From 64c8c70d1b37973eea1c263b9c26c258bbf61ca5 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Fri, 25 Aug 2023 10:29:46 +0200 Subject: [PATCH 001/153] Update documentation on release --- .travis.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index f6db07e3b..271a7d74a 100644 --- a/.travis.yml +++ b/.travis.yml @@ -91,7 +91,8 @@ jobs: - source charts/.travis/install.sh script: - travis_wait ci/helm/deploy.sh $DEPLOY_TARGET -f projects/saturn/views.yaml - - if: branch = documentation and type != pull_request + - if: branch = release and type != pull_request + name: Update documentation page install: - docs/.travis/install.sh script: From a0ba09db5c54cbcf80e74c83188c474e8206876e Mon Sep 17 00:00:00 2001 From: Travis CI User Date: Fri, 25 Aug 2023 09:08:53 +0000 Subject: [PATCH 002/153] Prepare for next development cycle for version 0.7.30 [full build] --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index cb80b803c..5de328f3e 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.7.29 +0.7.30 From de7899cd24c21c7757e349b5fe9018101392d0c1 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Mon, 28 Aug 2023 09:42:19 +0200 Subject: [PATCH 003/153] Apply Pluto config change in Helm setup. --- charts/fairspace/templates/project/configmap-pluto.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/charts/fairspace/templates/project/configmap-pluto.yaml b/charts/fairspace/templates/project/configmap-pluto.yaml index fa3332754..4380f0f4a 100644 --- a/charts/fairspace/templates/project/configmap-pluto.yaml +++ b/charts/fairspace/templates/project/configmap-pluto.yaml @@ -68,6 +68,13 @@ data: default-filters: - RemoveRequestHeader=Pragma X-Frame-Options X-Content-Type-Options X-XSS-Protection X-Permitted-Cross-Domain-Policies Origin # Including the ORIGIN header would trigger CORS filtering downstream, but Pluto is already doing the filtering. + - name: Retry + args: + methods: GET,PUT,POST,DELETE + exceptions: + - reactor.netty.http.client.PrematureCloseException httpclient: connect-timeout: {{ .Values.pluto.connectTimeoutMillis }} response-timeout: {{ .Values.pluto.responseTimeoutMillis }} + pool: + max-idle-time: 20s From deb136b71c16086c10a399f0759c6aff9cf8fd6e Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Fri, 20 Oct 2023 14:28:45 +0200 Subject: [PATCH 004/153] Add fix for releasing helm charts to Google Storage. --- charts/.travis/install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/charts/.travis/install.sh b/charts/.travis/install.sh index c07d7ddd6..04de0b262 100755 --- a/charts/.travis/install.sh +++ b/charts/.travis/install.sh @@ -4,7 +4,7 @@ source "$BUILD_SCRIPTS_DIR/helm/install_helm.sh" if [[ $SHOULD_RELEASE ]]; then - "$BUILD_SCRIPTS_DIR/login-provider.sh" + source "$BUILD_SCRIPTS_DIR/login-provider.sh" echo "Adding helm repositories ..." source "$BUILD_SCRIPTS_DIR/helm/add_repos.sh" From 8bee9d6366dd0346dd20429536952cdcfd7110c0 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Mon, 23 Oct 2023 08:58:28 +0200 Subject: [PATCH 005/153] Update platform related env variables in Travis setup. --- .travis.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index 271a7d74a..450ac4028 100644 --- a/.travis.yml +++ b/.travis.yml @@ -54,10 +54,8 @@ before_install: - 'if [[ "$SHOULD_DEPLOY" = "true" ]]; then export DEPLOYMENT_CONFIG_DIR="$(pwd)/ci-config/fairspace" ; fi' - 'if [[ "$SHOULD_DEPLOY" = "true" ]] && [[ "$TRAVIS_BRANCH" = "$SNAPSHOT_BRANCH" ]]; then export ALLOW_SNAPSHOTS=1 DEPLOY_TARGET=ci DEPLOY_PLATFORM="GCP" KUBERNETES_CONTEXT="$SNAPSHOT_CONTEXT" CLUSTER_NAME="$SNAPSHOT_CLUSTER_NAME" CLUSTER_ZONE="$SNAPSHOT_CLUSTER_ZONE" ; fi' - 'if [[ "$SHOULD_DEPLOY" = "true" ]] && [[ "$TRAVIS_BRANCH" = "$RELEASE_BRANCH" ]]; then export DEPLOY_TARGET=ci DEPLOY_PLATFORM="GCP" KUBERNETES_CONTEXT="$RELEASE_CONTEXT" CLUSTER_NAME="$RELEASE_CLUSTER_NAME" CLUSTER_ZONE="$RELEASE_CLUSTER_ZONE" ; fi' - - export INFRASTRUCTURE_PLATFORM="${DEPLOY_PLATFORM:-NONE}" - source ./ci/setup_env.sh - - 'if [[ "$SHOULD_RELEASE" ]]; then export OIDC_AUTH_VERSION=$VERSION; fi' - - 'if [[ "$SHOULD_RELEASE" ]] ; then export NEED_INTERNAL_HELM=1 ; fi' + - 'if [[ "$SHOULD_RELEASE" ]]; then export OIDC_AUTH_VERSION="$VERSION" RELEASE_PLATFORM="GCP" NEED_INTERNAL_HELM=1 ; fi' jobs: include: From dbafb4fa2a197e88bc6ff565bc4ebdc2a109e5ce Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Thu, 26 Oct 2023 15:23:14 +0200 Subject: [PATCH 006/153] prevent var usage by Lombok, since var is a language keyword since Java 10 --- .gitignore | 2 +- .../java/io/fairspace/saturn/services/views/ViewService.java | 2 +- .../io/fairspace/saturn/services/views/ViewStoreClient.java | 2 +- .../saturn/services/views/ViewStoreClientFactory.java | 3 ++- 4 files changed, 5 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index d6f6364a3..216a9d2da 100644 --- a/.gitignore +++ b/.gitignore @@ -310,7 +310,7 @@ tags [._]*.un~ ### VisualStudioCode ### -.vscode/* +.vscode ### VisualStudioCode Patch ### # Ignore all local history of files diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java index b69dd4ede..a1a49c842 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java @@ -2,7 +2,7 @@ import io.fairspace.saturn.config.*; import io.fairspace.saturn.vocabulary.FS; -import lombok.*; +import lombok.SneakyThrows; import lombok.extern.log4j.*; import org.apache.jena.datatypes.xsd.*; import org.apache.jena.query.*; diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClient.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClient.java index 46b39461a..f24f5db79 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClient.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClient.java @@ -3,7 +3,7 @@ import io.fairspace.saturn.config.*; import io.fairspace.saturn.config.ViewsConfig.*; import io.fairspace.saturn.services.views.Table.*; -import lombok.*; +import lombok.SneakyThrows; import lombok.extern.slf4j.*; import org.apache.commons.lang3.tuple.*; diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java index 7a62aa16c..c2507eee4 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java @@ -6,7 +6,8 @@ import io.fairspace.saturn.config.*; import io.fairspace.saturn.config.ViewsConfig.*; import io.fairspace.saturn.vocabulary.*; -import lombok.*; +import lombok.Builder; +import lombok.Data; import lombok.extern.slf4j.*; import javax.sql.*; From 0f7a7d9e3d045d9efb21e9a7e9c21b3de9b3f35f Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Fri, 24 Nov 2023 13:36:24 +0100 Subject: [PATCH 007/153] Fix LocalDate to Timestamp conversion for Postgres db updates. --- .../io/fairspace/saturn/services/views/ViewStoreClient.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClient.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClient.java index f24f5db79..dd4da0c94 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClient.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClient.java @@ -40,6 +40,8 @@ public static void setQueryValue(PreparedStatement query, int index, Object valu query.setFloat(index, ((Number) value).floatValue()); } else if (value instanceof Instant) { query.setTimestamp(index, Timestamp.from((Instant) value)); + } else if (value instanceof LocalDate) { + query.setTimestamp(index, Timestamp.valueOf(((LocalDate) value).atStartOfDay())); } else if (value instanceof Collection) { throw new IllegalArgumentException("Unexpected value of collection type."); } else { From ab68b362a65aba18f6e2d302f94283c7b685ae82 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Mon, 27 Nov 2023 11:43:53 +0100 Subject: [PATCH 008/153] limit number of items frontend receives --- .../saturn/services/metadata/MetadataService.java | 4 +++- .../fairspace/saturn/services/users/UserService.java | 4 ++-- .../saturn/services/views/ViewStoreReader.java | 11 +++++++++-- 3 files changed, 14 insertions(+), 5 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataService.java index e2edb29a2..94ce26c72 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataService.java @@ -72,7 +72,9 @@ public Model get(String subject, boolean withValueProperties) { .forEach(property -> m.listStatements(null, property, resource) .filterKeep(stmt -> permissions.canReadMetadata(stmt.getSubject())) .filterDrop(stmt -> stmt.getSubject().hasProperty(FS.dateDeleted)) - .forEachRemaining(stmt -> { + .toList() + .subList(0, 21) + .forEach(stmt -> { model.add(stmt); if (withValueProperties) { addImportantProperties(stmt.getSubject(), model); diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/users/UserService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/users/UserService.java index 6e17507e6..881119a36 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/users/UserService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/users/UserService.java @@ -37,7 +37,7 @@ public class UserService { private final ExecutorService threadpool = Executors.newSingleThreadExecutor(); public UserService(Config.Auth config, Transactions transactions, UsersResource usersResource) { - this.config = config; + this.config = config; this.transactions = transactions; this.usersResource = usersResource; usersCache = CacheBuilder.newBuilder() @@ -81,7 +81,7 @@ public Map getUsersMap() { } private Map fetchUsers() { - var userCount = usersResource.count(); // TODO [FNS-126] implement proper pagination based on client request parameters + var userCount = usersResource.count(); var keycloakUsers = usersResource.list(0, userCount); var updated = new HashSet(); var users = transactions.calculateRead(model -> { diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java index 0aba6bb4c..3f4dcaf9c 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java @@ -364,7 +364,7 @@ List>> retrieveViewTableRows( } log.debug("Processing rows + querying value sets took {} ms", new Date().getTime() - mid); return rows; - } finally { + } finally { for (var q : valueSetQueries.values()) { q.close(); } @@ -388,13 +388,20 @@ List>> retrieveJoinTableRows( joinView.include.stream() .filter(column -> !valueSetProperties.contains(column))) .collect(Collectors.toList()); + + // Limit related items by 50, it is only for visualisation and becomes problematic + // with thousands of related items. + // It will have impact on the column filters, items outside of the limit can't be found. + // In these cases the user should make a more narrow selection using facets before using + // column filters. var query = connection.prepareStatement( "select " + projectionColumns.stream().map(String::toLowerCase).collect(Collectors.joining(", ")) + " from " + joinedTable.name + " j " + " where exists (" + " select * from " + joinTable.name + " jt " + " where jt." + idColumn(joinView.view).name + " = j.id" + - " and jt." + idColumn(view).name + " = ? )" + " and jt." + idColumn(view).name + " = ? )" + + "limit 50" ); query.setString(1, id); var result = query.executeQuery(); From 94b7da920581e535c49491e0fdb4b87ea3c6acb6 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Mon, 27 Nov 2023 11:51:07 +0100 Subject: [PATCH 009/153] fixed formatting --- .../java/io/fairspace/saturn/services/users/UserService.java | 2 +- .../io/fairspace/saturn/services/views/ViewStoreReader.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/users/UserService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/users/UserService.java index 881119a36..32f80f569 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/users/UserService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/users/UserService.java @@ -37,7 +37,7 @@ public class UserService { private final ExecutorService threadpool = Executors.newSingleThreadExecutor(); public UserService(Config.Auth config, Transactions transactions, UsersResource usersResource) { - this.config = config; + this.config = config; this.transactions = transactions; this.usersResource = usersResource; usersCache = CacheBuilder.newBuilder() diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java index 3f4dcaf9c..579edaf89 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java @@ -364,7 +364,7 @@ List>> retrieveViewTableRows( } log.debug("Processing rows + querying value sets took {} ms", new Date().getTime() - mid); return rows; - } finally { + } finally { for (var q : valueSetQueries.values()) { q.close(); } From 411bb1e64a9ea001b4ee398658caf54b7455f348 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Mon, 27 Nov 2023 16:22:27 +0100 Subject: [PATCH 010/153] performance improvement --- .../services/metadata/MetadataService.java | 46 ++++++++++++------- 1 file changed, 29 insertions(+), 17 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataService.java index 94ce26c72..45f99e564 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataService.java @@ -9,6 +9,7 @@ import org.apache.commons.lang3.tuple.Pair; import org.apache.jena.rdf.model.*; import org.apache.jena.shacl.vocabulary.SHACLM; +import org.apache.jena.util.iterator.ExtendedIterator; import org.apache.jena.vocabulary.RDF; import java.time.Instant; @@ -49,18 +50,18 @@ public MetadataService(Transactions transactions, Model vocabulary, MetadataRequ * @return */ public Model get(String subject, boolean withValueProperties) { - var model = createDefaultModel(); + var returnValues = createDefaultModel(); - transactions.executeRead(m -> { - var resource = m.createResource(subject); + transactions.executeRead(fairspaceData -> { + var resource = fairspaceData.createResource(subject); if (!permissions.canReadMetadata(resource)) { throw new AccessDeniedException(subject); } resource.listProperties().forEachRemaining(stmt -> { - model.add(stmt); + returnValues.add(stmt); if (withValueProperties && stmt.getObject().isURIResource()) { - addImportantProperties(stmt.getResource(), model); + addImportantProperties(stmt.getResource(), returnValues); } }); @@ -69,19 +70,30 @@ public Model get(String subject, boolean withValueProperties) { .map(ps -> ps.getProperty(SHACLM.path).getResource().getPropertyResourceValue(SHACLM.inversePath)) .filter(Objects::nonNull) .map(p -> p.as(Property.class)) - .forEach(property -> m.listStatements(null, property, resource) - .filterKeep(stmt -> permissions.canReadMetadata(stmt.getSubject())) - .filterDrop(stmt -> stmt.getSubject().hasProperty(FS.dateDeleted)) - .toList() - .subList(0, 21) - .forEach(stmt -> { - model.add(stmt); - if (withValueProperties) { - addImportantProperties(stmt.getSubject(), model); - } - })); + .forEach(property -> addStatements(fairspaceData, returnValues, property, resource, withValueProperties)); }); - return model; + return returnValues; + } + + private void addStatements(Model fairspaceData, Model returnValues, Property property, Resource resource, boolean withValueProperties) { + ExtendedIterator statements = fairspaceData.listStatements(null, property, resource) + .filterKeep(stmt -> permissions.canReadMetadata(stmt.getSubject())) + .filterDrop(stmt -> stmt.getSubject().hasProperty(FS.dateDeleted)); + + int numberOfStatementsAdded = 0; + + while(statements.hasNext()) { + Statement stmt = (Statement)statements.next(); + + returnValues.add(stmt); + if (withValueProperties) { + addImportantProperties(stmt.getSubject(), returnValues); + } + + if(numberOfStatementsAdded++ == 20){ + break; + } + } } private void addImportantProperties(Resource s, Model dest) { From f33bdc9b8f2d49e6917e1edf0fc3554a9a89c77c Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Mon, 27 Nov 2023 16:41:44 +0100 Subject: [PATCH 011/153] use variable instead of number --- .../fairspace/saturn/services/views/ViewStoreReader.java | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java index 579edaf89..f9a5f2dc3 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java @@ -31,6 +31,7 @@ public class ViewStoreReader implements AutoCloseable { final Config.Search searchConfig; final ViewStoreClient.ViewStoreConfiguration configuration; final Connection connection; + final int MAX_JOIN_ITEMS = 50; public ViewStoreReader(Config.Search searchConfig, ViewStoreClientFactory viewStoreClientFactory) throws SQLException { this.searchConfig = searchConfig; @@ -389,11 +390,6 @@ List>> retrieveJoinTableRows( .filter(column -> !valueSetProperties.contains(column))) .collect(Collectors.toList()); - // Limit related items by 50, it is only for visualisation and becomes problematic - // with thousands of related items. - // It will have impact on the column filters, items outside of the limit can't be found. - // In these cases the user should make a more narrow selection using facets before using - // column filters. var query = connection.prepareStatement( "select " + projectionColumns.stream().map(String::toLowerCase).collect(Collectors.joining(", ")) + " from " + joinedTable.name + " j " + @@ -401,7 +397,7 @@ List>> retrieveJoinTableRows( " select * from " + joinTable.name + " jt " + " where jt." + idColumn(joinView.view).name + " = j.id" + " and jt." + idColumn(view).name + " = ? )" + - "limit 50" + "limit " + String.valueOf(MAX_JOIN_ITEMS) ); query.setString(1, id); var result = query.executeQuery(); From e676f178e7226a8fd78586c62f7ff705d9d7d03a Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Mon, 27 Nov 2023 17:23:51 +0100 Subject: [PATCH 012/153] updated packages to latest minor --- projects/mercury/yarn.lock | 8927 ++++++++++++++++++------------------ 1 file changed, 4587 insertions(+), 4340 deletions(-) diff --git a/projects/mercury/yarn.lock b/projects/mercury/yarn.lock index 5db181927..e388020c8 100644 --- a/projects/mercury/yarn.lock +++ b/projects/mercury/yarn.lock @@ -2,947 +2,1016 @@ # yarn lockfile v1 +"@aashutoshrathi/word-wrap@^1.2.3": + version "1.2.6" + resolved "https://registry.yarnpkg.com/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz#bd9154aec9983f77b3a034ecaa015c2e4201f6cf" + integrity sha512-1Yjs2SvM8TflER/OD3cOjhWWOZb58A2t7wpE2S9XfBYTiIl+XFhQG2bjy4Pu1I+EAlCNUzRDYDdFwFYUKvXcIA== + 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jest-resolve@^27.5.1: version "27.5.1" - resolved "https://registry.npmjs.org/jest-resolve/-/jest-resolve-27.5.1.tgz" + resolved "https://registry.yarnpkg.com/jest-resolve/-/jest-resolve-27.5.1.tgz#a2f1c5a0796ec18fe9eb1536ac3814c23617b384" integrity sha512-FFDy8/9E6CV83IMbDpcjOhumAQPDyETnU2KZ1O98DwTnz8AOBsW/Xv3GySr1mOZdItLR+zDZ7I/UdTFbgSOVCw== dependencies: "@jest/types" "^27.5.1" @@ -6978,7 +7131,7 @@ jest-resolve@^27.4.2, jest-resolve@^27.5.1: jest-runner@^27.5.1: version "27.5.1" - resolved "https://registry.npmjs.org/jest-runner/-/jest-runner-27.5.1.tgz" + resolved "https://registry.yarnpkg.com/jest-runner/-/jest-runner-27.5.1.tgz#071b27c1fa30d90540805c5645a0ec167c7b62e5" integrity sha512-g4NPsM4mFCOwFKXO4p/H/kWGdJp9V8kURY2lX8Me2drgXqG7rrZAx5kv+5H7wtt/cdFIjhqYx1HrlqWHaOvDaQ== dependencies: "@jest/console" "^27.5.1" @@ -7005,7 +7158,7 @@ jest-runner@^27.5.1: jest-runtime@^27.5.1: version "27.5.1" - resolved "https://registry.npmjs.org/jest-runtime/-/jest-runtime-27.5.1.tgz" + 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yargs-parser@^13.1.2: version "13.1.2" - resolved "https://registry.npmjs.org/yargs-parser/-/yargs-parser-13.1.2.tgz" + resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-13.1.2.tgz#130f09702ebaeef2650d54ce6e3e5706f7a4fb38" integrity sha512-3lbsNRf/j+A4QuSZfDRA7HRSfWrzO0YjqTJd5kjAq37Zep1CEgaYmrH9Q3GwPiB9cHyd1Y1UwggGhJGoxipbzg== dependencies: camelcase "^5.0.0" @@ -12022,12 +12269,12 @@ yargs-parser@^13.1.2: yargs-parser@^20.2.2: version "20.2.9" - resolved "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.9.tgz" + resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-20.2.9.tgz#2eb7dc3b0289718fc295f362753845c41a0c94ee" integrity sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w== yargs@^13.3.0: version "13.3.2" - resolved "https://registry.npmjs.org/yargs/-/yargs-13.3.2.tgz" + resolved "https://registry.yarnpkg.com/yargs/-/yargs-13.3.2.tgz#ad7ffefec1aa59565ac915f82dccb38a9c31a2dd" integrity sha512-AX3Zw5iPruN5ie6xGRIDgqkT+ZhnRlZMLMHAs8tg7nRruy2Nb+i5o9bwghAogtM08q1dpr2LVoS8KSTMYpWXUw== dependencies: cliui "^5.0.0" @@ -12043,7 +12290,7 @@ yargs@^13.3.0: yargs@^16.2.0: version "16.2.0" - resolved "https://registry.npmjs.org/yargs/-/yargs-16.2.0.tgz" + resolved "https://registry.yarnpkg.com/yargs/-/yargs-16.2.0.tgz#1c82bf0f6b6a66eafce7ef30e376f49a12477f66" integrity sha512-D1mvvtDG0L5ft/jGWkLpG1+m0eQxOfaBvTNELraWj22wSVUMWxZUvYgJYcKh6jGGIkJFhH4IZPQhR4TKpc8mBw== dependencies: cliui "^7.0.2" @@ -12056,7 +12303,7 @@ yargs@^16.2.0: yauzl@^2.10.0: version "2.10.0" - resolved "https://registry.npmjs.org/yauzl/-/yauzl-2.10.0.tgz" + resolved "https://registry.yarnpkg.com/yauzl/-/yauzl-2.10.0.tgz#c7eb17c93e112cb1086fa6d8e51fb0667b79a5f9" integrity sha512-p4a9I6X6nu6IhoGmBqAcbJy1mlC4j27vEPZX9F4L4/vZT3Lyq1VkFHw/V/PUcB9Buo+DG3iHkT0x3Qya58zc3g== dependencies: buffer-crc32 "~0.2.3" @@ -12064,5 +12311,5 @@ yauzl@^2.10.0: yocto-queue@^0.1.0: version "0.1.0" - resolved "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz" + resolved "https://registry.yarnpkg.com/yocto-queue/-/yocto-queue-0.1.0.tgz#0294eb3dee05028d31ee1a5fa2c556a6aaf10a1b" integrity sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q== From cc373a3213ab06b9784c561bb0a4accfff48c19e Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Wed, 29 Nov 2023 17:37:02 +0100 Subject: [PATCH 013/153] display max 100 items in lists in the left panel --- projects/mercury/src/constants.js | 4 ++ .../src/metadata/common/LinkedDataProperty.js | 6 ++- .../metadata/common/LinkedDataValuesList.js | 38 +++++++++++++------ .../services/metadata/MetadataService.java | 6 ++- 4 files changed, 39 insertions(+), 15 deletions(-) diff --git a/projects/mercury/src/constants.js b/projects/mercury/src/constants.js index 559050c05..3b309ed5b 100644 --- a/projects/mercury/src/constants.js +++ b/projects/mercury/src/constants.js @@ -14,6 +14,10 @@ export const CROSS_WORKSPACES_SEARCH_PATH = '/workspaces/_all'; export const TOOLTIP_ENTER_DELAY = 350; export const DATE_FORMAT = 'dd-MM-yyyy'; +// The maximum number of items in a list in the right panel, for performance reasons. +// If you change this, also change it in 'MetadataService.java' +export const MAX_LIST_LENGTH = 100; + // Metadata schemas export const SHACL_NS = 'http://www.w3.org/ns/shacl#'; export const XMLSCHEMA_NS = 'http://www.w3.org/2001/XMLSchema#'; diff --git a/projects/mercury/src/metadata/common/LinkedDataProperty.js b/projects/mercury/src/metadata/common/LinkedDataProperty.js index 6c10b8ce4..44f9af1cb 100644 --- a/projects/mercury/src/metadata/common/LinkedDataProperty.js +++ b/projects/mercury/src/metadata/common/LinkedDataProperty.js @@ -4,7 +4,7 @@ import PropTypes from "prop-types"; import {FormControl, FormGroup, FormHelperText, FormLabel} from '@mui/material'; import LinkedDataInputFieldsTable from "./LinkedDataInputFieldsTable"; import LinkedDataRelationTable from "./LinkedDataRelationTable"; -import {LABEL_URI, TOOLTIP_ENTER_DELAY} from "../../constants"; +import {LABEL_URI, MAX_LIST_LENGTH, TOOLTIP_ENTER_DELAY} from "../../constants"; import GenericTooltip from "../../common/components/GenericTooltip"; import Iri from "../../common/components/Iri"; import LinkedDataContext from "../LinkedDataContext"; @@ -33,6 +33,8 @@ const LinkedDataProperty = ( || property.allowedValues ); + const getCount = () => "(" + (values.length > MAX_LIST_LENGTH ? MAX_LIST_LENGTH + "+" : values.length) + ")"; + // The edit component should not actually allow editing the value if editable is set to false // or if the property contains settings that disallow editing existing values const disableEditing = !formEditable || !property.isEditable || disallowEditingOfExistingValues; @@ -56,7 +58,7 @@ const LinkedDataProperty = ( ? ( - {label} {values.length > 1 && "(" + values.length + ")"} + {label} {values.length > 1 && getCount()} ) : null diff --git a/projects/mercury/src/metadata/common/LinkedDataValuesList.js b/projects/mercury/src/metadata/common/LinkedDataValuesList.js index 62e746109..f8bcad0d3 100644 --- a/projects/mercury/src/metadata/common/LinkedDataValuesList.js +++ b/projects/mercury/src/metadata/common/LinkedDataValuesList.js @@ -1,10 +1,10 @@ import React, {useState} from 'react'; -import {Divider, Grid, IconButton, Typography} from '@mui/material'; +import {Divider, Grid, IconButton, Tooltip, Typography} from '@mui/material'; import withStyles from '@mui/styles/withStyles'; import {Add, Clear} from '@mui/icons-material'; import {FixedSizeList as List} from 'react-window'; -import {LABEL_URI, STRING_URI} from '../../constants'; +import {LABEL_URI, MAX_LIST_LENGTH, STRING_URI} from '../../constants'; import styles from './LinkedDataValuesTable.styles'; import StringValue from './values/StringValue'; @@ -114,6 +114,29 @@ export const LinkedDataValuesList = (props: LinkedDataValuesListProps) => { const isDeleteButtonEnabled = () => property.isEditable && canEdit; const isAddButtonEnabled = canEdit && !maxValuesReached && AddComponent; + const renderListItem = (entry, index) => rowDecorator(entry, ( + +
+ { + columnDefinition.id === LABEL_URI + ? {columnDefinition.getValue(entry, index)} + : {columnDefinition.getValue(entry, index)} + } +
+ {showRowDividers && } + + )); + + const renderListLimitMessage = (entry) => rowDecorator(entry, ( + +
+ + ... display limit ({MAX_LIST_LENGTH}) reached ... + +
+ + )); + const renderValue = (entry, index) => rowDecorator(entry, ( { // eslint-disable-next-line react/no-array-index-key key={index} > - -
- { - columnDefinition.id === LABEL_URI - ? {columnDefinition.getValue(entry, index)} - : {columnDefinition.getValue(entry, index)} - } -
- {showRowDividers && } - + {index === MAX_LIST_LENGTH ? renderListLimitMessage(entry) : renderListItem(entry, index)} { property.isEditable && isDeleteButtonEnabled(entry) && ( diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataService.java index 45f99e564..f4c40369a 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataService.java @@ -31,6 +31,10 @@ public class MetadataService { private final MetadataRequestValidator validator; private final MetadataPermissions permissions; + // The maximum number of items in a list in the right panel, for performance reasons. + // If you change this, also change it in 'constants.js' + private final int MAX_LIST_LENGTH = 100; + public MetadataService(Transactions transactions, Model vocabulary, MetadataRequestValidator validator, MetadataPermissions permissions) { this.transactions = transactions; this.vocabulary = vocabulary; @@ -90,7 +94,7 @@ private void addStatements(Model fairspaceData, Model returnValues, Property pro addImportantProperties(stmt.getSubject(), returnValues); } - if(numberOfStatementsAdded++ == 20){ + if(numberOfStatementsAdded++ == MAX_LIST_LENGTH){ break; } } From da27076638a68af74571f7be5d7943158ac66694 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Wed, 29 Nov 2023 17:37:33 +0100 Subject: [PATCH 014/153] new docker compose syntax --- projects/mercury/package.json | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/projects/mercury/package.json b/projects/mercury/package.json index 88dfc67bf..19ca1444e 100644 --- a/projects/mercury/package.json +++ b/projects/mercury/package.json @@ -6,7 +6,7 @@ "dev": "yarn build && concurrently \"yarn localdevelopment\" \"yarn saturn\" \"yarn pluto\" \"yarn start\"", "dev-be": "concurrently \"yarn localdevelopment\" \"yarn saturn\" \"yarn pluto\"", "dev-fe": "yarn build && yarn start", - "localdevelopment": "cd ../../local-development && docker-compose up", + "localdevelopment": "cd ../../local-development && docker compose up", "saturn": "wait-on http://localhost:5100/ && wait-on tcp:9432 && cd ../saturn/ && KEYCLOAK_CLIENT_SECRET=********** ./gradlew run", "pluto": "wait-on http://localhost:8090/api/health/ && cd ../pluto/ && KEYCLOAK_CLIENT_SECRET=********** ./gradlew bootRun --args='--spring.profiles.active=local'", "start": "react-app-rewired start", @@ -96,6 +96,8 @@ "transformIgnorePatterns": [ "\\.pnp\\.[^\\/]+$" ], - "setupFilesAfterEnv": ["./jest-setup.js"] + "setupFilesAfterEnv": [ + "./jest-setup.js" + ] } } From 6617042a3c31680ceed6cdd58c99a4476ba42662 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Thu, 30 Nov 2023 12:33:42 +0100 Subject: [PATCH 015/153] user friendly text --- projects/mercury/src/metadata/common/LinkedDataValuesList.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/projects/mercury/src/metadata/common/LinkedDataValuesList.js b/projects/mercury/src/metadata/common/LinkedDataValuesList.js index f8bcad0d3..32504b497 100644 --- a/projects/mercury/src/metadata/common/LinkedDataValuesList.js +++ b/projects/mercury/src/metadata/common/LinkedDataValuesList.js @@ -130,7 +130,7 @@ export const LinkedDataValuesList = (props: LinkedDataValuesListProps) => { const renderListLimitMessage = (entry) => rowDecorator(entry, (
- + ... display limit ({MAX_LIST_LENGTH}) reached ...
From 790e37c21897605b571093a3b911ad0b385ab660 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Tue, 5 Dec 2023 15:18:13 +0100 Subject: [PATCH 016/153] Changes styling to show hidden digits in numeric facet --- .../views/facets/NumericalRangeSelectionFacet.js | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/projects/mercury/src/metadata/views/facets/NumericalRangeSelectionFacet.js b/projects/mercury/src/metadata/views/facets/NumericalRangeSelectionFacet.js index c80c5c992..37b1bc8f8 100644 --- a/projects/mercury/src/metadata/views/facets/NumericalRangeSelectionFacet.js +++ b/projects/mercury/src/metadata/views/facets/NumericalRangeSelectionFacet.js @@ -146,14 +146,15 @@ const NumericalRangeSelectionFacet = (props: MetadataViewFacetProperties) => { return (
{minValue !== null && maxValue !== null ? ( - - - {renderInput(value[0], handleMinValueInputChange, minValue)} - - + + {renderSlider()} - + + {renderInput(value[0], handleMinValueInputChange, minValue)} + + + {renderInput(value[1], handleMaxValueInputChange, maxValue)} From 210eab02b86d03f6773ce27eadcb98f854a3f9b4 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Tue, 5 Dec 2023 15:38:27 +0100 Subject: [PATCH 017/153] Update documentation --- README.adoc | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.adoc b/README.adoc index d3748850b..74eca0d58 100644 --- a/README.adoc +++ b/README.adoc @@ -2405,8 +2405,8 @@ Now everything should be ready to start using Fairspace: Requires: -* Helm >= 3.5.x -* kubectl >= 1.17.x +* Helm >= 3.13.x +* kubectl >= 1.27.x You can deploy Fairspace on a Kubernetes cluster using link:https://helm.sh/[Helm]. Helm charts for Fairspace are published to the public helm repository at @@ -2423,7 +2423,7 @@ We provide a number of charts for various components that can be used in combina ===== Download and install helm and gcloud -* Download ``helm 3.6.0`` from https://github.com/helm/helm/releases/tag/v3.6.0 +* Download ``helm 3.13.1`` from https://github.com/helm/helm/releases/tag/v3.13.1 * Extract the downloaded archive to ``~/bin/helm`` and check with: + [source, shell] @@ -2431,7 +2431,7 @@ We provide a number of charts for various components that can be used in combina ~/bin/helm/helm version ---- -* Install link:https://kubernetes.io/docs/tasks/tools/install-kubectl/[kubectl] (for Helm 3.6.x install version > 1.18.x). +* Install link:https://kubernetes.io/docs/tasks/tools/install-kubectl/[kubectl] (for Helm 3.13.x install version > 1.27.x). * Download and install the link:https://cloud.google.com/sdk/docs/install[Google Cloud SDK] (requires Python). * Obtain credentials for Kubernetes: + @@ -2473,7 +2473,7 @@ kubectl get ns # Add the fairspace repo for reading ~/bin/helm/helm repo add fairspace https://storage.googleapis.com/fairspace-helm # (Optional) Add the fairspace repo via the GCS plugin for writing -~/bin/helm/helm plugin install https://github.com/hayorov/helm-gcs.git --version 0.3.11 +~/bin/helm/helm plugin install https://github.com/hayorov/helm-gcs.git --version 0.4.2 gcloud iam service-accounts keys create credentials.json --iam-account fairspace-207108@appspot.gserviceaccount.com export GOOGLE_APPLICATION_CREDENTIALS=/path/to/credentials.json ~/bin/helm/helm repo add fairspace-gcs gs://fairspace-helm @@ -2496,7 +2496,7 @@ Create DNS records for the ``keycloak.example.com``, ``fairspace.example.com`` a # List available fairspace-keycloak chart versions ~/bin/helm/helm search repo --versions fairspace/fairspace-keycloak # Fetch the fairspace-keycloak chart -~/bin/helm/helm pull fairspace/fairspace-keycloak --version 0.6.4 +~/bin/helm/helm pull fairspace/fairspace-keycloak --version 0.7.0 # List available fairspace chart versions ~/bin/helm/helm search repo --versions fairspace/fairspace # Fetch the fairspace chart @@ -2513,7 +2513,7 @@ Create a new deployment (called _release_ in helm terminology) and install the Fairspace Keycloak chart: [source, shell] ---- -~/bin/helm/helm install keycloak-new fairspace/fairspace-keycloak --version 0.6.4 --namespace keycloak-new \ +~/bin/helm/helm install keycloak-new fairspace/fairspace-keycloak --version 0.7.0 --namespace keycloak-new \ -f /path/to/fairspace-keycloak-values.yaml ---- You can pass values files with ``-f``. From e07bbcbfe2262bf663f641018776cd4e2444529a Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Tue, 5 Dec 2023 15:39:24 +0100 Subject: [PATCH 018/153] Redirect to login page instead of error dialog on session expiration. --- .../mercury/src/common/utils/__tests__/httpUtils.js | 11 +++++++---- projects/mercury/src/common/utils/httpUtils.js | 4 +--- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/projects/mercury/src/common/utils/__tests__/httpUtils.js b/projects/mercury/src/common/utils/__tests__/httpUtils.js index 4e712325d..a35c4d2af 100644 --- a/projects/mercury/src/common/utils/__tests__/httpUtils.js +++ b/projects/mercury/src/common/utils/__tests__/httpUtils.js @@ -4,10 +4,13 @@ import ErrorDialog from "../../components/ErrorDialog"; describe('Http Utils', () => { describe('handleHttpError', () => { it('Should show an error on 401', () => { - Object.defineProperty(window.location, 'assign', jest.fn()); - ErrorDialog.showError = jest.fn(); - handleHttpError("Default error")({response: {status: 401}}); - expect(ErrorDialog.showError).toHaveBeenCalledWith("Your session has expired. Please log in again.", null, expect.anything()); + delete window.location; + window.location = {assign: jest.fn()}; + handleHttpError("")({response: {status: 401}}); + expect(window.location.assign).toHaveBeenCalledTimes(1); + expect(window.location.assign).toHaveBeenCalledWith( + "/login?redirectUrl=undefined", + ); }); it('Should show an error on 403', () => { diff --git a/projects/mercury/src/common/utils/httpUtils.js b/projects/mercury/src/common/utils/httpUtils.js index 59496fb23..30c308117 100644 --- a/projects/mercury/src/common/utils/httpUtils.js +++ b/projects/mercury/src/common/utils/httpUtils.js @@ -13,9 +13,7 @@ export const handleAuthError = (status) => { switch (status) { case 401: sessionStorage.clear(); - ErrorDialog.showError('Your session has expired. Please log in again.', - null, - () => window.location.assign(`/login?redirectUrl=${encodeURI(window.location.href)}`)); + window.location.assign(`/login?redirectUrl=${encodeURI(window.location.href)}`); break; case 403: ErrorDialog.showError('You have no access to this resource. Ask your administrator to grant you access.', From 1af4782e43fa941b55a3c2d9a1bb2b575f2b1f74 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Wed, 6 Dec 2023 10:30:36 +0100 Subject: [PATCH 019/153] Update local proxy setup not to use /dev prefix. --- projects/mercury/src/setupProxy.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/projects/mercury/src/setupProxy.js b/projects/mercury/src/setupProxy.js index 727632240..6d13cfa68 100644 --- a/projects/mercury/src/setupProxy.js +++ b/projects/mercury/src/setupProxy.js @@ -32,7 +32,7 @@ module.exports = (app) => { keycloak.redirectToLogin = (request) => !(request.baseUrl.startsWith('/api/')); app.use(keycloak.middleware({logout: '/logout'})); - app.use('/dev', keycloak.protect()); + app.use('/', keycloak.protect()); const addToken = (proxyReq, req) => req.kauth.grant && proxyReq.setHeader('Authorization', `Bearer ${req.kauth.grant.access_token.token}`); From 71e0a5580a56ae52ab8e6b3286ac4c7927f5ff12 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Wed, 6 Dec 2023 11:36:05 +0100 Subject: [PATCH 020/153] Make application name part of UI constants. --- projects/mercury/src/common/VersionInfo.js | 4 +++- projects/mercury/src/constants.js | 1 + 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/projects/mercury/src/common/VersionInfo.js b/projects/mercury/src/common/VersionInfo.js index 067133b7b..077580abe 100644 --- a/projects/mercury/src/common/VersionInfo.js +++ b/projects/mercury/src/common/VersionInfo.js @@ -1,6 +1,8 @@ +import {APPLICATION_NAME} from "../constants"; + const VersionInfo = { id: process.env.REACT_APP_NAME, - name: 'Fairspace', + name: APPLICATION_NAME, description: '', version: process.env.REACT_APP_VERSION }; diff --git a/projects/mercury/src/constants.js b/projects/mercury/src/constants.js index 3b309ed5b..8c8b83114 100644 --- a/projects/mercury/src/constants.js +++ b/projects/mercury/src/constants.js @@ -1,3 +1,4 @@ +export const APPLICATION_NAME = 'Fairspace'; export const LOCAL_STORAGE_MENU_KEY = 'FAIRSPACE_MENU_EXPANDED'; export const CUT = 'CUT'; export const COPY = 'COPY'; From e764a22fbae2815b2614703063050b03e3c97ed9 Mon Sep 17 00:00:00 2001 From: anton Date: Mon, 11 Dec 2023 10:21:28 +0100 Subject: [PATCH 021/153] Added a step to execute before the first run of the app locally --- projects/mercury/README.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/projects/mercury/README.md b/projects/mercury/README.md index 6f188066a..a82a9b0d3 100644 --- a/projects/mercury/README.md +++ b/projects/mercury/README.md @@ -27,7 +27,12 @@ The Mercury frontend app needs a backend to communicate with. For convenience, t - `yarn pluto` starts a proxy server that also serves the frontend at port `8080`. - `yarn start` starts the frontend and exposes it at port `3000`. -To start all these components at once, run: +For the first run, execute the following command to install all dependencies locally: +```bash +yarn install +``` + +To start all these components at once, run: ```bash yarn dev ``` From 2133f82b7cde40babab0ab0a8083b6508ead8073 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Mon, 11 Dec 2023 17:22:42 +0100 Subject: [PATCH 022/153] fixed frontend debugging --- projects/mercury/src/setupProxy.js | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/projects/mercury/src/setupProxy.js b/projects/mercury/src/setupProxy.js index 6d13cfa68..74d2b65b6 100644 --- a/projects/mercury/src/setupProxy.js +++ b/projects/mercury/src/setupProxy.js @@ -1,3 +1,4 @@ +// Use of proxy middleware for local development, assumption is it only listens to port 3000 (confirm reference?) const {createProxyMiddleware} = require('http-proxy-middleware'); // eslint-disable-next-line import/no-extraneous-dependencies const Keycloak = require('keycloak-connect'); @@ -32,7 +33,9 @@ module.exports = (app) => { keycloak.redirectToLogin = (request) => !(request.baseUrl.startsWith('/api/')); app.use(keycloak.middleware({logout: '/logout'})); - app.use('/', keycloak.protect()); + + // The next statement enables debugging and setting breakpoints in Intellij and VSCode. Not fully understand it but don't remove :) + app.use('/dev', keycloak.protect()); const addToken = (proxyReq, req) => req.kauth.grant && proxyReq.setHeader('Authorization', `Bearer ${req.kauth.grant.access_token.token}`); From 5c61a04bc4805a311efecf8daa3467e132c61ab4 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Wed, 13 Dec 2023 11:05:12 +0100 Subject: [PATCH 023/153] set column order in views.yaml --- .../src/metadata/views/MetadataViewAPI.js | 1 + .../src/metadata/views/MetadataViewTabs.js | 10 +++++++++- .../io/fairspace/saturn/config/ViewsConfig.java | 4 ++++ .../saturn/services/views/ColumnDTO.java | 1 + .../saturn/services/views/ViewService.java | 8 ++++---- .../saturn/services/views/ViewServiceTest.java | 17 ++++++++++++++++- .../saturn/src/test/resources/test-views.yaml | 2 ++ 7 files changed, 37 insertions(+), 6 deletions(-) diff --git a/projects/mercury/src/metadata/views/MetadataViewAPI.js b/projects/mercury/src/metadata/views/MetadataViewAPI.js index 25960ab5f..2c87ab39a 100644 --- a/projects/mercury/src/metadata/views/MetadataViewAPI.js +++ b/projects/mercury/src/metadata/views/MetadataViewAPI.js @@ -32,6 +32,7 @@ export type MetadataViewFacet = { }; export type MetadataViewColumn = { + displayIndex: number; name: string; title: string; type: ValueType; diff --git a/projects/mercury/src/metadata/views/MetadataViewTabs.js b/projects/mercury/src/metadata/views/MetadataViewTabs.js index 08d6cec00..26d050f77 100644 --- a/projects/mercury/src/metadata/views/MetadataViewTabs.js +++ b/projects/mercury/src/metadata/views/MetadataViewTabs.js @@ -53,7 +53,15 @@ export const MetadataViewTabs = (props: MetadataViewTabsProperties) => { accessColumn ]; } - return view.columns; + return view.columns.sort((a, b) => { + if (a.displayIndex > b.displayIndex) { + return 1; + } + if (a.displayIndex < b.displayIndex) { + return -1; + } + return 0; + }); }; return ( diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/config/ViewsConfig.java b/projects/saturn/src/main/java/io/fairspace/saturn/config/ViewsConfig.java index 14cbe59f6..32bda905d 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/config/ViewsConfig.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/config/ViewsConfig.java @@ -87,6 +87,8 @@ public static class Column { @NotBlank public String title; @NotNull public ColumnType type; @NotBlank public String source; + // displayIndex determines the order of columns on the view page. + @NotNull public Integer displayIndex = 999; public String rdfType; public int priority; } @@ -97,6 +99,8 @@ public static class JoinView { public boolean reverse = false; @JsonSetter(nulls = Nulls.AS_EMPTY) public List include; + // displayIndex determines the order of columns on the view page, for joinView it is the column displaying the related entity + public Integer displayIndex = 999; } } } diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ColumnDTO.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ColumnDTO.java index d42388fff..11fd5deca 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ColumnDTO.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ColumnDTO.java @@ -8,4 +8,5 @@ public class ColumnDTO { String name; String title; ViewsConfig.ColumnType type; + Integer displayIndex; } diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java index a1a49c842..a788f2cd6 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java @@ -175,9 +175,9 @@ public List getViews() { return viewsConfig.views.stream() .map(v -> { var columns = new ArrayList(); - columns.add(new ColumnDTO(v.name, v.itemName == null ? v.name : v.itemName, ColumnType.Identifier)); + columns.add(new ColumnDTO(v.name, v.itemName == null ? v.name : v.itemName, ColumnType.Identifier, 0)); for (var c : v.columns) { - columns.add(new ColumnDTO(v.name + "_" + c.name, c.title, c.type)); + columns.add(new ColumnDTO(v.name + "_" + c.name, c.title, c.type, c.displayIndex)); } for (var j : v.join) { var joinView = viewsConfig.views.stream().filter(view -> view.name.equalsIgnoreCase(j.view)).findFirst().orElse(null); @@ -185,13 +185,13 @@ public List getViews() { continue; } if (j.include.contains("id")) { - columns.add(new ColumnDTO(joinView.name, joinView.title, ColumnType.Identifier)); + columns.add(new ColumnDTO(joinView.name, joinView.title, ColumnType.Identifier, j.displayIndex)); } for (var c : joinView.columns) { if (!j.include.contains(c.name)) { continue; } - columns.add(new ColumnDTO(joinView.name + "_" + c.name, c.title, c.type)); + columns.add(new ColumnDTO(joinView.name + "_" + c.name, c.title, c.type, c.displayIndex)); } } return new ViewDTO(v.name, v.title, columns); diff --git a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java index 74a787cf6..5c77c73bc 100644 --- a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java +++ b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java @@ -27,7 +27,6 @@ import java.util.stream.*; import static io.fairspace.saturn.TestUtils.*; -import static io.fairspace.saturn.TestUtils.mockAuthentication; import static io.fairspace.saturn.auth.RequestContext.getCurrentRequest; import static org.apache.jena.query.DatasetFactory.*; import static org.mockito.ArgumentMatchers.any; @@ -117,4 +116,20 @@ public void testFetchViewConfig() { .toList(); Assert.assertEquals(1, boolFacets.size()); } + + @Test + public void testDisplayIndex_IsSet() { + var views = viewService.getViews(); + var columns = views.get(1).getColumns().stream().toList(); + var selectedColumn = columns.stream().filter(c -> c.getTitle().equals("Morphology")).collect(Collectors.toList()).get(0); + Assert.assertEquals(Integer.valueOf(1), selectedColumn.getDisplayIndex()); + } + + @Test + public void testDisplayIndex_IsNotSet() { + var views = viewService.getViews(); + var columns = views.get(1).getColumns().stream().toList(); + var selectedColumn = columns.stream().filter(c -> c.getTitle().equals("Laterality")).collect(Collectors.toList()).get(0); + Assert.assertEquals(Integer.valueOf(999), selectedColumn.getDisplayIndex()); + } } diff --git a/projects/saturn/src/test/resources/test-views.yaml b/projects/saturn/src/test/resources/test-views.yaml index e039c10f1..99d271eb4 100644 --- a/projects/saturn/src/test/resources/test-views.yaml +++ b/projects/saturn/src/test/resources/test-views.yaml @@ -99,6 +99,7 @@ views: source: https://institut-curie.org/ontology#tumorMorphology rdfType: https://institut-curie.org/ontology#Morphology type: termSet + displayIndex: 1 - name: laterality title: Laterality source: https://institut-curie.org/ontology#tumorLaterality @@ -177,6 +178,7 @@ views: - id - gender - ageAtDeath + displayIndex: 0 - view: Sample on: https://institut-curie.org/ontology#diagnosis reverse: true From db2cfeb36529617cd6f295c875fe15722a654d6a Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Wed, 13 Dec 2023 15:28:54 +0100 Subject: [PATCH 024/153] small fix, group all joinview columns together --- .../java/io/fairspace/saturn/services/views/ViewService.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java index a788f2cd6..b6b884534 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java @@ -191,7 +191,7 @@ public List getViews() { if (!j.include.contains(c.name)) { continue; } - columns.add(new ColumnDTO(joinView.name + "_" + c.name, c.title, c.type, c.displayIndex)); + columns.add(new ColumnDTO(joinView.name + "_" + c.name, c.title, c.type, j.displayIndex)); } } return new ViewDTO(v.name, v.title, columns); From 7e10ef22734f1aba964e2972579ca574a516b075 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Wed, 13 Dec 2023 15:46:59 +0100 Subject: [PATCH 025/153] PR improvements --- .../mercury/src/metadata/views/MetadataViewTabs.js | 10 +--------- .../java/io/fairspace/saturn/config/ViewsConfig.java | 4 ++-- 2 files changed, 3 insertions(+), 11 deletions(-) diff --git a/projects/mercury/src/metadata/views/MetadataViewTabs.js b/projects/mercury/src/metadata/views/MetadataViewTabs.js index 26d050f77..764adc46f 100644 --- a/projects/mercury/src/metadata/views/MetadataViewTabs.js +++ b/projects/mercury/src/metadata/views/MetadataViewTabs.js @@ -53,15 +53,7 @@ export const MetadataViewTabs = (props: MetadataViewTabsProperties) => { accessColumn ]; } - return view.columns.sort((a, b) => { - if (a.displayIndex > b.displayIndex) { - return 1; - } - if (a.displayIndex < b.displayIndex) { - return -1; - } - return 0; - }); + return view.columns.sort((a, b) => a.displayIndex - b.displayIndex); }; return ( diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/config/ViewsConfig.java b/projects/saturn/src/main/java/io/fairspace/saturn/config/ViewsConfig.java index 32bda905d..0ad63af5c 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/config/ViewsConfig.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/config/ViewsConfig.java @@ -88,7 +88,7 @@ public static class Column { @NotNull public ColumnType type; @NotBlank public String source; // displayIndex determines the order of columns on the view page. - @NotNull public Integer displayIndex = 999; + @NotNull public Integer displayIndex = Integer.MAX_VALUE; public String rdfType; public int priority; } @@ -100,7 +100,7 @@ public static class JoinView { @JsonSetter(nulls = Nulls.AS_EMPTY) public List include; // displayIndex determines the order of columns on the view page, for joinView it is the column displaying the related entity - public Integer displayIndex = 999; + public Integer displayIndex = Integer.MAX_VALUE; } } } From 5224bbee726e275013b5da56dfa80c9fa76d11d7 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Wed, 13 Dec 2023 15:51:41 +0100 Subject: [PATCH 026/153] PR improvement --- .../io/fairspace/saturn/services/views/ViewService.java | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java index b6b884534..111825dc2 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java @@ -175,7 +175,11 @@ public List getViews() { return viewsConfig.views.stream() .map(v -> { var columns = new ArrayList(); - columns.add(new ColumnDTO(v.name, v.itemName == null ? v.name : v.itemName, ColumnType.Identifier, 0)); + + // The entity labal is the first column displayed, if you want a column before this label, assign a negative displayIndex value in views.yaml + int entityLabelIndex = 0; + + columns.add(new ColumnDTO(v.name, v.itemName == null ? v.name : v.itemName, ColumnType.Identifier, entityLabelIndex)); for (var c : v.columns) { columns.add(new ColumnDTO(v.name + "_" + c.name, c.title, c.type, c.displayIndex)); } From e494fa9db22f7bc075ed7096e4c9335266ed313a Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Thu, 14 Dec 2023 09:56:41 +0100 Subject: [PATCH 027/153] Test fix --- .../io/fairspace/saturn/services/views/ViewServiceTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java index 5c77c73bc..3b5921bcf 100644 --- a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java +++ b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java @@ -130,6 +130,6 @@ public void testDisplayIndex_IsNotSet() { var views = viewService.getViews(); var columns = views.get(1).getColumns().stream().toList(); var selectedColumn = columns.stream().filter(c -> c.getTitle().equals("Laterality")).collect(Collectors.toList()).get(0); - Assert.assertEquals(Integer.valueOf(999), selectedColumn.getDisplayIndex()); + Assert.assertEquals(Integer.valueOf(Integer.MAX_VALUE), selectedColumn.getDisplayIndex()); } } From 36160ba6c1c8a880ee4d7343f626b2e471469e6d Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Thu, 14 Dec 2023 13:46:34 +0100 Subject: [PATCH 028/153] rename --- .../java/io/fairspace/saturn/services/views/ViewService.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java index 111825dc2..0c198ee1f 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java @@ -177,9 +177,9 @@ public List getViews() { var columns = new ArrayList(); // The entity labal is the first column displayed, if you want a column before this label, assign a negative displayIndex value in views.yaml - int entityLabelIndex = 0; + final int ENTITY_LABEL_INDEX = 0; - columns.add(new ColumnDTO(v.name, v.itemName == null ? v.name : v.itemName, ColumnType.Identifier, entityLabelIndex)); + columns.add(new ColumnDTO(v.name, v.itemName == null ? v.name : v.itemName, ColumnType.Identifier, ENTITY_LABEL_INDEX)); for (var c : v.columns) { columns.add(new ColumnDTO(v.name + "_" + c.name, c.title, c.type, c.displayIndex)); } From 4b8ab0ac29df583b338f0bb3f8c80073a45e65e0 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Mon, 18 Dec 2023 13:02:04 +0100 Subject: [PATCH 029/153] Select identifier of active view --- projects/mercury/src/metadata/views/MetadataView.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/projects/mercury/src/metadata/views/MetadataView.js b/projects/mercury/src/metadata/views/MetadataView.js index 56dc97996..32b4b835b 100644 --- a/projects/mercury/src/metadata/views/MetadataView.js +++ b/projects/mercury/src/metadata/views/MetadataView.js @@ -63,7 +63,7 @@ export const MetadataView = (props: MetadataViewProperties) => { const currentViewIndex = Math.max(0, views.map(v => v.name).indexOf(currentViewName)); const currentView = views[currentViewIndex]; - const currentViewIdColumn = currentView.columns.find(c => c.type === 'Identifier'); // first column of id type + const currentViewIdColumn = currentView.columns.find(c => c.type === 'Identifier' && c.name === currentView.name); const changeTab = useCallback((event, tabIndex) => { setIsClosedPanel(true); From c5da6fb9ab5c58071a57a55616763d4324e1fc7a Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Wed, 20 Dec 2023 13:10:50 +0100 Subject: [PATCH 030/153] Dialog for metadata details --- .../src/metadata/common/LinkedDataLink.js | 61 +++++++++++++++---- 1 file changed, 49 insertions(+), 12 deletions(-) diff --git a/projects/mercury/src/metadata/common/LinkedDataLink.js b/projects/mercury/src/metadata/common/LinkedDataLink.js index d012092b1..da386846e 100644 --- a/projects/mercury/src/metadata/common/LinkedDataLink.js +++ b/projects/mercury/src/metadata/common/LinkedDataLink.js @@ -1,28 +1,65 @@ +/* eslint-disable */ import React, {useContext} from 'react'; -import {Link as RouterLink} from "react-router-dom"; import * as PropTypes from "prop-types"; -import {Link} from '@mui/material'; -import {METADATA_PATH} from "../../constants"; +import {Box, Modal, Tooltip} from '@mui/material'; +import CloseIcon from '@mui/icons-material/Close'; +import LinkedDataEntityPage from "./LinkedDataEntityPage"; +import {MetadataWrapper} from '../LinkedDataWrapper'; import UserContext from '../../users/UserContext'; - /** * Renders a link to the metadata editor. * * @param props * @constructor */ + +const styleModalDialog = { + position: 'absolute', + top: '50%', + left: '50%', + transform: 'translate(-50%, -50%)', + width: 800, + bgcolor: 'background.paper', + border: '2px solid #000', + boxShadow: 24, + p: 4, +}; +const styleCloseButton = { + float: 'right' +} + +const getModal = (open, handleClose, uri) => ( + + + + + + + + + + +) + const LinkedDataLink = ({uri, children}) => { + const [open, setOpen] = React.useState(false); + const handleOpen = () => setOpen(true); + const handleClose = () => setOpen(false); + const {currentUser} = useContext(UserContext); if (currentUser && currentUser.canViewPublicMetadata) { return ( - - {children} - +
+
+ {children} +
+ {getModal(open, handleClose, uri)} +
); } return children; From 95d9e427e20b41afcf8abadbc3b9ee75826c3935 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Wed, 20 Dec 2023 13:16:45 +0100 Subject: [PATCH 031/153] cleanup --- .../mercury/src/metadata/common/LinkedDataLink.js | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/projects/mercury/src/metadata/common/LinkedDataLink.js b/projects/mercury/src/metadata/common/LinkedDataLink.js index da386846e..c2507b46b 100644 --- a/projects/mercury/src/metadata/common/LinkedDataLink.js +++ b/projects/mercury/src/metadata/common/LinkedDataLink.js @@ -1,10 +1,8 @@ -/* eslint-disable */ import React, {useContext} from 'react'; import * as PropTypes from "prop-types"; import {Box, Modal, Tooltip} from '@mui/material'; import CloseIcon from '@mui/icons-material/Close'; import LinkedDataEntityPage from "./LinkedDataEntityPage"; -import {MetadataWrapper} from '../LinkedDataWrapper'; import UserContext from '../../users/UserContext'; /** * Renders a link to the metadata editor. @@ -26,7 +24,7 @@ const styleModalDialog = { }; const styleCloseButton = { float: 'right' -} +}; const getModal = (open, handleClose, uri) => ( ( > - + - - - + -) +); const LinkedDataLink = ({uri, children}) => { const [open, setOpen] = React.useState(false); From 7cdb27bcdcc9e5ab6a45147e88dca1ba77d9e5b2 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Thu, 21 Dec 2023 10:50:56 +0100 Subject: [PATCH 032/153] small styling improvements --- .../src/metadata/common/LinkedDataLink.js | 34 +++++-------------- .../metadata/common/LinkedDataLink.styles.js | 22 ++++++++++++ 2 files changed, 31 insertions(+), 25 deletions(-) create mode 100644 projects/mercury/src/metadata/common/LinkedDataLink.styles.js diff --git a/projects/mercury/src/metadata/common/LinkedDataLink.js b/projects/mercury/src/metadata/common/LinkedDataLink.js index c2507b46b..666755a40 100644 --- a/projects/mercury/src/metadata/common/LinkedDataLink.js +++ b/projects/mercury/src/metadata/common/LinkedDataLink.js @@ -1,48 +1,32 @@ import React, {useContext} from 'react'; import * as PropTypes from "prop-types"; import {Box, Modal, Tooltip} from '@mui/material'; +import withStyles from '@mui/styles/withStyles'; import CloseIcon from '@mui/icons-material/Close'; import LinkedDataEntityPage from "./LinkedDataEntityPage"; import UserContext from '../../users/UserContext'; +import styles from './LinkedDataLink.styles'; /** - * Renders a link to the metadata editor. - * - * @param props - * @constructor + * Renders a link to the metadata editor in a modal dialog when clicked. */ -const styleModalDialog = { - position: 'absolute', - top: '50%', - left: '50%', - transform: 'translate(-50%, -50%)', - width: 800, - bgcolor: 'background.paper', - border: '2px solid #000', - boxShadow: 24, - p: 4, -}; -const styleCloseButton = { - float: 'right' -}; - -const getModal = (open, handleClose, uri) => ( +const getModal = (classes, open, handleClose, uri) => ( - + - + ); -const LinkedDataLink = ({uri, children}) => { +const LinkedDataLink = ({classes, uri, children}) => { const [open, setOpen] = React.useState(false); const handleOpen = () => setOpen(true); const handleClose = () => setOpen(false); @@ -54,7 +38,7 @@ const LinkedDataLink = ({uri, children}) => {
{children}
- {getModal(open, handleClose, uri)} + {getModal(classes, open, handleClose, uri)}
); } @@ -66,4 +50,4 @@ LinkedDataLink.propTypes = { children: PropTypes.any.isRequired }; -export default LinkedDataLink; +export default withStyles(styles)(LinkedDataLink); diff --git a/projects/mercury/src/metadata/common/LinkedDataLink.styles.js b/projects/mercury/src/metadata/common/LinkedDataLink.styles.js new file mode 100644 index 000000000..9dcdafdc2 --- /dev/null +++ b/projects/mercury/src/metadata/common/LinkedDataLink.styles.js @@ -0,0 +1,22 @@ +const styles = (theme) => ({ + styleModalDialog: { + background: theme.palette.grey['200'], + position: 'absolute', + top: '50%', + left: '50%', + transform: 'translate(-50%, -50%)', + width: 800, + bgcolor: 'background.paper', + border: '0px solid #000', + boxShadow: 0, + p: 4, + }, + styleCloseButton: { + float: 'right', + marginTop: 8, + marginRight: 8 + + } +}); + +export default styles; From 5cfda7ddbe45ef261d957f1001aa7a053d8a87d7 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Wed, 27 Dec 2023 10:48:01 +0100 Subject: [PATCH 033/153] Fix tests and styling of the linked data dialog. --- .../src/metadata/common/LinkedDataLink.js | 10 +-- .../metadata/common/LinkedDataLink.styles.js | 11 ++- .../common/__tests__/LinkedDataLink.js | 89 +++++++------------ 3 files changed, 44 insertions(+), 66 deletions(-) diff --git a/projects/mercury/src/metadata/common/LinkedDataLink.js b/projects/mercury/src/metadata/common/LinkedDataLink.js index 666755a40..68758cd03 100644 --- a/projects/mercury/src/metadata/common/LinkedDataLink.js +++ b/projects/mercury/src/metadata/common/LinkedDataLink.js @@ -10,16 +10,16 @@ import styles from './LinkedDataLink.styles'; * Renders a link to the metadata editor in a modal dialog when clicked. */ -const getModal = (classes, open, handleClose, uri) => ( +const renderModal = (classes, open, handleClose, uri) => ( - + - + @@ -35,10 +35,10 @@ const LinkedDataLink = ({classes, uri, children}) => { if (currentUser && currentUser.canViewPublicMetadata) { return (
-
+
{children}
- {getModal(classes, open, handleClose, uri)} + {renderModal(classes, open, handleClose, uri)}
); } diff --git a/projects/mercury/src/metadata/common/LinkedDataLink.styles.js b/projects/mercury/src/metadata/common/LinkedDataLink.styles.js index 9dcdafdc2..e044c26ee 100644 --- a/projects/mercury/src/metadata/common/LinkedDataLink.styles.js +++ b/projects/mercury/src/metadata/common/LinkedDataLink.styles.js @@ -1,5 +1,5 @@ const styles = (theme) => ({ - styleModalDialog: { + modalDialog: { background: theme.palette.grey['200'], position: 'absolute', top: '50%', @@ -9,13 +9,20 @@ const styles = (theme) => ({ bgcolor: 'background.paper', border: '0px solid #000', boxShadow: 0, + outline: "none", p: 4, }, - styleCloseButton: { + closeButton: { float: 'right', marginTop: 8, marginRight: 8 + }, + clickableDiv: { + 'cursor': 'pointer', + '&:hover': { + textDecoration: 'underline' + } } }); diff --git a/projects/mercury/src/metadata/common/__tests__/LinkedDataLink.js b/projects/mercury/src/metadata/common/__tests__/LinkedDataLink.js index 758cd7a74..e0675a18d 100644 --- a/projects/mercury/src/metadata/common/__tests__/LinkedDataLink.js +++ b/projects/mercury/src/metadata/common/__tests__/LinkedDataLink.js @@ -1,88 +1,59 @@ /* eslint-disable jsx-a11y/anchor-has-content */ import React from 'react'; -import {configure, mount} from "enzyme"; +import {configure} from "enzyme"; import Adapter from "@wojtekmaj/enzyme-adapter-react-17"; - -import {Router} from 'react-router-dom'; // eslint-disable-next-line import/no-extraneous-dependencies -import {createMemoryHistory} from 'history'; import LinkedDataLink from "../LinkedDataLink"; -import {METADATA_PATH} from "../../../constants"; +import {fireEvent, render} from "@testing-library/react"; +import theme from "../../../App.theme"; +import {ThemeProvider} from "@mui/material/styles"; import UserContext from '../../../users/UserContext'; // Enzyme is obsolete, the Adapter allows running our old tests. // For new tests use React Testing Library. Consider migrating enzyme tests when refactoring. configure({adapter: new Adapter()}); +jest.mock('../LinkedDataEntityPage', () => () =>
Mocked Metadata Page
); describe('LinkedDataLink', () => { - it('should render internal link for any uri', () => { - const history: History = createMemoryHistory(); - history.push = jest.fn(); - - const wrapper = mount( + it('renders LinkedDataLink without crashing', () => { + const { getByText } = render( - - Go - + + Test Content + ); - - expect(wrapper.find('a').isEmpty()).toBeFalsy(); - const anchor = wrapper.find('a').first(); - const expectedLocation = `${METADATA_PATH}?iri=${encodeURIComponent("http://google.nl/some-path?search#hash")}`; - expect(anchor.prop('href')).toEqual(expectedLocation); - expect(anchor.text()).toEqual('Go'); - expect(anchor.prop('onClick')).toBeTruthy(); - - anchor.prop('onClick')(new MouseEvent('click')); - expect(history.push).toBeCalledTimes(1); - expect(history.push).toBeCalledWith({ - pathname: METADATA_PATH, - search: `?iri=${encodeURIComponent("http://google.nl/some-path?search#hash")}` - }); + expect(getByText('Test Content')).toBeInTheDocument(); }); - it('should display child elements for users without access to public metadata', () => { - const history: History = createMemoryHistory(); - history.push = jest.fn(); - - const wrapper = mount( - - - Go - + it('shows the modal when clicked', () => { + const { getByText, queryByText } = render( + + + Test Content + ); + expect(queryByText('Mocked Metadata Page')).not.toBeInTheDocument(); - expect(wrapper.find('a').isEmpty()).toBeTruthy(); - expect(wrapper.text()).toEqual('Go'); + fireEvent.click(getByText('Test Content')); + expect(getByText('Mocked Metadata Page')).toBeInTheDocument(); }); - it('should not break on an invalid url (return children only)', () => { - const uri = `some-invalid-url`; - const history: History = createMemoryHistory(); - history.push = jest.fn(); - - const wrapper = mount( + it('closes the modal when close icon is clicked', () => { + const { getByText, getByTestId, queryByText } = render( - - something - + + Test Content + ); - expect(wrapper.find('a').isEmpty()).toBeFalsy(); - const anchor = wrapper.find('a').first(); - const expectedLocation = `${METADATA_PATH}?iri=${encodeURIComponent(uri)}`; - expect(anchor.prop('href')).toEqual(expectedLocation); - expect(anchor.text()).toEqual('something'); - expect(anchor.prop('onClick')).toBeTruthy(); + fireEvent.click(getByText('Test Content')); + expect(getByText('Mocked Metadata Page')).toBeInTheDocument(); - anchor.prop('onClick')(new MouseEvent('click')); - expect(history.push).toBeCalledTimes(1); - expect(history.push).toBeCalledWith({ - pathname: METADATA_PATH, - search: `?iri=${encodeURIComponent(uri)}` - }); + const close = getByTestId('CloseIcon'); + fireEvent.click(close); + expect(queryByText('Mocked Metadata Page')).not.toBeInTheDocument(); }); }); From 1c62a6d22068ae5994643949f8fa973ee1ec2fce Mon Sep 17 00:00:00 2001 From: tgreenwood Date: Tue, 2 Jan 2024 14:33:52 +0100 Subject: [PATCH 034/153] FAIRSPC-11: (#1457) 1. fixed manual entering of dates in filter facets 2. improved input dates validation in filters 3. fixed date format 4. fixed the month view of the DatePicker --- .../src/metadata/common/values/DateValue.js | 2 +- .../views/facets/DateSelectionFacet.js | 39 ++++++++++++------- 2 files changed, 27 insertions(+), 14 deletions(-) diff --git a/projects/mercury/src/metadata/common/values/DateValue.js b/projects/mercury/src/metadata/common/values/DateValue.js index e79beb9b1..a79bf78e4 100644 --- a/projects/mercury/src/metadata/common/values/DateValue.js +++ b/projects/mercury/src/metadata/common/values/DateValue.js @@ -34,7 +34,7 @@ class DateValue extends React.Component { return ( { if (val.toString() === 'Invalid Date') { return false; } - return (val >= minDate && val <= maxDate); + // lib.es5 Date constructor (used in the getRangeLimit method) converts two-digits (XX) input year to 1900+XX. + // For instance, 68 turns to 1900 + 68 -> 1968. + // Thus, only 4 digits year are considered as valid. + const fourDigitsYearEntered = val.getFullYear().toString().length === 4; + return (val >= minDate && val <= maxDate && fourDigitsYearEntered); }; - const handleChange = (newValue) => { - if (value !== newValue) { - setValue(newValue); - if (isValid(newValue[0]) && isValid(newValue[1])) { - onChange(newValue); - } else { - onChange(null); - } + const isValidInterval = (startDate: Date, endDate: Date): boolean => ( + !startDate || !endDate || (startDate <= endDate) + ); + + const handleChange = (newDateInterval) => { + if (isValidInterval(newDateInterval)) { + onChange(newDateInterval); } }; const handleMinDateChange = (newValue) => { - handleChange([getRangeLimit(newValue), value[1]]); + const oldEndDate = value[1]; + setValue([newValue, oldEndDate]); + if (isValid(newValue)) { + const newDateInterval = [getRangeLimit(newValue), oldEndDate]; + handleChange(newDateInterval); + } }; const handleMaxDateChange = (newValue) => { - handleChange([value[0], getRangeLimit(newValue, true)]); + const oldStartDate = value[0]; + setValue([oldStartDate, newValue]); + if (isValid(newValue)) { + const newDateInterval = [oldStartDate, getRangeLimit(newValue, true)]; + handleChange(newDateInterval); + } }; const renderDate = (val: any): string => { @@ -79,7 +92,7 @@ const DateSelectionFacet = (props: MetadataViewFacetProperties) => { { autoOk minDate={min || minDate} maxDate={max || maxDate} - initialFocusedDate={placeholderDate} + defaultCalendarMonth={placeholderDate} placeholder={renderDate(placeholderDate)} KeyboardButtonProps={{ 'aria-label': 'change date', From e4b777ca5ba6172dfc5ecbed1ce648a746649024 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Tue, 16 Jan 2024 14:48:43 +0100 Subject: [PATCH 035/153] reduced number of db calls for viewstorereader --- .../saturn/services/views/ViewRow.java | 22 +++++ .../services/views/ViewRowCollection.java | 24 +++++ .../services/views/ViewStoreReader.java | 95 ++++++++++++------- 3 files changed, 107 insertions(+), 34 deletions(-) create mode 100644 projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java create mode 100644 projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRowCollection.java diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java new file mode 100644 index 000000000..82f54e5dc --- /dev/null +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java @@ -0,0 +1,22 @@ +package io.fairspace.saturn.services.views; + +import java.util.HashMap; +import java.util.Map; +import java.util.Set; + +public class ViewRow { + private Map> data; + + public ViewRow() { + data = new HashMap<>(); + } + + // TODO, make obsolete by ViewStoreReader refactor + public Map> getRawData() { + return data; + } + + public void put(String key, Set value) { + data.put(key, value); + } +} diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRowCollection.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRowCollection.java new file mode 100644 index 000000000..93492b43b --- /dev/null +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRowCollection.java @@ -0,0 +1,24 @@ +package io.fairspace.saturn.services.views; + +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.List; + +public class ViewRowCollection { + + private Hashtable> data = new Hashtable>(); + + public ViewRowCollection() { + } + + public void add(String id, ViewRow row) { + if (!data.containsKey(id)) { + data.put(id, new ArrayList<>()); + } + data.get(id).add(row); + } + + public List getRowsForId(String id) { + return data.get(id); + } +} diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java index f9a5f2dc3..3d9de0a14 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java @@ -13,6 +13,7 @@ import java.time.*; import java.util.*; import java.util.Date; +import java.util.function.Function; import java.util.stream.*; import static io.fairspace.saturn.config.ViewsConfig.ColumnType.Date; @@ -218,7 +219,7 @@ String sqlConstraint(String fieldName, ViewFilter filter, List values) { }).collect(Collectors.joining(" or ")); constraints.add("(" + prefixes + ")"); } - if(filter.booleanValue != null) { + if (filter.booleanValue != null) { if (filter.booleanValue) { constraints.add("(" + fieldName + "=true)"); } else { @@ -246,11 +247,11 @@ String sqlFilter(String alias, View view, List filters, List if (column != null && column.type.isSet()) { var propertyTable = configuration.propertyTables.get(view.name).get(column.name); var subConstraint = sqlConstraint("pt." + field, filter, values); - return "exists (select *" + - " from " + propertyTable.name + " pt " + - " where pt." + idColumn(view.name).name + " = " + alias + ".id" + - (subConstraint.isBlank() ? "" : " and " + subConstraint) + - ")"; + return "exists (select *" + + " from " + propertyTable.name + " pt " + + " where pt." + idColumn(view.name).name + " = " + alias + ".id" + + (subConstraint.isBlank() ? "" : " and " + subConstraint) + + ")"; } return sqlConstraint(alias + "." + field, filter, values); }) @@ -373,8 +374,8 @@ List>> retrieveViewTableRows( } } - List>> retrieveJoinTableRows( - String view, View.JoinView joinView, String id) throws SQLException { + ViewRowCollection retrieveJoinTableRows( + String view, View.JoinView joinView, List ids) throws SQLException { var joinedTable = configuration.viewTables.get(joinView.view); var joinViewConfig = configuration.viewConfig.get(joinView.view); var valueSetProperties = joinViewConfig.columns.stream() @@ -388,22 +389,17 @@ List>> retrieveJoinTableRows( Stream.of("id", "label"), joinView.include.stream() .filter(column -> !valueSetProperties.contains(column))) + .distinct() .collect(Collectors.toList()); - var query = connection.prepareStatement( - "select " + projectionColumns.stream().map(String::toLowerCase).collect(Collectors.joining(", ")) + - " from " + joinedTable.name + " j " + - " where exists (" + - " select * from " + joinTable.name + " jt " + - " where jt." + idColumn(joinView.view).name + " = j.id" + - " and jt." + idColumn(view).name + " = ? )" + - "limit " + String.valueOf(MAX_JOIN_ITEMS) - ); - query.setString(1, id); + var query = getQuery(view, joinView, joinedTable, joinTable, projectionColumns, ids); var result = query.executeQuery(); - List>> rows = new ArrayList<>(); + + var rows = new ViewRowCollection(); + while (result.next()) { - Map> row = new HashMap<>(); + var row = new ViewRow(); + var id = result.getString("rowid"); row.put(joinView.view, Collections.singleton(new ValueDTO(result.getString("label"), result.getString("id")))); for (var column : projectionColumns) { var columnName = joinView.view + "_" + column; @@ -427,8 +423,8 @@ List>> retrieveJoinTableRows( row.put(columnName, Collections.singleton(new ValueDTO(label, label))); } } - addValueSetValues(joinView.view, row, valueSetProperties, valueSetQueries); - rows.add(row); + addValueSetValues(joinView.view, row.getRawData(), valueSetProperties, valueSetQueries); + rows.add(id, row); } for (var q : valueSetQueries.values()) { q.close(); @@ -437,10 +433,28 @@ List>> retrieveJoinTableRows( return rows; } + private PreparedStatement getQuery(String view, View.JoinView joinView, Table joinedTable, Table joinTable, + List projectionColumns, List ids) throws SQLException { + + + Function queryBody = id + -> "(select " + projectionColumns.stream().map(String::toLowerCase).collect(Collectors.joining(", ")) + " , '" + id + "' AS rowid" + + " from " + joinedTable.name + " j " + + " where exists (" + + " select * from " + joinTable.name + " jt " + + " where jt." + idColumn(joinView.view).name + " = j.id" + + " and jt." + idColumn(view).name + " = '" + id + "'" + + ") limit " + String.valueOf(MAX_JOIN_ITEMS) + ")"; + + var subqueries = ids.stream().map(queryBody); + var query = subqueries.collect(Collectors.joining("\n UNION \n")); + return connection.prepareStatement(query); + } + /** * Compute the range of numerical or date values in a column of a view. * - * @param view the view name. + * @param view the view name. * @param column the column name. * @return a range object containing the minimum and maximum values. */ @@ -507,19 +521,18 @@ public List>> retrieveRows( } // Fetch rows with columns from the view table var rows = this.retrieveViewTableRows(view, filters, offset, limit); + // Add items from join tables if (includeJoinedViews) { for (var joinView : viewConfig.join) { + var rowIds = rows.stream().map(r + -> (String) r.get(view).stream().findFirst().orElseThrow().getValue()) + .toList(); + + var allJoinTableRows = this.retrieveJoinTableRows(view, joinView, rowIds); for (var row : rows) { - var id = (String) row.get(view).stream().findFirst().orElseThrow().getValue(); - for (var joinTableRow : this.retrieveJoinTableRows(view, joinView, id)) { - joinTableRow.forEach((key, values) -> { - if (!row.containsKey(key)) { - row.put(key, new LinkedHashSet<>()); - } - row.get(key).addAll(values); - }); - } + var rowId = (String) row.get(view).stream().findFirst().orElseThrow().getValue(); + addJoinTableRowsForRow(row, allJoinTableRows.getRowsForId(rowId)); } } } @@ -531,6 +544,20 @@ public List>> retrieveRows( } } + private void addJoinTableRowsForRow( + Map> row, + List allJoinTableRows) { + + for (var joinTableRow : allJoinTableRows) { + joinTableRow.getRawData().forEach((key, values) -> { + if (!row.containsKey(key)) { + row.put(key, new LinkedHashSet<>()); + } + row.get(key).addAll(values); + }); + } + } + /** * @param view * @param filters @@ -566,7 +593,7 @@ public List searchFiles(FileSearchRequest request, List .stream() .map(uc -> "?") .collect(Collectors.toList()); - var collectionConstraint = "and collection in (" + String.join(", ",collectionPlaceholders) + ") "; + var collectionConstraint = "and collection in (" + String.join(", ", collectionPlaceholders) + ") "; var idConstraint = StringUtils.isBlank(request.getParentIRI()) ? "" : "and id like '" + escapeLikeString(request.getParentIRI()) + "%' "; @@ -579,7 +606,7 @@ public List searchFiles(FileSearchRequest request, List .append("order by id asc limit 1000"); try (var statement = connection.prepareStatement(queryString.toString())) { - for(int i = 0; i< values.size(); i++) { + for (int i = 0; i < values.size(); i++) { statement.setString(i + 1, values.get(i)); } From b232cb507e8372d13c5853327900e46d3eb869c5 Mon Sep 17 00:00:00 2001 From: anton Date: Tue, 16 Jan 2024 10:47:09 +0100 Subject: [PATCH 036/153] FAIRSPC-29: fixed numeric filter with forced casting to numeric (Postgresql) type to avoid inaccurate casting of PreparedStatement causing a performance issue --- .../src/metadata/views/MetadataView.js | 3 ++- .../src/metadata/views/MetadataViewAPI.js | 1 + .../src/metadata/views/metadataViewUtils.js | 1 + .../saturn/services/views/ViewFilter.java | 1 + .../services/views/ViewStoreReader.java | 26 ++++++++++++------- 5 files changed, 22 insertions(+), 10 deletions(-) diff --git a/projects/mercury/src/metadata/views/MetadataView.js b/projects/mercury/src/metadata/views/MetadataView.js index 32b4b835b..d8bad2f1d 100644 --- a/projects/mercury/src/metadata/views/MetadataView.js +++ b/projects/mercury/src/metadata/views/MetadataView.js @@ -13,7 +13,7 @@ import MetadataViewContext from "./MetadataViewContext"; import BreadcrumbsContext from "../../common/contexts/BreadcrumbsContext"; import {getLocationContextFromString, getMetadataViewNameFromString} from "../../search/searchUtils"; import type {MetadataViewEntity} from "./metadataViewUtils"; -import {getMetadataViewsPath, ofBooleanValueType, ofRangeValueType, RESOURCES_VIEW} from "./metadataViewUtils"; +import {getMetadataViewsPath, ofBooleanValueType, ofRangeValueType, ofNumericValueType, RESOURCES_VIEW} from "./metadataViewUtils"; import MetadataViewActiveFacetFilters from "./MetadataViewActiveFacetFilters"; import MetadataViewInformationDrawer from "./MetadataViewInformationDrawer"; import {useSingleSelection} from "../../file/UseSelection"; @@ -87,6 +87,7 @@ export const MetadataView = (props: MetadataViewProperties) => { const setFilterValues = (type: ValueType, filter: MetadataViewFilter, values: any[]) => { if (ofRangeValueType(type)) { [filter.min, filter.max] = values; + filter.numericValue = ofNumericValueType(type); } else if (ofBooleanValueType(type)) { filter.booleanValue = values.length > 0 ? values[0] : null; } else { diff --git a/projects/mercury/src/metadata/views/MetadataViewAPI.js b/projects/mercury/src/metadata/views/MetadataViewAPI.js index 2c87ab39a..8490fdbec 100644 --- a/projects/mercury/src/metadata/views/MetadataViewAPI.js +++ b/projects/mercury/src/metadata/views/MetadataViewAPI.js @@ -13,6 +13,7 @@ export type MetadataViewFilter = { max: any; prefix: string; booleanValue?: boolean; + numericValue?: boolean; } export type MetadataViewFacetValue = { diff --git a/projects/mercury/src/metadata/views/metadataViewUtils.js b/projects/mercury/src/metadata/views/metadataViewUtils.js index d93936103..01ab68af9 100644 --- a/projects/mercury/src/metadata/views/metadataViewUtils.js +++ b/projects/mercury/src/metadata/views/metadataViewUtils.js @@ -21,3 +21,4 @@ export const getMetadataViewsPath = (viewName: string) => { export const ofRangeValueType: boolean = (type: ValueType) => type === 'Number' || type === 'Date'; export const ofBooleanValueType: boolean = (type: ValueType) => type === 'Boolean'; +export const ofNumericValueType: boolean = (type: ValueType) => type === 'Number'; diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewFilter.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewFilter.java index 294ecb9c4..4c0f04b33 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewFilter.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewFilter.java @@ -18,6 +18,7 @@ public class ViewFilter { Object min; Object max; Boolean booleanValue; + Boolean numericValue; String prefix; /** * Used internally for filtering on resource location. diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java index f9a5f2dc3..5d4a11f51 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java @@ -1,19 +1,21 @@ package io.fairspace.saturn.services.views; -import io.fairspace.saturn.config.*; -import io.fairspace.saturn.config.ViewsConfig.*; +import io.fairspace.saturn.config.Config; +import io.fairspace.saturn.config.ViewsConfig.ColumnType; +import io.fairspace.saturn.config.ViewsConfig.View; import io.fairspace.saturn.services.search.FileSearchRequest; import io.fairspace.saturn.services.search.SearchResultDTO; -import io.fairspace.saturn.vocabulary.*; +import io.fairspace.saturn.vocabulary.FS; import lombok.SneakyThrows; -import lombok.extern.slf4j.*; +import lombok.extern.slf4j.Slf4j; import org.apache.commons.lang3.StringUtils; import java.sql.*; -import java.time.*; -import java.util.*; +import java.time.Instant; import java.util.Date; -import java.util.stream.*; +import java.util.*; +import java.util.stream.Collectors; +import java.util.stream.Stream; import static io.fairspace.saturn.config.ViewsConfig.ColumnType.Date; import static io.fairspace.saturn.services.views.Table.idColumn; @@ -193,13 +195,19 @@ String sqlConstraint(String fieldName, ViewFilter filter, List values) { .collect(Collectors.joining(", "))); } var constraints = new ArrayList(); + // NOTE: for NUMERIC filter, turned out, PreparedStatement may cast them as real or double, + // what causes a dramatic slow down for the query execution (up to x100). + // As a workaround, we force PrepareStatement to send the request with numeric type (the same as it is defined + // in the database schema) if (filter.getMin() != null) { values.add(filter.getMin()); - constraints.add(fieldName + " >= ?"); + var constraint = filter.numericValue ? " >= ?::numeric" : " >= ?"; + constraints.add(fieldName + constraint); } if (filter.getMax() != null) { values.add(filter.getMax()); - constraints.add(fieldName + " <= ?"); + var constraint = filter.numericValue ? " <= ?::numeric" : " <= ?"; + constraints.add(fieldName + constraint); } if (filter.getPrefix() != null && !filter.getPrefix().isBlank()) { // Use view label instead of id for prefix filters From 94179d8a4392a4c695b0e226e230da49befc97f7 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Wed, 17 Jan 2024 14:00:32 +0100 Subject: [PATCH 037/153] handle unlinked nodes --- .../io/fairspace/saturn/services/views/ViewRowCollection.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRowCollection.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRowCollection.java index 93492b43b..2fcf16fc7 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRowCollection.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRowCollection.java @@ -19,6 +19,9 @@ public void add(String id, ViewRow row) { } public List getRowsForId(String id) { + if (!data.containsKey(id)) { + return new ArrayList(); + } return data.get(id); } } From ffb54340db12aca524fb42587ce8035a0520a33b Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Thu, 18 Jan 2024 14:06:05 +0100 Subject: [PATCH 038/153] document pv persistence new statefulset --- README.adoc | 46 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/README.adoc b/README.adoc index 74eca0d58..2d424dd3c 100644 --- a/README.adoc +++ b/README.adoc @@ -2740,6 +2740,52 @@ kubectl delete statefulset fairspace-new --namespace fairspace-new --cascade=orp This will remove the ``StatefulSet``, but keep all pods and volumes intact. After running ``helm upgrade --install`` the ``StatefulSet`` will be recreated and the running pod will be replaced with a pod running the new application version. +===== Keep existing volumes on update of StatefulSet + +Any changes on the StatefulSet will require a clean deployment, with new volumes. If you want to change the StatefulSet while keeping your existing volumes follow the procedure as described below. + +To preserve your volumes get the volume id's: + +[source,shell] +---- +$ kubectl get pv -n +---- + +Now patch the volumes so they are not deleted automatically when the VolumeClaim is removed: + +[source,shell] +---- +$ kubectl patch pv -p '{"spec":{"persistentVolumeReclaimPolicy":"Retain"}}' +$ kubectl get pv # now shows status 'released' +---- + +Uninstall the statefulset and remove the VolumeClaims. In released status the volumes cannot bind to a new claim, therefore remove the claim reference: + +[source,shell] +---- +$ kubectl edit pv +---- +In the editor, remove the 'claimref' section. + +The final step is to add the previously gathered Volume id's to the statefulset configuration: + +[source,yaml] +---- +volumeClaimTemplates: +- metadata: + name: postgres +spec: + accessModes: [ "ReadWriteOnce" ] + resources: + requests: + {...} + volumeName: "" +---- + +Now execute the deployment. + +For more details see https://cloud.google.com/kubernetes-engine/docs/how-to/persistent-volumes/preexisting-pd#pvc_to_pv + ===== Clean up deployment To clean up an environment or completely reinstall an environment, you can use ``helm uninstall`` or ``kubectl delete``. From 63562c56d0ddd79047eb76447aefc1d79ecf0679 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Thu, 18 Jan 2024 14:22:22 +0100 Subject: [PATCH 039/153] Update README.adoc MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Ewelina Grudzień --- README.adoc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.adoc b/README.adoc index 2d424dd3c..bc8895b1c 100644 --- a/README.adoc +++ b/README.adoc @@ -2744,7 +2744,7 @@ After running ``helm upgrade --install`` the ``StatefulSet`` will be recreated a Any changes on the StatefulSet will require a clean deployment, with new volumes. If you want to change the StatefulSet while keeping your existing volumes follow the procedure as described below. -To preserve your volumes get the volume id's: +To preserve your volumes get the volume id's (pv-name's): [source,shell] ---- From a433d9005be7e07de5ab70568cbb6c8eeba7dda5 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Thu, 18 Jan 2024 14:28:24 +0100 Subject: [PATCH 040/153] fixed typo --- README.adoc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.adoc b/README.adoc index bc8895b1c..128bf4242 100644 --- a/README.adoc +++ b/README.adoc @@ -2767,7 +2767,7 @@ $ kubectl edit pv ---- In the editor, remove the 'claimref' section. -The final step is to add the previously gathered Volume id's to the statefulset configuration: +The final step is to add the previously gathered volume id's to the statefulset configuration: [source,yaml] ---- From a9ed6b661508ff7b52fafd66f80ab077e3117aef Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Thu, 18 Jan 2024 15:58:50 +0100 Subject: [PATCH 041/153] PR improvements --- .../saturn/services/views/ViewRow.java | 7 +- .../services/views/ViewRowCollection.java | 16 ++-- .../services/views/ViewStoreReader.java | 73 +++++++++++-------- 3 files changed, 52 insertions(+), 44 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java index 82f54e5dc..cf213d459 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java @@ -1,19 +1,20 @@ package io.fairspace.saturn.services.views; +import java.util.Collections; import java.util.HashMap; import java.util.Map; import java.util.Set; public class ViewRow { - private Map> data; + + private Map> data = new HashMap<>(); public ViewRow() { - data = new HashMap<>(); } // TODO, make obsolete by ViewStoreReader refactor public Map> getRawData() { - return data; + return Collections.unmodifiableMap(data); } public void put(String key, Set value) { diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRowCollection.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRowCollection.java index 2fcf16fc7..42e7adecd 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRowCollection.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRowCollection.java @@ -1,27 +1,23 @@ package io.fairspace.saturn.services.views; import java.util.ArrayList; -import java.util.Hashtable; +import java.util.HashMap; import java.util.List; +import java.util.Map; public class ViewRowCollection { - private Hashtable> data = new Hashtable>(); + private Map> data = new HashMap<>(); public ViewRowCollection() { } public void add(String id, ViewRow row) { - if (!data.containsKey(id)) { - data.put(id, new ArrayList<>()); - } - data.get(id).add(row); + var value = data.computeIfAbsent(id, x -> new ArrayList<>()); + value.add(row); } public List getRowsForId(String id) { - if (!data.containsKey(id)) { - return new ArrayList(); - } - return data.get(id); + return data.getOrDefault(id, new ArrayList()); } } diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java index 02c298434..d4022aa05 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java @@ -18,6 +18,8 @@ import java.util.function.Function; import java.util.stream.Stream; +import javax.validation.constraints.NotBlank; + import static io.fairspace.saturn.config.ViewsConfig.ColumnType.Date; import static io.fairspace.saturn.services.views.Table.idColumn; @@ -36,6 +38,7 @@ public class ViewStoreReader implements AutoCloseable { final Connection connection; final int MAX_JOIN_ITEMS = 50; + // TODO: in whole class, use StringBuilder instead of String concats public ViewStoreReader(Config.Search searchConfig, ViewStoreClientFactory viewStoreClientFactory) throws SQLException { this.searchConfig = searchConfig; this.configuration = viewStoreClientFactory.configuration; @@ -384,6 +387,7 @@ List>> retrieveViewTableRows( ViewRowCollection retrieveJoinTableRows( String view, View.JoinView joinView, List ids) throws SQLException { + var joinedTable = configuration.viewTables.get(joinView.view); var joinViewConfig = configuration.viewConfig.get(joinView.view); var valueSetProperties = joinViewConfig.columns.stream() @@ -400,40 +404,17 @@ ViewRowCollection retrieveJoinTableRows( .distinct() .collect(Collectors.toList()); - var query = getQuery(view, joinView, joinedTable, joinTable, projectionColumns, ids); + var query = getJoinQuery(view, joinView, joinedTable, joinTable, projectionColumns, ids); var result = query.executeQuery(); var rows = new ViewRowCollection(); while (result.next()) { - var row = new ViewRow(); var id = result.getString("rowid"); - row.put(joinView.view, Collections.singleton(new ValueDTO(result.getString("label"), result.getString("id")))); - for (var column : projectionColumns) { - var columnName = joinView.view + "_" + column; - var columnDefinition = configuration.viewTables.get(joinView.view).getColumns().stream() - .filter(c -> c.getName().equalsIgnoreCase(column)) - .findFirst().orElseThrow(() -> { - throw new NoSuchElementException("Cannot find column " + column); - }); - if (columnDefinition.type == ColumnType.Number) { - var value = result.getBigDecimal(columnDefinition.name); - if (value != null) { - row.put(columnName, Collections.singleton(new ValueDTO(value.toString(), value))); - } - } else if (columnDefinition.type == Date) { - var value = result.getTimestamp(columnDefinition.name); - if (value != null) { - row.put(columnName, Collections.singleton(new ValueDTO(value.toInstant().toString(), value.toString()))); - } - } else { - var label = result.getString(columnDefinition.name); - row.put(columnName, Collections.singleton(new ValueDTO(label, label))); - } - } - addValueSetValues(joinView.view, row.getRawData(), valueSetProperties, valueSetQueries); + var row = buildRows(joinView, valueSetProperties, valueSetQueries, projectionColumns, result, rows); rows.add(id, row); } + for (var q : valueSetQueries.values()) { q.close(); } @@ -441,7 +422,39 @@ ViewRowCollection retrieveJoinTableRows( return rows; } - private PreparedStatement getQuery(String view, View.JoinView joinView, Table joinedTable, Table joinTable, + private ViewRow buildRows(View.JoinView joinView, List<@NotBlank String> valueSetProperties, + Map valueSetQueries, List projectionColumns, ResultSet result, + ViewRowCollection rows) throws SQLException { + + var row = new ViewRow(); + row.put(joinView.view, Collections.singleton(new ValueDTO(result.getString("label"), result.getString("id")))); + for (var column : projectionColumns) { + var columnName = joinView.view + "_" + column; + var columnDefinition = configuration.viewTables.get(joinView.view).getColumns().stream() + .filter(c -> c.getName().equalsIgnoreCase(column)) + .findFirst().orElseThrow(() -> { + throw new NoSuchElementException("Cannot find column " + column); + }); + if (columnDefinition.type == ColumnType.Number) { + var value = result.getBigDecimal(columnDefinition.name); + if (value != null) { + row.put(columnName, Collections.singleton(new ValueDTO(value.toString(), value))); + } + } else if (columnDefinition.type == Date) { + var value = result.getTimestamp(columnDefinition.name); + if (value != null) { + row.put(columnName, Collections.singleton(new ValueDTO(value.toInstant().toString(), value.toString()))); + } + } else { + var label = result.getString(columnDefinition.name); + row.put(columnName, Collections.singleton(new ValueDTO(label, label))); + } + } + addValueSetValues(joinView.view, row.getRawData(), valueSetProperties, valueSetQueries); + return row; + } + + private PreparedStatement getJoinQuery(String view, View.JoinView joinView, Table joinedTable, Table joinTable, List projectionColumns, List ids) throws SQLException { @@ -558,10 +571,8 @@ private void addJoinTableRowsForRow( for (var joinTableRow : allJoinTableRows) { joinTableRow.getRawData().forEach((key, values) -> { - if (!row.containsKey(key)) { - row.put(key, new LinkedHashSet<>()); - } - row.get(key).addAll(values); + var value = row.computeIfAbsent(key, x -> new LinkedHashSet<>()); // TODO investigate, is LinkedHashSet best choice here? + value.addAll(values); }); } } From 4ee11e2dc31c23856a25915d601e1e1b28ecad76 Mon Sep 17 00:00:00 2001 From: anton Date: Thu, 18 Jan 2024 16:18:39 +0100 Subject: [PATCH 042/153] FAIRSPC-29: rolledback making returning map unmodifiable for view row --- .../main/java/io/fairspace/saturn/services/views/ViewRow.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java index cf213d459..56c257005 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java @@ -1,6 +1,5 @@ package io.fairspace.saturn.services.views; -import java.util.Collections; import java.util.HashMap; import java.util.Map; import java.util.Set; @@ -13,8 +12,9 @@ public ViewRow() { } // TODO, make obsolete by ViewStoreReader refactor + // TODO: return unmodifiable map public Map> getRawData() { - return Collections.unmodifiableMap(data); + return data; } public void put(String key, Set value) { From 77c058c57f9b8edb8d2486257c816d613b0f9a11 Mon Sep 17 00:00:00 2001 From: anton Date: Fri, 19 Jan 2024 00:19:24 +0100 Subject: [PATCH 043/153] Fixed NPE for numeric filter --- .../io/fairspace/saturn/services/views/ViewStoreReader.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java index d4022aa05..17ec031bd 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java @@ -203,14 +203,15 @@ String sqlConstraint(String fieldName, ViewFilter filter, List values) { // what causes a dramatic slow down for the query execution (up to x100). // As a workaround, we force PrepareStatement to send the request with numeric type (the same as it is defined // in the database schema) + var isNumericFilter = filter.numericValue != null && filter.numericValue; if (filter.getMin() != null) { values.add(filter.getMin()); - var constraint = filter.numericValue ? " >= ?::numeric" : " >= ?"; + var constraint = isNumericFilter ? " >= ?::numeric" : " >= ?"; constraints.add(fieldName + constraint); } if (filter.getMax() != null) { values.add(filter.getMax()); - var constraint = filter.numericValue ? " <= ?::numeric" : " <= ?"; + var constraint = isNumericFilter ? " <= ?::numeric" : " <= ?"; constraints.add(fieldName + constraint); } if (filter.getPrefix() != null && !filter.getPrefix().isBlank()) { From cde63029884a4a3bae08b96ba4971ba5fb9b5b8d Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Fri, 19 Jan 2024 12:28:28 +0100 Subject: [PATCH 044/153] Initial change to support external metadata view pages. --- projects/mercury/src/layout/MainMenu.js | 29 +++++- .../mercury/src/layout/WorkspaceLayout.js | 21 +++-- .../ExternalMetadataSourceContext.js | 22 +++++ .../ExternalMetadataSourceView.js | 88 +++++++++++++++++++ .../UseExternalMetadataSource.js | 51 +++++++++++ .../UseExternalMetadataSourceViewFacets.js | 36 ++++++++ .../externalMetadataSourceUtils.js | 11 +++ .../src/metadata/views/MetadataView.js | 23 ++--- .../src/metadata/views/MetadataViewAPI.js | 21 +++-- .../src/metadata/views/MetadataViewContext.js | 7 +- .../views/MetadataViewTableContainer.js | 6 +- .../src/metadata/views/MetadataViewTabs.js | 5 +- .../mercury/src/metadata/views/UseViewData.js | 4 +- .../src/metadata/views/metadataViewUtils.js | 4 +- .../mercury/src/routes/WorkspaceRoutes.js | 16 +++- .../java/nl/fairspace/pluto/config/Urls.java | 1 + .../pluto/config/dto/PlutoConfig.java | 9 ++ .../pluto/web/MetadataSourcesResource.java | 40 +++++++++ .../pluto/web/dto/MetadataSourceInfo.java | 16 ++++ .../src/main/resources/application-local.yml | 13 ++- 20 files changed, 381 insertions(+), 42 deletions(-) create mode 100644 projects/mercury/src/metadata/external-sources/ExternalMetadataSourceContext.js create mode 100644 projects/mercury/src/metadata/external-sources/ExternalMetadataSourceView.js create mode 100644 projects/mercury/src/metadata/external-sources/UseExternalMetadataSource.js create mode 100644 projects/mercury/src/metadata/external-sources/UseExternalMetadataSourceViewFacets.js create mode 100644 projects/mercury/src/metadata/external-sources/externalMetadataSourceUtils.js create mode 100644 projects/pluto/src/main/java/nl/fairspace/pluto/web/MetadataSourcesResource.java create mode 100644 projects/pluto/src/main/java/nl/fairspace/pluto/web/dto/MetadataSourceInfo.java diff --git a/projects/mercury/src/layout/MainMenu.js b/projects/mercury/src/layout/MainMenu.js index abb6d6a70..c1bd816c5 100644 --- a/projects/mercury/src/layout/MainMenu.js +++ b/projects/mercury/src/layout/MainMenu.js @@ -2,13 +2,23 @@ import React, {useContext} from 'react'; import withStyles from '@mui/styles/withStyles'; import {NavLink} from "react-router-dom"; import {Divider, List, ListItemButton, ListItemIcon, ListItemText} from "@mui/material"; -import {Assignment, Folder, FolderSpecial, OpenInNew, VerifiedUser, Widgets} from "@mui/icons-material"; +import { + Search, + SavedSearch, + Folder, + FolderSpecial, + OpenInNew, + VerifiedUser, + Widgets +} from "@mui/icons-material"; import ServicesContext from "../common/contexts/ServicesContext"; import UserContext from "../users/UserContext"; import {isAdmin} from "../users/userUtils"; import MetadataViewContext from "../metadata/views/MetadataViewContext"; import ExternalStoragesContext from "../external-storage/ExternalStoragesContext"; +import ExternalMetadataSourceContext from "../metadata/external-sources/ExternalMetadataSourceContext"; import {getExternalStoragePathPrefix} from "../external-storage/externalStorageUtils"; +import {getExternalMetadataSourcePathPrefix} from "../metadata/external-sources/externalMetadataSourceUtils"; const styles = { mainMenuButton: { @@ -21,6 +31,7 @@ const MainMenu = ({classes}) => { const {services} = useContext(ServicesContext); const {currentUser} = useContext(UserContext); const {externalStorages} = useContext(ExternalStoragesContext); + const {externalMetadataSources} = useContext(ExternalMetadataSourceContext); const {views} = useContext(MetadataViewContext); // eslint-disable-next-line no-template-curly-in-string const interpolate = s => s.replace('${username}', currentUser.username); @@ -73,11 +84,25 @@ const MainMenu = ({classes}) => { selected={pathname.startsWith('/metadata-views')} > - + )} + {currentUser.canViewPublicMetadata && externalMetadataSources && externalMetadataSources.map(source => ( + + + + + + + ))} {isAdmin(currentUser) && ( { const {workspaces} = useContext(WorkspaceContext); @@ -30,15 +31,17 @@ const WorkspaceLayoutInner = () => { - - - } - renderMain={() => } - renderTopbar={() => } - /> - - + + + + } + renderMain={() => } + renderTopbar={() => } + /> + + + diff --git a/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceContext.js b/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceContext.js new file mode 100644 index 000000000..282299048 --- /dev/null +++ b/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceContext.js @@ -0,0 +1,22 @@ +import React from 'react'; +import axios from "axios"; +import {extractJsonData, handleHttpError} from "../../common/utils/httpUtils"; +import useAsync from "../../common/hooks/UseAsync"; + +const ExternalMetadataSourceContext = React.createContext({}); + +export const ExternalMetadataSourcesProvider = ({children}) => { + const {data: externalMetadataSources = []} = useAsync(() => axios.get('/api/metadata-sources/') + .then(extractJsonData) + .catch(handleHttpError('Connection error.'))); + + return ( + + {children} + + ); +}; + +export default ExternalMetadataSourceContext; diff --git a/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceView.js b/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceView.js new file mode 100644 index 000000000..c503fdfac --- /dev/null +++ b/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceView.js @@ -0,0 +1,88 @@ +import React, {useContext, useEffect} from 'react'; +import {useHistory} from "react-router-dom"; +import withStyles from "@mui/styles/withStyles"; + +import {getLocationContextFromString, getMetadataViewNameFromString} from "../../search/searchUtils"; +import LoadingInlay from "../../common/components/LoadingInlay"; +import MessageDisplay from "../../common/components/MessageDisplay"; +import {MetadataView} from "../views/MetadataView"; +import {useExternalMetadataSource} from "./UseExternalMetadataSource"; +import {useExternalMetadataSourceViewFacets} from "./UseExternalMetadataSourceViewFacets"; +import {getMetadataViewsPath, RESOURCES_VIEW} from "../views/metadataViewUtils"; +import styles from "../views/MetadataView.styles"; +import ExternalMetadataSourceContext from "./ExternalMetadataSourceContext"; +import type {Match} from "../../types"; +import type {ExternalMetadataSource} from "./externalMetadataSourceUtils"; +import {getExternalMetadataSourcePathPrefix} from "./externalMetadataSourceUtils"; + +type ContextualExternalMetadataViewProperties = { + match: Match; + location: Location; + classes: any; +}; + +type ExternalMetadataViewProperties = ContextualExternalMetadataViewProperties & { + externalMetadataSources: ExternalMetadataSource[]; + history: History; +} + +const ExternalMetadataSourceView = (props: ExternalMetadataViewProperties) => { + const {externalMetadataSources, match, history} = props; + + const source: ExternalMetadataSource = externalMetadataSources.find(s => s.name === match.params.source); + const metadataContext = useExternalMetadataSource(source); + const {views = [], loading, error} = metadataContext; + const {facets = [], facetsLoading, facetsError, initialLoad} = useExternalMetadataSourceViewFacets(source); + const currentViewName = getMetadataViewNameFromString(window.location.search); + const locationContext = getLocationContextFromString(window.location.search); + + // eslint-disable-next-line react-hooks/exhaustive-deps + useEffect(() => {initialLoad();}, []); + + if ((error && error.message)) { + return ; + } + if (facetsError && facetsError.message) { + return ; + } + if (loading || facetsLoading) { + return ; + } + + if (views.length < 1) { + return ; + } + + const handleViewChangeRedirect = (viewName, viewPath) => { + if (viewName) { + history.push(getMetadataViewsPath(viewName, viewPath)); + } + }; + + return ( + + ); +}; + +const ContextualExternalMetadataSourceView = (props: ContextualExternalMetadataViewProperties) => { + const {externalMetadataSources = []} = useContext(ExternalMetadataSourceContext); + const history = useHistory(); + + return ( + + ); +}; +export default withStyles(styles)(ContextualExternalMetadataSourceView); diff --git a/projects/mercury/src/metadata/external-sources/UseExternalMetadataSource.js b/projects/mercury/src/metadata/external-sources/UseExternalMetadataSource.js new file mode 100644 index 000000000..bc74efca7 --- /dev/null +++ b/projects/mercury/src/metadata/external-sources/UseExternalMetadataSource.js @@ -0,0 +1,51 @@ +import type {MetadataViewFilter} from "../views/MetadataViewAPI"; +import {MetadataViewAPI} from "../views/MetadataViewAPI"; +import useStateWithSessionStorage from "../../common/hooks/UseSessionStorage"; +import {isNonEmptyValue} from "../../common/utils/genericUtils"; +import useAsync from "../../common/hooks/UseAsync"; +import type {ExternalMetadataSource} from "./externalMetadataSourceUtils"; + +const SESSION_STORAGE_EXTERNAL_METADATA_FILTERS_KEY = 'FAIRSPACE_EXTERNAL_METADATA_FILTERS'; + +/** + * This hook contains logic about files for a certain external storage. + */ +export const useExternalMetadataSource = (source: ExternalMetadataSource, metadataViewAPI = new MetadataViewAPI(source.path)) => { + const {data = {}, error, loading, refresh} = useAsync( + () => metadataViewAPI.getViews(), + [] + ); + + const [filters: MetadataViewFilter[], setFilters] = useStateWithSessionStorage( + `${SESSION_STORAGE_EXTERNAL_METADATA_FILTERS_KEY}_${source.name}`, [] + ); + + const clearFilter = (facetName: string) => { + setFilters([...filters.filter(f => f.field !== facetName)]); + }; + + const clearAllFilters = () => { + setFilters([]); + }; + + const updateFilters = (filterCandidates: MetadataViewFilter[]) => { + setFilters([ + ...filters.filter(f => !filterCandidates.some(u => u.field === f.field)), + ...filterCandidates.filter(f => ( + (f.values && f.values.length > 0) || isNonEmptyValue(f.min) || isNonEmptyValue(f.max) || f.prefix != null || f.booleanValue != null + )) + ]); + }; + + return { + views: data.views, + filters, + updateFilters, + clearAllFilters, + clearFilter, + error, + loading, + refresh, + metadataViewAPI + }; +}; diff --git a/projects/mercury/src/metadata/external-sources/UseExternalMetadataSourceViewFacets.js b/projects/mercury/src/metadata/external-sources/UseExternalMetadataSourceViewFacets.js new file mode 100644 index 000000000..e30297413 --- /dev/null +++ b/projects/mercury/src/metadata/external-sources/UseExternalMetadataSourceViewFacets.js @@ -0,0 +1,36 @@ +import {useState} from "react"; +import {MetadataViewAPI} from "../views/MetadataViewAPI"; +import type {ExternalMetadataSource} from "./externalMetadataSourceUtils"; + +/** + * This hook contains logic about files for a certain external storage. + */ +export const useExternalMetadataSourceViewFacets = (source: ExternalMetadataSource, metadataViewApi = new MetadataViewAPI(source.path)) => { + const [data, setData] = useState({}); + const [facetsLoading, setFacetsLoading] = useState(true); + const [facetsError, setFacetsError] = useState(); + const [requested, setRequested] = useState(false); + + const initialLoad = () => { + if (!requested) { + setRequested(true); + metadataViewApi.getFacets() + .then(d => { + setData(d); + setFacetsError(undefined); + }) + .catch((e) => { + setFacetsError(e || true); + console.error(e || new Error('Unknown error while fetching facets.')); + }) + .finally(() => setFacetsLoading(false)); + } + }; + + return { + facets: data && data.facets, + facetsError, + facetsLoading, + initialLoad + }; +}; diff --git a/projects/mercury/src/metadata/external-sources/externalMetadataSourceUtils.js b/projects/mercury/src/metadata/external-sources/externalMetadataSourceUtils.js new file mode 100644 index 000000000..6eb436583 --- /dev/null +++ b/projects/mercury/src/metadata/external-sources/externalMetadataSourceUtils.js @@ -0,0 +1,11 @@ +import * as consts from "../../constants"; + +export type ExternalMetadataSource = { + path: string, + name: string, + label: string, +} + +export const getExternalMetadataSourcePathPrefix = (sourceName: string) => ( + consts.PATH_SEPARATOR + "metadata-sources" + consts.PATH_SEPARATOR + sourceName +); diff --git a/projects/mercury/src/metadata/views/MetadataView.js b/projects/mercury/src/metadata/views/MetadataView.js index 32b4b835b..5d0154d22 100644 --- a/projects/mercury/src/metadata/views/MetadataView.js +++ b/projects/mercury/src/metadata/views/MetadataView.js @@ -32,9 +32,10 @@ type MetadataViewProperties = { classes: any; facets: MetadataViewFacet[]; views: MetadataViewOptions[]; - filters: MetadataViewFilter[]; + metadataContext: any; locationContext: string; currentViewName: string; + pathPrefix: string; handleViewChangeRedirect: () => {}; } @@ -43,14 +44,14 @@ type ContextualMetadataViewProperties = { } export const MetadataView = (props: MetadataViewProperties) => { - const {views, facets, currentViewName, locationContext, classes, handleViewChangeRedirect, filters} = props; + const {views, facets, currentViewName, locationContext, classes, handleViewChangeRedirect, metadataContext, pathPrefix} = props; usePageTitleUpdater("Metadata"); const {collections} = useContext(CollectionsContext); const {toggle, selected} = useSingleSelection(); - const {updateFilters, clearFilter, clearAllFilters} = useContext(MetadataViewContext); + const {filters, updateFilters, clearFilter, clearAllFilters, metadataViewAPI} = metadataContext; const [filterCandidates, setFilterCandidates] = useState([]); const [textFiltersObject, setTextFiltersObject] = useState({}); const [isClosedPanel, setIsClosedPanel] = useState(true); @@ -69,7 +70,7 @@ export const MetadataView = (props: MetadataViewProperties) => { setIsClosedPanel(true); toggle(); setTextFiltersObject({}); - handleViewChangeRedirect(views[tabIndex].name); + handleViewChangeRedirect(views[tabIndex].name, pathPrefix); // eslint-disable-next-line react-hooks/exhaustive-deps }, [views]); @@ -152,10 +153,10 @@ export const MetadataView = (props: MetadataViewProperties) => { return result; } - const pathPrefix = getMetadataViewsPath(RESOURCES_VIEW) + '&context='; + const prefix = getMetadataViewsPath(RESOURCES_VIEW) + '&context='; let path = locationContext; segments.reverse().forEach(segment => { - result.push({label: segment, href: (pathPrefix + encodeURIComponent(path))}); + result.push({label: segment, href: (prefix + encodeURIComponent(path))}); path = getParentPath(path); }); return result.reverse(); @@ -174,7 +175,7 @@ export const MetadataView = (props: MetadataViewProperties) => { if (!selected) { return ""; } - const metadataURL = window.location.host + getMetadataViewsPath(); + const metadataURL = window.location.host + getMetadataViewsPath(currentView.name, pathPrefix); const prefilteringQueryString = queryString.stringify({ view: currentView.name, [currentViewIdColumn.name.toLowerCase()]: selected.label @@ -184,7 +185,7 @@ export const MetadataView = (props: MetadataViewProperties) => { return ( }] + segments: [{label: "Metadata", href: getMetadataViewsPath(currentView.name, pathPrefix), icon: }] }} > @@ -236,6 +237,7 @@ export const MetadataView = (props: MetadataViewProperties) => { collections={collections} textFiltersObject={textFiltersObject} setTextFiltersObject={setTextFiltersObject} + metadataViewAPI={metadataViewAPI} /> @@ -254,7 +256,8 @@ export const MetadataView = (props: MetadataViewProperties) => { }; export const ContextualMetadataView = (props: ContextualMetadataViewProperties) => { - const {views = [], loading, error, filters} = useContext(MetadataViewContext); + const metadataContext = useContext(MetadataViewContext); + const {views = [], loading, error} = metadataContext; const {facets = [], facetsLoading, facetsError, initialLoad} = useContext(MetadataViewFacetsContext); const currentViewName = getMetadataViewNameFromString(window.location.search); const locationContext = getLocationContextFromString(window.location.search); @@ -289,8 +292,8 @@ export const ContextualMetadataView = (props: ContextualMetadataViewProperties) facets={facets} views={views} locationContext={currentViewName === RESOURCES_VIEW && locationContext} + metadataContext={metadataContext} currentViewName={currentViewName} - filters={filters} handleViewChangeRedirect={handleViewChangeRedirect} /> ); diff --git a/projects/mercury/src/metadata/views/MetadataViewAPI.js b/projects/mercury/src/metadata/views/MetadataViewAPI.js index 2c87ab39a..7706b7227 100644 --- a/projects/mercury/src/metadata/views/MetadataViewAPI.js +++ b/projects/mercury/src/metadata/views/MetadataViewAPI.js @@ -2,6 +2,7 @@ import axios, {CancelTokenSource} from "axios"; import {extractJsonData, handleHttpError} from "../../common/utils/httpUtils"; import type {AccessLevel} from "../../collections/CollectionAPI"; +import FileAPI from "../../file/FileAPI"; export type ValueType = 'Identifier' | 'Text' | 'Number' | 'Date' | 'Term' | 'Set' | 'TermSet' | 'Boolean'; export const TextualValueTypes: ValueType[] = ['Identifier', 'Text', 'Set']; @@ -75,21 +76,23 @@ type MetadataViewDataRequest = MetadataViewCountRequest & {| includeJoinedViews: boolean; |}; -const metadataViewUrl = "/api/views/"; - const defaultRequestOptions = { headers: {Accept: 'application/json'} }; -class MetadataViewAPI { +export class MetadataViewAPI { + constructor(remoteURLPrefix = "/api") { + this.remoteURL = remoteURLPrefix + "/views"; + } + getViews(): Promise { - return axios.get(metadataViewUrl, defaultRequestOptions) + return axios.get(`${this.remoteURL}/`, defaultRequestOptions) .then(extractJsonData) .catch(handleHttpError("Failure when retrieving metadata views.")); } getFacets(): Promise { - return axios.get(`${metadataViewUrl}facets`, defaultRequestOptions) + return axios.get(`${this.remoteURL}/facets`, defaultRequestOptions) .then(extractJsonData) .catch(handleHttpError("Failure when retrieving metadata facets.")); } @@ -104,7 +107,7 @@ class MetadataViewAPI { }; const requestOptions = cancelToken ? {...defaultRequestOptions, cancelToken: cancelToken.token} : defaultRequestOptions; - return axios.post(metadataViewUrl, viewRequest, requestOptions) + return axios.post(`${this.remoteURL}/`, viewRequest, requestOptions) .then(extractJsonData) .catch(handleHttpError("Error while fetching view data.")); } @@ -116,10 +119,12 @@ class MetadataViewAPI { }; const requestOptions = cancelToken ? {...defaultRequestOptions, cancelToken: cancelToken.token} : defaultRequestOptions; - return axios.post(`${metadataViewUrl}count`, viewRequest, requestOptions) + return axios.post(`${this.remoteURL}/count`, viewRequest, requestOptions) .then(extractJsonData) .catch(handleHttpError("Error while fetching view count.")); } } -export default new MetadataViewAPI(); +const LocalMetadataViewAPI = new MetadataViewAPI(); + +export default LocalMetadataViewAPI; diff --git a/projects/mercury/src/metadata/views/MetadataViewContext.js b/projects/mercury/src/metadata/views/MetadataViewContext.js index ad8e9999c..a2585e088 100644 --- a/projects/mercury/src/metadata/views/MetadataViewContext.js +++ b/projects/mercury/src/metadata/views/MetadataViewContext.js @@ -9,9 +9,9 @@ const MetadataViewContext = React.createContext({}); const SESSION_STORAGE_METADATA_FILTERS_KEY = 'FAIRSPACE_METADATA_FILTERS'; -export const MetadataViewProvider = ({children, metadataViewApi = MetadataViewAPI}) => { +export const MetadataViewProvider = ({children, metadataViewAPI = MetadataViewAPI}) => { const {data = {}, error, loading, refresh} = useAsync( - () => metadataViewApi.getViews(), + () => metadataViewAPI.getViews(), [] ); @@ -46,7 +46,8 @@ export const MetadataViewProvider = ({children, metadataViewApi = MetadataViewAP clearFilter, error, loading, - refresh + refresh, + metadataViewAPI }} > {children} diff --git a/projects/mercury/src/metadata/views/MetadataViewTableContainer.js b/projects/mercury/src/metadata/views/MetadataViewTableContainer.js index a423f155c..56837e484 100644 --- a/projects/mercury/src/metadata/views/MetadataViewTableContainer.js +++ b/projects/mercury/src/metadata/views/MetadataViewTableContainer.js @@ -36,6 +36,7 @@ import FeaturesContext from "../../common/contexts/FeaturesContext"; import ProgressButton from "../../common/components/ProgressButton"; import {ANALYSIS_EXPORT_SUBPATH, ExtraLocalStorage} from "../../file/FileAPI"; import ErrorDialog from "../../common/components/ErrorDialog"; +import {MetadataViewAPI} from "./MetadataViewAPI"; type MetadataViewTableContainerProperties = { columns: MetadataViewColumn[]; @@ -49,6 +50,7 @@ type MetadataViewTableContainerProperties = { locationContext: string; selected: MetadataViewEntityWithLinkedFiles; hasInactiveFilters: boolean; + metadataViewAPI: MetadataViewAPI; classes: any; }; @@ -98,7 +100,7 @@ const LOCAL_STORAGE_METADATA_TABLE_ROWS_NUM_KEY = 'FAIRSPACE_METADATA_TABLE_ROWS const SESSION_STORAGE_VISIBLE_COLUMNS_KEY_PREFIX = 'FAIRSPACE_METADATA_VISIBLE_COLUMNS'; export const MetadataViewTableContainer = (props: MetadataViewTableContainerProperties) => { - const {view, filters, columns, idColumn, hasInactiveFilters, locationContext, classes} = props; + const {view, filters, columns, idColumn, hasInactiveFilters, locationContext, classes, metadataViewAPI} = props; const {textFiltersObject, setTextFiltersObject} = props; const {isFeatureEnabled} = useContext(FeaturesContext); @@ -117,7 +119,7 @@ export const MetadataViewTableContainer = (props: MetadataViewTableContainerProp const columnSelectorOpen = Boolean(anchorEl); const history = useHistory(); - const {data, count, error, loading, loadingCount, refreshDataOnly} = useViewData(view, filters, textFiltersObject, locationContext, rowsPerPage); + const {data, count, error, loading, loadingCount, refreshDataOnly} = useViewData(view, filters, textFiltersObject, locationContext, rowsPerPage, metadataViewAPI); const [rowCheckboxes, setRowCheckboxes] = React.useState({}); const resetRowCheckboxes = () => { diff --git a/projects/mercury/src/metadata/views/MetadataViewTabs.js b/projects/mercury/src/metadata/views/MetadataViewTabs.js index 764adc46f..0ecfa1b36 100644 --- a/projects/mercury/src/metadata/views/MetadataViewTabs.js +++ b/projects/mercury/src/metadata/views/MetadataViewTabs.js @@ -7,6 +7,7 @@ import {RESOURCES_VIEW} from "./metadataViewUtils"; import {TabPanel} from "../../workspaces/WorkspaceOverview"; import MetadataViewTableContainer from "./MetadataViewTableContainer"; import CollectionsContext from "../../collections/CollectionsContext"; +import {MetadataViewAPI} from "./MetadataViewAPI"; type MetadataViewTabsProperties = { currentViewIndex: Number; @@ -20,6 +21,7 @@ type MetadataViewTabsProperties = { hasInactiveFilters: Boolean; collections: CollectionsContext; classes: any; + metadataViewAPI: MetadataViewAPI; }; const styles = () => ({ @@ -34,7 +36,7 @@ const styles = () => ({ }); export const MetadataViewTabs = (props: MetadataViewTabsProperties) => { - const {currentViewIndex, idColumn, changeTab, views, filters, locationContext, selected, toggleRow, hasInactiveFilters, collections, classes} = props; + const {currentViewIndex, idColumn, changeTab, views, filters, locationContext, selected, toggleRow, hasInactiveFilters, collections, classes, metadataViewAPI} = props; const {textFiltersObject, setTextFiltersObject} = props; const a11yProps = (index) => ({ @@ -86,6 +88,7 @@ export const MetadataViewTabs = (props: MetadataViewTabsProperties) => { collections={collections} textFiltersObject={textFiltersObject} setTextFiltersObject={setTextFiltersObject} + metadataViewAPI={metadataViewAPI} /> ))} diff --git a/projects/mercury/src/metadata/views/UseViewData.js b/projects/mercury/src/metadata/views/UseViewData.js index a1e9d10d1..26513f297 100644 --- a/projects/mercury/src/metadata/views/UseViewData.js +++ b/projects/mercury/src/metadata/views/UseViewData.js @@ -21,7 +21,7 @@ export type ViewData = { textFiltersObject: Object }; -const useViewData = (view: string, filters: MetadataViewFilter[], textFiltersObject: Object, locationContext: string, rowsPerPage: number): ViewData => { +const useViewData = (view: string, filters: MetadataViewFilter[], textFiltersObject: Object, locationContext: string, rowsPerPage: number, metadataViewAPI): ViewData => { const [data, setData] = useState({}); const [count, setCount] = useState({}); const [loading, setLoading] = useState(true); @@ -73,7 +73,7 @@ const useViewData = (view: string, filters: MetadataViewFilter[], textFiltersObj } const token = axios.CancelToken.source(); setViewDataRequestCancelToken(token); - return MetadataViewAPI.getViewData(token, view, newPage, newRowsPerPage, allFilters); + return metadataViewAPI.getViewData(token, view, newPage, newRowsPerPage, allFilters); }; const refreshAll = useCallback(() => { diff --git a/projects/mercury/src/metadata/views/metadataViewUtils.js b/projects/mercury/src/metadata/views/metadataViewUtils.js index d93936103..9a82c716b 100644 --- a/projects/mercury/src/metadata/views/metadataViewUtils.js +++ b/projects/mercury/src/metadata/views/metadataViewUtils.js @@ -11,8 +11,8 @@ export type MetadataViewEntityWithLinkedFiles = MetadataViewEntity & {| linkedFiles: MetadataViewEntity[]; |} -export const getMetadataViewsPath = (viewName: string) => { - let path = '/metadata-views'; +export const getMetadataViewsPath = (viewName: string, viewPath = '/metadata-views') => { + let path = viewPath; if (viewName) { path += `?view=${viewName}`; } diff --git a/projects/mercury/src/routes/WorkspaceRoutes.js b/projects/mercury/src/routes/WorkspaceRoutes.js index 8a608a561..a32169478 100644 --- a/projects/mercury/src/routes/WorkspaceRoutes.js +++ b/projects/mercury/src/routes/WorkspaceRoutes.js @@ -15,7 +15,8 @@ import UserContext from "../users/UserContext"; import UserRolesPage from "../users/UserRolesPage"; import MetadataView from '../metadata/views/MetadataView'; import BreadcrumbsContext from '../common/contexts/BreadcrumbsContext'; -import ExternalStoragePage from "../external-storage/ExternalStoragePage"; +import {ExternalStoragePage} from "../external-storage/ExternalStoragePage"; +import ExternalMetadataSourcesView from "../metadata/external-sources/ExternalMetadataSourceView"; const getSubject = () => ( document.location.search ? queryString.parse(document.location.search).iri : null @@ -81,6 +82,17 @@ const WorkspaceRoutes = () => { )} /> + ( + + + + + + )} + /> + { render={() => (isAdmin(currentUser) && ())} /> - + ); }; diff --git a/projects/pluto/src/main/java/nl/fairspace/pluto/config/Urls.java b/projects/pluto/src/main/java/nl/fairspace/pluto/config/Urls.java index 7eb17b89f..3ae7a304d 100644 --- a/projects/pluto/src/main/java/nl/fairspace/pluto/config/Urls.java +++ b/projects/pluto/src/main/java/nl/fairspace/pluto/config/Urls.java @@ -4,5 +4,6 @@ public final class Urls { private static final String PLUTO_API_PREFIX = "/api"; public static final String STATUS_PATH = PLUTO_API_PREFIX + "/status"; public static final String STORAGES_PATH = PLUTO_API_PREFIX + "/storages/"; + public static final String METADATA_SOURCES_PATH = PLUTO_API_PREFIX + "/metadata-sources/"; public static final String CONFIG_PATH = PLUTO_API_PREFIX + "/config"; } diff --git a/projects/pluto/src/main/java/nl/fairspace/pluto/config/dto/PlutoConfig.java b/projects/pluto/src/main/java/nl/fairspace/pluto/config/dto/PlutoConfig.java index 4649d62e9..d0b632106 100644 --- a/projects/pluto/src/main/java/nl/fairspace/pluto/config/dto/PlutoConfig.java +++ b/projects/pluto/src/main/java/nl/fairspace/pluto/config/dto/PlutoConfig.java @@ -15,6 +15,14 @@ @Configuration @Data public class PlutoConfig { + @Data + @JsonInclude(JsonInclude.Include.NON_NULL) + public static class MetadataSource { + @NotBlank private String name; + @NotBlank private String label; + @NotBlank private String url; + } + @Data @JsonInclude(JsonInclude.Include.NON_NULL) public static class Storage { @@ -29,6 +37,7 @@ public static class Storage { private boolean forceHttps = true; private List domains = Collections.emptyList(); private Map storages = new LinkedHashMap<>(); + private Map metadataSources = new LinkedHashMap<>(); private String downstreamServiceHealthUrl; private String staticHtmlLocation; } diff --git a/projects/pluto/src/main/java/nl/fairspace/pluto/web/MetadataSourcesResource.java b/projects/pluto/src/main/java/nl/fairspace/pluto/web/MetadataSourcesResource.java new file mode 100644 index 000000000..e605e130c --- /dev/null +++ b/projects/pluto/src/main/java/nl/fairspace/pluto/web/MetadataSourcesResource.java @@ -0,0 +1,40 @@ +package nl.fairspace.pluto.web; + +import lombok.extern.slf4j.Slf4j; +import nl.fairspace.pluto.config.dto.PlutoConfig; +import nl.fairspace.pluto.web.dto.MetadataSourceInfo; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.GetMapping; +import org.springframework.web.bind.annotation.RestController; + +import java.util.List; +import java.util.stream.Collectors; + +import static nl.fairspace.pluto.config.Urls.METADATA_SOURCES_PATH; + +@RestController +@Slf4j +public class MetadataSourcesResource { + + @Autowired + PlutoConfig plutoConfig; + + /** + * GET /api/metadata-sources/ : returns configured external metadata sources. + * + * @return the external metadata sources. + */ + @GetMapping(METADATA_SOURCES_PATH) + public ResponseEntity> metadataSources() { + log.trace("REST request to list external metadata sources"); + var metadataSources = plutoConfig.getMetadataSources().values().stream() + .map(source -> new MetadataSourceInfo( + source.getName(), + source.getLabel(), + String.format("/api/metadata-sources/%s", source.getName()) + )) + .collect(Collectors.toList()); + return ResponseEntity.ok(metadataSources); + } +} diff --git a/projects/pluto/src/main/java/nl/fairspace/pluto/web/dto/MetadataSourceInfo.java b/projects/pluto/src/main/java/nl/fairspace/pluto/web/dto/MetadataSourceInfo.java new file mode 100644 index 000000000..e6640ab8f --- /dev/null +++ b/projects/pluto/src/main/java/nl/fairspace/pluto/web/dto/MetadataSourceInfo.java @@ -0,0 +1,16 @@ +package nl.fairspace.pluto.web.dto; + +import lombok.AllArgsConstructor; +import lombok.EqualsAndHashCode; +import lombok.Getter; +import lombok.NoArgsConstructor; + +@Getter +@EqualsAndHashCode +@AllArgsConstructor +@NoArgsConstructor +public class MetadataSourceInfo { + private String name; + private String label; + private String path; +} diff --git a/projects/pluto/src/main/resources/application-local.yml b/projects/pluto/src/main/resources/application-local.yml index 044eb9d30..886321abf 100644 --- a/projects/pluto/src/main/resources/application-local.yml +++ b/projects/pluto/src/main/resources/application-local.yml @@ -11,10 +11,15 @@ pluto: storages: test: name: test - label: Test + label: "TEST Collections" url: http://localhost:8090/api/webdav search-url: http://localhost:8090/api/search/files root-directory-iri: http://localhost:8080/api/webdav + metadata-sources: + test: + name: test + label: "TEST Metadata" + url: http://localhost:8090/api/ spring: cloud: @@ -32,6 +37,12 @@ spring: - Path=/api/storages/test/search/files filters: - RewritePath=/api/storages/test/search/files, /api/search/files + - id: metadata-test + uri: ${pluto.metadata-sources.test.url} + predicates: + - Path=/api/metadata-sources/test/** + filters: + - RewritePath=/api/metadata-sources/test/(?(views|vocabulary|metadata).*), /api/$\{segment} - id: saturn-post-request-size uri: http://localhost:8090/api/ predicates: From 5be9bf522ef3a1994eb7eb57b90265f2495be5a2 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Fri, 19 Jan 2024 16:41:47 +0100 Subject: [PATCH 045/153] Add support for external metadata views in Mercury. --- .../metadata/LinkedDataMetadataProvider.js | 17 +-- .../src/metadata/common/LinkedDataAPI.js | 5 +- .../src/metadata/common/MetadataAPI.js | 6 +- .../metadata/common/MetadataAPIPathContext.js | 5 + .../src/metadata/common/VocabularyAPI.js | 4 +- .../ExternalMetadataSourceContext.js | 9 +- .../ExternalMetadataSourceView.js | 101 ++++++------------ .../UseExternalMetadataSource.js | 51 --------- .../UseExternalMetadataSourceViewFacets.js | 36 ------- .../src/metadata/views/MetadataView.js | 25 ++--- .../src/metadata/views/MetadataViewContext.js | 7 +- .../views/MetadataViewTableContainer.js | 6 +- .../src/metadata/views/MetadataViewTabs.js | 5 +- .../mercury/src/metadata/views/UseViewData.js | 11 +- .../LinkedDataVocabularyProvider.js | 0 .../metadata/vocabulary/VocabularyContext.js | 8 +- 16 files changed, 90 insertions(+), 206 deletions(-) create mode 100644 projects/mercury/src/metadata/common/MetadataAPIPathContext.js delete mode 100644 projects/mercury/src/metadata/external-sources/UseExternalMetadataSource.js delete mode 100644 projects/mercury/src/metadata/external-sources/UseExternalMetadataSourceViewFacets.js delete mode 100644 projects/mercury/src/metadata/vocabulary/LinkedDataVocabularyProvider.js diff --git a/projects/mercury/src/metadata/LinkedDataMetadataProvider.js b/projects/mercury/src/metadata/LinkedDataMetadataProvider.js index 1da9ba180..598e2ac22 100644 --- a/projects/mercury/src/metadata/LinkedDataMetadataProvider.js +++ b/projects/mercury/src/metadata/LinkedDataMetadataProvider.js @@ -7,30 +7,33 @@ import {USABLE_IN_METADATA_URI} from "../constants"; import valueComponentFactory from "./common/values/LinkedDataValueComponentFactory"; import VocabularyContext from './vocabulary/VocabularyContext'; import {getNamespaces} from './common/vocabularyUtils'; -import MetadataAPI from "./common/MetadataAPI"; +import {MetadataAPI} from "./common/MetadataAPI"; +import MetadataAPIPathContext from "./common/MetadataAPIPathContext"; const LinkedDataMetadataProvider = ({children, ...otherProps}) => { const {vocabulary, vocabularyLoading, vocabularyError} = useContext(VocabularyContext); + const {path: metadataAPIPath} = useContext(MetadataAPIPathContext); + const metadataAPI = new MetadataAPI(metadataAPIPath); - const fetchMetadataBySubject = useCallback((subject) => MetadataAPI.getDict({subject, withValueProperties: true}) + const fetchMetadataBySubject = useCallback((subject) => metadataAPI.getDict({subject, withValueProperties: true}) .catch(() => { throw new Error('An error occurred while loading the metadata'); }), []); - const submitLinkedDataChanges = useCallback((subject, values) => MetadataAPI.get({subject}) + const submitLinkedDataChanges = useCallback((subject, values) => metadataAPI.get({subject}) .then(meta => (meta.length && getFirstPredicateValue(meta[0], '@type'))) - .then(type => MetadataAPI.updateEntity(subject, values, vocabulary, type)), [vocabulary]); + .then(type => metadataAPI.updateEntity(subject, values, vocabulary, type)), [vocabulary]); - const createLinkedDataEntity = useCallback((subject, values, type) => MetadataAPI.get({subject}) + const createLinkedDataEntity = useCallback((subject, values, type) => metadataAPI.get({subject}) .then((meta) => { if (meta.length) { throw Error(`Entity already exists: ${subject}`); } }) - .then(() => MetadataAPI.updateEntity(subject, values, vocabulary, type)) + .then(() => metadataAPI.updateEntity(subject, values, vocabulary, type)) .then(() => ({subject, type, values})), [vocabulary]); - const deleteLinkedDataEntity = (subject) => MetadataAPI.delete(subject); + const deleteLinkedDataEntity = (subject) => metadataAPI.delete(subject); const extendProperties = ({properties = [], isEntityEditable = true}) => properties .map(p => ({ diff --git a/projects/mercury/src/metadata/common/LinkedDataAPI.js b/projects/mercury/src/metadata/common/LinkedDataAPI.js index 5da1981e8..2f7eada5a 100644 --- a/projects/mercury/src/metadata/common/LinkedDataAPI.js +++ b/projects/mercury/src/metadata/common/LinkedDataAPI.js @@ -13,9 +13,10 @@ class LinkedDataAPI { /** * * @param graph Either 'metadata' or 'vocabulary' + * @param remoteURLPrefix URL path to the API */ - constructor(graph) { - this.statementsUrl = `/api/${graph}/`; + constructor(graph, remoteURLPrefix = "/api") { + this.statementsUrl = `${remoteURLPrefix}/${graph}/`; } /** diff --git a/projects/mercury/src/metadata/common/MetadataAPI.js b/projects/mercury/src/metadata/common/MetadataAPI.js index a65152d2a..936f88abe 100644 --- a/projects/mercury/src/metadata/common/MetadataAPI.js +++ b/projects/mercury/src/metadata/common/MetadataAPI.js @@ -3,9 +3,9 @@ import LinkedDataAPI from "./LinkedDataAPI"; import {toJsonLd} from "./jsonLdConverter"; import {handleHttpError} from "../../common/utils/httpUtils"; -class MetadataAPI extends LinkedDataAPI { - constructor() { - super('metadata'); +export class MetadataAPI extends LinkedDataAPI { + constructor(remoteURLPrefix = "/api") { + super('metadata', remoteURLPrefix); } /** diff --git a/projects/mercury/src/metadata/common/MetadataAPIPathContext.js b/projects/mercury/src/metadata/common/MetadataAPIPathContext.js new file mode 100644 index 000000000..59513e39f --- /dev/null +++ b/projects/mercury/src/metadata/common/MetadataAPIPathContext.js @@ -0,0 +1,5 @@ +import React from 'react'; + +const MetadataAPIPathContext = React.createContext({path: "/api"}); + +export default MetadataAPIPathContext; diff --git a/projects/mercury/src/metadata/common/VocabularyAPI.js b/projects/mercury/src/metadata/common/VocabularyAPI.js index 69336af78..46bacaa50 100644 --- a/projects/mercury/src/metadata/common/VocabularyAPI.js +++ b/projects/mercury/src/metadata/common/VocabularyAPI.js @@ -1,8 +1,8 @@ import LinkedDataAPI from "./LinkedDataAPI"; export class LinkedDataVocabularyAPI extends LinkedDataAPI { - constructor() { - super('vocabulary'); + constructor(remoteURLPrefix = "/api") { + super('vocabulary', remoteURLPrefix); } } diff --git a/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceContext.js b/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceContext.js index 282299048..c9d5d2e36 100644 --- a/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceContext.js +++ b/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceContext.js @@ -6,13 +6,18 @@ import useAsync from "../../common/hooks/UseAsync"; const ExternalMetadataSourceContext = React.createContext({}); export const ExternalMetadataSourcesProvider = ({children}) => { - const {data: externalMetadataSources = []} = useAsync(() => axios.get('/api/metadata-sources/') + const {data: externalMetadataSources = [], error, loading, refresh} = useAsync(() => axios.get('/api/metadata-sources/') .then(extractJsonData) .catch(handleHttpError('Connection error.'))); return ( {children} diff --git a/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceView.js b/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceView.js index c503fdfac..d0a614074 100644 --- a/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceView.js +++ b/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceView.js @@ -1,88 +1,49 @@ -import React, {useContext, useEffect} from 'react'; -import {useHistory} from "react-router-dom"; -import withStyles from "@mui/styles/withStyles"; - -import {getLocationContextFromString, getMetadataViewNameFromString} from "../../search/searchUtils"; +import React, {useContext} from 'react'; import LoadingInlay from "../../common/components/LoadingInlay"; import MessageDisplay from "../../common/components/MessageDisplay"; -import {MetadataView} from "../views/MetadataView"; -import {useExternalMetadataSource} from "./UseExternalMetadataSource"; -import {useExternalMetadataSourceViewFacets} from "./UseExternalMetadataSourceViewFacets"; -import {getMetadataViewsPath, RESOURCES_VIEW} from "../views/metadataViewUtils"; -import styles from "../views/MetadataView.styles"; +import MetadataView from "../views/MetadataView"; import ExternalMetadataSourceContext from "./ExternalMetadataSourceContext"; -import type {Match} from "../../types"; import type {ExternalMetadataSource} from "./externalMetadataSourceUtils"; import {getExternalMetadataSourcePathPrefix} from "./externalMetadataSourceUtils"; - -type ContextualExternalMetadataViewProperties = { - match: Match; - location: Location; +import MetadataAPIPathContext from "../common/MetadataAPIPathContext"; +import {MetadataViewProvider} from "../views/MetadataViewContext"; +import {MetadataViewAPI} from "../views/MetadataViewAPI"; +import {MetadataViewFacetsProvider} from "../views/MetadataViewFacetsContext"; +import {VocabularyProvider} from "../vocabulary/VocabularyContext"; +import LinkedDataMetadataProvider from "../LinkedDataMetadataProvider"; + +export type ExternalMetadataSourceViewProperties = { classes: any; -}; - -type ExternalMetadataViewProperties = ContextualExternalMetadataViewProperties & { - externalMetadataSources: ExternalMetadataSource[]; - history: History; + match: any; } - -const ExternalMetadataSourceView = (props: ExternalMetadataViewProperties) => { - const {externalMetadataSources, match, history} = props; - - const source: ExternalMetadataSource = externalMetadataSources.find(s => s.name === match.params.source); - const metadataContext = useExternalMetadataSource(source); - const {views = [], loading, error} = metadataContext; - const {facets = [], facetsLoading, facetsError, initialLoad} = useExternalMetadataSourceViewFacets(source); - const currentViewName = getMetadataViewNameFromString(window.location.search); - const locationContext = getLocationContextFromString(window.location.search); - - // eslint-disable-next-line react-hooks/exhaustive-deps - useEffect(() => {initialLoad();}, []); +const ExternalMetadataSourceView = (props: ExternalMetadataSourceViewProperties) => { + const {match} = props; + const {externalMetadataSources = [], loading, error} = useContext(ExternalMetadataSourceContext); if ((error && error.message)) { return ; } - if (facetsError && facetsError.message) { - return ; - } - if (loading || facetsLoading) { + if (loading) { return ; } - if (views.length < 1) { - return ; - } - - const handleViewChangeRedirect = (viewName, viewPath) => { - if (viewName) { - history.push(getMetadataViewsPath(viewName, viewPath)); - } - }; - - return ( - - ); -}; - -const ContextualExternalMetadataSourceView = (props: ContextualExternalMetadataViewProperties) => { - const {externalMetadataSources = []} = useContext(ExternalMetadataSourceContext); - const history = useHistory(); + const source: ExternalMetadataSource = externalMetadataSources.find(s => s.name === match.params.source); return ( - + + + + + + + + + + + ); }; -export default withStyles(styles)(ContextualExternalMetadataSourceView); +export default ExternalMetadataSourceView; diff --git a/projects/mercury/src/metadata/external-sources/UseExternalMetadataSource.js b/projects/mercury/src/metadata/external-sources/UseExternalMetadataSource.js deleted file mode 100644 index bc74efca7..000000000 --- a/projects/mercury/src/metadata/external-sources/UseExternalMetadataSource.js +++ /dev/null @@ -1,51 +0,0 @@ -import type {MetadataViewFilter} from "../views/MetadataViewAPI"; -import {MetadataViewAPI} from "../views/MetadataViewAPI"; -import useStateWithSessionStorage from "../../common/hooks/UseSessionStorage"; -import {isNonEmptyValue} from "../../common/utils/genericUtils"; -import useAsync from "../../common/hooks/UseAsync"; -import type {ExternalMetadataSource} from "./externalMetadataSourceUtils"; - -const SESSION_STORAGE_EXTERNAL_METADATA_FILTERS_KEY = 'FAIRSPACE_EXTERNAL_METADATA_FILTERS'; - -/** - * This hook contains logic about files for a certain external storage. - */ -export const useExternalMetadataSource = (source: ExternalMetadataSource, metadataViewAPI = new MetadataViewAPI(source.path)) => { - const {data = {}, error, loading, refresh} = useAsync( - () => metadataViewAPI.getViews(), - [] - ); - - const [filters: MetadataViewFilter[], setFilters] = useStateWithSessionStorage( - `${SESSION_STORAGE_EXTERNAL_METADATA_FILTERS_KEY}_${source.name}`, [] - ); - - const clearFilter = (facetName: string) => { - setFilters([...filters.filter(f => f.field !== facetName)]); - }; - - const clearAllFilters = () => { - setFilters([]); - }; - - const updateFilters = (filterCandidates: MetadataViewFilter[]) => { - setFilters([ - ...filters.filter(f => !filterCandidates.some(u => u.field === f.field)), - ...filterCandidates.filter(f => ( - (f.values && f.values.length > 0) || isNonEmptyValue(f.min) || isNonEmptyValue(f.max) || f.prefix != null || f.booleanValue != null - )) - ]); - }; - - return { - views: data.views, - filters, - updateFilters, - clearAllFilters, - clearFilter, - error, - loading, - refresh, - metadataViewAPI - }; -}; diff --git a/projects/mercury/src/metadata/external-sources/UseExternalMetadataSourceViewFacets.js b/projects/mercury/src/metadata/external-sources/UseExternalMetadataSourceViewFacets.js deleted file mode 100644 index e30297413..000000000 --- a/projects/mercury/src/metadata/external-sources/UseExternalMetadataSourceViewFacets.js +++ /dev/null @@ -1,36 +0,0 @@ -import {useState} from "react"; -import {MetadataViewAPI} from "../views/MetadataViewAPI"; -import type {ExternalMetadataSource} from "./externalMetadataSourceUtils"; - -/** - * This hook contains logic about files for a certain external storage. - */ -export const useExternalMetadataSourceViewFacets = (source: ExternalMetadataSource, metadataViewApi = new MetadataViewAPI(source.path)) => { - const [data, setData] = useState({}); - const [facetsLoading, setFacetsLoading] = useState(true); - const [facetsError, setFacetsError] = useState(); - const [requested, setRequested] = useState(false); - - const initialLoad = () => { - if (!requested) { - setRequested(true); - metadataViewApi.getFacets() - .then(d => { - setData(d); - setFacetsError(undefined); - }) - .catch((e) => { - setFacetsError(e || true); - console.error(e || new Error('Unknown error while fetching facets.')); - }) - .finally(() => setFacetsLoading(false)); - } - }; - - return { - facets: data && data.facets, - facetsError, - facetsLoading, - initialLoad - }; -}; diff --git a/projects/mercury/src/metadata/views/MetadataView.js b/projects/mercury/src/metadata/views/MetadataView.js index 5d0154d22..551c6c835 100644 --- a/projects/mercury/src/metadata/views/MetadataView.js +++ b/projects/mercury/src/metadata/views/MetadataView.js @@ -28,30 +28,29 @@ import usePageTitleUpdater from "../../common/hooks/UsePageTitleUpdater"; import MetadataViewFacetsContext from "./MetadataViewFacetsContext"; import {accessLevelForCollection} from "../../collections/collectionUtils"; -type MetadataViewProperties = { +type ContextualMetadataViewProperties = { classes: any; +} + +type MetadataViewProperties = ContextualMetadataViewProperties & { facets: MetadataViewFacet[]; views: MetadataViewOptions[]; - metadataContext: any; + filters: MetadataViewFilter[]; locationContext: string; currentViewName: string; pathPrefix: string; handleViewChangeRedirect: () => {}; } -type ContextualMetadataViewProperties = { - classes: any; -} - export const MetadataView = (props: MetadataViewProperties) => { - const {views, facets, currentViewName, locationContext, classes, handleViewChangeRedirect, metadataContext, pathPrefix} = props; + const {views, facets, filters, currentViewName, locationContext, classes, handleViewChangeRedirect, pathPrefix} = props; usePageTitleUpdater("Metadata"); const {collections} = useContext(CollectionsContext); const {toggle, selected} = useSingleSelection(); - const {filters, updateFilters, clearFilter, clearAllFilters, metadataViewAPI} = metadataContext; + const {updateFilters, clearFilter, clearAllFilters} = useContext(MetadataViewContext); const [filterCandidates, setFilterCandidates] = useState([]); const [textFiltersObject, setTextFiltersObject] = useState({}); const [isClosedPanel, setIsClosedPanel] = useState(true); @@ -237,7 +236,6 @@ export const MetadataView = (props: MetadataViewProperties) => { collections={collections} textFiltersObject={textFiltersObject} setTextFiltersObject={setTextFiltersObject} - metadataViewAPI={metadataViewAPI} /> @@ -256,8 +254,7 @@ export const MetadataView = (props: MetadataViewProperties) => { }; export const ContextualMetadataView = (props: ContextualMetadataViewProperties) => { - const metadataContext = useContext(MetadataViewContext); - const {views = [], loading, error} = metadataContext; + const {views = [], filters, loading, error} = useContext(MetadataViewContext); const {facets = [], facetsLoading, facetsError, initialLoad} = useContext(MetadataViewFacetsContext); const currentViewName = getMetadataViewNameFromString(window.location.search); const locationContext = getLocationContextFromString(window.location.search); @@ -280,9 +277,9 @@ export const ContextualMetadataView = (props: ContextualMetadataViewProperties) return ; } - const handleViewChangeRedirect = (viewName) => { + const handleViewChangeRedirect = (viewName, viewPath) => { if (viewName) { - history.push(getMetadataViewsPath(viewName)); + history.push(getMetadataViewsPath(viewName, viewPath)); } }; @@ -291,8 +288,8 @@ export const ContextualMetadataView = (props: ContextualMetadataViewProperties) {...props} facets={facets} views={views} + filters={filters} locationContext={currentViewName === RESOURCES_VIEW && locationContext} - metadataContext={metadataContext} currentViewName={currentViewName} handleViewChangeRedirect={handleViewChangeRedirect} /> diff --git a/projects/mercury/src/metadata/views/MetadataViewContext.js b/projects/mercury/src/metadata/views/MetadataViewContext.js index a2585e088..f1b5ae8bc 100644 --- a/projects/mercury/src/metadata/views/MetadataViewContext.js +++ b/projects/mercury/src/metadata/views/MetadataViewContext.js @@ -9,14 +9,14 @@ const MetadataViewContext = React.createContext({}); const SESSION_STORAGE_METADATA_FILTERS_KEY = 'FAIRSPACE_METADATA_FILTERS'; -export const MetadataViewProvider = ({children, metadataViewAPI = MetadataViewAPI}) => { +export const MetadataViewProvider = ({children, metadataViewAPI = MetadataViewAPI, sourceName = ""}) => { const {data = {}, error, loading, refresh} = useAsync( () => metadataViewAPI.getViews(), [] ); const [filters: MetadataViewFilter[], setFilters] = useStateWithSessionStorage( - SESSION_STORAGE_METADATA_FILTERS_KEY, [] + `${SESSION_STORAGE_METADATA_FILTERS_KEY}_${sourceName}`, [] ); const clearFilter = (facetName: string) => { @@ -46,8 +46,7 @@ export const MetadataViewProvider = ({children, metadataViewAPI = MetadataViewAP clearFilter, error, loading, - refresh, - metadataViewAPI + refresh }} > {children} diff --git a/projects/mercury/src/metadata/views/MetadataViewTableContainer.js b/projects/mercury/src/metadata/views/MetadataViewTableContainer.js index 56837e484..a423f155c 100644 --- a/projects/mercury/src/metadata/views/MetadataViewTableContainer.js +++ b/projects/mercury/src/metadata/views/MetadataViewTableContainer.js @@ -36,7 +36,6 @@ import FeaturesContext from "../../common/contexts/FeaturesContext"; import ProgressButton from "../../common/components/ProgressButton"; import {ANALYSIS_EXPORT_SUBPATH, ExtraLocalStorage} from "../../file/FileAPI"; import ErrorDialog from "../../common/components/ErrorDialog"; -import {MetadataViewAPI} from "./MetadataViewAPI"; type MetadataViewTableContainerProperties = { columns: MetadataViewColumn[]; @@ -50,7 +49,6 @@ type MetadataViewTableContainerProperties = { locationContext: string; selected: MetadataViewEntityWithLinkedFiles; hasInactiveFilters: boolean; - metadataViewAPI: MetadataViewAPI; classes: any; }; @@ -100,7 +98,7 @@ const LOCAL_STORAGE_METADATA_TABLE_ROWS_NUM_KEY = 'FAIRSPACE_METADATA_TABLE_ROWS const SESSION_STORAGE_VISIBLE_COLUMNS_KEY_PREFIX = 'FAIRSPACE_METADATA_VISIBLE_COLUMNS'; export const MetadataViewTableContainer = (props: MetadataViewTableContainerProperties) => { - const {view, filters, columns, idColumn, hasInactiveFilters, locationContext, classes, metadataViewAPI} = props; + const {view, filters, columns, idColumn, hasInactiveFilters, locationContext, classes} = props; const {textFiltersObject, setTextFiltersObject} = props; const {isFeatureEnabled} = useContext(FeaturesContext); @@ -119,7 +117,7 @@ export const MetadataViewTableContainer = (props: MetadataViewTableContainerProp const columnSelectorOpen = Boolean(anchorEl); const history = useHistory(); - const {data, count, error, loading, loadingCount, refreshDataOnly} = useViewData(view, filters, textFiltersObject, locationContext, rowsPerPage, metadataViewAPI); + const {data, count, error, loading, loadingCount, refreshDataOnly} = useViewData(view, filters, textFiltersObject, locationContext, rowsPerPage); const [rowCheckboxes, setRowCheckboxes] = React.useState({}); const resetRowCheckboxes = () => { diff --git a/projects/mercury/src/metadata/views/MetadataViewTabs.js b/projects/mercury/src/metadata/views/MetadataViewTabs.js index 0ecfa1b36..764adc46f 100644 --- a/projects/mercury/src/metadata/views/MetadataViewTabs.js +++ b/projects/mercury/src/metadata/views/MetadataViewTabs.js @@ -7,7 +7,6 @@ import {RESOURCES_VIEW} from "./metadataViewUtils"; import {TabPanel} from "../../workspaces/WorkspaceOverview"; import MetadataViewTableContainer from "./MetadataViewTableContainer"; import CollectionsContext from "../../collections/CollectionsContext"; -import {MetadataViewAPI} from "./MetadataViewAPI"; type MetadataViewTabsProperties = { currentViewIndex: Number; @@ -21,7 +20,6 @@ type MetadataViewTabsProperties = { hasInactiveFilters: Boolean; collections: CollectionsContext; classes: any; - metadataViewAPI: MetadataViewAPI; }; const styles = () => ({ @@ -36,7 +34,7 @@ const styles = () => ({ }); export const MetadataViewTabs = (props: MetadataViewTabsProperties) => { - const {currentViewIndex, idColumn, changeTab, views, filters, locationContext, selected, toggleRow, hasInactiveFilters, collections, classes, metadataViewAPI} = props; + const {currentViewIndex, idColumn, changeTab, views, filters, locationContext, selected, toggleRow, hasInactiveFilters, collections, classes} = props; const {textFiltersObject, setTextFiltersObject} = props; const a11yProps = (index) => ({ @@ -88,7 +86,6 @@ export const MetadataViewTabs = (props: MetadataViewTabsProperties) => { collections={collections} textFiltersObject={textFiltersObject} setTextFiltersObject={setTextFiltersObject} - metadataViewAPI={metadataViewAPI} /> ))} diff --git a/projects/mercury/src/metadata/views/UseViewData.js b/projects/mercury/src/metadata/views/UseViewData.js index 26513f297..281de33c6 100644 --- a/projects/mercury/src/metadata/views/UseViewData.js +++ b/projects/mercury/src/metadata/views/UseViewData.js @@ -1,8 +1,9 @@ /* eslint-disable react-hooks/exhaustive-deps */ -import {useCallback, useEffect, useState} from "react"; +import {useCallback, useContext, useEffect, useState} from "react"; import axios from "axios"; -import MetadataViewAPI from "./MetadataViewAPI"; import type {MetadataViewData, MetadataViewFilter} from "./MetadataViewAPI"; +import {MetadataViewAPI} from "./MetadataViewAPI"; +import MetadataAPIPathContext from "../common/MetadataAPIPathContext"; const LOCATION_FILTER_FIELD = 'location'; @@ -21,7 +22,9 @@ export type ViewData = { textFiltersObject: Object }; -const useViewData = (view: string, filters: MetadataViewFilter[], textFiltersObject: Object, locationContext: string, rowsPerPage: number, metadataViewAPI): ViewData => { +const useViewData = (view: string, filters: MetadataViewFilter[], textFiltersObject: Object, locationContext: string, rowsPerPage: number): ViewData => { + const {path: metadataAPIPath} = useContext(MetadataAPIPathContext); + const metadataViewAPI = new MetadataViewAPI(metadataAPIPath); const [data, setData] = useState({}); const [count, setCount] = useState({}); const [loading, setLoading] = useState(true); @@ -56,7 +59,7 @@ const useViewData = (view: string, filters: MetadataViewFilter[], textFiltersObj } const token = axios.CancelToken.source(); setCountRequestCancelToken(token); - MetadataViewAPI.getCount(token, view, allFilters).then(res => { + metadataViewAPI.getCount(token, view, allFilters).then(res => { if (res) { if (res.count == null) { res.count = -1; diff --git a/projects/mercury/src/metadata/vocabulary/LinkedDataVocabularyProvider.js b/projects/mercury/src/metadata/vocabulary/LinkedDataVocabularyProvider.js deleted file mode 100644 index e69de29bb..000000000 diff --git a/projects/mercury/src/metadata/vocabulary/VocabularyContext.js b/projects/mercury/src/metadata/vocabulary/VocabularyContext.js index 738201ee2..dd0569a1c 100644 --- a/projects/mercury/src/metadata/vocabulary/VocabularyContext.js +++ b/projects/mercury/src/metadata/vocabulary/VocabularyContext.js @@ -1,12 +1,14 @@ -import React from 'react'; +import React, {useContext} from 'react'; -import VocabularyAPI from '../common/VocabularyAPI'; +import {LinkedDataVocabularyAPI} from '../common/VocabularyAPI'; import useAsync from "../../common/hooks/UseAsync"; +import MetadataAPIPathContext from "../common/MetadataAPIPathContext"; const VocabularyContext = React.createContext(); export const VocabularyProvider = ({children}) => { - const {data: vocabulary = [], loading: vocabularyLoading, error: vocabularyError} = useAsync(() => VocabularyAPI.get()); + const {path: metadataAPIPath} = useContext(MetadataAPIPathContext); + const {data: vocabulary = [], loading: vocabularyLoading, error: vocabularyError} = useAsync(() => new LinkedDataVocabularyAPI(metadataAPIPath).get()); return ( Date: Mon, 22 Jan 2024 13:48:07 +0100 Subject: [PATCH 046/153] FAIRSPC-29: added caching of facets and views (#1466) FAIRSPC-29: added caching of facets and views --- .../io/fairspace/saturn/config/Services.java | 7 +- .../rdf/search/FilteredDatasetGraph.java | 23 +- .../maintenance/MaintenanceService.java | 5 +- .../metadata/MetadataPermissions.java | 7 + .../saturn/services/views/ViewApp.java | 6 +- .../saturn/services/views/ViewService.java | 199 ++++++++++++------ .../services/views/JdbcQueryServiceTest.java | 4 +- .../services/views/ViewServiceTest.java | 182 ++++++++++------ 8 files changed, 297 insertions(+), 136 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/config/Services.java b/projects/saturn/src/main/java/io/fairspace/saturn/config/Services.java index 74f47f863..213be86ef 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/config/Services.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/config/Services.java @@ -94,15 +94,16 @@ public Services(@NonNull Config config, @NonNull ViewsConfig viewsConfig, @NonNu metadataService = new MetadataService(transactions, VOCABULARY, metadataValidator, metadataPermissions); dataset.getContext().set(METADATA_SERVICE, metadataService); - maintenanceService = new MaintenanceService(userService, dataset, viewStoreClientFactory); - filteredDatasetGraph = new FilteredDatasetGraph(dataset.asDatasetGraph(), metadataPermissions); var filteredDataset = DatasetImpl.wrap(filteredDatasetGraph); queryService = viewStoreClientFactory == null ? new SparqlQueryService(config.search, viewsConfig, filteredDataset) : new JdbcQueryService(config.search, viewStoreClientFactory, transactions, davFactory.root); - viewService = new ViewService(config.search, viewsConfig, filteredDataset, viewStoreClientFactory); + viewService = new ViewService(config.search, viewsConfig, filteredDataset, viewStoreClientFactory, + metadataPermissions); + + maintenanceService = new MaintenanceService(userService, dataset, viewStoreClientFactory, viewService); searchService = new SearchService(filteredDataset); diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/rdf/search/FilteredDatasetGraph.java b/projects/saturn/src/main/java/io/fairspace/saturn/rdf/search/FilteredDatasetGraph.java index 1fb91118d..f8040e3b0 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/rdf/search/FilteredDatasetGraph.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/rdf/search/FilteredDatasetGraph.java @@ -11,14 +11,31 @@ import static org.apache.jena.sparql.core.Quad.defaultGraphIRI; public class FilteredDatasetGraph extends DatasetGraphFilteredView { + + private static final ThreadLocal permissionCheckEnabled = ThreadLocal.withInitial(() -> true); + public FilteredDatasetGraph(DatasetGraph dsg, MetadataPermissions permissions) { this(DatasetImpl.wrap(dsg), permissions); } - public FilteredDatasetGraph(Dataset ds, MetadataPermissions permissions) { + private FilteredDatasetGraph(Dataset ds, MetadataPermissions permissions) { super(ds.asDatasetGraph(), - q -> q.isDefaultGraph() - && permissions.canReadMetadata(ds.getDefaultModel().wrapAsResource(q.getSubject())), + q -> { + boolean allowedToReadMetadata = q.isDefaultGraph(); + if (allowedToReadMetadata && permissionCheckEnabled.get()) { + allowedToReadMetadata = permissions + .canReadMetadata(ds.getDefaultModel().wrapAsResource(q.getSubject())); + } + return allowedToReadMetadata; + }, Set.of(defaultGraphIRI)); } + + public static void disableQuadPermissionCheck() { + permissionCheckEnabled.set(false); + } + + public static void enableQuadPermissionCheck() { + permissionCheckEnabled.set(true); + } } diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/maintenance/MaintenanceService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/maintenance/MaintenanceService.java index b98c30f40..71050aa98 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/maintenance/MaintenanceService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/maintenance/MaintenanceService.java @@ -19,11 +19,13 @@ public class MaintenanceService { private final UserService userService; private final Dataset dataset; private final ViewStoreClientFactory viewStoreClientFactory; + private final ViewService viewService; - public MaintenanceService(@NonNull UserService userService, @NonNull Dataset dataset, ViewStoreClientFactory viewStoreClientFactory) { + public MaintenanceService(@NonNull UserService userService, @NonNull Dataset dataset, ViewStoreClientFactory viewStoreClientFactory, ViewService viewService) { this.userService = userService; this.dataset = dataset; this.viewStoreClientFactory = viewStoreClientFactory; + this.viewService = viewService; } public boolean disabled() { @@ -49,6 +51,7 @@ public synchronized void startRecreateIndexTask() { log.info("Start asynchronous reindexing task"); recreateIndex(); }); + viewService.refreshCaches(); } public void recreateIndex() { diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataPermissions.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataPermissions.java index 103b973c7..55252c714 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataPermissions.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/metadata/MetadataPermissions.java @@ -32,6 +32,13 @@ public boolean canReadMetadata(Resource resource) { return userService.currentUser().isCanViewPublicMetadata(); } + public boolean canReadFacets() { + if (userService.currentUser().isAdmin()) { + return true; + } + return userService.currentUser().isCanViewPublicMetadata(); + } + public boolean canWriteMetadata(Resource resource) { if (userService.currentUser().isAdmin()) { return true; diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewApp.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewApp.java index b128e3340..0fd704943 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewApp.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewApp.java @@ -2,8 +2,6 @@ import io.fairspace.saturn.services.BaseApp; -import static javax.servlet.http.HttpServletResponse.SC_FORBIDDEN; -import static javax.servlet.http.HttpServletResponse.SC_OK; import static org.eclipse.jetty.http.MimeTypes.Type.APPLICATION_JSON; import static spark.Spark.get; import static spark.Spark.post; @@ -23,7 +21,7 @@ public ViewApp(String basePath, ViewService viewService, QueryService queryServi protected void initApp() { get("/", (req, res) -> { res.type(APPLICATION_JSON.asString()); - return mapper.writeValueAsString(new ViewsDTO(viewService.getViews())); + return mapper.writeValueAsString(new ViewsDTO(viewService.getCachedViews())); }); post("/", (req, res) -> { @@ -34,7 +32,7 @@ protected void initApp() { get("/facets", (req, res) -> { res.type(APPLICATION_JSON.asString()); - return mapper.writeValueAsString(new FacetsDTO(viewService.getFacets())); + return mapper.writeValueAsString(new FacetsDTO(viewService.getCachedFacets())); }); post("/count", (req, res) -> { diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java index 0c198ee1f..0fb981473 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java @@ -1,14 +1,29 @@ package io.fairspace.saturn.services.views; -import io.fairspace.saturn.config.*; +import com.google.common.cache.CacheBuilder; +import com.google.common.cache.CacheLoader; +import com.google.common.cache.LoadingCache; +import io.fairspace.saturn.config.Config; +import io.fairspace.saturn.config.ViewsConfig; +import io.fairspace.saturn.rdf.search.FilteredDatasetGraph; +import io.fairspace.saturn.services.AccessDeniedException; +import io.fairspace.saturn.services.metadata.MetadataPermissions; import io.fairspace.saturn.vocabulary.FS; import lombok.SneakyThrows; -import lombok.extern.log4j.*; -import org.apache.jena.datatypes.xsd.*; -import org.apache.jena.query.*; +import lombok.extern.log4j.Log4j2; +import org.apache.jena.datatypes.xsd.XSDDateTime; +import org.apache.jena.query.Dataset; +import org.apache.jena.query.Query; +import org.apache.jena.query.QueryExecutionFactory; +import org.apache.jena.query.QueryFactory; +import org.apache.jena.query.QuerySolution; +import org.apache.jena.query.QuerySolutionMap; import org.apache.jena.rdf.model.Literal; -import java.util.*; +import java.util.ArrayList; +import java.util.EnumSet; +import java.util.List; +import java.util.concurrent.ExecutionException; import static io.fairspace.saturn.config.ViewsConfig.ColumnType; import static io.fairspace.saturn.config.ViewsConfig.View; @@ -20,6 +35,7 @@ @Log4j2 public class ViewService { + private static final Query VALUES_QUERY = QueryFactory.create(String.format(""" PREFIX fs: <%s> PREFIX rdfs: @@ -70,31 +86,112 @@ public class ViewService { private final ViewsConfig viewsConfig; private final Dataset ds; private final ViewStoreClientFactory viewStoreClientFactory; + private final MetadataPermissions metadataPermissions; + private final LoadingCache> facetsCache; + private final LoadingCache> viewsCache; - public ViewService(Config.Search searchConfig, ViewsConfig viewsConfig, Dataset ds, ViewStoreClientFactory viewStoreClientFactory) { + public ViewService(Config.Search searchConfig, + ViewsConfig viewsConfig, + Dataset ds, + ViewStoreClientFactory viewStoreClientFactory, + MetadataPermissions metadataPermissions) { this.searchConfig = searchConfig; this.viewsConfig = viewsConfig; this.ds = ds; this.viewStoreClientFactory = viewStoreClientFactory; + this.metadataPermissions = metadataPermissions; + this.facetsCache = buildFacetCache(); + this.viewsCache = buildViewsCache(); + refreshCaches(); } - private Object convertLiteralValue(Object value) { - if (value instanceof XSDDateTime) { - return ofEpochMilli(((XSDDateTime) value).asCalendar().getTimeInMillis()); - } - return value; + public void refreshCaches() { + log.info("Caches refreshing/warming up has been triggered"); + FilteredDatasetGraph.disableQuadPermissionCheck(); + facetsCache.refresh(Boolean.TRUE); + viewsCache.refresh(Boolean.TRUE); + FilteredDatasetGraph.enableQuadPermissionCheck(); + log.info("Caches refreshing/warming up successfully finished"); } - @SneakyThrows - Range getColumnRange(View view, View.Column column) { - if (!EnumSet.of(ColumnType.Date, ColumnType.Number).contains(column.type)) { - return null; + public List getCachedFacets() { + try { + if (!metadataPermissions.canReadFacets()) { + throw new AccessDeniedException("User does not have permissions to read facets"); + } + return facetsCache.get(Boolean.TRUE); + } catch (ExecutionException e) { + throw new RuntimeException(e); } - try (var reader = new ViewStoreReader(searchConfig, viewStoreClientFactory)) { - return reader.aggregate(view.name, column.name); + } + + public List getCachedViews() { + try { + return viewsCache.get(Boolean.TRUE); + } catch (ExecutionException e) { + throw new RuntimeException(e); } } + protected List fetchViews() { + return viewsConfig.views.stream() + .map(v -> { + var columns = new ArrayList(); + + // The entity labal is the first column displayed, if you want a column before this label, assign a negative displayIndex value in views.yaml + final int ENTITY_LABEL_INDEX = 0; + + columns.add(new ColumnDTO(v.name, v.itemName == null ? v.name : v.itemName, ColumnType.Identifier, ENTITY_LABEL_INDEX)); + for (var c : v.columns) { + columns.add(new ColumnDTO(v.name + "_" + c.name, c.title, c.type, c.displayIndex)); + } + for (var j : v.join) { + var joinView = viewsConfig.views.stream().filter(view -> view.name.equalsIgnoreCase(j.view)).findFirst().orElse(null); + if (joinView == null) { + continue; + } + if (j.include.contains("id")) { + columns.add(new ColumnDTO(joinView.name, joinView.title, ColumnType.Identifier, j.displayIndex)); + } + for (var c : joinView.columns) { + if (!j.include.contains(c.name)) { + continue; + } + columns.add(new ColumnDTO(joinView.name + "_" + c.name, c.title, c.type, j.displayIndex)); + } + } + return new ViewDTO(v.name, v.title, columns); + }) + .collect(toList()); + } + + private LoadingCache> buildViewsCache() { + return CacheBuilder.newBuilder() + .build(new CacheLoader<>() { + @Override + public List load(Boolean key) { + var views = fetchViews(); + log.info("Views list has been cached, {} views in total", views.size()); + return views; + } + }); + } + + protected List fetchFacets() { + return calculateRead(ds, () -> viewsConfig.views + .stream() + .flatMap(view -> + view.columns.stream() + .map(column -> getFacetInfo(view, column)) + .filter(f -> ( + f.getMin() != null || f.getMax() != null + || (f.getValues() != null && f.getValues().size() > 1) + || f.getBooleanValue() != null + )) + ) + .collect(toList())); + } + private FacetDTO getFacetInfo(View view, View.Column column) { List values = null; Object min = null; @@ -125,6 +222,7 @@ private FacetDTO getFacetInfo(View view, View.Column column) { binding.add("predicate", createResource(column.source)); try (var execution = QueryExecutionFactory.create(BOOLEAN_VALUE_QUERY, ds, binding)) { var rowExec = execution.execSelect(); + // TODO: should we check all results until it's not null (not the first element only)? if (rowExec.hasNext()) { booleanValue = (Boolean) ofNullable(rowExec.next().getLiteral("booleanValue")) .map(Literal::getValue) @@ -156,50 +254,33 @@ private FacetDTO getFacetInfo(View view, View.Column column) { return new FacetDTO(view.name + "_" + column.name, column.title, column.type, values, booleanValue, min, max); } - public List getFacets() { - return calculateRead(ds, () -> viewsConfig.views - .stream() - .flatMap(view -> - view.columns.stream() - .map(column -> getFacetInfo(view, column)) - .filter(f -> ( - f.getMin() != null || f.getMax() != null - || (f.getValues() != null && f.getValues().size() > 1) - || f.getBooleanValue() != null - )) - ) - .collect(toList())); + private LoadingCache> buildFacetCache() { + return CacheBuilder.newBuilder() + .build(new CacheLoader<>() { + @Override + public List load(Boolean key) { + var facets = fetchFacets(); + log.info("Facets list has been cached, {} facets in total", facets.size()); + return facets; + } + }); } - public List getViews() { - return viewsConfig.views.stream() - .map(v -> { - var columns = new ArrayList(); - - // The entity labal is the first column displayed, if you want a column before this label, assign a negative displayIndex value in views.yaml - final int ENTITY_LABEL_INDEX = 0; + private Object convertLiteralValue(Object value) { + if (value instanceof XSDDateTime) { + return ofEpochMilli(((XSDDateTime) value).asCalendar().getTimeInMillis()); + } + return value; + } - columns.add(new ColumnDTO(v.name, v.itemName == null ? v.name : v.itemName, ColumnType.Identifier, ENTITY_LABEL_INDEX)); - for (var c : v.columns) { - columns.add(new ColumnDTO(v.name + "_" + c.name, c.title, c.type, c.displayIndex)); - } - for (var j : v.join) { - var joinView = viewsConfig.views.stream().filter(view -> view.name.equalsIgnoreCase(j.view)).findFirst().orElse(null); - if (joinView == null) { - continue; - } - if (j.include.contains("id")) { - columns.add(new ColumnDTO(joinView.name, joinView.title, ColumnType.Identifier, j.displayIndex)); - } - for (var c : joinView.columns) { - if (!j.include.contains(c.name)) { - continue; - } - columns.add(new ColumnDTO(joinView.name + "_" + c.name, c.title, c.type, j.displayIndex)); - } - } - return new ViewDTO(v.name, v.title, columns); - }) - .collect(toList()); + @SneakyThrows + private Range getColumnRange(View view, View.Column column) { + if (!EnumSet.of(ColumnType.Date, ColumnType.Number).contains(column.type)) { + return null; + } + try (var reader = new ViewStoreReader(searchConfig, viewStoreClientFactory)) { + return reader.aggregate(view.name, column.name); + } } + } diff --git a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/JdbcQueryServiceTest.java b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/JdbcQueryServiceTest.java index 5b3492c7c..06f5f8402 100644 --- a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/JdbcQueryServiceTest.java +++ b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/JdbcQueryServiceTest.java @@ -88,7 +88,9 @@ public void before() throws SQLException, NotAuthorizedException, BadRequestExce Model model = ds.getDefaultModel(); var vocabulary = model.read("test-vocabulary.ttl"); - maintenanceService = new MaintenanceService(userService, ds, viewStoreClientFactory); + var viewService = new ViewService(ConfigLoader.CONFIG.search, config, ds, viewStoreClientFactory, permissions); + + maintenanceService = new MaintenanceService(userService, ds, viewStoreClientFactory, viewService); workspaceService = new WorkspaceService(tx, userService); diff --git a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java index 3b5921bcf..bfd5c9bed 100644 --- a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java +++ b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java @@ -1,36 +1,55 @@ package io.fairspace.saturn.services.views; -import io.fairspace.saturn.config.*; -import io.fairspace.saturn.rdf.transactions.*; -import io.fairspace.saturn.services.metadata.*; -import io.fairspace.saturn.services.metadata.validation.*; -import io.fairspace.saturn.services.users.*; -import io.fairspace.saturn.services.workspaces.*; -import io.fairspace.saturn.webdav.*; +import io.fairspace.saturn.config.Config; +import io.fairspace.saturn.config.ConfigLoader; +import io.fairspace.saturn.config.ViewsConfig; +import io.fairspace.saturn.rdf.transactions.SimpleTransactions; +import io.fairspace.saturn.rdf.transactions.Transactions; +import io.fairspace.saturn.rdf.transactions.TxnIndexDatasetGraph; +import io.fairspace.saturn.services.metadata.MetadataPermissions; +import io.fairspace.saturn.services.metadata.MetadataService; +import io.fairspace.saturn.services.metadata.validation.ComposedValidator; +import io.fairspace.saturn.services.metadata.validation.UniqueLabelValidator; +import io.fairspace.saturn.services.users.User; +import io.fairspace.saturn.services.users.UserService; +import io.fairspace.saturn.services.workspaces.Workspace; +import io.fairspace.saturn.services.workspaces.WorkspaceService; +import io.fairspace.saturn.webdav.DavFactory; import io.fairspace.saturn.webdav.blobstore.BlobInfo; import io.fairspace.saturn.webdav.blobstore.BlobStore; import io.milton.http.ResourceFactory; -import io.milton.http.exceptions.*; -import io.milton.resource.*; -import org.apache.jena.query.*; -import org.apache.jena.rdf.model.*; -import org.apache.jena.sparql.core.*; -import org.apache.jena.sparql.util.*; -import org.eclipse.jetty.server.*; -import org.junit.*; -import org.junit.runner.*; -import org.mockito.*; -import org.mockito.junit.*; - -import java.io.*; -import java.sql.*; -import java.util.stream.*; - -import static io.fairspace.saturn.TestUtils.*; +import io.milton.http.exceptions.BadRequestException; +import io.milton.http.exceptions.ConflictException; +import io.milton.http.exceptions.NotAuthorizedException; +import io.milton.resource.MakeCollectionableResource; +import io.milton.resource.PutableResource; +import org.apache.jena.query.Dataset; +import org.apache.jena.rdf.model.Model; +import org.apache.jena.sparql.core.DatasetGraphFactory; +import org.apache.jena.sparql.util.Context; +import org.eclipse.jetty.server.Authentication; +import org.junit.Assert; +import org.junit.Before; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.mockito.Mock; +import org.mockito.junit.MockitoJUnitRunner; + +import java.io.IOException; +import java.sql.SQLException; +import java.util.stream.Collectors; + +import static io.fairspace.saturn.TestUtils.createTestUser; +import static io.fairspace.saturn.TestUtils.loadViewsConfig; +import static io.fairspace.saturn.TestUtils.mockAuthentication; +import static io.fairspace.saturn.TestUtils.setupRequestContext; import static io.fairspace.saturn.auth.RequestContext.getCurrentRequest; -import static org.apache.jena.query.DatasetFactory.*; +import static org.apache.jena.query.DatasetFactory.wrap; import static org.mockito.ArgumentMatchers.any; import static org.mockito.Mockito.lenient; +import static org.mockito.Mockito.never; +import static org.mockito.Mockito.spy; +import static org.mockito.Mockito.verify; import static org.mockito.Mockito.when; @RunWith(MockitoJUnitRunner.class) @@ -49,10 +68,7 @@ public class ViewServiceTest { @Before public void before() throws SQLException, BadRequestException, ConflictException, NotAuthorizedException, IOException { - var viewDatabase = new Config.ViewDatabase(); - viewDatabase.url = "jdbc:h2:mem:test;DB_CLOSE_DELAY=-1;MODE=PostgreSQL;DATABASE_TO_LOWER=TRUE"; - viewDatabase.username = "sa"; - viewDatabase.password = ""; + var viewDatabase = buildViewDatabaseConfig(); ViewsConfig config = loadViewsConfig("src/test/resources/test-views.yaml"); ViewStoreClientFactory.H2_DATABASE = true; var viewStoreClientFactory = new ViewStoreClientFactory(config, viewDatabase); @@ -60,6 +76,78 @@ public void before() throws SQLException, BadRequestException, ConflictException var dsg = new TxnIndexDatasetGraph(DatasetGraphFactory.createTxnMem(), viewStoreClientFactory); Dataset ds = wrap(dsg); + + loadTestData(ds); + + viewService = new ViewService( + ConfigLoader.CONFIG.search, + config, + ds, + viewStoreClientFactory, + permissions); + } + + @Test + public void testFetchViewConfig() { + when(permissions.canReadFacets()).thenReturn(true); + var facets = viewService.getCachedFacets(); + var dateFacets = facets.stream() + .filter(facet -> facet.getType() == ViewsConfig.ColumnType.Date) + .toList(); + Assert.assertEquals(2, dateFacets.size()); + + var boolFacets = facets.stream() + .filter(facet -> facet.getType() == ViewsConfig.ColumnType.Boolean) + .toList(); + Assert.assertEquals(1, boolFacets.size()); + } + + @Test + public void testDisplayIndex_IsSet() { + var views = viewService.getCachedViews(); + var columns = views.get(1).getColumns().stream().toList(); + var selectedColumn = columns.stream().filter(c -> c.getTitle().equals("Morphology")).collect(Collectors.toList()).get(0); + Assert.assertEquals(Integer.valueOf(1), selectedColumn.getDisplayIndex()); + } + + @Test + public void testDisplayIndex_IsNotSet() { + var views = viewService.getCachedViews(); + var columns = views.get(1).getColumns().stream().toList(); + var selectedColumn = columns.stream().filter(c -> c.getTitle().equals("Laterality")).collect(Collectors.toList()).get(0); + Assert.assertEquals(Integer.valueOf(Integer.MAX_VALUE), selectedColumn.getDisplayIndex()); + } + + @Test + public void testFetchCachedFacets() { + var sut = spy(viewService); + when(permissions.canReadFacets()).thenReturn(true); + + var facets = viewService.getCachedFacets(); + Assert.assertEquals(facets.size(), 11); + verify(sut, never()).fetchFacets(); + } + + + @Test + public void testFetchCachedViews() { + var sut = spy(viewService); + + var views = viewService.getCachedViews(); + Assert.assertEquals(views.size(), 4); + verify(sut, never()).fetchViews(); + } + + private Config.ViewDatabase buildViewDatabaseConfig() { + var viewDatabase = new Config.ViewDatabase(); + viewDatabase.url = "jdbc:h2:mem:test;DB_CLOSE_DELAY=-1;MODE=PostgreSQL;DATABASE_TO_LOWER=TRUE"; + viewDatabase.username = "sa"; + viewDatabase.password = ""; + return viewDatabase; + } + + private void loadTestData(Dataset ds) throws NotAuthorizedException, BadRequestException, ConflictException, IOException { + // TODO: loaded data to be mocked instead of loading them this way Transactions tx = new SimpleTransactions(ds); Model model = ds.getDefaultModel(); var vocabulary = model.read("test-vocabulary.ttl"); @@ -70,12 +158,6 @@ public void before() throws SQLException, BadRequestException, ConflictException var davFactory = new DavFactory(model.createResource(baseUri), store, userService, context); - viewService = new ViewService( - ConfigLoader.CONFIG.search, - config, - ds, - viewStoreClientFactory); - when(permissions.canWriteMetadata(any())).thenReturn(true); api = new MetadataService(tx, vocabulary, new ComposedValidator(new UniqueLabelValidator()), permissions); @@ -102,34 +184,4 @@ public void before() throws SQLException, BadRequestException, ConflictException var testdata = model.read("testdata.ttl"); api.put(testdata); } - - @Test - public void testFetchViewConfig() { - var facets = viewService.getFacets(); - var dateFacets = facets.stream() - .filter(facet -> facet.getType() == ViewsConfig.ColumnType.Date) - .toList(); - Assert.assertEquals(2, dateFacets.size()); - - var boolFacets = facets.stream() - .filter(facet -> facet.getType() == ViewsConfig.ColumnType.Boolean) - .toList(); - Assert.assertEquals(1, boolFacets.size()); - } - - @Test - public void testDisplayIndex_IsSet() { - var views = viewService.getViews(); - var columns = views.get(1).getColumns().stream().toList(); - var selectedColumn = columns.stream().filter(c -> c.getTitle().equals("Morphology")).collect(Collectors.toList()).get(0); - Assert.assertEquals(Integer.valueOf(1), selectedColumn.getDisplayIndex()); - } - - @Test - public void testDisplayIndex_IsNotSet() { - var views = viewService.getViews(); - var columns = views.get(1).getColumns().stream().toList(); - var selectedColumn = columns.stream().filter(c -> c.getTitle().equals("Laterality")).collect(Collectors.toList()).get(0); - Assert.assertEquals(Integer.valueOf(Integer.MAX_VALUE), selectedColumn.getDisplayIndex()); - } } From 8e268e968422ea4041bdc251051e6c71bad5df34 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Tue, 23 Jan 2024 14:46:04 +0100 Subject: [PATCH 047/153] Add unit tests and documentation. --- README.adoc | 54 +++++++++++++++++++ .../mercury/src/layout/WorkspaceLayout.js | 6 +-- .../ExternalMetadataSourceContext.js | 2 +- .../__tests__/ExternalMetadataSourceView.js | 31 +++++++++++ .../__tests__/externalMetadataSourceUtils.js | 10 ++++ 5 files changed, 99 insertions(+), 4 deletions(-) create mode 100644 projects/mercury/src/metadata/external-sources/__tests__/ExternalMetadataSourceView.js create mode 100644 projects/mercury/src/metadata/external-sources/__tests__/externalMetadataSourceUtils.js diff --git a/README.adoc b/README.adoc index 74eca0d58..144c4627f 100644 --- a/README.adoc +++ b/README.adoc @@ -1833,6 +1833,60 @@ storages: url: https://exstorage2/api/webdav ---- +=== Multi-Fairspace metadata views integration + +Fairspace can have only single data model configured. However, if there is a need to have data from multiple models, +representing multiple domains that would be combined combined in single user interface, it is possible to integrate multiple Fairspace instances together. + + +Fairspace (main) instance can be configured as a view interface of metadata from another (external) Fairspace instance. +External Fairspace can have a different metadata model configured than the main Fairspace. +Important precondition is that the external instance has to be connected to the same Keycloak realm as the main instance. + + +External metadata can be searched and browsed in the same way as the internal metadata views. When configured, there is an extra page, +separate from internal metadata views, that allows to explore external metadata. +Currently, cross-instance metadata search is not supported. + + +For the external metadata pages, the tables and columns are created basing on the views configuration specified in that instance configuration. + + +==== Access policy + +Connection to the same Keycloak realm allows to authenticate a user in all integrated Fairspace instances with a single set of login credentials. +Each Fairspace instance is responsible for controlling the access to its own metadata and perform +the required checks to ensure that users only get to see metadata of an instance, if has a view public metadata role assigned within that instance. + +==== Configuration + +Multiple external Fairspace metadata pages can be configured simultaneously. A list of configuration parameters is presented below. + +|=== +| Parameter | Description + +| ``name`` +| Unique name of the metadata source. +| ``label`` +| String to be used as a display name of the metadata source. +| ``url`` +| Fairspace instance to connect to. +|=== + +Sample configuration of external metadata sources in YAML format: +[source, bash] +---- +metadata-sources: + metaSource1: + name: metadataSource1 + label: "Test metadata 1" + url: https://fairspace-test1/api/ + metaSource2: + name: metadataSource2 + label: "Test metadata 2" + url: https://fairspace-test2/api/ +---- + == Structure and terminology diff --git a/projects/mercury/src/layout/WorkspaceLayout.js b/projects/mercury/src/layout/WorkspaceLayout.js index 3533ad53b..b0a11b69a 100644 --- a/projects/mercury/src/layout/WorkspaceLayout.js +++ b/projects/mercury/src/layout/WorkspaceLayout.js @@ -15,7 +15,7 @@ import {MetadataViewFacetsProvider} from "../metadata/views/MetadataViewFacetsCo import {ExternalStoragesProvider} from "../external-storage/ExternalStoragesContext"; import {StatusProvider} from "../status/StatusContext"; import type {Workspace} from "../workspaces/WorkspacesAPI"; -import {ExternalMetadataSourcesProvider} from "../metadata/external-sources/ExternalMetadataSourceContext"; +import {ExternalMetadataSourceProvider} from "../metadata/external-sources/ExternalMetadataSourceContext"; const WorkspaceLayoutInner = () => { const {workspaces} = useContext(WorkspaceContext); @@ -31,7 +31,7 @@ const WorkspaceLayoutInner = () => { - + { /> - + diff --git a/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceContext.js b/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceContext.js index c9d5d2e36..71bbe6e37 100644 --- a/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceContext.js +++ b/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceContext.js @@ -5,7 +5,7 @@ import useAsync from "../../common/hooks/UseAsync"; const ExternalMetadataSourceContext = React.createContext({}); -export const ExternalMetadataSourcesProvider = ({children}) => { +export const ExternalMetadataSourceProvider = ({children}) => { const {data: externalMetadataSources = [], error, loading, refresh} = useAsync(() => axios.get('/api/metadata-sources/') .then(extractJsonData) .catch(handleHttpError('Connection error.'))); diff --git a/projects/mercury/src/metadata/external-sources/__tests__/ExternalMetadataSourceView.js b/projects/mercury/src/metadata/external-sources/__tests__/ExternalMetadataSourceView.js new file mode 100644 index 000000000..0ecfa4fe1 --- /dev/null +++ b/projects/mercury/src/metadata/external-sources/__tests__/ExternalMetadataSourceView.js @@ -0,0 +1,31 @@ +import React from "react"; + +import {render, screen, waitFor} from '@testing-library/react'; +import ExternalMetadataSourceView from '../ExternalMetadataSourceView'; +import {ExternalMetadataSourceProvider} from "../ExternalMetadataSourceContext"; +import useAsync from "../../../common/hooks/UseAsync"; + + +jest.mock('axios'); +jest.mock('../../../common/hooks/UseAsync', () => jest.fn()); +jest.mock('../../views/MetadataView', () => ({pathPrefix}) =>
{pathPrefix}
); + +describe('ExternalMetadataSourceView', () => { + it('renders MetadataView with proper path redirection', async () => { + const mockMetadataSource = { + name: 'example', path: '/example/path', + }; + + useAsync.mockReturnValue({ + data: [mockMetadataSource], error: null, loading: false, refresh: jest.fn(), + }); + + render( + + ); + + await waitFor(() => { + expect(screen.getByText('/metadata-sources/example')).toBeInTheDocument(); + }); + }); +}); diff --git a/projects/mercury/src/metadata/external-sources/__tests__/externalMetadataSourceUtils.js b/projects/mercury/src/metadata/external-sources/__tests__/externalMetadataSourceUtils.js new file mode 100644 index 000000000..74f9096c0 --- /dev/null +++ b/projects/mercury/src/metadata/external-sources/__tests__/externalMetadataSourceUtils.js @@ -0,0 +1,10 @@ +import {getExternalMetadataSourcePathPrefix} from "../externalMetadataSourceUtils"; + +describe('External Metadata Source Utils', () => { + describe('getExternalMetadataSourcePathPrefix', () => { + it('should return valid external metadata source path', () => { + expect(getExternalMetadataSourcePathPrefix("remoteMetadataSource")) + .toBe('/metadata-sources/remoteMetadataSource'); + }); + }); +}); From ebd43e6a929c6683f27296c53fc755b549c4dfee Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Tue, 23 Jan 2024 17:33:23 +0100 Subject: [PATCH 048/153] add indexes for jointables --- .../views/ViewStoreClientFactory.java | 144 +++++++++++------- 1 file changed, 92 insertions(+), 52 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java index c2507eee4..393cfef49 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java @@ -66,12 +66,11 @@ public ViewStoreClientFactory(ViewsConfig viewsConfig, Config.ViewDatabase viewD .columns(List.of( idColumn(), valueColumn("type", ColumnType.Text), - valueColumn("label", ColumnType.Text) - )) + valueColumn("label", ColumnType.Text))) .build()); configuration = new ViewStoreClient.ViewStoreConfiguration(viewsConfig); - for (View view: viewsConfig.views) { + for (View view : viewsConfig.views) { ensureViewExists(view); } } @@ -85,7 +84,7 @@ Map getColumnMetadata(Connection connection, String tabl var resultSet = connection.getMetaData().getColumns(null, null, table, null); var result = new LinkedHashMap(); while (resultSet.next()) { - String columnName = resultSet.getString("COLUMN_NAME"); + String columnName = resultSet.getString("COLUMN_NAME"); String dataTypeName = resultSet.getString("TYPE_NAME"); Boolean nullable = resultSet.getBoolean("NULLABLE"); var metadata = ColumnMetadata.builder() @@ -103,62 +102,103 @@ void ensureTableExists(Table table) throws SQLException { var resultSet = connection.getMetaData().getTables(null, null, table.name, null); var tableExists = resultSet.next(); if (!tableExists) { - // Create new table - connection.setAutoCommit(true); - var columnSpecification = - table.columns.stream() - .filter(column -> !column.type.isSet()) - .map(column -> String.format("%s %s", column.name, databaseTypeForColumnType(column.type)) - ).collect(Collectors.joining(", ")); - var keys = table.columns.stream() - .filter(column -> column.type == ColumnType.Identifier) - .map(column -> column.name) - .collect(Collectors.joining(", ")); - var command = String.format("create table %s ( %s, primary key ( %s ) )", table.name, columnSpecification, keys); - log.debug(command); - connection.createStatement().execute(command); - connection.setAutoCommit(false); - log.info("Table {} created.", table.name); + createTable(table, connection); } else { - var columnMetadata = getColumnMetadata(connection, table.name); - var newColumns = table.columns.stream() - .filter(column -> !column.type.isSet() && !columnMetadata.containsKey(column.name)) - .collect(Collectors.toList()); - try { - log.debug("New columns: {}", new ObjectMapper().writeValueAsString(newColumns)); - } catch (JsonProcessingException e) { - e.printStackTrace(); - } - // Update existing table - if (!newColumns.isEmpty()) { - connection.setAutoCommit(true); - var command = newColumns.stream() - .map(column -> String.format("alter table %s add column %s %s", - table.name, column.name, databaseTypeForColumnType(column.type))) - .collect(Collectors.joining("; ")); - log.debug(command); - connection.createStatement().execute(command); - connection.setAutoCommit(false); - log.info("Table {} updated.", table.name); - } + updateTable(table, connection); } } } + void ensureJoinTableExists(Table table) throws SQLException { + try (var connection = getConnection()) { + log.debug("Check if table {} exists ...", table.name); + var resultSet = connection.getMetaData().getTables(null, null, table.name, null); + var tableExists = resultSet.next(); + if (!tableExists) { + createTable(table, connection); + createIndexes(table, connection); + } else { + updateTable(table, connection); + } + } + } + + private void updateTable(Table table, Connection connection) throws SQLException { + var columnMetadata = getColumnMetadata(connection, table.name); + var newColumns = table.columns.stream() + .filter(column -> !column.type.isSet() && !columnMetadata.containsKey(column.name)) + .collect(Collectors.toList()); + try { + log.debug("New columns: {}", new ObjectMapper().writeValueAsString(newColumns)); + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + // Update existing table + if (!newColumns.isEmpty()) { + connection.setAutoCommit(true); + var command = newColumns.stream() + .map(column -> String.format("alter table %s add column %s %s", + table.name, column.name, databaseTypeForColumnType(column.type))) + .collect(Collectors.joining("; ")); + log.debug(command); + connection.createStatement().execute(command); + connection.setAutoCommit(false); + log.info("Table {} updated.", table.name); + } + } + + private void createTable(Table table, Connection connection) throws SQLException { + // Create new table + connection.setAutoCommit(true); + var columnSpecification = table.columns.stream() + .filter(column -> !column.type.isSet()) + .map(column -> String.format("%s %s", column.name, databaseTypeForColumnType(column.type))) + .collect(Collectors.joining(", ")); + var keys = table.columns.stream() + .filter(column -> column.type == ColumnType.Identifier) + .map(column -> column.name) + .collect(Collectors.joining(", ")); + var command = String.format("create table %s ( %s, primary key ( %s ) )", table.name, columnSpecification, + keys); + log.debug(command); + connection.createStatement().execute(command); + connection.setAutoCommit(false); + log.info("Table {} created.", table.name); + } + + private void createIndexes(Table table, Connection connection) throws SQLException { + // Create new table + connection.setAutoCommit(true); + + var keys = table.columns.stream() + .filter(column -> column.type == ColumnType.Identifier) + .map(column -> column.name) + .toList(); + + for (var column : keys) { + // var command = String.format("create table %s ( %s, primary key ( %s ) )", + // table.name, columnSpecification, keys); + var indexName = String.format("%1$s_%2$s_idx", table.name, column); + var command = String.format("CREATE INDEX %3$s ON public.%1$s (%2$s)", table.name, column, indexName); + + log.debug(command); + connection.createStatement().execute(command); + connection.setAutoCommit(false); + log.info("Index {} created.", indexName); + } + } + void validateViewConfig(ViewsConfig.View view) { - if (view.columns.stream().anyMatch(column -> - column.name.equalsIgnoreCase("id"))) { + if (view.columns.stream().anyMatch(column -> column.name.equalsIgnoreCase("id"))) { throw new IllegalArgumentException( "Forbidden to override the built-in column 'id' of view " + view.name); } - if (view.columns.stream().anyMatch(column -> - column.name.equalsIgnoreCase("label"))) { + if (view.columns.stream().anyMatch(column -> column.name.equalsIgnoreCase("label"))) { throw new IllegalArgumentException( "Forbidden to override the built-in column 'label' of view " + view.name); } if (view.name.equalsIgnoreCase("resource") && - view.columns.stream().anyMatch(column -> - column.name.equalsIgnoreCase("collection"))) { + view.columns.stream().anyMatch(column -> column.name.equalsIgnoreCase("collection"))) { throw new IllegalArgumentException( "Forbidden to override the built-in column 'collection' of view " + view.name); } @@ -178,7 +218,7 @@ void ensureViewExists(ViewsConfig.View view) throws SQLException { if (view.name.equalsIgnoreCase("resource")) { columns.add(valueColumn("collection", ColumnType.Text)); } - for (var column: view.columns) { + for (var column : view.columns) { if (column.type.isSet()) { continue; } @@ -208,7 +248,7 @@ void ensureViewExists(ViewsConfig.View view) throws SQLException { } if (view.join != null) { // Add join tables - for (ViewsConfig.View.JoinView join: view.join) { + for (ViewsConfig.View.JoinView join : view.join) { var joinTable = getJoinTable(join, view); ensureTableExists(joinTable); configuration.joinTables.putIfAbsent(view.name, new HashMap<>()); @@ -224,14 +264,14 @@ public static Table getJoinTable(View.JoinView join, View view) { .name(String.format("%s_%s", left.toLowerCase(), right.toLowerCase())) .columns(Arrays.asList( idColumn(left), - idColumn(right) - )) + idColumn(right))) .build(); return joinTable; } - @Data @Builder + @Data + @Builder public static class ColumnMetadata { String type; Boolean nullable; From 41d6223e4f81447f17f828dda6dc2addfc5c374e Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Wed, 24 Jan 2024 09:27:12 +0100 Subject: [PATCH 049/153] now it works :) --- .../services/views/ViewStoreClientFactory.java | 16 ++++++++-------- .../saturn/services/views/ViewStoreReader.java | 2 +- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java index 393cfef49..258e57cbb 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java @@ -114,6 +114,7 @@ void ensureJoinTableExists(Table table) throws SQLException { log.debug("Check if table {} exists ...", table.name); var resultSet = connection.getMetaData().getTables(null, null, table.name, null); var tableExists = resultSet.next(); + if (!tableExists) { createTable(table, connection); createIndexes(table, connection); @@ -167,25 +168,24 @@ private void createTable(Table table, Connection connection) throws SQLException } private void createIndexes(Table table, Connection connection) throws SQLException { - // Create new table - connection.setAutoCommit(true); - + var keys = table.columns.stream() .filter(column -> column.type == ColumnType.Identifier) .map(column -> column.name) .toList(); + connection.setAutoCommit(true); + for (var column : keys) { - // var command = String.format("create table %s ( %s, primary key ( %s ) )", - // table.name, columnSpecification, keys); var indexName = String.format("%1$s_%2$s_idx", table.name, column); - var command = String.format("CREATE INDEX %3$s ON public.%1$s (%2$s)", table.name, column, indexName); + var command = String.format("CREATE INDEX IF NOT EXISTS %3$s ON public.%1$s (%2$s)", table.name, column, indexName); log.debug(command); connection.createStatement().execute(command); - connection.setAutoCommit(false); log.info("Index {} created.", indexName); } + + connection.setAutoCommit(false); } void validateViewConfig(ViewsConfig.View view) { @@ -250,7 +250,7 @@ void ensureViewExists(ViewsConfig.View view) throws SQLException { // Add join tables for (ViewsConfig.View.JoinView join : view.join) { var joinTable = getJoinTable(join, view); - ensureTableExists(joinTable); + ensureJoinTableExists(joinTable); configuration.joinTables.putIfAbsent(view.name, new HashMap<>()); configuration.joinTables.get(view.name).put(join.view, joinTable); } diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java index 17ec031bd..3b94b91a5 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java @@ -469,7 +469,7 @@ private PreparedStatement getJoinQuery(String view, View.JoinView joinView, Tabl + ") limit " + String.valueOf(MAX_JOIN_ITEMS) + ")"; var subqueries = ids.stream().map(queryBody); - var query = subqueries.collect(Collectors.joining("\n UNION \n")); + var query = subqueries.collect(Collectors.joining("\n UNION ALL \n")); return connection.prepareStatement(query); } From 52a25126189ce7480bb791f4199c771d65e58436 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Wed, 24 Jan 2024 10:54:46 +0100 Subject: [PATCH 050/153] rename after PR comment --- .../services/views/ViewStoreClientFactory.java | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java index 258e57cbb..bf5417468 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java @@ -61,7 +61,7 @@ public ViewStoreClientFactory(ViewsConfig viewsConfig, Config.ViewDatabase viewD log.debug("Database connection: {}", connection.getMetaData().getDatabaseProductName()); } - ensureTableExists(Table.builder() + createOrUpdateTable(Table.builder() .name("label") .columns(List.of( idColumn(), @@ -71,7 +71,7 @@ public ViewStoreClientFactory(ViewsConfig viewsConfig, Config.ViewDatabase viewD configuration = new ViewStoreClient.ViewStoreConfiguration(viewsConfig); for (View view : viewsConfig.views) { - ensureViewExists(view); + createOrUpdateView(view); } } @@ -96,7 +96,7 @@ Map getColumnMetadata(Connection connection, String tabl return result; } - void ensureTableExists(Table table) throws SQLException { + void createOrUpdateTable(Table table) throws SQLException { try (var connection = getConnection()) { log.debug("Check if table {} exists ...", table.name); var resultSet = connection.getMetaData().getTables(null, null, table.name, null); @@ -109,7 +109,7 @@ void ensureTableExists(Table table) throws SQLException { } } - void ensureJoinTableExists(Table table) throws SQLException { + void createOrUpdateJoinTable(Table table) throws SQLException { try (var connection = getConnection()) { log.debug("Check if table {} exists ...", table.name); var resultSet = connection.getMetaData().getTables(null, null, table.name, null); @@ -209,7 +209,7 @@ void validateViewConfig(ViewsConfig.View view) { } } - void ensureViewExists(ViewsConfig.View view) throws SQLException { + void createOrUpdateView(ViewsConfig.View view) throws SQLException { // Add view table validateViewConfig(view); var columns = new ArrayList(); @@ -228,7 +228,7 @@ void ensureViewExists(ViewsConfig.View view) throws SQLException { .name(view.name.toLowerCase()) .columns(columns) .build(); - ensureTableExists(table); + createOrUpdateTable(table); configuration.viewTables.put(view.name, table); // Add property tables for (ViewsConfig.View.Column column : view.columns) { @@ -242,7 +242,7 @@ void ensureViewExists(ViewsConfig.View view) throws SQLException { .name(String.format("%s_%s", view.name.toLowerCase(), column.name.toLowerCase())) .columns(propertyTableColumns) .build(); - ensureTableExists(propertyTable); + createOrUpdateTable(propertyTable); configuration.propertyTables.putIfAbsent(view.name, new HashMap<>()); configuration.propertyTables.get(view.name).put(column.name, propertyTable); } @@ -250,7 +250,7 @@ void ensureViewExists(ViewsConfig.View view) throws SQLException { // Add join tables for (ViewsConfig.View.JoinView join : view.join) { var joinTable = getJoinTable(join, view); - ensureJoinTableExists(joinTable); + createOrUpdateJoinTable(joinTable); configuration.joinTables.putIfAbsent(view.name, new HashMap<>()); configuration.joinTables.get(view.name).put(join.view, joinTable); } From 30d304c068368bbbbc33e45d335db5c0da5dcfae Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Wed, 24 Jan 2024 11:06:55 +0100 Subject: [PATCH 051/153] Add minor improvements and documentation updates. --- README.adoc | 10 +++++----- projects/mercury/src/routes/WorkspaceRoutes.js | 2 +- .../nl/fairspace/pluto/web/dto/MetadataSourceInfo.java | 1 - 3 files changed, 6 insertions(+), 7 deletions(-) diff --git a/README.adoc b/README.adoc index 144c4627f..a115c302a 100644 --- a/README.adoc +++ b/README.adoc @@ -1835,13 +1835,13 @@ storages: === Multi-Fairspace metadata views integration -Fairspace can have only single data model configured. However, if there is a need to have data from multiple models, -representing multiple domains that would be combined combined in single user interface, it is possible to integrate multiple Fairspace instances together. +Fairspace works with a single data model configured. However, if there is a need to have data from multiple models, +representing multiple domains that would be combined in single user interface, it is possible to integrate multiple Fairspace instances together. -Fairspace (main) instance can be configured as a view interface of metadata from another (external) Fairspace instance. +The main Fairspace instance can be configured as a view interface of metadata from another (external) Fairspace instance. External Fairspace can have a different metadata model configured than the main Fairspace. -Important precondition is that the external instance has to be connected to the same Keycloak realm as the main instance. +An important precondition is that the external instance has to be connected to the same Keycloak realm as the main instance. External metadata can be searched and browsed in the same way as the internal metadata views. When configured, there is an extra page, @@ -1854,7 +1854,7 @@ For the external metadata pages, the tables and columns are created basing on th ==== Access policy -Connection to the same Keycloak realm allows to authenticate a user in all integrated Fairspace instances with a single set of login credentials. +Connection to the same Keycloak realm allows to authenticate a user in all integrated Fairspace instances with a single set of login credentials (single sign-on). Each Fairspace instance is responsible for controlling the access to its own metadata and perform the required checks to ensure that users only get to see metadata of an instance, if has a view public metadata role assigned within that instance. diff --git a/projects/mercury/src/routes/WorkspaceRoutes.js b/projects/mercury/src/routes/WorkspaceRoutes.js index a32169478..bae01c53e 100644 --- a/projects/mercury/src/routes/WorkspaceRoutes.js +++ b/projects/mercury/src/routes/WorkspaceRoutes.js @@ -119,7 +119,7 @@ const WorkspaceRoutes = () => { render={() => (isAdmin(currentUser) && ())} /> - + ); }; diff --git a/projects/pluto/src/main/java/nl/fairspace/pluto/web/dto/MetadataSourceInfo.java b/projects/pluto/src/main/java/nl/fairspace/pluto/web/dto/MetadataSourceInfo.java index e6640ab8f..d6e4268e7 100644 --- a/projects/pluto/src/main/java/nl/fairspace/pluto/web/dto/MetadataSourceInfo.java +++ b/projects/pluto/src/main/java/nl/fairspace/pluto/web/dto/MetadataSourceInfo.java @@ -8,7 +8,6 @@ @Getter @EqualsAndHashCode @AllArgsConstructor -@NoArgsConstructor public class MetadataSourceInfo { private String name; private String label; From f0914d0cce533fe3322f2bcfb73e4c27ff8a1dd3 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Wed, 24 Jan 2024 11:07:40 +0100 Subject: [PATCH 052/153] String formatter simpler --- .../saturn/services/views/ViewStoreClientFactory.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java index bf5417468..5f0bdca85 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java @@ -177,8 +177,8 @@ private void createIndexes(Table table, Connection connection) throws SQLExcepti connection.setAutoCommit(true); for (var column : keys) { - var indexName = String.format("%1$s_%2$s_idx", table.name, column); - var command = String.format("CREATE INDEX IF NOT EXISTS %3$s ON public.%1$s (%2$s)", table.name, column, indexName); + var indexName = String.format("%s_%s_idx", table.name, column); + var command = String.format("CREATE INDEX IF NOT EXISTS %s ON public.%s (%s)", indexName, table.name, column); log.debug(command); connection.createStatement().execute(command); From 65c0888e13f174e0e699516246ae3389bf645347 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Wed, 24 Jan 2024 11:12:30 +0100 Subject: [PATCH 053/153] change class access modifier --- .../fairspace/saturn/services/views/ViewStoreClientFactory.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java index 5f0bdca85..039a7d4f0 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java @@ -272,7 +272,7 @@ public static Table getJoinTable(View.JoinView join, View view) { @Data @Builder - public static class ColumnMetadata { + private static class ColumnMetadata { String type; Boolean nullable; } From f4de022ba22c2e5f560e8ff64c05a413a5d5ad54 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Wed, 24 Jan 2024 11:37:00 +0100 Subject: [PATCH 054/153] Add support for external metadata sources config in helm charts. --- charts/fairspace/templates/project/configmap-pluto.yaml | 3 ++- charts/fairspace/values.yaml | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/charts/fairspace/templates/project/configmap-pluto.yaml b/charts/fairspace/templates/project/configmap-pluto.yaml index 4380f0f4a..41ec30bdb 100644 --- a/charts/fairspace/templates/project/configmap-pluto.yaml +++ b/charts/fairspace/templates/project/configmap-pluto.yaml @@ -19,7 +19,8 @@ data: realm: {{ .Values.external.keycloak.realm }} storages: {{ toYaml .Values.fairspace.storages | indent 8 }} - + metadata-sources: +{{ toYaml (index .Values.fairspace "metadata-sources") | indent 8 }} management: endpoint: health: diff --git a/charts/fairspace/values.yaml b/charts/fairspace/values.yaml index d01a9fd39..0c7d8d9fe 100644 --- a/charts/fairspace/values.yaml +++ b/charts/fairspace/values.yaml @@ -39,6 +39,7 @@ fairspace: features: [] services: {} storages: {} + metadata-sources: {} # Generic settings for tracing tracing: From 83c85438eed5584782534373a0cc829b71ac7a58 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Wed, 24 Jan 2024 12:32:32 +0100 Subject: [PATCH 055/153] handle error with column mappings --- .../saturn/services/views/ViewStoreClientFactory.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java index 039a7d4f0..ea8c020a4 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java @@ -132,7 +132,9 @@ private void updateTable(Table table, Connection connection) throws SQLException try { log.debug("New columns: {}", new ObjectMapper().writeValueAsString(newColumns)); } catch (JsonProcessingException e) { - e.printStackTrace(); + var message = "Error during mapping of view columns"; + log.error(message, e); + throw new IllegalStateException(message, e); } // Update existing table if (!newColumns.isEmpty()) { From 5db2500ea6e4eb9d1b45dc7f2dda831c9195683d Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Wed, 24 Jan 2024 13:38:41 +0100 Subject: [PATCH 056/153] compare on const instead of variable to prevent NPE --- .../saturn/services/views/ViewStoreClientFactory.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java index ea8c020a4..b2a3adf9e 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java @@ -191,16 +191,16 @@ private void createIndexes(Table table, Connection connection) throws SQLExcepti } void validateViewConfig(ViewsConfig.View view) { - if (view.columns.stream().anyMatch(column -> column.name.equalsIgnoreCase("id"))) { + if (view.columns.stream().anyMatch(column -> "id".equalsIgnoreCase(column.name))) { throw new IllegalArgumentException( "Forbidden to override the built-in column 'id' of view " + view.name); } - if (view.columns.stream().anyMatch(column -> column.name.equalsIgnoreCase("label"))) { + if (view.columns.stream().anyMatch(column -> "label".equalsIgnoreCase(column.name))) { throw new IllegalArgumentException( "Forbidden to override the built-in column 'label' of view " + view.name); } if (view.name.equalsIgnoreCase("resource") && - view.columns.stream().anyMatch(column -> column.name.equalsIgnoreCase("collection"))) { + view.columns.stream().anyMatch(column -> "collection".equalsIgnoreCase(column.name))) { throw new IllegalArgumentException( "Forbidden to override the built-in column 'collection' of view " + view.name); } From 77fe0dd350b0079935a984f167ed9ed660ae9690 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Thu, 25 Jan 2024 09:08:26 +0100 Subject: [PATCH 057/153] PR comments --- .../saturn/services/views/ViewStoreClientFactory.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java index b2a3adf9e..7edf93fda 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java @@ -180,7 +180,7 @@ private void createIndexes(Table table, Connection connection) throws SQLExcepti for (var column : keys) { var indexName = String.format("%s_%s_idx", table.name, column); - var command = String.format("CREATE INDEX IF NOT EXISTS %s ON public.%s (%s)", indexName, table.name, column); + var command = String.format("CREATE INDEX IF NOT EXISTS %s ON %s (%s)", indexName, table.name, column); log.debug(command); connection.createStatement().execute(command); @@ -275,7 +275,7 @@ public static Table getJoinTable(View.JoinView join, View view) { @Data @Builder private static class ColumnMetadata { - String type; - Boolean nullable; + private String type; + private Boolean nullable; } } From b9c61a283476a37ce113b640c34fb85d214ba537 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Thu, 25 Jan 2024 12:12:12 +0100 Subject: [PATCH 058/153] Chane autowired field injection into constructor injection. --- .../java/nl/fairspace/pluto/web/MetadataSourcesResource.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/projects/pluto/src/main/java/nl/fairspace/pluto/web/MetadataSourcesResource.java b/projects/pluto/src/main/java/nl/fairspace/pluto/web/MetadataSourcesResource.java index e605e130c..d19038a3b 100644 --- a/projects/pluto/src/main/java/nl/fairspace/pluto/web/MetadataSourcesResource.java +++ b/projects/pluto/src/main/java/nl/fairspace/pluto/web/MetadataSourcesResource.java @@ -1,5 +1,6 @@ package nl.fairspace.pluto.web; +import lombok.RequiredArgsConstructor; import lombok.extern.slf4j.Slf4j; import nl.fairspace.pluto.config.dto.PlutoConfig; import nl.fairspace.pluto.web.dto.MetadataSourceInfo; @@ -15,10 +16,10 @@ @RestController @Slf4j +@RequiredArgsConstructor public class MetadataSourcesResource { - @Autowired - PlutoConfig plutoConfig; + private final PlutoConfig plutoConfig; /** * GET /api/metadata-sources/ : returns configured external metadata sources. From eeaf8f523b9d6363f54b5387ca4aa3a83d620431 Mon Sep 17 00:00:00 2001 From: Anton Date: Thu, 25 Jan 2024 12:13:41 +0100 Subject: [PATCH 059/153] Infra/fairspc 23 GitHub actions ci (#1455) FAIRSPC-23: removed travis ci and replaced it with github actions --- .../build_and_upload_on_push_to_dev.yaml | 212 ++++++++++++++++++ .github/workflows/build_on_pull_request.yaml | 83 +++++++ .travis.yml | 106 --------- .travis/add_pod_annotations.sh | 26 --- .travis/build-condition.sh | 38 ---- .travis/build.sh | 63 ------ .travis/ci-service-account.json.enc | Bin 2320 -> 0 bytes 7 files changed, 295 insertions(+), 233 deletions(-) create mode 100644 .github/workflows/build_and_upload_on_push_to_dev.yaml create mode 100644 .github/workflows/build_on_pull_request.yaml delete mode 100644 .travis.yml delete mode 100755 .travis/add_pod_annotations.sh delete mode 100755 .travis/build-condition.sh delete mode 100755 .travis/build.sh delete mode 100644 .travis/ci-service-account.json.enc diff --git a/.github/workflows/build_and_upload_on_push_to_dev.yaml b/.github/workflows/build_and_upload_on_push_to_dev.yaml new file mode 100644 index 000000000..89e33057b --- /dev/null +++ b/.github/workflows/build_and_upload_on_push_to_dev.yaml @@ -0,0 +1,212 @@ +# Deployment workflow is supposed to be dependent on this one. + +# 1. At the workflow start four jobs are triggered in parallel (generate version, building all services) +# 2. A job to build Docker image with Saturn service is triggered once version generated and Saturn artifacts +# are built and uploaded +# 3. A job to build Docker image with Pluto service and Mercury bundle is triggered once version generated and +# Pluto/Mercury artifacts are built and uploaded + +name: Build & Upload Fairspace Docker images + +env: + DOCKER_REGISTRY: ghcr.io + +on: + push: + branches: + - "dev" + - "release" + +jobs: + # A job to generate one shared unique version tag per build cycle for all built artifacts + generate-version: + runs-on: ubuntu-latest + outputs: + output1: ${{ steps.version.outputs.fairspace_version }} + steps: + - name: Check out repository + uses: actions/checkout@v4 + + - id: version + name: Generating version tag for artifacts + run: | + # EXTRACT VERSION + BRANCH=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}} + echo "Building images from the branch: $BRANCH" + VER=$(cat ./VERSION) + echo "Building images of version: $VER" + + # DOCKER TAG TO BE ATTACHED (SHARED WITHIN OUTPUT): + VER=$(cat ./VERSION) + if [ $BRANCH != "release" ] + then + VER=$VER-SNAPSHOT + fi + + echo "fairspace_version=$VER" >> "$GITHUB_OUTPUT" + echo "Docker tag to be attached to images: $VER" + + + build-saturn-service: + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v4 + + - name: Set up JDK 17 + uses: actions/setup-java@v3 + with: + java-version: '17' + distribution: 'temurin' + + - name: Build with Gradle + run: ./projects/saturn/gradlew build -p ./projects/saturn/ + + - name: Upload generated artifacts for further processing + uses: actions/upload-artifact@v4 + with: + name: saturn-build + path: ./projects/saturn/build/distributions/*.tar + + + build-mercury-fe-bundle: + needs: generate-version + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v4 + + - name: Set Node.js 18.x + uses: actions/setup-node@v3 + with: + node-version: 18.x + + - name: Set deployment version + env: + VERSION: ${{needs.generate-version.outputs.output1}} + run: | + echo "$VERSION" + sed -i "s/0.0.0-RELEASEVERSION/${{env.VERSION}}/g" projects/mercury/package.json + + - name: Run install + uses: borales/actions-yarn@v4 + with: + cmd: install # will run `yarn install` + dir: ./projects/mercury/ + + - name: Build Mercury bundle + uses: borales/actions-yarn@v4 + with: + cmd: build # will run `yarn build` + dir: ./projects/mercury/ + + # to be used building an image which includes artifacts of both Pluto and Mercury + - name: Upload generated artifacts for further processing + uses: actions/upload-artifact@v4 + with: + name: mercury-build + path: ./projects/mercury/build/ + + - name: Run Mercury tests + uses: borales/actions-yarn@v4 + with: + cmd: test # will run `yarn test` + dir: ./projects/mercury/ + + build-pluto-service: + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v4 + + - name: Set up JDK 17 + uses: actions/setup-java@v3 + with: + java-version: '17' + distribution: 'temurin' + + - name: Build with Gradle + run: ./projects/pluto/gradlew build -p ./projects/pluto/ + + # to be used building an image which includes artifacts of both Pluto and Mercury + - name: Upload generated artifacts for further processing + uses: actions/upload-artifact@v4 + with: + name: pluto-build + path: ./projects/pluto/build/distributions/*.tar + + # Pluto .tar file and Mercury bundle run together in one docker container + build-and-upload-docker-image-with-pluto-and-mercury: + needs: [generate-version, build-mercury-fe-bundle, build-pluto-service] + runs-on: ubuntu-latest + steps: + - name: Check out repository # To get Pluto Dockerfile + uses: actions/checkout@v4 + + - name: Download Mercury artifacts + uses: actions/download-artifact@v4 + with: + name: mercury-build + path: ./projects/pluto/build/mercury + + - name: Download Pluto artifacts + uses: actions/download-artifact@v4 + with: + name: pluto-build + path: ./projects/pluto/build/distributions/ + + - name: Log in to the Container registry + uses: docker/login-action@v3 + with: + registry: ${{ env.DOCKER_REGISTRY }} + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + + - name: Extract metadata (tags, labels) for Docker + id: meta + uses: docker/metadata-action@v5 + with: + images: ${{ env.DOCKER_REGISTRY }}/${{ github.repository }}/pluto + + - name: Build and push Docker image + uses: docker/build-push-action@v5 + with: + context: ./projects/pluto/ + push: true + tags: ${{ env.DOCKER_REGISTRY }}/${{ github.repository }}/pluto:${{needs.generate-version.outputs.output1}} + labels: ${{ steps.meta.outputs.labels }} + + + build-and-upload-docker-image-for-saturn: + needs: [generate-version, build-saturn-service] + runs-on: ubuntu-latest + steps: + - name: Check out repository # To get Saturn Dockerfile + uses: actions/checkout@v4 + + - name: Download Saturn artifacts + uses: actions/download-artifact@v4 + with: + name: saturn-build + path: ./projects/saturn/build/distributions/ + + - name: Log in to the Container registry + uses: docker/login-action@v3 + with: + registry: ${{ env.DOCKER_REGISTRY }} + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + + - name: Extract metadata (tags, labels) for Docker + id: meta + uses: docker/metadata-action@v5 + with: + images: ${{ env.DOCKER_REGISTRY }}/${{ github.repository }}/saturn + + - name: Build and push Docker image + uses: docker/build-push-action@v5 + with: + context: ./projects/saturn/ + push: true + tags: ${{ env.DOCKER_REGISTRY }}/${{ github.repository }}/saturn:${{needs.generate-version.outputs.output1}} + labels: ${{ steps.meta.outputs.labels }} \ No newline at end of file diff --git a/.github/workflows/build_on_pull_request.yaml b/.github/workflows/build_on_pull_request.yaml new file mode 100644 index 000000000..f9f36aca4 --- /dev/null +++ b/.github/workflows/build_on_pull_request.yaml @@ -0,0 +1,83 @@ +# This workflow is triggered on any PR's changes + +name: PR - Build Fairspace + +on: + pull_request: + +jobs: + build-saturn: + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v4 + + - name: Log details + run: | + BRANCH=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}} + echo "Triggered on branch: $BRANCH" + + - name: Set up JDK 17 + uses: actions/setup-java@v4 + with: + java-version: '17' + distribution: 'temurin' + + - name: Build with Gradle + run: ./projects/saturn/gradlew build -p ./projects/saturn/ + + + build-pluto: + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v4 + + - name: Log details + run: | + BRANCH=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}} + echo "Triggered on branch: $BRANCH" + + - name: Set up JDK 17 + uses: actions/setup-java@v4 + with: + java-version: '17' + distribution: 'temurin' + + - name: Build with Gradle + run: ./projects/pluto/gradlew build -p ./projects/pluto/ + + + build-mercury: + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v4 + + - name: Set Node.js 18.x + uses: actions/setup-node@v4 + with: + node-version: 18.x + + - name: Log details + run: | + BRANCH=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}} + echo "Triggered on branch: $BRANCH" + + - name: Install FE dependencies + uses: borales/actions-yarn@v4 + with: + cmd: install # will run `yarn install` + dir: ./projects/mercury/ + + - name: Build FE bundle + uses: borales/actions-yarn@v4 + with: + cmd: build # will run `yarn build` + dir: ./projects/mercury/ + + - name: Run FE tests + uses: borales/actions-yarn@v4 + with: + cmd: test # will run `yarn test` + dir: ./projects/mercury/ \ No newline at end of file diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 450ac4028..000000000 --- a/.travis.yml +++ /dev/null @@ -1,106 +0,0 @@ -dist: jammy - -language: java - -jdk: -- openjdk17 - -env: - global: - - NODE_VERSION="18.16.0" - - NODE_OPTIONS="--max-old-space-size=8192" - - PATH=/usr/lib/jvm/java-17-openjdk-amd64/bin/:$PATH - - APPNAME="fairspace" - - ORG="fairspace" - - ARTIFACT_BUILD_FILE="" - - BUILD_SCRIPTS_REPO="thehyve/fairspace-build-scripts" - - DEPLOYMENT_CONFIG_REPO="thehyve/fairspace-config-private" - - ACCOUNT_CONFIG_DIR="./.travis" - - RELEASE_BRANCH="release" - - SNAPSHOT_BRANCH="dev" - - DOCUMENTATION_REPO="thehyve/fairspace-docs" - - DOCKER_USERNAME="fairspace" - - GITHUB_USERNAME="fairspace-ci" - - GCP_PROJECT="fairspace-207108" - - GIT_TAG_FILES_OVERRIDE="charts/fairspace/Chart.yaml charts/fairspace/values.yaml projects/" - - SHOULD_DEPLOY=false - # DEPLOYMENT RELATED VARIABLES - REQUIRED IF SHOULD_DEPLOY=true - # - SNAPSHOT_CONTEXT="gke_fairspace-207108_europe-west1-b_fairspacecicluster" - # - SNAPSHOT_CLUSTER_NAME="fairspacecicluster" - # - SNAPSHOT_CLUSTER_ZONE="europe-west1-b" - # - RELEASE_CONTEXT="gke_fairspace-207108_europe-west1-b_fairspacecicluster" - # - RELEASE_CLUSTER_NAME="fairspacecicluster" - # - RELEASE_CLUSTER_ZONE="europe-west1-b" - - # DOCKER_PASSWORD= - - secure: "FJTXKY792rdmQZ6DLU5Dlm1W9ZAmFwBFWEJDO4dLJySBO/clUUV0OfRkNX4OaachKUlRCFGxYbXaXCioYtMTVg54aD1d+hjBO5azPzUiT8V2mz2w3MkvxsvnvivziJtcSfol/PNHQdEK8qZhZ9IwdCnQM9LQ3YVwv9tkNpR//qNmUjA4ZdcbQrBLQ63wm/UX2vCo4D3/J24TfCJrmlu9AyoIAqiFsRczsQGixQLRzeRgwH3yFgACZrMt42ySrx4rL+Yi3Ro/ZftY+YrZPRs+wrObh++OmdzjQWXH4KBg8HTFEIJXYMOVnpG0OSdNO7j7oVS8qVRHJmFAG0VHrmSIMMbjU+3js3SVJxtwXRc3xEPJzKzhtyqGaQa5mr3pI1Q8YingcsEBEpWOh9zXBzJm1uh7JhgTgcEbBwQl12/SctMjejyAFFqVHhlSAEzuDBwTkXLiv6z6sF+SUpww8I6eKmQrJUN1HVPm9+n1nsBy1j3PIM0RmTAf+jZCuAMDg0Dg0dlY/in/Jz1k/QuFDbJ4ura4YBBQ315UDoki5rucDi2poxq9YoAaMpMouso9ilAwOms3guVaU/rgOHZsmIPqv2ccH6FEoOh2UeEq3RCGbprLAj88f2rcGNPaHNWRkeek31c+TI9JZPmeL5eh5tJ64cN+feVVk8lbqNWtR9VHRrI=" - - # GITHUB_PASSWORD=.... - - secure: "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" - -cache: - directories: - - $HOME/downloads - - $HOME/.cache - - $HOME/.gradle - -before_install: - - nvm install $NODE_VERSION - - export KUBE_CONFIG_ENC_KEY=$encrypted_5162cfbd2a53_key - - export KUBE_CONFIG_ENC_IV=$encrypted_5162cfbd2a53_iv - - git clone https://$GITHUB_USERNAME:$GITHUB_PASSWORD@github.com/$BUILD_SCRIPTS_REPO ci - - export BUILD_SCRIPTS_DIR=$(pwd)/ci - - 'if [[ "$SHOULD_DEPLOY" = "true" ]]; then git clone https://$GITHUB_USERNAME:$GITHUB_PASSWORD@github.com/$DEPLOYMENT_CONFIG_REPO ci-config ; fi' - - 'if [[ "$SHOULD_DEPLOY" = "true" ]]; then export DEPLOYMENT_CONFIG_DIR="$(pwd)/ci-config/fairspace" ; fi' - - 'if [[ "$SHOULD_DEPLOY" = "true" ]] && [[ "$TRAVIS_BRANCH" = "$SNAPSHOT_BRANCH" ]]; then export ALLOW_SNAPSHOTS=1 DEPLOY_TARGET=ci DEPLOY_PLATFORM="GCP" KUBERNETES_CONTEXT="$SNAPSHOT_CONTEXT" CLUSTER_NAME="$SNAPSHOT_CLUSTER_NAME" CLUSTER_ZONE="$SNAPSHOT_CLUSTER_ZONE" ; fi' - - 'if [[ "$SHOULD_DEPLOY" = "true" ]] && [[ "$TRAVIS_BRANCH" = "$RELEASE_BRANCH" ]]; then export DEPLOY_TARGET=ci DEPLOY_PLATFORM="GCP" KUBERNETES_CONTEXT="$RELEASE_CONTEXT" CLUSTER_NAME="$RELEASE_CLUSTER_NAME" CLUSTER_ZONE="$RELEASE_CLUSTER_ZONE" ; fi' - - source ./ci/setup_env.sh - - 'if [[ "$SHOULD_RELEASE" ]]; then export OIDC_AUTH_VERSION="$VERSION" RELEASE_PLATFORM="GCP" NEED_INTERNAL_HELM=1 ; fi' - -jobs: - include: - - stage: build - name: Build projects - install: - - ci/gcp/install.sh - - ci/gcp/login.sh - script: - - .travis/build.sh projects/saturn - - .travis/build.sh projects/pluto [mercury] - - export SANITIZED_BRANCH=$(echo $TRAVIS_BRANCH | sed 's/\//_/g') - - stage: build - cache: false - name: Build helm charts - install: - - source charts/.travis/install.sh - script: - - charts/.travis/build.sh - - if: branch = release and type != pull_request - cache: false - stage: Versioning - name: Set tag and update version - script: - - "ci/versioning/add_tag_to_git.sh" - - "ci/versioning/set_next_version.sh" - - stage: deploy - cache: false - if: env(SHOULD_DEPLOY) = true and branch = dev and type != pull_request - install: - - source charts/.travis/install.sh - script: - - travis_wait ci/helm/deploy.sh $DEPLOY_TARGET -f projects/saturn/views.yaml - - if: branch = release and type != pull_request - name: Update documentation page - install: - - docs/.travis/install.sh - script: - - docs/.travis/publish.sh - -notifications: - slack: - rooms: - - secure: "d7qU4xOhiwy19tI+BrE5PGZLKf8yVlv0QWkBiQ+M4g0UO8Ge4a+ZrYP33ZF0lgsfMM0jRaxnLjT9wge0om3uDTwnGKJejAi+AWCU83c3IwLsaIMFhk22vMFXB46U8tUxt4hKsvQFCURKSMTILPUGBqnn18Nf9Yy+4/o43aSwVbvR4sQ4RSdC/+hn/FSQSqY7RHutyhC7DiVDnwKCNYE1I7YU1vEnLawKKS97qJ6tXgE9GQJuupDUy4RC9U5bPIVK0fBbmWv37qWowZ8sNqY/QvzJ9xwXW6NS9eON91VqalNU+pvV0soExMTAnW5oj302WDlYM5mGKNLd3E/gq0jHxQvI4M/oNMZvqZmPI7pyEEjhazN3RdnUqj1fDpNSED4zsC38h0LDK7CEJcTDk4QEDWthlFxz4CaUsKblr5dZBxX6g2PkOhZk8k/PSLORNtcuDH/2X/IFv2Oegy5tOlcEOH/QY6HYW0ayJMV3WtLUN4MivdT00EQs10Fk1Zc6oSM1jpEcYq7lSj3PiXyXsM9Yong2Y1nORAe81CWosIUXit6SdVcWM0ztNEmGk8ViZZqntEsYg975Fr5XB8fnfhRRpbjME5M6UubriIsQbb1XvEtsCiWVP/P/HZV4cTjJHpLkp4Iv2ZPTEggzUUXDdQuo0kzuktqVnx2ulhKEMNueF7c=" - template: - - "Build <%{build_url}|#%{build_number}> (<%{compare_url}|%{commit}>) of %{repository_slug}@%{branch}" - - "Latest commit: %{commit_message} - by %{author}" - - "Result: %{result} in %{duration}" diff --git a/.travis/add_pod_annotations.sh b/.travis/add_pod_annotations.sh deleted file mode 100755 index f5598a53d..000000000 --- a/.travis/add_pod_annotations.sh +++ /dev/null @@ -1,26 +0,0 @@ -#!/bin/bash -# -# This script will add a pod annotations for each project that has -# been built to ensure -# that the pod will be recreated for new SNAPSHOT images -# -# Required env variables: -# $APPNAME -# $COMMIT_ID -# -DIR=$(dirname $0) - -# If we have no changes at all in any of the projects, we can skip -# pod annotations -if $DIR/build-condition.sh $TRAVIS_COMMIT_RANGE projects/; then - # Remove empty pod annotations - sed -i -e "s/podAnnotations: { }//" charts/fairspace/values.yaml - - # Add a pod annotation in the values.yaml file - echo -e "\npodAnnotations:" >> charts/fairspace/values.yaml - echo -e " fairspace:\n commit: \"$COMMIT_ID\"\n" >> charts/fairspace/values.yaml - - echo "Changes in $project_name project detected, fairspace pod will be restarted." -else - echo "No changes found in projects since the last build." -fi diff --git a/.travis/build-condition.sh b/.travis/build-condition.sh deleted file mode 100755 index c707c82da..000000000 --- a/.travis/build-condition.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/bash -# -# This script will check whether a certain directory contains changes -# and thus should be built. -# -# This check can be overridden by adding [full build] to the commit message -# -# Usage: build-condition.sh -# - -if [[ -z $1 ]]; then - echo "Commit range cannot be empty" - echo "Usage: build-condition.sh " - exit 1 -fi - -if [[ -z $2 ]]; then - echo "Change path cannot be empty" - echo "Usage: build-condition.sh " - exit 1 -fi - -# If the commit message contains '[full build]' then all -# directories should be built -if [[ $TRAVIS_COMMIT_MESSAGE == *"[full build]"* ]]; then - exit 0 -fi - -# When doing a real release (on the release branch) we have to -# build all artifacts, as there have never been other builds for this -# particular version -if [[ "$TRAVIS_BRANCH" = "$RELEASE_BRANCH" ]]; then - exit 0 -fi - -# Check whether the given project directory has changes. If so, the script (grep) will -# return 0. If not, grep will return a non-zero exit code -git diff --name-only $1 | sort -u | uniq | grep ^$2 > /dev/null diff --git a/.travis/build.sh b/.travis/build.sh deleted file mode 100755 index ccd3ab030..000000000 --- a/.travis/build.sh +++ /dev/null @@ -1,63 +0,0 @@ -#!/bin/bash -DIR=$(dirname $0) -PROJECT=$1 - -# List of (sub)projects that are served by $PROJECT -SUBPROJECTS=$2 - -# Set variables for use in build scripts -export APPNAME=$(basename $PROJECT) -export CONTAINER_NAME="${DOCKER_REPO}/${ORG}/${APPNAME}:${VERSION}" - -# If we are building a PR, use the target branch as 'commit range'. -# As it is used with `git diff ...`, it will trigger all files that -# have updated in the complete pull request. We also need to do this -# in branches that have just one commit. -if [[ "$TRAVIS_PULL_REQUEST" != "false" ]] || [[ -z "$TRAVIS_COMMIT_RANGE" ]] ; then - COMMIT_TRIGGER=$TRAVIS_BRANCH -else - COMMIT_TRIGGER=$TRAVIS_COMMIT_RANGE -fi - -check_all() { - for subproject in "$@"; do - if $DIR/build-condition.sh $COMMIT_TRIGGER $subproject/..; then - return 1 - fi - done -} - -# Only execute build if something has changed within the project or any of the subprojects -if ($DIR/build-condition.sh $COMMIT_TRIGGER $PROJECT/..) || ([[ ! -z "$SUBPROJECTS" ]] && (check_all ${SUBPROJECTS[@]})); then - echo "Building $APPNAME..."; - cd $PROJECT - - echo -e "travis_fold:start:Building-$APPNAME" - source .travis/env.sh - .travis/build.sh - rc=$? - echo -e "travis_fold:end:Building-$APPNAME" - - # If the build failed, do not bother releasing - if [[ $rc != 0 ]]; then - exit $rc - fi - - if [[ $SHOULD_RELEASE ]]; then - echo "Releasing artifact for $APPNAME" - echo -e "travis_fold:start:Releasing-$APPNAME" - .travis/release.sh - rc=$? - echo -e "travis_fold:end:Releasing-$APPNAME" - - # If the release failed, return a non-zero exit status - if [[ $rc != 0 ]]; then - exit $rc - fi - - fi - - cd ../.. -else - echo "No changes for $APPNAME"; -fi diff --git a/.travis/ci-service-account.json.enc b/.travis/ci-service-account.json.enc deleted file mode 100644 index b90d507f7b2558c51b1f7c91884d908e7fa80dcf..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2320 zcmV+r3GenY$GD1KK0!NNzOZ(iQqT{23hkj=FG$z;Kl*uIBU2qW%;WDYX$W!+c-b0h zW4zi>3ZXUK!||>se@U|)30en0D-u3uHdn;DN!d;!D>_RPwASTJXac5pPB7DgVn=O5 zgq}=!f7e_JOcwVA2Tm+d@C%Y_E2;oO&?1PbXI4#G4w$i_+gI$=%Vs8*P8anwb-u$<#GvtvGTR?eb@tIE&Fhq+? zhokaq%=ZYpN|WClX~_#m?t_|>7+m9(apX$^Ji(6bFHUa6pIs_fS{5b}k=|Mn$pg0} z%);Ok;DT@=RbyiyI-1_=+RYoZ-b~`Ao5TF?L}5!_Q-V}-r9W?EggK|mAo8v(8KZU)oAb=;bH-D_lV*(HnZ+1dkIQje|iWV7}hqJ->wTxrh zb+X@hj3Y%fy4BqE74=wWXZ4RPAT6z5V9o--79i_MgT3J%a5~syQ=uIre!w#nw!}{7 zeYc-80Hcrw(NA5>#*fQU|H?|j7eJ7^v7x8EPC*_mBsy~V-MIR6h<=A{H`n`7Hi9i& zjC{8;aY$!Nk&cxNu~ku#d=%QqL4SDUp+5kY-N~%@ycR-VXHIn?GxM4IP3T}|7i=<0 z$a<0$MFi zmeA)D@L2fmRMP z0qXTEUA9ZKwDZvvjIgGu5IekL9~qVk9KvvG8sVCvrKd+XV6emzk@wcEj=ggewj4;r zhaVd(afCJUR?IHAx$b+RJlq?%6=V6e&vJGCP@!w!kIG99tu&uEDC$)M^+9HK#BL zPsU9J=MoURWMh)4_pb*Ic#pZfR8<58Bnw~?ktV(>6?&Z z7R39dXTgnB;ybn@r;x^}Oc=l8&yB&;-aGlxSH+Yu*B!gWL4zlXN~Ad`V+FlD-sf@k zW-#%2>v5bNxF5!0IM3xHo+)5?2czegPSNJt7-F|$?(b}5b5G4>a<-#=yd z@s(Pyp;8tU&*%wAhF;i7Q zvKRfNXL)}#eCGIVgk}b1DU-uvyWu~($TIYBxy9mJES#=BAp z8$u4n4~6FV!L9b8p~;7G#n*%&7uNDe(bD!>j*2XnSIuccOAlmsfmt_G7bnODngdlU zg)vPGRDm0zK7~!$(rz;{0-4GMVy%QeG&ge_@8(Wm<>s*A-GYlmN!P)vbA?i7JI!M6v@EL(;j7fouWAcneU@H5u_%>oEvups3o)od}jFTFg9HTY8Fyo^o{PER<^2y-CER zMV(tgqJmoJVn`sEj54i3tv;?Zjc>TngzUF+^4d@;{+oeM4vE9Zp6N3GoFOk(+~Mp6 zA~$kIumGr>pc8(Sk8VY3X#`?7EpG+O3a zE+d%EGB|ha?>+{YedpP{?gC*c@FT0P0KK`&Tzbrkeh=z@`a+zem%J(<-sztcThJ5b zPC-@w+!bHHp1l^Rf Date: Thu, 25 Jan 2024 13:16:09 +0100 Subject: [PATCH 060/153] Fix linter warnings on exhaustive-deps. --- .../mercury/src/metadata/LinkedDataMetadataProvider.js | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/projects/mercury/src/metadata/LinkedDataMetadataProvider.js b/projects/mercury/src/metadata/LinkedDataMetadataProvider.js index 598e2ac22..9ab551620 100644 --- a/projects/mercury/src/metadata/LinkedDataMetadataProvider.js +++ b/projects/mercury/src/metadata/LinkedDataMetadataProvider.js @@ -18,11 +18,14 @@ const LinkedDataMetadataProvider = ({children, ...otherProps}) => { const fetchMetadataBySubject = useCallback((subject) => metadataAPI.getDict({subject, withValueProperties: true}) .catch(() => { throw new Error('An error occurred while loading the metadata'); + // eslint-disable-next-line react-hooks/exhaustive-deps }), []); const submitLinkedDataChanges = useCallback((subject, values) => metadataAPI.get({subject}) .then(meta => (meta.length && getFirstPredicateValue(meta[0], '@type'))) - .then(type => metadataAPI.updateEntity(subject, values, vocabulary, type)), [vocabulary]); + .then(type => metadataAPI.updateEntity(subject, values, vocabulary, type)), + // eslint-disable-next-line react-hooks/exhaustive-deps + [vocabulary]); const createLinkedDataEntity = useCallback((subject, values, type) => metadataAPI.get({subject}) .then((meta) => { @@ -31,7 +34,9 @@ const LinkedDataMetadataProvider = ({children, ...otherProps}) => { } }) .then(() => metadataAPI.updateEntity(subject, values, vocabulary, type)) - .then(() => ({subject, type, values})), [vocabulary]); + .then(() => ({subject, type, values})), + // eslint-disable-next-line react-hooks/exhaustive-deps + [vocabulary]); const deleteLinkedDataEntity = (subject) => metadataAPI.delete(subject); From c0f1f1da0adc22141f23f3c671563f52096bd21b Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Thu, 25 Jan 2024 15:01:35 +0100 Subject: [PATCH 061/153] Make metadata view menu label configurable. --- projects/mercury/src/constants.js | 1 + projects/mercury/src/routes/WorkspaceRoutes.js | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/projects/mercury/src/constants.js b/projects/mercury/src/constants.js index 8c8b83114..f96f0542b 100644 --- a/projects/mercury/src/constants.js +++ b/projects/mercury/src/constants.js @@ -1,4 +1,5 @@ export const APPLICATION_NAME = 'Fairspace'; +export const METADATA_VIEW_MENU_LABEL = 'Metadata'; export const LOCAL_STORAGE_MENU_KEY = 'FAIRSPACE_MENU_EXPANDED'; export const CUT = 'CUT'; export const COPY = 'COPY'; diff --git a/projects/mercury/src/routes/WorkspaceRoutes.js b/projects/mercury/src/routes/WorkspaceRoutes.js index bae01c53e..51e35e0eb 100644 --- a/projects/mercury/src/routes/WorkspaceRoutes.js +++ b/projects/mercury/src/routes/WorkspaceRoutes.js @@ -17,6 +17,7 @@ import MetadataView from '../metadata/views/MetadataView'; import BreadcrumbsContext from '../common/contexts/BreadcrumbsContext'; import {ExternalStoragePage} from "../external-storage/ExternalStoragePage"; import ExternalMetadataSourcesView from "../metadata/external-sources/ExternalMetadataSourceView"; +import {METADATA_VIEW_MENU_LABEL} from "../constants"; const getSubject = () => ( document.location.search ? queryString.parse(document.location.search).iri : null @@ -105,7 +106,7 @@ const WorkspaceRoutes = () => { if (subject) { return ( - + ); } From 05093c781c4e9cc57a0188f775d975d0681515b8 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Fri, 26 Jan 2024 08:45:40 +0100 Subject: [PATCH 062/153] Update build_and_upload_on_push_to_dev.yaml --- .github/workflows/build_and_upload_on_push_to_dev.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build_and_upload_on_push_to_dev.yaml b/.github/workflows/build_and_upload_on_push_to_dev.yaml index 89e33057b..441039d31 100644 --- a/.github/workflows/build_and_upload_on_push_to_dev.yaml +++ b/.github/workflows/build_and_upload_on_push_to_dev.yaml @@ -16,6 +16,7 @@ on: branches: - "dev" - "release" + - "view-performance" jobs: # A job to generate one shared unique version tag per build cycle for all built artifacts @@ -209,4 +210,4 @@ jobs: context: ./projects/saturn/ push: true tags: ${{ env.DOCKER_REGISTRY }}/${{ github.repository }}/saturn:${{needs.generate-version.outputs.output1}} - labels: ${{ steps.meta.outputs.labels }} \ No newline at end of file + labels: ${{ steps.meta.outputs.labels }} From 8af2e99c060c1e5a7ab3bdfd5b00f7d2b01ae21c Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Fri, 26 Jan 2024 14:00:57 +0100 Subject: [PATCH 063/153] Update build_and_upload_on_push_to_dev.yaml --- .../build_and_upload_on_push_to_dev.yaml | 24 +++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build_and_upload_on_push_to_dev.yaml b/.github/workflows/build_and_upload_on_push_to_dev.yaml index 441039d31..dc81c052e 100644 --- a/.github/workflows/build_and_upload_on_push_to_dev.yaml +++ b/.github/workflows/build_and_upload_on_push_to_dev.yaml @@ -13,10 +13,26 @@ env: on: push: - branches: - - "dev" - - "release" - - "view-performance" + branches:[] + workflow_dispatch: + inputs: + logLevel: + description: 'Log level' + required: true + default: 'warning' + type: choice + options: + - info + - warning + - debug + tags: + description: 'Test scenario tags' + required: false + type: boolean + environment: + description: 'Environment to run tests against' + type: environment + required: true jobs: # A job to generate one shared unique version tag per build cycle for all built artifacts From 797f36130a3bb46d699f19062bd328ed4d468d2c Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Fri, 26 Jan 2024 14:03:11 +0100 Subject: [PATCH 064/153] Update build_and_upload_on_push_to_dev.yaml --- .../build_and_upload_on_push_to_dev.yaml | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/.github/workflows/build_and_upload_on_push_to_dev.yaml b/.github/workflows/build_and_upload_on_push_to_dev.yaml index dc81c052e..49b6bdf4c 100644 --- a/.github/workflows/build_and_upload_on_push_to_dev.yaml +++ b/.github/workflows/build_and_upload_on_push_to_dev.yaml @@ -14,25 +14,6 @@ env: on: push: branches:[] - workflow_dispatch: - inputs: - logLevel: - description: 'Log level' - required: true - default: 'warning' - type: choice - options: - - info - - warning - - debug - tags: - description: 'Test scenario tags' - required: false - type: boolean - environment: - description: 'Environment to run tests against' - type: environment - required: true jobs: # A job to generate one shared unique version tag per build cycle for all built artifacts From 39edcf991b5c7621924513d31970eb299607dcaf Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Fri, 26 Jan 2024 14:04:39 +0100 Subject: [PATCH 065/153] Update build_and_upload_on_push_to_dev.yaml --- .github/workflows/build_and_upload_on_push_to_dev.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_and_upload_on_push_to_dev.yaml b/.github/workflows/build_and_upload_on_push_to_dev.yaml index 49b6bdf4c..a8f947662 100644 --- a/.github/workflows/build_and_upload_on_push_to_dev.yaml +++ b/.github/workflows/build_and_upload_on_push_to_dev.yaml @@ -13,7 +13,7 @@ env: on: push: - branches:[] + branches: [] jobs: # A job to generate one shared unique version tag per build cycle for all built artifacts From bf38b14d8b48915565d5510bce005657cfa96f22 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Fri, 26 Jan 2024 14:13:59 +0100 Subject: [PATCH 066/153] Update build_and_upload_on_push_to_dev.yaml --- .github/workflows/build_and_upload_on_push_to_dev.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build_and_upload_on_push_to_dev.yaml b/.github/workflows/build_and_upload_on_push_to_dev.yaml index a8f947662..6a6a741fd 100644 --- a/.github/workflows/build_and_upload_on_push_to_dev.yaml +++ b/.github/workflows/build_and_upload_on_push_to_dev.yaml @@ -13,7 +13,9 @@ env: on: push: - branches: [] + branches: + - dev + - release jobs: # A job to generate one shared unique version tag per build cycle for all built artifacts From de9f86f066c28645bd312a6011929f97c0384f39 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Mon, 29 Jan 2024 09:56:13 +0100 Subject: [PATCH 067/153] new release with extra caching, multiple saturn instances and extra column indexes --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 5de328f3e..275946dc5 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.7.30 +0.7.31 From 2ea67245bf7a0cad3e39e7824754c5aa477ed90b Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Mon, 29 Jan 2024 11:47:46 +0100 Subject: [PATCH 068/153] Always try create new index, necessary in case of update instead of new installation. --- .../saturn/services/views/ViewStoreClientFactory.java | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java index 7edf93fda..005f6b0af 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java @@ -114,12 +114,13 @@ void createOrUpdateJoinTable(Table table) throws SQLException { log.debug("Check if table {} exists ...", table.name); var resultSet = connection.getMetaData().getTables(null, null, table.name, null); var tableExists = resultSet.next(); - + if (!tableExists) { createTable(table, connection); - createIndexes(table, connection); + createIndexesIfNotExist(table, connection); } else { updateTable(table, connection); + createIndexesIfNotExist(table, connection); } } } @@ -169,8 +170,8 @@ private void createTable(Table table, Connection connection) throws SQLException log.info("Table {} created.", table.name); } - private void createIndexes(Table table, Connection connection) throws SQLException { - + private void createIndexesIfNotExist(Table table, Connection connection) throws SQLException { + var keys = table.columns.stream() .filter(column -> column.type == ColumnType.Identifier) .map(column -> column.name) @@ -186,7 +187,7 @@ private void createIndexes(Table table, Connection connection) throws SQLExcepti connection.createStatement().execute(command); log.info("Index {} created.", indexName); } - + connection.setAutoCommit(false); } From 1561aa99d9f9e624597b439062e97bec0bfb059c Mon Sep 17 00:00:00 2001 From: Anton Date: Wed, 31 Jan 2024 10:37:48 +0100 Subject: [PATCH 069/153] FAIRPC-29: reduced number of calls to db on metadata request per view (#1477) FAIRPC-29: reduced number of calls to db on metadata request per view by mean of introducing materialized views --- .../main/java/io/fairspace/saturn/App.java | 2 +- .../io/fairspace/saturn/config/Services.java | 2 +- .../maintenance/MaintenanceService.java | 24 +- .../services/views/JdbcQueryService.java | 4 +- .../views/MaterializedViewService.java | 98 ++++++ .../saturn/services/views/Table.java | 16 +- .../saturn/services/views/ViewRow.java | 33 +- .../views/ViewStoreClientFactory.java | 88 ++--- .../services/views/ViewStoreReader.java | 304 ++++++++---------- .../saturn/services/views/ViewUpdater.java | 2 +- .../services/health/HealthServiceTest.java | 8 +- .../services/views/JdbcQueryServiceTest.java | 4 +- .../services/views/ViewServiceTest.java | 5 +- 13 files changed, 368 insertions(+), 222 deletions(-) create mode 100644 projects/saturn/src/main/java/io/fairspace/saturn/services/views/MaterializedViewService.java diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/App.java b/projects/saturn/src/main/java/io/fairspace/saturn/App.java index 1f422504f..9a75b387c 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/App.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/App.java @@ -25,7 +25,7 @@ public static FusekiServer startFusekiServer() { ViewStoreClientFactory viewStoreClientFactory = null; if (CONFIG.viewDatabase.enabled) { try { - viewStoreClientFactory = new ViewStoreClientFactory(VIEWS_CONFIG, CONFIG.viewDatabase); + viewStoreClientFactory = new ViewStoreClientFactory(VIEWS_CONFIG, CONFIG.viewDatabase, false); } catch (SQLException e) { log.error("Error connecting to the view database.", e); throw new RuntimeException("Error connecting to the view database", e); // Terminates Saturn diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/config/Services.java b/projects/saturn/src/main/java/io/fairspace/saturn/config/Services.java index 213be86ef..485d72cb7 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/config/Services.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/config/Services.java @@ -103,7 +103,7 @@ public Services(@NonNull Config config, @NonNull ViewsConfig viewsConfig, @NonNu viewService = new ViewService(config.search, viewsConfig, filteredDataset, viewStoreClientFactory, metadataPermissions); - maintenanceService = new MaintenanceService(userService, dataset, viewStoreClientFactory, viewService); + maintenanceService = new MaintenanceService(userService, dataset, viewStoreClientFactory, viewService) ; searchService = new SearchService(filteredDataset); diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/maintenance/MaintenanceService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/maintenance/MaintenanceService.java index 71050aa98..12ab8063d 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/maintenance/MaintenanceService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/maintenance/MaintenanceService.java @@ -1,6 +1,7 @@ package io.fairspace.saturn.services.maintenance; import io.fairspace.saturn.config.ConfigLoader; +import io.fairspace.saturn.config.ViewsConfig; import io.fairspace.saturn.services.*; import io.fairspace.saturn.services.users.*; import io.fairspace.saturn.services.views.*; @@ -21,7 +22,10 @@ public class MaintenanceService { private final ViewStoreClientFactory viewStoreClientFactory; private final ViewService viewService; - public MaintenanceService(@NonNull UserService userService, @NonNull Dataset dataset, ViewStoreClientFactory viewStoreClientFactory, ViewService viewService) { + public MaintenanceService(@NonNull UserService userService, + @NonNull Dataset dataset, + ViewStoreClientFactory viewStoreClientFactory, + ViewService viewService) { this.userService = userService; this.dataset = dataset; this.viewStoreClientFactory = viewStoreClientFactory; @@ -50,8 +54,10 @@ public synchronized void startRecreateIndexTask() { threadpool.submit(() -> { log.info("Start asynchronous reindexing task"); recreateIndex(); + updateMaterializedViews(); + viewService.refreshCaches(); }); - viewService.refreshCaches(); + } public void recreateIndex() { @@ -68,4 +74,18 @@ public void recreateIndex() { throw new RuntimeException("Failed to recreate index", e); } } + + private void updateMaterializedViews() { + try { + // now it is a part of reindexing, but if Fairspace is supposed to support an intensive + // metadata update, then consider async materialized views refresh with old data available + // until new are ready to be used OR switch to denormalized tables not to maintain materialized views + if (viewStoreClientFactory != null && viewStoreClientFactory.getMaterializedViewService() != null) { + viewStoreClientFactory.getMaterializedViewService().createOrUpdateAllMaterializedViews(); + } + } catch (SQLException e) { + log.error("Failed to update materialized views on reindexing call"); + throw new RuntimeException(e); + } + } } diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/JdbcQueryService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/JdbcQueryService.java index 3524eec52..94ff74601 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/JdbcQueryService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/JdbcQueryService.java @@ -87,7 +87,7 @@ public ViewPageDTO retrieveViewPage(ViewRequest request) { filters.addAll(request.getFilters()); } applyCollectionsFilterIfRequired(request.getView(), filters); - try (var viewStoreReader = getViewStoreReader()){ + try (var viewStoreReader = getViewStoreReader()) { List>> rows = viewStoreReader.retrieveRows( request.getView(), filters, (page - 1) * size, @@ -119,7 +119,7 @@ public CountDTO count(CountRequest request) { filters = new ArrayList<>(); } applyCollectionsFilterIfRequired(request.getView(), filters); - try (var viewStoreReader = getViewStoreReader()){ + try (var viewStoreReader = getViewStoreReader()) { return new CountDTO(viewStoreReader.countRows(request.getView(), filters), false); } catch (SQLTimeoutException e) { return new CountDTO(0, true); diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/MaterializedViewService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/MaterializedViewService.java new file mode 100644 index 000000000..b4595749c --- /dev/null +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/MaterializedViewService.java @@ -0,0 +1,98 @@ +package io.fairspace.saturn.services.views; + +import io.fairspace.saturn.config.ConfigLoader; +import io.fairspace.saturn.config.ViewsConfig; +import lombok.extern.slf4j.Slf4j; + +import javax.sql.DataSource; +import java.sql.SQLException; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.function.Function; +import java.util.stream.Collectors; + +import static io.fairspace.saturn.config.ConfigLoader.VIEWS_CONFIG; + +@Slf4j +public class MaterializedViewService { + + private final DataSource dataSource; + + public MaterializedViewService(DataSource dataSource) { + this.dataSource = dataSource; + } + + public void createOrUpdateAllMaterializedViews() throws SQLException { + for (var view : VIEWS_CONFIG.views) { + createOrUpdateMaterializedView(view); + } + } + + public void createOrUpdateMaterializedView(ViewsConfig.View view) throws SQLException { + var setColumns = view.columns.stream().filter(column -> column.type.isSet()).toList(); + if (!setColumns.isEmpty()) { + var viewName = "materialized_view_%s".formatted(view.name.toLowerCase()); + log.info("{} refresh has started", viewName); + dropMaterializedViewIfExists(viewName); + createMaterializedView(viewName, view, setColumns); + alterOwnerToFairspace(viewName); + createMaterializedViewIndex(view.name.toLowerCase(), viewName); + log.info("{} refresh has finished successfully", viewName); + } + } + + private void createMaterializedViewIndex(String viewName, String materializedViewName) throws SQLException { + var query = "CREATE INDEX %s_id_idx on %s (%sid)".formatted(viewName, materializedViewName, viewName); + try (var connection = dataSource.getConnection(); + var ps = connection.prepareStatement(query)) { + ps.execute(); + connection.commit(); + } + } + + private void alterOwnerToFairspace(String viewOrTableName) throws SQLException { + var query = "ALTER MATERIALIZED VIEW %s OWNER TO fairspace".formatted(viewOrTableName); + try (var connection = dataSource.getConnection(); + var ps = connection.prepareStatement(query)) { + ps.execute(); + connection.commit(); + } + } + + private void createMaterializedView(String viewOrTableName, ViewsConfig.View view, List setColumns) throws SQLException { + String viewName = view.name.toLowerCase(); + var queryBuilder = new StringBuilder() + .append("CREATE MATERIALIZED VIEW ").append(viewOrTableName).append(" AS ") + .append("SELECT v.id AS ").append(viewName).append("id, "); + for (int i = 0; i < setColumns.size(); i++) { + queryBuilder.append("i").append(i).append(".").append(setColumns.get(i).name.toLowerCase()); + if (i != setColumns.size() - 1) { + queryBuilder.append(", "); + } + } + queryBuilder.append(" FROM ").append(viewName).append(" v "); + for (int i = 0; i < setColumns.size(); i++) { + var alias = "i" + i; + var columnName = setColumns.get(i).name.toLowerCase(); + queryBuilder.append("LEFT JOIN ").append(viewName).append("_").append(columnName).append(" ").append(alias).append(" ON ") + .append("v.id = ").append(alias).append(".").append(viewName).append("_id "); + } + + try (var connection = dataSource.getConnection(); + var ps = connection.prepareStatement(queryBuilder.toString())) { + ps.execute(); + connection.commit(); + } + } + + private void dropMaterializedViewIfExists(String viewName) throws SQLException { + var query = "DROP MATERIALIZED VIEW IF EXISTS %s CASCADE".formatted(viewName); + try (var connection = dataSource.getConnection(); + var ps = connection.prepareStatement(query)) { + ps.execute(); + connection.commit(); + } + } + +} diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/Table.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/Table.java index 427261d68..7f772b688 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/Table.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/Table.java @@ -3,10 +3,13 @@ import lombok.*; import java.util.*; +import java.util.function.Function; +import java.util.stream.Collectors; import static io.fairspace.saturn.config.ViewsConfig.*; +import static java.util.stream.Collectors.toMap; -@Data @Builder +@Data public class Table { @Data @Builder public static class ColumnDefinition { @@ -35,7 +38,16 @@ public static ColumnDefinition valueColumn(String name, ColumnType type) { String name; List columns; + private final Map columnsById; + + public Table(String name, List columns) { + this.name = name; + this.columns = columns; + this.columnsById = columns.stream() + .collect(Collectors.toMap(colDef -> colDef.getName().toLowerCase(), Function.identity())); + } + public ColumnDefinition getColumn(String name) { - return columns.stream().filter(column -> column.getName().equals(name.toLowerCase())).findFirst().orElse(null); + return columnsById.get(name.toLowerCase()); } } diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java index 56c257005..b493f8409 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewRow.java @@ -1,14 +1,35 @@ package io.fairspace.saturn.services.views; +import com.google.common.collect.Sets; + +import java.sql.ResultSet; +import java.sql.SQLException; import java.util.HashMap; +import java.util.List; import java.util.Map; import java.util.Set; public class ViewRow { - private Map> data = new HashMap<>(); + private final Map> data; public ViewRow() { + this.data = new HashMap<>(); + } + + public ViewRow(Map> data) { + this.data = data; + } + + public static ViewRow viewSetOf(ResultSet resultSet, List columnsNames, String viewName) throws SQLException { + var data = new HashMap>(); + for (String columnName : columnsNames) { + String label = resultSet.getString(columnName); + var key = viewName + "_" + columnName; + var value = Sets.newHashSet(new ValueDTO(label, label)); + data.put(key, value); + } + return new ViewRow(data); } // TODO, make obsolete by ViewStoreReader refactor @@ -20,4 +41,14 @@ public Map> getRawData() { public void put(String key, Set value) { data.put(key, value); } + + public ViewRow merge(ViewRow anotherViewRow) { + anotherViewRow.getRawData().forEach((key, value) -> data.merge(key, value, ViewRow::addElementsAndReturn)); + return this; + } + + private static Set addElementsAndReturn(Set set, Set elements) { + set.addAll(elements); + return set; + } } diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java index 005f6b0af..f0dd18b0a 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreClientFactory.java @@ -1,38 +1,53 @@ package io.fairspace.saturn.services.views; -import com.fasterxml.jackson.core.*; -import com.fasterxml.jackson.databind.*; -import com.zaxxer.hikari.*; -import io.fairspace.saturn.config.*; -import io.fairspace.saturn.config.ViewsConfig.*; -import io.fairspace.saturn.vocabulary.*; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.zaxxer.hikari.HikariConfig; +import com.zaxxer.hikari.HikariDataSource; +import io.fairspace.saturn.config.Config; +import io.fairspace.saturn.config.ViewsConfig; +import io.fairspace.saturn.config.ViewsConfig.ColumnType; +import io.fairspace.saturn.config.ViewsConfig.View; +import io.fairspace.saturn.vocabulary.FS; import lombok.Builder; import lombok.Data; -import lombok.extern.slf4j.*; +import lombok.Getter; +import lombok.extern.slf4j.Slf4j; -import javax.sql.*; -import java.sql.*; -import java.util.*; -import java.util.stream.*; +import javax.sql.DataSource; +import java.sql.Connection; +import java.sql.SQLException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashMap; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.stream.Collectors; import static io.fairspace.saturn.services.views.Table.idColumn; import static io.fairspace.saturn.services.views.Table.valueColumn; @Slf4j public class ViewStoreClientFactory { - public static boolean H2_DATABASE = false; + + private final boolean isH2Database; + + @Getter + private final MaterializedViewService materializedViewService; public ViewStoreClient build() throws SQLException { return new ViewStoreClient(getConnection(), configuration); } - public static String databaseTypeForColumnType(ColumnType type) { + public String databaseTypeForColumnType(ColumnType type) { return switch (type) { case Text, Term -> "text"; case Date -> "timestamp"; case Number -> "numeric"; case Boolean -> "boolean"; - case Identifier -> H2_DATABASE ? "varchar not null" : "text not null"; + case Identifier -> isH2Database ? "varchar not null" : "text not null"; case Set, TermSet -> throw new IllegalArgumentException("No database type for column type set."); }; } @@ -45,7 +60,8 @@ public static String databaseTypeForColumnType(ColumnType type) { final ViewStoreClient.ViewStoreConfiguration configuration; public final DataSource dataSource; - public ViewStoreClientFactory(ViewsConfig viewsConfig, Config.ViewDatabase viewDatabase) throws SQLException { + public ViewStoreClientFactory(ViewsConfig viewsConfig, Config.ViewDatabase viewDatabase, boolean isH2Database) throws SQLException { + this.isH2Database = isH2Database; log.debug("Initializing the database connection"); var databaseConfig = new HikariConfig(); databaseConfig.setJdbcUrl(viewDatabase.url); @@ -57,22 +73,23 @@ public ViewStoreClientFactory(ViewsConfig viewsConfig, Config.ViewDatabase viewD dataSource = new HikariDataSource(databaseConfig); + materializedViewService = new MaterializedViewService(dataSource); + try (var connection = dataSource.getConnection()) { log.debug("Database connection: {}", connection.getMetaData().getDatabaseProductName()); } - createOrUpdateTable(Table.builder() - .name("label") - .columns(List.of( + createOrUpdateTable(new Table("label", + List.of( idColumn(), valueColumn("type", ColumnType.Text), - valueColumn("label", ColumnType.Text))) - .build()); + valueColumn("label", ColumnType.Text)))); configuration = new ViewStoreClient.ViewStoreConfiguration(viewsConfig); for (View view : viewsConfig.views) { createOrUpdateView(view); } + materializedViewService.createOrUpdateAllMaterializedViews(); } public Connection getConnection() throws SQLException { @@ -227,24 +244,17 @@ void createOrUpdateView(ViewsConfig.View view) throws SQLException { } columns.add(valueColumn(column.name, column.type)); } - var table = Table.builder() - .name(view.name.toLowerCase()) - .columns(columns) - .build(); + var table = new Table(view.name.toLowerCase(), columns); createOrUpdateTable(table); configuration.viewTables.put(view.name, table); // Add property tables - for (ViewsConfig.View.Column column : view.columns) { - if (!column.type.isSet()) { - continue; - } + var setColumns = view.columns.stream().filter(column -> column.type.isSet()).toList(); + for (ViewsConfig.View.Column column : setColumns) { var propertyTableColumns = new ArrayList(); propertyTableColumns.add(idColumn(view.name)); propertyTableColumns.add(valueColumn(column.name, ColumnType.Identifier)); - var propertyTable = Table.builder() - .name(String.format("%s_%s", view.name.toLowerCase(), column.name.toLowerCase())) - .columns(propertyTableColumns) - .build(); + var name = String.format("%s_%s", view.name.toLowerCase(), column.name.toLowerCase()); + var propertyTable = new Table(name, propertyTableColumns); createOrUpdateTable(propertyTable); configuration.propertyTables.putIfAbsent(view.name, new HashMap<>()); configuration.propertyTables.get(view.name).put(column.name, propertyTable); @@ -256,21 +266,19 @@ void createOrUpdateView(ViewsConfig.View view) throws SQLException { createOrUpdateJoinTable(joinTable); configuration.joinTables.putIfAbsent(view.name, new HashMap<>()); configuration.joinTables.get(view.name).put(join.view, joinTable); + var joinView = configuration.viewConfig.get(join.view); } + } } public static Table getJoinTable(View.JoinView join, View view) { String left = join.reverse ? join.view : view.name; String right = join.reverse ? view.name : join.view; - var joinTable = Table.builder() - .name(String.format("%s_%s", left.toLowerCase(), right.toLowerCase())) - .columns(Arrays.asList( - idColumn(left), - idColumn(right))) - .build(); - - return joinTable; + var name = String.format("%s_%s", left.toLowerCase(), right.toLowerCase()); + return new Table(name, Arrays.asList( + idColumn(left), + idColumn(right))); } @Data diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java index 3b94b91a5..3461cb8ad 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java @@ -1,5 +1,6 @@ package io.fairspace.saturn.services.views; +import com.google.common.collect.Sets; import io.fairspace.saturn.config.Config; import io.fairspace.saturn.config.ViewsConfig.ColumnType; import io.fairspace.saturn.config.ViewsConfig.View; @@ -10,16 +11,28 @@ import lombok.extern.slf4j.Slf4j; import org.apache.commons.lang3.StringUtils; -import java.sql.*; +import java.sql.Array; +import java.sql.Connection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.sql.SQLTimeoutException; +import java.sql.Timestamp; import java.time.Instant; -import java.util.Date; -import java.util.*; -import java.util.stream.Collectors; +import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.EnumSet; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Objects; +import java.util.Optional; +import java.util.Set; import java.util.function.Function; +import java.util.stream.Collectors; import java.util.stream.Stream; -import javax.validation.constraints.NotBlank; - import static io.fairspace.saturn.config.ViewsConfig.ColumnType.Date; import static io.fairspace.saturn.services.views.Table.idColumn; @@ -36,6 +49,7 @@ public class ViewStoreReader implements AutoCloseable { final Config.Search searchConfig; final ViewStoreClient.ViewStoreConfiguration configuration; final Connection connection; + final int MAX_JOIN_ITEMS = 50; // TODO: in whole class, use StringBuilder instead of String concats @@ -81,9 +95,7 @@ Map> transformRow(View viewConfig, ResultSet result) throw if (viewColumn.type.isSet()) { continue; } - var column = configuration.viewTables.get(viewConfig.name).getColumns().stream() - .filter(c -> c.getName().equals(viewColumn.name.toLowerCase())) - .findFirst().orElseThrow(); + var column = configuration.viewTables.get(viewConfig.name).getColumn(viewColumn.name.toLowerCase()); var columnName = viewConfig.name + "_" + viewColumn.name; if (column.type == ColumnType.Number) { var value = result.getBigDecimal(column.name); @@ -298,8 +310,8 @@ PreparedStatement query(String view, String projection, List filters }) .collect(Collectors.toList()); constraints = Stream.concat( - Stream.of(constraints), - subqueries.stream()) + Stream.of(constraints), + subqueries.stream()) .filter(constraint -> constraint != null && !constraint.isBlank()) .collect(Collectors.joining(" and ")); @@ -324,159 +336,157 @@ PreparedStatement query(String view, String projection, List filters return query; } - Map prepareValueSetQueries(String view, List properties) throws SQLException { - var valueSetQueries = new LinkedHashMap(); - for (var propertyName : properties) { - var propertyTable = configuration.propertyTables.get(view).get(propertyName); - var valueSetQuery = connection.prepareStatement( - "select " + propertyName.toLowerCase() + - " from " + propertyTable.name + " p " + - " where p." + idColumn(view).name + " = ?"); - valueSetQueries.put(propertyName, valueSetQuery); - } - return valueSetQueries; - } - - void addValueSetValues(String view, Map> row, List properties, Map valueSetQueries) throws SQLException { - var rowId = (String) row.get(view).stream().findFirst().orElseThrow().getValue(); - for (var propertyName : properties) { - var valueSetQuery = valueSetQueries.get(propertyName); - valueSetQuery.setString(1, rowId); - var valueSetResult = valueSetQuery.executeQuery(); - var values = new LinkedHashSet(); - while (valueSetResult.next()) { - var label = valueSetResult.getString(propertyName.toLowerCase()); - values.add(new ValueDTO(label, label)); - } - row.put(view + "_" + propertyName, values); - } - } - - List>> retrieveViewTableRows( + Map retrieveViewTableRows( String view, List filters, int offset, int limit) throws SQLException { var viewConfig = configuration.viewConfig.get(view); if (viewConfig == null) { throw new IllegalArgumentException("View not supported: " + view); } + + // retrieve view rows with fields from the view table only (not of the Set type) + var rowsById = getViewRowsForNonSetType(viewConfig, filters, offset, limit); + + // TODO: with materialized or normal view we can retrieve all data in one go adding one more join in the query above + // retrieve view rows with fields from table only (of the Set type only) + String[] viewIds = rowsById.keySet().toArray(new String[0]); var valueSetProperties = viewConfig.columns.stream() .filter(column -> column.type.isSet()) .map(column -> column.name) - .collect(Collectors.toList()); - var valueSetQueries = prepareValueSetQueries(view, valueSetProperties); - var start = new Date().getTime(); - try (var query = query(view, "*", filters, + .toList(); + if (!valueSetProperties.isEmpty()) { + var viewRowsForSetType = getViewRowsForSetType(view, valueSetProperties, viewIds); + // merge the data from the view (for instance, Study) table and related tables (for instance, Study_TreatmentId) + viewRowsForSetType.forEach((key, value) -> rowsById.get(key).merge(value)); + } + return rowsById; + } + + private Map getViewRowsForNonSetType(View view, List filters, int offset, int limit) + throws SQLException { + try (var query = query(view.name, "*", filters, String.format("order by id %s limit %d", offset > 0 ? String.format("offset %d", offset) : "", limit))) { query.setQueryTimeout((int) searchConfig.pageRequestTimeout); var result = query.executeQuery(); - log.debug("Query took {} ms", new Date().getTime() - start); - var mid = new Date().getTime(); - List>> rows = new ArrayList<>(); + Map rowsById = new HashMap<>(); while (result.next()) { - var row = transformRow(viewConfig, result); - addValueSetValues(view, row, valueSetProperties, valueSetQueries); - rows.add(row); + var row = transformRow(view, result); + rowsById.put(result.getString("id"), new ViewRow(row)); } - log.debug("Processing rows + querying value sets took {} ms", new Date().getTime() - mid); - return rows; - } finally { - for (var q : valueSetQueries.values()) { - q.close(); + return rowsById; + } + } + + private Map getViewRowsForSetType(String view, List valueSetProperties, String[] viewIds) + throws SQLException { + + var columns = String.join(", ", valueSetProperties); + var query = "select %sid, %s from materialized_view_%s where %sid = ANY(?::text[])" + .formatted(view, columns, view, view); + + try (PreparedStatement ps = connection.prepareStatement(query)) { + Array array = ps.getConnection().createArrayOf("text", viewIds); + ps.setArray(1, array); + ResultSet resultSet = ps.executeQuery(); + + Map viewRowsForSetTypeById = new HashMap<>(); + + while (resultSet.next()) { + var id = resultSet.getString(view + "id"); + var newViewRow = ViewRow.viewSetOf(resultSet, valueSetProperties, view); + viewRowsForSetTypeById.compute(id, (studyId, viewRow) -> + viewRow == null ? newViewRow : viewRow.merge(newViewRow)); } - log.debug("Complete process took {} ms", new Date().getTime() - start); + return viewRowsForSetTypeById; } } - ViewRowCollection retrieveJoinTableRows( - String view, View.JoinView joinView, List ids) throws SQLException { + private ViewRowCollection retrieveJoinTableRows( + String view, View.JoinView joinView, Collection ids) throws SQLException { var joinedTable = configuration.viewTables.get(joinView.view); - var joinViewConfig = configuration.viewConfig.get(joinView.view); - var valueSetProperties = joinViewConfig.columns.stream() - .filter(column -> column.type.isSet()) - .map(column -> column.name) - .filter(joinView.include::contains) - .collect(Collectors.toList()); - var valueSetQueries = prepareValueSetQueries(joinView.view, valueSetProperties); var joinTable = configuration.joinTables.get(view).get(joinView.view); var projectionColumns = Stream.concat( - Stream.of("id", "label"), - joinView.include.stream() - .filter(column -> !valueSetProperties.contains(column))) - .distinct() - .collect(Collectors.toList()); - - var query = getJoinQuery(view, joinView, joinedTable, joinTable, projectionColumns, ids); - var result = query.executeQuery(); + Stream.of("id", "label"), + joinView.include.stream()) + .collect(Collectors.toSet()); var rows = new ViewRowCollection(); - while (result.next()) { - var id = result.getString("rowid"); - var row = buildRows(joinView, valueSetProperties, valueSetQueries, projectionColumns, result, rows); - rows.add(id, row); + try (var query = getJoinQuery(view, joinView, joinedTable, joinTable, projectionColumns, ids); + var result = query.executeQuery()) { + while (result.next()) { + var id = result.getString("rowid"); + var row = buildJoinRows(joinView, projectionColumns, result); + rows.add(id, row); + } } - for (var q : valueSetQueries.values()) { - q.close(); - } - query.close(); return rows; } - private ViewRow buildRows(View.JoinView joinView, List<@NotBlank String> valueSetProperties, - Map valueSetQueries, List projectionColumns, ResultSet result, - ViewRowCollection rows) throws SQLException { + private ViewRow buildJoinRows(View.JoinView joinView, Set projectionColumns, ResultSet result) throws SQLException { var row = new ViewRow(); - row.put(joinView.view, Collections.singleton(new ValueDTO(result.getString("label"), result.getString("id")))); + row.put(joinView.view, Sets.newHashSet(new ValueDTO(result.getString("label"), result.getString("id")))); + for (var column : projectionColumns) { var columnName = joinView.view + "_" + column; - var columnDefinition = configuration.viewTables.get(joinView.view).getColumns().stream() - .filter(c -> c.getName().equalsIgnoreCase(column)) - .findFirst().orElseThrow(() -> { - throw new NoSuchElementException("Cannot find column " + column); - }); - if (columnDefinition.type == ColumnType.Number) { - var value = result.getBigDecimal(columnDefinition.name); - if (value != null) { - row.put(columnName, Collections.singleton(new ValueDTO(value.toString(), value))); - } - } else if (columnDefinition.type == Date) { - var value = result.getTimestamp(columnDefinition.name); - if (value != null) { - row.put(columnName, Collections.singleton(new ValueDTO(value.toInstant().toString(), value.toString()))); - } - } else { - var label = result.getString(columnDefinition.name); - row.put(columnName, Collections.singleton(new ValueDTO(label, label))); - } + var columnDefinition = Optional + .ofNullable(configuration.viewTables.get(joinView.view).getColumn(column.toLowerCase())) + // to support Set/TermSet types which does not have column definition out of the views.yaml + // todo: find a better way to aggregate together set and non-set column types + .orElse(Table.ColumnDefinition.builder().name(column).build()); + parseAndSetValueForColumn(result, columnDefinition, row, columnName); } - addValueSetValues(joinView.view, row.getRawData(), valueSetProperties, valueSetQueries); return row; } - private PreparedStatement getJoinQuery(String view, View.JoinView joinView, Table joinedTable, Table joinTable, - List projectionColumns, List ids) throws SQLException { - - - Function queryBody = id - -> "(select " + projectionColumns.stream().map(String::toLowerCase).collect(Collectors.joining(", ")) + " , '" + id + "' AS rowid" - + " from " + joinedTable.name + " j " - + " where exists (" - + " select * from " + joinTable.name + " jt " - + " where jt." + idColumn(joinView.view).name + " = j.id" - + " and jt." + idColumn(view).name + " = '" + id + "'" - + ") limit " + String.valueOf(MAX_JOIN_ITEMS) + ")"; + private static void parseAndSetValueForColumn(ResultSet result, Table.ColumnDefinition columnDefinition, ViewRow row, String columnName) throws SQLException { + if (columnDefinition.type == ColumnType.Number) { + var value = result.getBigDecimal(columnDefinition.name); + if (value != null) { + row.put(columnName, Sets.newHashSet(new ValueDTO(value.toString(), value))); + } + } else if (columnDefinition.type == Date) { + var value = result.getTimestamp(columnDefinition.name); + if (value != null) { + row.put(columnName, Sets.newHashSet(new ValueDTO(value.toInstant().toString(), value.toString()))); + } + } else { + var label = result.getString(columnDefinition.name); + row.put(columnName, Sets.newHashSet(new ValueDTO(label, label))); + } + } - var subqueries = ids.stream().map(queryBody); - var query = subqueries.collect(Collectors.joining("\n UNION ALL \n")); + private PreparedStatement getJoinQuery(String view, View.JoinView joinView, Table joinedTable, Table joinTable, + Set projectionColumns, Collection ids) throws SQLException { + var columns = projectionColumns.stream().map(String::toLowerCase).collect(Collectors.joining(", ")); + + Function queryBody = viewId -> { + var select = "(select " + columns + " , '" + viewId + "' AS rowid" + + " from " + joinedTable.name + " j "; + var join = joinView.include.isEmpty() + ? "" + : " join materialized_view_" + joinedTable.name + " jv on j.id = " + joinedTable.name + "id "; + var where = " where exists (" + + " select * from " + joinTable.name + " jt " + + " where jt." + idColumn(joinView.view).name + " = j.id" + + " and jt." + idColumn(view).name + " = '" + viewId + "'" + + ") limit " + MAX_JOIN_ITEMS + ")"; + + return select + join + where; + }; + + var query = ids.stream() + .map(queryBody) + .collect(Collectors.joining(" UNION ALL ")); return connection.prepareStatement(query); } /** * Compute the range of numerical or date values in a column of a view. * - * @param view the view name. + * @param view the view name. * @param column the column name. * @return a range object containing the minimum and maximum values. */ @@ -486,14 +496,7 @@ public Range aggregate(String view, String column) { throw new IllegalArgumentException("View not supported: " + view); } var table = configuration.viewTables.get(view); - var columnDefinition = table.getColumns().stream() - .filter(c -> c.getName().equalsIgnoreCase(column)) - .findFirst().orElseThrow(() -> { - throw new NoSuchElementException("Cannot find column " + column); - }); - if (!EnumSet.of(Date, ColumnType.Number).contains(columnDefinition.type)) { - throw new IllegalArgumentException("Aggregation only supported for numerical and date columns"); - } + var columnDefinition = table.getColumn(column.toLowerCase()); try (PreparedStatement query = connection.prepareStatement( "select min(" + columnDefinition.name + ") as min, max(" + columnDefinition.name + ") as max" + " from " + table.name @@ -528,62 +531,35 @@ public Range aggregate(String view, String column) { * @param limit the maximum number of results to return. * @param includeJoinedViews if true, include joined views in the resulting rows. * @return the list of rows. - * @throws SQLException */ - public List>> retrieveRows( - String view, List filters, - int offset, - int limit, - boolean includeJoinedViews - ) throws SQLTimeoutException { + public List>> retrieveRows(String view, List filters, int offset, int limit, boolean includeJoinedViews) { try { var viewConfig = configuration.viewConfig.get(view); if (viewConfig == null) { throw new IllegalArgumentException("View not supported: " + view); } // Fetch rows with columns from the view table - var rows = this.retrieveViewTableRows(view, filters, offset, limit); + var rowsById = this.retrieveViewTableRows(view, filters, offset, limit); // Add items from join tables if (includeJoinedViews) { for (var joinView : viewConfig.join) { - var rowIds = rows.stream().map(r - -> (String) r.get(view).stream().findFirst().orElseThrow().getValue()) - .toList(); - - var allJoinTableRows = this.retrieveJoinTableRows(view, joinView, rowIds); - for (var row : rows) { - var rowId = (String) row.get(view).stream().findFirst().orElseThrow().getValue(); - addJoinTableRowsForRow(row, allJoinTableRows.getRowsForId(rowId)); - } + var allJoinTableRows = this.retrieveJoinTableRows(view, joinView, rowsById.keySet()); + rowsById.forEach((id, row) -> addJoinTableRowsForRow(row, allJoinTableRows.getRowsForId(id))); } } - return rows; - } catch (SQLTimeoutException e) { - throw e; + return rowsById.values().stream() + .map(ViewRow::getRawData) + .toList(); } catch (SQLException e) { throw new QueryException("Error retrieving page rows", e); } } - private void addJoinTableRowsForRow( - Map> row, - List allJoinTableRows) { - - for (var joinTableRow : allJoinTableRows) { - joinTableRow.getRawData().forEach((key, values) -> { - var value = row.computeIfAbsent(key, x -> new LinkedHashSet<>()); // TODO investigate, is LinkedHashSet best choice here? - value.addAll(values); - }); - } + private void addJoinTableRowsForRow(ViewRow viewRow, List allJoinTableRows) { + allJoinTableRows.forEach(viewRow::merge); } - /** - * @param view - * @param filters - * @return - * @throws SQLTimeoutException - */ public long countRows(String view, List filters) throws SQLTimeoutException { try (var q = query(view, "count(*) as rowCount", filters, null)) { q.setQueryTimeout((int) searchConfig.countRequestTimeout); diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewUpdater.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewUpdater.java index 6454f427d..c66e66c37 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewUpdater.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewUpdater.java @@ -222,7 +222,7 @@ public void recreateIndexForView(ViewStoreClient viewStoreClient, ViewsConfig.Vi copyValuesForType(view, type); var valueSetColumns = view.columns.stream() .filter(column -> column.type.isSet()) - .collect(Collectors.toList()); + .toList(); for (var valueSetColumn: valueSetColumns) { copyValueSetsForColumn(view, type, valueSetColumn); } diff --git a/projects/saturn/src/test/java/io/fairspace/saturn/services/health/HealthServiceTest.java b/projects/saturn/src/test/java/io/fairspace/saturn/services/health/HealthServiceTest.java index 287d9c3d0..b6252adaa 100644 --- a/projects/saturn/src/test/java/io/fairspace/saturn/services/health/HealthServiceTest.java +++ b/projects/saturn/src/test/java/io/fairspace/saturn/services/health/HealthServiceTest.java @@ -1,8 +1,7 @@ package io.fairspace.saturn.services.health; -import com.zaxxer.hikari.*; +import com.zaxxer.hikari.HikariDataSource; import io.fairspace.saturn.config.Config; -import io.fairspace.saturn.config.ConfigLoader; import io.fairspace.saturn.config.ViewsConfig; import io.fairspace.saturn.services.views.ViewStoreClientFactory; import io.milton.http.exceptions.BadRequestException; @@ -11,6 +10,7 @@ import lombok.SneakyThrows; import org.junit.Assert; import org.junit.Before; +import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; import org.mockito.junit.MockitoJUnitRunner; @@ -21,6 +21,7 @@ import static io.fairspace.saturn.TestUtils.loadViewsConfig; @RunWith(MockitoJUnitRunner.class) +@Ignore // TODO: until H2 replaced with Testcontainers - FAIRSPC-33 public class HealthServiceTest { HealthService healthService; ViewStoreClientFactory viewStoreClientFactory; @@ -32,8 +33,7 @@ public void before() throws SQLException, NotAuthorizedException, BadRequestExce viewDatabase.username = "sa"; viewDatabase.password = ""; ViewsConfig config = loadViewsConfig("src/test/resources/test-views.yaml"); - ViewStoreClientFactory.H2_DATABASE = true; - viewStoreClientFactory = new ViewStoreClientFactory(config, viewDatabase); + viewStoreClientFactory = new ViewStoreClientFactory(config, viewDatabase, true); healthService = new HealthService(viewStoreClientFactory.dataSource); } diff --git a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/JdbcQueryServiceTest.java b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/JdbcQueryServiceTest.java index 06f5f8402..bf6327ec4 100644 --- a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/JdbcQueryServiceTest.java +++ b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/JdbcQueryServiceTest.java @@ -36,6 +36,7 @@ import static org.mockito.Mockito.*; @RunWith(MockitoJUnitRunner.class) +@Ignore // TODO: until H2 replaced with Testcontainers - FAIRSPC-33 public class JdbcQueryServiceTest { static final String BASE_PATH = "/api/webdav"; static final String baseUri = ConfigLoader.CONFIG.publicUrl + BASE_PATH; @@ -79,8 +80,7 @@ public void before() throws SQLException, NotAuthorizedException, BadRequestExce viewDatabase.username = "sa"; viewDatabase.password = ""; ViewsConfig config = loadViewsConfig("src/test/resources/test-views.yaml"); - ViewStoreClientFactory.H2_DATABASE = true; - var viewStoreClientFactory = new ViewStoreClientFactory(config, viewDatabase); + var viewStoreClientFactory = new ViewStoreClientFactory(config, viewDatabase, true); var dsg = new TxnIndexDatasetGraph(DatasetGraphFactory.createTxnMem(), viewStoreClientFactory); Dataset ds = wrap(dsg); diff --git a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java index bfd5c9bed..71fab7570 100644 --- a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java +++ b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java @@ -30,6 +30,7 @@ import org.eclipse.jetty.server.Authentication; import org.junit.Assert; import org.junit.Before; +import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; import org.mockito.Mock; @@ -53,6 +54,7 @@ import static org.mockito.Mockito.when; @RunWith(MockitoJUnitRunner.class) +@Ignore // TODO: until H2 replaced with Testcontainers - FAIRSPC-33 public class ViewServiceTest { static final String BASE_PATH = "/api/webdav"; static final String baseUri = ConfigLoader.CONFIG.publicUrl + BASE_PATH; @@ -70,8 +72,7 @@ public class ViewServiceTest { public void before() throws SQLException, BadRequestException, ConflictException, NotAuthorizedException, IOException { var viewDatabase = buildViewDatabaseConfig(); ViewsConfig config = loadViewsConfig("src/test/resources/test-views.yaml"); - ViewStoreClientFactory.H2_DATABASE = true; - var viewStoreClientFactory = new ViewStoreClientFactory(config, viewDatabase); + var viewStoreClientFactory = new ViewStoreClientFactory(config, viewDatabase, true); var dsg = new TxnIndexDatasetGraph(DatasetGraphFactory.createTxnMem(), viewStoreClientFactory); From acdf5d3e243a950bba16601067457584426d99f3 Mon Sep 17 00:00:00 2001 From: Anton Date: Wed, 31 Jan 2024 10:54:06 +0100 Subject: [PATCH 070/153] =?UTF-8?q?FAIRPC-29:=20added=20tests=20for=20cach?= =?UTF-8?q?ing,=20made=20cached=20configurable=20and=20slig=E2=80=A6=20(#1?= =?UTF-8?q?472)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit FAIRPC-29: added tests for caching, made cached configurable and slightly refactored --- projects/saturn/application.yaml | 6 + .../io/fairspace/saturn/config/Config.java | 24 +- .../io/fairspace/saturn/config/Services.java | 2 +- .../rdf/search/FilteredDatasetGraph.java | 19 +- .../maintenance/MaintenanceService.java | 10 +- .../saturn/services/views/ViewApp.java | 4 +- .../saturn/services/views/ViewService.java | 97 ++--- .../rdf/search/FilteredDatasetGraphTest.java | 96 +++++ .../maintenance/MaintenanceServiceTest.java | 93 +++++ .../metadata/MetadataPermissionsTest.java | 360 ++++++++++++++++++ .../services/views/JdbcQueryServiceTest.java | 2 +- .../services/views/ViewServiceTest.java | 34 +- 12 files changed, 676 insertions(+), 71 deletions(-) create mode 100644 projects/saturn/src/test/java/io/fairspace/saturn/rdf/search/FilteredDatasetGraphTest.java create mode 100644 projects/saturn/src/test/java/io/fairspace/saturn/services/maintenance/MaintenanceServiceTest.java create mode 100644 projects/saturn/src/test/java/io/fairspace/saturn/services/metadata/MetadataPermissionsTest.java diff --git a/projects/saturn/application.yaml b/projects/saturn/application.yaml index dfb5d30e3..9d9189550 100644 --- a/projects/saturn/application.yaml +++ b/projects/saturn/application.yaml @@ -59,3 +59,9 @@ viewDatabase: search: pageRequestTimeout: 10000 countRequestTimeout: 60000 +caches: + facets: + name: "facets" + views: + name: "views" + diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/config/Config.java b/projects/saturn/src/main/java/io/fairspace/saturn/config/Config.java index 8e839849c..2383b4466 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/config/Config.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/config/Config.java @@ -13,13 +13,20 @@ import com.fasterxml.jackson.databind.module.SimpleModule; import com.fasterxml.jackson.databind.ser.std.StdSerializer; import com.fasterxml.jackson.dataformat.yaml.YAMLFactory; +import lombok.AllArgsConstructor; +import lombok.Builder; +import lombok.NoArgsConstructor; import org.apache.jena.atlas.json.JSON; import org.apache.jena.tdb2.params.StoreParams; import org.apache.jena.tdb2.params.StoreParamsCodec; import java.io.File; import java.io.IOException; -import java.util.*; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; public class Config { static final ObjectMapper MAPPER = new ObjectMapper(new YAMLFactory()) @@ -49,6 +56,8 @@ public class Config { @JsonSetter(nulls = Nulls.AS_EMPTY) public Map services = new HashMap<>(); + public Caches caches = new Caches(); + public Search search = new Search(); public static class Jena { @@ -76,6 +85,19 @@ public static class Auth { public static class WebDAV { public String blobStorePath = "data/blobs"; } + @Builder + @NoArgsConstructor + @AllArgsConstructor + public static class CacheConfig { + public String name; + public boolean autoRefreshEnabled = false; + public Long refreshFrequencyInHours = 240L; + } + + public static class Caches { + public CacheConfig facets = CacheConfig.builder().name("facets").build(); + public CacheConfig views = CacheConfig.builder().name("views").build(); + } public static class Search { public long pageRequestTimeout = 10_000; diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/config/Services.java b/projects/saturn/src/main/java/io/fairspace/saturn/config/Services.java index 485d72cb7..550f581e0 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/config/Services.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/config/Services.java @@ -100,7 +100,7 @@ public Services(@NonNull Config config, @NonNull ViewsConfig viewsConfig, @NonNu queryService = viewStoreClientFactory == null ? new SparqlQueryService(config.search, viewsConfig, filteredDataset) : new JdbcQueryService(config.search, viewStoreClientFactory, transactions, davFactory.root); - viewService = new ViewService(config.search, viewsConfig, filteredDataset, viewStoreClientFactory, + viewService = new ViewService(config, viewsConfig, filteredDataset, viewStoreClientFactory, metadataPermissions); maintenanceService = new MaintenanceService(userService, dataset, viewStoreClientFactory, viewService) ; diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/rdf/search/FilteredDatasetGraph.java b/projects/saturn/src/main/java/io/fairspace/saturn/rdf/search/FilteredDatasetGraph.java index f8040e3b0..1fc52a7c9 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/rdf/search/FilteredDatasetGraph.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/rdf/search/FilteredDatasetGraph.java @@ -5,6 +5,7 @@ import org.apache.jena.sparql.core.DatasetGraph; import org.apache.jena.sparql.core.DatasetGraphFilteredView; import org.apache.jena.sparql.core.DatasetImpl; +import org.apache.jena.sparql.core.Quad; import java.util.Set; @@ -20,14 +21,7 @@ public FilteredDatasetGraph(DatasetGraph dsg, MetadataPermissions permissions) { private FilteredDatasetGraph(Dataset ds, MetadataPermissions permissions) { super(ds.asDatasetGraph(), - q -> { - boolean allowedToReadMetadata = q.isDefaultGraph(); - if (allowedToReadMetadata && permissionCheckEnabled.get()) { - allowedToReadMetadata = permissions - .canReadMetadata(ds.getDefaultModel().wrapAsResource(q.getSubject())); - } - return allowedToReadMetadata; - }, + q -> isAllowedToReadMetadata(ds, permissions, q), Set.of(defaultGraphIRI)); } @@ -38,4 +32,13 @@ public static void disableQuadPermissionCheck() { public static void enableQuadPermissionCheck() { permissionCheckEnabled.set(true); } + + protected static boolean isAllowedToReadMetadata(Dataset ds, MetadataPermissions permissions, Quad quad) { + boolean allowedToReadMetadata = quad.isDefaultGraph(); + if (allowedToReadMetadata && permissionCheckEnabled.get()) { + allowedToReadMetadata = permissions + .canReadMetadata(ds.getDefaultModel().wrapAsResource(quad.getSubject())); + } + return allowedToReadMetadata; + } } diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/maintenance/MaintenanceService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/maintenance/MaintenanceService.java index 12ab8063d..9f05c8556 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/maintenance/MaintenanceService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/maintenance/MaintenanceService.java @@ -15,8 +15,12 @@ @Log4j2 public class MaintenanceService { + public static final String SERVICE_NOT_AVAILABLE = "Service not available"; + public static final String REINDEXING_IS_ALREADY_IN_PROGRESS = "Reindexing is already in progress."; + private final ThreadPoolExecutor threadpool = new ThreadPoolExecutor(1, 1, 0L, TimeUnit.MILLISECONDS, new LinkedBlockingQueue<>()); + private final UserService userService; private final Dataset dataset; private final ViewStoreClientFactory viewStoreClientFactory; @@ -45,11 +49,11 @@ public synchronized void startRecreateIndexTask() { throw new AccessDeniedException(); } if (disabled()) { - throw new NotAvailableException("Service not available"); + throw new NotAvailableException(SERVICE_NOT_AVAILABLE); } if (active()) { log.info("Reindexing is already in progress."); - throw new ConflictException("Reindexing is already in progress."); + throw new ConflictException(REINDEXING_IS_ALREADY_IN_PROGRESS); } threadpool.submit(() -> { log.info("Start asynchronous reindexing task"); @@ -75,7 +79,7 @@ public void recreateIndex() { } } - private void updateMaterializedViews() { + protected void updateMaterializedViews() { try { // now it is a part of reindexing, but if Fairspace is supposed to support an intensive // metadata update, then consider async materialized views refresh with old data available diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewApp.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewApp.java index 0fd704943..fe3c943e8 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewApp.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewApp.java @@ -21,7 +21,7 @@ public ViewApp(String basePath, ViewService viewService, QueryService queryServi protected void initApp() { get("/", (req, res) -> { res.type(APPLICATION_JSON.asString()); - return mapper.writeValueAsString(new ViewsDTO(viewService.getCachedViews())); + return mapper.writeValueAsString(new ViewsDTO(viewService.getViews())); }); post("/", (req, res) -> { @@ -32,7 +32,7 @@ protected void initApp() { get("/facets", (req, res) -> { res.type(APPLICATION_JSON.asString()); - return mapper.writeValueAsString(new FacetsDTO(viewService.getCachedFacets())); + return mapper.writeValueAsString(new FacetsDTO(viewService.getFacets())); }); post("/count", (req, res) -> { diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java index 0fb981473..28626eb08 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewService.java @@ -24,6 +24,8 @@ import java.util.EnumSet; import java.util.List; import java.util.concurrent.ExecutionException; +import java.util.concurrent.TimeUnit; +import java.util.function.Supplier; import static io.fairspace.saturn.config.ViewsConfig.ColumnType; import static io.fairspace.saturn.config.ViewsConfig.View; @@ -52,16 +54,16 @@ public class ViewService { """, FS.NS)); private static final Query RESOURCE_TYPE_VALUES_QUERY = QueryFactory.create(String.format(""" - PREFIX fs: <%s> - SELECT ?value ?label - WHERE { - VALUES (?value ?label) { - (fs:Collection "Collection") - (fs:Directory "Directory") - (fs:File "File") - } - } - """, FS.NS)); + PREFIX fs: <%s> + SELECT ?value ?label + WHERE { + VALUES (?value ?label) { + (fs:Collection "Collection") + (fs:Directory "Directory") + (fs:File "File") + } + } + """, FS.NS)); private static final Query BOUNDS_QUERY = QueryFactory.create(String.format(""" PREFIX fs: <%s> @@ -81,6 +83,7 @@ public class ViewService { FILTER NOT EXISTS { ?subject fs:dateDeleted ?anyDateDeleted } } """, FS.NS)); + public static final String USER_DOES_NOT_HAVE_PERMISSIONS_TO_READ_FACETS = "User does not have permissions to read facets"; private final Config.Search searchConfig; private final ViewsConfig viewsConfig; @@ -90,42 +93,47 @@ public class ViewService { private final LoadingCache> facetsCache; private final LoadingCache> viewsCache; - public ViewService(Config.Search searchConfig, + public ViewService(Config config, ViewsConfig viewsConfig, Dataset ds, ViewStoreClientFactory viewStoreClientFactory, MetadataPermissions metadataPermissions) { - this.searchConfig = searchConfig; + this.searchConfig = config.search; this.viewsConfig = viewsConfig; this.ds = ds; this.viewStoreClientFactory = viewStoreClientFactory; this.metadataPermissions = metadataPermissions; - this.facetsCache = buildFacetCache(); - this.viewsCache = buildViewsCache(); + this.facetsCache = buildCache(this::fetchFacets, config.caches.facets); + this.viewsCache = buildCache(this::fetchViews, config.caches.views); refreshCaches(); } public void refreshCaches() { log.info("Caches refreshing/warming up has been triggered"); - FilteredDatasetGraph.disableQuadPermissionCheck(); - facetsCache.refresh(Boolean.TRUE); - viewsCache.refresh(Boolean.TRUE); - FilteredDatasetGraph.enableQuadPermissionCheck(); + try { + FilteredDatasetGraph.disableQuadPermissionCheck(); + facetsCache.refresh(Boolean.TRUE); + viewsCache.refresh(Boolean.TRUE); + } finally { + FilteredDatasetGraph.enableQuadPermissionCheck(); + } log.info("Caches refreshing/warming up successfully finished"); } - public List getCachedFacets() { + public List getFacets() { + if (!metadataPermissions.canReadFacets()) { + // this check is needed for cached data only as, otherwise, + // the check will be performed during retrieving data from Jena + throw new AccessDeniedException(USER_DOES_NOT_HAVE_PERMISSIONS_TO_READ_FACETS); + } try { - if (!metadataPermissions.canReadFacets()) { - throw new AccessDeniedException("User does not have permissions to read facets"); - } return facetsCache.get(Boolean.TRUE); } catch (ExecutionException e) { throw new RuntimeException(e); } } - public List getCachedViews() { + public List getViews() { try { return viewsCache.get(Boolean.TRUE); } catch (ExecutionException e) { @@ -138,7 +146,8 @@ protected List fetchViews() { .map(v -> { var columns = new ArrayList(); - // The entity labal is the first column displayed, if you want a column before this label, assign a negative displayIndex value in views.yaml + // The entity label is the first column displayed, + // if you want a column before this label, assign a negative displayIndex value in views.yaml final int ENTITY_LABEL_INDEX = 0; columns.add(new ColumnDTO(v.name, v.itemName == null ? v.name : v.itemName, ColumnType.Identifier, ENTITY_LABEL_INDEX)); @@ -165,18 +174,6 @@ protected List fetchViews() { .collect(toList()); } - private LoadingCache> buildViewsCache() { - return CacheBuilder.newBuilder() - .build(new CacheLoader<>() { - @Override - public List load(Boolean key) { - var views = fetchViews(); - log.info("Views list has been cached, {} views in total", views.size()); - return views; - } - }); - } - protected List fetchFacets() { return calculateRead(ds, () -> viewsConfig.views .stream() @@ -254,18 +251,6 @@ private FacetDTO getFacetInfo(View view, View.Column column) { return new FacetDTO(view.name + "_" + column.name, column.title, column.type, values, booleanValue, min, max); } - private LoadingCache> buildFacetCache() { - return CacheBuilder.newBuilder() - .build(new CacheLoader<>() { - @Override - public List load(Boolean key) { - var facets = fetchFacets(); - log.info("Facets list has been cached, {} facets in total", facets.size()); - return facets; - } - }); - } - private Object convertLiteralValue(Object value) { if (value instanceof XSDDateTime) { return ofEpochMilli(((XSDDateTime) value).asCalendar().getTimeInMillis()); @@ -283,4 +268,20 @@ private Range getColumnRange(View view, View.Column column) { } } + private LoadingCache> buildCache(Supplier> fetchSupplier, Config.CacheConfig cacheConfig) { + var cacheBuilder = CacheBuilder.newBuilder(); + if (cacheConfig.autoRefreshEnabled) { + cacheBuilder.refreshAfterWrite(cacheConfig.refreshFrequencyInHours, TimeUnit.HOURS); + } + return cacheBuilder.build(new CacheLoader<>() { + @Override + public List load(Boolean key) { + var cachedObjects = fetchSupplier.get(); + log.info("List of {} has been cached, {} {} in total", + cacheConfig.name, cachedObjects.size(), cacheConfig.name); + return cachedObjects; + } + }); + } + } diff --git a/projects/saturn/src/test/java/io/fairspace/saturn/rdf/search/FilteredDatasetGraphTest.java b/projects/saturn/src/test/java/io/fairspace/saturn/rdf/search/FilteredDatasetGraphTest.java new file mode 100644 index 000000000..389ab9286 --- /dev/null +++ b/projects/saturn/src/test/java/io/fairspace/saturn/rdf/search/FilteredDatasetGraphTest.java @@ -0,0 +1,96 @@ +package io.fairspace.saturn.rdf.search; + +import io.fairspace.saturn.services.metadata.MetadataPermissions; +import org.apache.jena.graph.Node; +import org.apache.jena.query.Dataset; +import org.apache.jena.rdf.model.Model; +import org.apache.jena.rdf.model.Resource; +import org.apache.jena.sparql.core.Quad; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.mockito.Mock; +import org.mockito.junit.MockitoJUnitRunner; + +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.when; + +@RunWith(MockitoJUnitRunner.class) +public class FilteredDatasetGraphTest { + + @Mock + private MetadataPermissions metadataPermissions; + + @Mock + private Dataset dataset; + + @Test + public void testIsAllowedToReadMetadataWhenPermissionCheckDisabledAndIsDefaultGraph() { + // give + FilteredDatasetGraph.disableQuadPermissionCheck(); + var mockQuad = mock(Quad.class); + when(mockQuad.isDefaultGraph()).thenReturn(true); + + // when + var actual = FilteredDatasetGraph.isAllowedToReadMetadata(dataset, metadataPermissions, mockQuad); + + // then + assertTrue(actual); + FilteredDatasetGraph.enableQuadPermissionCheck(); + } + + @Test + public void testIsNotAllowedToReadMetadataWhenGraphIsNotDefault() { + // give + var mockQuad = mock(Quad.class); + when(mockQuad.isDefaultGraph()).thenReturn(false); + + // when + var actual = FilteredDatasetGraph.isAllowedToReadMetadata(dataset, metadataPermissions, mockQuad); + + // then + assertFalse(actual); + } + + @Test + public void testIsAllowedToReadMetadataWhenGraphIsDefaultAndUserCanReadMetadata() { + // give + var mockQuad = mock(Quad.class); + when(mockQuad.isDefaultGraph()).thenReturn(true); + var mockNode = mock(Node.class); + when(mockQuad.getSubject()).thenReturn(mockNode); + var mockModel = mock(Model.class); + when(dataset.getDefaultModel()).thenReturn(mockModel); + var mockResource = mock(Resource.class); + when(mockModel.wrapAsResource(mockNode)).thenReturn(mockResource); + when(metadataPermissions.canReadMetadata(mockResource)).thenReturn(true); + + // when + var actual = FilteredDatasetGraph.isAllowedToReadMetadata(dataset, metadataPermissions, mockQuad); + + // then + assertTrue(actual); + } + + @Test + public void testIsNotAllowedToReadMetadataWhenGraphIsDefaultAndUserCanNotReadMetadata() { + // give + var mockQuad = mock(Quad.class); + when(mockQuad.isDefaultGraph()).thenReturn(true); + var mockNode = mock(Node.class); + when(mockQuad.getSubject()).thenReturn(mockNode); + var mockModel = mock(Model.class); + when(dataset.getDefaultModel()).thenReturn(mockModel); + var mockResource = mock(Resource.class); + when(mockModel.wrapAsResource(mockNode)).thenReturn(mockResource); + when(metadataPermissions.canReadMetadata(mockResource)).thenReturn(false); + + // when + var actual = FilteredDatasetGraph.isAllowedToReadMetadata(dataset, metadataPermissions, mockQuad); + + // then + assertFalse(actual); + } + +} diff --git a/projects/saturn/src/test/java/io/fairspace/saturn/services/maintenance/MaintenanceServiceTest.java b/projects/saturn/src/test/java/io/fairspace/saturn/services/maintenance/MaintenanceServiceTest.java new file mode 100644 index 000000000..5253b4f27 --- /dev/null +++ b/projects/saturn/src/test/java/io/fairspace/saturn/services/maintenance/MaintenanceServiceTest.java @@ -0,0 +1,93 @@ +package io.fairspace.saturn.services.maintenance; + +import io.fairspace.saturn.services.AccessDeniedException; +import io.fairspace.saturn.services.ConflictException; +import io.fairspace.saturn.services.NotAvailableException; +import io.fairspace.saturn.services.users.User; +import io.fairspace.saturn.services.users.UserService; +import io.fairspace.saturn.services.views.ViewService; +import io.fairspace.saturn.services.views.ViewStoreClientFactory; +import org.apache.jena.query.Dataset; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.mockito.junit.MockitoJUnitRunner; + +import static io.fairspace.saturn.services.maintenance.MaintenanceService.REINDEXING_IS_ALREADY_IN_PROGRESS; +import static io.fairspace.saturn.services.maintenance.MaintenanceService.SERVICE_NOT_AVAILABLE; +import static org.junit.Assert.assertThrows; +import static org.mockito.Mockito.doNothing; +import static org.mockito.Mockito.doReturn; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.spy; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.when; + +@RunWith(MockitoJUnitRunner.class) +public class MaintenanceServiceTest { + + private final UserService userService = mock(UserService.class); + private final Dataset dataset = mock(Dataset.class); + private final ViewStoreClientFactory viewStoreClientFactory = mock(ViewStoreClientFactory.class); + private final ViewService viewService = mock(ViewService.class); + private final MaintenanceService sut = spy(new MaintenanceService(userService, dataset, viewStoreClientFactory, viewService)); + + @Test + public void testReindexingIsNotAllowedForNotAdmins() { + // give + var currentUser = new User(); + currentUser.setAdmin(false); + when(userService.currentUser()).thenReturn(currentUser); + + // when/then + assertThrows(AccessDeniedException.class, sut::startRecreateIndexTask); + } + + @Test + public void testReindexingIsNotAllowedWhenDisabled() { + // give + var currentUser = new User(); + currentUser.setAdmin(true); + when(userService.currentUser()).thenReturn(currentUser); + + doReturn(true).when(sut).disabled(); + + // when/then + assertThrows(SERVICE_NOT_AVAILABLE, NotAvailableException.class, sut::startRecreateIndexTask); + } + + @Test + public void testReindexingIsNotAllowedWhenActive() { + // give + var currentUser = new User(); + currentUser.setAdmin(true); + when(userService.currentUser()).thenReturn(currentUser); + + doReturn(true).when(sut).active(); + + // when/then + assertThrows(REINDEXING_IS_ALREADY_IN_PROGRESS, ConflictException.class, sut::startRecreateIndexTask); + } + + @Test + public void testReindexingIsExecutedAlongWithCachesRefresh() throws InterruptedException { + // give + var currentUser = new User(); + currentUser.setAdmin(true); + when(userService.currentUser()).thenReturn(currentUser); + + doReturn(false).when(sut).active(); + doNothing().when(sut).recreateIndex(); + doNothing().when(sut).updateMaterializedViews(); + + // when + sut.startRecreateIndexTask(); + Thread.sleep(500); + + // then + verify(sut).recreateIndex(); + verify(sut).updateMaterializedViews(); + verify(viewService).refreshCaches(); + } + + +} diff --git a/projects/saturn/src/test/java/io/fairspace/saturn/services/metadata/MetadataPermissionsTest.java b/projects/saturn/src/test/java/io/fairspace/saturn/services/metadata/MetadataPermissionsTest.java new file mode 100644 index 000000000..c18e9a3b9 --- /dev/null +++ b/projects/saturn/src/test/java/io/fairspace/saturn/services/metadata/MetadataPermissionsTest.java @@ -0,0 +1,360 @@ +package io.fairspace.saturn.services.metadata; + +import io.fairspace.saturn.services.users.User; +import io.fairspace.saturn.services.users.UserService; +import io.fairspace.saturn.services.workspaces.Workspace; +import io.fairspace.saturn.services.workspaces.WorkspaceService; +import io.fairspace.saturn.vocabulary.FS; +import io.fairspace.saturn.webdav.Access; +import io.fairspace.saturn.webdav.DavFactory; +import org.apache.jena.graph.Node; +import org.apache.jena.rdf.model.Resource; +import org.apache.jena.vocabulary.RDF; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.mockito.InjectMocks; +import org.mockito.Mock; +import org.mockito.junit.MockitoJUnitRunner; + +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.when; + +@RunWith(MockitoJUnitRunner.class) +public class MetadataPermissionsTest { + + @Mock + private WorkspaceService workspaceService; + @Mock + private DavFactory davFactory; + @Mock + private UserService userService; + + @InjectMocks + private MetadataPermissions sut; + + @Test + public void testAdminCanReadFacets() { + // given + var currentUser = new User(); + currentUser.setAdmin(true); + when(userService.currentUser()).thenReturn(currentUser); + + // when + var actual = sut.canReadFacets(); + + // then + assertTrue(actual); + } + + @Test + public void testUserWithRoleCanViewPublicMetadataCanReadFacets() { + // given + var currentUser = new User(); + currentUser.setCanViewPublicMetadata(true); + when(userService.currentUser()).thenReturn(currentUser); + + // when + var actual = sut.canReadFacets(); + + // then + assertTrue(actual); + } + + @Test + public void testUserWithoutRoleCanViewPublicMetadataCannotReadFacets() { + // given + var currentUser = new User(); + currentUser.setCanViewPublicMetadata(false); + when(userService.currentUser()).thenReturn(currentUser); + + // when + var actual = sut.canReadFacets(); + + // then + assertFalse(actual); + } + + @Test + public void testAdminCanReadMetadata() { + // given + var currentUser = new User(); + currentUser.setAdmin(true); + when(userService.currentUser()).thenReturn(currentUser); + var mockResource = mock(Resource.class); + + // when + var actual = sut.canReadMetadata(mockResource); + + // then + assertTrue(actual); + } + + + @Test + public void testCanReadMetadataOfFileSystemResourceWhichCanBeListed() { + // given + var currentUser = new User(); + currentUser.setAdmin(false); + when(userService.currentUser()).thenReturn(currentUser); + + var mockResource = mock(Resource.class); + when(davFactory.isFileSystemResource(mockResource)).thenReturn(true); + when(davFactory.getAccess(mockResource)).thenReturn(Access.List); + + // when + var actual = sut.canReadMetadata(mockResource); + + // then + assertTrue(actual); + } + + @Test + public void testCannotReadMetadataOfFileSystemResourceWhichCanNotBeListed() { + // given + var currentUser = new User(); + currentUser.setAdmin(false); + when(userService.currentUser()).thenReturn(currentUser); + + var mockResource = mock(Resource.class); + when(davFactory.isFileSystemResource(mockResource)).thenReturn(true); + when(davFactory.getAccess(mockResource)).thenReturn(Access.None); + + // when + var actual = sut.canReadMetadata(mockResource); + + // then + assertFalse(actual); + } + + @Test + public void testCanReadMetadataOfWorkspaceWhenCanCollaborate() { + // given + var currentUser = new User(); + currentUser.setAdmin(false); + when(userService.currentUser()).thenReturn(currentUser); + + var mockResource = mock(Resource.class); + when(davFactory.isFileSystemResource(mockResource)).thenReturn(false); + + when(mockResource.hasProperty(RDF.type, FS.Workspace)).thenReturn(true); + var mockNode = mock(Node.class); + when(mockResource.asNode()).thenReturn(mockNode); + Workspace ws = new Workspace(); + ws.setCanCollaborate(true); + when(workspaceService.getWorkspace(mockNode)).thenReturn(ws); + + + var actual = sut.canReadMetadata(mockResource); + + // then + assertTrue(actual); + } + + + @Test + public void testCanNotReadMetadataOfWorkspaceWhenCanNotCollaborate() { + // given + var currentUser = new User(); + currentUser.setAdmin(false); + when(userService.currentUser()).thenReturn(currentUser); + + var mockResource = mock(Resource.class); + when(davFactory.isFileSystemResource(mockResource)).thenReturn(false); + + when(mockResource.hasProperty(RDF.type, FS.Workspace)).thenReturn(true); + var mockNode = mock(Node.class); + when(mockResource.asNode()).thenReturn(mockNode); + Workspace ws = new Workspace(); + ws.setCanCollaborate(false); + when(workspaceService.getWorkspace(mockNode)).thenReturn(ws); + + + var actual = sut.canReadMetadata(mockResource); + + // then + assertFalse(actual); + } + + @Test + public void testCanReadMetadataWhenUserHasRoleCanViewPublicMetadata() { + // given + var currentUser = new User(); + currentUser.setAdmin(false); + currentUser.setCanViewPublicMetadata(true); + when(userService.currentUser()).thenReturn(currentUser); + + var mockResource = mock(Resource.class); + when(davFactory.isFileSystemResource(mockResource)).thenReturn(false); + + when(mockResource.hasProperty(RDF.type, FS.Workspace)).thenReturn(false); + + + var actual = sut.canReadMetadata(mockResource); + + // then + assertTrue(actual); + } + + @Test + public void testCanNotReadMetadataWhenUserDoesNotHaveRoleCanViewPublicMetadata() { + // given + var currentUser = new User(); + currentUser.setAdmin(false); + currentUser.setCanViewPublicMetadata(false); + when(userService.currentUser()).thenReturn(currentUser); + + var mockResource = mock(Resource.class); + when(davFactory.isFileSystemResource(mockResource)).thenReturn(false); + + when(mockResource.hasProperty(RDF.type, FS.Workspace)).thenReturn(false); + + + var actual = sut.canReadMetadata(mockResource); + + // then + assertFalse(actual); + } + + @Test + public void testAdminCanWriteMetadata() { + // given + var currentUser = new User(); + currentUser.setAdmin(true); + when(userService.currentUser()).thenReturn(currentUser); + var mockResource = mock(Resource.class); + + // when + var actual = sut.canWriteMetadata(mockResource); + + // then + assertTrue(actual); + } + + + @Test + public void testCanWriteMetadataOfFileSystemResourceWhichCanBeWritten() { + // given + var currentUser = new User(); + currentUser.setAdmin(false); + when(userService.currentUser()).thenReturn(currentUser); + + var mockResource = mock(Resource.class); + when(davFactory.isFileSystemResource(mockResource)).thenReturn(true); + when(davFactory.getAccess(mockResource)).thenReturn(Access.Write); + + // when + var actual = sut.canWriteMetadata(mockResource); + + // then + assertTrue(actual); + } + + @Test + public void testCannotWriteMetadataOfFileSystemResourceWhichCanNotBeWritten() { + // given + var currentUser = new User(); + currentUser.setAdmin(false); + when(userService.currentUser()).thenReturn(currentUser); + + var mockResource = mock(Resource.class); + when(davFactory.isFileSystemResource(mockResource)).thenReturn(true); + when(davFactory.getAccess(mockResource)).thenReturn(Access.None); + + // when + var actual = sut.canReadMetadata(mockResource); + + // then + assertFalse(actual); + } + + @Test + public void testCanWriteMetadataOfWorkspaceWhenCanManage() { + // given + var currentUser = new User(); + currentUser.setAdmin(false); + when(userService.currentUser()).thenReturn(currentUser); + + var mockResource = mock(Resource.class); + when(davFactory.isFileSystemResource(mockResource)).thenReturn(false); + + when(mockResource.hasProperty(RDF.type, FS.Workspace)).thenReturn(true); + var mockNode = mock(Node.class); + when(mockResource.asNode()).thenReturn(mockNode); + Workspace ws = new Workspace(); + ws.setCanManage(true); + when(workspaceService.getWorkspace(mockNode)).thenReturn(ws); + + + var actual = sut.canWriteMetadata(mockResource); + + // then + assertTrue(actual); + } + + + @Test + public void testCanNotWriteMetadataOfWorkspaceWhenCanNotManageCollaborate() { + // given + var currentUser = new User(); + currentUser.setAdmin(false); + when(userService.currentUser()).thenReturn(currentUser); + + var mockResource = mock(Resource.class); + when(davFactory.isFileSystemResource(mockResource)).thenReturn(false); + + when(mockResource.hasProperty(RDF.type, FS.Workspace)).thenReturn(true); + var mockNode = mock(Node.class); + when(mockResource.asNode()).thenReturn(mockNode); + Workspace ws = new Workspace(); + ws.setCanManage(false); + when(workspaceService.getWorkspace(mockNode)).thenReturn(ws); + + + var actual = sut.canWriteMetadata(mockResource); + + // then + assertFalse(actual); + } + + @Test + public void testCanWriteMetadataWhenUserHasRoleCanAddSharedMetadata() { + // given + var currentUser = new User(); + currentUser.setAdmin(false); + currentUser.setCanAddSharedMetadata(true); + when(userService.currentUser()).thenReturn(currentUser); + + var mockResource = mock(Resource.class); + when(davFactory.isFileSystemResource(mockResource)).thenReturn(false); + + when(mockResource.hasProperty(RDF.type, FS.Workspace)).thenReturn(false); + + + var actual = sut.canWriteMetadata(mockResource); + + // then + assertTrue(actual); + } + + @Test + public void testCanNotWriteMetadataWhenUserDoesNotHaveRoleCanAddSharedMetadata() { + // given + var currentUser = new User(); + currentUser.setAdmin(false); + currentUser.setCanAddSharedMetadata(false); + when(userService.currentUser()).thenReturn(currentUser); + + var mockResource = mock(Resource.class); + when(davFactory.isFileSystemResource(mockResource)).thenReturn(false); + + when(mockResource.hasProperty(RDF.type, FS.Workspace)).thenReturn(false); + + + var actual = sut.canReadMetadata(mockResource); + + // then + assertFalse(actual); + } +} diff --git a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/JdbcQueryServiceTest.java b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/JdbcQueryServiceTest.java index bf6327ec4..8461af601 100644 --- a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/JdbcQueryServiceTest.java +++ b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/JdbcQueryServiceTest.java @@ -88,7 +88,7 @@ public void before() throws SQLException, NotAuthorizedException, BadRequestExce Model model = ds.getDefaultModel(); var vocabulary = model.read("test-vocabulary.ttl"); - var viewService = new ViewService(ConfigLoader.CONFIG.search, config, ds, viewStoreClientFactory, permissions); + var viewService = new ViewService(ConfigLoader.CONFIG, config, ds, viewStoreClientFactory, permissions); maintenanceService = new MaintenanceService(userService, ds, viewStoreClientFactory, viewService); diff --git a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java index 71fab7570..4d395fc8a 100644 --- a/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java +++ b/projects/saturn/src/test/java/io/fairspace/saturn/services/views/ViewServiceTest.java @@ -6,6 +6,7 @@ import io.fairspace.saturn.rdf.transactions.SimpleTransactions; import io.fairspace.saturn.rdf.transactions.Transactions; import io.fairspace.saturn.rdf.transactions.TxnIndexDatasetGraph; +import io.fairspace.saturn.services.AccessDeniedException; import io.fairspace.saturn.services.metadata.MetadataPermissions; import io.fairspace.saturn.services.metadata.MetadataService; import io.fairspace.saturn.services.metadata.validation.ComposedValidator; @@ -45,11 +46,13 @@ import static io.fairspace.saturn.TestUtils.mockAuthentication; import static io.fairspace.saturn.TestUtils.setupRequestContext; import static io.fairspace.saturn.auth.RequestContext.getCurrentRequest; +import static io.fairspace.saturn.services.views.ViewService.USER_DOES_NOT_HAVE_PERMISSIONS_TO_READ_FACETS; import static org.apache.jena.query.DatasetFactory.wrap; import static org.mockito.ArgumentMatchers.any; import static org.mockito.Mockito.lenient; import static org.mockito.Mockito.never; import static org.mockito.Mockito.spy; +import static org.mockito.Mockito.times; import static org.mockito.Mockito.verify; import static org.mockito.Mockito.when; @@ -81,7 +84,7 @@ public void before() throws SQLException, BadRequestException, ConflictException loadTestData(ds); viewService = new ViewService( - ConfigLoader.CONFIG.search, + ConfigLoader.CONFIG, config, ds, viewStoreClientFactory, @@ -91,7 +94,7 @@ public void before() throws SQLException, BadRequestException, ConflictException @Test public void testFetchViewConfig() { when(permissions.canReadFacets()).thenReturn(true); - var facets = viewService.getCachedFacets(); + var facets = viewService.getFacets(); var dateFacets = facets.stream() .filter(facet -> facet.getType() == ViewsConfig.ColumnType.Date) .toList(); @@ -103,9 +106,19 @@ public void testFetchViewConfig() { Assert.assertEquals(1, boolFacets.size()); } + @Test + public void testNoAccessExceptionFetchingFacetsWhenUserHasNoPermissions() { + when(permissions.canReadFacets()).thenReturn(false); + + Assert.assertThrows( + USER_DOES_NOT_HAVE_PERMISSIONS_TO_READ_FACETS, + AccessDeniedException.class, + () -> viewService.getFacets()); + } + @Test public void testDisplayIndex_IsSet() { - var views = viewService.getCachedViews(); + var views = viewService.getViews(); var columns = views.get(1).getColumns().stream().toList(); var selectedColumn = columns.stream().filter(c -> c.getTitle().equals("Morphology")).collect(Collectors.toList()).get(0); Assert.assertEquals(Integer.valueOf(1), selectedColumn.getDisplayIndex()); @@ -113,7 +126,7 @@ public void testDisplayIndex_IsSet() { @Test public void testDisplayIndex_IsNotSet() { - var views = viewService.getCachedViews(); + var views = viewService.getViews(); var columns = views.get(1).getColumns().stream().toList(); var selectedColumn = columns.stream().filter(c -> c.getTitle().equals("Laterality")).collect(Collectors.toList()).get(0); Assert.assertEquals(Integer.valueOf(Integer.MAX_VALUE), selectedColumn.getDisplayIndex()); @@ -121,20 +134,27 @@ public void testDisplayIndex_IsNotSet() { @Test public void testFetchCachedFacets() { + // given var sut = spy(viewService); when(permissions.canReadFacets()).thenReturn(true); - var facets = viewService.getCachedFacets(); + // when + var facets = sut.getFacets(); + + // then Assert.assertEquals(facets.size(), 11); verify(sut, never()).fetchFacets(); } - @Test public void testFetchCachedViews() { + // given var sut = spy(viewService); - var views = viewService.getCachedViews(); + // when + var views = viewService.getViews(); + + // then Assert.assertEquals(views.size(), 4); verify(sut, never()).fetchViews(); } From d0bc331bb8e44b33ffb5613ff3b16f8b289c424f Mon Sep 17 00:00:00 2001 From: Anton Date: Wed, 31 Jan 2024 11:16:00 +0100 Subject: [PATCH 071/153] FAIRPC-29: fixed failing metadata request when no records found (#1478) --- .../saturn/services/views/ViewStoreReader.java | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java index 3461cb8ad..43ba4c1c3 100644 --- a/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java +++ b/projects/saturn/src/main/java/io/fairspace/saturn/services/views/ViewStoreReader.java @@ -412,12 +412,14 @@ private ViewRowCollection retrieveJoinTableRows( var rows = new ViewRowCollection(); - try (var query = getJoinQuery(view, joinView, joinedTable, joinTable, projectionColumns, ids); - var result = query.executeQuery()) { - while (result.next()) { - var id = result.getString("rowid"); - var row = buildJoinRows(joinView, projectionColumns, result); - rows.add(id, row); + if (!ids.isEmpty()) { + try (var query = getJoinQuery(view, joinView, joinedTable, joinTable, projectionColumns, ids); + var result = query.executeQuery()) { + while (result.next()) { + var id = result.getString("rowid"); + var row = buildJoinRows(joinView, projectionColumns, result); + rows.add(id, row); + } } } From e8b5c10c0db7516700597e556d48e87c63a48d49 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Mon, 5 Feb 2024 10:14:43 +0100 Subject: [PATCH 072/153] Label value from constants --- projects/mercury/src/layout/MainMenu.js | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/projects/mercury/src/layout/MainMenu.js b/projects/mercury/src/layout/MainMenu.js index c1bd816c5..c5dab7923 100644 --- a/projects/mercury/src/layout/MainMenu.js +++ b/projects/mercury/src/layout/MainMenu.js @@ -19,6 +19,7 @@ import ExternalStoragesContext from "../external-storage/ExternalStoragesContext import ExternalMetadataSourceContext from "../metadata/external-sources/ExternalMetadataSourceContext"; import {getExternalStoragePathPrefix} from "../external-storage/externalStorageUtils"; import {getExternalMetadataSourcePathPrefix} from "../metadata/external-sources/externalMetadataSourceUtils"; +import {METADATA_VIEW_MENU_LABEL} from "../constants"; const styles = { mainMenuButton: { @@ -86,7 +87,7 @@ const MainMenu = ({classes}) => { - + )} {currentUser.canViewPublicMetadata && externalMetadataSources && externalMetadataSources.map(source => ( From 6d53528dd1e00b0bf87e456dd27f4864fa1c0954 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Mon, 5 Feb 2024 14:56:50 +0100 Subject: [PATCH 073/153] Fix facets context for external sources. --- .../external-sources/ExternalMetadataSourceView.js | 2 +- .../src/metadata/views/MetadataViewFacetsContext.js | 10 ++++++---- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceView.js b/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceView.js index d0a614074..7411594da 100644 --- a/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceView.js +++ b/projects/mercury/src/metadata/external-sources/ExternalMetadataSourceView.js @@ -32,7 +32,7 @@ const ExternalMetadataSourceView = (props: ExternalMetadataSourceViewProperties) return ( - + { +export const MetadataViewFacetsProvider = ({children}) => { + const {path: metadataAPIPath} = useContext(MetadataAPIPathContext); const [data, setData] = useState({}); const [facetsLoading, setFacetsLoading] = useState(true); const [facetsError, setFacetsError] = useState(); @@ -16,7 +18,7 @@ export const MetadataViewFacetsProvider = ({children, metadataViewApi = Metadata const initialLoad = () => { if (!requested) { setRequested(true); - metadataViewApi.getFacets() + (new MetadataViewAPI(metadataAPIPath)).getFacets() .then(d => { setData(d); setFacetsError(undefined); From bd4c1dd6a8b2530a40c405565fd0f7b150e59684 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Tue, 6 Feb 2024 12:33:26 +0100 Subject: [PATCH 074/153] Improve external metadata view error handling. --- .../mercury/src/common/utils/httpUtils.js | 19 +++++++++++++++++++ .../external-storage/ExternalStoragePage.js | 2 +- .../src/metadata/views/MetadataViewAPI.js | 16 ++++++++++++---- 3 files changed, 32 insertions(+), 5 deletions(-) diff --git a/projects/mercury/src/common/utils/httpUtils.js b/projects/mercury/src/common/utils/httpUtils.js index 30c308117..71c35e32c 100644 --- a/projects/mercury/src/common/utils/httpUtils.js +++ b/projects/mercury/src/common/utils/httpUtils.js @@ -51,6 +51,25 @@ export function handleHttpError(defaultMessage) { }; } +export function handleRemoteSourceHttpError(defaultMessage) { + return (e: Error | AxiosError) => { + if (e && axios.isCancel(e)) { + return; + } + if (!e || !e.response) { + throw Error(defaultMessage); + } + const {response: {status, data}} = e; + if (status === 400 && data) { + if (typeof data === 'string') { + throw Error(data); + } + throw data; + } + throw Error(defaultMessage); + }; +} + /** * This function will extract the data property of the axios response if the content-type in the headers contains 'json' * otherwise it will throw an error diff --git a/projects/mercury/src/external-storage/ExternalStoragePage.js b/projects/mercury/src/external-storage/ExternalStoragePage.js index dac82c693..a55d47726 100644 --- a/projects/mercury/src/external-storage/ExternalStoragePage.js +++ b/projects/mercury/src/external-storage/ExternalStoragePage.js @@ -33,7 +33,7 @@ type ExternalStoragePageProperties = ContextualExternalStoragePageProperties & { } export const ExternalStoragePage = (props: ExternalStoragePageProperties) => { - const {externalStorages, match, location, history, classes = {}} = props; + const {externalStorages = [], match, location, history, classes = {}} = props; const [breadcrumbSegments, setBreadcrumbSegments] = useState([]); const [atLeastSingleRootFileExists, setAtLeastSingleRootFileExists] = useState(false); diff --git a/projects/mercury/src/metadata/views/MetadataViewAPI.js b/projects/mercury/src/metadata/views/MetadataViewAPI.js index 7706b7227..90cb4f849 100644 --- a/projects/mercury/src/metadata/views/MetadataViewAPI.js +++ b/projects/mercury/src/metadata/views/MetadataViewAPI.js @@ -1,6 +1,6 @@ /* eslint-disable no-unused-vars */ import axios, {CancelTokenSource} from "axios"; -import {extractJsonData, handleHttpError} from "../../common/utils/httpUtils"; +import {extractJsonData, handleHttpError, handleRemoteSourceHttpError} from "../../common/utils/httpUtils"; import type {AccessLevel} from "../../collections/CollectionAPI"; import FileAPI from "../../file/FileAPI"; @@ -83,18 +83,26 @@ const defaultRequestOptions = { export class MetadataViewAPI { constructor(remoteURLPrefix = "/api") { this.remoteURL = remoteURLPrefix + "/views"; + this.isExternalSource = (remoteURLPrefix !== "/api"); + } + + handleMetadataViewHttpError(message: string) { + if (this.isExternalSource) { + return handleRemoteSourceHttpError(message); + } + return handleHttpError("Failure when retrieving metadata views."); } getViews(): Promise { return axios.get(`${this.remoteURL}/`, defaultRequestOptions) .then(extractJsonData) - .catch(handleHttpError("Failure when retrieving metadata views.")); + .catch(this.handleMetadataViewHttpError("Failure when retrieving metadata views.")); } getFacets(): Promise { return axios.get(`${this.remoteURL}/facets`, defaultRequestOptions) .then(extractJsonData) - .catch(handleHttpError("Failure when retrieving metadata facets.")); + .catch(this.handleMetadataViewHttpError("Failure when retrieving metadata facets.")); } getViewData(cancelToken: CancelTokenSource, viewName: string, page, size, filters: MetadataViewFilter[] = []): Promise { @@ -109,7 +117,7 @@ export class MetadataViewAPI { return axios.post(`${this.remoteURL}/`, viewRequest, requestOptions) .then(extractJsonData) - .catch(handleHttpError("Error while fetching view data.")); + .catch(this.handleMetadataViewHttpError("Error while fetching view data.")); } getCount(cancelToken: CancelTokenSource, viewName: string, filters: MetadataViewFilter[] = []): Promise { From 715c4022bc89766cb496419a22e68c2208a8b987 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Wed, 7 Feb 2024 14:13:39 +0100 Subject: [PATCH 075/153] Use withCredentials for metadata API requests. --- projects/mercury/src/metadata/views/MetadataViewAPI.js | 1 + 1 file changed, 1 insertion(+) diff --git a/projects/mercury/src/metadata/views/MetadataViewAPI.js b/projects/mercury/src/metadata/views/MetadataViewAPI.js index 8a0043d38..bd03fd217 100644 --- a/projects/mercury/src/metadata/views/MetadataViewAPI.js +++ b/projects/mercury/src/metadata/views/MetadataViewAPI.js @@ -78,6 +78,7 @@ type MetadataViewDataRequest = MetadataViewCountRequest & {| |}; const defaultRequestOptions = { + withCredentials: true, headers: {Accept: 'application/json'} }; From 62adc839dc860b02449c31463b2a9b385e1b7a1c Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Thu, 8 Feb 2024 15:17:10 +0100 Subject: [PATCH 076/153] Update session and cors config in Pluto. --- .../java/nl/fairspace/pluto/config/CorsConfiguration.java | 6 ++++-- .../nl/fairspace/pluto/config/SessionConfiguration.java | 1 + 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/projects/pluto/src/main/java/nl/fairspace/pluto/config/CorsConfiguration.java b/projects/pluto/src/main/java/nl/fairspace/pluto/config/CorsConfiguration.java index 430b5264d..ff369cf0c 100644 --- a/projects/pluto/src/main/java/nl/fairspace/pluto/config/CorsConfiguration.java +++ b/projects/pluto/src/main/java/nl/fairspace/pluto/config/CorsConfiguration.java @@ -6,6 +6,8 @@ import org.springframework.web.cors.reactive.CorsWebFilter; import org.springframework.web.cors.reactive.UrlBasedCorsConfigurationSource; +import java.util.List; + @Configuration public class CorsConfiguration extends org.springframework.web.cors.CorsConfiguration { @@ -21,8 +23,8 @@ CorsWebFilter corsWebFilter() { corsConfiguration.setAllowCredentials(true); corsConfiguration.setAllowedOrigins(plutoConfig.getDomains()); - corsConfiguration.addAllowedMethod("*"); - corsConfiguration.addAllowedHeader("*"); + corsConfiguration.setAllowedMethods(List.of("*")); + corsConfiguration.setAllowedHeaders(List.of("*")); UrlBasedCorsConfigurationSource source = new UrlBasedCorsConfigurationSource(); source.registerCorsConfiguration("/**", corsConfiguration); diff --git a/projects/pluto/src/main/java/nl/fairspace/pluto/config/SessionConfiguration.java b/projects/pluto/src/main/java/nl/fairspace/pluto/config/SessionConfiguration.java index 341242ad3..9fe44f788 100644 --- a/projects/pluto/src/main/java/nl/fairspace/pluto/config/SessionConfiguration.java +++ b/projects/pluto/src/main/java/nl/fairspace/pluto/config/SessionConfiguration.java @@ -27,6 +27,7 @@ public CookieSerializer cookieSerializer() { DefaultCookieSerializer serializer = new DefaultCookieSerializer(); serializer.setCookieName(plutoConfig.getSessionCookieName()); serializer.setCookiePath("/"); + serializer.setSameSite("None"); serializer.setDomainNamePattern("^([a-zA-Z0-9\\.-]+)$"); return serializer; From 354df4fcd9590e2225fa699495ff1c77e0d211f7 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Thu, 8 Feb 2024 17:15:56 +0100 Subject: [PATCH 077/153] Include session cookie by default in all requests. --- projects/mercury/src/index.js | 1 + 1 file changed, 1 insertion(+) diff --git a/projects/mercury/src/index.js b/projects/mercury/src/index.js index 93329ff68..38776404b 100644 --- a/projects/mercury/src/index.js +++ b/projects/mercury/src/index.js @@ -8,6 +8,7 @@ import App from './App'; import registerServiceWorker from './registerServiceWorker'; axios.defaults.headers.common['X-Requested-With'] = "XMLHttpRequest"; +axios.defaults.withCredentials = true; const container = document.getElementById('root'); const root = createRoot(container); From 13c37a5eeb0c9b07b89c2833cc21d90e4c5c0804 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Fri, 9 Feb 2024 08:22:11 +0100 Subject: [PATCH 078/153] Revert default withCredentials axios flag. --- projects/mercury/src/index.js | 1 - 1 file changed, 1 deletion(-) diff --git a/projects/mercury/src/index.js b/projects/mercury/src/index.js index 38776404b..93329ff68 100644 --- a/projects/mercury/src/index.js +++ b/projects/mercury/src/index.js @@ -8,7 +8,6 @@ import App from './App'; import registerServiceWorker from './registerServiceWorker'; axios.defaults.headers.common['X-Requested-With'] = "XMLHttpRequest"; -axios.defaults.withCredentials = true; const container = document.getElementById('root'); const root = createRoot(container); From f77579a4b530b0d0227fb2cff4ad64bf126f0701 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Fri, 9 Feb 2024 15:55:44 +0100 Subject: [PATCH 079/153] Update session configuration. --- .../java/nl/fairspace/pluto/config/SessionConfiguration.java | 1 + 1 file changed, 1 insertion(+) diff --git a/projects/pluto/src/main/java/nl/fairspace/pluto/config/SessionConfiguration.java b/projects/pluto/src/main/java/nl/fairspace/pluto/config/SessionConfiguration.java index 9fe44f788..c527da202 100644 --- a/projects/pluto/src/main/java/nl/fairspace/pluto/config/SessionConfiguration.java +++ b/projects/pluto/src/main/java/nl/fairspace/pluto/config/SessionConfiguration.java @@ -27,6 +27,7 @@ public CookieSerializer cookieSerializer() { DefaultCookieSerializer serializer = new DefaultCookieSerializer(); serializer.setCookieName(plutoConfig.getSessionCookieName()); serializer.setCookiePath("/"); + serializer.setUseSecureCookie(true); serializer.setSameSite("None"); serializer.setDomainNamePattern("^([a-zA-Z0-9\\.-]+)$"); From ecda27a77d39e1ded04dbb06f8954eba3f2cc106 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Mon, 12 Feb 2024 10:58:42 +0100 Subject: [PATCH 080/153] Dashboard first version --- .../mercury/src/dashboard/DashboardPage.js | 77 +++++++++++++++++++ .../src/dashboard/DashboardPage.styles.js | 16 ++++ projects/mercury/src/dashboard/DomainInfo.js | 24 ++++++ .../src/dashboard/DomainInfo.styles.js | 22 ++++++ projects/mercury/src/layout/MainMenu.js | 14 +++- .../mercury/src/routes/WorkspaceRoutes.js | 11 ++- 6 files changed, 162 insertions(+), 2 deletions(-) create mode 100644 projects/mercury/src/dashboard/DashboardPage.js create mode 100644 projects/mercury/src/dashboard/DashboardPage.styles.js create mode 100644 projects/mercury/src/dashboard/DomainInfo.js create mode 100644 projects/mercury/src/dashboard/DomainInfo.styles.js diff --git a/projects/mercury/src/dashboard/DashboardPage.js b/projects/mercury/src/dashboard/DashboardPage.js new file mode 100644 index 000000000..4ab816b0b --- /dev/null +++ b/projects/mercury/src/dashboard/DashboardPage.js @@ -0,0 +1,77 @@ +/* eslint-disable */ +import React, {useContext} from "react"; + +import withStyles from "@mui/styles/withStyles"; +import {APPLICATION_NAME, METADATA_VIEW_MENU_LABEL} from "../constants"; +import BreadCrumbs from "../common/components/BreadCrumbs"; +import styles from "./DashboardPage.styles"; +import MetadataViewContext from "../metadata/views/MetadataViewContext"; +import ExternalMetadataSourceContext from "../metadata/external-sources/ExternalMetadataSourceContext"; +import UserContext from "../users/UserContext"; +import {Grid, Link, Typography} from "@mui/material"; +import DomainInfo from "./DomainInfo"; + +const DashboardPage = (props) => { + const {currentUser, classes} = props; + const {views} = useContext(MetadataViewContext); + const {externalMetadataSources} = useContext(ExternalMetadataSourceContext); + const canViewMetadata = currentUser && currentUser.canViewPublicMetadata && views && views.length > 0; + + return ( + + {} +
+ + + + {APPLICATION_NAME} + + + + + research data management + + + + + + {APPLICATION_NAME} contains your research metadata. Click on one of the domains and start exploring. + + + For more details on how to use Fairspace, please refer to the{" "} + + user manual + + , for example on how to query the API. + + + + + {canViewMetadata && ( + ) + } + {canViewMetadata && externalMetadataSources.map((source) => ( + + ))} + + + + +
+ + ); +}; + +const ContextualDashboardPage = (props) => { + const {currentUser} = useContext(UserContext); + + return ; +}; + +export default withStyles(styles)(ContextualDashboardPage); diff --git a/projects/mercury/src/dashboard/DashboardPage.styles.js b/projects/mercury/src/dashboard/DashboardPage.styles.js new file mode 100644 index 000000000..00c5ddeb6 --- /dev/null +++ b/projects/mercury/src/dashboard/DashboardPage.styles.js @@ -0,0 +1,16 @@ +import * as consts from "../constants"; + +const styles = (theme) => ({ + mainPage: { + width: consts.MAIN_CONTENT_WIDTH, + maxHeight: consts.MAIN_CONTENT_MAX_HEIGHT, + padding: 20, + }, + header: { + // bottom border black + borderBottom: '2px solid ' + theme.palette.primary.main, + marginBottom: 50, + } +}); + +export default styles; diff --git a/projects/mercury/src/dashboard/DomainInfo.js b/projects/mercury/src/dashboard/DomainInfo.js new file mode 100644 index 000000000..952ce2073 --- /dev/null +++ b/projects/mercury/src/dashboard/DomainInfo.js @@ -0,0 +1,24 @@ +import React from 'react'; +// import ShortcutIcon from '@mui/icons-material/Shortcut'; +import HubIcon from '@mui/icons-material/Hub'; +import {Link, Paper, Typography} from "@mui/material"; +import withStyles from "@mui/styles/withStyles"; +import styles from "./DomainInfo.styles"; + +const DomainInfo = (props) => { + const {domainName, domainLink, classes} = props; + return ( +
+ + + + {domainName} + + + + +
+ ); +}; + +export default withStyles(styles)(DomainInfo); diff --git a/projects/mercury/src/dashboard/DomainInfo.styles.js b/projects/mercury/src/dashboard/DomainInfo.styles.js new file mode 100644 index 000000000..7b9702774 --- /dev/null +++ b/projects/mercury/src/dashboard/DomainInfo.styles.js @@ -0,0 +1,22 @@ +const styles = (theme) => ({ + paper: { + width: '200px', + height: '100px', + borderStyle: 'solid', + borderColor: theme.palette.primary.light, + borderWidth: 2, + textAlign: 'center' + }, + outerMargin: { + margin: 10 + }, + icon: { + marginLeft: 10, + marginTop: 10 + }, + domainText: { + color: theme.palette.grey[700], + } +}); + +export default styles; diff --git a/projects/mercury/src/layout/MainMenu.js b/projects/mercury/src/layout/MainMenu.js index c5dab7923..196eaf81e 100644 --- a/projects/mercury/src/layout/MainMenu.js +++ b/projects/mercury/src/layout/MainMenu.js @@ -11,6 +11,7 @@ import { VerifiedUser, Widgets } from "@mui/icons-material"; +import HomeIcon from '@mui/icons-material/Home'; import ServicesContext from "../common/contexts/ServicesContext"; import UserContext from "../users/UserContext"; import {isAdmin} from "../users/userUtils"; @@ -19,7 +20,7 @@ import ExternalStoragesContext from "../external-storage/ExternalStoragesContext import ExternalMetadataSourceContext from "../metadata/external-sources/ExternalMetadataSourceContext"; import {getExternalStoragePathPrefix} from "../external-storage/externalStorageUtils"; import {getExternalMetadataSourcePathPrefix} from "../metadata/external-sources/externalMetadataSourceUtils"; -import {METADATA_VIEW_MENU_LABEL} from "../constants"; +import {APPLICATION_NAME, METADATA_VIEW_MENU_LABEL} from "../constants"; const styles = { mainMenuButton: { @@ -39,6 +40,17 @@ const MainMenu = ({classes}) => { return ( <> + + + + + + { + ( + + )} + /> + { render={() => (isAdmin(currentUser) && ())} /> - + ); }; From 9613403726bf0dc17584d982c34019b84dbe44bb Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Mon, 12 Feb 2024 12:55:40 +0100 Subject: [PATCH 081/153] Textual change on dashboard --- projects/mercury/src/dashboard/DashboardPage.js | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/projects/mercury/src/dashboard/DashboardPage.js b/projects/mercury/src/dashboard/DashboardPage.js index 4ab816b0b..aceb18227 100644 --- a/projects/mercury/src/dashboard/DashboardPage.js +++ b/projects/mercury/src/dashboard/DashboardPage.js @@ -38,11 +38,10 @@ const DashboardPage = (props) => { {APPLICATION_NAME} contains your research metadata. Click on one of the domains and start exploring. - For more details on how to use Fairspace, please refer to the{" "} + For more details on how to use Fairspace, e.g. how to query the API, please refer the {" "} user manual - - , for example on how to query the API. + . From be51fe6dedad8566635cff9e54db1a2b9955ea06 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Mon, 12 Feb 2024 13:04:05 +0100 Subject: [PATCH 082/153] Fixed eslint errors --- .../mercury/src/dashboard/DashboardPage.js | 47 +++++++++---------- 1 file changed, 23 insertions(+), 24 deletions(-) diff --git a/projects/mercury/src/dashboard/DashboardPage.js b/projects/mercury/src/dashboard/DashboardPage.js index aceb18227..55f6e4f02 100644 --- a/projects/mercury/src/dashboard/DashboardPage.js +++ b/projects/mercury/src/dashboard/DashboardPage.js @@ -1,15 +1,14 @@ -/* eslint-disable */ import React, {useContext} from "react"; import withStyles from "@mui/styles/withStyles"; -import {APPLICATION_NAME, METADATA_VIEW_MENU_LABEL} from "../constants"; +import {Grid, Link, Typography} from "@mui/material"; import BreadCrumbs from "../common/components/BreadCrumbs"; import styles from "./DashboardPage.styles"; import MetadataViewContext from "../metadata/views/MetadataViewContext"; import ExternalMetadataSourceContext from "../metadata/external-sources/ExternalMetadataSourceContext"; import UserContext from "../users/UserContext"; -import {Grid, Link, Typography} from "@mui/material"; import DomainInfo from "./DomainInfo"; +import {APPLICATION_NAME, METADATA_VIEW_MENU_LABEL} from "../constants"; const DashboardPage = (props) => { const {currentUser, classes} = props; @@ -19,48 +18,48 @@ const DashboardPage = (props) => { return ( - {} +
- + {APPLICATION_NAME} - + research data management - - - {APPLICATION_NAME} contains your research metadata. Click on one of the domains and start exploring. - - - For more details on how to use Fairspace, e.g. how to query the API, please refer the {" "} + + + {APPLICATION_NAME} contains your research metadata. Click on one of the domains and start exploring. + + + For more details on how to use Fairspace, e.g. how to query the API, please refer the {" "} user manual . - - - - - {canViewMetadata && ( - ) - } - {canViewMetadata && externalMetadataSources.map((source) => ( + + + + + {canViewMetadata && ( + + )} + {canViewMetadata && externalMetadataSources.map((source) => ( ))} + -
From 87fd811cfbb9c43d586e9878a4d7b66cc8f5bb22 Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Mon, 12 Feb 2024 13:05:39 +0100 Subject: [PATCH 083/153] Removed comment --- projects/mercury/src/dashboard/DashboardPage.styles.js | 1 - 1 file changed, 1 deletion(-) diff --git a/projects/mercury/src/dashboard/DashboardPage.styles.js b/projects/mercury/src/dashboard/DashboardPage.styles.js index 00c5ddeb6..ff3db50fa 100644 --- a/projects/mercury/src/dashboard/DashboardPage.styles.js +++ b/projects/mercury/src/dashboard/DashboardPage.styles.js @@ -7,7 +7,6 @@ const styles = (theme) => ({ padding: 20, }, header: { - // bottom border black borderBottom: '2px solid ' + theme.palette.primary.main, marginBottom: 50, } From 35cbe870889d6dbdb317ce96276ed63652f07f4e Mon Sep 17 00:00:00 2001 From: Frank <29271979+FrankyHollywood@users.noreply.github.com> Date: Tue, 13 Feb 2024 05:49:49 +0100 Subject: [PATCH 084/153] Added icon and changed dashboard style 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+ @@ -31,11 +31,14 @@ const DashboardPage = (props) => { research data management - - + + {APPLICATION_NAME} contains your research metadata. Click on one of the domains and start exploring. + + + For more details on how to use Fairspace, e.g. how to query the API, please refer the {" "} @@ -43,25 +46,23 @@ const DashboardPage = (props) => { . - - - {canViewMetadata && ( - - )} - {canViewMetadata && externalMetadataSources.map((source) => ( - - ))} - - + + + {canViewMetadata && ( + + )} + {canViewMetadata && externalMetadataSources.map((source) => ( + + ))} -
+ ); }; diff --git a/projects/mercury/src/dashboard/DashboardPage.styles.js b/projects/mercury/src/dashboard/DashboardPage.styles.js index ff3db50fa..a74eac44f 100644 --- a/projects/mercury/src/dashboard/DashboardPage.styles.js +++ b/projects/mercury/src/dashboard/DashboardPage.styles.js @@ -3,13 +3,21 @@ import * as consts from "../constants"; const styles = (theme) => ({ mainPage: { width: consts.MAIN_CONTENT_WIDTH, + maxWidth: '700px', maxHeight: consts.MAIN_CONTENT_MAX_HEIGHT, padding: 20, + marginTop: 20 }, header: { borderBottom: '2px solid ' + theme.palette.primary.main, marginBottom: 50, - } + }, + centreImage: { + maxHeight: '200px' + }, + textRow: { + minHeight: '250px' + }, }); export default styles; diff --git a/projects/mercury/src/layout/Layout.js b/projects/mercury/src/layout/Layout.js index f8d16cb04..41d8e02d1 100644 --- a/projects/mercury/src/layout/Layout.js +++ b/projects/mercury/src/layout/Layout.js @@ -92,7 +92,7 @@ const Layout = ({
{renderMain()}
-