Merge pull request #41 from akaene/main

Records import

src/main/java/cz/cvut/kbss/study/dto/RecordImportResult.java

@@ -0,0 +1,76 @@
+package cz.cvut.kbss.study.dto;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Represents the result of importing records to this instance.
+ */
+public class RecordImportResult {
+
+    /**
+     * Total number of processed records.
+     */
+    private int totalCount;
+
+    /**
+     * Number of successfully imported records.
+     */
+    private int importedCount;
+
+    /**
+     * Errors that occurred during import.
+     */
+    private List<String> errors;
+
+    public RecordImportResult() {
+    }
+
+    public RecordImportResult(int totalCount) {
+        this.totalCount = totalCount;
+    }
+
+    public int getTotalCount() {
+        return totalCount;
+    }
+
+    public void setTotalCount(int totalCount) {
+        this.totalCount = totalCount;
+    }
+
+    public int getImportedCount() {
+        return importedCount;
+    }
+
+    public void setImportedCount(int importedCount) {
+        this.importedCount = importedCount;
+    }
+
+    public void incrementImportedCount() {
+        this.importedCount++;
+    }
+
+    public List<String> getErrors() {
+        return errors;
+    }
+
+    public void setErrors(List<String> errors) {
+        this.errors = errors;
+    }
+
+    public void addError(String error) {
+        if (this.errors == null) {
+            this.errors = new ArrayList<>();
+        }
+        errors.add(error);
+    }
+
+    @Override
+    public String toString() {
+        return "RecordImportResult{" +
+                "totalCount=" + totalCount +
+                ", importedCount=" + importedCount +
+                (errors != null ? ", errors=" + errors : "") +
+                '}';
+    }
+}

src/main/java/cz/cvut/kbss/study/exception/RecordAuthorNotFoundException.java

@@ -0,0 +1,11 @@
+package cz.cvut.kbss.study.exception;
+
+/**
+ * Indicates that the application is attempting to import a record with a nonexistent author.
+ */
+public class RecordAuthorNotFoundException extends RecordManagerException {
+
+    public RecordAuthorNotFoundException(String message) {
+        super(message);
+    }
+}

src/main/java/cz/cvut/kbss/study/model/RecordPhase.java

@@ -23,4 +23,20 @@ public enum RecordPhase {
     public String getIri() {
         return iri;
     }
+
+    /**
+     * Returns {@link RecordPhase} with the specified IRI.
+     *
+     * @param iri record phase identifier
+     * @return matching {@code RecordPhase}
+     * @throws IllegalArgumentException When no matching phase is found
+     */
+    public static RecordPhase fromString(String iri) {
+        for (RecordPhase p : values()) {
+            if (p.getIri().equals(iri)) {
+                return p;
+            }
+        }
+        throw new IllegalArgumentException("Unknown record phase identifier '" + iri + "'.");
+    }
 }

src/main/java/cz/cvut/kbss/study/model/User.java

@@ -1,7 +1,13 @@
 package cz.cvut.kbss.study.model;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
-import cz.cvut.kbss.jopa.model.annotations.*;
+import cz.cvut.kbss.jopa.model.annotations.FetchType;
+import cz.cvut.kbss.jopa.model.annotations.Id;
+import cz.cvut.kbss.jopa.model.annotations.OWLClass;
+import cz.cvut.kbss.jopa.model.annotations.OWLDataProperty;
+import cz.cvut.kbss.jopa.model.annotations.OWLObjectProperty;
+import cz.cvut.kbss.jopa.model.annotations.ParticipationConstraints;
+import cz.cvut.kbss.jopa.model.annotations.Types;
 import cz.cvut.kbss.study.model.util.HasDerivableUri;
 import cz.cvut.kbss.study.util.Constants;
 import cz.cvut.kbss.study.util.IdentificationUtils;
@@ -148,6 +154,18 @@ public void addType(String type) {
         getTypes().add(type);
     }
 
+    /**
+     * Returns true if this user is an admin.
+     * <p>
+     * That is, it has an admin type.
+     *
+     * @return {@code true} if this is admin, {@code false} otherwise
+     */
+    public boolean isAdmin() {
+        assert types != null;
+        return getTypes().contains(Vocabulary.s_c_administrator);
+    }
+
     public String getToken() {
         return token;
     }

src/main/java/cz/cvut/kbss/study/persistence/dao/PatientRecordDao.java

@@ -63,8 +63,12 @@ public PatientRecord findByKey(String key) {
     @Override
     public void persist(PatientRecord entity) {
         Objects.requireNonNull(entity);
-        entity.setKey(IdentificationUtils.generateKey());
-        entity.setUri(generateRecordUriFromKey(entity.getKey()));
+        if (entity.getKey() == null) {
+            entity.setKey(IdentificationUtils.generateKey());
+        }
+        if (entity.getUri() == null) {
+            entity.setUri(generateRecordUriFromKey(entity.getKey()));
+        }
         try {
             final Descriptor descriptor = getDescriptor(entity.getUri());
             em.persist(entity, descriptor);

src/main/java/cz/cvut/kbss/study/rest/PatientRecordController.java

@@ -1,9 +1,11 @@
 package cz.cvut.kbss.study.rest;
 
 import cz.cvut.kbss.study.dto.PatientRecordDto;
+import cz.cvut.kbss.study.dto.RecordImportResult;
 import cz.cvut.kbss.study.exception.NotFoundException;
 import cz.cvut.kbss.study.model.Institution;
 import cz.cvut.kbss.study.model.PatientRecord;
+import cz.cvut.kbss.study.model.RecordPhase;
 import cz.cvut.kbss.study.rest.exception.BadRequestException;
 import cz.cvut.kbss.study.rest.util.RecordFilterMapper;
 import cz.cvut.kbss.study.rest.util.RestUtils;
@@ -94,6 +96,20 @@ public ResponseEntity<Void> createRecord(@RequestBody PatientRecord record) {
         return new ResponseEntity<>(headers, HttpStatus.CREATED);
     }
 
+    @PostMapping(value = "/import", consumes = MediaType.APPLICATION_JSON_VALUE)
+    public RecordImportResult importRecords(@RequestBody List<PatientRecord> records,
+                                            @RequestParam(name = "phase", required = false) String phaseIri) {
+        final RecordImportResult importResult;
+        if (phaseIri != null) {
+            final RecordPhase targetPhase = RecordPhase.fromString(phaseIri);
+            importResult = recordService.importRecords(records, targetPhase);
+        } else {
+            importResult = recordService.importRecords(records);
+        }
+        LOG.trace("Records imported with result: {}.", importResult);
+        return importResult;
+    }
+
     @PutMapping(value = "/{key}", consumes = MediaType.APPLICATION_JSON_VALUE)
     @ResponseStatus(HttpStatus.NO_CONTENT)
     public void updateRecord(@PathVariable("key") String key, @RequestBody PatientRecord record) {

src/main/java/cz/cvut/kbss/study/rest/handler/RestExceptionHandler.java

@@ -1,6 +1,11 @@
 package cz.cvut.kbss.study.rest.handler;
 
-import cz.cvut.kbss.study.exception.*;
+import cz.cvut.kbss.study.exception.EntityExistsException;
+import cz.cvut.kbss.study.exception.NotFoundException;
+import cz.cvut.kbss.study.exception.PersistenceException;
+import cz.cvut.kbss.study.exception.RecordAuthorNotFoundException;
+import cz.cvut.kbss.study.exception.ValidationException;
+import cz.cvut.kbss.study.exception.WebServiceIntegrationException;
 import jakarta.servlet.http.HttpServletRequest;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -83,13 +88,14 @@ public ResponseEntity<ErrorInfo> persistenceException(HttpServletRequest request
         return new ResponseEntity<>(errorInfo(request, e.getCause()), HttpStatus.INTERNAL_SERVER_ERROR);
     }
 
+    @ExceptionHandler(RecordAuthorNotFoundException.class)
+    public ResponseEntity<ErrorInfo> recordAuthorNotFoundException(HttpServletRequest request,
+                                                                   RecordAuthorNotFoundException e) {
+        logException(request, e);
+        return new ResponseEntity<>(errorInfo(request, e), HttpStatus.CONFLICT);
+    }
+
     void logException(HttpServletRequest request, RuntimeException e) {
-        LOG.debug(
-            String.format(
-                "Request to '%s' failed due to error: %s",
-                request.getRequestURI(),
-                e.getMessage()
-            )
-        );
+        LOG.debug("Request to '{}' failed due to error: {}", request.getRequestURI(), e.getMessage());
     }
 }

src/main/java/cz/cvut/kbss/study/service/PatientRecordService.java

@@ -1,8 +1,10 @@
 package cz.cvut.kbss.study.service;
 
 import cz.cvut.kbss.study.dto.PatientRecordDto;
+import cz.cvut.kbss.study.dto.RecordImportResult;
 import cz.cvut.kbss.study.model.Institution;
 import cz.cvut.kbss.study.model.PatientRecord;
+import cz.cvut.kbss.study.model.RecordPhase;
 import cz.cvut.kbss.study.model.User;
 import cz.cvut.kbss.study.persistence.dao.util.RecordFilterParams;
 
@@ -51,4 +53,42 @@ public interface PatientRecordService extends BaseService<PatientRecord> {
      * @see #findAllRecords()
      */
     List<PatientRecord> findAllFull(RecordFilterParams filterParams);
+
+    /**
+     * Imports the specified records.
+     * <p>
+     * Only records whose identifiers do not already exist in the repository are imported. Existing records are skipped
+     * and the returned object contains a note that the record already exists.
+     * <p>
+     * This method, in contrast to {@link #importRecords(List, RecordPhase)}, preserves the phase of the imported
+     * records.
+     * <p>
+     * If the current user is an admin, the import procedure retains provenance data of the record. Otherwise, the
+     * current user is set as the record's author. Also, if the current user is not an admin, the phase of all
+     * the imported records is set to {@link RecordPhase#open}, for admin, the phase of the records is retained.
+     *
+     * @param records Records to import
+     * @return Instance representing the import result
+     * @throws cz.cvut.kbss.study.exception.RecordAuthorNotFoundException Thrown when importing a record whose author
+     *                                                                    does not exist in this application instance's
+     *                                                                    repository
+     */
+    RecordImportResult importRecords(List<PatientRecord> records);
+
+    /**
+     * Imports the specified records and sets them all to the specified phase.
+     * <p>
+     * Only records whose identifiers do not already exist in the repository are imported. Existing records are skipped
+     * and the returned object contains a note that the record already exists.
+     * <p>
+     * If the current user is an admin, the import procedure retains provenance data of the record. Otherwise, the
+     * current user is set as the record's author.
+     *
+     * @param records Records to import
+     * @return Instance representing the import result
+     * @throws cz.cvut.kbss.study.exception.RecordAuthorNotFoundException Thrown when importing a record whose author
+     *                                                                    does not exist in this application instance's
+     *                                                                    repository
+     */
+    RecordImportResult importRecords(List<PatientRecord> records, RecordPhase targetPhase);
 }

src/main/java/cz/cvut/kbss/study/service/repository/RepositoryPatientRecordService.java

@@ -1,33 +1,46 @@
 package cz.cvut.kbss.study.service.repository;
 
 import cz.cvut.kbss.study.dto.PatientRecordDto;
+import cz.cvut.kbss.study.dto.RecordImportResult;
+import cz.cvut.kbss.study.exception.RecordAuthorNotFoundException;
 import cz.cvut.kbss.study.model.Institution;
 import cz.cvut.kbss.study.model.PatientRecord;
+import cz.cvut.kbss.study.model.RecordPhase;
 import cz.cvut.kbss.study.model.User;
 import cz.cvut.kbss.study.persistence.dao.OwlKeySupportingDao;
 import cz.cvut.kbss.study.persistence.dao.PatientRecordDao;
 import cz.cvut.kbss.study.persistence.dao.util.RecordFilterParams;
 import cz.cvut.kbss.study.service.PatientRecordService;
+import cz.cvut.kbss.study.service.UserService;
 import cz.cvut.kbss.study.service.security.SecurityUtils;
-import cz.cvut.kbss.study.util.IdentificationUtils;
+import cz.cvut.kbss.study.util.Utils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
 import java.util.Date;
 import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
 
 @Service
 public class RepositoryPatientRecordService extends KeySupportingRepositoryService<PatientRecord>
         implements PatientRecordService {
 
+    private static final Logger LOG = LoggerFactory.getLogger(RepositoryPatientRecordService.class);
+
     private final PatientRecordDao recordDao;
 
     private final SecurityUtils securityUtils;
 
-    public RepositoryPatientRecordService(PatientRecordDao recordDao,
-                                          SecurityUtils securityUtils) {
+    private final UserService userService;
+
+    public RepositoryPatientRecordService(PatientRecordDao recordDao, SecurityUtils securityUtils,
+                                          UserService userService) {
         this.recordDao = recordDao;
         this.securityUtils = securityUtils;
+        this.userService = userService;
     }
 
     @Override
@@ -65,7 +78,6 @@ protected void prePersist(PatientRecord instance) {
         instance.setAuthor(author);
         instance.setDateCreated(new Date());
         instance.setInstitution(author.getInstitution());
-        instance.setKey(IdentificationUtils.generateKey());
         recordDao.requireUniqueNonEmptyLocalName(instance);
     }
 
@@ -75,4 +87,53 @@ protected void preUpdate(PatientRecord instance) {
         instance.setLastModified(new Date());
         recordDao.requireUniqueNonEmptyLocalName(instance);
     }
+
+    @Transactional
+    @Override
+    public RecordImportResult importRecords(List<PatientRecord> records) {
+        Objects.requireNonNull(records);
+        LOG.debug("Importing records.");
+        return importRecordsImpl(records, Optional.empty());
+    }
+
+    private RecordImportResult importRecordsImpl(List<PatientRecord> records, Optional<RecordPhase> targetPhase) {
+        final User author = securityUtils.getCurrentUser();
+        final Date created = new Date();
+        final RecordImportResult result = new RecordImportResult(records.size());
+        records.forEach(r -> {
+            setImportedRecordProvenance(author, created, targetPhase, r);
+            if (recordDao.exists(r.getUri())) {
+                LOG.warn("Record {} already exists. Skipping it.", Utils.uriToString(r.getUri()));
+                result.addError("Record " + Utils.uriToString(r.getUri()) + " already exists.");
+            } else {
+                recordDao.persist(r);
+                result.incrementImportedCount();
+            }
+        });
+        return result;
+    }
+
+    private void setImportedRecordProvenance(User currentUser, Date now, Optional<RecordPhase> targetPhase,
+                                             PatientRecord record) {
+        if (!currentUser.isAdmin()) {
+            record.setAuthor(currentUser);
+            record.setInstitution(currentUser.getInstitution());
+            record.setDateCreated(now);
+            targetPhase.ifPresentOrElse(record::setPhase, () -> record.setPhase(RecordPhase.open));
+        } else {
+            targetPhase.ifPresent(record::setPhase);
+            if (!userService.exists(record.getAuthor().getUri())) {
+                throw new RecordAuthorNotFoundException("Author of record " + record + "not found during import.");
+            }
+        }
+    }
+
+
+    @Transactional
+    @Override
+    public RecordImportResult importRecords(List<PatientRecord> records, RecordPhase targetPhase) {
+        Objects.requireNonNull(records);
+        LOG.debug("Importing records to target phase '{}'.", targetPhase);
+        return importRecordsImpl(records, Optional.ofNullable(targetPhase));
+    }
 }