Release 2.1.0 (PR #302)

Merge pull request #302 from virtual-imaging-platform/develop
virtual-imaging-platform · Sep 7, 2021 · 33cd0a9 · 33cd0a9
2 parents 6016063 + 76cd68c
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diff --git a/README.md b/README.md
@@ -24,8 +24,55 @@ You may name your branch anything except master, develop, release-*, or hotfix-*
 * Push your commits to Github (your fork).
 * Make a pull request to merge feature branch (in your fork) to development branch (in the base repository).
 
-# Installation instructions
+# Production installation instructions
+
+You can follow the instruction [here](https://github.com/virtual-imaging-platform/Complementary-tools/blob/develop/README.md)
+
+You can contact us at [[email protected]]([email protected]) for precisions.
+
+# Local test installation instructions
+
+It is possible to launch a local vip instance in a tomcat on a linux machine.
+This is only useful for testing purposes as most of the features are simulated and many are still to be implemented and do not work yet.
+Here are the instructions to configure a local vip instance :
+- create a empty folder that will contain all the configuration files and simulated data. `/path/to/vip/local/folder` will be its path used in the next instructions
+- unzip the `local-config.zip` archive available in `vip-local/src/main/resources` in `/path/to/vip/local/folder`. This should contain 3 `.conf` files
+- create a `$HOME/.vip` directory and a `$HOME/.vip/local-config-folder.properties` file
+- put `vipConfigFolder = /path/to/vip/local/folder` in the `$HOME/.vip/local-config-folder.properties` file
+
+Then, install vip in your local tomcat :
+
+1. Build the vip-local war with `mvn clean package` at the root of the `VIP-portal` project.
+2. Put the `vip-portal/target/vip-portal-[...]-local.war` file in the `$TOMCAT_HOME/webapps` directory
+3. Add the folowing lines in `$TOMCAT_HOME/conf/context.xml` (database jndi configuration), and edit `path/to/vip/local/folder/vip` to the real path in `url`
+```
+<Resource name="jdbc/vip" auth="Container"  type="javax.sql.DataSource" 
+       username="sa"     
+       password="" 
+       driverClassName="org.h2.Driver" 
+       description="VIP local h2 Connection" 
+       url="jdbc:h2:/path/to/vip/local/folder/vip" 
+       maxActive="100" 
+       maxIdle="50" />
+```
+4. Create or adapt the `$TOMCAT_HOME/bin/setenv.sh` file with these lines (edit `path/to/vip/local/folder/vip` to the real path) :
+
+```
+export CATALINA_OPTS="$CATALINA_OPTS -Dspring.profiles.active=local,config-file,jndi-db"
+export CATALINA_OPTS="$CATALINA_OPTS -DvipConfigFolder=/path/to/vip/local/folder"
+```
+
+5. That's it, start tomcat (`bin/startup.sh`). Access vip on `localhost:8080/vip-portal-[...]-local` (adapt with the war name and your tomcat host/port configuration)
+
+### Local instance notes
+
+- The default admin email/password is `[email protected]`/`localAdminPassword`.
+- all is not working perfectly yet, expect to see some error messages. The home page, files transfers and execution launchs shoud work, but application imports and the page with execution details are not implemented at the moment.
+- vip do not send email but logs them
+- at the moment, logging is done in the `$HOME/.vip/vip.log` file
+
+
+
+
+
 
-To be done. Until this section is written, install at your own risks or
-contact us at
-[[email protected]]([email protected]).
diff --git a/pom.xml b/pom.xml
@@ -43,7 +43,7 @@ knowledge of the CeCILL-B license and that you accept its terms.
     <properties>
         <!-- project version. Only to change it here (and in CoreConstants.java
            Follow this practice : https://maven.apache.org/maven-ci-friendly.html-->
-        <revision>2.0</revision>
+        <revision>2.1</revision>
         <changelist/>
         <sha1/>
 
@@ -57,6 +57,7 @@ knowledge of the CeCILL-B license and that you accept its terms.
         <spring-framework.version>5.2.6.RELEASE</spring-framework.version>
         <springsecurity.version>5.3.2.RELEASE</springsecurity.version>
         <jackson.version>2.11.0</jackson.version>
+        <h2database.version>1.3.173</h2database.version>
     </properties>
 
     <description>VIP</description>
@@ -149,7 +150,7 @@ knowledge of the CeCILL-B license and that you accept its terms.
         <dependency>
             <groupId>com.h2database</groupId>
             <artifactId>h2</artifactId>
-            <version>1.4.200</version>
+            <version>${h2database.version}</version>
             <scope>test</scope>
         </dependency>
         <dependency>
@@ -192,21 +193,9 @@ knowledge of the CeCILL-B license and that you accept its terms.
     <repositories>
 
         <repository>
-            <id>creatis-releases</id>
-            <name>Creatis Insa Lyon repository [creatis]</name>
-            <url>http://vip.creatis.insa-lyon.fr:9007/nexus/content/repositories/releases</url>
-        </repository>
-
-        <repository>
-            <id>creatis-thirdparty</id>
-            <name>Creatis Insa Lyon repository [creatis]</name>
-            <url>http://vip.creatis.insa-lyon.fr:9007/nexus/content/repositories/thirdparty</url>
-        </repository>
-
-        <repository>
-            <id>creatis-snapshots</id>
+            <id>creatis</id>
             <name>Creatis Insa Lyon repository [creatis]</name>
-            <url>http://vip.creatis.insa-lyon.fr:9007/nexus/content/repositories/snapshots</url>
+            <url>https://vip.creatis.insa-lyon.fr:9007/nexus/repository/public</url>
         </repository>
 
         <!-- repo used to get empty jar for commons logging and log4j -->
@@ -221,13 +210,13 @@ knowledge of the CeCILL-B license and that you accept its terms.
         <repository>
             <id>creatis-releases</id>
             <name>Internal Releases</name>
-            <url>http://vip.creatis.insa-lyon.fr:9007/nexus/content/repositories/releases</url>
+            <url>https://vip.creatis.insa-lyon.fr:9007/nexus/repository/releases</url>
         </repository>
 
         <snapshotRepository>
             <id>creatis-snapshots</id>
             <name>Internal Snapshots</name>
-            <url>http://vip.creatis.insa-lyon.fr:9007/nexus/content/repositories/snapshots</url>
+            <url>https://vip.creatis.insa-lyon.fr:9007/nexus/repository/snapshots</url>
         </snapshotRepository>
 
     </distributionManagement>

diff --git a/vip-api/src/main/java/fr/insalyon/creatis/vip/api/ApiPropertiesInitializer.java b/vip-api/src/main/java/fr/insalyon/creatis/vip/api/ApiPropertiesInitializer.java
@@ -39,6 +39,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.ConfigurableApplicationContext;
+import org.springframework.context.annotation.Profile;
 import org.springframework.core.env.ConfigurableEnvironment;
 import org.springframework.core.io.FileSystemResource;
 import org.springframework.core.io.Resource;

diff --git a/vip-api/src/main/java/fr/insalyon/creatis/vip/api/SpringSecurityConfig.java b/vip-api/src/main/java/fr/insalyon/creatis/vip/api/SpringSecurityConfig.java
@@ -31,23 +31,20 @@
  */
 package fr.insalyon.creatis.vip.api;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
-import fr.insalyon.creatis.vip.api.CarminProperties;
 import fr.insalyon.creatis.vip.api.security.SpringCompatibleUser;
-import fr.insalyon.creatis.vip.api.security.apikey.*;
+import fr.insalyon.creatis.vip.api.security.apikey.ApikeyAuthenticationEntryPoint;
+import fr.insalyon.creatis.vip.api.security.apikey.ApikeyAuthentificationConfigurer;
 import fr.insalyon.creatis.vip.core.client.bean.User;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.core.env.Environment;
-import org.springframework.http.converter.json.Jackson2ObjectMapperBuilder;
 import org.springframework.security.config.annotation.web.builders.HttpSecurity;
-import org.springframework.security.config.annotation.web.builders.WebSecurity;
-import org.springframework.security.config.annotation.web.configuration.*;
+import org.springframework.security.config.annotation.web.configuration.EnableWebSecurity;
+import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
 import org.springframework.security.config.http.SessionCreationPolicy;
 import org.springframework.security.core.Authentication;
 import org.springframework.security.core.context.SecurityContextHolder;
 import org.springframework.security.web.firewall.DefaultHttpFirewall;
-import org.springframework.security.web.firewall.StrictHttpFirewall;
 
 import java.util.function.Supplier;
 
@@ -66,11 +63,15 @@ public class SpringSecurityConfig extends WebSecurityConfigurerAdapter {
 
     // authentication done by bean LimitigDaoAuthenticationProvider
 
-    @Autowired
-    private ApikeyAuthenticationEntryPoint apikeyAuthenticationEntryPoint;
+    private final ApikeyAuthenticationEntryPoint apikeyAuthenticationEntryPoint;
+
+    private final Environment env;
 
     @Autowired
-    private Environment env;
+    public SpringSecurityConfig(ApikeyAuthenticationEntryPoint apikeyAuthenticationEntryPoint, Environment env) {
+        this.apikeyAuthenticationEntryPoint = apikeyAuthenticationEntryPoint;
+        this.env = env;
+    }
 
     @Override
     protected void configure(HttpSecurity http) throws Exception {
@@ -110,11 +111,6 @@ public Supplier<User> currentUserProvider() {
         };
     }
 
-    @Bean
-    public ObjectMapper objectMapper() {
-        return Jackson2ObjectMapperBuilder.json().build();
-    }
-
     /*
         Do not use the default firewall (StrictHttpFirewall) because it blocks
         "//" in url and it is used in gwt rpc calls

diff --git a/vip-api/src/main/java/fr/insalyon/creatis/vip/api/SpringWebConfig.java b/vip-api/src/main/java/fr/insalyon/creatis/vip/api/SpringWebConfig.java
@@ -31,6 +31,7 @@
  */
 package fr.insalyon.creatis.vip.api;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import fr.insalyon.creatis.vip.api.business.VipConfigurer;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
@@ -43,6 +44,7 @@
 import org.springframework.core.env.PropertiesPropertySource;
 import org.springframework.core.io.ClassPathResource;
 import org.springframework.core.io.support.ResourcePropertySource;
+import org.springframework.http.converter.json.Jackson2ObjectMapperBuilder;
 import org.springframework.web.servlet.config.annotation.*;
 
 import java.io.IOException;
@@ -102,4 +104,8 @@ public void addInterceptors(InterceptorRegistry registry) {
         registry.addInterceptor(vipConfigurer);
     }
 
+    @Bean
+    public ObjectMapper objectMapper() {
+        return Jackson2ObjectMapperBuilder.json().build();
+    }
 }
diff --git a/vip-api/src/main/java/fr/insalyon/creatis/vip/api/business/DataApiBusiness.java b/vip-api/src/main/java/fr/insalyon/creatis/vip/api/business/DataApiBusiness.java
@@ -33,6 +33,7 @@
 
 import fr.insalyon.creatis.vip.api.CarminProperties;
 import fr.insalyon.creatis.vip.api.exception.ApiException;
+import fr.insalyon.creatis.vip.api.exception.ApiException.ApiError;
 import fr.insalyon.creatis.vip.api.model.PathProperties;
 import fr.insalyon.creatis.vip.api.model.UploadData;
 import fr.insalyon.creatis.vip.api.model.UploadDataType;
@@ -281,12 +282,13 @@ private void checkDownloadPermission(String path) throws ApiException {
     private void checkPermission(String path, LFCAccessType accessType)
             throws ApiException {
         try {
-            lfcPermissionBusiness.checkPermission(
-                currentUserProvider.get(), path, accessType);
+            if ( ! lfcPermissionBusiness.isLFCPathAllowed(
+                currentUserProvider.get(), path, accessType, true)) {
+                throw new ApiException(ApiError.UNAUTHORIZED_DATA_ACCESS, path);
+            }
         } catch (BusinessException e) {
-            throw new ApiException("API Permission error", e);
+            throw new ApiException("Error when checking permissions", e);
         }
-        // all check passed : all good !
     }
 
     // #### DOWNLOAD STUFF

diff --git a/vip-api/src/main/java/fr/insalyon/creatis/vip/api/exception/ApiException.java b/vip-api/src/main/java/fr/insalyon/creatis/vip/api/exception/ApiException.java
@@ -55,7 +55,8 @@ public enum ApiError implements VipError{
         INPUT_FIELD_NOT_VALID(8009),
         WRONG_DATE_FORMAT(8010),
         WRONG_STAT_SERVICE(8011),
-        COUNTRY_UNKNOWN(8012);
+        COUNTRY_UNKNOWN(8012),
+        UNAUTHORIZED_DATA_ACCESS(8013);
 
         private Integer code;
         ApiError(Integer code) { this.code = code; }
@@ -75,6 +76,7 @@ public enum ApiError implements VipError{
             addMessage(ApiError.WRONG_DATE_FORMAT, "The date {} have a wrong format (needed : {})", 2);
             addMessage(ApiError.WRONG_STAT_SERVICE, "The service {} is unknown, only 'vip' is possible", 1);
             addMessage(ApiError.COUNTRY_UNKNOWN, "Country unknown : {}", 1);
+            addMessage(ApiError.UNAUTHORIZED_DATA_ACCESS, "Unauthorized data access to : {}", 1);
         }
 
         public Optional<String> getMessage() {

diff --git a/...main/java/fr/insalyon/creatis/vip/api/security/apikey/ApikeyAuthenticationEntryPoint.java b/...main/java/fr/insalyon/creatis/vip/api/security/apikey/ApikeyAuthenticationEntryPoint.java
@@ -56,6 +56,7 @@ public class ApikeyAuthenticationEntryPoint implements AuthenticationEntryPoint
 
     private final ObjectMapper objectMapper;
 
+    @Autowired
     public ApikeyAuthenticationEntryPoint(ObjectMapper objectMapper) {
         this.objectMapper = objectMapper;
     }

diff --git a/...va/fr/insalyon/creatis/vip/applicationimporter/client/rpc/ApplicationImporterService.java b/...va/fr/insalyon/creatis/vip/applicationimporter/client/rpc/ApplicationImporterService.java
@@ -55,8 +55,8 @@ public static ApplicationImporterServiceAsync getInstance() {
 
     String readAndValidateBoutiquesFile(String fileLFN) throws ApplicationImporterException;
 
-    void createApplication(BoutiquesTool bt, String type, String tag, HashMap<String, BoutiquesTool> bts, boolean isRunOnGrid, boolean overwriteVersion, boolean challenge) throws ApplicationImporterException;
-   
+    void createApplication(BoutiquesTool bt, String type, String tag, boolean isRunOnGrid, boolean overwriteVersion) throws ApplicationImporterException;
+
     String getApplicationImporterRootFolder() throws ApplicationImporterException;
 
     List<String> getApplicationImporterRequirements() throws ApplicationImporterException;

diff --git a/.../insalyon/creatis/vip/applicationimporter/client/rpc/ApplicationImporterServiceAsync.java b/.../insalyon/creatis/vip/applicationimporter/client/rpc/ApplicationImporterServiceAsync.java
@@ -40,7 +40,7 @@ public interface ApplicationImporterServiceAsync {
 
     public void readAndValidateBoutiquesFile(String fileLFN, AsyncCallback<String> callback);
 
-    public void createApplication(BoutiquesTool bt, String type, String tag, HashMap<String, BoutiquesTool> bts, boolean isRunOnGrid, boolean overwriteVersion, boolean challenge, AsyncCallback<Void> callback);
+    public void createApplication(BoutiquesTool bt, String type, String tag, boolean isRunOnGrid, boolean overwriteVersion, AsyncCallback<Void> callback);
 
     public void getApplicationImporterRootFolder(AsyncCallback<String> asyncCallback);
 

diff --git a/...rter/src/main/java/fr/insalyon/creatis/vip/applicationimporter/client/view/Constants.java b/...rter/src/main/java/fr/insalyon/creatis/vip/applicationimporter/client/view/Constants.java
@@ -74,11 +74,8 @@ public class Constants {
     public static final String VM_GASW = "gasw.vm";
     //LFN access to SegPerfAnalyzer
     public static final String LNF_PATH = "";
-    // Application Importer Challenge Descriptor Path
-    public static final String APP_IMPORTER_CHALLENGE_PATH_MSSEG = "/vip/MSEG-admin/applications/templates";
-    public static final String APP_IMPORTER_CHALLENGE_PATH_PETSEG = "/vip/PETSEG-admin/applications/templates";
-    // Application Importer Challenge Descriptor
-    public static final String APP_IMPORTER_CHALLENGE_METRIC = "SegPerfAnalyzer.json";
-    public static final String APP_IMPORTER_CHALLENGE_METADATA = "metadata-updater.json";
+    // Application Importer types
+    public static final String APP_IMPORTER_STANDALONE_TYPE = "app-importer-standalone-type";
+    public static final String APP_IMPORTER_DOT_INPUTS_TYPE = "app-importer-dot-inputs-type";
 
 }
diff --git a/...r/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/DisplayTab.java b/...r/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/DisplayTab.java
@@ -58,7 +58,6 @@ public class DisplayTab extends Tab {
     private VIPLayout vipLayout;
     private final ModalWindow modal;
     private BoutiquesTool boutiquesTool;
-    private HashMap<String, BoutiquesTool> bts = null;
 
     public DisplayTab(String tabIcon, String tabId, String tabName) {
         this.setTitle(Canvas.imgHTML(tabIcon) + " " + tabName.trim());
@@ -107,70 +106,13 @@ private void configure() {
             @Override
             public void onClick(ClickEvent event) {
                 boutiquesTool.setApplicationLFN(vipLayout.getApplicationLocation() + "/" + boutiquesTool.getName());
-                if (!vipLayout.getApplicationType().contains("standalone")) {
-                    createApplicationWithAddDesc();
-                } else {
-                    createApplication();
-                }
-
+                createApplication();
             }
         });
         createApplicationButton.setWidth(120);
         globalLayout.addMember(createApplicationButton);
     }
 
-    /**
-     * Creates an application depending on other descriptors for the MICCAI
-     * challenge. The results of application should be evaluated to different
-     * metric methods.
-     *
-     */
-    public void createApplicationWithAddDesc() {
-        bts = new HashMap<String, BoutiquesTool>();
-        // Fisrt callback to get mectric descriptor
-        final AsyncCallback<String> callback = new AsyncCallback<String>() {
-            @Override
-            public void onFailure(Throwable caught) {
-                Layout.getInstance().setWarningMessage("Unable to read JSON file :" + caught.getMessage());
-            }
-
-            @Override
-            public void onSuccess(String jsonFileContent) {
-                try {
-                    bts.put("metric", JSONUtil.parseBoutiquesTool(JSONParser.parseStrict(jsonFileContent).isObject()));
-                    bts.get("metric").setApplicationLFN(vipLayout.getApplicationLocation() + "/" + boutiquesTool.getName());
-
-                    //second callback to get metadata descripotr
-                    final AsyncCallback<String> callback2 = new AsyncCallback<String>() {
-                        @Override
-                        public void onFailure(Throwable caught) {
-                            Layout.getInstance().setWarningMessage("Unable to read JSON file :" + caught.getMessage());
-                        }
-
-                        @Override
-                        public void onSuccess(String jsonFileContent) {
-                            try {
-                                bts.put("adaptater", JSONUtil.parseBoutiquesTool(JSONParser.parseStrict(jsonFileContent).isObject()));
-                                bts.get("adaptater").setApplicationLFN(vipLayout.getApplicationLocation() + "/" + boutiquesTool.getName());
-                                //Finally, launch
-                                createApplication();
-                            } catch (ApplicationImporterException ex) {
-                                Logger.getLogger(DisplayTab.class.getName()).log(Level.SEVERE, null, ex);
-                            }
-
-                        }
-                    };
-                    ApplicationImporterService.Util.getInstance().readAndValidateBoutiquesFile(vipLayout.getDescriptorLocation() + "/" + Constants.APP_IMPORTER_CHALLENGE_METADATA,
-                            callback2);
-                } catch (ApplicationImporterException ex) {
-                    Logger.getLogger(DisplayTab.class.getName()).log(Level.SEVERE, null, ex);
-                }
-
-            }
-        };
-        ApplicationImporterService.Util.getInstance().readAndValidateBoutiquesFile(vipLayout.getDescriptorLocation() + "/" + Constants.APP_IMPORTER_CHALLENGE_METRIC, callback);
-    }
-
     public static BoutiquesTool parseJSON(JSONObject jsonObject)
         throws ApplicationImporterException {
 
@@ -232,10 +174,8 @@ public void onSuccess(Void result) {
             boutiquesTool,
             vipLayout.getApplicationType(),
             vipLayout.getTag(),
-            bts,
             vipLayout.getIsRunOnGrid(),
             vipLayout.getOverwrite(),
-            false,
             callback);
     }
 }