SPI mica-source testing

obiba · Jan 19, 2023 · 108d3ae · 108d3ae
1 parent dcf168b
commit 108d3ae
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Showing 11 changed files with 136 additions and 26 deletions.
diff --git a/mica-core/src/main/java/org/obiba/mica/core/service/StudyTableSourceServiceRegistry.java b/mica-core/src/main/java/org/obiba/mica/core/service/StudyTableSourceServiceRegistry.java
@@ -84,7 +84,6 @@ private StudyTableSource makeStudyTableSourceInternal(StudyTableContext context,
     Optional<StudyTableSourceService> serviceOptional = pluginsService.getStudyTableSourceServices().stream()
       .filter(service -> service.isFor(source)).findFirst();
     if (serviceOptional.isPresent()) {
-      // TODO add a context to the study table source
       StudyTableSource tableSource = serviceOptional.get().makeSource(source);
       tableSource.setStudyTableContext(context);
       if (tableSource instanceof StudyTableFileSource) {

diff --git a/mica-core/src/main/java/org/obiba/mica/core/source/ExcelTableSource.java b/mica-core/src/main/java/org/obiba/mica/core/source/ExcelTableSource.java
@@ -29,7 +29,6 @@ public class ExcelTableSource extends AbstractStudyTableSource implements StudyT
   @NotNull
   private String path;
 
-  @NotNull
   private String table;
 
   private boolean initialized;
@@ -73,22 +72,12 @@ public String getTable() {
 
   @Override
   public ValueTable getValueTable() {
-    ensureInitialzed();
+    ensureInitialized();
     return Strings.isNullOrEmpty(table) ?
       excelDatasource.getValueTables().stream().findFirst().get() :
       excelDatasource.getValueTable(table);
   }
 
-  @Override
-  public Mica.DatasetVariableContingencyDto getContingency(IVariable variable, IVariable crossVariable) {
-    throw new UnsupportedOperationException("Contingency search not available from an Excel file");
-  }
-
-  @Override
-  public Mica.DatasetVariableAggregationDto getVariableSummary(String variableName) {
-    throw new UnsupportedOperationException("Summary statistics not available from an Excel file");
-  }
-
   @Override
   public String getURN() {
     return Strings.isNullOrEmpty(table) ? String.format("urn:file:%s", path) : String.format("urn:file:%s:%s", path, table);
@@ -99,7 +88,7 @@ public void initialise(InputStream in) {
     excelDatasource = new ExcelDatasource(path, in);
   }
 
-  private void ensureInitialzed() {
+  private void ensureInitialized() {
     if (!initialized) {
       Initialisables.initialise(excelDatasource);
       initialized = true;

diff --git a/mica-core/src/main/java/org/obiba/mica/core/source/OpalTableSource.java b/mica-core/src/main/java/org/obiba/mica/core/source/OpalTableSource.java
@@ -62,13 +62,23 @@ public ValueTable getValueTable() {
     return getDatasource().getValueTable(table);
   }
 
+  @Override
+  public boolean providesContingency() {
+    return true;
+  }
+
   @Override
   public Mica.DatasetVariableContingencyDto getContingency(IVariable variable, IVariable crossVariable) {
     Search.QueryTermsDto query = QueryTermsUtil.getContingencyQuery(variable, crossVariable);
     Search.QueryResultDto results = getRestValueTable().getFacets(query);
     return OpalDtos.asDto(variable, crossVariable, getContext().getPrivacyThreshold(), results);
   }
 
+  @Override
+  public boolean providesVariableSummary() {
+    return true;
+  }
+
   @Override
   public Mica.DatasetVariableAggregationDto getVariableSummary(String variableName) {
     RestValueTable.RestVariableValueSource variableValueSource = (RestValueTable.RestVariableValueSource) getRestValueTable().getVariableValueSource(variableName);

diff --git a/mica-core/src/main/java/org/obiba/mica/dataset/service/CollectedDatasetService.java b/mica-core/src/main/java/org/obiba/mica/dataset/service/CollectedDatasetService.java
@@ -40,6 +40,7 @@
 import org.obiba.mica.micaConfig.service.MicaConfigService;
 import org.obiba.mica.micaConfig.service.OpalService;
 import org.obiba.mica.network.service.NetworkService;
+import org.obiba.mica.spi.source.StudyTableSource;
 import org.obiba.mica.study.NoSuchStudyException;
 import org.obiba.mica.study.domain.BaseStudy;
 import org.obiba.mica.study.domain.DataCollectionEvent;
@@ -429,12 +430,15 @@ public DatasetVariable getDatasetVariable(StudyDataset dataset, String variableN
   @Cacheable(value = "dataset-variables", cacheResolver = "datasetVariablesCacheResolver", key = "#variableName")
   public Mica.DatasetVariableAggregationDto getVariableSummary(@NotNull StudyDataset dataset, String variableName) {
     log.info("Caching variable summary {} {}", dataset.getId(), variableName);
-    return getStudyTableSource(dataset, dataset.getSafeStudyTable()).getVariableSummary(variableName);
+    StudyTableSource tableSource = getStudyTableSource(dataset, dataset.getSafeStudyTable());
+    return tableSource.providesVariableSummary() ? tableSource.getVariableSummary(variableName) : null;
   }
 
   public Mica.DatasetVariableContingencyDto getContingencyTable(@NotNull StudyDataset dataset, DatasetVariable variable,
                                                                 DatasetVariable crossVariable) throws NoSuchValueTableException, NoSuchVariableException {
-    return getStudyTableSource(dataset, dataset.getSafeStudyTable()).getContingency(variable, crossVariable);
+
+    StudyTableSource tableSource = getStudyTableSource(dataset, dataset.getSafeStudyTable());
+    return tableSource.providesContingency() ? tableSource.getContingency(variable, crossVariable) : null;
   }
 
   public void delete(String id) {

diff --git a/mica-core/src/main/java/org/obiba/mica/dataset/service/HarmonizedDatasetService.java b/mica-core/src/main/java/org/obiba/mica/dataset/service/HarmonizedDatasetService.java
@@ -36,6 +36,7 @@
 import org.obiba.mica.micaConfig.service.MicaConfigService;
 import org.obiba.mica.micaConfig.service.OpalService;
 import org.obiba.mica.network.service.NetworkService;
+import org.obiba.mica.spi.source.StudyTableSource;
 import org.obiba.mica.study.NoSuchStudyException;
 import org.obiba.mica.study.domain.BaseStudy;
 import org.obiba.mica.study.domain.HarmonizationStudy;
@@ -380,8 +381,9 @@ public DatasetVariable getDatasetVariable(HarmonizationDataset dataset, String v
   public Mica.DatasetVariableAggregationDto getVariableSummary(@NotNull HarmonizationDataset dataset, String variableName, String studyId, String source) {
     for(BaseStudyTable baseTable : dataset.getBaseStudyTables()) {
       if(baseTable.isFor(studyId, source)) {
-        log.info("Caching variable summary {} {} {} {} {}", dataset.getId(), variableName, studyId, source);
-        return getStudyTableSource(dataset, baseTable).getVariableSummary(variableName);
+        log.info("Caching variable summary {} {} {} {}", dataset.getId(), variableName, studyId, source);
+        StudyTableSource tableSource = getStudyTableSource(dataset, baseTable);
+        return tableSource.providesVariableSummary() ? tableSource.getVariableSummary(variableName) : null;
       }
     }
 
@@ -390,7 +392,8 @@ public Mica.DatasetVariableAggregationDto getVariableSummary(@NotNull Harmonizat
 
   public Mica.DatasetVariableContingencyDto getContingencyTable(@NotNull HarmonizationDataset dataset, @NotNull BaseStudyTable studyTable, DatasetVariable variable,
                                                                 DatasetVariable crossVariable) throws NoSuchStudyException, NoSuchValueTableException {
-    return getStudyTableSource(dataset, studyTable).getContingency(variable, crossVariable);
+    StudyTableSource tableSource = getStudyTableSource(dataset, studyTable);
+    return tableSource.providesContingency() ? tableSource.getContingency(variable, crossVariable) : null;
   }
 
   @Override

diff --git a/mica-core/src/main/java/org/obiba/mica/micaConfig/service/PluginsService.java b/mica-core/src/main/java/org/obiba/mica/micaConfig/service/PluginsService.java
@@ -118,16 +118,16 @@ public void init() {
    */
   private void initPlugins() {
     Collection<PluginResources> plugins = getPlugins(true);
-    String pluginName = environment.getProperty(MICA_SEARCH_PLUGIN_NAME, DEFAULT_MICA_SEARCH_PLUGIN_NAME);
+    String searchPluginName = environment.getProperty(MICA_SEARCH_PLUGIN_NAME, DEFAULT_MICA_SEARCH_PLUGIN_NAME);
 
     try {
-      String pluginLatestVersion = getPluginRepositoryCache().getPluginLatestVersion(pluginName);
+      String pluginLatestVersion = getPluginRepositoryCache().getPluginLatestVersion(searchPluginName);
       // ensure there is a mica-search plugin installed
       if (plugins.stream().noneMatch(p -> "mica-search".equals(p.getType()))
         || plugins.stream()
-            .filter(plugin -> pluginName.equals(plugin.getName()))
+            .filter(plugin -> searchPluginName.equals(plugin.getName()))
             .filter(plugin -> plugin.getVersion().compareTo(new Version(pluginLatestVersion)) >= 0).count() == 0) {
-        installPlugin(pluginName, null);
+        installPlugin(searchPluginName, null);
         // rescan plugins
         plugins = getPlugins(true);
       }
@@ -137,14 +137,16 @@ private void initPlugins() {
 
     boolean micaSearchFound = false; // mica-search plugin is a singleton
     List<PluginResources> filteredPlugins =
-      plugins.stream().filter(plugin -> pluginName.equals(plugin.getName()))
+      plugins.stream().filter(plugin -> searchPluginName.equals(plugin.getName()) || "mica-source".equals(plugin.getType()))
         .sorted(Comparator.comparing(PluginResources::getVersion))
         .collect(Collectors.toList());
 
     for (PluginResources plugin : filteredPlugins) {
       if ("mica-search".equals(plugin.getType()) && !micaSearchFound) {
         initSearchEngineServicePlugin(plugin);
         micaSearchFound = true;
+      } else if ("mica-source".equals(plugin.getType())) {
+        initStudyTableSourceServicePlugin(plugin);
       }
     }
   }
@@ -162,8 +164,12 @@ private void initSearchEngineServicePlugin(PluginResources plugin) {
     servicePlugins.add(service);
   }
 
-  private void initStudyTableSourceServicePlugins(PluginResources plugin) {
+  private void initStudyTableSourceServicePlugin(PluginResources plugin) {
     StudyTableSourceServiceLoader.get(plugin.getURLClassLoader(false)).forEach(service -> {
+      Properties properties = plugin.getProperties();
+      properties.setProperty("MICA_HOME", properties.getProperty("OPAL_HOME"));
+      properties.remove("OPAL_HOME");
+      service.configure(properties);
       service.start();
       servicePlugins.add(service);
     });

diff --git a/...rest/src/main/java/org/obiba/mica/dataset/rest/DatasourceNotAvailableExceptionMapper.java b/...rest/src/main/java/org/obiba/mica/dataset/rest/DatasourceNotAvailableExceptionMapper.java
@@ -21,6 +21,6 @@
 public class DatasourceNotAvailableExceptionMapper implements ExceptionMapper<DatasourceNotAvailableException> {
   @Override
   public Response toResponse(DatasourceNotAvailableException e) {
-    return Response.status(Status.SERVICE_UNAVAILABLE).entity("Verify the datasource is available.").build();
+    return Response.status(Status.SERVICE_UNAVAILABLE).entity("Verify the datasource is available. " + e.getMessage()).build();
   }
 }
diff --git a/mica-spi/src/main/java/org/obiba/mica/spi/source/AbstractStudyTableSource.java b/mica-spi/src/main/java/org/obiba/mica/spi/source/AbstractStudyTableSource.java
@@ -10,6 +10,8 @@
 
 package org.obiba.mica.spi.source;
 
+import org.obiba.mica.web.model.Mica;
+
 /**
  * Helper class for implementing  {@link StudyTableSource}.
  */
@@ -26,4 +28,23 @@ protected StudyTableContext getContext() {
     return context;
   }
 
+  @Override
+  public boolean providesContingency() {
+    return false;
+  }
+
+  @Override
+  public Mica.DatasetVariableContingencyDto getContingency(IVariable variable, IVariable crossVariable) {
+    throw new UnsupportedOperationException("Contingency search not provided by: " + getClass().getSimpleName());
+  }
+
+  @Override
+  public boolean providesVariableSummary() {
+    return false;
+  }
+
+  @Override
+  public Mica.DatasetVariableAggregationDto getVariableSummary(String variableName) {
+    throw new UnsupportedOperationException("Summary statistics not provided by: " + getClass().getSimpleName());
+  }
 }
diff --git a/mica-spi/src/main/java/org/obiba/mica/spi/source/AbstractStudyTableSourceService.java b/mica-spi/src/main/java/org/obiba/mica/spi/source/AbstractStudyTableSourceService.java
@@ -0,0 +1,48 @@
+/*
+ * Copyright (c) 2022 OBiBa. All rights reserved.
+ *
+ * This program and the accompanying materials
+ * are made available under the terms of the GNU Public License v3.0.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.obiba.mica.spi.source;
+
+import java.util.Properties;
+
+/**
+ * Helper class.
+ */
+public abstract class AbstractStudyTableSourceService implements StudyTableSourceService {
+
+  protected Properties properties;
+
+  protected boolean running;
+
+  @Override
+  public Properties getProperties() {
+    return properties;
+  }
+
+  @Override
+  public void configure(Properties properties) {
+    this.properties = properties;
+  }
+
+  @Override
+  public boolean isRunning() {
+    return running;
+  }
+
+  @Override
+  public void start() {
+    this.running = true;
+  }
+
+  @Override
+  public void stop() {
+    this.running = false;
+  }
+}
diff --git a/mica-spi/src/main/java/org/obiba/mica/spi/source/StudyTableSource.java b/mica-spi/src/main/java/org/obiba/mica/spi/source/StudyTableSource.java
@@ -33,6 +33,13 @@ public interface StudyTableSource {
    */
   ValueTable getValueTable();
 
+  /**
+   * Whether crossing variables is supported.
+   *
+   * @return
+   */
+  boolean providesContingency();
+
   /**
    * Make a contingency query and return results.
    *
@@ -42,6 +49,13 @@ public interface StudyTableSource {
    */
   Mica.DatasetVariableContingencyDto getContingency(IVariable variable, IVariable crossVariable);
 
+  /**
+   * Whether variable summaries are supported.
+   *
+   * @return
+   */
+  boolean providesVariableSummary();
+
   /**
    * Get a variable summary statistics.
    *
@@ -57,6 +71,11 @@ public interface StudyTableSource {
    */
   String getURN();
 
+  /**
+   * Set context in which the study table is defined.
+   *
+   * @param context
+   */
   void setStudyTableContext(StudyTableContext context);
 
 }
diff --git a/mica-spi/src/main/java/org/obiba/mica/spi/source/StudyTableSourceService.java b/mica-spi/src/main/java/org/obiba/mica/spi/source/StudyTableSourceService.java
@@ -17,8 +17,19 @@
  */
 public interface StudyTableSourceService extends ServicePlugin {
 
+  /**
+   * Whether this service plugin can handle the study table source's URN.
+   * @param source
+   * @return
+   */
   boolean isFor(String source);
 
+  /**
+   * Make a {@link StudyTableSource} from the source URN.
+   *
+   * @param source
+   * @return
+   */
   StudyTableSource makeSource(String source);
 
 }