#4376 WIP. StudyTableSource interface added. New property sourceURN r…

…eplaces opal project/table in dataset's study tables and variables. Requires ES index config update.

mica-core/src/main/java/org/obiba/mica/core/domain/BaseStudyTable.java

@@ -13,16 +13,30 @@
 import com.google.common.base.MoreObjects;
 import com.google.common.base.Strings;
 
-import java.io.Serializable;
-
-public class BaseStudyTable extends OpalTable {
+public class BaseStudyTable {
 
   protected String studyId;
 
   protected String populationId;
 
   protected int populationWeight;
 
+  private LocalizedString name;
+
+  private LocalizedString description;
+
+  private LocalizedString additionalInformation;
+
+  private int weight;
+
+  private String sourceURN;
+
+  // legacy
+  private String project;
+
+  // legacy
+  private String table;
+
   public String getStudyId() {
     return studyId;
   }
@@ -72,13 +86,66 @@ public void setPopulationWeight(int populationWeight) {
 
   @Override
   public String toString() {
-    return MoreObjects.toStringHelper(this).add("project", getProject()).add("table", getTable())
+    return MoreObjects.toStringHelper(this).add("source", getSourceURN())
       .add("studyId", getStudyId()).add("populationId", getPopulationId())
       .toString();
   }
 
-  @Override
-  protected String getEntityId() {
-    return studyId;
+  public void setName(LocalizedString name) {
+    this.name = name;
+  }
+
+  public LocalizedString getName() {
+    return name;
+  }
+
+  public void setDescription(LocalizedString description) {
+    this.description = description;
+  }
+
+  public LocalizedString getDescription() {
+    return description;
+  }
+
+  public LocalizedString getAdditionalInformation() {
+    return additionalInformation;
+  }
+
+  public void setAdditionalInformation(LocalizedString additionalInformation) {
+    this.additionalInformation = additionalInformation;
+  }
+
+  public int getWeight() {
+    return weight;
+  }
+
+  public void setWeight(int weight) {
+    this.weight = weight;
+  }
+
+  public boolean isFor(String studyId, String sourceURN) {
+    return this.studyId.equals(studyId) && getSourceURN().equals(sourceURN);
+  }
+
+  public void setSourceURN(String sourceURN) {
+    this.sourceURN = sourceURN;
+  }
+
+  public String getSourceURN() {
+    // legacy
+    if (Strings.isNullOrEmpty(sourceURN)) {
+      this.sourceURN = OpalTableSource.newSource(project, table).getURN();
+    }
+    return sourceURN;
+  }
+
+  @Deprecated
+  public void setProject(String project) {
+    this.project = project;
+  }
+
+  @Deprecated
+  public void setTable(String table) {
+    this.table = table;
   }
 }

mica-core/src/main/java/org/obiba/mica/core/domain/OpalTableSource.java

@@ -0,0 +1,113 @@
+/*
+ * 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.core.domain;
+
+import com.google.common.base.Strings;
+import org.obiba.magma.ValueTable;
+import org.obiba.mica.micaConfig.service.OpalService;
+import org.obiba.mica.spi.dataset.StudyTableSource;
+import org.obiba.opal.rest.client.magma.RestDatasource;
+import org.obiba.opal.rest.client.magma.RestValueTable;
+import org.obiba.opal.web.model.Math;
+import org.obiba.opal.web.model.Search;
+
+import javax.validation.constraints.NotNull;
+
+/**
+ * Connector to an Opal server, to retrieve value table and summary statistics.
+ */
+public class OpalTableSource implements StudyTableSource {
+
+  private OpalService opalService;
+
+  private String opalUrl;
+
+  @NotNull
+  private String project;
+
+  @NotNull
+  private String table;
+
+  public String getProject() {
+    return project;
+  }
+
+  public void setProject(String project) {
+    this.project = project;
+  }
+
+  public String getTable() {
+    return table;
+  }
+
+  public void setTable(String table) {
+    this.table = table;
+  }
+
+  @Override
+  public ValueTable getValueTable() {
+    return getDatasource().getValueTable(table);
+  }
+
+  @Override
+  public Search.QueryResultDto getFacets(Search.QueryTermsDto query) {
+    return getRestValueTable().getFacets(query);
+  }
+
+  @Override
+  public Math.SummaryStatisticsDto getVariableSummary(String variableName) {
+    return ((RestValueTable.RestVariableValueSource)getRestValueTable().getVariableValueSource(variableName)).getSummary();
+  }
+
+  @Override
+  public String getURN() {
+    return String.format("urn:opal:%s.%s", project, table);
+  }
+
+  public static boolean isFor(String sourceURN) {
+    return !Strings.isNullOrEmpty(sourceURN) && sourceURN.startsWith("urn:opal:");
+  }
+
+  public static OpalTableSource newSource(String project, String table) {
+    OpalTableSource source = new OpalTableSource();
+    source.setProject(project);
+    source.setTable(table);
+    return source;
+  }
+
+  public static OpalTableSource fromURN(String sourceURN) {
+    if (Strings.isNullOrEmpty(sourceURN) || !sourceURN.startsWith("urn:opal:"))
+      throw new IllegalArgumentException("Not a valid Opal table source URN: " + sourceURN);
+
+    String fullName = toTableName(sourceURN);
+    int sep = fullName.indexOf(".");
+    String project = fullName.substring(0, sep);
+    String table = fullName.substring(sep + 1);
+    return OpalTableSource.newSource(project, table);
+  }
+
+  public static String toTableName(String sourceURN) {
+    return sourceURN.replace("urn:opal:", "");
+  }
+
+  public void init(OpalService opalService, String opalUrl) {
+    this.opalService = opalService;
+    this.opalUrl = opalUrl;
+  }
+
+  private RestDatasource getDatasource() {
+    return opalService.getDatasource(opalUrl, project);
+  }
+
+  private RestValueTable getRestValueTable() {
+    return (RestValueTable) getDatasource().getValueTable(table);
+  }
+}

mica-core/src/main/java/org/obiba/mica/core/domain/StudyTable.java

@@ -10,10 +10,10 @@
 
 package org.obiba.mica.core.domain;
 
-import java.io.Serializable;
-
 import com.google.common.base.MoreObjects;
 
+import java.io.Serializable;
+
 /**
  * Represents a opal table that is associated to a {@link org.obiba.mica.study.domain.Study}
  * {@link org.obiba.mica.study.domain.Population} {@link org.obiba.mica.study.domain.DataCollectionEvent}.
@@ -63,7 +63,7 @@ public boolean appliesTo(String studyId, String populationId, String dataCollect
 
   @Override
   public String toString() {
-    return MoreObjects.toStringHelper(this).add("project", getProject()).add("table", getTable())
+    return MoreObjects.toStringHelper(this).add("source", getSourceURN())
       .add("dceId", getDataCollectionEventUId()).toString();
   }
 

mica-core/src/main/java/org/obiba/mica/core/service/StudyTableSourceServiceRegistry.java

@@ -0,0 +1,50 @@
+/*
+ * 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.core.service;
+
+import org.obiba.mica.core.domain.BaseStudyTable;
+import org.obiba.mica.core.domain.OpalTableSource;
+import org.obiba.mica.micaConfig.service.OpalService;
+import org.obiba.mica.micaConfig.service.PluginsService;
+import org.obiba.mica.spi.dataset.StudyTableSource;
+import org.obiba.mica.spi.dataset.StudyTableSourceService;
+import org.obiba.mica.study.domain.BaseStudy;
+import org.springframework.stereotype.Service;
+
+import javax.inject.Inject;
+import java.util.NoSuchElementException;
+import java.util.Optional;
+
+@Service
+public class StudyTableSourceServiceRegistry {
+
+  @Inject
+  private PluginsService pluginsService;
+
+  @Inject
+  private OpalService opalService;
+
+  public StudyTableSource makeSource(BaseStudy study, String sourceURN) {
+    if (OpalTableSource.isFor(sourceURN)) {
+      OpalTableSource source = OpalTableSource.fromURN(sourceURN);
+      source.init(opalService, study.getOpal());
+      return source;
+    }
+    Optional<StudyTableSourceService> serviceOptional = pluginsService.getStudyTableSourceServices().stream()
+      .filter(service -> service.isFor(sourceURN)).findFirst();
+    if (serviceOptional.isPresent()) {
+      // TODO add a context to the study table source
+      return serviceOptional.get().makeSource(sourceURN);
+    }
+    throw new NoSuchElementException("Missing study-table-source plugin to handle source: " + sourceURN);
+  }
+
+}

mica-core/src/main/java/org/obiba/mica/dataset/domain/Dataset.java

@@ -28,7 +28,7 @@
 import java.util.Map;
 
 /**
- * Proxy to Opal tables.
+ * Proxy to value tables.
  */
 public abstract class Dataset extends AbstractModelAware implements AttributeAware, Indexable {