feat: added global summary statistics policy #4467

obiba · Dec 4, 2024 · a832731 · a832731
1 parent f6fc0ac
commit a832731
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Showing 20 changed files with 172 additions and 37 deletions.
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
@@ -15,6 +15,7 @@
 import com.google.common.collect.Sets;
 import com.google.common.eventbus.EventBus;
 import com.google.common.eventbus.Subscribe;
+import org.apache.shiro.SecurityUtils;
 import org.obiba.magma.NoSuchValueTableException;
 import org.obiba.magma.NoSuchVariableException;
 import org.obiba.magma.ValueTable;
@@ -40,6 +41,8 @@
 import org.obiba.mica.dataset.event.DatasetUpdatedEvent;
 import org.obiba.mica.file.FileUtils;
 import org.obiba.mica.file.service.FileSystemService;
+import org.obiba.mica.micaConfig.domain.MicaConfig;
+import org.obiba.mica.micaConfig.domain.SummaryStatisticsAccessPolicy;
 import org.obiba.mica.micaConfig.service.MicaConfigService;
 import org.obiba.mica.micaConfig.service.OpalService;
 import org.obiba.mica.network.service.NetworkService;
@@ -518,6 +521,11 @@ protected EventBus getEventBus() {
     return eventBus;
   }
 
+  @Override
+  protected MicaConfig getMicaConfig() {
+    return micaConfigService.getConfig();
+  }
+
   //
   // Private methods
   //

diff --git a/mica-core/src/main/java/org/obiba/mica/dataset/service/DatasetService.java b/mica-core/src/main/java/org/obiba/mica/dataset/service/DatasetService.java
@@ -12,6 +12,7 @@
 
 import com.google.common.base.Strings;
 import com.google.common.eventbus.EventBus;
+import org.apache.shiro.SecurityUtils;
 import org.obiba.magma.MagmaRuntimeException;
 import org.obiba.magma.NoSuchValueTableException;
 import org.obiba.magma.NoSuchVariableException;
@@ -26,10 +27,13 @@
 import org.obiba.mica.dataset.NoSuchDatasetException;
 import org.obiba.mica.dataset.domain.Dataset;
 import org.obiba.mica.dataset.domain.DatasetVariable;
+import org.obiba.mica.micaConfig.domain.MicaConfig;
+import org.obiba.mica.micaConfig.domain.SummaryStatisticsAccessPolicy;
 import org.obiba.mica.micaConfig.service.OpalService;
 import org.obiba.mica.network.service.NetworkService;
 import org.obiba.mica.spi.tables.StudyTableSource;
 import org.obiba.mica.study.service.StudyService;
+import org.obiba.mica.web.model.Mica;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -77,6 +81,44 @@ public abstract DatasetVariable getDatasetVariable(T dataset, String name)
 
   protected abstract EventBus getEventBus();
 
+  protected abstract MicaConfig getMicaConfig();
+
+  /**
+   * Apply summary statistics visibility policy.
+   *
+   * @param summary
+   * @return
+   */
+  public Mica.DatasetVariableAggregationDto getFilteredVariableSummary(Mica.DatasetVariableAggregationDto summary) {
+    SummaryStatisticsAccessPolicy policy = getMicaConfig().getSummaryStatisticsAccessPolicy();
+    if (summary == null || policy.equals(SummaryStatisticsAccessPolicy.OPEN_ALL)) return summary;
+    if (!SecurityUtils.getSubject().isAuthenticated()) {
+      if (policy.equals(SummaryStatisticsAccessPolicy.OPEN_STATS)) return summary;
+      // strip out detailed stats because user is not authenticated
+      summary = summary.toBuilder().clearFrequencies().build();
+      summary = summary.toBuilder().clearStatistics().build();
+    }
+    return summary;
+  }
+
+  /**
+   * Apply summary statistics visibility policy.
+   * 
+   * @param summary
+   * @return
+   */
+  public Mica.DatasetVariableAggregationsDto getFilteredVariableSummary(Mica.DatasetVariableAggregationsDto summary) {
+    SummaryStatisticsAccessPolicy policy = getMicaConfig().getSummaryStatisticsAccessPolicy();
+    if (summary == null || policy.equals(SummaryStatisticsAccessPolicy.OPEN_ALL)) return summary;
+    if (!SecurityUtils.getSubject().isAuthenticated()) {
+      if (policy.equals(SummaryStatisticsAccessPolicy.OPEN_STATS)) return summary;
+      // strip out detailed stats because user is not authenticated
+      summary = summary.toBuilder().clearFrequencies().build();
+      summary = summary.toBuilder().clearStatistics().build();
+    }
+    return summary;
+  }
+
   /**
    * Find all dataset identifiers.
    *

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
@@ -15,6 +15,7 @@
 import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
 import com.google.common.eventbus.EventBus;
+import org.apache.shiro.SecurityUtils;
 import org.obiba.magma.*;
 import org.obiba.magma.support.Disposables;
 import org.obiba.mica.NoSuchEntityException;
@@ -35,6 +36,8 @@
 import org.obiba.mica.dataset.event.DatasetUpdatedEvent;
 import org.obiba.mica.file.FileUtils;
 import org.obiba.mica.file.service.FileSystemService;
+import org.obiba.mica.micaConfig.domain.MicaConfig;
+import org.obiba.mica.micaConfig.domain.SummaryStatisticsAccessPolicy;
 import org.obiba.mica.micaConfig.service.MicaConfigService;
 import org.obiba.mica.micaConfig.service.OpalService;
 import org.obiba.mica.network.service.NetworkService;
@@ -438,6 +441,11 @@ protected EventBus getEventBus() {
     return eventBus;
   }
 
+  @Override
+  protected MicaConfig getMicaConfig() {
+    return micaConfigService.getConfig();
+  }
+
   //
   // Private methods
   //

diff --git a/mica-core/src/main/java/org/obiba/mica/micaConfig/domain/MicaConfig.java b/mica-core/src/main/java/org/obiba/mica/micaConfig/domain/MicaConfig.java
@@ -131,6 +131,8 @@ public class MicaConfig extends AbstractAuditableDocument implements Serializabl
 
   private boolean variableSummaryRequiresAuthentication = false;
 
+  private SummaryStatisticsAccessPolicy summaryStatisticsAccessPolicy;
+
   private boolean usePublicUrlForSharedLink = true;
 
   private String style;
@@ -543,6 +545,21 @@ public boolean isVariableSummaryRequiresAuthentication() {
 
   public void setVariableSummaryRequiresAuthentication(boolean variableSummaryRequiresAuthentication) {
     this.variableSummaryRequiresAuthentication = variableSummaryRequiresAuthentication;
+    if (summaryStatisticsAccessPolicy == null) {
+      summaryStatisticsAccessPolicy = variableSummaryRequiresAuthentication ? SummaryStatisticsAccessPolicy.RESTRICTED_ALL : SummaryStatisticsAccessPolicy.OPEN_ALL;
+    }
+  }
+
+  public SummaryStatisticsAccessPolicy getSummaryStatisticsAccessPolicy() {
+    if (summaryStatisticsAccessPolicy == null) {
+      summaryStatisticsAccessPolicy = variableSummaryRequiresAuthentication ? SummaryStatisticsAccessPolicy.RESTRICTED_ALL : SummaryStatisticsAccessPolicy.OPEN_ALL;
+    }
+    return summaryStatisticsAccessPolicy;
+  }
+
+  public void setSummaryStatisticsAccessPolicy(SummaryStatisticsAccessPolicy summaryStatisticsAccessPolicy) {
+    this.summaryStatisticsAccessPolicy = summaryStatisticsAccessPolicy;
+    this.variableSummaryRequiresAuthentication = !SummaryStatisticsAccessPolicy.OPEN_ALL.equals(summaryStatisticsAccessPolicy);
   }
 
   public boolean hasStyle() {

diff --git a/mica-core/src/main/java/org/obiba/mica/micaConfig/domain/SummaryStatisticsAccessPolicy.java b/mica-core/src/main/java/org/obiba/mica/micaConfig/domain/SummaryStatisticsAccessPolicy.java
@@ -0,0 +1,26 @@
+/*
+ * 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.micaConfig.domain;
+
+/**
+ * Specify the access policy to the variable stats.
+ */
+public enum SummaryStatisticsAccessPolicy {
+
+  OPEN_ALL, // open basic counts, detailed stats and contingency
+
+  OPEN_STATS, // open basic counts and detailed stats, restricted contingency
+
+  OPEN_BASICS, // open basic counts, restricted detailed stats and contingency
+
+  RESTRICTED_ALL, // restricted basic counts, detailed stats and contingency
+
+}
diff --git a/mica-core/src/main/java/org/obiba/mica/web/model/MicaConfigDtos.java b/mica-core/src/main/java/org/obiba/mica/web/model/MicaConfigDtos.java
@@ -149,6 +149,7 @@ Mica.MicaConfigDto asDto(@NotNull MicaConfig config, String language) {
     builder.setIsCollectedDatasetEnabled(config.isStudyDatasetEnabled());
     builder.setIsHarmonizedDatasetEnabled(config.isHarmonizationDatasetEnabled());
     builder.setVariableSummaryRequiresAuthentication(config.isVariableSummaryRequiresAuthentication());
+    builder.setSummaryStatisticsAccessPolicy(config.getSummaryStatisticsAccessPolicy().name());
     builder.setIsImportStudiesFeatureEnabled(config.isImportStudiesFeatureEnabled());
 
     if(config.hasStyle()) builder.setStyle(config.getStyle());
@@ -249,6 +250,7 @@ MicaConfig fromDto(@NotNull Mica.MicaConfigDtoOrBuilder dto) {
     config.setHarmonizationDatasetEnabled(dto.getIsHarmonizedDatasetEnabled());
     config.setImportStudiesFeatureEnabled(dto.getIsImportStudiesFeatureEnabled());
     if (dto.hasVariableSummaryRequiresAuthentication()) config.setVariableSummaryRequiresAuthentication(dto.getVariableSummaryRequiresAuthentication());
+    config.setSummaryStatisticsAccessPolicy(SummaryStatisticsAccessPolicy.valueOf(dto.getSummaryStatisticsAccessPolicy()));
 
     if (dto.hasSignupEnabled()) config.setSignupEnabled(dto.getSignupEnabled());
     config.setSignupWithPassword(dto.getSignupWithPassword());

diff --git a/mica-rest/src/main/java/org/obiba/mica/dataset/rest/PublishedDatasetResource.java b/mica-rest/src/main/java/org/obiba/mica/dataset/rest/PublishedDatasetResource.java
@@ -74,7 +74,8 @@ public DatasetVariable getVariable(@PathParam("id") String id, @PathParam("proje
   @Path("/collected/{project}/{table}/{variableName}/_summary")
   public Mica.DatasetVariableAggregationDto getVariableSummary(@PathParam("id") String id, @PathParam("project") String project, @PathParam("table") String table, @PathParam("variableName") String variableName) {
     checkVariableSummaryAccess();
-    return collectedDatasetService.getVariableSummary(alternativeStudyDataset(id, project, table), variableName);
+    Mica.DatasetVariableAggregationDto summary = collectedDatasetService.getVariableSummary(alternativeStudyDataset(id, project, table), variableName);
+    return collectedDatasetService.getFilteredVariableSummary(summary);
   }
 
   private Dataset getDataset(String id) {

diff --git a/...ch/src/main/java/org/obiba/mica/dataset/search/rest/AbstractPublishedDatasetResource.java b/...ch/src/main/java/org/obiba/mica/dataset/search/rest/AbstractPublishedDatasetResource.java
@@ -20,6 +20,7 @@
 import org.obiba.mica.dataset.domain.Dataset;
 import org.obiba.mica.dataset.domain.DatasetVariable;
 import org.obiba.mica.dataset.domain.HarmonizationDataset;
+import org.obiba.mica.micaConfig.domain.SummaryStatisticsAccessPolicy;
 import org.obiba.mica.micaConfig.service.MicaConfigService;
 import org.obiba.mica.micaConfig.service.TaxonomiesService;
 import org.obiba.mica.security.service.SubjectAclService;
@@ -308,10 +309,18 @@ protected List<Taxonomy> getTaxonomies() {
   protected void checkContingencyAccess() {
     if (!micaConfigService.getConfig().isContingencyEnabled())
       throw new ForbiddenException();
+    if (micaConfigService.getConfig().getSummaryStatisticsAccessPolicy().equals(SummaryStatisticsAccessPolicy.OPEN_ALL))
+      return;
+    // other require authentication
+    if (!SecurityUtils.getSubject().isAuthenticated())
+      throw new ForbiddenException();
   }
 
   protected void checkVariableSummaryAccess() {
-    if (!SecurityUtils.getSubject().isAuthenticated() && micaConfigService.getConfig().isVariableSummaryRequiresAuthentication())
+    if (micaConfigService.getConfig().getSummaryStatisticsAccessPolicy().name().startsWith("OPEN_"))
+      return;
+    // other require authentication
+    if (!SecurityUtils.getSubject().isAuthenticated())
       throw new ForbiddenException();
   }
 

diff --git a/.../obiba/mica/dataset/search/rest/collection/PublishedCollectedDatasetVariableResource.java b/.../obiba/mica/dataset/search/rest/collection/PublishedCollectedDatasetVariableResource.java
@@ -67,7 +67,8 @@ public Mica.DatasetVariableAggregationDto getVariableAggregations(@QueryParam("s
     StudyDataset dataset = getDataset(StudyDataset.class, datasetId);
     StudyTable studyTable = dataset.getSafeStudyTable();
     try {
-      return dtos.asDto(studyTable, datasetService.getVariableSummary(dataset, variableName), withStudySummary).build();
+      Mica.DatasetVariableAggregationDto summary = datasetService.getVariableSummary(dataset, variableName);
+      return dtos.asDto(studyTable, datasetService.getFilteredVariableSummary(summary), withStudySummary).build();
     } catch (Exception e) {
       if (log.isDebugEnabled())
         log.warn("Unable to retrieve statistics: {}", e.getMessage(), e);

diff --git a/...ba/mica/dataset/search/rest/harmonization/PublishedDataschemaDatasetVariableResource.java b/...ba/mica/dataset/search/rest/harmonization/PublishedDataschemaDatasetVariableResource.java
@@ -16,12 +16,7 @@
 import com.google.common.collect.LinkedListMultimap;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Multimap;
-import jakarta.ws.rs.BadRequestException;
-import jakarta.ws.rs.DefaultValue;
-import jakarta.ws.rs.GET;
-import jakarta.ws.rs.Path;
-import jakarta.ws.rs.Produces;
-import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.*;
 import jakarta.ws.rs.core.Response;
 import org.apache.commons.math3.util.Pair;
 import org.obiba.mica.core.domain.BaseStudyTable;
@@ -36,13 +31,13 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.context.annotation.Scope;
 import org.springframework.scheduling.annotation.Async;
-import org.springframework.scheduling.annotation.AsyncResult;
 import org.springframework.stereotype.Component;
 
 import javax.inject.Inject;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.util.List;
+import java.util.concurrent.CompletableFuture;
 import java.util.concurrent.Future;
 import java.util.stream.Collectors;
 
@@ -91,7 +86,8 @@ public Mica.DatasetVariableAggregationsDto getVariableAggregations(@QueryParam("
       BaseStudyTable opalTable = studyTables.get(i);
       Future<Mica.DatasetVariableAggregationDto> futureResult = results.get(i);
       try {
-        builder.add(dtos.asDto(opalTable, futureResult.get(), withStudySummary).build());
+        Mica.DatasetVariableAggregationDto summary = futureResult.get();
+        builder.add(dtos.asDto(opalTable, summary, withStudySummary).build());
       } catch (Exception e) {
         if (log.isDebugEnabled())
           log.warn("Unable to retrieve statistics: {}", e.getMessage(), e);
@@ -108,9 +104,9 @@ public Mica.DatasetVariableAggregationsDto getVariableAggregations(@QueryParam("
     if (allAggDto.hasStatistics()) aggDto.setStatistics(allAggDto.getStatistics());
     aggDto.addAllFrequencies(allAggDto.getFrequenciesList());
 
-    aggDto.addAllAggregations(aggsDto);
+    aggDto.addAllAggregations(aggsDto.stream().map((summary) -> datasetService.getFilteredVariableSummary(summary)).toList());
 
-    return aggDto.build();
+    return datasetService.getFilteredVariableSummary(aggDto.build());
   }
 
   @GET
@@ -259,24 +255,25 @@ protected Future<Mica.DatasetVariableAggregationDto> getVariableFacet(Harmonizat
                                                                  BaseStudyTable table) {
       try {
         String studyId = table.getStudyId();
-        return new AsyncResult<>(datasetService.getVariableSummary(dataset, variableName, studyId, table.getSource()));
+        Mica.DatasetVariableAggregationDto summary = datasetService.getVariableSummary(dataset, variableName, studyId, table.getSource());
+        return CompletableFuture.supplyAsync(() -> summary);
       } catch (Exception e) {
         if (log.isDebugEnabled())
           log.warn("Unable to retrieve statistics: {}", e.getMessage(), e);
         else
           log.warn("Unable to retrieve statistics: {}", e.getMessage());
-        return new AsyncResult<>(null);
+        return CompletableFuture.supplyAsync(() -> null);
       }
     }
 
     @Async
     protected Future<Mica.DatasetVariableContingencyDto> getContingencyTable(HarmonizationDataset dataset, DatasetVariable var,
                                                                 DatasetVariable crossVar, BaseStudyTable studyTable) {
       try {
-        return new AsyncResult<>(datasetService.getContingencyTable(dataset, studyTable, var, crossVar));
+        return CompletableFuture.supplyAsync(() -> datasetService.getContingencyTable(dataset, studyTable, var, crossVar));
       } catch (Exception e) {
         log.warn("Unable to retrieve contingency statistics: " + e.getMessage(), e);
-        return new AsyncResult<>(null);
+        return CompletableFuture.supplyAsync(() -> null);
       }
     }
   }

diff --git a/...ba/mica/dataset/search/rest/harmonization/PublishedHarmonizedDatasetVariableResource.java b/...ba/mica/dataset/search/rest/harmonization/PublishedHarmonizedDatasetVariableResource.java
@@ -80,8 +80,8 @@ public Mica.DatasetVariableAggregationDto getVariableAggregations(@QueryParam("s
     for (BaseStudyTable baseTable : getBaseStudyTables(dataset)) {
       if (baseTable.isFor(studyId, source)) {
         try {
-          return dtos.asDto(baseTable,
-            datasetService.getVariableSummary(dataset, variableName, studyId, source), withStudySummary).build();
+          Mica.DatasetVariableAggregationDto summary = datasetService.getVariableSummary(dataset, variableName, studyId, source);
+          return dtos.asDto(baseTable, datasetService.getFilteredVariableSummary(summary), withStudySummary).build();
         } catch (Exception e) {
           if (log.isDebugEnabled())
             log.warn("Unable to retrieve statistics: {}", e.getMessage(), e);

diff --git a/mica-web-model/src/main/protobuf/Mica.proto b/mica-web-model/src/main/protobuf/Mica.proto
@@ -452,6 +452,7 @@ message MicaConfigDto {
   required bool isStudiesExportEnabled = 68;
   required bool isNetworksExportEnabled = 69;
   repeated string usableVariableTaxonomiesForConceptTagging = 70;
+  required string summaryStatisticsAccessPolicy = 71;
 }
 
 message PublicMicaConfigDto {

diff --git a/mica-webapp/src/main/resources/_templates/libs/variable-scripts.ftl b/mica-webapp/src/main/resources/_templates/libs/variable-scripts.ftl
@@ -119,9 +119,6 @@
       });
     </#if>
 
-    <#if showVariableStatistics && (user?? || !config.variableSummaryRequiresAuthentication)>
-      makeSummary(${showHarmonizedVariableSummarySelector?c});
-    </#if>
-
+    makeSummary('${config.summaryStatisticsAccessPolicy}', ${showHarmonizedVariableSummarySelector?c});
   });
 </script>
diff --git a/mica-webapp/src/main/resources/_templates/variable.ftl b/mica-webapp/src/main/resources/_templates/variable.ftl
@@ -308,9 +308,10 @@
                   </#if>
                 </div>
                 <div class="card-body">
-                  <#if user?? || !config.variableSummaryRequiresAuthentication>
+                  <#if config.summaryStatisticsAccessPolicy?starts_with("OPEN_") || user??>
                     <@variableSummary variable=variable/>
-                  <#else>
+                  </#if>
+                  <#if config.summaryStatisticsAccessPolicy.name() != "OPEN_ALL" && config.summaryStatisticsAccessPolicy.name() != "OPEN_STATS" && user?? == false>
                     <@message "sign-in-for-variable-statistics"/>
                     <a href="${contextPath}/signin?redirect=${contextPath}/variable/${variable.id}" class="btn btn-info"><@message "sign-in"/></a>
                   </#if>

diff --git a/mica-webapp/src/main/resources/i18n/en.json b/mica-webapp/src/main/resources/i18n/en.json
@@ -432,8 +432,14 @@
     },
     "openAccess": "Open access",
     "openAccess-help": "Access to published documents is opened to everyone.",
-    "variableSummaryRequiresAuthentication": "Restricted access to variable summary statistics",
-    "variableSummaryRequiresAuthentication-help": "The user needs to be identified when accessing to the variable summary statistics (and related operations like contingency table).",
+    "variableSummaryRequiresAuthentication": "Access to variable summary statistics",
+    "variableSummaryRequiresAuthentication-help": "The user may need to be identified when accessing to the variable summary statistics (and related operations like contingency table).",
+    "summaryStatisticsAccessPolicy-label": {
+      "OPEN_ALL": "Open",
+      "OPEN_STATS": "Open basic counts open and detailed statistics and restricted contingency table",
+      "OPEN_BASICS": "Open basic counts open, restricted detailed statistics and contingency table",
+      "RESTRICTED_ALL": "Restricted statistics and contingency table"
+    },
     "sections": "Sections",
     "repository-enabled": "Repository enabled",
     "repository-enabled-help": "Show network, initiative, study, protocol, dataset, variable pages with the search interface.",