Merge pull request #343 from VEuPathDB/explicit-network-thresholds

return explicit network thresholds

api.raml

@@ -540,7 +540,7 @@ securitySchemes:
           200:
             body:
               application/json:
-                type: lib.BipartiteNetworkPostResponse
+                type: lib.CorrelationBipartiteNetworkPostResponse
 
   /correlationassaymetadata/visualizations:
     displayName: Visualizations for discovering corrleations between assay data and sample metadata
@@ -555,7 +555,7 @@ securitySchemes:
           200:
             body:
               application/json:
-                type: lib.BipartiteNetworkPostResponse
+                type: lib.CorrelationBipartiteNetworkPostResponse
 
   /distributions/visualizations:
     displayName: Visualizations for exploring distributions of data.

schema/library.raml

@@ -866,6 +866,12 @@ types:
       correlationCoefThreshold:
         type: number
         required: false
+  CorrelationBipartiteNetworkPostResponse:
+    type: BipartiteNetworkPostResponse
+    additionalProperties: false
+    properties:
+      significanceThreshold: number
+      correlationCoefThreshold: number
   CorrelationAssayAssayBipartitenetworkPostRequest:
     type: DataPluginRequestBase
     properties:
@@ -920,7 +926,7 @@ types:
     properties:
       source: NodeData
       target: NodeData
-      strokeWidth: string
+      weight: string
       color: string
   NetworkData:
     type: object

schema/url/correlation/correlation.raml

@@ -10,4 +10,11 @@ types:
         required: false
       correlationCoefThreshold:
         type: number
-        required: false
+        required: false
+
+  CorrelationBipartiteNetworkPostResponse:
+    additionalProperties: false
+    type: BipartiteNetworkPostResponse
+    properties:
+      significanceThreshold: number
+      correlationCoefThreshold: number

schema/url/networks.raml

@@ -11,7 +11,7 @@ types:
     properties:
       source: NodeData
       target: NodeData
-      strokeWidth: string
+      weight: string
       color: string
 
   NetworkData:

src/main/java/org/veupathdb/service/eda/ds/core/AbstractPlugin.java

@@ -724,9 +724,6 @@ public boolean validateImputeZeroesRequest(Map<String, DynamicDataSpec> dataSpec
 
     List<DynamicDataSpec> dataSpecsWithStudyDependentVocabs = dataSpecs.entrySet().stream().filter(entry -> hasStudyDependentVocabulary(entry.getValue())).map(Map.Entry::getValue).toList();
     List<String> entities = dataSpecsWithStudyDependentVocabs.stream().map(data -> getDynamicDataSpecEntityId(data)).toList();
-    //if (entities.size() == 0) {
-    //  return false;
-    //}
 
     boolean allEqualEntities = entities.isEmpty() || Collections.frequency(entities, entities.get(0)) == entities.size();
     if (!allEqualEntities) { 

src/main/java/org/veupathdb/service/eda/ds/plugin/correlation/AbstractCorrelationBipartiteNetwork.java

@@ -96,7 +96,7 @@ protected void writeResults(OutputStream out, Map<String, InputStream> dataStrea
       LinkData link = new LinkDataImpl();
       link.setSource(sourceNode);
       link.setTarget(targetNode);
-      link.setStrokeWidth(String.valueOf(Math.abs(Float.parseFloat(correlationRow.getCorrelationCoef()))));
+      link.setWeight(String.valueOf(Math.abs(Float.parseFloat(correlationRow.getCorrelationCoef()))));
       // Link color is the sign of the correlation
       String color = Float.parseFloat(correlationRow.getCorrelationCoef()) < 0 ? "-1" : "1";
       link.setColor(color);
@@ -131,8 +131,10 @@ protected void writeResults(OutputStream out, Map<String, InputStream> dataStrea
     bipartiteNetwork.setData(bipartiteNetworkData);
     bipartiteNetwork.setConfig(bipartiteNetworkConfig);
 
-    BipartiteNetworkPostResponse response = new BipartiteNetworkPostResponseImpl();
+    CorrelationBipartiteNetworkPostResponse response = new CorrelationBipartiteNetworkPostResponseImpl();
     response.setBipartitenetwork(bipartiteNetwork);
+    response.setSignificanceThreshold(pValueThreshold);
+    response.setCorrelationCoefThreshold(correlationCoefThreshold);
 
     JsonUtil.Jackson.writeValue(out, response);
     out.flush();

src/main/java/org/veupathdb/service/eda/ds/service/AppsService.java

@@ -348,14 +348,14 @@ public PostAppsDifferentialabundanceVisualizationsVolcanoplotResponse postAppsDi
   @Override
   public PostAppsCorrelationassaymetadataVisualizationsBipartitenetworkResponse postAppsCorrelationassaymetadataVisualizationsBipartitenetwork(CorrelationAssayMetadataBipartitenetworkPostRequest entity) {
     return wrapPlugin(() -> PostAppsCorrelationassaymetadataVisualizationsBipartitenetworkResponse.respond200WithApplicationJson(
-        new BipartiteNetworkPostResponseStream(processRequest(new CorrelationAssayMetadataBipartitenetworkPlugin(), entity))));
+        new CorrelationBipartiteNetworkPostResponseStream(processRequest(new CorrelationAssayMetadataBipartitenetworkPlugin(), entity))));
   }
 
   @DisableJackson
   @Override
   public PostAppsCorrelationassayassayVisualizationsBipartitenetworkResponse postAppsCorrelationassayassayVisualizationsBipartitenetwork(CorrelationAssayAssayBipartitenetworkPostRequest entity) {
     return wrapPlugin(() -> PostAppsCorrelationassayassayVisualizationsBipartitenetworkResponse.respond200WithApplicationJson(
-        new BipartiteNetworkPostResponseStream(processRequest(new CorrelationAssayAssayBipartitenetworkPlugin(), entity))));
+        new CorrelationBipartiteNetworkPostResponseStream(processRequest(new CorrelationAssayAssayBipartitenetworkPlugin(), entity))));
   }
 
   @DisableJackson