Merge pull request #347 from VEuPathDB/bipartite-network-api-update

Bipartite network api update
VEuPathDB · Jan 30, 2024 · 0d5e8c1 · 0d5e8c1
2 parents 97b37ef + 024392b
commit 0d5e8c1
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Showing 5 changed files with 104 additions and 21 deletions.
diff --git a/docs/api.html b/docs/api.html
diff --git a/schema/library.raml b/schema/library.raml
@@ -646,10 +646,18 @@ types:
     type: object
     properties:
       pcoaVariance: number[]
+  FeaturePrefilterThresholds:
+    type: object
+    additionalProperties: false
+    properties:
+      proportionNonZero?: number
+      variance?: number
+      standardDeviation?: number
   CorrelationComputeConfig:
     type: object
     properties:
       correlationMethod: CorrelationMethod
+      prefilterThresholds?: FeaturePrefilterThresholds
   CorrelationMethod:
     type: string
     enum:
@@ -778,6 +786,15 @@ types:
     additionalProperties: false
     properties:
       isCutoff: boolean
+  InternalJob:
+    type: object
+    properties:
+      jobId: JobID
+      status: JobStatus
+      owned: boolean
+      created: datetime
+      grabbed: datetime
+      finished: datetime
   PluginOverview:
     displayName: Plugin Overview
     type: object
@@ -939,16 +956,44 @@ types:
       variables:
         type: VariableMapping[]
         required: false
+  KPartiteNetworkConfig:
+    type: NetworkConfig
+    properties:
+      partitionsMetadata: string[]
+  NodeIdList:
+    type: object
+    additionalProperties: false
+    properties:
+      nodeIds: string[]
+  KPartiteNetworkData:
+    type: NetworkData
+    properties:
+      partitions: NodeIdList[]
+  KPartiteNetwork:
+    type: object
+    additionalProperties: false
+    properties:
+      data: KPartiteNetworkData
+      config: KPartiteNetworkConfig
+  KPartiteNetworkPostResponse:
+    type: object
+    additionalProperties: false
+    properties:
+      kpartitenetwork: KPartiteNetwork
   BipartiteNetworkConfig:
     type: NetworkConfig
     properties:
-      column1Metadata: string
-      column2Metadata: string
+      partitionsMetadata:
+        type: string[]
+        minItems: 2
+        maxItems: 2
   BipartiteNetworkData:
     type: NetworkData
     properties:
-      column1NodeIDs: string[]
-      column2NodeIDs: string[]
+      partitions:
+        type: NodeIdList[]
+        maxItems: 2
+        minItems: 2
   BipartiteNetwork:
     type: object
     additionalProperties: false

diff --git a/schema/url/networks.raml b/schema/url/networks.raml
@@ -28,18 +28,48 @@ types:
         type: VariableMapping[]
         required: false
 
+  KPartiteNetworkConfig:
+    type: NetworkConfig
+    properties:
+      partitionsMetadata: string[]
+
+  NodeIdList:
+    additionalProperties: false
+    properties:
+      nodeIds: string[]
+
+  KPartiteNetworkData:
+    type: NetworkData
+    properties:
+      partitions: NodeIdList[]
+
+  KPartiteNetwork:
+    additionalProperties: false
+    properties:
+      data: KPartiteNetworkData
+      config: KPartiteNetworkConfig
+
+  KPartiteNetworkPostResponse:
+    additionalProperties: false
+    properties:
+      kpartitenetwork: KPartiteNetwork
+
+  # a specific case of a KPartiteNetwork w two partitions
   BipartiteNetworkConfig:
     type: NetworkConfig
     properties:
-      column1Metadata: string
-      column2Metadata: string
+      partitionsMetadata: 
+        type: string[]
+        minItems: 2
+        maxItems: 2      
 
   BipartiteNetworkData:
     type: NetworkData
     properties:
-      column1NodeIDs: string[]
-      column2NodeIDs: string[]
-
+      partitions:
+        type: NodeIdList[]
+        maxItems: 2
+        minItems: 2
 
   BipartiteNetwork:
     additionalProperties: false

diff --git a/.../org/veupathdb/service/eda/ds/plugin/correlation/AbstractCorrelationBipartiteNetwork.java b/.../org/veupathdb/service/eda/ds/plugin/correlation/AbstractCorrelationBipartiteNetwork.java
@@ -120,12 +120,20 @@ protected void writeResults(OutputStream out, Map<String, InputStream> dataStrea
     BipartiteNetworkData bipartiteNetworkData = new BipartiteNetworkDataImpl();
     bipartiteNetworkData.setLinks(links);
     bipartiteNetworkData.setNodes(nodes);
-    bipartiteNetworkData.setColumn1NodeIDs(uniqueColumn1IDs);
-    bipartiteNetworkData.setColumn2NodeIDs(uniqueColumn2IDs);
+    NodeIdList partition1NodeIdList = new NodeIdListImpl();
+    partition1NodeIdList.setNodeIds(uniqueColumn1IDs);
+    NodeIdList partition2NodeIdList = new NodeIdListImpl();
+    partition2NodeIdList.setNodeIds(uniqueColumn2IDs);
+    List<NodeIdList> partitions = new ArrayList<NodeIdList>();
+    partitions.add(partition1NodeIdList);
+    partitions.add(partition2NodeIdList);
+    bipartiteNetworkData.setPartitions(partitions);
 
     BipartiteNetworkConfig bipartiteNetworkConfig = new BipartiteNetworkConfigImpl();
-    bipartiteNetworkConfig.setColumn1Metadata(stats.getData1Metadata());
-    bipartiteNetworkConfig.setColumn2Metadata(stats.getData2Metadata());
+    List<String> partitionsMetadata = new ArrayList<String>();
+    partitionsMetadata.add(stats.getData1Metadata());
+    partitionsMetadata.add(stats.getData2Metadata());
+    bipartiteNetworkConfig.setPartitionsMetadata(partitionsMetadata);
 
     BipartiteNetwork bipartiteNetwork = new BipartiteNetworkImpl();
     bipartiteNetwork.setData(bipartiteNetworkData);

diff --git a/src/main/resources/api.html b/src/main/resources/api.html