Merge pull request #70 from daisybio/transcriptInteraction_fix

Transcript interaction fix

app/controllers/transcriptInteraction.py

@@ -1,7 +1,7 @@
 import sqlalchemy as sa
 import os
 from flask import jsonify
-from sqlalchemy import desc, or_, and_
+from sqlalchemy import desc, and_
 from sqlalchemy.sql import text
 import app.models as models
 from app.config import LATEST, db
@@ -966,7 +966,7 @@ def get_transcript_network(dataset_ID: int = None, disease_name=None,
     nodes = db.session.execute(node_query).scalars().all()
     node_tr_ids = set([node.transcript_ID for node in nodes])
     edge_query = db.select(models.TranscriptInteraction).filter(
-        or_(
+        and_(
             models.TranscriptInteraction.transcript_ID_1.in_(node_tr_ids),
             models.TranscriptInteraction.transcript_ID_2.in_(node_tr_ids)
         )

swagger.yml

@@ -1518,85 +1518,68 @@ paths:
           required: false
           schema:
             type: number
-        - name: pValue
+        - name: maxPValue
           in: query
           required: false
           description: Threshold of the FDR adjusted p-value. Default is 0.05.
           schema:
             type: number
             default: 0.05
-        - name: pValueDirection
-          in: query
-          required: false
-          description: Direction of the FDR adjusted p-value threshold (<=, >=).
-          schema:
-            type: string
-            enum:
-              - <
-              - ">"
-            default: <
-        - name: mscor
+        - name: minMscor
           in: query
           required: false
           description: Threshold of the 'multiple sensitivity correlation' (mscor).
           schema:
             type: number
-        - name: mscorDirection
-          in: query
-          required: false
-          description: Direction of the mscor threshold (<=, >=).
-          schema:
-            type: string
-            enum:
-              - < 
-              - ">"
-            default: <
-        - name: correlation
+        - name: minCorrelation
           in: query
           required: false
           description: Threshold of the correlation.
           schema:
             type: number
-        - name: correlationDirection
+        - name: edgeSorting
           in: query
           required: false
-          description: Direction of the correlation threshold (<=, >=).
+          description: Possibilities for sorting of the edges.
           schema:
             type: string
             enum:
-              - <
-              - ">"
-            default: <
-        - name: sorting
+              - pValue
+              - mscor
+              - correlation
+        - name: nodeSorting
           in: query
           required: false
-          description: Possibilities for sorting of the results.
+          description: Possibilities for sorting of the nodes.
           schema:
             type: string
             enum:
-              - pValue
-              - mscor
-              - correlation
               - betweenness
               - degree
               - eigenvector
-        - name: descending
+        - name: maxNodes
           in: query
+          description: Number of nodes that should be shown. Default value is 100 and can be up to 1000. For more results please use batches, the provided offset parameter or download the whole dataset.
           required: false
-          description: Descending (true) or ascending (false) ordering of the results.
           schema:
-            type: boolean
-            default: true
-        - name: limit
+            type: integer
+            default: 100
+        - name: maxEdges
           in: query
-          description: Number of results that should be shown. Default value is 100 and can be up to 1000. For more results please use batches, the provided offset parameter or download the whole dataset.
+          description: Number of edges that should be shown. Default value is 100 and can be up to 1000. For more results please use batches, the provided offset parameter or download the whole dataset.
           required: false
           schema:
             type: integer
             default: 100
-        - name: offset
+        - name: offsetNodes
           in: query
-          description: Starting point from where results should be shown.
+          description: Starting point from where nodes should be shown.
+          required: false
+          schema:
+            type: integer
+        - name: offsetEdges
+          in: query
+          description: Starting point from where edges should be shown.
           required: false
           schema:
             type: integer