Merge pull request #54 from daisybio/dev

Add Sponge logging and node sorting
daisybio · Dec 20, 2024 · 657e313 · 657e313
2 parents 7569035 + c1856da
commit 657e313
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Showing 2 changed files with 13 additions and 11 deletions.
diff --git a/app/controllers/spongEffects.py b/app/controllers/spongEffects.py
@@ -9,6 +9,7 @@
 from app.controllers.externalInformation import get_genes, get_transcripts
 import app.models as models
 from app.config import LATEST, db
+from server import logger
 
 
 def get_spongEffects_run_ID(dataset_ID: int = None, disease_name: str = None, level: str = "gene", sponge_db_version: int = LATEST):
@@ -361,6 +362,7 @@ def run_spongEffects(file_path, out_path, params: Params = None, log: bool = Fal
         process = subprocess.run(cmd, capture_output=True, text=True, check=True)
         # get prediction output
         stderr = process.stderr
+        logger.info(stderr)
         with open(out_path, 'r') as json_file:
             return json.load(json_file)
     except subprocess.CalledProcessError as e:

diff --git a/app/controllers/transcriptInteraction.py b/app/controllers/transcriptInteraction.py
@@ -285,21 +285,21 @@ def read_all_transcript_network_analysis(dataset_ID: int = None, disease_name=No
     # add all sorting if given:
     sort = [models.networkAnalysisTranscript.sponge_run_ID]
     if sorting is not None:
-        if sort == "betweenness":
+        if sorting == "betweenness":
             if descending:
                 sort.append(models.networkAnalysisTranscript.betweenness.desc())
             else:
                 sort.append(models.networkAnalysisTranscript.betweenness.asc())
-            if sort == "degree":
-                if descending:
-                    sort.append(models.networkAnalysisTranscript.node_degree.desc())
-                else:
-                    sort.append(models.networkAnalysisTranscript.node_degree.asc())
-            if sort == "eigenvector":
-                if descending:
-                    sort.append(models.networkAnalysisTranscript.eigenvector.desc())
-                else:
-                    sort.append(models.networkAnalysisTranscript.eigenvector.asc())
+        if sorting == "degree":
+            if descending:
+                sort.append(models.networkAnalysisTranscript.node_degree.desc())
+            else:
+                sort.append(models.networkAnalysisTranscript.node_degree.asc())
+        if sorting == "eigenvector":
+            if descending:
+                sort.append(models.networkAnalysisTranscript.eigenvector.desc())
+            else:
+                sort.append(models.networkAnalysisTranscript.eigenvector.asc())
 
     result = models.networkAnalysisTranscript.query \
         .join(models.Transcript, models.Transcript.transcript_ID == models.networkAnalysisTranscript.transcript_ID) \