Merge pull request #51 from BackofenLab/workNico

Frontend update.

backend/src/enrichment.py

@@ -83,7 +83,6 @@ def functional_enrichment(driver: neo4j.Driver, in_genes, species_id: Any):
     csv.field_size_limit(sys.maxsize)
 
     # Read Terms and put into Dataframe
-    df_terms = pd.DataFrame(queries.get_enrichment_terms(driver, species_id))
     tot_tests = len(df_terms)
 
     stopwatch.round("setup_enrichment")

backend/src/enrichment_graph.py

@@ -27,6 +27,8 @@ def get_functional_graph(list_enrichment, species_id):
     terms, source, target, score = queries.get_terms_connected_by_overlap(driver, list_term, species_id)
 
     stopwatch.round("Neo4j")
+
+    if len(terms) == 0: return
 
     nodes = pd.DataFrame(terms).rename(columns={"Term": "external_id"}).drop_duplicates(subset="external_id")
 

backend/src/main.py

@@ -19,6 +19,7 @@
 import queries
 import signal
 from util.stopwatch import Stopwatch
+import g4f, asyncio
 
 app = Flask(__name__)
 
@@ -73,7 +74,6 @@ def proteins_enrichment():
     json_str = json.dumps(list_enrichment.to_dict("records"), ensure_ascii=False, separators=(",", ":"))
     return Response(json_str, mimetype="application/json")
 
-
 # ====================== Subgraph API ======================
 # request comes from home.js
 # TODO Refactor this
@@ -110,6 +110,7 @@ def proteins_subgraph_api():
         pd.DataFrame(proteins).rename(columns={"ENSEMBL_PROTEIN": "external_id"}).drop_duplicates(subset="external_id")
     )
 
+
     edges = pd.DataFrame({"source": source, "target": target, "score": score})
     edges = edges.drop_duplicates(subset=["source", "target"])
 

backend/src/queries.py

@@ -111,7 +111,6 @@ def get_protein_associations(
         result = session.run(query)
         return _convert_to_connection_info_score(result=result, _int=True, protein=True)
 
-
 def get_enrichment_terms(driver: neo4j.Driver, species_id: int) -> list[dict[str, Any]]:
     if species_id == 10090:
         species = "Mus_Musculus"

frontend/package.json

@@ -12,12 +12,13 @@
     "3d-force-graph": "^1.71.1",
     "axios": "^1.3.2",
     "core-js": "^3.8.3",
-    "d3": "^7.8.4",
+    "d3": "^7.8.5",
     "file-saver": "^2.0.5",
     "graphology": "^0.25.1",
     "imports-loader": "^4.0.1",
     "jquery": "^3.6.3",
     "mitt": "^3.0.0",
+    "ml-hclust": "^3.1.0",
     "random-color-rgb": "^1.1.1",
     "sigma": "^1.2.2",
     "smallest-enclosing-circle": "^1.0.2",
@@ -33,7 +34,7 @@
     "@vue/cli-plugin-babel": "~5.0.0",
     "@vue/cli-plugin-eslint": "~5.0.0",
     "@vue/cli-plugin-router": "~5.0.0",
-    "@vue/cli-service": "~5.0.0",
+    "@vue/cli-service": "^5.0.8",
     "eslint": "^7.32.0",
     "eslint-plugin-vue": "^8.0.3",
     "versions": "^10.4.1"

frontend/src/App.vue

@@ -1,5 +1,5 @@
 <template>
-  <div class="container">
+  <div class="container" id="container">
     <router-view v-slot="{ Component }">
     <keep-alive exclude="HomeView">
       <component :is="Component" />