Dependency migration

Dockerfile

@@ -1,8 +1,12 @@
 FROM python:3.12.6-bullseye
 
 # Install required packages using apt
+# RUN apt-get update && apt-get install -y \
+#     libmariadb3 libmariadb-dev build-essential linux-headers-amd64 mariadb-connector-c \
+#     && rm -rf /var/lib/apt/lists/*
+
 RUN apt-get update && apt-get install -y \
-    libmariadb3 libmariadb-dev build-essential linux-headers-amd64 \
+    default-mysql-client default-libmysqlclient-dev build-essential linux-headers-amd64 \
     && rm -rf /var/lib/apt/lists/*
 
 # Upgrade pip
@@ -12,11 +16,13 @@ WORKDIR /server
 COPY . /server
 
 RUN pip3 --no-cache-dir install -r requirements.txt
+RUN pip install debugpy
+
 
 # the mariadb plugin directory seems to be misconfigured
 # bei default. In order to work properly we manually adjust
 # the path.
-ENV MARIADB_PLUGIN_DIR=/usr/lib/mariadb/plugin
+# ENV MARIADB_PLUGIN_DIR /usr/lib/mariadb/plugin
 
 # EXPOSE 5000
 # CMD ["python3", "server.py"]

config.py

@@ -31,6 +31,9 @@
 MODEL_PATH = os.getenv("SPONGEFFECTS_MODEL_PATH")
 SPONGEFFECTS_PREDICT_SCRIPT = os.getenv("SPONGEFFECTS_PREDICT_SCRIPT")
 
+# latest database version 
+LATEST = 2
+
 # Configure the SQLAlchemy part of the app instance
 app.config['SQLALCHEMY_ECHO'] = False
 app.config['SQLALCHEMY_DATABASE_URI'] = "mysql://root:[email protected]:9669/SPONGEdb_v2"  # os.getenv("SPONGE_DB_URI")

externalInformation.py

@@ -1,6 +1,9 @@
 from flask import abort
 import models
 from flask import Response
+from sqlalchemy.sql import text
+import sqlalchemy as sa
+import os
 
 
 def getAutocomplete(searchString):
@@ -43,8 +46,6 @@ def getAutocomplete(searchString):
         else:
             abort(404, "No gene symbol found for the given String")
 
-import sqlalchemy as sa
-import os
 
 def getGeneInformation(ensg_number=None, gene_symbol=None):
     """
@@ -120,7 +121,7 @@ def getOverallCount():
     session = Session()
     # test for each dataset if the gene(s) of interest are included in the ceRNA network
 
-    count = session.execute(
+    count = session.execute(text(
             "select * "
             " from (select sum(count_all)/2 as count_interactions, sum(count_sign)/2 as count_interactions_sign, run_ID "
                 "from gene_counts group by run_ID) as t1 "
@@ -129,7 +130,7 @@ def getOverallCount():
             "using(run_ID) "
             "join "
             "(SELECT dataset.disease_name, run.run_ID from dataset join run where dataset.dataset_ID = run.dataset_ID) as t3 "
-            "using(run_ID);").fetchall()
+            "using(run_ID);")).fetchall()
 
     session.close()
     some_engine.dispose()

geneInteraction.py

@@ -649,10 +649,10 @@ def read_mirna_for_specific_interaction(disease_name=None, ensg_number=None, gen
         session = Session()
         # test for each dataset if the gene(s) of interest are included in the ceRNA network
 
-        mirna_filter = session.execute(text(text("select mirna_ID from interactions_genemirna where sponge_run_ID IN ( "
+        mirna_filter = session.execute(text("select mirna_ID from interactions_genemirna where sponge_run_ID IN ( "
                                        + ','.join(str(e) for e in run_IDs) + ") and gene_ID IN ( "
                                        + ','.join(str(e) for e in gene_IDs)
-                                       + ") group by mirna_ID HAVING count(mirna_ID) >= 2;"))).fetchall()
+                                       + ") group by mirna_ID HAVING count(mirna_ID) >= 2;")).fetchall()
 
         session.close()
         some_engine.dispose()
@@ -811,5 +811,3 @@ def get_distinc_ceRNA_sets(disease_name):
     #else:
         #abort(404, "No data found with input parameter")
     return
-
-get_distinc_ceRNA_sets(disease_name="kidney clear")

gsea.py

@@ -1,6 +1,5 @@
 from flask import abort
 import models
-import gseapy as gp
 from gseapy.plot import GSEAPlot
 import base64
 import io 

requirements.txt

@@ -19,6 +19,7 @@ flask-marshmallow==1.2.1
 Flask-SQLAlchemy==3.1.1
 fonttools==4.54.1
 greenlet==3.1.1
+gseapy==1.1.3
 gunicorn==23.0.0
 h11==0.14.0
 h2==4.1.0
@@ -80,7 +81,6 @@ typing_extensions==4.12.2
 tzdata==2024.2
 urllib3==2.2.3
 uvicorn==0.30.6
-uWSGI==2.0.23
 Werkzeug==3.0.4
 wheel==0.44.0
 zipp==3.20.2

survivalAnalysis.py

@@ -113,7 +113,7 @@ def get_survival_rate(disease_name, ensg_number = None, gene_symbol = None, samp
 
     # database version 
     if db_version is not None: 
-
+        queries.append(models.Dataset.version == db_version)
 
     result = models.SurvivalRate.query \
         .filter(*queries) \

swagger.yml

@@ -269,7 +269,7 @@ paths:
           content:
             application/json:
               schema:
-                type: array
+                type: object
                 items:
                   properties:
                     data_origin: