biotransformer package updates

.dockerignore

@@ -0,0 +1,5 @@
+env/
+__pycache__/
+.idea/
+ExtractedJar/
+.github/

Dockerfile

@@ -18,7 +18,17 @@ RUN apt-get update -y && \
 COPY . /src/
 WORKDIR /src
 
-RUN chown -R $APP_USER:$APP_USER /src /tmp
+# RUN rm -rf \
+# 	/usr/local/lib/python3.11/site-packages/pip-23.1.2.dist-info \
+# 	/root/.cache/pip \
+# 	/usr/local/lib/python3.11/site-packages/pip \
+# 	/usr/local/pip3.11 \
+# 	/usr/local/pip3 \
+# 	/usr/local/pip
+
+RUN mkdir -p /var/www
+
+RUN chown -R $APP_USER:$APP_USER /src /tmp /var/www
 
 RUN chmod 755 /src/start_flask.sh
 

bt_cli.py

@@ -62,13 +62,23 @@ def execute_bt3(self, smiles, pred_type, gen_limit, predictions_filename):
 		"""
 		Executes biotransformer jar file for predictions.
 		"""
+
+		logging.warning("Using the following jar: {}".format(BT_JAR_NAME))
+
+		# subprocess.run(["java", "-jar", BT_JAR_NAME,
+		# 	"--task", "pred",
+		# 	"--btType", pred_type,
+		# 	"--ismiles", smiles,
+		# 	"--csvoutput", predictions_filename,
+		# 	"--nsteps", str(gen_limit),
+		# 	"-useDB", "false"
+		# ], cwd=BT_JAR_PATH)
 		subprocess.run(["java", "-jar", BT_JAR_NAME,
 			"--task", "pred",
 			"--btType", pred_type,
 			"--ismiles", smiles,
 			"--csvoutput", predictions_filename,
-			"--nsteps", str(gen_limit),
-			"-useDB", "false"
+			"--nsteps", str(gen_limit)
 		], cwd=BT_JAR_PATH)
 
 	def build_endpoint_args(self):

docker-compose.yml

@@ -16,4 +16,4 @@ services:
     #   - ./:/src
     environment:
       - BT_JAR_PATH=/src/biotransformer3.0jar
-      - BT_JAR_NAME=BioTransformer3.0_20230525.jar
+      - BT_JAR_NAME=biotransformer.jar  # name of .jar in biotransformer3.0jar/