From 879cdb4ca28b7356c6f02a0cd3ef7bdc5d7bbe47 Mon Sep 17 00:00:00 2001
From: popenc <i.nickpope@gmail.com>
Date: Wed, 7 Aug 2024 11:10:52 -0400
Subject: [PATCH] biotransformer package updates

---
 .dockerignore      |  5 +++++
 .gitmodules        |  3 ---
 Dockerfile         | 12 +++++++++++-
 bt_cli.py          | 14 ++++++++++++--
 docker-compose.yml |  2 +-
 5 files changed, 29 insertions(+), 7 deletions(-)
 create mode 100644 .dockerignore
 delete mode 100644 .gitmodules

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..704385c
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,5 @@
+env/
+__pycache__/
+.idea/
+ExtractedJar/
+.github/
\ No newline at end of file
diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index 51f4aa6..0000000
--- a/.gitmodules
+++ /dev/null
@@ -1,3 +0,0 @@
-[submodule "biotransformer3.0jar"]
-	path = biotransformer3.0jar
-	url = https://bitbucket.org/wishartlab/biotransformer3.0jar
diff --git a/Dockerfile b/Dockerfile
index ef96bcc..4c2cb5c 100644
--- a/Dockerfile
+++ b/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
 
diff --git a/bt_cli.py b/bt_cli.py
index bef8f76..6548f03 100644
--- a/bt_cli.py
+++ b/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):
diff --git a/docker-compose.yml b/docker-compose.yml
index 3e3f2ef..40394a0 100644
--- a/docker-compose.yml
+++ b/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/