docker refactor and pin versions

Dockerfile

@@ -1,24 +1,26 @@
 FROM ubuntu:22.04
-MAINTAINER Mingxun Wang "mwang87@gmail.com"
+LABEL maintainer="Mingxun Wang <mwang87@gmail.com>"
 
 WORKDIR /app
 RUN apt-get update -y && \
         apt-get install -y libxrender-dev && \
         apt-get install -y git-core libarchive-dev build-essential wget vim curl
 
 # Install Mamba
-ENV CONDA_DIR /opt/conda
+ENV CONDA_DIR=/opt/conda
 RUN wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -O ~/miniforge.sh && /bin/bash ~/miniforge.sh -b -p /opt/conda
 ENV PATH=$CONDA_DIR/bin:$PATH
 RUN echo "export PATH=$CONDA_DIR:$PATH" >> ~/.bashrc
 
 RUN mamba create -y -n usi -c conda-forge -c bioconda -c defaults celery==5.3.6 \
         dash=1.20.0 dash-bootstrap-components=0.9.2 flask gunicorn \
         joblib matplotlib==3.6.3 numba numpy openssl qrcode rdkit requests \
-        requests-cache scipy spectrum_utils==0.3.5 werkzeug==2.0.0
+        requests-cache scipy setuptools spectrum_utils==0.3.5 werkzeug==2.0.0 \
+        python=3.11
+
 
 # install redis with pypi
-RUN /bin/bash -c 'source activate usi && pip install redis'
+RUN /bin/bash -c 'source activate usi && pip install redis "setuptools<81"'
 
 # installing hash
 RUN /bin/bash -c 'source activate usi && pip install "git+https://github.com/berlinguyinca/spectra-hash.git#subdirectory=python" && pip install celery-once'

Makefile

@@ -26,6 +26,10 @@ server-compose-interactive:
 	docker-compose --compatibility build
 	docker-compose --compatibility up
 
+server-compose-autotest-interactive:
+	docker-compose --compatibility build
+	docker-compose -f docker-compose.yml -f docker-compose-autotest.yml --compatibility up
+
 server-compose:
 	docker-compose --compatibility build
 	docker-compose --compatibility up -d

docker-compose-autotest.yml

@@ -0,0 +1,16 @@
+services:
+  metabolomicsusi-web:
+    command: /app/run_dev_server.sh
+    restart: "no"
+
+  metabolomicsusi-api1:
+    restart: "no"
+
+  metabolomicsusi-worker:
+    restart: "no"
+
+
+networks:
+  nginx-net:
+    name: nginx-net
+    external: true

docker-compose-production.yml

@@ -1,4 +1,3 @@
-version: '3'
 services:
   metabolomicsusi-web:
     networks:
@@ -64,5 +63,5 @@ services:
 
 networks:
   nginx-net:
-    external:
-      name: nginx-net
+    name: nginx-net
+    external: true

docker-compose.yml

@@ -1,4 +1,3 @@
-version: '3'
 services:
   metabolomicsusi-web:
     build:
@@ -72,6 +71,6 @@ services:
 
 networks:
   nginx-net:
-    external:
-      name: nginx-net
+    name: nginx-net
+    external: true
 

requirements.txt

@@ -18,6 +18,7 @@ redis
 requests
 requests_cache
 scipy
+setuptools
 umami-analytics
 spectrum_utils
 werkzeug==2.0.0

test/debug_script.py

@@ -0,0 +1,19 @@
+import functools
+import json
+import sys
+
+sys.path.insert(0, "../")  # Add the parent directory to the path
+
+from metabolomics_spectrum_resolver import parsing, similarity, views
+
+
+
+def debug():
+    usi = "mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00017443251"
+    # Parse the USI
+    parsed_usi = parsing.parse_usi(usi)
+    print("Parsed USI:", parsed_usi)
+
+
+if __name__ == "__main__":
+    debug()

test/test_unit.py

@@ -491,3 +491,5 @@ def test_cosine():
         + intensity[2] * intensity[3]
     )
     assert peak_matches == [(2, 3), (1, 1), (0, 0)]
+
+