Development Branch

.env_template

@@ -0,0 +1 @@
+HOSTNAME=de.metabolomics-usi.gnps2.org

.github/workflows/build.yml

@@ -0,0 +1,29 @@
+name: Docker Build Test
+
+on:
+  push:
+    branches:
+      master
+  pull_request:
+    branches:
+      master
+  schedule:
+      - cron:  '0 0 * * 1'
+
+jobs:
+  build-test:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: [3.8]
+# TODO: We probably should switch to using the Docker version.
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Build Docker
+      run: |
+        docker build . 

Dockerfile

@@ -1,14 +1,20 @@
-FROM continuumio/miniconda3:4.8.2
+FROM continuumio/miniconda3:4.10.3
 MAINTAINER Mingxun Wang "[email protected]"
 
 WORKDIR /app
 RUN apt-get update -y && \
         apt-get install -y libxrender-dev && \
-        apt-get install -y git-core
-RUN conda create -y -n usi -c conda-forge -c bioconda -c defaults celery \
+        apt-get install -y git-core libarchive-dev
+RUN conda install -c conda-forge mamba
+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 numba numpy openssl qrcode rdkit requests \
-        requests-cache scipy spectrum_utils werkzeug
+        joblib matplotlib==3.6.3 numba numpy openssl qrcode rdkit requests \
+        requests-cache scipy spectrum_utils==0.3.5 werkzeug==2.0.0
+
+# install redis with pypi
+RUN /bin/bash -c 'source activate usi && pip install redis'
+
+# 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'
 
 RUN echo "source activate usi" > ~/.bashrc

Makefile

@@ -23,19 +23,19 @@ clear-cache:
 
 #Docker Compose
 server-compose-interactive:
-	docker-compose build
-	docker-compose up
+	docker-compose --compatibility build
+	docker-compose --compatibility up
 
 server-compose:
-	docker-compose build
-	docker-compose up -d
+	docker-compose --compatibility build
+	docker-compose --compatibility up -d
 
 server-compose-production-interactive:
-	docker-compose build
+	docker-compose --compatibility build
 	docker-compose -f docker-compose.yml -f docker-compose-production.yml --compatibility up
 
 server-compose-production:
-	docker-compose build
+	docker-compose --compatibility build
 	docker-compose -f docker-compose.yml -f docker-compose-production.yml --compatibility up -d
 
 attach:

docker-compose-production.yml

@@ -5,29 +5,44 @@ services:
       - default
       - nginx-net
     environment:
-      VIRTUAL_HOST: metabolomics-usi.ucsd.edu,metabolomics-usi.gnps2.org
-      VIRTUAL_PORT: 5087
-      LETSENCRYPT_HOST: metabolomics-usi.ucsd.edu,metabolomics-usi.gnps2.org
+      VIRTUAL_HOST: ${HOSTNAME:-metabolomics-usi.gnps2.org}
+      VIRTUAL_PORT: 5000
+      LETSENCRYPT_HOST: ${HOSTNAME:-metabolomics-usi.gnps2.org}
       LETSENCRYPT_EMAIL: [email protected]
     command: /app/run_server.sh
     deploy:
       resources:
         limits:
           memory: 16000M
+    logging:
+      driver: "json-file"
+      options:
+        max-size: "10m"
+        max-file: "3"
 
   metabolomicsusi-worker:
     deploy:
       resources:
         limits:
           memory: 16000M
+    logging:
+      driver: "json-file"
+      options:
+        max-size: "10m"
+        max-file: "3"
 
   metabolomicsusi-redis:
     deploy:
       resources:
         limits:
           memory: 4000M
+    logging:
+      driver: "json-file"
+      options:
+        max-size: "10m"
+        max-file: "3"
 
 networks:
   nginx-net:
     external:
-      name: nginx-net
+      name: nginx-net

docker-compose.yml

@@ -12,7 +12,7 @@ services:
         - ./logs/:/app/logs:rw
     networks:
       - default
-    restart: on-failure
+    restart: always
     command: /app/run_dev_server.sh
 
   metabolomicsusi-worker:
@@ -24,7 +24,7 @@ services:
       - ./tmp:/app/tmp:rw
       - ./logs:/app/logs:rw
     command: /app/run_worker.sh
-    restart: on-failure
+    restart: always
     depends_on:
       - metabolomicsusi-redis
     networks:
@@ -33,10 +33,11 @@ services:
 
   metabolomicsusi-redis:
     container_name: metabolomicsusi-redis
-    image: redis
+    #image: valkey/valkey:alpine3.20
+    image: redis:alpine
     networks:
       - default
-    restart: on-failure
+    restart: always
 
 networks:
   nginx-net:

metabolomics_spectrum_resolver/dashinterface.py

@@ -39,6 +39,8 @@
 
         gtag('config', 'UA-8412213-8');
         </script>
+
+        <script async defer data-website-id="ce3d7d73-8edf-480d-83f6-5c3eab60deac" src="https://analytics.gnps2.org/umami.js"></script>
 
         {%metas%}
         <title>{%title%}</title>
@@ -59,10 +61,10 @@
     children=[
         dbc.NavbarBrand(
             html.Img(
-                src="https://gnps-cytoscape.ucsd.edu/static/img/GNPS_logo.png",
+                src="https://gnps2.org/static/img/logo.png",
                 width="120px",
             ),
-            href="https://gnps.ucsd.edu",
+            href="https://gnps2.org",
         ),
         dbc.Nav(
             [
@@ -426,7 +428,7 @@
     dbc.CardHeader(html.H5("Contributors")),
     dbc.CardBody(
         [
-            "Mingxun Wang, PhD – UC San Diego",
+            "Mingxun Wang, PhD – UC Riverside",
             html.Br(),
             "Wout Bittremieux, PhD – UC San Diego",
             html.Br(),