For Bartweb deployment

Dockerfile_uwsgi.dockerfile

@@ -0,0 +1,56 @@
+# Base OS with Python and tools
+FROM debian:latest
+# Metadata: Wenjing Ma
+LABEL MAINTAINER="mawenjing1993@gmail.com"
+
+# Update OS
+RUN apt-get update -y
+
+# Install Python + build tools (keep as-is, just drop Apache)
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    python3 \
+    python3-dev \
+    python3-pip \
+    vim \
+ && apt-get clean \
+ && apt-get autoremove \
+ && rm -rf /var/lib/apt/lists/*
+
+# Install uwsgi
+RUN pip3 install --no-cache-dir --break-system-packages uwsgi
+
+# App deps
+COPY ./requirements.txt /BARTweb/requirements.txt
+RUN pip3 install --break-system-packages -r /BARTweb/requirements.txt
+
+# App code
+RUN mkdir -p /BARTweb
+COPY . /BARTweb/
+
+# Prepare a writable usercase root (same fix that solved the 500)
+RUN mkdir -p /BARTweb/usercase \
+ && chown -R www-data:www-data /BARTweb/usercase \
+ && chmod -R 775 /BARTweb/usercase
+
+# Logs
+RUN mkdir -p /log /BARTweb/usercase/log \
+ && touch /log/bartweb.log /BARTweb/usercase/log/bartweb.log \
+ && chown -R www-data:www-data /log /BARTweb/usercase/log \
+ && chmod -R 775 /BARTweb/usercase/log
+
+WORKDIR /BARTweb/
+
+# Root stuff
+# Create a non-root user and group called "app"
+RUN groupadd -g 1001 app && useradd -u 1001 -g app -m app
+# Give ownersip of app + log dirs to user
+RUN chown -R app:app /BARTweb /log
+# Switch to new user
+USER app
+
+# Flask default port
+EXPOSE 5000
+
+# Run Flask app (app.py already has host='0.0.0.0')
+CMD ["uwsgi", "--ini", "uwsgi.ini"]

app.py

@@ -261,9 +261,9 @@ def help():
                 logger.error("Retrieve result: did not find the result.")
                 err_msg = "Job does not exist, make sure you enter the right key."
                 return redirect(url_for('error_page', msg=err_msg))
-
     return render_template('help.html')
 
+
 #############################################
 
 @app.route('/result', methods=['GET', 'POST'])
@@ -291,6 +291,11 @@ def get_result():
 
         results = parseIO.generate_results(user_data)
         results['sample'] = False
+
+        ## @marvinquite 02/25/2024, debug purpose
+        # logger.info(results)
+        ## Results can be accurately retrieved 04/16/2024 
+        ## end 
         return render_template('result_demonstration.html', results=results, key=request.args['user_key'])
 
 @app.route('/error', methods=['GET', 'POST'])
@@ -333,10 +338,10 @@ def download_sample_file(sample_type):
     if sample_type == 'genelist':
         sample_name = "genelist.txt"
         sample_path = os.path.join(PROJECT_DIR, 'sample/genelist/upload')
-    elif sample_type == 'ChIPseq.bam':
+    elif sample_type == 'ChIPdata':
         sample_name = "ChIPseq.bam"
-        sample_path = os.path.join(PROJECT_DIR, 'sample/ChIPdata')
-    elif sample_type == 'ChIPpeaks.bed':
+        sample_path = os.path.join(PROJECT_DIR, 'sample/ChIPdata/upload')
+    elif sample_type == 'ChIPpeaks':
         sample_name = "ChIPpeaks.bed"
         sample_path = os.path.join(PROJECT_DIR, 'sample/Region')
 
@@ -351,7 +356,7 @@ def sample_result(sample_type):
 
     user_data = {}
     with open(config_file, 'r') as fopen:
-        user_data = yaml.load(fopen)
+        user_data = yaml.load(fopen, Loader=yaml.FullLoader)
 
     if user_data:
         results = parseIO.generate_results(user_data)

Dockerfile → archived/Dockerfile

@@ -1,29 +1,10 @@
-FROM debian:latest
-MAINTAINER Yifan Zhang
-
-# Update OS
-RUN apt-get update -y
-
-# Install Python other things
-#RUN apt-get install -y python-pip python-dev build-essential
-RUN apt-get update && apt-get install -y apache2 \
-    libapache2-mod-wsgi-py3 \
-    build-essential \
-    python3 \
-    python3-dev\
-    python3-pip \
-    vim \
- && apt-get clean \
- && apt-get autoremove \
- && rm -rf /var/lib/apt/lists/*
-
-# && do not continue if any fails
-
+# FROM Dockerfile_debian_20240506_fixed  # not sure if this would be the correct name for it
+# MAINTAINER Wenjing Ma mawenjing1993@gmail.com
 
 # ADD . /app
 COPY ./requirements.txt /BARTweb/requirements.txt
 # RUN pip install uwsgi
-RUN pip3 install -r /BARTweb/requirements.txt
+RUN pip3 install --break-system-packages -r /BARTweb/requirements.txt
 
 # Copy over the apache configuration file and enable the site
 COPY ./apache-flask.conf /etc/apache2/sites-available/apache-flask.conf
@@ -42,12 +23,14 @@ EXPOSE 80
 # ENV HOME /app change to apache-flask
 WORKDIR /BARTweb/
 
-# For log
+# For log -> in 20230401j docker image
+RUN mkdir /log && touch /log/bartweb.log
+RUN chown -R www-data:www-data /log
+# original For log
 RUN mkdir -p usercase/log
 RUN touch usercase/log/bartweb.log
 RUN chown -R www-data:www-data usercase/log
 RUN chmod -R 775 usercase/log
 
 #run apache, this directory is present with installation of apache
 CMD ["/usr/sbin/apache2ctl", "-D", "FOREGROUND"]
-

archived/Dockerfile_debian_20240506_fixed

@@ -0,0 +1,20 @@
+FROM debian:latest
+MAINTAINER Wenjing Ma mawenjing1993@gmail.com
+
+# Update OS
+RUN apt-get update -y
+
+# Install Python other things
+#RUN apt-get install -y python-pip python-dev build-essential
+RUN apt-get update && apt-get install -y apache2 \
+    libapache2-mod-wsgi-py3 \
+    build-essential \
+    python3 \
+    python3-dev\
+    python3-pip \
+    vim \
+ && apt-get clean \
+ && apt-get autoremove \
+ && rm -rf /var/lib/apt/lists/*
+
+# && do not continue if any fails