V2.1.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MIRA
 Type: Package
 Title: Portable, Interactive Application for High-Quality Influenza, SARS-CoV-2, & RSV Genome Assembly, Annotation, and Curation
-Version: 2.0.0
+Version: 2.1.0
 Date: 2024-09-23
 Authors@R: 
   c(person(given="Kristine", family="Lacek", role=c("cre", "aut"), 

Dockerfile

@@ -14,11 +14,7 @@ RUN if [ -n "$APT_MIRROR_NAME" ]; then sed -i.bak -E '/security/! s^https?://.+?
 # Install and update system libraries of general use
 RUN apt-get update --allow-releaseinfo-change --fix-missing \
   && apt-get install --no-install-recommends -y \
-  build-essential \ 
-  iptables \
-  python3.7 \
-  python3-pip \
-  python3-setuptools \
+  vim \
   dos2unix
 
 # Create a working directory variable
@@ -41,11 +37,46 @@ COPY . ${MIRA_PROGRAM_DIR}
 
 ############# Install python packages ##################
 
-# Copy python requirements file to docker images
+# Copy all files to docker images
 COPY requirements.txt ${MIRA_PROGRAM_DIR}/requirements.txt
 
-# Install python requirements
-RUN pip3 install --no-cache-dir -r ${MIRA_PROGRAM_DIR}/requirements.txt
+# Update pip and setuptools and then install python packages
+RUN pip install --no-cache-dir --upgrade pip \
+  && pip install --no-cache-dir -r ${MIRA_PROGRAM_DIR}/requirements.txt  
+
+############# Fix vulnerablities pkgs ##################
+
+# Copy all files to docker images
+COPY fixed_vulnerability_pkgs.txt ${MIRA_PROGRAM_DIR}/fixed_vulnerability_pkgs.txt
+
+# Copy all files to docker images
+COPY fixed_vulnerability_pkgs.sh ${MIRA_PROGRAM_DIR}/fixed_vulnerability_pkgs.sh
+
+# Convert bash script from Windows style line endings to Unix-like control characters
+RUN dos2unix ${MIRA_PROGRAM_DIR}/fixed_vulnerability_pkgs.sh
+
+# Allow permission to excute the bash script
+RUN chmod a+x ${MIRA_PROGRAM_DIR}/fixed_vulnerability_pkgs.sh
+
+# Execute bash script to wget the file and tar the package
+RUN bash ${MIRA_PROGRAM_DIR}/fixed_vulnerability_pkgs.sh    
+
+############# Remove vulnerability pkgs ##################
+
+# Copy all files to docker images
+COPY remove_vulnerability_pkgs.txt ${MIRA_PROGRAM_DIR}/remove_vulnerability_pkgs.txt
+
+# Copy all files to docker images
+COPY remove_vulnerability_pkgs.sh ${MIRA_PROGRAM_DIR}/remove_vulnerability_pkgs.sh
+
+# Convert bash script from Windows style line endings to Unix-like control characters
+RUN dos2unix ${MIRA_PROGRAM_DIR}/remove_vulnerability_pkgs.sh
+
+# Allow permission to excute the bash script
+RUN chmod a+x ${MIRA_PROGRAM_DIR}/remove_vulnerability_pkgs.sh
+
+# Execute bash script to wget the file and tar the package
+RUN bash ${MIRA_PROGRAM_DIR}/remove_vulnerability_pkgs.sh
 
 ############# Launch MIRA dashboard ##################
 

NEWS.md

@@ -1,9 +1,14 @@
 
-# MIRA 2.0.0
+# MIRA 2.1.0
 
 * Github Repo: https://github.com/CDCgov/MIRA
 * Documentation: https://cdcgov.github.io/MIRA
 
+### v2.1.0
+- Artic RSV primers added
+- VIDRL RSV primers added
+- Containers rebuilt without vulnerability
+
 ### v2.0.0
 - Single container distribution (previously 4 docker images)
 - RSV Illumina module

app.py

@@ -460,6 +460,8 @@ def run_snake_script_onClick(
             docker_cmd += f"-p {Amplicon_Library_SC2} "
         elif  "rsv-illumina" in experiment_type.lower():
             docker_cmd += f"-p {Amplicon_Library_RSV} "
+        elif "sc2-spike-only-illumina" in experiment_type.lower():
+            docker_cmd += f"-p s_gene "
         docker_cmd += f"-c CLEANUP-FOOTPRINT"
         print(f'launching docker_cmd == "{docker_cmd}"\n\n')
         subprocess.Popen(docker_cmd.split(), close_fds=True)
@@ -1055,12 +1057,13 @@ def blank_fig():
             dcc.Dropdown(
                 [
                     {"label": "Flu-ONT", "value": "Flu-ONT"},
-                    {"label": "SC2-Spike-Only-ONT", "value": "SC2-Spike-Only-ONT"},
                     {"label": "Flu-Illumina", "value": "Flu-Illumina"},
+                    {"label": "SC2-Spike-Only-ONT", "value": "SC2-Spike-Only-ONT"},
+                    {"label": "SC2-Spike-Only-Illumina", "value":"SC2-Spike-Only-Illumina"},
                     {"label": "SC2-Whole-Genome-ONT", "value":"SC2-Whole-Genome-ONT"},
                     {"label": "SC2-Whole-Genome-Illumina", "value": "SC2-Whole-Genome-Illumina"},
                     {"label": "RSV-Illumina", "value": "RSV-Illumina"},
-                    {"label": "RSV-ONT", "value": "RSV-ONT",},
+                    {"label": "RSV-ONT", "value": "RSV-ONT"},
                 ],
                 id="experiment_type",
                 placeholder="What kind of data is this?",
@@ -1094,8 +1097,9 @@ def blank_fig():
             dcc.Dropdown(
                 [
                     {"label": "RSV CDC 8 amplicon 230901", "value": "RSV_CDC_8amplicon_230901"},
-                    {"label": "Dong et al. 230312", "value": "dong_et_al"},
+                    {"label": "WHO-CC Australia | 2024", "value": "australia_cc_2024"},
                     {"label": "Davina-Nunez et al. - WG pools", "value": "davina_nunez_wgs"},
+                    {"label": "Artic V1", "value":"artic_v1"}
                 ],  # add handling here for no primers used
                 id="Amplicon_Library_RSV",
                 placeholder="For Illumina RSV, which primer schema was used?",

docker-compose-cdcgov.yml

@@ -1,8 +1,7 @@
-version: "3.9"
 
 x-mira-image:
   &mira-image
-  cdcgov/mira:v2.0.0
+  cdcgov/mira:latest
 
 x-data-volume:
   &data-volume
@@ -19,3 +18,4 @@ services:
       - 8020:8050
     volumes:
       - *data-volume
+    command: tail -f /dev/null

docker-compose-dev.yml

@@ -1,20 +1,7 @@
-version: "3.9"
 
 x-spyne-image:
   &spyne-image
-  spyne_image: cdcgov/spyne-dev:v2.0.0
-
-x-mira-volume:
-  &mira-volume
-  type: bind
-  source: /home/snu3/Github/MIRA
-  target: /MIRA
-
-x-spyne-volume:
-  &spyne-volume
-  type: bind
-  source: /home/snu3/Github/spyne
-  target: /spyne
+  spyne_image: spyne:latest
 
 x-data-volume:
   &data-volume
@@ -36,5 +23,4 @@ services:
       - 8020:8050
     volumes:
       - *data-volume
-      - *mira-volume
-      - *spyne-volume
+    command: tail -f /dev/null

docker-compose-git.yml

@@ -1,4 +1,3 @@
-version: "3.9"
 
 x-spyne-git-repo:
   &spyne-git-repo
@@ -8,21 +7,29 @@ x-mira-git-repo:
   &mira-git-repo
   https://github.com/CDCgov/MIRA.git#prod
 
+x-base-image:
+  &base-image
+  base_image: python:3.10-slim-bookworm
+
+x-python-version:
+  &python-version
+  python_version: python3.10
+
 x-irma-image:
   &irma-image
-  cdcgov/irma:v1.2.0
- 
+  irma_image: cdcgov/irma:v1.2.1
+
 x-dais-image:
   &dais-image
-  cdcgov/dais-ribosome:v1.5.4
- 
+  dais_image: cdcgov/dais-ribosome:v1.5.5
+
 x-spyne-image:
   &spyne-image
-  spyne:v2.0.0  
+  spyne:latest  
 
 x-mira-image:
   &mira-image
-  mira:v2.0.0    
+  mira:latest   
 
 x-data-volume:
   &data-volume
@@ -38,8 +45,7 @@ services:
       context: *spyne-git-repo
       dockerfile: Dockerfile
       args:
-        irma_image: *irma-image
-        dais_image: *dais-image
+        << : [*base-image, *python-version, *irma-image, *dais-image]
     restart: always
     networks:
       - backend
@@ -65,6 +71,7 @@ services:
       - 8020:8050
     volumes:
       - *data-volume
+    command: tail -f /dev/null
 
 networks:
   backend:

docker-compose.yml

@@ -1,13 +1,12 @@
-version: "3.9"
 
 x-spyne-image:
   &spyne-image
-  spyne_image: cdcgov/spyne:v2.0.0
+  spyne_image: cdcgov/spyne:latest
 
 x-data-volume:
   &data-volume
   type: bind
-  source: ~/FLU_SC2_SEQUENCING
+  source: /home/snu3/Github/FLU_SC2_SEQUENCING
   target: /data
 
 services:
@@ -24,3 +23,4 @@ services:
       - 8020:8050
     volumes:
       - *data-volume
+    command: tail -f /dev/null

fixed_vulnerability_pkgs.sh

@@ -0,0 +1,49 @@
+
+#!/bin/bash
+# Wrapper to install python packages 
+
+# Path to requirement file
+SPYNE_PROGRAM_DIR=${SPYNE_PROGRAM_DIR:-/spyne}
+fixed_pkgs=${SPYNE_PROGRAM_DIR}/fixed_vulnerability_pkgs.txt
+fixed_pkgs_clean=${SPYNE_PROGRAM_DIR}/fixed_vulnerability_pkgs_clean.txt
+
+# Install updated version of python pkgs
+if [[ -f ${fixed_pkgs} ]]
+then
+
+    echo "Update python packages"
+
+	# Remove blank lines from the file and save a cleaner version of it
+	awk NF < ${fixed_pkgs} > ${fixed_pkgs_clean}
+
+	# Get number of packages in the file
+	n=`wc -l < ${fixed_pkgs_clean}`
+	i=1
+
+    while [[ i -le $n ]];
+	do
+		echo $i
+		# Get the name of the package and its version
+		updated_pkg=$(head -${i} ${fixed_pkgs_clean} | tail -1 | sed -e 's,\r,,g')
+		echo $updated_pkg
+        # Get the package name only
+        pkg_name=$(echo ${updated_pkg} | sed -e "s/\(.*\)\(==\)\(.*\)/\1/g")
+		echo $pkg_name
+        # Check if package already existed in pip install
+        check_pip_pkg=$(pip list | grep -w ${pkg_name} | sed -e "s/\s\+/==/g")
+		echo $check_pip_pkg
+        # If package exists, update to new version
+        case ${check_pip_pkg} in
+            "") ;;
+            *)  pip install --no-cache-dir ${updated_pkg};;
+        esac
+        # Go to next pkg
+        i=$(($i+1))
+    done
+
+	# Return message to keep the process going
+    echo "Done"
+
+fi
+
+

fixed_vulnerability_pkgs.txt

@@ -0,0 +1,2 @@
+setuptools==70.0.0
+idna==3.10

remove_vulnerability_pkgs.sh

@@ -0,0 +1,38 @@
+
+#!/bin/bash
+# Wrapper to remove vulnerability packages 
+
+SPYNE_PROGRAM_DIR=${SPYNE_PROGRAM_DIR:-/spyne}
+remove_pkgs=${SPYNE_PROGRAM_DIR}/remove_vulnerability_pkgs.txt
+remove_pkgs_clean=${SPYNE_PROGRAM_DIR}/remove_vulnerability_pkgs_clean.txt
+python_version=${python_version:-python3.10}
+
+# Extract bbmap package to the bbtools directory
+if [[ -f ${remove_pkgs} ]]
+then
+
+	echo "Remove vulnerability packages"
+
+	# Remove blank lines from the file and save a cleaner version of it
+	awk NF < ${remove_pkgs} > ${remove_pkgs_clean}
+
+	# Get number of packages in the file
+	n=`wc -l < ${remove_pkgs_clean}`
+	i=1
+
+	while [[ i -le $n ]];
+	do
+		echo $i
+		# Get the name of the package
+		pkg_name=$(head -${i} ${remove_pkgs_clean} | tail -1 | sed 's,\r,,g')
+		echo $pkg_name
+		# Remove the package if it exists
+		find /usr/local/lib/${python_version}/site-packages -name "*${pkg_name}*" -exec rm -rf {} \;
+		# Go to next file
+		i=$(($i+1))
+	done
+
+	# Return message to keep the process going
+	echo "Done"
+
+fi

requirements.txt

@@ -1,18 +1,18 @@
 colorlover
-dash==2.11.0
+dash==2.15.0
 dash-bio==0.2.0
 dash-bootstrap-components==1.2.1
 dash-core-components==2.0.0
 dash-daq==0.5.0
 dash-html-components==2.0.0
 dash-table==5.0.0
-flask==2.1.3
+flask==3.0.3
 flask-caching==1.10.1
 flask-compress==1.5.0
-numpy==1.19.5
-openpyxl==3.0.10
-pandas==1.1.0
+numpy==1.23.1
+openpyxl==3.1.0
+pandas==2.0.3
 plotly==5.11.0
-pyyaml==6.0
-requests==2.28.1
-Werkzeug==2.2.2
+pyyaml==6.0.2
+requests==2.32.0
+Werkzeug==3.0.6