Merge pull request #87 from openvar/v3.2.0

V3.2.0

Author: Peter J. Freeman

Dockerfile

@@ -1,6 +1,6 @@
 
 # Use an official Python runtime as a parent image
-FROM python:3.8
+FROM python:3.10
 
 # Set the working directory to /app
 WORKDIR /app
@@ -30,5 +30,4 @@ RUN pip install -e .
 COPY configuration/docker.ini /root/.variantvalidator
 
 # Start the application with gunicorn
-# CMD gunicorn -b 0.0.0.0:8000 app --workers=3 --threads=5 --worker-class=gthread --chdir ./rest_VariantValidator/
 CMD gunicorn  -b 0.0.0.0:8000 app --threads=5 --chdir ./rest_VariantValidator/

configuration/docker.ini

@@ -4,30 +4,30 @@ port = 3306
 database = validator
 user = vvadmin
 password = var1ant
-version = vvdb_2022_04
+version = vvdb_2022_11
 
 [seqrepo]
-version = VV_SR_2022_02/master
+version = VV_SR_2022_11/master
 location = /usr/local/share/seqrepo
+require_threading = True
 
 [postgres]
 host = vvta
 port = 5432
 database = vvta
-version = vvta_2022_02
+version = vvta_2022_11
 user = uta_admin
 password = uta_admin
 
 [logging]
-#Levels control verbosity and can be set to "CRITICAL" "ERROR" "WARNING" "INFO" or "DEBUG".
-log_to = /usr/local/share/logs
+# Levels control verbosity and can be set to "CRITICAL" "ERROR" "WARNING" "INFO" or "DEBUG".
 log = True
 console = WARNING
 file = ERROR
 
 [Entrez]
-email = None
-api_key = None
+email = OPTIONAL
+api_key = OPTIONAL
 
 
 # <LICENSE>

docker-compose.yml

@@ -6,17 +6,17 @@ services:
       context: .
       dockerfile: vdb_docker.df
     ports:
-      - "33060:3306"
+      - "33061:3306"
     expose:
-      - "33060"
+      - "33061"
   vvta:
     build:
       context: .
       dockerfile: vvta_docker.df
     ports:
-      - "54320:5432"
+      - "54321:5432"
     expose:
-      - "54320"
+      - "54321"
   seqrepo:
     build:
       context: .

docs/DOCKER.md

@@ -37,6 +37,17 @@ do not update your container for more than 12 months; else leave as `None`. See
 Note: Reconfiguration can be achieved by accessing the docker container through bash. See below for entry and the 
 VariantValidator [manual](https://github.com/openvar/variantValidator/blob/master/docs/MANUAL.md) for details
 
+- Edit the `vdb_docker.df` file 
+
+You need to select your chip set e.g. Arm or Intel and remove the relevant hash. Default is intel
+
+```
+# For Arm chips e.g. Apple M1
+# FROM biarms/mysql:5.7
+
+# For Intel chips
+FROM mysql:5.7
+```
 
 ## Build the container
 
@@ -53,6 +64,7 @@ $ docker-compose pull
 ```bash
 $ mkdir ~/variantvalidator_data
 $ mkdir ~/variantvalidator_data/share
+$ mkdir ~/variantvalidator_data/share/logs
 ```
 *i.e.* a directory called `variantvalidator_data/share` in your `home` directory
 
@@ -66,7 +78,7 @@ $ docker-compose build --no-cache
     - The first time you do this, it will complete the build process, for example, populating the required the databases
     - The build takes a while because the  vv databases are large. However, this is a significant improvement on previou
     s versions. Build time is ~30 minutes (depending on the speed of you computer and internet connection)
-    - The build has completed when you see the message ***"naming to docker.io/library/rest_variantvalidator_restvv"***
+    - The build has completed when you see the message ***"Use 'docker scan' to run Snyk tests against images to find vulnerabilities and learn how to fix them"***
 
 ```bash
 # If you have previously installed this software you will need to remove old SeqRepo databases
@@ -216,6 +228,7 @@ $ exit
     - Note: Under the terms and conditions of our [license](https://github.com/openvar/rest_variantValidator/blob/master/LICENSE.txt) changes to the code and improvements must be made available to the community so that we can integrate them for the good of all our users 
     - See instructions on VariantValidator development in Docker 
 
+3. For other commands that you can run using bash, see the [VariantValidator DOCKER.md](https://github.com/openvar/variantValidator/blob/master/docs/DOCKER.md)
 
 ## Developing VariantValidator in Docker
 The container has been configured with git installed. This means that you can clone Repos directly into the container

vdb_docker.df

@@ -1,4 +1,8 @@
-FROM mysql:latest
+# For Arm chips e.g. Apple M1
+# FROM biarms/mysql:5.7
+
+# For Intel chips
+FROM mysql:5.7
 
 ENV MYSQL_RANDOM_ROOT_PASSWORD yes
 
@@ -10,5 +14,4 @@ ENV MYSQL_PASSWORD var1ant
 
 RUN apt-get update && apt-get install -y wget && rm -rf /var/lib/apt/lists/*
 
-RUN wget --output-document=validator_2022_04.sql.gz https://www528.lamp.le.ac.uk/vvdata/validator/validator_2022_04.sql.gz -O /docker-entrypoint-initdb.d/validator_2022_04.sql.gz
-
+RUN wget https://www528.lamp.le.ac.uk/vvdata/validator/validator_2022_11.sql.gz -O /docker-entrypoint-initdb.d/validator_2022_11.sql.gz

vvsr_docker.df

@@ -6,8 +6,8 @@ RUN apt-get install -y wget
 
 RUN mkdir -p /usr/local/share/seqrepo
 
-RUN wget --output-document=/usr/local/share/seqrepo/VV_SR_2022_02.tar https://www528.lamp.le.ac.uk/vvdata/vv_seqrepo/VV_SR_2022_02.tar
+RUN wget --output-document=/usr/local/share/seqrepo/VV_SR_2022_11.tar https://www528.lamp.le.ac.uk/vvdata/vv_seqrepo/VV_SR_2022_11.tar
 
-RUN tar -xvf /usr/local/share/seqrepo/VV_SR_2022_02.tar --directory /usr/local/share/seqrepo
+RUN tar -xvf /usr/local/share/seqrepo/VV_SR_2022_11.tar --directory /usr/local/share/seqrepo
 
-RUN rm /usr/local/share/seqrepo/VV_SR_2022_02.tar
+RUN rm /usr/local/share/seqrepo/VV_SR_2022_11.tar

vvta_docker.df

@@ -1,4 +1,4 @@
-FROM postgres:11.15
+FROM postgres:12.6
 
 ENV POSTGRES_DB=vvta
 
@@ -8,4 +8,5 @@ ENV POSTGRES_PASSWORD=uta_admin
 
 RUN apt-get update && apt-get install -y wget && rm -rf /var/lib/apt/lists/*
 
-RUN wget --output-document=VVTA_2022_02_noseq.sql.gz https://www528.lamp.le.ac.uk/vvdata/vvta/VVTA_2022_02_noseq.sql.gz -O /docker-entrypoint-initdb.d/VVTA_2022_02_noseq.sql.gz
+RUN wget --output-document=vvta_2022_11_noseq.sql.gz  https://www528.lamp.le.ac.uk/vvdata/vvta/vvta_2022_11_no_seq.sql.gz  -O /docker-entrypoint-initdb.d/vvta_2022_11_noseq.sql.gz
+