Docker vn

.github/workflows/checks.yml → .github/workflows/checks.yaml

@@ -7,7 +7,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v3
 

.github/workflows/pr-priority-label.yaml

@@ -0,0 +1,23 @@
+name: Pull Request Has Priority Label
+on:
+  pull_request:
+    types: [opened, labeled, unlabeled, synchronize]
+jobs:
+  pr-priority-label:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    outputs:
+      status: ${{ steps.check-labels.outputs.status }}
+    steps:
+      - id: check-labels
+        uses: mheap/github-action-required-labels@v5
+        with:
+          mode: exactly
+          count: 1
+          labels: "priority:*"
+          use_regex: true
+          add_comment: true
+          message: "PRs require a priority label. Please add one."
+          exit_type: failure

Dockerfile

@@ -2,9 +2,14 @@
 # Runs service on port 80.
 # Healthchecks service up every 5m.  
 
-FROM python:3.7
+FROM python:3.9
 RUN apt update ; apt install -y rsync
 RUN pip install pipenv uvicorn[standard]
+ENV SEQREPO_ROOT_DIR=/usr/local/share/seqrepo/2021-01-29
+ENV GENE_NORM_DB_URL=http://dynamodb:8001
+ENV AWS_ACCESS_KEY_ID = 'DUMMYIDEXAMPLE'
+ENV AWS_SECRET_ACCESS_KEY = 'DUMMYEXAMPLEKEY'
+ENV AWS_DEFAULT_REGION = 'us-west-2'
 COPY . /app
 WORKDIR /app
 RUN if [ ! -f "Pipfile.lock" ] ; then pipenv lock ; else echo Pipfile.lock exists ; fi
@@ -13,4 +18,4 @@ EXPOSE 80
 HEALTHCHECK --interval=5m --timeout=3s \
     CMD curl -f http://localhost/variation || exit 1
 
-CMD pipenv run uvicorn variation.main:app  --port 80 --host 0.0.0.0
+CMD cd src pipenv run uvicorn variation.main:app --log-level debug --port 80 --host 0.0.0.0

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018-2023 VICC
+Copyright (c) 2018-2024 VICC
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,25 +1,28 @@
 # Variation Normalization
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5894937.svg)](https://doi.org/10.5281/zenodo.5894937)
+[![image](https://img.shields.io/pypi/v/variation-normalizer.svg)](https://pypi.python.org/pypi/variation-normalizer) [![image](https://img.shields.io/pypi/l/variation-normalizer.svg)](https://pypi.python.org/pypi/variation-normalizer) [![image](https://img.shields.io/pypi/pyversions/variation-normalizer.svg)](https://pypi.python.org/pypi/variation-normalizer) [![Actions status](https://github.com/cancervariants/variation-normalization/actions/workflows/checks.yaml/badge.svg)](https://github.com/cancervariants/variation-normalization/actions/checks.yaml)[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5894937.svg)](https://doi.org/10.5281/zenodo.5894937)
 
-Services and guidelines for normalizing variation terms to [VRS](https://vrs.ga4gh.org/en/latest) compatible representations.
+<!-- description -->
+The Variation Normalizer parses and translates free-text descriptions of genomic variations into computable objects conforming to the [Variation Representation Specification (VRS)](https://vrs.ga4gh.org/en/latest), enabling consistent and accurate variant harmonization across a diversity of genomic knowledge resources.
+<!-- /description -->
 
-Public OpenAPI endpoint: <https://normalize.cancervariants.org/variation>
+---
 
-Installing with pip:
+[Live OpenAPI endpoint](https://normalize.cancervariants.org/variation)
+
+---
+
+## Installation
+
+Install from [PyPI](https://pypi.org/project/variation-normalizer):
 
 ```shell
-pip install variation-normalizer
+python3 -m pip install variation-normalizer
 ```
 
-The variation-normalization repo depends on VRS models, and therefore each variation-normalizer package on PyPI uses a particular version of VRS. The correspondences between packages may be summarized as:
+---
 
-| variation-normalization branch | variation-normalizer version | gene-normalizer version | VRS version |
-| ---- | --- | ---- | --- |
-| [main](https://github.com/cancervariants/variation-normalization/tree/main) | 0.6.X | 0.1.X | [1.X.X](https://github.com/ga4gh/vrs) |
-| [staging](https://github.com/cancervariants/variation-normalization/tree/staging) | 0.8.X | 0.3.X | [2.0-alpha](https://github.com/ga4gh/vrs/tree/2.0-alpha) |
-
-## About
+## Normalization
 
 Variation Normalization works by using four main steps: tokenization, classification, validation, and translation. During tokenization, we split strings on whitespace and parse to determine the type of token. During classification, we specify the order of tokens a classification can have. We then do validation checks such as ensuring references for a nucleotide or amino acid matches the expected value and validating a position exists on the given transcript. During translation, we return a VRS Allele object.
 
@@ -36,7 +39,18 @@ Variation Normalizer accepts input from GRCh37 or GRCh8 assemblies.
 
 We are working towards adding more types of variations, coordinates, and representations.
 
-### Endpoints
+
+### VRS Versioning
+
+The variation-normalization repo depends on VRS models, and therefore each variation-normalizer package on PyPI uses a particular version of VRS. The correspondences between packages may be summarized as:
+
+| variation-normalization branch | variation-normalizer version | gene-normalizer version | VRS version |
+| ---- | --- | ---- | --- |
+| [main](https://github.com/cancervariants/variation-normalization/tree/main) | 0.6.X | 0.1.X | [1.X.X](https://github.com/ga4gh/vrs) |
+| [staging](https://github.com/cancervariants/variation-normalization/tree/staging) | 0.8.X | 0.3.X | [2.0-alpha](https://github.com/ga4gh/vrs/tree/2.0-alpha) |
+
+
+### Available Endpoints
 
 #### `/to_vrs`
 
@@ -48,7 +62,7 @@ Returns a VRS Variation aligned to the prioritized transcript. The Variation Nor
 
 If a genomic variation query _is_ given a gene (E.g. `BRAF g.140753336A>T`), the associated cDNA representation will be returned. This is because the gene provides additional strand context. If a genomic variation query is _not_ given a gene, the GRCh38 representation will be returned.
 
-## Developer Instructions
+## Development
 
 Clone the repo:
 
@@ -68,7 +82,7 @@ pipenv shell
 pipenv update && pipenv install --dev
 ```
 
-### Backend Services
+### Required resources
 
 Variation Normalization relies on some local data caches which you will need to set up. It uses pipenv to manage its environment, which you will also need to install.
 
@@ -154,11 +168,11 @@ uvicorn variation.main:app --reload
 Next, view the OpenAPI docs on your local machine:
 <http://127.0.0.1:8000/variation>
 
-### Init coding style tests
+### Code QC
 
 Code style is managed by [Ruff](https://docs.astral.sh/ruff/) and checked prior to commit.
 
-Check style with `ruff`:
+To perform formatting and check style:
 
 ```shell
 python3 -m ruff format . && python3 -m ruff check --fix .
@@ -186,3 +200,44 @@ From the _root_ directory of the repository:
 ```shell
 pytest tests/
 ```
+
+## Docker Setup:  
+This section deals with setting up Variation Normalizer's backend dependencies via Docker. You must have Docker installed for this section. See more [here](https://docs.docker.com/engine/install/).
+
+To create a new Docker network, use the [docker network create](https://docs.docker.com/reference/cli/docker/network/create/) command. For example, `docker network create tulip-net`
+
+## SeqRepo  
+Variation Normalizer depends on [Biocommons SeqRepo](https://github.com/biocommons/biocommons.seqrepo).  It is recommended to have the image as a volume attached to SeqRepo since the size exceeds 10 GB and can take a while to download.
+1. Pull the image from Docker Hub Repository: 
+
+```shell
+docker pull biocommons/seqrepo
+
+## UTA  
+The Postgres UTA instance is another dependancy required for Variation Normalizer. To setup Container for UTA postgres Db instance. Follow the following steps:  
+a.) Pull the image from Docker Hub Repository by typing following command in terminal.  
+Set the uta_v env variable by typing command uta_v=<"name of the version>. For eg uta_v=uta_20210129b.  
+Command : docker pull biocommons/uta:$uta_v  
+b.) Once the image is downnloaded, Start the container with the command :  
+docker run  
+-d  
+-e POSTGRES_PASSWORD=some-password-that-you-make-up  
+-v /tmp:/tmp  
+-v uta_vol:/var/lib/postgresql/data  
+--name $uta_v  
+--net=<"name of the network> \  
+biocommons/uta:$uta_v  
+
+### DynamoDB 
+AWS provides a docker image for the local instance. The DynamoDB local instance requires credentials (`AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY`). You can provide dummy values for these if you do not have an AWS account.
+1. Pull the image from Docker Hub repository and start the container:
+
+```shell
+docker run --net tulip-net -d --name dynamodb -p 8001:8001 amazon/dynamodb-local:1.18.0 -jar DynamoDBLocal.jar -port 8001  
+
+### Running the Dockerfile locally
+
+1. Build the image from the docker file:
+
+```shell
+docker build -t variation-normalization .