Merge pull request #112 from cancervariants/issue-106

Issue 106

Author: korikuzma

.flake8

@@ -7,3 +7,4 @@ exclude =
   source
   outputs
   docs/*
+  variant/version.py

Pipfile

@@ -17,6 +17,7 @@ pyyaml = "*"
 jupyter = "*"
 ipykernel = "*"
 twine = "*"
+matplotlib = "*"
 
 [packages]
 hgvs = "*"
@@ -30,5 +31,5 @@ uvicorn = "*"
 pydantic = "*"
 uvloop = "*"
 httptools = "*"
-"ga4gh.vrs" = {extras = ["extras"], version = "*"}
+"ga4gh.vrs" = {version = "==0.7.0rc3", extras = ["extras"]}
 gene-normalizer = "*"

README.md

@@ -19,6 +19,16 @@ seqrepo_date_dir=$(ls -d */)
 sudo mv $seqrepo_date_dir latest
 ```
 
+Variant Normalizer also uses [uta](https://github.com/biocommons/uta).
+
+To install:
+```
+uta_v=uta_20180821
+docker pull biocommons/uta:$uta_v
+export UTA_DB_URL=postgresql://anonymous@localhost:5432/uta/uta_20180821
+docker-compose -f docker-compose.yml up
+```
+
 ### Data
 Variant Normalization uses [Ensembl BioMart](http://www.ensembl.org/biomart/martview) to retrieve `variant/data/transcript_mappings.tsv`. We currently use `Human Genes (GRCh38.p13)` for the dataset and the following attributes we use are: Gene stable ID, Gene stable ID version, Transcript stable ID, Transcript stable ID version, Protein stable ID, Protein stable ID version, RefSeq match transcript (MANE Select), Gene name. 
 
@@ -60,6 +70,12 @@ pytest tests/
 ```
 
 ### Starting the Variant Normalization Service
+
+`gene-normalizer`s dynamodb must be running and run the following:
+```
+docker-compose -f docker-compose.yml up
+```
+
 From the _root_ directory of the repository:
 ```
 uvicorn variant.main:app --reload

docker-compose.yml

@@ -0,0 +1,33 @@
+version: "3"
+
+services:
+  seqrepo-rest-service:
+    # Test: curl http://localhost:5000/seqrepo/1/sequence/refseq:NM_000551.3
+    expose:
+      - 5000
+    ports:
+      - 5000:5000
+    image: biocommons/seqrepo-rest-service:latest
+    volumes:
+      - ./variant/data/seqrepo:/usr/local/share/seqrepo
+
+  uta:
+    # Test:
+    # psql -XAt postgres://anonymous@localhost/uta -c 'select count(*) from transcript'
+    # 249909
+    expose:
+      - 5432
+    ports:
+      - 5432:5432
+    environment:
+      - POSTGRES_PASSWORD=password
+      - POSTGRES_USER=user
+    image: biocommons/uta:uta_20180821
+    volumes:
+      - ./variant/data/uta_20180821:/var/lib/postgresql/data
+
+volumes:
+  seqrepo_vol:
+    external: true
+  uta_vol:
+    external: true

requirements-dev.txt

@@ -10,92 +10,99 @@
 
 -i https://pypi.org/simple
 -e .
-anyio==2.2.0; python_full_version >= '3.6.2'
+anyio==3.1.0; python_full_version >= '3.6.2'
 appdirs==1.4.4
 appnope==0.1.2; sys_platform == 'darwin'
-argcomplete==1.12.2
+argcomplete==1.12.3
 argh==0.26.2
 argon2-cffi==20.1.0
 async-generator==1.10; python_version >= '3.5'
-attrs==20.3.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-babel==2.9.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+attrs==21.2.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+babel==2.9.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 backcall==0.2.0
 backports-datetime-fromisoformat==1.0.0
 beautifulsoup4==4.9.3
-biocommons.seqrepo==0.6.3
-bioutils==0.5.2.post3; python_version >= '3.6'
+biocommons.seqrepo==0.6.3.post1
+bioutils==0.5.5; python_version >= '3.6'
 bleach==3.3.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-boto3==1.17.50; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
-botocore==1.20.50; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
+boto3==1.17.79; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
+botocore==1.20.79; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 bs4==0.0.1
 canonicaljson==1.4.0; python_version ~= '3.5'
 certifi==2020.12.5
 cffi==1.14.5
-cfgv==3.2.0; python_full_version >= '3.6.1'
+cfgv==3.3.0; python_full_version >= '3.6.1'
 chardet==4.0.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 civicpy==1.1.3; python_version >= '3.5'
 click==7.1.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+colorama==0.4.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 coloredlogs==15.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 configparser==5.0.2; python_version >= '3.6'
-coverage==5.5
-coveralls==3.0.1
+coverage[toml]==5.5
+coveralls==3.1.0
 cssselect==1.1.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+cycler==0.10.0
 decorator==4.4.2
 defusedxml==0.7.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 deprecation==2.1.0
 distlib==0.3.1
 docopt==0.6.2
+docutils==0.17.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 entrypoints==0.3; python_version >= '2.7'
 fake-useragent==0.1.11
-fastapi==0.63.0
+fastapi==0.65.1
 filelock==3.0.12
 flake8-docstrings==1.6.0
-flake8==3.9.0
-frozendict==1.2
-ga4gh.vrs[extras]==0.6.4
+flake8==3.9.2
+frozendict==2.0.2; python_version >= '3.6'
+ga4gh.vrs[extras]==0.7.0rc3
 gene-normalizer==0.1.5
 gffutils==0.10.1
 h11==0.12.0; python_version >= '3.6'
 hgvs==1.5.1
-httptools==0.1.1
+httptools==0.2.0
 humanfriendly==9.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-identify==2.2.3; python_full_version >= '3.6.1'
+identify==2.2.6; python_full_version >= '3.6.1'
 idna==2.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+importlib-metadata==4.0.1; python_version >= '3.6'
 inflection==0.5.1; python_version >= '3.5'
 iniconfig==1.1.1
-ipykernel==5.5.3
+ipykernel==5.5.5
 ipython-genutils==0.2.0
-ipython==7.22.0; python_version >= '3.7'
+ipython==7.23.1; python_version >= '3.7'
 ipywidgets==7.6.3
 jedi==0.18.0; python_version >= '3.6'
-jinja2==2.11.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+jinja2==3.0.1; python_version >= '3.6'
 jmespath==0.10.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
 json5==0.9.5
 jsonschema==3.2.0
 jupyter-client==6.1.12; python_version >= '3.5'
 jupyter-console==6.4.0; python_version >= '3.6'
 jupyter-core==4.7.1; python_version >= '3.6'
-jupyter-packaging==0.9.1; python_version >= '3.6'
-jupyter-server==1.6.1; python_version >= '3.6'
+jupyter-server==1.8.0; python_version >= '3.6'
 jupyter==1.0.0
 jupyterlab-pygments==0.1.2
-jupyterlab-server==2.4.0; python_version >= '3.6'
+jupyterlab-server==2.5.2; python_version >= '3.6'
 jupyterlab-widgets==1.0.0; python_version >= '3.6'
-jupyterlab==3.0.14
+jupyterlab==3.0.16
+keyring==23.0.1; python_version >= '3.6'
+kiwisolver==1.3.1; python_version >= '3.6'
 lxml==4.6.3
 markdown==3.3.4; python_version >= '3.6'
-markupsafe==1.1.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+markupsafe==2.0.1; python_version >= '3.6'
+matplotlib-inline==0.1.2; python_version >= '3.5'
+matplotlib==3.4.2
 mccabe==0.6.1
 mistune==0.8.4
-nbclassic==0.2.7; python_version >= '3.6'
+nbclassic==0.3.1; python_version >= '3.6'
 nbclient==0.5.3; python_full_version >= '3.6.1'
 nbconvert==6.0.7; python_version >= '3.6'
 nbformat==5.1.3; python_version >= '3.5'
 nest-asyncio==1.5.1; python_version >= '3.5'
 networkx==2.5.1; python_version >= '3.6'
 nodeenv==1.6.0
-notebook==6.3.0; python_version >= '3.6'
-numpy==1.20.2; python_version >= '3.7'
+notebook==6.4.0; python_version >= '3.6'
+numpy==1.20.3; python_version >= '3.7'
 obonet==0.3.0; python_version >= '3.5'
 packaging==20.9; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pandas==1.2.4; python_full_version >= '3.7.1'
@@ -105,64 +112,70 @@ parsley==1.3
 parso==0.8.2; python_version >= '3.6'
 pexpect==4.8.0; sys_platform != 'win32'
 pickleshare==0.7.5
+pillow==8.2.0; python_version >= '3.6'
+pkginfo==1.7.0
 pluggy==0.13.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pre-commit==2.12.0
+pre-commit==2.13.0
 prometheus-client==0.10.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 prompt-toolkit==3.0.18; python_full_version >= '3.6.1'
 psycopg2-binary==2.8.6; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 ptyprocess==0.7.0
 py==1.10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pycodestyle==2.7.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pycparser==2.20; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pydantic==1.8.1
-pydocstyle==6.0.0; python_version >= '3.6'
+pydantic==1.8.2
+pydocstyle==6.1.1; python_version >= '3.6'
 pyee==8.1.0
 pyfaidx==0.5.9.5
 pyflakes==2.3.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pygments==2.8.1; python_version >= '3.5'
+pygments==2.9.0; python_version >= '3.5'
 pyparsing==2.4.7; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pyppeteer==0.2.5; python_version < '4' and python_full_version >= '3.6.1'
 pyquery==1.4.3
 pyrsistent==0.17.3; python_version >= '3.5'
 pysam==0.16.0.1
-pytest-cov==2.11.1
-pytest==6.2.3
+pytest-cov==2.12.0
+pytest==6.2.4
 python-dateutil==2.8.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 python-jsonschema-objects==0.3.10
 pytz==2021.1
 pyyaml==5.4.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 pyzmq==22.0.3; python_version >= '3.6'
-qtconsole==5.0.3; python_version >= '3.6'
+qtconsole==5.1.0; python_version >= '3.6'
 qtpy==1.9.0
+readme-renderer==29.0
 requests-html==0.10.0; python_version >= '3.6'
+requests-toolbelt==0.9.1
 requests==2.25.1
-s3transfer==0.3.6
+rfc3986==1.5.0
+s3transfer==0.4.2
 send2trash==1.5.0
 simplejson==3.17.2; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
-six==1.15.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+six==1.16.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 sniffio==1.2.0; python_version >= '3.5'
 snowballstemmer==2.1.0
 soupsieve==2.2.1; python_version >= '3'
 sqlparse==0.4.1; python_version >= '3.5'
-starlette==0.13.6; python_version >= '3.6'
+starlette==0.14.2; python_version >= '3.6'
 tabulate==0.8.9
-terminado==0.9.4; python_version >= '3.6'
-testpath==0.4.4
+terminado==0.10.0; python_version >= '3.6'
+testpath==0.5.0; python_version >= '3.5'
 toml==0.10.2; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
-tomlkit==0.7.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 tornado==6.1; python_version >= '3.5'
-tqdm==4.60.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+tqdm==4.61.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 traitlets==5.0.5; python_version >= '3.7'
-typing-extensions==3.7.4.3
+twine==3.4.1
+typing-extensions==3.10.0.0
 urllib3==1.26.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'
 uvicorn==0.13.4
 uvloop==0.15.2
 vcfpy==0.13.3
-virtualenv==20.4.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+virtualenv==20.4.7; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 w3lib==1.22.0
 wcwidth==0.2.5
 webencodings==0.5.1
+websocket-client==1.0.1; python_version >= '3.6'
 websockets==8.1
-wheel==0.36.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 widgetsnbextension==3.5.1
-yoyo-migrations==7.3.1
+yoyo-migrations==7.3.2
+zipp==3.4.1; python_version >= '3.6'

requirements.txt

@@ -8,16 +8,16 @@
 -i https://pypi.org/simple
 appdirs==1.4.4
 appnope==0.1.2; sys_platform == 'darwin'
-argcomplete==1.12.2
+argcomplete==1.12.3
 argh==0.26.2
-attrs==20.3.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+attrs==21.2.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 backcall==0.2.0
 backports-datetime-fromisoformat==1.0.0
 beautifulsoup4==4.9.3
-biocommons.seqrepo==0.6.3
-bioutils==0.5.2.post3; python_version >= '3.6'
-boto3==1.17.50; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
-botocore==1.20.50; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
+biocommons.seqrepo==0.6.3.post1
+bioutils==0.5.5; python_version >= '3.6'
+boto3==1.17.79; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
+botocore==1.20.79; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 bs4==0.0.1
 canonicaljson==1.4.0; python_version ~= '3.5'
 certifi==2020.12.5
@@ -30,26 +30,27 @@ cssselect==1.1.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3
 decorator==4.4.2
 deprecation==2.1.0
 fake-useragent==0.1.11
-fastapi==0.63.0
-frozendict==1.2
-ga4gh.vrs[extras]==0.6.4
+fastapi==0.65.1
+frozendict==2.0.2; python_version >= '3.6'
+ga4gh.vrs[extras]==0.7.0rc3
 gene-normalizer==0.1.5
 gffutils==0.10.1
 h11==0.12.0; python_version >= '3.6'
 hgvs==1.5.1
-httptools==0.1.1
+httptools==0.2.0
 humanfriendly==9.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 idna==2.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 inflection==0.5.1; python_version >= '3.5'
 ipython-genutils==0.2.0
-ipython==7.22.0; python_version >= '3.7'
+ipython==7.23.1; python_version >= '3.7'
 jedi==0.18.0; python_version >= '3.6'
 jmespath==0.10.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
 jsonschema==3.2.0
 lxml==4.6.3
 markdown==3.3.4; python_version >= '3.6'
+matplotlib-inline==0.1.2; python_version >= '3.5'
 networkx==2.5.1; python_version >= '3.6'
-numpy==1.20.2; python_version >= '3.7'
+numpy==1.20.3; python_version >= '3.7'
 obonet==0.3.0; python_version >= '3.5'
 packaging==20.9; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pandas==1.2.4; python_full_version >= '3.7.1'
@@ -61,10 +62,10 @@ pickleshare==0.7.5
 prompt-toolkit==3.0.18; python_full_version >= '3.6.1'
 psycopg2-binary==2.8.6; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 ptyprocess==0.7.0
-pydantic==1.8.1
+pydantic==1.8.2
 pyee==8.1.0
 pyfaidx==0.5.9.5
-pygments==2.8.1; python_version >= '3.5'
+pygments==2.9.0; python_version >= '3.5'
 pyparsing==2.4.7; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pyppeteer==0.2.5; python_version < '4' and python_full_version >= '3.6.1'
 pyquery==1.4.3
@@ -76,21 +77,21 @@ pytz==2021.1
 pyyaml==5.4.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 requests-html==0.10.0; python_version >= '3.6'
 requests==2.25.1
-s3transfer==0.3.6
+s3transfer==0.4.2
 simplejson==3.17.2; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
-six==1.15.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+six==1.16.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 soupsieve==2.2.1; python_version >= '3'
 sqlparse==0.4.1; python_version >= '3.5'
-starlette==0.13.6; python_version >= '3.6'
+starlette==0.14.2; python_version >= '3.6'
 tabulate==0.8.9
-tqdm==4.60.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+tqdm==4.61.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 traitlets==5.0.5; python_version >= '3.7'
-typing-extensions==3.7.4.3
+typing-extensions==3.10.0.0
 urllib3==1.26.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'
 uvicorn==0.13.4
 uvloop==0.15.2
 vcfpy==0.13.3
 w3lib==1.22.0
 wcwidth==0.2.5
 websockets==8.1
-yoyo-migrations==7.3.1
+yoyo-migrations==7.3.2