Merge pull request #92 from cancervariants/staging

Staging

Pipfile

@@ -13,7 +13,6 @@ beautifulsoup4 = "*"
 gffutils = "*"
 requests = "*"
 "biocommons.seqrepo" = "*"
-seqrepo = "*"
 "ga4gh.vrs" = {version = "==0.7.0rc3", extras = ["extras"]}
 uvloop = "*"
 websockets = "*"

README.md

@@ -12,21 +12,18 @@ for direction on installing pipenv in your compute environment.
 Once installed, from the project root dir, just run:
 
 ```commandline
-pipenv sync
+pipenv shell
+pipenv lock && pipenv sync
 ```
 
 Gene Normalization relies on [SeqRepo](https://github.com/biocommons/biocommons.seqrepo) data. 
 
-From the _gene_ directory of the repository:
-```commandline
-pip install seqrepo
-mkdir -p data/seqrepo
-seqrepo -r data/seqrepo pull -i 2021-01-29
-sudo chmod -R u+w data/seqrepo
-cd data/seqrepo
-seqrepo_date_dir=$(ls -d */)
-mv $seqrepo_date_dir latest
+From the _root_ directory:
 ```
+pip install seqrepo
+sudo mkdir /usr/local/share/seqrepo
+sudo chown $USER /usr/local/share/seqrepo
+seqrepo pull -i 2021-01-29
 
 ### Deploying DynamoDB Locally
 

gene/__init__.py

@@ -24,6 +24,9 @@
     logger.addHandler(ch)
 
 
+SEQREPO_DATA_PATH = '/usr/local/share/seqrepo/latest'
+
+
 class DownloadException(Exception):
     """Exception for failures relating to source file downloads."""
 

gene/etl/base.py

@@ -2,7 +2,7 @@
 from abc import ABC, abstractmethod
 from typing import Optional, List
 from gene.database import Database
-from gene import PREFIX_LOOKUP, ITEM_TYPES, APP_ROOT
+from gene import PREFIX_LOOKUP, ITEM_TYPES, SEQREPO_DATA_PATH
 from biocommons.seqrepo import SeqRepo
 from pathlib import Path
 from ftplib import FTP
@@ -25,7 +25,7 @@ class Base(ABC):
 
     def __init__(self, database: Database, host: str, data_dir: str,
                  src_data_dir: Path,
-                 seqrepo_dir=APP_ROOT / 'data' / 'seqrepo' / 'latest',
+                 seqrepo_dir=SEQREPO_DATA_PATH,
                  *args, **kwargs) -> None:
         """Instantiate Base class.
 

gene/version.py

@@ -1 +1 @@
-__version__ = "0.1.21"
+__version__ = "0.1.22"

requirements-dev.txt

@@ -10,152 +10,151 @@
 
 -i https://pypi.org/simple
 -e .
-anyio==3.3.2; python_full_version >= '3.6.2'
+anyio==3.3.4; python_full_version >= '3.6.2'
 appdirs==1.4.4
 appnope==0.1.2; sys_platform == 'darwin'
 argcomplete==1.12.3
 argh==0.26.2
 argon2-cffi==21.1.0; python_version >= '3.5'
-asgiref==3.4.1; python_full_version >= '3.6.0'
+asgiref==3.4.1; python_version >= '3.6'
 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.entry-points-selectable==1.1.0; python_version >= '2.7'
 beautifulsoup4==4.10.0
 biocommons.seqrepo==0.6.4
-bioutils==0.5.5; python_full_version >= '3.6.0'
+bioutils==0.5.5; python_version >= '3.6'
 bleach==4.1.0; python_version >= '3.6'
-boto3==1.18.57
-botocore==1.21.57; python_full_version >= '3.6.0'
+boto3==1.19.7
+botocore==1.22.7; python_version >= '3.6'
 bs4==0.0.1
-canonicaljson==1.4.0; python_version ~= '3.5'
-certifi==2021.5.30
-cffi==1.14.6
+canonicaljson==1.5.0; python_version ~= '3.5'
+certifi==2021.10.8
+cffi==1.15.0
 cfgv==3.3.1; python_full_version >= '3.6.1'
-charset-normalizer==2.0.6; python_version >= '3'
-click==8.0.1
+charset-normalizer==2.0.7; python_version >= '3'
+click==8.0.3
 coloredlogs==15.0.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-configparser==5.0.2; python_full_version >= '3.6.0'
+configparser==5.0.2; python_version >= '3.6'
 coverage[toml]==5.5
 coveralls==3.2.0
 cssselect==1.1.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-debugpy==1.5.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+debugpy==1.5.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 decorator==5.1.0; python_version >= '3.5'
 defusedxml==0.7.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 distlib==0.3.3
 docopt==0.6.2
 entrypoints==0.3; python_version >= '2.7'
 fake-useragent==0.1.11
 fastapi==0.70.0
-filelock==3.3.0; python_version >= '3.6'
+filelock==3.3.2; python_version >= '3.6'
 flake8-docstrings==1.6.0
-flake8==3.9.2
-frozendict==2.0.6; python_full_version >= '3.6.0'
+flake8==4.0.1
+frozendict==2.0.7; python_version >= '3.6'
 ga4gh.vrs[extras]==0.7.0rc3
 ga4gh.vrsatile.pydantic==0.0.3
 gffutils==0.10.1
-h11==0.12.0; python_full_version >= '3.6.0'
+h11==0.12.0; python_version >= '3.6'
 hgvs==1.5.1
 httptools==0.3.0
 humanfriendly==10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-identify==2.3.0; python_full_version >= '3.6.1'
-idna==3.2; python_version >= '3'
-importlib-metadata==4.8.1; python_full_version >= '3.6.0'
+identify==2.3.1; python_full_version >= '3.6.1'
+idna==3.3; python_version >= '3'
+importlib-metadata==4.8.1; python_version >= '3.6'
 inflection==0.5.1; python_version >= '3.5'
 iniconfig==1.1.1
-ipykernel==6.4.1; python_version >= '3.7'
+ipykernel==6.4.2; python_version >= '3.7'
 ipython-genutils==0.2.0
-ipython==7.28.0; python_version >= '3.7'
-jedi==0.18.0; python_full_version >= '3.6.0'
+ipython==7.29.0; python_version >= '3.7'
+jedi==0.18.0; python_version >= '3.6'
 jinja2==3.0.2; 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==0.9.6
 jsonschema==3.2.0
 jupyter-client==7.0.6; python_full_version >= '3.6.1'
-jupyter-core==4.8.1; python_version >= '3.6'
+jupyter-core==4.9.1; python_version >= '3.6'
 jupyter-server==1.11.1; python_version >= '3.6'
 jupyterlab-pygments==0.1.2
 jupyterlab-server==2.8.2; python_version >= '3.6'
-jupyterlab==3.1.18
+jupyterlab==3.2.1
 lxml==4.6.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-markdown==3.3.4; python_full_version >= '3.6.0'
+markdown==3.3.4; python_version >= '3.6'
 markupsafe==2.0.1; python_version >= '3.6'
 matplotlib-inline==0.1.3; python_version >= '3.5'
 mccabe==0.6.1
 mistune==0.8.4
 mock==4.0.3
-nbclassic==0.3.2; python_version >= '3.6'
+nbclassic==0.3.4; python_version >= '3.6'
 nbclient==0.5.4; python_full_version >= '3.6.1'
 nbconvert==6.2.0; python_version >= '3.7'
 nbformat==5.1.3; python_version >= '3.5'
 nest-asyncio==1.5.1; python_version >= '3.5'
 nodeenv==1.6.0
-notebook==6.4.4; python_version >= '3.6'
-numpy==1.21.2; python_version < '3.11' and python_version >= '3.7'
-packaging==21.0; python_version >= '3.6'
+notebook==6.4.5; python_version >= '3.6'
+numpy==1.21.3; python_version < '3.11' and python_version >= '3.7'
+packaging==21.2; python_version >= '3.6'
 pandocfilters==1.5.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 parse==1.19.0
 parsley==1.3
-parso==0.8.2; python_full_version >= '3.6.0'
+parso==0.8.2; python_version >= '3.6'
 pexpect==4.8.0; sys_platform != 'win32'
 pickleshare==0.7.5
 platformdirs==2.4.0; python_version >= '3.6'
 pluggy==1.0.0; python_version >= '3.6'
 pre-commit==2.15.0
-prometheus-client==0.11.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-prompt-toolkit==3.0.20; python_full_version >= '3.6.2'
-psycopg2-binary==2.9.1; python_full_version >= '3.6.0'
+prometheus-client==0.12.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+prompt-toolkit==3.0.21; python_full_version >= '3.6.2'
+psycopg2-binary==2.9.1; python_version >= '3.6'
 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'
+pycodestyle==2.8.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 pycparser==2.20; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pydantic==1.8.2
 pydocstyle==6.1.1; python_version >= '3.6'
 pyee==8.2.2
-pyfaidx==0.6.2
-pyflakes==2.3.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+pyfaidx==0.6.3.1
+pyflakes==2.4.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pygments==2.10.0; 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==0.2.6; python_full_version >= '3.6.1' and python_full_version < '4.0.0'
 pyquery==1.4.3
-pyrsistent==0.18.0; python_full_version >= '3.6.0'
+pyrsistent==0.18.0; python_version >= '3.6'
 pysam==0.17.0
 pytest-cov==3.0.0
 pytest==6.2.5
 python-dateutil==2.8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 python-jsonschema-objects==0.3.10
 pytz==2021.3
-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'
+pyyaml==6.0; python_version >= '3.6'
 pyzmq==22.3.0; python_version >= '3.6'
-requests-html==0.10.0; python_full_version >= '3.6.0'
+requests-html==0.10.0; python_version >= '3.6'
 requests-unixsocket==0.2.0
 requests==2.26.0
-s3transfer==0.5.0; python_full_version >= '3.6.0'
+s3transfer==0.5.0; python_version >= '3.6'
 send2trash==1.8.0
-seqrepo==0.0.0
 simplejson==3.17.5; python_version >= '2.5' 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_full_version >= '3.6.0'
+soupsieve==2.2.1; python_version >= '3.6'
 sqlparse==0.4.2; python_version >= '3.5'
-starlette==0.16.0; python_full_version >= '3.6.0'
+starlette==0.16.0; python_version >= '3.6'
 tabulate==0.8.9
 terminado==0.12.1; 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'
 tornado==6.1; python_version >= '3.5'
 tqdm==4.62.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-traitlets==5.1.0; python_version >= '3.7'
+traitlets==5.1.1; python_version >= '3.7'
 typing-extensions==3.10.0.2
 urllib3==1.26.7; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_full_version < '4.0.0'
 uvicorn==0.15.0
 uvloop==0.16.0
-virtualenv==20.8.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+virtualenv==20.9.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 w3lib==1.22.0
 wcwidth==0.2.5
 webencodings==0.5.1
 websocket-client==1.2.1; python_version >= '3.6'
 websockets==9.1
 yoyo-migrations==7.3.2
-zipp==3.6.0; python_full_version >= '3.6.0'
+zipp==3.6.0; python_version >= '3.6'

requirements.txt

@@ -6,81 +6,80 @@
 #
 
 -i https://pypi.org/simple
-anyio==3.3.2; python_full_version >= '3.6.2'
+anyio==3.3.4; python_full_version >= '3.6.2'
 appdirs==1.4.4
 appnope==0.1.2; sys_platform == 'darwin'
 argcomplete==1.12.3
 argh==0.26.2
-asgiref==3.4.1; python_full_version >= '3.6.0'
+asgiref==3.4.1; python_version >= '3.6'
 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
 beautifulsoup4==4.10.0
 biocommons.seqrepo==0.6.4
-bioutils==0.5.5; python_full_version >= '3.6.0'
-boto3==1.18.57
-botocore==1.21.57; python_full_version >= '3.6.0'
+bioutils==0.5.5; python_version >= '3.6'
+boto3==1.19.7
+botocore==1.22.7; python_version >= '3.6'
 bs4==0.0.1
-canonicaljson==1.4.0; python_version ~= '3.5'
-certifi==2021.5.30
-charset-normalizer==2.0.6; python_version >= '3'
-click==8.0.1
+canonicaljson==1.5.0; python_version ~= '3.5'
+certifi==2021.10.8
+charset-normalizer==2.0.7; python_version >= '3'
+click==8.0.3
 coloredlogs==15.0.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-configparser==5.0.2; python_full_version >= '3.6.0'
+configparser==5.0.2; python_version >= '3.6'
 cssselect==1.1.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 decorator==5.1.0; python_version >= '3.5'
 fake-useragent==0.1.11
 fastapi==0.70.0
-frozendict==2.0.6; python_full_version >= '3.6.0'
+frozendict==2.0.7; python_version >= '3.6'
 ga4gh.vrs[extras]==0.7.0rc3
 ga4gh.vrsatile.pydantic==0.0.3
 gffutils==0.10.1
-h11==0.12.0; python_full_version >= '3.6.0'
+h11==0.12.0; python_version >= '3.6'
 hgvs==1.5.1
 httptools==0.3.0
 humanfriendly==10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-idna==3.2; python_version >= '3'
-importlib-metadata==4.8.1; python_full_version >= '3.6.0'
+idna==3.3; python_version >= '3'
+importlib-metadata==4.8.1; python_version >= '3.6'
 inflection==0.5.1; python_version >= '3.5'
-ipython==7.28.0; python_version >= '3.7'
-jedi==0.18.0; python_full_version >= '3.6.0'
+ipython==7.29.0; 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; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-markdown==3.3.4; python_full_version >= '3.6.0'
+markdown==3.3.4; python_version >= '3.6'
 matplotlib-inline==0.1.3; python_version >= '3.5'
-numpy==1.21.2; python_version < '3.11' and python_version >= '3.7'
+numpy==1.21.3; python_version < '3.11' and python_version >= '3.7'
 parse==1.19.0
 parsley==1.3
-parso==0.8.2; python_full_version >= '3.6.0'
+parso==0.8.2; python_version >= '3.6'
 pexpect==4.8.0; sys_platform != 'win32'
 pickleshare==0.7.5
-prompt-toolkit==3.0.20; python_full_version >= '3.6.2'
-psycopg2-binary==2.9.1; python_full_version >= '3.6.0'
+prompt-toolkit==3.0.21; python_full_version >= '3.6.2'
+psycopg2-binary==2.9.1; python_version >= '3.6'
 ptyprocess==0.7.0
 pydantic==1.8.2
 pyee==8.2.2
-pyfaidx==0.6.2
+pyfaidx==0.6.3.1
 pygments==2.10.0; python_version >= '3.5'
 pyppeteer==0.2.6; python_full_version >= '3.6.1' and python_full_version < '4.0.0'
 pyquery==1.4.3
-pyrsistent==0.18.0; python_full_version >= '3.6.0'
+pyrsistent==0.18.0; python_version >= '3.6'
 pysam==0.17.0
 python-dateutil==2.8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 python-jsonschema-objects==0.3.10
-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_full_version >= '3.6.0'
+pyyaml==6.0; python_version >= '3.6'
+requests-html==0.10.0; python_version >= '3.6'
 requests==2.26.0
-s3transfer==0.5.0; python_full_version >= '3.6.0'
-seqrepo==0.0.0
+s3transfer==0.5.0; python_version >= '3.6'
 simplejson==3.17.5; python_version >= '2.5' 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'
-soupsieve==2.2.1; python_full_version >= '3.6.0'
+soupsieve==2.2.1; python_version >= '3.6'
 sqlparse==0.4.2; python_version >= '3.5'
-starlette==0.16.0; python_full_version >= '3.6.0'
+starlette==0.16.0; python_version >= '3.6'
 tabulate==0.8.9
 tqdm==4.62.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-traitlets==5.1.0; python_version >= '3.7'
+traitlets==5.1.1; python_version >= '3.7'
 typing-extensions==3.10.0.2
 urllib3==1.26.7; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_full_version < '4.0.0'
 uvicorn==0.15.0
@@ -89,4 +88,4 @@ w3lib==1.22.0
 wcwidth==0.2.5
 websockets==9.1
 yoyo-migrations==7.3.2
-zipp==3.6.0; python_full_version >= '3.6.0'
+zipp==3.6.0; python_version >= '3.6'