Merge pull request #243 from cancervariants/staging

Staging

.flake8

@@ -1,5 +1,6 @@
 [flake8]
 ignore = D205, D400
+max-line-length = 88
 exclude =
   .git
   venv

Dockerfile

@@ -0,0 +1,16 @@
+# A simple container for variant-service.
+# Runs service on port 80.
+# Healthchecks service up every 5m.  
+
+FROM python:3.7
+RUN apt update ; apt install -y rsync
+RUN pip install pipenv uvicorn[standard]
+COPY . /app
+WORKDIR /app
+RUN if [ ! -f "Pipfile.lock" ] ; then pipenv lock ; else echo Pipfile.lock exists ; fi
+RUN pipenv sync
+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

Pipfile

@@ -36,6 +36,5 @@ httptools = "*"
 gene-normalizer = ">=0.1.23"
 pyliftover = "*"
 boto3 = "*"
-"ga4gh.vrsatile.pydantic" = ">=0.0.8"
+"ga4gh.vrsatile.pydantic" = ">=0.0.9"
 pandas = "*"
-sqlalchemy = "*"

requirements-dev.txt

@@ -27,19 +27,19 @@ biocommons.seqrepo==0.6.5
 bioutils==0.5.5; python_version >= '3.6'
 black==22.1.0; python_full_version >= '3.6.2'
 bleach==4.1.0; python_version >= '3.6'
-boto3==1.20.46
-botocore==1.23.46; python_version >= '3.6'
+boto3==1.21.3
+botocore==1.24.3; python_version >= '3.6'
 bs4==0.0.1
 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==2.0.11; python_version >= '3'
-click==8.0.3; python_version >= '3.6'
+charset-normalizer==2.0.12; python_version >= '3'
+click==8.0.4; python_version >= '3.6'
 colorama==0.4.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 coloredlogs==15.0.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 configparser==5.2.0; python_version >= '3.6'
-coverage==6.3
+coverage==6.3.1
 coveralls==3.3.1
 cssselect==1.1.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 cycler==0.11.0; python_version >= '3.6'
@@ -49,30 +49,29 @@ defusedxml==0.7.1; python_version >= '2.7' and python_version not in '3.0, 3.1,
 distlib==0.3.4
 docopt==0.6.2
 docutils==0.18.1; 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'
+entrypoints==0.4; python_version >= '3.6'
 executing==0.8.2
 fake-useragent==0.1.11
-fastapi==0.73.0
-filelock==3.4.2; python_version >= '3.7'
+fastapi==0.74.0
+filelock==3.6.0; python_version >= '3.7'
 flake8-docstrings==1.6.0
 flake8==4.0.1
 fonttools==4.29.1; python_version >= '3.7'
-frozendict==2.2.1; python_version >= '3.6'
+frozendict==2.3.0; python_version >= '3.6'
 ga4gh.vrs[extras]==0.7.2
-ga4gh.vrsatile.pydantic==0.0.8
+ga4gh.vrsatile.pydantic==0.0.9
 gene-normalizer==0.1.24
 gffutils==0.10.1
-greenlet==1.1.2; python_version >= '3' and platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32')))))
 h11==0.13.0; python_version >= '3.6'
 hgvs==1.5.2
 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==2.4.7; python_version >= '3.7'
+identify==2.4.10; python_version >= '3.7'
 idna==3.3; python_version >= '3'
-importlib-metadata==4.10.1; python_version < '3.10'
+importlib-metadata==4.11.1; python_version < '3.10'
 inflection==0.5.1; python_version >= '3.5'
 iniconfig==1.1.1
-ipykernel==6.8.0
+ipykernel==6.9.1
 ipython-genutils==0.2.0
 ipython==8.0.1; python_version >= '3.8'
 ipywidgets==7.6.5
@@ -83,47 +82,47 @@ json5==0.9.6
 jsonschema==3.2.0
 jupyter-client==7.1.2; python_full_version >= '3.6.1'
 jupyter-console==6.4.0; python_version >= '3.6'
-jupyter-core==4.9.1; python_version >= '3.6'
-jupyter-server==1.13.4; python_version >= '3.7'
+jupyter-core==4.9.2; python_version >= '3.6'
+jupyter-server==1.13.5; python_version >= '3.7'
 jupyter==1.0.0
 jupyterlab-pygments==0.1.2
 jupyterlab-server==2.10.3; python_version >= '3.6'
 jupyterlab-widgets==1.0.2; python_version >= '3.6'
-jupyterlab==3.2.8
+jupyterlab==3.2.9
 keyring==23.5.0; python_version >= '3.7'
 kiwisolver==1.3.2; python_version >= '3.7'
-lxml==4.7.1
+lxml==4.8.0
 markdown==3.3.6; python_version >= '3.6'
-markupsafe==2.0.1; python_version >= '3.6'
+markupsafe==2.1.0; python_version >= '3.7'
 matplotlib-inline==0.1.3; python_version >= '3.5'
 matplotlib==3.5.1
 mccabe==0.6.1
 mistune==0.8.4
 mypy-extensions==0.4.3
 nbclassic==0.3.5; python_version >= '3.6'
-nbclient==0.5.10; python_version >= '3.7'
-nbconvert==6.4.1; python_version >= '3.7'
+nbclient==0.5.11; python_version >= '3.7'
+nbconvert==6.4.2; python_version >= '3.7'
 nbformat==5.1.3; python_version >= '3.5'
 nest-asyncio==1.5.4; python_version >= '3.5'
 nodeenv==1.6.0
 notebook==6.4.8; python_version >= '3.6'
-numpy==1.22.1; python_version >= '3.8'
+numpy==1.22.2; python_version < '3.10' and platform_machine != 'aarch64' and platform_machine != 'arm64'
 packaging==21.3; python_version >= '3.6'
-pandas==1.4.0
+pandas==1.4.1
 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==0.8.3; python_version >= '3.6'
 pathspec==0.9.0
 pexpect==4.8.0; sys_platform != 'win32'
 pickleshare==0.7.5
-pillow==9.0.0; python_version >= '3.7'
+pillow==9.0.1; python_version >= '3.7'
 pkginfo==1.8.2
-platformdirs==2.4.1; python_version >= '3.7'
+platformdirs==2.5.1; python_version >= '3.7'
 pluggy==1.0.0; python_version >= '3.6'
 pre-commit==2.17.0
 prometheus-client==0.13.1; python_version >= '3.6'
-prompt-toolkit==3.0.26; python_full_version >= '3.6.2'
+prompt-toolkit==3.0.28; python_full_version >= '3.6.2'
 psycopg2-binary==2.9.3
 psycopg2==2.9.3; python_version >= '3.6'
 ptyprocess==0.7.0
@@ -139,50 +138,49 @@ pyflakes==2.4.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.
 pygments==2.11.2; python_version >= '3.5'
 pyliftover==0.4
 pyparsing==3.0.7; python_version >= '3.6'
-pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4'
+pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4.0'
 pyquery==1.4.3
 pyrsistent==0.18.1; python_version >= '3.7'
 pysam==0.18.0
 pytest-cov==3.0.0
-pytest==6.2.5
+pytest==7.0.1
 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==0.4.1
 pytz==2021.3
 pyyaml==6.0; python_version >= '3.6'
 pyzmq==22.3.0; python_version >= '3.6'
 qtconsole==5.2.2; python_version >= '3.6'
-qtpy==2.0.0; python_version >= '3.6'
+qtpy==2.0.1; python_version >= '3.6'
 readme-renderer==32.0; python_version >= '3.6'
 requests-html==0.10.0; python_version >= '3.6'
 requests-toolbelt==0.9.1
 requests==2.27.1
 rfc3986==2.0.0; python_version >= '3.7'
-s3transfer==0.5.0; python_version >= '3.6'
+s3transfer==0.5.1; python_version >= '3.6'
 send2trash==1.8.0
-setuptools==60.6.0; python_version >= '3.7'
+setuptools==60.9.3; python_version >= '3.7'
 simplejson==3.17.6; 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==2.2.0
 soupsieve==2.3.1; python_version >= '3.6'
-sqlalchemy==1.4.31
 sqlparse==0.4.2; python_version >= '3.5'
-stack-data==0.1.4
+stack-data==0.2.0
 starlette==0.17.1; python_version >= '3.6'
 tabulate==0.8.9
 terminado==0.13.1; python_version >= '3.7'
 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'
-tomli==2.0.0; python_version >= '3.7'
+tomli==2.0.1; python_version >= '3.7'
 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==5.1.1; python_version >= '3.7'
-twine==3.7.1
-typing-extensions==4.0.1
-urllib3==1.26.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'
-uvicorn==0.17.1
+twine==3.8.0
+typing-extensions==4.1.1
+urllib3==1.26.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4.0'
+uvicorn==0.17.5
 uvloop==0.16.0
-virtualenv==20.13.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+virtualenv==20.13.1; 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

requirements.txt

@@ -19,51 +19,50 @@ beautifulsoup4==4.10.0; python_version >= '3.1'
 biocommons.seqrepo==0.6.5
 bioutils==0.5.5; python_version >= '3.6'
 black==22.1.0; python_full_version >= '3.6.2'
-boto3==1.20.46
-botocore==1.23.46; python_version >= '3.6'
+boto3==1.21.3
+botocore==1.24.3; python_version >= '3.6'
 bs4==0.0.1
 canonicaljson==1.5.0; python_version ~= '3.5'
 certifi==2021.10.8
-charset-normalizer==2.0.11; python_version >= '3'
-click==8.0.3; python_version >= '3.6'
+charset-normalizer==2.0.12; python_version >= '3'
+click==8.0.4; python_version >= '3.6'
 coloredlogs==15.0.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 configparser==5.2.0; 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==5.1.1; python_version >= '3.5'
 executing==0.8.2
 fake-useragent==0.1.11
-fastapi==0.73.0
-frozendict==2.2.1; python_version >= '3.6'
+fastapi==0.74.0
+frozendict==2.3.0; python_version >= '3.6'
 ga4gh.vrs[extras]==0.7.2
-ga4gh.vrsatile.pydantic==0.0.8
+ga4gh.vrsatile.pydantic==0.0.9
 gene-normalizer==0.1.24
 gffutils==0.10.1
-greenlet==1.1.2; python_version >= '3' and platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32')))))
 h11==0.13.0; python_version >= '3.6'
 hgvs==1.5.2
 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==3.3; python_version >= '3'
-importlib-metadata==4.10.1; python_version < '3.10'
+importlib-metadata==4.11.1; python_version < '3.10'
 inflection==0.5.1; python_version >= '3.5'
 ipython==8.0.1; python_version >= '3.8'
 jedi==0.18.1; 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'
 jsonschema==3.2.0
-lxml==4.7.1
+lxml==4.8.0
 markdown==3.3.6; python_version >= '3.6'
 matplotlib-inline==0.1.3; python_version >= '3.5'
 mypy-extensions==0.4.3
-numpy==1.22.1; python_version >= '3.8'
-pandas==1.4.0
+numpy==1.22.2; python_version < '3.10' and platform_machine != 'aarch64' and platform_machine != 'arm64'
+pandas==1.4.1
 parse==1.19.0
 parsley==1.3
 parso==0.8.3; python_version >= '3.6'
 pathspec==0.9.0
 pexpect==4.8.0; sys_platform != 'win32'
 pickleshare==0.7.5
-platformdirs==2.4.1; python_version >= '3.7'
-prompt-toolkit==3.0.26; python_full_version >= '3.6.2'
+platformdirs==2.5.1; python_version >= '3.7'
+prompt-toolkit==3.0.28; python_full_version >= '3.6.2'
 psycopg2==2.9.3; python_version >= '3.6'
 ptyprocess==0.7.0
 pure-eval==0.2.2
@@ -72,7 +71,7 @@ pyee==8.2.2
 pyfaidx==0.6.4
 pygments==2.11.2; python_version >= '3.5'
 pyliftover==0.4
-pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4'
+pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4.0'
 pyquery==1.4.3
 pyrsistent==0.18.1; python_version >= '3.7'
 pysam==0.18.0
@@ -82,23 +81,22 @@ pytz==2021.3
 pyyaml==6.0; python_version >= '3.6'
 requests-html==0.10.0; python_version >= '3.6'
 requests==2.27.1
-s3transfer==0.5.0; python_version >= '3.6'
-setuptools==60.6.0; python_version >= '3.7'
+s3transfer==0.5.1; python_version >= '3.6'
+setuptools==60.9.3; python_version >= '3.7'
 simplejson==3.17.6; 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==2.3.1; python_version >= '3.6'
-sqlalchemy==1.4.31
 sqlparse==0.4.2; python_version >= '3.5'
-stack-data==0.1.4
+stack-data==0.2.0
 starlette==0.17.1; python_version >= '3.6'
 tabulate==0.8.9
-tomli==2.0.0; python_version >= '3.7'
+tomli==2.0.1; python_version >= '3.7'
 tqdm==4.62.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 traitlets==5.1.1; python_version >= '3.7'
-typing-extensions==4.0.1
-urllib3==1.26.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'
-uvicorn==0.17.1
+typing-extensions==4.1.1
+urllib3==1.26.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4.0'
+uvicorn==0.17.5
 uvloop==0.16.0
 w3lib==1.22.0
 wcwidth==0.2.5

setup.cfg

@@ -35,9 +35,8 @@ install_requires =
     gene-normalizer >= 0.1.23
     pyliftover
     boto3
-    ga4gh.vrsatile.pydantic >= 0.0.8
+    ga4gh.vrsatile.pydantic >= 0.0.9
     pandas
-    sqlalchemy
 
 tests_require =
     pytest