From 7dac4c68daf025cf169be61f82c1030016cd6729 Mon Sep 17 00:00:00 2001
From: James Stevenson <james.stevenson@nationwidechildrens.org>
Date: Mon, 17 Jan 2022 07:24:11 -0500
Subject: [PATCH 1/3] Enable parameter entry in swaggerui by default
---
Pipfile | 2 +-
gene/main.py | 6 +-
requirements-dev.txt | 133 +++++++++++++++++++++++--------------------
requirements.txt | 72 +++++++++++++----------
setup.cfg | 2 +-
5 files changed, 119 insertions(+), 96 deletions(-)
diff --git a/Pipfile b/Pipfile
index d852221e..2b17634c 100644
--- a/Pipfile
+++ b/Pipfile
@@ -5,7 +5,7 @@ name = "pypi"
[packages]
pydantic = "*"
-fastapi = "*"
+fastapi = ">=0.72.0"
uvicorn = "*"
click = "*"
boto3 = "*"
diff --git a/gene/main.py b/gene/main.py
index 49a6f001..4679b2b8 100644
--- a/gene/main.py
+++ b/gene/main.py
@@ -9,7 +9,11 @@
query_handler = QueryHandler()
-app = FastAPI(docs_url='/gene', openapi_url='/gene/openapi.json')
+app = FastAPI(
+ docs_url="/gene",
+ openapi_url="/gene/openapi.json",
+ swagger_ui_parameters={"tryItOutEnabled": True}
+)
def custom_openapi():
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 297907e9..b9ee403a 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -10,115 +10,122 @@
-i https://pypi.org/simple
-e .
-anyio==3.3.4; python_full_version >= '3.6.2'
+-e .
+anyio==3.5.0; python_full_version >= '3.6.2'
appdirs==1.4.4
appnope==0.1.2; sys_platform == 'darwin'
-argcomplete==1.12.3
+argcomplete==2.0.0; python_version >= '3.6'
argh==0.26.2
-argon2-cffi==21.1.0; python_version >= '3.5'
+argon2-cffi-bindings==21.2.0; python_version >= '3.6'
+argon2-cffi==21.3.0; python_version >= '3.6'
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'
+asttokens==2.0.5
+attrs==21.4.0; 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==1.1.1; python_version >= '2.7'
beautifulsoup4==4.10.0
-biocommons.seqrepo==0.6.4
+biocommons.seqrepo==0.6.5
bioutils==0.5.5; python_version >= '3.6'
-bleach==4.1.0; python_full_version >= '3.6.0'
-boto3==1.20.8
-botocore==1.23.8; python_version >= '3.6'
+black==21.12b0; python_full_version >= '3.6.2'
+bleach==4.1.0; python_version >= '3.6'
+boto3==1.20.37
+botocore==1.23.37; 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==2.0.7; python_version >= '3'
+charset-normalizer==2.0.10; 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==5.1.0; python_version >= '3.6'
-coverage[toml]==6.1.2
+configparser==5.2.0; python_version >= '3.6'
+coverage==6.2
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'
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'
+decorator==5.1.1; 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
+distlib==0.3.4
docopt==0.6.2
entrypoints==0.3; python_version >= '2.7'
+executing==0.8.2
fake-useragent==0.1.11
-fastapi==0.70.0
-filelock==3.4.0; python_full_version >= '3.6.0'
+fastapi==0.72.0
+filelock==3.4.2; python_version >= '3.7'
flake8-docstrings==1.6.0
flake8==4.0.1
-frozendict==2.0.7; python_version >= '3.6'
+frozendict==2.2.0; python_version >= '3.6'
ga4gh.vrs[extras]==0.7.2
-ga4gh.vrsatile.pydantic==0.0.5
+ga4gh.vrsatile.pydantic==0.0.6
gffutils==0.10.1
h11==0.12.0; python_version >= '3.6'
-hgvs==1.5.1
+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==2.3.6; python_full_version >= '3.6.1'
+identify==2.4.4; python_full_version >= '3.6.1'
idna==3.3; python_version >= '3'
-importlib-metadata==4.8.2; python_version < '3.10'
+importlib-metadata==4.10.1; python_version < '3.10'
inflection==0.5.1; python_version >= '3.5'
iniconfig==1.1.1
-ipykernel==6.5.0; python_version >= '3.7'
+ipykernel==6.7.0; python_version >= '3.7'
ipython-genutils==0.2.0
-ipython==7.29.0; python_version >= '3.7'
+ipython==8.0.0; python_version >= '3.8'
jedi==0.18.1; python_version >= '3.6'
-jinja2==3.0.3; python_full_version >= '3.6.0'
+jinja2==3.0.3; 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==4.9.1; python_full_version >= '3.6.0'
-jupyter-server==1.11.2; python_full_version >= '3.6.0'
+jupyter-client==7.1.1; python_full_version >= '3.6.1'
+jupyter-core==4.9.1; python_version >= '3.6'
+jupyter-server==1.13.3; python_version >= '3.7'
jupyterlab-pygments==0.1.2
-jupyterlab-server==2.8.2; python_full_version >= '3.6.0'
-jupyterlab==3.2.4
-lxml==4.6.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+jupyterlab-server==2.10.3; python_version >= '3.6'
+jupyterlab==3.2.8
+lxml==4.7.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
markdown==3.3.6; python_version >= '3.6'
-markupsafe==2.0.1; python_full_version >= '3.6.0'
+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==0.3.4; python_full_version >= '3.6.0'
-nbclient==0.5.8; python_full_version >= '3.6.1'
-nbconvert==6.3.0; python_version >= '3.7'
+mypy-extensions==0.4.3
+nbclassic==0.3.5; python_version >= '3.6'
+nbclient==0.5.10; python_version >= '3.7'
+nbconvert==6.4.0; python_version >= '3.7'
nbformat==5.1.3; python_version >= '3.5'
-nest-asyncio==1.5.1; python_version >= '3.5'
+nest-asyncio==1.5.4; python_version >= '3.5'
nodeenv==1.6.0
-notebook==6.4.6; python_full_version >= '3.6.0'
-numpy==1.21.4; python_version < '3.11' and python_version >= '3.7'
-packaging==21.3; python_full_version >= '3.6.0'
+notebook==6.4.7; python_version >= '3.6'
+numpy==1.22.1; python_version >= '3.8'
+packaging==21.3; 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_version >= '3.6'
+parso==0.8.3; python_version >= '3.6'
+pathspec==0.9.0
pexpect==4.8.0; sys_platform != 'win32'
pickleshare==0.7.5
-platformdirs==2.4.0; python_full_version >= '3.6.0'
-pluggy==1.0.0; python_full_version >= '3.6.0'
-pre-commit==2.15.0
+platformdirs==2.4.1; python_version >= '3.7'
+pluggy==1.0.0; python_version >= '3.6'
+pre-commit==2.16.0
prometheus-client==0.12.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-prompt-toolkit==3.0.22; python_full_version >= '3.6.2'
-psycopg2-binary==2.9.2; python_version >= '3.6'
+prompt-toolkit==3.0.24; python_full_version >= '3.6.2'
+psycopg2==2.9.3; python_version >= '3.6'
ptyprocess==0.7.0
+pure-eval==0.2.1
py==1.11.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
pycodestyle==2.8.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
pycparser==2.21; 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_full_version >= '3.6.0'
+pydantic==1.9.0
+pydocstyle==6.1.1; python_version >= '3.6'
pyee==8.2.2
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==3.0.6; python_full_version >= '3.6.0'
-pyppeteer==0.2.6; python_version < '4' and python_full_version >= '3.6.1'
+pygments==2.11.2; python_version >= '3.5'
+pyparsing==3.0.6; python_version >= '3.6'
+pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4'
pyquery==1.4.3
-pyrsistent==0.18.0; python_version >= '3.6'
+pyrsistent==0.18.1; python_version >= '3.7'
pysam==0.18.0
pytest-cov==3.0.0
pytest==6.2.5
@@ -126,35 +133,37 @@ python-dateutil==2.8.2; python_version >= '2.7' and python_version not in '3.0,
python-jsonschema-objects==0.4.1
pytz==2021.3
pyyaml==6.0; python_version >= '3.6'
-pyzmq==22.3.0; python_full_version >= '3.6.0'
+pyzmq==22.3.0; python_version >= '3.6'
requests-html==0.10.0; python_version >= '3.6'
-requests==2.26.0
+requests==2.27.1
s3transfer==0.5.0; python_version >= '3.6'
send2trash==1.8.0
+setuptools==60.5.0; 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'
sqlparse==0.4.2; python_version >= '3.5'
-starlette==0.16.0; python_version >= '3.6'
+stack-data==0.1.4
+starlette==0.17.1; python_version >= '3.6'
tabulate==0.8.9
-terminado==0.12.1; python_full_version >= '3.6.0'
+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'
-tomli==1.2.2; python_full_version >= '3.6.0'
+tomli==1.2.3; python_version >= '3.6'
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'
-typing-extensions==4.0.0
-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_version < '4'
-uvicorn==0.15.0
+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==0.17.0
uvloop==0.16.0
-virtualenv==20.10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+virtualenv==20.13.0; 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_full_version >= '3.6.0'
-websockets==9.1
+websocket-client==1.2.3; python_version >= '3.6'
+websockets==10.1
yoyo-migrations==7.3.2
-zipp==3.6.0; python_version >= '3.6'
+zipp==3.7.0; python_version >= '3.7'
diff --git a/requirements.txt b/requirements.txt
index 220e9b55..90291adc 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,86 +6,96 @@
#
-i https://pypi.org/simple
-anyio==3.3.4; python_full_version >= '3.6.2'
+anyio==3.5.0; python_full_version >= '3.6.2'
appdirs==1.4.4
appnope==0.1.2; sys_platform == 'darwin'
-argcomplete==1.12.3
+argcomplete==2.0.0; python_version >= '3.6'
argh==0.26.2
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'
+asttokens==2.0.5
+attrs==21.4.0; 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
+biocommons.seqrepo==0.6.5
bioutils==0.5.5; python_version >= '3.6'
-boto3==1.20.8
-botocore==1.23.8; python_version >= '3.6'
+black==21.12b0; python_full_version >= '3.6.2'
+boto3==1.20.37
+botocore==1.23.37; python_version >= '3.6'
bs4==0.0.1
canonicaljson==1.5.0; python_version ~= '3.5'
certifi==2021.10.8
-charset-normalizer==2.0.7; python_version >= '3'
+charset-normalizer==2.0.10; 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==5.1.0; python_version >= '3.6'
+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==5.1.0; python_version >= '3.5'
+decorator==5.1.1; python_version >= '3.5'
+executing==0.8.2
fake-useragent==0.1.11
-fastapi==0.70.0
-frozendict==2.0.7; python_version >= '3.6'
+fastapi==0.72.0
+frozendict==2.2.0; python_version >= '3.6'
ga4gh.vrs[extras]==0.7.2
-ga4gh.vrsatile.pydantic==0.0.5
+ga4gh.vrsatile.pydantic==0.0.6
gffutils==0.10.1
h11==0.12.0; python_version >= '3.6'
-hgvs==1.5.1
+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==4.8.2; python_version < '3.10'
+importlib-metadata==4.10.1; python_version < '3.10'
inflection==0.5.1; python_version >= '3.5'
-ipython==7.29.0; python_version >= '3.7'
+ipython==8.0.0; 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==4.6.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+lxml==4.7.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
markdown==3.3.6; python_version >= '3.6'
matplotlib-inline==0.1.3; python_version >= '3.5'
-numpy==1.21.4; python_version < '3.11' and python_version >= '3.7'
+mypy-extensions==0.4.3
+numpy==1.22.1; python_version >= '3.8'
parse==1.19.0
parsley==1.3
-parso==0.8.2; python_version >= '3.6'
+parso==0.8.3; python_version >= '3.6'
+pathspec==0.9.0
pexpect==4.8.0; sys_platform != 'win32'
pickleshare==0.7.5
-prompt-toolkit==3.0.22; python_full_version >= '3.6.2'
-psycopg2-binary==2.9.2; python_version >= '3.6'
+platformdirs==2.4.1; python_version >= '3.7'
+prompt-toolkit==3.0.24; python_full_version >= '3.6.2'
+psycopg2==2.9.3; python_version >= '3.6'
ptyprocess==0.7.0
-pydantic==1.8.2
+pure-eval==0.2.1
+pydantic==1.9.0
pyee==8.2.2
pyfaidx==0.6.3.1
-pygments==2.10.0; python_version >= '3.5'
-pyppeteer==0.2.6; python_version < '4' and python_full_version >= '3.6.1'
+pygments==2.11.2; python_version >= '3.5'
+pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4'
pyquery==1.4.3
-pyrsistent==0.18.0; python_version >= '3.6'
+pyrsistent==0.18.1; python_version >= '3.7'
pysam==0.18.0
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==0.4.1
pyyaml==6.0; python_version >= '3.6'
requests-html==0.10.0; python_version >= '3.6'
-requests==2.26.0
+requests==2.27.1
s3transfer==0.5.0; python_version >= '3.6'
+setuptools==60.5.0; 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'
sqlparse==0.4.2; python_version >= '3.5'
-starlette==0.16.0; python_version >= '3.6'
+stack-data==0.1.4
+starlette==0.17.1; python_version >= '3.6'
tabulate==0.8.9
+tomli==1.2.3; python_version >= '3.6'
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==4.0.0
-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_version < '4'
-uvicorn==0.15.0
+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==0.17.0
uvloop==0.16.0
w3lib==1.22.0
wcwidth==0.2.5
-websockets==9.1
+websockets==10.1
yoyo-migrations==7.3.2
-zipp==3.6.0; python_version >= '3.6'
+zipp==3.7.0; python_version >= '3.7'
diff --git a/setup.cfg b/setup.cfg
index 169f1896..7e21cdaa 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -25,7 +25,7 @@ zip_safe = False
install_requires =
pydantic
- fastapi
+ fastapi >= 0.72.0
uvicorn
click
boto3
From 81e8ae69e1e6ca626f872fdcdd4721123ad0c4da Mon Sep 17 00:00:00 2001
From: korikuzma <korikuzma@gmail.com>
Date: Thu, 24 Mar 2022 10:11:47 -0400
Subject: [PATCH 2/3] Set use_enum_values, response_datetime is a str, update
packages
---
Pipfile | 7 +-
gene/__init__.py | 7 ++
gene/query.py | 4 +-
gene/schemas.py | 23 +++-
gene/version.py | 2 +-
gene/vrs_locations/chromosome_location.py | 6 +-
gene/vrs_locations/sequence_location.py | 9 +-
requirements-dev.txt | 133 +++++++++++-----------
requirements.txt | 76 ++++++-------
setup.cfg | 9 +-
tests/unit/test_ensembl_source.py | 2 +-
tests/unit/test_hgnc_source.py | 2 +-
tests/unit/test_ncbi_source.py | 2 +-
tests/unit/test_query.py | 85 ++++++++------
14 files changed, 198 insertions(+), 169 deletions(-)
diff --git a/Pipfile b/Pipfile
index 2b17634c..08a75ee7 100644
--- a/Pipfile
+++ b/Pipfile
@@ -5,7 +5,7 @@ name = "pypi"
[packages]
pydantic = "*"
-fastapi = ">=0.72.0"
+fastapi = "*"
uvicorn = "*"
click = "*"
boto3 = "*"
@@ -13,13 +13,12 @@ beautifulsoup4 = "*"
gffutils = "*"
requests = "*"
"biocommons.seqrepo" = "*"
-"ga4gh.vrs" = {version = ">=0.7.2", extras = ["extras"]}
+"ga4gh.vrs" = {version = ">=0.7.5.dev1", extras = ["extras"]}
uvloop = "*"
websockets = "*"
httptools = "*"
typing-extensions = "*"
-"ga4gh.vrsatile.pydantic" = ">=0.0.5"
-jsonschema = ">=2.3, <4.0"
+"ga4gh.vrsatile.pydantic" = ">=0.0.10"
[dev-packages]
gene = {editable = true, path = "."}
diff --git a/gene/__init__.py b/gene/__init__.py
index 3864de11..fb923279 100644
--- a/gene/__init__.py
+++ b/gene/__init__.py
@@ -18,6 +18,13 @@
logger.setLevel(logging.DEBUG)
logger.handlers = []
+logging.getLogger("boto3").setLevel(logging.INFO)
+logging.getLogger("botocore").setLevel(logging.INFO)
+logging.getLogger("urllib3").setLevel(logging.INFO)
+logging.getLogger("python_jsonschema_objects").setLevel(logging.INFO)
+logging.getLogger("biocommons.seqrepo.seqaliasdb.seqaliasdb").setLevel(logging.INFO) # noqa: E501
+logging.getLogger("biocommons.seqrepo.fastadir.fastadir").setLevel(logging.INFO) # noqa: E501
+
if 'GENE_NORM_EB_PROD' in environ:
ch = logging.StreamHandler()
ch.setLevel(logging.INFO)
diff --git a/gene/query.py b/gene/query.py
index dfd40067..102f1bbb 100644
--- a/gene/query.py
+++ b/gene/query.py
@@ -2,7 +2,6 @@
import re
from typing import List, Dict, Set
from urllib.parse import quote
-from uvicorn.config import logger
from .version import __version__
from gene import NAMESPACE_LOOKUP, PREFIX_LOOKUP, ITEM_TYPES
from gene.database import Database
@@ -12,6 +11,7 @@
from botocore.exceptions import ClientError
from boto3.dynamodb.conditions import Key
from datetime import datetime
+from gene import logger
class InvalidParameterException(Exception):
@@ -241,7 +241,7 @@ def _get_service_meta() -> ServiceMeta:
"""
return ServiceMeta(
version=__version__,
- response_datetime=datetime.now()
+ response_datetime=str(datetime.now())
)
def search(self, query_str: str, keyed: bool = False,
diff --git a/gene/schemas.py b/gene/schemas.py
index 3ed832a6..7842d412 100644
--- a/gene/schemas.py
+++ b/gene/schemas.py
@@ -8,7 +8,6 @@
from ga4gh.vrsatile.pydantic.vrs_models import SequenceLocation, \
ChromosomeLocation, CURIE
from ga4gh.vrsatile.pydantic.vrsatile_models import GeneDescriptor
-from datetime import datetime
from pydantic.types import StrictStr
@@ -82,6 +81,8 @@ class Gene(BaseModel):
class Config:
"""Configure model example"""
+ use_enum_values = True
+
@staticmethod
def schema_extra(schema: Dict[str, Any],
model: Type['Gene']) -> None:
@@ -201,6 +202,8 @@ class SourceMeta(BaseModel):
class Config:
"""Configure model example"""
+ use_enum_values = True
+
@staticmethod
def schema_extra(schema: Dict[str, Any],
model: Type['SourceMeta']) -> None:
@@ -235,6 +238,8 @@ class MatchesKeyed(BaseModel):
class Config:
"""Configure model example"""
+ use_enum_values = True
+
@staticmethod
def schema_extra(schema: Dict[str, Any],
model: Type['MatchesKeyed']) -> None:
@@ -276,6 +281,8 @@ class MatchesListed(BaseModel):
class Config:
"""Configure model example"""
+ use_enum_values = True
+
@staticmethod
def schema_extra(schema: Dict[str, Any],
model: Type['MatchesListed']) -> None:
@@ -309,12 +316,14 @@ class ServiceMeta(BaseModel):
name = 'gene-normalizer'
version: StrictStr
- response_datetime: datetime
+ response_datetime: StrictStr
url = 'https://github.com/cancervariants/gene-normalization'
class Config:
"""Configure model example"""
+ use_enum_values = True
+
@staticmethod
def schema_extra(schema: Dict[str, Any],
model: Type['ServiceMeta']) -> None:
@@ -326,7 +335,7 @@ def schema_extra(schema: Dict[str, Any],
schema['example'] = {
'name': 'gene-normalizer',
'version': '0.1.0',
- 'response_datetime': '2021-04-05T16:44:15.367831',
+ 'response_datetime': '2022-03-23 15:57:14.180908',
'url': 'https://github.com/cancervariants/gene-normalization'
}
@@ -342,6 +351,8 @@ class SearchService(BaseModel):
class Config:
"""Configure model example"""
+ use_enum_values = True
+
@staticmethod
def schema_extra(schema: Dict[str, Any],
model: Type['SearchService']) -> None:
@@ -388,7 +399,7 @@ def schema_extra(schema: Dict[str, Any],
"service_meta_": {
'name': 'gene-normalizer',
'version': '0.1.0',
- 'response_datetime': '2021-04-05T16:44:15.367831',
+ 'response_datetime': '2022-03-23 15:57:14.180908',
'url': 'https://github.com/cancervariants/gene-normalization' # noqa: E501
}
}
@@ -407,6 +418,8 @@ class NormalizeService(BaseModel):
class Config:
"""Configure model example"""
+ use_enum_values = True
+
@staticmethod
def schema_extra(schema: Dict[str, Any],
model: Type['NormalizeService']) -> None:
@@ -533,7 +546,7 @@ def schema_extra(schema: Dict[str, Any],
"service_meta_": {
'name': 'gene-normalizer',
'version': '0.1.19',
- 'response_datetime': '2021-09-06T10:52:20.334720',
+ 'response_datetime': '2022-03-23 15:57:14.180908',
'url': 'https://github.com/cancervariants/gene-normalization' # noqa: E501
}
}
diff --git a/gene/version.py b/gene/version.py
index f545e732..e206f1dc 100644
--- a/gene/version.py
+++ b/gene/version.py
@@ -1,2 +1,2 @@
"""Gene normalizer version"""
-__version__ = "0.1.24"
+__version__ = "0.1.25"
diff --git a/gene/vrs_locations/chromosome_location.py b/gene/vrs_locations/chromosome_location.py
index a753a0d7..e2c36e02 100644
--- a/gene/vrs_locations/chromosome_location.py
+++ b/gene/vrs_locations/chromosome_location.py
@@ -23,8 +23,10 @@ def add_location(self, location):
chr=location['chr'],
interval=models.CytobandInterval(
start=location['start'],
- end=location['end']
- )
+ end=location['end'],
+ type="CytobandInterval"
+ ),
+ type="ChromosomeLocation"
)
chr_location._id = ga4gh_identify(chr_location)
return chr_location.as_dict()
diff --git a/gene/vrs_locations/sequence_location.py b/gene/vrs_locations/sequence_location.py
index 3deeb2a3..2dcc8f3e 100644
--- a/gene/vrs_locations/sequence_location.py
+++ b/gene/vrs_locations/sequence_location.py
@@ -38,9 +38,12 @@ def add_location(self, seqid, gene, params, sr):
seq_location = models.SequenceLocation(
sequence_id=sequence_id,
interval=models.SequenceInterval(
- start=models.Number(value=gene.start - 1),
- end=models.Number(value=gene.end)
- )
+ start=models.Number(value=gene.start - 1,
+ type="Number"),
+ end=models.Number(value=gene.end, type="Number"),
+ type="SequenceInterval"
+ ),
+ type="SequenceLocation"
)
seq_location._id = ga4gh_identify(seq_location)
location = seq_location.as_dict()
diff --git a/requirements-dev.txt b/requirements-dev.txt
index b9ee403a..b44f818d 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -10,7 +10,6 @@
-i https://pypi.org/simple
-e .
--e .
anyio==3.5.0; python_full_version >= '3.6.2'
appdirs==1.4.4
appnope==0.1.2; sys_platform == 'darwin'
@@ -18,7 +17,7 @@ argcomplete==2.0.0; python_version >= '3.6'
argh==0.26.2
argon2-cffi-bindings==21.2.0; python_version >= '3.6'
argon2-cffi==21.3.0; python_version >= '3.6'
-asgiref==3.4.1; python_version >= '3.6'
+asgiref==3.5.0; python_version >= '3.7'
asttokens==2.0.5
attrs==21.4.0; 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'
@@ -26,144 +25,142 @@ backcall==0.2.0
beautifulsoup4==4.10.0
biocommons.seqrepo==0.6.5
bioutils==0.5.5; python_version >= '3.6'
-black==21.12b0; python_full_version >= '3.6.2'
bleach==4.1.0; python_version >= '3.6'
-boto3==1.20.37
-botocore==1.23.37; python_version >= '3.6'
+boto3==1.21.25
+botocore==1.24.25; python_version >= '3.6'
bs4==0.0.1
-canonicaljson==1.5.0; python_version ~= '3.5'
+canonicaljson==1.6.0; python_version ~= '3.7'
certifi==2021.10.8
cffi==1.15.0
cfgv==3.3.1; python_full_version >= '3.6.1'
-charset-normalizer==2.0.10; python_version >= '3'
-click==8.0.3
+charset-normalizer==2.0.12; python_version >= '3'
+click==8.0.4
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==6.2
+coverage==6.3.2
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'
debugpy==1.5.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-decorator==5.1.1; python_version >= '3.5'
+decorator==5.1.1; python_full_version >= '3.5.0'
defusedxml==0.7.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
distlib==0.3.4
docopt==0.6.2
-entrypoints==0.3; python_version >= '2.7'
-executing==0.8.2
+entrypoints==0.4; python_version >= '3.6'
+executing==0.8.3
fake-useragent==0.1.11
-fastapi==0.72.0
-filelock==3.4.2; python_version >= '3.7'
+fastapi==0.75.0
+filelock==3.6.0; python_version >= '3.7'
flake8-docstrings==1.6.0
flake8==4.0.1
-frozendict==2.2.0; python_version >= '3.6'
-ga4gh.vrs[extras]==0.7.2
-ga4gh.vrsatile.pydantic==0.0.6
+ga4gh.vrs[extras]==0.8.0.dev0
+ga4gh.vrsatile.pydantic==0.0.10
gffutils==0.10.1
-h11==0.12.0; python_version >= '3.6'
+h11==0.13.0; python_version >= '3.6'
hgvs==1.5.2
-httptools==0.3.0
+httptools==0.4.0
humanfriendly==10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-identify==2.4.4; python_full_version >= '3.6.1'
+identify==2.4.12; python_version >= '3.7'
idna==3.3; python_version >= '3'
-importlib-metadata==4.10.1; python_version < '3.10'
-inflection==0.5.1; python_version >= '3.5'
+importlib-metadata==4.11.3; python_version < '3.10'
+inflection==0.5.1; python_full_version >= '3.5.0'
iniconfig==1.1.1
-ipykernel==6.7.0; python_version >= '3.7'
+ipykernel==6.9.2; python_version >= '3.7'
ipython-genutils==0.2.0
-ipython==8.0.0; python_version >= '3.8'
+ipython==8.1.1; python_version >= '3.8'
jedi==0.18.1; python_version >= '3.6'
jinja2==3.0.3; 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'
+jmespath==1.0.0; python_version >= '3.7'
json5==0.9.6
jsonschema==3.2.0
-jupyter-client==7.1.1; python_full_version >= '3.6.1'
-jupyter-core==4.9.1; python_version >= '3.6'
-jupyter-server==1.13.3; python_version >= '3.7'
+jupyter-client==7.1.2; python_full_version >= '3.6.1'
+jupyter-core==4.9.2; python_version >= '3.6'
+jupyter-server==1.15.6; python_version >= '3.7'
jupyterlab-pygments==0.1.2
-jupyterlab-server==2.10.3; python_version >= '3.6'
-jupyterlab==3.2.8
-lxml==4.7.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+jupyterlab-server==2.11.2; python_version >= '3.7'
+jupyterlab==3.3.2
+lxml==4.8.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
markdown==3.3.6; python_version >= '3.6'
-markupsafe==2.0.1; python_version >= '3.6'
-matplotlib-inline==0.1.3; python_version >= '3.5'
+markupsafe==2.1.1; python_version >= '3.7'
+matplotlib-inline==0.1.3; python_full_version >= '3.5.0'
mccabe==0.6.1
mistune==0.8.4
mock==4.0.3
-mypy-extensions==0.4.3
-nbclassic==0.3.5; python_version >= '3.6'
-nbclient==0.5.10; python_version >= '3.7'
-nbconvert==6.4.0; python_version >= '3.7'
-nbformat==5.1.3; python_version >= '3.5'
+nbclassic==0.3.7; python_version >= '3.7'
+nbclient==0.5.13; python_version >= '3.7'
+nbconvert==6.4.4; python_version >= '3.7'
+nbformat==5.2.0; python_version >= '3.7'
nest-asyncio==1.5.4; python_version >= '3.5'
nodeenv==1.6.0
-notebook==6.4.7; python_version >= '3.6'
-numpy==1.22.1; python_version >= '3.8'
+notebook-shim==0.1.0; python_version >= '3.7'
+notebook==6.4.10; python_version >= '3.6'
+numpy==1.22.3; python_version >= '3.8'
packaging==21.3; 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==0.8.3; 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'
+platformdirs==2.5.1; python_version >= '3.7'
pluggy==1.0.0; python_version >= '3.6'
-pre-commit==2.16.0
-prometheus-client==0.12.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-prompt-toolkit==3.0.24; python_full_version >= '3.6.2'
+pre-commit==2.17.0
+prometheus-client==0.13.1; python_version >= '3.6'
+prompt-toolkit==3.0.28; python_full_version >= '3.6.2'
+psutil==5.9.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
psycopg2==2.9.3; python_version >= '3.6'
ptyprocess==0.7.0
-pure-eval==0.2.1
+pure-eval==0.2.2
py==1.11.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
pycodestyle==2.8.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-pycparser==2.21; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+pycparser==2.21
pydantic==1.9.0
pydocstyle==6.1.1; python_version >= '3.6'
pyee==8.2.2
-pyfaidx==0.6.3.1
+pyfaidx==0.6.4
pyflakes==2.4.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pygments==2.11.2; python_version >= '3.5'
-pyparsing==3.0.6; python_version >= '3.6'
-pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4'
+pygments==2.11.2; python_full_version >= '3.5.0'
+pyparsing==3.0.7; python_version >= '3.6'
+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==7.1.1
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
+pytz==2022.1
pyyaml==6.0; python_version >= '3.6'
pyzmq==22.3.0; 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'
+s3transfer==0.5.2; python_version >= '3.6'
send2trash==1.8.0
-setuptools==60.5.0; python_version >= '3.7'
+setuptools==60.10.0; 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'
+sniffio==1.2.0; python_full_version >= '3.5.0'
snowballstemmer==2.2.0
soupsieve==2.3.1; python_version >= '3.6'
-sqlparse==0.4.2; python_version >= '3.5'
-stack-data==0.1.4
+sqlparse==0.4.2; python_full_version >= '3.5.0'
+stack-data==0.2.0
starlette==0.17.1; python_version >= '3.6'
tabulate==0.8.9
-terminado==0.12.1; python_version >= '3.6'
-testpath==0.5.0; python_version >= '3.5'
+terminado==0.13.3; python_version >= '3.7'
+testpath==0.6.0; 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==1.2.3; python_version >= '3.6'
+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'
+tqdm==4.63.1; 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==0.17.0
+typing-extensions==4.1.1
+urllib3==1.26.9; 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==0.17.6
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==20.13.4; 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==1.2.3; python_version >= '3.6'
-websockets==10.1
+websocket-client==1.3.1; python_version >= '3.6'
+websockets==10.2
yoyo-migrations==7.3.2
zipp==3.7.0; python_version >= '3.7'
diff --git a/requirements.txt b/requirements.txt
index 90291adc..cefe51b7 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -11,64 +11,59 @@ appdirs==1.4.4
appnope==0.1.2; sys_platform == 'darwin'
argcomplete==2.0.0; python_version >= '3.6'
argh==0.26.2
-asgiref==3.4.1; python_version >= '3.6'
+asgiref==3.5.0; python_version >= '3.7'
asttokens==2.0.5
attrs==21.4.0; 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==0.6.5
bioutils==0.5.5; python_version >= '3.6'
-black==21.12b0; python_full_version >= '3.6.2'
-boto3==1.20.37
-botocore==1.23.37; python_version >= '3.6'
+boto3==1.21.25
+botocore==1.24.25; python_version >= '3.6'
bs4==0.0.1
-canonicaljson==1.5.0; python_version ~= '3.5'
+canonicaljson==1.6.0; python_version ~= '3.7'
certifi==2021.10.8
-charset-normalizer==2.0.10; python_version >= '3'
-click==8.0.3
+charset-normalizer==2.0.12; python_version >= '3'
+click==8.0.4
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'
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
+decorator==5.1.1; python_full_version >= '3.5.0'
+executing==0.8.3
fake-useragent==0.1.11
-fastapi==0.72.0
-frozendict==2.2.0; python_version >= '3.6'
-ga4gh.vrs[extras]==0.7.2
-ga4gh.vrsatile.pydantic==0.0.6
+fastapi==0.75.0
+ga4gh.vrs[extras]==0.8.0.dev0
+ga4gh.vrsatile.pydantic==0.0.10
gffutils==0.10.1
-h11==0.12.0; python_version >= '3.6'
+h11==0.13.0; python_version >= '3.6'
hgvs==1.5.2
-httptools==0.3.0
+httptools==0.4.0
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'
-inflection==0.5.1; python_version >= '3.5'
-ipython==8.0.0; python_version >= '3.8'
+importlib-metadata==4.11.3; python_version < '3.10'
+inflection==0.5.1; python_full_version >= '3.5.0'
+ipython==8.1.1; 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'
+jmespath==1.0.0; python_version >= '3.7'
jsonschema==3.2.0
-lxml==4.7.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+lxml==4.8.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
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'
+matplotlib-inline==0.1.3; python_full_version >= '3.5.0'
+numpy==1.22.3; python_version >= '3.8'
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==3.0.24; python_full_version >= '3.6.2'
+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==0.2.1
+pure-eval==0.2.2
pydantic==1.9.0
pyee==8.2.2
-pyfaidx==0.6.3.1
-pygments==2.11.2; python_version >= '3.5'
-pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4'
+pyfaidx==0.6.4
+pygments==2.11.2; python_full_version >= '3.5.0'
+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
@@ -77,25 +72,24 @@ python-jsonschema-objects==0.4.1
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==60.5.0; python_version >= '3.7'
+s3transfer==0.5.2; python_version >= '3.6'
+setuptools==60.10.0; 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'
+sniffio==1.2.0; python_full_version >= '3.5.0'
soupsieve==2.3.1; python_version >= '3.6'
-sqlparse==0.4.2; python_version >= '3.5'
-stack-data==0.1.4
+sqlparse==0.4.2; python_full_version >= '3.5.0'
+stack-data==0.2.0
starlette==0.17.1; python_version >= '3.6'
tabulate==0.8.9
-tomli==1.2.3; python_version >= '3.6'
-tqdm==4.62.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+tqdm==4.63.1; 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==0.17.0
+typing-extensions==4.1.1
+urllib3==1.26.9; 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==0.17.6
uvloop==0.16.0
w3lib==1.22.0
wcwidth==0.2.5
-websockets==10.1
+websockets==10.2
yoyo-migrations==7.3.2
zipp==3.7.0; python_version >= '3.7'
diff --git a/setup.cfg b/setup.cfg
index 7e21cdaa..1dfcc3c0 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -25,7 +25,7 @@ zip_safe = False
install_requires =
pydantic
- fastapi >= 0.72.0
+ fastapi
uvicorn
click
boto3
@@ -33,9 +33,8 @@ install_requires =
gffutils
requests
biocommons.seqrepo
- ga4gh.vrs[extras] >= 0.7.2
- jsonschema >=2.3, <4.0
- ga4gh.vrsatile.pydantic >= 0.0.5
+ ga4gh.vrs[extras] >= 0.7.5.dev1
+ ga4gh.vrsatile.pydantic >= 0.0.10
tests_require =
@@ -44,4 +43,4 @@ tests_require =
mock
[tool:pytest]
-addopts = --ignore setup.py --doctest-modules --cov-report term-missing --cov .
+addopts = --ignore setup.py --ignore codebuild/ --ignore dynamodb_local_latest/ --doctest-modules --cov-report term-missing --cov .
diff --git a/tests/unit/test_ensembl_source.py b/tests/unit/test_ensembl_source.py
index cf22ef04..d740f3f4 100644
--- a/tests/unit/test_ensembl_source.py
+++ b/tests/unit/test_ensembl_source.py
@@ -14,7 +14,7 @@ def __init__(self):
def search(self, query_str, incl='ensembl'):
resp = self.query_handler.search(query_str, keyed=True, incl=incl)
- return resp.source_matches[SourceName.ENSEMBL]
+ return resp.source_matches[SourceName.ENSEMBL.value]
e = QueryGetter()
return e
diff --git a/tests/unit/test_hgnc_source.py b/tests/unit/test_hgnc_source.py
index 502d92f4..4a469fcf 100644
--- a/tests/unit/test_hgnc_source.py
+++ b/tests/unit/test_hgnc_source.py
@@ -15,7 +15,7 @@ def __init__(self):
def search(self, query_str, incl='hgnc'):
resp = self.query_handler.search(query_str, keyed=True, incl=incl)
- return resp.source_matches[SourceName.HGNC]
+ return resp.source_matches[SourceName.HGNC.value]
h = QueryGetter()
return h
diff --git a/tests/unit/test_ncbi_source.py b/tests/unit/test_ncbi_source.py
index c5156431..10d1c199 100644
--- a/tests/unit/test_ncbi_source.py
+++ b/tests/unit/test_ncbi_source.py
@@ -16,7 +16,7 @@ def __init__(self):
def search(self, query_str, incl='ncbi'):
resp = self.query_handler.search(query_str, keyed=True, incl=incl)
- return resp.source_matches[SourceName.NCBI]
+ return resp.source_matches[SourceName.NCBI.value]
n = QueryGetter()
return n
diff --git a/tests/unit/test_query.py b/tests/unit/test_query.py
index 8cda65a0..0b86d030 100644
--- a/tests/unit/test_query.py
+++ b/tests/unit/test_query.py
@@ -4,7 +4,6 @@
from gene.schemas import SourceName, MatchType
import copy
import pytest
-from datetime import datetime
@pytest.fixture(scope='module')
@@ -327,7 +326,8 @@ def num_sources():
@pytest.fixture(scope="module")
def source_meta():
"""Create test fixture for source meta"""
- return [SourceName.HGNC, SourceName.ENSEMBL, SourceName.NCBI]
+ return [SourceName.HGNC.value, SourceName.ENSEMBL.value,
+ SourceName.NCBI.value]
def compare_normalize_resp(resp, expected_query, expected_match_type,
@@ -365,7 +365,7 @@ def compare_service_meta(service_meta):
"""Check that service metadata is correct."""
assert service_meta.name == "gene-normalizer"
assert service_meta.version >= "0.1.0"
- assert isinstance(service_meta.response_datetime, datetime)
+ assert isinstance(service_meta.response_datetime, str)
assert service_meta.url == \
'https://github.com/cancervariants/gene-normalization'
@@ -430,15 +430,15 @@ def test_search_query_inc_exc(query_handler, num_sources):
resp = query_handler.search('BRAF', keyed=True, incl=sources)
matches = resp.source_matches
assert len(matches) == len(sources.split())
- assert SourceName.HGNC in matches
- assert SourceName.NCBI in matches
+ assert SourceName.HGNC.value in matches
+ assert SourceName.NCBI.value in matches
sources = 'HGnC'
resp = query_handler.search('BRAF', keyed=True, excl=sources)
matches = resp.source_matches
assert len(matches) == num_sources - len(sources.split())
- assert SourceName.ENSEMBL in matches
- assert SourceName.NCBI in matches
+ assert SourceName.ENSEMBL.value in matches
+ assert SourceName.NCBI.value in matches
def test_search_invalid_parameter_exception(query_handler):
@@ -456,26 +456,31 @@ def test_ache_query(query_handler, num_sources, normalized_ache, source_meta):
resp = query_handler.search('ncbigene:43', keyed=True)
matches = resp.source_matches
assert len(matches) == num_sources
- assert matches[SourceName.HGNC].records[0].match_type == MatchType.XREF
- assert len(matches[SourceName.ENSEMBL].records) == 0
- assert matches[SourceName.NCBI].records[0].match_type == \
+ assert matches[SourceName.HGNC.value].records[0].match_type == \
+ MatchType.XREF
+ assert len(matches[SourceName.ENSEMBL.value].records) == 0
+ assert matches[SourceName.NCBI.value].records[0].match_type == \
MatchType.CONCEPT_ID
resp = query_handler.search('hgnc:108', keyed=True)
matches = resp.source_matches
assert len(matches) == num_sources
- assert matches[SourceName.HGNC].records[0].match_type == \
+ assert matches[SourceName.HGNC.value].records[0].match_type == \
MatchType.CONCEPT_ID
- assert matches[SourceName.ENSEMBL].records[0].match_type == MatchType.XREF
- assert matches[SourceName.NCBI].records[0].match_type == MatchType.XREF
+ assert matches[SourceName.ENSEMBL.value].records[0].match_type == \
+ MatchType.XREF
+ assert matches[SourceName.NCBI.value].records[0].match_type == \
+ MatchType.XREF
resp = query_handler.search('ensembl:ENSG00000087085', keyed=True)
matches = resp.source_matches
assert len(matches) == num_sources
- assert matches[SourceName.HGNC].records[0].match_type == MatchType.XREF
- assert matches[SourceName.ENSEMBL].records[0].match_type == \
+ assert matches[SourceName.HGNC.value].records[0].match_type == \
+ MatchType.XREF
+ assert matches[SourceName.ENSEMBL.value].records[0].match_type == \
MatchType.CONCEPT_ID
- assert matches[SourceName.NCBI].records[0].match_type == MatchType.XREF
+ assert matches[SourceName.NCBI.value].records[0].match_type == \
+ MatchType.XREF
# Normalize
q = "ACHE"
@@ -546,26 +551,31 @@ def test_braf_query(query_handler, num_sources, normalized_braf, source_meta):
resp = query_handler.search('ncbigene:673', keyed=True)
matches = resp.source_matches
assert len(matches) == num_sources
- assert matches[SourceName.HGNC].records[0].match_type == MatchType.XREF
- assert len(matches[SourceName.ENSEMBL].records) == 0
- assert matches[SourceName.NCBI].records[0].match_type == \
+ assert matches[SourceName.HGNC.value].records[0].match_type == \
+ MatchType.XREF
+ assert len(matches[SourceName.ENSEMBL.value].records) == 0
+ assert matches[SourceName.NCBI.value].records[0].match_type == \
MatchType.CONCEPT_ID
resp = query_handler.search('hgnc:1097', keyed=True)
matches = resp.source_matches
assert len(matches) == num_sources
- assert matches[SourceName.HGNC].records[0].match_type ==\
+ assert matches[SourceName.HGNC.value].records[0].match_type ==\
MatchType.CONCEPT_ID
- assert matches[SourceName.ENSEMBL].records[0].match_type == MatchType.XREF
- assert matches[SourceName.NCBI].records[0].match_type == MatchType.XREF
+ assert matches[SourceName.ENSEMBL.value].records[0].match_type == \
+ MatchType.XREF
+ assert matches[SourceName.NCBI.value].records[0].match_type == \
+ MatchType.XREF
resp = query_handler.search('ensembl:ENSG00000157764', keyed=True)
matches = resp.source_matches
assert len(matches) == num_sources
- assert matches[SourceName.HGNC].records[0].match_type == MatchType.XREF
- assert matches[SourceName.ENSEMBL].records[0].match_type == \
+ assert matches[SourceName.HGNC.value].records[0].match_type == \
+ MatchType.XREF
+ assert matches[SourceName.ENSEMBL.value].records[0].match_type == \
MatchType.CONCEPT_ID
- assert matches[SourceName.NCBI].records[0].match_type == MatchType.XREF
+ assert matches[SourceName.NCBI.value].records[0].match_type == \
+ MatchType.XREF
# Normalize
q = "BRAF"
@@ -624,26 +634,31 @@ def test_abl1_query(query_handler, num_sources, normalized_abl1, source_meta):
resp = query_handler.search('ncbigene:25', keyed=True)
matches = resp.source_matches
assert len(matches) == num_sources
- assert matches[SourceName.HGNC].records[0].match_type == MatchType.XREF
- assert len(matches[SourceName.ENSEMBL].records) == 0
- assert matches[SourceName.NCBI].records[0].match_type == \
+ assert matches[SourceName.HGNC.value].records[0].match_type == \
+ MatchType.XREF
+ assert len(matches[SourceName.ENSEMBL.value].records) == 0
+ assert matches[SourceName.NCBI.value].records[0].match_type == \
MatchType.CONCEPT_ID
resp = query_handler.search('hgnc:76', keyed=True)
matches = resp.source_matches
assert len(matches) == num_sources
- assert matches[SourceName.HGNC].records[0].match_type == \
+ assert matches[SourceName.HGNC.value].records[0].match_type == \
MatchType.CONCEPT_ID
- assert matches[SourceName.ENSEMBL].records[0].match_type == MatchType.XREF
- assert matches[SourceName.NCBI].records[0].match_type == MatchType.XREF
+ assert matches[SourceName.ENSEMBL.value].records[0].match_type == \
+ MatchType.XREF
+ assert matches[SourceName.NCBI.value].records[0].match_type == \
+ MatchType.XREF
resp = query_handler.search('ensembl:ENSG00000097007', keyed=True)
matches = resp.source_matches
assert len(matches) == num_sources
- assert matches[SourceName.HGNC].records[0].match_type == MatchType.XREF
- assert matches[SourceName.ENSEMBL].records[0].match_type == \
+ assert matches[SourceName.HGNC.value].records[0].match_type == \
+ MatchType.XREF
+ assert matches[SourceName.ENSEMBL.value].records[0].match_type == \
MatchType.CONCEPT_ID
- assert matches[SourceName.NCBI].records[0].match_type == MatchType.XREF
+ assert matches[SourceName.NCBI.value].records[0].match_type == \
+ MatchType.XREF
# Normalize
q = "ABL1"
@@ -724,7 +739,7 @@ def test_multiple_norm_concepts(query_handler, normalized_p150, source_meta):
def test_invalid_queries(query_handler):
"""Test invalid queries"""
resp = query_handler.normalize("B R A F")
- assert resp.match_type is MatchType.NO_MATCH
+ assert resp.match_type is MatchType.NO_MATCH.value
with pytest.raises(TypeError):
resp["match_type"]
From 79a897a4575bd1215a780b800de5669fa78526ad Mon Sep 17 00:00:00 2001
From: korikuzma <korikuzma@gmail.com>
Date: Thu, 24 Mar 2022 13:23:24 -0400
Subject: [PATCH 3/3] Install python-devel and postgresql-devel in eb
---
.ebextensions/01app.config | 3 +++
1 file changed, 3 insertions(+)
create mode 100644 .ebextensions/01app.config
diff --git a/.ebextensions/01app.config b/.ebextensions/01app.config
new file mode 100644
index 00000000..fd4dc15a
--- /dev/null
+++ b/.ebextensions/01app.config
@@ -0,0 +1,3 @@
+commands:
+ 01_install_postgresql_devel:
+ command: "yum install -y python-devel postgresql-devel"
\ No newline at end of file