Merge pull request #275 from cancervariants/staging

Staging

Author: korikuzma

Pipfile

@@ -31,8 +31,8 @@ fastapi = "*"
 uvicorn = "*"
 pydantic = "*"
 "ga4gh.vrs" = {version = ">=0.7.5.dev1", extras = ["extras"]}
-gene-normalizer = ">=0.1.23"
+gene-normalizer = ">=0.1.26"
 pyliftover = "*"
 boto3 = "*"
-"ga4gh.vrsatile.pydantic" = ">=0.0.10"
+"ga4gh.vrsatile.pydantic" = ">=0.0.11"
 uta-tools = ">=0.0.15"

README.md

@@ -2,7 +2,7 @@
 
 # Variation Normalization
 
-Services and guidelines for normalizing variation terms into [VRS (v1.2.0)](https://vrs.ga4gh.org/en/1.2.0) and [VRSATILE (latest)](https://vrsatile.readthedocs.io/en/latest/) compatible representations.
+Services and guidelines for normalizing variation terms into [VRS](https://vrs.ga4gh.org/en/latest) and [VRSATILE](https://vrsatile.readthedocs.io/en/latest/) compatible representations.
 
 Public OpenAPI endpoint: https://normalize.cancervariants.org/variation
 
@@ -26,8 +26,8 @@ Variation Normalization is limited to the following types of variants:
 We are working towards adding more types of variations, coordinates, and representations.
 
 ### Endpoints
-#### /toVRS
-The `/toVRS` endpoint returns a list of validated VRS [Variations](https://vrs.ga4gh.org/en/1.2.0/terms_and_model.html#variation).
+#### /to_vrs
+The `/to_vrs` endpoint returns a list of validated VRS [Variations](https://vrs.ga4gh.org/en/1.2.0/terms_and_model.html#variation).
 
 The `/normalize` endpoint returns a [Variation Descriptor](https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/vod_index.html#variation-descriptor) containing the MANE Transcript, if one is found. If a genomic query is not given a gene, `normalize` will return its GRCh38 representation.
 

requirements-dev.txt

@@ -24,12 +24,12 @@ asyncpg==0.25.0; python_version >= '3.6'
 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
-beautifulsoup4==4.10.0; python_version >= '3.1'
+beautifulsoup4==4.11.1; python_version >= '3.6'
 biocommons.seqrepo==0.6.5
 bioutils==0.5.5; python_version >= '3.6'
-bleach==4.1.0; python_version >= '3.6'
-boto3==1.21.32
-botocore==1.24.32; python_version >= '3.6'
+bleach==5.0.0; python_version >= '3.7'
+boto3==1.21.37
+botocore==1.24.37; python_version >= '3.6'
 bs4==0.0.1
 canonicaljson==1.6.0; python_version ~= '3.7'
 certifi==2021.10.8
@@ -61,10 +61,10 @@ flake8-docstrings==1.6.0
 flake8-import-order==0.18.1
 flake8-quotes==3.3.1
 flake8==4.0.1
-fonttools==4.31.2; python_version >= '3.7'
+fonttools==4.32.0; python_version >= '3.7'
 ga4gh.vrs[extras]==0.8a0
-ga4gh.vrsatile.pydantic==0.0.10
-gene-normalizer==0.1.24
+ga4gh.vrsatile.pydantic==0.0.11
+gene-normalizer==0.1.26
 gffutils==0.10.1
 h11==0.13.0; python_version >= '3.6'
 hgvs==1.5.2
@@ -74,7 +74,7 @@ idna==3.3; python_version >= '3.5'
 importlib-metadata==4.11.3; python_version < '3.10'
 inflection==0.5.1; python_version >= '3.5'
 iniconfig==1.1.1
-ipykernel==6.12.1
+ipykernel==6.13.0
 ipython-genutils==0.2.0
 ipython==8.2.0; python_version >= '3.8'
 ipywidgets==7.7.0
@@ -83,15 +83,15 @@ jinja2==3.1.1; python_version >= '3.7'
 jmespath==1.0.0; python_version >= '3.7'
 json5==0.9.6
 jsonschema==3.2.0
-jupyter-client==7.2.1; python_version >= '3.7'
+jupyter-client==7.2.2; python_version >= '3.7'
 jupyter-console==6.4.3; python_version >= '3.6'
 jupyter-core==4.9.2; python_version >= '3.6'
 jupyter-server==1.16.0; python_version >= '3.7'
 jupyter==1.0.0
-jupyterlab-pygments==0.1.2
+jupyterlab-pygments==0.2.0; python_version >= '3.7'
 jupyterlab-server==2.12.0; python_version >= '3.7'
 jupyterlab-widgets==1.1.0; python_version >= '3.6'
-jupyterlab==3.3.2
+jupyterlab==3.3.3
 keyring==23.5.0; python_version >= '3.7'
 kiwisolver==1.4.2; python_version >= '3.7'
 lxml==4.8.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
@@ -103,7 +103,7 @@ mccabe==0.6.1
 mistune==0.8.4
 nbclassic==0.3.7; python_version >= '3.7'
 nbclient==0.5.13; python_version >= '3.7'
-nbconvert==6.4.5; python_version >= '3.7'
+nbconvert==6.5.0; python_version >= '3.7'
 nbformat==5.3.0; python_version >= '3.7'
 nest-asyncio==1.5.5; python_version >= '3.5'
 nodeenv==1.6.0
@@ -123,7 +123,7 @@ pkginfo==1.8.2
 platformdirs==2.5.1; python_version >= '3.7'
 pluggy==1.0.0; python_version >= '3.6'
 pre-commit==2.18.1
-prometheus-client==0.13.1; python_version >= '3.6'
+prometheus-client==0.14.1; python_version >= '3.6'
 prompt-toolkit==3.0.29; 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-binary==2.9.3
@@ -140,7 +140,7 @@ 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'
 pyliftover==0.4
-pyparsing==3.0.7; python_version >= '3.6'
+pyparsing==3.0.8; python_full_version >= '3.6.8'
 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'
@@ -160,21 +160,21 @@ requests-html==0.10.0; python_version >= '3.6'
 requests-toolbelt==0.9.1
 requests==2.27.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 rfc3986==2.0.0; python_version >= '3.7'
-rich==12.1.0; python_version < '4' and python_full_version >= '3.6.2'
+rich==12.2.0; python_version < '4' and python_full_version >= '3.6.3'
 s3transfer==0.5.2; python_version >= '3.6'
 send2trash==1.8.0
-setuptools==62.0.0; python_version >= '3.7'
+setuptools==62.1.0; 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'
+soupsieve==2.3.2; python_version >= '3.6'
 sqlparse==0.4.2; python_version >= '3.5'
 stack-data==0.2.0
 starlette==0.17.1; python_version >= '3.6'
 tabulate==0.8.9
 terminado==0.13.3; python_version >= '3.7'
-testpath==0.6.0; python_version >= '3.5'
+tinycss2==1.1.1; python_version >= '3.6'
 toml==0.10.2; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
 tomli==2.0.1; python_version >= '3.7'
 tornado==6.1; python_version >= '3.5'
@@ -185,7 +185,7 @@ typing-extensions==4.1.1; python_version >= '3.6'
 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'
 uta-tools==0.0.15
 uvicorn==0.17.6
-virtualenv==20.14.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+virtualenv==20.14.1; 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

@@ -17,11 +17,11 @@ asttokens==2.0.5
 asyncpg==0.25.0; python_version >= '3.6'
 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; python_version >= '3.1'
+beautifulsoup4==4.11.1; python_version >= '3.6'
 biocommons.seqrepo==0.6.5
 bioutils==0.5.5; python_version >= '3.6'
-boto3==1.21.32
-botocore==1.24.32; python_version >= '3.6'
+boto3==1.21.37
+botocore==1.24.37; python_version >= '3.6'
 bs4==0.0.1
 canonicaljson==1.6.0; python_version ~= '3.7'
 certifi==2021.10.8
@@ -35,8 +35,8 @@ executing==0.8.3
 fake-useragent==0.1.11
 fastapi==0.75.1
 ga4gh.vrs[extras]==0.8a0
-ga4gh.vrsatile.pydantic==0.0.10
-gene-normalizer==0.1.24
+ga4gh.vrsatile.pydantic==0.0.11
+gene-normalizer==0.1.26
 gffutils==0.10.1
 h11==0.13.0; python_version >= '3.6'
 hgvs==1.5.2
@@ -78,11 +78,11 @@ pyyaml==6.0; python_version >= '3.6'
 requests-html==0.10.0; python_version >= '3.6'
 requests==2.27.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 s3transfer==0.5.2; python_version >= '3.6'
-setuptools==62.0.0; python_version >= '3.7'
+setuptools==62.1.0; 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'
+soupsieve==2.3.2; python_version >= '3.6'
 sqlparse==0.4.2; python_version >= '3.5'
 stack-data==0.2.0
 starlette==0.17.1; python_version >= '3.6'

setup.cfg

@@ -31,10 +31,10 @@ install_requires =
     uvicorn
     pydantic
     ga4gh.vrs[extras] >= 0.7.5.dev1
-    gene-normalizer >= 0.1.23
+    gene-normalizer >= 0.1.26
     pyliftover
     boto3
-    ga4gh.vrsatile.pydantic >= 0.0.10
+    ga4gh.vrsatile.pydantic >= 0.0.11
     uta-tools >= 0.0.15
 
 tests_require =