Adding endpoint for vrs-python translate_from method

Pipfile

@@ -32,7 +32,7 @@ uvicorn = "*"
 pydantic = "*"
 uvloop = "*"
 httptools = "*"
-"ga4gh.vrs" = {version = ">=0.7.2", extras = ["extras"]}
+"ga4gh.vrs" = {version = ">=0.7.4", extras = ["extras"]}
 gene-normalizer = ">=0.1.23"
 pyliftover = "*"
 boto3 = "*"

requirements-dev.txt

@@ -25,10 +25,9 @@ backcall==0.2.0
 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'
 bleach==4.1.0; python_version >= '3.6'
-boto3==1.21.3
-botocore==1.24.3; python_version >= '3.6'
+boto3==1.21.12
+botocore==1.24.12; python_version >= '3.6'
 bs4==0.0.1
 canonicaljson==1.5.0; python_version ~= '3.5'
 certifi==2021.10.8
@@ -39,41 +38,41 @@ 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==6.3.1
+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'
 cycler==0.11.0; python_version >= '3.6'
 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
 docutils==0.18.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 entrypoints==0.4; python_version >= '3.6'
-executing==0.8.2
+executing==0.8.3
 fake-useragent==0.1.11
-fastapi==0.74.0
-filelock==3.6.0; python_version >= '3.7'
+fastapi==0.74.1
+filelock==3.6.0; python_full_version >= '3.7.0'
 flake8-docstrings==1.6.0
 flake8==4.0.1
-fonttools==4.29.1; python_version >= '3.7'
+fonttools==4.29.1; python_full_version >= '3.7.0'
 frozendict==2.3.0; python_version >= '3.6'
-ga4gh.vrs[extras]==0.7.2
+ga4gh.vrs[extras]==0.7.4
 ga4gh.vrsatile.pydantic==0.0.9
 gene-normalizer==0.1.24
 gffutils==0.10.1
 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==2.4.10; python_version >= '3.7'
+identify==2.4.11; python_full_version >= '3.7.0'
 idna==3.3; python_version >= '3'
-importlib-metadata==4.11.1; python_version < '3.10'
-inflection==0.5.1; python_version >= '3.5'
+importlib-metadata==4.11.2; python_version < '3.10'
+inflection==0.5.1; python_full_version >= '3.5.0'
 iniconfig==1.1.1
 ipykernel==6.9.1
 ipython-genutils==0.2.0
-ipython==8.0.1; python_version >= '3.8'
+ipython==8.1.1; python_version >= '3.8'
 ipywidgets==7.6.5
 jedi==0.18.1; python_version >= '3.6'
 jinja2==3.0.3; python_version >= '3.6'
@@ -83,42 +82,41 @@ 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==4.9.2; python_version >= '3.6'
-jupyter-server==1.13.5; python_version >= '3.7'
+jupyter-server==1.13.5; python_full_version >= '3.7.0'
 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==3.2.9
-keyring==23.5.0; python_version >= '3.7'
-kiwisolver==1.3.2; python_version >= '3.7'
+jupyterlab==3.3.0
+keyring==23.5.0; python_full_version >= '3.7.0'
+kiwisolver==1.3.2; python_full_version >= '3.7.0'
 lxml==4.8.0
 markdown==3.3.6; python_version >= '3.6'
-markupsafe==2.1.0; python_version >= '3.7'
-matplotlib-inline==0.1.3; python_version >= '3.5'
+markupsafe==2.1.0; python_full_version >= '3.7.0'
+matplotlib-inline==0.1.3; python_full_version >= '3.5.0'
 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==0.5.11; python_version >= '3.7'
-nbconvert==6.4.2; python_version >= '3.7'
+nbclassic==0.3.6; python_full_version >= '3.7.0'
+nbclient==0.5.11; python_full_version >= '3.7.0'
+nbconvert==6.4.2; python_full_version >= '3.7.0'
 nbformat==5.1.3; python_version >= '3.5'
 nest-asyncio==1.5.4; python_version >= '3.5'
 nodeenv==1.6.0
+notebook-shim==0.1.0; python_full_version >= '3.7.0'
 notebook==6.4.8; python_version >= '3.6'
-numpy==1.22.2; python_version < '3.10' and platform_machine != 'aarch64' and platform_machine != 'arm64'
+numpy==1.22.2; python_version >= '3.8'
 packaging==21.3; python_version >= '3.6'
 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==9.0.1; python_version >= '3.7'
+pillow==9.0.1; python_full_version >= '3.7.0'
 pkginfo==1.8.2
-platformdirs==2.5.1; python_version >= '3.7'
+platformdirs==2.5.1; python_full_version >= '3.7.0'
 pluggy==1.0.0; python_version >= '3.6'
 pre-commit==2.17.0
 prometheus-client==0.13.1; python_version >= '3.6'
@@ -135,7 +133,7 @@ pydocstyle==6.1.1; python_version >= '3.6'
 pyee==8.2.2
 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'
+pygments==2.11.2; python_full_version >= '3.5.0'
 pyliftover==0.4
 pyparsing==3.0.7; python_version >= '3.6'
 pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4.0'
@@ -155,37 +153,37 @@ 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==0.5.1; python_version >= '3.6'
+rfc3986==2.0.0; python_full_version >= '3.7.0'
+s3transfer==0.5.2; python_version >= '3.6'
 send2trash==1.8.0
 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'
+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'
+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==0.13.1; python_version >= '3.7'
-testpath==0.5.0; python_version >= '3.5'
+terminado==0.13.2; python_full_version >= '3.7.0'
+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==2.0.1; python_version >= '3.7'
+tomli==2.0.1; python_full_version >= '3.7.0'
 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==4.63.0; 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==3.8.0
 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==20.13.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+virtualenv==20.13.2; 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
 widgetsnbextension==3.5.2
 yoyo-migrations==7.3.2
 zipp==3.7.0; python_version >= '3.7'

requirements.txt

@@ -18,9 +18,8 @@ backcall==0.2.0
 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==1.21.3
-botocore==1.24.3; python_version >= '3.6'
+boto3==1.21.12
+botocore==1.24.12; python_version >= '3.6'
 bs4==0.0.1
 canonicaljson==1.5.0; python_version ~= '3.5'
 certifi==2021.10.8
@@ -29,47 +28,44 @@ 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
+decorator==5.1.1; python_full_version >= '3.5.0'
+executing==0.8.3
 fake-useragent==0.1.11
-fastapi==0.74.0
+fastapi==0.74.1
 frozendict==2.3.0; python_version >= '3.6'
-ga4gh.vrs[extras]==0.7.2
+ga4gh.vrs[extras]==0.7.4
 ga4gh.vrsatile.pydantic==0.0.9
 gene-normalizer==0.1.24
 gffutils==0.10.1
 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==4.11.1; python_version < '3.10'
-inflection==0.5.1; python_version >= '3.5'
-ipython==8.0.1; python_version >= '3.8'
+importlib-metadata==4.11.2; 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'
 jsonschema==3.2.0
 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==1.22.2; python_version < '3.10' and platform_machine != 'aarch64' and platform_machine != 'arm64'
+matplotlib-inline==0.1.3; python_full_version >= '3.5.0'
+numpy==1.22.2; python_version >= '3.8'
 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==2.5.1; 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
 pydantic==1.9.0
 pyee==8.2.2
 pyfaidx==0.6.4
-pygments==2.11.2; python_version >= '3.5'
+pygments==2.11.2; python_full_version >= '3.5.0'
 pyliftover==0.4
 pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4.0'
 pyquery==1.4.3
@@ -81,25 +77,24 @@ pytz==2021.3
 pyyaml==6.0; python_version >= '3.6'
 requests-html==0.10.0; python_version >= '3.6'
 requests==2.27.1
-s3transfer==0.5.1; python_version >= '3.6'
+s3transfer==0.5.2; 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'
+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'
+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==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'
+tqdm==4.63.0; 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==4.1.1
 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
-websockets==10.1
+websockets==10.2
 yoyo-migrations==7.3.2
 zipp==3.7.0; python_version >= '3.7'

setup.cfg

@@ -31,7 +31,7 @@ install_requires =
     fastapi >= 0.72.0
     uvicorn
     pydantic
-    ga4gh.vrs[extras] >= 0.7.2
+    ga4gh.vrs[extras] >= 0.7.4
     gene-normalizer >= 0.1.23
     pyliftover
     boto3

variation/data_sources/uta.py

@@ -64,7 +64,9 @@ def _update_db_url(self, db_pwd, db_url) -> Optional[str]:
             else:
                 if uta_password_in_environ and not db_pwd:
                     db_pwd = environ['UTA_PASSWORD']
-            return f"{db_url[0]}:{db_pwd}@{db_url[1]}"
+            uta_db_url = f"{db_url[0]}:{db_pwd}@{db_url[1]}"
+            environ["UTA_DB_URL"] = uta_db_url
+            return uta_db_url
 
     def _get_conn_args(self, is_prod, db_pwd, db_url) -> Dict:
         """Return connection arguments.
@@ -82,14 +84,17 @@ def _get_conn_args(self, is_prod, db_pwd, db_url) -> Dict:
             self.schema = environ['UTA_SCHEMA']
             region = 'us-east-2'
             client = boto3.client('rds', region_name=region)
+            host = environ['UTA_HOST']
+            port = environ['UTA_PORT']
+            user = environ['UTA_USER']
+            db = environ['UTA_DATABASE']
             token = client.generate_db_auth_token(
-                DBHostname=environ['UTA_HOST'], Port=environ['UTA_PORT'],
-                DBUsername=environ['UTA_USER'], Region=region
+                DBHostname=host, Port=port, DBUsername=user, Region=region
             )
-            return self._get_args(environ['UTA_HOST'],
-                                  int(environ['UTA_PORT']),
-                                  environ['UTA_DATABASE'], environ['UTA_USER'],
-                                  token)
+            # TODO: Resolve in issue-252
+            # environ['UTA_DB_URL'] = \
+            #     f"postgresql://{user}:{token}@{host}/{db}/{self.schema}"
+            return self._get_args(host, int(port), db, user, token)
 
     def _url_encode_password(self, db_url) -> str:
         """Update DB URL to url encode password.