refactor: update to lastest version of gene-normalizer (#146)

* gene-normalizer versions allowed: >= 0.1.34 OR >= 0.2.9
  * QueryHandler now accepts Database instance in the latest version
* CoolSeqTool now has a gene_query_handler instance var

Author: korikuzma

Pipfile

@@ -14,7 +14,7 @@ hgvs = "*"
 pydantic = "*"
 fastapi = "*"
 uvicorn = "*"
-gene-normalizer = "*"
+gene-normalizer = ">=0.1.34, != 0.2.0, != 0.2.1, != 0.2.2, != 0.2.3, != 0.2.4, != 0.2.5, != 0.2.6, != 0.2.7, != 0.2.8"
 "ga4gh.vrs" = "*"
 
 [dev-packages]

cool_seq_tool/cool_seq_tool.py

@@ -59,6 +59,7 @@ def __init__(
         self.uta_db = UTADatabase(db_url=db_url, db_pwd=db_pwd)
         gene_normalizer = GeneNormalizer(gene_query_handler, gene_db_url,
                                          gene_db_region)
+        self.gene_query_handler = gene_normalizer.query_handler
         self.alignment_mapper = AlignmentMapper(
             self.seqrepo_access, self.transcript_mappings, self.uta_db)
         self.mane_transcript = MANETranscript(

cool_seq_tool/data_sources/gene_normalizer.py

@@ -1,6 +1,7 @@
 """Module for accessing Gene Normalizer"""
 from typing import Dict
 
+from gene.database.dynamodb import DynamoDbDatabase
 from gene.query import QueryHandler
 from gene.schemas import SourceName
 
@@ -27,7 +28,8 @@ def __init__(
         if query_handler:
             self.query_handler = query_handler
         else:
-            self.query_handler = QueryHandler(db_url, db_region)
+            ddb = DynamoDbDatabase(db_url=db_url, region_name=db_region)
+            self.query_handler = QueryHandler(ddb)
 
     def get_hgnc_data(self, gene: str) -> Dict:
         """Return HGNC data for a given gene

cool_seq_tool/version.py

@@ -1 +1 @@
-__version__ = "0.1.11"
+__version__ = "0.1.12"

requirements-dev.txt

@@ -5,13 +5,13 @@ appdirs==1.4.4
 appnope==0.1.3 ; sys_platform == 'darwin'
 asttokens==2.2.1
 asyncpg==0.27.0
-attrs==22.2.0 ; python_version >= '3.6'
+attrs==23.1.0 ; python_version >= '3.7'
 backcall==0.2.0
-beautifulsoup4==4.12.0 ; python_full_version >= '3.6.0'
+beautifulsoup4==4.12.2 ; python_full_version >= '3.6.0'
 biocommons.seqrepo==0.6.5
 bioutils==0.5.7 ; python_version >= '3.6'
-boto3==1.26.103
-botocore==1.29.103 ; python_version >= '3.7'
+boto3==1.26.115
+botocore==1.29.115 ; python_version >= '3.7'
 bs4==0.0.1
 canonicaljson==2.0.0 ; python_version >= '3.7'
 certifi==2022.12.7 ; python_version >= '3.6'
@@ -22,78 +22,79 @@ coloredlogs==15.0.1 ; python_version >= '2.7' and python_version not in '3.0, 3.
 comm==0.1.3 ; python_version >= '3.6'
 configparser==5.3.0 ; python_version >= '3.7'
 -e .
-coverage[toml]==7.2.2 ; python_version >= '3.7'
+coverage[toml]==7.2.3 ; python_version >= '3.7'
 cssselect==1.2.0 ; python_version >= '3.7'
-debugpy==1.6.6 ; python_version >= '3.7'
+cython==0.29.34 ; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'
+debugpy==1.6.7 ; python_version >= '3.7'
 decorator==5.1.1 ; python_version >= '3.5'
 distlib==0.3.6
 exceptiongroup==1.1.1 ; python_version < '3.11'
 executing==1.2.0
 fake-useragent==1.1.3
-fastapi==0.95.0
-filelock==3.10.7 ; python_version >= '3.7'
+fastapi==0.95.1
+filelock==3.12.0 ; python_version >= '3.7'
 flake8==6.0.0
 flake8-annotations==3.0.0
 flake8-docstrings==1.7.0
 flake8-import-order==0.18.2
 flake8-quotes==3.3.2
 ga4gh.vrs==0.9.0.dev0
 ga4gh.vrsatile.pydantic==0.1.0.dev7 ; python_version >= '3.8'
-gene-normalizer==0.2.8
+gene-normalizer==0.2.9
 h11==0.14.0 ; python_version >= '3.7'
 hgvs==1.5.4
 humanfriendly==10.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 identify==2.5.22 ; python_version >= '3.7'
 idna==3.4 ; python_version >= '3.5'
-importlib-metadata==6.1.0 ; python_version >= '3.7'
+importlib-metadata==6.5.0 ; python_version >= '3.7'
 inflection==0.5.1 ; python_version >= '3.5'
 iniconfig==2.0.0 ; python_version >= '3.7'
 ipykernel==6.22.0
 ipython==8.12.0 ; python_version >= '3.8'
 jedi==0.18.2 ; python_version >= '3.6'
 jmespath==1.0.1 ; python_version >= '3.7'
 jsonschema==3.2.0
-jupyter-client==8.1.0 ; python_version >= '3.8'
+jupyter-client==8.2.0 ; python_version >= '3.8'
 jupyter-core==5.3.0 ; python_version >= '3.8'
 lxml==4.9.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 markdown==3.4.3 ; python_version >= '3.7'
 matplotlib-inline==0.1.6 ; python_version >= '3.5'
 mccabe==0.7.0 ; python_version >= '3.6'
-mock==5.0.1
+mock==5.0.2
 nest-asyncio==1.5.6 ; python_version >= '3.5'
 nodeenv==1.7.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6'
 numpy==1.24.2 ; python_version >= '3.8'
-packaging==23.0 ; python_version >= '3.7'
-pandas==1.5.3
+packaging==23.1 ; python_version >= '3.7'
+pandas==2.0.0
 parse==1.19.0
 parsley==1.3
 parso==0.8.3 ; python_version >= '3.6'
 pexpect==4.8.0 ; sys_platform != 'win32'
 pickleshare==0.7.5
 platformdirs==3.2.0 ; python_version >= '3.7'
 pluggy==1.0.0 ; python_version >= '3.6'
-pre-commit==3.2.1
+pre-commit==3.2.2
 prompt-toolkit==3.0.38 ; python_full_version >= '3.7.0'
-psutil==5.9.4 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-psycopg2==2.9.5 ; python_version >= '3.6'
-psycopg2-binary==2.9.5
+psutil==5.9.5 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+psycopg2==2.9.6 ; python_version >= '3.6'
+psycopg2-binary==2.9.6
 ptyprocess==0.7.0
 pure-eval==0.2.2
 pycodestyle==2.10.0 ; python_version >= '3.6'
 pydantic==1.10.7
 pydocstyle==6.3.0 ; python_version >= '3.6'
 pyee==8.2.2
 pyflakes==3.0.1 ; python_version >= '3.6'
-pygments==2.14.0 ; python_version >= '3.6'
+pygments==2.15.1 ; python_version >= '3.7'
 pyliftover==0.4
 pyppeteer==1.0.2 ; python_version >= '3.7' and python_version < '4.0'
 pyquery==2.0.0
 pyrsistent==0.19.3 ; python_version >= '3.7'
-pysam==0.20.0
-pytest==7.2.2
+pysam==0.21.0 ; python_version >= '3.6'
+pytest==7.3.1
 pytest-asyncio==0.18.3
 pytest-cov==4.0.0
-python-dateutil==2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+python-dateutil==2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
 python-jsonschema-objects==0.4.1
 pytz==2023.3
 pyyaml==6.0 ; python_version >= '3.6'
@@ -102,19 +103,20 @@ requests==2.28.2 ; python_version >= '3.7' and python_version < '4'
 requests-html==0.10.0 ; python_full_version >= '3.6.0'
 s3transfer==0.6.0 ; python_version >= '3.7'
 setuptools==67.6.1 ; python_version >= '3.7'
-six==1.16.0 ; python_version >= '2.7' 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'
 sniffio==1.3.0 ; python_version >= '3.7'
 snowballstemmer==2.2.0
-soupsieve==2.4 ; python_version >= '3.7'
-sqlparse==0.4.3 ; python_version >= '3.5'
+soupsieve==2.4.1 ; python_version >= '3.7'
+sqlparse==0.4.4 ; python_version >= '3.5'
 stack-data==0.6.2
 starlette==0.26.1 ; python_version >= '3.7'
 tabulate==0.9.0 ; python_version >= '3.7'
 tomli==2.0.1 ; python_version < '3.11'
-tornado==6.2 ; python_version >= '3.7'
+tornado==6.3 ; python_version >= '3.8'
 tqdm==4.65.0 ; python_version >= '3.7'
 traitlets==5.9.0 ; python_version >= '3.7'
 typing-extensions==4.5.0 ; python_version >= '3.7'
+tzdata==2023.3 ; python_version >= '2'
 urllib3==1.26.15 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 uvicorn==0.21.1
 virtualenv==20.21.0 ; python_version >= '3.7'

requirements.txt

@@ -5,13 +5,13 @@ appdirs==1.4.4
 appnope==0.1.3 ; sys_platform == 'darwin'
 asttokens==2.2.1
 asyncpg==0.27.0
-attrs==22.2.0 ; python_version >= '3.6'
+attrs==23.1.0 ; python_version >= '3.7'
 backcall==0.2.0
-beautifulsoup4==4.12.0 ; python_full_version >= '3.6.0'
+beautifulsoup4==4.12.2 ; python_full_version >= '3.6.0'
 biocommons.seqrepo==0.6.5
 bioutils==0.5.7 ; python_version >= '3.6'
-boto3==1.26.103
-botocore==1.29.103 ; python_version >= '3.7'
+boto3==1.26.115
+botocore==1.29.115 ; python_version >= '3.7'
 bs4==0.0.1
 canonicaljson==2.0.0 ; python_version >= '3.7'
 certifi==2022.12.7 ; python_version >= '3.6'
@@ -20,18 +20,19 @@ click==8.1.3 ; python_version >= '3.7'
 coloredlogs==15.0.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 configparser==5.3.0 ; python_version >= '3.7'
 cssselect==1.2.0 ; python_version >= '3.7'
+cython==0.29.34 ; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'
 decorator==5.1.1 ; python_version >= '3.5'
 executing==1.2.0
 fake-useragent==1.1.3
-fastapi==0.95.0
+fastapi==0.95.1
 ga4gh.vrs==0.9.0.dev0
 ga4gh.vrsatile.pydantic==0.1.0.dev7 ; python_version >= '3.8'
-gene-normalizer==0.2.8
+gene-normalizer==0.2.9
 h11==0.14.0 ; python_version >= '3.7'
 hgvs==1.5.4
 humanfriendly==10.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 idna==3.4 ; python_version >= '3.5'
-importlib-metadata==6.1.0 ; python_version >= '3.7'
+importlib-metadata==6.5.0 ; python_version >= '3.7'
 inflection==0.5.1 ; python_version >= '3.5'
 ipython==8.12.0 ; python_version >= '3.8'
 jedi==0.18.2 ; python_version >= '3.6'
@@ -41,42 +42,43 @@ lxml==4.9.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2,
 markdown==3.4.3 ; python_version >= '3.7'
 matplotlib-inline==0.1.6 ; python_version >= '3.5'
 numpy==1.24.2 ; python_version >= '3.8'
-pandas==1.5.3
+pandas==2.0.0
 parse==1.19.0
 parsley==1.3
 parso==0.8.3 ; python_version >= '3.6'
 pexpect==4.8.0 ; sys_platform != 'win32'
 pickleshare==0.7.5
 prompt-toolkit==3.0.38 ; python_full_version >= '3.7.0'
-psycopg2==2.9.5 ; python_version >= '3.6'
+psycopg2==2.9.6 ; python_version >= '3.6'
 ptyprocess==0.7.0
 pure-eval==0.2.2
 pydantic==1.10.7
 pyee==8.2.2
-pygments==2.14.0 ; python_version >= '3.6'
+pygments==2.15.1 ; python_version >= '3.7'
 pyliftover==0.4
 pyppeteer==1.0.2 ; python_version >= '3.7' and python_version < '4.0'
 pyquery==2.0.0
 pyrsistent==0.19.3 ; python_version >= '3.7'
-pysam==0.20.0
-python-dateutil==2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+pysam==0.21.0 ; python_version >= '3.6'
+python-dateutil==2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
 python-jsonschema-objects==0.4.1
 pytz==2023.3
 pyyaml==6.0 ; python_version >= '3.6'
 requests==2.28.2 ; python_version >= '3.7' and python_version < '4'
 requests-html==0.10.0 ; python_full_version >= '3.6.0'
 s3transfer==0.6.0 ; python_version >= '3.7'
 setuptools==67.6.1 ; python_version >= '3.7'
-six==1.16.0 ; python_version >= '2.7' 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'
 sniffio==1.3.0 ; python_version >= '3.7'
-soupsieve==2.4 ; python_version >= '3.7'
-sqlparse==0.4.3 ; python_version >= '3.5'
+soupsieve==2.4.1 ; python_version >= '3.7'
+sqlparse==0.4.4 ; python_version >= '3.5'
 stack-data==0.6.2
 starlette==0.26.1 ; python_version >= '3.7'
 tabulate==0.9.0 ; python_version >= '3.7'
 tqdm==4.65.0 ; python_version >= '3.7'
 traitlets==5.9.0 ; python_version >= '3.7'
 typing-extensions==4.5.0 ; python_version >= '3.7'
+tzdata==2023.3 ; python_version >= '2'
 urllib3==1.26.15 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 uvicorn==0.21.1
 w3lib==2.1.1 ; python_version >= '3.7'

setup.cfg

@@ -23,7 +23,7 @@ install_requires =
     pydantic
     uvicorn
     fastapi
-    gene-normalizer
+    gene-normalizer >=0.1.34, != 0.2.0, != 0.2.1, != 0.2.2, != 0.2.3, != 0.2.4, != 0.2.5, != 0.2.6, != 0.2.7, != 0.2.8
     ga4gh.vrs
 
 [options.package_data]