Merge pull request #96 from cancervariants/staging

Staging

Pipfile

@@ -13,12 +13,12 @@ beautifulsoup4 = "*"
 gffutils = "*"
 requests = "*"
 "biocommons.seqrepo" = "*"
-"ga4gh.vrs" = {version = "==0.7.0rc3", extras = ["extras"]}
+"ga4gh.vrs" = {version = ">=0.7.2", extras = ["extras"]}
 uvloop = "*"
 websockets = "*"
 httptools = "*"
 typing-extensions = "*"
-"ga4gh.vrsatile.pydantic" = ">=0.0.3"
+"ga4gh.vrsatile.pydantic" = ">=0.0.5"
 jsonschema = ">=2.3, <4.0"
 
 [dev-packages]

codebuild/deploy_eb_env_dev.py

@@ -0,0 +1,52 @@
+"""Module for deploying staging EB environment."""
+import boto3
+import time
+
+elasticbeanstalk = boto3.client('elasticbeanstalk')
+servicecatalog = boto3.client('servicecatalog')
+terminate_time = 12
+eb_app_name = "GeneNormalization"
+eb_env_name = "GeneNormalization-dev-env"
+sc_product_id = "prod-mmw6ymv2ntzl2"
+print(f'Launching new Service Catalog Product for staging environment:'
+      f' {eb_app_name}')
+sc_product_artifacts = \
+    servicecatalog.list_provisioning_artifacts(ProductId=sc_product_id)
+for artifact in sc_product_artifacts['ProvisioningArtifactDetails']:
+    if artifact['Active']:
+        provisioning_artifact_id = artifact['Id']
+try:
+    eb_provisioned_product = servicecatalog.provision_product(
+        ProductId=sc_product_id,
+        ProvisioningArtifactId=provisioning_artifact_id,
+        ProvisionedProductName=eb_env_name,
+        ProvisioningParameters=[
+            {
+                'Key': 'Env',
+                'Value': eb_app_name
+            },
+            {
+                'Key': 'EnvType',
+                'Value': 'dev'
+            },
+            {
+                'Key': 'TerminateTime',
+                'Value': str(terminate_time)
+            }
+        ]
+    )
+    eb_provisioned_product_Id = \
+        eb_provisioned_product['RecordDetail']['ProvisionedProductId']
+    product_status = servicecatalog.describe_provisioned_product(
+        Id=eb_provisioned_product_Id)
+    eb_provisioned_product_status = \
+        product_status['ProvisionedProductDetail']['Status']
+    while eb_provisioned_product_status == "UNDER_CHANGE":
+        time.sleep(10)
+        product_status = servicecatalog.describe_provisioned_product(
+            Id=eb_provisioned_product_Id)
+        eb_provisioned_product_status = \
+            product_status['ProvisionedProductDetail']['Status']
+        print(eb_provisioned_product_status)
+except:  # noqa: E722
+    print("The EB environment is already running...")

codebuild/terminate_eb_env_dev.py

@@ -0,0 +1,30 @@
+"""Module for terminating staging EB environment."""
+import boto3
+import json
+import time
+
+client = boto3.client('lambda')
+servicecatalog = boto3.client('servicecatalog')
+eb_env_name = "GeneNormalization-dev-env"
+data = {"sc_provisioned_name": eb_env_name}
+client.invoke(FunctionName='igm-inf-terminate-provisioned-product',
+              Payload=json.dumps(data))
+time.sleep(10)
+provisioned_product = \
+    servicecatalog.describe_provisioned_product(Name=eb_env_name)
+eb_provisioned_product_Id =\
+    provisioned_product['ProvisionedProductDetail']['Id']
+product_status = servicecatalog.describe_provisioned_product(
+    Id=eb_provisioned_product_Id)
+eb_provisioned_product_status =\
+    product_status['ProvisionedProductDetail']['Status']
+while eb_provisioned_product_status == "UNDER_CHANGE":
+    time.sleep(10)
+    try:
+        product_status = servicecatalog.describe_provisioned_product(
+            Id=eb_provisioned_product_Id)
+        eb_provisioned_product_status = \
+            product_status['ProvisionedProductDetail']['Status']
+    except:  # noqa: E722
+        eb_provisioned_product_status = "PRODUCT NOT FOUND"
+    print(eb_provisioned_product_status)

gene/etl/base.py

@@ -164,6 +164,6 @@ def get_seqrepo(self, seqrepo_dir) -> SeqRepo:
         :param Path seqrepo_dir: Path to seqrepo directory
         :return: SeqRepo instance
         """
-        if not seqrepo_dir.exists():
+        if not Path(seqrepo_dir).exists():
             raise NotADirectoryError(f"Could not find {seqrepo_dir}")
         return SeqRepo(seqrepo_dir)

gene/query.py

@@ -8,7 +8,7 @@
 from gene.database import Database
 from gene.schemas import Gene, SourceMeta, MatchType, SourceName, \
     ServiceMeta, SourcePriority, NormalizeService, SearchService
-from ga4gh.vrsatile.pydantic.vrsatile_model import GeneDescriptor, Extension
+from ga4gh.vrsatile.pydantic.vrsatile_models import GeneDescriptor, Extension
 from botocore.exceptions import ClientError
 from boto3.dynamodb.conditions import Key
 from datetime import datetime

gene/schemas.py

@@ -5,9 +5,9 @@
 from pydantic import BaseModel, StrictBool, validator
 from enum import Enum, IntEnum
 from ga4gh.vrsatile.pydantic import return_value
-from ga4gh.vrsatile.pydantic.vrs_model import SequenceLocation, \
+from ga4gh.vrsatile.pydantic.vrs_models import SequenceLocation, \
     ChromosomeLocation, CURIE
-from ga4gh.vrsatile.pydantic.vrsatile_model import GeneDescriptor
+from ga4gh.vrsatile.pydantic.vrsatile_models import GeneDescriptor
 from datetime import datetime
 from pydantic.types import StrictStr
 

gene/version.py

@@ -1 +1,2 @@
-__version__ = "0.1.22"
+"""Gene normalizer version"""
+__version__ = "0.1.23"

requirements-dev.txt

@@ -20,13 +20,13 @@ 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'
 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==1.1.0; python_version >= '2.7'
+backports.entry-points-selectable==1.1.1; python_version >= '2.7'
 beautifulsoup4==4.10.0
 biocommons.seqrepo==0.6.4
 bioutils==0.5.5; python_version >= '3.6'
-bleach==4.1.0; python_version >= '3.6'
-boto3==1.19.7
-botocore==1.22.7; 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'
 bs4==0.0.1
 canonicaljson==1.5.0; python_version ~= '3.5'
 certifi==2021.10.8
@@ -35,9 +35,9 @@ cfgv==3.3.1; python_full_version >= '3.6.1'
 charset-normalizer==2.0.7; 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==5.0.2; python_version >= '3.6'
-coverage[toml]==5.5
-coveralls==3.2.0
+configparser==5.1.0; python_version >= '3.6'
+coverage[toml]==6.1.2
+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'
@@ -47,114 +47,114 @@ docopt==0.6.2
 entrypoints==0.3; python_version >= '2.7'
 fake-useragent==0.1.11
 fastapi==0.70.0
-filelock==3.3.2; python_version >= '3.6'
+filelock==3.4.0; python_full_version >= '3.6.0'
 flake8-docstrings==1.6.0
 flake8==4.0.1
 frozendict==2.0.7; python_version >= '3.6'
-ga4gh.vrs[extras]==0.7.0rc3
-ga4gh.vrsatile.pydantic==0.0.3
+ga4gh.vrs[extras]==0.7.2
+ga4gh.vrsatile.pydantic==0.0.5
 gffutils==0.10.1
 h11==0.12.0; python_version >= '3.6'
 hgvs==1.5.1
 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==2.3.1; python_full_version >= '3.6.1'
+identify==2.3.6; python_full_version >= '3.6.1'
 idna==3.3; python_version >= '3'
-importlib-metadata==4.8.1; python_version >= '3.6'
+importlib-metadata==4.8.2; python_version < '3.10'
 inflection==0.5.1; python_version >= '3.5'
 iniconfig==1.1.1
-ipykernel==6.4.2; python_version >= '3.7'
+ipykernel==6.5.0; python_version >= '3.7'
 ipython-genutils==0.2.0
 ipython==7.29.0; python_version >= '3.7'
-jedi==0.18.0; python_version >= '3.6'
-jinja2==3.0.2; python_version >= '3.6'
+jedi==0.18.1; python_version >= '3.6'
+jinja2==3.0.3; python_full_version >= '3.6.0'
 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_version >= '3.6'
-jupyter-server==1.11.1; python_version >= '3.6'
+jupyter-core==4.9.1; python_full_version >= '3.6.0'
+jupyter-server==1.11.2; python_full_version >= '3.6.0'
 jupyterlab-pygments==0.1.2
-jupyterlab-server==2.8.2; python_version >= '3.6'
-jupyterlab==3.2.1
-lxml==4.6.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-markdown==3.3.4; python_version >= '3.6'
-markupsafe==2.0.1; python_version >= '3.6'
+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'
+markdown==3.3.6; python_version >= '3.6'
+markupsafe==2.0.1; python_full_version >= '3.6.0'
 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_version >= '3.6'
-nbclient==0.5.4; python_full_version >= '3.6.1'
-nbconvert==6.2.0; python_version >= '3.7'
+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'
 nbformat==5.1.3; python_version >= '3.5'
 nest-asyncio==1.5.1; python_version >= '3.5'
 nodeenv==1.6.0
-notebook==6.4.5; python_version >= '3.6'
-numpy==1.21.3; python_version < '3.11' and python_version >= '3.7'
-packaging==21.2; python_version >= '3.6'
+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'
 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'
 pexpect==4.8.0; sys_platform != 'win32'
 pickleshare==0.7.5
-platformdirs==2.4.0; python_version >= '3.6'
-pluggy==1.0.0; python_version >= '3.6'
+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
 prometheus-client==0.12.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-prompt-toolkit==3.0.21; python_full_version >= '3.6.2'
-psycopg2-binary==2.9.1; python_version >= '3.6'
+prompt-toolkit==3.0.22; python_full_version >= '3.6.2'
+psycopg2-binary==2.9.2; python_version >= '3.6'
 ptyprocess==0.7.0
-py==1.10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+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==2.20; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+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_version >= '3.6'
+pydocstyle==6.1.1; python_full_version >= '3.6.0'
 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==2.4.7; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pyppeteer==0.2.6; python_full_version >= '3.6.1' and python_full_version < '4.0.0'
+pyparsing==3.0.6; python_full_version >= '3.6.0'
+pyppeteer==0.2.6; python_version < '4' and python_full_version >= '3.6.1'
 pyquery==1.4.3
 pyrsistent==0.18.0; python_version >= '3.6'
-pysam==0.17.0
+pysam==0.18.0
 pytest-cov==3.0.0
 pytest==6.2.5
 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==0.3.10
+python-jsonschema-objects==0.4.1
 pytz==2021.3
 pyyaml==6.0; python_version >= '3.6'
-pyzmq==22.3.0; python_version >= '3.6'
+pyzmq==22.3.0; python_full_version >= '3.6.0'
 requests-html==0.10.0; python_version >= '3.6'
-requests-unixsocket==0.2.0
 requests==2.26.0
 s3transfer==0.5.0; python_version >= '3.6'
 send2trash==1.8.0
-simplejson==3.17.5; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
+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==2.1.0
-soupsieve==2.2.1; python_version >= '3.6'
+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'
 tabulate==0.8.9
-terminado==0.12.1; python_version >= '3.6'
+terminado==0.12.1; python_full_version >= '3.6.0'
 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'
 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==3.10.0.2
-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_full_version < '4.0.0'
+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
 uvloop==0.16.0
-virtualenv==20.9.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+virtualenv==20.10.0; 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_version >= '3.6'
+websocket-client==1.2.1; python_full_version >= '3.6.0'
 websockets==9.1
 yoyo-migrations==7.3.2
 zipp==3.6.0; python_version >= '3.6'