Merge pull request #107 from cancervariants/staging

Staging
cancervariants · Mar 24, 2022 · b17a54d · b17a54d
2 parents 4559e96 + b0bfbd7
commit b17a54d
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Showing 16 changed files with 242 additions and 187 deletions.
diff --git a/.ebextensions/01app.config b/.ebextensions/01app.config
@@ -0,0 +1,3 @@
+commands:
+    01_install_postgresql_devel:
+        command: "yum install -y python-devel postgresql-devel"
diff --git a/Pipfile b/Pipfile
@@ -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
@@ -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/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/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
@@ -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
@@ -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
@@ -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
@@ -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()