Merge pull request #649 from populationgenomics/dev

Release

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 6.6.0
+current_version = 6.6.2
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>[A-z0-9-]+)

api/graphql/schema.py

@@ -484,7 +484,7 @@ class GraphQLSequencingGroup:
     technology: str
     platform: str
     meta: strawberry.scalars.JSON
-    external_ids: strawberry.scalars.JSON | None
+    external_ids: strawberry.scalars.JSON
 
     internal_id: strawberry.Private[int]
     sample_id: strawberry.Private[int]
@@ -498,7 +498,7 @@ def from_internal(internal: SequencingGroupInternal) -> 'GraphQLSequencingGroup'
             technology=internal.technology,
             platform=internal.platform,
             meta=internal.meta,
-            external_ids=internal.external_ids,
+            external_ids=internal.external_ids or {},
             # internal
             internal_id=internal.id,
             sample_id=internal.sample_id,
@@ -575,7 +575,7 @@ def from_internal(internal: AssayInternal) -> 'GraphQLAssay':
             id=internal.id,
             type=internal.type,
             meta=internal.meta,
-            external_ids=internal.external_ids,
+            external_ids=internal.external_ids or {},
             # internal
             sample_id=internal.sample_id,
         )

api/server.py

@@ -20,7 +20,7 @@
 from api.settings import PROFILE_REQUESTS, SKIP_DATABASE_CONNECTION
 
 # This tag is automatically updated by bump2version
-_VERSION = '6.6.0'
+_VERSION = '6.6.2'
 
 logger = get_logger()
 

deploy/python/version.txt

@@ -1 +1 @@
-6.6.0
+6.6.2

metamist/graphql/__init__.py

@@ -9,7 +9,9 @@
 
 from gql import Client, gql as gql_constructor
 from gql.transport.aiohttp import AIOHTTPTransport
+from gql.transport.aiohttp import log as aiohttp_logger
 from gql.transport.requests import RequestsHTTPTransport
+from gql.transport.requests import log as requests_logger
 
 from cpg_utils.cloud import get_google_identity_token
 
@@ -54,13 +56,18 @@ def configure_sync_client(
     if _sync_client and not force_recreate:
         return _sync_client
 
-    token = auth_token or get_google_identity_token(
-        target_audience=metamist.configuration.sm_url
-    )
-    transport = RequestsHTTPTransport(
-        url=url or get_sm_url(),
-        headers={'Authorization': f'Bearer {token}'},
-    )
+    env = os.getenv('SM_ENVIRONMENT', 'PRODUCTION').lower()
+    if env == 'local':
+        transport = RequestsHTTPTransport(url=url or get_sm_url())
+    else:
+        token = auth_token or get_google_identity_token(
+            target_audience=metamist.configuration.sm_url
+        )
+        transport = RequestsHTTPTransport(
+            url=url or get_sm_url(),
+            headers={'Authorization': f'Bearer {token}'},
+        )
+
     _sync_client = Client(
         transport=transport, schema=schema, fetch_schema_from_transport=schema is None
     )
@@ -78,13 +85,18 @@ async def configure_async_client(
     if _async_client and not force_recreate:
         return _async_client
 
-    token = auth_token or get_google_identity_token(
-        target_audience=metamist.configuration.sm_url
-    )
-    transport = AIOHTTPTransport(
-        url=url or get_sm_url(),
-        headers={'Authorization': f'Bearer {token}'},
-    )
+    env = os.getenv('SM_ENVIRONMENT', 'PRODUCTION').lower()
+    if env == 'local':
+        transport = AIOHTTPTransport(url=url or get_sm_url())
+    else:
+        token = auth_token or get_google_identity_token(
+            target_audience=metamist.configuration.sm_url
+        )
+        transport = AIOHTTPTransport(
+            url=url or get_sm_url(),
+            headers={'Authorization': f'Bearer {token}'},
+        )
+
     _async_client = Client(
         transport=transport, schema=schema, fetch_schema_from_transport=schema is None
     )
@@ -126,31 +138,48 @@ def validate(doc: DocumentNode, client=None, use_local_schema=False):
 
 # use older style typing to broaden supported Python versions
 def query(
-    _query: str | DocumentNode, variables: Dict = None, client: Client = None
+    _query: str | DocumentNode, variables: Dict = None, client: Client = None, log_response: bool = False
 ) -> Dict[str, Any]:
     """Query the metamist GraphQL API"""
     if variables is None:
         variables = {}
 
+    # disable logging for gql
+    current_level = aiohttp_logger.level
+    if not log_response:
+        requests_logger.setLevel('WARNING')
+
     response = (client or configure_sync_client()).execute_sync(
         _query if isinstance(_query, DocumentNode) else gql(_query),
         variable_values=variables,
     )
+
+    if not log_response:
+        requests_logger.setLevel(current_level)
     return response
 
 
 async def query_async(
-    _query: str | DocumentNode, variables: Dict = None, client: Client = None
+    _query: str | DocumentNode, variables: Dict = None, client: Client = None, log_response: bool = False
 ) -> Dict[str, Any]:
     """Asynchronously query the Metamist GraphQL API"""
     if variables is None:
         variables = {}
 
+    # disable logging for gql
+    current_level = aiohttp_logger.level
+    if log_response:
+        aiohttp_logger.setLevel('WARNING')
+
     if not client:
         client = await configure_async_client()
 
     response = await client.execute_async(
         _query if isinstance(_query, DocumentNode) else gql(_query),
         variable_values=variables,
     )
+
+    if log_response:
+        aiohttp_logger.setLevel(current_level)
+
     return response

models/models/assay.py

@@ -12,7 +12,7 @@ class AssayInternal(SMBase):
     sample_id: int
     meta: dict[str, Any] | None
     type: str
-    external_ids: dict[str, str] | None = None
+    external_ids: dict[str, str] | None = {}
 
     def __repr__(self):
         return ', '.join(f'{k}={v}' for k, v in vars(self).items())

models/models/sequencing_group.py

@@ -37,7 +37,7 @@ class SequencingGroupInternal(SMBase):
     platform: str | None = None
     meta: dict[str, str] | None = None
     sample_id: int | None = None
-    external_ids: dict[str, str] | None = None
+    external_ids: dict[str, str] | None = {}
     archived: bool | None = None
 
     project: int | None = None

openapi-templates/configuration.mustache

@@ -24,10 +24,10 @@ JSON_SCHEMA_VALIDATION_KEYWORDS = {
 
 sm_url = getenv('SM_URL')
 if not sm_url:
-    env = getenv('SM_ENVIRONMENT', 'PRODUCTION')
-    if 'local' in env.lower():
+    env = getenv('SM_ENVIRONMENT', 'PRODUCTION').lower()
+    if 'local' in env:
         sm_url = "http://localhost:8000"
-    elif 'dev' in env.lower():
+    elif 'dev' in env:
         sm_url = 'https://sample-metadata-api-dev-mnrpw3mdza-ts.a.run.app'
     else:
         sm_url = 'https://sample-metadata-api-mnrpw3mdza-ts.a.run.app'
@@ -192,7 +192,7 @@ conf = {{{packageName}}}.Configuration(
                  ):
         """Constructor
         """
-        env = getenv('SM_ENVIRONMENT', 'PRODUCTION')
+        self.env = getenv('SM_ENVIRONMENT', 'PRODUCTION').lower()
         self._base_path = host or sm_url
 
         """Default Base url
@@ -491,6 +491,9 @@ conf = {{{packageName}}}.Configuration(
 
         :return: The Auth Settings information dict.
         """
+        if self.env == 'local':
+            return {}
+
         auth = {
             'HTTPBearer': {
                 'type': 'bearer',

setup.py

@@ -19,7 +19,7 @@
 setup(
     name=PKG,
     # This tag is automatically updated by bump2version
-    version='6.6.0',
+    version='6.6.2',
     description='Python API for interacting with the Sample API system',
     long_description=readme,
     long_description_content_type='text/markdown',

web/package.json

@@ -1,6 +1,6 @@
 {
     "name": "metamist",
-    "version": "6.6.0",
+    "version": "6.6.2",
     "private": true,
     "dependencies": {
         "@apollo/client": "^3.7.3",