Update project based db connections

api/routes/analysis.py

@@ -11,7 +11,7 @@
 from api.utils.dates import parse_date_only_string
 from api.utils.db import (
     Connection,
-    get_project_readonly_connection,
+    get_project_read_connection,
     get_project_write_connection,
     get_projectless_db_connection,
 )
@@ -141,7 +141,7 @@ async def update_analysis(
 )
 async def get_all_sample_ids_without_analysis_type(
     analysis_type: str,
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = get_project_read_connection,
 ):
     """get_all_sample_ids_without_analysis_type"""
     atable = AnalysisLayer(connection)
@@ -161,7 +161,7 @@ async def get_all_sample_ids_without_analysis_type(
     operation_id='getIncompleteAnalyses',
 )
 async def get_incomplete_analyses(
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = get_project_read_connection,
 ):
     """Get analyses with status queued or in-progress"""
     atable = AnalysisLayer(connection)
@@ -176,7 +176,7 @@ async def get_incomplete_analyses(
 )
 async def get_latest_complete_analysis_for_type(
     analysis_type: str,
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = get_project_read_connection,
 ):
     """Get (SINGLE) latest complete analysis for some analysis type"""
     alayer = AnalysisLayer(connection)
@@ -194,7 +194,7 @@ async def get_latest_complete_analysis_for_type(
 async def get_latest_complete_analysis_for_type_post(
     analysis_type: str,
     meta: dict[str, Any] = Body(..., embed=True),  # type: ignore[assignment]
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = get_project_read_connection,
 ):
     """
     Get SINGLE latest complete analysis for some analysis type
@@ -280,7 +280,7 @@ async def get_analysis_runner_log(
 async def get_sample_reads_map(
     export_type: ExportType = ExportType.JSON,
     sequencing_types: list[str] = Query(None),  # type: ignore
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = get_project_read_connection,
 ):
     """
     Get map of ExternalSampleId  pathToCram  InternalSeqGroupID for seqr

api/routes/assay.py

@@ -2,7 +2,7 @@
 
 from fastapi import APIRouter
 
-from api.utils import get_project_readonly_connection
+from api.utils import get_project_read_connection
 from api.utils.db import Connection, get_projectless_db_connection
 from db.python.layers.assay import AssayLayer
 from db.python.tables.assay import AssayFilter
@@ -52,7 +52,7 @@ async def get_assay_by_id(
     '/{project}/external_id/{external_id}/details', operation_id='getAssayByExternalId'
 )
 async def get_assay_by_external_id(
-    external_id: str, connection=get_project_readonly_connection
+    external_id: str, connection=get_project_read_connection
 ):
     """Get an assay by ONE of its external identifiers"""
     assay_layer = AssayLayer(connection)
@@ -86,13 +86,13 @@ async def get_assays_by_criteria(
         unwrapped_sample_ids = sample_id_transform_to_raw_list(sample_ids)
 
     filter_ = AssayFilter(
-        sample_id=GenericFilter(in_=unwrapped_sample_ids)
-        if unwrapped_sample_ids
-        else None,
+        sample_id=(
+            GenericFilter(in_=unwrapped_sample_ids) if unwrapped_sample_ids else None
+        ),
         id=GenericFilter(in_=assay_ids) if assay_ids else None,
-        external_id=GenericFilter(in_=external_assay_ids)
-        if external_assay_ids
-        else None,
+        external_id=(
+            GenericFilter(in_=external_assay_ids) if external_assay_ids else None
+        ),
         meta=assay_meta,
         sample_meta=sample_meta,
         project=GenericFilter(in_=pids) if pids else None,

api/routes/family.py

@@ -12,7 +12,7 @@
 from api.utils import get_projectless_db_connection
 from api.utils.db import (
     Connection,
-    get_project_readonly_connection,
+    get_project_read_connection,
     get_project_write_connection,
 )
 from api.utils.export import ExportType
@@ -73,7 +73,7 @@ async def get_pedigree(
     replace_with_family_external_ids: bool = True,
     include_header: bool = True,
     empty_participant_value: Optional[str] = None,
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = get_project_read_connection,
     include_participants_not_in_families: bool = False,
 ):
     """
@@ -140,7 +140,7 @@ async def get_pedigree(
 async def get_families(
     participant_ids: Optional[List[int]] = Query(None),
     sample_ids: Optional[List[str]] = Query(None),
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = get_project_read_connection,
 ) -> List[Family]:
     """Get families for some project"""
     family_layer = FamilyLayer(connection)

api/routes/participant.py

@@ -9,7 +9,7 @@
 from api.utils import get_projectless_db_connection
 from api.utils.db import (
     Connection,
-    get_project_readonly_connection,
+    get_project_read_connection,
     get_project_write_connection,
 )
 from api.utils.export import ExportType
@@ -46,7 +46,7 @@ async def get_individual_metadata_template_for_seqr(
     external_participant_ids: list[str] | None = Query(default=None),  # type: ignore[assignment]
     # pylint: disable=invalid-name
     replace_with_participant_external_ids: bool = True,
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = get_project_read_connection,
 ):
     """Get individual metadata template for SEQR as a CSV"""
     participant_layer = ParticipantLayer(connection)
@@ -89,7 +89,7 @@ async def get_individual_metadata_template_for_seqr(
 async def get_id_map_by_external_ids(
     external_participant_ids: list[str],
     allow_missing: bool = False,
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = get_project_read_connection,
 ):
     """Get ID map of participants, by external_id"""
     player = ParticipantLayer(connection)
@@ -120,7 +120,7 @@ async def get_external_participant_id_to_sequencing_group_id(
     sequencing_type: str = None,
     export_type: ExportType = ExportType.JSON,
     flip_columns: bool = False,
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = get_project_read_connection,
 ):
     """
     Get csv / tsv export of external_participant_id to sequencing_group_id
@@ -153,7 +153,9 @@ async def get_external_participant_id_to_sequencing_group_id(
     writer.writerows(rows)
 
     ext = export_type.get_extension()
-    filename = f'{project}-participant-to-sequencing-group-map-{date.today().isoformat()}{ext}'
+    filename = (
+        f'{project}-participant-to-sequencing-group-map-{date.today().isoformat()}{ext}'
+    )
     if sequencing_type:
         filename = f'{project}-{sequencing_type}-participant-to-sequencing-group-map-{date.today().isoformat()}{ext}'
     return StreamingResponse(
@@ -205,7 +207,7 @@ async def upsert_participants(
 async def get_participants(
     external_participant_ids: list[str] = None,
     internal_participant_ids: list[int] = None,
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = get_project_read_connection,
 ):
     """Get participants, default ALL participants in project"""
     player = ParticipantLayer(connection)

api/routes/sample.py

@@ -2,7 +2,7 @@
 
 from api.utils.db import (
     Connection,
-    get_project_readonly_connection,
+    get_project_read_connection,
     get_project_write_connection,
     get_projectless_db_connection,
 )
@@ -61,7 +61,7 @@ async def upsert_samples(
 async def get_sample_id_map_by_external(
     external_ids: list[str],
     allow_missing: bool = False,
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = get_project_read_connection,
 ):
     """Get map of sample IDs, { [externalId]: internal_sample_id }"""
     st = SampleLayer(connection)
@@ -90,7 +90,7 @@ async def get_sample_id_map_by_internal(
     '/{project}/id-map/internal/all', operation_id='getAllSampleIdMapByInternal'
 )
 async def get_all_sample_id_map_by_internal(
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = get_project_read_connection,
 ):
     """Get map of ALL sample IDs, { [internal_id]: external_sample_id }"""
     st = SampleLayer(connection)
@@ -106,7 +106,7 @@ async def get_all_sample_id_map_by_internal(
     operation_id='getSampleByExternalId',
 )
 async def get_sample_by_external_id(
-    external_id: str, connection: Connection = get_project_readonly_connection
+    external_id: str, connection: Connection = get_project_read_connection
 ):
     """Get sample by external ID"""
     st = SampleLayer(connection)

api/routes/sequencing_groups.py

@@ -5,7 +5,7 @@
 
 from api.utils.db import (
     Connection,
-    get_project_readonly_connection,
+    get_project_read_connection,
     get_project_write_connection,
     get_projectless_db_connection,
 )
@@ -42,7 +42,7 @@ async def get_sequencing_group(
 
 @router.get('/project/{project}', operation_id='getAllSequencingGroupIdsBySampleByType')
 async def get_all_sequencing_group_ids_by_sample_by_type(
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = get_project_read_connection,
 ) -> dict[str, dict[str, list[str]]]:
     """Creates a new sample, and returns the internal sample ID"""
     st = SequencingGroupLayer(connection)

api/routes/web.py

@@ -1,14 +1,15 @@
 """
 Web routes
 """
+
 from typing import Optional
 
 from fastapi import APIRouter, Request
 from pydantic import BaseModel
 
 from api.utils.db import (
     Connection,
-    get_project_readonly_connection,
+    get_project_read_connection,
     get_project_write_connection,
     get_projectless_db_connection,
 )
@@ -39,7 +40,7 @@ async def get_project_summary(
     grid_filter: list[SearchItem],
     limit: int = 20,
     token: Optional[int] = 0,
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = get_project_read_connection,
 ) -> ProjectSummary:
     """Creates a new sample, and returns the internal sample ID"""
     st = WebLayer(connection)
@@ -56,11 +57,11 @@ async def get_project_summary(
         new_token = max(int(sample.id) for p in participants for sample in p.samples)
 
     links = PagingLinks(
-        next=str(request.base_url)
-        + request.url.path.lstrip('/')
-        + f'?token={new_token}'
-        if new_token
-        else None,
+        next=(
+            str(request.base_url) + request.url.path.lstrip('/') + f'?token={new_token}'
+            if new_token
+            else None
+        ),
         self=str(request.url),
         token=str(new_token) if new_token else None,
     )

api/utils/db.py

@@ -11,6 +11,7 @@
 from db.python.connect import Connection, SMConnections
 from db.python.gcp_connect import BqConnection, PubSubConnection
 from db.python.tables.project import ProjectPermissionsTable
+from models.models.group import GroupProjectRole
 
 EXPECTED_AUDIENCE = getenv('SM_OAUTHAUDIENCE')
 
@@ -78,23 +79,50 @@ async def dependable_get_write_project_connection(
     return await ProjectPermissionsTable.get_project_connection(
         project_name=project,
         author=author,
-        readonly=False,
+        allowed_roles={GroupProjectRole.write},
         ar_guid=ar_guid,
         on_behalf_of=on_behalf_of,
         meta=meta,
     )
 
 
-async def dependable_get_readonly_project_connection(
+async def dependable_get_read_project_connection(
     project: str,
+    request: Request,
     author: str = Depends(authenticate),
     ar_guid: str = Depends(get_ar_guid),
 ) -> Connection:
     """FastAPI handler for getting connection WITH project"""
+    meta = {"path": request.url.path}
+    if request.client:
+        meta["ip"] = request.client.host
+    return await ProjectPermissionsTable.get_project_connection(
+        project_name=project,
+        author=author,
+        allowed_roles={
+            GroupProjectRole.read,
+            GroupProjectRole.write,
+            GroupProjectRole.contribute,
+        },
+        on_behalf_of=None,
+        ar_guid=ar_guid,
+    )
+
+
+async def dependable_get_contribute_project_connection(
+    project: str,
+    request: Request,
+    author: str = Depends(authenticate),
+    ar_guid: str = Depends(get_ar_guid),
+) -> Connection:
+    """FastAPI handler for getting connection WITH project"""
+    meta = {"path": request.url.path}
+    if request.client:
+        meta["ip"] = request.client.host
     return await ProjectPermissionsTable.get_project_connection(
         project_name=project,
         author=author,
-        readonly=True,
+        allowed_roles={GroupProjectRole.write, GroupProjectRole.contribute},
         on_behalf_of=None,
         ar_guid=ar_guid,
     )
@@ -150,7 +178,10 @@ def validate_iap_jwt_and_get_email(iap_jwt, audience):
 
 
 get_author = Depends(authenticate)
-get_project_readonly_connection = Depends(dependable_get_readonly_project_connection)
+get_project_read_connection = Depends(dependable_get_read_project_connection)
+get_project_contribute_connection = Depends(
+    dependable_get_contribute_project_connection
+)
 get_project_write_connection = Depends(dependable_get_write_project_connection)
 get_projectless_db_connection = Depends(dependable_get_connection)
 get_projectless_bq_connection = Depends(dependable_get_bq_connection)