Update routes, layers and table files to work with new permissions

Author: dancoates

api/routes/analysis.py

@@ -11,22 +11,16 @@
 from api.utils.dates import parse_date_only_string
 from api.utils.db import (
     Connection,
-    get_project_read_connection,
-    get_project_write_connection,
+    get_project_db_connection,
     get_projectless_db_connection,
 )
 from api.utils.export import ExportType
 from db.python.layers.analysis import AnalysisLayer
 from db.python.tables.analysis import AnalysisFilter
-from db.python.tables.project import ProjectPermissionsTable
 from db.python.utils import GenericFilter
 from models.enums import AnalysisStatus
-from models.models.analysis import (
-    Analysis,
-    AnalysisInternal,
-    ProportionalDateTemporalMethod,
-)
-from models.models.group import ReadAccessRoles
+from models.models.analysis import Analysis, ProportionalDateTemporalMethod
+from models.models.project import FullWriteAccessRoles, ReadAccessRoles
 from models.utils.sequencing_group_id_format import (
     sequencing_group_id_format,
     sequencing_group_id_format_list,
@@ -96,7 +90,8 @@ def to_filter(self, project_id_map: dict[str, int]) -> AnalysisFilter:
 
 @router.put('/{project}/', operation_id='createAnalysis', response_model=int)
 async def create_analysis(
-    analysis: Analysis, connection: Connection = get_project_write_connection
+    analysis: Analysis,
+    connection: Connection = get_project_db_connection(FullWriteAccessRoles),
 ) -> int:
     """Create a new analysis"""
 
@@ -136,14 +131,14 @@ async def update_analysis(
 )
 async def get_all_sample_ids_without_analysis_type(
     analysis_type: str,
-    connection: Connection = get_project_read_connection,
+    connection: Connection = get_project_db_connection(ReadAccessRoles),
 ):
     """get_all_sample_ids_without_analysis_type"""
     atable = AnalysisLayer(connection)
-    assert connection.project
+    assert connection.project_id
     sequencing_group_ids = (
         await atable.get_all_sequencing_group_ids_without_analysis_type(
-            connection.project, analysis_type
+            connection.project_id, analysis_type
         )
     )
     return {
@@ -156,12 +151,12 @@ async def get_all_sample_ids_without_analysis_type(
     operation_id='getIncompleteAnalyses',
 )
 async def get_incomplete_analyses(
-    connection: Connection = get_project_read_connection,
+    connection: Connection = get_project_db_connection(ReadAccessRoles),
 ):
     """Get analyses with status queued or in-progress"""
     atable = AnalysisLayer(connection)
-    assert connection.project
-    results = await atable.get_incomplete_analyses(project=connection.project)
+    assert connection.project_id
+    results = await atable.get_incomplete_analyses(project=connection.project_id)
     return [r.to_external() for r in results]
 
 
@@ -171,13 +166,13 @@ async def get_incomplete_analyses(
 )
 async def get_latest_complete_analysis_for_type(
     analysis_type: str,
-    connection: Connection = get_project_read_connection,
+    connection: Connection = get_project_db_connection(ReadAccessRoles),
 ):
     """Get (SINGLE) latest complete analysis for some analysis type"""
     alayer = AnalysisLayer(connection)
-    assert connection.project
+    assert connection.project_id
     analysis = await alayer.get_latest_complete_analysis_for_type(
-        project=connection.project, analysis_type=analysis_type
+        project=connection.project_id, analysis_type=analysis_type
     )
     return analysis.to_external()
 
@@ -189,16 +184,16 @@ 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_read_connection,
+    connection: Connection = get_project_db_connection(ReadAccessRoles),
 ):
     """
     Get SINGLE latest complete analysis for some analysis type
     (you can specify meta attributes in this route)
     """
     alayer = AnalysisLayer(connection)
-    assert connection.project
+    assert connection.project_id
     analysis = await alayer.get_latest_complete_analysis_for_type(
-        project=connection.project,
+        project=connection.project_id,
         analysis_type=analysis_type,
         meta=meta,
     )
@@ -229,11 +224,8 @@ async def query_analyses(
     if not query.projects:
         raise ValueError('Must specify "projects"')
 
-    pt = ProjectPermissionsTable(connection)
-    projects = await pt.get_and_check_access_to_projects_for_names(
-        user=connection.author,
-        project_names=query.projects,
-        allowed_roles=ReadAccessRoles,
+    projects = connection.get_and_check_access_to_projects_for_names(
+        query.projects, ReadAccessRoles
     )
     project_name_map = {p.name: p.id for p in projects}
     atable = AnalysisLayer(connection)
@@ -243,27 +235,24 @@ async def query_analyses(
 
 @router.get('/analysis-runner', operation_id='getAnalysisRunnerLog')
 async def get_analysis_runner_log(
-    project_names: list[str] = Query(None),  # type: ignore
-    # author: str = None, # not implemented yet, uncomment when we do
-    output_dir: str = None,
-    ar_guid: str = None,
+    project_names: list[str],
+    output_dir: str,
+    ar_guid: str | None = None,
     connection: Connection = get_projectless_db_connection,
-) -> list[AnalysisInternal]:
+) -> list[Analysis]:
     """
     Get log for the analysis-runner, useful for checking this history of analysis
     """
     atable = AnalysisLayer(connection)
     project_ids = None
-    if project_names:
-        pt = ProjectPermissionsTable(connection)
-        projects = await pt.get_and_check_access_to_projects_for_names(
-            connection.author, project_names, allowed_roles=ReadAccessRoles
-        )
-        project_ids = [p.id for p in projects]
+
+    projects = connection.get_and_check_access_to_projects_for_names(
+        project_names, allowed_roles=ReadAccessRoles
+    )
+    project_ids = [p.id for p in projects]
 
     results = await atable.get_analysis_runner_log(
         project_ids=project_ids,
-        # author=author,
         output_dir=output_dir,
         ar_guid=ar_guid,
     )
@@ -278,7 +267,7 @@ 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_read_connection,
+    connection: Connection = get_project_db_connection(ReadAccessRoles),
 ):
     """
     Get map of ExternalSampleId  pathToCram  InternalSeqGroupID for seqr
@@ -293,9 +282,9 @@ async def get_sample_reads_map(
     """
 
     at = AnalysisLayer(connection)
-    assert connection.project
+    assert connection.project_id
     objs = await at.get_sample_cram_path_map_for_seqr(
-        project=connection.project, sequencing_types=sequencing_types
+        project=connection.project_id, sequencing_types=sequencing_types
     )
 
     for r in objs:
@@ -311,7 +300,7 @@ async def get_sample_reads_map(
     writer = csv.writer(output, delimiter=export_type.get_delimiter())
     writer.writerows(rows)
 
-    basefn = f'{connection.project}-seqr-igv-paths-{date.today().isoformat()}'
+    basefn = f'{connection.project_id}-seqr-igv-paths-{date.today().isoformat()}'
 
     return StreamingResponse(
         iter([output.getvalue()]),
@@ -345,9 +334,8 @@ async def get_proportionate_map(
         }
     }
     """
-    pt = ProjectPermissionsTable(connection)
-    project_list = await pt.get_and_check_access_to_projects_for_names(
-        connection.author, projects, allowed_roles=ReadAccessRoles
+    project_list = connection.get_and_check_access_to_projects_for_names(
+        projects, allowed_roles=ReadAccessRoles
     )
     project_ids = [p.id for p in project_list]
 

api/routes/analysis_runner.py

@@ -2,15 +2,12 @@
 
 from fastapi import APIRouter
 
-from api.utils.db import (
-    Connection,
-    get_project_read_connection,
-    get_project_write_connection,
-)
+from api.utils.db import Connection, get_project_db_connection
 from db.python.layers.analysis_runner import AnalysisRunnerLayer
 from db.python.tables.analysis_runner import AnalysisRunnerFilter
 from db.python.utils import GenericFilter
 from models.models.analysis_runner import AnalysisRunner, AnalysisRunnerInternal
+from models.models.project import FullWriteAccessRoles, ReadAccessRoles
 
 router = APIRouter(prefix='/analysis-runner', tags=['analysis-runner'])
 
@@ -32,13 +29,13 @@ async def create_analysis_runner_log(  # pylint: disable=too-many-arguments
     output_path: str,
     hail_version: str | None = None,
     cwd: str | None = None,
-    connection: Connection = get_project_write_connection,
+    connection: Connection = get_project_db_connection(FullWriteAccessRoles),
 ) -> str:
     """Create a new analysis runner log"""
 
     alayer = AnalysisRunnerLayer(connection)
 
-    if not connection.project:
+    if not connection.project_id:
         raise ValueError('Project not set')
 
     analysis_id = await alayer.insert_analysis_runner_entry(
@@ -58,7 +55,7 @@ async def create_analysis_runner_log(  # pylint: disable=too-many-arguments
             batch_url=batch_url,
             submitting_user=submitting_user,
             meta=meta,
-            project=connection.project,
+            project=connection.project_id,
             audit_log_id=None,
             output_path=output_path,
         )
@@ -75,13 +72,13 @@ async def get_analysis_runner_logs(
     repository: str | None = None,
     access_level: str | None = None,
     environment: str | None = None,
-    connection: Connection = get_project_read_connection,
+    connection: Connection = get_project_db_connection(ReadAccessRoles),
 ) -> list[AnalysisRunner]:
     """Get analysis runner logs"""
 
     atable = AnalysisRunnerLayer(connection)
 
-    if not connection.project:
+    if not connection.project_id:
         raise ValueError('Project not set')
 
     filter_ = AnalysisRunnerFilter(
@@ -90,9 +87,9 @@ async def get_analysis_runner_logs(
         repository=GenericFilter(eq=repository),
         access_level=GenericFilter(eq=access_level),
         environment=GenericFilter(eq=environment),
-        project=GenericFilter(eq=connection.project),
+        project=GenericFilter(eq=connection.project_id),
     )
 
     logs = await atable.query(filter_)
 
-    return [log.to_external({connection.project: project}) for log in logs]
+    return [log.to_external({connection.project_id: project}) for log in logs]

api/routes/assay.py

@@ -4,16 +4,15 @@
 
 from api.utils.db import (
     Connection,
-    get_project_read_connection,
+    get_project_db_connection,
     get_projectless_db_connection,
 )
 from db.python.layers.assay import AssayLayer
 from db.python.tables.assay import AssayFilter
-from db.python.tables.project import ProjectPermissionsTable
 from db.python.utils import GenericFilter
 from models.base import SMBase
 from models.models.assay import AssayUpsert
-from models.models.group import ReadAccessRoles
+from models.models.project import ReadAccessRoles
 from models.utils.sample_id_format import sample_id_transform_to_raw_list
 
 router = APIRouter(prefix='/assay', tags=['assay'])
@@ -57,7 +56,8 @@ 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_read_connection
+    external_id: str,
+    connection: Connection = get_project_db_connection(ReadAccessRoles),
 ):
     """Get an assay by ONE of its external identifiers"""
     assay_layer = AssayLayer(connection)
@@ -84,12 +84,11 @@ async def get_assays_by_criteria(
 ):
     """Get assays by criteria"""
     assay_layer = AssayLayer(connection)
-    pt = ProjectPermissionsTable(connection)
 
     pids: list[int] | None = None
     if criteria.projects:
-        project_list = await pt.get_and_check_access_to_projects_for_names(
-            connection.author, criteria.projects, allowed_roles=ReadAccessRoles
+        project_list = connection.get_and_check_access_to_projects_for_names(
+            criteria.projects, allowed_roles=ReadAccessRoles
         )
         pids = [p.id for p in project_list]