Merging dev changes.

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 6.5.0
+current_version = 6.6.2
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>[A-z0-9-]+)

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-yaml
         exclude: '\.*conda/.*'
@@ -14,13 +14,13 @@ repos:
       - id: check-added-large-files
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.33.0
+    rev: v0.38.0
     hooks:
       - id: markdownlint
         args: ["--config", ".markdownlint.json"]
 
   - repo: https://github.com/ambv/black
-    rev: 23.3.0
+    rev: 23.12.1
     hooks:
       - id: black
         args: [.]
@@ -29,7 +29,7 @@ repos:
         exclude: ^metamist/
 
   - repo: https://github.com/PyCQA/flake8
-    rev: "6.0.0"
+    rev: "6.1.0"
     hooks:
       - id: flake8
         additional_dependencies: [flake8-bugbear, flake8-quotes]
@@ -45,7 +45,7 @@ repos:
 
   # mypy
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.8.0
     hooks:
       - id: mypy
         args: [

api/graphql/loaders.py

@@ -10,10 +10,10 @@
 from strawberry.dataloader import DataLoader
 
 from api.utils import get_projectless_db_connection, group_by
-from db.python.connect import NotFoundError
 from db.python.layers import (
     AnalysisLayer,
     AssayLayer,
+    AuditLogLayer,
     FamilyLayer,
     ParticipantLayer,
     SampleLayer,
@@ -24,16 +24,18 @@
 from db.python.tables.project import ProjectPermissionsTable
 from db.python.tables.sample import SampleFilter
 from db.python.tables.sequencing_group import SequencingGroupFilter
-from db.python.utils import GenericFilter, ProjectId
+from db.python.utils import GenericFilter, NotFoundError
 from models.models import (
     AnalysisInternal,
     AssayInternal,
     FamilyInternal,
     ParticipantInternal,
     Project,
+    ProjectId,
     SampleInternal,
     SequencingGroupInternal,
 )
+from models.models.audit_log import AuditLogInternal
 
 
 class LoaderKeys(enum.Enum):
@@ -44,6 +46,9 @@ class LoaderKeys(enum.Enum):
 
     PROJECTS_FOR_IDS = 'projects_for_id'
 
+    AUDIT_LOGS_BY_IDS = 'audit_logs_by_ids'
+    AUDIT_LOGS_BY_ANALYSIS_IDS = 'audit_logs_by_analysis_ids'
+
     ANALYSES_FOR_SEQUENCING_GROUPS = 'analyses_for_sequencing_groups'
 
     ASSAYS_FOR_SAMPLES = 'sequences_for_samples'
@@ -168,6 +173,31 @@ async def wrapped(query: list[dict[str, Any]]) -> list[Any]:
     return connected_data_loader_caller
 
 
+@connected_data_loader(LoaderKeys.AUDIT_LOGS_BY_IDS)
+async def load_audit_logs_by_ids(
+    audit_log_ids: list[int], connection
+) -> list[AuditLogInternal | None]:
+    """
+    DataLoader: get_audit_logs_by_ids
+    """
+    alayer = AuditLogLayer(connection)
+    logs = await alayer.get_for_ids(audit_log_ids)
+    logs_by_id = {log.id: log for log in logs}
+    return [logs_by_id.get(a) for a in audit_log_ids]
+
+
+@connected_data_loader(LoaderKeys.AUDIT_LOGS_BY_ANALYSIS_IDS)
+async def load_audit_logs_by_analysis_ids(
+    analysis_ids: list[int], connection
+) -> list[list[AuditLogInternal]]:
+    """
+    DataLoader: get_audit_logs_by_analysis_ids
+    """
+    alayer = AnalysisLayer(connection)
+    logs = await alayer.get_audit_logs_by_analysis_ids(analysis_ids)
+    return [logs.get(a) or [] for a in analysis_ids]
+
+
 @connected_data_loader_with_params(LoaderKeys.ASSAYS_FOR_SAMPLES, default_factory=list)
 async def load_assays_by_samples(
     connection, ids, filter: AssayFilter
@@ -332,7 +362,7 @@ async def load_projects_for_ids(project_ids: list[int], connection) -> list[Proj
     """
     Get projects by IDs
     """
-    pttable = ProjectPermissionsTable(connection.connection)
+    pttable = ProjectPermissionsTable(connection)
     projects = await pttable.get_and_check_access_to_projects_for_ids(
         user=connection.user, project_ids=project_ids, readonly=True
     )

api/graphql/schema.py

@@ -31,6 +31,7 @@
 from models.models import (
     AnalysisInternal,
     AssayInternal,
+    AuditLogInternal,
     FamilyInternal,
     ParticipantInternal,
     Project,
@@ -204,6 +205,29 @@ async def analyses(
         return [GraphQLAnalysis.from_internal(a) for a in internal_analysis]
 
 
+@strawberry.type
+class GraphQLAuditLog:
+    """AuditLog GraphQL model"""
+
+    id: int
+    author: str
+    timestamp: datetime.datetime
+    ar_guid: str | None
+    comment: str | None
+    meta: strawberry.scalars.JSON
+
+    @staticmethod
+    def from_internal(audit_log: AuditLogInternal) -> 'GraphQLAuditLog':
+        return GraphQLAuditLog(
+            id=audit_log.id,
+            author=audit_log.author,
+            timestamp=audit_log.timestamp,
+            ar_guid=audit_log.ar_guid,
+            comment=audit_log.comment,
+            meta=audit_log.meta,
+        )
+
+
 @strawberry.type
 class GraphQLAnalysis:
     """Analysis GraphQL model"""
@@ -215,7 +239,6 @@ class GraphQLAnalysis:
     timestamp_completed: datetime.datetime | None = None
     active: bool
     meta: strawberry.scalars.JSON
-    author: str
 
     @staticmethod
     def from_internal(internal: AnalysisInternal) -> 'GraphQLAnalysis':
@@ -227,7 +250,6 @@ def from_internal(internal: AnalysisInternal) -> 'GraphQLAnalysis':
             timestamp_completed=internal.timestamp_completed,
             active=internal.active,
             meta=internal.meta,
-            author=internal.author,
         )
 
     @strawberry.field
@@ -244,6 +266,14 @@ async def project(self, info: Info, root: 'GraphQLAnalysis') -> GraphQLProject:
         project = await loader.load(root.project)
         return GraphQLProject.from_internal(project)
 
+    @strawberry.field
+    async def audit_logs(
+        self, info: Info, root: 'GraphQLAnalysis'
+    ) -> list[GraphQLAuditLog]:
+        loader = info.context[LoaderKeys.AUDIT_LOGS_BY_ANALYSIS_IDS]
+        audit_logs = await loader.load(root.id)
+        return [GraphQLAuditLog.from_internal(audit_log) for audit_log in audit_logs]
+
 
 @strawberry.type
 class GraphQLFamily:
@@ -297,6 +327,7 @@ class GraphQLParticipant:
     karyotype: str | None
 
     project_id: strawberry.Private[int]
+    audit_log_id: strawberry.Private[int | None]
 
     @staticmethod
     def from_internal(internal: ParticipantInternal) -> 'GraphQLParticipant':
@@ -308,6 +339,7 @@ def from_internal(internal: ParticipantInternal) -> 'GraphQLParticipant':
             reported_gender=internal.reported_gender,
             karyotype=internal.karyotype,
             project_id=internal.project,
+            audit_log_id=internal.audit_log_id,
         )
 
     @strawberry.field
@@ -349,6 +381,16 @@ async def project(self, info: Info, root: 'GraphQLParticipant') -> GraphQLProjec
         project = await loader.load(root.project_id)
         return GraphQLProject.from_internal(project)
 
+    @strawberry.field
+    async def audit_log(
+        self, info: Info, root: 'GraphQLParticipant'
+    ) -> GraphQLAuditLog | None:
+        if root.audit_log_id is None:
+            return None
+        loader = info.context[LoaderKeys.AUDIT_LOGS_BY_IDS]
+        audit_log = await loader.load(root.audit_log_id)
+        return GraphQLAuditLog.from_internal(audit_log)
+
 
 @strawberry.type
 class GraphQLSample:
@@ -359,22 +401,20 @@ class GraphQLSample:
     active: bool
     meta: strawberry.scalars.JSON
     type: str
-    author: str | None
 
     # keep as integers, because they're useful to reference in the fields below
     internal_id: strawberry.Private[int]
     participant_id: strawberry.Private[int]
     project_id: strawberry.Private[int]
 
     @staticmethod
-    def from_internal(sample: SampleInternal):
+    def from_internal(sample: SampleInternal) -> 'GraphQLSample':
         return GraphQLSample(
             id=sample_id_format(sample.id),
             external_id=sample.external_id,
             active=sample.active,
             meta=sample.meta,
             type=sample.type,
-            author=sample.author,
             # internals
             internal_id=sample.id,
             participant_id=sample.participant_id,
@@ -450,7 +490,7 @@ 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]
@@ -464,7 +504,7 @@ 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,
@@ -491,7 +531,7 @@ async def analyses(
         loader = info.context[LoaderKeys.ANALYSES_FOR_SEQUENCING_GROUPS]
         project_id_map = {}
         if project:
-            ptable = ProjectPermissionsTable(connection.connection)
+            ptable = ProjectPermissionsTable(connection)
             project_ids = project.all_values()
             projects = await ptable.get_and_check_access_to_projects_for_names(
                 user=connection.author, project_names=project_ids, readonly=True
@@ -541,7 +581,7 @@ 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,
         )
@@ -564,7 +604,7 @@ def enum(self, info: Info) -> GraphQLEnum:
     @strawberry.field()
     async def project(self, info: Info, name: str) -> GraphQLProject:
         connection = info.context['connection']
-        ptable = ProjectPermissionsTable(connection.connection)
+        ptable = ProjectPermissionsTable(connection)
         project = await ptable.get_and_check_access_to_project_for_name(
             user=connection.author, project_name=name, readonly=True
         )
@@ -583,7 +623,7 @@ async def sample(
         active: GraphQLFilter[bool] | None = None,
     ) -> list[GraphQLSample]:
         connection = info.context['connection']
-        ptable = ProjectPermissionsTable(connection.connection)
+        ptable = ProjectPermissionsTable(connection)
         slayer = SampleLayer(connection)
 
         if not id and not project:
@@ -631,7 +671,7 @@ async def sequencing_groups(
     ) -> list[GraphQLSequencingGroup]:
         connection = info.context['connection']
         sglayer = SequencingGroupLayer(connection)
-        ptable = ProjectPermissionsTable(connection.connection)
+        ptable = ProjectPermissionsTable(connection)
         if not (project or sample_id or id):
             raise ValueError('Must filter by project, sample or id')
 
@@ -685,7 +725,7 @@ async def family(self, info: Info, family_id: int) -> GraphQLFamily:
     @strawberry.field
     async def my_projects(self, info: Info) -> list[GraphQLProject]:
         connection = info.context['connection']
-        ptable = ProjectPermissionsTable(connection.connection)
+        ptable = ProjectPermissionsTable(connection)
         projects = await ptable.get_projects_accessible_by_user(
             connection.author, readonly=True
         )

api/routes/analysis.py

@@ -104,10 +104,12 @@ async def create_analysis(
 
     atable = AnalysisLayer(connection)
 
+    if analysis.author:
+        # special tracking here, if we can't catch it through the header
+        connection.on_behalf_of = analysis.author
+
     analysis_id = await atable.create_analysis(
         analysis.to_internal(),
-        # analysis-runner: usage is tracked through `on_behalf_of`
-        author=analysis.author,
     )
 
     return analysis_id
@@ -226,7 +228,7 @@ async def query_analyses(
     if not query.projects:
         raise ValueError('Must specify "projects"')
 
-    pt = ProjectPermissionsTable(connection=connection.connection)
+    pt = ProjectPermissionsTable(connection)
     projects = await pt.get_and_check_access_to_projects_for_names(
         user=connection.author, project_names=query.projects, readonly=True
     )
@@ -249,7 +251,7 @@ async def get_analysis_runner_log(
     atable = AnalysisLayer(connection)
     project_ids = None
     if project_names:
-        pt = ProjectPermissionsTable(connection=connection.connection)
+        pt = ProjectPermissionsTable(connection)
         project_ids = await pt.get_project_ids_from_names_and_user(
             connection.author, project_names, readonly=True
         )
@@ -335,7 +337,7 @@ async def get_proportionate_map(
         }
     }
     """
-    pt = ProjectPermissionsTable(connection=connection.connection)
+    pt = ProjectPermissionsTable(connection)
     project_ids = await pt.get_project_ids_from_names_and_user(
         connection.author, projects, readonly=True
     )

api/routes/assay.py

@@ -79,7 +79,7 @@ async def get_assays_by_criteria(
 ):
     """Get assays by criteria"""
     assay_layer = AssayLayer(connection)
-    pt = ProjectPermissionsTable(connection.connection)
+    pt = ProjectPermissionsTable(connection)
 
     pids: list[int] | None = None
     if projects: