From 60d67d19b67ac86f964bb1ef812d44cf9f100c5c Mon Sep 17 00:00:00 2001
From: EddieLF <34049565+EddieLF@users.noreply.github.com>
Date: Tue, 14 May 2024 13:51:58 +1000
Subject: [PATCH 1/2] Fix individual metadata for seqr layer headers (#774)

* Fix individual metadata for seqr layer headers

* Clean up fix
---
 db/python/layers/participant.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/db/python/layers/participant.py b/db/python/layers/participant.py
index 25b2f8fed..6b1bffd71 100644
--- a/db/python/layers/participant.py
+++ b/db/python/layers/participant.py
@@ -767,7 +767,8 @@ async def get_seqr_individual_template(
         rows = [{h: r.get(h) for h in set_headers if h in r} for r in rows]
         headers = []  # get ordered headers if we have data for it
         for h in SeqrMetadataKeys.get_ordered_headers():
-            if header := lheader_to_json.get(h.value.lower()) in set_headers:
+            header = lheader_to_json.get(h.value.lower())
+            if header in set_headers:
                 headers.append(header)
 
         return {

From d21e39903ff06d650bedf91b4fc71a4f9e29c285 Mon Sep 17 00:00:00 2001
From: Michael Franklin <22381693+illusional@users.noreply.github.com>
Date: Wed, 15 May 2024 10:48:40 +1000
Subject: [PATCH 2/2] Add pseudo contributor role w/o readonly reqs, but write
 access (#777)

* Add pseudo contributor role w/o readonly reqs, but write access

* duhhh

* Don't throw away all provided values

* Fix linting error

---------

Co-authored-by: Michael Franklin <illusional@users.noreply.github.com>
---
 api/routes/cohort.py       |  6 +++---
 api/utils/db.py            | 32 ++++++++++++++++++++++++++++++++
 db/python/tables/family.py |  1 +
 3 files changed, 36 insertions(+), 3 deletions(-)

diff --git a/api/routes/cohort.py b/api/routes/cohort.py
index a8cb7ec25..fd500984d 100644
--- a/api/routes/cohort.py
+++ b/api/routes/cohort.py
@@ -1,6 +1,6 @@
 from fastapi import APIRouter
 
-from api.utils.db import Connection, get_project_readonly_connection
+from api.utils.db import Connection, HACK_get_project_contributor_connection
 from db.python.layers.cohort import CohortLayer
 from db.python.tables.project import ProjectPermissionsTable
 from models.models.cohort import CohortBody, CohortCriteria, CohortTemplate, NewCohort
@@ -17,7 +17,7 @@
 async def create_cohort_from_criteria(
     cohort_spec: CohortBody,
     cohort_criteria: CohortCriteria | None = None,
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = HACK_get_project_contributor_connection,
     dry_run: bool = False,
 ) -> NewCohort:
     """
@@ -70,7 +70,7 @@ async def create_cohort_from_criteria(
 @router.post('/{project}/cohort_template', operation_id='createCohortTemplate')
 async def create_cohort_template(
     template: CohortTemplate,
-    connection: Connection = get_project_readonly_connection,
+    connection: Connection = HACK_get_project_contributor_connection,
 ) -> str:
     """
     Create a cohort template with the given name and sample/sequencing group IDs.
diff --git a/api/utils/db.py b/api/utils/db.py
index c574c1278..608a49888 100644
--- a/api/utils/db.py
+++ b/api/utils/db.py
@@ -103,6 +103,35 @@ async def dependable_get_write_project_connection(
     )
 
 
+async def HACK_dependable_contributor_project_connection(
+    project: str,
+    author: str = Depends(authenticate),
+    ar_guid: str = Depends(get_ar_guid),
+    extra_values: dict | None = Depends(get_extra_audit_log_values),
+) -> Connection:
+    """FastAPI handler for getting connection WITH project"""
+    meta = {}
+    if extra_values:
+        meta.update(extra_values)
+
+    meta['role'] = 'contributor'
+
+    # hack by making it appear readonly
+    connection = await ProjectPermissionsTable.get_project_connection(
+        project_name=project,
+        author=author,
+        readonly=True,
+        on_behalf_of=None,
+        ar_guid=ar_guid,
+        meta=meta,
+    )
+
+    # then hack it so
+    connection.readonly = False
+
+    return connection
+
+
 async def dependable_get_readonly_project_connection(
     project: str,
     author: str = Depends(authenticate),
@@ -179,6 +208,9 @@ def validate_iap_jwt_and_get_email(iap_jwt, audience):
 
 get_author = Depends(authenticate)
 get_project_readonly_connection = Depends(dependable_get_readonly_project_connection)
+HACK_get_project_contributor_connection = Depends(
+    HACK_dependable_contributor_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)
diff --git a/db/python/tables/family.py b/db/python/tables/family.py
index 3aef7545f..219c375fa 100644
--- a/db/python/tables/family.py
+++ b/db/python/tables/family.py
@@ -65,6 +65,7 @@ async def query(
         if not filter_.project and not filter_.id:
             raise ValueError('Project or ID filter is required for family queries')
 
+        has_participant_join = False
         field_overrides = {'id': 'f.id', 'external_id': 'f.external_id'}
 
         if filter_.participant_id: