Merge pull request #447 from VariantEffect/bugfix/estelle/61/numScoreSetsAndExperiments

Bugfix/estelle/61/num score sets and experiments

Author: EstelleDa

docker-compose-dev.yml

@@ -23,7 +23,6 @@ services:
       - "8002:8000"
     volumes:
       - .:/code
-      - mavedb-seqrepo-dev:/usr/local/share/seqrepo
 
   worker:
     image: mavedb-api/mavedb-worker:dev
@@ -42,7 +41,6 @@ services:
       LOG_CONFIG: dev
     volumes:
       - .:/code
-      - mavedb-seqrepo-dev:/usr/local/share/seqrepo
     depends_on:
       - db
       - redis

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "mavedb"
-version = "2025.1.1"
+version = "2025.1.2"
 description = "API for MaveDB, the database of Multiplexed Assays of Variant Effect."
 license = "AGPL-3.0-only"
 readme = "README.md"

src/mavedb/__init__.py

@@ -6,6 +6,6 @@
 logger = module_logging.getLogger(__name__)
 
 __project__ = "mavedb-api"
-__version__ = "2025.1.1"
+__version__ = "2025.1.2"
 
 logger.info(f"MaveDB {__version__}")

src/mavedb/lib/experiments.py

@@ -4,7 +4,10 @@
 from sqlalchemy import func, or_, not_
 from sqlalchemy.orm import Session
 
+from mavedb.lib.authentication import UserData
 from mavedb.lib.logging.context import logging_context, save_to_logging_context
+from mavedb.lib.permissions import Action
+from mavedb.lib.score_sets import find_superseded_score_set_tail
 from mavedb.models.contributor import Contributor
 from mavedb.models.controlled_keyword import ControlledKeyword
 from mavedb.models.experiment import Experiment
@@ -14,6 +17,7 @@
 from mavedb.models.publication_identifier import PublicationIdentifier
 from mavedb.models.score_set import ScoreSet
 from mavedb.models.user import User
+from mavedb.view_models import experiment
 from mavedb.view_models.search import ExperimentsSearch
 
 logger = logging.getLogger(__name__)
@@ -108,7 +112,7 @@ def search_experiments(
                     # Keep experiments without any score sets
                     not_(Experiment.score_sets.any()),
                     # Keep experiments where score sets exist but have no meta_analyzes_score_sets
-                    Experiment.score_sets.any(not_(ScoreSet.meta_analyzes_score_sets.any()))
+                    Experiment.score_sets.any(not_(ScoreSet.meta_analyzes_score_sets.any())),
                 )
             )
         else:
@@ -125,3 +129,30 @@ def search_experiments(
     )
 
     return items
+
+
+def enrich_experiment_with_num_score_sets(
+    item_update: Experiment, user_data: Optional[UserData]
+) -> experiment.Experiment:
+    """
+    Validate and update the number of score set in experiment. The superseded score set is excluded.
+    Data structure: experiment{score_set_urns, num_score_sets}
+    """
+    filter_superseded_score_set_tails = [
+        find_superseded_score_set_tail(score_set, Action.READ, user_data) for score_set in item_update.score_sets
+    ]
+    filtered_score_set_urns = sorted(
+        {
+            score_set.urn
+            for score_set in filter_superseded_score_set_tails
+            if score_set is not None and score_set.urn is not None
+        }
+    )
+
+    updated_experiment = experiment.Experiment.from_orm(item_update).copy(
+        update={
+            "num_score_sets": len(filtered_score_set_urns),
+            "score_set_urns": filtered_score_set_urns,
+        }
+    )
+    return updated_experiment

src/mavedb/routers/experiment_sets.py

@@ -7,6 +7,7 @@
 
 from mavedb import deps
 from mavedb.lib.authentication import UserData, get_current_user
+from mavedb.lib.experiments import enrich_experiment_with_num_score_sets
 from mavedb.lib.logging import LoggedRoute
 from mavedb.lib.logging.context import logging_context, save_to_logging_context
 from mavedb.lib.permissions import Action, has_permission
@@ -51,5 +52,13 @@ def fetch_experiment_set(
 
     # Filter experiment sub-resources to only those experiments readable by the requesting user.
     item.experiments[:] = [exp for exp in item.experiments if has_permission(user_data, exp, Action.READ).permitted]
+    enriched_experiments = [
+        enrich_experiment_with_num_score_sets(exp, user_data)
+        for exp in item.experiments
+    ]
+    enriched_item = experiment_set.ExperimentSet.from_orm(item).copy(update={
+        "experiments": enriched_experiments,
+        "numExperiments": len(enriched_experiments)
+    })
 
-    return item
+    return enriched_item

src/mavedb/routers/experiments.py

@@ -14,7 +14,7 @@
 from mavedb.lib.authorization import require_current_user, require_current_user_with_email
 from mavedb.lib.contributors import find_or_create_contributor
 from mavedb.lib.exceptions import NonexistentOrcidUserError
-from mavedb.lib.experiments import search_experiments as _search_experiments
+from mavedb.lib.experiments import search_experiments as _search_experiments, enrich_experiment_with_num_score_sets
 from mavedb.lib.identifiers import (
     find_or_create_doi_identifier,
     find_or_create_publication_identifier,
@@ -89,7 +89,11 @@ def search_experiments(search: ExperimentsSearch, db: Session = Depends(deps.get
     """
     Search experiments.
     """
-    return _search_experiments(db, None, search)
+    items = _search_experiments(db, None, search)
+    return [
+        enrich_experiment_with_num_score_sets(exp, None)
+        for exp in items
+    ]
 
 
 @router.post(
@@ -105,7 +109,11 @@ def search_my_experiments(
     """
     Search experiments created by the current user..
     """
-    return _search_experiments(db, user_data.user, search)
+    items = _search_experiments(db, user_data.user, search)
+    return [
+            enrich_experiment_with_num_score_sets(exp, user_data)
+            for exp in items
+        ]
 
 
 @router.get(
@@ -120,7 +128,7 @@ def fetch_experiment(
     urn: str,
     db: Session = Depends(deps.get_db),
     user_data: Optional[UserData] = Depends(get_current_user),
-) -> Experiment:
+) -> experiment.Experiment:
     """
     Fetch a single experiment by URN.
     """
@@ -133,7 +141,7 @@ def fetch_experiment(
         raise HTTPException(status_code=404, detail=f"Experiment with URN {urn} not found")
 
     assert_permission(user_data, item, Action.READ)
-    return item
+    return enrich_experiment_with_num_score_sets(item, user_data)
 
 
 @router.get(
@@ -184,6 +192,13 @@ def get_experiment_score_sets(
     else:
         filtered_score_sets.sort(key=attrgetter("urn"))
         save_to_logging_context({"associated_resources": [item.urn for item in score_set_result]})
+        enriched_score_sets = []
+        for fs in filtered_score_sets:
+            enriched_experiment = enrich_experiment_with_num_score_sets(fs.experiment, user_data)
+            response_item = score_set.ScoreSet.from_orm(fs).copy(update={"experiment": enriched_experiment})
+            enriched_score_sets.append(response_item)
+
+        return enriched_score_sets
 
     return filtered_score_sets
 
@@ -429,7 +444,7 @@ async def update_experiment(
     db.refresh(item)
 
     save_to_logging_context({"updated_resource": item.urn})
-    return item
+    return enrich_experiment_with_num_score_sets(item, user_data)
 
 
 @router.delete("/experiments/{urn}", response_model=None, responses={422: {}})

src/mavedb/routers/mapped_variant.py

@@ -26,7 +26,7 @@ async def fetch_mapped_variant_by_variant_urn(db, urn: str) -> Optional[MappedVa
             db.query(MappedVariant)
             .filter(Variant.urn == urn)
             .filter(MappedVariant.variant_id == Variant.id)
-            .filter(MappedVariant.current is True)
+            .filter(MappedVariant.current)  # filter current is true
             .one_or_none()
         )
     except MultipleResultsFound:

src/mavedb/routers/score_sets.py

@@ -23,6 +23,7 @@
 )
 from mavedb.lib.contributors import find_or_create_contributor
 from mavedb.lib.exceptions import MixedTargetError, NonexistentOrcidUserError, ValidationError
+from mavedb.lib.experiments import enrich_experiment_with_num_score_sets
 from mavedb.lib.identifiers import (
     create_external_gene_identifier_offset,
     find_or_create_doi_identifier,
@@ -72,7 +73,7 @@
 
 async def fetch_score_set_by_urn(
     db, urn: str, user: Optional[UserData], owner_or_contributor: Optional[UserData], only_published: bool
-) -> Optional[ScoreSet]:
+) -> ScoreSet:
     """
     Fetch one score set by URN, ensuring that the user has read permission.
 
@@ -135,7 +136,15 @@ def search_score_sets(
     Search score sets.
     """
     score_sets = _search_score_sets(db, None, search)
-    return fetch_superseding_score_set_in_search_result(score_sets, user_data, search)
+    updated_score_sets = fetch_superseding_score_set_in_search_result(score_sets, user_data, search)
+    enriched_score_sets = []
+    if updated_score_sets:
+        for u in updated_score_sets:
+            enriched_experiment = enrich_experiment_with_num_score_sets(u.experiment, user_data)
+            response_item = score_set.ScoreSet.from_orm(u).copy(update={"experiment": enriched_experiment})
+            enriched_score_sets.append(response_item)
+
+    return enriched_score_sets
 
 
 @router.get("/score-sets/mapped-genes", status_code=200, response_model=dict[str, list[str]])
@@ -183,7 +192,15 @@ def search_my_score_sets(
     Search score sets created by the current user..
     """
     score_sets = _search_score_sets(db, user_data.user, search)
-    return fetch_superseding_score_set_in_search_result(score_sets, user_data, search)
+    updated_score_sets = fetch_superseding_score_set_in_search_result(score_sets, user_data, search)
+    enriched_score_sets = []
+    if updated_score_sets:
+        for u in updated_score_sets:
+            enriched_experiment = enrich_experiment_with_num_score_sets(u.experiment, user_data)
+            response_item = score_set.ScoreSet.from_orm(u).copy(update={"experiment": enriched_experiment})
+            enriched_score_sets.append(response_item)
+
+    return enriched_score_sets
 
 
 @router.get(
@@ -203,7 +220,9 @@ async def show_score_set(
     Fetch a single score set by URN.
     """
     save_to_logging_context({"requested_resource": urn})
-    return await fetch_score_set_by_urn(db, urn, user_data, None, False)
+    item = await fetch_score_set_by_urn(db, urn, user_data, None, False)
+    enriched_experiment = enrich_experiment_with_num_score_sets(item.experiment, user_data)
+    return score_set.ScoreSet.from_orm(item).copy(update={"experiment": enriched_experiment})
 
 
 @router.get(
@@ -647,7 +666,9 @@ async def create_score_set(
     db.refresh(item)
 
     save_to_logging_context({"created_resource": item.urn})
-    return item
+
+    enriched_experiment = enrich_experiment_with_num_score_sets(item.experiment, user_data)
+    return score_set.ScoreSet.from_orm(item).copy(update={"experiment": enriched_experiment})
 
 
 @router.post(
@@ -711,7 +732,8 @@ async def upload_score_set_variant_data(
     db.add(item)
     db.commit()
     db.refresh(item)
-    return item
+    enriched_experiment = enrich_experiment_with_num_score_sets(item.experiment, user_data)
+    return score_set.ScoreSet.from_orm(item).copy(update={"experiment": enriched_experiment})
 
 
 @router.post(
@@ -748,7 +770,8 @@ async def update_score_set_calibration_data(
     db.refresh(item)
 
     save_to_logging_context({"updated_resource": item.urn})
-    return item
+    enriched_experiment = enrich_experiment_with_num_score_sets(item.experiment, user_data)
+    return score_set.ScoreSet.from_orm(item).copy(update={"experiment": enriched_experiment})
 
 
 @router.put(
@@ -1004,7 +1027,9 @@ async def update_score_set(
     db.refresh(item)
 
     save_to_logging_context({"updated_resource": item.urn})
-    return item
+
+    enriched_experiment = enrich_experiment_with_num_score_sets(item.experiment, user_data)
+    return score_set.ScoreSet.from_orm(item).copy(update={"experiment": enriched_experiment})
 
 
 @router.delete("/score-sets/{urn}", responses={422: {}})
@@ -1142,7 +1167,8 @@ async def publish_score_set(
             msg="Failed to enqueue published variant materialized view refresh job.", extra=logging_context()
         )
 
-    return item
+    enriched_experiment = enrich_experiment_with_num_score_sets(item.experiment, user_data)
+    return score_set.ScoreSet.from_orm(item).copy(update={"experiment": enriched_experiment})
 
 
 @router.get(
@@ -1276,3 +1302,4 @@ async def get_clinical_controls_options_for_score_set(
         dict(zip(("db_name", "available_versions"), (db_name, db_versions)))
         for db_name, db_versions in clinical_control_options.items()
     ]
+

src/mavedb/view_models/experiment.py

@@ -132,6 +132,7 @@ def publication_identifiers_validator(cls, value, values, field) -> list[Publica
 
 # Properties to return to non-admin clients
 class Experiment(SavedExperiment):
+    num_score_sets: Optional[int] = None
     score_set_urns: list[str]
     processing_state: Optional[str]
     doi_identifiers: Sequence[DoiIdentifier]

src/mavedb/view_models/experiment_set.py

@@ -45,6 +45,7 @@ class ExperimentSet(SavedExperimentSet):
     created_by: Optional[User]
     modified_by: Optional[User]
     experiments: Sequence[Experiment]
+    num_experiments: Optional[int] = None
 
 
 # Properties to return to admin clients