Do release-2025.5.1 in release-2025.6.0

alembic/versions/00dab0f5f498_add_external_links_property_to_.py

@@ -0,0 +1,33 @@
+"""add external links property to experiments
+
+Revision ID: 00dab0f5f498
+Revises: b22b450d409c
+Create Date: 2025-12-16 12:06:15.265947
+
+"""
+
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "00dab0f5f498"
+down_revision = "b22b450d409c"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column(
+        "experiments",
+        sa.Column("external_links", postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default="{}"),
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column("experiments", "external_links")
+    # ### end Alembic commands ###

src/mavedb/models/experiment.py

@@ -73,6 +73,7 @@ class Experiment(Base):
     abstract_text = Column(String, nullable=False)
     method_text = Column(String, nullable=False)
     extra_metadata = Column(JSONB, nullable=False)
+    external_links = Column(JSONB, nullable=False, default={})
 
     private = Column(Boolean, nullable=False, default=True)
     approved = Column(Boolean, nullable=False, default=False)

src/mavedb/routers/experiments.py

@@ -459,6 +459,7 @@ async def update_experiment(
     item.raw_read_identifiers = raw_read_identifiers
 
     if item_update.keywords:
+        keywords: list[ExperimentControlledKeywordAssociation] = []
         all_labels_none = all(k.keyword.label is None for k in item_update.keywords)
         if all_labels_none is False:
             # Users may choose part of keywords from dropdown menu. Remove not chosen keywords from the list.
@@ -467,10 +468,18 @@ async def update_experiment(
                 validate_keyword_list(filtered_keywords)
             except ValidationError as e:
                 raise HTTPException(status_code=422, detail=str(e))
-            try:
-                await item.set_keywords(db, filtered_keywords)
-            except Exception as e:
-                raise HTTPException(status_code=500, detail=f"Invalid keywords: {str(e)}")
+            for upload_keyword in filtered_keywords:
+                try:
+                    description = upload_keyword.description
+                    controlled_keyword = search_keyword(db, upload_keyword.keyword.key, upload_keyword.keyword.label)
+                    experiment_controlled_keyword = ExperimentControlledKeywordAssociation(
+                        controlled_keyword=controlled_keyword,
+                        description=description,
+                    )
+                    keywords.append(experiment_controlled_keyword)
+                except ValueError as e:
+                    raise HTTPException(status_code=422, detail=str(e))
+        item.keyword_objs = keywords
 
     item.modified_by = user_data.user
 

src/mavedb/view_models/collection.py

@@ -1,5 +1,5 @@
 from datetime import date
-from typing import Any, Sequence, Optional
+from typing import Any, Optional, Sequence
 
 from pydantic import Field, model_validator
 
@@ -132,3 +132,14 @@ class Collection(SavedCollection):
 # NOTE: Coupled to ContributionRole enum
 class AdminCollection(Collection):
     pass
+
+
+# Properties to return for official collections
+class OfficialCollection(BaseModel):
+    badge_name: str
+    name: str
+    urn: str
+
+    class Config:
+        arbitrary_types_allowed = True
+        from_attributes = True

src/mavedb/view_models/components/external_link.py

@@ -0,0 +1,15 @@
+from typing import Optional
+
+from mavedb.view_models.base.base import BaseModel
+
+
+class ExternalLink(BaseModel):
+    """
+    Represents an external hyperlink for view models.
+
+    Attributes:
+        url (Optional[str]): Fully qualified URL for the external resource.
+            May be None if no link is available or applicable.
+    """
+
+    url: Optional[str] = None

src/mavedb/view_models/experiment.py

@@ -1,18 +1,20 @@
 from datetime import date
 from typing import Any, Collection, Optional, Sequence
 
-from pydantic import field_validator, model_validator, ValidationInfo
+from pydantic import ValidationInfo, field_validator, model_validator
 
+from mavedb.lib.validation import urn_re
 from mavedb.lib.validation.exceptions import ValidationError
 from mavedb.lib.validation.transform import (
     transform_experiment_set_to_urn,
-    transform_score_set_list_to_urn_list,
     transform_record_publication_identifiers,
+    transform_score_set_list_to_urn_list,
 )
-from mavedb.lib.validation import urn_re
 from mavedb.lib.validation.utilities import is_null
 from mavedb.view_models import record_type_validator, set_record_type
 from mavedb.view_models.base.base import BaseModel
+from mavedb.view_models.collection import OfficialCollection
+from mavedb.view_models.components.external_link import ExternalLink
 from mavedb.view_models.contributor import Contributor, ContributorCreate
 from mavedb.view_models.doi_identifier import (
     DoiIdentifier,
@@ -37,16 +39,6 @@
 from mavedb.view_models.user import SavedUser, User
 
 
-class OfficialCollection(BaseModel):
-    badge_name: str
-    name: str
-    urn: str
-
-    class Config:
-        arbitrary_types_allowed = True
-        from_attributes = True
-
-
 class ExperimentBase(BaseModel):
     title: str
     short_description: str
@@ -115,6 +107,7 @@ class SavedExperiment(ExperimentBase):
     contributors: list[Contributor]
     keywords: Sequence[SavedExperimentControlledKeyword]
     score_set_urns: list[str]
+    external_links: dict[str, ExternalLink]
 
     _record_type_factory = record_type_validator()(set_record_type)
 

src/mavedb/view_models/score_set.py

@@ -19,6 +19,8 @@
 from mavedb.models.enums.processing_state import ProcessingState
 from mavedb.view_models import record_type_validator, set_record_type
 from mavedb.view_models.base.base import BaseModel
+from mavedb.view_models.collection import OfficialCollection
+from mavedb.view_models.components.external_link import ExternalLink
 from mavedb.view_models.contributor import Contributor, ContributorCreate
 from mavedb.view_models.doi_identifier import (
     DoiIdentifier,
@@ -49,20 +51,6 @@
 UnboundedRange = tuple[Union[float, None], Union[float, None]]
 
 
-class ExternalLink(BaseModel):
-    url: Optional[str] = None
-
-
-class OfficialCollection(BaseModel):
-    badge_name: str
-    name: str
-    urn: str
-
-    class Config:
-        arbitrary_types_allowed = True
-        from_attributes = True
-
-
 class ScoreSetBase(BaseModel):
     """Base class for score set view models."""
 
@@ -109,7 +97,7 @@ def targets_need_labels_when_multiple_targets_exist(self) -> Self:
                         "Target sequence labels cannot be empty when multiple targets are defined.",
                         custom_loc=[
                             "body",
-                            "targetGene",
+                            "targetGenes",
                             idx,
                             "targetSequence",
                             "label",
@@ -134,7 +122,7 @@ def target_labels_are_unique(self) -> Self:
                     "Target sequence labels cannot be duplicated.",
                     custom_loc=[
                         "body",
-                        "targetGene",
+                        "targetGenes",
                         dup_indices[-1],
                         "targetSequence",
                         "label",
@@ -161,7 +149,7 @@ def target_accession_base_editor_targets_are_consistent(cls, field_value, values
                     "All target accessions must be of the same base editor type.",
                     custom_loc=[
                         "body",
-                        "targetGene",
+                        "targetGenes",
                         0,
                         "targetAccession",
                         "isBaseEditor",

tests/helpers/constants.py

@@ -427,7 +427,7 @@
         "special": False,
         "description": "Description",
     },
-    {"key": "Delivery method", "label": "Other", "special": False, "description": "Description"},
+    {"key": "Delivery Method", "label": "Other", "special": False, "description": "Description"},
     {
         "key": "Phenotypic Assay Mechanism",
         "label": "Other",
@@ -442,6 +442,13 @@
         "special": False,
         "description": "Description",
     },
+    {
+        "key": "Phenotypic Assay Profiling Strategy",
+        "label": "Shotgun sequencing",
+        "code": None,
+        "special": False,
+        "description": "Description",
+    },
 ]
 
 TEST_KEYWORDS = [
@@ -470,7 +477,7 @@
         },
     },
     {
-        "keyword": {"key": "Delivery method", "label": "Other", "special": False, "description": "Description"},
+        "keyword": {"key": "Delivery Method", "label": "Other", "special": False, "description": "Description"},
         "description": "Details of delivery method",
     },
 ]
@@ -492,7 +499,7 @@
     "methodText": "Methods",
     "keywords": [
         {
-            "keyword": {"key": "Delivery method", "label": "Other", "special": False, "description": "Description"},
+            "keyword": {"key": "Delivery Method", "label": "Other", "special": False, "description": "Description"},
             "description": "Details of delivery method",
         },
     ],
@@ -540,6 +547,7 @@
     "primaryPublicationIdentifiers": [],
     "secondaryPublicationIdentifiers": [],
     "rawReadIdentifiers": [],
+    "externalLinks": {},
     # keys to be set after receiving response
     "urn": None,
     "experimentSetUrn": None,
@@ -572,14 +580,60 @@
     "keywords": [
         {
             "recordType": "ExperimentControlledKeyword",
-            "keyword": {"key": "Delivery method", "label": "Other", "special": False, "description": "Description"},
+            "keyword": {"key": "Delivery Method", "label": "Other", "special": False, "description": "Description"},
             "description": "Details of delivery method",
         },
     ],
     "doiIdentifiers": [],
     "primaryPublicationIdentifiers": [],
     "secondaryPublicationIdentifiers": [],
     "rawReadIdentifiers": [],
+    "externalLinks": {},
+    # keys to be set after receiving response
+    "urn": None,
+    "experimentSetUrn": None,
+    "officialCollections": [],
+    "numScoreSets": 0,  # NOTE: This is context-dependent and may need overriding per test
+}
+
+TEST_EXPERIMENT_WITH_UPDATE_KEYWORD_RESPONSE = {
+    "recordType": "Experiment",
+    "title": "Test Experiment Title",
+    "shortDescription": "Test experiment",
+    "abstractText": "Abstract",
+    "methodText": "Methods",
+    "createdBy": {
+        "recordType": "User",
+        "firstName": TEST_USER["first_name"],
+        "lastName": TEST_USER["last_name"],
+        "orcidId": TEST_USER["username"],
+    },
+    "modifiedBy": {
+        "recordType": "User",
+        "firstName": TEST_USER["first_name"],
+        "lastName": TEST_USER["last_name"],
+        "orcidId": TEST_USER["username"],
+    },
+    "creationDate": date.today().isoformat(),
+    "modificationDate": date.today().isoformat(),
+    "scoreSetUrns": [],
+    "contributors": [],
+    "keywords": [
+        {
+            "recordType": "ExperimentControlledKeyword",
+            "keyword": {
+                "key": "Phenotypic Assay Profiling Strategy",
+                "label": "Shotgun sequencing",
+                "special": False,
+                "description": "Description"
+            },
+            "description": "Details of phenotypic assay profiling strategy",
+        },
+    ],
+    "doiIdentifiers": [],
+    "primaryPublicationIdentifiers": [],
+    "secondaryPublicationIdentifiers": [],
+    "rawReadIdentifiers": [],
     # keys to be set after receiving response
     "urn": None,
     "experimentSetUrn": None,
@@ -622,14 +676,15 @@
         },
         {
             "recordType": "ExperimentControlledKeyword",
-            "keyword": {"key": "Delivery method", "label": "Other", "special": False, "description": "Description"},
+            "keyword": {"key": "Delivery Method", "label": "Other", "special": False, "description": "Description"},
             "description": "Description",
         },
     ],
     "doiIdentifiers": [],
     "primaryPublicationIdentifiers": [],
     "secondaryPublicationIdentifiers": [],
     "rawReadIdentifiers": [],
+    "externalLinks": {},
     # keys to be set after receiving response
     "urn": None,
     "experimentSetUrn": None,