fix: 🐛 maganing organization table (#53)

* feat: added managing organization table

* fix: api for managing org

* fix: api for managing org

* fix: test for managing org

* fix: model classes of managing organization

* style: format

apis/dataset_metadata/dataset_managing_organization.py

@@ -11,8 +11,10 @@
 dataset_managing_organization = api.model(
     "DatasetManagingOrganization",
     {
-        "managing_organization_name": fields.String(required=True),
-        "managing_organization_ror_id": fields.String(required=True),
+        "name": fields.String(required=True),
+        "identifier": fields.String(required=True),
+        "identifier_scheme": fields.String(required=True),
+        "identifier_scheme_uri": fields.String(required=True),
     },
 )
 
@@ -28,7 +30,7 @@ class DatasetManagingOrganization(Resource):
     def get(self, study_id: int, dataset_id: int):  # pylint: disable= unused-argument
         """Get dataset publisher metadata"""
         dataset_ = model.Dataset.query.get(dataset_id)
-        managing_organization_ = dataset_.dataset_other
+        managing_organization_ = dataset_.dataset_managing_organization
         return managing_organization_.to_dict(), 200
 
     @api.doc("update organization")
@@ -46,12 +48,17 @@ def put(self, study_id: int, dataset_id: int):
             "type": "object",
             "additionalProperties": False,
             "properties": {
-                "managing_organization_name": {"type": "string", "minLength": 1},
-                "managing_organization_ror_id": {
-                    "type": "string",
-                },
+                "name": {"type": "string", "minLength": 1},
+                "identifier": {"type": "string"},
+                "identifier_scheme": {"type": "string"},
+                "identifier_scheme_uri": {"type": "string"},
             },
-            "required": ["managing_organization_name", "managing_organization_ror_id"],
+            "required": [
+                "name",
+                "identifier",
+                "identifier_scheme",
+                "identifier_scheme_uri",
+            ],
         }
         try:
             validate(instance=request.json, schema=schema)
@@ -60,7 +67,7 @@ def put(self, study_id: int, dataset_id: int):
 
         data = request.json
         dataset_ = model.Dataset.query.get(dataset_id)
-        dataset_.dataset_other.update(data)
+        dataset_.dataset_managing_organization.update(data)
 
         model.db.session.commit()
-        return dataset_.dataset_other.to_dict(), 200
+        return dataset_.dataset_managing_organization.to_dict(), 200

model/__init__.py

@@ -10,6 +10,7 @@
 from .dataset_metadata.dataset_description import DatasetDescription
 from .dataset_metadata.dataset_funder import DatasetFunder
 from .dataset_metadata.dataset_healthsheet import DatasetHealthsheet
+from .dataset_metadata.dataset_managing_organization import DatasetManagingOrganization
 from .dataset_metadata.dataset_other import DatasetOther
 from .dataset_metadata.dataset_rights import DatasetRights
 from .dataset_metadata.dataset_subject import DatasetSubject
@@ -60,6 +61,7 @@
     "DatasetContributor",
     "StudyContributor",
     "DatasetOther",
+    "DatasetManagingOrganization",
     "DatasetAccess",
     "DatasetConsent",
     "DatasetHealthsheet",

model/dataset.py

@@ -21,6 +21,7 @@ def __init__(self, study):
         self.dataset_consent = model.DatasetConsent(self)
         self.dataset_healthsheet = model.DatasetHealthsheet(self)
         self.dataset_other = model.DatasetOther(self)
+        self.dataset_managing_organization = model.DatasetManagingOrganization(self)
 
         self.dataset_title.append(model.DatasetTitle(self))
         self.dataset_description.append(model.DatasetDescription(self))
@@ -94,6 +95,12 @@ def __init__(self, study):
     dataset_other = db.relationship(
         "DatasetOther", back_populates="dataset", uselist=False, cascade="all, delete"
     )
+    dataset_managing_organization = db.relationship(
+        "DatasetManagingOrganization",
+        back_populates="dataset",
+        uselist=False,
+        cascade="all, delete",
+    )
     dataset_related_identifier = db.relationship(
         "DatasetRelatedIdentifier", back_populates="dataset", cascade="all, delete"
     )
@@ -131,7 +138,7 @@ def to_dict_dataset_metadata(self):
                 if not i.creator
             ],
             "about": self.dataset_other.to_dict_metadata(),
-            "managing_organization": self.dataset_other.to_dict_managing_organization(),  # type: ignore
+            "managing_organization": self.dataset_managing_organization.to_dict_metadata(),  # type: ignore
             "access": self.dataset_access.to_dict_metadata(),
             "consent": self.dataset_consent.to_dict_metadata(),
             "dates": [i.to_dict_metadata() for i in self.dataset_date],  # type: ignore

model/dataset_metadata/dataset_managing_organization.py

@@ -0,0 +1,52 @@
+from ..db import db
+
+
+class DatasetManagingOrganization(db.Model):  # type: ignore
+    def __init__(self, dataset):
+        self.dataset = dataset
+        self.name = ""
+        self.identifier = ""
+        self.identifier_scheme = ""
+        self.identifier_scheme_uri = ""
+
+    __tablename__ = "dataset_managing_organization"
+
+    name = db.Column(db.String, nullable=False)
+    identifier = db.Column(db.String, nullable=False)
+    identifier_scheme = db.Column(db.String, nullable=False)
+    identifier_scheme_uri = db.Column(db.String, nullable=False)
+
+    dataset_id = db.Column(
+        db.CHAR(36), db.ForeignKey("dataset.id"), primary_key=True, nullable=False
+    )
+    dataset = db.relationship("Dataset", back_populates="dataset_managing_organization")
+
+    def to_dict(self):
+        return {
+            "name": self.name,
+            "identifier": self.identifier,
+            "identifier_scheme": self.identifier_scheme,
+            "identifier_scheme_uri": self.identifier_scheme_uri,
+        }
+
+    def to_dict_metadata(self):
+        return {
+            "name": self.name,
+            "identifier": self.identifier,
+        }
+
+    @staticmethod
+    def from_data(dataset, data: dict):
+        dataset_other = DatasetManagingOrganization(dataset)
+        dataset_other.update(data)
+        return dataset_other
+
+    def update(self, data: dict):
+        if "name" in data:
+            self.name = data["name"]
+        if "identifier" in data:
+            self.identifier = data["identifier"]
+        if "identifier_scheme" in data:
+            self.identifier_scheme = data["identifier_scheme"]
+        if "identifier_scheme_uri" in data:
+            self.identifier_scheme_uri = data["identifier_scheme_uri"]

model/dataset_metadata/dataset_other.py

@@ -9,8 +9,6 @@ def __init__(self, dataset):
         self.dataset = dataset
         self.resource_type = ""
         self.language = None
-        self.managing_organization_name = ""
-        self.managing_organization_ror_id = ""
         self.size = ""
         self.format = ""
         self.standards_followed = ""
@@ -20,8 +18,6 @@ def __init__(self, dataset):
 
     resource_type = db.Column(db.String, nullable=False)
     language = db.Column(db.String, nullable=True)
-    managing_organization_name = db.Column(db.String, nullable=False)
-    managing_organization_ror_id = db.Column(db.String, nullable=False)
     size = db.Column(ARRAY(String), nullable=False)
     format = db.Column(ARRAY(String), nullable=False)
     standards_followed = db.Column(db.String, nullable=False)
@@ -35,8 +31,6 @@ def __init__(self, dataset):
     def to_dict(self):
         return {
             "language": self.language,
-            "managing_organization_name": self.managing_organization_name,
-            "managing_organization_ror_id": self.managing_organization_ror_id,
             "standards_followed": self.standards_followed,
             "acknowledgement": self.acknowledgement,
             "size": self.size,
@@ -51,11 +45,6 @@ def to_dict_metadata(self):
             "resource_type": self.resource_type,
         }
 
-    def to_dict_managing_organization(self):
-        return {
-            "managing_organization_name": self.managing_organization_name,
-        }
-
     @staticmethod
     def from_data(dataset, data: dict):
         dataset_other = DatasetOther(dataset)
@@ -65,10 +54,6 @@ def from_data(dataset, data: dict):
     def update(self, data: dict):
         if "language" in data:
             self.language = data["language"]
-        if "managing_organization_name" in data:
-            self.managing_organization_name = data["managing_organization_name"]
-        if "managing_organization_ror_id" in data:
-            self.managing_organization_ror_id = data["managing_organization_ror_id"]
         if "size" in data:
             self.size = data["size"]
         if "format" in data:

tests/functional/test_study_dataset_metadata_api.py

@@ -2866,64 +2866,64 @@ def test_put_dataset_managing_organization_metadata(clients):
     response = _logged_in_client.put(
         f"/study/{study_id}/dataset/{dataset_id}/metadata/managing-organization",
         json={
-            "managing_organization_name": "Managing Organization Name",
-            "managing_organization_ror_id": "Managing Organization ROR ID",
+            "name": "Managing Organization Name",
+            "identifier": "identifier",
+            "identifier_scheme": "identifier scheme",
+            "identifier_scheme_uri": "identifier scheme_uri",
         },
     )
 
     assert response.status_code == 200
     response_data = json.loads(response.data)
 
-    assert response_data["managing_organization_name"] == "Managing Organization Name"
-    assert (
-        response_data["managing_organization_ror_id"] == "Managing Organization ROR ID"
-    )
+    assert response_data["name"] == "Managing Organization Name"
+    assert response_data["identifier"] == "identifier"
+    assert response_data["identifier_scheme"] == "identifier scheme"
+    assert response_data["identifier_scheme_uri"] == "identifier scheme_uri"
 
     admin_response = _admin_client.put(
         f"/study/{study_id}/dataset/{dataset_id}/metadata/managing-organization",
         json={
-            "managing_organization_name": "Managing Admin Organization Name",
-            "managing_organization_ror_id": "Managing Organization ROR ID",
+            "name": "admin Managing Organization Name",
+            "identifier": "identifier",
+            "identifier_scheme": "identifier scheme",
+            "identifier_scheme_uri": "identifier scheme_uri",
         },
     )
 
     assert admin_response.status_code == 200
     admin_response_data = json.loads(admin_response.data)
 
-    assert (
-        admin_response_data["managing_organization_name"]
-        == "Managing Admin Organization Name"
-    )
-    assert (
-        admin_response_data["managing_organization_ror_id"]
-        == "Managing Organization ROR ID"
-    )
+    assert admin_response_data["name"] == "admin Managing Organization Name"
+    assert admin_response_data["identifier"] == "identifier"
+    assert admin_response_data["identifier_scheme"] == "identifier scheme"
+    assert admin_response_data["identifier_scheme_uri"] == "identifier scheme_uri"
 
     editor_response = _editor_client.put(
         f"/study/{study_id}/dataset/{dataset_id}/metadata/managing-organization",
         json={
-            "managing_organization_name": "Managing Editor Organization Name",
-            "managing_organization_ror_id": "Managing Organization ROR ID",
+            "name": "editor Managing Organization Name",
+            "identifier": "identifier",
+            "identifier_scheme": "identifier scheme",
+            "identifier_scheme_uri": "identifier scheme_uri",
         },
     )
 
     assert editor_response.status_code == 200
     editor_response_data = json.loads(editor_response.data)
 
-    assert (
-        editor_response_data["managing_organization_name"]
-        == "Managing Editor Organization Name"
-    )
-    assert (
-        editor_response_data["managing_organization_ror_id"]
-        == "Managing Organization ROR ID"
-    )
+    assert editor_response_data["name"] == "editor Managing Organization Name"
+    assert editor_response_data["identifier"] == "identifier"
+    assert editor_response_data["identifier_scheme"] == "identifier scheme"
+    assert editor_response_data["identifier_scheme_uri"] == "identifier scheme_uri"
 
     viewer_response = _viewer_client.put(
         f"/study/{study_id}/dataset/{dataset_id}/metadata/managing-organization",
         json={
-            "managing_organization_name": "Managing Viewer Organization Name",
-            "managing_organization_ror_id": "Managing Organization ROR ID",
+            "name": "editor Managing Organization Name",
+            "identifier": "identifier",
+            "identifier_scheme": "identifier scheme",
+            "identifier_scheme_uri": "identifier scheme_uri",
         },
     )
 
@@ -2967,40 +2967,25 @@ def test_get_dataset_managing_organization_metadata(clients):
 
     # Editor was the last to update the metadata successfully so
     # the response should reflect that
-    assert (
-        response_data["managing_organization_name"]
-        == "Managing Editor Organization Name"
-    )
-    assert (
-        response_data["managing_organization_ror_id"] == "Managing Organization ROR ID"
-    )
-
-    assert (
-        admin_response_data["managing_organization_name"]
-        == "Managing Editor Organization Name"
-    )
-    assert (
-        admin_response_data["managing_organization_ror_id"]
-        == "Managing Organization ROR ID"
-    )
-
-    assert (
-        editor_response_data["managing_organization_name"]
-        == "Managing Editor Organization Name"
-    )
-    assert (
-        editor_response_data["managing_organization_ror_id"]
-        == "Managing Organization ROR ID"
-    )
-
-    assert (
-        viewer_response_data["managing_organization_name"]
-        == "Managing Editor Organization Name"
-    )
-    assert (
-        viewer_response_data["managing_organization_ror_id"]
-        == "Managing Organization ROR ID"
-    )
+    assert response_data["name"] == "editor Managing Organization Name"
+    assert response_data["identifier"] == "identifier"
+    assert response_data["identifier_scheme"] == "identifier scheme"
+    assert response_data["identifier_scheme_uri"] == "identifier scheme_uri"
+
+    assert admin_response_data["name"] == "editor Managing Organization Name"
+    assert admin_response_data["identifier"] == "identifier"
+    assert admin_response_data["identifier_scheme"] == "identifier scheme"
+    assert admin_response_data["identifier_scheme_uri"] == "identifier scheme_uri"
+
+    assert editor_response_data["name"] == "editor Managing Organization Name"
+    assert editor_response_data["identifier"] == "identifier"
+    assert editor_response_data["identifier_scheme"] == "identifier scheme"
+    assert editor_response_data["identifier_scheme_uri"] == "identifier scheme_uri"
+
+    assert viewer_response_data["name"] == "editor Managing Organization Name"
+    assert viewer_response_data["identifier"] == "identifier"
+    assert viewer_response_data["identifier_scheme"] == "identifier scheme"
+    assert viewer_response_data["identifier_scheme_uri"] == "identifier scheme_uri"
 
 
 # ------------------- RELATED IDENTIFIER METADATA ------------------- #

tests/functional/test_study_version_api.py

@@ -855,9 +855,10 @@ def test_get_version_dataset_metadata(clients):
     assert response_data["de_identification"]["type"] == "Level"
 
     assert (
-        response_data["managing_organization"]["managing_organization_name"]
-        == "Managing Editor Organization Name"
+        response_data["managing_organization"]["name"]
+        == "editor Managing Organization Name"
     )
+    assert response_data["managing_organization"]["identifier"] == "identifier"
     assert response_data["identifiers"][0]["identifier"] == "identifier test"
     assert response_data["identifiers"][0]["type"] == "ARK"
 
@@ -895,9 +896,10 @@ def test_get_version_dataset_metadata(clients):
     assert admin_response_data["de_identification"]["direct"] is True
     assert admin_response_data["de_identification"]["type"] == "Level"
     assert (
-        admin_response_data["managing_organization"]["managing_organization_name"]
-        == "Managing Editor Organization Name"
+        admin_response_data["managing_organization"]["name"]
+        == "editor Managing Organization Name"
     )
+    assert admin_response_data["managing_organization"]["identifier"] == "identifier"
 
     assert admin_response_data["identifiers"][0]["identifier"] == "identifier test"
     assert admin_response_data["identifiers"][0]["type"] == "ARK"
@@ -938,9 +940,10 @@ def test_get_version_dataset_metadata(clients):
     assert editor_response_data["de_identification"]["direct"] is True
     assert editor_response_data["de_identification"]["type"] == "Level"
     assert (
-        editor_response_data["managing_organization"]["managing_organization_name"]
-        == "Managing Editor Organization Name"
+        editor_response_data["managing_organization"]["name"]
+        == "editor Managing Organization Name"
     )
+    assert editor_response_data["managing_organization"]["identifier"] == "identifier"
 
     assert editor_response_data["identifiers"][0]["identifier"] == "identifier test"
     assert editor_response_data["identifiers"][0]["type"] == "ARK"