[#78] Handle HydroShare Collection Resources

dspback/api.py

@@ -3,11 +3,10 @@
 from fastapi import FastAPI, status
 from fastapi.openapi.utils import get_openapi
 from fastapi.staticfiles import StaticFiles
+from pydantic import ValidationError
 from starlette.middleware.cors import CORSMiddleware
 from starlette.middleware.sessions import SessionMiddleware
 from starlette.responses import PlainTextResponse
-from pydantic import ValidationError
-
 
 from dspback.config import get_settings
 from dspback.dependencies import RepositoryException
@@ -52,10 +51,10 @@
 async def http_exception_handler(request, exc):
     return PlainTextResponse(f"Repository exception response[{str(exc.detail)}]", status_code=exc.status_code)
 
+
 @app.exception_handler(ValidationError)
 async def validation_exception_handler(request, exc: ValidationError):
-    return PlainTextResponse(f"Request data validation errors: {str(exc)}",
-                             status_code=status.HTTP_400_BAD_REQUEST)
+    return PlainTextResponse(f"Request data validation errors: {str(exc)}", status_code=status.HTTP_400_BAD_REQUEST)
 
 
 @app.on_event("startup")

dspback/config/__init__.py

@@ -44,6 +44,7 @@ class Settings(BaseSettings):
     zenodo_file_delete_url: HttpUrl
     zenodo_file_read_url: HttpUrl
     zenodo_view_url: HttpUrl
+    zenodo_public_view_url: HttpUrl
     zenodo_move_or_rename_url: HttpUrl
     zenodo_health_url: HttpUrl
 
@@ -145,6 +146,7 @@ def get_settings():
         "file_read": settings.zenodo_file_read_url,
         "move_or_rename_url": settings.zenodo_move_or_rename_url,
         "view_url": settings.zenodo_view_url,
+        "public_view_url": settings.zenodo_public_view_url,
         "schema": "/api/schema/zenodo/schema.json",
         "uischema": "/api/schema/zenodo/uischema.json",
         "schema_defaults": "/api/schema/zenodo/defaults.json",
@@ -164,6 +166,7 @@ def get_settings():
         "folder_delete": settings.hydroshare_folder_read_url,
         "move_or_rename_url": settings.hydroshare_move_or_rename_url,
         "view_url": settings.hydroshare_view_url,
+        "public_view_url": settings.hydroshare_view_url,
         "schema": "/api/schema/hydroshare/schema.json",
         "uischema": "/api/schema/hydroshare/uischema.json",
         "schema_defaults": "/api/schema/hydroshare/defaults.json",
@@ -179,6 +182,7 @@ def get_settings():
         "file_delete": settings.earthchem_file_delete_url,
         "file_read": settings.earthchem_file_read_url,
         "view_url": settings.earthchem_view_url,
+        "public_view_url": settings.earthchem_public_view_url,
         "schema": "/api/schema/earthchem/schema.json",
         "uischema": "/api/schema/earthchem/uischema.json",
         "schema_defaults": "/api/schema/earthchem/defaults.json",

dspback/pydantic_schemas.py

@@ -141,7 +141,11 @@ def parse_publication_date(cls, value):
 
     def to_submission(self, identifier) -> Submission:
         settings = get_settings()
-        view_url = settings.zenodo_view_url % identifier
+        view_url = (
+            settings.zenodo_public_view_url % identifier
+            if self.publication_date
+            else settings.zenodo_view_url % identifier
+        )
         return Submission(
             title=self.title,
             authors=[creator.name for creator in self.creators],
@@ -264,7 +268,11 @@ class License(BaseModel):
 
     def to_submission(self, identifier) -> Submission:
         settings = get_settings()
-        view_url = settings.earthchem_public_view_url % identifier
+        view_url = (
+            settings.earthchem_public_view_url % identifier
+            if self.datePublished
+            else settings.earthchem_view_url % identifier
+        )
         authors = [contributor.name for contributor in self.contributors]
         authors.insert(0, self.leadAuthor.name)
         return Submission(

dspback/routers/earthchem.py

@@ -131,6 +131,16 @@ async def get_metadata_repository(self, request: Request, identifier) -> respons
         await self.submit(request, identifier=identifier, json_metadata=json_metadata)
         return json_metadata
 
+    @router.get(
+        '/submission/earthchem/{identifier}',
+        tags=["EarthChem"],
+        summary="Update and get an EarthChem record Submission",
+        description="Retrieves the metadata for the EarthChem record and returns the updated Submission in the database.",
+    )
+    async def update_and_get_submission(self, request: Request, identifier):
+        await self.get_metadata_repository(request, identifier)
+        return self.user.submission(identifier)
+
     @router.delete(
         '/metadata/earthchem/{identifier}',
         tags=["EarthChem"],

dspback/routers/hydroshare.py

@@ -142,6 +142,16 @@ async def _retrieve_metadata_from_repository(self, request: Request, identifier)
         if response.status_code >= 300:
             raise RepositoryException(status_code=response.status_code, detail=response.text)
 
+        """
+        HydroShare maintenance mode
+          Parsing the response can fail if HydroShare is in maintenance mode.
+          The request to HydroShare will return status code 200, but contain an HTML response.
+        """
+        try:
+            json_metadata = json.loads(response.text)
+        except:
+            raise RepositoryException(status_code=500, detail="Failed to parse JSON response")
+
         json_metadata = json.loads(response.text)
         json_metadata = from_hydroshare_format(json_metadata)
         return self.wrap_metadata(json_metadata, exists_and_is("published", json_metadata))
@@ -159,6 +169,16 @@ async def get_metadata_repository(self, request: Request, identifier):
         await self.submit(request, identifier=identifier, json_metadata=json_metadata)
         return json_metadata
 
+    @router.get(
+        '/submission/hydroshare/{identifier}',
+        tags=["HydroShare"],
+        summary="Update and get a HydroShare resource Submission",
+        description="Retrieves the metadata for the HydroShare resource and returns the updated Submission in the database.",
+    )
+    async def update_and_get_submission(self, request: Request, identifier):
+        await self.get_metadata_repository(request, identifier)
+        return self.user.submission(identifier)
+
     @router.delete(
         '/metadata/hydroshare/{identifier}',
         tags=["HydroShare"],

dspback/routers/zenodo.py

@@ -123,6 +123,16 @@ async def get_metadata_repository(self, request: Request, identifier):
 
         return json_metadata
 
+    @router.get(
+        '/submission/zenodo/{identifier}',
+        tags=["Zenodo"],
+        summary="Update and get a Zenodo record Submission",
+        description="Retrieves the metadata for the Zenodo record and returns the updated Submission in the database.",
+    )
+    async def update_and_get_submission(self, request: Request, identifier):
+        await self.get_metadata_repository(request, identifier)
+        return self.user.submission(identifier)
+
     @router.delete(
         '/metadata/zenodo/{identifier}',
         tags=["Zenodo"],

dspback/schemas/earthchem/schema.json

@@ -28,8 +28,7 @@
     "description": {
       "title": "Abstract or Description",
       "type": "string",
-      "description": "Describe measurements, location, and purpose of the dataset",
-      "maxLength": 250
+      "description": "Describe measurements, location, and purpose of the dataset"
     },
     "community": {
       "title": "Community",

dspback/schemas/external/schema.json

@@ -172,9 +172,6 @@
           "format": "date-time",
           "options": {
             "placeholder": "YYYY-MM-DDTHH:MM"
-          },
-          "formatMinimum": {
-            "$data": "1/start"
           }
         }
       },

dspback/schemas/external/uischema.json

@@ -149,7 +149,31 @@
     {
       "type": "Control",
       "label": "Temporal coverage",
-      "scope": "#/properties/temporalCoverage"
+      "scope": "#/properties/temporalCoverage",
+      "options": {
+        "detail": {
+          "type": "VerticalLayout",
+          "elements": [
+            {
+              "type": "Control",
+              "scope": "#/properties/name"
+            },
+            {
+              "type": "HorizontalLayout",
+              "elements": [
+                {
+                  "type": "Control",
+                  "scope": "#/properties/start"
+                },
+                {
+                  "type": "Control",
+                  "scope": "#/properties/end"
+                }
+              ]
+            }
+          ]
+        }
+      }
     },
     {
       "type": "Control",

dspback/schemas/hydroshare/schema.json

@@ -624,9 +624,6 @@
           "format": "date-time",
           "options": {
             "placeholder": "YYYY-MM-DDTHH:MM"
-          },
-          "formatMinimum": {
-            "$data": "1/start"
           }
         }
       },

dspback/schemas/hydroshare/uischema.json

@@ -316,6 +316,7 @@
       "scope": "#/properties/relations",
       "options": {
         "showSortButtons": true,
+        "collapsed": true,
         "elementLabelProp": [
           "type",
           "value"

tests/test_records.py

@@ -24,6 +24,7 @@ async def test_hydroshare_to_submission(hydroshare):
 
 async def test_zenodo_to_submission(zenodo):
     zenodo_record = ZenodoRecord(**zenodo)
+    zenodo_record.publication_date = None
     zenodo_submission = zenodo_record.to_submission("947940")
 
     assert zenodo_submission.title == zenodo_record.title
@@ -34,6 +35,18 @@ async def test_zenodo_to_submission(zenodo):
     assert zenodo_submission.url == get_settings().zenodo_view_url % zenodo_record.record_id
 
 
+async def test_zenodo_published_to_submission(zenodo):
+    zenodo_record = ZenodoRecord(**zenodo)
+    zenodo_submission = zenodo_record.to_submission("947940")
+
+    assert zenodo_submission.title == zenodo_record.title
+    assert zenodo_submission.authors == [creator.name for creator in zenodo_record.creators]
+    assert zenodo_submission.repo_type == RepositoryType.ZENODO
+    assert zenodo_submission.submitted <= datetime.utcnow()
+    assert zenodo_submission.identifier == zenodo_record.record_id
+    assert zenodo_submission.url == get_settings().zenodo_public_view_url % zenodo_record.record_id
+
+
 async def test_external_to_submission(external):
     external_record = ExternalRecord(**external)
     external_submission = external_record.to_submission("947940")
@@ -71,6 +84,21 @@ async def test_external_to_jsonld(external):
 
 
 async def test_earthchem_to_submission(earthchem):
+    earthchem_record = EarthChemRecord(**earthchem)
+    earthchem_record.datePublished = None
+    earthchem_submission = earthchem_record.to_submission("947940")
+
+    assert earthchem_submission.title == earthchem_record.title
+    authors = [f"{contributor.familyName}, {contributor.givenName}" for contributor in earthchem_record.contributors]
+    authors.insert(0, f"{earthchem_record.leadAuthor.familyName}, {earthchem_record.leadAuthor.givenName}")
+    assert earthchem_submission.authors == authors
+    assert earthchem_submission.repo_type == RepositoryType.EARTHCHEM
+    assert earthchem_submission.submitted <= datetime.utcnow()
+    assert earthchem_submission.identifier == "947940"
+    assert earthchem_submission.url == get_settings().earthchem_view_url % "947940"
+
+
+async def test_earthchem_published_to_submission(earthchem):
     earthchem_record = EarthChemRecord(**earthchem)
     earthchem_submission = earthchem_record.to_submission("947940")