[#38] merge branch 'develop' of https://github.com/I-GUIDE/catalogapi …

…into 38-update-to-pydantic-v2
I-GUIDE · Sep 12, 2023 · d997914 · d997914
2 parents 00be384 + e2daeca
commit d997914
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Showing 31 changed files with 8,339 additions and 343 deletions.
diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
@@ -52,8 +52,9 @@ jobs:
         VUE_APP_URL: ${{ secrets.VUE_APP_URL }}
         VUE_APP_LOGIN_URL: ${{ secrets.VUE_APP_LOGIN_URL }}
         VUE_APP_CLIENT_ID: ${{ secrets.VUE_APP_CLIENT_ID }}
+        VUE_APP_GOOGLE_MAPS_API_KEY: ${{ secrets.VUE_APP_GOOGLE_MAPS_API_KEY }}
       run: |
-        variables=("VUE_APP_NAME" "VUE_APP_API_URL" "VUE_APP_SUPPORT_EMAIL" "VUE_APP_URL" "VUE_APP_LOGIN_URL" "VUE_APP_CLIENT_ID")
+        variables=("VUE_APP_NAME" "VUE_APP_API_URL" "VUE_APP_SUPPORT_EMAIL" "VUE_APP_URL" "VUE_APP_LOGIN_URL" "VUE_APP_CLIENT_ID" "VUE_APP_GOOGLE_MAPS_API_KEY")
 
         # Empty the .env file
         > frontend/.env

diff --git a/api/adapters/__init__.py b/api/adapters/__init__.py
@@ -0,0 +1,2 @@
+# import all adapters here to get them registered
+from api.adapters import hydroshare
diff --git a/api/adapters/hydroshare.py b/api/adapters/hydroshare.py
@@ -1,10 +1,11 @@
 import requests
-from starlette import status
+# from starlette import status
 from datetime import datetime
 from typing import List, Optional, Union
 from pydantic import BaseModel, EmailStr, HttpUrl
+
 from api.adapters.base import AbstractRepositoryMetadataAdapter, AbstractRepositoryRequestHandler
-from api.adapters.utils import RepositoryType
+from api.adapters.utils import RepositoryType, register_adapter
 from api.exceptions import RepositoryException
 from api.models import schema
 from api.models.catalog import DatasetMetadataDOC
@@ -169,7 +170,7 @@ def get_metadata(self, record_id: str):
 
         def make_request(url, file_list=False) -> Union[dict, List[dict]]:
             response = requests.get(url)
-            if response.status_code != status.HTTP_200_OK:
+            if response.status_code != 200:
                 raise RepositoryException(status_code=response.status_code, detail=response.text)
             if not file_list:
                 return response.json()
@@ -179,7 +180,7 @@ def make_request(url, file_list=False) -> Union[dict, List[dict]]:
             # check if there are more results to fetch - by default, 100 files are returned from HydroShare
             while response.json()["next"]:
                 response = requests.get(response.json()["next"])
-                if response.status_code != status.HTTP_200_OK:
+                if response.status_code != 200:
                     raise RepositoryException(status_code=response.status_code, detail=response.text)
                 content_files.extend(response.json()["results"])
             return content_files
@@ -213,6 +214,9 @@ def update_submission(submission: Submission, repo_record_id: str) -> Submission
         return submission
 
 
+register_adapter(RepositoryType.HYDROSHARE, HydroshareMetadataAdapter)
+
+
 class _HydroshareResourceMetadata(BaseModel):
     title: str
     abstract: str

diff --git a/api/adapters/utils.py b/api/adapters/utils.py
@@ -1,5 +1,22 @@
 from enum import Enum
+from typing import Type, Union
+
+from api.adapters.base import AbstractRepositoryMetadataAdapter
 
 
 class RepositoryType(str, Enum):
     HYDROSHARE = 'HYDROSHARE'
+
+
+_adapter_registry = {}
+
+
+def register_adapter(repository_type: RepositoryType, adapter_class: Type[AbstractRepositoryMetadataAdapter]) -> None:
+    _adapter_registry[repository_type] = adapter_class
+
+
+def get_adapter_by_type(repository_type: RepositoryType) -> Union[AbstractRepositoryMetadataAdapter, None]:
+    adapter_cls = _adapter_registry.get(repository_type, None)
+    if adapter_cls:
+        return adapter_cls()
+    return None
diff --git a/api/exceptions.py b/api/exceptions.py
@@ -1,7 +1,4 @@
-from fastapi import HTTPException
-
-
-class RepositoryException(HTTPException):
+class RepositoryException(Exception):
     def __init__(self, status_code: int, detail: str):
         self._status_code = status_code
         self._detail = detail

diff --git a/api/models/catalog.py b/api/models/catalog.py
@@ -1,4 +1,5 @@
 import datetime
+from typing import Optional
 
 from beanie import Document
 
@@ -37,4 +38,4 @@ def delete_revision_id(self):
 
 
 class DatasetMetadataDOC(CoreMetadataDOC):
-    repository_identifier: str = None
+    repository_identifier: Optional[str] = None
diff --git a/api/models/management/change_streams_pre_and_post.py b/api/models/management/change_streams_pre_and_post.py
@@ -0,0 +1,20 @@
+import asyncio
+from api.config import get_settings
+from api.models.catalog import DatasetMetadataDOC
+
+from beanie import init_beanie
+from motor.motor_asyncio import AsyncIOMotorClient
+
+
+async def main():
+    db = AsyncIOMotorClient(get_settings().db_connection_string)
+    await init_beanie(database=db[get_settings().database_name], document_models=[DatasetMetadataDOC])
+    # https://www.mongodb.com/docs/manual/reference/command/collMod/#change-streams-with-document-pre--and-post-images
+    # This enables us to get the record id of a deleted submission within a trigger.  We need this for removing
+    # discovery records when a submission is deleted
+    await db[get_settings().database_name].command(
+        ({'collMod': DatasetMetadataDOC.get_collection_name(), "changeStreamPreAndPostImages": {'enabled': True}}))
+    db.close()
+
+if __name__ == "__main__":
+    asyncio.run(main())
diff --git a/api/models/schemas/schema.json b/api/models/schemas/schema.json
@@ -183,7 +183,7 @@
           "title": "@Type"
         },
         "name": {
-          "description": "Name of the organization.",
+          "description": "Name of the provider organization or repository.",
           "title": "Name",
           "type": "string"
         },
@@ -219,7 +219,7 @@
         "name"
       ],
       "title": "Funding Organization",
-      "type": "string"
+      "type": "object"
     },
     "GeoCoordinates": {
       "properties": {
@@ -314,7 +314,7 @@
                   "title": "@Type"
                 },
                 "name": {
-                  "description": "Name of the organization.",
+                  "description": "Name of the provider organization or repository.",
                   "title": "Name",
                   "type": "string"
                 },
@@ -350,7 +350,7 @@
                 "name"
               ],
               "title": "Funding Organization",
-              "type": "string"
+              "type": "object"
             },
             {
               "type": "null"
@@ -483,6 +483,7 @@
       "type": "object"
     },
     "LanguageEnum": {
+      "description": "",
       "enum": [
         "eng",
         "esp"
@@ -970,9 +971,6 @@
             }
           ],
           "description": "A date/time object containing the instant corresponding to the termination of the time interval (ISO8601 formatted date - YYYY-MM-DDTHH:MM). If the ending date is left off, that means the temporal coverage is ongoing.",
-          "formatMinimum": {
-            "$data": "1/startDate"
-          },
           "title": "End date"
         }
       },
@@ -1032,6 +1030,7 @@
       "anyOf": [
         {
           "items": {
+            "title": "Identifier",
             "type": "string"
           },
           "type": "array"
@@ -1567,6 +1566,7 @@
     "inLanguage": {
       "anyOf": [
         {
+          "description": "",
           "enum": [
             "eng",
             "esp"
@@ -1750,7 +1750,7 @@
                         "title": "@Type"
                       },
                       "name": {
-                        "description": "Name of the organization.",
+                        "description": "Name of the provider organization or repository.",
                         "title": "Name",
                         "type": "string"
                       },
@@ -1786,7 +1786,7 @@
                       "name"
                     ],
                     "title": "Funding Organization",
-                    "type": "string"
+                    "type": "object"
                   },
                   {
                     "type": "null"
@@ -1831,9 +1831,6 @@
                 }
               ],
               "description": "A date/time object containing the instant corresponding to the termination of the time interval (ISO8601 formatted date - YYYY-MM-DDTHH:MM). If the ending date is left off, that means the temporal coverage is ongoing.",
-              "formatMinimum": {
-                "$data": "1/startDate"
-              },
               "title": "End date"
             }
           },

diff --git a/api/models/schemas/ui-schema.json b/api/models/schemas/ui-schema.json
@@ -449,28 +449,22 @@
                         "options": {
                           "map": {
                             "type": "box",
-                            "northlimit": "northlimit",
-                            "eastlimit": "eastlimit",
-                            "southlimit": "southlimit",
-                            "westlimit": "westlimit"
+                            "format": "GeoShape",
+                            "box": "box"
                           }
                         },
                         "elements": [
                           {
                             "type": "Control",
-                            "scope": "#/properties/northlimit"
-                          },
-                          {
-                            "type": "Control",
-                            "scope": "#/properties/eastlimit"
-                          },
-                          {
-                            "type": "Control",
-                            "scope": "#/properties/southlimit"
+                            "scope": "#/properties/@type",
+                            "rule": {
+                              "effect": "HIDE",
+                              "condition": {}
+                            }
                           },
                           {
                             "type": "Control",
-                            "scope": "#/properties/westlimit"
+                            "scope": "#/properties/box"
                           }
                         ]
                       }
@@ -792,67 +786,35 @@
               "scope": "#/properties/funder",
               "options": {
                 "detail": {
-                  "0": {
-                    "type": "VerticalLayout",
-                    "elements": [
-                      {
-                        "type": "Control",
-                        "scope": "#/properties/@type",
-                        "rule": {
-                          "effect": "HIDE",
-                          "condition": {}
-                        }
-                      },
-                      {
-                        "type": "Control",
-                        "scope": "#/properties/name"
-                      },
-                      {
-                        "type": "HorizontalLayout",
-                        "elements": [
-                          {
-                            "type": "Control",
-                            "scope": "#/properties/email"
-                          },
-                          {
-                            "type": "Control",
-                            "scope": "#/properties/identifier"
-                          }
-                        ]
+                  "label": "Organization",
+                  "type": "VerticalLayout",
+                  "elements": [
+                    {
+                      "type": "Control",
+                      "scope": "#/properties/@type",
+                      "rule": {
+                        "effect": "HIDE",
+                        "condition": {}
                       }
-                    ]
-                  },
-                  "1": {
-                    "label": "Organization",
-                    "type": "VerticalLayout",
-                    "elements": [
-                      {
-                        "type": "Control",
-                        "scope": "#/properties/@type",
-                        "rule": {
-                          "effect": "HIDE",
-                          "condition": {}
+                    },
+                    {
+                      "type": "HorizontalLayout",
+                      "elements": [
+                        {
+                          "type": "Control",
+                          "scope": "#/properties/name"
+                        },
+                        {
+                          "type": "Control",
+                          "scope": "#/properties/url"
                         }
-                      },
-                      {
-                        "type": "HorizontalLayout",
-                        "elements": [
-                          {
-                            "type": "Control",
-                            "scope": "#/properties/name"
-                          },
-                          {
-                            "type": "Control",
-                            "scope": "#/properties/url"
-                          }
-                        ]
-                      },
-                      {
-                        "type": "Control",
-                        "scope": "#/properties/address"
-                      }
-                    ]
-                  }
+                      ]
+                    },
+                    {
+                      "type": "Control",
+                      "scope": "#/properties/address"
+                    }
+                  ]
                 }
               }
             }

diff --git a/api/models/user.py b/api/models/user.py
@@ -1,10 +1,12 @@
 from datetime import datetime
-from typing import List, Optional
+from typing import List, Optional, TYPE_CHECKING
 
 from beanie import Document, Link, PydanticObjectId
 from pydantic import HttpUrl, model_validator
 
-from api.adapters.utils import RepositoryType
+if TYPE_CHECKING:
+    # this avoids circular imports
+    from api.adapters.utils import RepositoryType
 
 
 class Submission(Document):
@@ -31,7 +33,7 @@ class User(Document):
     def submission(self, identifier: PydanticObjectId) -> Submission:
         return next(filter(lambda submission: submission.identifier == identifier, self.submissions), None)
 
-    def submission_by_repository(self, repo_type: RepositoryType, identifier: str) -> Submission:
+    def submission_by_repository(self, repo_type: 'RepositoryType', identifier: str) -> Submission:
         return next(
             filter(
                 lambda submission: submission.repository_identifier == identifier