251 full provenance info to metadata

src/lib/datacite_doi_helper.py

@@ -7,7 +7,7 @@
 import logging
 from flask import Flask
 from api.datacite_api import DataCiteApi
-from hubmap_sdk import EntitySdk
+from hubmap_sdk import Entity, EntitySdk
 from hubmap_commons.exceptions import HTTPException
 import ast
 
@@ -120,7 +120,6 @@ def build_doi_creators(self, dataset: object) -> list:
 
         return creators
 
-
     """
     Register a draft DOI with DataCite
 
@@ -181,21 +180,28 @@ def create_dataset_draft_doi(self, dataset: dict, check_publication_status=True)
             raise KeyError('Either the entity_type of the given Dataset is missing or the entity is not a Dataset')
 
     """
-    Move the DOI state from draft to findable, meaning publish this dataset 
-    
+    Move the DOI state from draft to findable (publish) in DataCite
+
     Parameters
     ----------
     dataset: dict
         The dataset dict to be published
     user_token: str
         The user's globus nexus token
-    
+
     Returns
     -------
     dict
-        The published datset entity dict with updated DOI properties
+        The updated DOI properties
+
+    Raises
+    ------
+    requests.exceptions.RequestException
+        If the request to entity-api fails
+    KeyError
+        If the entity_type of the given Dataset is missing or the entity is not a Dataset
     """
-    def move_doi_state_from_draft_to_findable(self, dataset: dict, user_token: str) -> object:
+    def move_doi_state_from_draft_to_findable(self, dataset: dict, user_token: str) -> dict:
         if ('entity_type' in dataset) and (dataset['entity_type'] == 'Dataset'):
             datacite_api = DataCiteApi(self.datacite_repository_id, self.datacite_repository_password,
                                        self.datacite_hubmap_prefix, self.datacite_api_url, self.entity_api_url)
@@ -207,19 +213,16 @@ def move_doi_state_from_draft_to_findable(self, dataset: dict, user_token: str)
                 logger.debug("======resulting json from DataCite======")
                 logger.debug(doi_data)
 
-                # Then update the dataset DOI properties via entity-api after the DOI gets published
-                try:
-                    doi_name = datacite_api.build_doi_name(dataset['sennet_id'])
-                    entity_api = EntitySdk(user_token, self.entity_api_url)
-                    updated_dataset = self.update_dataset_after_doi_published(dataset['uuid'], doi_name, entity_api)
-
-                    return updated_dataset
-                except requests.exceptions.RequestException as e:
-                    raise requests.exceptions.RequestException(e)
+                doi_name = datacite_api.build_doi_name(dataset['sennet_id'])
+                doi_info = {
+                    'registered_doi': doi_name,
+                    'doi_url': f'https://doi.org/{doi_name}'
+                }
+                return doi_info
             else:
                 # Log the full stack trace, prepend a line with our message
                 logger.exception(f"Unable to publish DOI for dataset {dataset['uuid']} via DataCite")
-                logger.debug(f'======Status code from DataCite {response.status_code} ======')
+                logger.debug(f'======Status code from DataCite {response.status_code}======')
                 logger.debug("======response text from DataCite======")
                 logger.debug(response.text)
 
@@ -229,8 +232,8 @@ def move_doi_state_from_draft_to_findable(self, dataset: dict, user_token: str)
             raise KeyError('Either the entity_type of the given Dataset is missing or the entity is not a Dataset')
 
     """
-    Update the dataset's properties after DOI is published (Draft -> Findable) 
-    
+    Update the dataset's properties in Entity-API after DOI is published (Draft -> Findable)
+
     Parameters
     ----------
     dataset_uuid: str
@@ -239,35 +242,32 @@ def move_doi_state_from_draft_to_findable(self, dataset: dict, user_token: str)
         The registered doi: prefix/suffix
     entity_api
         The EntitySdk object instance
-    
+
     Returns
     -------
-    dict
-        The entity dict with updated DOI properties
-    """
-    def update_dataset_after_doi_published(self, dataset_uuid: str, doi_name: str, entity_api: EntitySdk) -> object:
+    hubmap_sdk.Entity
+        The updated dataset entity
 
+    Raises
+    ------
+    requests.exceptions.RequestException
+        If the request to entity-api fails
+    """
+    def update_dataset_after_doi_published(self, dataset_uuid: dict, doi_info: str, entity_api: EntitySdk) -> Entity:
         # Update the registered_doi, and doi_url properties after DOI made findable
         # Changing Dataset.status to "Published" and setting the published_* properties
         # are handled by another script
         # See https://github.com/hubmapconsortium/ingest-ui/issues/354
-        dataset_properties_to_update = {
-            'registered_doi': doi_name,
-            'doi_url': f'https://doi.org/{doi_name}'
-        }
-
         try:
-            entity = entity_api.update_entity(dataset_uuid, dataset_properties_to_update)
+            # Entity update via PUT call only returns a json message, no entity details
+            result = entity_api.update_entity(dataset_uuid, doi_info)
             logger.info("======The dataset {dataset['uuid']}  has been updated with DOI info======")
-            updated_entity = vars(entity)
-            logger.debug("======updated_entity======")
-            logger.debug(updated_entity)
-            return updated_entity
-
+            logger.info(doi_info)
+            return result
         except HTTPException as e:
             # Log the full stack trace, prepend a line with our message
             logger.exception(f"Unable to update the DOI properties of dataset {dataset_uuid}")
-            logger.debug(f'======Status code from DataCite {e.status_code} ======')
+            logger.debug(f'======Status code from DataCite {e.status_code}======')
             logger.debug("======response text from entity-api======")
             logger.debug(e.description)
 
@@ -283,7 +283,7 @@ def update_dataset_after_doi_published(self, dataset_uuid: str, doi_name: str, e
 
     try:
         user_token = sys.argv[1]
-    except IndexError as e:
+    except IndexError:
         msg = "Missing user token argument"
         # Log the full stack trace, prepend a line with our message
         logger.exception(msg)
@@ -295,7 +295,7 @@ def update_dataset_after_doi_published(self, dataset_uuid: str, doi_name: str, e
 
     count = 1
     for dataset_uuid in datasets:
-        logger.debug(f"Begin {count}: ========================= {dataset_uuid} =========================")
+        logger.debug(f"Begin {count}: ========================={dataset_uuid}=========================")
         try:
             entity = entity_api.get_entity_by_id(dataset_uuid)
             dataset = vars(entity)
@@ -306,7 +306,7 @@ def update_dataset_after_doi_published(self, dataset_uuid: str, doi_name: str, e
                 logger.debug("Create Draft DOI")
 
                 # DISABLED
-                #data_cite_doi_helper.create_dataset_draft_doi(dataset)
+                # data_cite_doi_helper.create_dataset_draft_doi(dataset)
             except Exception as e:
                 logger.exception(e)
                 sys.exit(e)
@@ -316,7 +316,7 @@ def update_dataset_after_doi_published(self, dataset_uuid: str, doi_name: str, e
 
                 # DISABLED
                 # To publish an existing draft DOI (change the state from draft to findable)
-                #data_cite_doi_helper.move_doi_state_from_draft_to_findable(dataset, user_token)
+                # data_cite_doi_helper.move_doi_state_from_draft_to_findable(dataset, user_token)
             except Exception as e:
                 logger.exception(e)
                 sys.exit(e)
@@ -330,8 +330,8 @@ def update_dataset_after_doi_published(self, dataset_uuid: str, doi_name: str, e
             logger.debug("======response text from entity-api======")
             logger.debug(e.description)
 
-        logger.debug(f"End {count}: ========================= {dataset_uuid} =========================")
+        logger.debug(f"End {count}: ========================={dataset_uuid}=========================")
 
         time.sleep(1)
 
-        count = count + 1
+        count = count + 1

src/lib/services.py

@@ -1,5 +1,6 @@
-from typing import Optional, Union
+from typing import List, Optional, Union
 
+import requests
 from flask import current_app
 from hubmap_sdk import Entity, EntitySdk, SearchSdk
 from hubmap_sdk.sdk_helper import HTTPException as SDKException
@@ -90,3 +91,44 @@ def get_entity_from_search_api(
 
     except SDKException:
         raise
+
+
+def get_associated_sources_from_dataset(
+    dataset_id: str, token: str, as_dict: bool = False
+) -> Union[List[Entity], dict]:
+    """Get the associated sources for the given dataset.
+
+    Parameters
+    ----------
+    dataset_id : str
+        The uuid of the dataset.
+    token : str
+        The groups token for the request.
+    as_dict : bool, optional
+        Should entity be returned as a dictionary, by default False
+
+    Returns
+    -------
+    Union[List[Entity], dict]
+        The associated sources for the given dataset.
+
+    Raises
+    ------
+    hubmap_sdk.sdk_helper.HTTPException
+        If the entiti-api request fails or entity not found
+    """
+    entity_api_url = current_app.config["ENTITY_WEBSERVICE_URL"]
+    url = f"{entity_api_url}/datasets/{dataset_id}/sources"
+    headers = {"Authorization": f"Bearer {token}"}
+    res = requests.get(url, headers=headers)
+    if not res.ok:
+        raise SDKException(f"Failed to get associated source for dataset {dataset_id}")
+    body = res.json()
+
+    if as_dict:
+        return body
+
+    if isinstance(body, list):
+        return [Entity(entity) for entity in res.json()]
+
+    return [Entity(body)]

src/requirements.txt

@@ -1,6 +1,6 @@
 Flask==2.1.3
 globus_sdk==2.0.1
-hubmap-sdk==1.0.4
+hubmap-sdk==1.0.7
 Werkzeug==2.3.7
 
 # For interacting with memcached