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Updating doi publishing function to match hubmap
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@tjmadonna
tjmadonna committed Feb 14, 2024
1 parent 02b754d commit dcc86f3
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84 changes: 42 additions & 42 deletions src/lib/datacite_doi_helper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -120,7 +120,6 @@ def build_doi_creators(self, dataset: object) -> list:

return creators


"""
Register a draft DOI with DataCite
Expand Down Expand Up @@ -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)
Expand All @@ -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['hubmap_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)

Expand All @@ -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
Expand All @@ -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)

Expand All @@ -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)
Expand All @@ -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)
Expand All @@ -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)
Expand All @@ -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)
Expand All @@ -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
18 changes: 8 additions & 10 deletions src/routes/entity_CRUD/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -879,27 +879,25 @@ def publish_datastage(identifier):
try:
datacite_doi_helper.create_dataset_draft_doi(entity_dict, check_publication_status=False)
except Exception as e:
return jsonify({"error": f"Error occurred while trying to create a draft doi for{dataset_uuid}. {e}"}), 500
logger.exception(f"Exception while creating a draft doi for {dataset_uuid}: {e}")
return jsonify({"error": f"Error occurred while trying to create a draft doi for {dataset_uuid}. {e}"}), 500

# This will make the draft DOI created above 'findable'....
try:
doi_info = datacite_doi_helper.move_doi_state_from_draft_to_findable(entity_dict, auth_tokens)
except Exception as e:
return jsonify({"error": f"Error occurred while trying to change doi draft state to findable doi for{dataset_uuid}. {e}"}), 500
logger.exception(f"Exception while creating making doi findable and saving to entity for {dataset_uuid}: {e}")
return jsonify({"error": f"Error occurred while trying to change doi draft state to findable doi for {dataset_uuid}. {e}"}), 500

doi_update_clause = ""
if doi_info is not None:
doi_update_clause = f", e.registered_doi = '{doi_info['registered_doi']}', e.doi_url = '{doi_info['doi_url']}'"

# set up a status_history list to add a "Published" entry to below
if 'status_history' in rval[0]:
status_history_str = rval[0]['status_history']
if status_history_str is None:
status_history_list = []
else:
status_history_list = string_helper.convert_str_literal(status_history_str)
else:
status_history_list = []
status_history_list = []
status_history_str = rval[0].get('status_history')
if status_history_str is not None:
status_history_list = string_helper.convert_str_literal(status_history_str)

# add Published status change to status history
status_update = {
Expand Down

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