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Update related ids upon dataSet change. Fixes #402 #403

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merged 1 commit into from Mar 6, 2020
Merged

Update related ids upon dataSet change. Fixes #402 #403

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37 changes: 22 additions & 15 deletions server/lib/__init__.py
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Expand Up @@ -48,7 +48,7 @@ def pids_to_entities(pids, user=None, base_url=None, lookup=True):
try:
for pid in pids:
entity = Entity(pid.strip(), user)
entity['base_url'] = base_url
entity["base_url"] = base_url
entity = RESOLVERS.resolve(entity)
provider = IMPORT_PROVIDERS.getProvider(entity)
if lookup:
Expand Down Expand Up @@ -80,30 +80,30 @@ def register_dataMap(dataMaps, parent, parentType, user=None, base_url=None):
"""
progress = True
importedData = []
with ProgressContext(progress, user=user, title='Registering resources') as ctx:
with ProgressContext(progress, user=user, title="Registering resources") as ctx:
for dataMap in DataMap.fromList(dataMaps):
# probably would be nicer if Entity kept all details and the dataMap
# would be merged into it
provider = IMPORT_PROVIDERS.getFromDataMap(dataMap)
objType, obj = provider.register(
parent, parentType, ctx, user, dataMap, base_url=base_url
)
importedData.append(obj['_id'])
importedData.append(obj["_id"])
return importedData


def update_citation(event):
tale = event.info['tale']
user = event.info['user']
tale = event.info["tale"]
user = event.info["user"]

dataset_top_identifiers = set()
for obj in tale.get('dataSet', []):
for obj in tale.get("dataSet", []):
try:
doc = ModelImporter.model(obj['_modelType']).load(
obj['itemId'], user=user, level=AccessType.READ, exc=True
doc = ModelImporter.model(obj["_modelType"]).load(
obj["itemId"], user=user, level=AccessType.READ, exc=True
)
provider_name = doc['meta']['provider']
if provider_name.startswith('HTTP'):
provider_name = doc["meta"]["provider"]
if provider_name.startswith("HTTP"):
continue
provider = IMPORT_PROVIDERS.providerMap[provider_name]
except (KeyError, ValidationException):
Expand All @@ -113,22 +113,29 @@ def update_citation(event):
dataset_top_identifiers.add(top_identifier)

citations = []
related_ids = [
related_id
for related_id in tale["relatedIdentifiers"]
if related_id["relation"] != "Cites"
]
for doi in dataset_top_identifiers:
if doi.startswith('doi:'):
related_ids.append(dict(identifier=doi, relation="Cites"))
if doi.startswith("doi:"):
doi = doi[4:]
try:
url = (
'https://api.datacite.org/dois/'
'text/x-bibliography/{}?style=harvard-cite-them-right'
"https://api.datacite.org/dois/"
"text/x-bibliography/{}?style=harvard-cite-them-right"
)
citations.append(
html2markdown.convert(urlopen(url.format(doi)).read().decode())
)
except Exception as ex:
logger.info('Unable to get a citation for %s, getting "%s"', doi, str(ex))

tale['dataSetCitation'] = citations
tale["dataSetCitation"] = citations
tale["relatedIdentifiers"] = related_ids
event.preventDefault().addResponse(tale)


events.bind('tale.update_citation', 'wholetale', update_citation)
events.bind("tale.update_citation", "wholetale", update_citation)