def get_doc_prov(j, gcis_url, refList, personList, reportList, webpageList):#organizationList, activityList):
"""Generate PROV-ES JSON from GCIS doc metadata."""
gcis_ns = "http://data.globalchange.gov/gcis.owl#"
doc = ProvEsDocument()
dataset = requests.get(j['href']).json()
datasetID = 'bibo:%s' % j['identifier']
doc_attrs = [
("prov:type", 'gcis:Dataset'),
("prov:label", j['name']),
("prov:location", "%s%s"%(gcis_url, j['uri'])),
]
doc.entity('bibo:%s' % j['identifier'], doc_attrs)
agent_ids = {}
org_ids = {}
#contributors
if 'contributors' in dataset:
for contributor in dataset['contributors']:
personID = None
if contributor['person_uri'] is not None:
name = " ".join([contributor['person'][i]
for i in ('first_name', 'middle_name', 'last_name')
if contributor['person'].get(i, None) is not None])
personAttrs = [
("prov:type", 'gcis:Person'),
("prov:label", "%s"%name),# %s"%(contributor['person']['first_name'],contributor['person']['last_name'])),
("prov:location", "%s%s"%(gcis_url,contributor['person_uri'])),
("gcis:id", str(contributor['person_id'])),
("gcis:orcid", contributor['person']['orcid'])
]
personID = 'bibo:%s'%contributor['person_id']
agent_ids[personID] = []
doc.agent(personID, personAttrs)
if contributor['organization'] is not None:
#make org
org_attrs = [
("prov:type", "gcis:organization"),
("prov:label", contributor["organization"]["name"]),
("prov:location", "%s%s"%(gcis_url, contributor["organization_uri"])),
("gcis:organization_type_identifier", contributor["organization"]["organization_type_identifier"]),
("gcis:country_code", contributor["organization"]["country_code"]),
]
orgID = 'bibo:%s'%contributor['organization']['identifier']
#doc.entity(orgID, org_attrs)
doc.governingOrganization(orgID, contributor['organization']['name'])
org_ids[orgID] = True
if personID in agent_ids:
agent_ids[personID].append(orgID)
#create actvity
if dataset['start_time'] is not None:
start_time = str(dataset['start_time'])
else:
start_time = ""
if dataset['end_time'] is not None:
end_time = str(dataset['end_time'])
else:
end_time = ""
act_id = GCIS["generate-%s"%j['identifier'].replace('/', '-')]
attrs = []
for agent_id in agent_ids:
waw_id = GCIS["%s"%get_uuid("%s:%s"%(act_id, agent_id))]
doc.wasAssociatedWith(act_id, agent_id, None, waw_id, {'prov:role':GCIS['Author']})
for org_id in agent_ids[agent_id]:
del_id = GCIS["%s"%get_uuid("%s:%s:%s"%(agent_id, org_id, act_id))]
doc.delegation(agent_id, org_id, act_id, del_id, {'prov:type':'gcis:worksAt'})
for org_id in org_ids:
waw_id = GCIS["%s"%get_uuid("%s:%s"%(act_id, org_id))]
doc.wasAssociatedWith(act_id, org_id, None, waw_id, {'prov:role':GCIS['Contributor']})
act = doc.activity(act_id, start_time, end_time, attrs)
doc.wasGeneratedBy(datasetID, act, end_time, GCIS["%s"%get_uuid("%s:%s"%(datasetID, act_id))])
#aliases
#instrument measurements
"""
role_ids = {}
agent_ids = {}
org_ids = {}
personID = None
#contributors
if 'contributors' in dataset:
for contributor in dataset['contributors']:
if contributor['person_uri'] is not None:
name = " ".join([contributor['person'][i]
for i in ('first_name', 'middle_name', 'last_name')
if contributor['person'].get(i, None) is not None])
personAttrs = [
("prov:type", 'gcis:Person'),
("prov:label", "%s"%name),# %s"%(contributor['person']['first_name'],contributor['person']['last_name'])),
("prov:location", "%s%s"%(gcis_url,contributor['person_uri'])),
("gcis:id", str(contributor['person_id'])),
("gcis:orcid", contributor['person']['orcid'])
]
personID = 'bibo:%s'%contributor['person_id']
role_ids[personID] = contributor['role_type_identifier']
doc.agent(personID, personAttrs)
agent_ids[personID] = []
#doc.wasAssociatedWith(datasetID, personID, None, None,{"prov:role": contributor['role_type_identifier']} )
if contributor['organization'] is not None:
org_attrs = [
("prov:type", "gcis:organization"),
("prov:label", contributor["organization"]["name"]),
("prov:location", "%s%s"%(gcis_url, contributor["organization_uri"])),
("gcis:organization_type_identifier", contributor["organization"]["organization_type_identifier"]),
("gcis:country_code", contributor["organization"]["country_code"]),
]
orgID = 'bibo:%s'%contributor['organization']['identifier']
doc.agent(orgID, org_attrs)
doc.governingOrganization(orgID, contributor['organization']['name'])
if personID in agent_ids:
agent_ids[personID].append(orgID)
if dataset['start_time'] is not None:
start_time = str(dataset['start_time'])
else:
start_time = ""
if dataset['end_time'] is not None:
end_time = str(dataset['end_time'])
else:
end_time = ""
# print j['identifier']
#else:
# start_time = None
# end_time = None
act_id = GCIS["generate-%s"%j['identifier'].replace('/', '-')]
attrs = []
for agent_id in agent_ids:
waw_id = GCIS["%s"%get_uuid("%s:%s"%(act_id, agent_id))]
doc.wasAssociatedWith(act_id, agent_id, None, waw_id, {'prov:role': GCIS[role_ids[agent_id]] })
for org_id in agent_ids[agent_id]:
del_id = GCIS["%s"%get_uuid("%s:%s:%s"%(agent_id, org_id, act_id))]
doc.delegation(agent_id, org_id, act_id, del_id, {'prov:type':'gcis:worksAt'})
for org_id in org_ids:
waw_id = GCIS["%s"%get_uuid("%s:%s"%(act_id, org_id))]
doc.wasAssociatedWith(act_id, org_id, None, waw_id, {'prov:role':GCIS['Contributor']})
act = doc.activity(act_id, start_time, end_time, attrs)
doc.wasGeneratedBy(datasetID, act, end_time, GCIS["%s"%get_uuid("%s:%s"%(datasetID, act_id))])
"""
#cited by
if 'cited_by' in dataset:
for citation in dataset['cited_by']:
if 'publication' in citation:
#pub_uri = "%s%s"%(gcis_url, citation['publication'])
itemType = citation['publication'].split("/")[1]
itemList = get_itemList(dump_dir, itemType)
if any(item['uri'] == citation['publication'] for item in itemList):
item = next(obj for obj in itemList if obj['uri'] == citation['publication'])
item_id = 'bibo:%s'%item['identifier']
doc.wasDerivedFrom(item_id, datasetID)
prov_json = json.loads(doc.serialize())
return prov_json
def get_doc_prov(j, gcis_url, refList, journalList, organizationList, personList, dump_dir):
"""Generate PROV-ES JSON from GCIS doc metadata."""
gcis_ns = "https://gcis-search-stage.jpl.net:3000/gcis.owl#"
doc = ProvEsDocument()
bndl = None
article = requests.get(j['href']).json()
journalID = None
#make journal
if any(journal['identifier'] == article['journal_identifier'] for journal in journalList):
journal = next(jour for jour in journalList if jour['identifier'] == article['journal_identifier'])
journalAttrs = [
("prov:type", 'gcis:Journal'),
("prov:label", journal['title']),
("prov:location", "%s%s"%(gcis_url,journal['uri'])),
("gcis:online_issn", journal['online_issn']),
("gcis:print_issn", journal['print_issn']),
("gcis:publisher", journal['publisher']),
]
journalID = 'bibo:%s'%journal['identifier']
doc.entity(journalID, journalAttrs)
#get organization/publisher if any
if journal['publisher'] is not None:
if any(organization['name'] == journal['publisher'] for organization in organizationList):
organization = next(org for org in organizationList if org['name'] == journal['publisher'])
org_attrs = [
("prov:type", 'gcis:organization'),
("prov:label", organization['name']),
("prov:location", "%s%s"%(gcis_url,organization['uri'])),
("gcis:organization_type_identifier", organization['organization_type_identifier']),
("gcis:country_code", organization['country_code']),
]
org_id = 'bibo:%s'%organization['identifier']
doc.entity(org_id, org_attrs)
doc.governingOrganization(org_id, organization['name'])
#make article
articleAttrs = [
("prov:type", 'gcis:Article'),
("prov:label", article['title']),
("prov:location","%s%s"%(gcis_url, article['uri'])),
("dcterms:isPartOf", journalID),
]
articleID = 'bibo:%s'%article['identifier']
doc.entity(articleID, articleAttrs)
#link journal to article
if journalID is not None:
doc.hadMember(journalID, articleID)
agent_ids = {}
org_ids = {}
#contributors
if 'contributors' in article:
for contributor in article['contributors']:
personID = None
if contributor['person_uri'] is not None:
name = " ".join([contributor['person'][i]
for i in ('first_name', 'middle_name', 'last_name')
if contributor['person'].get(i, None) is not None])
personAttrs = [
("prov:type", 'gcis:Person'),
("prov:label", "%s"%name),# %s"%(contributor['person']['first_name'],contributor['person']['last_name'])),
("prov:location", "%s%s"%(gcis_url,contributor['person_uri'])),
("gcis:id", str(contributor['person_id'])),
("gcis:orcid", contributor['person']['orcid'])
]
personID = 'bibo:%s'%contributor['person_id']
agent_ids[personID] = []
doc.agent(personID, personAttrs)
if contributor['organization'] is not None:
#make org
org_attrs = [
("prov:type", "gcis:organization"),
("prov:label", contributor["organization"]["name"]),
("prov:location", "%s%s"%(gcis_url, contributor["organization_uri"])),
("gcis:organization_type_identifier", contributor["organization"]["organization_type_identifier"]),
("gcis:country_code", contributor["organization"]["country_code"]),
]
orgID = 'bibo:%s'%contributor['organization']['identifier']
#doc.entity(orgID, org_attrs)
doc.governingOrganization(orgID, contributor['organization']['name'])
org_ids[orgID] = True
if personID in agent_ids:
agent_ids[personID].append(orgID)
#create actvity
if isinstance(j['year'], int):
start_time = str(j['year'])
end_time = str(j['year'])
else:
start_time = None
end_time = None
act_id = GCIS["generate-%s"%j['identifier'].replace('/', '-')]
attrs = []
for agent_id in agent_ids:
waw_id = GCIS["%s"%get_uuid("%s:%s"%(act_id, agent_id))]
doc.wasAssociatedWith(act_id, agent_id, None, waw_id, {'prov:role':GCIS['Author']})
for org_id in agent_ids[agent_id]:
del_id = GCIS["%s"%get_uuid("%s:%s:%s"%(agent_id, org_id, act_id))]
doc.delegation(agent_id, org_id, act_id, del_id, {'prov:type':'gcis:worksAt'})
for org_id in org_ids:
waw_id = GCIS["%s"%get_uuid("%s:%s"%(act_id, org_id))]
doc.wasAssociatedWith(act_id, org_id, None, waw_id, {'prov:role':GCIS['Contributor']})
act = doc.activity(act_id, start_time, end_time, attrs)
doc.wasGeneratedBy(articleID, act, end_time, GCIS["%s"%get_uuid("%s:%s"%(articleID, act_id))])
#cited by?
if 'cited_by' in article:
for citation in article['cited_by']:
if 'publication' in citation:
#pub_uri = "%s%s"%(gcis_url, citation['publication'])
itemType = citation['publication'].split("/")[1]
itemList = get_itemList(dump_dir, itemType)
if any(item['uri'] == citation['publication'] for item in itemList):
item = next(obj for obj in itemList if obj['uri'] == citation['publication'])
item_id = 'bibo:%s'%item['identifier']
doc.wasDerivedFrom(item_id, articleID)
print articleID
prov_json = json.loads(doc.serialize())
return prov_json
