def get_context_data(self, **kwargs):
"""
Update context data to add publication.
"""
context = super(DataDepotPublishedView, self).get_context_data(**kwargs)
logger.info('Get context Data')
pub = BaseESPublication(project_id=kwargs['project_id'].strip('/'))
logger.debug('pub: %s', pub.to_dict())
context['projectId'] = pub.projectId
context['citation_title'] = pub.project.value.title
context['citation_date'] = pub.created
if pub.project.value.to_dict().get('dois') != None: #This is for newer publications
context['doi'] = pub.project.value.dois[0]
elif pub.project.to_dict().get('doi') != None: #This is for older publications
context['doi'] = pub.project.doi
context['keywords'] = pub.project.value.keywords.split(',')
if 'users' in pub.to_dict():
context['authors'] = [{
'full_name': '{last_name}, {first_name}'.format(
last_name=user['last_name'], first_name=user['first_name']
),
'institution': getattr(getattr(user, 'profile', ''), 'institution', '')
} for user in getattr(pub, 'users', [])]
elif 'authors' in pub.to_dict():
context['authors'] = [{
'full_name': '{last_name}, {first_name}'.format(
last_name=author['lname'], first_name=author['fname']
),
'institution': getattr(author, 'inst', '')
} for author in getattr(pub, 'authors',[])]
else:
context['authors'] = [{
'full_name': '{last_name}, {first_name}'.format(
last_name=author['lname'], first_name=author['fname']
),
'institution': getattr(author, 'inst', '')
} for author in getattr(pub.project.value, 'teamOrder', [])]
context['publication'] = pub
context['description'] = pub.project.value.description
context['experiments'] = getattr(pub, 'experimentsList', [])
context['missions'] = getattr(pub, 'missions', [])
context['reports'] = getattr(pub, 'reports', [])
context['simulations'] = getattr(pub, 'simulations', [])
context['hybrid_simulations'] = getattr(pub, 'hybrid_simulations',[])
proj = ProjectsManager(service_account()).get_project_by_id(pub.projectId)
context['dc_json'] = json.dumps(proj.to_dataset_json())
if self.request.user.is_authenticated:
context['angular_init'] = json.dumps({
'authenticated': True,
})
else:
context['angular_init'] = json.dumps({
'authenticated': False,
})
return context
def get(self, request, project_id, revision=None):
"""
Get a publication. If a revision is not supplied, return
the "Original" publication. Include the latest version if it
is not being queried.
"""
es_client = new_es_client()
pub = BaseESPublication(project_id=project_id,
revision=revision,
using=es_client)
latest_revision = IndexedPublication.max_revision(
project_id=project_id, using=es_client)
latest_pub_dict = None
if latest_revision > 0 and latest_revision != revision:
latest_pub = BaseESPublication(project_id=project_id,
revision=latest_revision,
using=es_client)
if latest_pub is not None and hasattr(latest_pub, 'project'):
latest_pub_dict = latest_pub.to_dict()
if pub is not None and hasattr(pub, 'project'):
pub_dict = pub.to_dict()
if pub_dict['project']['value']['projectType'] != 'other':
metrics.info('Data Depot',
extra={
'user':
request.user.username,
'sessionId':
getattr(request.session, 'session_key', ''),
'operation':
'listing',
'agent':
request.META.get('HTTP_USER_AGENT'),
'ip':
get_client_ip(request),
'info': {
'api': 'agave',
'systemId':
'designsafe.storage.published',
'filePath': project_id,
'query': {}
}
})
if latest_pub_dict:
pub_dict['latestRevision'] = latest_pub_dict
return JsonResponse(pub_dict)
else:
return JsonResponse({
'status': 404,
'message': 'Not found'
},
status=404)
def get_context_data(self, **kwargs):
"""Update context data to add publication."""
context = super(DataDepotPublishedView, self).get_context_data(**kwargs)
logger.info('Get context Data')
pub = BaseESPublication(project_id=kwargs['project_id'].strip('/'))
logger.debug('pub: %s', pub.to_dict())
context['projectId'] = pub.projectId
context['citation_title'] = pub.project.value.title
context['citation_date'] = pub.created
context['doi'] = pub.project.doi
context['keywords'] = pub.project.value.keywords.split(',')
context['authors'] = [{
'full_name': '{last_name}, {first_name}'.format(
last_name=user['last_name'], first_name=user['first_name']
),
'institution': getattr(getattr(user, 'profile'), 'institution', '')
} for user in getattr(pub, 'users', [])]
context['publication'] = pub
context['description'] = pub.project.value.description
if self.request.user.is_authenticated:
context['angular_init'] = json.dumps({
'authenticated': True,
})
else:
context['angular_init'] = json.dumps({
'authenticated': False,
})
return context
def freeze_project_and_entity_metadata(project_id, entity_uuids=None):
"""Freeze project and entity metadata.
Given a project id and an entity uuid (should be a main entity) this function
retrieves all metadata related to these entities and stores it into Elasticsearch
as :class:`~designafe.libs.elasticsearch.docs.publications.BaseESPublication`
:param str project_id: Project id.
:param list of entity_uuid strings: Entity uuids.
"""
mgr = ProjectsManager(service_account())
prj = mgr.get_project_by_id(project_id)
pub_doc = BaseESPublication(project_id=project_id)
publication = pub_doc.to_dict()
if entity_uuids:
# clear any existing entities in publication
entity = mgr.get_entity_by_uuid(entity_uuids[0])
pub_entities_field_name = FIELD_MAP[entity.name]
publication[pub_entities_field_name] = []
for ent_uuid in entity_uuids:
entity = None
entity = mgr.get_entity_by_uuid(ent_uuid)
entity_json = entity.to_body_dict()
if entity:
pub_entities_field_name = FIELD_MAP[entity.name]
publication['authors'] = entity_json['value']['authors'][:]
entity_json['authors'] = []
_populate_entities_in_publication(entity, publication)
_transform_authors(entity_json, publication)
if entity_json['value']['dois']:
entity_json['doi'] = entity_json['value']['dois'][-1]
_delete_unused_fields(entity_json)
publication[pub_entities_field_name].append(entity_json)
prj_json = prj.to_body_dict()
_delete_unused_fields(prj_json)
award_number = publication.get('project', {}).get('value', {}).pop(
'awardNumber', []) or []
if not isinstance(award_number, list):
award_number = []
prj_json['value']['awardNumbers'] = award_number
prj_json['value'].pop('awardNumber', None)
if publication.get('project'):
publication['project'].update(prj_json)
else:
publication['project'] = prj_json
pub_doc.update(**publication)
return pub_doc
def amend_publication(project_id, amendments=None, authors=None, revision=None):
"""Amend a Publication
Update Amendable fields on a publication and the corrosponding DataCite
records. These changes do not produce a new version of a publication, but
they do allow for limited changes to a published project. This is currently
configured to support "Other" publications only.
:param str project_id: Project uuid to amend
:param int revision: Revision number to amend
"""
es_client = new_es_client()
mgr = ProjectsManager(service_account())
prj = mgr.get_project_by_id(project_id)
pub = BaseESPublication(project_id=project_id, revision=revision, using=es_client)
prj_dict = prj.to_body_dict()
pub_dict = pub.to_dict()
_delete_unused_fields(prj_dict)
if pub.project.value.projectType != 'other':
pub_entity_uuids = pub.entities()
for uuid in pub_entity_uuids:
if uuid in amendments:
entity = amendments[uuid]
else:
entity = mgr.get_entity_by_uuid(uuid)
entity = entity.to_body_dict()
_delete_unused_fields(entity)
for pub_ent in pub_dict[FIELD_MAP[entity['name']]]:
if pub_ent['uuid'] == entity['uuid']:
for key in entity['value']:
ent_type = 'entity' if 'dois' in entity['value'] else 'subentity'
if key not in UNAMENDABLE_FIELDS[ent_type]:
pub_ent['value'][key] = entity['value'][key]
if 'authors' in entity['value']:
pub_ent['value']['authors'] = authors[entity['uuid']]
_set_authors(pub_ent, pub_dict)
# weird key swap for old issues with awardnumber(s)
award_number = prj.award_number or []
if not isinstance(award_number, list):
award_number = []
prj_dict['value']['awardNumbers'] = award_number
prj_dict['value'].pop('awardNumber', None)
for key in prj_dict['value']:
if key not in UNAMENDABLE_FIELDS['project']:
pub_dict['project']['value'][key] = prj_dict['value'][key]
if authors and prj_dict['value']['projectType'] == 'other':
pub_dict['project']['value']['teamOrder'] = authors
pub.update(**pub_dict)
IndexedPublication._index.refresh(using=es_client)
return pub
def get(self, request, project_id):
pub = BaseESPublication(project_id=project_id)
if pub is not None and hasattr(pub, 'project'):
return JsonResponse(pub.to_dict())
else:
return JsonResponse({
'status': 404,
'message': 'Not found'
},
status=404)
def freeze_project_and_entity_metadata(project_id, entity_uuids=None):
"""Freeze project and entity metadata.
Given a project id and an entity uuid (should be a main entity) this function
retrieves all metadata related to these entities and stores it into Elasticsearch
as :class:`~designafe.libs.elasticsearch.docs.publications.BaseESPublication`
When publishing for the first time or publishing over an existing publication. We
will clear any existing entities (if any) from the published metadata. We'll use entity_uuids
(the entities getting DOIs) to rebuild the rest of the publication. These entities
usually do not have files associated to them (except published reports/documents).
:param str project_id: Project id.
:param list of entity_uuid strings: Entity uuids.
"""
mgr = ProjectsManager(service_account())
prj = mgr.get_project_by_id(project_id)
pub_doc = BaseESPublication(project_id=project_id)
publication = pub_doc.to_dict()
if entity_uuids:
# clear any existing sub entities in publication and keep updated fileObjs
fields_to_clear = []
entities_with_files = []
for key in list(FIELD_MAP.keys()):
if FIELD_MAP[key] in list(publication.keys()):
fields_to_clear.append(FIELD_MAP[key])
fields_to_clear = set(fields_to_clear)
for field in fields_to_clear:
for ent in publication[field]:
if 'fileObjs' in ent:
entities_with_files.append(ent)
if ent['uuid'] in entity_uuids:
publication[field] = []
for ent_uuid in entity_uuids:
entity = None
entity = mgr.get_entity_by_uuid(ent_uuid)
if entity:
entity_json = entity.to_body_dict()
pub_entities_field_name = FIELD_MAP[entity.name]
for e in entities_with_files:
if e['uuid'] == entity_json['uuid']:
entity_json['fileObjs'] = e['fileObjs']
publication['authors'] = list(entity_json['value']['authors'])
entity_json['authors'] = []
_populate_entities_in_publication(entity, publication)
_transform_authors(entity_json, publication)
if entity_json['value']['dois']:
entity_json['doi'] = entity_json['value']['dois'][-1]
_delete_unused_fields(entity_json)
publication[pub_entities_field_name].append(entity_json)
prj_json = prj.to_body_dict()
_delete_unused_fields(prj_json)
award_number = publication.get('project', {}).get('value', {}).pop(
'awardNumber', []
) or []
if not isinstance(award_number, list):
award_number = []
prj_json['value']['awardNumbers'] = award_number
prj_json['value'].pop('awardNumber', None)
if publication.get('project'):
publication['project'].update(prj_json)
else:
publication['project'] = prj_json
pub_doc.update(**publication)
return pub_doc
def fix_file_tags(project_id):
pub = BaseESPublication(project_id=project_id)
pub_dict = pub.to_dict()
entities_to_check = list(set(pub_dict.keys()).intersection(list(FIELD_MAP.values())))
entities_to_check.append('project')
def check_complete_tags(tags):
for tag in tags:
if 'path' not in tag:
return False
return True
def fix_tags_path(entity):
for tag in entity['value']['fileTags']:
try:
pub_file = BaseFileResource.listing(
service_account(),
system="designsafe.storage.published",
path="{}{}".format(project_id, tag['path'])
)
tag['fileUuid'] = pub_file.uuid
except Exception as err:
LOG.info('error: {}'.format(err))
continue
def fix_tags_no_path(entity):
if entity['name'] == 'designsafe.project':
proj_other = BaseFileResource.listing(service_account(), system="project-{}".format(entity['uuid']), path="")
for child in proj_other.children:
try:
pub_file = BaseFileResource.listing(service_account(), system="designsafe.storage.published", path="{}{}".format(project_id, child.path))
proj_file = BaseFileResource.listing(service_account(), system="project-{}".format(entity['uuid']), path=child.path)
for tag in entity['value']['fileTags']:
if tag['fileUuid'] == proj_file.uuid:
tag['fileUuid'] = pub_file.uuid
except Exception as err:
LOG.info('error: {}'.format(err))
continue
else:
for fobj in entity['fileObjs']:
try:
pub_file = BaseFileResource.listing(service_account(), system="designsafe.storage.published", path="{}{}".format(project_id, fobj['path']))
proj_file = BaseFileResource.listing(service_account(), system="project-{}".format(pub_dict['project']['uuid']), path=fobj['path'])
for tag in entity['value']['fileTags']:
if tag['fileUuid'] == proj_file.uuid:
tag['fileUuid'] = pub_file.uuid
except Exception as err:
LOG.info('error: {}'.format(err))
continue
for entname in entities_to_check:
if type(pub_dict[entname]) == list:
for entity in pub_dict[entname]:
if 'value' in entity and 'fileTags' in entity['value'] and check_complete_tags(entity['value']['fileTags']):
fix_tags_path(entity)
elif 'value' in entity and 'fileTags' in entity['value']:
fix_tags_no_path(entity)
else:
if 'value' in pub_dict[entname] and 'fileTags' in pub_dict[entname]['value'] and check_complete_tags(pub_dict[entname]['value']['fileTags']):
fix_tags_path(pub_dict[entname])
elif 'value' in pub_dict[entname] and 'fileTags' in pub_dict[entname]['value']:
fix_tags_no_path(pub_dict[entname])
pub.update(**pub_dict)
