def execute_query(project_id, query_id):
"""
executes the defined and saved query in scopus
:param project_id: the ID of the current project
:return: 'finished' with a status of 204 when the query was executed successfully
"""
app.logger.info('project {}: running query {}'.format(
project_id, query_id))
# reads the saved Scopus search string from disk
scopus_queries = query_service.load_scopus_queries(project_id, query_id)
# retrieve the project from disk, set the booleans and save the project
project = project_service.load_project(project_id)
project.isEidsCollected = False
project.isEidsCollecting = True
project_service.save_project(project)
eids = scopus_service.execute_query(scopus_queries)
# print the results to the command line for logging
app.logger.info('project {}: found {} entries in Scopus'.format(
project_id, len(eids)))
# persist EIDs to file
identifier_service.save_id_list(project_id=project_id,
query_id=query_id,
identifiers=eids)
# set the project boolean and save the project
project.isEidslist = True
project.isEidsCollected = True
project.isEidsCollecting = False
project_service.save_project(project)
return Response({"status": "FINISHED"}, status=204)
def set_survey_id(project_id):
survey_id = request.form['survey_id']
project = project_service.load_project(project_id)
project.survey_id = survey_id
project_service.save_project(project)
app.logger.info('project {}: connecting with survey {}'.format(
project_id, survey_id))
return Response('survey ID saved', status=204)
def upload_sample_judgement_file(project_id):
with app.app_context():
location = app.config.get("LIBINTEL_DATA_DIR")
print("saving sample test file for " + project_id)
project = project_service.load_project(project_id)
file = request.files['sample-judgement-file']
path_to_save = location + '/out/' + project_id + '/'
if not os.path.exists(path_to_save):
os.makedirs(path_to_save)
file.save(path_to_save + 'sample_judgement_eids_list.csv')
project.isSampledata = True
project_service.save_project(project)
return Response('list saved', status=204)
def upload_test_file(project_id):
with app.app_context():
location = app.config.get("LIBINTEL_DATA_DIR")
print("saving test file for " + project_id)
project = project_service.load_project(project_id)
file = request.files['test-file']
path_to_save = location + '/out/' + project_id + '/'
if not os.path.exists(path_to_save):
os.makedirs(path_to_save)
file.save(path_to_save + 'test_eids_list.txt')
project['isTestdata'] = True
project_service.save_project(project)
return Response('list saved', status=204)
def save_project():
# Get the client provided project
project = get_project_from_req(request)
response_body = {}
if project:
operation = "save" if "_id" in project else "create"
project = project_service.save_project(project)
if project:
populate_response_with_project(response_body, project)
else:
response_body["error"] = True
response_body["message"] = "Error saving the project"
now = str(datetime.now())
print ">> %s\t%s\t%s_project()\t[%s]" % \
(request.remote_addr, now, operation, project["_id"])
else:
response_body["error"] = True
response_body["message"] = "No project provided to save"
# Create the response object
response = make_response(jsonify(response_body))
return response
def upload_xml_file(project_id):
"""
retrieves the query xml file from the request and saves it to disc
:param project_id: the ID of the current project
:return: returns a status of 204 when the file could be saved
"""
with app.app_context():
location = app.config.get("LIBINTEL_DATA_DIR")
app.logger.info("project {}: saving uploaded xml file".format(project_id))
if request.method == 'POST':
project = project_service.load_project(project_id)
file = request.files['query_xml']
path_to_save = location + '/out/' + project_id + '/'
if not os.path.exists(path_to_save):
os.makedirs(path_to_save)
file.save(path_to_save + 'query.xml')
project.isQueryDefined = True
project_service.save_project(project)
return Response("OK", status=204)
def save_query_as_xml(project_id):
"""
saves the query as xml document in the working directory as query.json file. Creates a scopus search string and
saves it as scopus_search_string.txt. Sets project.isQueryDefined = True
:param project_id: the ID of the current project
:return: the saved query
"""
project = project_service.load_project(project_id)
query_json = request.get_json(silent=True)
query = query_service.from_json(query_json)
try:
query_service.save_query_to_xml(project_id, query)
app.logger.info(
'project {}: successfully saved query to xml'.format(project_id))
except IOError:
app.logger.warn(
'project {}: could not save query to xml'.format(project_id))
return Response("could not save query", status=500)
query_service.create_scopus_queries(project_id, query)
project.isQueryDefined = True
app.logger.info('project {}: scopus queried defined'.format(project_id))
project_service.save_project(project)
return json.dumps(query, default=lambda o: o.__getstate__())
def data_collection_execution(project_id):
"""
run the data collection
:parameter project_id the id of the current project
"""
mode = ''
if request.args.get('mode') is not None:
mode = request.args.get('mode')
app.logger.info('project {}: collecting data with mode {}'.format(
project_id, mode))
# load project, set status bools, and load and eid list. initialize missed eid list
project = project_service.load_project(project_id)
project.isDataCollecting = True
project.isDataCollected = False
eids = eids_service.load_eid_list(project_id, mode)
missed_eids = []
with app.app_context():
keys = app.config.get("LIBINTEL_SCOPUS_KEYS")
# initialize status, set to collecting and save status
status = Status("DATA_COLLECTING")
status.total = len(eids)
status_service.save_status(project_id, status)
if status.total > 0:
if mode != 'missed':
elasticsearch_service.delete_index(project.project_id)
else:
eids_service.deleteMissedEids()
if type(keys) is tuple:
# the number of threads is given by the number of available API keys
number_of_threads = len(keys)
app.logger.info('project {}: collecting data in {} threads'.format(
project_id, number_of_threads))
# gather the individual chunks provided to each process
length_of_chunks = math.ceil(status.total / number_of_threads)
list_chunks = list(chunks(eids, length_of_chunks))
# make asynchronous calls and delegate the individual collection to the individual threads
for key_index, key in enumerate(keys):
if len(list_chunks) > key_index:
thread = Thread(target=collect_data,
args=(list_chunks[key_index],
project.project_id, project.name,
key_index, key,
app._get_current_object()))
thread.start()
return Response('finished', status=204)
collect_data(eids=eids,
project_id=project.project_id,
project_name=project.name,
i=0,
key=keys,
app=app._get_current_object())
# if only one API-Key is given, collect data sequentially
for idx, eid in enumerate(eids):
# set scopus api-key to the provided key
scopus.config['Authentication']['APIKEy'] = keys
# update the progress status and save the status to disk
status.progress = idx + 1
status_service.save_status(project_id, status)
# print progress
app.logger.info('project {}: processing entry ' + str(idx) +
'of ' + str(status.total) + ' entries: ' +
str(idx / status.total * 100) + '%')
# retrieve data from scopus
try:
scopus_abstract = scopus.AbstractRetrieval(identifier=eid,
id_type='eid',
view="FULL",
refresh=True)
app.logger.info(
'project {}: collected scopus data for EID {}'.format(
project_id, eid))
except Exception as inst:
app.logger.error(
'project {}: could not collect scopus data for EID {}, exception: {}'
.format(project_id, eid, type(inst)))
missed_eids.append(eid)
continue
# create new AllResponses object to hold the individual information
response = AllResponses(eid, project.name, project.project_id)
# add scopus abstract to AllResponses object
response.scopus_abstract_retrieval = scopus_abstract
# get doi and collect unpaywall data and Altmetric data
doi = scopus_abstract.doi
if doi is not None:
if doi != "":
response.unpaywall_response = Unpaywall(doi)
response.altmetric_response = Altmetric(doi)
response.scival_data = Scival([])
# send response to elastic search index
elasticsearch_service.send_to_index(response, project.project_id)
app.logger.info('project {}: saved EID {} to elasticsearch'.format(
project_id, eid))
eids_service.save_eid_list(project_id=project.project_id,
eids=missed_eids,
prefix='missed_')
app.logger.info('project {}: all EID data collected'.format(project_id))
status.status = "DATA_COLLECTED"
status_service.save_status(project_id, status)
project.isDataCollecting = False
project.isDataCollected = True
project_service.save_project(project)
return Response({"status": "FINISHED"}, status=204)
def references_collection_execution(project_id):
"""
collects the references for a given collection of publications
:param project_id: the ID of the current project
:return: 204 if successful
"""
# initialize lists, read sample size from request and load eid list
sample_size = int(request.args.get('sample_size'))
missed_eids = []
references_eids = []
eids = eids_service.load_eid_list(project_id)
# load project and set booleans
project = project_service.load_project(project_id)
project.isReferencesCollecting = True
project.isReferencesCollected = False
project_service.save_project(project)
# prepare status
status = Status("REFERENCES_COLLECTING")
status.total = eids.__len__()
status_service.save_status(project_id, status)
# if eids are given, cycle through all of them
if status.total > 0:
for idx, eid in enumerate(eids):
# update the progress status and save the status to disk
status.progress = idx + 1
status_service.save_status(project_id, status)
# print progress
app.logger.info('project {}: processing entry ' + str(idx) +
'of ' + str(status.total) + ' entries: ' +
str(idx / status.total * 100) + '%')
# retrieve refereces from scopus
try:
scopus_abstract = scopus.AbstractRetrieval(eid, view="FULL")
app.logger.info(
'project {}: collected scopus data for EID {}'.format(
project_id, eid))
if scopus_abstract.references is not None:
references_eids = references_eids + scopus_abstract.references
else:
app.logger.warn(
'project {}: no references given in scopus export for EID {}.'
.format(project_id, eid))
except IOError:
app.logger.error(
'project {}: could not collect scopus data for EID {}'.
format(project_id, eid))
missed_eids.append(eid)
continue
# transform references eids into tuple and calculate the occurences
references_eids_tuple = tuple(references_eids)
occurences = Counter(references_eids_tuple)
most_occurences = occurences.most_common(sample_size)
# save the counter with the most occurences to disk
counter_service.save_counter(project_id, most_occurences, 'references_')
eids_service.save_eid_list(project_id, missed_eids, prefix='missed_')
# set the status and save it to disk
status.status = "DATA_COLLECTED"
status_service.save_status(project_id, status)
# set the project booleans and save it to disk
project.isReferencesCollecting = False
project.isReferencesCollected = True
project_service.save_project(project)
return Response({"status": "FINISHED"}, status=204)
def query_execution(project_id):
"""
executes the defined and saved query in scopus
:param project_id: the ID of the current project
:return: 'finished' with a status of 204 when the query was executed successfully
"""
app.logger.info('project {}: running queries'.format(project_id))
# reads the saved Scopus search string from disk
scopus_queries = query_service.load_scopus_queries(project_id)
# retrieve the project from disk, set the booleans and save the project
project = project_service.load_project(project_id)
project.isEidsCollected = False
project.isEidsCollecting = True
project_service.save_project(project)
# prepares the status file
status = Status("EIDS_COLLECTING")
status_service.save_status(project_id, status)
# prepare EIDs list
eids = []
for index, search_strings in enumerate(scopus_queries.search_strings):
individual_eids = []
for search_string in search_strings:
app.logger.info('project {}: executing search {} - {}'.format(
project_id, index, search_string))
search = scopus.ScopusSearch(search_string,
refresh=True,
field='eid',
view='STANDARD')
if search.results is not None:
app.logger.info(
'project {}: result search {} - {} entries found'.format(
project_id, index, len(search.results)))
for result in search.results:
# add EID if it is not already in the list (from a former search)
eids.append(result.eid)
individual_eids.append(result.eid)
eids_service.save_eid_list(
project_id=project_id,
eids=set(individual_eids),
prefix=(str(scopus_queries.search_ids[index]) + '_'))
# convert to set in order to remove duplicates
eids = set(eids)
# print the results to the command line for logging
app.logger.info('project {}: found {} eids in Scopus'.format(
project_id, len(eids)))
# persist EIDs to file
eids_service.save_eid_list(project_id=project_id, eids=eids)
# set the total number of results to the relevance_measures measure save it to disk
relevance_measure = RelevanceMeasure(
number_of_search_results=eids.__len__())
relevance_measure_service.save_relevance_measures(project_id,
relevance_measure)
# set the total number of results to the status save it to disk
status.total = relevance_measure.number_of_search_results
status_service.save_status(project_id, status)
# set the status and save it to disk
status = Status("EIDS_COLLECTED")
status_service.save_status(project_id, status)
# set the project boolean and save the project
project.isEidslist = True
project.isEidsCollected = True
project.isEidsCollecting = False
project_service.save_project(project)
return Response({"status": "FINISHED"}, status=204)