def start_bibupload_job(id_pairs):
""" Submits the append job to bibupload
id_pairs - {local_recid: remote_recid} """
bibupload = ChunkedBibUpload(mode='a', user=SCRIPT_NAME, notimechange=True)
for local, remote in id_pairs.iteritems():
bibupload.add(generate_marc_to_append(local, remote))
bibupload.cleanup() # This initiates the job
def start_bibupload_job(id_pairs):
""" Submits the append job to bibupload
id_pairs - {local_recid: remote_recid} """
bibupload = ChunkedBibUpload(mode='a', user=SCRIPT_NAME, notimechange=True)
for local, remote in id_pairs.iteritems():
bibupload.add(generate_marc_to_append(local, remote))
bibupload.cleanup() # This initiates the job
def bst_hepnames_orcid_sync():
bai_orcids = run_sql("SELECT bai.data, orcid.data FROM aidPERSONIDDATA as bai JOIN aidPERSONIDDATA as orcid ON bai.personid=orcid.personid WHERE orcid.tag='extid:ORCID' AND bai.tag='canonical_name'")
recs = []
not_matched_profiles = 0
enhanced_records = 0
conflicting_orcids = 0
for bai, orcid in bai_orcids:
recids = perform_request_search(p="035:%s" % bai, cc="HepNames")
if len(recids) > 1:
write_message("WARNING: %s/author/profile/%s, %s matches more than one HepNames: %s" % (CFG_SITE_URL, bai, orcid, recids), stream=sys.stderr)
not_matched_profiles += 1
elif not recids:
write_message("WARNING: %s/author/profile/%s, %s does not match any HepName" % (CFG_SITE_URL, bai, orcid), stream=sys.stderr)
not_matched_profiles += 1
else:
recid = recids[0]
record = get_record(recid)
for field in record_get_field_instances(record, tag="035"):
subfields = field_get_subfield_instances(field)
subfields_dict = dict(subfields)
if subfields_dict.get('9') == 'ORCID':
if subfields_dict.get('a') != orcid:
if not subfields_dict.get('a', '').strip():
write_message("WARNING: record %s/record/%s has an empty ORCID" % (CFG_SITE_URL, recid), stream=sys.stderr)
continue
write_message("WARNING: record %s/record/%s matched by BAI %s/author/profile/%s has a different ORCID %s than the profile one: %s" % (CFG_SITE_URL, recid, CFG_SITE_URL, bai, subfields_dict.get('a'), orcid), stream=sys.stderr)
conflicting_orcids += 1
break
else:
new_record = {}
record_add_field(new_record, tag="001", controlfield_value=str(recid))
record_add_field(new_record, tag="035", subfields=[('a', orcid), ('9', 'ORCID')])
recs.append(new_record)
write_message("INFO: adding ORCID %s to record %s/record/%s matched by BAI %s/author/profile/%s" % (orcid, CFG_SITE_URL, recid, CFG_SITE_URL, bai))
enhanced_records += 1
if recs:
write_message("INFO: initiating uploads")
bibupload = ChunkedBibUpload(mode="a", user='******')
for record in recs:
bibupload.add(record_xml_output(record))
bibupload.cleanup()
else:
write_message("INFO: no modification are necessary")
write_message("INFO: not_matched_profiles: %s, enhanced_records: %s, conflicting_orcids: %s" % (not_matched_profiles, enhanced_records, conflicting_orcids))
def bst_arxiv_doi_update(input_uri=None,
log_dir=CFG_TMPSHAREDDIR,
logging=True,
asana_key=CFG_ASANA_API_KEY,
asana_parent_id=ASANA_PARENT_TASK_ID,
skip_result_types='missing'):
"""Update DOIs on documents harvested from ArXiv.
Parameters:
:param input_uri: Link to new URI data
DEFAULT: https://vendor.ridge.aps.org/arXiv/latest_pub.xml
NOTE: Test data can be taken from http://arxiv.org/schemas/doi_feed_test.xml
:param log_dir: Directory to store log files in
:param logging: True or False, default True
:param asana_key: The Asana API, by default uses the value of CFG_ASANA_API_KEY
NOTE: Passing the value of None for this parameter will skip writing
to Asana and instead email the instance admin
:param asana_parent_id: The taskID of the task in Asana to log subtasks to
:param skip_result_types: Error messages to not bother with during
reporting, input as Comma Seperated Values CSVs
Possible values: missing, ambigous, incorrect
"""
skip_results = verify_skip_results(skip_result_types)
if input_uri is None:
_print("Notice: No URI specified, defaulting to " + URI_DEFAULT)
input_uri = URI_DEFAULT
task_update_progress("Resolving URI: %s" % (input_uri,))
# Testing builds characters
bibupload = ChunkedBibUpload(mode='a', user=SCRIPT_NAME, notimechange=False)
# open url and parse xml
try:
tree = ET.parse(urllib.urlopen(input_uri))
_print('Opened DOI file ' + input_uri)
except IOError:
_print("FATAL ERROR: Could not open URL: " + input_uri, 1)
task_update_progress("Failed retrieving DOI data")
return False
except ExpatError:
_print("FATAL ERROR: Could not parse XML from: " + input_uri, 1)
task_update_progress("Failed parsing DOI data")
return False
root = tree.getroot()
try:
date_el = root.find('date')
date_str = '%s-%s-%s' % (date_el.get('year'), date_el.get('month'),
date_el.get('day'))
_print("Processing DOIs last updated on date %s" % date_str)
except AttributeError:
_print("Warning: Couldn't get last published date of Arxiv DOI feed.")
doi_count = 0
new_count = 0
# Stores any DOIs with have issues with in structure:
# Missing: (doi, arxiv preprint_id, published date)
# Ambiguous: (doi, arxiv preprint_id, rec_ids)
# Incorrect: (rec_id, old-doi, new-doi)
problem_dois = {'missing': [], 'ambiguous': [], 'incorrect': []}
task_update_progress("Processing records...")
# NB: Element.getiterator() is deprecated since version 2.7: Use
# method Element.iter() instead.
for item in root.getiterator('article'):
doi_count += 1
doi = item.get('doi')
arxiv = item.get('preprint_id')
published_date = item.get('published')
_print("XML entry #%s: %s" % (str(doi_count), arxiv), 6)
rec_id = get_record_by_arxiv_id(arxiv)
if len(rec_id) == 1:
rec_id = rec_id[0]
try:
record_xml = append_to_record(rec_id, doi, published_date)
except DOIError as ex:
problem_dois['incorrect'].append((rec_id, ex.message, doi))
continue
if record_xml:
new_count += 1
_print("* Now we will run the bibupload for " +
"%s record" % rec_id, 5)
_print("** We will upload the following xml code %s" %
repr(record_xml), 9)
bibupload.add(record_xml)
elif len(rec_id) > 1:
_print('ERROR: %d records found with matching arXiv ID %s' %
(len(rec_id), arxiv))
problem_dois['ambiguous'].append((doi, arxiv, repr(rec_id)))
else:
_print('No record found matching arxiv ID: %s' % arxiv, 9)
problem_dois['missing'].append((doi, arxiv, published_date))
_print("========================| FINAL SCORE |=======================", 1)
_print("DOIs found and processed: %d" % doi_count, 1)
_print("Arxiv IDs without corresponding records: %d"
% len(problem_dois['missing']), 1)
_print("Arxiv IDs corresponding to multiple records (duplicates): %d"
% len(problem_dois['ambiguous']), 1)
_print("Inspire records with an incorrect DOI: %d"
% len(problem_dois['incorrect']), 1)
_print("Records without DOIs requiring appends: %d" % new_count, 1)
_print("==============================================================", 1)
bibupload.cleanup()
notify_on_errors(problem_dois, log_dir, doi_count, new_count,
asana_key, asana_parent_id, skip_results)
return True
def bst_arxiv_doi_update(input_uri=None,
log_dir=CFG_TMPSHAREDDIR,
logging=True,
asana_key=CFG_ASANA_API_KEY,
asana_parent_id=ASANA_PARENT_TASK_ID,
skip_result_types='missing'):
"""Update DOIs on documents harvested from ArXiv.
Parameters:
:param input_uri: Link to new URI data
DEFAULT: https://vendor.ridge.aps.org/arXiv/latest_pub.xml
NOTE: Test data can be taken from http://arxiv.org/schemas/doi_feed_test.xml
:param log_dir: Directory to store log files in
:param logging: True or False, default True
:param asana_key: The Asana API, by default uses the value of CFG_ASANA_API_KEY
NOTE: Passing the value of None for this parameter will skip writing
to Asana and instead email the instance admin
:param asana_parent_id: The taskID of the task in Asana to log subtasks to
:param skip_result_types: Error messages to not bother with during
reporting, input as Comma Seperated Values CSVs
Possible values: missing, ambigous, incorrect
"""
skip_results = verify_skip_results(skip_result_types)
if input_uri is None:
_print("Notice: No URI specified, defaulting to " + URI_DEFAULT)
input_uri = URI_DEFAULT
task_update_progress("Resolving URI: %s" % (input_uri, ))
# Testing builds characters
bibupload = ChunkedBibUpload(mode='a',
user=SCRIPT_NAME,
notimechange=False)
# open url and parse xml
try:
tree = ET.parse(urllib.urlopen(input_uri))
_print('Opened DOI file ' + input_uri)
except IOError:
_print("FATAL ERROR: Could not open URL: " + input_uri, 1)
task_update_progress("Failed retrieving DOI data")
return False
except ExpatError:
_print("FATAL ERROR: Could not parse XML from: " + input_uri, 1)
task_update_progress("Failed parsing DOI data")
return False
root = tree.getroot()
try:
date_el = root.find('date')
date_str = '%s-%s-%s' % (date_el.get('year'), date_el.get('month'),
date_el.get('day'))
_print("Processing DOIs last updated on date %s" % date_str)
except AttributeError:
_print("Warning: Couldn't get last published date of Arxiv DOI feed.")
doi_count = 0
new_count = 0
# Stores any DOIs with have issues with in structure:
# Missing: (doi, arxiv preprint_id, published date)
# Ambiguous: (doi, arxiv preprint_id, rec_ids)
# Incorrect: (rec_id, old-doi, new-doi)
problem_dois = {'missing': [], 'ambiguous': [], 'incorrect': []}
task_update_progress("Processing records...")
# NB: Element.getiterator() is deprecated since version 2.7: Use
# method Element.iter() instead.
for item in root.getiterator('article'):
doi_count += 1
doi = item.get('doi')
arxiv = item.get('preprint_id')
published_date = item.get('published')
_print("XML entry #%s: %s" % (str(doi_count), arxiv), 6)
rec_id = get_record_by_arxiv_id(arxiv)
if len(rec_id) == 1:
rec_id = rec_id[0]
try:
record_xml = append_to_record(rec_id, doi, published_date)
except DOIError as ex:
problem_dois['incorrect'].append((rec_id, ex.message, doi))
continue
if record_xml:
new_count += 1
_print(
"* Now we will run the bibupload for " +
"%s record" % rec_id, 5)
_print(
"** We will upload the following xml code %s" %
repr(record_xml), 9)
bibupload.add(record_xml)
elif len(rec_id) > 1:
_print('ERROR: %d records found with matching arXiv ID %s' %
(len(rec_id), arxiv))
problem_dois['ambiguous'].append((doi, arxiv, repr(rec_id)))
else:
_print('No record found matching arxiv ID: %s' % arxiv, 9)
problem_dois['missing'].append((doi, arxiv, published_date))
_print("========================| FINAL SCORE |=======================", 1)
_print("DOIs found and processed: %d" % doi_count, 1)
_print(
"Arxiv IDs without corresponding records: %d" %
len(problem_dois['missing']), 1)
_print(
"Arxiv IDs corresponding to multiple records (duplicates): %d" %
len(problem_dois['ambiguous']), 1)
_print(
"Inspire records with an incorrect DOI: %d" %
len(problem_dois['incorrect']), 1)
_print("Records without DOIs requiring appends: %d" % new_count, 1)
_print("==============================================================", 1)
bibupload.cleanup()
notify_on_errors(problem_dois, log_dir, doi_count, new_count, asana_key,
asana_parent_id, skip_results)
return True