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'):
"""
bst_arxiv_doi_update
Updates 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=True)
bibindex = ChunkedBibIndex(indexes='year,global,journal',
user=SCRIPT_NAME)
# 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 retreiving DOI data")
task_update_status("FAILED")
return False
except ExpatError:
_print("FATAL ERROR: Could not parse XML from: " + input_uri, 1)
task_update_progress("Failed parsing DOI data")
task_update_status("FAILED")
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 and bibindex for " +
"%s record" % rec_id, 5)
_print("** We will upload the following xml code %s" %
repr(record_xml), 9)
bibupload.add(record_xml)
bibindex.add(rec_id)
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)
if logging:
task_update_progress("Logging...")
write_list_to_file(log_dir, 'errors', ERRORS)
write_list_to_file(log_dir, 'messages', MESSAGES)
notify_on_errors(problem_dois, log_dir, doi_count, new_count,
asana_key, asana_parent_id, skip_results)
task_update_progress("%s finished. %s DOIs processed, %s to add"
% (SCRIPT_NAME, str(doi_count), str(new_count)))
task_update_status("DONE")
bibupload.__del__()
bibindex.__del__()
return True
def bst_arxiv_doi_update(input_uri=None,
log_dir=CFG_TMPSHAREDDIR, logging=True):
"""
bst_arxiv_doi_update
Updates DOIs on documents harvested from ArXiv.
Parameters:
* 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
* log_dir - Directory to store log files in
* logging - True or False, default True
"""
if input_uri is None:
_print("Notice: No URI specified, defaulting to " + URI_DEFAULT)
input_uri = URI_DEFAULT
task_update_progress("Resolving URI...")
# Testing builds characters
bibupload = ChunkedBibUpload(mode='a', user=SCRIPT_NAME, notimechange=True)
bibindex = ChunkedBibIndex(indexes='year,global,journal',
user=SCRIPT_NAME)
# 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 retreiving DOI data")
task_update_status("FAILED")
return False
root = tree.getroot()
doi_count = 0
new_count = 0
missing_count = 0
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]
record_xml = append_to_record(rec_id, doi, published_date)
if record_xml:
new_count += 1
_print("* Now we will run the bibupload and bibindex for " +
str(rec_id) + " record", 5)
_print("** We will upload the following xml code " +
repr(record_xml), 9)
bibupload.add(record_xml)
bibindex.add(rec_id)
elif len(rec_id) > 1:
_print('ERROR: %d records found with matching arXiv ID %s' %
(len(rec_id), arxiv))
else:
missing_count += 1
_print('No record found matching arxiv ID: ' + arxiv, 9)
_print("======================== FINAL SCORE ========================", 1)
_print("DOIs found and processed: " + str(doi_count), 1)
_print("Arxiv IDs without corresponding records: " + str(missing_count), 1)
_print("Records requiring appends: " + str(new_count), 1)
if logging:
task_update_progress("Logging...")
write_list_to_file(log_dir, 'errors', ERRORS)
write_list_to_file(log_dir, 'messages', MESSAGES)
task_update_progress(SCRIPT_NAME + " finished. %s DOIs processed, %s to add"
% (str(doi_count), str(new_count)))
task_update_status("DONE")
bibupload.__del__()
bibindex.__del__()
return True
def bst_arxiv_doi_update(input_uri=None,
log_dir=CFG_TMPSHAREDDIR,
logging=True):
"""
bst_arxiv_doi_update
Updates DOIs on documents harvested from ArXiv.
Parameters:
* 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
* log_dir - Directory to store log files in
* logging - True or False, default True
"""
if input_uri is None:
_print("Notice: No URI specified, defaulting to " + URI_DEFAULT)
input_uri = URI_DEFAULT
task_update_progress("Resolving URI...")
# Testing builds characters
bibupload = ChunkedBibUpload(mode='a', user=SCRIPT_NAME, notimechange=True)
bibindex = ChunkedBibIndex(indexes='year,global,journal', user=SCRIPT_NAME)
# 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 retreiving DOI data")
task_update_status("FAILED")
return False
root = tree.getroot()
doi_count = 0
new_count = 0
missing_count = 0
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]
record_xml = append_to_record(rec_id, doi, published_date)
if record_xml:
new_count += 1
_print(
"* Now we will run the bibupload and bibindex for " +
str(rec_id) + " record", 5)
_print(
"** We will upload the following xml code " +
repr(record_xml), 9)
bibupload.add(record_xml)
bibindex.add(rec_id)
elif len(rec_id) > 1:
_print('ERROR: %d records found with matching arXiv ID %s' %
(len(rec_id), arxiv))
else:
missing_count += 1
_print('No record found matching arxiv ID: ' + arxiv, 9)
_print("======================== FINAL SCORE ========================", 1)
_print("DOIs found and processed: " + str(doi_count), 1)
_print("Arxiv IDs without corresponding records: " + str(missing_count), 1)
_print("Records requiring appends: " + str(new_count), 1)
if logging:
task_update_progress("Logging...")
write_list_to_file(log_dir, 'errors', ERRORS)
write_list_to_file(log_dir, 'messages', MESSAGES)
task_update_progress(SCRIPT_NAME +
" finished. %s DOIs processed, %s to add" %
(str(doi_count), str(new_count)))
task_update_status("DONE")
bibupload.__del__()
bibindex.__del__()
return True
