def merge_bibcodes(bibcodes, print_adsxml=False, print_marcxml=False, write_xml_to_disk=False):
"""
Returns a merged version of the record identified by bibcode.
"""
# Extract the record from ADS.
records = ADSRecords('full', 'XML')
for bibcode in bibcodes:
records.addCompleteRecord(bibcode)
ads_xml_obj = records.export()
if print_adsxml:
print ads_xml_obj.serialize('UTF-8')
if write_xml_to_disk:
with open('/tmp/adsxml.xml', 'w') as f:
f.write(ads_xml_obj.serialize('UTF-8'))
# Convert to MarcXML.
stylesheet = libxslt.parseStylesheetDoc(libxml2.parseFile(XSLT))
xml_object = stylesheet.applyStylesheet(ads_xml_obj, None)
if print_marcxml:
print xml_object.serialize('UTF-8')
if write_xml_to_disk:
with open('/tmp/marcxml.xml', 'w') as f:
f.write(xml_object.serialize('UTF-8'))
merged_records, bibcodes_with_problems = merge_records_xml(xml_object)
return merged_records
def readRecords(records,LOGGER=settings.LOGGER):
'''
records: [(bibcode,JSON_fingerprint),...]
'''
h = hash(json.dumps(records))
if not records:
LOGGER.debug("No records given")
return []
targets = dict(records)
s = time.time()
records = ADSRecords('full','XML')
failures = []
for bibcode in targets.keys():
try:
records.addCompleteRecord(bibcode)
except KeyboardInterrupt:
raise
except:
failures.append(bibcode)
LOGGER.warning("[%s] ADSRecords failed" % bibcode)
records = records.export()
if not records.content:
return []
ttc = time.time()-s
rate = len(targets)/ttc
if failures:
LOGGER.warning('ADSRecords failed to retrieve %s records' % len(failures))
LOGGER.info('ADSRecords took %0.1fs to query %s records (%0.1f rec/s)\t[%s]' % (ttc,len(targets),rate,h))
records = ensureList(xmltodict.parse(records.__str__())['records']['record'])
assert(len(records)==len(targets)-len(failures))
# with open('%s.pickle' % uuid.uuid4(),'w') as fp:
# pickle.dump(records,fp)
return records,targets
def extractor_process(q_todo, q_done, q_probl, q_uplfile, lock_stdout, lock_createdfiles, q_life, extraction_directory, extraction_name):
"""Worker function for the extraction of bibcodes from ADS
it has been defined outside any class because it's more simple to treat with multiprocessing """
logger.warning(multiprocessing.current_process().name + ' (worker) Process started')
#I create a local logger
fh = logging.FileHandler(os.path.join(pipeline_settings.BASE_OUTPUT_PATH, extraction_directory, pipeline_settings.BASE_LOGGING_PATH, multiprocessing.current_process().name+'_worker.log'))
fmt = logging.Formatter(pipeline_settings.LOGGING_FORMAT)
fh.setFormatter(fmt)
local_logger = logging.getLogger(pipeline_settings.LOGGING_WORKER_NAME)
local_logger.addHandler(fh)
local_logger.setLevel(logger.level)
local_logger.propagate = False
#I print the same message for the local logger
local_logger.warning(multiprocessing.current_process().name + ' Process started')
#I remove the automatic join from the queue of the files to upload
q_uplfile.cancel_join_thread()
#I get the maximum number of groups I can process
max_num_groups = settings.MAX_NUMBER_OF_GROUP_TO_PROCESS
#variable used to know if I'm exiting because the queue is empty or because I reached the maximum number of groups to process
queue_empty = False
#while there is something to process or I reach the maximum number of groups I can process, I try to process
for grpnum in range(max_num_groups):
task_todo = q_todo.get()
if task_todo[0] == 'STOP':
queue_empty = True
#I exit the loop
break
#I print when I'm starting the extraction
local_logger.warning(multiprocessing.current_process().name + (' starting to process group %s' % task_todo[0]))
############
#then I process the bibcodes
# I define a couple of lists where to store the bibcodes processed
bibcodes_ok = []
bibcodes_probl = []
#I define a ADSEXPORT object
recs = ADSRecords('full', 'XML')
# I define a maximum amount of bibcodes I can skip per each cicle: the number of bibcodes per group / 10 (minimum 500)
# if i skip more than this amount it means that there is something
# wrong with the access to the data and it's better to stop everything
max_number_of_bibs_to_skip = max(settings.NUMBER_OF_BIBCODES_PER_GROUP / 10, settings.MAX_SKIPPED_BIBCODES)
for bibcode in task_todo[1]:
try:
recs.addCompleteRecord(bibcode)
bibcodes_ok.append(bibcode)
except Exception, error:
local_logger.error(': problem retrieving the bibcode "%s" in group %s' % (bibcode, task_todo[0]))
#I catch the exception type name
exc_type, exc_obj, exc_tb = sys.exc_info()
try:
str_error_to_print = exc_type.__name__ + '\t' + str(error)
except:
try:
str_error_to_print = u'%s\t%s' % (unicode(exc_type.__name__), unicode(error))
except:
local_logger.error(' Cannot log error for bibcode %s ' % bibcode)
str_error_to_print = ''
bibcodes_probl.append((bibcode, str_error_to_print))
max_number_of_bibs_to_skip = max_number_of_bibs_to_skip - 1
#If i=I reach 0 It means that I skipped 1k bibcodes and probably there is a problem: so I simulate an exit for empty queue
if max_number_of_bibs_to_skip == 0:
break
#I exit from both loops
if max_number_of_bibs_to_skip == 0:
local_logger.warning(' Detected possible error with ADS data access: skipped %s bibcodes in one group' % max(settings.NUMBER_OF_BIBCODES_PER_GROUP / 10, settings.MAX_SKIPPED_BIBCODES))
queue_empty = True
break
#I extract the object I created
xmlobj = recs.export()
del recs
try:
#I define a transformation object
transf = xml_transformer.XmlTransformer(local_logger)
#and I transform my object
marcxml = transf.transform(xmlobj)
except:
err_msg = ' Impossible to transform the XML!'
local_logger.critical(err_msg)
raise GenericError(err_msg)
if marcxml:
#I merge the records
merged_records, records_with_merging_probl = merger.merge_records_xml(marcxml)
#If I had problems to merge some records I remove the bibcodes from the list "bibcodes_ok" and I add them to "bibcodes_probl"
for elem in records_with_merging_probl:
try:
bibcodes_ok.remove(elem[0])
except ValueError:
local_logger.warning(' Problems to remove bibcode "%s" in group "%s" from the list of bibcodes extracted after merging' % (elem[0], task_todo[0]) )
if elem[0] in bibcodes_probl:
local_logger.error(': bibcode "%s" reached the merger but was in problematic bibcodes!' % elem[0])
bibcodes_probl = bibcodes_probl + records_with_merging_probl
#########
#I write the object in a file
##########
filepath = os.path.join(settings.BASE_OUTPUT_PATH, extraction_directory, pipeline_settings.BASE_BIBRECORD_FILES_DIR, pipeline_settings.BIBREC_FILE_BASE_NAME+'_'+extraction_name+'_'+task_todo[0])
output = open(filepath, 'wb')
pickle.dump(merged_records, output)
output.close()
#then I write the filepath to a file for eventual future recovery
lock_createdfiles.acquire()
bibrec_file_obj = open(os.path.join(settings.BASE_OUTPUT_PATH, extraction_directory,settings.LIST_BIBREC_CREATED), 'a')
bibrec_file_obj.write(filepath + '\n')
bibrec_file_obj.close()
lock_createdfiles.release()
#finally I append the file to the queue
local_logger.info('Insert in queue for upload the file "%s" of the group "%s" ' % (filepath, task_todo[0]))
q_uplfile.put((task_todo[0],filepath))
#logger.info('record created, merged but not uploaded')
#bibupload_merger(merged_records, local_logger, 'replace_or_insert')
#otherwise I put all the bibcodes in the problematic
else:
bibcodes_probl = bibcodes_probl + [(bib, 'Bibcode extraction ok, but xml generation failed') for bib in bibcodes_ok]
bibcodes_ok = []
#finally I pass to the done bibcodes to the proper file
q_done.put([task_todo[0], bibcodes_ok])
#and the problematic bibcodes
q_probl.put([task_todo[0], bibcodes_probl])
local_logger.warning(multiprocessing.current_process().name + (' finished to process group %s' % task_todo[0]))
def updateRecords(records,LOGGER=settings.LOGGER):
if not records:
LOGGER.debug("No records given")
return []
targets = dict(records)
s = time.time()
records = ADSRecords('full','XML')
failures = []
for bibcode in targets.keys():
try:
records.addCompleteRecord(bibcode)
except KeyboardInterrupt:
raise
except:
failures.append(bibcode)
LOGGER.warning("[%s] ADSRecords failed" % bibcode)
records = records.export()
if not records.content:
return []
ttc = time.time()-s
rate = len(targets)/ttc
if failures:
LOGGER.warning('ADSRecords failed to retrieve %s records' % len(failures))
LOGGER.info('ADSRecords took %0.1fs to query %s records (%0.1f rec/s)' % (ttc,len(targets),rate))
records = ensureList(xmltodict.parse(records.__str__())['records']['record'])
with open('raw.txt','a') as fp:
for r in records:
fp.write('%s' % r)
fp.write('\n\n')
assert(len(records)==len(targets)-len(failures))
#Could send these tasks out on a queue
completeRecords = []
for r in records:
#Define top-level schema that will go in mongo
cr = {
'bibcode': r['@bibcode'],
'JSON_fingerprint': targets[r['@bibcode']],
'metadata' : {},
}
#Find metadata blocks that need merging
metadataCounter = collections.Counter([entry['@type'] for entry in r['metadata']])
needsMerging = dict([(k,[]) for k,v in metadataCounter.iteritems() if v>1])
#Iterate over metadata blocks; directly input single defined blocks
#and build a 'needsMerging' list to merge in the next step
for metadataBlock in r['metadata']:
for field,data in metadataBlock.iteritems():
if field in NORMALIZE_SCHEMA:
metadataBlock[field] = NORMALIZE_SCHEMA[field](data)
if metadataBlock['@type'] not in needsMerging:
cr['metadata'].update({metadataBlock['@type']:metadataBlock})
else: #If it shows up more than once, it needs merging.
needsMerging[metadataBlock['@type']].append(metadataBlock)
#Now merge the multiply defined metadataBlocks
for entryType,data in needsMerging.iteritems():
cr['metadata'].update({entryType:merge(data,r['@bibcode'],entryType,LOGGER)})
#Finally, we have a complete record
completeRecords.append(enforceSchema(cr))
LOGGER.info('Added %s complete records' % len(completeRecords))
return completeRecords
