def get_coden_formatted(bfo, separator=','):
"""Produces a SPIRES-style coden reference for a record
This typically looks like JOURNAL-CODEN,VOLUME,FIRSTPAGE
If this is impossible (for example if we lack sufficient information about
the reference or lack a CODEN lookup KB), produces empty string.
@param separator A string used to join the pieces of the reference
"""
coden = ''
publication_info = bfo.fields('773__')
if publication_info:
publication_info = publication_info[0]
else:
return ''
journal = publication_info.get('p', '')
volume = publication_info.get('v', '')
pages = publication_info.get('c', '')
if pages:
dashpos = pages.find('-')
if dashpos > -1:
pages = pages[:dashpos]
try:
if journal and (volume != '' or pages != ''):
coden = separator.join([get_kbr_keys("CODENS", searchvalue=journal, searchtype='e')[0][0], volume, pages])
except:
return ''
return coden
def authorships(self, req, form):
"""
Return list of authors used for auto-completion
in the authors field.
Return response as JSON.
"""
argd = wash_urlargd(form, {"publicationid": (str, ""), "term": (str, "")})
user_info = collect_user_info(req)
uid = user_info["uid"]
req.content_type = "application/json"
term = argd["term"]
publicationid = argd["publicationid"]
ret = get_favourite_authorships_for_user(uid, publicationid, term)
if ret:
return json.dumps(ret)
if ":" in term:
## an institution is being typed
name, institute = term.split(":", 1)
institute = institute.strip()
if len(institute) > 1:
institutes = [row[0] for row in get_kbr_keys("institutes", searchkey=institute, searchtype="s")]
institutes.sort()
return json.dumps(["%s: %s" % (name, institute) for institute in institutes[:100]])
return json.dumps([])
def authorships(self, req, form):
"""
Return list of authors used for auto-completion
in the authors field.
Return response as JSON.
"""
argd = wash_urlargd(
form, {'publicationid': (str, ''), 'term': (str, '')})
user_info = collect_user_info(req)
uid = user_info['uid']
req.content_type = 'application/json'
term = argd['term']
publicationid = argd['publicationid']
ret = get_favourite_authorships_for_user(uid, publicationid, term)
if ret:
return json.dumps(ret)
if ':' in term:
## an institution is being typed
name, institute = term.split(':', 1)
institute = institute.strip()
if len(institute) > 1:
institutes = [row[0] for row in get_kbr_keys(
'institutes', searchkey=institute, searchtype='s')]
institutes.sort()
return json.dumps(["%s: %s" % (name, institute) for institute in institutes[:100]])
return json.dumps([])
def authorships(self, req, form):
"""
Return list of authors used for auto-completion
in the authors field.
Return response as JSON.
"""
argd = wash_urlargd(form, {
'publicationid': (str, ''),
'term': (str, '')
})
user_info = collect_user_info(req)
uid = user_info['uid']
req.content_type = 'application/json'
term = argd['term']
publicationid = argd['publicationid']
ret = get_favourite_authorships_for_user(uid, publicationid, term)
if ret:
return json.dumps(ret)
if ':' in term:
## an institution is being typed
name, institute = term.split(':', 1)
institute = institute.strip()
if len(institute) > 1:
institutes = [
row[0] for row in get_kbr_keys(
'institutes', searchkey=institute, searchtype='s')
]
institutes.sort()
return json.dumps([
"%s: %s" % (name, institute)
for institute in institutes[:100]
])
return json.dumps([])
def get_coden_formatted(bfo, separator=','):
"""Produces a SPIRES-style coden reference for a record
This typically looks like JOURNAL-CODEN,VOLUME,FIRSTPAGE
If this is impossible (for example if we lack sufficient information about
the reference or lack a CODEN lookup KB), produces empty string.
@param separator A string used to join the pieces of the reference
"""
coden = ''
publication_info = bfo.fields('773__')
if publication_info:
publication_info = publication_info[0]
else:
return ''
journal = publication_info.get('p', '')
volume = publication_info.get('v', '')
pages = publication_info.get('c', '')
if pages:
dashpos = pages.find('-')
if dashpos > -1:
pages = pages[:dashpos]
try:
if journal and (volume != '' or pages != ''):
coden = separator.join([
get_kbr_keys("CODENS", searchvalue=journal,
searchtype='e')[0][0], volume, pages
])
except:
return ''
return coden
def test_EJOURNALS_keys(self):
"""bibknowledge - test left/right rules (key lookups)"""
mykeys = get_kbr_keys("EJOURNALS", "Acta")
self.assertEqual(2, len(mykeys))
mykeys = get_kbr_values("EJOURNALS", '', searchtype='e')
self.assertEqual(0, len(mykeys))
mykeys = get_kbr_values("EJOURNALS", searchtype='s')
self.assertEqual(327, len(mykeys))
mykeys = get_kbr_values("EJOURNALS", searchkey='', searchtype='s')
self.assertEqual(327, len(mykeys))
def test_EJOURNALS_keys(self):
"""bibknowledge - test left/right rules (key lookups)"""
mykeys = get_kbr_keys("EJOURNALS", "Acta")
self.assertEqual(2, len(mykeys))
mykeys = get_kbr_values("EJOURNALS", '', searchtype='e')
self.assertEqual(0, len(mykeys))
mykeys = get_kbr_values("EJOURNALS", searchtype='s')
self.assertEqual(327, len(mykeys))
mykeys = get_kbr_values("EJOURNALS", searchkey='', searchtype='s')
self.assertEqual(327, len(mykeys))
def test_EJOURNALS_keys(self):
"""bibknowledge - test a left/right rule"""
mykeys = get_kbr_keys("EJOURNALS", "Acta")
self.assertEqual(2, len(mykeys))
def test_EJOURNALS_keys(self):
"""bibknowledge - test a left/right rule"""
mykeys = get_kbr_keys("EJOURNALS", "Acta")
self.assertEqual(2, len(mykeys))
def load_kbs(cfg, run_sql, in_task=False):
for kb, query in cfg.iteritems():
task_sleep_now_if_required(can_stop_too=True)
if not kb_exists(kb):
add_kb(kb)
if in_task:
write_message("Updating %s KB..." % kb)
try:
if not in_task:
print "kb:", kb
print "kb beginning:", len(get_kb_mappings(kb))
if kb.startswith('json_'):
encoder = ComplexEncoder()
mapping, description = run_sql(query, with_desc=True)
if kb in CFG_ADDITIONAL_ENTRIES:
mapping += CFG_ADDITIONAL_ENTRIES[kb]
if not in_task:
print CFG_ADDITIONAL_ENTRIES[kb]
column_counter = {}
new_description = []
for column in description[1:]:
column = column[0]
counter = column_counter[column] = column_counter.get(
column, 0) + 1
if counter > 1:
new_description.append('%s%d' % (column, counter))
else:
new_description.append(column)
description = new_description
else:
mapping = run_sql(query)
if kb in CFG_ADDITIONAL_ENTRIES:
mapping += CFG_ADDITIONAL_ENTRIES[kb]
if not in_task:
print CFG_ADDITIONAL_ENTRIES[kb]
if not in_task:
print "mapping:", len(mapping)
if kb == 'projects':
mapping += [('000000', 'NO PROJECT')]
original_keys = set([key[0] for key in get_kbr_keys(kb)])
if not in_task:
print "original_keys before:", len(original_keys)
updated = 0
added = 0
for i, row in enumerate(mapping):
key, value = row[0], row[1:]
if kb.startswith('json_'):
value = encoder.encode(dict(zip(description, value)))
else:
value = value[0]
if value:
if key in original_keys:
original_keys.remove(key)
if in_task:
task_update_progress("%s - %s%%" %
(kb, i * 100 / len(mapping)))
if kb_mapping_exists(kb, key):
updated += 1
update_kb_mapping(kb, key, key, value)
else:
added += 1
add_kb_mapping(kb, key, value)
if not in_task:
print "updated:", updated, "added:", added
print "kb after update:", len(get_kb_mappings(kb))
print "original_keys after:", len(original_keys)
if in_task:
task_update_progress("Cleaning %s" % kb)
for key in original_keys:
remove_kb_mapping(kb, key)
if not in_task:
print "kb after remove:", len(get_kb_mappings(kb))
except:
register_exception(alert_admin=True,
prefix="Error when updating KB %s" % kb)
continue
def load_kbs(cfg, run_sql, in_task=False):
for kb, query in cfg.iteritems():
task_sleep_now_if_required(can_stop_too=True)
if not kb_exists(kb):
add_kb(kb)
if in_task:
write_message("Updating %s KB..." % kb)
try:
if not in_task:
print "kb:", kb
print "kb beginning:", len(get_kb_mappings(kb))
if kb.startswith('json_'):
encoder = ComplexEncoder()
mapping, description = run_sql(query, with_desc=True)
if kb in CFG_ADDITIONAL_ENTRIES:
mapping += CFG_ADDITIONAL_ENTRIES[kb]
if not in_task:
print CFG_ADDITIONAL_ENTRIES[kb]
column_counter = {}
new_description = []
for column in description[1:]:
column = column[0]
counter = column_counter[column] = column_counter.get(column, 0) + 1
if counter > 1:
new_description.append('%s%d' % (column, counter))
else:
new_description.append(column)
description = new_description
else:
mapping = run_sql(query)
if kb in CFG_ADDITIONAL_ENTRIES:
mapping += CFG_ADDITIONAL_ENTRIES[kb]
if not in_task:
print CFG_ADDITIONAL_ENTRIES[kb]
if not in_task:
print "mapping:", len(mapping)
if kb == 'projects':
mapping += [('000000', 'NO PROJECT')]
original_keys = set([key[0] for key in get_kbr_keys(kb)])
if not in_task:
print "original_keys before:", len(original_keys)
updated = 0
added = 0
for i, row in enumerate(mapping):
key, value = row[0], row[1:]
if kb.startswith('json_'):
value = encoder.encode(dict(zip(description, value)))
else:
value = value[0]
if value:
if key in original_keys:
original_keys.remove(key)
if in_task:
task_update_progress("%s - %s%%" % (kb, i * 100 / len(mapping)))
if kb_mapping_exists(kb, key):
updated += 1
update_kb_mapping(kb, key, key, value)
else:
added += 1
add_kb_mapping(kb, key, value)
if not in_task:
print "updated:", updated, "added:", added
print "kb after update:", len(get_kb_mappings(kb))
print "original_keys after:", len(original_keys)
if in_task:
task_update_progress("Cleaning %s" % kb)
for key in original_keys:
remove_kb_mapping(kb, key)
if not in_task:
print "kb after remove:", len(get_kb_mappings(kb))
except:
register_exception(alert_admin=True, prefix="Error when updating KB %s" % kb)
continue
