def records_by_author (context, author):
cursor = context.get_cursor()
queued_records = []
source_catalog = context.get_source_catalog()
complete_mapping = source_catalog.get_complete_mapping()
term_list = complete_mapping['author']
term_clause = ' OR '.join(['queued_record_metadata.term_id=%s' % term.uid for term in term_list])
try:
select_clause = """
SELECT queued_records.uid
FROM queued_records, queued_record_metadata, studies
WHERE queued_records.uid = queued_record_metadata.queued_record_id
AND queued_records.uid = studies.record_id
AND queued_records.status = 2
AND studies.article_type >= 2
AND studies.article_type < 8
AND (%s)
""" % term_clause
cursor.execute(select_clause + """
AND value LIKE %s
""", str(author) + '%'
)
rows = cursor.fetchall()
for row in rows:
queued_record = QueuedRecord(context, row[0])
queued_records.append(queued_record)
except Exception, e:
context.logger.error('Records by author: %s', e)
def records_by_year (context, year, term_map={}):
cursor = context.get_cursor()
queued_records = []
year_terms = term_map['pubdate']
year_clause = ' OR '.join(['queued_record_metadata.term_id=%s' % term.uid for term in year_terms])
try:
select_clause = """
SELECT queued_records.uid
FROM queued_records, queued_record_metadata, studies
WHERE queued_records.uid = queued_record_metadata.queued_record_id
AND queued_records.uid = studies.record_id
AND queued_records.status = 2
AND studies.article_type >= 2
AND studies.article_type < 8
AND (%s)
""" % year_clause
cursor.execute(select_clause + """
AND SUBSTRING(queued_record_metadata.value, 1, 4) LIKE %s
""", str(year) + '%'
)
rows = cursor.fetchall()
for row in rows:
queued_record = QueuedRecord(context, row[0])
queued_records.append(queued_record)
except Exception, e:
context.logger.error('Records by year: %s', e)
def records_by_journal (context, issn, term_map={}):
journal_title = ''
queued_records = []
issn_terms = term_map['issn']
issn_clause = ' OR '.join(['queued_record_metadata.term_id=%s' % term.uid for term in issn_terms])
cursor = context.get_cursor()
cursor.execute("""
SELECT journal_title
FROM medline_journals
WHERE issn = %s
""", issn)
try:
rows = cursor.fetchall()
if len(rows) != 1:
raise Exception('Journal %s not found' % issn)
journal_title = rows[0][0]
select_clause = """
SELECT queued_records.uid
FROM queued_records, queued_record_metadata, studies
WHERE queued_record_metadata.queued_record_id = queued_records.uid
AND queued_records.uid = studies.record_id
AND queued_records.status = 2
AND studies.article_type >= 2
AND studies.article_type < 8
AND (%s)
""" % issn_clause
cursor.execute(select_clause + """
AND queued_record_metadata.value = %s
""", issn
)
rows = cursor.fetchall()
for row in rows:
queued_record = QueuedRecord(context, row[0])
queued_records.append(queued_record)
except Exception, e:
context.logger.error('Records by journal: %s', e)
def records_by_methodology (context, methodology_id):
queued_records = []
cursor = context.get_cursor()
try:
cursor.execute("""
SELECT queued_records.uid
FROM queued_records, studies, methodologies
WHERE queued_records.uid = studies.record_id
AND studies.uid = methodologies.study_id
AND queued_records.status = 2
AND studies.article_type >= 2
AND studies.article_type < 8
AND methodologies.study_type_id = %s
""", methodology_id
)
rows = cursor.fetchall()
for row in rows:
queued_record = QueuedRecord(context, row[0])
queued_records.append(queued_record)
except Exception, e:
context.logger.error('Records by methodology: %s', e)
def records_by_concept (context, concept, concept_id):
cursor = context.get_cursor()
queued_records = []
table_name = concept_tables[concept]
try:
select_clause = """
SELECT queued_records.uid
FROM queued_records, studies, %s
WHERE %s.study_id = studies.uid
AND studies.record_id = queued_records.uid
AND %s.concept_id = %s
AND queued_records.status = 2
AND studies.article_type >= 2
AND studies.article_type < 8
""" % (table_name,
table_name,
table_name, concept_id)
cursor.execute(select_clause)
rows = cursor.fetchall()
for row in rows:
queued_record = QueuedRecord(context, row[0])
queued_records.append(queued_record)
except Exception, e:
context.logger.error('Records by concept: %s', e)
sys.exit(0)
query_str = options.boolean.join(
[' "%s" [%s] ' % (term, options.field) for term in args])
#print query_str.strip()
search_index = SearchIndex(context)
hit_list = []
hits, searcher = search_index.search(query_str)
for i, doc in hits:
hit_list.append(doc.get('uid'))
searcher.close()
output = []
for id in hit_list:
rec = QueuedRecord(context, int(id))
if options.locations:
study = Study(context, rec.study_id)
for loc in study.locations:
out = []
out.extend((id, loc.uid, loc.study_id, loc.feature_id))
feature = Feature(uid=loc.feature_id)
feature.load(context)
out.extend((feature.latitude, feature.longitude, feature.name,
feature.feature_type, feature.country_code))
output.append('\t'.join([str(v) for v in out]))
else:
mm = rec.get_mapped_metadata(ctm)
if mm['author']:
first_author = mm['author'][0]
else:
# for query by ArcGIS.
#
# $Id$
import canary.context
from canary.gazeteer import Feature
from canary.loader import QueuedRecord
from canary.study import Study
if __name__ == '__main__':
out_file = open('/tmp/export-location-info.txt', 'w')
all = {}
context = canary.context.Context()
for i in range(4000):
try:
rec = QueuedRecord(context, i)
if not rec \
or not rec.status == rec.STATUS_CURATED:
raise 'ValueError'
study = Study(context, rec.study_id)
if not study.status == study.STATUS_TYPES['curated'] \
or not (study.article_type >= study.ARTICLE_TYPES['traditional'] \
and study.article_type <= study.ARTICLE_TYPES['curated']):
raise 'ValueError'
for loc in study.locations:
out = []
out.extend((loc.uid, loc.study_id, loc.feature_id))
feature = Feature(uid=loc.feature_id)
search_index = SearchIndex(context)
searches = (
'Lead [exposure]',
'Hantavirus [exposure]',
'peromyscus [species]',
'Michigan [location]',
'DDT [exposure]',
'2003 [year]',
'cats and dogs',
'"Burger J" [author]',
'cross-sectional [methodology]',
'case-control [methodology] and cattle [species]',
'disease-model [methodology]',
'"age factors" [risk_factors]',
'Sarin [exposure]',
'Arsenic [exposure]',
'"Bacillus anthracis" [exposure]',
'"West Nile Virus" [exposure]',
'"Water Pollutants, Chemical" [exposure]',
)
for t in searches:
hits, searcher = search_index.search(t)
result_set = []
for i, doc in hits:
uid = doc.get(str('uid'))
record = QueuedRecord(context, uid)
if record.status == record.STATUS_CURATED:
result_set.append(record)
searcher.close()
makeplot(context, t, result_set)
pubmed_source = source_catalog.get_source(13)
pubmed_search = PubmedSearch()
if options.canary_id:
rows = [[options.canary_id,],]
else:
# get all active queuedrecord ids
cursor.execute("""
SELECT uid
FROM queued_records
""")
rows = cursor.fetchall()
parser = Parser(pubmed_source)
for row in rows:
qr = QueuedRecord(context, row[0])
print 'Fetching pubmed data for ui %s' % qr.unique_identifier
pm_data = pubmed_search.fetch(qr.unique_identifier)
fetched_records = parser.parse(mapped_terms=complete_mapping,
is_email=False, data=pm_data)
if len(fetched_records) != 1:
print 'Fetch for %s (%s) found %s records, ignoring' % (ui,
qr.uid, len(fetched_records))
else:
print 'Orig metadata:', qr.metadata
fetched_rec = fetched_records[0]
print 'Fetched metadata:', fetched_rec.metadata
fetched_rec_metadata = fetched_rec.get_mapped_metadata(complete_mapping)
print 'Fetched metadata, mapped:', fetched_rec_metadata
if options.update:
rows = [
[
options.canary_id,
],
]
else:
# get all active queuedrecord ids
cursor.execute("""
SELECT uid
FROM queued_records
""")
rows = cursor.fetchall()
parser = Parser(pubmed_source)
for row in rows:
qr = QueuedRecord(context, row[0])
print 'Fetching pubmed data for ui %s' % qr.unique_identifier
pm_data = pubmed_search.fetch(qr.unique_identifier)
fetched_records = parser.parse(mapped_terms=complete_mapping,
is_email=False,
data=pm_data)
if len(fetched_records) != 1:
print 'Fetch for %s (%s) found %s records, ignoring' % (
ui, qr.uid, len(fetched_records))
else:
print 'Orig metadata:', qr.metadata
fetched_rec = fetched_records[0]
print 'Fetched metadata:', fetched_rec.metadata
fetched_rec_metadata = fetched_rec.get_mapped_metadata(
complete_mapping)