def delete (self, context):
cursor = context.get_cursor()
try:
# First, remove the study (connected table records will
# also be deleted). But don't delete non-existent studies.
if self.study_id >= 0:
study = Study(context, self.study_id)
study.delete(context)
# Next, unindex it.
search_index = canary.search.SearchIndex(context)
search_index.unindex_record(self)
# Then, remove the metadata
cursor.execute("""
DELETE FROM queued_record_metadata
WHERE queued_record_id = %s
""", self.uid)
# Finally, remove this record itself.
cursor.execute("""
DELETE FROM queued_records
WHERE uid = %s
""", self.uid)
if context.config.use_cache:
context.cache_delete('record:%s' % self.uid)
except Exception, e:
context.logger.error('Delete queued record %s (%s)', self.uid, e)
def delete(self, context):
cursor = context.get_cursor()
try:
# First, remove the study (connected table records will
# also be deleted). But don't delete non-existent studies.
if self.study_id >= 0:
study = Study(context, self.study_id)
study.delete(context)
# Next, unindex it.
search_index = canary.search.SearchIndex(context)
search_index.unindex_record(self)
# Then, remove the metadata
cursor.execute(
"""
DELETE FROM queued_record_metadata
WHERE queued_record_id = %s
""", self.uid)
# Finally, remove this record itself.
cursor.execute(
"""
DELETE FROM queued_records
WHERE uid = %s
""", self.uid)
if context.config.use_cache:
context.cache_delete('record:%s' % self.uid)
except Exception, e:
context.logger.error('Delete queued record %s (%s)', self.uid, e)
def search(self, query):
"""perform a lucene search for studies
"""
studies = []
for record in self.searcher.search(query, curated_only=True):
studies.append(Study(self.context, record.study_id))
return studies
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:
first_author = '-'
output.append('\t'.join(
#!/usr/bin/env python
# $Id$
from canary.context import Context
from canary.loader import QueuedRecord
from canary.study import Study
context = Context()
cursor = context.get_cursor()
cursor.execute("""
SELECT studies.record_id, study_history.study_id, study_history.modified
FROM study_history, studies
WHERE study_history.message = 'Set record status to curated'
AND study_history.study_id = studies.uid
ORDER BY studies.record_id ASC, study_history.modified ASC
""")
for row in cursor:
print "record_id:%i; study_id:%i; curated:%s" % row
# update either QUEUED_RECORDS or STUDIES with curated time
# r = QueuedRecord(con,row[0])
# r.date_curated = row[2]
# r.save
s = Study(context, row[1])
s.date_curated = row[2]
s.save(context)
#!/usr/bin/env python
# $Id$
from canary.context import Context
from canary.loader import QueuedRecord
from canary.study import Study
context = Context()
cursor = context.get_cursor()
cursor.execute("""
SELECT studies.record_id, study_history.study_id, study_history.modified
FROM study_history, studies
WHERE study_history.message = 'Set record status to curated'
AND study_history.study_id = studies.uid
ORDER BY studies.record_id ASC, study_history.modified ASC
""")
for row in cursor:
print "record_id:%i; study_id:%i; curated:%s" % row
# update either QUEUED_RECORDS or STUDIES with curated time
# r = QueuedRecord(con,row[0])
# r.date_curated = row[2]
# r.save
s = Study(context, row[1])
s.date_curated = row[2]
s.save(context)
pmid_list.sort()
for pmid in pmid_list:
cursor.execute("""
SELECT studies.uid AS study_id, queued_records.uid AS queued_record_id
FROM queued_records, studies
WHERE queued_records.study_id = studies.uid
AND studies.status = 2
AND queued_records.unique_identifier = %s
""", pmid)
fields = [d[0] for d in cursor.description]
desc = dtuple.TupleDescriptor([[f] for f in fields])
row = cursor.fetchone()
if row:
row = dtuple.DatabaseTuple(desc, row)
study = Study(row['study_id'])
study.load(cursor)
studies.append((study, pmid))
else:
# sort by unique_identifier for easier side-by-side comparison
cursor.execute("""
SELECT studies.uid AS study_id, queued_records.uid AS queued_record_id,
queued_records.unique_identifier
FROM studies, queued_records
WHERE studies.uid = queued_records.study_id
AND studies.status = 2
AND studies.curator_user_id = %s
ORDER BY ABS(queued_records.unique_identifier)
""", curator_id)
def makeplot(context, token, records):
this_module = sys.modules[__name__]
N = len(linkage_keys)
ind = arange(N)
width = 0.35
meth_type_count = {}
study_count = dict(zip(linkages, array([0] * len(linkages))))
for id, type in linkages_attrs:
meth_type_count[id] = start.copy()
for rec in records:
study = Study(context, rec.study_id)
for attr, key in linkages_attrs:
if getattr(study, 'has_%s' % key):
study_count[attr] += 1
for meth in study.methodologies:
meth_type_count[attr][meth.study_type_id] += 1
rc('grid', color=0.85, linestyle='-', linewidth=0.3)
grid(True)
yoff = array([0] * N)
s = """
'experimental' : 1,
'descriptive' : 2,
'aggregate' : 3,
'cross sectional' : 4,
'cohort' : 5,
'case control' : 6,
'disease model' : 7,
"""
print['%s %s\n' % (k, v) for k, v in meth_type_count.items()]
p_exp_x = [meth_type_count[key][1] for key in linkage_keys]
p_exp = bar(ind, p_exp_x, width, color='#993333', bottom=yoff)
yoff = yoff + p_exp_x
p_coh_x = [meth_type_count[key][5] for key in linkage_keys]
p_coh = bar(ind, p_coh_x, width, color='#FF9933', bottom=yoff)
yoff = yoff + p_coh_x
p_csec_x = [meth_type_count[key][4] for key in linkage_keys]
p_csec = bar(ind, p_csec_x, width, color='#99CC99', bottom=yoff)
yoff = yoff + p_csec_x
p_desc_x = [meth_type_count[key][2] for key in linkage_keys]
p_desc = bar(ind, p_desc_x, width, color='#6666CC', bottom=yoff)
yoff = yoff + p_desc_x
#p_agg_x = [meth_type_count[key][3] for key in linkage_keys]
#p_agg = bar(ind, p_agg_x, width, color='#CCCC00', bottom=yoff)
#yoff = yoff + p_agg_x
#p_cc_x = [meth_type_count[key][6] for key in linkage_keys]
#p_cc = bar(ind, p_cc_x, width, color='#CC66FF', bottom=yoff)
#yoff = yoff + p_cc_x
#p_dm_x = [meth_type_count[key][7] for key in linkage_keys]
#p_dm = bar(ind, p_dm_x, width, color='#993366', bottom=yoff)
#yoff = yoff + p_dm_x
precords_x = array([len(records)] * N)
#precords = bar(ind+width/3, precords_x, width/3, color='#999999', bottom=0)
precords = plot(precords_x, color='#AAAAAA', marker='-', linewidth=1.5)
pstudies_x = [study_count[k] for k in linkage_keys]
pstudies = bar(ind + width / 3,
pstudies_x,
width / 3,
color='#EEEEEE',
bottom=0)
max_val = max(yoff)
xlabel('Linkages to Human Health')
ylabel('# Methodologies by Type for Studies with Linkages')
title('Animal Sentinels for "%s" (%s records)' % (token, len(records)),
size=12)
xticks(ind + width / 2, [linkages[k] for k in linkage_keys],
rotation=20,
size=6)
step = max_val / 5
yticks(arange(0, max_val + (step * 3), step))
legend(
(p_exp[0], p_coh[0], p_csec[0], p_desc[0], precords[0], pstudies[0]),
('Experimental', 'Cohort', 'Cross-Sectional', 'Descriptive',
'# Studies Total', '# Records w/Linkage'))
## legend((p_exp[0], p_desc[0], p_agg[0], p_csec[0], p_coh[0],
## p_cc[0], p_dm[0], precords[0], pstudies[0]),
## ('Experimental', 'Descriptive', 'Aggregate',
## 'Cross-Sectional', 'Cohort', 'Case-Control', 'Disease Model',
#savefig(('%s' % token.replace(' ', '_')))
show()
cla()
def index_record(self, record, writer=None):
# field, value, store?, index?, token?
try:
if not writer:
had_writer = False
writer = self.context.get_search_index_writer(False)
else:
had_writer = True
study = Study(self.context, record.study_id)
self.logger.debug('starting document')
doc = PyLucene.Document()
# First, we need to create a unique key so we can later delete
# if necessary. Will try simply uid for now.
doc.add(PyLucene.Field('uid', str(record.uid), True, True, False))
doc.add(PyLucene.Field('all', str(record.uid), True, True, False))
# Second, save internal-use metadata. These should probably
# be x'd out at Query-time.
doc.add(
PyLucene.Field('record-status', str(record.status), False,
True, False))
doc.add(
PyLucene.Field('article-type', str(study.article_type), False,
True, False))
source_catalog = self.context.get_source_catalog()
complete_term_map = source_catalog.get_complete_mapping()
mapped_metadata = record.get_mapped_metadata(complete_term_map)
# First index all the non-multiple metadata fields
for field in ('abstract', 'affiliation', 'issn', 'journal',
'pubdate', 'issue', 'pages', 'title', 'volume'):
val = mapped_metadata.get(field, None)
if val:
doc.add(PyLucene.Field(field, val, False, True, True))
doc.add(PyLucene.Field('all', val, False, True, True))
# Be sure to index all of (abbrev, full title, issn) as "journal"
issn = mapped_metadata.get('issn')
if issn:
j = Journal()
j.load_from_issn(self.context, issn)
no_dash = j.no_dash()
self.logger.debug('indexing journal: %s, abbv:%s, issn:%s' % \
(j.journal_title, j.abbreviation, issn))
doc.add(PyLucene.Field('journal', issn, False, True, True))
doc.add(PyLucene.Field('journal', no_dash, False, True, True))
doc.add(PyLucene.Field('all', issn, False, True, True))
doc.add(PyLucene.Field('all', no_dash, False, True, True))
if j.abbreviation:
doc.add(
PyLucene.Field('journal', j.abbreviation, False, True,
True))
doc.add(
PyLucene.Field('all', j.abbreviation, False, True,
True))
if j.journal_title:
doc.add(
PyLucene.Field('journal', j.journal_title, False, True,
True))
doc.add(
PyLucene.Field('all', j.journal_title, False, True,
True))
# If a page range is given, index the first page, assuming
# the delimiter is '-'
pages = mapped_metadata.get('pages', None)
if pages \
and '-' in pages:
first_page = pages[0:pages.index('-')]
doc.add(PyLucene.Field('pages', first_page, False, True, True))
doc.add(PyLucene.Field('all', first_page, False, True, True))
# 'unique_identifier' must be specially treated because
# of the '_'
val = mapped_metadata.get('unique_identifier', None)
if val:
doc.add(
PyLucene.Field('unique-identifier', val, False, True,
True))
doc.add(PyLucene.Field('all', val, False, True, True))
# Next, index all the possibly-multiple metadata fields
# Give these (especially for author and subject) a little
# boost, less than for canary UMLS concepts
for field in ('author', 'grantnum', 'keyword', 'registrynum',
'subject'):
vals = mapped_metadata.get(field, None)
for val in vals:
doc.add(PyLucene.Field(field, val, False, True, True))
f = PyLucene.Field('all', val, False, True, True)
f.setBoost(1.3)
doc.add(f)
# If at least one author name is available, index the first
# author to support first-author searching. Also, boost it
# slightly higher than the other authors.
authors = mapped_metadata.get('author', None)
if authors:
doc.add(
PyLucene.Field('first-author', authors[0], False, True,
True))
f = PyLucene.Field('all', authors[0], False, True, True)
f.setBoost(1.5)
doc.add(f)
# All the booleans
for bool in ('has_outcomes', 'has_exposures', 'has_relationships',
'has_interspecies', 'has_exposure_linkage',
'has_outcome_linkage', 'has_genomic'):
val = getattr(study, bool)
# NOTE: I think lucene dislikes '_' in field names ??
boolstr = bool.replace('_', '-')
doc.add(
PyLucene.Field(boolstr, str(int(val)), False, True, False))
# NOTE: no need to add this to 'all'. I think.
# Now, all the UMLS concepts. Simpler approach to
# lucene "synonym injection", but it works! Give it
# slightly bigger boost than keywords/subjects
for ctype in ('exposures', 'outcomes', 'risk_factors', 'species'):
# NOTE: I think lucene dislikes '_' in field names ??
ctype_search = ctype.replace('_', '-')
for val in getattr(study, ctype):
concept = Concept(self.context, val.concept_id)
for syn in concept.synonyms:
doc.add(
PyLucene.Field(ctype_search,
unicode(syn, 'latin-1'), False,
True, True))
f = PyLucene.Field('all', unicode(syn, 'latin-1'),
False, True, True)
f.setBoost(2.0)
doc.add(f)
# And, the locations
gazeteer = self.context.get_gazeteer()
locs = []
for location in study.locations:
feature = Feature(self.context, uid=location.feature_id)
feature.load(self.context)
if gazeteer.fips_codes.has_key(
(feature.country_code, feature.adm1)):
region_name = gazeteer.fips_codes[(feature.country_code,
feature.adm1)]
else:
region_name = ''
full_name = '%s (%s, %s, %s)' % (
feature.name, gazeteer.feature_codes[feature.feature_type],
render_capitalized(region_name),
render_capitalized(
gazeteer.country_codes[feature.country_code]))
doc.add(
PyLucene.Field('location', unicode(full_name, 'latin-1'),
False, True, True))
doc.add(
PyLucene.Field('all', unicode(full_name, 'latin-1'), False,
True, True))
# Finally, the methodologies
for meth in study.methodologies:
doc.add(
PyLucene.Field('methodology',
meth.get_study_type(text=True), False, True,
True))
doc.add(
PyLucene.Field('all', meth.get_study_type(text=True),
False, True, True))
# And each exposure route term
for route in meth.get_routes(True):
doc.add(
PyLucene.Field('exposure_route', route, False, True,
True))
doc.add(PyLucene.Field('all', route, False, True, True))
writer.addDocument(doc)
if not had_writer:
writer.close()
except Exception, e:
self.logger.error('Failed to index record: %s', e)
self.logger.error(traceback.print_exc())
if __name__ == '__main__':
cmdline = CommandLine()
cmdline.parse_args()
context = cmdline.context()
collector = StatCollector(context)
collector.add_handlers(
CuratorHandler(),
ArticleTypeHandler(),
ExposureHandler(),
OutcomeHandler(),
RiskFactorHandler(),
SpeciesHandler(),
LocationHandler(),
MethodologyTypeHandler(),
)
searcher = RecordSearcher(context)
records = searcher.search('record-status:%i' % QueuedRecord.STATUS_CURATED)
today = datetime.now()
one_weeks_records = [
rec for rec in records
if today - Study(context, rec.study_id).date_modified <= timedelta(7)
]
collector.process(one_weeks_records)
for handler in collector.handlers:
print handler.__class__, handler.stats