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sdGetRawPrimTriage.py
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sdGetRawPrimTriage.py
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'''
Purpose:
run sql to get lit triage relevance training set
(minor) Data transformations include:
replacing non-ascii chars with ' '
replacing FIELDSEP and RECORDSEP chars in the doc text w/ ' '
Outputs: Delimited file to stdout
See sampleDataLib.ClassifiedSample for output format
'''
#-----------------------------------
import sys
import os
import string
import re
import time
import argparse
import db
import sampleDataLib
from utilsLib import removeNonAscii
import ExtractedTextSet
#-----------------------------------
sampleObjType = sampleDataLib.PrimTriageClassifiedSample
# for the Sample output file
outputSampleSet = sampleDataLib.ClassifiedSampleSet(sampleObjType=sampleObjType)
RECORDEND = sampleObjType.getRecordEnd()
FIELDSEP = sampleObjType.getFieldSep()
#-----------------------------------
def getArgs():
parser = argparse.ArgumentParser( \
description='Get littriage relevance training samples, write to stdout')
parser.add_argument('--test', dest='test', action='store_true',
required=False,
help="just run ad hoc test code")
parser.add_argument('option', action='store', default='counts',
choices=['discard_after', 'keep_after', 'keep_before',
'keep_tumor', 'test_2020', 'counts'],
help='which subset of training samples to get or "counts" (default)')
parser.add_argument('-l', '--limit', dest='nResults',
required=False, type=int, default=0, # 0 means ALL
help="limit results to n references. Default is no limit")
parser.add_argument('--textlength', dest='maxTextLength',
type=int, required=False, default=None,
help="only include the 1st n chars of text fields (for debugging)")
parser.add_argument('--norestrict', dest='restrictArticles',
action='store_false', required=False,
help="include all articles, default: skip review and non-peer reviewed")
parser.add_argument('-q', '--quiet', dest='verbose', action='store_false',
required=False, help="skip helpful messages to stderr")
defaultHost = os.environ.get('PG_DBSERVER', 'bhmgidevdb01')
defaultDatabase = os.environ.get('PG_DBNAME', 'prod')
parser.add_argument('-s', '--server', dest='server', action='store',
required=False, default=defaultHost,
help='db server. Shortcuts: adhoc, prod, dev, test. (Default %s)' %
defaultHost)
parser.add_argument('-d', '--database', dest='database', action='store',
required=False, default=defaultDatabase,
help='which database. Example: mgd (Default %s)' % defaultDatabase)
args = parser.parse_args()
if args.server == 'adhoc':
args.host = 'mgi-adhoc.jax.org'
args.db = 'mgd'
elif args.server == 'prod':
args.host = 'bhmgidb01.jax.org'
args.db = 'prod'
elif args.server == 'dev':
args.host = 'mgi-testdb4.jax.org'
args.db = 'jak'
elif args.server == 'test':
args.host = 'bhmgidevdb01.jax.org'
args.db = 'prod'
else:
args.host = args.server + '.jax.org'
args.db = args.database
return args
#-----------------------------------
args = getArgs()
####################
# SQL fragments used to build up queries
# We build the queries in the following steps:
# 1) A tmp OMIT_TABLE of references to omit from the training set because
# their ground truth may be questionable
# 2) a tmp BASE_TABLE of all refs NOT in the OMIT_TABLE and build an
# index on creation_date for that table. This speeds things dramatically
# 3) a final tmp table pulled from the BASE_TABLE with specific where clause
# criteria for the specific training sample option
# 4) using the final tmp table,
# do a "select *" to get the basic reference data
# use ExtractedTextSet.getExtractedTextSetForTable() to get their
# extracted text
# do select count(*) to get data set counts.
####################
LIT_TRIAGE_DATE = "10/31/2017" # when we switched to new lit triage
START_DATE = "1/01/2017" # earliest date for refs to get
# before lit Triage
TUMOR_START_DATE = "07/01/2013" # date to get add'l tumor papers from
END_DATE = "12/31/2019" # last date to get training data from
#----------------
OMIT_TEXT = "Omitted refs\n" + \
"\t(GOA loaded or only pm2gene indexed or MGI:Mice_in_references_only)"
BUILD_OMIT_TABLE = [ \
# Tmp table of samples to omit.
# Currently, reasons to omit:
# (1) articles "indexed" by pm2gene & not selected by a group other than GO
#
# (2) created by the goa load and not selected by a group other than GO.
# In these cases, no curator has selected the paper, so we don't really
# know if these are relevant (not good ground truth)
#
# (3) articles marked as discard with MGI:Mice_in_references_only tag
# Since these articles are discarded for a different reason, and they
# will not go through relevance classification, it seems we should not
# train on them.
'''
create temporary table tmp_omit
as
select r._refs_key, a.accid pubmed
from bib_refs r join bib_workflow_status bs
on (r._refs_key = bs._refs_key and bs.iscurrent=1 )
join bib_status_view bsv on (r._refs_key = bsv._refs_key)
left join bib_workflow_tag bt on (r._refs_key = bt._refs_key)
join bib_workflow_relevance wr on (r._refs_key = wr._refs_key
and wr.iscurrent=1)
join acc_accession a
on (a._object_key = r._refs_key and a._logicaldb_key=29 -- pubmed
and a._mgitype_key=1 )
where
( ( (bs._status_key = 31576673 and bs._group_key = 31576666 and
bs._createdby_key = 1571 -- index for GO by pm2geneload
)
or r._createdby_key = 1575 -- created by littriage_go
)
and -- not selected by any other group
(
bsv.ap_status in ('Not Routed', 'Rejected')
and bsv.gxd_status in ('Not Routed', 'Rejected')
and bsv.tumor_status in ('Not Routed', 'Rejected')
and bsv.qtl_status in ('Not Routed', 'Rejected')
and r.creation_date >= '%s'
)
)
or
(
wr._relevance_key = 70594666 -- discard
and bt._tag_key = 49170000 -- MGI:Mice_in_references_only
)
''' % (START_DATE),
'''
create index tmp_idx1 on tmp_omit(_refs_key)
''',
]
#----------------
BUILD_BASE_TABLE = [ \
'''
create temporary table tmp_refs
as
select distinct r._refs_key, r.creation_date
from bib_refs r join bib_workflow_data bd on (r._refs_key = bd._refs_key)
where r._createdby_key != 1609 -- not littriage_discard user
and bd.extractedtext is not null
and not exists (select 1 from tmp_omit t where t._refs_key = r._refs_key)
''',
'''
create index tmp_idx2 on tmp_refs(_refs_key)
''',
# this index is important for speed since bib_refs does not have an index on
# creation_date
'''
create index tmp_idx3 on tmp_refs(creation_date)
''',
]
#----------------
FINAL_TMP_TABLE_SQL = \
'''
create temporary table %s
as
select distinct r._refs_key,
rt.term as knownClassName,
r.year,
to_char(r.creation_date, 'MM/DD/YYYY') as "creation_date",
r.isreviewarticle,
typeTerm.term as ref_type,
'ignore supp term' as supp_status,
-- suppTerm.term as supp_status,
r.journal, r.title, r.abstract,
a.accid pubmed,
bsv.ap_status,
bsv.gxd_status,
bsv.go_status,
bsv.tumor_status,
bsv.qtl_status
from bib_refs r join tmp_refs tr on (r._refs_key = tr._refs_key)
join bib_workflow_data bd on (r._refs_key = bd._refs_key)
join bib_status_view bsv on (r._refs_key = bsv._refs_key)
-- join voc_term suppTerm on (bd._supplemental_key = suppTerm._term_key)
-- (was originally including supp status term for analysis, but
-- sometimes there were duplicate status rcds in bib_workflow_data,
-- so I'm skipping this for now)
join bib_workflow_relevance wr on (r._refs_key = wr._refs_key
and wr.iscurrent=1)
join voc_term rt on (wr._relevance_key = rt._term_key)
join voc_term typeTerm on (r._referencetype_key = typeTerm._term_key)
join acc_accession a on
(a._object_key = r._refs_key and a._logicaldb_key=29 -- pubmed
and a._mgitype_key=1 and a.preferred=1 )
'''
RESTRICT_REF_TYPE = \
'''
and r._referencetype_key=31576687 -- peer reviewed article
and r.isreviewarticle != 1
'''
#----------------
# Dict of where clause components for specific query options,
# these should be non-overlapping result sets
WHERE_CLAUSES = { \
'discard_after' :
'''
where -- discard_after
wr._relevance_key = 70594666 -- discard
-- Note: using rt.term = 'discard', I could not get the query to return
and tr.creation_date > '%s' -- After lit triage release
and tr.creation_date <= '%s' -- before end date
''' % (LIT_TRIAGE_DATE, END_DATE),
'keep_after' :
'''
where -- keep_after
(bsv.ap_status in ('Chosen', 'Indexed', 'Full-coded')
or bsv.go_status in ('Chosen', 'Indexed', 'Full-coded')
or bsv.gxd_status in ('Chosen', 'Indexed', 'Full-coded')
or bsv.qtl_status in ('Chosen', 'Indexed', 'Full-coded')
or bsv.tumor_status in ('Chosen', 'Indexed', 'Full-coded')
)
and tr.creation_date > '%s' -- After lit triage release
and tr.creation_date <= '%s' -- before end date
''' % (LIT_TRIAGE_DATE, END_DATE),
'keep_before' :
'''
where -- keep_before
(bsv.ap_status in ('Chosen', 'Indexed', 'Full-coded')
or bsv.go_status in ('Chosen', 'Indexed', 'Full-coded')
or bsv.gxd_status in ('Chosen', 'Indexed', 'Full-coded')
or bsv.qtl_status in ('Chosen', 'Indexed', 'Full-coded')
or bsv.tumor_status in ('Chosen', 'Indexed', 'Full-coded')
)
and tr.creation_date >= '%s' -- after start date
and tr.creation_date <= '%s' -- before lit triage release
''' % (START_DATE, LIT_TRIAGE_DATE, ),
'keep_tumor' :
'''
where -- keep_tumor
bsv.tumor_status in ('Chosen', 'Indexed', 'Full-coded')
and tr.creation_date >= '%s' -- after tumor start date
and tr.creation_date <= '%s' -- before start date
''' % (TUMOR_START_DATE, START_DATE, ),
'test_2020' :
'''
where -- test set of 2020 refs
tr.creation_date > '%s' -- After end date
and tr.creation_date <= '12/31/2020' -- before end of 2020
and
(
(wr._relevance_key = 70594666) -- discard
or
(bsv.ap_status in ('Chosen', 'Indexed', 'Full-coded')
or bsv.go_status in ('Chosen', 'Indexed', 'Full-coded')
or bsv.gxd_status in ('Chosen', 'Indexed', 'Full-coded')
or bsv.qtl_status in ('Chosen', 'Indexed', 'Full-coded')
or bsv.tumor_status in ('Chosen', 'Indexed', 'Full-coded')
)
)
''' % (END_DATE),
} # end WHERE_CLAUSES
#-----------------------------------
def doCounts():
'''
Get counts of sample records from db and write them to stdout
'''
sys.stdout.write(time.ctime() + '\n')
sys.stdout.write("Hitting database %s %s as mgd_public\n" % \
(args.host, args.db))
sys.stdout.write(getRestrictedArticleText())
selectCountSQL = 'select count(distinct _refs_key) as num from %s\n'
db.sql(BUILD_OMIT_TABLE, 'auto')
db.sql(BUILD_BASE_TABLE, 'auto')
doCount(OMIT_TEXT, [selectCountSQL % "tmp_omit"])
tmpTableName, finalTmpTableSQL = buildFinalTmpTableSQL('discard_after')
doCount("Discard after: %s - %s" % (LIT_TRIAGE_DATE, END_DATE),
finalTmpTableSQL + [selectCountSQL % tmpTableName])
tmpTableName, finalTmpTableSQL = buildFinalTmpTableSQL('keep_after')
doCount("Keep after: %s - %s" % (LIT_TRIAGE_DATE, END_DATE),
finalTmpTableSQL + [selectCountSQL % tmpTableName])
tmpTableName, finalTmpTableSQL = buildFinalTmpTableSQL('keep_before')
doCount("Keep before: %s - %s" % (START_DATE, LIT_TRIAGE_DATE),
finalTmpTableSQL + [selectCountSQL % tmpTableName])
tmpTableName, finalTmpTableSQL = buildFinalTmpTableSQL('keep_tumor')
doCount("Tumor papers: %s - %s" % (TUMOR_START_DATE, START_DATE),
finalTmpTableSQL + [selectCountSQL % tmpTableName])
tmpTableName, finalTmpTableSQL = buildFinalTmpTableSQL('test_2020')
doCount("Test set from 2020" ,
finalTmpTableSQL + [selectCountSQL % tmpTableName])
#-----------------------------------
def doCount(label, q # list of sql stmts. last one being 'select count as num'
):
results = db.sql(q, 'auto')
num = results[-1][0]['num']
sys.stdout.write("%7d\t%s\n" % (num, label))
#-----------------------------------
def getRestrictedArticleText():
if args.restrictArticles:
text = "Omitting review and non-peer reviewed articles\n"
else:
text = "Including review and non-peer reviewed articles\n"
return text
#-----------------------------------
def buildFinalTmpTableSQL(queryKey):
"""
Assemble SQL statements to build final tmp table with the references from
the desired queryKey
Return tmpTableName and list of SQL stmts
"""
if args.restrictArticles: restrict = RESTRICT_REF_TYPE
else: restrict = ''
if args.nResults > 0: limitSQL = "\nlimit %d\n" % args.nResults
else: limitSQL = ''
finalTmpTableName = 'tmp_' + queryKey
finalTmpTableSQL = (FINAL_TMP_TABLE_SQL % finalTmpTableName) + \
WHERE_CLAUSES[queryKey] + restrict + limitSQL
buildIndexSQL = 'create index tmp_idx_%s on %s(_refs_key)' % \
(queryKey, finalTmpTableName)
return finalTmpTableName, [finalTmpTableSQL, buildIndexSQL]
#-----------------------------------
####################
def main():
####################
db.set_sqlServer (args.host)
db.set_sqlDatabase(args.db)
db.set_sqlUser ("mgd_public")
db.set_sqlPassword("mgdpub")
startTime = time.time()
if args.option == 'counts': doCounts()
else: doSamples()
verbose("Total time: %8.3f seconds\n\n" % (time.time()-startTime))
#-----------------------------------
def doSamples():
'''
Run SQL to get samples from DB and output them to stdout
'''
verbose("Hitting database %s %s as mgd_public\n" % (args.host, args.db))
verbose(getRestrictedArticleText())
verbose("Retreiving reference set: %s\n" % args.option)
startTime = time.time()
# build initial tmp tables
db.sql(BUILD_OMIT_TABLE, 'auto')
db.sql(BUILD_BASE_TABLE, 'auto')
# build final tmp tbl with the desired references
tmpTableName, finalTmpTableSQL = buildFinalTmpTableSQL(args.option)
db.sql(finalTmpTableSQL, 'auto')
# get the result set
refRcds = db.sql(['select * from %s' % tmpTableName], 'auto')[-1]
verbose("%d references retrieved\n" % (len(refRcds)))
verbose("SQL time: %8.3f seconds\n\n" % (time.time()-startTime))
# get their extracted text and join it to refRcds
verbose("Getting extracted text\n")
startTime = time.time()
extTextSet = ExtractedTextSet.getExtractedTextSetForTable(db, tmpTableName)
extTextSet.joinRefs2ExtText(refRcds, allowNoText=True)
verbose("%8.3f seconds\n\n" % (time.time()-startTime))
# build Sample objects and write SampleSet
global outputSampleSet
startTime = time.time()
verbose("constructing and writing samples:\n")
for r in refRcds:
sample = sqlRecord2ClassifiedSample(r)
outputSampleSet.addSample(sample)
writeSamples(outputSampleSet)
verbose("wrote %d samples:\n" % outputSampleSet.getNumSamples())
verbose("%8.3f seconds\n\n" % (time.time()-startTime))
return
#-----------------------------------
def writeSamples(sampleSet):
sampleSet.setMetaItem('host', args.host)
sampleSet.setMetaItem('db', args.db)
sampleSet.setMetaItem('time', time.strftime("%Y/%m/%d-%H:%M:%S"))
sampleSet.write(sys.stdout)
#-----------------------------------
def sqlRecord2ClassifiedSample(r, # sql Result record
):
"""
Encapsulates knowledge of ClassifiedSample.setFields() field names
"""
newR = {}
newSample = sampleObjType()
newR['knownClassName']= str(r['knownClassName'])
newR['ID'] = str(r['pubmed'])
newR['creationDate'] = str(r['creation_date'])
newR['year'] = str(r['year'])
newR['journal'] = '_'.join(str(r['journal']).split(' '))
newR['title'] = cleanUpTextField(r, 'title')
newR['abstract'] = cleanUpTextField(r, 'abstract')
newR['extractedText'] = cleanUpTextField(r, 'ext_text')
if args.maxTextLength: newR['extractedText'] += '\n'
newR['isReview'] = str(r['isreviewarticle'])
newR['refType'] = str(r['ref_type'])
newR['suppStatus'] = str(r['supp_status'])
newR['apStatus'] = str(r['ap_status'])
newR['gxdStatus'] = str(r['gxd_status'])
newR['goStatus'] = str(r['go_status'])
newR['tumorStatus'] = str(r['tumor_status'])
newR['qtlStatus'] = str(r['qtl_status'])
return newSample.setFields(newR)
#-----------------------------------
def cleanUpTextField(rcd,
textFieldName,
):
# in case we omit this text field during debugging, check if defined
if rcd.has_key(textFieldName): # 2to3 note: rcd is not a python dict,
# it has a has_key() method
text = str(rcd[textFieldName])
else: text = ''
if args.maxTextLength: # handy for debugging
text = text[:args.maxTextLength]
text = text.replace('\n', ' ')
text = removeNonAscii(cleanDelimiters(text))
return text
#-----------------------------------
def cleanDelimiters(text):
""" remove RECORDEND and FIELDSEPs from text (replace w/ ' ')
"""
return text.replace(RECORDEND,' ').replace(FIELDSEP,' ')
#-----------------------------------
def verbose(text):
if args.verbose:
sys.stderr.write(text)
sys.stderr.flush()
#-----------------------------------
if __name__ == "__main__":
if not (len(sys.argv) > 1 and sys.argv[1] == '--test'):
main()
else: # ad hoc test code
if True: # debug SQL
for query in WHERE_CLAUSES.keys():
tmpTableName, finalTmpTableSQL = buildFinalTmpTableSQL(query)
print('||'.join(finalTmpTableSQL))
print()