def getAccessionByAccID(id, inMGITypeKeys=[]):
# split and prep the IDs
accidsToSearch = splitCommaInput(id.lower())
# build accid query
query = Accession.query
query = query.filter(
db.and_(
db.func.lower(Accession.accid).in_((accidsToSearch)),
Accession._logicaldb_key.in_((ACCEPTED_LDBS))))
# add keys to filter, if have have any
if inMGITypeKeys:
query = query.filter(Accession._mgitype_key.in_(inMGITypeKeys))
# setting sort
query = query.order_by(Accession._mgitype_key)
#gather accession objects
return query.all()
def getAccessionByMarkerSymbol(symbolSearch):
"""
Return acc_accession objects that match on symbol
"""
# split on comma, but still include original string,
# because some symbols have commas
symbolsToSearch = set([symbolSearch.lower()])
tokens = splitCommaInput(symbolSearch.lower())
symbolsToSearch = symbolsToSearch.union(tokens)
app.logger.debug("symbols to search = %s" % symbolsToSearch)
# join marker via primary mgiid
query = Accession.query
query = query.join(Marker.mgiid_object) \
.filter(Marker._organism_key==1)
query = query.filter(db.func.lower(Marker.symbol).in_(symbolsToSearch))
return query.all()
def getAccessionByMarkerSymbol(symbolSearch):
"""
Return acc_accession objects that match on symbol
"""
# split on comma, but still include original string,
# because some symbols have commas
symbolsToSearch = set([symbolSearch.lower()])
tokens = splitCommaInput(symbolSearch.lower())
symbolsToSearch = symbolsToSearch.union(tokens)
app.logger.debug("symbols to search = %s" % symbolsToSearch)
# join marker via primary mgiid
query = Accession.query
query = query.join(Marker.mgiid_object) \
.filter(Marker._organism_key==1)
query = query.filter(db.func.lower(Marker.symbol).in_(symbolsToSearch))
return query.all()
def getAccessionByAccID(id, inMGITypeKeys=[]):
# split and prep the IDs
accidsToSearch = splitCommaInput(id.lower())
# build accid query
query = Accession.query
query = query.filter(
db.and_(
db.func.lower(Accession.accid).in_((accidsToSearch)),
Accession._logicaldb_key.in_((ACCEPTED_LDBS))
)
)
# add keys to filter, if have have any
if inMGITypeKeys:
query = query.filter(Accession._mgitype_key.in_(inMGITypeKeys))
# setting sort
query = query.order_by(Accession._mgitype_key)
#gather accession objects
return query.all()
def search(self, accids=None,
journal=None,
title=None,
authors=None,
primeAuthor=None,
volume=None,
year=None,
marker_id=None,
allele_id=None,
limit=None):
"""
Search references by
accids,
journal,
title,
authors,
primAuthor,
volume,
year,
marker_id,
allele_id
"""
query = Reference.query
if authors:
authors = authors.lower()
query = query.filter(
db.func.lower(Reference.authors).like(authors),
)
if primeAuthor:
primeAuthor = primeAuthor.lower()
query = query.filter(
db.func.lower(Reference._primary).like(primeAuthor),
)
if journal:
journal = journal.lower()
query = query.filter(
db.func.lower(Reference.journal).like(journal),
)
if title:
title = title.lower()
query = query.filter(
db.func.lower(Reference.title).like(title),
)
if volume:
volume = volume.lower()
query = query.filter(db.func.lower(Reference.vol)==volume)
if year:
query = query.filter(Reference.year==int(year))
if marker_id:
marker_accession = db.aliased(Accession)
sub_reference = db.aliased(Reference)
sq = db.session.query(sub_reference) \
.join(sub_reference.all_markers) \
.join(marker_accession, Marker.mgiid_object) \
.filter(marker_accession.accid==marker_id) \
.filter(sub_reference._refs_key==Reference._refs_key) \
.correlate(Reference)
query = query.filter(
sq.exists()
)
if allele_id:
allele_accession = db.aliased(Accession)
sub_reference = db.aliased(Reference)
sq = db.session.query(sub_reference) \
.join(sub_reference.explicit_alleles) \
.join(allele_accession, Allele.mgiid_object) \
.filter(allele_accession.accid==allele_id) \
.filter(sub_reference._refs_key==Reference._refs_key) \
.correlate(Reference)
query = query.filter(
sq.exists()
)
if accids:
# split and prep the IDs
accids = accids.lower()
accidsToSearch = splitCommaInput(accids)
jnum_accession = db.aliased(Accession)
sub_ref1 = db.aliased(Reference)
ref_sq = db.session.query(sub_ref1) \
.join(jnum_accession, sub_ref1.jnumid_object) \
.filter(db.func.lower(jnum_accession.accid).in_(accidsToSearch)) \
.filter(sub_ref1._refs_key==Reference._refs_key) \
.correlate(Reference)
pmed_accession = db.aliased(Accession)
sub_ref2 = db.aliased(Reference)
pmed_sq = db.session.query(sub_ref2) \
.join(pmed_accession, sub_ref2.pubmedid_object) \
.filter(db.func.lower(pmed_accession.accid).in_(accidsToSearch)) \
.filter(sub_ref2._refs_key==Reference._refs_key) \
.correlate(Reference)
query1 = query.filter(ref_sq.exists())
query2 = query.filter(pmed_sq.exists())
query = query1.union(query2)
# setting sort
query = query.order_by(Reference._refs_key.desc())
# setting limit on number of returned references
if limit:
query = query.limit(limit)
references = query.all()
return references