def alleleDetailById(id):
allele = allele_hunter.getAlleleByMGIID(id)
if allele:
return renderAlleleDetail(allele)
return error_template('No allele found for ID = %s' % id)
def convert(note, anchorClass=''):
"""
Takes a string and runs various regular
expressions against it, to convert any special
MGI notes tags into links
"""
if not note:
return ''
for regex, template in NOTES_TAG_CONVERSIONS:
match = regex.search(note)
while match:
args = match.groups()[0].split('|')
start = match.start()
end = match.end()
if not args[1]:
# default to ID field, if link text blank
args[1] = args[0]
# convert the note tag
# This shouldn't match unless we have 3 args in the first place
converted = template % (anchorClass, args[0], args[1])
# insert converted tag
note = note[:start] + converted + note[end:]
match = regex.search(note)
# special handling for non-standard \AlleleSymbol tag
match = alleleSymbolRegex.search(note)
while match:
args = match.groups()[0].split('|')
start = match.start()
end = match.end()
allele = allele_hunter.getAlleleByMGIID(args[0])
if allele is None:
note = note[:start] + "<span style='color: red;'>Allele ID Error</span> " + note[end:]
else:
# insert converted tag
note = note[:start] + superscript(allele.symbol) + note[end:]
match = alleleSymbolRegex.search(note)
# special handling for non-standard \Elsevier tag
match = elsevierRegex.search(note)
while match:
args = match.groups()[0].split('|')
start = match.start()
end = match.end()
app.logger.warn('match! %s' % args[0])
ref = reference_service.get_by_jnum_id(args[0])
# generate replacement text
journal = ref.journal or ''
vol = ref.vol or ''
pgs = ref.pgs or ''
title = ref.title or ''
authors = ref.authors or ''
year = ref.year or ''
replacementText = "%s %s: %s, %s, %s Copyright %s" % \
(journal, vol, pgs, authors, title, year)
# insert converted tag
note = note[:start] + replacementText + note[end:]
match = elsevierRegex.search(note)
return note
def queryAllele(self):
params = self._getParams()
return allele_hunter.getAlleleByMGIID(params['allele_id'])
def alleleDetailById(id):
allele = allele_hunter.getAlleleByMGIID(id)
if allele:
return renderAlleleDetail(allele)
return error_template('No allele found for ID = %s' % id)
def queryAllele(self):
params = self._getParams()
return allele_hunter.getAlleleByMGIID(params['allele_id'])
def convert(note, anchorClass=''):
"""
Takes a string and runs various regular
expressions against it, to convert any special
MGI notes tags into links
"""
if not note:
return ''
for regex, template in NOTES_TAG_CONVERSIONS:
match = regex.search(note)
while match:
args = match.groups()[0].split('|')
start = match.start()
end = match.end()
if not args[1]:
# default to ID field, if link text blank
args[1] = args[0]
# convert the note tag
# This shouldn't match unless we have 3 args in the first place
converted = template % (anchorClass, args[0], args[1])
# insert converted tag
note = note[:start] + converted + note[end:]
match = regex.search(note)
# special handling for non-standard \AlleleSymbol tag
match = alleleSymbolRegex.search(note)
while match:
args = match.groups()[0].split('|')
start = match.start()
end = match.end()
allele = allele_hunter.getAlleleByMGIID(args[0])
if allele is None:
note = note[:
start] + "<span style='color: red;'>Allele ID Error</span> " + note[
end:]
else:
# insert converted tag
note = note[:start] + superscript(allele.symbol) + note[end:]
match = alleleSymbolRegex.search(note)
# special handling for non-standard \Elsevier tag
match = elsevierRegex.search(note)
while match:
args = match.groups()[0].split('|')
start = match.start()
end = match.end()
app.logger.warn('match! %s' % args[0])
ref = reference_service.get_by_jnum_id(args[0])
# generate replacement text
journal = ref.journal or ''
vol = ref.vol or ''
pgs = ref.pgs or ''
title = ref.title or ''
authors = ref.authors or ''
year = ref.year or ''
replacementText = "%s %s: %s, %s, %s Copyright %s" % \
(journal, vol, pgs, authors, title, year)
# insert converted tag
note = note[:start] + replacementText + note[end:]
match = elsevierRegex.search(note)
return note
