w = GlycoMotifWiki()
gtc = None
def accs():
global gtc
if len(sys.argv) > 1:
gtc = GlyTouCan(prefetch=False, usecache=False)
for acc in sys.argv[1:]:
yield acc
else:
gtc = GlyTouCan(prefetch=True, usecache=False)
for m in w.itermotif():
yield m.get('id')
for acc in accs():
m = w.get(acc)
gtcacc = m.get('glytoucan')
wurcs = gtc.getseq(gtcacc, 'wurcs')
glycoct = gtc.getseq(gtcacc, 'glycoct')
if not glycoct:
glycoct = gtc.glycoct(gtcacc)
if wurcs:
m.set('wurcs', wurcs)
if glycoct:
m.set('glycoct', glycoct)
if w.put(m):
print acc
page = theart['Pagination']['MedlinePgn']
if issue:
volume = "%s(%s)" % (vol, issue)
else:
volume = vol
if isinstance(ref, int):
citedby = (
'Cummings_(2009)_The_repertoire_of_glycan_determinants_in_the_human_glycome',
ref)
elif isinstance(ref, basestring) and ref.startswith('EP'):
citedby = ('GE', ref)
else:
citedby = None
pub = Publication(authors=authors,
title=title,
journal=journal,
year=year,
volume=volume,
pages=page,
pmid=pmid,
doi=doi,
citedby=citedby)
print Publication.pagename(**pub.data)
print pub.astemplate()
if w.put(pub):
print >> sys.stderr, pmid
time.sleep(5)
assert towiki in ("PROD", "DEV", "TEST")
assert fromwiki != towiki
w1 = GlycoMotifWiki(smwenv=fromwiki, quiet=True)
print >> sys.stderr, "from: %s" % (w1.title(), )
w2 = GlycoMotifWiki(smwenv=towiki, quiet=True)
print >> sys.stderr, " to: %s" % (w2.title(), )
dummy = raw_input("Enter to proceed, <Ctrl-C> to abort:")
currentcoll = set()
for c1 in w1.itercollection():
id = c1.get('id')
assert (id)
currentcoll.add(id)
if w2.put(c1):
print >> sys.stderr, "Pushing %s to %s" % (id, w2.title())
else:
print >> sys.stderr, "No change to %s in %s" % (id, w2.title())
currentmotif = set()
for m1 in w1.itermotif():
id = m1.get('id')
assert (id)
currentmotif.add(id)
if w2.put(m1):
print >> sys.stderr, "Pushing %s to %s" % (id, w2.title())
else:
print >> sys.stderr, "No change to %s in %s" % (id, w2.title())
for c2 in w2.itercollection():
#!/bin/env python27
from getwiki import GlycoMotifWiki, Collection, GlyTouCanMotif, CCRCMotif, GlycoEpitopeMotif, AllMotif, GlyGenMotif
from getwiki import GlydinMotif, GlydinCummingsMotif, GlydinHayesMotif, GlydinCermavMotif, GlydinSugarbindMotif, GlydinBioligoMotif
from getwiki import UniCarbMotif
import sys
w = GlycoMotifWiki()
current = set()
w.put(
Collection(id=GlyTouCanMotif.id,
name="GlyTouCan Motifs",
contact="Kiyoko Aoki-Kinoshita",
email="*****@*****.**",
url="https://glytoucan.org/Motifs/listAll"))
current.add(GlyTouCanMotif.id)
w.put(
Collection(
id=CCRCMotif.id,
name="CCRC Motifs",
contact="Rene Ranzinger",
email="*****@*****.**",
url=
"https://github.com/glygen-glycan-data/PyGly/raw/master/smw/glycomotif/data/MotifsMP2.xlsx"
))
current.add(CCRCMotif.id)
w.put(
Collection(id=GlycoEpitopeMotif.id,
name="GlycoEpitope Epitopes",
contact="Toshisuke Kawasaki",
email="*****@*****.**",