def fetchKegg(project):
from ductape.kegg.kegg import KeggNet, KeggAPI
from ductape.terminal import RunThread
# Check if we have to fetch the whole kegg DB
fetch = False
proj = Project(project)
k = KeggAPI()
try:
k.getDBVersion()
release = k.result[1]
except Exception as e:
logger.warning("Could not fetch the KEGG DB version (%s)" % str(e))
release = None
if proj.isKegg():
if release and proj.kegg < release:
logger.warning("A new KEGG DB version is available (%s, was %s)" % (str(release), str(proj.kegg)))
fetch = True
else:
fetch = True
if fetch:
logger.info("Fetching the whole KEGG metabolic map")
if release:
logger.info("KEGG DB release %s" % str(release))
kegg = Kegg(project)
avoid = [kid for kid in kegg.getAllIDs()]
knet = KeggNet(avoid=avoid)
if not RunThread(knet):
return False
# Details
kegg.addPathways(knet.result.path)
logger.info("Added %d Path IDs" % len(knet.result.path))
kegg.addReactions(knet.result.react)
logger.info("Added %d Re IDs" % len(knet.result.react))
kegg.addCompounds(knet.result.comp)
logger.info("Added %d Co IDs" % len(knet.result.comp))
kegg.addRPairs(knet.result.rpair)
logger.info("Added %d RPair IDs" % len(knet.result.rpair))
# Links
kegg.addPathReacts(knet.result.pathreact)
kegg.addReactComps(knet.result.reactcomp)
kegg.addCompReacts(knet.result.compreact)
kegg.addPathComps(knet.result.pathcomp)
kegg.addReactRPairs(knet.result.reactrpair)
kegg.addRPairReacts(knet.result.rpairreact)
logger.info("Added Kegg links")
# HTML maps
kegg.addPathHtml(knet.result.pathmaps)
logger.info("Added Kegg maps")
# Add the release version
if release:
proj.setKegg(release)
else:
logger.info("KEGG db is up-to-date")
from ductape.kegg.kegg import KeggNet, KeggAPI, BaseKegg
from ductape.terminal import RunThread
# Check if we have to fetch the whole kegg DB
fetch = False
proj = Project(project)
logger.info('Checking connectivity')
bk = BaseKegg()
try:
bk.checkConnection()
except Exception, e:
logger.error(str(e))
return False
k = KeggAPI()
try:
k.getDBVersion()
release = k.result[1]
except Exception as e:
logger.warning('Could not fetch the KEGG DB version (%s)'%str(e))
release = None
if proj.isKegg():
if release and proj.kegg < release:
logger.warning('A new KEGG DB version is available (%s, was %s)'%
(str(release), str(proj.kegg)))
fetch = True
else:
fetch = True
if fetch:
def fetchKegg(project, keeptrying=False):
from ductape.kegg.kegg import KeggNet, KeggAPI, BaseKegg
from ductape.terminal import RunThread
# Check if we have to fetch the whole kegg DB
fetch = False
proj = Project(project)
logger.info('Checking connectivity')
bk = BaseKegg()
try:
bk.checkConnection()
except Exception as e:
logger.error(str(e))
return False
k = KeggAPI()
try:
k.getDBVersion()
release = k.result[1]
except Exception as e:
logger.warning('Could not fetch the KEGG DB version (%s)'%str(e))
release = None
if proj.isKegg():
if release and proj.kegg < release:
logger.warning('A new KEGG DB version is available (%s, was %s)'%
(str(release), str(proj.kegg)))
fetch = True
else:
fetch = True
if fetch:
logger.info('Fetching the whole KEGG metabolic map')
if release:
logger.info('KEGG DB release %s'%str(release))
kegg = Kegg(project)
knet = KeggNet(keeptrying=keeptrying)
if not RunThread(knet):
return False
# Details
kegg.addPathways(knet.result.path)
logger.info('Added %d Path IDs'%len(knet.result.path))
kegg.addReactions(knet.result.react)
logger.info('Added %d Re IDs'%len(knet.result.react))
kegg.addCompounds(knet.result.comp)
logger.info('Added %d Co IDs'%len(knet.result.comp))
kegg.addRPairs(knet.result.rpair)
logger.info('Added %d RPair IDs'%len(knet.result.rpair))
# Links
kegg.addPathReacts(knet.result.pathreact)
kegg.addReactComps(knet.result.reactcomp)
kegg.addCompReacts(knet.result.compreact)
kegg.addPathComps(knet.result.pathcomp)
kegg.addReactRPairs(knet.result.reactrpair)
kegg.addRPairReacts(knet.result.rpairreact)
logger.info('Added Kegg links')
# HTML maps
kegg.addPathHtml(knet.result.pathmaps)
logger.info('Added Kegg maps')
# Add the release version
if release:
proj.setKegg(release)
else:
logger.info('KEGG db is up-to-date')
return True
def fetchKegg(project, keeptrying=False):
from ductape.kegg.kegg import KeggNet, KeggAPI, BaseKegg
from ductape.terminal import RunThread
# Check if we have to fetch the whole kegg DB
fetch = False
proj = Project(project)
logger.info('Checking connectivity')
bk = BaseKegg()
try:
bk.checkConnection()
except Exception as e:
logger.error(str(e))
return False
k = KeggAPI()
try:
k.getDBVersion()
release = k.result[1]
except Exception as e:
logger.warning('Could not fetch the KEGG DB version (%s)' % str(e))
release = None
if proj.isKegg():
if release and proj.kegg < release:
logger.warning('A new KEGG DB version is available (%s, was %s)' %
(str(release), str(proj.kegg)))
fetch = True
else:
fetch = True
if fetch:
logger.info('Fetching the whole KEGG metabolic map')
if release:
logger.info('KEGG DB release %s' % str(release))
kegg = Kegg(project)
knet = KeggNet(keeptrying=keeptrying)
if not RunThread(knet):
return False
# Details
kegg.addPathways(knet.result.path)
logger.info('Added %d Path IDs' % len(knet.result.path))
kegg.addReactions(knet.result.react)
logger.info('Added %d Re IDs' % len(knet.result.react))
kegg.addCompounds(knet.result.comp)
logger.info('Added %d Co IDs' % len(knet.result.comp))
kegg.addRPairs(knet.result.rpair)
logger.info('Added %d RPair IDs' % len(knet.result.rpair))
# Links
kegg.addPathReacts(knet.result.pathreact)
kegg.addReactComps(knet.result.reactcomp)
kegg.addCompReacts(knet.result.compreact)
kegg.addPathComps(knet.result.pathcomp)
kegg.addReactRPairs(knet.result.reactrpair)
kegg.addRPairReacts(knet.result.rpairreact)
logger.info('Added Kegg links')
# HTML maps
kegg.addPathHtml(knet.result.pathmaps)
logger.info('Added Kegg maps')
# Add the release version
if release:
proj.setKegg(release)
else:
logger.info('KEGG db is up-to-date')
return True