def do_add_dir(self, args):
dir = args
result = list(list_exp_files(dir))
print 'found files for %d experiments in %s' % (len(result), dir)
with DomDb(self.session_factory, self.ion_mode, self.config) as domdb:
for d in result:
name = d['name']
path = os.path.join(dir,d['data'])
mdpath = os.path.join(dir,d['metadata'])
print 'loading experiment %s from:' % name
print '- data file %s' % path
print '- metadata file %s' % mdpath
etl(domdb.session,name,path,mdpath,self.ion_mode,log=console_log)
n = domdb.mtab_count(self.ion_mode)
print '%d metabolites in database' % n
def do_add_dir(self, args):
dir = args
result = list(list_exp_files(dir))
print 'found files for %d experiments in %s' % (len(result), dir)
with DomDb(self.session_factory, self.ion_mode, self.config) as domdb:
for d in result:
name = d['name']
path = os.path.join(dir, d['data'])
mdpath = os.path.join(dir, d['metadata'])
print 'loading experiment %s from:' % name
print '- data file %s' % path
print '- metadata file %s' % mdpath
etl(domdb.session,
name,
path,
mdpath,
self.ion_mode,
log=console_log)
n = domdb.mtab_count(self.ion_mode)
print '%d metabolites in database' % n
def do_add(self,args):
try:
exp, path, mdpath = args.split(' ')
except ValueError:
print 'ERROR: add takes [exp name] [data file] [metadata file]'
return
if not os.path.exists(path):
print 'data file %s does not exist' % path
return
if not os.path.exists(mdpath):
print 'metadata file %s does not exist' % mdpath
return
print 'loading experiment %s from:' % exp
print 'data file %s' % path
print 'metadata file %s' % mdpath
session = self.session_factory()
etl(session,exp,path,mdpath,self.ion_mode,log=console_log)
session.close()
with DomDb(self.session_factory, self.ion_mode, self.config) as domdb:
n = domdb.mtab_count()
print '%d metabolites in database' % n
def do_add(self, args):
try:
exp, path, mdpath = args.split(' ')
except ValueError:
print 'ERROR: add takes [exp name] [data file] [metadata file]'
return
if not os.path.exists(path):
print 'data file %s does not exist' % path
return
if not os.path.exists(mdpath):
print 'metadata file %s does not exist' % mdpath
return
print 'loading experiment %s from:' % exp
print 'data file %s' % path
print 'metadata file %s' % mdpath
session = self.session_factory()
etl(session, exp, path, mdpath, self.ion_mode, log=console_log)
session.close()
with DomDb(self.session_factory, self.ion_mode, self.config) as domdb:
n = domdb.mtab_count()
print '%d metabolites in database' % n