def expIdLine(args, expId, t):
samplefiles = 0
samplesize = 0
submittedfiles = 0
for stanza in expId:
for fname in stanza['fileName'].split(','):
if fname in t.files:
file = t.files[fname]
samplesize = samplesize + file.size
samplefiles = samplefiles + 1
if 'geoSampleAccession' in stanza:
submittedfiles = submittedfiles + 1
if expId.title == None:
title = styles.style('Inconsistent', 'red')
else:
title = expId.title
return expId.name.rjust(12) + ' ' + title + ' [%s]' % filesize(samplesize) + ' - %d files' % samplefiles
def trackLine(args, t):
nametext = t.name.ljust(25)
try:
sub = 0
tot = 0
wantSubmit = 1
for exp in t.alphaMetaDb.experiments.iterkeys():
submitted = 0
samples = 0
for stanza in t.alphaMetaDb.experiments[exp]:
if 'objStatus' in stanza:
continue
if 'Aln' not in stanza['metaObject']:
if 'geoSampleAccession' in stanza:
submitted += 1
samples += 1
if (not args.pessimistic and submitted > 0) or (submitted == samples and submitted != 0):
sub += 1
args.totalsubmitted += 1
if samples > 0:
tot += 1
args.totalexps += 1
#for stanza in t.alphaMetaDb.filter2(lambda s: s['objType'] != 'composite').itervalues():
# if 'geoSampleAccession' in stanza:
# sub += 1
# tot += 1
#subtext = '%d%%' % int((float(sub) / tot) * 100)
subtext = ('%d/%d' % (sub, tot)).ljust(10)
#subtext = ' ' * (4 - len(subtext)) + subtext
filestext = '%d' % tot
filestext = ' ' * (4 - len(filestext)) + filestext + ' files'
if sub == 0:
subtext = styles.style(subtext, 'red')
elif sub < tot:
subtext = styles.style(subtext, 'yellow')
else:
subtext = styles.style(subtext, 'green')
wantSubmit = 0
status = styles.style('Public ', 'green')
#just randomization for testing, replace with
# /cluster/home/mmaddren/kent/src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
if (tot % 2 == 0):
status = styles.style('Unreleased', 'blue')
wantSubmit = 0
datatype = styles.style('Not Found'.ljust(16), 'red')
if t.alphaMetaDb.dataType != None:
datatype = t.alphaMetaDb.dataType.name
if t.alphaMetaDb.dataType.type == 'MicroArray':
datatype = styles.style(datatype.ljust(16), 'yellow')
args.totaltracks += 1
elif t.alphaMetaDb.dataType.valid:
datatype = styles.style(datatype.ljust(16), 'green')
args.totaltracks += 1
else:
if t.alphaMetaDb.dataType.shouldSubmit:
datatype = styles.style(datatype.ljust(16), 'red')
else:
datatype = styles.style(datatype.ljust(16), 'blue')
#subtext = ''
args.totalexps -= tot
wantSubmit = 0
if datatype == '' and len(t.alphaMetaDb.experiments) == 0:
datatype = styles.style('no expIds'.ljust(16), 'red')
#if wantSubmit:
# nametext = styles.style(nametext, 'green')
geouptodate = ''
if args.geo and t.geo != None:
exps = dict()
local = 0
offsite = 0
mismatch = 0
matched = 0
for expId in t.alphaMetaDb.experiments.iterkeys():
k = t.alphaMetaDb.experiments[expId].title
exps[k] = t.alphaMetaDb.experiments[expId]
if k in t.geo.accessions.iterkeys():
happened = 0
for stanza in exps[k]:
if 'geoSampleAccession' in stanza and stanza['geoSampleAccession'] != t.geo.accessions[k]:
mismatch += 1
happened = 1
break
if happened == 0:
for stanza in exps[k]:
if 'geoSampleAccession' not in stanza:
offsite += 1
happened = 1
break
if happened == 0:
matched += 1
else:
local += 1
geouptodate = '%d GSMs, %d expIds, %d match, %d local, %d on geo, %d mismatch' % (len(t.geo.accessions.keys()), len(t.alphaMetaDb.experiments.keys()), matched, local, offsite, mismatch)
releases = ''
for release in t.releaseObjects:
if release.onPublic:
releases += styles.style(str(release.index), 'green')
else:
releases += styles.style(str(release.index), 'red')
if 'geoSeriesAccession' in t.alphaMetaDb.compositeStanza:
args.submittedtracks += 1
return nametext + styles.style(t.alphaMetaDb.compositeStanza['geoSeriesAccession'].ljust(12), 'green') + subtext + datatype + releases + ' ' + geouptodate
else:
return nametext + styles.style('Unsubmitted'.ljust(12), 'blue') + subtext + datatype + releases
except KeyError as e:
return styles.style(nametext, 'red') + styles.style('Error ' + str(e), 'red')
