def gdv_create(self,ex):
from bbcflib import gdv
project = gdv.get_project(mail=self.globals['gdv']['email'],
key=self.globals['gdv']['key'],
project_key=self.job.options['gdv_key'])
if 'error' in project:
self.log_write("Creating GDV project.")
project = gdv.new_project( self.globals['gdv']['email'],
self.globals['gdv']['key'],
self.job.description,
self.job.assembly.id,
self.globals['gdv']['url'] )
self.debug_write("\nGDV project: "+json.dumps(project))
add_pickle( ex, project, description=set_file_descr("gdv_json",step='gdv',type='py',view='admin') )
self.job.options['gdv_project'] = project
return True
def main(argv=None):
parser = None
try:
parser = optparse.OptionParser(usage=usage, description=description)
for opt in opts:
parser.add_option(opt[0],opt[1],help=opt[2],**opt[3])
(options, args) = parser.parse_args()
if options.minilims in module_list:
M = MiniLIMS(os.path.join(options.basepath,options.minilims+"_minilims"))
elif os.path.exists(options.minilims):
M = MiniLIMS(options.minilims)
else:
raise Usage("Minilims not found, please specify a path or a module with -m.")
tags = options.tag
if tags:
tags = tags.split(",")
if tags[0].count("="):
tags = dict(x.split("=") for x in tags)
elif tags[0].count(":"):
tags = dict(x.split(":") for x in tags)
if options.gdv:
if tags: tags['type'] = 'sql'
else: tags = {'type': 'sql'}
if options.programs:
if isinstance(options.execution, basestring):
exlist = M.search_executions(with_description=options.execution)
if len(exlist) == 0:
exlist = M.search_executions(with_text=options.execution)
if len(exlist) == 0:
raise Usage("Execution with key %s not found in %s." %(options.execution,options.minilims))
exid = max(exlist)
else:
exid = int(options.execution or 0)
exec_data = M.fetch_execution(exid)['programs']
outfile = options.output and open(options.output,"w") or sys.stdout
for prog in exec_data:
pargs = prog['arguments']
if tags and all([t not in x for x in pargs for t in tags]):
continue
stout = prog['stdout'].encode('ascii','ignore')
sterr = prog['stderr'].encode('ascii','ignore')
if pargs[0] == 'bsub': pargs = str(pargs[-1])
else: pargs = str(" ".join(pargs))
outfile.write("\n".join([pargs,stout,'',sterr,'','-'*40,'']))
outfile.close()
return 0
files = get_files(options.execution,M,select_param=tags)
fprefix = ''
if options.list:
if options.output and os.path.isdir(options.output):
options.output = os.path.join(options.output,options.execution+".txt")
outfile = options.output and open(options.output,"w") or sys.stdout
outfile.write("\t".join(["type","group","name","path","comment"])+"\n")
else:
if not(options.output): options.output = "./"
if not(os.path.isdir(options.output)):
options.output, fprefix = os.path.split(options.output)
if options.gdv:
gdvpaths = []
gdvnames = []
for t in sorted(files.keys()):
for k,v in files[t].iteritems():
fpath = os.path.join(M.file_path,k)
vv = v.split("[")
fname = fprefix+vv.pop(0)
comment = ''
par_dict = {}
if vv:
vv = vv[0].split("]")
par_dict = dict(x.split(":") for x in vv.pop(0).split(","))
if vv: comment = vv[0].strip().strip("()")
if not(options.admin) and par_dict.get('view') == 'admin': continue
if options.list: outfile.write("\t".join([t,par_dict.get('groupId',''),fname,fpath,comment])+"\n")
if options.copy: shutil.copy(fpath, os.path.join(options.output,fname))
if options.symlink: os.symlink(fpath, os.path.join(options.output,fname))
if options.gdv:
gdvpaths.append(fpath)
gdvnames.append(re.sub('\.sql.*','',str(fname)))
if options.list and options.output: outfile.close()
if options.gdv:
from bbcflib import gdv
gdvurl = options.gdvurl or gdv.default_url
gdvproject = gdv.get_project(mail=options.email, key=options.key,
project_key=options.gdv)
if gdvproject.get('project',{}).get('id',0)>0:
try:
tr = gdv.multiple_tracks( mail=options.email, key=options.key,
project_id=gdvproject['project']['id'],
urls=gdvpaths, names=gdvnames, extensions=['sql']*len(gdvpaths),
force=True, serv_url=gdvurl )
except Exception, err:
raise Usage("GDV Tracks Failed: %s\n" %err)
print """
*********** GDV project at: ***********
%s/public/project?k=%s&id=%s
***************************************
""" %(gdvurl,gdvproject['project']['download_key'],gdvproject['project']['id'])
return 0