def main(*args, **kwargs):
#check to make sure everything is set up properly
if not os.path.exists(converted):
os.makedirs(converted)
if len(parameters.PROTEIN_DATABASES) > 0:
if os.path.exists(parameters.HOME + "/bin/blastdbcmd") and os.path.exists(parameters.HOME + "/bin/makeblastdb"):
print " + Validating protein databases indexes"
for f in parameters.PROTEIN_DATABASES:
p = subprocess.Popen([parameters.HOME + "/bin/blastdbcmd", "-db", f, "-info"], stderr=subprocess.PIPE, stdout=subprocess.PIPE)
(out, err) = p.communicate()
p.stderr.close()
p.stdout.close()
if p.wait() != 0:
subprocess.call([parameters.HOME + "/bin/makeblastdb", "-in", f, "-parse_seqids", "-dbtype", "prot"])
Jobs.start()
session_factory = UnencryptedCookieSessionFactoryConfig(parameters.SECRET_KEY)
config = Configurator(renderer_globals_factory=RendererGlobals, session_factory=session_factory)
#Routes: give each URL a name
config.add_route("index", "/")
config.add_route("upload", "/init")
config.add_route("convert", "/init_local")
config.add_route("convert_url", "/init_url")
config.add_route("query_init", "/query_init")
config.add_route("add", "/add")
config.add_route("merge", "/merge")
config.add_route("view", "/view")
config.add_route("results", "/results")
config.add_route("peptide", "/peptide")
config.add_route("select", "/select")
config.add_route("spectrum", "/spectrum")
config.add_route("lc", "/lc")
config.add_route("tooltip", "/tooltip/{type}")
config.add_route("gpmdb_peptide", "/gpmdb_peptide")
#Views: now associate a function with each route name
#config.add_view(SearchHit, route_name="search_hit")
config.add_view(Index, route_name="index")
config.add_view(Upload, route_name="upload")
config.add_view(Convert, route_name="convert")
config.add_view(ConvertUrl, route_name="convert_url")
config.add_view(QueryInitStatus, route_name="query_init")
config.add_view(AddFile, route_name="add")
config.add_view(MergeFile, route_name="merge")
config.add_view(View, route_name="view")
config.add_view(ListResults, route_name="results")
config.add_view(ListPeptide, route_name="peptide")
config.add_view(SelectInfo, route_name="select")
config.add_view(Spectrum, route_name="spectrum")
config.add_view(SpectumLC, route_name="lc")
config.add_view(Tooltip, route_name="tooltip")
config.add_view(GPMDB.GetObservationsForPeptide, route_name="gpmdb_peptide", renderer="json")
#these views provide content which does not change, such as images and javascript
config.add_static_view("/favicon.ico", parameters.HOME + "/res/favicon.ico", cache_max_age=3600 * 24 * 7)
config.add_static_view("res", parameters.HOME + "/res", cache_max_age=3600 * 24 * 7)
config.add_static_view("test", parameters.HOME + "/test", cache_max_age=0)
return config.make_wsgi_app()
def Convert(req):
#for when this is running on the same server as galaxy
#just use the local files directly
try:
fs = binascii.unhexlify(req.GET["file"])
except:
return HTTPBadRequest_Param("file")
try:
ref = Referencers[req.GET["type"]]
except:
return HTTPBadRequest_Param("type")
#Build the index file
if not os.path.exists(converted):
os.makedirs(converted)
(jobid, f) = Jobs.add_job("local", fs, 7 * 24 * 60 * 60, ref=ref)
resp = render_to_response(templates + "upload.pt", {"file": f, "jobid": str(jobid)}, request=req)
resp.cache_expires(0)
return resp
def Upload(req):
#uploading from a remote server
fs = req.POST.getall("uploadedfiles[]")
if platform.system() == "Windows": # Windows has an extra .file in here for some reason
for f in fs:
if hasattr(f.file, "file"):
f.file = f.file.file
for f in fs:
f.file.seek(0)
#Build the index file
if not os.path.exists(converted):
os.makedirs(converted)
try:
cleanup = req.POST["delete"]
except:
cleanup = 7
(jobid, f) = Jobs.add_job("remote", fs, cleanup * 24 * 60 * 60)
json_response = '{"file":"' + f + '","jobid":' + str(jobid) + '}\r\n'
resp = Response(json_response)
resp.cache_expires(0)
return resp
def ConvertUrl(req):
_read_shortcut_params(req)
default_hash = ""
try:
req_scan = req.GET["scan"]
default_hash = "#S0;None;%s" % req_scan
except KeyError:
pass
try:
url = req.GET["url"]
except:
return HTTPBadRequest_Param("url")
try:
ref = Referencers[req.GET["type"]]
except:
return HTTPBadRequest_Param("type")
#Build the index file
if not os.path.exists(converted):
os.makedirs(converted)
(jobid, f) = Jobs.add_job("url", str(url), 7 * 24 * 60 * 60, ref=ref)
resp = render_to_response(templates + "upload.pt", {"file": f, "jobid": str(jobid), "default_hash": default_hash}, request=req)
resp.cache_expires(0)
return resp
def run(argv):
parser = getParser()
args = parser.parse_args(argv[1:])
config = yaml.load(open(args.config,'r'))
for ky in ['force','rootdir','rundir','verbose','flush_interval',
'writers_hang', 'masters_hang', 'num_samples']:
val = getattr(args,ky)
if val in [None, False]: continue
print("replacing config[%s] with %s (from command line)" % (ky,val))
config[ky]=val
jobs = Jobs(config)
if args.kill:
jobs.kill_all()
return
prepare_output_directory(config)
config_filename = copy_config_to_rundir(config)
daq_writer_hosts = assign_hosts('daq_writer', config)
daq_master_hosts = assign_hosts('daq_master', config)
ana_reader_hosts = assign_hosts('daq_master', config)
jobs.launch('daq_writer', daq_writer_hosts)
time.sleep(2)
jobs.launch('daq_master', daq_master_hosts)
time.sleep(2)
jobs.launch('ana_reader_master', ana_reader_hosts)
jobs.wait()
