def main():
if len(sys.argv) != 1 or sys.argv[1] == "-h" or sys.argv[1] == "--help":
usage(sys.argv[0])
sys.exit()
ini_file = sys.argv.pop(1)
conf_parser = configparser.ConfigParser({'here': os.getcwd()})
conf_parser.read(ini_file)
configuration = {}
for key, value in conf_parser.items("app:main"):
configuration[key] = value
app = galaxy.app.UniverseApplication(global_conf=ini_file, **configuration)
# Step through Datasets, determining size on disk for each.
print("Determining the size of each dataset...")
for row in app.model.Dataset.table.select().execute():
purged = app.model.Dataset.get(row.id).purged
file_size = app.model.Dataset.get(row.id).file_size
if file_size is None and not purged:
size_on_disk = app.model.Dataset.get(row.id).get_size()
print("Updating Dataset.%d with file_size: %d" %
(row.id, size_on_disk))
app.model.Dataset.table.update(
app.model.Dataset.table.c.id == row.id).execute(
file_size=size_on_disk)
app.shutdown()
sys.exit(0)
def main():
if len(sys.argv) != 2 or sys.argv[1] == "-h" or sys.argv[1] == "--help" :
usage(sys.argv[0])
sys.exit()
ini_file = sys.argv.pop(1)
conf_parser = ConfigParser.ConfigParser({'here': os.getcwd()})
conf_parser.read(ini_file)
configuration = {}
for key, value in conf_parser.items("app:main"):
configuration[key] = value
app = galaxy.app.UniverseApplication( global_conf=ini_file, **configuration )
# Search out tabular datatypes (and subclasses) and initialize metadata
print "Seeking out tabular based files and initializing metadata"
for row in app.model.Dataset.table.select().execute():
data = app.model.Dataset.get(row.id)
if issubclass(type(data.datatype), type(app.datatypes_registry.get_datatype_by_extension('tabular'))):
print row.id, data.extension
# Call meta_data for all tabular files
# special case interval type where we do not want to overwrite chr, start, end, etc assignments
if issubclass(type(data.datatype), type(app.datatypes_registry.get_datatype_by_extension('interval'))):
galaxy.datatypes.tabular.Tabular().set_meta(data)
else:
data.set_meta()
app.model.context.add( data )
app.model.context.flush()
app.shutdown()
sys.exit(0)
def main():
ini_file = sys.argv.pop(1)
conf_parser = ConfigParser.ConfigParser({'here':os.getcwd()})
conf_parser.read(ini_file)
configuration = {}
for key, value in conf_parser.items("app:main"): configuration[key] = value
app = galaxy.app.UniverseApplication( global_conf = ini_file, **configuration )
#Step through Database, turning metadata bunches into dictionaries.
#print "Changing metadata bunches to dictionaries."
#for row in app.model.Dataset.table.select().execute():
# if isinstance (row.metadata, Bunch):
# print row.id
# app.model.Dataset.table.update(app.model.Dataset.table.c.id == row.id).execute( _metadata = row.metadata.__dict__ )
#Make sure all metadata is jsonified
#print "Rewriting all metadata to database, setting metadata dbkey, to ensure JSONified storage."
#for row in app.model.Dataset.table.select().execute():
# print row.id
# data = app.model.Dataset.get(row.id)
# dbkey = data.old_dbkey
# if not dbkey or data.metadata.dbkey not in ["?", ["?"], None, []]:
# dbkey = data.metadata.dbkey
# if not dbkey: dbkey = "?"
# #change dbkey then flush, then change to real value and flush, ensures that metadata is rewritten to database
# data.dbkey="~"
# data.flush()
# data.dbkey=dbkey
# data.flush()
#Search out tabular datatypes (and subclasses) and initialize metadata
print "Seeking out tabular based files and initializing metadata"
for row in app.model.Dataset.table.select().execute():
data = app.model.Dataset.get(row.id)
if issubclass(type(data.datatype), type(app.datatypes_registry.get_datatype_by_extension('tabular'))):
print row.id, data.extension
#Call meta_data for all tabular files
#special case interval type where we do not want to overwrite chr, start, end, etc assignments
if issubclass(type(data.datatype), type(app.datatypes_registry.get_datatype_by_extension('interval'))):
galaxy.datatypes.tabular.Tabular().set_meta(data)
else:
data.set_meta()
app.model.context.add( data )
app.model.context.flush()
#Search out maf datatypes and make sure that available species is set.
#print "Seeking out maf files and setting available species."
#for row in app.model.Dataset.table.select(app.model.Dataset.table.c.extension == 'maf').execute():
# print row.id
# sys.stdout.flush()
# data = app.model.Dataset.get(row.id)
# if data.missing_meta:
# data.set_meta() #Call maf set metadata method, setting available species
# data.flush()
app.shutdown()
sys.exit(0)
def main():
ini_file = sys.argv.pop(1)
conf_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} )
conf_parser.read( ini_file )
configuration = {}
for key, value in conf_parser.items( "app:main" ):
configuration[key] = value
app = galaxy.app.UniverseApplication( global_conf = ini_file, **configuration )
#Step through Datasets, determining size on disk for each.
print "Determining the size of each dataset..."
for row in app.model.Dataset.table.select().execute():
purged = app.model.Dataset.get( row.id ).purged
file_size = app.model.Dataset.get( row.id ).file_size
if file_size is None and not purged:
size_on_disk = app.model.Dataset.get( row.id ).get_size()
print "Updating Dataset.%d with file_size: %d" %( row.id, size_on_disk )
app.model.Dataset.table.update( app.model.Dataset.table.c.id == row.id ).execute( file_size=size_on_disk )
app.shutdown()
sys.exit(0)
def main():
if len(sys.argv) != 2 or sys.argv[1] == "-h" or sys.argv[1] == "--help":
usage(sys.argv[0])
sys.exit()
ini_file = sys.argv.pop(1)
conf_parser = configparser.ConfigParser({'here': os.getcwd()})
conf_parser.read(ini_file)
configuration = {}
for key, value in conf_parser.items("app:main"):
configuration[key] = value
app = galaxy.app.UniverseApplication(global_conf=ini_file, **configuration)
# Search out tabular datatypes (and subclasses) and initialize metadata
print("Seeking out tabular based files and initializing metadata")
for row in app.model.Dataset.table.select().execute():
data = app.model.Dataset.get(row.id)
if issubclass(
type(data.datatype),
type(
app.datatypes_registry.get_datatype_by_extension(
'tabular'))):
print(row.id, data.extension)
# Call meta_data for all tabular files
# special case interval type where we do not want to overwrite chr, start, end, etc assignments
if issubclass(
type(data.datatype),
type(
app.datatypes_registry.get_datatype_by_extension(
'interval'))):
galaxy.datatypes.tabular.Tabular().set_meta(data)
else:
data.set_meta()
app.model.context.add(data)
app.model.context.flush()
app.shutdown()
sys.exit(0)
if galaxy_test_file_dir:
os.environ['GALAXY_TEST_FILE_DIR'] = galaxy_test_file_dir
success = _run_functional_test()
except:
log.exception("Failure running tests")
log.info("Shutting down")
# ---- Tear down -----------------------------------------------------------
if server:
log.info("Shutting down embedded web server")
server.server_close()
server = None
log.info("Embedded web server stopped")
if app:
log.info("Shutting down app")
app.shutdown()
app = None
log.info("Embedded Universe application stopped")
try:
if os.path.exists(
tempdir) and 'GALAXY_TEST_NO_CLEANUP' not in os.environ:
log.info("Cleaning up temporary files in %s" % tempdir)
shutil.rmtree(tempdir)
else:
log.info("GALAXY_TEST_NO_CLEANUP is on. Temporary files in %s" %
tempdir)
except:
pass
if success:
return 0
else:
if galaxy_test_file_dir:
os.environ[ 'GALAXY_TEST_FILE_DIR' ] = galaxy_test_file_dir
success = _run_functional_test( )
except:
log.exception( "Failure running tests" )
log.info( "Shutting down" )
# ---- Tear down -----------------------------------------------------------
if server:
log.info( "Shutting down embedded web server" )
server.server_close()
server = None
log.info( "Embedded web server stopped" )
if app:
log.info( "Shutting down app" )
app.shutdown()
app = None
log.info( "Embedded Universe application stopped" )
try:
if os.path.exists( tempdir ) and 'GALAXY_TEST_NO_CLEANUP' not in os.environ:
log.info( "Cleaning up temporary files in %s" % tempdir )
shutil.rmtree( tempdir )
else:
log.info( "GALAXY_TEST_NO_CLEANUP is on. Temporary files in %s" % tempdir )
except:
pass
if psu_production and 'GALAXY_TEST_NO_CLEANUP' not in os.environ:
for dir in ( file_path, new_file_path ):
try:
if os.path.exists( dir ):
log.info( 'Cleaning up temporary files in %s' % dir )
