def vampsupload(runobj):
"""
Upload data files to VAMPS database
"""
# for vamps 'new_lane_keys' will be prefix
# of the uniques and names file
# that was just created in vamps_gast.py
# or we can get the 'lane_keys' directly from the config_file
# for illumina:
# a unique idx_key is a concatenation of barcode_index and run_key
idx_keys = get_keys(runobj)
# if(runobj.vamps_user_upload):
# idx_keys = [runobj.user+runobj.runcode]
# else:
# idx_keys = convert_unicode_dictionary_to_str(json.loads(open(runobj.trim_status_file_name,"r").read()))["new_lane_keys"]
# NOT NEEDED HERE: Find duplicate project names
# if vamps user uploads this has already been done and this project is
# already in vamps_upload_info table
# if data from a csv file (illumina and 454) this also is not needed
# as data is checked in metadata.py
myvamps = Vamps(runobj, idx_keys)
# Create files
myvamps.create_vamps_files()
# put files in db
myvamps.load_vamps_db()
def new_vamps(runobj):
"""
"""
logger.info("STARTING NEW_VAMPS()")
idx_keys = get_keys(runobj)
myvamps = Vamps(runobj, idx_keys)
myvamps.create_vamps_files()
def new_vamps(runobj):
"""
"""
logger.info("STARTING NEW_VAMPS()")
idx_keys = get_keys(runobj)
myvamps = Vamps(runobj, idx_keys)
myvamps.create_vamps_files()
def vampsupload(runobj):
"""
Upload data files to VAMPS database
"""
# for vamps 'new_lane_keys' will be prefix
# of the uniques and names file
# that was just created in vamps_gast.py
# or we can get the 'lane_keys' directly from the config_file
# for illumina:
# a unique idx_key is a concatenation of barcode_index and run_key
idx_keys = get_keys(runobj)
# if(runobj.vamps_user_upload):
# idx_keys = [runobj.user+runobj.runcode]
# else:
# idx_keys = convert_unicode_dictionary_to_str(json.loads(open(runobj.trim_status_file_name,"r").read()))["new_lane_keys"]
# NOT NEEDED HERE: Find duplicate project names
# if vamps user uploads this has already been done and this project is
# already in vamps_upload_info table
# if data from a csv file (illumina and 454) this also is not needed
# as data is checked in metadata.py
myvamps = Vamps(runobj, idx_keys)
# Create files
myvamps.create_vamps_files()
# put files in db
result_code = myvamps.load_vamps_db()
if result_code[:5] == 'ERROR':
logger.error("load_vamps_db failed")
if runobj.vamps_user_upload:
write_status_to_vamps_db(runobj.site, runobj.run, "GAST_ERROR",
result_code)
sys.exit("load_vamps_db failed")
elif runobj.vamps_user_upload:
logger.debug("Finished loading VAMPS data. %s" % result_code)
write_status_to_vamps_db(runobj.site, runobj.run, 'GAST_SUCCESS',
'Loading VAMPS Finished')
def vampsupload(runobj):
"""
Upload data files to VAMPS database
"""
# for vamps 'new_lane_keys' will be prefix
# of the uniques and names file
# that was just created in vamps_gast.py
# or we can get the 'lane_keys' directly from the config_file
# for illumina:
# a unique idx_key is a concatenation of barcode_index and run_key
idx_keys = get_keys(runobj)
# if(runobj.vamps_user_upload):
# idx_keys = [runobj.user+runobj.runcode]
# else:
# idx_keys = convert_unicode_dictionary_to_str(json.loads(open(runobj.trim_status_file_name,"r").read()))["new_lane_keys"]
# NOT NEEDED HERE: Find duplicate project names
# if vamps user uploads this has already been done and this project is
# already in vamps_upload_info table
# if data from a csv file (illumina and 454) this also is not needed
# as data is checked in metadata.py
myvamps = Vamps(runobj, idx_keys)
# Create files
myvamps.create_vamps_files()
# put files in db
result_code = myvamps.load_vamps_db()
if result_code[:5] == 'ERROR':
logger.error("load_vamps_db failed")
sys.exit("load_vamps_db failed")
if runobj.vamps_user_upload:
write_status_to_vamps_db( runobj.site, runobj.run, "GAST_ERROR", result_code )
elif runobj.vamps_user_upload:
print "Finished loading VAMPS data",result_code
write_status_to_vamps_db( runobj.site, runobj.run, 'GAST_SUCCESS', 'Loading VAMPS Finished' )
def vampsupload(runobj):
"""
Upload data files to VAMPS database
"""
# for vamps 'new_lane_keys' will be prefix
# of the uniques and names file
# that was just created in vamps_gast.py
# or we can get the 'lane_keys' directly from the config_file
# for illumina:
# a unique idx_key is a concatenation of barcode_index and run_key
idx_keys = get_keys(runobj)
# if(runobj.vamps_user_upload):
# idx_keys = [runobj.user+runobj.runcode]
# else:
# idx_keys = convert_unicode_dictionary_to_str(json.loads(open(runobj.trim_status_file_name,"r").read()))["new_lane_keys"]
myvamps = Vamps(runobj)
myvamps.taxonomy(idx_keys)
myvamps.sequences(idx_keys)
myvamps.exports(idx_keys)
myvamps.projects(idx_keys)
myvamps.info(idx_keys)
