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 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' )