import re
import os
-from htsworkflow.pipelines.retrieve_config import getCombinedOptions, saveConfigFile
-from htsworkflow.pipelines.retrieve_config import FlowCellNotFound, WebError404
+from htsworkflow.pipelines.retrieve_config import \
+ CONFIG_SYSTEM, CONFIG_USER, \
+ FlowCellNotFound, getCombinedOptions, saveConfigFile, WebError404
from htsworkflow.pipelines.genome_mapper import DuplicateGenome, getAvailableGenomes, constructMapperDict
from htsworkflow.pipelines.run_status import GARunStatus
return False
-def retrieve_config(conf_info, flowcell, cfg_filepath, genome_dir):
+def retrieve_config(conf_info, flowcell, cfg_filepath, genome_dir,
+ cfg_defaults=None):
"""
Gets the config file from server...
requires config file in:
return True if successful, False is failure
"""
- options = getCombinedOptions()
+ options = getCombinedOptions(cfg_defaults)
if options.url is None:
- logging.error("~/.ga_frontend.conf or /etc/ga_frontend/ga_frontend.conf" \
- " missing base_host_url option")
+ logging.error("%s or %s missing base_host_url option" % \
+ (CONFIG_USER, CONFIG_SYSTEM))
return False
try: