def check_configuration(cfg):
"""
checks the validity of configuration elements
:param cfg: the configuration object (ConfigParser)
:return: True or False
"""
# general job configuration
if not utility.check_config(cfg, "job_config", ["name", "action_on_failure", "mapper_memory"]):
return False
if not utility.check_upload_config(cfg["job_config"], 'upload_script', 'script',
'script_local_location', 'script_s3_location'):
return False
# preprocessing script args
if not utility.check_config(cfg, "script_arguments", ["manifest", "input_location",
"output_location", "report_location",
"region"]):
return False
if not utility.check_s3_region(cfg["script_arguments"]['region']):
return False
# user files
# Note that the "files" item is optional
if not utility.check_config(cfg, "user_script_config", []) and \
not utility.check_upload_config(cfg["user_script_config"], 'upload_user_files', 'script','user_files_local_location', 'user_files_s3_location', 'supporting_files', 'min_trim'):
return False
return True
def check_configuration(cfg):
"""
checks the validity of configuration elements
:param cfg: the configuration object (ConfigParser)
:return: True or False
"""
# general job configuration
if not utility.check_config(cfg, "job_config", ["name", "action_on_failure", "mapper_memory"]):
return False
if not utility.check_upload_config(cfg["job_config"], 'upload_script', 'script',
'script_local_location', 'script_s3_location'):
return False
# preprocessing script args
if not utility.check_config(cfg, "script_arguments", ["manifest", "input_location",
"output_location", "report_location",
"region"]):
return False
if not utility.check_s3_region(cfg["script_arguments"]['region']):
return False
# user files
# Note that the "files" item is optional
if not utility.check_config(cfg, "user_script_config", []) and \
not utility.check_upload_config(cfg["user_script_config"], 'upload_user_files', 'script',
'user_files_local_location', 'user_files_s3_location', 'supporting_files'):
return False
return True
def check_configuration(config):
if not utility.check_config(config, "job_config", [
"name", "action_on_failure", "analysis_script",
"analysis_script_s3_location", "upload_analysis_script"
]):
return False
if not utility.check_upload_config(
config["job_config"], "upload_analysis_script", "analysis_script",
"analysis_script_local_location", "analysis_script_s3_location"):
return False
if not utility.check_config(config, "spark_config",
["driver_memory", "executor_memory"]):
return False
if not utility.check_config(config, "script_arguments", [
"input_location", "output_location", "annotation_file", "region",
"strand_specificity", "aligner_tool", "counter_tool"
]):
return False
if not utility.check_s3_region(config["script_arguments"]["region"]):
return False
return True
def check_configuration(config):
if not utility.check_config(config, "EMR", [
"release_label", "software_installer_location",
"genome_folder_location"
]):
return False
if not utility.check_upload_config(
config["EMR"], "upload_bootstrap_scripts", "bootstrap_scripts",
"bootstrap_scripts_local_location",
"bootstrap_scripts_s3_location"):
return False
if not utility.check_config(config, "EMR_nodes", [
"key_name", "service_role", "instance_profile",
"master_instance_type", "master_instance_count",
"core_instance_type", "core_instance_count"
]):
return False
release_version = config["EMR"]["release_label"].split("-")[-1].split(".")
major_release_version = int(release_version[0])
minor_release_version = int(release_version[1])
if config["EMR_nodes"].get("custom_ami_id", "").strip() != "" \
and not (major_release_version >= 5 and minor_release_version >= 7):
print(
"\033[31mERROR: \033[0mCustom AMI can only be used with EMR release >= 5.7"
)
return False
return True
def check_configuration(config):
if not utility.check_config(config, "job_config", [
"name", "action_on_failure", "assembly_script",
"assembly_script_s3_location", "upload_assembly_script"
]):
return False
if not utility.check_upload_config(
config["job_config"], "upload_assembly_script", "assembly_script",
"assembly_script_local_location", "assembly_script_s3_location"):
return False
if not utility.check_config(config, "spark_config",
["driver_memory", "executor_memory"]):
return False
if not utility.check_config(config, "script_arguments", [
"input_location", "output_location", "annotation_file",
"enable_tiling", "enable_analysis", "region", "aligner_tool",
"assembler_tool", "assembler_extra_args",
"assembler_merge_extra_args"
]):
return False
if not utility.check_s3_region(config["script_arguments"]["region"]):
return False
return True
def check_configuration(config):
if not utility.check_config(config, "EMR", ["release_label", "software_installer_location",
"genome_folder_location"]):
return False
if not utility.check_upload_config(config["EMR"], "upload_bootstrap_scripts", "bootstrap_scripts",
"bootstrap_scripts_local_location", "bootstrap_scripts_s3_location"):
return False
if not utility.check_config(config, "EMR_nodes", ["key_name", "service_role", "instance_profile",
"master_instance_type", "master_instance_count",
"core_instance_type", "core_instance_count"]):
return False
return True
def check_configuration(config):
if not utility.check_config(config, "EMR", ["release_label", "software_installer_location",
"genome_folder_location"]):
return False
if not utility.check_upload_config(config["EMR"], "upload_bootstrap_scripts", "bootstrap_scripts",
"bootstrap_scripts_local_location", "bootstrap_scripts_s3_location"):
return False
if not utility.check_config(config, "EMR_nodes", ["key_name", "service_role", "instance_profile",
"master_instance_type", "master_instance_count",
"core_instance_type", "core_instance_count"]):
return False
return True
def check_configuration(config):
if not utility.check_config(config, "job_config", ["name", "action_on_failure", "downloader_script",
"downloader_script_s3_location", "upload_downloader_script"]):
return False
if not utility.check_upload_config(config["job_config"], "upload_downloader_script", "downloader_script",
"downloader_script_local_location", "downloader_script_s3_location"):
return False
if not utility.check_config(config, "script_arguments", ["accession_list", "output_location", "report_location",
"region"]):
return False
if not utility.check_s3_region(config["script_arguments"]["region"]):
return False
return True
def check_configuration(config):
if not utility.check_config(config, "job_config", ["name", "action_on_failure", "splitter_script",
"splitter_script_s3_location", "upload_splitter_script"]):
return False
if not utility.check_upload_config(config["job_config"], "upload_splitter_script", "splitter_script",
"splitter_script_local_location", "splitter_script_s3_location"):
return False
if not utility.check_config(config, "script_arguments", ["manifest", "input_location", "output_location",
"report_location", "region"]):
return False
if not utility.check_s3_region(config["script_arguments"]["region"]):
return False
return True
def check_configuration(config):
if not utility.check_config(config, "job_config", ["name", "action_on_failure", "analysis_script",
"analysis_script_s3_location", "upload_analysis_script"]):
return False
if not utility.check_upload_config(config["job_config"], "upload_analysis_script", "analysis_script",
"analysis_script_local_location", "analysis_script_s3_location"):
return False
if not utility.check_config(config, "spark_config", ["driver_memory", "executor_memory"]):
return False
if not utility.check_config(config, "script_arguments", ["input_location", "output_location", "annotation_file",
"region", "strand_specificity", "aligner_tool",
"counter_tool"]):
return False
if not utility.check_s3_region(config["script_arguments"]["region"]):
return False
return True
def check_configuration(config):
if not utility.check_config(config, "job_config", ["name", "action_on_failure", "classify_script",
"classify_script_s3_location", "upload_classify_script"]):
return False
if not utility.check_upload_config(config["job_config"], "upload_classify_script", "classify_script",
"classify_script_local_location", "classify_script_s3_location"):
return False
if not utility.check_config(config, "spark_config", ["driver_memory", "executor_memory"]):
return False
if not utility.check_config(config, "script_arguments", ["output_location", "region"]):
return False
if not utility.check_s3_region(config["script_arguments"]["region"]):
return False
if all(x not in config["script_arguments"] for x in ["input_location", "organism", "and_keywords", "or_keywords"]):
print("At least one of the following script arguments are required: input_location, organism, and_keywords, "
"or_keywords")
return False
return True