Index

A

add_config_args() (in module config_utilities) (in module sanitize_utilities) add_file_config_args() (in module config_utilities) add_mysql_config_args() (in module config_utilities) add_redis_config_args() (in module config_utilities)

add_run_config_args() (in module config_utilities) aliases (check_utilities.SrcClass attribute), [1] AppURLopener (class in fetch_utilities) ARCHIVES (in module fetch_utilities) args (job_utilities.Job attribute)

C

check() (in module check_utilities) check_utilities (module) chronos_parent_str() (in module job_utilities) chunk() (in module fetch_utilities) cjobfile (job_utilities.Job attribute) cjobstr (job_utilities.Job attribute) close() (mysql_utilities.MySQL method) combine_tables() (in module mysql_utilities) compare_versions() (in module check_utilities) config_args() (in module config_utilities) config_utilities (module) conn (mysql_utilities.MySQL attribute) conv_gene() (in module redis_utilities)

conv_utilities (module) convert_nodes() (in module export_utilities) copy_table() (mysql_utilities.MySQL method) create_db() (mysql_utilities.MySQL method) create_dictionary() (in module mysql_utilities) create_KnowNet() (in module mysql_utilities) create_mapping_dict() (check_utilities.SrcClass method) create_mapping_dicts() (in module mysql_utilities) create_table() (mysql_utilities.MySQL method) create_temp_table() (mysql_utilities.MySQL method) csu() (in module table_utilities) CURL_PREFIX (in module job_utilities) cursor (mysql_utilities.MySQL attribute)

D

database (mysql_utilities.MySQL attribute) DEFAULT_HINT (in module conv_utilities) DEFAULT_START_STEP (in module workflow_utilities) DEFAULT_TAXON (in module conv_utilities) deploy_container() (in module mysql_utilities) (in module redis_utilities) DIR (in module fetch_utilities)

disable_keys() (mysql_utilities.MySQL method) download() (in module fetch_utilities) drop_db() (mysql_utilities.MySQL method) drop_duplicates_by_type_or_node() (in module sanitize_utilities) drop_table() (mysql_utilities.MySQL method) drop_temp_table() (mysql_utilities.MySQL method) dump_table() (mysql_utilities.MySQL method)

E

enable_keys() (in module import_utilities) (mysql_utilities.MySQL method)

export_utilities (module)

F

fetch_utilities (module)

figure_out_class() (in module export_utilities) format_raw_line() (in module fetch_utilities)

G

generic_dict() (in module workflow_utilities) get_aliases() (check_utilities.SrcClass method) get_database() (in module mysql_utilities) (in module redis_utilities) get_dependencies() (check_utilities.SrcClass method) get_file_meta() (in module mysql_utilities) get_gg() (in module export_utilities) get_insert_cmd() (in module mysql_utilities) get_line_count() (in module fetch_utilities) get_local_file_info() (check_utilities.SrcClass method)

get_local_version_info() (check_utilities.SrcClass method) get_md5_hash() (in module fetch_utilities) get_metadata() (in module export_utilities) get_node_info() (in module redis_utilities) get_pg() (in module export_utilities) get_remote_file_modified() (check_utilities.SrcClass method) get_remote_file_size() (check_utilities.SrcClass method) get_remote_url() (check_utilities.SrcClass method) get_source_version() (check_utilities.SrcClass method) get_sources() (in module export_utilities) get_SrcClass() (in module check_utilities)

H

host (mysql_utilities.MySQL attribute)

I

import_edge() (in module import_utilities) import_ensembl() (in module mysql_utilities) (in module redis_utilities) import_file() (in module import_utilities) import_file_nokeys() (in module import_utilities) import_filemeta() (in module import_utilities) import_gene_nodes() (in module redis_utilities) import_node_meta() (in module redis_utilities) import_nodemeta() (in module import_utilities) import_nodes() (in module mysql_utilities)

import_pnode() (in module import_utilities) import_production_edges() (in module import_utilities) import_schema() (mysql_utilities.MySQL method) import_status() (in module import_utilities) import_table() (mysql_utilities.MySQL method) import_utilities (module) init_knownet() (mysql_utilities.MySQL method) insert() (mysql_utilities.MySQL method) insert_ignore() (mysql_utilities.MySQL method) is_map() (check_utilities.SrcClass method)

J

Job (class in job_utilities) job_utilities (module)

jobname (job_utilities.Job attribute) jobtype (job_utilities.Job attribute)

L

license (check_utilities.SrcClass attribute), [1]

list_sources() (in module workflow_utilities) load_data() (mysql_utilities.MySQL method)

M

main() (in module conv_utilities) (in module export_utilities) (in module fetch_utilities) (in module import_utilities) (in module mysql_utilities) (in module redis_utilities) (in module table_utilities) (in module workflow_utilities) main_parse_args() (in module check_utilities) (in module conv_utilities) (in module fetch_utilities) (in module import_utilities) (in module table_utilities) (in module workflow_utilities)

make_network_undirected() (in module sanitize_utilities) make_network_unweighted() (in module sanitize_utilities) map_list() (in module conv_utilities) MAX_CHUNKS (in module fetch_utilities) merge() (in module import_utilities) merge_logs() (in module import_utilities) move_table() (mysql_utilities.MySQL method) MySQL (class in mysql_utilities) mysql_utilities (module)

N

name (check_utilities.SrcClass attribute), [1] node_desc() (in module redis_utilities)

norm_edges() (in module export_utilities) normalize_network_by_type() (in module sanitize_utilities) num_connected_components() (in module export_utilities)

P

passw (mysql_utilities.MySQL attribute) pmid (check_utilities.SrcClass attribute), [1] port (mysql_utilities.MySQL attribute)

POSSIBLE_STEPS (in module workflow_utilities) pretty_name() (in module config_utilities) print_chronos_job() (job_utilities.Job method)

Q

query_all_mappings() (in module mysql_utilities) query_distinct() (mysql_utilities.MySQL method)

queue_chronos_job() (job_utilities.Job method) queue_starter_job() (in module job_utilities)

R

redis_utilities (module) reference (check_utilities.SrcClass attribute), [1] remote_file (check_utilities.SrcClass attribute), [1] replace() (mysql_utilities.MySQL method) replace_jobtmp() (job_utilities.Job method) replace_safe() (mysql_utilities.MySQL method) run() (mysql_utilities.MySQL method) run_check() (in module workflow_utilities)

run_docker_job() (job_utilities.Job method) run_export() (in module workflow_utilities) run_fetch() (in module workflow_utilities) run_import() (in module workflow_utilities) run_job() (job_utilities.Job method) run_job_step() (in module job_utilities) run_local_job() (job_utilities.Job method) run_map() (in module workflow_utilities) run_table() (in module workflow_utilities)

S

sanitize_utilities (module) set_isolation() (mysql_utilities.MySQL method) SETUP_FILES (in module workflow_utilities) should_skip() (in module export_utilities)

sort_network() (in module sanitize_utilities) source_url (check_utilities.SrcClass attribute), [1] SPECIAL_MODES (in module workflow_utilities) SrcClass (class in check_utilities) start_transaction() (mysql_utilities.MySQL method)

T

table() (check_utilities.SrcClass method)

table_utilities (module) tmpdict (job_utilities.Job attribute)

U

update_filemeta() (in module import_utilities) upper_triangle() (in module sanitize_utilities)

url_base (check_utilities.SrcClass attribute), [1] use_db() (mysql_utilities.MySQL method) user (mysql_utilities.MySQL attribute)

V

version (check_utilities.SrcClass attribute), [1]

W

workflow_utilities (module)