This script stores file path constants and functions to retrieve those paths.

Functions beginning with an underscore are intended to be called through the supported function or are just helpers.

Author: Parker Hicks Date: 2025-04-15

Last updated: 2026-02-02 by Parker Hicks

na_entities()

Return annotations not to include

disease_ontologies()

Return available disease ontologies.

sexes()

Return available sexes.

species_map()

Return species common and scientific names.

get_annotations(level)

Returns the annotations database file for a given level.

get_config()

Loads the MetaHQ config file.

get_config_file()

Returns the path to the MetaHQ config file if it exists.

get_config_file_no_check()

Only used to initialize MetaHQ.

get_data_dir()

Extracts the MetaHQ data directory from the config.

get_default_data_dir()

Return the default data directory.

get_database_version()

Return the current version of the database.

get_log_dir()

Return log directory defined in config.

get_default_log_dir()

Returns path to default logging directory.

get_default_log_file()

Returns the path to the default logging file.

geo_metadata(level)

Returns the MetaHQ metadata file for the specified level.

get_metadata_path()

Returns the path to MetaHQ metadata.

get_metahq_home()

Returns the home directory for MetaHQ.

Makes the directory if it doesn't exist.

get_ontology_dirs(onto)

Returns the path to the specified ontology directory.

get_ontology_files(onto)

Returns the path to the specified ontology obo file.

get_ontology_search_db()

Returns the path to the ontology search database.

get_ontology_families(onto)

Returns the path to files outlining ontology relationships.

get_technologies()

Returns the file to technology relationships.

attributes(query)

Returns default keys to collect attribute values.

database_ids(query)

Returns supported accession IDs for SRA or GEO.

ecodes(query)

Checks if query is in the supported evidence codes.

levels(query)

Check if queried level is supported.

metadata_fields(level)

Returns supported metadata fields for a specified level.

ontologies(query)

Returns the path to a queried ontology.

onto_relations(query, relatives)

Returns the path to a queried ontology.

species(query)

Checks if a species is supported by MetaHQ.

technologies(query)

Returns supported technologies in MetaHQ.

supported(entity)

Returns supported items for a specified entity.