def names(directory: str, zenodo: bool, no_strict: bool, force: bool): """Make the prefix-identifier-name dump.""" paths = db_output_helper( _iter_ooh_na_na, 'names', ('prefix', 'identifier', 'name'), strict=not no_strict, force=force, directory=directory, ) if zenodo: # see https://zenodo.org/record/4020486 update_zenodo(OOH_NA_NA_RECORD, paths)
def properties(directory: str, zenodo: bool, force: bool, no_strict: bool): """Make the properties dump.""" paths = db_output_helper( _iter_properties, 'properties', ('prefix', 'identifier', 'property', 'value'), directory=directory, force=force, strict=not no_strict, summary_detailed=(0, 2), # second column corresponds to property type ) if zenodo: # see https://zenodo.org/record/4625172 update_zenodo(PROPERTIES_RECORD, paths)
def synonyms(directory: str, zenodo: bool, force: bool, no_strict: bool): """Make the prefix-identifier-synonym dump.""" paths = db_output_helper( _iter_synonyms, 'synonyms', ('prefix', 'identifier', 'synonym'), directory=directory, force=force, strict=not no_strict, skip_set={'kegg.pathway', 'kegg.genes', 'kegg.genome'}, ) if zenodo: # see https://zenodo.org/record/4021482 update_zenodo(SYNONYMS_RECORD, paths)
def alts(directory: str, zenodo: bool, force: bool, no_strict: bool): """Make the prefix-alt-id dump.""" paths = db_output_helper( _iter_alts, 'alts', ('prefix', 'identifier', 'alt'), directory=directory, force=force, strict=not no_strict, skip_set={'kegg.pathway', 'kegg.genes', 'kegg.genome', 'umls'}, ) if zenodo: # see https://zenodo.org/record/4021476 update_zenodo(ALTS_DATA_RECORD, paths)
def definitions(directory: str, zenodo: bool, no_strict: bool, force: bool): """Make the prefix-identifier-definition dump.""" paths = db_output_helper( _iter_definitions, 'definitions', ('prefix', 'identifier', 'definition'), strict=not no_strict, force=force, directory=directory, skip_set={'kegg.pathway', 'kegg.genes', 'kegg.genome', 'umls'}, ) if zenodo: # see https://zenodo.org/record/4637061 update_zenodo(DEFINITIONS_RECORD, paths)
def species(directory: str, zenodo: bool, no_strict: bool, force: bool): """Make the prefix-identifier-species dump.""" with logging_redirect_tqdm(): paths = db_output_helper( _iter_species, "species", ("prefix", "identifier", "species"), strict=not no_strict, force=force, directory=directory, ) if zenodo: # see https://zenodo.org/record/5334738 update_zenodo(SPECIES_RECORD, paths)
def alts(directory: str, zenodo: bool, force: bool, no_strict: bool): """Make the prefix-alt-id dump.""" paths = db_output_helper( _iter_alts, "alts", ("prefix", "identifier", "alt"), directory=directory, force=force, strict=not no_strict, skip_set={"kegg.pathway", "kegg.genes", "kegg.genome", "umls"}, ) if zenodo: # see https://zenodo.org/record/4021476 update_zenodo(ALTS_DATA_RECORD, paths)
def definitions(directory: str, zenodo: bool, no_strict: bool, force: bool): """Make the prefix-identifier-definition dump.""" paths = db_output_helper( _iter_definitions, "definitions", ("prefix", "identifier", "definition"), strict=not no_strict, force=force, directory=directory, skip_set={"kegg.pathway", "kegg.genes", "kegg.genome", "umls"}, ) if zenodo: # see https://zenodo.org/record/4637061 update_zenodo(DEFINITIONS_RECORD, paths)
def typedefs(directory: str, zenodo: bool, no_strict: bool, force: bool): """Make the typedef prefix-identifier-name dump.""" paths = db_output_helper( _iter_typedefs, 'typedefs', ('prefix', 'typedef_prefix', 'identifier', 'name'), strict=not no_strict, force=force, directory=directory, use_gzip=False, skip_set={'ncbigene', 'kegg.pathway', 'kegg.genes', 'kegg.genome'}, ) if zenodo: # see https://zenodo.org/record/4644013 update_zenodo(TYPEDEFS_RECORD, paths)
def xrefs(directory: str, zenodo: bool, force: bool, no_strict: bool): # noqa: D202 """Make the prefix-identifier-xref dump.""" with logging_redirect_tqdm(): paths = db_output_helper( _iter_xrefs, "xrefs", ("prefix", "identifier", "xref_prefix", "xref_identifier", "provenance"), directory=directory, force=force, strict=not no_strict, summary_detailed=(0, 2), # second column corresponds to xref prefix ) if zenodo: # see https://zenodo.org/record/4021477 update_zenodo(JAVERT_RECORD, paths)
def properties(directory: str, zenodo: bool, force: bool, no_strict: bool): """Make the properties dump.""" with logging_redirect_tqdm(): paths = db_output_helper( _iter_properties, "properties", ("prefix", "identifier", "property", "value"), directory=directory, force=force, strict=not no_strict, summary_detailed=(0, 2), # second column corresponds to property type ) if zenodo: # see https://zenodo.org/record/4625172 update_zenodo(PROPERTIES_RECORD, paths)
def synonyms(directory: str, zenodo: bool, force: bool, no_strict: bool): """Make the prefix-identifier-synonym dump.""" with logging_redirect_tqdm(): paths = db_output_helper( _iter_synonyms, "synonyms", ("prefix", "identifier", "synonym"), directory=directory, force=force, strict=not no_strict, skip_set={"kegg.pathway", "kegg.genes", "kegg.genome"}, ) if zenodo: # see https://zenodo.org/record/4021482 update_zenodo(SYNONYMS_RECORD, paths)
def typedefs(directory: str, zenodo: bool, no_strict: bool, force: bool): """Make the typedef prefix-identifier-name dump.""" paths = db_output_helper( _iter_typedefs, "typedefs", ("prefix", "typedef_prefix", "identifier", "name"), strict=not no_strict, force=force, directory=directory, use_gzip=False, skip_set={"ncbigene", "kegg.pathway", "kegg.genes", "kegg.genome"}, ) if zenodo: # see https://zenodo.org/record/4644013 update_zenodo(TYPEDEFS_RECORD, paths)
def relations(directory: str, zenodo: bool, force: bool, no_strict: bool): """Make the relation dump.""" paths = db_output_helper( _iter_relations, 'relations', ( 'source_prefix', 'source_identifier', 'relation_prefix', 'relation_identifier', 'target_prefix', 'target_identifier', ), directory=directory, force=force, strict=not no_strict, summary_detailed=(0, 2, 3), # second column corresponds to relation type ) if zenodo: # see https://zenodo.org/record/4625167 update_zenodo(RELATIONS_RECORD, paths)
def names( directory: str, zenodo: bool, no_strict: bool, force: bool, skip_below: Optional[str], skip_below_exclusive: bool, ): """Make the prefix-identifier-name dump.""" with logging_redirect_tqdm(): paths = db_output_helper( _iter_names, "names", ("prefix", "identifier", "name"), strict=not no_strict, force=force, directory=directory, skip_below=skip_below, skip_below_inclusive=not skip_below_exclusive, ) if zenodo: # see https://zenodo.org/record/4020486 update_zenodo(OOH_NA_NA_RECORD, paths)