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)