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"""Base for the metadata module."""
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
SUPPORTED_COLUMN_TYPES = {"categorical", "numeric"}
SUPPORTED_ID_HEADERS = {
"case_insensitive": {
"id",
"sampleid",
"sample id",
"sample-id",
"featureid",
"feature id",
"feature-id",
},
# For backwards-compatibility with existing formats.
"exact_match": {
# QIIME 1 mapping files. "#Sample ID" was never supported, but
# we're including it here for symmetry with the other supported
# headers that allow a space between words.
"#SampleID",
"#Sample ID",
# biom-format: observation metadata and "classic" (TSV) OTU tables.
"#OTUID",
"#OTU ID",
# Qiita sample/prep information files.
"sample_name",
},
}
FORMATTED_ID_HEADERS = "Case-insensitive: %s\n\nCase-sensitive: %s" % (
", ".join(repr(e) for e in sorted(SUPPORTED_ID_HEADERS["case_insensitive"])),
", ".join(repr(e) for e in sorted(SUPPORTED_ID_HEADERS["exact_match"])),
)
def is_id_header(name):
"""Determine if a name is a valid ID column header.
This function may be used to determine if a value in a metadata file is a
valid ID column header, or if a pandas ``Index.name`` matches the ID header
requirements. The "ID header" corresponds to the ``Metadata.id_header``
and ``MetadataColumn.id_header`` properties.
Parameters
----------
name : string or None
Name to check against ID header requirements.
Returns
-------
bool
``True`` if `name` is a valid ID column header, ``False`` otherwise.
"""
return name and (
name in SUPPORTED_ID_HEADERS["exact_match"]
or name.lower() in SUPPORTED_ID_HEADERS["case_insensitive"]
)
|
