LoomValidator (class)

Validate the content of a Loom file against the file format specification and/or attrubute conventions.

>>> lv = loompy.LoomValidator()
>>> if not lv.validate(d+f, strictness="conventions"):
>>>     for warn in lv.warnings:
>>>         print("WARNING:", warn)
>>>     for err in lv.errors:
>>>         print("ERROR:", err)

WARNING: Optional global attribute 'Description' is missing
WARNING: Optional global attribute 'Journal' is missing
WARNING: Optional global attribute 'Authors' is missing
WARNING: Optional global attribute 'Title' is missing
WARNING: Optional global attribute 'Year' is missing
WARNING: Optional column attribute 'ClusterName' is missing
WARNING: Optional column attribute 'Valid' is missing
WARNING: Optional row attribute 'Valid' is missing
WARNING: Optional row attribute 'Selected' is missing
ERROR: Column attribute 'ClusterID' is missing
ERROR: Column attribute 'CellID' cannot contain duplicate values
ERROR: For help, see http://linnarssonlab.org/loompy/conventions/
class loompy.LoomValidator(version: str = '2.0.1')[source]
__init__(version: str = '2.0.1') → None[source]
Parameters:version – The Loom file format version to validate against (“2.0.1” or “old”)
Remarks:
“old” version will accept files that lack the “row_graphs” and “col_graphs” groups
version = None

Version of the spec to validate against

errors = None

Errors found during validation

warnings = None

Warnings triggered during validation

summary = None

Summary of the file structure

validate(path: str, strictness: str = 'speconly') → bool[source]

Validate a file for conformance to the Loom specification

Parameters:
  • path – Full path to the file to be validated
  • strictness – “speconly” or “conventions”
Remarks:
In “speconly” mode, conformance is assessed relative to the file format specification at http://linnarssonlab.org/loompy/format/. In “conventions” mode, conformance is additionally assessed relative to attribute name and data type conventions given at http://linnarssonlab.org/loompy/conventions/.
validate_conventions(ds: loompy.loompy.LoomConnection) → bool[source]

Validate the LoomConnection object against the attribute name/dtype conventions.

Parameters:ds – LoomConnection object
Returns:True if the file conforms to the conventions, else False
Remarks:
Upon return, the instance attributes ‘self.errors’ and ‘self.warnings’ contain lists of errors and warnings.
validate_spec(file: h5py._hl.files.File) → bool[source]

Validate the LoomConnection object against the format specification.

Parameters:file – h5py File object
Returns:True if the file conforms to the specs, else False
Remarks:
Upon return, the instance attributes ‘self.errors’ and ‘self.warnings’ contain lists of errors and warnings, and the ‘self.summary’ attribute contains a summary of the file contents.