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 = None)

__init__(version: str = None) → None

Parameters

version – The Loom file format version to validate against (“3.0.0”, “2.0.1”, “old”), or None to infer from file

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

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

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

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.