validator¶
Validation of SBGN documents.
validate_xsd validates against the SBGN XSD schema, the packaged SBGN-ML 0.3
schema in libsbgnpy/schema/SBGN.xsd. Documents in the earlier namespaces are
upconverted before they are validated, i.e., the same documents are read and
validated. validate adds the rules of the SBGN specifications which the
schema cannot express, see libsbgnpy.specification. The schematron rules of
the SBGN languages are checked separately, see libsbgnpy.schematron.
from pathlib import Path
from libsbgnpy import validate
errors = validate(Path("map.sbgn"))
if errors:
for error in errors:
print(error)
Validate an SBGN file against the SBGN XSD schema.
The file is decoded with the encoding its XML declaration names, UTF-8 by default; a file which is no well-formed XML is reported as a single error.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
f
|
Path
|
path of the SBGN file |
required |
Returns:
| Type | Description |
|---|---|
list[str]
|
The validation errors, empty if the document is valid. |
Raises:
| Type | Description |
|---|---|
OSError
|
if the file cannot be read |
Validate an SBGN file against the schema and the SBGN specifications.
The errors of validate_xsd are
followed by the errors of
check_sbgn, i.e., of the rules of
the specifications which the schema cannot express. A document which cannot
be read is only checked against the schema.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
f
|
Path
|
path of the SBGN file |
required |
Returns:
| Type | Description |
|---|---|
list[str]
|
The validation errors, empty if the document is valid. |
Raises:
| Type | Description |
|---|---|
OSError
|
if the file cannot be read |