defineutils

CDISC Define-XML v2.1 utilities

The defineutils package currently includes 2 modules:

1. definehtml.py: transforms a define.xml into a define.html using the stylesheet
2. validate.py: schema validates a define.xml file

The definehtml.py module includes the Define-XML v2.1 style sheet to simplify usage. It generates a define.html file, or alternatively will generate an HTML string.

The validate.py module includes the Define-XML v2.1 schema to simplify usage. It schema validates a define.xml file and returns a define.xml is valid message to indicate success, or a detailed message documenting the schema validation issues.

Using defineutils

Currently, defineutils contains 2 modules, one for generating an HTML rendition and one for schema validation.

Example code used to generate a define.html from a define.xml:

from pathlib import Path
from defineutils.definehtml import DefineHtml, DefineHtmlGenerationError

out_file = Path(__file__).parent.joinpath("define.html")
dh = DefineHtml(Path(__file__).parent.joinpath("define.xml"))
dh.transform_to_html_file(out_file)

The above code applies the Define-XML v2.1 stylesheet to the define.xml to generation the define.html file. The stylesheet is embedded in the module. For error handling, use the custom DefineHtmlGenerationError exception.

Example code used to schema validate a define.xml:

from pathlib import Path
from defineutils.validate import DefineSchemaValidator, DefineSchemaValidationError

validator = DefineSchemaValidator(Path(__file__).parent.joinpath("define.xml"))
try:
    result = validator.validate_define_file()
except DefineSchemaValidationError as e:
    print(e)

The above code schema validates the specified define.xml file. The Define-XML v2.1 schema is embedded into the module. The schema validation errors are reported via the DefineSchemaValidationError exception.

Running defineutils from the Command-line

When you run a module with the -m switch it will execute the defineutils modules from the command-line. For example, to transform a define.xml file into HTML using the stylesheet, the following command-line example executes the module to generate define.html. The -m parameter instructs Python to run the module as an application. The definehtml program uses the -d parameter to specify the define.xml file path and the -o to specify the define.html file path.

python3 -m defineutils.definehtml -d tests/define.xml -o tests/define.html

The validate command can be executed using the command-line the same way. For validate, only the -d parameter is required to indicate the file path of the define.xml to validate.

python3 -m defineutils.validate -d tests/define.xml

If you are running defineutils from the source code using a virtual environment, you may need to activate that virtual environment before running the code from the command-line.

source .venv/bin/activate
python3 -m defineutils.validate -d tests/define.xml