library_xml

library_xml

Introduction

library_xml retrieves a standard from the CDISC Library as Library-XML (an ODM media type) and loads it into odmlib for processing, writing the result out as JSON.

Its main value as an example is that it shows how to use external/local odmlib extension models. The two model packages bundled here —

• library_odm_1_0/ — Library-XML based on ODM (e.g. CDASHIG)
• library_define_1_0/ — Library-XML based on Define-XML (e.g. SDTMIG)

— are loaded with the odmlib v0.2.0 local_model=True loader option, so they make a good template for implementing your own ODM extensions. (For a from-scratch walkthrough of building a local extension model, see ../snippets/custom-extension/.)

v0.2.0 features shown

• Loading documents against a local extension model: XMLDefineLoader(model_package=..., local_model=True) / XMLODMLoader(model_package=..., local_model=True).
• Namespace declaration via odmlib.ns_registry.NamespaceRegistry.
• create_document_from_string() to parse XML retrieved over HTTP, and to_json() to serialize.

Prerequisites

pip install -r requirements.txt

(installs odmlib>=0.2.0 and requests)

You also need a CDISC Library API key — create an account at library.cdisc.org and use your own key in place of YOUR_API_KEY below.

Run

Retrieve SDTMIG v3.4 (Define-XML flavor of Library-XML — note the -d flag):

cd library_xml
python library_xml.py -d -e "/mdr/sdtmig/3-4" -k YOUR_API_KEY

Retrieve CDASHIG v2.2 (ODM flavor) to a named output file:

python library_xml.py -e "/mdr/cdashig/2-2" -f library-odmlib-cdashig2-2.json -k YOUR_API_KEY

The -d flag selects the Define-XML model for Library-XML; omit it for the ODM model. The endpoint is given by -e, and -f sets the output JSON filename (a default is used when omitted).

Limitations

This is a demonstration program, not a production application. It exercises the metadata sections of Library-XML and could be extended to address additional use cases. Using the CDISC Library API requires your own account and credentials.