validate_cdisc_submission()

Check a CDISC submission with the CDISC CORE engine.

Usage

validate_cdisc_submission(
    source,
    standard=None,
    version=None,
    define=None,
    controlled_terminology=None,
    agency=None,
    ct_version=None,
    study_id=None,
    core=None,
    core_cwd=None,
    cache=None,
    workdir=None,
)

CDISC CORE is CDISC’s open-source engine for its conformance rules, and it has the published rules of CDISC and of the FDA and PMDA. The validate_cdisc_submission() function runs CORE on a submission in a single call: it makes a SubmissionPackage from the source (unless it is one already), runs CORE on it, and reads CORE’s results into a ConformanceReport. This is the same as calling the package’s validate_conformance() method with engine="core".

CORE is a separate command-line tool (cdisc-rules-engine) that has to be installed. If it isn’t on the PATH, give the command with core= or in the POINTBLANK_CDISC_CORE environment variable. For checks that need no other software, use validate_sdtmig(), which runs Pointblank’s bundled SDTMIG rules.

Parameters

source: str | Path | dict | SubmissionPackage: The submission to check. This can be the path of a folder of datasets (.xpt or Dataset-JSON files, which are read with SubmissionPackage.from_folder()), a dict of DataFrames keyed by dataset name, or a SubmissionPackage.
standard: str | None = None: The CDISC standard, such as "sdtmig". The default is "sdtmig", or the package’s standard if source is a SubmissionPackage.
version: str | None = None: The version of the standard, such as "3.4". The default is "3.4", or the package’s standard_version if source is a SubmissionPackage.
define: str | Path | Any | None = None: The path of the study’s Define-XML, which CORE uses in its checks. For a folder, a define*.xml file in it is found without this. It is ignored if source is a SubmissionPackage, whose own define is used. The default is None.
controlled_terminology: str | Sequence[str] | None = None: The controlled terminology package or packages for CORE’s -ct option, such as "sdtmct-2024-03-29". The default is None.
agency: str | None = None: The regulatory agency, such as "FDA" or "PMDA", which is shown in the report. It doesn’t change the rules that CORE runs. The default is None.
ct_version: str | None = None: The controlled terminology version to record in the package. It is only shown in the package’s summary and isn’t given to CORE. It is ignored if source is a SubmissionPackage. The default is None.
study_id: str | None = None: A study identifier to record in the package. It is ignored if source is a SubmissionPackage. The default is None.
core: str | Sequence[str] | None = None: How to run CORE. This can be the path or name of the CORE executable, or a command as a list (such as ["python", "core.py"]). With the default of None, the command is taken from the POINTBLANK_CDISC_CORE environment variable, or else CORE is looked for on the PATH.
core_cwd: str | Path | None = None: The directory to run CORE from. This is needed when CORE is run from a checkout of its repository, since it looks for its resources/ folder in the current directory. The default is None.
cache: str | Path | None = None: The path to CORE’s rules cache (its -ca option). The default is None.
workdir: str | Path | None = None: A directory for the XPT files that the datasets are written to and for CORE’s report. With the default of None, a temporary directory is used and then deleted.

Returns

ConformanceReport: A report of CORE’s results, whose is_core is True.

Raises

NotADirectoryError: If source is a path that isn’t a folder.
TypeError: If source isn’t a path, a dict or a SubmissionPackage.

Examples

CORE has to be installed for this function, so these examples aren’t run here. Let’s check a folder of SDTM datasets against SDTMIG 3.4, for a submission to the FDA:

import pointblank as pb

report = pb.validate_cdisc_submission(
    "study_xyz/sdtm/",
    standard="sdtmig",
    version="3.4",
    controlled_terminology="sdtmct-2024-03-29",
    agency="FDA",
)

print(report)

Printing the report gives the standard, the version of CORE, the number of rules with each of CORE’s statuses and the total number of issues. The issues and the failing records can then be looked at, and the report saved for review:

for issue in report.issues(status="ISSUE REPORTED"):
    print(issue["dataset"], issue["rule_id"], issue["issues"], issue["message"])

report.to_excel("study_xyz/conformance/core_report.xlsx")

If CORE was installed from a checkout of its repository, it has to be run from that directory, as in core=["python", "core.py"], core_cwd="path/to/cdisc-rules-engine". A report that CORE wrote on its own can be read with ConformanceReport.from_core_report(), which has an example that runs without CORE.

Parameters

Returns

Raises

Examples

See Also