Validate an RDF file or directory containing RDF (in turtle format) against the expected FHIR Schema
This package can be used to validate a single RDF file or a directory containing RDF (turtle) files using:
- ShEx - FHIR Shape Expressions definitions of resources and/or
- RDF - Compare two RDF files or directories
validate --help
usage: validate [-h] [-i [INFILE [INFILE ...]]] [-id INDIR]
[-o [OUTFILE [OUTFILE ...]]] [-od OUTDIR] [-f] [-s]
[--shex] [-sd SHEXDIR] [-cd CACHEDIR]
Validate FHIR RDF
optional arguments:
-h, --help show this help message and exit
-i [INFILE [INFILE ...]], --infile [INFILE [INFILE ...]]
Input file(s)
-id INDIR, --indir INDIR
Input directory
-o [OUTFILE [OUTFILE ...]], --outfile [OUTFILE [OUTFILE ...]]
Output file(s)
-od OUTDIR, --outdir OUTDIR
Output directory
-f, --flatten Flatten output directory
-s, --stoponerror Stop on processing error
--shex Do ShEx validaton
-sd SHEXDIR, --shexdir SHEXDIR
Base directory of ShEx definitions. Default: indir
-cd CACHEDIR, --cachedir CACHEDIR
Cache directory for cached ShEx
- Check out, unzip or otherwise create a FHIR
publishdirectory, which contains RDF (.ttl) and ShEx (.shex) FHIR files. - Run
validate -id <fhir directory> --sd <fhir directory> --shex -od <other comparison directory> -cd cache
Note that the run can take a long time if doing ShEx validation and the cache directory hasn't been loaded.
- The PyShEx parser takes a long time to parse the FHIR ShEx Schema definitions. For this reason, you can specify a cache directory that carries the parsed (ShExJ) representation of the schemas. The cache directory that is a part of this project currently contains a fairly recent version of the FHIR R5 build.