def main(argv: List[str] = None):
"""
Process RDF files in indir, doing ShEx validation and/or comparing the RDF to the files in outdir
:param argv: Argument list. If None, use sys.argv
:return: 0 if all RDF files that had valid FHIR in them were successful, 1 otherwise
"""
dlp = dirlistproc.DirectoryListProcessor(argv, "Validate FHIR RDF", ".ttl", None, addargs=addargs,
postparse=add_cache)
if not (dlp.opts.infile or dlp.opts.indir):
dirlistproc.DirectoryListProcessor(["--help"], "Validate FHIR RDF", ".ttl", None, addargs=addargs)
nfiles, nsuccess = dlp.run(validate_rdf, file_filter_2=input_filter)
print(f"Total={nfiles} Successful={nsuccess}")
return 0 if nfiles == nsuccess else 1
def main(argv: List[str] = None):
"""
Turn any ShEx files in indir into ShExJ in outdir
:param argv: Argument list. If None, use sys.argv
:return: 0 if conversion was successful, 1 if errors
"""
dlp = dirlistproc.DirectoryListProcessor(argv, "ShEx to ShExJ converter",
".shex", ".shexj")
if not (dlp.opts.infile or dlp.opts.indir):
dirlistproc.DirectoryListProcessor(["--help"],
"ShEx to ShExJ converter", ".shex",
".shexj")
nfiles, nsuccess = dlp.run(do_shex)
print(f"Total={nfiles} Successful={nsuccess}")
return 0 if nfiles == nsuccess else 1
def gen_dlp(args: List[str]) -> dirlistproc.DirectoryListProcessor:
return dirlistproc.DirectoryListProcessor(
args,
"Add FHIR R4 edits to JSON file",
'.json',
'.json',
addargs=addargs)
def main(argv: List[str] = None):
"""
Convert RDF files into JSON-LD format
:param argv: Argument list. If None, use sys.argv
:return: 0 if all RDF files that had valid FHIR in them were successful, 1 otherwise
"""
def dlp(args: List[str]) -> dirlistproc.DirectoryListProcessor:
return dirlistproc.DirectoryListProcessor(args,
"RDF Format Converter",
'.ttl',
'jsonld',
addargs=addargs)
def set_suffix(fname: Optional[List[str]],
fmt: Optional[str]) -> Optional[Tuple[str, str]]:
"""
If a format isn't explicated, see whether it can be determined from the list of file names. Also deal with the
".json" / ".json-ld" issue.
:param fname: possible list of file names
:param fmt: user specified format
:return: File suffix / conversion format. None if undeterminable
"""
if fname and not fmt:
if '.' in fname[0]:
fmt = fname[0].rsplit('.', 1)[1]
return \
(".json", "json-ld") if fmt == 'json' else\
(".jsonld", "json-ld") if fmt == 'jsonld' else \
(".xml", "pretty-xml") if fmt == "xml" else\
(('' if fmt.startswith('.') else '.') + fmt, (fmt[1:] if fmt.startswith('.') else fmt)) if fmt else\
(None, None)
dlp = dlp(argv)
if not (dlp.opts.infile or dlp.opts.indir):
dirlistproc.DirectoryListProcessor(argv + ["--help"])
dlp.infile_suffix, dlp.opts.informat = set_suffix(dlp.opts.infile,
dlp.opts.informat)
dlp.outfile_suffix, dlp.opts.outformat = set_suffix(
dlp.opts.outfile, dlp.opts.outformat)
if not dlp.opts.informat:
print("Unable to determine input format", file=sys.stderr)
if not dlp.opts.outformat:
print("Unable to determine output format", file=sys.stderr)
nfiles, nsuccess = dlp.run(
convert_rdf, file_filter=file_filter
) if dlp.opts.informat and dlp.opts.outformat else (0, 0)
print(f"Total={nfiles} Successful={nsuccess}")
return 0 if nfiles == nsuccess else 1
def main(argv: List[str], default_exit: bool = True) -> bool:
""" Entry point for command line utility """
dlp = dirlistproc.DirectoryListProcessor(
argv,
description="Convert FHIR JSON into RDF",
infile_suffix=".json",
outfile_suffix=".ttl",
addargs=addargs,
noexit=not default_exit)
if not dlp.successful_parse:
return False
# Version
if dlp.opts.version:
print("FHIR to RDF Conversion Tool -- Version {}".format(__version__))
# We either have to have an input file or an input directory
if not dlp.opts.infile and not dlp.opts.indir:
if not dlp.opts.version:
dlp.parser.error(
"Either an input file or an input directory must be supplied")
return dlp.opts.version
# Create the output directory if needed
if dlp.opts.outdir and not os.path.exists(dlp.opts.outdir):
os.makedirs(dlp.opts.outdir)
# If we are going to a single output file or stdout, gather all the input
dlp.opts.graph = Graph() if (not dlp.opts.outfile and not dlp.opts.outdir) or\
(dlp.opts.outfile and len(dlp.opts.outfile) == 1) else None
dlp.opts.fhir_metavoc = load_fhir_ontology(dlp.opts)
# If it looks like we're processing a URL as an input file, skip the suffix check
if dlp.opts.infile and len(
dlp.opts.infile
) == 1 and not dlp.opts.indir and "://" in dlp.opts.infile[0]:
dlp.infile_suffix = ""
dlp.outfile_suffix = '.' + suffix_for(dlp.opts.format)
nfiles, nsuccess = dlp.run(proc=proc_file, file_filter_2=file_filter)
if nfiles:
if dlp.opts.graph:
serialize_graph(dlp.opts.graph,
dlp.opts.outfile[0] if dlp.opts.outfile else None,
dlp.opts)
return nsuccess > 0
return False
def dlp(args: List[str]) -> dirlistproc.DirectoryListProcessor:
return dirlistproc.DirectoryListProcessor(args,
"RDF Format Converter",
'.ttl',
'jsonld',
addargs=addargs)
def testSpecSchema(self):
dlp = dirlistproc.DirectoryListProcessor(["-id", testDir], "Validate ShExJ", ".json", None)
nfiles, nsuccess = dlp.run(lambda *argv: proc_shexj(*argv), file_filter_2=file_filter)
print("Files: {}, Errors: {}".format(nfiles, nfiles-nsuccess))