def _verify_schema1_content(
self,
schema: SchemaDefinition,
source_file,
addl_checks: Callable[[SchemaDefinition], None] = None) -> None:
expected = loads(f"""{{
"default_prefix": "http://example.org/{source_file}/",
"name": "{source_file}",
"id": "http://example.org/{source_file}",
"title": "Load Raw Schema Test",
"metamodel_version": "0.5.0",
"source_file": "{source_file}.yaml",
"source_file_date": "Mon Dec 31 11:25:38 2018",
"source_file_size": 76,
"generation_date": "2018-12-31 11:50"
}}""")
schema.source_file = os.path.basename(schema.source_file)
if addl_checks:
addl_checks(schema)
self.assertTrue(isinstance(schema.metamodel_version, str))
expected.metamodel_version = schema.metamodel_version
self.assertTrue(isinstance(schema.source_file_date, str))
expected.source_file_date = schema.source_file_date
self.assertTrue(isinstance(schema.source_file_size, int))
expected.source_file_size = schema.source_file_size
self.assertTrue(isinstance(schema.generation_date, str))
expected.generation_date = schema.generation_date
self.assertEqual(expected, loads(as_json(schema)))
def test_merge_contexts_base(self):
self.assertEqual(
JsonObj(**{'@context': JsonObj(**{'@base': 'file://relloc'})}),
merge_contexts(base='file://relloc'))
self.assertEqual(
loads(f'{{"@context": {{"@base": "{META_BASE_URI}"}}}}'),
merge_contexts(base=META_BASE_URI))
self.assertEqual(
loads("""
{"@context": [
"https://w3id.org/biolink/biolinkml/context.jsonld",
{
"ex": "http://example.org/test/",
"ex2": "http://example.org/test2/"
},
{
"ex": "http://example.org/test3/",
"ex2": {
"@id": "http://example.org/test4/"
}
},
{
"@base": "https://w3id.org/biolink/biolinkml/"
}
]
}"""),
merge_contexts([METAMODEL_CONTEXT_URI, json_1, json_2],
base=META_BASE_URI))
def check_json(ifn: str, ifdir: str, opts: Namespace) -> bool:
"""
Check whether ifn is a valid FHIR file
:param ifn: file name
:param ifdir: file directory
:param opts: options - we add in_json to it if the file passes
:return: True if a valid FHIR resource
"""
if '://' in ifn:
infilename = ifn
resp = requests.get(ifn)
if not resp.ok:
print(f"Error {resp.status_code}: {ifn} {resp.reason}")
return False
in_json = loads(resp.text)
else:
infilename = os.path.join(ifdir, ifn)
with open(infilename) as infile:
in_json = loads(infile.read())
if not (hasattr(in_json, 'resourceType') or hasattr(in_json, 'id')):
print(f"{infilename} is not a FHIR resource - processing skipped",
file=sys.stderr)
return False
opts.in_json = in_json
return True
def test_default_vocab(self):
json_ld_text = ContextGenerator(without_default).serialize()
json_ld = loads(json_ld_text)
self.assertEqual('http://example.org/sssom/schema/', json_ld['@context']['@vocab'])
self.assertEqual('http://example.org/sssom/schema/name', json_ld['@context']['name']['@id'])
json_ld_text2 = ContextGenerator(with_default).serialize()
json_ld2 = loads(json_ld_text2)
self.assertEqual('https://w3id.org/sssom/', json_ld2['@context']['@vocab'])
self.assertNotIn('name', json_ld2['@context']['@vocab'])
def check_types(s: SchemaDefinition) -> None:
output = os.path.join(outputdir, 'schema4.json')
if not os.path.exists(output):
with open(output, 'w') as f:
f.write(as_json(JsonObj(**{k: as_dict(loads(as_json(v))) for k, v in s.types.items()})))
self.fail(f"File {output} created - rerun test")
with open(output) as f:
expected = as_dict(load(f))
self.assertEqual(expected, {k: as_dict(loads(as_json(v))) for k, v in s.types.items()})
s.types = None
def compare_shexj(
shex: Union[ShExJ.Schema, str],
shexj: Union[ShExJ.Schema, str]) -> Tuple[bool, StringIO]:
d1 = loads(as_json(shex) if isinstance(shex, ShExJ.Schema) else shex)
d2 = loads(
as_json(shexj) if isinstance(shexj, ShExJ.Schema) else shexj)
log = StringIO()
with redirect_stdout(log):
return compare_dicts(d1._as_dict,
d2._as_dict,
d1name="expected",
d2name="actual ",
filtr=json_filtr), log
def dumpit(argv: Optional[Union[str, List[str]]] = None,
prog: Optional[str] = None) -> int:
"""
Dump resources from a FHIR server
:param argv: command line arguments
:param prog: program name for testing help output
:return: number of resource instances dumped
"""
if isinstance(argv, str):
argv = argv.split()
opts = genargs(prog).parse_args(argv if argv is not None else sys.argv[1:])
os.makedirs(os.path.join(opts.outdir, opts.resource), exist_ok=True)
url = f"{opts.server}/{opts.resource}?_format=json&_summary=false"
if opts.max:
url += f"&_count={opts.max}"
nwritten = 0
while True:
resp = requests.get(url)
url = None
if resp.ok:
rslts = loads(resp.text)
nwritten = save_instances(opts, rslts, nwritten)
if opts.max is None or nwritten < opts.max:
for l in rslts.link:
if l.relation == "next":
url = l.url
else:
print(resp.reason)
if not url:
break
if opts.verbose:
print(f"{nwritten} instances written to {opts.outdir}")
return nwritten
def test_uri_type(self):
""" URI datatype should map to ShEx URI instead of NONLITERAL """
shex = loads(
ShExGenerator(LOCAL_TYPES_YAML_FILE, format='json').serialize())
uri_shape = [s for s in shex.shapes if s.id == str(METATYPE.Uri)]
self.assertEqual(1, len(uri_shape))
self.assertEqual('iri', uri_shape[0].nodeKind)
def test_issue_types(self):
""" Make sure that types are generated as part of the output """
def generator() -> str:
gen = JsonSchemaGenerator(env.input_path('issue_129.yaml'))
gen.topCls = 'c'
return gen.serialize()
sobj_str = env.generate_single_file('issue_129.json',
lambda: generator(),
value_is_returned=True)
sobj = jsonasobj.loads(sobj_str)
defs = sobj['definitions']
C = defs['C']
props = C['properties']
assert props['age_in_years']['type'] == 'integer'
assert props['has_prop']['type'] == 'boolean'
# multivalued primitive type, inlined
assert props['scores']['type'] == 'array'
assert props['scores']['items']['type'] == 'number'
# single-valued complex type, inlined
assert props['has_d']['$ref'] == "#/definitions/D"
# multi-valued, inlined
assert props['has_ds']['type'] == 'array'
assert props['has_ds']['items']['$ref'] == "#/definitions/D"
# single-valued, non-inlined (foreign key)
assert props['parent']['type'] == "string"
# multi-valued, non-inlined (foreign key)
assert props['children']['type'] == 'array'
assert props['children']['items']['type'] == "string"
def test_andras_loop():
manifast = \
"https://raw.githubusercontent.com/SuLab/Genewiki-ShEx/master/pathways/wikipathways/manifest_all.json"
manifest = jsonasobj.loads(requests.get(manifast).text)
for case in manifest:
print(case._as_json_dumps())
if case.data.startswith("Endpoint:"):
sparql_endpoint = case.data.replace("Endpoint: ", "")
schema = requests.get(case.schemaURL).text
shex = ShExC(schema).schema
print("==== Schema =====")
# print(shex._as_json_dumps())
evaluator = ShExEvaluator(schema=shex, debug=True)
sparql_query = case.queryMap.replace("SPARQL '''",
"").replace("'''@START", "")
df = get_sparql_dataframe(sparql_endpoint, sparql_query)
for wdid in df.item:
slurpeddata = requests.get(wdid + ".ttl")
results = evaluator.evaluate(rdf=slurpeddata.text,
focus=wdid,
debug=False)
for result in results:
if result.result:
print(str(result.focus) + ": CONFORMS")
else:
print("item with issue: " + str(result.focus) + " - " +
"shape applied: " + str(result.start))
def resource_url(server: str, text: str) -> str:
""" Create a URL out of the resource text """
def as_url(resource_name: str, resource_format: str,
resource_id: str) -> str:
# Note that the 'json' below defines the response format. The server is clever enough to figure out
# what you are shipping...
return f"{server}{'/' if not server.endswith('/') else ''}{resource_name}" \
f"/{resource_id}?_format=json&_pretty=true"
""" Create a server URL for uploading text """
if text.startswith('<'):
# XML
doc = ElementTree().parse(source=StringIO(text))
'{http://hl7.org/fhir}ClinicalProfile'
typ = doc.tag.replace(f'{{{FHIR_XML_URI}}}', '')
res_id = doc.findall('{http://hl7.org/fhir}id')[0].attrib['value']
return as_url(typ, 'xml', res_id)
elif text.startswith('{'):
# JSON
json_text = loads(text)
return as_url(json_text.resourceType, 'json', json_text.id)
elif text.startswith('@'):
g = Graph()
g.parse(data=text, format='turtle')
focus = g.value(predicate=FHIR.nodeRole, object=FHIR.treeRoot)
typ_uri = g.value(subject=focus, predicate=RDF.type)
res_id = g.value(subject=focus, predicate=FHIR.id)
typ = str(typ_uri).replace(str(FHIR), '')
return as_url(typ, 'ttl', res_id)
else:
raise ValueError("Unrecognized file type")
def nb_filter(s: str) -> str:
""" Filter for jupyter (ipynb) notebooks """
# It is easier to deal with notebook content in JSON
s_json = loads(ldcontext_metadata_filter(s))
for cell in s_json.cells:
if hasattr(cell, 'execution_count'):
cell.execution_count = 1
if hasattr(cell, 'metadata'):
delattr(cell, 'metadata')
if hasattr(cell, 'outputs'):
del_outputs = []
for output in cell.outputs:
to_del = []
if hasattr(output, 'text'):
for line in output.text:
if 'WARNING: You are using pip' in line or\
'You should consider upgrading via' in line or\
'Requirement already satisfied:' in line:
to_del.append(line)
for del_line in to_del:
output.text.remove(del_line)
if not output.text:
del_outputs.append(output)
if del_outputs:
for del_output in del_outputs:
cell.outputs.remove(del_output)
if hasattr(s_json.metadata, 'language_info'):
if hasattr(s_json.metadata.language_info, 'version'):
s_json.metadata.language_info.version = '3'
return as_json(s_json)
def test_get(self):
py_obj = jsonasobj.loads(test_json)
self.assertEqual(1, py_obj.k1)
with self.assertRaises(AttributeError):
py_obj.e1
self.assertIsNone(py_obj._get('e1'))
self.assertEqual("abc", py_obj._get('e2', 'abc'))
def test_merge_contexts(self):
self.assertIsNone(merge_contexts())
self.assertEqual('file://local.jsonld', merge_contexts("local.jsonld")['@context'])
self.assertEqual('file://local.jsonld', merge_contexts(["local.jsonld"])['@context'])
self.assertEqual(METAMODEL_CONTEXT_URI, merge_contexts(METAMODEL_CONTEXT_URI)['@context'])
self.assertEqual(METAMODEL_CONTEXT_URI, merge_contexts([METAMODEL_CONTEXT_URI])['@context'])
self.assertEqual(JsonObj(ex='http://example.org/test/', ex2='http://example.org/test2/'),
merge_contexts(json_1)['@context'])
self.assertEqual(JsonObj(ex='http://example.org/test/', ex2='http://example.org/test2/'),
merge_contexts([json_1])['@context'])
self.assertEqual(JsonObj(ex='http://example.org/test3/', ex2=JsonObj(**{'@id': 'http://example.org/test4/'})),
merge_contexts(json_2)['@context'])
self.assertEqual(JsonObj(ex='http://example.org/test3/', ex2=JsonObj(**{'@id': 'http://example.org/test4/'})),
merge_contexts([json_2])['@context'])
self.assertEqual([f'file://local.jsonld',
'https://w3id.org/linkml/meta.context.jsonld',
JsonObj(ex='http://example.org/test/', ex2='http://example.org/test2/'),
JsonObj(ex='http://example.org/test3/', ex2=JsonObj(**{'@id': 'http://example.org/test4/'}))],
merge_contexts(["local.jsonld", METAMODEL_CONTEXT_URI, json_1, json_2])['@context'])
self.assertEqual(loads(context_output),
merge_contexts(["local.jsonld", METAMODEL_CONTEXT_URI, json_1, json_2]))
# Dups are not removed
self.assertEqual(
JsonObj(**{'@context': [JsonObj(ex='http://example.org/test/', ex2='http://example.org/test2/'),
JsonObj(ex='http://example.org/test/', ex2='http://example.org/test2/')]}),
merge_contexts([json_1, json_1]))
self.assertEqual('file://local.jsonld', merge_contexts("local.jsonld")['@context'])
def test_uri_and_curie(self):
""" Compile a model of URI's and Curies and then test the various types """
self.single_file_generator('py',
PythonGenerator,
filtr=metadata_filter,
comparator=compare_python)
# Check that the interpretations are correct
self.single_file_generator(
'jsonld',
ContextGenerator,
filtr=ldcontext_metadata_filter,
comparator=lambda expected, actual: compare_rdf(
expected, actual, fmt="json-ld"))
self.single_file_generator('json',
JSONLDGenerator,
filtr=json_metadata_filter)
module = compile_python(env.expected_path(self.model_name + '.py'))
curie_obj = module.C1("ex:obj1",
hasCurie="ex:curie",
hasURI="http://example.org/test/uri",
hasNcName="A123",
id2="ex:id2")
instance_jsonld = loads('{ "ex": "http://example.org/test/inst#" }')
g = as_rdf(
curie_obj,
[env.input_path(self.model_name + '.jsonld'), instance_jsonld])
env.eval_single_file(env.expected_path('uriandcurie.ttl'),
g.serialize(format='ttl').decode(), lambda s: s,
compare_rdf)
def test_basic_json_read(self) -> None:
""" Test the basic JSON level read
"""
py_obj = jsonasobj.loads(test_json)
self.assertEqual("Markus Lanthaler", py_obj.name)
self.assertEqual("Dave Longley", py_obj.knows[0].name)
self.assertEqual("http://xmlns.com/foaf/0.1/name", py_obj["@context"].name)
self.assertEqual("http://me.markus-lanthaler.com/", py_obj["@id"])
def test_decimal(self):
test_json = loads(json_data)
from fhirtordf.loaders.fhirresourceloader import FHIRResource
test_rdf = FHIRResource(FHIRGraph(), None, "http://hl7.org/fhir", test_json, add_ontology_header=False)
g = test_rdf.graph
self.assertEqual({URIRef('http://hl7.org/fhir/Bundle/bundle-example'),
URIRef('https://example.com/base/MedicationRequest/3123')},
set(s for s in g.subjects() if isinstance(s, URIRef)))
def test_reference(self):
test_json = loads(data)
from fhirtordf.loaders.fhirresourceloader import FHIRResource
test_rdf = FHIRResource(FHIRGraph(), None, "http://hl7.org/fhir", test_json)
g = test_rdf.graph
expected_graph = Graph()
diffs = rdf_compare(expected_graph, test_rdf.graph, ignore_owl_version=True, ignore_type_arcs=True)
self.assertEqual("", diffs)
def check_types(s: SchemaDefinition) -> None:
self.assertEqual({
'integer': {'base': 'int',
'from_schema': 'http://example.org/schema5',
'name': 'integer'},
'string': {'base': 'str',
'from_schema': 'http://example.org/schema4',
'name': 'string'}},
{k: as_dict(loads(as_json(v))) for k, v in s.types.items()})
s.types = None
def test_reference(self):
test_json = loads(data)
from fhirtordf.loaders.fhirresourceloader import FHIRResource
fmv_loc = "http://build.fhir.org/fhir.ttl"
test_rdf = FHIRResource(FHIRMetaVoc(fmv_loc).g, None, "http://hl7.org/fhir", test_json)
g = test_rdf.graph
subj = URIRef("http://hl7.org/fhir/CoverageEligibilityResponse/E2500")
self.assertEqual("http://www.BenefitsInc.com/fhir/coverageeligibilityrequest/225476332402",
str(g.value(g.value(subj, FHIR.CoverageEligibilityResponse.request), FHIR.link)))
def proc_response(response: Response) -> Optional[str]:
if response.status_code != 200:
return response.reason
elif response.status_code == 400:
outcome = loads(response.text)
rval = []
for issue in outcome.issue:
rval.append(f"Severity: {issue.severity} - {issue.diagnostics}")
return '\n'.join(rval)
return None
def test_example(self):
pyobj = jsonasobj.loads(str(test_json))
self.assertEqual('Markus Lanthaler', pyobj.name)
self.assertEqual(pyobj.name, pyobj['name'])
self.assertEqual('Dave Longley', pyobj.knows[0].name)
self.assertEqual('http://xmlns.com/foaf/0.1/name', pyobj['@context'].name)
self.assertEqual(json.loads(test_json), json.loads(pyobj._as_json))
self.assertEqual(json.loads(pyobj._as_json), json.loads(as_json(pyobj)))
self.assertTrue(compare_dicts(test_data, pyobj._as_dict))
self.assertTrue(compare_dicts(test_data, as_dict(pyobj)))
def test_dct_prefix(self):
""" Make sure prefixes are handled correctly """
with self.assertRaises(ValueError,
msg="A colon in an identifier is illegal"):
shex = loads(
ShExGenerator(env.input_path('Issue_6.yaml'),
format='json').serialize())
shex = loads(
ShExGenerator(env.input_path('Issue_6_fixed.yaml'),
format='json').serialize())
company_shape = [s for s in shex.shapes if 'Company' in s.id][0]
for expr in company_shape.expression.expressions:
if expr.min == 0:
self.assertEqual(
str(DCT.created),
expr.predicate,
)
return
self.assertFalse(True, "DCT.created predicate not found")
def check_types(s: SchemaDefinition) -> None:
output = env.expected_path('schema4.json')
if not os.path.exists(output):
with open(output, 'w') as f:
f.write(
as_json(
JsonObj(
**{
k: as_dict(loads(as_json(v)))
for k, v in s.types.items()
})))
with open(output) as f:
expected = as_dict(load(f))
self.assertEqual(
expected,
{k: as_dict(loads(as_json(v)))
for k, v in s.types.items()})
s.types = None
def end_schema(self, context: str = biolink_context) -> None:
# self._visit(self.schema)
json_str = as_json(self.schema)
json_obj = loads(json_str)
if '://' not in context:
context = urljoin('file:', pathname2url(os.path.abspath(context)))
base_prefix = self.default_uri()
json_obj["@context"] = [context, {'@base': base_prefix}] if base_prefix else context
json_obj["@id"] = self.schema.id
print(as_json(json_obj, indent=" "))
def test_as_json(self):
schema = self.fix_schema_metadata(
load_raw_schema(os.path.join(inputdir, 'schema6.yaml')))
outfile = os.path.join(outputdir, 'schema6.json')
if not os.path.exists(outfile):
with open(outfile, 'w') as f:
f.write(as_json(schema))
self.fail(f"Generated {outfile} - run test again")
else:
self.assertEqual(load(outfile), loads(as_json(schema)))
def test_reference(self):
test_json = loads(data)
from fhirtordf.loaders.fhirresourceloader import FHIRResource
test_rdf = FHIRResource(FHIRGraph(), None, "http://hl7.org/fhir",
test_json)
g = test_rdf.graph
subj = URIRef("http://hl7.org/fhir/EligibilityResponse/E2500")
self.assertEqual(
"http://www.BenefitsInc.com/fhir/eligibility/225476332402",
str(
g.value(g.value(subj, FHIR.EligibilityResponse.request),
FHIR.link)))
def loinc_name_for(code: str) -> str:
userAndPass = b64encode(b"hsolbrig:instill-geminate-tehran").decode(
"ascii")
headers = {'Authorization': 'Basic %s' % userAndPass}
resp = requests.get(
f"https://fhir.loinc.org/CodeSystem/$lookup?system=http://loinc.org&code={code}",
headers=headers)
if resp.status_code == 200:
vals = map_parameters(loads(resp.text))
if vals:
return vals.display
else:
return "Unknown Code"
def __init__(self, source: Union[fname, json_txt]) -> None:
""" Construct a FHIR StructuredDefinition from a source file name, file or string
:param source: JSON source
"""
valueset_directory = None
if hasattr(source, 'read'): # an open file
self._obj = load(source)
elif source.strip().startswith('{'): # a dictionary in text form
self._obj = loads(source)
else:
self._obj = load(open(source)) # a file name
valueset_directory = os.path.dirname(source)
self.elements = [FHIRElement(self._obj, e, valueset_directory) for e in self._obj.snapshot.element
if '.' in e.path and self._significant_differential(e)]
def test_issue_177(self):
def generator() -> str:
gen = JsonSchemaGenerator(env.input_path('issue_177.yaml'))
return gen.serialize()
json_str = env.generate_single_file(
'issue_177.json',
lambda: JsonSchemaGenerator(env.input_path('issue_177.yaml')
).serialize(),
value_is_returned=True)
sobj = jsonasobj.loads(json_str)
props = sobj['properties']
assert props['sa']['type'] == 'string'
assert props['sb']['type'] == 'integer'
def test_as_json(self):
schema = self.fix_schema_metadata(
load_raw_schema(os.path.join(datadir, 'schema6.yaml')))
self.assertEqual(
loads("""{
"name": "schema6",
"id": "http://example.org/schema6.fuzz",
"title": "Load Raw Schema Test",
"types": [
{
"name": "foo",
"from_schema": "http://example.org/schema6.fuzz",
"base": "str",
"uri": "http://example.org/types/String"
}
],
"slots": [
{
"name": "s1",
"from_schema": "http://example.org/schema6.fuzz",
"domain": "c1",
"range": "foo"
}
],
"classes": [
{
"name": "c1",
"from_schema": "http://example.org/schema6.fuzz"
}
],
"metamodel_version": "0.5.0",
"source_file": "schema6.yaml",
"source_file_date": "2018-12-31 17:23",
"source_file_size": 259,
"generation_date": "2018-12-31 17:23"
}"""), loads(as_json(schema)))
def get(self,
relurl: Optional[str],
params: Optional[Dict[str, str]] = None) -> Optional[JsonObj]:
url = self.url + relurl
resp = requests.get(url,
params=params,
auth=(self._user,
self._password) if self._user else None)
if self.show_urls:
print(f"GET {resp.url}")
if resp.ok:
return loads(resp.text)
else:
print(f"{resp.url}: Error: {resp.reason}", file=sys.stderr)
return None
def run_test(self, manifest_uri: str, num_entries: Optional[int]=None, verbose: bool=True, debug: bool=False,
stop_on_fail: bool=False, debug_slurps: bool=False, save_graph_dir: Optional[str]=None) \
-> List[EvaluationResult]:
""" Run the test identified by manifest_uri
:param manifest_uri: uri of manifest
:param num_entries: number of manifest elements to test
:param verbose: True means talk about it
:param debug: debug setting for shex evaluator
:param stop_on_fail: True means run until failure
:param debug_slurps: True means emit SPARQL_slurper statistics
:param save_graph_dir: If present, save the final graph in this directory
:return:
"""
manifest = loads(self.fetch_uri(manifest_uri))
rval: List[EvaluationResult] = []
for case in manifest:
if verbose:
print(case._as_json_dumps())
sparql_endpoint = case.data.replace("Endpoint: ", "")
shex = self.fetch_uri(case.schemaURL)
evaluator = ShExEvaluator(schema=shex, debug=debug)
prefixes = PrefixLibrary(shex, SKOS=SKOS)
sparql_query = case.queryMap.replace("SPARQL '''",
"").replace("'''@START", "")
dfs: List[str] = self.get_sparql_dataframe(sparql_endpoint,
sparql_query)
dfs_slice = dfs[:num_entries] if num_entries is not None else dfs
for df in dfs_slice:
slurper = SlurpyGraphWithAgent(sparql_endpoint)
# slurper.debug_slurps = debug_slurps
prefixes.add_bindings(slurper)
print(f"Evaluating: {df}")
results = evaluator.evaluate(rdf=slurper,
focus=df,
debug=debug,
debug_slurps=debug_slurps,
over_slurp=False)
rval += results
if save_graph_dir:
element_name = df.rsplit('/', 1)[1]
file_name = os.path.join(save_graph_dir,
element_name + '.ttl')
print(f"Writing: {file_name}")
slurper.serialize(file_name, format="turtle")
if stop_on_fail and not all(r.result for r in results):
break
return rval
def __init__(self, source: Union[fname, json_txt]) -> None:
""" Construct a FHIR StructuredDefinition from a source file name, file or string
:param source: JSON source
"""
valueset_directory = None
if hasattr(source, 'read'): # an open file
self._obj = load(source)
elif source.strip().startswith('{'): # a dictionary in text form
self._obj = loads(source)
else:
self._obj = load(open(source)) # a file name
valueset_directory = os.path.dirname(source)
self.elements = [
FHIRElement(self._obj, e, valueset_directory)
for e in self._obj.snapshot.element
if '.' in e.path and self._significant_differential(e)
]
def sdo_valueset(self) -> str:
""" Return a schema.org representation of the value set
:return:
"""
# TODO: This URL should really be a terminology service expand call, but the documented method doesn't work
rval = ''
vsdef = self.sdo_valueset_file()
if not vsdef:
resp = get(self._reference, headers={'accept': 'application/json'})
if resp.ok:
vsdef = loads(resp.text)
else:
print("ValueSet access error: %s (%s)" % (self._reference, resp.reason))
if vsdef:
rval = self.sdo_valueset_header(vsdef.url, vsdef.id, vsdef.name)
if 'codeSystem' in vsdef and 'concept' in vsdef.codeSystem:
cs = vsdef.codeSystem
rval += '\n\t'.join([self.sdo_concept(vsdef.url, vsdef.id, cs.system, c) for c in cs.concept])
return rval
def test_as_json(self):
""" Test the JSON serialization
"""
py_obj = jsonasobj.loads(test_json)
self.assertEqual(json.loads(test_json), json.loads(py_obj._as_json))
self.assertEqual(json.loads(test_json), json.loads(as_json(py_obj)))
"@id": "name:foo",
"@type": "@id"
}
},
"@id": "http://me.markus-lanthaler.com/",
"name": "Markus Lanthaler",
"knows": [
{
"name": "Dave Longley",
"menu": "something",
"modelDate" : "01/01/2015"
}
]
}"""
py_obj = jsonasobj.loads(test_json)
py_obj.knows[0].extra = {'age': 17}
py_obj.knows.append(dict(name='Barack Obama'))
del py_obj.knows[0]['menu']
print(py_obj.name)
print(py_obj['name'])
print(py_obj.knows[0].name)
print(py_obj['@context'].name)
print(as_json(py_obj))
print(as_dict(py_obj))
'''
Result:
Markus Lanthaler
Markus Lanthaler
Dave Longley
