def merge(files):
"""Merge a set of Feils FILES.
This will expand out the felis FILES so that it is easy to
override values (using @Id), then normalize to a single
output.
"""
graph = []
for file in files:
schema_obj = yaml.load(file, Loader=yaml.SafeLoader)
if "@graph" not in schema_obj:
schema_obj["@type"] = "felis:Schema"
schema_obj["@context"] = DEFAULT_CONTEXT
graph.extend(jsonld.flatten(schema_obj))
updated_map = {}
for item in graph:
_id = item["@id"]
item_to_update = updated_map.get(_id, item)
if item_to_update and item_to_update != item:
logger.debug(f"Overwriting {_id}")
item_to_update.update(item)
updated_map[_id] = item_to_update
merged = {
"@context": DEFAULT_CONTEXT,
"@graph": list(updated_map.values())
}
normalized = _normalize(merged)
_dump(normalized)
def do_flatten(doc):
# flatten a document
# see: https://json-ld.org/spec/latest/json-ld/#flattened-document-form
flattened = jsonld.flatten(doc)
# all deep-level trees flattened to the top-level
print("FLATTENED")
print(json.dumps(flattened, indent=2))
async def retrieve(request):
"""Retrieve data specific to an acronym, URL should be persistent."""
db_pool = request.app['pool']
term = request.match_info['acronymid']
term_type = request.match_info['acronymtype']
LOG.info('retrieve')
data = await fetch_acronym(db_pool, term, term_type)
doc = {
"@id": f'acr:{data[0]["index"]}',
"dc:title": data[0]["title"],
"skos:label": data[0]["title"],
"dc:type": {
"@id": f'acr:{data[0]["acronymtype"]}',
"@type": 'skos:Concept',
"skos:label": data[0]["acronymtype"]
},
"dc:language": data[0]["language"],
"dc:description": data[0]["description"]
}
if request.content_type == 'application/ld+json':
response = jsonld.flatten(doc, context)
return web.json_response(response,
content_type='application/ld+json',
dumps=json.dumps)
elif request.content_type == 'application/n-quads':
response = jsonld.normalize(doc, {
'algorithm': 'URDNA2015',
'format': 'application/n-quads'
})
return web.Response(text=response, content_type='application/n-quads')
else:
response = {"data": data}
return web.json_response(response,
content_type='application/json',
dumps=json.dumps)
def __init__(self,
name: str,
document: Any,
url: Optional[str] = None,
soup: Optional[BeautifulSoup] = None):
if '@context' not in document or 'schema.org' in document['@context']:
# schema.org, as it is commonly used, has a bug.
# Very often 'http://schema.org' is used as the '@context' value, but the website does not ever return a valid JSON-LD schema.
# It appears it used to, with the help of content-negotiation: https://webmasters.stackexchange.com/questions/123409
# But this has stopped working. So we hard code in this default context to fix.
document['@context'] = JSONLD.DEFAULT_CONTEXT
else:
# TODO: Support other schemas
logging.warning(
f"You're using a schema which is not schema.org ({document['@context']}). Support is limited at the moment (particularly for introspection)."
)
super().__init__(name)
self.context = document['@context']
self.graph = jsonld.flatten(document, self.context)['@graph']
self._introspect()
if url:
self.url = url
if soup:
self.soup = soup
def _introspect(self):
schema = None
if self.context == JSONLD.DEFAULT_CONTEXT:
schema = get_schemaorg_schema()
else:
# TODO: Support other schemas
schema = None
if schema:
self.introspection_graph = jsonld.flatten(schema,
self.context)['@graph']
def process_jsonld(self, data, original, **kwargs):
if isinstance(original, (list, tuple)):
return data
method = request.args.get("process", "compact")
context = {"@context": {"@vocab": "http://neurostore.org/nimads/"}}
if method == "flatten":
return jsonld.flatten(data, context)
elif method == "expand":
return jsonld.expand(data)
else:
return jsonld.compact(data, context)
def _serialize(self,
obj: typing.Union[_T, typing.Iterable[_T]],
*,
many: bool = False):
"""Serialize ``obj`` to jsonld."""
if many and obj is not None:
return [
self._serialize(d, many=False)
for d in typing.cast(typing.Iterable[_T], obj)
]
if isinstance(obj, Proxy):
proxy_schema = obj.__proxy_schema__
if (not obj.__proxy_initialized__
and isinstance(proxy_schema, type(self))
and proxy_schema.flattened == self.flattened):
# if proxy was not accessed and we use the same schema, return original data
return obj.__proxy_original_data__
# resolve Proxy object
obj = obj.__wrapped__
ret = self.dict_class()
for attr_name, field_obj in self.dump_fields.items():
value = field_obj.serialize(attr_name,
obj,
accessor=self.get_attribute)
if value is missing:
continue
key = field_obj.data_key if field_obj.data_key is not None else attr_name
reverse = getattr(field_obj, "reverse", False)
if reverse:
if "@reverse" not in ret:
ret["@reverse"] = self.dict_class()
ret["@reverse"][key] = value
else:
ret[key] = value
if "@id" not in ret or not ret["@id"]:
ret["@id"] = self.opts.id_generation_strategy(ret, obj)
# add type
rdf_type = self.opts.rdf_type
if not rdf_type:
raise ValueError("No class type specified for schema")
ret["@type"] = normalize_type(rdf_type)
if self.flattened and self._top_level:
ret = jsonld.flatten(ret)
return ret
def flatten_metadata_graph(obj):
from pyld import jsonld
# simplify graph into a sequence of one dict per known dataset, even
# if multiple meta data set from different sources exist for the same
# dataset.
# cache schema requests; this also avoid the need for network access
# for previously "visited" schemas
jsonld.set_document_loader(_cached_load_document)
# TODO cache entire graphs to prevent repeated term resolution for
# subsequent calls
return jsonld.flatten(obj, ctx={"@context": "http://schema.org/"})
def flatten_metadata_graph(obj):
from pyld import jsonld
# simplify graph into a sequence of one dict per known dataset, even
# if multiple meta data set from different sources exist for the same
# dataset.
# cache schema requests; this also avoid the need for network access
# for previously "visited" schemas
jsonld.set_document_loader(_cached_load_document)
# TODO cache entire graphs to prevent repeated term resolution for
# subsequent calls
return jsonld.flatten(obj, ctx={"@context": "http://schema.org/"})
def as_quad_stream(
self,
raw_data: TextIO,
iri: Optional[URIRef],
context: LDContext,
root_loader: Loader,
) -> Iterable[Quad]:
"""Read JSON-LD data into a quad stream."""
document = self.as_jsonld_document(raw_data)
document = assign_key_if_not_present(
document=document,
key='@id',
default_value=str(iri),
)
document = assign_key_if_not_present(
document=document,
key=str(OCTA.subjectOf),
default_value={
'@id': str(iri),
},
)
try:
document = jsonld.expand(
document,
options={
'expandContext': context,
'documentLoader': root_loader,
# Explanation:
# https://github.com/digitalbazaar/pyld/issues/143
'base': str(LOCAL),
},
)
except JsonLdError as err:
raise ExpandError(
message=str(err),
document=document,
context=context,
iri=iri,
) from err
document = jsonld.flatten(document)
return list(
parse_quads(
quads_document=jsonld.to_rdf(document),
graph=iri,
blank_node_prefix=str(iri),
), )
def test_import_jsonld_into_named_graph(flatten_before_import: bool):
"""Test named graphs we use."""
graph = ConjunctiveGraph()
jsonld_document = JSONLD_DOCUMENT
if flatten_before_import:
jsonld_document = jsonld.flatten(jsonld_document)
serialized_document = json.dumps(jsonld_document, indent=4)
graph.parse(
data=serialized_document,
format='json-ld',
publicID=PUBLIC_ID,
)
print(graph.serialize(format='n3').decode('utf-8'))
# Make sure only one NAMED GRAPH is created on import.
assert list(map(
operator.itemgetter(Variable('g')),
graph.query(
'SELECT DISTINCT ?g WHERE { GRAPH ?g { ?s ?p ?o . } } ORDER BY ?g',
).bindings,
)) == [
URIRef('https://myblog.net/rdf/'),
]
# The information in @included section was properly parsed.
assert graph.query('''
SELECT * WHERE {
GRAPH ?g {
ex:Rover rdfs:subClassOf ex:Robot .
}
}
''', initNs=NAMESPACES).bindings == [{
Variable('g'): PUBLIC_ID,
}]
# The information in the root was properly parsed.
assert graph.query('''
SELECT * WHERE {
GRAPH ?g {
blog:JSONLD-and-named-graphs a schema:blogPost .
}
}
''', initNs=NAMESPACES).bindings == [{
Variable('g'): PUBLIC_ID,
}]
def parse(self):
try:
jsonld_flat = jsonld.flatten(
self.feed,Feed.jsonld_ctx,{"base":self.base}
)
except Exception as e:
raise Exception(
"Could not flatten JSON-LD for feed: '{0}' [{1}]".format(
self.base,
str(e)
)
)
for node in jsonld_flat["@graph"]:
if self.hasType(node, "simplevod:SimpleVoD"):
self.title = node["title"]
if (
"hasMemberGroup" in node and
"@list" in node["hasMemberGroup"]
):
for group in node["hasMemberGroup"]["@list"]:
self.categories.append(self.get(group["@id"]))
elif self.hasType(node, "simplevod:SimpleVoDCategory"):
category = self.get(node["@id"])
category.update({
"isCategory": True,
"title": node["title"],
"items": []
})
if "hasMember" in node and "@list" in node["hasMember"]:
for item in node["hasMember"]["@list"]:
category["items"].append(self.get(item["@id"]))
elif self.hasType(node, "TVProgramme"):
item = self.get(node["@id"])
item.update({
"isItem": True,
"title": node["title"],
"video": self.get(node["isInstantiatedBy"]["@id"]),
"productcode": node["videodb:productcode"]
})
elif self.hasType(node, "MediaResource"):
video = self.get(node["@id"])
video.update({
"videoref": node["videodb:videoref"]
})
def get_jsonld(self, context, new_context={}, format="full"):
"""Return the JSON-LD serialization.
:param: context the context to use for raw publishing; each SmartJsonLD
instance is expected to have a default context associated.
:param: new_context the context to use for formatted publishing,
usually supplied by the client; used by the 'compacted', 'framed',
and 'normalized' formats.
:param: format the publishing format; can be 'full', 'inline',
'compacted', 'expanded', 'flattened', 'framed' or 'normalized'.
Note that 'full' and 'inline' are synonims, referring to the
document form which includes the context; for more information see:
[http://www.w3.org/TR/json-ld/]
"""
from pyld import jsonld
if isinstance(context, six.string_types):
ctx = self.get_context(context)
elif isinstance(context, dict):
ctx = context
else:
raise TypeError('JSON-LD context must be a string or dictionary')
try:
doc = self.translate(context, ctx)
except NotImplementedError:
# model does not require translation
doc = self.dumps(clean=True)
doc["@context"] = ctx
if format in ["full", "inline"]:
return doc
if format == "compacted":
return jsonld.compact(doc, new_context)
elif format == "expanded":
return jsonld.expand(doc)
elif format == "flattened":
return jsonld.flatten(doc)
elif format == "framed":
return jsonld.frame(doc, new_context)
elif format == "normalized":
return jsonld.normalize(doc, new_context)
raise ValueError('Invalid JSON-LD serialization format')
def get_jsonld(self, context, new_context={}, format="full"):
"""Return the JSON-LD serialization.
:param: context the context to use for raw publishing; each SmartJsonLD
instance is expected to have a default context associated.
:param: new_context the context to use for formatted publishing,
usually supplied by the client; used by the 'compacted', 'framed',
and 'normalized' formats.
:param: format the publishing format; can be 'full', 'inline',
'compacted', 'expanded', 'flattened', 'framed' or 'normalized'.
Note that 'full' and 'inline' are synonims, referring to the
document form which includes the context; for more information see:
[http://www.w3.org/TR/json-ld/]
"""
from pyld import jsonld
if isinstance(context, six.string_types):
ctx = self.get_context(context)
elif isinstance(context, dict):
ctx = context
else:
raise TypeError('JSON-LD context must be a string or dictionary')
try:
doc = self.translate(context, ctx)
except NotImplementedError:
# model does not require translation
doc = self.dumps(clean=True)
doc["@context"] = ctx
if format in ["full", "inline"]:
return doc
if format == "compacted":
return jsonld.compact(doc, new_context)
elif format == "expanded":
return jsonld.expand(doc)
elif format == "flattened":
return jsonld.flatten(doc)
elif format == "framed":
return jsonld.frame(doc, new_context)
elif format == "normalized":
return jsonld.normalize(doc, new_context)
raise ValueError('Invalid JSON-LD serialization format')
def flat_map(response):
"""
Transform a response using JSON-LD's "flatten" operation, and return a
dictionary mapping resources (as fully-qualified URLs) to their values
(also containing fully-qualified URLs).
"""
# The URL in '@context' may not be available yet, because we probably
# haven't deployed. So replace the response's "@context" with the
# contents of that file.
response['@context'] = CONTEXT['@context']
# jsonld.flatten gives us a list of objects, which all have @id values
# (unless they're awkward "blank nodes", like definitions of features).
# The @id values are unique after flattening, so we can make a dictionary
# keyed by them.
result = {}
flat_objects = jsonld.flatten(response)
for obj in flat_objects:
if '@id' in obj:
result[obj['@id']] = obj
return result
def modify_tap(start_schema_at, files):
"""Modify TAP information in Felis schema FILES.
This command has some utilities to aid in rewriting felis FILES
in specific ways. It will write out a merged version of these files.
"""
count = 0
graph = []
for file in files:
schema_obj = yaml.load(file, Loader=yaml.SafeLoader)
if "@graph" not in schema_obj:
schema_obj["@type"] = "felis:Schema"
schema_obj["@context"] = DEFAULT_CONTEXT
schema_index = schema_obj.get("tap:schema_index")
if not schema_index or (schema_index
and schema_index > start_schema_at):
schema_index = start_schema_at + count
count += 1
schema_obj["tap:schema_index"] = schema_index
graph.extend(jsonld.flatten(schema_obj))
merged = {"@context": DEFAULT_CONTEXT, "@graph": graph}
normalized = _normalize(merged)
_dump(normalized)
def _serialize(self,
obj: typing.Union[_T, typing.Iterable[_T]],
*,
many: bool = False):
"""Serialize ``obj`` to jsonld."""
if many and obj is not None:
return [
self._serialize(d, many=False)
for d in typing.cast(typing.Iterable[_T], obj)
]
ret = self.dict_class()
for attr_name, field_obj in self.dump_fields.items():
value = field_obj.serialize(attr_name,
obj,
accessor=self.get_attribute)
if value is missing:
continue
key = field_obj.data_key if field_obj.data_key is not None else attr_name
reverse = getattr(field_obj, "reverse", False)
if reverse:
if "@reverse" not in ret:
ret["@reverse"] = self.dict_class()
ret["@reverse"][key] = value
else:
ret[key] = value
# add type
rdf_type = self.opts.rdf_type
if not rdf_type:
raise ValueError("No class type specified for schema")
ret["@type"] = normalize_type(rdf_type)
if self.flattened:
ret = jsonld.flatten(ret)
return ret
def main():
itemFile = sys.argv[1]
with open(itemFile, "r") as f:
item = json.load(f)
numItems = len(item.keys()) - 2 # -2 for context and id
context = {}
ctxtResolver(item["@context"], context)
doc = {k: v for k, v in item.items() if k not in "@context"}
item = {}
item["@context"] = context
item.update(doc)
expanded = jsonld.expand(item)
print("Expanded")
print(json.dumps(expanded, indent=2))
print("\n\n")
compacted = jsonld.compact(expanded, context)
print("Compacted")
print(json.dumps(compacted, indent=2))
print("\n\n")
flattened = jsonld.flatten(compacted, context)
print("Flattened")
print(json.dumps(flattened, indent=2))
print("\n\n")
normalized = jsonld.normalize(item, {
'algorithm': 'URDNA2015',
'format': 'application/n-quads'
})
print("Normalized")
print(json.dumps(normalized, indent=2))
print("\n\n")
inpPropNames = set(item.keys()) - set(["@context", "latestResourceData"])
expPropNames = set([k.split("/")[-1] for k in expanded[0].keys()])
compPropNames = set([k.split(":")[-1] for k in compacted.keys()])
print("Missing from expanded" + str(inpPropNames - expPropNames))
print("Missing from compacted" + str(inpPropNames - compPropNames))
def main(self):
print('PyLD Unit Tests')
print('Use -h or --help to view options.')
# add program options
self.parser.add_option('-f',
'--file',
dest='file',
help='The single test file to run',
metavar='FILE')
self.parser.add_option('-d',
'--directory',
dest='directory',
help='The directory full of test files',
metavar='DIR')
self.parser.add_option('-e',
'--earl',
dest='earl',
help='The filename to write the EARL report to',
metavar='EARL')
self.parser.add_option('-v',
'--verbose',
dest='verbose',
action='store_true',
default=False,
help='Prints verbose test data')
# parse options
(self.options, args) = self.parser.parse_args()
# check if file or directory were specified
if self.options.file == None and self.options.directory == None:
raise Exception('No test file or directory specified.')
# check if file was specified, exists, and is file
if self.options.file is not None:
if (os.path.exists(self.options.file)
and os.path.isfile(self.options.file)):
# add manifest file to the file list
self.manifest_files.append(os.path.abspath(self.options.file))
else:
raise Exception('Invalid test file: "%s"' % self.options.file)
# check if directory was specified, exists and is dir
if self.options.directory is not None:
if (os.path.exists(self.options.directory)
and os.path.isdir(self.options.directory)):
# load manifest files from test directory
for test_dir, dirs, files in os.walk(self.options.directory):
for manifest in files:
# add all .jsonld manifest files to the file list
if (manifest.find('manifest') != -1
and manifest.endswith('.jsonld')):
self.manifest_files.append(join(
test_dir, manifest))
else:
raise Exception('Invalid test directory: "%s"' %
self.options.directory)
# see if any manifests have been specified
if len(self.manifest_files) == 0:
raise Exception('No manifest files found.')
passed = 0
failed = 0
total = 0
# run the tests from each manifest file
for manifest_file in self.manifest_files:
test_dir = os.path.dirname(manifest_file)
manifest = json.load(open(manifest_file, 'r'))
count = 1
for test in manifest['sequence']:
# skip unsupported types
skip = True
test_type = test['@type']
for tt in test_type:
if tt in SKIP_TEST_TYPES:
skip = True
break
if tt in TEST_TYPES:
skip = False
if skip:
# print 'Skipping test: "%s" ...' % test['name']
continue
print('JSON-LD/%s %04d/%s...' %
(manifest['name'], count, test['name']),
end=' ')
total += 1
count += 1
# read input file
with open(join(test_dir, test['input'])) as f:
if test['input'].endswith('.jsonld'):
input = json.load(f)
else:
input = f.read().decode('utf8')
# read expect file
with open(join(test_dir, test['expect'])) as f:
if test['expect'].endswith('.jsonld'):
expect = json.load(f)
else:
expect = f.read().decode('utf8')
result = None
# JSON-LD options
options = {
'base':
'http://json-ld.org/test-suite/tests/' + test['input'],
'useNativeTypes': True
}
success = False
try:
if 'jld:ExpandTest' in test_type:
result = jsonld.expand(input, options)
elif 'jld:CompactTest' in test_type:
ctx = json.load(open(join(test_dir, test['context'])))
result = jsonld.compact(input, ctx, options)
elif 'jld:FlattenTest' in test_type:
result = jsonld.flatten(input, None, options)
elif 'jld:FrameTest' in test_type:
frame = json.load(open(join(test_dir, test['frame'])))
result = jsonld.frame(input, frame, options)
elif 'jld:FromRDFTest' in test_type:
result = jsonld.from_rdf(input, options)
elif 'jld:ToRDFTest' in test_type:
options['format'] = 'application/nquads'
result = jsonld.to_rdf(input, options)
elif 'jld:NormalizeTest' in test_type:
options['format'] = 'application/nquads'
result = jsonld.normalize(input, options)
# check the expected value against the test result
success = deep_compare(expect, result)
if success:
passed += 1
print('PASS')
else:
failed += 1
print('FAIL')
if not success or self.options.verbose:
print('Expect:', json.dumps(expect, indent=2))
print('Result:', json.dumps(result, indent=2))
except jsonld.JsonLdError as e:
print('\nError: ', e)
failed += 1
print('FAIL')
# add EARL report assertion
EARL['subjectOf'].append({
'@type':
'earl:Assertion',
'earl:assertedBy':
EARL['doap:developer']['@id'],
'earl:mode':
'earl:automatic',
'earl:test':
('http://json-ld.org/test-suite/tests/' +
os.path.basename(manifest_file) + test.get('@id', '')),
'earl:result': {
'@type':
'earl:TestResult',
'dc:date':
datetime.datetime.utcnow().isoformat(),
'earl:outcome':
('earl:' + 'passed' if success else 'failed')
}
})
if self.options.earl:
f = open(self.options.earl, 'w')
f.write(json.dumps(EARL, indent=2))
f.close()
print('Done. Total:%d Passed:%d Failed:%d' % (total, passed, failed))
# see: http://json-ld.org/spec/latest/json-ld/#expanded-document-form
expanded = jsonld.expand(compacted)
print(json.dumps(expanded, indent=2))
# Output:
# [{
# "http://schema.org/image": [{"@id": "http://manu.sporny.org/images/manu.png"}],
# "http://schema.org/name": [{"@value": "Manu Sporny"}],
# "http://schema.org/url": [{"@id": "http://manu.sporny.org/"}]
# }]
# expand using URLs
jsonld.expand('http://example.org/doc')
# flatten a document
# see: http://json-ld.org/spec/latest/json-ld/#flattened-document-form
flattened = jsonld.flatten(doc)
# all deep-level trees flattened to the top-level
# frame a document
# see: http://json-ld.org/spec/latest/json-ld-framing/#introduction
framed = jsonld.frame(doc, frame)
# document transformed into a particular tree structure per the given frame
# normalize a document using the RDF Dataset Normalization Algorithm
# (URDNA2015), see: http://json-ld.github.io/normalization/spec/
normalized = jsonld.normalize(
doc, {'algorithm': 'URDNA2015', 'format': 'application/n-quads'})
# normalized is a string that is a canonical representation of the document
# that can be used for hashing, comparison, etc.
from w3lib.html import get_base_url
import json
from pyld_document_loader import my_requests_document_loader
def get_schema_context():
r = requests.get('https://schema.org/docs/jsonldcontext.json')
return r.json()
def get_jsons(url):
r = requests.get(url)
base_url = get_base_url(r.text, r.url)
data = extruct.extract(r.text, base_url=base_url)
return data['json-ld']
if __name__ == '__main__':
jsonld.set_document_loader(my_requests_document_loader())
ctx = get_schema_context()
url = 'https://www.imdb.com/title/tt7126948/'
doc = get_jsons(url)
#compacted = jsonld.compact(doc, ctx)
data = jsonld.flatten(doc, ctx=ctx)
print(json.dumps(data, indent=2))
with open('imdb_pyld.json', 'w') as f:
f.write(json.dumps(data))
def test_page(ark):
global elements
elements = []
if request.cookies.get("fairscapeAuth") is None:
token = request.headers.get("Authorization")
else:
token = request.cookies.get("fairscapeAuth")
data_jsonld = requests.get(EG_URL + ark, headers={
"Authorization": token
}).json()
if 'error' in data_jsonld.keys():
return data_jsonld['error']
# try:
try:
data_jsonld_flat = jsonld.flatten(data_jsonld) #
except Exception as cause:
raise JsonLdError('Error flattening JSON-LD content ', cause)
# print("\nflattened JSON-LD content\n", json.dumps(data_jsonld_flat, indent=2))
elements = [] # contains nodes and edges
nodes = [] # vertices
edges = [] # links between vertices
id_position = {} # mapping of each @id to a number
counter = 0
# TODO: to check if http://schema.org/name missing
for level in data_jsonld_flat:
if level.get('@id') is None or '_:b' in level[
'@id']: # flattening generates a blank node _:b when @id is missing
print('Error: found blank node for missing @id at: ', level)
sys.exit()
if level.get(['@type'][0]) is None:
print('Error: missing @type at: ', level)
sys.exit()
nodes_data = {}
nodes_element = {}
nodes_element['id'] = counter
nodes_element['@id'] = level['@id']
if os.environ.get("LOCAL", False):
nodes_element['href'] = 'http://*****:*****@id'] # href in cytoscape to open as a URI
else:
nodes_element['href'] = MDS_URL + level[
'@id'] # href in cytoscape to open as a URI
nodes_element['@type'] = level['@type'][0]
nodes_element['type'] = level['@type'][
0] # @type cannot be retrieved as node(@type)
nodes_element['name'] = level['https://schema.org/name'][0]['@value']
nodes_element['info'] = 'Name: ' + level['https://schema.org/name'][0]['@value'] + '\nType: ' + level['@type'][0] \
+ '\nPID: ' + level['@id'] # all attributes together
nodes_data['data'] = nodes_element
nodes.append(nodes_data)
id_position[level['@id']] = counter
counter += 1
# print('\nNodes\n', json.dumps(nodes, indent=2))
# populate edges
for item in data_jsonld_flat:
source_id = item[
'@id'] # chooses @id as source at each level for an edge
for key, value in item.items(
): # iterates through each flattened level
if isinstance(value, list):
for i in value:
if isinstance(i, dict):
if '@id' in i.keys():
edges_data = {}
edges_element = {}
edges_element['source'] = id_position[source_id]
edges_element['target'] = id_position[i['@id']]
edges_element['label'] = key
edges_data['data'] = edges_element
edges.append(edges_data)
# print('\nEdges\n', json.dumps(edges, indent=2))
# copies all nodes and edges inside elements
elements = nodes.copy()
for element in edges:
elements.append(element)
# Convert multiple edges such that e1(v1, v2), e2(v1, v2), e3(v1, v2) =>
# Multiples edges between v1, v2 such as http://schema.org/founder, http://schema.org/member become [founder, member]
source = []
target = []
label = []
for edge_data in edges:
for edge in edge_data.values():
for key, value in edge.items():
if key == 'source':
source.append(value)
if key == 'target':
target.append(value)
if key == 'label':
label.append(value)
d = {'source': source, 'target': target, 'label': label}
df = pd.DataFrame(data=d)
# print('\nAll Edges\n', df)
df_edge_has_common_nodes = df[df.duplicated(subset=['source', 'target'],
keep=False)]
# print('\nEdges with common nodes\n', df_edge_has_common_nodes)
df_unique = df.drop_duplicates(subset=['source', 'target'], keep=False)
# print('\nUnique Edges\n', df_unique)
df_merged_edge_has_common_nodes = df_edge_has_common_nodes.groupby(['source', 'target'], as_index=False) \
.agg({'label': ','.join})
# print('\nMerged unique & non-unique edges\n', df_merged_edge_has_common_nodes)
uri_prefix_suffix_dict_list = [
] # Maps uri prefix to its suffix e.g. {http://schema.org/ : member"
# populate common edge labels within [...] e.g. [founder, member, ...]
def get_property_labels(labels):
property_list = str(labels).split(',')
if len(property_list) == 1:
uri_prefix_suffix_dict = {}
suffix = property_list[0].split('/')[-1]
prefix = property_list[0].replace(suffix, '')
uri_prefix_suffix_dict[prefix] = suffix
uri_prefix_suffix_dict_list.append(uri_prefix_suffix_dict)
return suffix
elif len(property_list) > 1:
property_list_size = len(property_list)
# prop_list = [] # sending as a list does not add [] around the labels
props_list = '[' # this string adds the anticipated []
for prop in property_list:
uri_prefix_suffix_dict = {}
suffix = prop.split('/')[-1]
prefix = prop.replace(suffix, '')
uri_prefix_suffix_dict[prefix] = suffix
uri_prefix_suffix_dict_list.append(uri_prefix_suffix_dict)
# prop_list.append(suffix)
property_list_size -= 1
if property_list_size > 0:
props_list += suffix + ', '
else:
props_list += suffix
# return prop_list
return props_list + ']'
elements = [] # reinitialize empty nodes and edges
# Populate only unique edges which are not shared between two nodes
for index, row in df_unique.iterrows():
edge_data = {}
edges_element = {}
edges_element['source'] = row['source']
edges_element['target'] = row['target']
property_label = get_property_labels(row['label'])
if property_label is None:
print('ERROR: Could not find property label!')
sys.exit()
edges_element['label'] = property_label
edge_data['data'] = edges_element
elements.append(edge_data)
# Populate only those edges which are shared between two vertices
for index, row in df_merged_edge_has_common_nodes.iterrows():
edge_data = {}
edges_element = {}
edges_element['source'] = row['source']
edges_element['target'] = row['target']
property_labels = get_property_labels(row['label'])
if property_labels is None:
print('ERROR: Could not find property labels!')
sys.exit()
edges_element['label'] = property_labels
edge_data['data'] = edges_element
elements.append(edge_data)
# print('\nRefined Edges\n', elements)
# Adding the nodes
def is_node_in_edges(node, edges):
edge_nodes = set()
for edge_data_value in edges:
edge_nodes.add(edge_data_value['data']['source'])
edge_nodes.add(edge_data_value['data']['target'])
if node['data']['id'] in edge_nodes:
return True
else:
return False
for node in nodes:
if is_node_in_edges(node, edges):
elements.append(node)
# except:
# return "Visual Failed. Probably missing type, name, or ID"
print('Made it to render.')
if os.environ.get("LOCAL", False):
return render_template('local_index.html')
return render_template('index.html')
from pyld import jsonld
import json
from os.path import join
doc = json.load(open(join("../json-instances/", "PDB-5AEM.jsonld")))
print("loaded jsonld", doc)
context = json.load(open(join("../json-schemas/contexts/", "dataset_sdo_context.jsonld")))
print("loaded context")
compacted = jsonld.compact(doc, context)
print("-------------COMPACTED")
print(json.dumps(compacted, indent=2))
expanded = jsonld.expand(compacted)
print("-------------EXPANDED")
print(json.dumps(expanded, indent=2))
flattened = jsonld.flatten(compacted)
def flatten(document):
"""Flatten OA JSON-LD."""
# See http://www.w3.org/TR/json-ld-api/#flattening
return jsonld.flatten(document)
uri_generator=UriPatternGenerator('http://id.trees.org/types/%s'),
concept_scheme=ConceptScheme('http://id.trees.org'))
# Generate a doc for a cs
doc = jsonld_dumper(provider, CONTEXT)
msg = 'Conceptscheme'
print(msg)
print(len(msg) * '=')
print(json.dumps(doc, indent=2))
# Print an expanded doc
expanded = jsonld.expand(doc, CONTEXT)
msg = 'Conceptscheme expanded'
print(msg)
print(len(msg) * '=')
print(json.dumps(expanded, indent=2))
# Compact the doc again
compacted = jsonld.compact(expanded, CONTEXT)
msg = 'Conceptscheme compacted again'
print(msg)
print(len(msg) * '=')
print(json.dumps(compacted, indent=2))
# And now flatten it
flattened = jsonld.flatten(compacted, CONTEXT)
msg = 'Conceptscheme flattened'
print(msg)
print(len(msg) * '=')
print(json.dumps(flattened, indent=2))
def the_function(self, source, context, expand_context):
""" actually flatten
"""
return jsonld.flatten(source, context,
dict(expandContext=expand_context))
def _norm(self, ld):
j = json.loads(ld)
flat = jsonld.flatten(j)
return json.dumps(flat)
# expand a document, removing its context
# see: http://json-ld.org/spec/latest/json-ld/#expanded-document-form
expanded = jsonld.expand(compacted)
print(json.dumps(expanded, indent=2))
# Output:
# {
# "http://schema.org/image": [{"@id": "http://manu.sporny.org/images/manu.png"}],
# "http://schema.org/name": [{"@value": "Manu Sporny"}],
# "http://schema.org/url": [{"@id": "http://manu.sporny.org/"}]
# }
# expand using URLs
jsonld.expand('http://example.org/doc')
# flatten a document
# see: http://json-ld.org/spec/latest/json-ld/#flattened-document-form
flattened = jsonld.flatten(doc)
# all deep-level trees flattened to the top-level
# frame a document
# see: http://json-ld.org/spec/latest/json-ld-framing/#introduction
framed = jsonld.frame(doc, frame)
# document transformed into a particular tree structure per the given frame
# normalize a document
normalized = jsonld.normalize(doc, {'format': 'application/nquads'})
# normalized is a string that is a canonical representation of the document
# that can be used for hashing
def test_import_jsonld_into_named_graph():
"""Test named graphs we use."""
graph = ConjunctiveGraph()
serialized_document = json.dumps(jsonld.expand(
jsonld.flatten(JSONLD_DOCUMENT, ), ),
indent=4)
graph.parse(
data=serialized_document,
format='json-ld',
# All the semantic data about my blog is stored in a particular
# named graph.
publicID=PUBLIC_ID,
)
assert list(
map(
operator.itemgetter(Variable('g')),
graph.query(
'SELECT DISTINCT ?g WHERE { GRAPH ?g { ?s ?p ?o . } } ORDER BY ?g',
).bindings,
)) == [
PUBLIC_ID,
]
assert graph.query('''
SELECT * WHERE {
?subclass_of_robot rdfs:subClassOf ex:Robot .
}
''',
initNs=NAMESPACES).bindings == [{
Variable('subclass_of_robot'):
URIRef('https://example.org/Rover'),
}]
# THIS FAILS!
# The information about ex:Rover cannot be found if I specify the GRAPH.
# Meaning, this information is not in one of the named graphs.
assert graph.query('''
SELECT * WHERE {
GRAPH ?g {
ex:Rover rdfs:subClassOf ex:Robot .
}
}
''',
initNs=NAMESPACES).bindings == [{
Variable('g'):
PUBLIC_ID,
}]
# `publicID` was used for the part of data which was on the top level
# of the document.
assert graph.query('''
SELECT * WHERE {
GRAPH ?g {
blog:JSONLD-and-named-graphs a schema:blogPost .
}
}
''',
initNs=NAMESPACES).bindings == [{
Variable('g'):
PUBLIC_ID,
}]
from pyld import jsonld
import json
import os
doc = json.load(open(os.join(".." + os.sep + "json-instances" + os.sep + "", "PDB-5AEM.jsonld")))
print("loaded jsonld", doc)
context = json.load(open(os.join(".." + os.sep + "json-schemas" + os.sep + "contexts" + os.sep, "dataset_sdo_context.jsonld")))
print("loaded context")
compacted = jsonld.compact(doc, context)
print("-------------COMPACTED")
print(json.dumps(compacted, indent=2))
expanded = jsonld.expand(compacted)
print("-------------EXPANDED")
print(json.dumps(expanded, indent=2))
flattened = jsonld.flatten(compacted)
def flatten(document):
"""Flatten OA JSON-LD."""
# See http://www.w3.org/TR/json-ld-api/#flattening
return jsonld.flatten(document)
def main(self):
print('PyLD Unit Tests')
print('Use -h or --help to view options.')
# add program options
self.parser.add_option('-f', '--file', dest='file',
help='The single test file to run', metavar='FILE')
self.parser.add_option('-d', '--directory', dest='directory',
help='The directory full of test files', metavar='DIR')
self.parser.add_option('-e', '--earl', dest='earl',
help='The filename to write the EARL report to', metavar='EARL')
self.parser.add_option('-v', '--verbose', dest='verbose',
action='store_true', default=False,
help='Prints verbose test data')
# parse options
(self.options, args) = self.parser.parse_args()
# check if file or directory were specified
if self.options.file == None and self.options.directory == None:
raise Exception('No test file or directory specified.')
# check if file was specified, exists, and is file
if self.options.file is not None:
if (os.path.exists(self.options.file) and
os.path.isfile(self.options.file)):
# add manifest file to the file list
self.manifest_files.append(os.path.abspath(self.options.file))
else:
raise Exception('Invalid test file: "%s"' % self.options.file)
# check if directory was specified, exists and is dir
if self.options.directory is not None:
if (os.path.exists(self.options.directory) and
os.path.isdir(self.options.directory)):
# load manifest files from test directory
for test_dir, dirs, files in os.walk(self.options.directory):
for manifest in files:
# add all .jsonld manifest files to the file list
if (manifest.find('manifest') != -1 and
manifest.endswith('.jsonld')):
self.manifest_files.append(
join(test_dir, manifest))
else:
raise Exception('Invalid test directory: "%s"' %
self.options.directory)
# see if any manifests have been specified
if len(self.manifest_files) == 0:
raise Exception('No manifest files found.')
passed = 0
failed = 0
total = 0
# run the tests from each manifest file
for manifest_file in self.manifest_files:
test_dir = os.path.dirname(manifest_file)
manifest = json.load(open(manifest_file, 'r'))
count = 1
for test in manifest['sequence']:
# skip unsupported types
skip = True
test_type = test['@type']
for tt in test_type:
if tt in SKIP_TEST_TYPES:
skip = True
break
if tt in TEST_TYPES:
skip = False
if skip:
# print 'Skipping test: "%s" ...' % test['name']
continue
print('JSON-LD/%s %04d/%s...' % (
manifest['name'], count, test['name']), end=' ')
total += 1
count += 1
# read input file
with open(join(test_dir, test['input'])) as f:
if test['input'].endswith('.jsonld'):
input = json.load(f)
else:
input = f.read().decode('utf8')
# read expect file
with open(join(test_dir, test['expect'])) as f:
if test['expect'].endswith('.jsonld'):
expect = json.load(f)
else:
expect = f.read().decode('utf8')
result = None
# JSON-LD options
options = {
'base': 'http://json-ld.org/test-suite/tests/' +
test['input'],
'useNativeTypes': True
}
success = False
try:
if 'jld:ExpandTest' in test_type:
result = jsonld.expand(input, options)
elif 'jld:CompactTest' in test_type:
ctx = json.load(open(join(test_dir, test['context'])))
result = jsonld.compact(input, ctx, options)
elif 'jld:FlattenTest' in test_type:
result = jsonld.flatten(input, None, options)
elif 'jld:FrameTest' in test_type:
frame = json.load(open(join(test_dir, test['frame'])))
result = jsonld.frame(input, frame, options)
elif 'jld:FromRDFTest' in test_type:
result = jsonld.from_rdf(input, options)
elif 'jld:ToRDFTest' in test_type:
options['format'] = 'application/nquads'
result = jsonld.to_rdf(input, options)
elif 'jld:NormalizeTest' in test_type:
options['format'] = 'application/nquads'
result = jsonld.normalize(input, options)
# check the expected value against the test result
success = deep_compare(expect, result)
if success:
passed += 1
print('PASS')
else:
failed += 1
print('FAIL')
if not success or self.options.verbose:
print('Expect:', json.dumps(expect, indent=2))
print('Result:', json.dumps(result, indent=2))
except jsonld.JsonLdError as e:
print('\nError: ', e)
failed += 1
print('FAIL')
# add EARL report assertion
EARL['subjectOf'].append({
'@type': 'earl:Assertion',
'earl:assertedBy': EARL['doap:developer']['@id'],
'earl:mode': 'earl:automatic',
'earl:test': ('http://json-ld.org/test-suite/tests/' +
os.path.basename(manifest_file) + test.get('@id', '')),
'earl:result': {
'@type': 'earl:TestResult',
'dc:date': datetime.datetime.utcnow().isoformat(),
'earl:outcome': ('earl:' + 'passed' if success else
'failed')
}
})
if self.options.earl:
f = open(self.options.earl, 'w')
f.write(json.dumps(EARL, indent=2))
f.close()
print('Done. Total:%d Passed:%d Failed:%d' % (total, passed, failed))
import os
import sys
import json
from pyld import jsonld
from pyld_document_loader import my_requests_document_loader
if __name__ == '__main__':
fjson = sys.argv[1]
with open(fjson, 'r') as f:
doc = json.loads(f.read())
jsonld.set_document_loader(my_requests_document_loader())
data = jsonld.flatten(doc)
jpath, jfile = os.path.split(fjson)
flatten_file = f'{jpath}{os.path.sep}flatten_{jfile}'
with open(flatten_file,'w') as f:
f.write(json.dumps(data))