def route_dynamic(path):
args = dict(request.args)
if 'direction' in args:
direction = args.pop('direction')
else:
direction = 'OUTGOING' # should always be outgoing here since we can't specify?
if 'format' in args:
format_ = args.pop('format')
else:
format_ = None
try:
j = sgd.dispatch(path, **args)
except rHTTPError as e:
log.exception(e)
abort(e.response.status_code) # DO NOT PASS ALONG THE MESSAGE
except ValueError as e:
log.exception(e)
abort(404)
if j is None or 'edges' not in j or not j['edges']:
log.error(pformat(j))
log.debug(sgd._last_url)
return abort(400)
prov = [
hfn.titletag(f'Dynamic query result for {path}'),
f'<meta name="date" content="{UTCNOWISO()}">',
f'<link rel="http://www.w3.org/ns/prov#wasGeneratedBy" href="{wgb}">',
'<meta name="representation" content="SciGraph">',
f'<link rel="http://www.w3.org/ns/prov#wasDerivedFrom" href="{sgd._last_url}">'
]
kwargs = {'json': cleanBad(j), 'html_head': prov}
tree, extras = creatTree(*Query(None, None, direction, None), **kwargs)
#print(extras.hierarhcy)
#print(tree)
if format_ is not None:
if format_ == 'table':
#breakpoint()
def nowrap(class_, tag=''):
return (f'{tag}.{class_}' '{ white-space: nowrap; }')
ots = [
OntTerm(n) for n in flatten_tree(extras.hierarchy)
if 'CYCLE' not in n
]
#rows = [[ot.label, ot.asId().atag(), ot.definition] for ot in ots]
rows = [[ot.label,
hfn.atag(ot.iri, ot.curie), ot.definition]
for ot in ots]
return hfn.htmldoc(hfn.render_table(rows, 'label', 'curie',
'definition'),
styles=(hfn.table_style,
nowrap('col-label', 'td')))
return hfn.htmldoc(extras.html, other=prov, styles=hfn.tree_styles)
def route_sparc_dynamic(path):
args = dict(request.args)
if 'direction' in args:
direction = args.pop('direction')
else:
direction = 'OUTGOING' # should always be outgoing here since we can't specify?
if 'format' in args:
format_ = args.pop('format')
else:
format_ = None
j = data_sgd.dispatch(path, **args)
#breakpoint()
if not j['edges']:
log.error(pprint(j))
return abort(400)
kwargs = {'json': j}
tree, extras = creatTree(*Query(None, None, direction, None), **kwargs)
#print(extras.hierarhcy)
print(tree)
if format_ is not None:
if format_ == 'table':
#breakpoint()
def nowrap(class_, tag=''):
return (f'{tag}.{class_}' '{ white-space: nowrap; }')
ots = [
OntTerm(n) for n in flatten_tree(extras.hierarchy)
if 'CYCLE' not in n
]
#rows = [[ot.label, ot.asId().atag(), ot.definition] for ot in ots]
rows = [[ot.label,
hfn.atag(ot.iri, ot.curie), ot.definition]
for ot in ots]
return htmldoc(hfn.render_table(rows, 'label', 'curie',
'definition'),
styles=(hfn.table_style,
nowrap('col-label', 'td')))
return htmldoc(extras.html, styles=hfn.tree_styles)
def render(pred, root, direction=None, depth=10, local_filepath=None,
branch='master', restriction=False, wgb='FIXME', local=False,
verbose=False, flatten=False,):
kwargs = {'local':local, 'verbose':verbose}
prov = makeProv(pred, root, wgb)
if local_filepath is not None:
github_link = ('https://github.com/SciCrunch/NIF-Ontology/raw/'
f'{branch}/{local_filepath}')
prov.append('<link rel="http://www.w3.org/ns/prov#wasDerivedFrom" '
f'href="{github_link}">')
graph = graphFromGithub(github_link, verbose)
qname = graph.namespace_manager._qhrm # FIXME
labels_index = {qname(s):str(o) for s, o in graph[:rdfs.label:]}
if pred == 'subClassOf':
pred = 'rdfs:subClassOf' # FIXME qname properly?
elif pred == 'subPropertyOf':
pred = 'rdfs:subPropertyOf'
try:
kwargs['json'] = graph.asOboGraph(pred, restriction=restriction)
kwargs['prefixes'] = {k:str(v) for k, v in graph.namespace_manager}
except KeyError as e:
if verbose:
log.error(str(e))
return abort(422, 'Unknown predicate.')
else:
kwargs['graph'] = sgg
# FIXME this does not work for a generic scigraph load ...
# and it should not be calculated every time anyway!
# oh look, here we are needed a class again
if False:
versionIRI = [
e['obj']
for e in sgg.getNeighbors('http://ontology.neuinfo.org/'
'NIF/ttl/nif.ttl')['edges']
if e['pred'] == 'versionIRI'][0]
#print(versionIRI)
prov.append('<link rel="http://www.w3.org/ns/prov#wasDerivedFrom" '
f'href="{versionIRI}">') # FIXME wrong and wont resolve
prov.append('<meta name="representation" content="SciGraph">') # FIXME :/
kwargs['html_head'] = prov
try:
if root.startswith('http'): # FIXME this codepath is completely busted?
if 'prefixes' in kwargs:
rec = None
for k, v in kwargs.items():
if root.startswith(v):
rec = k + 'r:' + root.strip(v) # FIXME what?!
break
if rec is None:
raise KeyError('no prefix found for {root}')
else:
rec = sgv.findById(root)
if 'curie' in rec:
root_curie = rec['curie']
# FIXME https://github.com/SciGraph/SciGraph/issues/268
if not root_curie.endswith(':') and '/' not in root_curie:
root = root_curie
else:
kwargs['curie'] = root_curie
elif 'prefixes' not in kwargs and root.endswith(':'):
kwargs['curie'] = root
root = sgc._curies[root.rstrip(':')] # also 268
tree, extras = creatTree(*Query(root, pred, direction, depth), **kwargs)
dematerialize(list(tree.keys())[0], tree)
if flatten:
if local_filepath is not None:
def safe_find(n):
return {'labels':[labels_index[n]],
'deprecated': False # FIXME inacurate
}
else:
def safe_find(n): # FIXME scigraph bug
if n.endswith(':'):
n = sgc._curies[n.rstrip(':')]
elif '/' in n:
prefix, suffix = n.split(':')
iriprefix = sgc._curies[prefix]
n = iriprefix + suffix
return sgv.findById(n)
out = set(n for n in flatten_tree(extras.hierarchy))
try:
lrecs = Async()(deferred(safe_find)(n) for n in out)
except RuntimeError:
asyncio.set_event_loop(current_app.config['loop'])
lrecs = Async()(deferred(safe_find)(n) for n in out)
rows = sorted(((r['labels'][0] if r['labels'] else '')
+ ',' + n for r, n in zip(lrecs, out)
# FIXME still stuff wrong, but better for non cache case
if not r['deprecated']), key=lambda lid: lid.lower())
return '\n'.join(rows), 200, {'Content-Type':'text/plain;charset=utf-8'}
else:
return hfn.htmldoc(extras.html,
other=prov,
styles=hfn.tree_styles)
except (KeyError, TypeError) as e:
if verbose:
log.error(f'{type(e)} {e}')
if sgg.getNode(root):
# FIXME distinguish these cases...
message = 'Unknown predicate or no results.'
elif 'json' in kwargs:
message = 'Unknown root.'
r = graph.namespace_manager.expand(root)
for s in graph.subjects():
if r == s:
message = ('No results. '
'You are querying a ttl file directly, '
'did you remember to set ?restriction=true?')
break
else:
message = 'Unknown root.'
return abort(422, message)
def sparc_dynamic(data_sgd, data_sgc, path, wgb, process=lambda coll, blob: blob):
args = dict(request.args)
if 'direction' in args:
direction = args.pop('direction')
else:
direction = 'OUTGOING' # should always be outgoing here since we can't specify?
if 'format' in args:
format_ = args.pop('format')
else:
format_ = None
if 'apinat' in path: # FIXME bad hardcoded hack
_old_get = data_sgd._get
try:
data_sgd._get = data_sgd._normal_get
j = data_sgd.dispatch(path, **args)
except ValueError as e:
log.exception(e)
abort(404)
except rHTTPError as e:
log.exception(e)
abort(e.response.status_code) # DO NOT PASS ALONG THE MESSAGE
finally:
data_sgd._get = _old_get
else:
try:
j = data_sgd.dispatch(path, **args)
except rHTTPError as e:
log.exception(e)
abort(e.response.status_code) # DO NOT PASS ALONG THE MESSAGE
except ValueError as e:
log.exception(e)
abort(404)
j = process(collapse_apinat, j)
if j is None or 'edges' not in j:
log.error(pformat(j))
return abort(400)
elif not j['edges']:
return node_list(j['nodes']) # FIXME ... really should error?
if path.endswith('housing-lyphs'): # FIXME hack
root = 'NLX:154731'
#direction = 'INCOMING'
else:
root = None
prov = [
hfn.titletag(f'Dynamic query result for {path}'),
f'<meta name="date" content="{UTCNOWISO()}">',
f'<link rel="http://www.w3.org/ns/prov#wasGeneratedBy" href="{wgb}">',
'<meta name="representation" content="SciGraph">',
('<link rel="http://www.w3.org/ns/prov#wasDerivedFrom" '
f'href="{data_sgd._last_url}">')]
kwargs = {'json': cleanBad(j),
'html_head': prov,
'prefixes': data_sgc.getCuries(), # FIXME efficiency
}
tree, extras = creatTree(*Query(root, None, direction, None), **kwargs)
#print(extras.hierarhcy)
#print(tree)
if format_ is not None:
if format_ == 'table':
#breakpoint()
def nowrap(class_, tag=''):
return (f'{tag}.{class_}'
'{ white-space: nowrap; }')
ots = [OntTerm(n)
for n in flatten_tree(extras.hierarchy)
if 'CYCLE' not in n]
#rows = [[ot.label, ot.asId().atag(), ot.definition] for ot in ots]
rows = [[ot.label, hfn.atag(ot.iri, ot.curie), ot.definition]
for ot in ots]
return hfn.htmldoc(hfn.render_table(rows, 'label', 'curie', 'definition'),
styles=(hfn.table_style, nowrap('col-label', 'td')))
return hfn.htmldoc(extras.html,
other=prov,
styles=hfn.tree_styles)