def route_examples():
links = hfn.render_table(
[[name,
hfn.atag(url_for("route_query", pred=pred, root=root) + (args[0] if args else ''),
f'../query/{pred}/{root}{args[0] if args else ""}')]
for name, pred, root, *args in examples],
'Root class',
'../query/{predicate-curie}/{root-curie}?direction=INCOMING&depth=10&branch=master&local=false',
halign='left')
flinks = hfn.render_table(
[[name,
hfn.atag(url_for("route_filequery", pred=pred, root=root, file=file) + (args[0] if args else ''),
f'../query/{pred}/{root}/{file}{args[0] if args else ""}')]
for name, pred, root, file, *args in file_examples],
'Root class',
'../query/{predicate-curie}/{root-curie}/{ontology-filepath}?direction=INCOMING&depth=10&branch=master&restriction=false',
halign='left')
dlinks = hfn.render_table(
[[name,
hfn.atag(url_for("route_dynamic", path=path) + (querystring if querystring else ''),
f'../query/dynamic/{path}{querystring if querystring else ""}')]
for name, path, querystring in dynamic_examples],
'Root class',
'../query/dynamic/{path}?direction=OUTGOING&dynamic=query&args=here',
halign='left')
return hfn.htmldoc(links, flinks, dlinks, title='Example hierarchy queries')
def route_sparc_index():
hyp_rows = hyperlink_tree(sparc_view)
return hfn.htmldoc(
hfn.render_table(hyp_rows),
title = 'SPARC Anatomical terms index',
metas = ({'name':'date', 'content':time()},),
)
def route_sparc_view():
hyp_rows = []
spaces = hfn.nbsp * 8
for tier1, tier2_on in sorted(sparc_view.items()):
url = url_for('route_sparc_view_query', tier1=tier1)
tier1_row = tier1.split(YML_DELIMITER)
tier1_row += tier2_on['CURIES']
tagged_tier1_row = tag_row(tier1_row, url)
hyp_rows.append(tagged_tier1_row)
if not tier2_on:
continue
# BUG: Will break what we want if more is added to spinal cord
if len(tier2_on.keys()) > 15:
continue
if tier1_row[0] == 'Nerve roots of spinal cord segments':
continue
for tier2, tier3_on in tier2_on.items():
if tier2 == 'CURIES':
continue
url = url_for('route_sparc_view_query', tier1=tier1, tier2=tier2)
tier2_row = tier2.split(YML_DELIMITER)
tier2_row += tier3_on['CURIES']
tagged_tier2_row = tag_row(row=tier2_row, url=url, tier_level=1)
if len(list(sparc_view[tier1_row[0]][tier2_row[0]].keys())) == 1:
tagged_tier2_row[0] = spaces+tier2_row[0]
hyp_rows.append(tagged_tier2_row)
return hfn.htmldoc(
hfn.render_table(hyp_rows),
title= 'Main Page Sparc',
styles= ["p {margin: 0px; padding: 0px;}"],
metas= ({'name':'date', 'content':time()},),
)
def route_sparc_demos_isan2019_flatmap_queries():
# lift up to load from an external source at some point
# from pyontutils.core import OntResPath
# orp = OntResPath('annotations.ttl')
# [i for i in sorted(set(OntId(e) for t in orp.graph for e in t)) if i.prefix in ('UBERON', 'FMA', 'ILX')]
query = """
MATCH (blank)-
[entrytype:ilxtr:hasSomaLocatedIn|ilxtr:hasAxonLocatedIn|ilxtr:hasDendriteLocatedIn|ilxtr:hasPresynapticTerminalsIn]
->(location:Class{{iri: "{iri}"}})
WITH entrytype, location, blank
MATCH (phenotype)<-[predicate]-(blank)<-[:equivalentClass]-(neuron)
WHERE NOT (phenotype.iri =~ ".*_:.*")
RETURN location, entrytype.iri, neuron.iri, predicate.iri, phenotype
"""
def fetch(iri, limit=10):
q = query.format(iri=iri)
log.debug(q)
blob = data_sgc.execute(q, limit, 'application/json')
# oh boy
# if there are less results than the limit scigraph segfaults
# and returns nothing
return blob
hrm = [fetch(oid) for oid in test_terms]
return hfn.htmldoc(hfn.render_table([[1, 2]],'oh', 'no'),
title='Simulated flatmap query results',
)
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_demos_isan2019_neuron_connectivity():
def connected(start):
log.debug(start)
blob = data_sgd.neurons_connectivity(start) #, limit=9999)
edges = blob['edges']
neurons = {}
types = {}
rows = []
start_type = None
sc = OntId(start).curie
for e in edges:
s, p, o = e['sub'], e['pred'], e['obj']
if p == 'operand':
continue
if s.startswith('_:'):
if s not in neurons:
neurons[s] = []
types[s] = {}
otp = OntTerm(p)
oto = OntTerm(o)
neurons[s].append((otp, oto))
if o == sc:
start_type = otp
if oto not in types[s]:
types[s][oto] = []
types[s][oto].append(otp)
for v in neurons.values():
v.sort()
return OntTerm(start), start_type, neurons, types
hrm = [connected(t) for t in set(test_terms)]
header = ['Start', 'Start Type', 'Neuron', 'Relation', 'Target']
rows = []
for start, start_type, neurons, types in sorted(hrm):
start = start.atag()
start_type = start_type.atag() if start_type is not None else ''
for i, v in enumerate(neurons.values(), 1):
neuron = i
for p, o in v:
relation = p.atag()
target = o.atag()
row = start, start_type, neuron, relation, target
rows.append(row)
rows.append(['|'] + [' '] * 4)
h = hfn.htmldoc(hfn.render_table(rows, *header),
title='neuron connectivity')
return h
def route_sparc_view_query(tier1, tier2=None):
journey = sparc_view
if tier1 not in journey:
return abort(404)
journey = journey[tier1]
if tier2 is not None:
if tier2 not in journey:
return abort(404)
journey = journey[tier2]
hyp_rows = hyperlink_tree(journey)
return hfn.htmldoc(
hfn.render_table(hyp_rows),
title = 'Terms for ' + (tier2 if tier2 is not None else tier1),
metas = ({'name':'date', 'content':time()},),
)
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 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)
