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
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 __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
# PLEASE DO NOT PUT PMIDs as external ids!!!
# FIXME idlib PMID(thing) urg the regex state machine is so simple ;_;
if self.id.startswith('PMID:'):
log.warning('PMIDs should never be External IDs!')
self._term = fake
self.s = OntId(self.id).URIRef
return
self._term = OntTerm(self.id)
self.s = self._term.URIRef
def query_scigraph_for_curies(self, label: str, prefixes:List[str] = ['UBERON', 'ILX']) -> list:
curies = []
# return []
# for prefix in prefixes:
# BUG: prefixes cant be used because it gives random errors if the prefix isn't exact
for prefix in prefixes:
neighbors = [v.OntTerm for v in OntTerm.query(label=label.strip(), prefix=prefix)]
if not neighbors:
continue
for neighbor in neighbors:
oid = OntId(neighbor)
curies.append(oid.curie)
return curies
def res_stats(res):
hrm = [(o, n['id']) for o, r in res for n in r['nodes']]
hrmt = len(hrm)
ntotal = len(set(hrm))
assert hrmt == ntotal
nunique = len(set(t for o, t in hrm))
dupes = [(t, c) for t, c in Counter([t for o, t in hrm]).most_common() if c > 1]
ndupes = len(dupes)
total_extra = sum(c for t, c in dupes) - ndupes
many = [(c, OntTerm(t)) for t, c in dupes if c > 2]
# the extra 7142 terms are the result of 6695 terms that
# appear more than once across multiple organs
breakpoint()
def get_curies_from_scigraph_label_query(label: str,
prefixes: List[str] = [
'UBERON', 'ILX', 'PAXRAT'
]) -> list:
curies = set()
for prefix in prefixes:
# TODO: if not stipped the label will return nothing. Seems to be trailing spaces
neighbors = [
v.OntTerm
for v in OntTerm.query(label=label.strip(), prefix=prefix)
]
if not neighbors:
continue
for neighbor in neighbors:
curies.add(OntId(neighbor).curie)
return list(curies)
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 server(api_key=None, verbose=False):
# data endpoint
#_dataBP = 'https://sparc.olympiangods.org/scigraph'
_dataBP = 'http://sparc-data.scicrunch.io:9000/scigraph'
scigraphd = moduleDirect(_dataBP, 'scigraphd')
data_sgd = scigraphd.Dynamic(cache=True, verbose=True, do_error=True)
data_sgd._basePath = _dataBP
data_sgc = scigraphd.Cypher(cache=True, verbose=True)
data_sgc._basePath = _dataBP
f = Path(__file__).resolve()
working_dir = get_working_dir(__file__)
resources = auth.get_path('resources')
if working_dir:
git_dir = working_dir / '.git'
else:
git_dir = Path('/dev/null')
try:
if working_dir is not None:
ref = subprocess.check_output(['git',
'--git-dir', git_dir.as_posix(),
'--work-tree', working_dir.as_posix(),
'rev-parse', 'HEAD'],
stderr=subprocess.DEVNULL).decode().rstrip()
else:
ver = __version__
if '+' in ver:
ref = ver.split('+', 1)[-1]
else:
ref = ver
except subprocess.CalledProcessError:
ref = 'master' # 'NO-REPO-AT-MOST-TODO-GET-LATEST-HASH'
wasGeneratedBy = ('https://github.com/tgbugs/pyontutils/blob/'
f'{ref}/pyontutils/{f.name}'
'#L{line}')
line = getSourceLine(render)
wgb = wasGeneratedBy.format(line=line)
importchain = ImportChain(sgg=sgg, sgc=sgc, wasGeneratedBy=wasGeneratedBy)
importchain.make_html() # run this once, restart services on a new release
loop = asyncio.get_event_loop()
app = Flask('ontology tree service')
app.config['loop'] = loop
# gsheets = GoogleSheets()
sparc_view = open_custom_sparc_view_yml()
# sparc_view_raw = open_custom_sparc_view_yml(False)
log.info('starting index load')
uot_terms = [OntTerm(t) for t in uot]
uot_lookup = {t.label:t for t in uot_terms}
uot_ordered = sorted(t.label for t in uot_terms)
basename = 'trees'
@app.route(f'/{basename}', methods=['GET'])
@app.route(f'/{basename}/', methods=['GET'])
def route_():
d = url_for('route_docs')
e = url_for('route_examples')
i = url_for('route_import_chain')
return hfn.htmldoc(hfn.atag(d, 'Docs'),
'<br>',
hfn.atag(e, 'Examples'),
'<br>',
hfn.atag(i, 'Import chain'),
title='NIF ontology hierarchies')
@app.route(f'/{basename}/docs', methods=['GET'])
def route_docs():
return redirect('https://github.com/SciCrunch/NIF-Ontology/blob/master/docs') # TODO
@app.route(f'/{basename}/examples', methods=['GET'])
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')
@app.route(f'/{basename}/sparc/demos/isan2019/neuron-connectivity', methods=['GET'])
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
@app.route(f'/{basename}/sparc/demos/isan2019/flatmap-queries', methods=['GET'])
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',
)
@app.route(f'/{basename}/sparc/demos/apinat', methods=['GET'])
@app.route(f'/{basename}/sparc/demos/apinat/', methods=['GET'])
def route_sparc_demos_apinat():
return 'apinat'
@app.route(f'/{basename}/sparc/connectivity/query', methods=['GET'])
def route_sparc_connectivity_query():
kwargs = request.args
log.debug(kwargs)
script = """
var ele = document.getElementById('model-selector')
ele.onselect
"""
return hfn.htmldoc(hfn.render_form(
[[('Model',), {}],
[None, None],
[
#('Kidney', 'Defensive breathing',), # TODO autopopulate
('Urinary Omega Tree',),
{'id':'model-selector', 'name': 'model'}]], # FIXME auto via js?
# FIXME must switch start and stop per model (argh)
# or hide/show depending on which model is selected
[[('start',), {}],
[None, None],
[
#('one', 'two', 'three'), # TODO auto populate
uot_ordered,
{'name': 'start'}]], # FIXME auto via js?
[[('end',), {}],
[None, None],
[
#('one', 'two', 'three'), # TODO auto populate
uot_ordered,
{'name': 'end'}]], # FIXME auto via js?
[[tuple(), {}],
[tuple(), {'type': 'submit', 'value': 'Query'}],
[None, None]] # FIXME auto via js?
, action='view', method='POST'
),
scripts=(script,),
title='Connectivity query')
@app.route(f'/{basename}/sparc/connectivity/view', methods=['POST'])
def route_sparc_connectivity_view():
kwargs = request.args
log.debug(kwargs)
# FIXME error handling for bad data
model = request.form['model']
start = request.form['start']
end = request.form['end']
sid = uot_lookup[start].curie
eid = uot_lookup[end].curie
#start = 'UBERON:0005157'
#end = 'UBERON:0001255'
return redirect(f'/{basename}/sparc/dynamic/shortestSimple?start_id={sid}'
f'&end_id={eid}&direction=INCOMING&format=table') # TODO
#return hfn.htmldoc(title='Connectivity view')
@app.route(f'/{basename}/sparc/simple/dynamic/<path:path>', methods=['GET'])
def route_sparc_simple_dynamic(path):
return sparc_dynamic(data_sgd, data_sgc, path, wgb, simplify)
@app.route(f'/{basename}/sparc/dynamic/<path:path>', methods=['GET'])
def route_sparc_dynamic(path):
return sparc_dynamic(data_sgd, data_sgc, path, wgb)
@app.route(f'/{basename}/dynamic/<path:path>', methods=['GET'])
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)
@app.route(f'/{basename}/imports/chain', methods=['GET'])
def route_import_chain():
return importchain.html
@app.route(f'/{basename}/query/<pred>/<root>', methods=['GET'])
def route_query(pred, root):
kwargs = getArgs(request)
kwargs['wgb'] = wgb
maybe_abort = sanitize(pred, kwargs)
if maybe_abort is not None:
return maybe_abort
if verbose:
kwargs['verbose'] = verbose
log.debug(str(kwargs))
return render(pred, root, **kwargs)
@app.route(f'/{basename}/query/<pred>/http:/<path:iri>', methods=['GET']) # one / due to nginx
@app.route(f'/{basename}/query/<pred>/https:/<path:iri>', methods=['GET']) # just in case
def route_iriquery(pred, iri): # TODO maybe in the future
root = 'http://' + iri # for now we have to normalize down can check request in future
if verbose:
log.debug(f'ROOOOT {root}')
kwargs = getArgs(request)
kwargs['wgb'] = wgb
maybe_abort = sanitize(pred, kwargs)
if maybe_abort is not None:
return maybe_abort
if verbose:
kwargs['verbose'] = verbose
log.debug(str(kwargs))
return render(pred, root, **kwargs)
@app.route(f'/{basename}/query/<pred>/<root>/<path:file>', methods=['GET'])
def route_filequery(pred, root, file):
kwargs = getArgs(request)
kwargs['local_filepath'] = file
kwargs['wgb'] = wgb
maybe_abort = sanitize(pred, kwargs)
if maybe_abort is not None:
return maybe_abort
if verbose:
kwargs['verbose'] = verbose
log.debug(str(kwargs))
try:
return render(pred, root, **kwargs)
except HTTPError:
return abort(404, 'Unknown ontology file.') # TODO 'Unknown git branch.'
@app.route(f'/{basename}/sparc/view/<tier1>', methods=['GET'])
@app.route(f'/{basename}/sparc/view/<tier1>/', methods=['GET'])
@app.route(f'/{basename}/sparc/view/<tier1>/<tier2>', methods=['GET'])
@app.route(f'/{basename}/sparc/view/<tier1>/<tier2>/', methods=['GET'])
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()},),
)
@app.route(f'/{basename}/sparc/view', methods=['GET'])
@app.route(f'/{basename}/sparc/view/', methods=['GET'])
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()},),
)
@app.route(f'/{basename}/sparc/index', methods=['GET'])
@app.route(f'/{basename}/sparc/index/', methods=['GET'])
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()},),
)
@app.route(f'/{basename}/sparc', methods=['GET'])
@app.route(f'/{basename}/sparc/', methods=['GET'])
def route_sparc():
# FIXME TODO route to compiled
p = Path('/var/www/ontology/trees/sparc/sawg.html')
if p.exists():
return send_from_directory(p.parent.as_posix(), p.name)
log.critical(f'{resources}/sawg.org has not been published')
return send_from_directory(resources.as_posix(), 'sawg.org')
#return hfn.htmldoc(
#atag(url_for('route_sparc_view'), 'Terms by region or atlas'), '<br>',
#atag(url_for('route_sparc_index'), 'Index'),
#title='SPARC Anatomical terms', styles=["p {margin: 0px; padding: 0px;}"],
#metas = ({'name':'date', 'content':time()},),
#)
return app
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)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._term = OntTerm(self.id)
self.s = self._term.URIRef
def main():
sparc_terms = convert_view_text_to_dict()
print('Linearizing graph')
sparc_terms_unpaired = list(linearize_graph(sparc_terms))
print('Adding ids to terms list')
sparc_terms_paired = pair_terms(sparc_terms_unpaired)
# embed()
avoid_in_bl = [
'Gross anatomy',
'Internal anatomy',
'Segmental Anatomy',
'Atlas Nomenclature',
'Allen Mouse Brainstem',
'Paxinos Rar Brainstem'
'Berman Cat Brainstem',
'Nerves (also includes Cranial)',
'UBERON',
]
accepted_prefixes_for_bl = [
'UBERON',
'PAXRAT',
]
print('Building sparc terms list txt')
sparc_terms_text, sparc_terms_bl = '', []
for term in sparc_terms_paired:
sparc_terms_text += ' ' * 4 * term.tier_level + '\t'.join(
[term.label] + term.curies) + '\n'
if not term.curies and term.label.strip() not in avoid_in_bl:
sparc_terms_bl.append(term.label)
# Labels with no ID
# Slow as heck
print(
f'Building list for terms with no IDs with len:{len(sparc_terms_bl)}')
for i, bl_term in enumerate(sparc_terms_bl):
neighbors = OntTerm.search(bl_term.split(' ')[0])
for neighbor in neighbors:
if set(neighbor.split(' ')) == set(bl_term.split(' ')):
# if neighbor.curie.split(':')[0] in accepted_prefixes_for_bl:
view_text_bl[i] += '\t' + neighbor.curie
# Original IDs with wrong label
print('Building list for terms with wrong IDs')
sparc_terms_with_bad_ids = []
for term in sparc_terms_unpaired:
for curie in term.curies:
onts = OntTerm.query(curie=curie)
if not onts:
continue
for ont in onts:
if term.label.lower().strip() != ont.label.lower().strip():
sparc_terms_with_bad_ids.append({
**vars(term), 'searched_label':
ont.label
})
# embed()
with open(resources / 'sparc_terms_populated3.txt', 'w') as outfile:
outfile.write(sparc_terms_text)
with open(resources / 'sparc_terms_unpopulated_terms3.txt',
'w') as outfile:
outfile.write('\n'.join(sorted(sparc_terms_bl)))
with open(resources / 'sparc_terms_with_bad_ids3.json', 'w') as outfile:
json.dump(sparc_terms_with_bad_ids, outfile, indent=4)
# methods helper (subset of the larger ontology to speed up development)
###
restHasValue = Restriction(None, owl.hasValue)
filename = 'methods-helper'
prefixes = None
OntCuries['HBP_MEM'] = 'http://www.hbp.FIXME.org/hbp_measurement_methods/'
#OntCuries['HBP_MEM'] = 'http://www.hbp.FIXME.org/hbp_measurement_methods/'
#imports = NIFTTL['nif_backend.ttl'],
imports = methods_core.iri,
comment = 'helper for methods development'
_repo = True
debug = True
triples = ((tech.injection, owl.equivalentClass, OntTerm('BIRNLEX:2135')), )
triples += ( # protocols
oc(prot.CLARITY, ilxtr.protocol),
oc(prot.deepSequencing, ilxtr.protocol),
oc(prot.sangerSequencing, ilxtr.protocol),
oc(prot.shotgunSequencing, ilxtr.protocol),
oc(prot.fMRI, ilxtr.protocol),
oc(prot.dwMRI, ilxtr.protocol),
oc(prot.DTI, ilxtr.protocol),
)
triples += ( # information entity
# information entities
oc(ilxtr.informationEntity),
def server(api_key=None, verbose=False):
f = Path(__file__).resolve()
working_dir = get_working_dir(__file__)
if working_dir:
git_dir = working_dir / '.git'
else:
git_dir = Path('/dev/null')
try:
commit = subprocess.check_output(
[
'git', '--git-dir',
git_dir.as_posix(), '--work-tree',
working_dir.as_posix(), 'rev-parse', 'HEAD'
],
stderr=subprocess.DEVNULL).decode().rstrip()
except subprocess.CalledProcessError:
commit = 'master' # 'NO-REPO-AT-MOST-TODO-GET-LATEST-HASH'
wasGeneratedBy = ('https://github.com/tgbugs/pyontutils/blob/'
f'{commit}/pyontutils/{f.name}'
'#L{line}')
line = getSourceLine(render)
wgb = wasGeneratedBy.format(line=line)
importchain = ImportChain(wasGeneratedBy=wasGeneratedBy)
importchain.make_html() # run this once, restart services on a new release
loop = asyncio.get_event_loop()
app = Flask('ontology tree service')
app.config['loop'] = loop
# gsheets = GoogleSheets()
sparc_view = open_custom_sparc_view_yml()
log.info('starting index load')
uot_terms = [OntTerm(t) for t in uot]
uot_lookup = {t.label: t for t in uot_terms}
uot_ordered = sorted(t.label for t in uot_terms)
basename = 'trees'
@app.route(f'/{basename}', methods=['GET'])
@app.route(f'/{basename}/', methods=['GET'])
def route_():
d = url_for('route_docs')
e = url_for('route_examples')
i = url_for('route_import_chain')
return htmldoc(atag(d, 'Docs'),
'<br>',
atag(e, 'Examples'),
'<br>',
atag(i, 'Import chain'),
title='NIF ontology hierarchies')
@app.route(f'/{basename}/docs', methods=['GET'])
def route_docs():
return redirect(
'https://github.com/SciCrunch/NIF-Ontology/blob/master/docs'
) # TODO
@app.route(f'/{basename}/examples', methods=['GET'])
def route_examples():
links = render_table(
[[
name,
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 = render_table(
[[
name,
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 = render_table(
[[
name,
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 htmldoc(links,
flinks,
dlinks,
title='Example hierarchy queries')
@app.route(f'/{basename}/sparc/connectivity/query', methods=['GET'])
def route_sparc_connectivity_query():
kwargs = request.args
log.debug(kwargs)
script = """
var ele = document.getElementById('model-selector')
ele.onselect
"""
return hfn.htmldoc(
hfn.render_form(
[
[('Model', ), {}],
[None, None],
[
#('Kidney', 'Defensive breathing',), # TODO autopopulate
(
'Urinary Omega Tree', ),
{
'id': 'model-selector',
'name': 'model'
}
]
], # FIXME auto via js?
# FIXME must switch start and stop per model (argh)
# or hide/show depending on which model is selected
[
[('start', ), {}],
[None, None],
[
#('one', 'two', 'three'), # TODO auto populate
uot_ordered,
{
'name': 'start'
}
]
], # FIXME auto via js?
[
[('end', ), {}],
[None, None],
[
#('one', 'two', 'three'), # TODO auto populate
uot_ordered,
{
'name': 'end'
}
]
], # FIXME auto via js?
[[tuple(), {}],
[tuple(), {
'type': 'submit',
'value': 'Query'
}], [None, None]] # FIXME auto via js?
,
action='view',
method='POST'),
scripts=(script, ),
title='Connectivity query')
@app.route(f'/{basename}/sparc/connectivity/view', methods=['POST'])
def route_sparc_connectivity_view():
kwargs = request.args
log.debug(kwargs)
# FIXME error handling for bad data
model = request.form['model']
start = request.form['start']
end = request.form['end']
sid = uot_lookup[start].curie
eid = uot_lookup[end].curie
#start = 'UBERON:0005157'
#end = 'UBERON:0001255'
return redirect(
f'/{basename}/sparc/dynamic/shortestSimple?start_id={sid}&end_id={eid}&direction=INCOMING&format=table'
) # TODO
#return hfn.htmldoc(title='Connectivity view')
@app.route(f'/{basename}/sparc/dynamic/<path:path>', methods=['GET'])
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)
@app.route(f'/{basename}/dynamic/<path:path>', methods=['GET'])
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
j = sgd.dispatch(path, **args)
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)
@app.route(f'/{basename}/imports/chain', methods=['GET'])
def route_import_chain():
return importchain.html
@app.route(f'/{basename}/query/<pred>/<root>', methods=['GET'])
def route_query(pred, root):
kwargs = getArgs(request)
kwargs['wgb'] = wgb
maybe_abort = sanitize(pred, kwargs)
if maybe_abort is not None:
return maybe_abort
if verbose:
kwargs['verbose'] = verbose
log.debug(str(kwargs))
return render(pred, root, **kwargs)
@app.route(f'/{basename}/query/<pred>/http:/<path:iri>',
methods=['GET']) # one / due to nginx
@app.route(f'/{basename}/query/<pred>/https:/<path:iri>',
methods=['GET']) # just in case
def route_iriquery(pred, iri): # TODO maybe in the future
root = 'http://' + iri # for now we have to normalize down can check request in future
if verbose:
log.debug(f'ROOOOT {root}')
kwargs = getArgs(request)
kwargs['wgb'] = wgb
maybe_abort = sanitize(pred, kwargs)
if maybe_abort is not None:
return maybe_abort
if verbose:
kwargs['verbose'] = verbose
log.debug(str(kwargs))
return render(pred, root, **kwargs)
@app.route(f'/{basename}/query/<pred>/<root>/<path:file>', methods=['GET'])
def route_filequery(pred, root, file):
kwargs = getArgs(request)
kwargs['local_filepath'] = file
kwargs['wgb'] = wgb
maybe_abort = sanitize(pred, kwargs)
if maybe_abort is not None:
return maybe_abort
if verbose:
kwargs['verbose'] = verbose
log.debug(str(kwargs))
try:
return render(pred, root, **kwargs)
except HTTPError:
return abort(
404, 'Unknown ontology file.') # TODO 'Unknown git branch.'
@app.route(f'/{basename}/sparc/view/<tier1>', methods=['GET'])
@app.route(f'/{basename}/sparc/view/<tier1>/', methods=['GET'])
@app.route(f'/{basename}/sparc/view/<tier1>/<tier2>', methods=['GET'])
@app.route(f'/{basename}/sparc/view/<tier1>/<tier2>/', methods=['GET'])
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 htmldoc(
render_table(hyp_rows),
title='Terms for ' + (tier2 if tier2 is not None else tier1),
metas=({
'name': 'date',
'content': time()
}, ),
)
@app.route(f'/{basename}/sparc/view', methods=['GET'])
@app.route(f'/{basename}/sparc/view/', methods=['GET'])
def route_sparc_view():
hyp_rows = []
spaces = 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()) > 6:
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)
hyp_rows.append(tagged_tier2_row)
return htmldoc(
render_table(hyp_rows),
title='Main Page Sparc',
styles=["p {margin: 0px; padding: 0px;}"],
metas=({
'name': 'date',
'content': time()
}, ),
)
@app.route(f'/{basename}/sparc/index', methods=['GET'])
@app.route(f'/{basename}/sparc/index/', methods=['GET'])
def route_sparc_index():
hyp_rows = hyperlink_tree(sparc_view)
return htmldoc(
render_table(hyp_rows),
title='SPARC Anatomical terms index',
metas=({
'name': 'date',
'content': time()
}, ),
)
@app.route(f'/{basename}/sparc', methods=['GET'])
@app.route(f'/{basename}/sparc/', methods=['GET'])
def route_sparc():
# FIXME TODO route to compiled
p = Path('/var/www/ontology/trees/sparc/sawg.html')
if p.exists():
return send_from_directory(p.parent.as_posix(), p.name)
log.critical(f'{devconfig.resources}/sawg.org has not been published')
return send_from_directory(
Path(devconfig.resources).as_posix(), 'sawg.org')
#return htmldoc(
#atag(url_for('route_sparc_view'), 'Terms by region or atlas'), '<br>',
#atag(url_for('route_sparc_index'), 'Index'),
#title='SPARC Anatomical terms', styles=["p {margin: 0px; padding: 0px;}"],
#metas = ({'name':'date', 'content':time()},),
#)
return app
