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ontree.py
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ontree.py
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#!/usr/bin/env python3
"""Render a tree from a predicate root pair.
Normally run as a web service.
Usage:
ontree server [options]
ontree [options] <predicate-curie> <root-curie>
ontree --test
Options:
-a --api=API Full url to SciGraph api endpoint
-k --key=APIKEY apikey for SciGraph instance
-p --port=PORT port on which to run the server [default: 8000]
-f --input-file=FILE don't use SciGraph, load an individual file instead
-o --outgoing if not specified defaults to incoming
-b --both if specified goes in both directions
-t --test run tests
-v --verbose print extra information
"""
import os
import asyncio
import subprocess
from pprint import pformat
from pathlib import Path
from datetime import datetime
from urllib.error import HTTPError
from urllib.parse import parse_qs
import htmlfn as hfn
from flask import (Flask,
url_for,
redirect,
request,
abort,
current_app,
send_from_directory)
from requests.exceptions import HTTPError as rHTTPError
from pyontutils import scigraph
from pyontutils.core import OntId, OntTerm, OntGraph
from pyontutils.scig import ImportChain, makeProv
from pyontutils.utils import getSourceLine, get_working_dir, makeSimpleLogger
from pyontutils.utils import Async, deferred, UTCNOWISO
from pyontutils.config import auth
from pyontutils.hierarchies import (Query,
creatTree,
dematerialize,
flatten as flatten_tree)
from pyontutils.namespaces import rdfs, OntCuries
from pyontutils.scigraph_codegen import moduleDirect
from nifstd_tools.sheets_sparc import (hyperlink_tree,
tag_row,
open_custom_sparc_view_yml,
YML_DELIMITER)
from nifstd_tools.simplify import simplify, apinat_deblob, cleanBad
from nifstd_tools import __version__
log = makeSimpleLogger('ontree')
# FIXME these will go to network which is :/
sgg = scigraph.Graph(cache=False, verbose=True)
sgv = scigraph.Vocabulary(cache=False, verbose=True)
sgc = scigraph.Cypher(cache=False, verbose=True)
sgd = scigraph.Dynamic(cache=False, verbose=True)
# This was for ttl creation extension for sparc view
# ixr.setup(instrumented=OntTerm)
a = 'rdfs:subClassOf'
_hpp = 'RO_OLD:has_proper_part' # and apparently this fails too
hpp = 'http://www.obofoundry.org/ro/ro.owl#has_proper_part'
hpp = 'NIFRID:has_proper_part'
po = 'BFO:0000050' # how?! WHY does this fail!? the curie is there!
_po = 'http://purl.obolibrary.org/obo/BFO_0000050'
hr = 'RO:0000087'
_hr = 'http://purl.obolibrary.org/obo/RO_0000087'
inc = 'INCOMING'
out = 'OUTGOING'
both = 'BOTH'
uot = (
"UBERON:0000056",
"UBERON:0000057",
"UBERON:0000074",
"UBERON:0001224",
"UBERON:0001226",
"UBERON:0001227",
"UBERON:0001255",
"UBERON:0001287",
"UBERON:0001290",
"UBERON:0001291",
"UBERON:0001292",
"UBERON:0004193",
"UBERON:0004203",
"UBERON:0004204",
"UBERON:0004205",
"UBERON:0004639",
"UBERON:0004640",
"UBERON:0005096",
"UBERON:0005097",
"UBERON:0005750",
"UBERON:0005751",
"UBERON:0009973",
"UBERON:0012240",
"UBERON:0012242",
)
def time():
''' Get current time in a year-month-day:meta format '''
return str(datetime.utcnow().isoformat()).replace('.', ',')
def node_list(nodes):
log.debug(pformat(nodes))
# FIXME why the heck are these coming in as lbl now?!?!
s = sorted([(n['lbl'], hfn.atag(n['id'], n['lbl'], new_tab=True))
for n in nodes])
return '<br>\n'.join([at for _, at in s])
def graphFromGithub(link, verbose=False):
# mmmm no validation
# also caching probably
if verbose:
log.info(link)
g = OntGraph().parse(f'{link}?raw=true', format='turtle')
OntCuries.populate(g)
return g
collapse_apinat = [ # FIXME config?
['apinatomy:conveys', 'apinatomy:source'],
['apinatomy:conveys', 'apinatomy:target'],
['apinatomy:conveys', 'apinatomy:source',
# FIXME if the final external is missing the rendering
# halts at layerIn and doesn't show the subtree
'apinatomy:internalIn', 'apinatomy:layerIn', 'apinatomy:external'],
['apinatomy:conveys', 'apinatomy:target',
'apinatomy:internalIn', 'apinatomy:layerIn', 'apinatomy:external'],
['apinatomy:fasciculatesIn', 'apinatomy:external'],
['apinatomy:fasciculatesIn', 'apinatomy:layerIn', 'apinatomy:external'],
['apinatomy:fasciculatesIn', 'apinatomy:supertype', 'apinatomy:external'],
['apinatomy:fasciculatesIn', 'apinatomy:cloneOf', 'apinatomy:supertype', 'apinatomy:external'],
]
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 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 getArgs(request):
want = {'direction':inc, # INCOMING OUTGOING BOTH
'depth':10,
'branch':'master',
'restriction':False, # True False
'local':False, # True False # canonoical vs scigraph ? interlex?
'flatten':False,
}
def convert(k):
if k in request.args:
v = request.args[k]
else:
return want[k]
if isinstance(want[k], bool):
if v.lower() == 'true':
return True
elif v.lower() == 'false':
return False
else:
raise TypeError(f'Expected a bool, got "{v}" instead.')
elif isinstance(want[k], int):
try:
return int(v)
except (TypeError, ValueError) as e:
raise TypeError(f'Expected an int, got "{v}" instead.') from e
else:
return v
return {k:convert(k)
for k, v in want.items()}
def sanitize(pred, kwargs):
if pred == 'isDefinedBy' and kwargs['depth'] > 1:
return abort(400, 'isDefinedBy not allowed for queries with depth > 1.')
examples = (
('Brain parts', hpp, 'UBERON:0000955', '?direction=OUTGOING'), # FIXME direction=lol doesn't cause issues...
('Brain parts alt', po, 'UBERON:0000955'),
('Brain parts alt flat', po, 'UBERON:0000955', '?flatten=true'),
('Anatomical entities', a, 'UBERON:0001062'),
('Cell parts', a, 'GO:0044464'),
('Cells', a, 'SAO:1813327414'),
('Proteins', a, 'SAO:26622963'),
('GPCRs', a, 'NIFEXT:5012'),
('Mulitmeric ion channels', a, 'NIFEXT:2502'),
('Monomeric ion channels', a, 'NIFEXT:2500'),
('Diseases', a, 'DOID:4'),
('Vertebrata', a, 'NCBITaxon:7742', '?depth=40'),
('Metazoa', a, 'NCBITaxon:33208', '?depth=40'),
('Rodentia', a, 'NCBITaxon:9989'),
('Insecta', a, 'NCBITaxon:50557', '?depth=40'),
('Neurotransmitters', hr, 'CHEBI:25512'),
('Neurotransmitters', a, 'NLXMOL:100306'),
('IRIs ok for roots', a, 'http://uri.neuinfo.org/nif/nifstd/nlx_mol_100306'),
('Provenance', 'isDefinedBy',
'http://ontology.neuinfo.org/NIF/ttl/generated/chebislim.ttl', '?depth=1'),
)
extra_examples = (
('No tech?', a, 'ilxtr:technique'),
('Cell septum', a, 'GO:0044457'),
('Old NIFGA part of', hpp, 'BIRNLEX:796'),
('Cereberal cortex parts', po, 'UBERON:0002749'),
('Broken iri of borken curie', a, 'http://uri.interlex.org/paxinos/uris/rat/labels/'),
('Broken curie', a, 'PAXRAT:'),
)
file_examples = (
('Resources', a, 'NLXRES:20090101', 'ttl/resources.ttl'),
('Staging branch', a, 'PAXRAT:',
'ttl/generated/parcellation/paxinos-rat-labels.ttl', '?branch=staging'),
('Restriction example', hpp, 'UBERON:0000955',
'ttl/bridge/uberon-bridge.ttl', '?direction=OUTGOING&restriction=true'),
)
dynamic_examples = (
('Shortest path', 'shortestSimple',
'?start_id=UBERON:0000955&end_id=UBERON:0001062&relationship=subClassOf'),
('Shortest path table', 'shortestSimple',
'?start_id=UBERON:0000955&end_id=UBERON:0001062&relationship=subClassOf&format=table'),
('Stomach parts', 'prod/sparc/organParts/FMA:7148', None),
('Parc graph', 'prod/sparc/parcellationGraph', '?direction=INCOMING'),
('Parc arts', 'prod/sparc/parcellationArtifacts/NCBITaxon:10116', '?direction=INCOMING'),
('Parc roots', 'prod/sparc/parcellationRoots/NCBITaxon:10116', '?direction=INCOMING'),
('Parc region roots', 'prod/sparc/parcellationRoots/NCBITaxon:10116/UBERON:0000955', '?direction=INCOMING'),
)
demo_examples = (
#('All connectivity', '/trees/sparc/demos/isan2019/flatmap-queries'), # broken due to scigraph segfault for json return
('Neuron connectivity', '/trees/sparc/demos/isan2019/neuron-connectivity'),
)
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):
if '/neru-' in path:
process = lambda x, blob: apinat_deblob(blob, remove_converge=True)[0]
else:
process = simplify
return sparc_dynamic(data_sgd, data_sgc, path, wgb, process)
@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
# for now hardcode
test_terms = [OntId('UBERON:0001759'),
OntId('UBERON:0000388'),
OntId('UBERON:0001629'),
OntId('UBERON:0001723'),
OntId('UBERON:0001737'),
OntId('UBERON:0001930'),
OntId('UBERON:0001989'),
OntId('UBERON:0001990'),
OntId('UBERON:0002024'),
OntId('UBERON:0002440'),
OntId('UBERON:0003126'),
OntId('UBERON:0003708'),
OntId('UBERON:0009050'),
OntId('UBERON:0011326'),
OntId('FMA:6240'),
OntId('FMA:6243'),
OntId('FMA:6474'),
OntId('FMA:6579'),
OntId('ILX:0738293'),
# # #
OntId('UBERON:0000388'),
OntId('UBERON:0000988'),
OntId('UBERON:0001103'),
OntId('UBERON:0001508'),
OntId('UBERON:0001629'),
OntId('UBERON:0001649'),
OntId('UBERON:0001650'),
OntId('UBERON:0001723'),
OntId('UBERON:0001737'),
OntId('UBERON:0001759'),
OntId('UBERON:0001884'),
OntId('UBERON:0001891'),
OntId('UBERON:0001896'),
OntId('UBERON:0001930'),
OntId('UBERON:0001990'),
OntId('UBERON:0002024'),
OntId('UBERON:0002126'),
OntId('UBERON:0002440'),
OntId('UBERON:0003126'),
OntId('UBERON:0003708'),
OntId('UBERON:0005807'),
OntId('UBERON:0006457'),
OntId('UBERON:0006469'),
OntId('UBERON:0006470'),
OntId('UBERON:0006488'),
OntId('UBERON:0006489'),
OntId('UBERON:0006490'),
OntId('UBERON:0006491'),
OntId('UBERON:0006492'),
OntId('UBERON:0006493'),
OntId('UBERON:0009009'),
OntId('UBERON:0009918'),
OntId('UBERON:0011326'),
OntId('FMA:67532'),
OntId('FMA:7643'),
OntId('ILX:0485722'),
OntId('ILX:0505839'),
OntId('ILX:0725956'),
OntId('ILX:0731873'),
OntId('ILX:0736966'),
OntId('ILX:0738279'),
OntId('ILX:0738290'),
OntId('ILX:0738291'),
OntId('ILX:0738292'),
OntId('ILX:0738293'),
OntId('ILX:0738308'),
OntId('ILX:0738309'),
OntId('ILX:0738312'),
OntId('ILX:0738313'),
OntId('ILX:0738315'),
OntId('ILX:0738319'),
OntId('ILX:0738324'),
OntId('ILX:0738325'),
OntId('ILX:0738342'),
OntId('ILX:0738371'),
OntId('ILX:0738372'),
OntId('ILX:0738373'),
OntId('ILX:0738374')]
class fakeRequest:
args = {}