def graph(self):
if not hasattr(self, '_graph'):
self._graph = populateFromJsonLd(OntGraph(), self.asJsonLd())
OntCuries.populate(self._graph)
self.populateHeader(self._graph)
return self._graph
def graph(self):
g = OntGraph()
OntCuries.populate(g)
self.populate(g)
g.bind('local', self.context)
g.bind('apinatomy', readable) # FIXME populate from store
g.bind('elements', elements)
return g
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
def populate(self, graph=None):
""" Populate a graph, or if no graph is provided
populate a new empty graph from the current
content. (Also useful for debug) """
if graph is None:
graph = OntGraph()
[graph.add(t) for t in self.triples]
OntCuries.populate(graph)
return graph
def import_tree(graph, ontologies, **kwargs):
for ontology in ontologies:
thisfile = Path(ontology).name
print(thisfile)
OntCuries.populate(graph)
j = graph.asOboGraph('owl:imports', restriction=False)
try:
t, te = creatTree(*Query(f'NIFTTL:{thisfile}', 'owl:imports', 'OUTGOING', 30), json=j, prefixes=dict(graph.namespace_manager), **kwargs)
#print(t)
yield t, te
except KeyError:
print(tc.red('WARNING:'), 'could not find', ontology, 'in import chain') # TODO zap onts w/o imports
def fromRdf(cls, graph):
iri = graph.boundIdentifier
context = rdflib.Namespace(iri + '/ids/')
# TODO removing things from the trie is not implemented ...
#d = OntCuries._dict
#d.pop('local', None)
#d['local'] = str(context)
#OntCuries.reset()
OntCuries({'local': str(context)})
_, id = iri.rsplit('/', 1)
resources = {}
for s in graph[:rdf.type:owl.NamedIndividual]:
for element in graph[s:rdf.type]:
if element != owl.NamedIndividual:
_, class_ = element.rsplit('/', 1)
resource = getattr(cls, class_).fromRdf(s, graph, context)
# FIXME we should really keep the internal representation
# around instead of just throwing it away
resources[resource.id] = resource.blob
for s in graph[:rdf.type:owl.Class]:
# FIXME s rdf:type elements:External ??
resource = External.fromRdf(s, graph, context)
resources[resource.id] = resource.blob
map = {'id': id, 'resources': resources}
return cls(map, {})
def normalize_prefixes(graph, curies):
new_graph = OntGraph()
oc = OntCuries.new()
curies.pop('', None)
curies['rdf'] = str(rdf)
curies['rdfs'] = str(rdfs)
oc(curies)
oc.populate(new_graph)
[new_graph.add(t) for t in graph]
return new_graph
#!/usr/bin/env python3.7
from pathlib import Path
import rdflib
from pyontutils.core import Ont, OntGraph
from pyontutils.config import auth
from pyontutils.sheets import Sheet
from pyontutils.namespaces import owl, rdf, rdfs, ilxtr, NIFRID, OntCuries, skos, makeNamespaces
from neurondm import OntTerm, OntId
from neurondm.models.allen_cell_types import AllenCellTypes
from neurondm.core import log
log = log.getChild('indicators')
OntCuries(AllenCellTypes.prefixes) # FIXME BAD
OntCuries({'TEMPIND': 'http://uri.interlex.org/temp/uris/phenotype-indicators/'})
NIFRAW, NIFTTL = makeNamespaces('NIFRAW', 'NIFTTL')
a = rdf.type
# TODO the proper way to do this in the future will be to write a populateIndicators
# for Neuron and Phenotype
class PhenotypeIndicators(Sheet):
name = 'phenotype-indicators'
sheet_name = 'indicators'
@property
def things(self):
def process(k, v):
sparc.middleName,
sparc.lastName,
xsd.minInclusive,
xsd.maxInclusive,
TEMP.hasValue,
TEMP.hasUnit,
))
OntCuries({
'orcid': 'https://orcid.org/',
'ORCID': 'https://orcid.org/',
'DOI': 'https://doi.org/',
'ror': 'https://ror.org/',
'dataset': 'https://api.blackfynn.io/datasets/N:dataset:',
'package': 'https://api.blackfynn.io/packages/N:package:',
'user': '******',
'unit': str(unit),
'dim': str(dim),
'asp': str(asp),
'tech': str(tech),
'awards': str(TEMP['awards/']),
'sparc': str(sparc),
})
class OntId(OIDB):
pass
#def atag(self, **kwargs):
#if 'curie' in kwargs:
#kwargs.pop('curie')
#return hfn.atag(self.iri, self.curie, **kwargs)
def new_index(self, referenceIndex, *, commit=True):
""" reference hosts have a single incrementing primary key index
to which everything is mapped
in theory these indexes could also be per 'prefix' aka
the sandboxed uri path or external uri path to which
something is mapped I don't see any reason not to do this
for this kind of implementation since a regular pattern
can be develop
"""
'''
QUESTION: do we force a remapping of external id sequences
into uris/ first? this seems like a bad idea? or rather,
it is actually a good idea, but it will have to be done with
a pattern based redirect instead of an actual materialization
the alternative is to do what ontobee does and pass the external
iri as a query parameter ... hrm tradoffs, well we certainly
can't make a nice /uberon/uris/obo/{UBERON_} folder if we include
the whole uri ... so this seems a reasonable tradeoff
http://purl.obolibrary.org/obo/ can wind up being mapped into
multiple uri spaces ... /obo/uris/obo/ would seem to make more sense
but how to indicate that other organizations/projects map there ...
/uberon/uris/obo/UBERON_ could indicate the latest sequence
ah, and of course in theory this gets us out of the very annoying
situation where /uberon/uris/obo/UBERON_ really IS different than
/doid/uris/obo/UBERON_ for some identifiers (sigh) and if they are
all mapped and masking based on presence then we can detect the issues
HOWEVER how do we enforce that in reality the _mapping_ is all to
/obo/uris/obo/ ??
'''
path = self.path_index(referenceIndex)
rrp = path.repo_relative_path
s = sncho[rrp.with_suffix('').as_posix()] # TODO check ownership
if path.exists():
raise FileExistsError(path)
g = OntGraph(path=path)
OntCuries.populate(g)
# TODO these are really identified by the follow:
# base/readable/
# {group}/uris/
# base/ontologies/
# {group}/ontologies/uris/
pos = (
(rdf.type, snchn.IndexGraph),
(rdfs.label, rdflib.Literal(f'IndexGraph for {referenceIndex}')),
(snchn.referenceIndex, rdflib.Literal(referenceIndex)), # TODO HRM
#(snchn.indexRemote, )
)
for po in pos:
g.add((s, *po)) # FIXME
g.path.parent.mkdir(parents=True)
g.write()
if commit:
path.commit(f'add new index for {referenceIndex}')
return path
xsd.minInclusive,
xsd.maxInclusive,
TEMP.hasValue,
TEMP.hasUnit,))
OntCuries({'orcid':'https://orcid.org/',
'ORCID':'https://orcid.org/',
'DOI':'https://doi.org/',
'ror':'https://ror.org/',
'pio.api': 'https://www.protocols.io/api/v3/protocols/',
'dataset':'https://api.blackfynn.io/datasets/N:dataset:',
'package':'https://api.blackfynn.io/packages/N:package:',
'user':'******',
'bibo': 'http://purl.org/ontology/bibo/', # crossref
'prism.basic': 'http://prismstandard.org/namespaces/basic/2.1/', # crossref
'unit': str(unit),
'dim': str(dim),
'asp': str(asp),
'protcur': 'https://uilx.org/tgbugs/u/protcur/',
'hyp-protcur': 'https://uilx.org/tgbugs/u/hypothesis/protcur/',
'aspect-raw': 'https://uilx.org/tgbugs/u/aspect-raw/',
'verb': 'https://uilx.org/tgbugs/u/executor-verb/',
'fuzzy': 'https://uilx.org/tgbugs/u/fuzzy-quantity/',
'tech': str(tech),
'awards':str(TEMP['awards/']),
'sparc':str(sparc),})
def curies_runtime(base):
""" base is .e.g https://api.blackfynn.io/datasets/{dataset_id}/ """
elements = rdflib.Namespace('https://apinatomy.org/uris/elements/')
readable = rdflib.Namespace('https://apinatomy.org/uris/readable/')
# add apinatomy:Graph to ttlser topClasses
tc = CustomTurtleSerializer.topClasses
if readable.Graph not in tc:
sec = CustomTurtleSerializer.SECTIONS
CustomTurtleSerializer.topClasses = [readable.Graph] + tc
CustomTurtleSerializer.SECTIONS = ('', ) + sec
# add apinatomy:Graph as a header section marker
OntGraph.metadata_type_markers.append(readable.Graph)
OntCuries({
'apinatomy': str(readable),
'elements': str(elements), # FIXME guranteed name collisions ...
# also just read this from the embedded local conventions
})
class NoIdError(Exception):
""" blob has no id """
apinscm = sc.ApiNATOMYSchema()
def make_classes(schema):
types = {}
def ref_to_list(ref):
sparc.lastName,
xsd.minInclusive,
xsd.maxInclusive,
TEMP.hasValue,
TEMP.hasUnit,
))
OntCuries({
'orcid': 'https://orcid.org/',
'ORCID': 'https://orcid.org/',
'DOI': 'https://doi.org/',
'ror': 'https://ror.org/',
'dataset': 'https://api.blackfynn.io/datasets/N:dataset:',
'package': 'https://api.blackfynn.io/packages/N:package:',
'user': '******',
'bibo': 'http://purl.org/ontology/bibo/', # crossref
'prism.basic':
'http://prismstandard.org/namespaces/basic/2.1/', # crossref
'unit': str(unit),
'dim': str(dim),
'asp': str(asp),
'tech': str(tech),
'awards': str(TEMP['awards/']),
'sparc': str(sparc),
})
class OntId(OIDB):
pass
#def atag(self, **kwargs):
#if 'curie' in kwargs:
#kwargs.pop('curie')
elements = rdflib.Namespace('https://apinatomy.org/uris/elements/')
readable = rdflib.Namespace('https://apinatomy.org/uris/readable/')
# add apinatomy:Graph to ttlser topClasses
tc = CustomTurtleSerializer.topClasses
if readable.Graph not in tc:
sec = CustomTurtleSerializer.SECTIONS
CustomTurtleSerializer.topClasses = [readable.Graph] + tc
CustomTurtleSerializer.SECTIONS = ('', ) + sec
# add apinatomy:Graph as a header section marker
OntGraph.metadata_type_markers.append(readable.Graph)
OntCuries({
'apinatomy': str(readable),
'elements': str(elements), # FIXME guranteed name collisions ...
'PMID': 'https://www.ncbi.nlm.nih.gov/pubmed/',
# also just read this from the embedded local conventions
})
class NoIdError(Exception):
""" blob has no id """
apinscm = sc.ApiNATOMYSchema()
def make_classes(schema):
types = {}
def ref_to_list(ref):
def parse_workflow():
# FIXME TODO these states should probably be compiled down to numbers???
docs = Path(__file__).parent.absolute().resolve().parent / 'docs'
rridpath = docs / 'workflow-rrid.graphml'
paperpath = docs / 'workflow-paper-id.graphml'
cgraph = ConjunctiveGraph()
gt.WorkflowMapping(rridpath.as_posix()).graph(cgraph)
gt.PaperIdMapping(paperpath.as_posix(), False).graph(cgraph)
write(cgraph, '/tmp/workflow.ttl')
predicates = set(cgraph.predicates())
OntCuries({cp:str(ip) for cp, ip in cgraph.namespaces()})
OntCuries({'RRID': 'https://scicrunch.org/resolver/RRID:',
'DOI': 'https://doi.org/',
'PMID': 'https://www.ncbi.nlm.nih.gov/pubmed/'})
hg = makeGraph('', graph=cgraph)
short = sorted(hg.qname(_) for _ in predicates)
wf.hasTag
wf.hasReplyTag
wf.hasTagOrReplyTag
wf.hasOutputTag
#if type isa wf.tag
tag_types = set(cgraph.transitive_subjects(rdfs.subClassOf, wf.tag))
tag_tokens = {tagType:sorted(set(t for t in cgraph.transitive_subjects(rdf.type, tagType)
if t != tagType))
for tagType in tag_types}
has_tag_types = set(cgraph.transitive_subjects(rdfs.subPropertyOf, wf.hasTagOrReplyTag))
has_tag_types.add(wf.hasOutputTag)
has_next_action_types = set(cgraph.transitive_subjects(rdfs.subPropertyOf, wf.hasOutput))
has_next_action_types.add(wf.hasNextStep)
terminals = sorted(tag
for ttype in tag_types
if ttype != wf.tagScibot # scibot is not 'terminal' for this part
for tag in cgraph[:rdf.type:ttype]
if not isinstance(tag, BNode)
and not any(o for httype in has_tag_types
for o in cgraph[tag:httype]))
endpoints = sorted(endpoint
for endpoint in cgraph[:rdf.type:wf.state]
if not isinstance(endpoint, BNode)
and not any(o for hnatype in has_next_action_types
for o in cgraph[endpoint:hnatype]))
complicated = sorted(a_given_tag
for tt in tag_types
for a_given_tag in cgraph[:rdf.type:tt]
if not isinstance(a_given_tag, BNode)
and not [successor_tag
for htt in has_tag_types
for successor_tag in chain(t
for t in cgraph[a_given_tag:htt]
#if not isinstance(t, BNode)
,
# we don't actually need this for terminals
# we will need it later
#(t for b in cgraph[a_given_tag:htt]
#if isinstance(b, BNode)
#for listhead in cgraph[b:owl.oneOf]
#for t in unlist(listhead, cgraph)),
)])
def topList(node, g):
for s in g[:rdf.rest:node]:
yield s
def getLists(node, g):
for linker in g[:rdf.first:node]:
top = None
for top in g.transitiveClosure(topList, linker):
pass
if top:
yield top
else:
yield linker
def getIsTagOf(node, g):
for htt in has_tag_types:
for parent_tag in g[:htt:node]:
yield parent_tag
def getIsOneOfTagOf(node, g):
for list_top in getLists(node, g):
for linker in g[:owl.oneOf:list_top]:
for parent_tag, _ in g[::linker]:
yield parent_tag
def getPreviousTag(node, g): # not quite what we need
yield from getIsOneOfTagOf(node, g)
yield from getIsTagOf(node, g)
def getTagChains(node, g, seen=tuple()):
# seen to prevent recursion cases where
# taggning can occur in either order e.g. PMID -> DOI
#print(tc.red(repr(OntId(node)))) # tc.red(OntId(node)) does weird stuff O_o
parent_tag = None
for parent_tag in chain(getIsOneOfTagOf(node, g),
getIsTagOf(node, g)):
if parent_tag in seen:
parent_tag = None
continue
ptt = next(g[parent_tag:rdf.type])
#if ptt in tag_types:
for pchain in getTagChains(parent_tag, g, seen + (node,)):
if ptt in tag_types:
out = parent_tag, *pchain
else:
out = pchain
yield out
if not ptt and not out:
parent_tag = None
if not parent_tag:
yield tuple()
def getInitiatesAction(node, g):
for action in g[:wf.initiatesAction:node]:
yield action
def getIsOneOfOutputOf(node, g):
for list_top in getLists(node, g):
for linker in g[:owl.oneOf:list_top]:
for hot in has_next_action_types:
for parent_thing in g[:hot:linker]:
yield parent_thing
def getActionChains(node, g):
parent_action = None
for parent_action in chain(getIsOneOfOutputOf(node, g), # works for actions too
getInitiatesAction(node, g)):
for pchain in getActionChains(parent_action, g): # NOTE may also be a tag...
out = parent_action, *pchain
#print(tuple(hg.qname(o) for o in out))
yield out
if not parent_action:
yield tuple()
def getRestSubjects(predicate, object, g):
""" invert restriction """
rsco = cmb.Restriction(rdfs.subClassOf)
for rt in rsco.parse(graph=g):
if rt.p == predicate and rt.o == object:
yield from g.transitive_subjects(rdfs.subClassOf, rt.s)
annoParts = list(getRestSubjects(wf.isAttachedTo, wf.annotation, cgraph))
partInstances = {OntId(a):set(t if isinstance(t, BNode) else OntId(t)
for t in cgraph.transitive_subjects(rdf.type, a)
if not isinstance(t, BNode) and t != a)
for a in annoParts}
_endpoint_chains = {OntId(endpoint):[[OntId(endpoint)] + [OntId(e) for e in chain]
for chain in getActionChains(endpoint, cgraph)]
for endpoint in endpoints}
#print([hg.qname(e) for e in endpoints])
#print([print([hg.qname(c) for c in getActionChains(endpoint, cgraph) if c])
#for endpoint in endpoints
#if endpoint])
#_ = [print(list(getActionChains(e, cgraph)) for e in endpoints)]
#return
wat = cgraph.transitiveClosure(getPreviousTag, RRIDCUR.Duplicate)
wat = list(wat)
#def invOneOf(tag, g):
fake_chains = {hg.qname(terminal):
[hg.qname(c)
for c in cgraph.transitiveClosure(getPreviousTag, terminal)]
for terminal in terminals}
def make_chains(things, getChains):
return {OntId(thing):[[OntId(thing)] + [OntId(e) for e in chain]
for chain in getChains(thing, cgraph)]
for thing in things
#if not print(thing)
}
def print_chains(thing_chains):
print('\nstart from beginning')
print('\n'.join(sorted(' -> '.join(hg.qname(e) for e in reversed(chain))
for chains in thing_chains.values()
for chain in chains)))
print('\nstart from end')
print('\n'.join(sorted(' <- '.join(e.curie for e in chain)
for chains in thing_chains.values()
for chain in chains)))
def valid_tagsets(all_chains):
# not the most efficient way to do this ...
transitions = defaultdict(set)
for end, chains in all_chains.items():
for chain in chains:
valid = set()
prior_state = None
for element in reversed(chain):
valid.add(element)
state = frozenset(valid)
transitions[prior_state].add(state)
prior_state = state
return {s:frozenset(n) for s, n in transitions.items()}
endpoint_chains = make_chains(endpoints, getActionChains)
#endpoint_transitions = valid_transitions(endpoint_chains) # not the right structure
print_chains(endpoint_chains)
terminal_chains = make_chains(terminals, getTagChains)
print_chains(terminal_chains)
tag_transitions = valid_tagsets(terminal_chains)
terminal_tags_to_endpoints = 'TODO'
def printq(*things):
print(*(OntId(t).curie for t in things))
from pprint import pprint
def get_linkers(s, o, g, linkerFunc): # FIXME not right
for p in g[s::o]:
yield p
for l in linkerFunc(o, g):
#print(tc.blue(f'{OntId(s).curie} {l if isinstance(l, BNode) else OntId(l).curie}'))
for p in g[s::l]:
#print(tc.red(f'{s} {l} {o} {p}'))
yield p
return
linkers = set(l for l in g.transitiveClosure(linkerFunc, o))
for p, o in g[s::]:
if o in linkers:
yield p
def edge_to_symbol(p, rev=False):
if p == wf.initiatesAction:
return '<<' if rev else '>>'
elif p == wf.hasReplyTag:
return '<' if rev else '>'
elif p == wf.hasTagOrReplyTag:
return '<=' if rev else '=>'
elif p == wf.hasOutputTag:
return '-<-' if rev else '->-'
else:
return '<??' if rev else '??>'
def chain_to_typed_chain(chain, g, func):
# duh...
#pprint(chain)
for s, o in zip(chain, chain[1:]):
# TODO deal with reversed case
s, o = s.u, o.u
p = None
#print(s, o)
printq(s, o)
for p in get_linkers(s, o, g, func):
#print(tc.yellow(p))
#yield (s, edge_to_symbol(p), o)
yield from (s, edge_to_symbol(p), o)
if not p:
for rp in get_linkers(o, s, g, func):
print(tc.blue(rp))
yield from (s, edge_to_symbol(rp, rev=True), o)
def tchains(thing_chains, func):
return sorted([OntId(e).curie if isinstance(e, URIRef) else e
for e in chain_to_typed_chain(list(reversed(chain)), cgraph, func)]
for chains in thing_chains.values()
for chain in chains)
def getLinkers(node, g):
for list_top in getLists(node, g):
for linker in g[:owl.oneOf:list_top]:
yield linker
def allSubjects(object, graph):
yield from (s for s, p in graph[::object])
yield from getLinkers(object, graph)
print()
ttc = tchains(terminal_chains, allSubjects)
tec = tchains(endpoint_chains, allSubjects)
pprint(ttc)
pprint(tec)
valid_tagsets = frozenset((t for s in tag_transitions.values() for t in s))
tts = valid_tagsets - frozenset(tag_transitions)
endtype = 'TODO' #
tt = {}
for endtype, chains in endpoint_chains.items():
for *_chain, tag in chains:
if _chain:
next_thing = _chain[-1]
for ets in tts:
if tag in ets:
tt[ets] = next_thing
terminal_tagsets = tt
#[print(wat) for wat in terminal_chains.values()]
#pprint(terminal_chains)
return tag_types, tag_tokens, partInstances, valid_tagsets, terminal_tagsets, tag_transitions
ilxtr.hasCircuitRolePhenotype)
"""
http://ontology.neuinfo.org/trees/query/swanr:hasPart1/SWAN:1/ttl/generated/swanson.ttl?restriction=true&depth=40&direction=OUTGOING
human cns gray matter regions
http://ontology.neuinfo.org/trees/query/swanr:hasPart3/SWAN:1/ttl/generated/swanson.ttl?restriction=true&depth=40&direction=OUTGOING
surface features, handy to have around
http://ontology.neuinfo.org/trees/query/swanr:hasPart5/SWAN:629/ttl/generated/swanson.ttl?restriction=true&depth=40&direction=OUTGOING
"""
sgraph = rdflib.Graph().parse(
(Neuron.local_base / 'ttl/generated/swanson.ttl').as_posix(), format='ttl')
# restriction.parse(sgraph) # FIXME this breaks with weird error message
OntCuries({**graphBase.prefixes, **PREFIXES})
rests = [r for r in restriction.parse(graph=sgraph) if r.p == swanr.hasPart3]
#restriction = Restriction2(rdfs.subClassOf)
class LocalGraphService(ontquery.services.BasicService):
def __init__(self, graph):
self.graph = graph
super().__init__()
def query(self,
curie=None,
iri=None,
label=None,
term=None,
search=None,