def fromYaml(cls, in_path):
in_path = aug.RepoPath(in_path).resolve()
with open(in_path, 'rt') as f:
blob = yaml.safe_load(f)
if 'include' in blob:
orgs = [
OntResGit(path=aug.RepoPath(subblob['path']),
ref=subblob['ref']) for subblob in blob['include']
]
else:
orgs = [
OntResGit(path=aug.RepoPath(subblob['path']),
ref=subblob['ref']) for subblob in blob['paths']
]
if not orgs:
raise ValueError(f'orgs is epty for {in_path}')
referenceIndex = blob['referenceIndex']
namespaces = blob['namespaces']
if isinstance(namespaces, str):
namespaces = namespaces.split(' ')
snchf = cls(orgs=orgs,
namespaces=namespaces,
referenceIndex=referenceIndex)
return cls(graph=snchf.populate(OntGraph()))
def methods_sneech():
# TODO the sneech files ?
org_m = OntResGit(methods)
org_h = OntResGit(helper)
org_c = OntResGit(core)
with org.repo.getRef('methods'):
pass
def methods_mapping():
from pyontutils.namespaces import TEMP, ilxtr, tech
from nifstd_tools import methods as m
import rdflib
# TODO add this to ibnode tests
_before = OntResGit(methods,
ref='8c30706cbc7ccc7443685a34dec026e8afbbedd1')
after = OntResGit(
methods,
ref='860c88a574d17e0d427c1101fa1947b730b613a9') # renaming commit
before = OntResGit(after.path, ref=after.ref + '~1')
assert before.graph.identity() == _before.graph.identity()
bg = before.graph
ag = after.graph
_, local = next(ag[:ilxtr.indexNamespace:])
local = rdflib.Namespace(str(local))
T0 = TEMP['0']
l0 = local['0']
b = OntGraph().populate_from_triples(bg.subjectGraph(T0))
a = OntGraph().populate_from_triples(ag.subjectGraph(l0))
b.debug()
a.debug()
it = b.subjectIdentity(T0)
il = a.subjectIdentity(l0)
assert it == il
assert it in (il, )
assert il in (it, ) # (it,) ni il # SIGH
assert it in {il: None}
assert il in {it: None}
r = b.subjectsRenamed(a)
renamed = before.graph.subjectsRenamed(after.graph)
assert (len(renamed) - 1 == max([
int(v.rsplit('/', 1)[-1]) for v in renamed.values()
if v != ilxtr.Something
]))
(OntGraph(
namespace_manager=after.graph.namespace_manager).populate_from_triples(
before.graph.subjectsRenamedTriples(after.graph)).debug())
return renamed
index_graph = OntGraph(path=olr / 'ttl/generated/index-methods.ttl')
# FIXME either use or record for posterity the commits where these
# transformations were run rather than pointing to the branch name
with org.repo.getRef('methods'):
input_graph = org.graph
output_graph = input_graph.mapTempToIndex(index_graph, TEMP, m.local)
a, r, c = output_graph.subjectsChanged(input_graph)
index_graph.write()
def test():
snchf = SnchFile.fromYaml('../test/sneech-file.yaml')
snchf.writeTtl(aug.RepoPath('../test/rando-sneech-ttl.ttl').resolve())
rp = aug.RepoPath(auth.get_path('ontology-local-repo'))
wrangler = SneechWrangler(aug.RepoPath('~/git/sneechenator').expanduser())
dir_snchn = wrangler.dir_process / 'test-sneechening'
if not dir_snchn.exists(): # FIXME bad workflow
dir_snchn.mkdir()
path_index = wrangler.path_index(snchf.index)
if not path_index.exists():
path_index = wrangler.new_index(
snchf.index) # FIXME move inside Sneechenator? or no
path_index.commit_from_working_tree(f'new index {snchf.index}')
org_index = OntResGit(path_index)
expanded = snchf.write(dir_snchn) # TODO commit
expanded.commit_from_working_tree(f'expanded snch file')
sncher = Sneechenator(org_index, snchf.namespaces, snchf.orgs)
#sncher.preSneechUpon(dir_snchn)
rg, maybe_sneeches = sncher.sneechReviewGraph()
# commit here I think ?
# consider using ilxtr.maybeHasIlxId ?
# TODO modified maybe_sneeches file + maybe list -> update list
breakpoint()
def _parse_graph(self, graph):
# there should be only one of each of these
graph.debug()
gen = graph[:rdf.type:snchn.SneechFile]
s = next(gen)
try:
next(gen)
raise ValueError('MORE THAN ONE SNEECH FILE IN A SINGLE FILE!')
except StopIteration:
pass
self.identity_metadata = graph.subjectIdentity(
s) # FIXME align naming with idlib when we get there
self.referenceIndex = next(graph[s:snchn.referenceIndex:])
self.namespaces = list(graph[s:snchn.namespaces:])
_orgs = []
orgs = []
for bn in graph[s:snchn['include']:]:
try:
path = aug.RepoPath(next(graph[bn:snchn.path:]))
except StopIteration:
iri = next(graph[bn:snchn.iri:])
for string_path in graph[iri:snchn.hasLocalPath:]:
path = aug.RepoPath(string_path).resolve()
if path.exists():
break
else:
# TODO OntResIri failover ??? probalby not
raise ValueError(f'could not find local path for {iri}')
ref = next(graph[bn:snchn.ref:])
# TODO if there is a bound name use that and move the raw paths
# to annotations for local sourcing of that file that can be
# edited manually if needs be
org = OntResGit(path, ref)
dorg = org.asDeRef()
_orgs.append(org)
orgs.append(dorg)
self._orgs = _orgs
self.orgs = orgs
def npokb_mapping():
index_graph = OntGraph(path=auth.get_path('ontology-local-repo') /
'ttl/generated/neurons/npokb-index.ttl')
if index_graph.path.exists():
index_graph.parse()
# testing
index_graph.bind('npokb', npokb)
#[index_graph.add((npokb[str(i)], rdf.type, owl.Class)) for i in range(1, 11)]
#[index_graph.add((npokb[str(i)], ilxtr.hasTemporaryId, TEMP[str(i)])) for i in range(1, 11)]
ios = []
for eff in (
'common-usage-types',
'huang-2017',
'markram-2015',
'allen-cell-types',
):
# FIXME if the index id is already being used it is still added as a temp id incorrectly
path = auth.get_path(
'ontology-local-repo') / f'ttl/generated/neurons/{eff}.ttl'
org = OntResGit(
path, ref='HEAD'
) # HEAD is default but just for clarity set it explicitly here
prev_graph = org.graph
input_graph = OntGraph(path=path)
input_graph.parse()
mapped_graph = input_graph.mapStableIdentifiers(
prev_graph, ilxtr.origLabel)
output_graph = mapped_graph.mapTempToIndex(index_graph, npokb, TEMP)
ios.append((mapped_graph, output_graph))
mapped_graph, output_graph = ios[0]
a, r, c = output_graph.subjectsChanged(mapped_graph)
index_graph.write()
[o.write() for i, o, in ios] # when ready
#from sparcur.paths import Path
#Path(index_graph.path).xopen()
breakpoint()