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 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 _todo(utr):
# real output
glb = auth.get_path('git-local-base')
uberon_edit = aug.RepoPath(
glb) / 'NOFORK/uberon/src/ontology/uberon-edit.obo'
of = oio.OboFile(path=uberon_edit, strict=False)
utr.submit_to_obofile(of, 'UBERON', uberon_id_range)
of.write(overwrite=True, version=oio.OBO_VER_ROBOT)
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 __init__(self, path_repo):
# TODO make sneech path configurable and passable via command line etc.
rpath = aug.RepoPath(path_repo)
if not rpath.exists():
self.rp_sneech = rpath
self.rp_sneech.init()
readme = self.rp_sneech / 'README.org'
with open(readme, 'wt') as f:
f.write('#+title: Sneechenator\n\nTrack the stars for your sneeches!')
readme.commit_from_working_tree('first commit')
self.dir_index.mkdir()
self.dir_process.mkdir()
else:
self.rp_sneech = rpath.working_dir
def main():
#ori = OntResIri('https://alt.olympiangods.org/sparc/ontologies/community-terms.ttl')
ori = OntResIri(
'http://localhost:8515/sparc/ontologies/community-terms.ttl')
rdfl = oq.plugin.get('rdflib')(ori.graph, OntId)
OntTerm.query_init(rdfl)
utr = UpstreamTermRequests()
_todo(utr)
return
# test output
tof = oio.OboFile()
utr.submit_to_obofile(tof, 'FIXME', (0, float('inf')))
tof.write(path=aug.RepoPath('/tmp/uberon-new-terms.obo'), overwrite=True)
ori_uberon = OntResIri('http://purl.obolibrary.org/obo/uberon.owl')
ori_uberon_meta = ori_uberon.metadata() # doap:GitRepository
breakpoint()
return
def metadata_events(self):
""" metadata about dois from the crossref events api """
events_endpoint = 'https://api.eventdata.crossref.org/v1/events'
rp = aug.RepoPath(__file__)
try:
email = rp.repo.config_reader().get_value('user', 'email')
log.warning(
f'your email {email} is being sent to crossref as part of the friendly way to use their api'
)
mailto = f'mailto={email}'
except aug.exceptions.NotInRepoError:
# TODO failover to the git repo api?
mailto = '*****@*****.**'
resp_obj = requests.get(
f'{events_endpoint}?{mailto}&obj-id={self.handle}')
resp_sub = requests.get(
f'{events_endpoint}?{mailto}&subj-id={self.handle}')
# TODO if > 1000 get the rest using the pagination token
yield from resp_sub.json()['message']['events']
yield from resp_obj.json()['message']['events']
this_repo.checkout_diff_tracked(),
)
else:
post_load = lambda: None
post_main = lambda: None
do_mains = True
default_dir = aug.AugmentedPath(__file__).parent
_test_ttl = (default_dir / 'graphload-test.ttl')
test_ttl = _test_ttl.as_posix()
_test_owl = (default_dir / 'owl-test.ttl')
test_owl = _test_owl.as_posix()
_temp_git = aug.RepoPath(temp_path) / 'git-test'
temp_git = _temp_git.as_posix()
nsmethodsobo = (glb /
'methodsOntology/source-material/ns_methods.obo').as_posix()
### build mains
mains = {
'scigraph':
None,
'combinators':
None,
'hierarchies':
None,
'closed_namespaces':
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()
olr = aug.RepoPath(auth.get_path('ontology-local-repo'))
ttl = olr / 'ttl'
methods = ttl / 'methods.ttl'
helper = ttl / 'methods-helper.ttl'
core = ttl / 'methods-core.ttl'
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(
import pprint
import unittest
import augpathlib as aug
from sparcur.datasets import (
Tabular,
DatasetDescriptionFile,
SubmissionFile,
SubjectsFile,
SamplesFile,
remove_rule,
)
from sparcur import pipelines as pipes
from sparcur import exceptions as exc
from .common import examples_root, template_root, project_path, temp_path, ddih
template_root = aug.RepoPath(template_root)
class TestTabular(unittest.TestCase):
def setUp(self):
self.pp = probject_path
class Helper:
refs = (
'd8a6aa5f83021b3b9ea208c295a19051ffe83cd9', # located in working dir not resources
'dataset-template-1.1',
'dataset-template-1.2',
'dataset-template-1.2.1',
'dataset-template-1.2.2',
'dataset-template-1.2.3',
def pathTtl(self):
olr = aug.RepoPath(auth.get_path('ontology-local-repo'))
path = olr / 'ttl' / 'modality.ttl'
return path
