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Merge pull request #4986 from njkim/3745_fix_load_ontology_extension
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fix load ontology extension re #3745
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@chiatt
chiatt authored Jul 9, 2019
2 parents 47bf804 + 69806ab commit 290790b
Showing 1 changed file with 31 additions and 28 deletions.
59 changes: 31 additions & 28 deletions arches/management/commands/load_ontology.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,9 +27,9 @@
from arches.app.models import models

from arches.app.models.system_settings import settings
# from rdflib import *
# from rdflib import *
from rdflib import Graph, RDF, RDFS
from rdflib.resource import Resource
from rdflib.resource import Resource
from rdflib.namespace import Namespace, NamespaceManager

class Command(BaseCommand):
Expand Down Expand Up @@ -61,51 +61,54 @@ def choose_ontology(message):
if len(available_ontologies) > 0:
selections = []
for index, ontology in enumerate(available_ontologies, start=1):
selections.append(('%s. %s (%s)') % (index, ontology.name, ontology.pk))
selections.append(('%s. %s (%s)') % (index, ontology.name, ontology.pk))
selected_ontology = raw_input(message + '\n'.join(selections)+'\n')
return available_ontologies[int(selected_ontology)-1]
else:
return None

if options['reload']:
ontology = None
if options['source'] is not None:
path = '.%s' % os.path.abspath(options['source']).replace(models.get_ontology_storage_system().location, '')
ontology = models.Ontology.objects.get(parentontology=None, path=path)
else:
ontology = choose_ontology(_('Select the number corresponding to the\nbase ontology which you want to reload.\n'))

if ontology:
self.run_loader(data_source=ontology.path.path, name=ontology.name, version=ontology.version, id=ontology.pk, extensions=None, verbosity=options['verbosity'])
return

if options['version'] is None:
print _('You must supply a version number using the -vn/--version argument.')
return
return

if options['source'] is not None:
self.run_loader(data_source=options['source'], name=options['ontology_name'], version=options['version'], id=options['id'], extensions=options['extensions'], verbosity=options['verbosity'])
return

if options['extensions'] is not None:
ontology = choose_ontology(_('Select the number corresponding to the\nbase ontology to which you want to add the extension.\n'))
if ontology:
for extension in options['extensions'].split(','):
path_to_check = self.get_relative_path(extension)
try:
proposed_path = models.Ontology.objects.get(path=path_to_check).path.path
print ''
print _('It looks like an ontology file has already been loaded with the same name.')
print _('The file currently loaded is located here:')
print ' %s' % proposed_path
print _('If you would simply like to reload the current ontology, you can run this command with the dash r (-r) flag')
print 'eg: python manage.py load_ontology -r\n'
return
except:
pass
self.run_loader(data_source=ontology.path.path, version=options['version'], id=ontology.pk, extensions=options['extensions'], verbosity=options['verbosity'])
if os.path.isfile(options['extensions']):
ontology = choose_ontology(_('Select the number corresponding to the\nbase ontology to which you want to add the extension.\n'))
if ontology:
for extension in options['extensions'].split(','):
path_to_check = self.get_relative_path(extension)
try:
proposed_path = models.Ontology.objects.get(path=path_to_check).path.path
print ''
print _('It looks like an ontology file has already been loaded with the same name.')
print _('The file currently loaded is located here:')
print ' %s' % proposed_path
print _('If you would simply like to reload the current ontology, you can run this command with the dash r (-r) flag')
print 'eg: python manage.py load_ontology -r\n'
return
except:
pass
self.run_loader(data_source=ontology.path.path, version=options['version'], id=ontology.pk, extensions=options['extensions'], verbosity=options['verbosity'])
else:
print _('You must first define a base ontology (using -s) before loading an extension using the (-x) argument')
else:
print _('You must first define a base ontology (using -s) before loading an extension using the (-x) argument')
print 'The File "%s" Not Found' % options['extensions']
return

def run_loader(self, data_source=None, version=None, name=None, id=None, extensions=None, verbosity=1):
Expand All @@ -127,7 +130,7 @@ def run_loader(self, data_source=None, version=None, name=None, id=None, extensi
self.graph = Graph()
self.namespace_manager = NamespaceManager(self.graph)
self.subclass_cache = {}

with transaction.atomic():
ontology = self.add_ontology(id=id, data_source=data_source, version=version, name=name)
loaded_extensions = [extension.path.path for extension in models.Ontology.objects.filter(parentontology=ontology)]
Expand All @@ -149,7 +152,7 @@ def run_loader(self, data_source=None, version=None, name=None, id=None, extensi
models.OntologyClass.objects.filter(ontology=ontology).delete()
for ontology_class, data in self.crawl_graph().iteritems():
models.OntologyClass.objects.update_or_create(source=ontology_class, ontology=ontology, defaults={'target': data})

def add_ontology(self, id=None, data_source=None, version=None, name=None, parentontology=None):
self.graph.parse(data_source)

Expand All @@ -159,7 +162,7 @@ def add_ontology(self, id=None, data_source=None, version=None, name=None, paren
name = os.path.splitext(filename)[0]

if models.get_ontology_storage_system().location in filepath:
# if the file we're referencing already exists in the location where we
# if the file we're referencing already exists in the location where we
# usually store them then leave it there and just save a reference to it
path = self.get_relative_path(data_source)
else:
Expand Down Expand Up @@ -220,5 +223,5 @@ def get_relative_path(self, data_source):
try:
ret = data_source.path
except:
pass
return ret
pass
return ret

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