def __call__(self, rdfDataSource=None):
'''Ingest and render a results page.'''
context = aq_inner(self.context)
if rdfDataSource is None:
rdfDataSource = context.rdfDataSource
if not rdfDataSource:
raise RDFIngestException(_(u'This folder has no RDF data source URL.'))
normalizerFunction = queryUtility(IIDNormalizer).normalize
graph = ConjunctiveGraph()
graph.parse(URLInputSource(rdfDataSource))
statements = self._parseRDF(graph)
createdObjects = []
for uri, predicates in statements.items():
typeURI = predicates[_typeURI][0]
handler = _handlers[typeURI]
objectID = handler.generateID(uri, predicates, normalizerFunction)
handler.deleteExistingObject(objectID, context, uri, predicates, statements)
title = handler.generateTitle(uri, predicates)
created = handler.createObjects(objectID, title, uri, predicates, statements, context)
for obj in created:
obj.reindex()
createdObjects.extend(created)
self.objects = createdObjects
return self.renderResults()
def __call__(self):
'''Ingest and render a results page.'''
context = aq_inner(self.context)
rdfDataSource, bmoDataSource, bmuDataSource, bmSumDataSource, idDataSource = context.rdfDataSource, context.bmoDataSource, context.bmuDataSource, context.bmSumDataSource, context.idDataSource
if bmSumDataSource:
context.dataSummary = self.getSummaryData(bmSumDataSource)
if not rdfDataSource or not bmoDataSource or not bmuDataSource:
raise RDFIngestException(
_(u'This biomarker folder lacks one or both of its RDF source URLs.'
))
# Weapons at ready
catalog = getToolByName(context, 'portal_catalog')
normalizerFunction = queryUtility(IIDNormalizer).normalize
graph = ConjunctiveGraph()
graph.parse(URLInputSource(rdfDataSource))
statements = self._parseRDF(graph)
# Add mutation-specific information
graph = ConjunctiveGraph()
graph.parse(URLInputSource(bmuDataSource))
mutationStatements = self._parseRDF(graph)
# Clean the slate (but not the subfolders)
results = catalog(path=dict(query='/'.join(context.getPhysicalPath()),
depth=1),
object_provides=IBiomarker.__identifier__)
context.manage_delObjects([i.id for i in results])
newBiomarkers = {}
# Make all the biomarker objects
for uri, predicates in statements.items():
try:
typeURI = predicates[_typeURI][0]
if typeURI != _biomarkerTypeURI:
continue
isPanel = bool(int(predicates[_isPanelPredicateURI][0]))
title = unicode(predicates[_bmTitlePredicateURI][0])
hgnc = predicates[_hgncPredicateURI][
0] if _hgncPredicateURI in predicates else None
if hgnc is not None:
hgnc = hgnc.strip()
objID = hgnc if hgnc else normalizerFunction(title)
objType = isPanel and 'Biomarker Panel' or 'Elemental Biomarker'
try:
obj = context[context.invokeFactory(objType, objID)]
except BadRequest:
obj = None
for appendedNumber in xrange(
1, MAX_NON_UNIQUE_BIOMARKER_IDS + 1):
try:
obj = context[context.invokeFactory(
objType, "%s-%d" % (objID, appendedNumber))]
break
except BadRequest:
pass
if obj is None:
raise BadRequest(
"Something's wrong. Got more than %d biomarkers with the same ID '%s'!"
% (MAX_NON_UNIQUE_BIOMARKER_IDS, objID))
if not isPanel:
#Append biomuta's predicates if gene symbol exists in biomuta's list as well
self.addMutationSpecificInformation(
objID, predicates, mutationStatements)
# Disabled because it causes the ingest to take multiple hours instead of just 1 hour
# See CA-1434 (kelly 2016-12-06)
# Re-enabled to because added blob storage to save existing queries. Only the first query might take 2 hours.
testpred = self.addExternaResourcesInformation(
objID, predicates, idDataSource)
predicates = testpred
#Add frequencies for biomarker associated with biomarker type (Gene, Protein, etc...)
#Update biomarker, if biomuta was added, biomuta predicates will be updated as well
self.updateBiomarker(obj, uri, predicates, context, statements)
newBiomarkers[uri] = obj
obj.reindexObject()
except KeyError:
pass
# Connect elementals to their panels
for uri, predicates in statements.items():
try:
typeURI = predicates[_typeURI][0]
if typeURI != _biomarkerTypeURI:
continue
biomarkerUID = newBiomarkers[uri].UID()
panelURIs = predicates[_memberOfPanelPredicateURI]
panels = self.findObjectsByIdentifiers(catalog, panelURIs)
for panel in panels:
current = [i.UID() for i in panel.members]
current.append(biomarkerUID)
panel.setMembers(current)
except KeyError:
pass
# Add organ-specific information
graph = ConjunctiveGraph()
graph.parse(URLInputSource(bmoDataSource))
organStatements = self._parseRDF(graph)
self.addOrganSpecificInformation(newBiomarkers, organStatements,
normalizerFunction, catalog)
# Update indicated organs:
for biomarker in newBiomarkers.values():
biomarker.updatedIndicatedBodySystems()
biomarker.reindexObject()
# Publish as necessary
for uri, predicates in statements.items():
if uri in newBiomarkers:
biomarker = newBiomarkers[uri]
if biomarker.qaState == 'Private':
self.retractBiomarker(context, biomarker, predicates)
else:
self.publishBiomarker(context, biomarker, predicates)
self.objects = [CreatedObject(i) for i in newBiomarkers.values()]
return self.render and self.template() or len(self.objects)
def __call__(self, request):
value = request.form.get('rdfDataSource', request.get('rdfDataSource', None))
if value and not _protocolsRegex.match(value):
return {'rdfDataSource': _(u'Please enter a valid URL to an RDF data source.')}
return None
from Products.Archetypes.interfaces import IObjectPostValidation
from zope.component import adapts
import re
_protocols = (
'http', 'ftp', 'irc', 'news', 'imap', 'gopher', 'jabber', 'webdav', 'smb', 'fish',
'ldap', 'pop3', 'smtp', 'sftp', 'ssh', 'feed', 'testscheme', 'file'
)
_protocolsRegex = re.compile(r'(%s)s?:(//)?[^\s\r\n]+' % '|'.join(_protocols))
KnowledgeFolderSchema = folder.ATFolderSchema.copy() + atapi.Schema((
atapi.StringField(
'rdfDataSource',
required=False,
storage=atapi.AnnotationStorage(),
widget=atapi.StringWidget(
label=_(u'RDF Data Source'),
description=_(u'URL to a source of Resource Description Format data that mandates the contents of this folder.'),
size=60,
),
),
))
KnowledgeFolderSchema['title'].storage = atapi.AnnotationStorage()
KnowledgeFolderSchema['description'].storage = atapi.AnnotationStorage()
finalizeATCTSchema(KnowledgeFolderSchema, folderish=True, moveDiscussion=False)
class KnowledgeFolder(folder.ATFolder):
'''Knowledge folder which contains knowledge objects.'''
implements(IKnowledgeFolder)
portal_type = 'Knowledge Folder'
_at_rename_after_creation = True
def __call__(self, request):
value = request.form.get('identifier', request.get('identifier', None))
if value and not _uriRegex.match(value):
return {'identifier': _(u'Please enter a valid URI.')}
return None
import re
_uriSchemes = (
'http', 'ftp', 'irc', 'news', 'imap', 'gopher', 'jabber', 'webdav', 'smb', 'fish',
'ldap', 'pop3', 'smtp', 'sftp', 'ssh', 'feed', 'testscheme', 'urn'
)
_uriRegex = re.compile(r'(%s)s?:(//)?[^\s\r\n]+' % '|'.join(_uriSchemes))
KnowledgeObjectSchema = schemata.ATContentTypeSchema.copy() + atapi.Schema((
atapi.StringField(
'identifier',
required=True,
default='http://',
storage=atapi.AnnotationStorage(),
predicateURI=dublincore.IDENTIFIER_URI,
widget=atapi.StringWidget(
label=_(u'Identifier'),
description=_(u'The Uniform Resource Identifier identifying the resource.'),
),
),
))
KnowledgeObjectSchema['title'].storage = atapi.AnnotationStorage()
# FIXME: Should be this:
# KnowledgeObjectSchema['title'].predicateURI = dublincore.TITLE_URI
# But BMDB uses this:
KnowledgeObjectSchema['title'].predicateURI = 'http://edrn.nci.nih.gov/rdf/rdfs/bmdb-1.0.0#Description'
KnowledgeObjectSchema['description'].storage = atapi.AnnotationStorage()
KnowledgeObjectSchema['description'].predicateURI = dublincore.DESCRIPTION_URI
finalizeATCTSchema(KnowledgeObjectSchema, folderish=False, moveDiscussion=False)
class KnowledgeObject(base.ATCTContent):
from zope.interface import implements, directlyProvides
from zope.schema.interfaces import IVocabularyFactory
from zope.schema.vocabulary import SimpleVocabulary
DiseaseSchema = knowledgeobject.KnowledgeObjectSchema.copy() + atapi.Schema((
atapi.ReferenceField(
'affectedOrgans',
enforceVocabulary=True,
multiValued=True,
relationship='affectsOrgan',
required=False,
storage=atapi.AnnotationStorage(),
vocabulary_factory=u'eke.knowledge.BodySystems',
vocabulary_display_path_bound=-1,
widget=atapi.ReferenceWidget(
label=_(u'Affected Body Systems'),
description=_(u'Body systems for which this disease is an ailment.'),
),
),
atapi.StringField(
'icd9Code',
required=False,
storage=atapi.AnnotationStorage(),
widget=atapi.StringWidget(
label=_(u'ICD9 Code'),
description=_(u'International Statistical Classifiction of Disease Code (version 9)'),
size=10,
),
predicateURI=u'http://edrn.nci.nih.gov/xml/rdf/edrn.rdf#icd9',
),
atapi.StringField(
def __call__(self):
'''Ingest and render a results page.'''
context = aq_inner(self.context)
rdfDataSource, bmoDataSource, bmuDataSource, bmSumDataSource, idDataSource = context.rdfDataSource, context.bmoDataSource, context.bmuDataSource, context.bmSumDataSource, context.idDataSource
if bmSumDataSource:
context.dataSummary = self.getSummaryData(bmSumDataSource)
if not rdfDataSource or not bmoDataSource or not bmuDataSource:
raise RDFIngestException(_(u'This biomarker folder lacks one or both of its RDF source URLs.'))
# Weapons at ready
catalog = getToolByName(context, 'portal_catalog')
normalizerFunction = queryUtility(IIDNormalizer).normalize
graph = ConjunctiveGraph()
graph.parse(URLInputSource(rdfDataSource))
statements = self._parseRDF(graph)
# Add mutation-specific information
graph = ConjunctiveGraph()
graph.parse(URLInputSource(bmuDataSource))
mutationStatements = self._parseRDF(graph)
# Clean the slate (but not the subfolders)
results = catalog(path=dict(query='/'.join(context.getPhysicalPath()), depth=1),
object_provides=IBiomarker.__identifier__)
context.manage_delObjects([i.id for i in results])
newBiomarkers = {}
# Make all the biomarker objects
for uri, predicates in statements.items():
try:
typeURI = predicates[_typeURI][0]
if typeURI != _biomarkerTypeURI:
continue
isPanel = bool(int(predicates[_isPanelPredicateURI][0]))
title = unicode(predicates[_bmTitlePredicateURI][0])
hgnc = predicates[_hgncPredicateURI][0] if _hgncPredicateURI in predicates else None
if hgnc is not None:
hgnc = hgnc.strip()
objID = hgnc if hgnc else normalizerFunction(title)
objType = isPanel and 'Biomarker Panel' or 'Elemental Biomarker'
try:
obj = context[context.invokeFactory(objType, objID)]
except BadRequest:
obj = None
for appendedNumber in xrange(1, MAX_NON_UNIQUE_BIOMARKER_IDS+1):
try:
obj = context[context.invokeFactory(objType, "%s-%d" % (objID, appendedNumber))]
break
except BadRequest:
pass
if obj is None:
raise BadRequest("Something's wrong. Got more than %d biomarkers with the same ID '%s'!" %
(MAX_NON_UNIQUE_BIOMARKER_IDS, objID))
if not isPanel:
#Append biomuta's predicates if gene symbol exists in biomuta's list as well
self.addMutationSpecificInformation(objID, predicates, mutationStatements)
# Disabled because it causes the ingest to take multiple hours instead of just 1 hour
# See CA-1434 (kelly 2016-12-06)
# Re-enabled to because added blob storage to save existing queries. Only the first query might take 2 hours.
testpred = self.addExternaResourcesInformation(objID, predicates, idDataSource)
predicates = testpred
#Add frequencies for biomarker associated with biomarker type (Gene, Protein, etc...)
#Update biomarker, if biomuta was added, biomuta predicates will be updated as well
self.updateBiomarker(obj, uri, predicates, context, statements)
newBiomarkers[uri] = obj
obj.reindexObject()
except KeyError:
pass
# Connect elementals to their panels
for uri, predicates in statements.items():
try:
typeURI = predicates[_typeURI][0]
if typeURI != _biomarkerTypeURI:
continue
biomarkerUID = newBiomarkers[uri].UID()
panelURIs = predicates[_memberOfPanelPredicateURI]
panels = self.findObjectsByIdentifiers(catalog, panelURIs)
for panel in panels:
current = [i.UID() for i in panel.members]
current.append(biomarkerUID)
panel.setMembers(current)
except KeyError:
pass
# Add organ-specific information
graph = ConjunctiveGraph()
graph.parse(URLInputSource(bmoDataSource))
organStatements = self._parseRDF(graph)
self.addOrganSpecificInformation(newBiomarkers, organStatements, normalizerFunction, catalog)
# Update indicated organs:
for biomarker in newBiomarkers.values():
biomarker.updatedIndicatedBodySystems()
biomarker.reindexObject()
# Publish as necessary
for uri, predicates in statements.items():
if uri in newBiomarkers:
biomarker = newBiomarkers[uri]
if biomarker.qaState == 'Private':
self.retractBiomarker(context, biomarker, predicates)
else:
self.publishBiomarker(context, biomarker, predicates)
self.objects = [CreatedObject(i) for i in newBiomarkers.values()]
return self.render and self.template() or len(self.objects)