class Assessment(Item):
item_type = 'assessment'
schema = load_schema('clincoded:schemas/assessment.json')
name_key = 'uuid'
embedded = [
'submitted_by',
'pathogenicity_assessed',
'experimental_assessed',
]
rev = {
'pathogenicity_assessed': ('pathogenicity', 'assessments'),
'experimental_assessed': ('experimental', 'assessments')
}
@calculated_property(
schema={
"title": "Pathogenicity Assessed",
"type": ["string", "object"],
"linkFrom": "pathogenicity.assessments"
})
def pathogenicity_assessed(self, request, pathogenicity_assessed):
return paths_filtered_by_status(request, pathogenicity_assessed)
@calculated_property(
schema={
"title": "Experimental Assessed",
"type": ["string", "object"],
"linkFrom": "experimental.assessments"
})
def experimental_assessed(self, request, experimental_assessed):
return paths_filtered_by_status(request, experimental_assessed)
class Experimental(Item):
item_type = 'experimental'
schema = load_schema('clincoded:schemas/experimental.json')
name_key = 'uuid'
embedded = [
'submitted_by', 'variants', 'variants.submitted_by',
'biochemicalFunction.geneWithSameFunctionSameDisease.genes',
'proteinInteractions.interactingGenes', 'associatedAnnotations',
'associatedAnnotations.article', 'associatedAnnotations.associatedGdm',
'associatedAnnotations.associatedGdm.disease',
'associatedAnnotations.associatedGdm.gene', 'assessments',
'assessments.submitted_by'
]
rev = {'associatedAnnotations': ('annotation', 'experimentalData')}
@calculated_property(
schema={
"title": "Associated annotations",
"type": "array",
"items": {
"type": ['string', 'object'],
"linkFrom": "annotation.experimentalData",
},
})
def associatedAnnotations(self, request, associatedAnnotations):
return paths_filtered_by_status(request, associatedAnnotations)
def test_biosample_upgrade_inline_unknown(testapp, biosample_1):
from contentbase.schema_utils import load_schema
schema = load_schema('encoded:schemas/biosample.json')
biosample_1['starting_amount'] = 'Unknown'
res = testapp.post_json('/biosample?validate=false&render=uuid', biosample_1)
location = res.location
res = testapp.patch_json(location, {})
res = testapp.get(location + '?frame=raw&upgrade=false').maybe_follow()
assert res.json['schema_version'] == schema['properties']['schema_version']['default']
assert 'starting_amount' not in res.json
def test_biosample_upgrade_inline_unknown(testapp, biosample_1):
from contentbase.schema_utils import load_schema
schema = load_schema('encoded:schemas/biosample.json')
biosample_1['starting_amount'] = 'Unknown'
res = testapp.post_json('/biosample?validate=false&render=uuid', biosample_1)
location = res.location
res = testapp.patch_json(location, {})
res = testapp.get(location + '?frame=raw&upgrade=false').maybe_follow()
assert res.json['schema_version'] == schema['properties']['schema_version']['default']
assert 'starting_amount' not in res.json
class Group(Item):
item_type = 'group'
schema = load_schema('clincoded:schemas/group.json')
name_key = 'uuid'
embedded = [
'commonDiagnosis',
'submitted_by',
'otherGenes',
'otherPMIDs',
'otherPMIDs.submitted_by',
#'statistic',
'familyIncluded',
'familyIncluded.commonDiagnosis',
'familyIncluded.submitted_by',
'familyIncluded.otherPMIDs',
'familyIncluded.otherPMIDs.submitted_by',
'familyIncluded.segregation.variants',
'familyIncluded.segregation.variants.submitted_by',
'familyIncluded.segregation.assessments',
'familyIncluded.segregation.assessments.submitted_by',
'familyIncluded.individualIncluded',
'familyIncluded.individualIncluded.diagnosis',
'familyIncluded.individualIncluded.submitted_by',
'familyIncluded.individualIncluded.variants',
'familyIncluded.individualIncluded.variants.submitted_by',
'familyIncluded.individualIncluded.otherPMIDs',
'familyIncluded.individualIncluded.otherPMIDs.submitted_by',
'individualIncluded',
'individualIncluded.diagnosis',
'individualIncluded.submitted_by',
'individualIncluded.otherPMIDs',
'individualIncluded.otherPMIDs.submitted_by',
'individualIncluded.variants',
'individualIncluded.variants.submitted_by',
'associatedAnnotations',
'associatedAnnotations.article',
'associatedAnnotations.associatedGdm',
'associatedAnnotations.associatedGdm.disease',
'associatedAnnotations.associatedGdm.gene'
#'control'
]
rev = {'associatedAnnotations': ('annotation', 'groups')}
@calculated_property(
schema={
"title": "Associated annotations",
"type": "array",
"items": {
"type": ['string', 'object'],
"linkFrom": "annotation.groups",
},
})
def associatedAnnotations(self, request, associatedAnnotations):
return paths_filtered_by_status(request, associatedAnnotations)
class User(Item):
item_type = 'user'
schema = load_schema('clincoded:schemas/user.json')
@calculated_property(schema={
"title": "Title",
"type": "string",
})
def title(self, first_name, last_name):
return u'{} {}'.format(first_name, last_name)
def __ac_local_roles__(self):
owner = 'userid.%s' % self.uuid
return {owner: 'role.owner'}
class Image(ItemWithAttachment, Item):
item_type = 'image'
schema = load_schema('clincoded:schemas/image.json')
schema['properties']['attachment']['properties']['type']['enum'] = [
'image/png',
'image/jpeg',
'image/gif',
]
embedded = ['submitted_by']
def unique_keys(self, properties):
keys = super(Image, self).unique_keys(properties)
value = properties['attachment']['download']
keys.setdefault('image:filename', []).append(value)
return keys
class AccessKey(Item):
item_type = 'access_key'
schema = load_schema('clincoded:schemas/access_key.json')
name_key = 'access_key_id'
def __ac_local_roles__(self):
owner = 'userid.%s' % self.properties['user']
return {owner: 'role.owner'}
def __json__(self, request):
properties = super(AccessKey, self).__json__(request)
del properties['secret_access_key_hash']
return properties
class Collection(Item.Collection):
pass
def test_biosample_upgrade_inline(testapp, biosample_1):
from contentbase.schema_utils import load_schema
schema = load_schema('encoded:schemas/biosample.json')
res = testapp.post_json('/biosample?validate=false&render=uuid', biosample_1)
location = res.location
# The properties are stored un-upgraded.
res = testapp.get(location + '?frame=raw&upgrade=false').maybe_follow()
assert res.json['schema_version'] == '1'
# When the item is fetched, it is upgraded automatically.
res = testapp.get(location).maybe_follow()
assert res.json['schema_version'] == schema['properties']['schema_version']['default']
res = testapp.patch_json(location, {})
# The stored properties are now upgraded.
res = testapp.get(location + '?frame=raw&upgrade=false').maybe_follow()
assert res.json['schema_version'] == schema['properties']['schema_version']['default']
def test_biosample_upgrade_inline(testapp, biosample_1):
from contentbase.schema_utils import load_schema
schema = load_schema('encoded:schemas/biosample.json')
res = testapp.post_json('/biosample?validate=false&render=uuid', biosample_1)
location = res.location
# The properties are stored un-upgraded.
res = testapp.get(location + '?frame=raw&upgrade=false').maybe_follow()
assert res.json['schema_version'] == '1'
# When the item is fetched, it is upgraded automatically.
res = testapp.get(location).maybe_follow()
assert res.json['schema_version'] == schema['properties']['schema_version']['default']
res = testapp.patch_json(location, {})
# The stored properties are now upgraded.
res = testapp.get(location + '?frame=raw&upgrade=false').maybe_follow()
assert res.json['schema_version'] == schema['properties']['schema_version']['default']
class Provisional(Item):
item_type = 'provisionalClassification'
schema = load_schema('clincoded:schemas/provisionalClassification.json')
name_key = 'uuid'
embedded = [
'submitted_by',
'gdm_associated',
]
rev = {
'gdm_associated': ('gdm', 'provisionalClassifications'),
}
@calculated_property(
schema={
"title": "GDM Associated",
"type": ["string", "object"],
"linkFrom": "gdm.provisionalClassifications"
})
def gdm_associated(self, request, gdm_associated):
return paths_filtered_by_status(request, gdm_associated)
class CuratorPage(Item):
item_type = 'curator_page'
schema = load_schema('clincoded:schemas/curator_page.json')
name_key = 'name'
STATUS_ACL = {
'public': ALLOW_EVERYONE_VIEW,
}
def unique_keys(self, properties):
keys = super(CuratorPage, self).unique_keys(properties)
parent = properties.get('parent')
name = properties['name']
value = name if parent is None else u'{}:{}'.format(parent, name)
keys.setdefault('curator_page:location', []).append(value)
return keys
@calculated_property(
condition=lambda context, request: request.resource_path(
context.__parent__) == '/curator-pages/',
schema={
"title": "Canonical URI",
"type": "string",
})
def canonical_uri(self, name):
if name == 'homepage':
return '/'
return '/%s/' % name
@property
def __parent__(self):
parent_uuid = self.properties.get('parent')
name = self.__name__
collections = self.registry[COLLECTIONS]
connection = self.registry[CONNECTION]
if parent_uuid: # explicit parent
return connection.get_by_uuid(parent_uuid)
elif name in collections or name == 'homepage':
# collection default page; use pages collection as canonical parent
return self.collection
else: # top level
return self.registry[ROOT]
class History(Item):
item_type = 'history'
schema = load_schema('clincoded:schemas/curatorHistory.json')
embedded = [
'primary',
'meta.gdm.gene',
'meta.gdm.disease',
'meta.article.gdm',
'meta.article.gdm.gene',
'meta.article.gdm.disease',
'meta.group.gdm',
'meta.group.gdm.gene',
'meta.group.gdm.disease',
'meta.group.article',
'meta.family.gdm',
'meta.family.gdm.gene',
'meta.family.gdm.disease',
'meta.family.group',
'meta.family.article',
'meta.individual.gdm',
'meta.individual.gdm.gene',
'meta.individual.gdm.disease',
'meta.individual.group',
'meta.individual.family',
'meta.individual.article',
'meta.experimental.gdm',
'meta.experimental.gdm.gene',
'meta.experimental.gdm.disease',
'meta.experimental.article',
'meta.provisionalClassification.gdm',
'meta.provisionalClassification.gdm.gene',
'meta.provisionalClassification.gdm.disease',
'meta.pathogenicity.variant',
'meta.pathogenicity.gdm',
'meta.assessment.gdm',
'meta.assessment.experimental',
'meta.assessment.family',
'meta.assessment.pathogenicity',
'meta.assessment.variant',
'submitted_by',
]
class AccessKey(Item):
item_type = 'access_key'
schema = load_schema('clincoded:schemas/access_key.json')
name_key = 'access_key_id'
STATUS_ACL = {
'current': [(Allow, 'role.owner', ['view', 'edit'])] + ONLY_ADMIN_VIEW,
'deleted': DELETED,
}
def __ac_local_roles__(self):
owner = 'userid.%s' % self.properties['user']
return {owner: 'role.owner'}
def __json__(self, request):
properties = super(AccessKey, self).__json__(request)
del properties['secret_access_key_hash']
return properties
class Collection(Item.Collection):
pass
class Pathogenicity(Item):
item_type = 'pathogenicity'
schema = load_schema('clincoded:schemas/pathogenicity.json')
name_key = 'uuid'
embedded = [
'submitted_by',
'variant',
'variant.submitted_by',
'variant.associatedPathogenicities',
'variant.associatedPathogenicities.assessments',
'variant.associatedPathogenicities.assessments.submitted_by',
'variant.associatedPathogenicities.submitted_by',
'variant.associatedPathogenicities.variant',
'assessments',
'assessments.submitted_by',
'associatedGdm',
]
rev = {
'associatedGdm': ('gdm', 'variantPathogenicity'),
}
@calculated_property(
schema={
"title": "Associated GDM",
"type": "object",
"linkFrom": "gdm.variantPathogenicity"
})
def associatedGdm(self, request, associatedGdm):
return paths_filtered_by_status(request, associatedGdm)
@calculated_property(schema={
"title": "Number of Assessment",
"type": "integer"
})
def numberOfAssessment(self, assessments):
if len(assessments) > 0:
return len(assessments)
return ''
class Variant(Item):
item_type = 'variant'
schema = load_schema('clincoded:schemas/variant.json')
name_key = 'uuid'
embedded = [
'submitted_by', 'associatedPathogenicities',
'associatedPathogenicities.assessments',
'associatedPathogenicities.assessments.submitted_by',
'associatedPathogenicities.variant',
'associatedPathogenicities.submitted_by'
]
rev = {'associatedPathogenicities': ('pathogenicity', 'variant')}
@calculated_property(
schema={
"title": "Associated pathogenicities",
"type": "array",
"items": {
"type": ['string', 'object'],
"linkFrom": "pathogenicity.variant",
},
})
def associatedPathogenicities(self, request, associatedPathogenicities):
return paths_filtered_by_status(request, associatedPathogenicities)
class Page(Item):
item_type = 'page'
schema = load_schema('clincoded:schemas/page.json')
name_key = 'name'
STATUS_ACL = {
'in progress': [],
'released': ALLOW_EVERYONE_VIEW,
'deleted': ONLY_ADMIN_VIEW,
}
embedded = [
'layout.blocks.image',
]
def unique_keys(self, properties):
keys = super(Page, self).unique_keys(properties)
parent = properties.get('parent')
name = properties['name']
value = name if parent is None else u'{}:{}'.format(parent, name)
keys.setdefault('page:location', []).append(value)
return keys
@calculated_property(condition=lambda context, request: request.
resource_path(context.__parent__) == '/pages/',
schema={
"title": "Canonical URI",
"type": "string",
})
def canonical_uri(self, name):
if name == 'homepage':
return '/'
return '/%s/' % name
@property
def __parent__(self):
parent_uuid = self.properties.get('parent')
name = self.__name__
collections = self.registry[COLLECTIONS]
connection = self.registry[CONNECTION]
if parent_uuid: # explicit parent
return connection.get_by_uuid(parent_uuid)
elif name in collections or name == 'homepage':
# collection default page; use pages collection as canonical parent
return self.collection
else: # top level
return self.registry[ROOT]
def is_default_page(self):
name = self.__name__
collections = self.registry[COLLECTIONS]
if self.properties.get('parent'):
return False
return name in collections or name == 'homepage'
# Handle traversal to nested pages
def __getitem__(self, name):
resource = self.get(name)
if resource is None:
raise KeyError(name)
return resource
def __contains__(self, name):
return self.get(name, None) is not None
def get(self, name, default=None):
location = str(self.uuid) + ':' + name
connection = self.registry[CONNECTION]
resource = connection.get_by_unique_key('page:location', location)
if resource is not None:
return resource
return default
def __resource_url__(self, request, info):
# Record ancestor uuids in linked_uuids so renames of ancestors
# invalidate linking objects.
for obj in lineage(self):
uuid = getattr(obj, 'uuid', None)
if uuid is not None:
request._linked_uuids.add(str(uuid))
return None
class Article(Item):
item_type = 'article'
schema = load_schema('clincoded:schemas/article.json')
name_key = 'pmid'
embedded = ['submitted_by']
class Document(ItemWithAttachment, Item):
item_type = 'document'
schema = load_schema('clincoded:schemas/document.json')
embedded = ['lab', 'award', 'submitted_by']
class Source(Item):
item_type = 'source'
schema = load_schema('clincoded:schemas/source.json')
name_key = 'name'
class Gene(Item):
item_type = 'gene'
schema = load_schema('clincoded:schemas/gene.json')
name_key = 'symbol'
def test_mixinProperties():
from contentbase.schema_utils import load_schema
schema = load_schema('encoded:schemas/access_key.json')
assert schema['properties']['uuid']['type'] == 'string'
def test_mixinProperties():
from contentbase.schema_utils import load_schema
schema = load_schema("encoded:schemas/access_key.json")
assert schema["properties"]["uuid"]["type"] == "string"
class Annotation(Item):
item_type = 'annotation'
schema = load_schema('clincoded:schemas/annotation.json')
name_key = 'uuid'
embedded = [
'article',
'article.submitted_by',
'submitted_by',
'groups',
'groups.commonDiagnosis',
'groups.submitted_by',
'groups.otherGenes',
'groups.otherPMIDs',
'groups.otherPMIDs.submitted_by',
'groups.familyIncluded.commonDiagnosis',
'groups.familyIncluded.submitted_by',
'groups.familyIncluded.otherPMIDs',
'groups.familyIncluded.otherPMIDs.submitted_by',
'groups.familyIncluded.segregation.variants',
'groups.familyIncluded.segregation.variants.submitted_by',
'groups.familyIncluded.segregation.assessments',
'groups.familyIncluded.segregation.assessments.submitted_by',
'groups.familyIncluded.individualIncluded',
'groups.familyIncluded.individualIncluded.diagnosis',
'groups.familyIncluded.individualIncluded.submitted_by',
'groups.familyIncluded.individualIncluded.variants',
'groups.familyIncluded.individualIncluded.variants.submitted_by',
'groups.familyIncluded.individualIncluded.otherPMIDs',
'groups.familyIncluded.individualIncluded.otherPMIDs.submitted_by',
'groups.individualIncluded',
'groups.individualIncluded.diagnosis',
'groups.individualIncluded.submitted_by',
'groups.individualIncluded.variants',
'groups.individualIncluded.variants.submitted_by',
'groups.individualIncluded.otherPMIDs',
'groups.individualIncluded.otherPMIDs.submitted_by',
# 'groups.control',
'families',
'families.associatedGroups',
'families.commonDiagnosis',
'families.submitted_by',
'families.otherPMIDs',
'families.otherPMIDs.submitted_by',
'families.segregation.variants',
'families.segregation.variants.submitted_by',
'families.segregation.assessments',
'families.segregation.assessments.submitted_by',
'families.individualIncluded',
'families.individualIncluded.diagnosis',
'families.individualIncluded.submitted_by',
'families.individualIncluded.variants',
'families.individualIncluded.variants.submitted_by',
'families.individualIncluded.otherPMIDs',
'families.individualIncluded.otherPMIDs.submitted_by',
'individuals',
'individuals.associatedGroups',
'individuals.associatedFamilies',
'individuals.diagnosis',
'individuals.submitted_by',
'individuals.variants',
'individuals.variants.submitted_by',
'individuals.otherPMIDs',
'individuals.otherPMIDs.submitted_by',
'experimentalData',
'experimentalData.submitted_by',
'experimentalData.variants',
'experimentalData.variants.submitted_by',
'experimentalData.biochemicalFunction.geneWithSameFunctionSameDisease.genes',
'experimentalData.proteinInteractions.interactingGenes',
'associatedGdm',
'experimentalData.assessments',
'experimentalData.assessments.submitted_by'
]
rev = {'associatedGdm': ('gdm', 'annotations')}
@calculated_property(
schema={
"title": "Associated gdm",
"type": "array",
"items": {
"type": ['string', 'object'],
"linkFrom": "gdm.annotations",
},
})
def associatedGdm(self, request, associatedGdm):
return paths_filtered_by_status(request, associatedGdm)
@calculated_property(schema={
"title": "Number of Group",
"type": "string",
})
def number_group(self, groups):
if len(groups) > 0:
return len(groups)
return ""
@calculated_property(schema={
"title": "Number of Family",
"type": "string",
})
def number_family(self, families):
if len(families) > 0:
return len(families)
return ""
@calculated_property(schema={
"title": "Number of Provisioinal Individual",
"type": "string",
})
def number_individual(self, individuals):
if len(individuals) > 0:
return len(individuals)
return ""
@calculated_property(schema={
"title": "Number of Experimental",
"type": "string",
})
def number_experimental(selft, experimentalData):
if len(experimentalData) > 0:
return len(experimentalData)
return ""
def test_load_schema(schema):
from contentbase.schema_utils import load_schema
assert load_schema("encoded:schemas/%s" % schema)
class Individual(Item):
item_type = 'individual'
schema = load_schema('clincoded:schemas/individual.json')
name_key = 'uuid'
embedded = [
'diagnosis', 'submitted_by', 'variants', 'variants.submitted_by',
'otherPMIDs', 'otherPMIDs.submitted_by', 'associatedGroups',
'associatedGroups.commonDiagnosis',
'associatedGroups.associatedAnnotations',
'associatedGroups.associatedAnnotations.article',
'associatedGroups.associatedAnnotations.associatedGdm',
'associatedGroups.associatedAnnotations.associatedGdm.disease',
'associatedGroups.associatedAnnotations.associatedGdm.gene',
'associatedFamilies', 'associatedFamilies.associatedGroups',
'associatedFamilies.associatedGroups.associatedAnnotations',
'associatedFamilies.associatedGroups.associatedAnnotations.article',
'associatedFamilies.associatedGroups.associatedAnnotations.associatedGdm',
'associatedFamilies.associatedGroups.associatedAnnotations.associatedGdm.disease',
'associatedFamilies.associatedGroups.associatedAnnotations.associatedGdm.gene',
'associatedFamilies.associatedAnnotations',
'associatedFamilies.associatedAnnotations.article',
'associatedFamilies.associatedAnnotations.associatedGdm',
'associatedFamilies.associatedAnnotations.associatedGdm.disease',
'associatedFamilies.associatedAnnotations.associatedGdm.gene',
'associatedFamilies.commonDiagnosis', 'associatedAnnotations',
'associatedAnnotations.article', 'associatedAnnotations.associatedGdm',
'associatedAnnotations.associatedGdm.disease',
'associatedAnnotations.associatedGdm.gene'
]
rev = {
'associatedGroups': ('group', 'individualIncluded'),
'associatedFamilies': ('family', 'individualIncluded'),
'associatedAnnotations': ('annotation', 'individuals')
}
@calculated_property(
schema={
"title": "Associated groups",
"type": "array",
"items": {
"type": ['string', 'object'],
"linkFrom": "group.individualIncluded",
},
})
def associatedGroups(self, request, associatedGroups):
return paths_filtered_by_status(request, associatedGroups)
@calculated_property(
schema={
"title": "Associated families",
"type": "array",
"items": {
"type": ['string', 'object'],
"linkFrom": "family.individualIncluded",
},
})
def associatedFamilies(self, request, associatedFamilies):
return paths_filtered_by_status(request, associatedFamilies)
@calculated_property(
schema={
"title": "Associated annotations",
"type": "array",
"items": {
"type": ['string', 'object'],
"linkFrom": "annotation.individuals",
},
})
def associatedAnnotations(self, request, associatedAnnotations):
return paths_filtered_by_status(request, associatedAnnotations)
@calculated_property(schema={"title": "Proband String", "type": "string"})
def is_proband(self, proband):
if proband:
return 'Yes'
else:
return 'No'
class OrphaPhenotype(Item):
item_type = 'orphaPhenotype'
schema = load_schema('clincoded:schemas/orphaPhenotype.json')
name_key = 'orphaNumber'
class Lab(Item):
item_type = 'lab'
schema = load_schema('clincoded:schemas/lab.json')
name_key = 'name'
embedded = ['awards']
class Award(Item):
item_type = 'award'
schema = load_schema('clincoded:schemas/award.json')
name_key = 'name'
def test_mixinProperties():
from contentbase.schema_utils import load_schema
schema = load_schema('clincoded:schemas/access_key.json')
assert schema['properties']['uuid']['type'] == 'string'
class Organism(Item):
item_type = 'organism'
schema = load_schema('clincoded:schemas/organism.json')
name_key = 'name'
def test_load_schema(schema):
from contentbase.schema_utils import load_schema
assert load_schema('encoded:schemas/%s' % schema)
class Gdm(Item):
item_type = 'gdm'
schema = load_schema('clincoded:schemas/gdm.json')
name_key = 'uuid'
embedded = [
'gene',
'disease',
'submitted_by',
'variantPathogenicity',
'variantPathogenicity.submitted_by',
'variantPathogenicity.variant',
'variantPathogenicity.variant.submitted_by',
'variantPathogenicity.assessments',
'variantPathogenicity.assessments.submitted_by',
'provisionalClassifications',
'provisionalClassifications.submitted_by',
'annotations',
'annotations.article',
'annotations.article.submitted_by',
'annotations.submitted_by',
'annotations.groups',
'annotations.groups.commonDiagnosis',
'annotations.groups.submitted_by',
'annotations.groups.otherGenes',
'annotations.groups.otherPMIDs',
'annotations.groups.otherPMIDs.submitted_by',
# 'annotations.groups.statistic',
# 'annotations.groups.statistic.variants',
'annotations.groups.familyIncluded',
'annotations.groups.familyIncluded.associatedGroups',
'annotations.groups.familyIncluded.commonDiagnosis',
'annotations.groups.familyIncluded.submitted_by',
'annotations.groups.familyIncluded.otherPMIDs',
'annotations.groups.familyIncluded.otherPMIDs.submitted_by',
'annotations.groups.familyIncluded.segregation.variants',
'annotations.groups.familyIncluded.segregation.variants.submitted_by',
'annotations.groups.familyIncluded.segregation.variants.associatedPathogenicities',
'annotations.groups.familyIncluded.segregation.variants.associatedPathogenicities.associatedGdm',
'annotations.groups.familyIncluded.segregation.variants.associatedPathogenicities.submitted_by',
'annotations.groups.familyIncluded.segregation.assessments',
'annotations.groups.familyIncluded.segregation.assessments.submitted_by',
'annotations.groups.familyIncluded.individualIncluded',
'annotations.groups.familyIncluded.individualIncluded.associatedGroups',
'annotations.groups.familyIncluded.individualIncluded.associatedFamilies',
'annotations.groups.familyIncluded.individualIncluded.associatedFamilies.associatedGroups',
'annotations.groups.familyIncluded.individualIncluded.diagnosis',
'annotations.groups.familyIncluded.individualIncluded.submitted_by',
'annotations.groups.familyIncluded.individualIncluded.variants',
'annotations.groups.familyIncluded.individualIncluded.variants.submitted_by',
'annotations.groups.familyIncluded.individualIncluded.variants.associatedPathogenicities',
'annotations.groups.familyIncluded.individualIncluded.variants.associatedPathogenicities.associatedGdm',
'annotations.groups.familyIncluded.individualIncluded.variants.associatedPathogenicities.submitted_by',
'annotations.groups.familyIncluded.individualIncluded.otherPMIDs',
'annotations.groups.familyIncluded.individualIncluded.otherPMIDs.submitted_by',
'annotations.groups.individualIncluded',
'annotations.groups.individualIncluded.associatedGroups',
'annotations.groups.individualIncluded.diagnosis',
'annotations.groups.individualIncluded.submitted_by',
'annotations.groups.individualIncluded.variants',
'annotations.groups.individualIncluded.variants.submitted_by',
'annotations.groups.individualIncluded.variants.associatedPathogenicities',
'annotations.groups.individualIncluded.variants.associatedPathogenicities.associatedGdm',
'annotations.groups.individualIncluded.variants.associatedPathogenicities.submitted_by',
'annotations.groups.individualIncluded.otherPMIDs',
'annotations.groups.individualIncluded.otherPMIDs.submitted_by',
# 'annotations.groups.control',
'annotations.families',
'annotations.families.associatedGroups',
'annotations.families.commonDiagnosis',
'annotations.families.submitted_by',
'annotations.families.otherPMIDs',
'annotations.families.otherPMIDs.submitted_by',
'annotations.families.segregation.variants',
'annotations.families.segregation.variants.submitted_by',
'annotations.families.segregation.variants.associatedPathogenicities',
'annotations.families.segregation.variants.associatedPathogenicities.associatedGdm',
'annotations.families.segregation.variants.associatedPathogenicities.submitted_by',
'annotations.families.segregation.assessments',
'annotations.families.segregation.assessments.submitted_by',
'annotations.families.individualIncluded',
'annotations.families.individualIncluded.associatedGroups',
'annotations.families.individualIncluded.associatedFamilies',
'annotations.families.individualIncluded.associatedFamilies.associatedGroups',
'annotations.families.individualIncluded.diagnosis',
'annotations.families.individualIncluded.submitted_by',
'annotations.families.individualIncluded.variants',
'annotations.families.individualIncluded.variants.submitted_by',
'annotations.families.individualIncluded.variants.associatedPathogenicities',
'annotations.families.individualIncluded.variants.associatedPathogenicities.associatedGdm',
'annotations.families.individualIncluded.variants.associatedPathogenicities.submitted_by',
'annotations.families.individualIncluded.otherPMIDs',
'annotations.families.individualIncluded.otherPMIDs.submitted_by',
'annotations.individuals',
'annotations.individuals.associatedGroups',
'annotations.individuals.associatedFamilies',
'annotations.individuals.associatedFamilies.associatedGroups',
'annotations.individuals.diagnosis',
'annotations.individuals.submitted_by',
'annotations.individuals.variants',
'annotations.individuals.variants.submitted_by',
'annotations.individuals.variants.associatedPathogenicities',
'annotations.individuals.variants.associatedPathogenicities.associatedGdm',
'annotations.individuals.variants.associatedPathogenicities.submitted_by',
'annotations.individuals.otherPMIDs',
'annotations.individuals.otherPMIDs.submitted_by',
'annotations.experimentalData',
'annotations.experimentalData.submitted_by',
'annotations.experimentalData.variants',
'annotations.experimentalData.variants.associatedPathogenicities',
'annotations.experimentalData.variants.associatedPathogenicities.associatedGdm',
'annotations.experimentalData.variants.submitted_by',
'annotations.experimentalData.assessments',
'annotations.experimentalData.assessments.submitted_by',
'annotations.experimentalData.biochemicalFunction.geneWithSameFunctionSameDisease.genes',
'annotations.experimentalData.proteinInteractions.interactingGenes',
'annotations.experimentalData.assessments',
'annotations.experimentalData.assessments.submitted_by'
]
@calculated_property(schema={
"title": "GDM Status",
"type": "string",
})
def gdm_status(self, finalClassification, draftClassification,
provisionalClassifications, annotations):
if finalClassification != '':
return 'Final Classification'
elif draftClassification != '':
return 'Draft Classification'
elif len(provisionalClassifications) > 0:
return 'Summary/Provisional Classifications'
elif len(annotations) > 0:
return 'In Progress'
else:
return 'Created'
@calculated_property(schema={
"title": "Number of Articles",
"type": "string",
})
def number_article(self, annotations):
if len(annotations) > 0:
return str(len(annotations))
return ""
@calculated_property(schema={
"title": "Number of Pathogenicity",
"type": "string",
})
def number_pathogenicity(self, variantPathogenicity):
if len(variantPathogenicity) > 0:
return str(len(variantPathogenicity))
return ""
@calculated_property(schema={
"title": "Number of Provisional",
"type": "string",
})
def number_provisional(self, provisionalClassifications):
if len(provisionalClassifications) > 0:
return str(len(provisionalClassifications))
return ""
@calculated_property(schema={
"title": "GDM",
"type": "string",
})
def gdm_title(self, gene, disease, modeCode):
gene_symbol = gene.replace('/genes/', '').replace('/', '')
orpha_id = disease.replace('/diseases/', '').replace('/', '')
return gene_symbol + '-' + orpha_id + '-' + modeCode
