def post(self):
"""
Biolink Model Relations
---
tags: [schema]
description: Get valid relations in the biolink model.
responses:
'200':
description: Array of relations
content:
application/json:
schema:
type: array
items:
type: string
"""
result = {}
try:
concept_model = ConceptModel("biolink-model")
result = sorted(list(concept_model.relations_by_name.keys()))
logging.debug(result)
except Exception as e:
#traceback.print_exc (e)
result = self.handle_exception(e)
return self.response(result)
def post(self):
"""
query
---
tag: validation
description: TranQL concept model relations query.
requestBody:
description: Input message
required: true
content:
application/json:
schema:
type: object
properties:
query:
type: string
responses:
'200':
description: Success
content:
text/plain:
schema:
type: string
example: "Successfully validated"
'400':
description: Malformed message
content:
text/plain:
schema:
type: string
"""
result = {}
try:
concept_model = ConceptModel("biolink-model")
result = sorted(list(concept_model.relations_by_name.keys()))
logging.debug(result)
except Exception as e:
#traceback.print_exc (e)
result = self.handle_exception(e)
return result
def post(self):
"""
query
---
tag: validation
description: TranQL Query
requestBody:
description: Input message
required: true
content:
application/json:
schema:
type: object
properties:
query:
type: string
responses:
'200':
description: Success
content:
text/plain:
schema:
type: string
example: "Successfully validated"
'400':
description: Malformed message
content:
text/plain:
schema:
type: string
"""
concept_model = ConceptModel("biolink-model")
concepts = sorted(list(concept_model.by_name.keys()))
logging.debug(concepts)
return concepts
class Query:
""" Model a query.
TODO:
- Model queries with arrows in both diretions.
- Model predicates
- Model arbitrary shaped graphs.
"""
""" Arrows in the query. """
back_arrow = "<-"
forward_arrow = "->"
""" The biolink model. Will use for query validation. """
concept_model = ConceptModel("biolink-model")
def __init__(self):
self.order = []
self.arrows = []
self.concepts = {}
self.disable = False
def add(self, key):
""" Add a token in the question graph to this query object. """
if key == self.forward_arrow or key == self.back_arrow:
""" It's a forward arrow, no predicate. """
self.arrows.append(Edge(direction=key))
elif isinstance(key, Concept):
self.order.append(key.name)
self.concepts[key.name] = key
elif isinstance(key, Edge):
self.arrows.append(key)
elif isinstance(key, list) and len(key) == 3:
if key[2].endswith(self.forward_arrow):
self.arrows.append(
Edge(direction=self.forward_arrow, predicate=key[1]))
elif key[0].startswith(self.back_arrow):
self.arrows.append(
Edge(direction=self.back_arrow, predicate=key[1]))
else:
""" It's a concept identifier, potentially named. """
type_name = key
name = key
if ':' in key:
if key.count(':') > 1:
raise IllegalConceptIdentifierError(
f"Illegal concept id: {key}")
name, type_name = key.split(':')
self.order.append(name)
""" Verify the type name is in the model we have. """
assert self.concept_model.get(type_name) != None
assert type_name in self.concept_model, f"Error: Concept {type_name} is not in the concept model."
self.concepts[name] = Concept(name=name, type_name=type_name)
def __getitem__(self, key):
return self.concepts[key]
def __setitem__(self, key, value):
raise ValueError("Not implemented")
def __delitem__(self, key):
del self.concepts[key]
def __contains__(self, key):
return key in self.concepts
def __repr__(self):
return f"{self.concepts} | {self.arrows}"