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Merge pull request #5 from iris-liu0312/master
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Json Editor
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iris-liu0312 authored Dec 24, 2021
2 parents 3f8f380 + 19736e0 commit 7a5f202
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2 changes: 1 addition & 1 deletion README.md
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## Introduction

This is a web tool to visualize KAIROS Schema Format generated schemas using Cytoscape.js and React.js. The tool also allows editing of these schemas for curation purpose. Current supported SDF version is **1.2**.
This is a web tool to visualize KAIROS Schema Format generated schemas using Cytoscape.js and React.js. The tool also allows editing of these schemas for curation purpose. Current supported SDF version is **1.3**.

**This project is currently a work in progress and is in alpha testing. Feedbacks and suggestions are welcome.**

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166 changes: 85 additions & 81 deletions app.py
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from flask import Flask, render_template, request
import json

# ===============================================
# app.py
# ------------
# reads json data to send to viewer
# ===============================================

app = Flask(__name__, static_folder='./static', template_folder='./static')

nodes = {}
edges = []

# TODO: look through SDF version documentation to decide what should be in the schema_key_dict
# TODO: move support to SDF version 1.3
# TODO: handle multiple root nodes

# SDF version 1.2
# SDF version 1.3
schema_key_dict = {
'root': ['@id', 'name', 'description', 'comment', 'qnode', '@type', 'minDuration', 'maxDuration', 'repeatable', 'TA1explanation', 'importance', 'qlabel'],
'root': ['@id', 'name', 'comment', 'description', 'aka', 'qnode', 'qlabel', 'minDuration',
'maxDuration', 'goal', 'ta1explanation', 'importance', 'children_gate'],
# TODO: handle xor children_gates
'participant': ['@id', 'roleName', 'entity'],
'child': ['child', 'comment', 'optional', 'importance', 'outlinks', 'outlink_gate', ]
'child': ['child', 'comment', 'optional', 'importance', 'outlinks', 'outlink_gate'],
'privateData': ['@type', 'template', 'repeatable', 'importance']
}

def create_node(_id, _label, _type, _shape=''):
Expand Down Expand Up @@ -72,58 +80,12 @@ def extend_node(node, obj):
node['classes'] = 'optional'
else:
node['data'][key] = obj[key]
if 'privateData' in obj.keys():
for key in obj['privateData'].keys():
if key in schema_key_dict['privateData']:
node['data'][key] = obj['privateData'][key]
return node

def handle_precondition(order, node_set, label='Precondition'):
"""Adds edges between multiple previous and next nodes.
Parameters:
order (dict): links to "before" and "after" nodes
node_set (dict): nodes to be linked
label (str): shows order on graph
"""
e = []
if isinstance(order['before'], list):
for before_id in order['before']:
if isinstance(order['after'], list):
for after_id in order['after']:
if before_id in node_set and after_id in node_set:
e.append(create_edge(before_id, after_id, label, 'step_child'))
else:
if before_id in node_set and order['after'] in node_set:
e.append(create_edge(before_id, order['after'], label, 'step_child'))
else:
if isinstance(order['after'], list):
for after_id in order['after']:
if order['before'] in node_set and after_id in node_set:
e.append(create_edge(order['before'], after_id, label, 'step_child'))
else:
if order['before'] in node_set and order['after'] in node_set:
e.append(create_edge(order['before'], order['after'], label, 'step_child'))
return e

def handle_optional(_order, node_set):
"""Calls handle_precondition with thet optional label.
"""
return handle_precondition(_order, node_set, 'Optional')

def handle_flags(_flag, _order, node_set):
"""Calls handle_precondition or handle_optional based on flag.
Parameters:
_flag (str): flag raised in order dictionary
_node_set (dict): set of nodes to be handled
"""
switcher={
'precondition': handle_precondition,
'optional': handle_optional
}
func = switcher.get(_flag.lower(), lambda *args: None)
return func(_order, node_set)

def get_nodes_and_edges(schema):
"""Creates lists of nodes and edges, through references and relations.
Expand All @@ -137,55 +99,97 @@ def get_nodes_and_edges(schema):
"""
nodes = {}
edges = []
containers = []

for scheme in schema:
# top node
# create event node
_label = scheme['name'].split('/')[-1].replace('_', ' ').replace('-', ' ')
nodes[scheme['@id']] = extend_node(create_node(scheme['@id'], _label, 'root', 'diamond'), scheme)
# not root node, change node type
if '@type' in nodes[scheme['@id']]['data']:
nodes[scheme['@id']]['data']['_type'] = 'parent'
# not hierarchical node, change node shape
scheme_id = scheme['@id']
# node already exists
if scheme_id in nodes:
# add information
nodes[scheme_id]['data']['_type'] = 'root'
nodes[scheme_id]['data']['_label'] = _label
nodes[scheme_id] = extend_node(nodes[scheme_id], scheme)
# change type back
if 'children' not in scheme:
nodes[scheme['@id']]['data']['_type'] = 'child'
nodes[scheme['@id']]['data']['_shape'] = 'ellipse'
if scheme['repeatable']:
edges.append(create_edge(scheme['@id'], scheme['@id'], _edge_type='child_outlink'))
nodes[scheme_id]['data']['_type'] = 'child'
elif 'outlinks' in nodes[scheme_id]['data']['name']:
nodes[scheme_id]['data']['_type'] = 'container'
containers.append(scheme_id)
else:
nodes[scheme_id]['data']['_type'] = 'parent'
nodes[scheme_id]['data']['_shape'] = 'diamond'
# new node
else:
nodes[scheme_id] = extend_node(create_node(scheme_id, _label, 'root', 'diamond'), scheme)

if '@type' in nodes[scheme_id]['data']:
# not root node, change node type
nodes[scheme_id]['data']['_type'] = 'parent'
nodes[scheme_id]['data']['_shape'] = 'diamond'
# not hierarchical node, change node shape
if 'children' not in scheme:
nodes[scheme_id]['data']['_type'] = 'child'
nodes[scheme_id]['data']['_shape'] = 'ellipse'
# handle repeatable
if nodes[scheme_id]['data']['repeatable']:
edges.append(create_edge(scheme_id, scheme_id, _edge_type='child_outlink'))

# participants
if 'participants' in scheme:
for participant in scheme['participants']:
_label = participant['roleName'].split('/')[-1].replace('_', '')
nodes[participant['@id']] = extend_node(create_node(participant['@id'], _label, 'participant', 'square'), participant)

edges.append(create_edge(scheme['@id'], participant['@id'], _edge_type='step_participant'))
edges.append(create_edge(scheme_id, participant['@id'], _edge_type='step_participant'))

# children
if 'children' in scheme:
for child in scheme['children']:
nodes[child['child']] = extend_node(create_node(child['child'], child['comment'], 'child', 'ellipse'), child)
edges.append(create_edge(scheme['@id'], child['child'], _edge_type='step_child'))

child_id = child['child']
# node already exists
if child_id in nodes:
prev_type = nodes[child_id]['data']['_type']
nodes[child_id]['data']['_type'] = 'child'
nodes[child_id] = extend_node(nodes[child_id], child)
nodes[child_id]['data']['_type'] = prev_type
# new node
else:
nodes[child_id] = extend_node(create_node(child_id, child['comment'], 'child', 'ellipse'), child)
edges.append(create_edge(scheme_id, child_id, _edge_type='step_child'))

# check for outlinks
if len(child['outlinks']):
for outlink in child['outlinks']:
if outlink not in nodes:
_label = outlink.split('/')[-1].replace('_', '')
nodes[outlink] = create_node(outlink, _label, 'child', 'ellipse')
edges.append(create_edge(child['child'], outlink, _edge_type='child_outlink'))

# TODO: and, xor gate
# TODO: optional nodes -- the option is in the cy-style json
# bug? it doesn't show up on parent node
# found: parent node does not have optional key and overwrites child node keys
edges.append(create_edge(child_id, outlink, _edge_type='child_outlink'))

# handle containers, ie. connect previous node to all their successors
edges_to_remove = []
for container in containers:
for edge in edges:
if 'searched' in edge['data'] and edge['data']['searched']:
continue
if edge['data']['target'] == container:
source_id = edge['data']['source']
nodes[source_id]['data']['children_gate'] = nodes[container]['data']['children_gate']
edges_to_remove.append(edge)
edge['data']['searched'] = True
if edge['data']['source'] == container:
edges.append(create_edge(source_id, edge['data']['target'], _edge_type='step_child'))
edges_to_remove.append(edge)
edge['data']['searched'] = True

for index in edges_to_remove:
edges.remove(index)

# === are these two necessary? / what are these for ===
# TODO: entities
# TODO: relations
# if 'relations' in schema and len(schema['relations']):
# # generalize, although at the moment UIUC Q7 only has these two predicates
# predicates = {'Q19267375':'proximity', 'Q6498684':'ownership'}
# for relation in schema['relations']:

# if 'entityRelations' in schema and isinstance(schema['entityRelations'], list):
# for entityRelation in schema['entityRelations']:
Expand Down Expand Up @@ -257,8 +261,8 @@ def homepage():
def upload():
file = request.files['file']
schema_string = file.read().decode("utf-8")
schemaJson = json.loads(schema_string)['events']
schema = schemaJson
schemaJson = json.loads(schema_string)
schema = schemaJson['events']
global nodes
global edges
nodes, edges = get_nodes_and_edges(schema)
Expand All @@ -284,7 +288,7 @@ def reload_schema():
"""Reloads schema; does the same thing as upload."""
schema_string = request.data.decode("utf-8")
schemaJson = json.loads(schema_string)
schema = schemaJson
schema = schemaJson['events']
global nodes
global edges
nodes, edges = get_nodes_and_edges(schema)
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