Source code for cameo.visualization.escher_ext

# Copyright 2015 Novo Nordisk Foundation Center for Biosustainability, DTU.

# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at

# http://www.apache.org/licenses/LICENSE-2.0

# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import json
import escher

from uuid import uuid4

try:
    from IPython.display import Javascript, display
except ImportError:
    pass


def _builders_var():
    js = Javascript("if(window.escher_builders == undefined) {\n"
                    "\twindow.escher_builders = {};\n"
                    "}")
    display(js)


[docs]class NotebookBuilder(escher.Builder): def __init__(self, *args, **kwargs): kwargs['id'] = "escher_" + str(uuid4()).replace("-", "_") super(NotebookBuilder, self).__init__(*args, **kwargs)
[docs] def update(self, reaction_data=None, metabolite_data=None, gene_data=None, reaction_scale=None): self.gene_data = gene_data if gene_data is not None else self.gene_data self.reaction_data = reaction_data if reaction_data is not None else self.reaction_data self.metabolite_data = metabolite_data if metabolite_data is not None else self.metabolite_data js = Javascript('var reaction_data_{the_id} = {reaction_data};\n' 'var metabolite_data_{the_id} = {metabolite_data};\n' 'var gene_data_{the_id} = {gene_data};\n' 'var builder = window.escher_builders["{the_id}"];\n' 'if(builder) {{\n' '\tbuilder.options.reaction_scale = {reaction_scale}\n' '\tbuilder.set_reaction_data(reaction_data_{the_id});\n' '\tbuilder.set_metabolite_data(metabolite_data_{the_id});\n' '\tbuilder.set_gene_data(gene_data_{the_id});\n' '}}'.format( the_id=self.the_id, reaction_data=(json.dumps(self.reaction_data) if self.reaction_data else 'null'), metabolite_data=(json.dumps(self.metabolite_data) if self.metabolite_data else 'null'), gene_data=(json.dumps(self.gene_data) if self.gene_data else 'null'), reaction_scale=json.dumps(reaction_scale) if reaction_scale else 'builder.options.reaction_scale')) display(js)
def _draw_js(self, the_id, enable_editing, menu, enable_keys, dev, fill_screen, scroll_behavior, never_ask_before_quit, static_site_index_json): _builders_var() draw = ("options = {{\n" "\tenable_editing: {enable_editing},\n" "\tmenu: {menu},\n" "\tenable_keys: {enable_keys},\n" "\tscroll_behavior: {scroll_behavior},\n" "\tfill_screen: {fill_screen},\n" "\treaction_data: reaction_data_{the_id},\n" "\tmetabolite_data: metabolite_data_{the_id},\n" "\tgene_data: gene_data_{the_id},\n" "\tnever_ask_before_quit: {never_ask_before_quit}\n").format( the_id=the_id, enable_editing=json.dumps(enable_editing), menu=json.dumps(menu), enable_keys=json.dumps(enable_keys), scroll_behavior=json.dumps(scroll_behavior), fill_screen=json.dumps(fill_screen), never_ask_before_quit=json.dumps(never_ask_before_quit)) # Add the specified options for option in self.options: val = getattr(self, option) if val is None: continue draw += ",\t{option}: {value}\n".format(option=option, value=json.dumps(val)) draw += "};\n\n" # dev needs escher. dev_str = '' if dev else 'escher.' # parse the url in javascript, for building a static site draw += ('window.escher_builders["{the_id}"] = {dev_str}Builder(\n' '\tmap_data_{the_id},\n' '\tmodel_data_{the_id},\n' '\tembedded_css_{the_id},\n' '\td3.select("#{the_id}"),\n' '\toptions);\n'.format(dev_str=dev_str, the_id=the_id)) return draw def _repr_html_(self): return self.display_in_notebook()