biggr_models.handlers.escher_handlers

Attributes

ESCHER_CSS

Classes

EscherHandler

Base RequestHandler that handles standard requests.

Functions

builder_to_html_string(builder, **kwargs)

Module Contents

biggr_models.handlers.escher_handlers.ESCHER_CSS = Multiline-String

Show Value

"""svg.escher-svg #mouse-node {
  fill: none;
}
svg.escher-svg #canvas {
  stroke: #ccc;
  stroke-width: 7px;
  fill: white;
}
svg.escher-svg .resize-rect {
  fill: black;
  opacity: 0;
  stroke: none;
}
svg.escher-svg .label {
  font-family: sans-serif;
  font-style: italic;
  font-weight: bold;
  font-size: 8px;
  fill: black;
  stroke: none;
  text-rendering: optimizelegibility;
  cursor: default;
}
svg.escher-svg .reaction-label {
  font-size: 30px;
  fill: rgb(13, 110, 253);
  text-rendering: optimizelegibility;
}
svg.escher-svg .node-label {
  font-size: 20px;
}
svg.escher-svg .gene-label {
  font-size: 18px;
  fill: rgb(32, 32, 120);
  text-rendering: optimizelegibility;
  cursor: default;
}
svg.escher-svg .text-label .label {
  font-size: 50px;
}
svg.escher-svg .text-label-input {
  font-size: 50px;
}
svg.escher-svg .node-circle {
  stroke-width: 4px;
}
svg.escher-svg .midmarker-circle, svg.escher-svg .multimarker-circle {
  fill: white;
  fill-opacity: 0.2;
  stroke: rgb(50, 50, 50);
  display: none !important;
}
svg.escher-svg g.selected .node-circle{
  stroke-width: 6px;
  stroke: rgb(20, 113, 199);
}
svg.escher-svg g.selected .label {
  fill: rgb(20, 113, 199);
}
svg.escher-svg .metabolite-circle {
  stroke: #d36b2a;
  fill: #ff883f;
}
svg.escher-svg g.selected .metabolite-circle {
  stroke: rgb(5, 2, 0);
}
svg.escher-svg .segment {
  stroke: #334E75;
  stroke-width: 10px;
  fill: none;
}
svg.escher-svg .arrowhead {
  fill: #334E75;
}
svg.escher-svg .stoichiometry-label-rect {
  fill: white;
  opacity: 0.5;
}
svg.escher-svg .stoichiometry-label {
  fill: #334E75;
  font-size: 17px;
}
svg.escher-svg .membrane {
  fill: none;
  stroke: rgb(255, 187, 0);
}
svg.escher-svg .brush .extent {
  fill-opacity: 0.1;
  fill: black;
  stroke: #fff;
  shape-rendering: crispEdges;
}
svg.escher-svg #brush-container .background {
  fill: none;
}
svg.escher-svg .bezier-circle {
  fill: rgb(255,255,255);
}
svg.escher-svg .bezier-circle.b1 {
  stroke: red;
}
svg.escher-svg .bezier-circle.b2 {
  stroke: blue;
}
svg.escher-svg .connect-line{
  stroke: rgb(200,200,200);
}
svg.escher-svg .direction-arrow {
  cursor: default;
  stroke: black;
  stroke-width: 1px;
  fill: white;
  opacity: 0.3;
}
svg.escher-svg .start-reaction-target {
  stroke: rgb(100,100,100);
  fill: none;
  opacity: 0.5;
}
svg.escher-svg .rotation-center-line {
  stroke: red;
  stroke-width: 5px;
}
svg.escher-svg .highlight {
  fill: #D97000;
  text-decoration: underline;
}
svg.escher-svg .node-to-combine {
  stroke-width: 12px !important;
}
.escher-container .button.btn, .escher-container .buttonGroup.btn {
  border-radius: none !important;
  background: rgb(51, 122, 183) !important;
  border: 1px solid rgb(43.35, 103.7, 155.55) !important;
  color: white !important;
  font-weight: normal !important;
}
.legend-container{
  display: none !important;
}
"""

biggr_models.handlers.escher_handlers.builder_to_html_string(builder: escher.plots.Builder, **kwargs)

class biggr_models.handlers.escher_handlers.EscherHandler(application: Application, request: tornado.httputil.HTTPServerRequest, **kwargs: Any)

Bases: biggr_models.handlers.utils.BaseHandler

Base RequestHandler that handles standard requests.

name = None

initialize(**kwargs)

Hook for subclass initialization. Called for each request.

A dictionary passed as the third argument of a URLSpec will be supplied as keyword arguments to initialize().

Example:

class ProfileHandler(RequestHandler):
    def initialize(self, database):
        self.database = database

    def get(self, username):
        ...

app = Application([
    (r'/user/(.*)', ProfileHandler, dict(database=database)),
    ])

prepare()

Called at the beginning of a request before get/post/etc.

Override this method to perform common initialization regardless of the request method. There is no guarantee that prepare will be called if an error occurs that is handled by the framework.

Asynchronous support: Use async def or decorate this method with .gen.coroutine to make it asynchronous. If this method returns an Awaitable execution will not proceed until the Awaitable is done.

Added in version 3.1: Asynchronous support.

get(model_bigg_id: str, map_bigg_id: str, **kwargs)

write_map(map_json: str, builder_opts: Dict[str, Any] = {}, **kwargs)