How can we embed n instances of Tree Illustrator into a notebook?

This is an attempt to do a simple thing.



In [2]:

    
from pprint import pprint
print("hello")









    



hello

Will this work with static notebooks?

Can we enable collaboration (esp. real-time) in these notebooks?

see Sage Notebooks for a pretty-good implementation, but won't show much inside of a TI instance.



In [1]:

    
test = "HI MOM"
print(test)
%qtconsole



In [2]:

    
# use a server-side support class to load the static stylist into an IFrame
from IPython.lib.display import IFrame
IFrame(
    src="http://rawgit.com/OpenTreeOfLife/tree-illustrator/master/stylist/stylist.html", 
    width="100%", 
    height=500,
    trees=[],
    data=[],
    ornaments=[]
)









    Out[2]:



In [4]:

    
# Let's try another, as a proper subclass of IFrame above
from IPython.lib.display import IFrame
class TreeIllustrator(IFrame):
    """Class for embedding an instance of Tree Illustrator in an IPython session
    This could optionally use keyword arguments to pass tree data, Vega specs, etc.
        ti2 = TreeIllustrator()
        display(ti2)
    To load an initial tree (in this case, a Newick string in the IPython session)::
        ti3 = TreeIllustrator(
            trees=[ myNewick ]
        )
        display(ti3)
    TODO: Add more options for insertion of style, Vega specs, maybe a complete illustration?
    We might consider using our Illustration JSON as the model for even partial specs here.
    """

    def __init__(self, id, width='100%', height=400, **kwargs):
        # tokenize? eg, src = "https://www.youtube.com/embed/{0}".format(id)
        src="http://rawgit.com/OpenTreeOfLife/tree-illustrator/master/stylist/stylist.html"
        super(TreeIllustrator, self).__init__(src, width, height, **kwargs)



In [5]:

    
TreeIllustrator('ti4')









    Out[5]:



In [9]:

    
%%javascript
// Load a JS file (for example, general support for Tree Illustrator instances) from a second gist at
// https://gist.github.com/jimallman/f16ef46d4d447e4bb74e
$.getScript('https://rawgit.com/jimallman/f16ef46d4d447e4bb74e/raw/4874dd6acd55df390e1aa6dde308914dbba4746b/js-import-test.js');

// here's a JS-only implementation of the TreeIllustrator class above
var elementID = 'ti5'; // expect this as an incoming argument? scan the DOM to pick a sensible default?
this.append_display_data({
    'data': {
        'text/html': '<iframe id="'+ elementID +'" width="100%" height="500" \
                       src="http://rawgit.com/OpenTreeOfLife/tree-illustrator/master/stylist/stylist.html?data=%5B%5D&amp;ornaments=%5B%5D&amp;trees=%5B%5D" \
                       frameborder="0" allowfullscreen="allowfullscreen"> \
                      </iframe>'
    } 
})

// Assign serial IDs? or maybe base these on the ID of the current cell (if it can be determined from JS)
var tiDomain = 'http://rawgit.com';
var ti5 = $('#ti5')[0];
var ti5window = ti5.contentWindow;

// add a listener for messages from the Tree Illustrator instance (its window)
window.addEventListener("message", receiveMessage, false);
// TODO: make sure we're not duplicating this? or allow one listener per instance?

function receiveMessage(event) {
    // the dispatched message has origin, data, source [sending window]
    if (event.origin !== tiDomain) {
        alert("Attempted inter-window message from an unexpected domain: ["+ event.origin +"], expected: ["+ tiDomain +"]");
        return;
    }

    // examine the payload to see what's what..
    if (event.source !== ti5window) {
        alert("Attempted inter-window message from an unexpected window: ["+ event.source +"], expected: ["+ ti5window +"]");
        return;
    }
    
    console.log(event);
    debugger;
}

// define methods for TreeIllustrator instances

function injectTree( data, treeIndex, options ) {
    // pass newick, other formats? bounce to peyotl for conversion, as needed?
    // specify nth tree to REPLACE an existing tree?
    ti5window.postMessage(
        {
            treeData: data,
            treeIndex: treeIndex,
            options: options        
        },
        tiDomain  // TODO: restrict to the domain extracted from 'src' URL above?
    );
    // TODO: consider a more general message 'addOrReplaceElement' with friendly JS wrappers
}

function useStyleGuide( data ) {
    // specify its name/label; complain if not found!
}

function listAllPossibleInputVars() {
    // return a list of variables in the current IPython session, so TI 
    // can offer these as sources for its trees, supplemental data, etc.
}

function saveIllustration() {
    // save everything? or just the main, monolithic JSON?
}

function loadIllustration(data) {
    // based on URL? or assume it's a local variable
}

function dumpSVG() {
    /* possibly options for 
     * - put SVG into (or append to?) output of this cell
     * - render it as literal SVG (plus available source?)
     * - save it to a "local" file for persistence & display
     * - show it in a new window/frame (current behavior)
     */
}

injectTree( {'size':'small', 'color':'blue'} );


/* Documentation used to build this:

    OutputArea class ('this' above) and its methods:
        https://github.com/jupyter/notebook/blob/master/notebook/static/notebook/js/outputarea.js

    basdf
        http:
*/

SVG output

Here's an example of literal SVG output from the Tree Illustrator above. We should support extracting this from a button (within the Tree Illustrator instance, or in the hosting page?), or perhaps a simple API call like

ti_3.dumpSVG( {showDiagnostics: true} );



In [19]:

    
%%html
<svg class="marks" width="9.010416666666666in" height="12.126953125in" viewBox="-50 -124.1875 865 1164.1875"><defs>
        <!-- Keep volatile masks, backdrops, etc. here -->
        <mask id="viewport-mask">
          <g id="mask-shapes">
            <rect id="viewport-bounds" fill="#888" x="-210.36532951289405" y="0" width="1185.730659025788" height="990"></rect>
            <rect id="illustration-bounds" fill="#fff" x="0" y="0" width="765" height="990"></rect>
          </g>
        </mask>
        <clipPath id="printing-clip-path">
            <use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#illustration-bounds"></use>
        </clipPath>
        <g id="printing-crop-marks">
            <g id="crop-mark-top-left">
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                <path stroke="black" stroke-width="0.25pt" fill="none" d="M -10 0 H -50"></path>
            </g>
            <g id="crop-mark-top-right" transform="translate(765, 0)">
                <path stroke="black" stroke-width="0.25pt" fill="none" d="M 0 -10 V -50"></path>
                <path stroke="black" stroke-width="0.25pt" fill="none" d="M 10 0 H 50"></path>
            </g>
            <g id="crop-mark-bottom-left" transform="translate(0, 990)">
                <path stroke="black" stroke-width="0.25pt" fill="none" d="M 0 10 V 50"></path>
                <path stroke="black" stroke-width="0.25pt" fill="none" d="M -10 0 H -50"></path>
            </g>
            <g id="crop-mark-bottom-right" transform="translate(765, 990)">
                <path stroke="black" stroke-width="0.25pt" fill="none" d="M 0 10 V 50"></path>
                <path stroke="black" stroke-width="0.25pt" fill="none" d="M 10 0 H 50"></path>
            </g>
        </g>
        <g id="printing-description">
            <text id="printing-description-name" x="-50" y="-110" style="font-family: sans-serif; font-weight: bold;">TODO: Add the actual illustration name, or 'Untitled'</text>
            <text id="printing-description-datetime" x="-50" y="-94" style="font-family: sans-serif; font-size: 0.8em;">Generated 8/3/2015 - 11:11:35 PM</text>
        </g>
        <g id="printing-rulers">
            <g id="ruler-cm">
                <text style="font-family: sans-serif; font-size: 0.5em; text-anchor: end;" x="-4" y="-16">cm</text>
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            </g>
            <g id="ruler-inches">
                <text style="font-family: sans-serif; font-size: 0.5em; text-anchor: end;" x="-4" y="-1">inches</text>
                <line x1="0" y1="0" x2="540" y2="0" stroke="#000" stroke-width="0.25pt" stroke-linecap="square"></line>
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            </g>
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            <line x1="0" y1="0" x2="0" y2="-5" stroke="#000" stroke-width="0.25pt" stroke-linecap="square"></line>
        </g>
      </defs><rect id="viewport-background" width="100%" height="100%" x="-210.36532951289405" y="0" style="fill: rgb(204, 204, 204); visibility: hidden;"></rect><use id="illustration-background" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#illustration-bounds" style="stroke: rgb(187, 187, 187); visibility: hidden;"></use><use id="crop-marks" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#printing-crop-marks"></use><use id="description" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#printing-description"></use><use id="rulers" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#printing-rulers" x="0" y="-60"></use><g transform="translate(0,0)"><g id="g34" class="type-group"><g transform="translate(0,0)"><rect class="background" width="800" height="900" style="pointer-events: none; fill: none;"></rect><g id="g35" class="type-group illustration-elements" style="clip-path: url(#printing-clip-path);"><g transform="translate(0,0)"><rect class="background" 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font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);">Lactuca</text><text x="-106.09101632727847" y="121.13699117683437" text-anchor="end" transform="rotate(311.8116718639026 -106.09101632727847,121.13699117683437)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);"></text><text x="-170.01648201288148" y="141.8509019796491" text-anchor="end" transform="rotate(320.7605355002663 -170.01648201288148,141.8509019796491)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);"></text><text x="-183.48976940869113" y="144.40829104433502" text-anchor="end" transform="rotate(322.39689913663005 -183.48976940869113,144.40829104433502)" style="font-style: normal; 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normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);">Nicotiana tomentosa</text><text x="-101.3878873066047" y="196.84455505799417" text-anchor="end" transform="rotate(297.85144459117555 -101.3878873066047,196.84455505799417)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);"></text><text x="-112.80293589899401" y="204.44497463270517" text-anchor="end" transform="rotate(299.48780822753906 -112.80293589899401,204.44497463270517)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);">Nicotiana sylvestris</text><text x="-100.947445545066" y="210.55133159855805" text-anchor="end" transform="rotate(296.2150809548118 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transform="rotate(279.03326277299357 -30.701552315199596,207.07856412832342)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);"></text><text x="-50.63481896151807" y="227.94377620091822" text-anchor="end" transform="rotate(283.1241718639026 -50.63481896151807,227.94377620091822)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);">Solanum lycopersicum</text><text x="-16.76508026203134" y="220.78544932192457" text-anchor="end" transform="rotate(274.94235368208456 -16.76508026203134,220.78544932192457)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);"></text><text x="-24.321135386031976" y="232.22991274496556" 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calamus</text><text x="47.729441533525886" y="128.27651808627402" text-anchor="start" transform="rotate(68.99064913663005 47.729441533525886,128.27651808627402)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);"></text><text x="50.3701216930918" y="228.002414111393" text-anchor="start" transform="rotate(76.94235368208444 50.3701216930918,228.002414111393)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);">Dioscorea</text><text x="70.75390124936091" y="131.06946256681027" text-anchor="start" transform="rotate(61.03894459117544 70.75390124936091,131.06946256681027)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);"></text><text x="78.04788959658657" y="207.20957863476173" text-anchor="start" transform="rotate(68.76053550026631 78.04788959658657,207.20957863476173)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);"></text><text x="76.03211255237481" y="220.7744728468919" text-anchor="start" transform="rotate(70.39689913663005 76.03211255237481,220.7744728468919)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);">Phalaenopsis</text><text x="88.51186420220913" y="216.07382973291723" text-anchor="start" transform="rotate(67.12417186390269 88.51186420220913,216.07382973291723)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);">Yucca</text><text x="94.83670749423939" y="130.13636420456578" text-anchor="start" transform="rotate(53.31735368208456 94.83670749423939,130.13636420456578)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);"></text><text x="112.56548093824993" y="204.5758111340158" text-anchor="start" transform="rotate(60.57871731844807 112.56548093824993,204.5758111340158)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);">Elaeis</text><text x="118.81550000656" y="125.89006748411543" text-anchor="start" transform="rotate(46.05599004572082 118.81550000656,125.89006748411543)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);"></text><text x="135.1516344835439" y="190.41083397860154" text-anchor="start" transform="rotate(54.03326277299357 135.1516344835439,190.41083397860154)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);">Musa</text><text x="144.5663875775445" y="115.73137608718753" text-anchor="start" transform="rotate(38.07871731844807 144.5663875775445,115.73137608718753)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);"></text><text x="155.9758797855584" y="173.76356040643574" text-anchor="start" transform="rotate(47.48780822753906 155.9758797855584,173.76356040643574)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);">Typha</text><text x="172.07829058980536" y="96.4459194071703" text-anchor="start" transform="rotate(28.669626409357306 172.07829058980536,96.4459194071703)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);"></text><text x="166.19019756547704" y="127.29860670548914" text-anchor="start" transform="rotate(36.85144459117532 166.19019756547704,127.29860670548914)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);"></text><text x="174.76674096020352" y="154.85101308725473" text-anchor="start" transform="rotate(40.942353682084445 174.76674096020352,154.85101308725473)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);">Zea</text><text x="184.93680351398876" y="121.76067203536937" text-anchor="start" transform="rotate(32.760535500266315 184.93680351398876,121.76067203536937)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);"></text><text x="191.27925039514813" y="133.91974599837863" text-anchor="start" transform="rotate(34.39689913662994 191.27925039514813,133.91974599837863)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: rgb(0, 0, 0);">Saccharum</text><text x="198.61261286675813" y="122.7814318626366" text-anchor="start" transform="rotate(31.124171863902802 198.61261286675813,122.7814318626366)" style="font-style: normal; font-variant: normal; font-weight: normal; font-stretch: normal; font-size: 12px; line-height: normal; font-family: sans-serif; fill: 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In [49]:

    
%%javascript 
// Load JS support for Tree Illustrator widgets 
$.getScript('https://rawgit.com/OpenTreeOfLife/tree-illustrator/master/stylist/ipynb-tree-illustrator.js');
// https://rawgit.com/OpenTreeOfLife/tree-illustrator/83999e2f924abac059042452e60c62152c262950/stylist/ipynb-tree-illustrator.js');
var ti = new IPythonTreeIllustrator.IllustratorWidget(this);



In [1]:

    
# define some variables in Python
test_int = 23
test_list = ['a','b','c']
test_tuple = ('A','B','C')
test_dict = {'Aa','Bb','Cc'}
test_dict









    Out[1]:





{'Aa', 'Bb', 'Cc'}



In [2]:

    
%%javascript
test_int



In [12]:

    
%%javascript
IPython.kernel



In [ ]: