915f56e3f34f66d58bf6573dc4dfddd068bd4090
angie
Tue Apr 19 13:36:48 2016 -0700
Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
refs #15277
diff --git src/hg/hgGateway/hgGateway.html src/hg/hgGateway/hgGateway.html
index ea52519..34f17de 100644
--- src/hg/hgGateway/hgGateway.html
+++ src/hg/hgGateway/hgGateway.html
@@ -1,245 +1,246 @@
<!-- For determining width of scrollbar (if there is one) -->
<div id="sbTestContainer">
<div id="sbTestContainerDPlain"></div>
<div id="sbTestContainerDScroll" style="overflow: scroll;">
<div id="sbTestContainerDInsideScroll"></div>
</div>
</div>
<div id="pageContent">
<div id="selectSpeciesSection" class="jwColumn" style="width: 450px;">
<div class="jwSectionTitle">
Browse/Select Species
</div>
<div class="jwSectionContents">
<div class="jwSubsectionTitle">
Popular Species
</div>
<div class="jwSubsectionContents">
<div class="jwIconWrapper">
<div class="jwIconSprite jwIconSpriteHuman"></div>
<div class="jwIconSpriteLabel">Human</div>
</div>
<div class="jwIconWrapper">
<div class="jwIconSprite jwIconSpriteMouse"></div>
<div class="jwIconSpriteLabel">Mouse</div>
</div>
<div class="jwIconWrapper">
<div class="jwIconSprite jwIconSpriteRat"></div>
<div class="jwIconSpriteLabel">Rat</div>
</div>
<div class="jwIconWrapper">
<div class="jwIconSprite jwIconSpriteFly"></div>
<div class="jwIconSpriteLabel">Fruitfly</div>
</div>
<div class="jwIconWrapper">
<div class="jwIconSprite jwIconSpriteWorm"></div>
<div class="jwIconSpriteLabel">Worm</div>
</div>
<div class="jwIconWrapper">
<div class="jwIconSprite jwIconSpriteYeast"></div>
<div class="jwIconSpriteLabel">Yeast</div>
</div>
<div>
<input id="speciesSearch" value="" size=40>
</div>
</div>
- <div class="jwSubsectionTitle">
+ <!-- This subsection is hidden unless hgGateway.js has a tree to draw. -->
+ <div id="representedSpeciesTitle" class="jwSubsectionTitle" style="display: none;">
Represented Species
</div>
- <div id="speciesGraphic" class="jwSubsectionContents">
+ <div id="speciesGraphic" class="jwSubsectionContents" style="display: none;">
<div id="sliderWidgetContainer" class="jwSliderWidget">
- <div id="sliderSvgContainer" class="jwSliderIcon" style="display: none;">
+ <div id="sliderSvgContainer" class="jwSliderIcon">
<svg id="sliderSvg"
xmlns:svg="http://www.w3.org/2000/svg"
xmlns="http://www.w3.org/2000/svg"
version="1.1"
height="53"
width="30">
<rect id="sliderRectangle"
ry="3"
y="1.5"
x="1.5"
height="50"
width="24"
style="fill: none; stroke: #222222; stroke-width: 3;"></rect>
<path id="sliderTriangle"
d="m 2.5,24 0,6 4,-3 z"
style="fill: #222222; stroke: #222222; stroke-width: 3"></path>
</svg>
</div> <!-- sliderSvgContainer -->
<div class="jwRainbowSlider" id="rainbowSlider">
<!-- JS will populate this -->
</div>
</div>
<div class="jwSpeciesPicker" id="speciesPicker">
<div id="speciesTreeContainer" class="jwColumn" style="overflow: visible;">
<svg id="speciesTree"
xmlns="http://www.w3.org/2000/svg"
xmlns:xlink="http://www.w3.org/1999/xlink">
<defs>
<!-- The y coordinates of these will be overwritten by JS. -->
<!-- I tried creating them in JS, but then the image style
url('#clipWhatever') didn't work. -->
<clipPath id="clipHuman">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipMouse">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipFly">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipWorm">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipYeast">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipMonkey">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipHedgehog">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipPig">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipCow">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipOrca">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipHorse">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipDog">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipWalrus">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipBat">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipElephant">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipManatee">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipArmadillo">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipKangaroo">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipBird">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipLizard">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipFrog">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipFish">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
<clipPath id="clipEbola">
<rect x="2" y="0" width="65" height="65"></rect>
</clipPath>
</defs>
<style>
text {
stroke:none;
fill: black;
font-size: 12px;
text-anchor: end;
letter-spacing: 0.025em;
cursor: pointer;
}
text:hover, text.selected {
fill: #31469A; /* rainbow dark blue: */
font-weight: bold;
}
text.trackHubsLink {
text-anchor: start;
}
line {
stroke: #4b759d;
stroke-width: 1;
}
line:hover {
stroke-width: 2;
}
</style>
<!-- Tree inserted here by JS -->
</svg>
</div> <!-- speciesTreeContainer -->
</div> <!-- speciesPicker -->
</div> <!-- subsection contents -->
</div>
</div>
<div id="findPositionSection" class ="jwColumn">
<div class="jwSectionTitle">
Find Position
</div>
<div id="findPositionContents" class="jwSectionContents"
style="display: none;"> <!-- To avoid empty containers jumping around, hide first. -->
<div id="findPosInputContainer" style="display: inline-block;">
<div id="selectAssemblyLabel" class="jwInputLabel">Assembly</div>
<select id="selectAssembly">
</select>
<div class="vertSpacerAbovePosition"></div>
<div class="jwInputLabel">
Position:
<span id="positionDisplay" class="jwPosDisplay"></span>
<i id="copyPosition" class="fa fa-copy jwTextBlue"
title="Copy the current position into the input below"></i>
</div>
<input id="positionInput" value="" size="40">
</div>
<div class="jwGoButtonContainer"
title="Go to the Genome Browser">
<div class="jwGoButton">
GO
</div>
<i class="jwGoIcon fa fa-play fa-2x"></i>
</div>
<div class="vertSpacerBelowPosition"></div>
<div id="descriptionTitle" class="jwDescriptionTitle">
<b><span id="descriptionGenome"></span> Genome Browser</b> -
<span id="descriptionDb"></span> assembly
<div class="jwFloatRight">
<a id="chromInfoLink" class="jwAnchor" href="hgTracks?chromInfoPage=&hgsid=$hgsid">
<div class="jwWhiteButton">
view sequences
</div>
</a>
</div>
</div>
<div id="descriptionText" class="jwDescriptionText">
</div>
</div>
</div>
</div>
<div style="clear: both;"></div>