XBio:D Javascript Library Reference

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Introduction

The xBio:D JavaScript library offers the functionality to create rich, dynamic, and interactive features for use with the OJ_Break API. The OJ_Break API provides procedures to retrieve data within the xBio:D database, and the xBio:D JS library is how that data gets presented. Users planning on working with the xBio:D JS library should be familiar with JavaScript programming and object-oriented programming.

Contents

API Access

All functionality in the xBio:D JS library depends on access of data from the OJ_Break API. See OJ_Break API Access for an overview of the API and how to obtain an API access key.

Example

An easy way to become familiar with the xBio:D JS library is to see a simple example of a web application which uses two xBio:D methods. The first is a Google Maps widget which takes data from the OJ_Break method getLocalities for a specified tnuid and displays the data onto an interactive map. Read more about the Google Maps JavaScript API. The second method used in the example is a listing of included taxa for a specified tnuid by using the OJ_Break method getIncludedTaxa. When you click on any of the linked taxa, that taxon's localities will be shown on the map, however this feature will not be explained in this bare bones example, as only the basics will be covered. 


 1 <!DOCTYPE HTML>
 2 <html>
 3 <head>
 4	<meta charset="UTF-8"/>
 5	<title>xBio:D API test</title>
 6	<link rel="stylesheet" type="text/css" href="xbiod.css">
 7	<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.8/jquery.min.js"></script>
 8	<script type="text/javascript" src="https://maps.googleapis.com/maps/api/js?sensor=false"></script>
 9	<script type="text/javascript" src="http://osuc.biosci.ohio-state.edu/JSLib/xbiod_lib/xbiod.js"></script>
10	<script>
11		// Call the loader for the current page
12		$(document).ready(loader);
13
14		function loader() {
15
16			// Initialize xBio:D library
17			xbiod.init(['visual','taxon'], '{API_KEY}', function() {
18				var tnuid = 605;
19
20				// Load xBio:D components
21				var visual = new xbiod.visual();
22				var taxon = new xbiod.taxon();
23		
24				// Load map
25				visual.showGoogleMap('map_id', tnuid);
26		
27				// Load included taxa
28				taxon.showIncludedTaxa('included_id', tnuid, {show_num_spms: 'Y',
29                                 taxonFormat: '<a href="test.html?tnuid=%tnuid%">%taxon%</a> %author% - %num_spms%'
30				});
31			});
32		}
33	</script>
34     <style  type="text/css">
35		html { height: 100% }
36		body { height: 100%; margin: 0; padding: 0 }
37		#map_id { height: 50% }
38		#included_id { height: 50% }
39     </style>
40 </head>
41 <body>
42	<div id="map_id"/>
43	<div id="included_id"/>
44 </body>
45 </html>

View simple example here (test.html)


There are a few things to note about this example:

  • The <!DOCTYPE html> tag is necessary for HTML 5 applications (line 1)
  • Jquery 1.8 library is included with a <script> tag (line 7)
  • The Google Map API JavaScript library is included with a <script> tag (line 8)
  • The xBio:D JS library is included with a <script> tag (line 9)
  • A function called loader intializes the xBio:D resources when the web page has finished loading (line 14)
  • Two objects where created to access the xBio:D components called visual and taxon (line 21 - 22)
  • The applications are created by calling there respective methods via the xBio:D library components (line 25 & 28 - 29)
  • In the <body> there are two <div> elements which create areas to hold the widgets. The first is called map_id and the second is included_id. (line 42 - 43)


These steps will be explained below.


Declaring Application as HTML 5

It is recommended for any web application to be declared as a true DOCTYPE. This can easily be done by using the HTML 5 DOCTYPE as seen below. This allows the application to be more cross-browser compliant. Please refer to the Google Maps Documentation on HTML 5 for more info. 

<!DOCTYPE html>

Loading JQuery Library

<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.8/jquery.min.js"></script>

The URL in the <script> tag above is the location of the JavaScript file which allows JQuery 1.8 to run on the web application. JQuery is used in the xBio:D JS library to get methods from the OJ_Break API and other scripts. It is a necessary component of any web app that intends to use xBio:D functionality.

Loading the Google Maps API

<script type="text/javascript" src="https://maps.googleapis.com/maps/api/js?sensor=false"></script>

The URL in the <script> tag above is the location of the JavaScript file which will load all the necessary defintions to allow access to the Maps API. Normally, an access key would need to be provided in order to use the Maps library. See Loading the Maps API for more info. This script file is necessary for web apps that use Google Maps as part of the application. It is a necessary file to have in this simple example, but is not required for all xBio:D applications.

Loading the xBio:D JavaScript Library

<script type="text/javascript" src="http://osuc.biosci.ohio-state.edu/JSLib/xbiod_lib/xbiod.js"></script>

The URL in the <script> tage above is the location of the xBio:D JavaScript Library which is a required file for this simple example and any web application that will be using xBio:D applications.

Initializing the xBio:D JS Library

<script>
    // Call the loader for the current page
    $(document).ready(loader);

        function loader() {

            // Initialize xBio:D library
            xbiod.init(['visual','taxon'], '{API_KEY}', function(){

To begin using the xBio:D library, first the components need to be loaded. This is done through the xBio:D init function which takes three parameters: an array of the components to be loaded, an API access key, and a callback function. In this example, the visual and taxon resources are passed to the init function for loading (all resources and their methods can be found in the Reference section below). This example also shows where a user would provide an OJ_Break API access key. See OJ_Break API Access for more information on access keys. Lastly, a callback method needs to be provided which will create the component objects.

Component Objects

// Load xBio:D components
var visual = new xbiod.visual();
var taxon = new xbiod.taxon();

An object derived from a namespace is instatiated using the new keyword and a namespace's constructor. The JavaScript namespace that represents the xBio:D visual applications is the visual namespace/component and similarly the namespace that represents the xBio:D taxon applications is the taxon namespace/component. Access to functionality from either of these components requires an object with a reference to that component. These objects allow methods from each component to be called to the web page.

Calling Application Methods

// Load map
visual.showGoogleMap('map_id', tnuid);
		
// Load included taxa
taxon.showIncludedTaxa('included_id', tnuid, {show_num_spms: 'Y', taxonFormat: '<a href="test.html?tnuid=%tnuid%">%taxon%</a> %author% - %num_spms%'});

Each application has a method associated with it which takes several parameters which will dictate what data it loads, where it will be contained, and options for how it should be presented. These methods and requirements can be found in the Reference section.

In the above example, the visual method showGoogleMap gets passed a <div> element id string which decides where it will be contained and a tnuid which will dictate which taxon data the map will locate.

The taxon method showIncludedTaxa gets passed similar parameters (a specified <div> element id string and a tnuid) however it also gets additional options in the form of a JavaScript object literal. In this example, the option show_num_spms is given the Boolean_flag 'Y' signifying that the application should display the number of specimens for that particular taxon and taxonFormat is assigned to present the data as links using the <a> tag.

Element Containers

Each method requires one or more unique <div> tag ids as string parameters (seen in the example <body> below). This will be used to specify where the resource will be contained in the web page. 

<body>
    <div id="map_id"/>
    <div id="included_id"/>
</body>

Reference

Person

showCollectingTripLocalityInfo

Description

Displays the locality info for a certain person's collecting trip.

Parameters
  • element_id (?)
  • loc_id (?)
  • per_id (?)
  • options
Options
  • tnuid (?)
  • inst_id (?)
  • pnid (?)
  • showChildren (?)
  • completeSpmInfo - Boolean_flag
  • generalFormat - string

showCollectingTrips

Description

Displays collecting trips for a specified collector.

Parameters
  • trips_element_id (?)
  • map_element_id (?)
  • collector_id (?)
  • options
Options
  • generalFormat - string
Additional Requirements

showDescribedTaxa

Description

Displays all taxa described by the specified author.

Parameters
  • element_id (?)
  • author_id (?)
  • options
Options
  • taxonFormat - string

showPublications

Description

Displays all publications for a particular author.

Parameters
  • element_id (?)
  • author_id (?)
  • options
Options

None


Record

showBiologicalInfo

Description

Displays both the habitat and associations for a selected occurrence identifier (cuid).

Parameters
  • element_id (?)
  • cuid (?)
  • options
Options
  • generalFormat - string

showCollectingTripsInfo

Description

Displays collecting trip info for a specified occurrence.

Parameters
  • element_id (?)
  • cuid (?)
  • options
Options
  • generalFormat - string

showDeterminations

Description

Displays determinations for a specified occurence.

Parameters
  • element_id (?)
  • cuid (?)
  • options
Options
  • generalFormat - string

showLocalityInfo

Description

Displays locality info for a specified occurrence.

Parameters
  • element_id (?)
  • cuid (?)
  • options
Options
  • generalFormat - string

showSpecimenInfo

Description

Displays specimen info for a specified occurrence.

Parameters
  • element_id (?)
  • cuid (?)
  • options
Options
  • generalFormat - string


Search

showSearch

Description

A JQuery UI autocomplete search bar which can search for taxa, cuids, institutions, agents, journals, organizations, collecting methods, localities, and places.

Parameters
  • element_id
  • options
Options
  • category - array of the below elements
    • type - a category keyword that will control which data gets searched for
    • handler_url - a URL that will be passed the ID of the selected search option
Additional Requirements
Additional Information
Category Options Formatting

Below is an example of how the categories should be input. 

// Load search
search.showSearch('search_id', {category: [{type: 'taxa', handler_url: 'http://hol.osu.edu/index.html'}, {type: 'cuids', handler_url: 'http://hol.osu.edu/spmInfo.html'}]});
Valid Category Keywords

Below is a list of available category keywords that the category array option can take (Note: the keyword spelling must match exactly what is seen below):

  • all - (if 'all' is chosen, it must be the only keyword chosen)
  • taxa
  • cuids
  • inst
  • agents
  • journals
  • orgs
  • coll_methods
  • locs
  • places


Taxon

showAssociations

Description

Displays all associations for a specified taxon.

Parameters
  • element_id (?)
  • tnuid (?)
  • options
Options
  • rank_grouping - string
  • taxonFormat - string

showCollections

Description

Displays all collections for which specimen of the selected taxon belong.

Parameters
  • element_id (?)
  • tnuid (?)
  • options
Options
  • generalFormat - string

showCollectingMethods

Description

Displays all the collecting methods performed to collect a specified taxon.

Parameters
  • element_id (?)
  • tnuid (?)
  • options
Options
  • generalFormat - string

showContributors

Description

Displays all contributors related to the occurrence, taxonomy, literature, and media of a taxon.

Parameters
  • element_id (?)
  • tnuid (?)
  • options
Options
  • inst_id (?)
  • generalFormat - string

showDeterminers

Description

Displays determiners for a specified taxon.

Parameters
  • element_id (?)
  • tnuid (?)
  • options
Options
  • generalFormat - string

showHabitats

Description

Displays all identified habitats for a selected taxon.

Parameters
  • element_id (?)
  • tnuid (?)
  • options
Options
  • generalFormat - string

showIncludedTaxa

Description

Displays taxa directly included within a taxon but not synonymous with it.

Parameters
  • element_id (?)
  • tnuid (?)
  • options
Options
  • inst_id (?)
  • showSyns (?)
  • showFossils (?)
  • types_only (?)
  • show_num_spms (?)
  • taxonFormat - string
  • useTaxonItalics - boolean

showLiterature

Description

Displays relevent publications for a specified taxon with links to the literature when available.

Parameters
  • element_id (?)
  • tnuid (?)
  • options
Options
  • showSyns (?)
  • taxonFormat - string
  • useTaxonItalics - boolean

showSubordinateTaxa

Description

Displays the count of valid taxa groups available below the current taxon rank.

Parameters
  • element_id (?)
  • tnuid (?)
  • options
Options
  • inst_id (?)
  • generalFormat - string

showSynonyms

Description

Displays all taxa which are objectively or subjectively synonymous with a selected taxon.

Parameters
  • element_id (?)
  • tnuid (?)
  • options
Options
  • showFossils (?)
  • taxonFormat - string
  • useTaxonItalics - boolean

showTaxonImages

Description

Displays a table of all images associated to a specific taxon.

Parameters
  • element_id (?)
  • tnuid (?)
  • options
Options
  • type - string
  • taxonFormat - string

showTypes

Description

Displays information and specimen types for a specified taxon.

Parameters
  • element_id (?)
  • tnuid (?)
  • options
Options
  • showSyns (?)
  • inst_id (?)
  • primary_only - Boolean_flag
  • taxon_author_search - string
  • offset - number
  • limit - number
  • useTaxonItalics - boolean
  • taxonFormat - string


Visual

showGoogleMap

Description

A Google map which displays locality markers for a specified taxon.

Parameters
  • element_id (?)
  • tnuid (?)
  • options
Options
  • pnids (?) - array of number
  • inst_id (?)
  • precDecimals (?)
  • showChildren (?)
Additional Requirements

showTaxonHierarchy

Description

An interactive, tree-based animation which allows a user to navigate through a selected taxon's hierarchy and all taxa available through the OJ_Break API.

Parameters
  • element_id (?)
  • tnuid (?)
  • requestedNode
  • options
Options
  • show_num_spms (?)
  • inst_id (?)
  • showSyns (?)
  • showFossils (?)
  • typesOnly (?)
  • node_color - string or hexadecimal number
  • background_color - string or hexadecimal number
  • handler_url - URL string
Additional Requirements
  • Processing.js 1.4.1+
  • Pass requestedNode parameter a value of null when calling function. See below:
// Load taxon hierarchy
visual.showTaxonHierarchy('canvas_id', tnuid, null, {backgroundColor: 'black'});
Additional Information
Valid Color Options

Below is a list of the available colors that can be used as the background or node color:

  • red
  • scarlet
  • orange
  • yellow
  • green
  • blue
  • cyan
  • violet
  • purple
  • grey/gray
  • white
  • black
URL Handler

The handler_url option can be used to allow the nodes to have links attached to them, so that a user may follow the link for more information on that specific taxon. 

// Load taxon hierarchy
visual.showTaxonHierarchy('canvas_id', tnuid, null, {backgroundColor: 'black', handler_url: 'http://hol.osu.edu/index.html'});

In this example, a default web page URL is given (note the use of http:// at the beginning). When provided a URL, the taxon hierachy animation will present a link button to the top right of the node that is currently being highlighted (see image below). This link will not be present if a URL is not specified.

Link button tut.png

If this button is clicked, the tnuid of the taxon will be appended to the handler_url and will be followed.


Portions of this page are modifications based on work created and shared by Google and used according to terms described in the Creative Commons 3.0 Attribution License.

Retrieved from "https://xbiod.osu.edu/index.php?title=XBio:D_Javascript_Library_Reference&oldid=1412"