Adjustments to jslib bower packaging.

Author: eapearson

.bowerrc

@@ -0,0 +1,3 @@
+{
+  "directory": "jslib/bower_components"
+}

.gitignore

@@ -2,6 +2,3 @@
 /temp/
 /dist/
 *.egg-info/
-/jslib/node_modules/
-/jslib/bower_components/
-/jslib/runtime/

jslib/bower.json bower.json

@@ -1,15 +1,26 @@
 {
   "name": "JsLibrary",
   "version": "0.0.1",
-  "main": "dist/bower/package/js/Taxon.js",
   "ignore": [
-    "src",
-    "package.json",
-    "Gruntfile.js",
-    "README.md",
-    ".gitignore",
-    "tools",
-    "test"
+     ".*",
+     "bin",
+     "build"
+     "CHANGELOG",
+     "config",
+     "data_loading",
+     "docs",
+     "examples",
+     "experiments",
+     "GolgiVolvox.png",
+     "jslib",
+     "lib",
+     "README.md",
+     "redis.conf",
+     "requirements*",
+     "run_tests.sh",
+     "setup.py",
+     "specs",
+     "temp"
   ],
   "dependencies": {
     "bluebird": "2.10.2",
@@ -18,7 +29,6 @@
     "thrift-binary-protocol": "eapearson/thrift-js-binary-protocol#master"
   },
   "devDependencies": {
-    "data-api": "eapearson/data_api#develop",
     "text": "requirejs-text#2.0.14",
     "requirejs-text": "2.0.14",
     "require-yaml": "0.1.2",

bower/Taxon.js

@@ -0,0 +1,241 @@
+/**
+ * @module Taxon
+ * @author Erik Pearson
+ * @version 0.1.0
+ * @param {TaxonLibrary} taxon
+ * @param {TriftLibrary} Thrift
+ * @param {BluebirdPromise} Promise
+ * @returns {Taxon_L12.factory}
+ */
+/*global define*/
+/*jslint white: true, browser: true*/
+define([
+    'bluebird',
+    'taxon_service',
+    'thrift',
+
+    // These don't have representations. Loading them causes the Thrift module
+    // to be enhanced with additional properties (typically just a single
+    //  property, the new capability added.)
+    'thrift_transport_xhr',
+    'thrift_protocol_binary'
+], function (Promise, taxon, Thrift) {
+    'use strict';
+
+    /**
+     * Represents an interface to the Taxon data service.
+     * @alias module:Taxon
+     * @constructs Taxon
+     * @param {object} config
+     * @param {ObjectReference} config.ref The object reference for the object to be accessed.
+     * @param {string} config.url The url for the Taxon Service endpoint.
+     * @param {string} config.token The KBase authorization token to be used to access the service.
+     * @returns {Taxon} A taxon api object
+     */
+    var Taxon = function (config) {
+        var objectReference,
+            dataAPIUrl,
+            authToken,
+            timeout;
+
+        // Construction argument contract enforcement, throw useful exceptions
+        if (!config) {
+            throw {
+                type: 'ArgumentError',
+                name: 'ConfigurationObjectMissing',
+                message: 'Configuration object missing',
+                suggestion: 'This is an API usage error; the taxon factory object is required to have a single configuration object as an argument.'
+            };
+        }
+        objectReference = config.ref;
+        if (!objectReference) {
+            throw {
+                type: 'ArgumentError',
+                name: 'ObjectReferenceMissing',
+                message: 'Object reference "ref" missing',
+                suggestion: 'The object reference is provided as in the "ref" argument to the config property'
+            };
+        }
+        dataAPIUrl = config.url;
+        if (!dataAPIUrl) {
+            throw {
+                type: 'ArgumentError',
+                name: 'UrlMissing',
+                message: 'Cannot find a url for the data api',
+                suggestion: 'The url is provided as in the "url" argument property'
+            };
+
+        }
+        authToken = config.token;
+        if (!authToken) {
+            throw {
+                type: 'ArgumentError',
+                name: 'AuthTokenMissing',
+                message: 'No Authorization found; Authorization is required for the data api',
+                suggestion: 'The authorization is provided in the "token" argument" property'
+            };
+        }
+        timeout = config.timeout;
+        if (!timeout) {
+            timeout = 30000;
+        }
+
+        /**
+         * Creates and returns an instance of the Taxon Thrift client. Note that
+         * this is
+         *
+         * @returns {Taxon_L22.taxon.thrift_serviceClient}
+         * @private
+         * @ignore
+         */
+        function client() {
+             try {
+                var transport = new Thrift.TXHRTransport(dataAPIUrl, {timeout: timeout}),
+                    protocol = new Thrift.TBinaryProtocol(transport),
+                    thriftClient = new taxon.thrift_serviceClient(protocol);
+                return thriftClient;
+            } catch (ex) {
+                // Rethrow exceptions in our format:
+                if (ex.type && ex.name) {
+                    throw ex;
+                } else {
+                    throw {
+                        type: 'ThriftError',
+                        message: 'An error was encountered creating the thrift client objects',
+                        suggestion: 'This could be a configuration or runtime error. Please consult the console for the error object',
+                        errorObject: ex
+                    };
+                }
+            }
+        }
+
+
+        /**
+         * If the Taxon has a parent object, this is returned. Otherwise,
+         * it is ...
+         *
+         * @returns {Promise<ObjectReference|Error>} An object reference string
+         * @throws {ThriftClientError} For networking and client side issues. These errors
+         * are detected by the front end (javascript) code.
+         * @throws {ThriftServiceError} For errors generated by the back end service.
+         *
+         */
+        function getParent() {
+            return Promise.resolve(client().get_parent(authToken, objectReference, true));
+        }
+
+        /**
+         * Get a array of object reference strings which are children (sub objects)
+         * of this Taxon.
+         *
+         * @returns {Array<ObjectReference>} An array of object references representing the children of this object.
+         */
+        function getChildren() {
+            return Promise.resolve(client().get_children(authToken, objectReference, true));
+        }
+
+        /**
+         *
+         * @returns {Array<String>} An array of genome annotation strings
+         */
+        function getGenomeAnnotations() {
+            return Promise.resolve(client().get_genome_annotations(authToken, objectReference, true));
+        }
+
+        /**
+         * Get a list of taxonomic groups the species belongs to, with least specific first,
+         * and most specific, that is the species itself, last.
+         *
+         * @returns {Array<String>} The lineage for this taxon, as an ordered list of taxonomic
+         * ranks from least specific to most specific.
+         *
+         * @example
+         *
+         * Life
+         *   Domain
+         *     Kingdom
+         *       Phylum
+         *         Clas
+         *           Order
+         *             Family
+         *               Genus
+         *                 Species
+         *
+         */
+        function getScientificLineage() {
+            return Promise.resolve(client().get_scientific_lineage(authToken, objectReference, true))
+                .then(function (data) {
+                    return data.split(';').map(function (x) {
+                        return x.trim(' ');
+                    });
+                });
+        }
+
+        /**
+         *
+         * @returns {String}
+         */
+        function getScientificName() {
+            return Promise.resolve(client().get_scientific_name(authToken, objectReference, true));
+        }
+
+        /**
+         *
+         * @returns {Number}
+         */
+        function getTaxonomicId() {
+            return Promise.resolve(client().get_taxonomic_id(authToken, objectReference, true));
+        }
+
+        /**
+         *
+         * @returns {String}
+         */
+        function getKingdom() {
+            return Promise.resolve(client().get_kingdom(authToken, objectReference, true));
+        }
+
+        /**
+         *
+         * @returns {String}
+         */
+        function getDomain() {
+            return Promise.resolve(client().get_domain(authToken, objectReference, true));
+        }
+
+        /**
+         * The NCBI genetic code for the species.
+         *
+         * @returns {Number}
+         * @see {@link http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi} NCBI "The Genetic Codes"
+         */
+        function getGeneticCode() {
+            return Promise.resolve(client().get_genetic_code(authToken, objectReference, true));
+        }
+
+        /**
+         *
+         * @returns {Array<String>}
+         */
+        function getAliases() {
+            return Promise.resolve(client().get_aliases(authToken, objectReference, true));
+        }
+
+        // API
+        return Object.freeze({
+            getParent: getParent,
+            getChildren: getChildren,
+            getGenomeAnnotations: getGenomeAnnotations,
+            getScientificLineage: getScientificLineage,
+            getScientificName: getScientificName,
+            getTaxonomicId: getTaxonomicId,
+            getKingdom: getKingdom,
+            getDomain: getDomain,
+            getGeneticCode: getGeneticCode,
+            getAliases: getAliases
+        });
+
+    };
+
+    return Taxon;
+});