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351 lines
19 KiB
JavaScript
351 lines
19 KiB
JavaScript
var require = patchRequire( require ),
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spaceghost = require( 'spaceghost' ).fromCasper( casper ),
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xpath = require( 'casper' ).selectXPath,
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utils = require( 'utils' ),
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format = utils.format;
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spaceghost.test.begin( 'Test the HDA API', 0, function suite( test ){
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spaceghost.start();
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// =================================================================== SET UP
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var email = spaceghost.user.getRandomEmail(),
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password = '123456';
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if( spaceghost.fixtureData.testUser ){
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email = spaceghost.fixtureData.testUser.email;
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password = spaceghost.fixtureData.testUser.password;
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}
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spaceghost.user.loginOrRegisterUser( email, password );
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spaceghost.openHomePage().api.tools.thenUploadToCurrent({
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filepath: '../../test-data/1.sam'
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});
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// =================================================================== TESTS
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var summaryKeys = [ 'id', 'name', 'history_id', 'state', 'deleted', 'purged', 'visible', 'url', 'type' ],
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detailKeys = [
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// the following are always present regardless of datatype
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'id', 'name', 'api_type', 'model_class',
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'history_id', 'hid',
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'accessible', 'deleted', 'visible', 'purged',
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'state', 'data_type', 'file_ext', 'file_size',
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'misc_info', 'misc_blurb',
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'download_url', 'visualizations', 'display_apps', 'display_types',
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'genome_build',
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// the following are NOT always present DEPENDING ON datatype
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'metadata_dbkey',
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'metadata_column_names', 'metadata_column_types', 'metadata_columns',
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'metadata_comment_lines', 'metadata_data_lines'
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];
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// ------------------------------------------------------------------------------------------- logged in user
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spaceghost.then( function(){
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// ------------------------------------------------------------------------------------------- INDEX
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this.test.comment( 'index should return a list of summary data for each hda' );
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var histories = this.api.histories.index(),
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lastHistory = histories[0],
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hdaIndex = this.api.hdas.index( lastHistory.id );
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//this.debug( 'hdaIndex:' + this.jsonStr( hdaIndex ) );
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this.test.assert( utils.isArray( hdaIndex ), "index returned an array: length " + hdaIndex.length );
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this.test.assert( hdaIndex.length >= 1, 'Has at least one hda' );
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var firstHda = hdaIndex[0];
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this.test.assert( this.hasKeys( firstHda, summaryKeys ), 'Has the proper keys' );
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this.test.assert( this.api.isEncodedId( firstHda.id ), 'Id appears well-formed: ' + firstHda.id );
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this.test.assert( firstHda.name === '1.sam', 'Title matches: ' + firstHda.name );
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// ------------------------------------------------------------------------------------------- SHOW
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this.test.comment( 'show should get an HDA details object' );
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var hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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//this.debug( this.jsonStr( hdaShow ) );
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this.test.assert( this.hasKeys( hdaShow, detailKeys ), 'Has the proper keys' );
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//TODO: validate data in each hdaShow attribute...
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// ------------------------------------------------------------------------------------------- INDEX (detailed)
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this.test.comment( 'index should return a list of detailed data for each hda in "ids" when passed' );
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hdaIndex = this.api.hdas.index( lastHistory.id, [ firstHda.id ] );
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this.debug( 'hdaIndex:' + this.jsonStr( hdaIndex ) );
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this.test.assert( utils.isArray( hdaIndex ), "index returned an array: length " + hdaIndex.length );
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this.test.assert( hdaIndex.length >= 1, 'Has at least one hda' );
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firstHda = hdaIndex[0];
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this.test.assert( this.hasKeys( firstHda, detailKeys ), 'Has the proper keys' );
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//TODO??: validate data in firstHda attribute? we ASSUME it's from a common method as show...
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// ------------------------------------------------------------------------------------------- CREATE
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//TODO: create from_ld_id
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this.test.comment( 'create should allow copying an accessible hda' );
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hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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var returned = this.api.hdas.create( lastHistory.id, {
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source : 'hda',
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content : hdaShow.id
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});
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//this.debug( 'returned:' + this.jsonStr( returned ) );
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this.test.assert( this.hasKeys( returned, detailKeys ), 'Has the proper keys' );
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this.test.assert( typeof returned.id !== 'number' && isNaN( Number( returned.id ) ),
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'id seems to be encoded: ' + returned.id );
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this.test.assert( typeof returned.history_id !== 'number' && isNaN( Number( returned.history_id ) ),
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'history_id seems to be encoded: ' + returned.history_id );
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// ------------------------------------------------------------------------------------------- UPDATE
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// ........................................................................................... idiot proofing
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this.test.comment( 'updating using a nonsense key should NOT fail with an error' );
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returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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konamiCode : 'uuddlrlrba'
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});
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this.test.assert( returned.id === firstHda.id );
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this.test.comment( 'updating by attempting to change type should cause an error' );
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this.api.assertRaises( function(){
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returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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//name : false
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deleted : 'sure why not'
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});
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}, 400, "must be a type: <type 'bool'>", 'changing deleted type failed' );
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// ........................................................................................... name
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this.test.comment( 'update should allow changing the name' );
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returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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name : 'New name'
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});
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//this.debug( 'returned:\n' + this.jsonStr( returned ) );
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hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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this.test.assert( hdaShow.name === 'New name', "Name successfully set via update: " + hdaShow.name );
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// no sanitizing input
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//this.test.comment( 'update should sanitize any new name' );
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this.test.comment( 'update should allow unicode in names' );
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var unicodeName = 'Ржевский сапоги';
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returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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name : unicodeName
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});
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//this.debug( 'returned:\n' + this.jsonStr( returned ) );
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hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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this.test.assert( hdaShow.name === unicodeName, "Update accepted unicode name: " + hdaShow.name );
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this.test.comment( 'update should allow escaped quotations in names' );
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var quotedName = '"Bler"';
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returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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name : quotedName
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});
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//this.debug( 'returned:\n' + this.jsonStr( returned ) );
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hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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this.test.assert( hdaShow.name === quotedName,
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"Update accepted escaped quotations in name: " + hdaShow.name );
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// ........................................................................................... deleted
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this.test.comment( 'update should allow changing the deleted flag' );
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returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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deleted: true
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});
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//this.debug( 'returned:\n' + this.jsonStr( returned ) );
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hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id, true );
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this.test.assert( hdaShow.deleted === true, "Update set the deleted flag: " + hdaShow.deleted );
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this.test.comment( 'update should allow changing the deleted flag back' );
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returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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deleted: false
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});
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//this.debug( 'returned:\n' + this.jsonStr( returned ) );
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hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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this.test.assert( hdaShow.deleted === false, "Update set the deleted flag: " + hdaShow.deleted );
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// ........................................................................................... visible/hidden
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this.test.comment( 'update should allow changing the visible flag' );
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returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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visible: false
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});
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//this.debug( 'returned:\n' + this.jsonStr( returned ) );
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hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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this.test.assert( hdaShow.visible === false, "Update set the visible flag: " + hdaShow.visible );
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// ........................................................................................... genome/dbkey
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this.test.comment( 'update should allow changing the genome_build' );
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returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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genome_build : 'hg18'
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});
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//this.debug( 'returned:\n' + this.jsonStr( returned ) );
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hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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//this.debug( 'hdaShow:\n' + this.jsonStr( hdaShow ) );
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this.test.assert( hdaShow.genome_build === 'hg18',
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"genome_build successfully set via update: " + hdaShow.genome_build );
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this.test.assert( hdaShow.metadata_dbkey === 'hg18',
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"metadata_dbkey successfully set via the same update: " + hdaShow.metadata_dbkey );
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// no sanitizing input
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//this.test.comment( 'update should sanitize any genome_build' );
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//TODO: this actually throws an 'invalid genome_build' error
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//this.test.comment( 'update should allow unicode in genome builds' );
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//var unicodeBuild = 'Ржевский18';
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//returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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// genome_build : unicodeBuild
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//});
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//this.debug( 'returned:\n' + this.jsonStr( returned ) );
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//hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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//this.debug( 'hdaShow:\n' + this.jsonStr( hdaShow ) );
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//this.test.assert( hdaShow.genome_build === unicodeBuild,
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// "Update accepted unicode genome_build: " + hdaShow.genome_build );
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// ........................................................................................... misc_info/info
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this.test.comment( 'update should allow changing the misc_info' );
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var newInfo = 'I\'ve made a huge mistake.';
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returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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misc_info : newInfo
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});
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//this.debug( 'returned:\n' + this.jsonStr( returned ) );
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hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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this.test.assert( hdaShow.misc_info === newInfo,
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"misc_info successfully set via update: " + hdaShow.misc_info );
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// no sanitizing input
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//this.test.comment( 'update should sanitize any misc_info' );
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this.test.comment( 'update should allow unicode in misc_info' );
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var unicodeInfo = '여보!';
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returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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misc_info : unicodeInfo
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});
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//this.debug( 'returned:\n' + this.jsonStr( returned ) );
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hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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this.test.assert( hdaShow.misc_info === unicodeInfo,
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"Update accepted unicode misc_info: " + hdaShow.misc_info );
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this.test.comment( 'update should set misc_info to the empty string if sent null/None' );
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returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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misc_info : null
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});
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//this.debug( 'returned:\n' + this.jsonStr( returned ) );
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hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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this.test.assert( hdaShow.misc_info === '',
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"Update used null as the empty string: " + hdaShow.misc_info );
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// ........................................................................................... annotation
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// currently fails because no annotation is returned in details
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this.test.comment( 'update should allow changing the annotation' );
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var newAnnotation = 'Found this sample on a movie theatre floor';
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returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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annotation : newAnnotation
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});
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//this.debug( 'returned:\n' + this.jsonStr( returned ) );
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hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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this.test.assert( hdaShow.annotation === newAnnotation,
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"Annotation successfully set via update: " + hdaShow.annotation );
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// no sanitizing input
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//this.test.comment( 'update should sanitize any new annotation' );
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this.test.comment( 'update should allow unicode in annotations' );
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var unicodeAnnotation = 'お願いは、それが落下させない';
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returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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annotation : unicodeAnnotation
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});
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//this.debug( 'returned:\n' + this.jsonStr( returned ) );
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hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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this.test.assert( hdaShow.annotation === unicodeAnnotation,
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"Update accepted unicode annotation: " + hdaShow.annotation );
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this.test.comment( 'update should allow escaped quotations in annotations' );
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var quotedAnnotation = '"Bler"';
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returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
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annotation : quotedAnnotation
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});
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//this.debug( 'returned:\n' + this.jsonStr( returned ) );
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hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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this.test.assert( hdaShow.annotation === quotedAnnotation,
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"Update accepted escaped quotations in annotation: " + hdaShow.annotation );
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// ------------------------------------------------------------------------------------------- ERRORS
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this.test.comment( 'create should error with "Please define the source" when the param "from_ld_id" is not used' );
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this.api.assertRaises( function(){
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this.api.hdas.create( lastHistory.id, { bler: 'bler' } );
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}, 400, "must be either 'library' or 'hda'", 'create with no source failed' );
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this.test.comment( 'updating using a nonsense key should fail silently' );
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returned = this.api.hdas.update( lastHistory.id, hdaShow.id, {
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konamiCode : 'uuddlrlrba'
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});
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this.test.assert( returned.konamiCode === undefined, 'key was not set: ' + returned.konamiCode );
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spaceghost.test.comment( 'A bad id should throw an error when using show' );
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this.api.assertRaises( function(){
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this.api.hdas.show( lastHistory.id, '1234123412341234' );
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}, 400, 'unable to decode', 'Bad Request with invalid id: show' );
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spaceghost.test.comment( 'A bad id should throw an error when using update' );
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this.api.assertRaises( function(){
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this.api.hdas.update( lastHistory.id, '1234123412341234', {} );
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}, 400, 'unable to decode', 'Bad Request with invalid id: update' );
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spaceghost.test.comment( 'A bad id should throw an error when using delete' );
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this.api.assertRaises( function(){
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this.api.hdas.delete_( lastHistory.id, '1234123412341234' );
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}, 400, 'unable to decode', 'Bad Request with invalid id: delete' );
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spaceghost.test.comment( 'A bad id should throw an error when using undelete' );
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this.test.comment( 'updating by attempting to change type should cause an error' );
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[ 'name', 'misc_info' ].forEach( function( key ){
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var updatedAttrs = {};
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updatedAttrs[ key ] = false;
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spaceghost.api.assertRaises( function(){
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returned = spaceghost.api.hdas.update( hdaShow.history_id, hdaShow.id, updatedAttrs );
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}, 400, "must be a type: <type 'basestring'>", 'type validation error' );
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});
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spaceghost.api.assertRaises( function(){
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returned = spaceghost.api.hdas.update( hdaShow.history_id, hdaShow.id, { annotation: false } );
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}, 400, "must be a type: (<type 'basestring'>, <type 'NoneType'>)", 'type validation error' );
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spaceghost.api.assertRaises( function(){
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returned = spaceghost.api.hdas.update( hdaShow.history_id, hdaShow.id, { genome_build: false } );
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}, 400, "must be a type: <type 'basestring'>", 'type validation error (genome_build must be string)' );
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[ 'deleted', 'visible' ].forEach( function( key ){
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var updatedAttrs = {};
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updatedAttrs[ key ] = 'straaang';
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spaceghost.api.assertRaises( function(){
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returned = spaceghost.api.hdas.update( hdaShow.history_id, hdaShow.id, updatedAttrs );
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}, 400, "must be a type: <type 'bool'>", 'type validation error' );
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});
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spaceghost.api.assertRaises( function(){
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returned = spaceghost.api.hdas.update( hdaShow.history_id, hdaShow.id, { tags: 'you\'re it' });
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}, 400, "must be a type: <type 'list'>", 'type validation error' );
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spaceghost.api.assertRaises( function(){
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returned = spaceghost.api.hdas.update( hdaShow.history_id, hdaShow.id, { tags: [ true ] });
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}, 400, "must be a type: <type 'basestring'>", 'type validation error' );
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// ------------------------------------------------------------------------------------------- DELETE
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this.test.comment( 'calling delete on an hda should mark it as deleted but not change the history size' );
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lastHistory = this.api.histories.show( lastHistory.id );
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var sizeBeforeDelete = lastHistory.nice_size;
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returned = this.api.hdas.delete_( lastHistory.id, firstHda.id );
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//this.debug( this.jsonStr( returned ) );
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hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id );
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this.test.assert( hdaShow.deleted, 'hda is marked deleted' );
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lastHistory = this.api.histories.show( lastHistory.id );
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this.test.assert( lastHistory.nice_size === sizeBeforeDelete, 'history size has not changed' );
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// by default, purging fails bc uni.ini:allow_user_dataset_purge=False
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this.api.assertRaises( function(){
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returned = this.api.hdas.delete_( lastHistory.id, firstHda.id, { purge : true });
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}, 403, 'This instance does not allow user dataset purging', 'Purge failed' );
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/*
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*/
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});
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//spaceghost.user.logout();
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// ===================================================================
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spaceghost.run( function(){ test.done(); });
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});
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