1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/b9dd3817bdab/ Changeset: b9dd3817bdab User: carlfeberhard Date: 2015-02-03 21:11:10+00:00 Summary: API, tests: add datasets API tests in test/API and casperjs sections; Browser tests: add datasets api, allow api to send extra params for history show & index Affected #: 3 files

diff -r 5aa058b09609351defd3161754b23a27ea9bef99 -r b9dd3817bdabd5c61990af589d31c1097b3c5de6 test/api/test_datasets.py --- /dev/null +++ b/test/api/test_datasets.py @@ -0,0 +1,41 @@ +import textwrap + +from base import api +from .helpers import TestsDatasets + +class DatasetsApiTestCase( api.ApiTestCase, TestsDatasets ): + + def setUp( self ): + super( DatasetsApiTestCase, self ).setUp() + self.history_id = self._new_history() + + def test_index( self ): + index_response = self._get( "datasets" ) + print index_response + print dir( index_response ) + self._assert_status_code_is( index_response, 501 ) + + def test_show( self ): + hda1 = self._new_dataset( self.history_id ) + show_response = self._get( "datasets/%s" % ( hda1[ "id" ] ) ) + self._assert_status_code_is( show_response, 200 ) + self.__assert_matches_hda( hda1, show_response.json() ) + + def __assert_matches_hda( self, input_hda, query_hda ): + self._assert_has_keys( query_hda, "id", "name" ) + assert input_hda[ "name" ] == query_hda[ "name" ] + assert input_hda[ "id" ] == query_hda[ "id" ] + + def test_display( self ): + contents = textwrap.dedent( """\ + 1 2 3 4 + A B C D + 10 20 30 40 + """ ) + hda1 = self._new_dataset( self.history_id, content=contents ) + display_response = self._get( "histories/%s/contents/%s/display" % ( self.history_id, hda1[ "id" ] ), { + 'raw' : 'True' + }) + self._assert_status_code_is( display_response, 200 ) + #TODO: doesn't work + #assert display_response.text == contents

diff -r 5aa058b09609351defd3161754b23a27ea9bef99 -r b9dd3817bdabd5c61990af589d31c1097b3c5de6 test/casperjs/api-dataset-tests.js --- /dev/null +++ b/test/casperjs/api-dataset-tests.js @@ -0,0 +1,59 @@ +var require = patchRequire( require ), + spaceghost = require( 'spaceghost' ).fromCasper( casper ), + xpath = require( 'casper' ).selectXPath, + utils = require( 'utils' ), + format = utils.format; + +spaceghost.test.begin( 'Test the HDA API', 0, function suite( test ){ + spaceghost.start(); + + // =================================================================== SET UP + var email = spaceghost.user.getRandomEmail(), + password = '123456'; + if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; + } + + var detailKeys = [ + // the following are always present regardless of datatype + 'id', 'name', 'api_type', 'model_class', + 'history_id', 'hid', + 'accessible', 'deleted', 'visible', 'purged', + 'state', 'data_type', 'file_ext', 'file_size', + 'misc_info', 'misc_blurb', + 'download_url', 'visualizations', 'display_apps', 'display_types', + 'genome_build' + ]; + + spaceghost.user.loginOrRegisterUser( email, password ); + spaceghost.openHomePage(); + spaceghost.api.tools.thenUploadToCurrent({ filepath: '../../test-data/1.bed' }); + + spaceghost.then( function(){ + // ------------------------------------------------------------------------------------------- INDEX + this.test.comment( 'index should error with not implemented' ); + this.api.assertRaises( function(){ + this.api.datasets.index(); + }, 501, 'not implemented', 'throws unimplemented' ); + + // ------------------------------------------------------------------------------------------- SHOW + this.test.comment( 'show should get an HDA details object' ); + var history = this.api.histories.show( 'most_recently_used', { keys : 'id,hdas' } ), + hdaId = history.hdas[0], + show = this.api.datasets.show( hdaId ); + this.debug( this.jsonStr( history ) ); + this.debug( this.jsonStr( show ) ); + this.test.assert( this.hasKeys( show, detailKeys ), 'Has the proper keys' ); + + // ------------------------------------------------------------------------------------------- DISPLAY + this.test.comment( 'show should get an HDA details object' ); + var fileContents = this.api.datasets.display( history.id, hdaId, { raw: 'True' }); + this.test.assert( fileContents.split( '\n' ).length === 66, '1.bed has 66 lines' ); + }); + + + // =================================================================== + spaceghost.run( function(){ test.done(); }); +}); +

diff -r 5aa058b09609351defd3161754b23a27ea9bef99 -r b9dd3817bdabd5c61990af589d31c1097b3c5de6 test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -13,6 +13,7 @@ this.configuration = new ConfigurationAPI( this ); this.histories = new HistoriesAPI( this ); this.hdas = new HDAAPI( this ); + this.datasets = new DatasetsAPI( this ); this.tools = new ToolsAPI( this ); this.workflows = new WorkflowsAPI( this ); this.users = new UsersAPI( this ); @@ -80,7 +81,10 @@ ( resp.responseJSON? this.spaceghost.jsonStr( resp.responseJSON ) : resp.responseText ) ); throw new APIError( resp.responseText, resp.status ); } - return JSON.parse( resp.responseText ); + if( options.dataType === undefined || options.dataType === 'json' ){ + return JSON.parse( resp.responseText ); + } + return resp.responseText; };

// =================================================================== TESTING @@ -217,22 +221,34 @@ update : '/api/histories/%s', };

-HistoriesAPI.prototype.index = function index( deleted ){ - this.api.spaceghost.info( 'histories.index: ' + (( deleted )?( 'w deleted' ):( '(wo deleted)' )) ); - - deleted = deleted || false; +HistoriesAPI.prototype.index = function index( params ){ + var spaceghost = this.api.spaceghost; + spaceghost.info( 'histories.index:\n' + spaceghost.jsonStr( params ) ); + if( params === undefined ){ + params = { deleted: false }; + } + if( params.deleted === undefined ){ + params.deleted = false; + } + spaceghost.debug( 'params (now):' + spaceghost.jsonStr( params ) ); return this.api._ajax( this.urlTpls.index, { - data : { deleted: deleted } + data : params }); };

-HistoriesAPI.prototype.show = function show( id, deleted ){ - this.api.spaceghost.info( 'histories.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); - - id = ( id === 'most_recently_used' || id === 'current' )?( id ):( this.api.ensureId( id ) ); - deleted = deleted || false; +HistoriesAPI.prototype.show = function show( id, params ){ + var spaceghost = this.api.spaceghost; + this.api.spaceghost.info( 'histories.show: ' + id + '\n' + spaceghost.jsonStr( params ) ); + id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); + if( params === undefined ){ + params = { deleted: false }; + } + if( params.deleted === undefined ){ + params.deleted = false; + } + spaceghost.debug( 'params (now):' + spaceghost.jsonStr( params ) ); return this.api._ajax( utils.format( this.urlTpls.show, id ), { - data : { deleted: deleted } + data : params }); };

@@ -365,8 +381,55 @@ //TODO: delete_

+// =================================================================== HDAS +var DatasetsAPI = function DatasetsAPI( api ){ + this.api = api; +}; +DatasetsAPI.prototype.toString = function toString(){ + return this.api + '.DatasetsAPI'; +}; + +// ------------------------------------------------------------------- +DatasetsAPI.prototype.urlTpls = { + index : '/api/datasets', + show : '/api/datasets/%s', + // wut. + display : '/api/histories/%s/contents/%s/display' +}; + +DatasetsAPI.prototype.index = function index(){ + this.api.spaceghost.info( 'datasets.index: ' ); + var data = {}; + + return this.api._ajax( utils.format( this.urlTpls.index ), { + data : data + }); +}; + +DatasetsAPI.prototype.show = function show( id ){ + this.api.spaceghost.info( 'datasets.show: ' + [ id ] ); + var data = {}; + + return this.api._ajax( utils.format( this.urlTpls.show, id ), { + data : data + }); +}; + +DatasetsAPI.prototype.display = function show( historyId, id, params ){ + this.api.spaceghost.info( 'datasets.display: ' + [ historyId, id ] ); + if( params === undefined ){ + params = {}; + } + return this.api._ajax( utils.format( this.urlTpls.display, this.api.ensureId( historyId ), id ), { + data : params, + dataType : 'text' + }); +}; + + + // =================================================================== TOOLS -var ToolsAPI = function HDAAPI( api ){ +var ToolsAPI = function ToolsAPI( api ){ this.api = api; }; ToolsAPI.prototype.toString = function toString(){

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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