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commit/galaxy-central: inithello: Tool shed functional tests for malformed XML in tool_dependencies.xml.
by Bitbucket 12 Feb '13

12 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/04b8060562f8/ changeset: 04b8060562f8 user: inithello date: 2013-02-12 21:00:28 summary: Tool shed functional tests for malformed XML in tool_dependencies.xml. affected #: 3 files diff -r 01e73b11a46f87b03af29581603378b06187051d -r 04b8060562f865fa5b3ec6dac4ecfe590bd3ec07 test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py @@ -63,20 +63,28 @@ 'freebayes/sam_fa_indices.loc.sample', strings_displayed=[], commit_message='Uploaded tool data table .loc file.' ) - def test_0025_upload_invalid_tool_dependency_xml( self ): + def test_0025_upload_malformed_tool_dependency_xml( self ): + '''Upload tool_dependencies.xml with bad characters in the readme tag.''' + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + self.upload_file( repository, + os.path.join( 'freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml' ), + valid_tools_only=False, + strings_displayed=[ 'Exception attempting to parse tool_dependencies.xml', 'not well-formed' ], + commit_message='Uploaded malformed tool dependency XML.' ) + def test_0030_upload_invalid_tool_dependency_xml( self ): '''Upload tool_dependencies.xml defining version 0.9.5 of the freebayes package.''' repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, os.path.join( 'freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml' ), strings_displayed=[ 'Name, version and type from a tool requirement tag does not match' ], commit_message='Uploaded invalid tool dependency XML.' ) - def test_0030_upload_valid_tool_dependency_xml( self ): + def test_0035_upload_valid_tool_dependency_xml( self ): '''Upload tool_dependencies.xml defining version 0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8 of the freebayes package.''' repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, os.path.join( 'freebayes', 'tool_dependencies.xml' ), commit_message='Uploaded valid tool dependency XML.' ) - def test_0035_verify_tool_dependencies( self ): + def test_0040_verify_tool_dependencies( self ): '''Verify that the uploaded tool_dependencies.xml specifies the correct package versions.''' repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.display_manage_repository_page( repository, diff -r 01e73b11a46f87b03af29581603378b06187051d -r 04b8060562f865fa5b3ec6dac4ecfe590bd3ec07 test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -57,6 +57,11 @@ commit_message="Uploaded invalid_tool_dependencies/tool_dependencies.xml.", remove_repo_files_not_in_tar='No' ) self.upload_file( repository, + os.path.join( 'freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml' ), + valid_tools_only=False, + strings_displayed=[ 'Exception attempting to parse tool_dependencies.xml', 'not well-formed' ], + commit_message='Uploaded malformed tool dependency XML.' ) + self.upload_file( repository, 'freebayes/tool_dependencies.xml', valid_tools_only=False, commit_message="Uploaded tool_dependencies.xml", diff -r 01e73b11a46f87b03af29581603378b06187051d -r 04b8060562f865fa5b3ec6dac4ecfe590bd3ec07 test/tool_shed/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml @@ -0,0 +1,46 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="freebayes" version="0.9.5"> + <install version="1.0"> + <actions> + <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> + <action type="shell_command">git reset --hard 9696d0ce8a962f7bb61c4791be5ce44312b81cf8</action> + <action type="shell_command">make</action> + <action type="move_directory_files"> + <source_directory>bin</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +FreeBayes requires g++ and the standard C and C++ development libraries. +Additionally, cmake is required for building the BamTools API. + </readme> + </package> + <package name="samtools" version="0.2.15"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> + <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>misc/maq2sam-long</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +This readme tag has invalid XML >< + </readme> + </package> +</tool_dependency> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Incorporate headless browser testing using CasperJS (casperjs.org) into galaxy functional testing
by Bitbucket 12 Feb '13

12 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/01e73b11a46f/ changeset: 01e73b11a46f user: carlfeberhard date: 2013-02-12 20:36:48 summary: Incorporate headless browser testing using CasperJS (casperjs.org) into galaxy functional testing affected #: 7 files diff -r ba8c49884f7daab5df8b62bd631157058c7ee910 -r 01e73b11a46f87b03af29581603378b06187051d test/casperjs/casperjs_runner.py --- /dev/null +++ b/test/casperjs/casperjs_runner.py @@ -0,0 +1,324 @@ +"""Test runner for casperjs headless browser tests with the Galaxy distribution. + +Allows integration of casperjs tests with buildbot, run_functional_tests.sh + +Tests can be run in any of the following ways: +* casperjs mytests.js --url='http://localhost:8080' +* python casperjs_runner.py +* nosetests +* sh run_functional_tests.sh test/casperjs/test_runner +* sh run_functional_tests.sh + +Note: that you can enable (lots) of debugging info using cli options: +* casperjs usertests.js --url='http://localhost:8080' --verbose=true --logLevel=debug + +(see casperjs.org for more information) +""" +# -------------------------------------------------------------------- can't do 2.5 +import sys +( major, minor, micro, releaselevel, serial ) = sys.version_info +if minor < 6: + msg = 'casperjs requires python 2.6 or newer. Using: %s' %( sys.version ) + try: + # if nose is installed do a skip test + from nose.plugins.skip import SkipTest + raise SkipTest( msg ) + except ImportError, i_err: + raise AssertionError( msg ) + +# -------------------------------------------------------------------- +import os +import subprocess +import json +import errno +import re + +import unittest +from server_env import TestEnvironment + +import pprint +import logging +logging.basicConfig( stream=sys.stderr, name=__name__ ) +log = logging.getLogger( __name__ ) + +# ==================================================================== MODULE VARS +_PATH_TO_HEADLESS = 'casperjs' + +_TODO = """ + get data back from js scripts (uploaded files, etc.) + use returned json to output list of failed assertions if code == 2 +""" + +# ==================================================================== +class HeadlessJSJavascriptError( Exception ): + """An error that occurrs in the javascript test file. + """ + pass + +class CasperJSTestCase( unittest.TestCase ): + """Casper tests running in a unittest framework. + """ + # casper uses a lot of escape codes to colorize output - these capture those and allow removal + escape_code_compiled_pattern = None + escape_code_pattern = r'\x1b\[[\d|;]+m' + + # info on where to get casper js - shown when the exec can't be found + casper_info = """ + CasperJS is a navigation scripting & testing utility for PhantomJS, written in Javascript. + More information is available at: casperjs.org + """ + + # debugging flag - set to true to have casperjs tests output with --verbose=true and --logLevel=debug + debug = False + # bit of a hack - this is the beginning of the last string when capserjs --verbose=true --logLevel=debug + # use this to get subprocess to stop waiting for output + casper_done_str = '[info] [phantom] Done' + + # convert js test results to unittest.TestResults + results_adapter = None #CasperJsonToUnittestResultsConverter() + + # ---------------------------------------------------------------- run the js script + def run_js_script( self, rel_script_path, *args, **kwargs ): + """Start the headless browser tests in a separate process and use both + the subprocess return code and the stdout output (formatted as JSON) + to determine which tests failed and which passed. + """ + log.debug( 'beginning headless browser tests: %s', rel_script_path ) + process_command_list = self.build_command_line( rel_script_path, *args, **kwargs ) + log.debug( 'process_command_list: %s', str( process_command_list ) ) + try: + process = subprocess.Popen( process_command_list, shell=False, + stdout=subprocess.PIPE, stderr=subprocess.PIPE ) + + # output from the browser (stderr only) immediately + while process.poll() == None: + stderr_msg = process.stderr.readline() + stderr_msg = self.strip_escape_codes( stderr_msg.strip() ) + log.debug( '(%s): %s', rel_script_path, stderr_msg ) + if stderr_msg.startswith( self.casper_done_str ): + break + + # stdout is assumed to have the json test data/results + ( stdout_output, stderr_output ) = process.communicate() + #log.debug( '%s stdout output:\n%s', rel_script_path, stdout_output ) + #log.debug( '%s stderr output:\n%s', rel_script_path, stderr_output ) + + log.debug( 'process.returncode: %d', process.returncode ) + if process.returncode == 1: + #TODO: this is a fail on first effect + raise self.browser_error_to_exception( rel_script_path, stdout_output ) + + # couldn't find the headless browser, + # provide information (as it won't be included by default with galaxy) + except OSError, os_err: + if os_err.errno == errno.ENOENT: + log.error( 'No path to headless browser executable: %s\n' + + 'These tests were designed to use the following headless browser:\n%s', + self.exec_path, self.casper_info ) + raise + + self.handle_js_results( stdout_output ) + + def build_command_line( self, rel_script_path, *args, **kwargs ): + """Build the headless browser command line list for subprocess. + """ + command_line_list = [ self.exec_path ] + + # make rel_script_path an absolute path (when this is not run from it's dir - i.e. run_functional_tests.sh) + curr_dir = os.path.dirname( __file__ ) + script_path = os.path.join( curr_dir, rel_script_path ) + command_line_list.append( script_path ) + + # let browser know where the server is (from the TestEnvironment created in setUp) + command_line_list.append( '--url=' + self.env.url ) + + # add the return json only option + # - has script send normal output to stderr and results, errors, logs to stdout as json + command_line_list.append( '--return-json' ) + + # check flag to output (very) verbose debugging messages from casperjs and tests + if self.debug: + command_line_list.extend([ '--verbose=true', '--logLevel=debug' ]) + + #TODO: allow casperjs cli options ('--includes='), ?in args, kwargs? + command_line_list.extend( args ) + + # send extra data - encode kwargs as json to pass to casper for decoding + command_line_list.append( json.dumps( kwargs ) ) + return command_line_list + + def strip_escape_codes( self, msg ): + """Removes colorizing escape codes from casper output strings. + """ + if not self.escape_code_compiled_pattern: + self.escape_code_compiled_pattern = re.compile( self.escape_code_pattern ) + return re.sub( self.escape_code_compiled_pattern, '', msg ) + + # ---------------------------------------------------------------- convert js error to python error + def browser_error_to_exception( self, script_path, stdout_output ): + """Converts the headless' error from JSON into a more informative + python HeadlessJSJavascriptError. + """ + get_error = lambda d: d[ 'errors' ][0] + get_msg = lambda err: err[ 'msg' ] + get_trace = lambda err: err[ 'backtrace' ] + try: + # assume it's json and located in errors (and first) + js_test_results = json.loads( stdout_output ) + last_error = get_error( js_test_results ) + err_string = ( "%s\n%s" %( get_msg( last_error ), + self.browser_backtrace_to_string( get_trace( last_error ) ) ) ) + + # if we couldn't parse json from what's returned on the error, raise a vanilla exc + except Exception, exc: + log.debug( '(failed to parse error returned from %s: %s)', _PATH_TO_HEADLESS, str( exc ) ) + return HeadlessJSJavascriptError( + "ERROR in headless browser script %s" %( script_path ) ) + + # otherwise, raise with msg and backtrace + return HeadlessJSJavascriptError( err_string ) + + def browser_backtrace_to_string( self, backtrace ): + """Converts list of trace dictionaries (as might be returned from + json results) to a string similar to a python backtrace. + """ + template = ' File "%s", line %s, in %s' + traces = [] + for trace in backtrace: + traces.append( template %( trace[ 'file' ], trace[ 'line' ], trace[ 'function' ] ) ) + return '\n'.join( traces ) + + # ---------------------------------------------------------------- results + def handle_js_results( self, results ): + """Handle the results of the js tests by either converting them + with the results adapter or checking for a failure list. + """ + # if given an adapter - use it + if self.results_adapter: + self.results_adapter.convert( results, self ) + + # - otherwise, assert no failures found + else: + js_test_results = json.loads( results ) + failures = js_test_results[ 'testResults' ][ 'failures' ] + assert len( failures ) == 0, ( + "Some assertions failed in the headless browser tests (see the log for details)" ) + + # ---------------------------------------------------------------- TestCase overrides + def setUp( self ): + # set up the env for each test + self.env = TestEnvironment.instance() + self.exec_path = _PATH_TO_HEADLESS + + def run( self, result=None ): + # wrap this in order to save ref to result + #TODO: gotta be a better way + self.result = result + unittest.TestCase.run( self, result=result ) + + +# ==================================================================== RESULTS CONVERSION +class CasperJsonToUnittestResultsConverter( object ): + """Convert casper failures, success to individual unittest.TestResults + """ + #TODO: So far I can add result instances - but each has the id, shortDescription + # of the TestCase.testMethod that called it. Can't find out how to change these. + + def convert( self, json_results, test ): + """Converts JSON test results into unittest.TestResults. + + precondition: test should have attribute 'result' which + is a unittest.TestResult (for that test). + """ + results_dict = json.loads( json_results ) + failures = results_dict[ 'testResults' ][ 'failures' ] + passes = results_dict[ 'testResults' ][ 'passes' ] + self.add_json_failures_to_results( failures, test ) + self.add_json_successes_to_results( passes, test ) + + def add_json_failures_to_results( self, failures, test ): + """Converts JSON test failures. + """ + #precondition: result should be an attr of test (a TestResult) + #TODO: no way to change test.desc, name in output? + for failure in failures: + #TODO: doesn't change shortDescription + #if 'standard' in failure: + # self.__doc__ = failure[ 'standard' ] + test.result.addFailure( test, self.casper_failure_to_unittest_failure( failure ) ) + test.result.testsRun += 1 + + def casper_failure_to_unittest_failure( self, casper_failure, failure_class=AssertionError ): + """Returns a casper test failure (in dictionary form) as a 3-tuple of + the form used by unittest.TestResult.addFailure. + + Used to add failures to a casperjs TestCase. + """ + #TODO: this is all too elaborate + fail_type = casper_failure[ 'type' ] + values = json.dumps( casper_failure[ 'values' ] ) + desc = casper_failure[ 'standard' ] + if 'messgae' in casper_failure: + desc = capser_failure[ 'message' ] + failure_msg = "(%s) %s: %s" %( fail_type, desc, values ) + #TODO: tb is empty ([]) - can we get file info from casper, covert to py trace? + return ( failure_class, failure_msg, [] ) + + def add_json_successes_to_results( self, successes, test ): + """Converts JSON test successes. + """ + for success in successes: + ## attempt to re-write test result description - doesn't work + #if 'standard' in success: + # self.__doc__ = success[ 'standard' ] + test.result.addSuccess( test ) + test.result.testsRun += 1 + + +# ==================================================================== MODULE FIXTURE +#NOTE: nose will run these automatically +def setup_module(): + log.debug( '\n--------------- setting up module' ) + +def teardown_module(): + log.debug( '\n--------------- tearing down module' ) + + +# ==================================================================== TESTCASE EXAMPLE +# these could be broken out into other files - shouldn't be necc. ATM +class UserTests( CasperJSTestCase ): + """TestCase that uses javascript and a headless browser to test dynamic pages. + """ + def test_10_registration( self ): + """User registration tests: register new user, logout, attempt bad registrations. + """ + # all keywords will be compiled into a single JSON obj and passed to the server + self.run_js_script( 'registration-tests.js', self.env.url, + testuser={ 'email': 'test1(a)test.test', 'password': '123456' }) + #TODO:?? could theoretically do db cleanup, checks here with SQLALX + #TODO: have run_js_script return other persistant fixture data (uploaded files, etc.) + + def test_20_login( self ): + """User log in tests. + """ + self.run_js_script( 'login-tests.js', self.env.url, + testuser={ 'email': 'test1(a)test.test', 'password': '123456' }) + + +class ToolTests( CasperJSTestCase ): + """(Minimal) casperjs tests for tools. + """ + #debug = True + def test_10_upload( self ): + """Tests uploading files + """ + self.run_js_script( 'upload-tests.js' ) + + +# ==================================================================== MAIN +if __name__ == '__main__': + log.setLevel( logging.DEBUG ) + setup_module() + #TODO: server_env config doesn't work with unittest's lame main fn + unittest.main() + # teardown_module() isn't called when unittest.main is used diff -r ba8c49884f7daab5df8b62bd631157058c7ee910 -r 01e73b11a46f87b03af29581603378b06187051d test/casperjs/login-tests.js --- /dev/null +++ b/test/casperjs/login-tests.js @@ -0,0 +1,142 @@ +// have to handle errors here - or phantom/casper won't bail but _HANG_ +//TODO: global error handler? +try { + var utils = require( 'utils' ), + xpath = require( 'casper' ).selectXPath, + format = utils.format, + + //...if there's a better way - please let me know, universe + scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + + spaceghost.start(); + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} + +// =================================================================== +/* TODO: + move selectors and assertText strings into global object for easier editing + + +*/ +// =================================================================== globals and helpers +var email = spaceghost.getRandomEmail(), + password = '123456'; +if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; +} + +// =================================================================== TESTS +spaceghost.thenOpen( spaceghost.baseUrl, function(){ + this.test.comment( 'loading galaxy homepage' ); + // can we load galaxy? + this.test.assertTitle( 'Galaxy' ); +}); + +// ------------------------------------------------------------------- should work + +// register a user (again...) +spaceghost.then( function(){ + this.test.comment( 'registering: ' + email ); + spaceghost.registerUser( email, password ); +}); +// capture a sshot +//spaceghost.then( function(){ +// this.clickLabel( 'User' ); +// this.capture( 'register.png' ); +//}); + +// log them out - check for empty logged in text +spaceghost.then( function(){ + this.test.comment( 'logging out: ' + email ); + spaceghost.logout(); +}); +spaceghost.then( function(){ + this.test.assertSelectorDoesntHaveText( + xpath( '//a[contains(text(),"Logged in as")]/span["id=#user-email"]' ), /\w/ ); + this.test.assert( spaceghost.loggedInAs() === '', 'loggedInAs() is empty string' ); +}); + +// log them back in - check for email in logged in text +spaceghost.then( function(){ + this.test.comment( 'logging back in: ' + email ); + spaceghost._submitLogin( email, password ); //No such user +}); +spaceghost.then( function(){ + this.test.assertSelectorHasText( + xpath( '//a[contains(text(),"Logged in as")]/span["id=#user-email"]' ), email ); + this.test.assert( spaceghost.loggedInAs() === email, 'loggedInAs() matches email' ); +}); + +// finally log back out for next tests +spaceghost.then( function(){ + this.test.comment( 'logging out: ' + email ); + spaceghost.logout(); +}); + +// ------------------------------------------------------------------- shouldn't work +// can't log in: users that don't exist, bad emails, sql injection (hurhur) +var badEmails = [ 'test2(a)test.org', 'test', '', "'; SELECT * FROM galaxy_user WHERE 'u' = 'u';" ]; +spaceghost.each( badEmails, function( self, badEmail ){ + self.then( function(){ + this.test.comment( 'attempting bad email: ' + badEmail ); + this._submitLogin( badEmail, password ); + }); + self.then(function(){ + this.assertErrorMessage( 'No such user' ); + }); +}); + +// can't use passwords that wouldn't be accepted in registration +var badPasswords = [ '1234', '', '; SELECT * FROM galaxy_user' ]; +spaceghost.each( badPasswords, function( self, badPassword ){ + self.then( function(){ + this.test.comment( 'attempting bad password: ' + badPassword ); + this._submitLogin( email, badPassword ); + }); + self.then(function(){ + this.assertErrorMessage( 'Invalid password' ); + }); +}); + +// ------------------------------------------------------------------- test yoself +// these versions are for conv. use in other tests, they should throw errors if used improperly +spaceghost.then( function(){ + this.assertStepsRaise( 'GalaxyError: LoginError', function(){ + this.then( function(){ + this.test.comment( 'testing (js) error thrown on bad email' ); + this.login( 'nihilist', '1234' ); + }); + }); +}); + +spaceghost.then( function(){ + this.assertStepsRaise( 'GalaxyError: LoginError', function(){ + this.then( function(){ + this.test.comment( 'testing (js) error thrown on bad password' ); + this.login( email, '1234' ); + }); + }); +}); + +spaceghost.then( function(){ + this.logout(); +}); + +// =================================================================== +spaceghost.run( function(){ + this.test.done(); +}); diff -r ba8c49884f7daab5df8b62bd631157058c7ee910 -r 01e73b11a46f87b03af29581603378b06187051d test/casperjs/registration-tests.js --- /dev/null +++ b/test/casperjs/registration-tests.js @@ -0,0 +1,182 @@ +// have to handle errors here - or phantom/casper won't bail but _HANG_ +try { + var utils = require( 'utils' ), + xpath = require( 'casper' ).selectXPath, + format = utils.format, + + //...if there's a better way - please let me know, universe + scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + + spaceghost.start(); + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} + + +// =================================================================== +/* TODO: + move selectors and assertText strings into global object for easier editing + pass email, etc. for first (successful) registration (for use with other tests) + + +*/ +// =================================================================== globals and helpers +var email = spaceghost.getRandomEmail(), + password = '123456', + confirm = password, + username = 'test' + Date.now(); + +// =================================================================== TESTS +spaceghost.thenOpen( spaceghost.baseUrl, function(){ + this.test.comment( 'loading galaxy homepage' ); + // can we load galaxy? + this.test.assertTitle( 'Galaxy' ); + // xpath selector use: + this.test.assertExists( xpath( "//div[@id='masthead']" ), 'found masthead' ); +}); + +// failing tests for...testing...the tests +//spaceghost.thenOpen( spaceghost.baseUrl, function(){ +// this.test.comment( 'loading galaxy homepage' ); +// // can we load galaxy? +// this.test.assertTitle( 'Blorgo' ); +// // xpath selector use: +// this.test.assertExists( xpath( "//div[@id='facebook']" ), 'found facebook' ); +//}); + + +// ------------------------------------------------------------------- register a new user +spaceghost.then( function(){ + this.test.comment( 'registering user: ' + email ); + this._submitUserRegistration( email, password, username, confirm ); +}); +spaceghost.thenOpen( spaceghost.baseUrl, function(){ + this.clickLabel( 'User' ); + this.test.assertSelectorHasText( 'a #user-email', email, '#user-email === ' + email ); +}); + + +// ------------------------------------------------------------------- log out that user +spaceghost.then( function(){ + this.test.comment( 'logging out user: ' + email ); + this.logout(); +}); +spaceghost.then( function(){ + this.debug( 'email:' + this.getElementInfo( 'a #user-email' ).html ); + this.test.assert( !this.getElementInfo( 'a #user-email' ).html, '#user-email is empty' ); +}); + + +// ------------------------------------------------------------------- bad user registrations +spaceghost.then( function(){ + this.test.comment( 'attempting to re-register user: ' + email ); + this._submitUserRegistration( email, password, username, confirm ); +}); +spaceghost.then(function(){ + this.assertErrorMessage( 'User with that email already exists' ); +}); + +// emails must be in the form -(a)-.- (which is an email on main, btw) +var badEmails = [ 'bob', 'bob@', 'bob@idontwanttocleanup', 'bob.cantmakeme' ]; +spaceghost.each( badEmails, function( self, badEmail ){ + self.then( function(){ + this.test.comment( 'attempting bad email: ' + badEmail ); + this._submitUserRegistration( badEmail, password, username, confirm ); + }); + self.then(function(){ + this.assertErrorMessage( 'Enter a real email address' ); + }); +}); + +// passwords must be at least 6 chars long +var badPasswords = [ '1234' ]; +spaceghost.each( badPasswords, function( self, badPassword ){ + self.then( function(){ + this.test.comment( 'attempting bad password: ' + badPassword ); + this._submitUserRegistration( spaceghost.getRandomEmail(), badPassword, username, confirm ); + }); + self.then(function(){ + this.assertErrorMessage( 'Use a password of at least 6 characters' ); + }); +}); + +// and confirm must match +var badConfirms = [ '1234', '12345678', '123456 7', '' ]; +spaceghost.each( badConfirms, function( self, badConfirm ){ + self.then( function(){ + this.test.comment( 'attempting bad password confirmation: ' + badConfirm ); + this._submitUserRegistration( spaceghost.getRandomEmail(), password, username, badConfirm ); + }); + self.then(function(){ + this.assertErrorMessage( 'Passwords do not match' ); + }); +}); + +// usernames must be >=4 chars... +//NOTE: that short username errors only show AFTER checking for existing/valid emails +// so: we need to generate new emails for each one +spaceghost.then( function(){ + var newEmail = spaceghost.getRandomEmail(), + badUsername = 'bob'; + this.test.comment( 'attempting short username: ' + badUsername ); + this._submitUserRegistration( newEmail, password, badUsername, confirm ); +}); +spaceghost.then(function(){ + this.assertErrorMessage( 'Public name must be at least 4 characters in length' ); +}); + +// ...and be lower-case letters, numbers and '-'... +var badUsernames = [ 'BOBERT', 'Robert Paulson', 'bobert!', 'bob_dobbs' ]; +spaceghost.each( badUsernames, function( self, badUsername ){ + self.then( function(){ + var newEmail = spaceghost.getRandomEmail(); + this.test.comment( 'attempting bad username: ' + badUsername ); + this._submitUserRegistration( newEmail, password, badUsername, confirm ); + }); + self.then(function(){ + this.assertErrorMessage( "Public name must contain only lower-case letters, numbers and '-'" ); + }); +}); + +// ...and the name can't be used already +spaceghost.then( function(){ + var newEmail = spaceghost.getRandomEmail(); + this.test.comment( 'attempting previously used username with new user: ' + newEmail ); + this._submitUserRegistration( newEmail, password, username, confirm ); +}); +spaceghost.then(function(){ + this.assertErrorMessage( 'Public name is taken; please choose another' ); +}); + + +// ------------------------------------------------------------------- test the tests +// these versions are for conv. use in other tests, they should throw errors if used improperly +spaceghost.then( function(){ + this.assertStepsRaise( 'GalaxyError: RegistrationError', function(){ + this.then( function(){ + this.test.comment( 'testing (js) error thrown on bad email' ); + this.registerUser( '@internet', '123456', 'ignobel' ); + }); + }); +}); + +spaceghost.then( function(){ + this.logout(); +}); + +// =================================================================== +spaceghost.run( function(){ + this.test.done(); +}); diff -r ba8c49884f7daab5df8b62bd631157058c7ee910 -r 01e73b11a46f87b03af29581603378b06187051d test/casperjs/server_env.py --- /dev/null +++ b/test/casperjs/server_env.py @@ -0,0 +1,97 @@ +""" +Classes to handle fetching the proper environment and urls for the selenium +tests to run against. +""" + +import os +import logging +log = logging.getLogger( __name__ ) + +class TestEnvironment( object ): + """Provides basic information on the server being tested. + + Implemented as a singleton class so that it may persist between tests + without needing to be reset/re-created. + """ + _instance = None + + ENV_PROTOCOL = None + ENV_HOST = 'GALAXY_TEST_HOST' + ENV_PORT = 'GALAXY_TEST_PORT' + ENV_HISTORY_ID = 'GALAXY_TEST_HISTORY_ID' + ENV_FILE_DIR = 'GALAXY_TEST_FILE_DIR' + ENV_TOOL_SHED_TEST_FILE = 'GALAXY_TOOL_SHED_TEST_FILE' + ENV_SAVED_FILES_DIR = 'GALAXY_TEST_SAVE' + + DEFAULT_PROTOCOL = 'http' + DEFAULT_HOST = 'localhost' + DEFAULT_PORT = '8080' + + @classmethod + def instance( cls, config=None ): + # singleton pattern + if( ( not cls._instance ) + or ( config ) ): + log.debug( 'creating singleton instance of "%s", config: %s', str( cls ), str( config ) ) + cls._instance = cls( config ) + return cls._instance + + @classmethod + def get_server_url( cls ): + return cls.instance().url + + def __init__( self, env_config_dict=None ): + self.config = env_config_dict or {} + + self.protocol = self._get_setting_from_config_or_env( 'protocol', self.ENV_PROTOCOL, self.DEFAULT_PROTOCOL ) + self.host = self._get_setting_from_config_or_env( 'host', self.ENV_HOST, self.DEFAULT_HOST ) + self.port = self._get_setting_from_config_or_env( 'port', self.ENV_PORT, self.DEFAULT_PORT ) + + self.history_id = self._get_setting_from_config_or_env( 'history_id', self.ENV_HISTORY_ID, default=None ) + self.file_dir = self._get_setting_from_config_or_env( 'file_dir', self.ENV_FILE_DIR, default=None ) + + self.tool_shed_test_file = self._get_setting_from_config_or_env( + 'tool_shed_test_file', self.ENV_TOOL_SHED_TEST_FILE, default=None ) + self.shed_tools_dict = self._get_shed_tools_dict() + + self.keepOutdir = self._get_setting_from_config_or_env( 'keepOutdir', self.ENV_SAVED_FILES_DIR, default=None ) + self._init_saved_files_dir() + + def _get_setting_from_config_or_env( self, config_name, env_name, default=False ): + """Try to get a setting from (in order): + TestEnvironment.config, the os env, or some default (if not False). + """ + config = self.config.get( config_name, None ) + env = os.environ.get( env_name, None ) + if( ( not ( config or env ) ) + and ( default == False ) ): + raise AttributeError( '"%s" was not set via config or %s or default' %( config_name, env_name ) ) + return config or env or default + + def _get_shed_tools_dict( self ): + """Read the shed tools from the tool shed test file if given, + otherwise an empty dict. + """ + if self.tool_shed_test_file: + f = open( self.tool_shed_test_file, 'r' ) + text = f.read() + f.close() + return from_json_string( text ) + else: + return {} + + def _init_saved_files_dir( self ): + """Set up the desired directory to save test output + """ + if self.keepOutdir > '': + try: + os.makedirs( self.keepOutdir ) + except: + log.debug( 'unable to create saved files directory: %s' %( self.keepOutDir ) ) + + @property + def url( self ): + url = '%s://%s' %( self.protocol, self.host ) + if self.port and self.port != 80: + url += ':%s' %( str( self.port ) ) + return url diff -r ba8c49884f7daab5df8b62bd631157058c7ee910 -r 01e73b11a46f87b03af29581603378b06187051d test/casperjs/spaceghost.js --- /dev/null +++ b/test/casperjs/spaceghost.js @@ -0,0 +1,1030 @@ +/* TODO: + Use in test command + + bug: assertStepsRaise raise errors (all the way) when used in 'casperjs test .' + + Does it run: + casperjs usertests.js --url='http://localhost:8080' + casperjs usertests.js --url='http://localhost:8080' --return-json + casperjs usertests.js --url='http://localhost:8080' --verbose=true --logLevel=debug + casperjs test test/casperjs --url='http://localhost:8080' + python casperjs_runner.py + nosetests + sh run_functional_tests.sh test/casperjs/ + sh run_functional_tests.sh + (buildbot) + + BUGS: + echo doesn't seem to work with python + trace not showing for errors here + + what if: + does an error saving a sshot bail the entire suite? + + Do the above handle: + test script errors + page errors (evaluate, find element, etc.) + failures + passes + python errors + + Does test_runner: + aggregate properly (passes, failures) + fail on first = false + + Test: + screenshotting + save html/sshots to GALAXY_TEST_SAVE (test_runner) + + can we pass the entire test_env (instead of just url) from test_runner to sg? + support method chaining pattern + move selectors, text to class level (spaceghost) + + modules? + May want to move common functions into PageObject-like subs of sg, e.g.: + spaceghost.loginPage.logout() + spaceghost.masthead.userMenu().login() // to click User -> Login + + more conv. functions: + withMainFrame( callback ) + getMessageInfo returns *message elementInfo or null + + frames in casper are a PITA (as are steps in gen.): is there a better way to select within a frame w/o a step? + waitFor (with progress and finally): a gen. form of waitForHdaState + +*/ +// =================================================================== +/** Extended version of casper object for use with Galaxy + */ + +// ------------------------------------------------------------------- modules +var Casper = require( 'casper' ).Casper; +var utils = require( 'utils' ); + +// ------------------------------------------------------------------- inheritance +/** + */ +function SpaceGhost(){ + SpaceGhost.super_.apply( this, arguments ); + this.init.apply( this, arguments ); +} +utils.inherits( SpaceGhost, Casper ); + +//console.debug( 'CasperError:' + CasperError ); + +// ------------------------------------------------------------------- error types +PageError.prototype = new CasperError(); +PageError.prototype.constructor = CasperError; +function PageError(){ + CasperError.apply( this, arguments ); + this.name = "PageError"; +} + +GalaxyError.prototype = new CasperError(); +GalaxyError.prototype.constructor = CasperError; +function GalaxyError(){ + CasperError.apply( this, arguments ); + this.name = "GalaxyError"; +} + +AlertError.prototype = new CasperError(); +AlertError.prototype.constructor = CasperError; +function AlertError(){ + CasperError.apply( this, arguments ); + this.name = "AlertError"; +} + +// =================================================================== METHODS / OVERRIDES +// ------------------------------------------------------------------- set up +/** More initialization: cli, event handlers, etc. + * @param {Object} options option hash + */ +SpaceGhost.prototype.init = function init( options ){ + //console.debug( 'init, options:', JSON.stringify( options, null, 2 ) ); + + //NOTE: cli will override in-script options + this._setOptionsFromCli(); + + // save errors for later output (needs to go before process CLI) + this.errors = []; + this.on( 'error', function( msg, backtrace ){ + //this.debug( 'adding error to stack: ' + msg + ', trace:' + JSON.stringify( backtrace, null, 2 ) ); + this.errors.push({ msg: msg, backtrace: backtrace }); + }); + this._processCLIArguments(); + this._setUpEventHandlers(); + + // inject these scripts by default + this.debug( 'this.options.scriptDir:' + this.options.scriptDir ); + this.options.clientScripts = [ + this.options.scriptDir + '../../static/scripts/libs/jquery/jquery.js' + //... + ].concat( this.options.clientScripts ); + this.debug( 'clientScripts:\n' + this.jsonStr( this.options.clientScripts ) ); + +}; + +/** Allow CLI arguments to set options if the proper option name is used. + * @example: + * casperjs myscript.js --verbose=true --logLevel=debug + */ +SpaceGhost.prototype._setOptionsFromCli = function setOptionsFromCli(){ + // get and remove any casper options passed on the command line + for( var optionName in this.options ){ + if( this.cli.has( optionName ) ){ + //console.debug( optionName + ':' + this.options[ optionName ] + ',' + this.cli.get( optionName ) ); + this.options[ optionName ] = this.cli.get( optionName ); + this.cli.drop( optionName ); + } + } +}; + +// ------------------------------------------------------------------- cli args and options +SpaceGhost.prototype._saveHtmlOnErrorHandler = function _saveHtmlOnErrorHandler( msg, backtrace ){ + // needs to output to a file in GALAXY_SAVE + //this.debugHTML(); +}; + +SpaceGhost.prototype._saveTextOnErrorHandler = function _saveTextOnErrorHandler( msg, backtrace ){ + // needs to output to a file in GALAXY_SAVE + //this.debugPage(); +}; + +SpaceGhost.prototype._saveScreenOnErrorHandler = function _saveScreenOnErrorHandler( msg, backtrace ){ + // needs to output to a pic in GALAXY_SAVE + //var filename = ...?? + //?? this.getCurrentUrl(), this.getCurrent + //this.capture( filename ); +}; + + +/** Set up any SG specific options passed in on the cli. + */ +SpaceGhost.prototype._processCLIArguments = function _processCLIArguments(){ + //TODO: init these programmitically + var CLI_OPTIONS = { + returnJsonOnly : { defaultsTo: false, flag: 'return-json', help: 'send output to stderr, json to stdout' }, + raisePageError : { defaultsTo: true, flag: 'page-error', help: 'raise errors thrown on the page' }, + errorOnAlert : { defaultsTo: false, flag: 'error-on-alert', help: 'throw errors when a page calls alert' }, + failOnAlert : { defaultsTo: true, flag: 'fail-on-alert', help: 'fail a test when a page calls alert' } + //screenOnError : { defaultsTo: false, flag: 'error-screen', help: 'capture a screenshot on a page error' }, + //textOnError : { defaultsTo: false, flag: 'error-text', help: 'output page text on a page error' }, + //htmlOnError : { defaultsTo: false, flag: 'error-html', help: 'output page html on a page error' } + }; + + // --url parameter required (the url of the server to test with) + if( !this.cli.has( 'url' ) ){ + this.die( 'Test server URL is required - ' + + 'Usage: capserjs <test_script.js> --url=<test_server_url>', 1 ); + } + this.baseUrl = this.cli.get( 'url' ); + + // --return-json: supress all output except for JSON logs, test results, and errors at finish + // this switch allows a testing suite to send JSON data back via stdout (w/o logs, echos interferring) + this.options.returnJsonOnly = CLI_OPTIONS.returnJsonOnly.defaultsTo; + if( this.cli.has( CLI_OPTIONS.returnJsonOnly.flag ) ){ + this.options.returnJsonOnly = true; + + //this._suppressOutput(); + this._redirectOutputToStderr(); + + // output json on fail-first error + this.on( 'error', function( msg, backtrace ){ + //console.debug( 'return-json caught error' ); + if( spaceghost.options.exitOnError ){ + this.outputStateAsJson(); + spaceghost.exit( 1 ); + } + }); + // non-error finshes/json-output are handled in run() for now + } + + // --error-on-alert=false: don't throw an error if the page calls alert (default: true) + this.options.raisePageError = CLI_OPTIONS.raisePageError.defaultsTo; + if( this.cli.has( CLI_OPTIONS.raisePageError.flag ) ){ + this.options.raisePageError = this.cli.get( CLI_OPTIONS.raisePageError.flag ); + } + + // --error-on-alert=false: don't throw an error if the page calls alert (default: true) + this.options.errorOnAlert = CLI_OPTIONS.errorOnAlert.defaultsTo; + if( this.cli.has( CLI_OPTIONS.errorOnAlert.flag ) ){ + this.options.errorOnAlert = this.cli.get( CLI_OPTIONS.errorOnAlert.flag ); + } + + // --fail-on-alert=false: don't fail a test if the page calls alert (default: true) + this.options.failOnAlert = CLI_OPTIONS.failOnAlert.defaultsTo; + if( this.cli.has( CLI_OPTIONS.failOnAlert.flag ) ){ + this.options.failOnAlert = this.cli.get( CLI_OPTIONS.failOnAlert.flag ); + } + + /* not implemented + // --error-page: print the casper.debugPage (the page's text) output on an error + if( this.cli.has( 'error-page' ) ){ + this.on( 'page.error', this._saveTextOnErrorHandler ); + + // --error-html: print the casper.debugHTML (the page's html) output on an error (mut.exc w error-text) + } else if( this.cli.has( 'error-html' ) ){ + this.on( 'page.error', this._saveHtmlOnErrorHandler ); + } + + // --error-screen: print the casper.debugPage (the page's text) output on an error + if( this.cli.has( 'error-screen' ) ){ + this.on( 'page.error', this._saveScreenOnErrorHandler ); + } + */ + + // get any fixture data passed in as JSON in args + // (NOTE: currently the 2nd arg (with the url being 1st?) + this.fixtureData = ( this.cli.has( 1 ) )?( JSON.parse( this.cli.get( 1 ) ) ):( {} ); + this.debug( 'fixtureData:' + this.jsonStr( this.fixtureData ) ); + +}; + +/** Suppress the normal output from the casper object (echo, errors) + */ +SpaceGhost.prototype._suppressOutput = function _suppressOutput(){ + // currently (1.0) the only way to suppress test pass/fail messages + // (no way to re-route to log either - circular) + this.echo = function( msg ){}; + + //this.removeListener( 'error', this.listeners( 'error' )[0] ); + // clear the casper listener that outputs formatted error messages + this.removeListener( 'error', this.listeners( 'error' )[1] ); +}; + +/** Suppress the normal output from the casper object (echo, errors) + */ +SpaceGhost.prototype._redirectOutputToStderr = function _redirectOutputToStderr(){ + // currently (1.0) the only way to suppress test pass/fail messages + // (no way to re-route to log either - circular) + var spaceghost = this; + this.echo = function( msg ){ + spaceghost.stderr( msg ); + }; + + //this.removeListener( 'error', this.listeners( 'error' )[0] ); + // clear the casper listener that outputs formatted error messages + this.removeListener( 'error', this.listeners( 'error' )[1] ); +}; + +/** Outputs logs, test results and errors in a single JSON formatted object. + */ +SpaceGhost.prototype.outputStateAsJson = function outputStateAsJson(){ + var returnedJSON = { + logs: this.result, + testResults: this.test.testResults, + errors: this.errors + }; + // use phantomjs console since echo can't be used (suppressed - see init) + console.debug( JSON.stringify( returnedJSON, null, 2 ) ); +}; + + +// ------------------------------------------------------------------- event handling +//note: using non-anon fns to allow removal if needed +// most of these are stubs (w logging) for later expansion + +/** Event handler for failed page loads + */ +SpaceGhost.prototype._loadFailedHandler = function _loadFailedHandler( object ){ + this.error( 'load.failed: ' + spaceghost.jsonStr( object ) ); + //TODO: throw error? +}; + +/** Event handler for page errors (js) - throws test scope as PageError + * NOTE: this has some special handling for DOM exc 12 which some casper selectors are throwing + * (even tho the selector still works) + */ +SpaceGhost.prototype._pageErrorHandler = function _pageErrorHandler( msg, backtrace ){ + // add a page error handler to catch page errors (what we're most interested with here) + // normally, casper seems to let these pass unhandled + //console.debug( 'page.error:' + msg ); + + //TODO:!! lots of casper selectors are throwing this - even tho they still work + if( msg === 'SYNTAX_ERR: DOM Exception 12: An invalid or illegal string was specified.' ){ + void( 0 ); // no op + + } else if( this.options.raisePageError ){ + //console.debug( '(page) Error: ' + msg ); + //this.bypassOnError = true; + + // ugh - these bounce back and forth between here and phantom.page.onError + // if we don't do this replace you end up with 'PageError: PageError: PageError: ...' + // I haven't found a great way to prevent the bouncing + msg = msg.replace( 'PageError: ', '' ); + throw new PageError( msg, backtrace ); + } +}; + +/** Event handler for console messages from the page. + */ +SpaceGhost.prototype._pageConsoleHandler = function _pageConsoleHandler(){ + // remote.message + var DELIM = '-'; + this.debug( this + '(page console) "' + Array.prototype.join.call( arguments, DELIM ) + '"' ); +}; + +/** Event handler for alerts + */ +SpaceGhost.prototype._alertHandler = function _alertHandler( message ){ + // casper info level already has outputs these + //this.warning( this + '(page alert)\n"' + message + '"' ); + var ALERT_MARKER = '(page alert) '; + + // either throw an error or fail the test + //console.debug( 'this.options.errorOnAlert: ' + this.options.errorOnAlert ); + this.stderr( 'this.options.failOnAlert: ' + this.options.failOnAlert ); + if( this.options.errorOnAlert ){ + throw new PageError( ALERT_MARKER + message ); + + } else if( this.options.failOnAlert ){ + //this.test.fail( ALERT_MARKER + message ); + //this.test.fail(); + this.test.assert( false, 'found alert message' ); + //this.stderr( 'this.options.failOnAlert: ' + this.options.failOnAlert ); + } +}; + +/** Event handler for navigation requested (loading of frames, redirects(?)) + */ +SpaceGhost.prototype._navHandler = function _navHandler( url, navigationType, navigationLocked, isMainFrame ){ + this.debug( 'navigation.requested: ' + url ); +}; + +/** Set up event handlers. + */ +SpaceGhost.prototype._setUpEventHandlers = function _setUpEventHandlers(){ + //console.debug( '_setUpEventHandlers' ); + + // ........................ page errors + this.on( 'page.error', this._pageErrorHandler ); + //this.on( 'load.failed', this._loadFailedHandler ); + + // ........................ page info/debugging + // these are already displayed at the casper info level + + //this.on( 'remote.message', this._pageConsoleHandler ); + this.on( 'remote.alert', this._alertHandler ); + + // these are already displayed at the casper debug level + //this.on( 'navigation.requested', this._navHandler ); + +}; + +// ------------------------------------------------------------------- page control +/** An override of casper.open specifically for Galaxy. + * (Currently only used to change language headers) + */ +SpaceGhost.prototype.open = function open(){ + //TODO: this can be moved to start (I think...?) + //!! override bc phantom has it's lang as 'en-US,*' and galaxy doesn't handle the '*' well (server error) + this.page.customHeaders = { 'Accept-Language': 'en-US' }; + return Casper.prototype.open.apply( this, arguments ); +}; + +/** An override to provide json output and more informative error codes + */ +SpaceGhost.prototype.run = function run( onComplete, time ){ + // wrap the onComplete to: + // return code 2 on test failure + // 0 on success + // (1 on js error - in error handler) + var new_onComplete = function(){ + onComplete.call( this ); + var returnCode = ( this.test.testResults.failed )?( 2 ):( 0 ); + + // if --return-json is used: output json and exit + if( this.options.returnJsonOnly ){ + this.outputStateAsJson(); + this.exit( returnCode ); + + // otherwise, render the nice casper output and exit + } else { + this.test.renderResults( true, returnCode ); + } + }; + Casper.prototype.run.call( this, new_onComplete, time ); +}; + +/** Install a function as an error handler temporarily, run a function with steps, then remove the handler. + * A rough stand-in for try catch with steps. + * CatchFn will be passed error's msg and trace. + * @param {Function} stepsFn a function that puts casper steps on the stack (then, thenOpen, etc.) + * @param {Function} catchFn some portion of the correct error msg + */ +SpaceGhost.prototype.tryStepsCatch = function tryStepsCatch( stepsFn, catchFn ){ + //TODO: * @param {Boolean} removeOtherListeners option to remove other listeners while this fires + // create three steps: 1) set up new error handler, 2) try the fn, 3) check for errors and rem. handler + var originalExitOnError, + errorMsg = '', errorTrace = [], + recordError = function( msg, trace ){ + errorMsg = msg; errorTrace = trace; + }; + + // dont bail on the error (but preserve option), install hndlr to simply record msg, trace + //NOTE: haven't had to remove other listeners yet + this.then( function(){ + originalExitOnError = this.options.exitOnError; + this.options.exitOnError = false; + this.on( 'error', recordError ); + }); + + // try the step... + this.then( stepsFn ); + + this.then( function(){ + // ...and if an error was recorded call the catch with the info + if( errorMsg ){ + catchFn.call( this, errorMsg, errorTrace ); + } + // remove that listener either way and restore the bail option + this.removeListener( 'error', recordError ); + this.options.exitOnError = originalExitOnError; + }); +}; + + +// =================================================================== TESTING +//TODO: form fill doesn't work as casperjs would want it - often a button -> controller url +//TODO: saveScreenshot (to GALAXY_TEST_SAVE) +//TODO: saveHtml (to GALAXY_TEST_SAVE) + +/** Casper has an (undocumented?) skip test feature. This is a conv. wrapper for that. + */ +SpaceGhost.prototype.skipTest = function(){ + //TODO: does this work? seems to... + throw this.test.SKIP_MESSAGE; +}; + +/** test helper - within frame, assert selector, and assert text in selector + * @param {CasperJS selector} selector what element in which to search for the text + * @param {String} text what text to search for + * @param {String} frame frame selector (gen. name) in which to search for selector (defaults to top) + */ +SpaceGhost.prototype.assertSelectorAndTextInFrame = function assertSelectorAndTextInFrame( selector, text, frame ){ + var spaceghost = this; + function assertSelectorAndText( selector, text ){ + spaceghost.test.assertExists( selector, + format( "found '%s' in %s", selector, frame ) ); + spaceghost.test.assertSelectorHasText( selector, text, + format( "%s contains '%s'", selector, text ) ); + } + if( frame ){ + this.withFrame( frame, function(){ + assertSelectorAndText( selector, text ); + }); + } else { + assertSelectorAndText( selector, text ); + } +} + +/** test helper - within frame, assert errormessage, and assert text in errormessage + * *message is a common UI feedback motif in Galaxy (often displayed in the main panel) + * @param {String} message what the message should contain + * @param {String} frame frame selector (gen. name) in which to search for selector (defaults to 'galaxy_main') + * @param {CasperJS selector} messageSelector what element in which to search for the text (defaults to '.errormessage') + */ +SpaceGhost.prototype.assertErrorMessage = function assertSelectorAndTextInFrame( message, frame, messageSelector ){ + messageSelector = messageSelector || this.selectors.messages.error; + frame = frame || this.selectors.frames.main; + this.assertSelectorAndTextInFrame( messageSelector, message, frame ); +}; + +/** Assert that stepsFn (which contains casper.then or some other casper step function) raises an error with + * a msg that contains some text (msgContains). + * @param {String} msgContains some portion of the correct error msg + * @param {Function} stepsFn a function that puts casper steps on the stack (then, thenOpen, etc.) + */ +SpaceGhost.prototype.assertStepsRaise = function assertStepsRaise( msgContains, stepsFn, removeOtherListeners ){ + // casper provides an assertRaises but this doesn't work well with steps + //TODO: * @param {Boolean} removeOtherListeners option to remove other listeners while this fires + var spaceghost = this; + function testTheError( msg, backtrace ){ + spaceghost.test.assert( msg.indexOf( msgContains ) != -1, 'Raised correct error: ' + msg ); + } + this.tryStepsCatch( stepsFn, testTheError ); +}; + +// =================================================================== CONVENIENCE +/** Wraps casper.getElementInfo in try, returning null if element not found instead of erroring. + * @param {String} selector css or xpath selector for the element to find + */ +SpaceGhost.prototype.elementInfoOrNull = function elementInfoOrNull( selector ){ + var found = null; + try { + found = this.getElementInfo( selector ); + } catch( err ){} + return found; +}; + +/** Wraps casper.click in try, returning true if element found and clicked, false if not instead of erroring. + * @param {String} selector css or xpath selector for the element to find + */ +SpaceGhost.prototype.tryClick = function tryClick( selector ){ + var done = false; + try { + found = this.click( selector ); + done = true; + } catch( err ){} + return done; +}; + + +// =================================================================== GALAXY CONVENIENCE +/** Gets a psuedo-random (unique?) email based on the time stamp. + * Helpful for testing registration. + * @param {String} username email user (defaults to 'test') + * @param {String} domain email domain (defaults to 'test.test') + */ +SpaceGhost.prototype.getRandomEmail = function getRandomEmail( username, domain ){ + username = username || 'test'; + domain = domain || 'test.test'; + return username + Date.now() + '@' + domain; +}; + + +/** Tests registering a new user on the Galaxy instance by submitting the registration form. + * NOTE: this version does NOT throw an error on a bad registration. + * It is meant for testing the registration functionality and, therefore, is marked as private. + * Other tests should use registerUser + * @param {String} email the users email address + * @param {String} password the users password + * @param {String} username the users ...username! (optional: will use 1st part of email) + * @param {String} confirm password confirmation (optional: defaults to password) + */ +SpaceGhost.prototype._submitUserRegistration = function _submitUserRegistration( email, password, username, confirm ){ + var userInfo = { + email : email, + password: password, + // default username to first part of email + username:( !username && email.match( /^\w*/ ) )?( email.match( /^\w*/ ) ):( username ), + // default confirm duplicate of password + confirm : ( confirm !== undefined )?( confirm ):( password ) + }; + this.debug( 'registering user:\n' + this.jsonStr( userInfo ) ); + + this.thenOpen( this.baseUrl, function(){ + + this.clickLabel( this.labels.masthead.menus.user ); + this.clickLabel( this.labels.masthead.userMenu.register ); + + this.withFrame( this.selectors.frames.main, function mainBeforeRegister(){ + this.debug( 'submitting registration... ' + this.getCurrentUrl() ); + this.fill( this.selectors.registrationPage.form, userInfo, false ); + // need manual up + this.click( xpath( this.selectors.registrationPage.submit_xpath ) ); + }); + + this.withFrame( this.selectors.frames.main, function mainAfterRegister(){ + var messageInfo = this.getElementInfo( this.selectors.messages.all ); + this.debug( 'post registration message:\n' + this.jsonStr( messageInfo ) ); + }); + }); +}; + +/** Register a new user on the Galaxy instance. + * @param {String} email the users email address + * @param {String} password the users password + * @param {String} username the users ...username! (optional: will use 1st part of email) + */ +SpaceGhost.prototype.registerUser = function registerUser( email, password, username ){ + this._submitUserRegistration( email, password, username ); + this.then( function(){ + this.withFrame( this.selectors.frames.main, function mainAfterRegister(){ + var messageInfo = this.getElementInfo( this.selectors.messages.all ); + this.debug( 'post registration message:\n' + this.jsonStr( messageInfo ) ); + + if( messageInfo.attributes[ 'class' ] === 'errormessage' ){ + throw new GalaxyError( 'RegistrationError: ' + messageInfo.html ); + } + }); + }); + return this; +}; + +/** Log out the current user + */ +SpaceGhost.prototype.logout = function logoutUser(){ + this.clickLabel( this.labels.masthead.menus.user ); + this.clickLabel( this.labels.masthead.userMenu.login ); + this.thenOpen( this.baseUrl, function(){ + //TODO: handle already logged out + this.clickLabel( this.labels.masthead.menus.user ); + this.clickLabel( this.labels.masthead.userMenu.logout ); + }); +}; + +/** Tests logging in a user on the Galaxy instance by submitting the login form. + * NOTE: this version does NOT throw an error on a bad login. + * It is meant for testing the login functionality and, therefore, is marked as private. + * Other tests should use login + * @param {String} email the users email address + * @param {String} password the users password + */ +SpaceGhost.prototype._submitLogin = function logoutUser( email, password ){ + var loginInfo = { + //NOTE: keys are used as name selectors in the fill fn - must match the names of the inputs + email: email, + password: password + }; + + this.thenOpen( this.baseUrl, function(){ + + this.clickLabel( this.labels.masthead.menus.user ); + this.clickLabel( this.labels.masthead.userMenu.login ); + + this.withFrame( this.selectors.frames.main, function mainBeforeLogin(){ + this.debug( '(' + this.getCurrentUrl() + ') logging in user:\n' + this.jsonStr( loginInfo ) ); + this.fill( this.selectors.loginPage.form, loginInfo, false ); + this.click( xpath( this.selectors.loginPage.submit_xpath ) ); + }); + this.withFrame( this.selectors.frames.main, function mainAfterLogin(){ + //TODO: prob. could use a more generalized form of this for url breakdown/checking + if( this.getCurrentUrl().search( this.selectors.loginPage.url_regex ) != -1 ){ + var messageInfo = this.getElementInfo( this.selectors.messages.all ); + this.debug( 'post login message:\n' + this.jsonStr( messageInfo ) ); + } + }); + }); +}; + +/** Logs in a user. Throws error on bad log in. + * @param {String} email the users email address + * @param {String} password the users password + */ +SpaceGhost.prototype.login = function login( email, password ){ + this._submitLogin( email, password ); + this.then( function(){ + this.withFrame( this.selectors.frames.main, function mainAfterLogin(){ + if( this.getCurrentUrl().search( this.selectors.loginPage.url_regex ) != -1 ){ + var messageInfo = this.getElementInfo( this.selectors.messages.all ); + if( messageInfo && messageInfo.attributes[ 'class' ] === 'errormessage' ){ + throw new GalaxyError( 'LoginError: ' + messageInfo.html ); + } + } + }); + if( this.loggedInAs() === email ){ + this.debug( 'logged in as ' + email ); + } + }); + return this; +}; + +/** Fetch the email of the currently logged in user (or '' if not logged in) + * @returns {String} email of currently logged in user or '' if no one logged in + */ +SpaceGhost.prototype.loggedInAs = function loggedInAs(){ + var userEmail = ''; + try { + var loggedInInfo = this.getElementInfo( xpath( this.selectors.masthead.userMenu.userEmail_xpath ) ); + userEmail = loggedInInfo.text; + } catch( err ){ + this.error( err ); + } + //console.debug( 'loggedInInfo:', this.jsonStr( loggedInInfo ) ); + return userEmail; +}; + +/** Attempts to login a user - if that raises an error (LoginError), register the user + * @param {String} email the users email address + * @param {String} password the users password + * @param {String} username the users ...username! (optional: will use 1st part of email) + */ +SpaceGhost.prototype.loginOrRegisterUser = function loginOrRegisterUser( email, password, username ){ + // attempt a login, if that fails - register + this.tryStepsCatch( function tryToLogin(){ + this.open( this.baseUrl ).login( email, password ); + + }, function failedLoginRegister(){ + this.open( this.baseUrl ).registerUser( email, password, username ); + }); + return this; +}; + +/** Tests uploading a file. + * NOTE: this version does NOT throw an error on a bad upload. + * It is meant for testing the upload functionality and, therefore, is marked as private. + * Other tests should use uploadFile + * @param {String} filepath the local filesystem path of the file to upload (absolute (?)) + */ +SpaceGhost.prototype._uploadFile = function _uploadFile( filepath ){ + var uploadInfo = {}; + //TODO: check file exists using phantom.fs + //TODO: pull from test data + uploadInfo[ this.tools.upload.fileInput ] = filepath; + this.debug( 'uploading file: ' + filepath ); + + spaceghost.then( function(){ + spaceghost.withFrame( this.selectors.frames.tools, function(){ + this.clickLabel( this.tools.upload.panelLabel ); + }); + }); + + this.then( function beginUpload(){ + spaceghost.withFrame( this.selectors.frames.main, function(){ + this.fill( this.tools.general.form, uploadInfo, false ); + + // the following throws: + // [error] [remote] Failed dispatching clickmouse event on xpath selector: //input[@value="Execute"]: + // PageError: TypeError: 'undefined' is not a function (evaluating '$(this).formSerialize()') + + // ...and yet the upload still seems to work + this.click( xpath( this.tools.general.executeButton_xpath ) ); + }); + }); + this.withFrame( this.selectors.frames.main, function afterUpload(){ + var messageInfo = this.elementInfoOrNull( this.selectors.messages.all ); + this.debug( 'post upload message:\n' + this.jsonStr( messageInfo ) ); + }); +}; + +/** Uploads a file. + * @param {String} filepath the local filesystem path of the file to upload (absolute (?)) + */ +SpaceGhost.prototype.uploadFile = function uploadFile( filepath ){ + this._uploadFile( filepath ); + this.then( function(){ + this.withFrame( this.selectors.frames.main, function mainAfterUpload(){ + var messageInfo = this.elementInfoOrNull( this.selectors.messages.all ); + if( ( !messageInfo ) + || ( messageInfo.attributes[ 'class' ] !== 'donemessagelarge' ) + || ( messageInfo.text.indexOf( this.text.upload.success ) === -1 ) ){ + throw new GalaxyError( 'UploadError: ' + this.jsonStr( messageInfo ) ); + } + }); + }); + return this; +}; + +/** Parses the hid and name of a newly uploaded file from the tool execution donemessagelarge + * @param {String} doneMsgText the text extracted from the donemessagelarge after a tool execution + */ +SpaceGhost.prototype.parseDoneMessageForTool = function parseDoneMessageForTool( doneMsgText ){ + //TODO: test on non-upload + var executionInfo = {}; + var textMatch = doneMsgText.match( /added to the queue:\n\n(\d+)\: (.*)\n/m ); + if( textMatch ){ + if( textMatch.length > 1 ){ + executionInfo.hid = parseInt( textMatch[1], 10 ); + } + if( textMatch.length > 2 ){ + executionInfo.name = textMatch[2]; + } + executionInfo.name = textMatch[2]; + } + return executionInfo; +}; + +/** Find the casper element info of the hda wrapper given the hda title and hid. + * NOTE: if more than one is found, will return the first found. + * precondition: you should wrap this with withFrame( 'galaxy_history' ) :( + * @param {String} title the title of the hda + * @param {Int} hid (optional) the hid of the hda to look for + * @returns {Object|null} ElementInfo of the historyItemWrapper found, null if not found + */ +SpaceGhost.prototype.hdaElementInfoByTitle = function hdaElementInfoByTitle( title, hid ){ + var spaceghost = this, + titleContains = ( hid !== undefined )?( hid + ': ' + title ):( title ), + wrapperInfo = null; + + wrapperInfo = spaceghost.evaluate( function( titleContains ){ + // find the title, then the wrapper (2 containers up) + var $title = $( '.historyItemTitle:contains(' + titleContains + ')' ); + var $wrapper = $title.parent().parent(); + return (( $wrapper.attr( 'id' ) )?( __utils__.getElementInfo( '#' + $wrapper.attr( 'id' ) )):( null )); + }, titleContains ); + + return wrapperInfo; +}; + +/** Wait for the hda with given id to move into the given state. + * @param {String} hdaSelector selector for hda (should be historyItemWrapper) + * @param {String} finalState hda state to wait for (e.g. 'ok', 'error', 'running', 'queued', etc.) + * @param {Function} whenInStateFn called when hda goes into finalState + * @param {Function} timeoutFn called when maxWaitMs have passed without the desired state + * @param {Int} maxWaitMs number of milliseconds to wait before timing out (defaults to options.waitTimeout) + */ +SpaceGhost.prototype.waitForHdaState = function waitForHdaState( hdaSelector, finalState, + whenInStateFn, timeoutFn, maxWaitMs ){ + //TODO:?? explicitly a historyWrapper id? + maxWaitMs = maxWaitMs || this.options.waitTimeout; + var finalStateClass = '.historyItem-' + finalState; + + this.then( function(){ + this.withFrame( this.selectors.frames.history, function(){ + // wait for state, preferrably debugging intermediate states + var spaceghost = this, + + // we need a larger timeout for these - it can take a bit + oldWaitTimeout = this.options.waitTimeout, + + // output some progress indicator within the test (debug) + progressIntervalId = setInterval( function progress(){ + var state = spaceghost.evaluate( function( hdaSelector ){ + var $wrapperClasses = $( hdaSelector ).attr( 'class' ); + return $wrapperClasses.match( /historyItem\-(\w+)/ )[1]; + }, hdaSelector ); + spaceghost.debug( hdaSelector + ': ' + state ); + }, 1000 ), + + // when done, close down the progress reporter and reset the wait timeout to what it was + finallyFn = function(){ + spaceghost.options.waitTimeout = oldWaitTimeout; + clearInterval( progressIntervalId ); + }; + + this.options.waitTimeout = maxWaitMs; + this.waitForSelector( hdaSelector + finalStateClass, function _whenInState(){ + this.debug( 'HDA now in state ' + finalState + ':\n' + + this.jsonStr( this.elementInfoOrNull( hdaSelector ) ) ); + whenInStateFn.call( this ); + finallyFn(); + + }, function timeout(){ + this.debug( 'timed out:\n' + + this.jsonStr( this.elementInfoOrNull( hdaSelector ) ) ); + timeoutFn.call( this ); + finallyFn(); + } + ); + }); + }); +}; + +// =================================================================== MISCELAIN +/** Send message to stderr + */ +SpaceGhost.prototype.stderr = function( msg ){ + var fs = require( 'fs' ); + fs.write( '/dev/stderr', msg + '\n', 'w' ); +}; + +// convenience logging funcs +/** log using level = 'debug' and default namespace = 'spaceghost' + */ +SpaceGhost.prototype.debug = function( msg, namespace ){ + namespace = namespace || 'spaceghost'; + this.log( msg, 'debug', namespace ); +}; + +/** log using level = 'info' and default namespace = 'spaceghost' + */ +SpaceGhost.prototype.info = function( msg, namespace ){ + namespace = namespace || 'spaceghost'; + this.log( msg, 'info', namespace ); +}; + +/** log using level = 'info' and default namespace = 'spaceghost' + */ +SpaceGhost.prototype.warning = function( msg, namespace ){ + namespace = namespace || 'spaceghost'; + this.log( msg, 'warning', namespace ); +}; + +/** log using level = 'info' and default namespace = 'spaceghost' + */ +SpaceGhost.prototype.error = function( msg, namespace ){ + namespace = namespace || 'spaceghost'; + this.log( msg, 'error', namespace ); +}; + +/** log despite logLevel settings, unless returnJsonOnly is set + */ +SpaceGhost.prototype.out = function( msg, namespace ){ + if( !this.options.returnJsonOnly ){ + console.debug( msg ); + } +}; + +/** JSON formatter + */ +SpaceGhost.prototype.jsonStr = function( obj ){ + return JSON.stringify( obj, null, 2 ); +}; + +/** Debug SG itself + */ +SpaceGhost.prototype.debugMe = function(){ + console.debug( 'options:\n' + this.jsonStr( this.options ) ); + console.debug( 'cli:\n' + this.jsonStr( this.cli ) ); +}; + +/** Get the last error on the stack. + */ +SpaceGhost.prototype.lastError = function(){ + return this.errors[( this.errors.length - 1 )]; +}; + +/** Get the last error from an assertRaises test (gen. for the message) + */ +SpaceGhost.prototype.getLastAssertRaisesError = function(){ + // assuming the test passed here... + var testsThatPassed = this.test.testResults.passes; + var test = null; + for( var i=( testsThatPassed.length - 1 ); i>=0; i-- ){ + currTest = testsThatPassed[i]; + if( currTest.type === 'assertRaises' ){ + test = currTest; break; + } + } + return ( ( test && test.values )?( test.values.error ):( undefined ) ); +}; + +/** String representation + */ +SpaceGhost.prototype.toString = function(){ + var currentUrl = ''; + try { + currentUrl = this.getCurrentUrl(); + } catch( err ){} + return 'SpaceGhost(' + currentUrl + ')'; +}; + + +// =================================================================== TEST DATA +// maintain selectors, labels, text here in one central location + +//TODO: to separate file? +SpaceGhost.prototype.selectors = { + masthead : { + userMenu : { + userEmail : 'a #user-email', + userEmail_xpath : '//a[contains(text(),"Logged in as")]/span["id=#user-email"]' + } + }, + frames : { + main : 'galaxy_main', + tools : 'galaxy_tools', + history : 'galaxy_history' + }, + messages : { + all : '[class*="message"]', + error : '.errormessage', + done : '.donemessage' + }, + loginPage : { + form : 'form#login', + submit_xpath : "//input[@value='Login']", + url_regex : /\/user\/login/ + }, + registrationPage : { + form : 'form#registration', + submit_xpath : "//input[@value='Submit']" + } +}; + +SpaceGhost.prototype.labels = { + masthead : { + menus : { + user : 'User' + }, + userMenu : { + register : 'Register', + login : 'Login', + logout : 'Logout' + } + } +}; + +SpaceGhost.prototype.tools = { + general : { + form : 'form#tool_form', + executeButton_xpath : '//input[@value="Execute"]' + }, + upload : { + panelLabel : 'Upload File', + fileInput : 'files_0|file_data' // is this general? + } +}; + +SpaceGhost.prototype.text = { + registrationPage : { + badEmailError : 'Enter a real email address' + //... + }, + upload : { + success : 'The following job has been successfully added to the queue' + } +}; + +// =================================================================== EXPORTS +/** + */ +exports.SpaceGhost = SpaceGhost; +exports.PageError = PageError; +exports.GalaxyError = GalaxyError; +exports.AlertError = AlertError; +/** + */ +exports.create = function create(options) { + "use strict"; + return new SpaceGhost(options); +}; + +// ------------------------------------------------------------------- included libs +//??: can we require underscore, etc. from the ../../static/scripts/lib? +// yep! +//var _ = require( '../../static/scripts/libs/underscore' ); +//var stooges = [{name : 'moe', age : 40}, {name : 'larry', age : 50}, {name : 'curly', age : 60}]; +//console.debug( JSON.stringify( _.pluck(stooges, 'name') ) ); +//exports._ = _; diff -r ba8c49884f7daab5df8b62bd631157058c7ee910 -r 01e73b11a46f87b03af29581603378b06187051d test/casperjs/upload-tests.js --- /dev/null +++ b/test/casperjs/upload-tests.js @@ -0,0 +1,132 @@ +// have to handle errors here - or phantom/casper won't bail but _HANG_ +try { + var utils = require( 'utils' ), + xpath = require( 'casper' ).selectXPath, + format = utils.format, + + //...if there's a better way - please let me know, universe + scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + + spaceghost.start(); + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} + + +// =================================================================== +/* TODO: + + find a way to error on bad upload? + general tool execution +*/ +// =================================================================== globals and helpers +var email = spaceghost.getRandomEmail(), + password = '123456'; +if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; +} + + +// =================================================================== TESTS +// ------------------------------------------------------------------- start a new user +spaceghost.loginOrRegisterUser( email, password ); +//??: why is a reload needed here? If we don't, loggedInAs === '' ... +spaceghost.thenOpen( spaceghost.baseUrl, function(){ + var loggedInAs = spaceghost.loggedInAs(); + this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); +}); + +// ------------------------------------------------------------------- get avail. tools +// list available tools +//spaceghost.then( function(){ +// spaceghost.withFrame( 'galaxy_tools', function(){ +// //var availableTools = this.fetchText( 'a.tool-link' ); +// +// var availableTools = this.evaluate( function(){ +// //var toolTitles = __utils__.findAll( 'div.toolTitle' ); +// //return Array.prototype.map.call( toolTitles, function( e ){ +// // //return e.innerHtml; +// // return e.textContent || e.innerText; +// //}).join( '\n' ); +// +// var toolLinks = __utils__.findAll( 'a.tool-link' ); +// return Array.prototype.map.call( toolLinks, function( e ){ +// //return e.innerHtml; +// return e.textContent || e.innerText; +// }).join( '\n' ); +// }); +// this.debug( 'availableTools: ' + availableTools ); +// }); +//}); + +// ------------------------------------------------------------------- upload from fs +// test uploading from the filesystem +var uploadInfo = {}; +spaceghost.then( function(){ + // strangely, this works with a non-existant file --> empty txt file + var filename = '1.sam'; + var filepath = this.options.scriptDir + '/../../test-data/' + filename; + this._uploadFile( filepath ); + + // when an upload begins successfully... + // 1. main should reload with a donemessagelarge + // 2. which contains the uploaded file's new hid + // 3. and the filename of the upload + this.withFrame( 'galaxy_main', function(){ + var doneElementInfo = this.elementInfoOrNull( '.donemessagelarge' ); + this.test.assert( doneElementInfo !== null, + "Found donemessagelarge after uploading file" ); + + uploadInfo = this.parseDoneMessageForTool( doneElementInfo.text ); + this.test.assert( uploadInfo.hid >= 0, + 'Found sensible hid from upload donemessagelarge: ' + uploadInfo.hid ); + this.test.assert( uploadInfo.name === filename, + 'Found matching name from upload donemessagelarge: ' + uploadInfo.name ); + }); + +}); + +// wait for upload to finish +spaceghost.then( function(){ + var hdaInfo = null; + + this.withFrame( 'galaxy_history', function(){ + hdaInfo = this.hdaElementInfoByTitle( uploadInfo.name, uploadInfo.hid ); + this.debug( 'hda:\n' + this.jsonStr( hdaInfo ) ); + }); + + this.then( function(){ + this.test.comment( 'Waiting for upload to move to ok state in history' ); + //precondition: needs class + var hdaStateClass = hdaInfo.attributes[ 'class' ].match( /historyItem\-(\w+)/ )[0]; + if( hdaStateClass !== 'historyItem-ok' ){ + this.waitForHdaState( '#' + hdaInfo.attributes.id, 'ok', + function whenInStateFn(){ + this.test.assert( true, 'Upload completed successfully for: ' + uploadInfo.name ); + + }, function timeoutFn(){ + this.test.fail( 'Test timedout for upload: ' + uploadInfo.name ); + + // wait a maximum of 30 secs + }, 30 * 1000 ); + } + }); +}); + +// =================================================================== +spaceghost.run( function(){ + this.test.done(); +}); diff -r ba8c49884f7daab5df8b62bd631157058c7ee910 -r 01e73b11a46f87b03af29581603378b06187051d test/casperjs/utils/simple-galaxy.js --- /dev/null +++ b/test/casperjs/utils/simple-galaxy.js @@ -0,0 +1,1 @@ +/Users/carleberhard/explore/phantom-casper/simple-galaxy.js \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Fix to trackster/util.js exports; Fix to docstring in history_contents; Fix alert text in hda-model
by Bitbucket 12 Feb '13

12 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ba8c49884f7d/ changeset: ba8c49884f7d user: carlfeberhard date: 2013-02-12 20:26:30 summary: Fix to trackster/util.js exports; Fix to docstring in history_contents; Fix alert text in hda-model affected #: 5 files diff -r d2e30720ba78cbee8b6a6a63daa91702778040bc -r ba8c49884f7daab5df8b62bd631157058c7ee910 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -113,11 +113,6 @@ """ Returns a dictionary for an HDA that raised an exception when it's dictionary was being built. - { - 'id' : < the encoded dataset id >, - 'type' : < name of the dataset >, - 'url' : < api url to retrieve this datasets full data >, - } """ return { 'id' : hda_id, diff -r d2e30720ba78cbee8b6a6a63daa91702778040bc -r ba8c49884f7daab5df8b62bd631157058c7ee910 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -191,7 +191,7 @@ // if not interruption by iframe reload //TODO: remove when iframes are removed if( !( ( xhr.readyState === 0 ) && ( xhr.status === 0 ) ) ){ - alert( _l( 'Error getting history updates from the server.' ) + '\n' + error ); + alert( _l( 'Error getting history updates from the server:' ) + '\n' + error ); history.log( 'stateUpdater error:', error, 'responseText:', xhr.responseText ); } }); diff -r d2e30720ba78cbee8b6a6a63daa91702778040bc -r ba8c49884f7daab5df8b62bd631157058c7ee910 static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b){if(_.isArray(b)){this.hdas.reset(b);this.checkForUpdates()}else{if(_.isString(b)&&(b.match(/error/i))){alert(_l("Error loading bootstrapped history")+":\n"+b)}}}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server.")+"\n"+e);c.log("stateUpdater error:",e,"responseText:",f.responseText)}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{var g=_l("ERROR updating hdas from api history contents")+": ";a.log(g,b,h,c,d,f);alert(g+b.join(","))}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b){if(_.isArray(b)){this.hdas.reset(b);this.checkForUpdates()}else{if(_.isString(b)&&(b.match(/error/i))){alert(_l("Error loading bootstrapped history")+":\n"+b)}}}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server:")+"\n"+e);c.log("stateUpdater error:",e,"responseText:",f.responseText)}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{var g=_l("ERROR updating hdas from api history contents")+": ";a.log(g,b,h,c,d,f);alert(g+b.join(","))}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file diff -r d2e30720ba78cbee8b6a6a63daa91702778040bc -r ba8c49884f7daab5df8b62bd631157058c7ee910 static/scripts/packed/viz/trackster/util.js --- a/static/scripts/packed/viz/trackster/util.js +++ b/static/scripts/packed/viz/trackster/util.js @@ -1,1 +1,1 @@ -define(function(){exports={};exports.ServerStateDeferred=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(a){return true}},go:function(){var d=$.Deferred(),c=this,f=c.get("ajax_settings"),e=c.get("success_fn"),b=c.get("interval"),a=function(){$.ajax(f).success(function(g){if(e(g)){d.resolve(g)}else{setTimeout(a,b)}})};a();return d}});exports.get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};return exports}); \ No newline at end of file +define(function(){var b=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(c){return true}},go:function(){var f=$.Deferred(),e=this,h=e.get("ajax_settings"),g=e.get("success_fn"),d=e.get("interval"),c=function(){$.ajax(h).success(function(i){if(g(i)){f.resolve(i)}else{setTimeout(c,d)}})};c();return f}});var a=function(c){if(!c){c="#ffffff"}if(typeof(c)==="string"){c=[c]}for(var l=0;l<c.length;l++){c[l]=parseInt(c[l].slice(1),16)}var p=function(v,u,i){return((v*299)+(u*587)+(i*114))/1000};var g=function(x,w,y,u,i,v){return(Math.max(x,u)-Math.min(x,u))+(Math.max(w,i)-Math.min(w,i))+(Math.max(y,v)-Math.min(y,v))};var j,q,h,m,s,k,t,e,f,d,r,o=false,n=0;do{j=Math.round(Math.random()*16777215);q=(j&16711680)>>16;h=(j&65280)>>8;m=j&255;f=p(q,h,m);o=true;for(l=0;l<c.length;l++){s=c[l];k=(s&16711680)>>16;t=(s&65280)>>8;e=s&255;d=p(k,t,e);r=g(q,h,m,k,t,e);if((Math.abs(f-d)<40)||(r<200)){o=false;break}}n++}while(!o&&n<=10);return"#"+(16777216+j).toString(16).substr(1,6)};return{ServerStateDeferred:b,get_random_color:a}}); \ No newline at end of file diff -r d2e30720ba78cbee8b6a6a63daa91702778040bc -r ba8c49884f7daab5df8b62bd631157058c7ee910 static/scripts/viz/trackster/util.js --- a/static/scripts/viz/trackster/util.js +++ b/static/scripts/viz/trackster/util.js @@ -1,12 +1,10 @@ define(function(){ -exports = {}; - /** * Implementation of a server-state based deferred. Server is repeatedly polled, and when * condition is met, deferred is resolved. */ -exports.ServerStateDeferred = Backbone.Model.extend({ +var ServerStateDeferred = Backbone.Model.extend({ defaults: { ajax_settings: {}, interval: 1000, @@ -44,7 +42,7 @@ * or set of colors. * @param colors a color or list of colors in the format '#RRGGBB' */ -exports.get_random_color = function(colors) { +var get_random_color = function(colors) { // Default for colors is white. if (!colors) { colors = "#ffffff"; } @@ -110,6 +108,9 @@ return '#' + ( 0x1000000 + new_color ).toString(16).substr(1,6); }; -return exports; +return { + ServerStateDeferred : ServerStateDeferred, + get_random_color : get_random_color +}; -}) \ No newline at end of file +}); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Pack scripts.
by Bitbucket 12 Feb '13

12 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d2e30720ba78/ changeset: d2e30720ba78 user: jgoecks date: 2013-02-12 18:01:37 summary: Pack scripts. affected #: 2 files diff -r a6fe104c109feea61995567336a1aaf515acf0d5 -r d2e30720ba78cbee8b6a6a63daa91702778040bc static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -define(["libs/backbone/backbone-relational"],function(){var b=Backbone.RelationalModel.extend({});var c=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){var f=new b();_.each(_.keys(this.attributes),function(g){if(g.indexOf("metadata_")===0){var h=g.split("metadata_")[1];f.set(h,this.attributes[g]);delete this.attributes[g]}},this);this.set("metadata",f)},get_metadata:function(f){return this.attributes.metadata.get(f)},urlRoot:galaxy_paths.get("datasets_url")});var a=c.extend({defaults:_.extend({},c.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(f){c.prototype.initialize.call(this);chunk_index=(this.attributes.first_data_chunk?1:0)},set_first_chunk:function(f){this.attributes.first_data_chunk=f;this.attributes.chunk_index=1},get_next_chunk:function(){if(this.attributes.at_eof){return null}var f=this,g=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:f.attributes.chunk_index++}).success(function(h){var i;if(h.ck_data!==""){i=h}else{f.attributes.at_eof=true;i=null}g.resolve(i)});return g}});var e=Backbone.Collection.extend({model:c});var d=Backbone.View.extend({initialize:function(f){},render:function(){this.$el.append($("<div/>").attr("id","loading_indicator"));var i=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(i);var f=this.model.get_metadata("column_names");if(f){i.append("<tr><th>"+f.join("</th><th>")+"</th></tr>")}var h=this.model.get("first_data_chunk");if(h){this._renderChunk(h)}var g=this;$(window).scroll(function(){if($(window).scrollTop()===$(document).height()-$(window).height()){$.when(g.model.get_next_chunk()).then(function(j){if(j){g._renderChunk(j)}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(h,f,i){var g=this.model.get_metadata("column_types");if(i!==undefined){return $("<td>").attr("colspan",i).addClass("stringalign").text(h)}else{if(g[f]==="str"||g==="list"){return $("<td>").addClass("stringalign").text(h)}else{return $("<td>").text(h)}}},_renderRow:function(f){var g=f.split("\t"),i=$("<tr>"),h=this.model.get_metadata("columns");if(g.length===h){_.each(g,function(k,j){i.append(this._renderCell(k,j))},this)}else{if(g.length>h){_.each(g.slice(0,h-1),function(k,j){i.append(this._renderCell(k,j))},this);i.append(this._renderCell(g.slice(h-1).join("\t"),h-1))}else{if(h>5&&g.length===h-1){_.each(g,function(k,j){i.append(this._renderCell(k,j))},this);i.append($("<td>"))}else{i.append(this._renderCell(f,0,h))}}}return i},_renderChunk:function(f){var g=this.$el.find("table");_.each(f.ck_data.split("\n"),function(h,i){g.append(this._renderRow(h))},this)}});return{Dataset:c,TabularDataset:a,DatasetCollection:e,TabularDatasetChunkedView:d}}); \ No newline at end of file +define(["libs/backbone/backbone-relational"],function(){var c=Backbone.RelationalModel.extend({});var d=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){var h=new c();_.each(_.keys(this.attributes),function(i){if(i.indexOf("metadata_")===0){var j=i.split("metadata_")[1];h.set(j,this.attributes[i]);delete this.attributes[i]}},this);this.set("metadata",h)},get_metadata:function(h){return this.attributes.metadata.get(h)},urlRoot:galaxy_paths.get("datasets_url")});var b=d.extend({defaults:_.extend({},d.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(h){d.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var h=this,i=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:h.attributes.chunk_index++}).success(function(j){var k;if(j.ck_data!==""){k=j}else{h.attributes.at_eof=true;k=null}i.resolve(k)});return i}});var f=Backbone.Collection.extend({model:d});var e=Backbone.View.extend({initialize:function(h){},render:function(){this.$el.append($("<div/>").attr("id","loading_indicator"));var l=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(l);var h=this.model.get_metadata("column_names");if(h){l.append("<tr><th>"+h.join("</th><th>")+"</th></tr>")}var j=this.model.get("first_data_chunk");if(j){this._renderChunk(j)}var i=this,m=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"}),k=false;if(!m){m=window}m=$(m);m.scroll(function(){if(!k&&(i.$el.height()-m.scrollTop()-m.height()<=0)){k=true;$.when(i.model.get_next_chunk()).then(function(n){if(n){i._renderChunk(n);k=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(j,h,k){var i=this.model.get_metadata("column_types");if(k!==undefined){return $("<td>").attr("colspan",k).addClass("stringalign").text(j)}else{if(i[h]==="str"||i==="list"){return $("<td>").addClass("stringalign").text(j)}else{return $("<td>").text(j)}}},_renderRow:function(h){var i=h.split("\t"),k=$("<tr>"),j=this.model.get_metadata("columns");if(i.length===j){_.each(i,function(m,l){k.append(this._renderCell(m,l))},this)}else{if(i.length>j){_.each(i.slice(0,j-1),function(m,l){k.append(this._renderCell(m,l))},this);k.append(this._renderCell(i.slice(j-1).join("\t"),j-1))}else{if(j>5&&i.length===j-1){_.each(i,function(m,l){k.append(this._renderCell(m,l))},this);k.append($("<td>"))}else{k.append(this._renderCell(h,0,j))}}}return k},_renderChunk:function(h){var i=this.$el.find("table");_.each(h.ck_data.split("\n"),function(j,k){i.append(this._renderRow(j))},this)}});var a=function(k,i,l,h){var j=new i({model:new k(l)});j.render();if(h){h.append(j.$el)}return j};var g=function(j,h){var i=$("<div/>").appendTo(h);return new e({el:i,model:new b(j)}).render()};return{Dataset:d,TabularDataset:b,DatasetCollection:f,TabularDatasetChunkedView:e,createTabularDatasetChunkedView:g}}); \ No newline at end of file diff -r a6fe104c109feea61995567336a1aaf515acf0d5 -r d2e30720ba78cbee8b6a6a63daa91702778040bc static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b){if(_.isArray(b)){this.hdas.reset(b);this.checkForUpdates()}else{if(_.isString(b)&&(b.match(/error/i))){alert(_l("Error loading bootstrapped history")+":\n"+b)}}}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server.")+"\n"+e);c.log("stateUpdater error:",e,"responseText:",f.responseText)}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{var g=_l("ERROR updating hdas from api history contents")+": ";a.log(g,b,h,c,d,errorJSON);alert(g+b.join(","))}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b){if(_.isArray(b)){this.hdas.reset(b);this.checkForUpdates()}else{if(_.isString(b)&&(b.match(/error/i))){alert(_l("Error loading bootstrapped history")+":\n"+b)}}}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server.")+"\n"+e);c.log("stateUpdater error:",e,"responseText:",f.responseText)}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{var g=_l("ERROR updating hdas from api history contents")+": ";a.log(g,b,h,c,d,f);alert(g+b.join(","))}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 12 Feb '13

12 Feb '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1f1072317efd/ changeset: 1f1072317efd branch: stable user: natefoo date: 2013-02-12 14:46:28 summary: Allow the CLI runner to handle command stdout >65K. affected #: 2 files diff -r 961ae35ba61230ac1f5991b7629e5da0559cd0b5 -r 1f1072317efd5cf82cb791d75ba968c4bacffaf4 lib/galaxy/jobs/runners/cli.py --- a/lib/galaxy/jobs/runners/cli.py +++ b/lib/galaxy/jobs/runners/cli.py @@ -316,6 +316,7 @@ if which_try == self.app.config.retry_job_output_collection: stdout = '' stderr = 'Job output not returned from cluster' + exit_code = 0 log.debug( stderr ) else: time.sleep(1) diff -r 961ae35ba61230ac1f5991b7629e5da0559cd0b5 -r 1f1072317efd5cf82cb791d75ba968c4bacffaf4 lib/galaxy/jobs/runners/cli_shell/rsh.py --- a/lib/galaxy/jobs/runners/cli_shell/rsh.py +++ b/lib/galaxy/jobs/runners/cli_shell/rsh.py @@ -4,6 +4,7 @@ import time import logging +import tempfile import subprocess from galaxy.util.bunch import Bunch @@ -28,7 +29,9 @@ fullcmd = '%s %s %s' % (self.rsh, self.hostname, cmd) else: fullcmd = '%s -l %s %s %s' % (self.rsh, self.username, self.hostname, cmd) - p = subprocess.Popen(fullcmd, shell=True, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + # Read stdout to a tempfile in case it's large (>65K) + outf = tempfile.TemporaryFile() + p = subprocess.Popen(fullcmd, shell=True, stdin=None, stdout=outf, stderr=subprocess.PIPE) # poll until timeout for i in range(timeout/3): r = p.poll() @@ -44,7 +47,8 @@ except: log.warning('Killing pid %s (cmd: "%s") with signal %s failed' % (p.pid, fullcmd, sig)) return Bunch(stdout='', stderr='Execution timed out', returncode=-1) - return Bunch(stdout=p.stdout.read(), stderr=p.stderr.read(), returncode=p.returncode) + outf.seek(0) + return Bunch(stdout=outf.read(), stderr=p.stderr.read(), returncode=p.returncode) class SecureShell(RemoteShell): https://bitbucket.org/galaxy/galaxy-central/commits/056ff69b05c4/ changeset: 056ff69b05c4 user: natefoo date: 2013-02-12 14:46:28 summary: Allow the CLI runner to handle command stdout >65K. affected #: 2 files diff -r e5dcefc328bb4fadcd0097787d167c7f43db5627 -r 056ff69b05c435f26650c5e7f65cffd764a40a08 lib/galaxy/jobs/runners/cli.py --- a/lib/galaxy/jobs/runners/cli.py +++ b/lib/galaxy/jobs/runners/cli.py @@ -316,6 +316,7 @@ if which_try == self.app.config.retry_job_output_collection: stdout = '' stderr = 'Job output not returned from cluster' + exit_code = 0 log.debug( stderr ) else: time.sleep(1) diff -r e5dcefc328bb4fadcd0097787d167c7f43db5627 -r 056ff69b05c435f26650c5e7f65cffd764a40a08 lib/galaxy/jobs/runners/cli_shell/rsh.py --- a/lib/galaxy/jobs/runners/cli_shell/rsh.py +++ b/lib/galaxy/jobs/runners/cli_shell/rsh.py @@ -4,6 +4,7 @@ import time import logging +import tempfile import subprocess from galaxy.util.bunch import Bunch @@ -28,7 +29,9 @@ fullcmd = '%s %s %s' % (self.rsh, self.hostname, cmd) else: fullcmd = '%s -l %s %s %s' % (self.rsh, self.username, self.hostname, cmd) - p = subprocess.Popen(fullcmd, shell=True, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + # Read stdout to a tempfile in case it's large (>65K) + outf = tempfile.TemporaryFile() + p = subprocess.Popen(fullcmd, shell=True, stdin=None, stdout=outf, stderr=subprocess.PIPE) # poll until timeout for i in range(timeout/3): r = p.poll() @@ -44,7 +47,8 @@ except: log.warning('Killing pid %s (cmd: "%s") with signal %s failed' % (p.pid, fullcmd, sig)) return Bunch(stdout='', stderr='Execution timed out', returncode=-1) - return Bunch(stdout=p.stdout.read(), stderr=p.stderr.read(), returncode=p.returncode) + outf.seek(0) + return Bunch(stdout=outf.read(), stderr=p.stderr.read(), returncode=p.returncode) class SecureShell(RemoteShell): https://bitbucket.org/galaxy/galaxy-central/commits/a6fe104c109f/ changeset: a6fe104c109f user: natefoo date: 2013-02-12 15:04:17 summary: Merged heads. affected #: 2 files diff -r 056ff69b05c435f26650c5e7f65cffd764a40a08 -r a6fe104c109feea61995567336a1aaf515acf0d5 tools/ngs_rna/tophat2_wrapper.py --- a/tools/ngs_rna/tophat2_wrapper.py +++ b/tools/ngs_rna/tophat2_wrapper.py @@ -22,7 +22,7 @@ parser.add_option( '', '--mate-std-dev', dest='mate_std_dev', help='Standard deviation of distribution on inner distances between male pairs.' ) parser.add_option( '', '--read-mismatches', dest='read_mismatches' ) parser.add_option( '', '--bowtie-n', action="store_true", dest='bowtie_n' ) - parser.add_option( '', '--report-discordant-pair-alignments', action="store_true", dest='report_discordant_pairs' ) + parser.add_option( '', '--no-discordant', action="store_true", dest='report_concordant_pairs_only' ) parser.add_option( '-a', '--min-anchor-length', dest='min_anchor_length', help='The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction.' ) parser.add_option( '-m', '--splice-mismatches', dest='splice_mismatches', help='The maximum number of mismatches that can appear in the anchor region of a spliced alignment.' ) @@ -141,8 +141,8 @@ opts = '-p %s %s' % ( options.num_threads, space ) if options.single_paired == 'paired': opts += ' -r %s' % options.mate_inner_dist - if options.report_discordant_pairs: - opts += ' --report-discordant-pair-alignments' + if options.report_concordant_pairs_only: + opts += ' --no-discordant' # Read group options. if options.rgid: if not options.rglb or not options.rgpl or not options.rgsm: diff -r 056ff69b05c435f26650c5e7f65cffd764a40a08 -r a6fe104c109feea61995567336a1aaf515acf0d5 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -37,8 +37,8 @@ -r $singlePaired.mate_inner_distance --mate-std-dev=$singlePaired.mate_std_dev - #if str($singlePaired.report_discordant_pairs) == "Yes": - --report-discordant-pair-alignments + #if str($singlePaired.report_discordant_pairs) == "No": + --no-discordant #end if #end if @@ -138,8 +138,8 @@ <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/><param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?"> - <option selected="true" value="No">No</option> - <option value="Yes">Yes</option> + <option value="No">No</option> + <option selected="True" value="Yes">Yes</option></param></when></conditional> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: joachimjacob: Fixed --no-discordant parameter in tophat2_wrapper.xml and .py.
by Bitbucket 12 Feb '13

12 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b1d3a6a907d1/ changeset: b1d3a6a907d1 user: joachimjacob date: 2013-02-12 09:55:44 summary: Fixed --no-discordant parameter in tophat2_wrapper.xml and .py. affected #: 2 files diff -r e5dcefc328bb4fadcd0097787d167c7f43db5627 -r b1d3a6a907d1ee4847fbcea61a162067b3be0f49 tools/ngs_rna/tophat2_wrapper.py --- a/tools/ngs_rna/tophat2_wrapper.py +++ b/tools/ngs_rna/tophat2_wrapper.py @@ -22,7 +22,7 @@ parser.add_option( '', '--mate-std-dev', dest='mate_std_dev', help='Standard deviation of distribution on inner distances between male pairs.' ) parser.add_option( '', '--read-mismatches', dest='read_mismatches' ) parser.add_option( '', '--bowtie-n', action="store_true", dest='bowtie_n' ) - parser.add_option( '', '--report-discordant-pair-alignments', action="store_true", dest='report_discordant_pairs' ) + parser.add_option( '', '--no-discordant', action="store_true", dest='report_concordant_pairs_only' ) parser.add_option( '-a', '--min-anchor-length', dest='min_anchor_length', help='The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction.' ) parser.add_option( '-m', '--splice-mismatches', dest='splice_mismatches', help='The maximum number of mismatches that can appear in the anchor region of a spliced alignment.' ) @@ -141,8 +141,8 @@ opts = '-p %s %s' % ( options.num_threads, space ) if options.single_paired == 'paired': opts += ' -r %s' % options.mate_inner_dist - if options.report_discordant_pairs: - opts += ' --report-discordant-pair-alignments' + if options.report_concordant_pairs_only: + opts += ' --no-discordant' # Read group options. if options.rgid: if not options.rglb or not options.rgpl or not options.rgsm: diff -r e5dcefc328bb4fadcd0097787d167c7f43db5627 -r b1d3a6a907d1ee4847fbcea61a162067b3be0f49 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -37,8 +37,8 @@ -r $singlePaired.mate_inner_distance --mate-std-dev=$singlePaired.mate_std_dev - #if str($singlePaired.report_discordant_pairs) == "Yes": - --report-discordant-pair-alignments + #if str($singlePaired.report_discordant_pairs) == "No": + --no-discordant #end if #end if @@ -138,8 +138,8 @@ <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/><param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?"> - <option selected="true" value="No">No</option> - <option value="Yes">Yes</option> + <option value="No">No</option> + <option selected="True" value="Yes">Yes</option></param></when></conditional> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Uncomment the previously added sentry_dsn.
by Bitbucket 11 Feb '13

11 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e5dcefc328bb/ changeset: e5dcefc328bb user: inithello date: 2013-02-12 05:17:13 summary: Uncomment the previously added sentry_dsn. affected #: 1 file diff -r 6be149267ed6016351819a0605213fb3d34b25ef -r e5dcefc328bb4fadcd0097787d167c7f43db5627 lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -41,7 +41,7 @@ self.log_events = False self.cookie_path = kwargs.get( "cookie_path", "/" ) # Error logging with sentry - # self.sentry_dsn = kwargs.get( 'sentry_dsn', None ) + self.sentry_dsn = kwargs.get( 'sentry_dsn', None ) #Parse global_conf global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Add sentry_dsn to reports webapp configuration.
by Bitbucket 11 Feb '13

11 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6be149267ed6/ changeset: 6be149267ed6 user: inithello date: 2013-02-12 05:15:34 summary: Add sentry_dsn to reports webapp configuration. affected #: 1 file diff -r 42e0e5d9b7a479d884f9556a59aadea7886c131e -r 6be149267ed6016351819a0605213fb3d34b25ef lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -40,6 +40,8 @@ self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.log_events = False self.cookie_path = kwargs.get( "cookie_path", "/" ) + # Error logging with sentry + # self.sentry_dsn = kwargs.get( 'sentry_dsn', None ) #Parse global_conf global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Return a dict instead of a list if a [galaxy:tool_*] section is missing from the config.
by Bitbucket 11 Feb '13

11 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/42e0e5d9b7a4/ changeset: 42e0e5d9b7a4 user: natefoo date: 2013-02-11 22:50:16 summary: Return a dict instead of a list if a [galaxy:tool_*] section is missing from the config. affected #: 1 file diff -r 41f4c9c9095919b080dc0e32a5d540865fdf0fa7 -r 42e0e5d9b7a479d884f9556a59aadea7886c131e lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -304,7 +304,7 @@ return rval except ConfigParser.NoSectionError: - return [] + return {} def get( self, key, default ): return self.config_dict.get( key, default ) def get_bool( self, key, default ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Use tabular chunked data diplay for shared/published datasets.
by Bitbucket 11 Feb '13

11 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/41f4c9c90959/ changeset: 41f4c9c90959 user: jgoecks date: 2013-02-11 21:56:50 summary: Use tabular chunked data diplay for shared/published datasets. affected #: 5 files diff -r 422f368eb0978b7d8ed5a320f1700603aea22ca1 -r 41f4c9c9095919b080dc0e32a5d540865fdf0fa7 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -69,6 +69,9 @@ <class 'galaxy.datatypes.metadata.MetadataParameter'> """ + # Data is not chunkable by default. + CHUNKABLE = False + #: dictionary of metadata fields for this datatype:: metadata_spec = None diff -r 422f368eb0978b7d8ed5a320f1700603aea22ca1 -r 41f4c9c9095919b080dc0e32a5d540865fdf0fa7 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -20,6 +20,9 @@ class Tabular( data.Text ): """Tab delimited data""" + + # All tabular data is chunkable. + CHUNKABLE = True CHUNK_SIZE = 50000 """Add metadata elements""" diff -r 422f368eb0978b7d8ed5a320f1700603aea22ca1 -r 41f4c9c9095919b080dc0e32a5d540865fdf0fa7 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -642,6 +642,11 @@ truncated, dataset_data = self.get_data( dataset, preview ) dataset.annotation = self.get_item_annotation_str( trans.sa_session, dataset.history.user, dataset ) + # If dataset is chunkable, get first chunk. + first_chunk = None + if dataset.datatype.CHUNKABLE: + first_chunk = dataset.datatype.get_chunk(trans, dataset, 0) + # If data is binary or an image, stream without template; otherwise, use display template. # TODO: figure out a way to display images in display template. if isinstance(dataset.datatype, datatypes.binary.Binary) or isinstance(dataset.datatype, datatypes.images.Image) or isinstance(dataset.datatype, datatypes.images.Html): @@ -658,8 +663,10 @@ user_item_rating = 0 ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, dataset ) - return trans.fill_template_mako( "/dataset/display.mako", item=dataset, item_data=dataset_data, truncated=truncated, - user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) + return trans.fill_template_mako( "/dataset/display.mako", item=dataset, item_data=dataset_data, + truncated=truncated, user_item_rating = user_item_rating, + ave_item_rating=ave_item_rating, num_ratings=num_ratings, + first_chunk=first_chunk ) else: raise web.httpexceptions.HTTPNotFound() diff -r 422f368eb0978b7d8ed5a320f1700603aea22ca1 -r 41f4c9c9095919b080dc0e32a5d540865fdf0fa7 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -102,7 +102,10 @@ }); /** - * Provides table-based, dynamic view of a tabular dataset. + * Provides table-based, dynamic view of a tabular dataset. + * NOTE: view's el must be in DOM already and provided when + * createing the view so that scrolling event can be attached + * to the correct container. */ var TabularDatasetChunkedView = Backbone.View.extend({ @@ -129,13 +132,31 @@ this._renderChunk(first_chunk); } - // Show new chunks during scrolling. - var self = this; - $(window).scroll(function() { - if ($(window).scrollTop() === $(document).height() - $(window).height()) { + // -- Show new chunks during scrolling. -- + + var self = this, + // Element that does the scrolling. + scroll_elt = _.find(this.$el.parents(), function(p) { + return $(p).css('overflow') === 'auto'; + }), + // Flag to ensure that only one chunk is loaded at a time. + loading_chunk = false; + + // If no scrolling element found, use window. + if (!scroll_elt) { scroll_elt = window; } + + // Wrap scrolling element for easy access. + scroll_elt = $(scroll_elt); + + // Set up chunk loading when scrolling using the scrolling element. + scroll_elt.scroll(function() { + // If not already loading a chunk and have scrolled to the bottom of this element, get next chunk. + if ( !loading_chunk && (self.$el.height() - scroll_elt.scrollTop() - scroll_elt.height() <= 0) ) { + loading_chunk = true; $.when(self.model.get_next_chunk()).then(function(result) { if (result) { self._renderChunk(result); + loading_chunk = false; } }); } @@ -218,7 +239,7 @@ if (parent_elt) { parent_elt.append(a_view.$el); } - + return a_view; }; @@ -227,7 +248,14 @@ * and appends to parent_elt. */ var createTabularDatasetChunkedView = function(dataset_config, parent_elt) { - return createModelAndView(TabularDataset, TabularDatasetChunkedView, dataset_config, parent_elt); + // Create view element and add to parent. + var view_div = $('<div/>').appendTo(parent_elt); + + // Create view with model, render, and return. + return new TabularDatasetChunkedView({ + el: view_div, + model: new TabularDataset(dataset_config) + }).render(); }; return { diff -r 422f368eb0978b7d8ed5a320f1700603aea22ca1 -r 41f4c9c9095919b080dc0e32a5d540865fdf0fa7 templates/webapps/galaxy/dataset/display.mako --- a/templates/webapps/galaxy/dataset/display.mako +++ b/templates/webapps/galaxy/dataset/display.mako @@ -5,6 +5,35 @@ <%def name="javascripts()"> ${parent.javascripts()} + ## If data is chunkable, use JavaScript for display. + %if item.datatype.CHUNKABLE: + + <script type="text/javascript"> + require.config({ + baseUrl: "${h.url_for('/static/scripts')}", + shim: { + "libs/backbone/backbone": { exports: "Backbone" }, + "libs/backbone/backbone-relational": ["libs/backbone/backbone"] + } + }); + + require(['mvc/data'], function(data) { + data.createTabularDatasetChunkedView( + // Dataset config. TODO: encode id. + _.extend( ${h.to_json_string( item.get_api_value() )}, + { + chunk_url: "${h.url_for( controller='/dataset', action='display', + dataset_id=trans.security.encode_id( item.id ))}", + first_data_chunk: ${first_chunk} + } + ), + // Append view to body. + $('.page-body') + ); + }); + </script> + + %endif </%def><%def name="init()"> @@ -31,14 +60,17 @@ </%def><%def name="render_item( data, data_to_render )"> - %if truncated: - <div class="warningmessagelarge"> - This dataset is large and only the first megabyte is shown below. | - <a href="${h.url_for( controller='dataset', action='display_by_username_and_slug', username=data.history.user.username, slug=trans.security.encode_id( data.id ), preview=False )}">Show all</a> - </div> + ## Chunkable data is rendered in JavaScript above; render unchunkable data below. + %if not data.datatype.CHUNKABLE: + %if truncated: + <div class="warningmessagelarge"> + This dataset is large and only the first megabyte is shown below. | + <a href="${h.url_for( controller='dataset', action='display_by_username_and_slug', username=data.history.user.username, slug=trans.security.encode_id( data.id ), preview=False )}">Show all</a> + </div> + %endif + ## TODO: why is the default font size so small? + <pre style="font-size: 135%">${ data_to_render | h }</pre> %endif - ## TODO: why is the default font size so small? - <pre style="font-size: 135%">${ data_to_render | h }</pre></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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