galaxy-commits March 2013

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commit/galaxy-central: inithello: Reference the right app.
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a7bd59964f50/ changeset: a7bd59964f50 user: inithello date: 2013-03-18 20:51:04 summary: Reference the right app. affected #: 1 file diff -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda -r a7bd59964f5053133897e6e7b89065a608e11d03 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -399,7 +399,7 @@ tool_panel_dict = tool_util.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) sample_files = metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files ) - tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) + tool_util.copy_sample_files( trans.app, tool_index_sample_files, tool_path=tool_path ) sample_files_copied = [ str( s ) for s in tool_index_sample_files ] repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata_dict ) if repository_tools_tups: 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: carlfeberhard: browser tests: refactoring, add api module
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f19741fdb9a6/ changeset: f19741fdb9a6 user: carlfeberhard date: 2013-03-18 20:14:22 summary: browser tests: refactoring, add api module affected #: 14 files diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda 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 @@ -175,15 +175,20 @@ if from_ld_id: try: ld = self.get_library_dataset( trans, from_ld_id, check_ownership=False, check_accessible=False ) - assert type( ld ) is trans.app.model.LibraryDataset, "Library content id ( %s ) is not a dataset" % from_ld_id + assert type( ld ) is trans.app.model.LibraryDataset, ( + "Library content id ( %s ) is not a dataset" % from_ld_id ) + except AssertionError, e: trans.response.status = 400 return str( e ) + except Exception, e: return str( e ) + hda = ld.library_dataset_dataset_association.to_history_dataset_association( history, add_to_history=True ) trans.sa_session.flush() return hda.get_api_value() + else: # TODO: implement other "upload" methods here. trans.response.status = 403 diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/anon-history-tests.js --- a/test/casperjs/anon-history-tests.js +++ b/test/casperjs/anon-history-tests.js @@ -68,15 +68,10 @@ }); // ------------------------------------------------------------------- check the empty history for well formedness -// grab the history frame bounds for mouse later tests -spaceghost.then( function(){ - historyFrameInfo = this.getElementInfo( 'iframe[name="galaxy_history"]' ); - //this.debug( 'historyFrameInfo:' + this.jsonStr( historyFrameInfo ) ); -}); - spaceghost.thenOpen( spaceghost.baseUrl, function testPanelStructure(){ this.test.comment( 'history panel for anonymous user, new history' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ + + this.withHistoryPanel( function(){ this.test.comment( "frame should have proper url and title: 'History'" ); this.test.assertMatch( this.getCurrentUrl(), /\/history/, 'Found history frame url' ); this.test.assertTitle( this.getTitle(), 'History', 'Found history frame title' ); @@ -103,15 +98,12 @@ 'Message contains "' + emptyMsgStr + '"' ); this.test.comment( 'name should have a tooltip with info on anon-user name editing' ); - // mouse over to find tooltip - this.historypanel.hoverOver( nameSelector, function testingHover(){ - this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); - this.test.assertSelectorHasText( tooltipSelector, anonNameTooltip ); - }, historyFrameInfo ); + this.historypanel.hoverOver( nameSelector ); + this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); + this.test.assertSelectorHasText( tooltipSelector, anonNameTooltip ); this.test.comment( 'name should NOT be editable when clicked by anon-user' ); - this.assertDoesntHaveClass( nameSelector, editableTextClass, - "Name field is not classed as editable text" ); + this.assertDoesntHaveClass( nameSelector, editableTextClass, "Name field is not classed as editable text" ); this.click( nameSelector ); this.test.assertDoesntExist( editableTextInput, "Clicking on name does not create an input" ); }); @@ -120,12 +112,13 @@ // ------------------------------------------------------------------- anon user can upload file spaceghost.then( function testAnonUpload(){ this.test.comment( 'anon-user should be able to upload files' ); + spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ - this.debug( 'uploaded HDA info: ' + this.jsonStr( _uploadInfo ) ); + this.debug( 'uploaded HDA info: ' + this.jsonStr( this.quickInfo( _uploadInfo.hdaElement ) ) ); var hasHda = _uploadInfo.hdaElement, hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( 'historyItem-ok' ) !== -1; - this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.name ); + this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.hdaElement.text ); testUploadInfo = _uploadInfo; }); }); @@ -134,19 +127,18 @@ this.test.assertNotVisible( emptyMsgSelector, 'Empty history message is not visible' ); }); - // ------------------------------------------------------------------- anon user can run tool on file // ------------------------------------------------------------------- anon user registers/logs in -> same history spaceghost.user.loginOrRegisterUser( email, password ); spaceghost.thenOpen( spaceghost.baseUrl, function(){ + this.test.comment( 'anon-user should login and be associated with previous history' ); - this.test.comment( 'anon-user should login and be associated with previous history' ); var loggedInAs = spaceghost.user.loggedInAs(); this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - var hdaInfo = this.historypanel.hdaElementInfoByTitle( testUploadInfo.name, testUploadInfo.hid ); + this.historypanel.waitForHdas( function(){ + var hdaInfo = this.historypanel.hdaElementInfoByTitle( testUploadInfo.hdaElement.text ); this.test.assert( hdaInfo !== null, "After logging in - found a matching hda by name and hid" ); if( hdaInfo ){ this.test.assert( testUploadInfo.hdaElement.attributes.id === hdaInfo.attributes.id, @@ -155,17 +147,18 @@ }); }); +// ------------------------------------------------------------------- logs out -> new history spaceghost.user.logout(); spaceghost.thenOpen( spaceghost.baseUrl, function(){ this.test.comment( 'logging out should create a new, anonymous history' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ + + this.historypanel.waitForHdas( function(){ this.test.assertSelectorHasText( nameSelector, unnamedName, 'History name is ' + unnamedName ); this.test.assertSelectorHasText( emptyMsgSelector, emptyMsgStr, 'Message contains "' + emptyMsgStr + '"' ); }); }); - // =================================================================== spaceghost.run( function(){ this.test.done(); diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/casperjs_runner.py --- a/test/casperjs/casperjs_runner.py +++ b/test/casperjs/casperjs_runner.py @@ -73,7 +73,7 @@ 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 = '# Tests complete' + casper_done_str = '# Stopping' # convert js test results to unittest.TestResults results_adapter = None #CasperJsonToUnittestResultsConverter() @@ -209,7 +209,8 @@ 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)" ) + "%d assertions failed in the headless browser tests" %( len( failures ) ) + + " (see the log for details)" ) # ---------------------------------------------------------------- TestCase overrides def setUp( self ): @@ -299,10 +300,12 @@ # ==================================================================== TESTCASE EXAMPLE # these could be broken out into other py files - shouldn't be necc. ATM class Test_01_User( CasperJSTestCase ): - """TestCase that uses javascript and a headless browser to test dynamic pages. + """Tests for the Galaxy user centered functionality: + registration, login, etc. """ def test_10_registration( self ): - """User registration tests: register new user, logout, attempt bad registrations. + """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', @@ -331,7 +334,7 @@ class Test_03_HistoryPanel( CasperJSTestCase ): - """(Minimal) casperjs tests for tools. + """Tests for History fetching, rendering, and modeling. """ def test_00_history_panel( self ): """Test history panel basics (controls, structure, refresh, history options menu, etc.). @@ -339,13 +342,18 @@ self.run_js_script( 'history-panel-tests.js' ) def test_10_anonymous_histories( self ): + """Test history options button. + """ + self.run_js_script( 'history-options-tests.js' ) + + def test_20_anonymous_histories( self ): """Test history panel basics with an anonymous user. """ self.run_js_script( 'anon-history-tests.js' ) class Test_04_HDAs( CasperJSTestCase ): - """(Minimal) casperjs tests for tools. + """Tests for HistoryDatasetAssociation fetching, rendering, and modeling. """ def test_00_HDA_states( self ): """Test structure rendering of HDAs in all the possible HDA states diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/hda-state-tests.js --- a/test/casperjs/hda-state-tests.js +++ b/test/casperjs/hda-state-tests.js @@ -55,17 +55,10 @@ // start a new user spaceghost.user.loginOrRegisterUser( email, password ); -// grab the history frame bounds for later mouse tests -spaceghost.then( function(){ - historyFrameInfo = this.getElementInfo( 'iframe[name="galaxy_history"]' ); - //this.debug( 'historyFrameInfo:' + this.jsonStr( historyFrameInfo ) ); -}); - // upload a file spaceghost.then( function upload(){ spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ testUploadInfo = _uploadInfo; - this.info( 'testUploadInfo:' + this.jsonStr( testUploadInfo ) ); }); }); @@ -73,13 +66,12 @@ // =================================================================== TEST HELPERS //NOTE: to be called with fn.call( spaceghost, ... ) -function testTitle( hdaSelector, hid, name ){ - var titleSelector = hdaSelector + ' ' + this.historypanel.data.selectors.hda.title, - titleShouldBe = hid + ': ' + name; +function testTitle( hdaSelector, name ){ + var titleSelector = hdaSelector + ' ' + this.historypanel.data.selectors.hda.title; this.test.assertVisible( titleSelector, 'HDA title is visible' ); - this.test.assertSelectorHasText( titleSelector, titleShouldBe, - 'HDA has proper hid and title' ); + this.test.assertSelectorHasText( titleSelector, name, + 'HDA contains name (' + name + '): ' + this.fetchText( titleSelector ) ); } function testTitleButtonStructure( hdaSelector, shouldHaveTheseButtons ){ @@ -87,28 +79,9 @@ shouldHaveTheseButtons = shouldHaveTheseButtons || [ 'display', 'edit', 'delete' ]; var hdaDbId = this.getElementAttribute( hdaSelector, 'id' ).split( '-' )[1], - buttonsArea = hdaSelector + ' ' + this.historypanel.data.selectors.hda.titleButtons, - buttons = { - // this seems backwards -> TODO: move buttonsArea concat into loop below, move this data to historypanel.data - display : { - nodeName : this.historypanel.data.text.hda.ok.nodeNames.displayButton, - selector : buttonsArea + ' ' + this.historypanel.data.selectors.hda.displayButton, - tooltip : this.historypanel.data.text.hda.ok.tooltips.displayButton, - hrefTpl : this.historypanel.data.text.hda.ok.hrefs.displayButton - }, - edit : { - nodeName : this.historypanel.data.text.hda.ok.nodeNames.editAttrButton, - selector : buttonsArea + ' ' + this.historypanel.data.selectors.hda.editAttrButton, - tooltip : this.historypanel.data.text.hda.ok.tooltips.editAttrButton, - hrefTpl : this.historypanel.data.text.hda.ok.hrefs.editAttrButton - }, - 'delete' : { - nodeName : this.historypanel.data.text.hda.ok.nodeNames.deleteButton, - selector : buttonsArea + ' ' + this.historypanel.data.selectors.hda.deleteButton, - tooltip : this.historypanel.data.text.hda.ok.tooltips.deleteButton, - hrefTpl : this.historypanel.data.text.hda.ok.hrefs.deleteButton - } - }; + buttonsArea = hdaSelector + ' ' + this.historypanel.data.selectors.hda.titleButtonArea, + buttons = this.historypanel.data.hdaTitleButtons; + this.test.assertVisible( buttonsArea, 'Button area is visible' ); for( var i=0; i<shouldHaveTheseButtons.length; i++ ){ @@ -123,7 +96,7 @@ this.test.assertVisible( button.selector, buttonName + ' button is visible' ); var buttonElement = this.getElementInfo( button.selector ); - this.debug( 'buttonElement:' + this.jsonStr( buttonElement ) ); + this.debug( 'buttonElement:' + this.jsonStr( this.quickInfo( buttonElement ) ) ); // should be an anchor this.test.assert( buttonElement.nodeName === button.nodeName, @@ -135,12 +108,13 @@ this.assertTextContains( href, hrefShouldBe, buttonName + ' has proper href (' + hrefShouldBe + '): ' + href ); - this.historypanel.hoverOver( button.selector, function testingHover(){ - var tooltipText = button.tooltip; - this.test.assertVisible( tooltipSelector, buttonName + ' button tooltip is visible when hovering' ); - this.test.assertSelectorHasText( tooltipSelector, tooltipText, - buttonName + ' button has tooltip text: "' + tooltipText + '"' ); - }, historyFrameInfo ); + this.historypanel.hoverOver( button.selector ); + var tooltipText = button.tooltip; + this.test.assertVisible( tooltipSelector, buttonName + ' button tooltip is visible when hovering' ); + this.test.assertSelectorHasText( tooltipSelector, tooltipText, + buttonName + ' button has tooltip text: "' + tooltipText + '"' ); + // clear the tooltip + this.page.sendEvent( 'mouseover', 0, 0 ); } } @@ -185,6 +159,7 @@ this.test.comment( 'Primary action buttons div should exist and be visible' ); this.test.assertExists( buttonsSelector, 'Primary action buttons div exists' ); this.test.assertVisible( buttonsSelector, 'Primary action buttons div is visible' ); + //TODO: ... } function testSecondaryActionButtons( hdaSelector ){ @@ -193,6 +168,7 @@ this.test.comment( 'Secondary action buttons div should exist and be visible' ); this.test.assertExists( buttonsSelector, 'Secondary action buttons div exists' ); this.test.assertVisible( buttonsSelector, 'Secondary action buttons div is visible' ); + //TODO: ... } function testPeek( hdaSelector, expectedPeekArray ){ @@ -239,112 +215,97 @@ // =================================================================== TESTS // ------------------------------------------------------------------- ok state -spaceghost.then( function checkOkState(){ +spaceghost.withHistoryPanel( function(){ this.test.comment( 'HDAs in the "ok" state should be well formed' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; - this.test.assertVisible( uploadSelector, 'HDA is visible' ); + var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + this.test.assertVisible( uploadSelector, 'HDA is visible' ); - this.test.comment( 'should have the proper state class' ); - this.assertHasClass( uploadSelector, this.historypanel.data.selectors.hda.wrapper.stateClasses.ok, - 'HDA has ok state class' ); + this.test.comment( 'should have the proper state class' ); + this.assertHasClass( uploadSelector, this.historypanel.data.selectors.hda.wrapper.stateClasses.ok, + 'HDA has ok state class' ); - // since we're using css there's no great way to test state icon (.state-icon is empty) + // since we're using css there's no great way to test state icon (.state-icon is empty) - this.test.comment( 'should have proper title and hid' ); - testTitle.call( spaceghost, uploadSelector, testUploadInfo.hid, testUploadInfo.name ); + this.test.comment( 'should have proper title and hid' ); + testTitle.call( spaceghost, uploadSelector, testUploadInfo.filename ); - this.test.comment( 'should have all of the three, main buttons' ); - testTitleButtonStructure.call( spaceghost, uploadSelector ); + this.test.comment( 'should have all of the three, main buttons' ); + testTitleButtonStructure.call( spaceghost, uploadSelector ); - this.test.comment( 'body is not visible before clicking the hda title' ); - var body = uploadSelector + ' ' + this.historypanel.data.selectors.hda.body; - this.test.assertNotVisible( body, 'body is not visible' ); + this.test.comment( 'body is not visible before clicking the hda title' ); + var body = uploadSelector + ' ' + this.historypanel.data.selectors.hda.body; + this.test.assertNotVisible( body, 'body is not visible' ); - this.test.comment( 'clicking the hda title should expand its body' ); - var hdaTitle = uploadSelector + ' ' + this.historypanel.data.selectors.hda.title; - this.click( hdaTitle ); - this.wait( 500, function(){ + this.test.comment( 'clicking the hda title should expand its body' ); + this.historypanel.thenExpandHda( uploadSelector, function(){ + // ugh. + this.jumpToHistory( function(){ testExpandedBody.call( spaceghost, uploadSelector, summaryShouldBeArray, infoShouldBe, false ); }); }); }); +// restore to collapsed +spaceghost.then( function(){ + this.test.comment( "Collapsing hda in 'ok' state should hide body again" ); + var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; -// restore to collapsed -spaceghost.then( function collapseOkState(){ - this.test.comment( "Collapsing hda in 'ok' state should hide body again" ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id, - hdaTitle = uploadSelector + ' ' + this.historypanel.data.selectors.hda.title; - body = uploadSelector + ' ' + this.historypanel.data.selectors.hda.body; - - this.click( hdaTitle ); - this.wait( 500, function(){ - this.test.assertNotVisible( body, 'body is not visible' ); - }); + spaceghost.historypanel.thenCollapseHda( uploadSelector, function collapseOkState(){ + this.test.assertNotVisible( uploadSelector + ' ' + this.historypanel.data.selectors.hda.body, + 'body is not visible' ); }); }); +// ------------------------------------------------------------------- new state +spaceghost.withHistoryPanel( function(){ + // set state directly through model, wait for re-render + //TODO: not ideal to test this + this.evaluate( function(){ + return Galaxy.currHistoryPanel.model.hdas.at( 0 ).set( 'state', 'new' ); + }); + this.wait( 1000, function(){ + this.test.comment( 'HDAs in the "new" state should be well formed' ); -// ------------------------------------------------------------------- new state -spaceghost.then( function checkNewState(){ - this.test.comment( 'HDAs in the "new" state should be well formed' ); + var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + this.test.assertVisible( uploadSelector, 'HDA is visible' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - // set state directly through model - //TODO: not ideal - this.evaluate( function(){ - return Galaxy.currHistoryPanel.model.hdas.at( 0 ).set( 'state', 'new' ); - }); - // wait for re-render - this.wait( 500, function(){ - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; - this.test.assertVisible( uploadSelector, 'HDA is visible' ); + // should have proper title and hid + testTitle.call( spaceghost, uploadSelector, testUploadInfo.filename ); - // should have proper title and hid - testTitle.call( spaceghost, uploadSelector, testUploadInfo.hid, testUploadInfo.name ); + this.test.comment( 'new HDA should have the new state class' ); + this.assertHasClass( uploadSelector, this.historypanel.data.selectors.hda.wrapper.stateClasses['new'], + 'HDA has new state class' ); - this.test.comment( 'new HDA should have the new state class' ); - this.assertHasClass( uploadSelector, this.historypanel.data.selectors.hda.wrapper.stateClasses['new'], - 'HDA has new state class' ); + this.test.comment( 'new HDA should NOT have any of the three, main buttons' ); + var buttonSelector = uploadSelector + ' ' + this.historypanel.data.selectors.hda.titleButtons + ' a'; + this.test.assertDoesntExist( buttonSelector, 'No display, edit, or delete buttons' ); - this.test.comment( 'new HDA should NOT have any of the three, main buttons' ); - var buttonSelector = uploadSelector + ' ' + this.historypanel.data.selectors.hda.titleButtons + ' a'; - this.test.assertDoesntExist( buttonSelector, 'No display, edit, or delete buttons' ); + this.test.comment( 'clicking the title of the new HDA will expand the body' ); - this.test.comment( 'clicking the title of the new HDA will expand the body' ); - var hdaTitle = uploadSelector + ' ' + this.historypanel.data.selectors.hda.title; - this.click( hdaTitle ); - this.wait( 500, function(){ - var bodySelector = uploadSelector + ' ' + this.historypanel.data.selectors.hda.body; - this.test.assertVisible( bodySelector, 'HDA body is visible (after expanding)' ); + this.historypanel.thenExpandHda( uploadSelector, function(){ + var bodySelector = uploadSelector + ' ' + this.historypanel.data.selectors.hda.body; + this.test.assertVisible( bodySelector, 'HDA body is visible (after expanding)' ); - var expectedBodyText = 'This is a new dataset'; - this.test.comment( 'the body should have the text: ' + expectedBodyText ); - this.test.assertSelectorHasText( bodySelector, expectedBodyText, - 'HDA body has text: ' + expectedBodyText ); - - // restore to collapsed - this.click( hdaTitle ); - }); + var expectedBodyText = 'This is a new dataset'; + this.test.comment( 'the body should have the text: ' + expectedBodyText ); + this.test.assertSelectorHasText( bodySelector, expectedBodyText, + 'HDA body has text: ' + expectedBodyText ); }); }); }); // restore state, collapse -spaceghost.then( function revertStateAndCollapse(){ - this.withFrame( spaceghost.data.selectors.frames.history, function(){ +spaceghost.withHistoryPanel( function revertStateAndCollapse(){ + var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + + this.historypanel.thenCollapseHda( uploadSelector, function(){ this.evaluate( function(){ return Galaxy.currHistoryPanel.model.hdas.at( 0 ).set( 'state', 'ok' ); }); - this.wait( 500, function(){ - var hdaTitle = '#' + testUploadInfo.hdaElement.attributes.id - + ' ' + this.historypanel.data.selectors.hda.title; - this.click( hdaTitle ); - }); }); + this.wait( 1000 ); }); - +/* +*/ // =================================================================== spaceghost.run( function(){ diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/history-options-tests.js --- /dev/null +++ b/test/casperjs/history-options-tests.js @@ -0,0 +1,145 @@ +// 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: + possibly break this file up +*/ +// =================================================================== globals and helpers +var email = spaceghost.user.getRandomEmail(), + password = '123456'; +if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; + spaceghost.info( 'Will use fixtureData.testUser: ' + email ); +} + +// selectors and labels +var includeDeletedOptionsLabel = spaceghost.historyoptions.data.labels.options.includeDeleted; + +// local +var filepathToUpload = '../../test-data/1.txt', + testUploadInfo = {}; + + +// =================================================================== TESTS +// ------------------------------------------------------------------- set up +// start a new user +spaceghost.user.loginOrRegisterUser( email, password ); + +spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ + testUploadInfo = _uploadInfo; +}); + +// ------------------------------------------------------------------- history options menu structure +//NOTE: options menu should be functionally tested elsewhere +spaceghost.historypanel.waitForHdas().then( function checkHistoryOptions(){ + this.test.comment( 'History options icon should be in place and menu should have the proper structure' ); + + // check the button and icon + this.test.assertExists( this.historyoptions.data.selectors.button, "Found history options button" ); + this.test.assertVisible( this.historyoptions.data.selectors.button, "History options button is visible" ); + this.test.assertVisible( this.historyoptions.data.selectors.buttonIcon, "History options icon is visible" ); + + // open the menu + this.click( this.historyoptions.data.selectors.button ); + this.test.assertVisible( this.historyoptions.data.selectors.menu, + "Menu is visible when options button is clicked" ); + + // check the options + var historyOptions = this.historyoptions.data.labels.options; + for( var optionKey in historyOptions ){ + if( historyOptions.hasOwnProperty( optionKey ) ){ + var optionLabel = historyOptions[ optionKey ]; + this.test.assertVisible( this.historyoptions.data.selectors.optionXpathByLabelFn( optionLabel ), + 'Option label is visible: ' + optionLabel ); + } + } + + // clear the menu + this.click( 'body' ); + this.test.assertNotVisible( this.historyoptions.data.selectors.menu, + "Clicking away from the menu closes it" ); +}); + +// ------------------------------------------------------------------- options allow showing/hiding deleted hdas +spaceghost.then( function(){ + this.test.comment( 'Deleting HDA' ); + var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + + this.historypanel.deleteHda( uploadSelector, function(){ + this.test.assertNotExists( uploadSelector, "Deleted HDA is NOT in the DOM" ); + }); +}); + +spaceghost.then( function(){ + this.test.comment( 'History options->' + includeDeletedOptionsLabel + ' shows deleted datasets' ); + var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + + this.historyoptions.includeDeleted( function(){ + this.test.assertExists( uploadSelector, + "Deleted HDA is in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); + this.test.assertVisible( uploadSelector, + "Deleted HDA is visible again (using history options -> " + includeDeletedOptionsLabel + ")" ); + }); +}); + +spaceghost.then( function(){ + this.test.comment( 'History options->' + includeDeletedOptionsLabel + ' (again) re-hides deleted datasets' ); + + this.historyoptions.excludeDeleted( function(){ + this.test.assertDoesntExist( '#' + testUploadInfo.hdaElement.attributes.id, + "Deleted HDA is not in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); + }); + // undelete the uploaded file + this.historypanel.undeleteHda( '#' + testUploadInfo.hdaElement.attributes.id ); +}); + +// ------------------------------------------------------------------- hidden hdas aren't shown +// ------------------------------------------------------------------- history options allows showing hidden hdas +// can't test this yet w/o a way to make hdas hidden thru the ui or api + + +// ------------------------------------------------------------------- history options collapses all expanded hdas +spaceghost.then( function(){ + this.historypanel.thenExpandHda( '#' + testUploadInfo.hdaElement.attributes.id ); +}); +spaceghost.then( function(){ + this.test.comment( 'History option collapses all expanded hdas' ); + + this.historyoptions.collapseExpanded( function(){ + var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; + this.withHistoryPanel( function(){ + this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is not visible" ); + }); + }); +}); + +// =================================================================== +spaceghost.run( function(){ + this.test.done(); +}); diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/history-panel-tests.js --- a/test/casperjs/history-panel-tests.js +++ b/test/casperjs/history-panel-tests.js @@ -72,177 +72,164 @@ // ------------------------------------------------------------------- set up // start a new user spaceghost.user.loginOrRegisterUser( email, password ); -//??: why is a reload needed here? If we don't, loggedInAs === '' ... -spaceghost.thenOpen( spaceghost.baseUrl, function(){ - var loggedInAs = spaceghost.user.loggedInAs(); - this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); + +// ------------------------------------------------------------------- check structure of empty history +spaceghost.thenOpen( spaceghost.baseUrl ).historypanel.waitForHdas( function(){ + this.test.comment( 'history panel with a new, empty history should be well formed' ); + this.test.comment( "frame should have proper url and title: 'History'" ); + this.test.assertMatch( this.getCurrentUrl(), /\/history/, 'Found history frame url' ); + this.test.assertTitle( this.getTitle(), 'History', 'Found history frame title' ); + + this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); + this.test.assertExists( nameSelector, nameSelector + ' exists' ); + this.test.assertVisible( nameSelector, 'History name is visible' ); + this.test.assertSelectorHasText( nameSelector, unnamedName, 'History name is ' + unnamedName ); + + this.test.comment( "history subtitle should display size and size should be: " + initialSizeStr ); + this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); + this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); + this.test.assertSelectorHasText( subtitleSelector, initialSizeStr, + 'History subtitle has "' + initialSizeStr + '"' ); + + this.test.comment( "tags and annotation icons should be available" ); + this.test.assertExists( tagIconSelector, 'Tag icon button found' ); + this.test.assertExists( annoIconSelector, 'Annotation icon button found' ); + + this.test.comment( "A message about the current history being empty should be displayed" ); + this.test.assertExists( emptyMsgSelector, emptyMsgSelector + ' exists' ); + this.test.assertVisible( emptyMsgSelector, 'Empty history message is visible' ); + this.test.assertSelectorHasText( emptyMsgSelector, emptyMsgStr, + 'Message contains "' + emptyMsgStr + '"' ); }); -// grab the history frame bounds for later mouse tests -spaceghost.then( function(){ - historyFrameInfo = this.getElementInfo( 'iframe[name="galaxy_history"]' ); - //this.debug( 'historyFrameInfo:' + this.jsonStr( historyFrameInfo ) ); -}); +// ------------------------------------------------------------------- name editing +spaceghost.withHistoryPanel( function(){ + this.test.comment( 'history panel, editing the history name' ); -// ------------------------------------------------------------------- check structure of empty history -spaceghost.thenOpen( spaceghost.baseUrl, function testPanelStructure(){ - this.test.comment( 'history panel, new history' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.test.comment( "frame should have proper url and title: 'History'" ); - this.test.assertMatch( this.getCurrentUrl(), /\/history/, 'Found history frame url' ); - this.test.assertTitle( this.getTitle(), 'History', 'Found history frame title' ); + this.test.comment( 'name should have a tooltip with proper info on name editing' ); + this.historypanel.hoverOver( nameSelector ); + this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); + this.test.assertSelectorHasText( tooltipSelector, nameTooltip ); + // clear the tooltip + this.page.sendEvent( 'mousemove', -1, -1 ); - this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); - this.test.assertExists( nameSelector, nameSelector + ' exists' ); - this.test.assertVisible( nameSelector, 'History name is visible' ); - this.test.assertSelectorHasText( nameSelector, unnamedName, 'History name is ' + unnamedName ); + this.test.comment( 'name should be create an input when clicked' ); + this.assertHasClass( nameSelector, editableTextClass, "Name field classed for editable text" ); + this.click( nameSelector ); + this.test.assertExists( editableTextInput, "Clicking on name creates an input" ); - this.test.comment( "history subtitle should display size and size should be: " + initialSizeStr ); - this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); - this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); - this.test.assertSelectorHasText( subtitleSelector, initialSizeStr, - 'History subtitle has "' + initialSizeStr + '"' ); - - this.test.comment( "tags and annotation icons should be available" ); - this.test.assertExists( tagIconSelector, 'Tag icon button found' ); - this.test.assertExists( annoIconSelector, 'Annotation icon button found' ); - - this.test.comment( "A message about the current history being empty should be displayed" ); - this.test.assertExists( emptyMsgSelector, emptyMsgSelector + ' exists' ); - this.test.assertVisible( emptyMsgSelector, 'Empty history message is visible' ); - this.test.assertSelectorHasText( emptyMsgSelector, emptyMsgStr, - 'Message contains "' + emptyMsgStr + '"' ); + this.test.comment( 'name should be editable by entering keys and pressing enter' ); + //NOTE: casperjs.sendKeys adds a click before and a selector.blur after sending - won't work here + this.page.sendEvent( 'keypress', newHistoryName ); + this.page.sendEvent( 'keypress', this.page.event.key.Enter ); + // wait for send and re-render name + this.wait( 1000, function(){ + this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is ' + newHistoryName ); + this.test.assertDoesntExist( editableTextInput, "Input disappears after pressing enter" ); }); }); -// ------------------------------------------------------------------- name editing -spaceghost.then( function(){ - this.test.comment( 'history panel, editing the history name' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.test.comment( 'name should have a tooltip with proper info on name editing' ); - var nameInfo = this.getElementInfo( nameSelector ); - this.page.sendEvent( 'mousemove', historyFrameInfo.x + nameInfo.x + 1, historyFrameInfo.y + nameInfo.y + 1 ); - this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); - this.test.assertSelectorHasText( tooltipSelector, nameTooltip ); +spaceghost.withHistoryPanel( function(){ + this.test.comment( 'name should revert if user clicks away while editing' ); - this.test.comment( 'name should be create an input when clicked' ); - this.assertHasClass( nameSelector, editableTextClass, "Name field classed for editable text" ); - this.click( nameSelector ); - this.test.assertExists( editableTextInput, "Clicking on name creates an input" ); + this.click( nameSelector ); + this.page.sendEvent( 'keypress', "Woodchipper metagenomics, Fargo, ND" ); - this.test.comment( 'name should be editable by entering keys and pressing enter' ); - //NOTE: casperjs.sendKeys adds a click before and a selector.blur after sending - won't work here - this.page.sendEvent( 'keypress', newHistoryName ); - this.page.sendEvent( 'keypress', this.page.event.key.Enter ); - this.wait( 1000, function(){ - this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is ' + newHistoryName ); - this.test.assertDoesntExist( editableTextInput, "Input disappears after pressing enter" ); - }); + this.page.sendEvent( 'mousedown', -1, -1 ); + this.wait( 1000, function(){ + this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is STILL ' + newHistoryName ); + this.test.assertDoesntExist( editableTextInput, "Input disappears after clicking away" ); }); }); -spaceghost.then( function(){ - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.test.comment( 'name should revert if user clicks away while editing' ); - this.click( nameSelector ); - this.page.sendEvent( 'keypress', "Woodchipper metagenomics, Fargo, ND" ); - // click above the name input element - var inputInfo = this.getElementInfo( editableTextInput ); - this.page.sendEvent( 'mousedown', historyFrameInfo.x + inputInfo.x + 1, historyFrameInfo.y + inputInfo.y - 5 ); +spaceghost.withHistoryPanel( function(){ + this.test.comment( 'name should revert if user hits ESC while editing' ); - this.wait( 1000, function(){ - this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is STILL ' + newHistoryName ); - this.test.assertDoesntExist( editableTextInput, "Input disappears after clicking away" ); - }); - }); -}); -spaceghost.then( function(){ - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.test.comment( 'name should revert if user hits ESC while editing' ); - this.click( nameSelector ); - this.page.sendEvent( 'keypress', "Arsenic Bacteria" ); + this.click( nameSelector ); + this.page.sendEvent( 'keypress', "Arsenic Bacteria" ); - this.page.sendEvent( 'keypress', this.page.event.key.Escape ); - this.wait( 1000, function(){ - this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is STILL ' + newHistoryName ); - this.test.assertDoesntExist( editableTextInput, "Input disappears after hitting ESC" ); - }); + this.page.sendEvent( 'keypress', this.page.event.key.Escape ); + this.wait( 1000, function(){ + this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is STILL ' + newHistoryName ); + this.test.assertDoesntExist( editableTextInput, "Input disappears after hitting ESC" ); }); }); // ------------------------------------------------------------------- check structure of NON empty history // upload file: 1.txt -spaceghost.then( function upload(){ +spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ this.test.comment( 'uploaded file should appear in history' ); - spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ - this.debug( 'uploaded HDA info: ' + this.jsonStr( _uploadInfo ) ); - var hasHda = _uploadInfo.hdaElement, - hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], - hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( wrapperOkClassName ) !== -1; - this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.name ); - testUploadInfo = _uploadInfo; - }); + + this.debug( 'uploaded HDA info: ' + this.jsonStr( _uploadInfo ) ); + var hasHda = _uploadInfo.hdaElement, + hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], + hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( wrapperOkClassName ) !== -1; + this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.name ); + testUploadInfo = _uploadInfo; }); -spaceghost.then( function checkPanelStructure(){ +spaceghost.withHistoryPanel( function checkPanelStructure(){ this.test.comment( 'checking structure of non-empty panel' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); - this.test.assertExists( nameSelector, nameSelector + ' exists' ); - this.test.assertVisible( nameSelector, 'History name is visible' ); - this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is ' + newHistoryName ); + this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); + this.test.assertExists( nameSelector, nameSelector + ' exists' ); + this.test.assertVisible( nameSelector, 'History name is visible' ); + this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is ' + newHistoryName ); - this.test.comment( "history subtitle should display size and size should be " + onetxtFilesize + " bytes" ); - var onetxtFilesize = require( 'fs' ).size( this.options.scriptDir + filepathToUpload ), - expectedSubtitle = onetxtFilesize + ' bytes'; - this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); - this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); - this.test.assertSelectorHasText( subtitleSelector, expectedSubtitle, - 'History subtitle has "' + expectedSubtitle + '"' ); + this.test.comment( "history subtitle should display size and size should be " + onetxtFilesize + " bytes" ); + var onetxtFilesize = require( 'fs' ).size( this.options.scriptDir + filepathToUpload ), + expectedSubtitle = onetxtFilesize + ' bytes'; + this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); + this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); + this.test.assertSelectorHasText( subtitleSelector, expectedSubtitle, + 'History subtitle has "' + expectedSubtitle + '": ' + this.fetchText( subtitleSelector ).trim() ); - this.test.comment( "tags and annotation icons should be available" ); - this.test.assertExists( tagIconSelector, 'Tag icon button found' ); - this.test.assertExists( annoIconSelector, 'Annotation icon button found' ); + this.test.comment( "tags and annotation icons should be available" ); + this.test.assertExists( tagIconSelector, 'Tag icon button found' ); + this.test.assertExists( annoIconSelector, 'Annotation icon button found' ); - this.test.comment( "A message about the current history being empty should NOT be displayed" ); - this.test.assertExists( emptyMsgSelector, emptyMsgSelector + ' exists' ); - this.test.assertNotVisible( emptyMsgSelector, 'Empty history message is NOT visible' ); - }); + this.test.comment( "A message about the current history being empty should NOT be displayed" ); + this.test.assertExists( emptyMsgSelector, emptyMsgSelector + ' exists' ); + this.test.assertNotVisible( emptyMsgSelector, 'Empty history message is NOT visible' ); }); // ------------------------------------------------------------------- tags // keeping this light here - better for it's own test file //TODO: check tooltips -spaceghost.then( function openTags(){ +spaceghost.withHistoryPanel( function openTags(){ this.test.comment( 'tag area should open when the history panel tag icon is clicked' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.mouseEvent( 'click', tagIconSelector ); - this.wait( 1000, function(){ - this.test.assertVisible( tagAreaSelector, 'Tag area is now displayed' ); - }); + + this.click( tagIconSelector ); + this.wait( 1000, function(){ + this.test.assertVisible( tagAreaSelector, 'Tag area is now displayed' ); + }); +}); +spaceghost.withHistoryPanel( function closeAnnotation(){ + this.test.comment( 'annotation area should close when the history panel tag icon is clicked again' ); + + this.click( tagIconSelector ); + this.wait( 1000, function(){ + this.test.assertNotVisible( tagAreaSelector, 'Tag area is now hidden' ); }); }); // ------------------------------------------------------------------- annotation // keeping this light here - better for it's own test file //TODO: check tooltips -spaceghost.then( function openAnnotation(){ +spaceghost.withHistoryPanel( function openAnnotation(){ this.test.comment( 'annotation area should open when the history panel annotation icon is clicked' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.mouseEvent( 'click', annoIconSelector ); - this.wait( 1000, function(){ - this.test.assertVisible( annoAreaSelector, 'Annotation area is now displayed' ); - }); + + this.click( annoIconSelector ); + this.wait( 1000, function(){ + this.test.assertVisible( annoAreaSelector, 'Annotation area is now displayed' ); }); }); -spaceghost.then( function closeAnnotation(){ +spaceghost.withHistoryPanel( function closeAnnotation(){ this.test.comment( 'annotation area should close when the history panel tag icon is clicked again' ); - this.withFrame( spaceghost.data.selectors.frames.history, function bler(){ - this.mouseEvent( 'click', annoIconSelector ); - this.wait( 1000, function(){ - this.test.assertNotVisible( annoAreaSelector, 'Tag area is now hidden' ); - }); + + this.click( annoIconSelector ); + this.wait( 1000, function(){ + this.test.assertNotVisible( annoAreaSelector, 'Annotation area is now hidden' ); }); }); @@ -261,96 +248,16 @@ }); }); -// ------------------------------------------------------------------- history options menu structure -//NOTE: options menu should be functionally tested elsewhere -spaceghost.then( function historyOptions(){ - this.test.comment( 'History options icon should be in place and menu should have the proper structure' ); - - // check the button and icon - this.test.assertExists( this.historyoptions.data.selectors.button, "Found history options button" ); - this.test.assertVisible( this.historyoptions.data.selectors.button, "History options button is visible" ); - this.test.assertVisible( this.historyoptions.data.selectors.buttonIcon, "History options icon is visible" ); - - // open the menu - this.click( this.historyoptions.data.selectors.button ); - this.test.assertVisible( this.historyoptions.data.selectors.menu, - "Menu is visible when options button is clicked" ); - - // check the options - for( var optionKey in this.historyoptions.data.labels.options ){ - if( this.historyoptions.data.labels.options.hasOwnProperty( optionKey ) ){ - var optionLabel = this.historyoptions.data.labels.options[ optionKey ], - optionXpath = this.historyoptions.data.selectors.optionXpathByLabelFn( optionLabel ); - this.test.assertVisible( optionXpath, 'Option label is visible: ' + optionLabel ); - } - } -}); - -// ------------------------------------------------------------------- deleted hdas aren't in the dom -spaceghost.then( function(){ - this.test.comment( 'deleted hdas shouldn\'t be in the history panel DOM' ); - - this.historypanel.deleteHda( '#' + testUploadInfo.hdaElement.attributes.id, function(){ - this.test.assertDoesntExist( '#' + testUploadInfo.hdaElement.attributes.id, - "Deleted HDA is not in the DOM" ); - }); -}); - -// ------------------------------------------------------------------- options allow showing/hiding deleted hdas -spaceghost.then( function(){ - this.test.comment( 'History options->' + includeDeletedOptionsLabel + ' shows deleted datasets' ); - - this.historyoptions.includeDeleted(); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.waitForSelector( nameSelector, function(){ - this.test.assertExists( '#' + testUploadInfo.hdaElement.attributes.id, - "Deleted HDA is in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); - this.test.assertVisible( '#' + testUploadInfo.hdaElement.attributes.id, - "Deleted HDA is visible again (using history options -> " + includeDeletedOptionsLabel + ")" ); - }); - }); -}); - -spaceghost.then( function(){ - this.test.comment( 'History options->' + includeDeletedOptionsLabel + ' (again) re-hides deleted datasets' ); - - this.historyoptions.includeDeleted(); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.waitForSelector( nameSelector, function(){ - this.test.assertDoesntExist( '#' + testUploadInfo.hdaElement.attributes.id, - "Deleted HDA is not in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); - }); - }); -}); - -// undelete the uploaded file -spaceghost.then( function(){ - this.historyoptions.includeDeleted(); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.waitForSelector( nameSelector, function(){ - //TODO: to conv. fn - this.click( '#' + testUploadInfo.hdaElement.attributes.id - + ' ' + this.historypanel.data.selectors.history.undeleteLink ); - }); - }); -}); - -// ------------------------------------------------------------------- hidden hdas aren't shown -// ------------------------------------------------------------------- history options allows showing hidden hdas -// can't test this yet w/o a way to make hdas hidden thru the ui or api - // ------------------------------------------------------------------- hdas can be expanded by clicking on the hda name // broken in webkit w/ jq 1.7 -spaceghost.then( function(){ +spaceghost.historypanel.waitForHdas( function(){ this.test.comment( 'HDAs can be expanded by clicking on the name' ); var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.click( uploadedSelector + ' .historyItemTitle' ); - this.wait( 1000, function(){ - this.test.assertVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, - "Body for uploaded file is visible" ); - }); + this.click( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.title ); + this.wait( 1000, function(){ + this.test.assertVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is visible" ); }); }); @@ -360,26 +267,22 @@ var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; this.click( refreshButtonSelector ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.waitForSelector( nameSelector, function(){ - this.test.assertVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, - "Body for uploaded file is visible" ); - }); + this.historypanel.waitForHdas( function(){ + this.test.assertVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is visible" ); }); // this will break: webkit + jq 1.7 }); // ------------------------------------------------------------------- expanded hdas collapse by clicking name again -spaceghost.then( function(){ +spaceghost.withHistoryPanel( function(){ this.test.comment( 'Expanded hdas collapse by clicking name again' ); var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.click( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.title ); - this.wait( 500, function(){ - this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, - "Body for uploaded file is not visible" ); - }); + this.click( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.title ); + this.wait( 500, function(){ + this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is not visible" ); }); }); @@ -389,32 +292,9 @@ var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; this.click( refreshButtonSelector ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.waitForSelector( nameSelector, function(){ - this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, - "Body for uploaded file is not visible" ); - }); - }); -}); - -// ------------------------------------------------------------------- history options collapses all expanded hdas -spaceghost.then( function(){ - // expand again - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.click( '#' + testUploadInfo.hdaElement.attributes.id + ' ' + this.historypanel.data.selectors.hda.title ); - this.wait( 500, function(){}); - }); -}); -spaceghost.then( function(){ - this.test.comment( 'History option collapses all expanded hdas' ); - var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; - - this.historyoptions.collapseExpanded(); - this.wait( 500, function(){ - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, - "Body for uploaded file is not visible" ); - }); + this.historypanel.waitForHdas( function(){ + this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is not visible" ); }); }); diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/login-tests.js --- a/test/casperjs/login-tests.js +++ b/test/casperjs/login-tests.js @@ -39,6 +39,8 @@ password = spaceghost.fixtureData.testUser.password; } +var userEmailSelector = '//a[contains(text(),"Logged in as")]/span["id=#user-email"]'; + // =================================================================== TESTS // register a user (again...) spaceghost.thenOpen( spaceghost.baseUrl, function(){ @@ -52,8 +54,7 @@ spaceghost.user.logout(); }); spaceghost.then( function(){ - this.test.assertSelectorDoesntHaveText( - xpath( '//a[contains(text(),"Logged in as")]/span["id=#user-email"]' ), /\w/ ); + this.test.assertSelectorDoesntHaveText( xpath( userEmailSelector ), /\w/ ); this.test.assert( spaceghost.user.loggedInAs() === '', 'loggedInAs() is empty string' ); }); @@ -63,8 +64,7 @@ spaceghost.user._submitLogin( email, password ); //No such user }); spaceghost.thenOpen( spaceghost.baseUrl, function(){ - this.test.assertSelectorHasText( - xpath( '//a[contains(text(),"Logged in as")]/span["id=#user-email"]' ), email ); + this.test.assertSelectorHasText( xpath( userEmailSelector ), email ); this.test.assert( spaceghost.user.loggedInAs() === email, 'loggedInAs() matches email' ); }); diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/modules/api.js --- /dev/null +++ b/test/casperjs/modules/api.js @@ -0,0 +1,231 @@ +// =================================================================== module object, exports +/** Creates a new api module object. + * @param {SpaceGhost} spaceghost a spaceghost instance + * @exported + */ +exports.create = function createAPI( spaceghost, apikey ){ + return new API( spaceghost ); +}; + +/** User object constructor. + * @param {SpaceGhost} spaceghost a spaceghost instance + * @param {String} apikey apikey for use when not using session authentication + */ +var API = function API( spaceghost, apikey ){ + this.spaceghost = spaceghost; + this.apikey = apikey; + + this.encodedIdExpectedLength = 16; + this.jQueryLocation = '../../static/scripts/libs/jquery/jquery.js'; + + this.histories = new HistoriesAPI( this ); + this.hdas = new HDAAPI( this ); +}; +exports.API = API; + +API.prototype.toString = function toString(){ + return ( this.spaceghost + '.API:' + + (( this.apikey )?( this.apikey ):( '(session)' )) ); +}; + +// ------------------------------------------------------------------- APIError +APIError.prototype = new Error(); +APIError.prototype.constructor = Error; +/** @class Thrown when Galaxy the API returns an error from a request */ +function APIError( msg ){ + Error.apply( this, arguments ); + this.name = "APIError"; + this.message = msg; +} +exports.APIError = APIError; + +/* ------------------------------------------------------------------- TODO: + can we component-ize this to become the basis for js-based api binding/resource + +*/ +// =================================================================== INTERNAL +var utils = require( 'utils' ); + +API.prototype._ajax = function _ajax( url, options ){ + options = options || {}; + options.async = false; + + this.ensureJQuery( '../../static/scripts/libs/jquery/jquery.js' ); + var resp = this.spaceghost.evaluate( function( url, options ){ + return jQuery.ajax( url, options ); + }, url, options ); + //this.spaceghost.debug( 'resp: ' + this.spaceghost.jsonStr( resp ) ); + + if( resp.status !== 200 ){ + // grrr... this doesn't lose the \n\r\t + throw new APIError( resp.responseText.replace( /[\s\n\r\t]+/gm, ' ' ).replace( /"/, '' ) ); + } + return JSON.parse( resp.responseText ); +}; + +// =================================================================== MISC +API.prototype.isEncodedId = function isEncodedId( id ){ + if( typeof id !== 'string' ){ return false; } + if( id.match( /[g-zG-Z]/ ) ){ return false; } + return ( id.length === this.encodedIdExpectedLength ); +}; + +// ------------------------------------------------------------------- is type or throw err +API.prototype.ensureId = function ensureId( id ){ + if( !this.isEncodedId( id ) ){ + throw new APIError( 'ID is not a valid encoded id: ' + id ); + } + return id; +}; + +API.prototype.ensureObject = function ensureObject( obj ){ + if( !utils.isObject( obj ) ){ + throw new APIError( 'Not a valid object: ' + obj ); + } + return obj; +}; + +// ------------------------------------------------------------------- jquery +// using jq for the ajax in this module - that's why these are here +//TODO:?? could go in spaceghost +API.prototype.hasJQuery = function hasJQuery(){ + return this.spaceghost.evaluate( function pageHasJQuery(){ + var has = false; + try { + has = typeof ( jQuery + '' ) === 'string'; + } catch( err ){} + return has; + }); +}; + +API.prototype.ensureJQuery = function ensureJQuery(){ + if( !this.hasJQuery() ){ + var absLoc = this.spaceghost.options.scriptDir + this.jQueryLocation, + injected = this.spaceghost.page.injectJs( absLoc ); + if( !injected ){ + throw new APIError( 'Could not inject jQuery' ); + } + } +}; + + +// =================================================================== HISTORIES +var HistoriesAPI = function HistoriesAPI( api ){ + this.api = api; +}; +HistoriesAPI.prototype.toString = function toString(){ + return this.api + '.HistoriesAPI'; +}; + +// ------------------------------------------------------------------- +HistoriesAPI.prototype.urlTpls = { + index : 'api/histories', + show : 'api/histories/%s', + create : 'api/histories', + delete_ : 'api/histories/%s', + undelete: 'api/histories/deleted/%s/undelete' +}; + +HistoriesAPI.prototype.index = function index( deleted ){ + this.api.spaceghost.info( 'history.index: ' + (( deleted )?( 'w deleted' ):( '(wo deleted)' )) ); + + deleted = deleted || false; + return this.api._ajax( this.urlTpls.index, { + data : { deleted: deleted } + }); +}; + +HistoriesAPI.prototype.show = function show( id, deleted ){ + this.api.spaceghost.info( 'history.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); + + id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); + deleted = deleted || false; + return this.api._ajax( utils.format( this.urlTpls.show, id ), { + data : { deleted: deleted } + }); +}; + +HistoriesAPI.prototype.create = function create( payload ){ + this.api.spaceghost.info( 'history.create: ' + this.api.spaceghost.jsonStr( payload ) ); + + // py.payload <-> ajax.data + payload = this.api.ensureObject( payload ); + return this.api._ajax( utils.format( this.urlTpls.create ), { + type : 'POST', + data : payload + }); +}; + +HistoriesAPI.prototype.delete_ = function delete_( id, purge ){ + this.api.spaceghost.info( 'history.delete: ' + [ id, (( purge )?( '(purge!)' ):( '' )) ] ); + + // py.payload <-> ajax.data + var payload = ( purge )?({ purge: true }):({}); + return this.api._ajax( utils.format( this.urlTpls.delete_, this.api.ensureId( id ) ), { + type : 'DELETE', + data : payload + }); +}; + +HistoriesAPI.prototype.undelete = function undelete( id ){ + //throw ( 'unimplemented' ); + this.api.spaceghost.info( 'history.undelete: ' + id ); + + return this.api._ajax( utils.format( this.urlTpls.undelete, this.api.ensureId( id ) ), { + type : 'POST' + }); +}; + + +// =================================================================== HDAS +var HDAAPI = function HDAAPI( api ){ + this.api = api; +}; +HDAAPI.prototype.toString = function toString(){ + return this.api + '.HDAAPI'; +}; + +// ------------------------------------------------------------------- +HDAAPI.prototype.urlTpls = { + index : 'api/histories/%s/contents', + show : 'api/histories/%s/contents/%s', + create : 'api/histories/%s/contents'//, + // not implemented + //delete_ : 'api/histories/%s', + //undelete: 'api/histories/deleted/%s/undelete' +}; + +HDAAPI.prototype.index = function index( historyId, ids ){ + this.api.spaceghost.info( 'history.index: ' + [ historyId, ids ] ); + var data = {}; + if( ids ){ + ids = ( utils.isArray( ids ) )?( ids.join( ',' ) ):( ids ); + data.ids = ids; + } + + return this.api._ajax( utils.format( this.urlTpls.index, this.api.ensureId( historyId ) ), { + data : data + }); +}; + +HDAAPI.prototype.show = function show( historyId, id, deleted ){ + this.api.spaceghost.info( 'history.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); + + id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); + deleted = deleted || false; + return this.api._ajax( utils.format( this.urlTpls.show, id ), { + data : { deleted: deleted } + }); +}; + +HDAAPI.prototype.create = function create( historyId, payload ){ + this.api.spaceghost.info( 'history.create: ' + this.api.spaceghost.jsonStr( payload ) ); + + // py.payload <-> ajax.data + payload = this.api.ensureObject( payload ); + return this.api._ajax( utils.format( this.urlTpls.create ), { + type : 'POST', + data : payload + }); +}; + diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/modules/historyoptions.js --- a/test/casperjs/modules/historyoptions.js +++ b/test/casperjs/modules/historyoptions.js @@ -21,23 +21,65 @@ // ------------------------------------------------------------------- /* TODO: + some of the fns below can be applied to any popup */ +// =================================================================== internal +var xpath = require( 'casper' ).selectXPath; + // =================================================================== API (external) /** Just open the menu + * @param {Function} fn function to call when the menu opens + * @returns {Any} the return value of fn */ -HistoryOptions.prototype.openMenu = function openMenu(){ - this.spaceghost.click( this.data.selectors.button ); +HistoryOptions.prototype.openMenu = function openMenu( fn ){ + return this.spaceghost.jumpToTop( function(){ + this.click( this.historyoptions.data.selectors.button ); + return fn.call( this ); + }); }; /** Click an option by Label + * @param {String} optionLabel the label of the option to click (can be partial?) + * @returns {SpaceGhost} for chaining */ HistoryOptions.prototype.clickOption = function clickOption( optionLabel ){ - this.openMenu(); - // casperjs clickLabel - var optionXpath = this.data.selectors.optionXpathByLabelFn( optionLabel ); - this.spaceghost.click( optionXpath ); + this.openMenu( function(){ + this.click( this.historyoptions.data.selectors.optionXpathByLabelFn( optionLabel ) ); + // shouldnt need to clear - clicking an option will do that + }); + return this.spaceghost; +}; + +/** Is the history option with the given label showing as toggled? + * @param {String} optionLabel the label of the option to check (can be partial?) + * @returns {Boolean} true if the option is on, false if off OR not a toggle + */ +HistoryOptions.prototype.isOn = function isOn( optionLabel ){ + return this.openMenu( function(){ + var toggleIconInfo = this.elementInfoOrNull( + this.historyoptions.data.selectors.optionIsOnXpathByLabelFn( optionLabel ) ); + // have to clear manually + this.click( 'body' ); + return !!toggleIconInfo; + }); +}; + +/** Toggle the option - optionally forcing to on or off. + * @param {String} optionLabel the label of the option to check (can be partial?) + * @param {Boolean} force if true ensure option is on, if false ensure it's off, + * if undefined simply toggle + * @returns {Boolean} true if the option is now on, false if now off or not a toggle + */ +HistoryOptions.prototype.toggle = function toggle( optionLabel, force ){ + var isOn = this.isOn( optionLabel ); + if( ( force === false && isOn ) + || ( force === true && !isOn ) + || ( force === undefined ) ){ + return this.clickOption( optionLabel ); + } + return force; }; // ------------------------------------------------------------------- @@ -101,22 +143,68 @@ //}; -// ------------------------------------------------------------------- +// ------------------------------------------------------------------- check the togglable options // these are easy, one click options (they don't open a new page) +/** Is 'Include Deleted Datasets' on (accrd. to the menu)? + */ +HistoryOptions.prototype.deletedAreIncluded = function deletedAreIncluded(){ + return this.isOn( this.data.labels.options.includeDeleted ); +}; +/** Is 'Include Deleted Datasets' on (accrd. to the menu)? + */ +HistoryOptions.prototype.hiddenAreIncluded = function hiddenAreIncluded(){ + return this.isOn( this.data.labels.options.includeHidden ); +}; + +// ------------------------------------------------------------------- options that control the hpanel /** corresponds to history options menu: 'Collapse Expanded Datasets' */ -HistoryOptions.prototype.collapseExpanded = function collapseExpanded(){ - this.clickOption( this.data.labels.options.collapseExpanded ); +HistoryOptions.prototype.collapseExpanded = function collapseExpanded( then ){ + return this.spaceghost.then( function(){ + this.historyoptions.clickOption( this.historyoptions.data.labels.options.collapseExpanded ); + this.wait( 500, then ); + }); }; -/** corresponds to history options menu: 'Include Deleted Datasets' + +/** set 'Include Deleted Datasets' to on + * @param {Function} then casper step to run when option is set */ -HistoryOptions.prototype.includeDeleted = function includeDeleted(){ - this.clickOption( this.data.labels.options.includeDeleted ); +HistoryOptions.prototype.includeDeleted = function includeDeleted( then ){ + return this.spaceghost.then( function(){ + this.historyoptions.toggle( this.historyoptions.data.labels.options.includeDeleted, true ); + this.historypanel.waitForHdas( then ); + }); }; -/** corresponds to history options menu: 'Include Hidden Datasets' + +/** set 'Include Deleted Datasets' to off + * @param {Function} then casper step to run when option is set */ -HistoryOptions.prototype.includeHidden = function includeHidden(){ - this.clickOption( this.data.labels.options.includeHidden ); +HistoryOptions.prototype.excludeDeleted = function excludeDeleted( then ){ + return this.spaceghost.then( function(){ + this.historyoptions.toggle( this.historyoptions.data.labels.options.includeDeleted, false ); + //TODO:?? this puts in the history frame. Is that what we want? + this.historypanel.waitForHdas( then ); + }); +}; + +/** set 'Include Hidden Datasets' to on + * @param {Function} then casper step to run when option is set + */ +HistoryOptions.prototype.includeHidden = function includeHidden( then ){ + return this.spaceghost.then( function(){ + this.historyoptions.toggle( this.historyoptions.data.labels.options.includeHidden, true ); + this.historypanel.waitForHdas( then ); + }); +}; + +/** set 'Include Hidden Datasets' to off + * @param {Function} then casper step to run when option is set + */ +HistoryOptions.prototype.excludeHidden = function excludeHidden( then ){ + return this.spaceghost.then( function(){ + this.historyoptions.toggle( this.historyoptions.data.labels.options.includeHidden, false ); + this.historypanel.waitForHdas( then ); + }); }; @@ -129,6 +217,10 @@ menu : '#history-options-button-menu', optionXpathByLabelFn : function optionXpathByLabelFn( label ){ return xpath( '//ul[@id="history-options-button-menu"]/li/a[text()[contains(.,"' + label + '")]]' ); + }, + optionIsOnXpathByLabelFn : function optionIsOnXpathByLabelFn( label ){ + return xpath( '//ul[@id="history-options-button-menu"]/li/a[text()[contains(.,"' + label + '")]]' + + '/span[@class="fa-icon-ok"]' ); } }, labels : { This diff is so big that we needed to truncate the remainder. 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: Fix unicode decoding error when displaying the contents of certain files. Catch any future errors.
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7b5f97700fdc/ changeset: 7b5f97700fdc branch: next-stable user: inithello date: 2013-03-18 19:32:06 summary: Fix unicode decoding error when displaying the contents of certain files. Catch any future errors. affected #: 1 file diff -r e0607a09d9fa9eb690e9b410d9c167072db0b55a -r 7b5f97700fdc8286db3e5ed6b6425127694ca42f lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1059,7 +1059,12 @@ """Translates the characters in text to an html string""" if text: if to_html: - escaped_text = str( markupsafe.escape( text ) ) + try: + escaped_text = text.decode( 'utf-8' ) + escaped_text = escaped_text.encode( 'ascii', 'ignore' ) + escaped_text = str( markupsafe.escape( escaped_text ) ) + except UnicodeDecodeError, e: + escaped_text = "Error decoding string: %s" % str( e ) else: escaped_text = str( text ) translated = [] 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: inithello: Fix unicode decoding error when displaying the contents of certain files. Catch any future errors.
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/51d3a88f45ee/ changeset: 51d3a88f45ee user: inithello date: 2013-03-18 19:32:06 summary: Fix unicode decoding error when displaying the contents of certain files. Catch any future errors. affected #: 1 file diff -r 7a4dd13dac9be2b3c9233b7a60e61d30d283744f -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1059,7 +1059,12 @@ """Translates the characters in text to an html string""" if text: if to_html: - escaped_text = str( markupsafe.escape( text ) ) + try: + escaped_text = text.decode( 'utf-8' ) + escaped_text = escaped_text.encode( 'ascii', 'ignore' ) + escaped_text = str( markupsafe.escape( escaped_text ) ) + except UnicodeDecodeError, e: + escaped_text = "Error decoding string: %s" % str( e ) else: escaped_text = str( text ) translated = [] 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: Include LWR and job running fixes from John Chilton in next-stable.
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e0607a09d9fa/ changeset: e0607a09d9fa branch: next-stable user: natefoo date: 2013-03-18 16:38:34 summary: Include LWR and job running fixes from John Chilton in next-stable. affected #: 10 files diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -7,6 +7,7 @@ <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/><plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/><plugin id="gridengine" type="runner" load="galaxy.jobs.runners.drmaa:DRMAARunner"/> + <plugin id="lwr" type="runner" load="galaxy.jobs.runners.lwr.LwrJobRunner" /></plugins><handlers default="handlers"> + <param id="private_token">123456789changeme</param> + </destination></destinations><tools><!-- Tools can be configured to use specific destinations or handlers, diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -126,7 +126,12 @@ for plugin in self.__findall_with_required(plugins, 'plugin', ('id', 'type', 'load')): if plugin.get('type') == 'runner': workers = plugin.get('workers', plugins.get('workers', JobConfiguration.DEFAULT_NWORKERS)) - self.runner_plugins.append(dict(id=plugin.get('id'), load=plugin.get('load'), workers=int(workers))) + runner_kwds = self.__get_params(plugin) + runner_info = dict(id=plugin.get('id'), + load=plugin.get('load'), + workers=int(workers), + kwds=runner_kwds) + self.runner_plugins.append(runner_info) else: log.error('Unknown plugin type: %s' % plugin.get('type')) # Load tasks if configured @@ -480,7 +485,7 @@ log.warning("Job runner classes must be subclassed from BaseJobRunner, %s has bases: %s" % (id, runner_class.__bases__)) continue try: - rval[id] = runner_class( self.app, runner['workers'] ) + rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) ) except TypeError: log.warning( "Job runner '%s:%s' has not been converted to a new-style runner" % ( module_name, class_name ) ) rval[id] = runner_class( self.app ) @@ -833,7 +838,7 @@ log.warning('set_runner() is deprecated, use set_job_destination()') self.set_job_destination(self.job_destination, external_id) - def set_job_destination(self, job_destination, external_id): + def set_job_destination(self, job_destination, external_id=None ): """ Persist job destination params in the database for recovery. diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -3,11 +3,12 @@ from galaxy import model from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner +from galaxy.jobs import JobDestination import errno from time import sleep -from lwr_client import FileStager, Client +from lwr_client import FileStager, Client, url_to_destination_params log = logging.getLogger( __name__ ) @@ -19,11 +20,16 @@ """ runner_name = "LWRRunner" - def __init__( self, app, nworkers ): + def __init__( self, app, nworkers, transport=None ): """Start the job runner """ super( LwrJobRunner, self ).__init__( app, nworkers ) self._init_monitor_thread() self._init_worker_threads() + self.transport_type = transport + + def url_to_destination( self, url ): + """Convert a legacy URL to a job destination""" + return JobDestination( runner="lwr", params=url_to_destination_params( url ) ) def check_watched_item(self, job_state): try: @@ -42,7 +48,7 @@ def queue_job(self, job_wrapper): stderr = stdout = command_line = '' - runner_url = job_wrapper.get_job_runner_url() + job_destination = job_wrapper.job_destination try: job_wrapper.prepare() @@ -74,7 +80,7 @@ rebuilt_command_line = file_stager.get_rewritten_command_line() job_id = file_stager.job_id client.launch( rebuilt_command_line ) - job_wrapper.set_runner( runner_url, job_id ) + job_wrapper.set_job_destination( job_destination, job_id ) job_wrapper.change_state( model.Job.states.RUNNING ) except Exception, exc: @@ -87,32 +93,26 @@ lwr_job_state.job_id = job_id lwr_job_state.old_state = True lwr_job_state.running = True - lwr_job_state.runner_url = runner_url + lwr_job_state.job_destination = job_destination self.monitor_job(lwr_job_state) def get_output_files(self, job_wrapper): output_fnames = job_wrapper.get_output_fnames() return [ str( o ) for o in output_fnames ] - - def determine_lwr_url(self, url): - lwr_url = url[ len( 'lwr://' ) : ] - return lwr_url - def get_client_from_wrapper(self, job_wrapper): job_id = job_wrapper.job_id if hasattr(job_wrapper, 'task_id'): job_id = "%s_%s" % (job_id, job_wrapper.task_id) - return self.get_client( job_wrapper.get_job_runner_url(), job_id ) + return self.get_client( job_wrapper.job_destination.params, job_id ) def get_client_from_state(self, job_state): - job_runner = job_state.runner_url + job_destination_params = job_state.job_destination.params job_id = job_state.job_id - return self.get_client(job_runner, job_id) + return self.get_client( job_destination_params, job_id ) - def get_client(self, job_runner, job_id): - lwr_url = self.determine_lwr_url( job_runner ) - return Client(lwr_url, job_id) + def get_client( self, job_destination_params, job_id ): + return Client( job_destination_params, job_id, transport_type=self.transport_type ) def finish_job( self, job_state ): stderr = stdout = command_line = '' @@ -210,7 +210,7 @@ lwr_url = job.job_runner_name job_id = job.job_runner_external_id log.debug("Attempt remote lwr kill of job with url %s and id %s" % (lwr_url, job_id)) - client = self.get_client(lwr_url, job_id) + client = self.get_client(job.destination_params, job_id) client.kill() @@ -219,6 +219,7 @@ job_state = AsynchronousJobState() job_state.job_id = str( job.get_job_runner_external_id() ) job_state.runner_url = job_wrapper.get_job_runner_url() + job_state.job_destination = job_wrapper.job_destination job_wrapper.command_line = job.get_command_line() job_state.job_wrapper = job_wrapper if job.get_state() == model.Job.states.RUNNING: diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/lwr_client/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py @@ -5,502 +5,9 @@ This module contains logic for interfacing with an external LWR server. """ -import os -import re -import time -import urllib -import simplejson +from .stager import FileStager +from .client import Client +from .destination import url_to_destination_params -from transport import get_transport - - -class JobInputs(object): - """ - Abstractions over dynamic inputs created for a given job (namely the command to - execute and created configfiles). - - **Parameters** - - command_line : str - Local command to execute for this job. (To be rewritten.) - config_files : str - Config files created for this job. (To be rewritten.) - - - >>> import tempfile - >>> tf = tempfile.NamedTemporaryFile() - >>> def setup_inputs(tf): - ... open(tf.name, "w").write("world /path/to/input the rest") - ... inputs = JobInputs("hello /path/to/input", [tf.name]) - ... return inputs - >>> inputs = setup_inputs(tf) - >>> inputs.rewrite_paths("/path/to/input", 'C:\\input') - >>> inputs.rewritten_command_line - 'hello C:\\\\input' - >>> inputs.rewritten_config_files[tf.name] - 'world C:\\\\input the rest' - >>> tf.close() - >>> tf = tempfile.NamedTemporaryFile() - >>> inputs = setup_inputs(tf) - >>> inputs.find_referenced_subfiles('/path/to') - ['/path/to/input'] - >>> inputs.path_referenced('/path/to') - True - >>> inputs.path_referenced('/path/to/input') - True - >>> inputs.path_referenced('/path/to/notinput') - False - >>> tf.close() - """ - - def __init__(self, command_line, config_files): - self.rewritten_command_line = command_line - self.rewritten_config_files = {} - for config_file in config_files or []: - config_contents = _read(config_file) - self.rewritten_config_files[config_file] = config_contents - - def find_referenced_subfiles(self, directory): - """ - Return list of files below specified `directory` in job inputs. Could - use more sophisticated logic (match quotes to handle spaces, handle - subdirectories, etc...). - - **Parameters** - - directory : str - Full path to directory to search. - - """ - pattern = r"(%s%s\S+)" % (directory, os.sep) - referenced_files = set() - for input_contents in self.__items(): - referenced_files.update(re.findall(pattern, input_contents)) - return list(referenced_files) - - def path_referenced(self, path): - pattern = r"%s" % path - found = False - for input_contents in self.__items(): - if re.findall(pattern, input_contents): - found = True - break - return found - - def rewrite_paths(self, local_path, remote_path): - """ - Rewrite references to `local_path` with `remote_path` in job inputs. - """ - self.__rewrite_command_line(local_path, remote_path) - self.__rewrite_config_files(local_path, remote_path) - - def __rewrite_command_line(self, local_path, remote_path): - self.rewritten_command_line = self.rewritten_command_line.replace(local_path, remote_path) - - def __rewrite_config_files(self, local_path, remote_path): - for config_file, rewritten_contents in self.rewritten_config_files.iteritems(): - self.rewritten_config_files[config_file] = rewritten_contents.replace(local_path, remote_path) - - def __items(self): - items = [self.rewritten_command_line] - items.extend(self.rewritten_config_files.values()) - return items - - -class FileStager(object): - """ - Objects of the FileStager class interact with an LWR client object to - stage the files required to run jobs on a remote LWR server. - - **Parameters** - - client : Client - LWR client object. - command_line : str - The local command line to execute, this will be rewritten for the remote server. - config_files : list - List of Galaxy 'configfile's produced for this job. These will be rewritten and sent to remote server. - input_files : list - List of input files used by job. These will be transferred and references rewritten. - output_files : list - List of output_files produced by job. - tool_dir : str - Directory containing tool to execute (if a wrapper is used, it will be transferred to remote server). - working_directory : str - Local path created by Galaxy for running this job. - - """ - - def __init__(self, client, tool, command_line, config_files, input_files, output_files, working_directory): - """ - """ - self.client = client - self.command_line = command_line - self.config_files = config_files - self.input_files = input_files - self.output_files = output_files - self.tool_id = tool.id - self.tool_version = tool.version - self.tool_dir = os.path.abspath(tool.tool_dir) - self.working_directory = working_directory - - # Setup job inputs, these will need to be rewritten before - # shipping off to remote LWR server. - self.job_inputs = JobInputs(self.command_line, self.config_files) - - self.file_renames = {} - - self.__handle_setup() - self.__initialize_referenced_tool_files() - self.__upload_tool_files() - self.__upload_input_files() - self.__upload_working_directory_files() - self.__initialize_output_file_renames() - self.__initialize_task_output_file_renames() - self.__initialize_config_file_renames() - self.__handle_rewrites() - self.__upload_rewritten_config_files() - - def __handle_setup(self): - job_config = self.client.setup(self.tool_id, self.tool_version) - - self.new_working_directory = job_config['working_directory'] - self.new_outputs_directory = job_config['outputs_directory'] - self.remote_path_separator = job_config['path_separator'] - # If remote LWR server assigned job id, use that otherwise - # just use local job_id assigned. - galaxy_job_id = self.client.job_id - self.job_id = job_config.get('job_id', galaxy_job_id) - if self.job_id != galaxy_job_id: - # Remote LWR server assigned an id different than the - # Galaxy job id, update client to reflect this. - self.client.job_id = self.job_id - - def __initialize_referenced_tool_files(self): - self.referenced_tool_files = self.job_inputs.find_referenced_subfiles(self.tool_dir) - - def __upload_tool_files(self): - for referenced_tool_file in self.referenced_tool_files: - tool_upload_response = self.client.upload_tool_file(referenced_tool_file) - self.file_renames[referenced_tool_file] = tool_upload_response['path'] - - def __upload_input_files(self): - for input_file in self.input_files: - self.__upload_input_file(input_file) - self.__upload_input_extra_files(input_file) - - def __upload_input_file(self, input_file): - if self.job_inputs.path_referenced(input_file): - input_upload_response = self.client.upload_input(input_file) - self.file_renames[input_file] = input_upload_response['path'] - - def __upload_input_extra_files(self, input_file): - # TODO: Determine if this is object store safe and what needs to be - # done if it is not. - files_path = "%s_files" % input_file[0:-len(".dat")] - if os.path.exists(files_path) and self.job_inputs.path_referenced(files_path): - for extra_file in os.listdir(files_path): - extra_file_path = os.path.join(files_path, extra_file) - relative_path = os.path.basename(files_path) - extra_file_relative_path = os.path.join(relative_path, extra_file) - response = self.client.upload_extra_input(extra_file_path, extra_file_relative_path) - self.file_renames[extra_file_path] = response['path'] - - def __upload_working_directory_files(self): - # Task manager stages files into working directory, these need to be - # uploaded if present. - for working_directory_file in os.listdir(self.working_directory): - path = os.path.join(self.working_directory, working_directory_file) - working_file_response = self.client.upload_working_directory_file(path) - self.file_renames[path] = working_file_response['path'] - - def __initialize_output_file_renames(self): - for output_file in self.output_files: - self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, - self.remote_path_separator, - os.path.basename(output_file)) - - def __initialize_task_output_file_renames(self): - for output_file in self.output_files: - name = os.path.basename(output_file) - self.file_renames[os.path.join(self.working_directory, name)] = r'%s%s%s' % (self.new_working_directory, - self.remote_path_separator, - name) - - def __initialize_config_file_renames(self): - for config_file in self.config_files: - self.file_renames[config_file] = r'%s%s%s' % (self.new_working_directory, - self.remote_path_separator, - os.path.basename(config_file)) - - def __rewrite_paths(self, contents): - new_contents = contents - for local_path, remote_path in self.file_renames.iteritems(): - new_contents = new_contents.replace(local_path, remote_path) - return new_contents - - def __handle_rewrites(self): - for local_path, remote_path in self.file_renames.iteritems(): - self.job_inputs.rewrite_paths(local_path, remote_path) - - def __upload_rewritten_config_files(self): - for config_file, new_config_contents in self.job_inputs.rewritten_config_files.iteritems(): - self.client.upload_config_file(config_file, new_config_contents) - - def get_rewritten_command_line(self): - """ - Returns the rewritten version of the command line to execute suitable - for remote host. - """ - return self.job_inputs.rewritten_command_line - - -class parseJson(object): - - def __init__(self): - pass - - def __call__(self, func): - def replacement(*args, **kwargs): - response = func(*args, **kwargs) - return simplejson.loads(response) - return replacement - - -class Client(object): - """ - Objects of this client class perform low-level communication with a remote LWR server. - - **Parameters** - - remote_host : str - Remote URL of the LWR server. - job_id : str - Galaxy job/task id. - private_key : str (optional) - Secret key the remote LWR server is configured with. - """ - - def __init__(self, remote_host, job_id, private_key=None): - if not remote_host.endswith("/"): - remote_host = remote_host + "/" - ## If we don't have an explicit private_key defined, check for - ## one embedded in the URL. A URL of the form - ## https://moo@cow:8913 will try to contact https://cow:8913 - ## with a private key of moo - private_key_format = "https?://(.*)@.*/?" - private_key_match = re.match(private_key_format, remote_host) - if not private_key and private_key_match: - private_key = private_key_match.group(1) - remote_host = remote_host.replace("%s@" % private_key, '', 1) - self.remote_host = remote_host - self.job_id = job_id - self.private_key = private_key - self.transport = get_transport() - - def __build_url(self, command, args): - if self.private_key: - args["private_key"] = self.private_key - data = urllib.urlencode(args) - url = self.remote_host + command + "?" + data - return url - - def __raw_execute(self, command, args={}, data=None, input_path=None, output_path=None): - url = self.__build_url(command, args) - response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) - return response - - @parseJson() - def __upload_file(self, action, path, name=None, contents=None): - if not name: - name = os.path.basename(path) - args = {"job_id": self.job_id, "name": name} - input_path = path - if contents: - input_path = None - return self.__raw_execute(action, args, contents, input_path) - - def upload_tool_file(self, path): - """ - Upload a tool related file (e.g. wrapper) required to run job. - - **Parameters** - - path : str - Local path tool. - """ - return self.__upload_file("upload_tool_file", path) - - def upload_input(self, path): - """ - Upload input dataset to remote server. - - **Parameters** - - path : str - Local path of input dataset. - """ - return self.__upload_file("upload_input", path) - - def upload_extra_input(self, path, relative_name): - """ - Upload extra input file to remote server. - - **Parameters** - - path : str - Extra files path of input dataset corresponding to this input. - relative_name : str - Relative path of extra file to upload relative to inputs extra files path. - """ - return self.__upload_file("upload_extra_input", path, name=relative_name) - - def upload_config_file(self, path, contents): - """ - Upload a job's config file to the remote server. - - **Parameters** - - path : str - Local path to the original config file. - contents : str - Rewritten contents of the config file to upload. - """ - return self.__upload_file("upload_config_file", path, contents=contents) - - def upload_working_directory_file(self, path): - """ - Upload the supplied file (path) from a job's working directory - to remote server. - - **Parameters** - - path : str - Path to file to upload. - """ - return self.__upload_file("upload_working_directory_file", path) - - @parseJson() - def _get_output_type(self, name): - return self.__raw_execute("get_output_type", {"name": name, - "job_id": self.job_id}) - - def download_work_dir_output(self, source, working_directory, output_path): - """ - Download an output dataset specified with from_work_dir from the - remote server. - - **Parameters** - - source : str - Path in job's working_directory to find output in. - working_directory : str - Local working_directory for the job. - output_path : str - Full path to output dataset. - """ - output = open(output_path, "wb") - name = os.path.basename(source) - self.__raw_download_output(name, self.job_id, "work_dir", output) - - def download_output(self, path, working_directory): - """ - Download an output dataset from the remote server. - - **Parameters** - - path : str - Local path of the dataset. - working_directory : str - Local working_directory for the job. - """ - name = os.path.basename(path) - output_type = self._get_output_type(name) - if output_type == "direct": - output_path = path - elif output_type == "task": - output_path = os.path.join(working_directory, name) - else: - raise Exception("No remote output found for dataset with path %s" % path) - self.__raw_download_output(name, self.job_id, output_type, output_path) - - def __raw_download_output(self, name, job_id, output_type, output_path): - self.__raw_execute("download_output", - {"name": name, - "job_id": self.job_id, - "output_type": output_type}, - output_path=output_path) - - def launch(self, command_line): - """ - Run or queue up the execution of the supplied - `command_line` on the remote server. - - **Parameters** - - command_line : str - Command to execute. - """ - return self.__raw_execute("launch", {"command_line": command_line, - "job_id": self.job_id}) - - def kill(self): - """ - Cancel remote job, either removing from the queue or killing it. - """ - return self.__raw_execute("kill", {"job_id": self.job_id}) - - def wait(self): - """ - Wait for job to finish. - """ - while True: - complete_response = self.raw_check_complete() - if complete_response["complete"] == "true": - return complete_response - time.sleep(1) - - @parseJson() - def raw_check_complete(self): - """ - Get check_complete response from the remote server. - """ - check_complete_response = self.__raw_execute("check_complete", {"job_id": self.job_id}) - return check_complete_response - - def check_complete(self): - """ - Return boolean indicating whether the job is complete. - """ - return self.raw_check_complete()["complete"] == "true" - - def clean(self): - """ - Cleanup the remote job. - """ - self.__raw_execute("clean", {"job_id": self.job_id}) - - @parseJson() - def setup(self, tool_id=None, tool_version=None): - """ - Setup remote LWR server to run this job. - """ - setup_args = {"job_id": self.job_id} - if tool_id: - setup_args["tool_id"] = tool_id - if tool_version: - setup_args["tool_version"] = tool_version - return self.__raw_execute("setup", setup_args) - - -def _read(path): - """ - Utility method to quickly read small files (config files and tool - wrappers) into memory as strings. - """ - input = open(path, "r") - try: - return input.read() - finally: - input.close() +__all__ = [Client, FileStager, url_to_destination_params] diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/lwr_client/client.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -0,0 +1,235 @@ +import os +import time +import urllib +import simplejson + +from .transport import get_transport +from .destination import url_to_destination_params + + +class parseJson(object): + + def __init__(self): + pass + + def __call__(self, func): + def replacement(*args, **kwargs): + response = func(*args, **kwargs) + return simplejson.loads(response) + return replacement + + +class Client(object): + """ + Objects of this client class perform low-level communication with a remote LWR server. + + **Parameters** + + destination_params : dict or str + connection parameters, either url with dict containing url (and optionally `private_token`). + job_id : str + Galaxy job/task id. + """ + + def __init__(self, destination_params, job_id, transport_type=None): + if isinstance(destination_params, str) or isinstance(destination_params, unicode): + destination_params = url_to_destination_params(destination_params) + self.remote_host = destination_params.get("url") + assert self.remote_host != None, "Failed to determine url for LWR client." + self.private_key = destination_params.get("private_token", None) + self.job_id = job_id + self.transport = get_transport(transport_type) + + def __build_url(self, command, args): + if self.private_key: + args["private_key"] = self.private_key + data = urllib.urlencode(args) + url = self.remote_host + command + "?" + data + return url + + def __raw_execute(self, command, args={}, data=None, input_path=None, output_path=None): + url = self.__build_url(command, args) + response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) + return response + + @parseJson() + def __upload_file(self, action, path, name=None, contents=None): + if not name: + name = os.path.basename(path) + args = {"job_id": self.job_id, "name": name} + input_path = path + if contents: + input_path = None + return self.__raw_execute(action, args, contents, input_path) + + def upload_tool_file(self, path): + """ + Upload a tool related file (e.g. wrapper) required to run job. + + **Parameters** + + path : str + Local path tool. + """ + return self.__upload_file("upload_tool_file", path) + + def upload_input(self, path): + """ + Upload input dataset to remote server. + + **Parameters** + + path : str + Local path of input dataset. + """ + return self.__upload_file("upload_input", path) + + def upload_extra_input(self, path, relative_name): + """ + Upload extra input file to remote server. + + **Parameters** + + path : str + Extra files path of input dataset corresponding to this input. + relative_name : str + Relative path of extra file to upload relative to inputs extra files path. + """ + return self.__upload_file("upload_extra_input", path, name=relative_name) + + def upload_config_file(self, path, contents): + """ + Upload a job's config file to the remote server. + + **Parameters** + + path : str + Local path to the original config file. + contents : str + Rewritten contents of the config file to upload. + """ + return self.__upload_file("upload_config_file", path, contents=contents) + + def upload_working_directory_file(self, path): + """ + Upload the supplied file (path) from a job's working directory + to remote server. + + **Parameters** + + path : str + Path to file to upload. + """ + return self.__upload_file("upload_working_directory_file", path) + + @parseJson() + def _get_output_type(self, name): + return self.__raw_execute("get_output_type", {"name": name, + "job_id": self.job_id}) + + def download_work_dir_output(self, source, working_directory, output_path): + """ + Download an output dataset specified with from_work_dir from the + remote server. + + **Parameters** + + source : str + Path in job's working_directory to find output in. + working_directory : str + Local working_directory for the job. + output_path : str + Full path to output dataset. + """ + output = open(output_path, "wb") + name = os.path.basename(source) + self.__raw_download_output(name, self.job_id, "work_dir", output) + + def download_output(self, path, working_directory): + """ + Download an output dataset from the remote server. + + **Parameters** + + path : str + Local path of the dataset. + working_directory : str + Local working_directory for the job. + """ + name = os.path.basename(path) + output_type = self._get_output_type(name) + if output_type == "direct": + output_path = path + elif output_type == "task": + output_path = os.path.join(working_directory, name) + else: + raise Exception("No remote output found for dataset with path %s" % path) + self.__raw_download_output(name, self.job_id, output_type, output_path) + + def __raw_download_output(self, name, job_id, output_type, output_path): + self.__raw_execute("download_output", + {"name": name, + "job_id": self.job_id, + "output_type": output_type}, + output_path=output_path) + + def launch(self, command_line): + """ + Run or queue up the execution of the supplied + `command_line` on the remote server. + + **Parameters** + + command_line : str + Command to execute. + """ + return self.__raw_execute("launch", {"command_line": command_line, + "job_id": self.job_id}) + + def kill(self): + """ + Cancel remote job, either removing from the queue or killing it. + """ + return self.__raw_execute("kill", {"job_id": self.job_id}) + + def wait(self): + """ + Wait for job to finish. + """ + while True: + complete_response = self.raw_check_complete() + if complete_response["complete"] == "true": + return complete_response + time.sleep(1) + + @parseJson() + def raw_check_complete(self): + """ + Get check_complete response from the remote server. + """ + check_complete_response = self.__raw_execute("check_complete", {"job_id": self.job_id}) + return check_complete_response + + def check_complete(self): + """ + Return boolean indicating whether the job is complete. + """ + return self.raw_check_complete()["complete"] == "true" + + def clean(self): + """ + Cleanup the remote job. + """ + self.__raw_execute("clean", {"job_id": self.job_id}) + + @parseJson() + def setup(self, tool_id=None, tool_version=None): + """ + Setup remote LWR server to run this job. + """ + setup_args = {"job_id": self.job_id} + if tool_id: + setup_args["tool_id"] = tool_id + if tool_version: + setup_args["tool_version"] = tool_version + return self.__raw_execute("setup", setup_args) diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/lwr_client/destination.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/destination.py @@ -0,0 +1,44 @@ + +from re import match + + +def url_to_destination_params(url): + """Convert a legacy runner URL to a job destination + + >>> params_simple = url_to_destination_params("http://localhost:8913/") + >>> params_simple["url"] + 'http://localhost:8913/' + >>> params_simple["private_token"] is None + True + >>> advanced_url = "https://1234x@example.com:8914/managers/longqueue" + >>> params_advanced = url_to_destination_params(advanced_url) + >>> params_advanced["url"] + 'https://example.com:8914/managers/longqueue/' + >>> params_advanced["private_token"] + '1234x' + >>> runner_url = "lwr://http://localhost:8913/" + >>> runner_params = url_to_destination_params(runner_url) + >>> runner_params['url'] + 'http://localhost:8913/' + """ + + if url.startswith("lwr://"): + url = url[len("lwr://"):] + + if not url.endswith("/"): + url += "/" + + ## Check for private token embedded in the URL. A URL of the form + ## https://moo@cow:8913 will try to contact https://cow:8913 + ## with a private key of moo + private_token_format = "https?://(.*)@.*/?" + private_token_match = match(private_token_format, url) + private_token = None + if private_token_match: + private_token = private_token_match.group(1) + url = url.replace("%s@" % private_token, '', 1) + + destination_args = {"url": url, + "private_token": private_token} + + return destination_args diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/lwr_client/stager.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/stager.py @@ -0,0 +1,256 @@ + +import os +from re import findall + + +class JobInputs(object): + """ + Abstractions over dynamic inputs created for a given job (namely the command to + execute and created configfiles). + + **Parameters** + + command_line : str + Local command to execute for this job. (To be rewritten.) + config_files : str + Config files created for this job. (To be rewritten.) + + + >>> import tempfile + >>> tf = tempfile.NamedTemporaryFile() + >>> def setup_inputs(tf): + ... open(tf.name, "w").write("world /path/to/input the rest") + ... inputs = JobInputs("hello /path/to/input", [tf.name]) + ... return inputs + >>> inputs = setup_inputs(tf) + >>> inputs.rewrite_paths("/path/to/input", 'C:\\input') + >>> inputs.rewritten_command_line + 'hello C:\\\\input' + >>> inputs.rewritten_config_files[tf.name] + 'world C:\\\\input the rest' + >>> tf.close() + >>> tf = tempfile.NamedTemporaryFile() + >>> inputs = setup_inputs(tf) + >>> inputs.find_referenced_subfiles('/path/to') + ['/path/to/input'] + >>> inputs.path_referenced('/path/to') + True + >>> inputs.path_referenced('/path/to/input') + True + >>> inputs.path_referenced('/path/to/notinput') + False + >>> tf.close() + """ + + def __init__(self, command_line, config_files): + self.rewritten_command_line = command_line + self.rewritten_config_files = {} + for config_file in config_files or []: + config_contents = _read(config_file) + self.rewritten_config_files[config_file] = config_contents + + def find_referenced_subfiles(self, directory): + """ + Return list of files below specified `directory` in job inputs. Could + use more sophisticated logic (match quotes to handle spaces, handle + subdirectories, etc...). + + **Parameters** + + directory : str + Full path to directory to search. + + """ + pattern = r"(%s%s\S+)" % (directory, os.sep) + referenced_files = set() + for input_contents in self.__items(): + referenced_files.update(findall(pattern, input_contents)) + return list(referenced_files) + + def path_referenced(self, path): + pattern = r"%s" % path + found = False + for input_contents in self.__items(): + if findall(pattern, input_contents): + found = True + break + return found + + def rewrite_paths(self, local_path, remote_path): + """ + Rewrite references to `local_path` with `remote_path` in job inputs. + """ + self.__rewrite_command_line(local_path, remote_path) + self.__rewrite_config_files(local_path, remote_path) + + def __rewrite_command_line(self, local_path, remote_path): + self.rewritten_command_line = self.rewritten_command_line.replace(local_path, remote_path) + + def __rewrite_config_files(self, local_path, remote_path): + for config_file, rewritten_contents in self.rewritten_config_files.iteritems(): + self.rewritten_config_files[config_file] = rewritten_contents.replace(local_path, remote_path) + + def __items(self): + items = [self.rewritten_command_line] + items.extend(self.rewritten_config_files.values()) + return items + + +class FileStager(object): + """ + Objects of the FileStager class interact with an LWR client object to + stage the files required to run jobs on a remote LWR server. + + **Parameters** + + client : Client + LWR client object. + command_line : str + The local command line to execute, this will be rewritten for the remote server. + config_files : list + List of Galaxy 'configfile's produced for this job. These will be rewritten and sent to remote server. + input_files : list + List of input files used by job. These will be transferred and references rewritten. + output_files : list + List of output_files produced by job. + tool_dir : str + Directory containing tool to execute (if a wrapper is used, it will be transferred to remote server). + working_directory : str + Local path created by Galaxy for running this job. + + """ + + def __init__(self, client, tool, command_line, config_files, input_files, output_files, working_directory): + """ + """ + self.client = client + self.command_line = command_line + self.config_files = config_files + self.input_files = input_files + self.output_files = output_files + self.tool_id = tool.id + self.tool_version = tool.version + self.tool_dir = os.path.abspath(tool.tool_dir) + self.working_directory = working_directory + + # Setup job inputs, these will need to be rewritten before + # shipping off to remote LWR server. + self.job_inputs = JobInputs(self.command_line, self.config_files) + + self.file_renames = {} + + self.__handle_setup() + self.__initialize_referenced_tool_files() + self.__upload_tool_files() + self.__upload_input_files() + self.__upload_working_directory_files() + self.__initialize_output_file_renames() + self.__initialize_task_output_file_renames() + self.__initialize_config_file_renames() + self.__handle_rewrites() + self.__upload_rewritten_config_files() + + def __handle_setup(self): + job_config = self.client.setup(self.tool_id, self.tool_version) + + self.new_working_directory = job_config['working_directory'] + self.new_outputs_directory = job_config['outputs_directory'] + self.remote_path_separator = job_config['path_separator'] + # If remote LWR server assigned job id, use that otherwise + # just use local job_id assigned. + galaxy_job_id = self.client.job_id + self.job_id = job_config.get('job_id', galaxy_job_id) + if self.job_id != galaxy_job_id: + # Remote LWR server assigned an id different than the + # Galaxy job id, update client to reflect this. + self.client.job_id = self.job_id + + def __initialize_referenced_tool_files(self): + self.referenced_tool_files = self.job_inputs.find_referenced_subfiles(self.tool_dir) + + def __upload_tool_files(self): + for referenced_tool_file in self.referenced_tool_files: + tool_upload_response = self.client.upload_tool_file(referenced_tool_file) + self.file_renames[referenced_tool_file] = tool_upload_response['path'] + + def __upload_input_files(self): + for input_file in self.input_files: + self.__upload_input_file(input_file) + self.__upload_input_extra_files(input_file) + + def __upload_input_file(self, input_file): + if self.job_inputs.path_referenced(input_file): + input_upload_response = self.client.upload_input(input_file) + self.file_renames[input_file] = input_upload_response['path'] + + def __upload_input_extra_files(self, input_file): + # TODO: Determine if this is object store safe and what needs to be + # done if it is not. + files_path = "%s_files" % input_file[0:-len(".dat")] + if os.path.exists(files_path) and self.job_inputs.path_referenced(files_path): + for extra_file in os.listdir(files_path): + extra_file_path = os.path.join(files_path, extra_file) + relative_path = os.path.basename(files_path) + extra_file_relative_path = os.path.join(relative_path, extra_file) + response = self.client.upload_extra_input(extra_file_path, extra_file_relative_path) + self.file_renames[extra_file_path] = response['path'] + + def __upload_working_directory_files(self): + # Task manager stages files into working directory, these need to be + # uploaded if present. + for working_directory_file in os.listdir(self.working_directory): + path = os.path.join(self.working_directory, working_directory_file) + working_file_response = self.client.upload_working_directory_file(path) + self.file_renames[path] = working_file_response['path'] + + def __initialize_output_file_renames(self): + for output_file in self.output_files: + self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, + self.remote_path_separator, + os.path.basename(output_file)) + + def __initialize_task_output_file_renames(self): + for output_file in self.output_files: + name = os.path.basename(output_file) + self.file_renames[os.path.join(self.working_directory, name)] = r'%s%s%s' % (self.new_working_directory, + self.remote_path_separator, + name) + + def __initialize_config_file_renames(self): + for config_file in self.config_files: + self.file_renames[config_file] = r'%s%s%s' % (self.new_working_directory, + self.remote_path_separator, + os.path.basename(config_file)) + + def __rewrite_paths(self, contents): + new_contents = contents + for local_path, remote_path in self.file_renames.iteritems(): + new_contents = new_contents.replace(local_path, remote_path) + return new_contents + + def __handle_rewrites(self): + for local_path, remote_path in self.file_renames.iteritems(): + self.job_inputs.rewrite_paths(local_path, remote_path) + + def __upload_rewritten_config_files(self): + for config_file, new_config_contents in self.job_inputs.rewritten_config_files.iteritems(): + self.client.upload_config_file(config_file, new_config_contents) + + def get_rewritten_command_line(self): + """ + Returns the rewritten version of the command line to execute suitable + for remote host. + """ + return self.job_inputs.rewritten_command_line + + +def _read(path): + """ + Utility method to quickly read small files (config files and tool + wrappers) into memory as strings. + """ + input = open(path, "r") + try: + return input.read() + finally: + input.close() diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/lwr_client/transport/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/transport/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/transport/__init__.py @@ -3,14 +3,24 @@ import os -def get_transport(os_module=os): - use_curl = os_module.getenv('LWR_CURL_TRANSPORT', "0") - ## If LWR_CURL_TRANSPORT is unset or set to 0, use default, - ## else use curl. - if use_curl.isdigit() and not int(use_curl): - return Urllib2Transport() +def get_transport(transport_type=None, os_module=os): + transport_type = __get_transport_type(transport_type, os_module) + if transport_type == 'urllib': + transport = Urllib2Transport() else: - return PycurlTransport() + transport = PycurlTransport() + return transport +def __get_transport_type(transport_type, os_module): + if not transport_type: + use_curl = os_module.getenv('LWR_CURL_TRANSPORT', "0") + ## If LWR_CURL_TRANSPORT is unset or set to 0, use default, + ## else use curl. + if use_curl.isdigit() and not int(use_curl): + transport_type = 'urllib' + else: + transport_type = 'curl' + return transport_type + __all__ = [get_transport] diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -173,7 +173,9 @@ return JobDestination(runner='pbs', params=params) def parse_destination_params(self, params): - """A wrapper method around __args_to_attrs() that allow administrators to define PBS params as either command-line options (as in ``qsub(1B)``) or more human-readable "long" args (as in ``pbs_submit(3B)``). + """A wrapper method around __args_to_attrs() that allow administrators to define PBS + params as either command-line options (as in ``qsub(1B)``) or more human-readable "long" + args (as in ``pbs_submit(3B)``). :returns: list of dicts -- The dicts map directly to pbs attropl structs (see ``pbs_submit(3B)``) """ @@ -185,7 +187,7 @@ arg = arg.lstrip('-') args[arg] = value except: - log.warning('Unrecognized long argument in destination params: %s' % k) + log.warning('Unrecognized long argument in destination params: %s' % arg) return self.__args_to_attrs(args) # Internal stuff diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/tasks.py --- a/lib/galaxy/jobs/runners/tasks.py +++ b/lib/galaxy/jobs/runners/tasks.py @@ -9,12 +9,13 @@ from time import sleep from galaxy.jobs import TaskWrapper +from galaxy.jobs.runners import BaseJobRunner log = logging.getLogger( __name__ ) __all__ = [ 'TaskedJobRunner' ] -class TaskedJobRunner( object ): +class TaskedJobRunner( BaseJobRunner ): """ Job runner backed by a finite pool of worker threads. FIFO scheduling """ @@ -25,7 +26,7 @@ self._init_worker_threads() def queue_job( self, job_wrapper ): - super( LocalJobRunner, self ).queue_job( job_wrapper ) + super( TaskedJobRunner, self ).queue_job( job_wrapper ) if not job_wrapper.is_ready: return 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: 8 new changesets
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

8 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/547d6844325a/ changeset: 547d6844325a user: jmchilton date: 2013-03-10 06:51:59 summary: Update LWR infrastructure for new destination based configuration of Galaxy runners. Implement legacy mapping functionality. Break lwr_client/__init__.py into separate smaller modules. Updates LWR client to LWR changeset https://bitbucket.org/jmchilton/lwr/commits/b0fbc1a299baa470b9346127767fcbe…. affected #: 5 files diff -r 2b4d6af45a04ddb49c2c87a0ead3874503d35832 -r 547d6844325ad305cc5d713365e3d66d75bbb5c1 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -3,11 +3,12 @@ from galaxy import model from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner +from galaxy.jobs import JobDestination import errno from time import sleep -from lwr_client import FileStager, Client +from lwr_client import FileStager, Client, url_to_destination_params log = logging.getLogger( __name__ ) @@ -25,6 +26,10 @@ self._init_monitor_thread() self._init_worker_threads() + def url_to_destination( self, url ): + """Convert a legacy URL to a job destination""" + return JobDestination( runner="lwr", params=url_to_destination_params( url ) ) + def check_watched_item(self, job_state): try: client = self.get_client_from_state(job_state) @@ -42,7 +47,7 @@ def queue_job(self, job_wrapper): stderr = stdout = command_line = '' - runner_url = job_wrapper.get_job_runner_url() + job_destination = job_wrapper.job_destination try: job_wrapper.prepare() @@ -74,7 +79,7 @@ rebuilt_command_line = file_stager.get_rewritten_command_line() job_id = file_stager.job_id client.launch( rebuilt_command_line ) - job_wrapper.set_runner( runner_url, job_id ) + job_wrapper.set_job_destination( job_destination, job_id ) job_wrapper.change_state( model.Job.states.RUNNING ) except Exception, exc: @@ -87,32 +92,26 @@ lwr_job_state.job_id = job_id lwr_job_state.old_state = True lwr_job_state.running = True - lwr_job_state.runner_url = runner_url + lwr_job_state.job_destination = job_destination self.monitor_job(lwr_job_state) def get_output_files(self, job_wrapper): output_fnames = job_wrapper.get_output_fnames() return [ str( o ) for o in output_fnames ] - - def determine_lwr_url(self, url): - lwr_url = url[ len( 'lwr://' ) : ] - return lwr_url - def get_client_from_wrapper(self, job_wrapper): job_id = job_wrapper.job_id if hasattr(job_wrapper, 'task_id'): job_id = "%s_%s" % (job_id, job_wrapper.task_id) - return self.get_client( job_wrapper.get_job_runner_url(), job_id ) + return self.get_client( job_wrapper.job_destination.params, job_id ) def get_client_from_state(self, job_state): - job_runner = job_state.runner_url + job_destination_params = job_state.job_destination.params job_id = job_state.job_id - return self.get_client(job_runner, job_id) + return self.get_client( job_destination_params, job_id ) - def get_client(self, job_runner, job_id): - lwr_url = self.determine_lwr_url( job_runner ) - return Client(lwr_url, job_id) + def get_client( self, job_destination_params, job_id ): + return Client( job_destination_params, job_id ) def finish_job( self, job_state ): stderr = stdout = command_line = '' @@ -210,7 +209,7 @@ lwr_url = job.job_runner_name job_id = job.job_runner_external_id log.debug("Attempt remote lwr kill of job with url %s and id %s" % (lwr_url, job_id)) - client = self.get_client(lwr_url, job_id) + client = self.get_client(job.destination_params, job_id) client.kill() @@ -219,6 +218,7 @@ job_state = AsynchronousJobState() job_state.job_id = str( job.get_job_runner_external_id() ) job_state.runner_url = job_wrapper.get_job_runner_url() + job_state.job_destination = job_wrapper.job_destination job_wrapper.command_line = job.get_command_line() job_state.job_wrapper = job_wrapper if job.get_state() == model.Job.states.RUNNING: diff -r 2b4d6af45a04ddb49c2c87a0ead3874503d35832 -r 547d6844325ad305cc5d713365e3d66d75bbb5c1 lib/galaxy/jobs/runners/lwr_client/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py @@ -5,502 +5,9 @@ This module contains logic for interfacing with an external LWR server. """ -import os -import re -import time -import urllib -import simplejson +from .stager import FileStager +from .client import Client +from .destination import url_to_destination_params -from transport import get_transport - - -class JobInputs(object): - """ - Abstractions over dynamic inputs created for a given job (namely the command to - execute and created configfiles). - - **Parameters** - - command_line : str - Local command to execute for this job. (To be rewritten.) - config_files : str - Config files created for this job. (To be rewritten.) - - - >>> import tempfile - >>> tf = tempfile.NamedTemporaryFile() - >>> def setup_inputs(tf): - ... open(tf.name, "w").write("world /path/to/input the rest") - ... inputs = JobInputs("hello /path/to/input", [tf.name]) - ... return inputs - >>> inputs = setup_inputs(tf) - >>> inputs.rewrite_paths("/path/to/input", 'C:\\input') - >>> inputs.rewritten_command_line - 'hello C:\\\\input' - >>> inputs.rewritten_config_files[tf.name] - 'world C:\\\\input the rest' - >>> tf.close() - >>> tf = tempfile.NamedTemporaryFile() - >>> inputs = setup_inputs(tf) - >>> inputs.find_referenced_subfiles('/path/to') - ['/path/to/input'] - >>> inputs.path_referenced('/path/to') - True - >>> inputs.path_referenced('/path/to/input') - True - >>> inputs.path_referenced('/path/to/notinput') - False - >>> tf.close() - """ - - def __init__(self, command_line, config_files): - self.rewritten_command_line = command_line - self.rewritten_config_files = {} - for config_file in config_files or []: - config_contents = _read(config_file) - self.rewritten_config_files[config_file] = config_contents - - def find_referenced_subfiles(self, directory): - """ - Return list of files below specified `directory` in job inputs. Could - use more sophisticated logic (match quotes to handle spaces, handle - subdirectories, etc...). - - **Parameters** - - directory : str - Full path to directory to search. - - """ - pattern = r"(%s%s\S+)" % (directory, os.sep) - referenced_files = set() - for input_contents in self.__items(): - referenced_files.update(re.findall(pattern, input_contents)) - return list(referenced_files) - - def path_referenced(self, path): - pattern = r"%s" % path - found = False - for input_contents in self.__items(): - if re.findall(pattern, input_contents): - found = True - break - return found - - def rewrite_paths(self, local_path, remote_path): - """ - Rewrite references to `local_path` with `remote_path` in job inputs. - """ - self.__rewrite_command_line(local_path, remote_path) - self.__rewrite_config_files(local_path, remote_path) - - def __rewrite_command_line(self, local_path, remote_path): - self.rewritten_command_line = self.rewritten_command_line.replace(local_path, remote_path) - - def __rewrite_config_files(self, local_path, remote_path): - for config_file, rewritten_contents in self.rewritten_config_files.iteritems(): - self.rewritten_config_files[config_file] = rewritten_contents.replace(local_path, remote_path) - - def __items(self): - items = [self.rewritten_command_line] - items.extend(self.rewritten_config_files.values()) - return items - - -class FileStager(object): - """ - Objects of the FileStager class interact with an LWR client object to - stage the files required to run jobs on a remote LWR server. - - **Parameters** - - client : Client - LWR client object. - command_line : str - The local command line to execute, this will be rewritten for the remote server. - config_files : list - List of Galaxy 'configfile's produced for this job. These will be rewritten and sent to remote server. - input_files : list - List of input files used by job. These will be transferred and references rewritten. - output_files : list - List of output_files produced by job. - tool_dir : str - Directory containing tool to execute (if a wrapper is used, it will be transferred to remote server). - working_directory : str - Local path created by Galaxy for running this job. - - """ - - def __init__(self, client, tool, command_line, config_files, input_files, output_files, working_directory): - """ - """ - self.client = client - self.command_line = command_line - self.config_files = config_files - self.input_files = input_files - self.output_files = output_files - self.tool_id = tool.id - self.tool_version = tool.version - self.tool_dir = os.path.abspath(tool.tool_dir) - self.working_directory = working_directory - - # Setup job inputs, these will need to be rewritten before - # shipping off to remote LWR server. - self.job_inputs = JobInputs(self.command_line, self.config_files) - - self.file_renames = {} - - self.__handle_setup() - self.__initialize_referenced_tool_files() - self.__upload_tool_files() - self.__upload_input_files() - self.__upload_working_directory_files() - self.__initialize_output_file_renames() - self.__initialize_task_output_file_renames() - self.__initialize_config_file_renames() - self.__handle_rewrites() - self.__upload_rewritten_config_files() - - def __handle_setup(self): - job_config = self.client.setup(self.tool_id, self.tool_version) - - self.new_working_directory = job_config['working_directory'] - self.new_outputs_directory = job_config['outputs_directory'] - self.remote_path_separator = job_config['path_separator'] - # If remote LWR server assigned job id, use that otherwise - # just use local job_id assigned. - galaxy_job_id = self.client.job_id - self.job_id = job_config.get('job_id', galaxy_job_id) - if self.job_id != galaxy_job_id: - # Remote LWR server assigned an id different than the - # Galaxy job id, update client to reflect this. - self.client.job_id = self.job_id - - def __initialize_referenced_tool_files(self): - self.referenced_tool_files = self.job_inputs.find_referenced_subfiles(self.tool_dir) - - def __upload_tool_files(self): - for referenced_tool_file in self.referenced_tool_files: - tool_upload_response = self.client.upload_tool_file(referenced_tool_file) - self.file_renames[referenced_tool_file] = tool_upload_response['path'] - - def __upload_input_files(self): - for input_file in self.input_files: - self.__upload_input_file(input_file) - self.__upload_input_extra_files(input_file) - - def __upload_input_file(self, input_file): - if self.job_inputs.path_referenced(input_file): - input_upload_response = self.client.upload_input(input_file) - self.file_renames[input_file] = input_upload_response['path'] - - def __upload_input_extra_files(self, input_file): - # TODO: Determine if this is object store safe and what needs to be - # done if it is not. - files_path = "%s_files" % input_file[0:-len(".dat")] - if os.path.exists(files_path) and self.job_inputs.path_referenced(files_path): - for extra_file in os.listdir(files_path): - extra_file_path = os.path.join(files_path, extra_file) - relative_path = os.path.basename(files_path) - extra_file_relative_path = os.path.join(relative_path, extra_file) - response = self.client.upload_extra_input(extra_file_path, extra_file_relative_path) - self.file_renames[extra_file_path] = response['path'] - - def __upload_working_directory_files(self): - # Task manager stages files into working directory, these need to be - # uploaded if present. - for working_directory_file in os.listdir(self.working_directory): - path = os.path.join(self.working_directory, working_directory_file) - working_file_response = self.client.upload_working_directory_file(path) - self.file_renames[path] = working_file_response['path'] - - def __initialize_output_file_renames(self): - for output_file in self.output_files: - self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, - self.remote_path_separator, - os.path.basename(output_file)) - - def __initialize_task_output_file_renames(self): - for output_file in self.output_files: - name = os.path.basename(output_file) - self.file_renames[os.path.join(self.working_directory, name)] = r'%s%s%s' % (self.new_working_directory, - self.remote_path_separator, - name) - - def __initialize_config_file_renames(self): - for config_file in self.config_files: - self.file_renames[config_file] = r'%s%s%s' % (self.new_working_directory, - self.remote_path_separator, - os.path.basename(config_file)) - - def __rewrite_paths(self, contents): - new_contents = contents - for local_path, remote_path in self.file_renames.iteritems(): - new_contents = new_contents.replace(local_path, remote_path) - return new_contents - - def __handle_rewrites(self): - for local_path, remote_path in self.file_renames.iteritems(): - self.job_inputs.rewrite_paths(local_path, remote_path) - - def __upload_rewritten_config_files(self): - for config_file, new_config_contents in self.job_inputs.rewritten_config_files.iteritems(): - self.client.upload_config_file(config_file, new_config_contents) - - def get_rewritten_command_line(self): - """ - Returns the rewritten version of the command line to execute suitable - for remote host. - """ - return self.job_inputs.rewritten_command_line - - -class parseJson(object): - - def __init__(self): - pass - - def __call__(self, func): - def replacement(*args, **kwargs): - response = func(*args, **kwargs) - return simplejson.loads(response) - return replacement - - -class Client(object): - """ - Objects of this client class perform low-level communication with a remote LWR server. - - **Parameters** - - remote_host : str - Remote URL of the LWR server. - job_id : str - Galaxy job/task id. - private_key : str (optional) - Secret key the remote LWR server is configured with. - """ - - def __init__(self, remote_host, job_id, private_key=None): - if not remote_host.endswith("/"): - remote_host = remote_host + "/" - ## If we don't have an explicit private_key defined, check for - ## one embedded in the URL. A URL of the form - ## https://moo@cow:8913 will try to contact https://cow:8913 - ## with a private key of moo - private_key_format = "https?://(.*)@.*/?" - private_key_match = re.match(private_key_format, remote_host) - if not private_key and private_key_match: - private_key = private_key_match.group(1) - remote_host = remote_host.replace("%s@" % private_key, '', 1) - self.remote_host = remote_host - self.job_id = job_id - self.private_key = private_key - self.transport = get_transport() - - def __build_url(self, command, args): - if self.private_key: - args["private_key"] = self.private_key - data = urllib.urlencode(args) - url = self.remote_host + command + "?" + data - return url - - def __raw_execute(self, command, args={}, data=None, input_path=None, output_path=None): - url = self.__build_url(command, args) - response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) - return response - - @parseJson() - def __upload_file(self, action, path, name=None, contents=None): - if not name: - name = os.path.basename(path) - args = {"job_id": self.job_id, "name": name} - input_path = path - if contents: - input_path = None - return self.__raw_execute(action, args, contents, input_path) - - def upload_tool_file(self, path): - """ - Upload a tool related file (e.g. wrapper) required to run job. - - **Parameters** - - path : str - Local path tool. - """ - return self.__upload_file("upload_tool_file", path) - - def upload_input(self, path): - """ - Upload input dataset to remote server. - - **Parameters** - - path : str - Local path of input dataset. - """ - return self.__upload_file("upload_input", path) - - def upload_extra_input(self, path, relative_name): - """ - Upload extra input file to remote server. - - **Parameters** - - path : str - Extra files path of input dataset corresponding to this input. - relative_name : str - Relative path of extra file to upload relative to inputs extra files path. - """ - return self.__upload_file("upload_extra_input", path, name=relative_name) - - def upload_config_file(self, path, contents): - """ - Upload a job's config file to the remote server. - - **Parameters** - - path : str - Local path to the original config file. - contents : str - Rewritten contents of the config file to upload. - """ - return self.__upload_file("upload_config_file", path, contents=contents) - - def upload_working_directory_file(self, path): - """ - Upload the supplied file (path) from a job's working directory - to remote server. - - **Parameters** - - path : str - Path to file to upload. - """ - return self.__upload_file("upload_working_directory_file", path) - - @parseJson() - def _get_output_type(self, name): - return self.__raw_execute("get_output_type", {"name": name, - "job_id": self.job_id}) - - def download_work_dir_output(self, source, working_directory, output_path): - """ - Download an output dataset specified with from_work_dir from the - remote server. - - **Parameters** - - source : str - Path in job's working_directory to find output in. - working_directory : str - Local working_directory for the job. - output_path : str - Full path to output dataset. - """ - output = open(output_path, "wb") - name = os.path.basename(source) - self.__raw_download_output(name, self.job_id, "work_dir", output) - - def download_output(self, path, working_directory): - """ - Download an output dataset from the remote server. - - **Parameters** - - path : str - Local path of the dataset. - working_directory : str - Local working_directory for the job. - """ - name = os.path.basename(path) - output_type = self._get_output_type(name) - if output_type == "direct": - output_path = path - elif output_type == "task": - output_path = os.path.join(working_directory, name) - else: - raise Exception("No remote output found for dataset with path %s" % path) - self.__raw_download_output(name, self.job_id, output_type, output_path) - - def __raw_download_output(self, name, job_id, output_type, output_path): - self.__raw_execute("download_output", - {"name": name, - "job_id": self.job_id, - "output_type": output_type}, - output_path=output_path) - - def launch(self, command_line): - """ - Run or queue up the execution of the supplied - `command_line` on the remote server. - - **Parameters** - - command_line : str - Command to execute. - """ - return self.__raw_execute("launch", {"command_line": command_line, - "job_id": self.job_id}) - - def kill(self): - """ - Cancel remote job, either removing from the queue or killing it. - """ - return self.__raw_execute("kill", {"job_id": self.job_id}) - - def wait(self): - """ - Wait for job to finish. - """ - while True: - complete_response = self.raw_check_complete() - if complete_response["complete"] == "true": - return complete_response - time.sleep(1) - - @parseJson() - def raw_check_complete(self): - """ - Get check_complete response from the remote server. - """ - check_complete_response = self.__raw_execute("check_complete", {"job_id": self.job_id}) - return check_complete_response - - def check_complete(self): - """ - Return boolean indicating whether the job is complete. - """ - return self.raw_check_complete()["complete"] == "true" - - def clean(self): - """ - Cleanup the remote job. - """ - self.__raw_execute("clean", {"job_id": self.job_id}) - - @parseJson() - def setup(self, tool_id=None, tool_version=None): - """ - Setup remote LWR server to run this job. - """ - setup_args = {"job_id": self.job_id} - if tool_id: - setup_args["tool_id"] = tool_id - if tool_version: - setup_args["tool_version"] = tool_version - return self.__raw_execute("setup", setup_args) - - -def _read(path): - """ - Utility method to quickly read small files (config files and tool - wrappers) into memory as strings. - """ - input = open(path, "r") - try: - return input.read() - finally: - input.close() +__all__ = [Client, FileStager, url_to_destination_params] diff -r 2b4d6af45a04ddb49c2c87a0ead3874503d35832 -r 547d6844325ad305cc5d713365e3d66d75bbb5c1 lib/galaxy/jobs/runners/lwr_client/client.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -0,0 +1,235 @@ +import os +import time +import urllib +import simplejson + +from .transport import get_transport +from .destination import url_to_destination_params + + +class parseJson(object): + + def __init__(self): + pass + + def __call__(self, func): + def replacement(*args, **kwargs): + response = func(*args, **kwargs) + return simplejson.loads(response) + return replacement + + +class Client(object): + """ + Objects of this client class perform low-level communication with a remote LWR server. + + **Parameters** + + destination_params : dict or str + connection parameters, either url with dict containing url (and optionally `private_token`). + job_id : str + Galaxy job/task id. + """ + + def __init__(self, destination_params, job_id): + if isinstance(destination_params, str) or isinstance(destination_params, unicode): + destination_params = url_to_destination_params(destination_params) + self.remote_host = destination_params.get("url") + assert self.remote_host != None, "Failed to determine url for LWR client." + self.private_key = destination_params.get("private_token", None) + self.job_id = job_id + self.transport = get_transport() + + def __build_url(self, command, args): + if self.private_key: + args["private_key"] = self.private_key + data = urllib.urlencode(args) + url = self.remote_host + command + "?" + data + return url + + def __raw_execute(self, command, args={}, data=None, input_path=None, output_path=None): + url = self.__build_url(command, args) + response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) + return response + + @parseJson() + def __upload_file(self, action, path, name=None, contents=None): + if not name: + name = os.path.basename(path) + args = {"job_id": self.job_id, "name": name} + input_path = path + if contents: + input_path = None + return self.__raw_execute(action, args, contents, input_path) + + def upload_tool_file(self, path): + """ + Upload a tool related file (e.g. wrapper) required to run job. + + **Parameters** + + path : str + Local path tool. + """ + return self.__upload_file("upload_tool_file", path) + + def upload_input(self, path): + """ + Upload input dataset to remote server. + + **Parameters** + + path : str + Local path of input dataset. + """ + return self.__upload_file("upload_input", path) + + def upload_extra_input(self, path, relative_name): + """ + Upload extra input file to remote server. + + **Parameters** + + path : str + Extra files path of input dataset corresponding to this input. + relative_name : str + Relative path of extra file to upload relative to inputs extra files path. + """ + return self.__upload_file("upload_extra_input", path, name=relative_name) + + def upload_config_file(self, path, contents): + """ + Upload a job's config file to the remote server. + + **Parameters** + + path : str + Local path to the original config file. + contents : str + Rewritten contents of the config file to upload. + """ + return self.__upload_file("upload_config_file", path, contents=contents) + + def upload_working_directory_file(self, path): + """ + Upload the supplied file (path) from a job's working directory + to remote server. + + **Parameters** + + path : str + Path to file to upload. + """ + return self.__upload_file("upload_working_directory_file", path) + + @parseJson() + def _get_output_type(self, name): + return self.__raw_execute("get_output_type", {"name": name, + "job_id": self.job_id}) + + def download_work_dir_output(self, source, working_directory, output_path): + """ + Download an output dataset specified with from_work_dir from the + remote server. + + **Parameters** + + source : str + Path in job's working_directory to find output in. + working_directory : str + Local working_directory for the job. + output_path : str + Full path to output dataset. + """ + output = open(output_path, "wb") + name = os.path.basename(source) + self.__raw_download_output(name, self.job_id, "work_dir", output) + + def download_output(self, path, working_directory): + """ + Download an output dataset from the remote server. + + **Parameters** + + path : str + Local path of the dataset. + working_directory : str + Local working_directory for the job. + """ + name = os.path.basename(path) + output_type = self._get_output_type(name) + if output_type == "direct": + output_path = path + elif output_type == "task": + output_path = os.path.join(working_directory, name) + else: + raise Exception("No remote output found for dataset with path %s" % path) + self.__raw_download_output(name, self.job_id, output_type, output_path) + + def __raw_download_output(self, name, job_id, output_type, output_path): + self.__raw_execute("download_output", + {"name": name, + "job_id": self.job_id, + "output_type": output_type}, + output_path=output_path) + + def launch(self, command_line): + """ + Run or queue up the execution of the supplied + `command_line` on the remote server. + + **Parameters** + + command_line : str + Command to execute. + """ + return self.__raw_execute("launch", {"command_line": command_line, + "job_id": self.job_id}) + + def kill(self): + """ + Cancel remote job, either removing from the queue or killing it. + """ + return self.__raw_execute("kill", {"job_id": self.job_id}) + + def wait(self): + """ + Wait for job to finish. + """ + while True: + complete_response = self.raw_check_complete() + if complete_response["complete"] == "true": + return complete_response + time.sleep(1) + + @parseJson() + def raw_check_complete(self): + """ + Get check_complete response from the remote server. + """ + check_complete_response = self.__raw_execute("check_complete", {"job_id": self.job_id}) + return check_complete_response + + def check_complete(self): + """ + Return boolean indicating whether the job is complete. + """ + return self.raw_check_complete()["complete"] == "true" + + def clean(self): + """ + Cleanup the remote job. + """ + self.__raw_execute("clean", {"job_id": self.job_id}) + + @parseJson() + def setup(self, tool_id=None, tool_version=None): + """ + Setup remote LWR server to run this job. + """ + setup_args = {"job_id": self.job_id} + if tool_id: + setup_args["tool_id"] = tool_id + if tool_version: + setup_args["tool_version"] = tool_version + return self.__raw_execute("setup", setup_args) diff -r 2b4d6af45a04ddb49c2c87a0ead3874503d35832 -r 547d6844325ad305cc5d713365e3d66d75bbb5c1 lib/galaxy/jobs/runners/lwr_client/destination.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/destination.py @@ -0,0 +1,40 @@ + +from re import match + + +def url_to_destination_params(url): + """Convert a legacy runner URL to a job destination + + >>> params_simple = url_to_destination_params("http://localhost:8913/") + >>> params_simple["url"] + 'http://localhost:8913/' + >>> params_simple["private_token"] is None + True + >>> advanced_url = "https://1234x@example.com:8914/managers/longqueue" + >>> params_advanced = url_to_destination_params(advanced_url) + >>> params_advanced["url"] + 'https://example.com:8914/managers/longqueue/' + >>> params_advanced["private_token"] + '1234x' + """ + + if url.startswith("lwr://"): + url = url[len("lwr://"):] + + if not url.endswith("/"): + url += "/" + + ## Check for private token embedded in the URL. A URL of the form + ## https://moo@cow:8913 will try to contact https://cow:8913 + ## with a private key of moo + private_token_format = "https?://(.*)@.*/?" + private_token_match = match(private_token_format, url) + private_token = None + if private_token_match: + private_token = private_token_match.group(1) + url = url.replace("%s@" % private_token, '', 1) + + destination_args = {"url": url, + "private_token": private_token} + + return destination_args diff -r 2b4d6af45a04ddb49c2c87a0ead3874503d35832 -r 547d6844325ad305cc5d713365e3d66d75bbb5c1 lib/galaxy/jobs/runners/lwr_client/stager.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/stager.py @@ -0,0 +1,256 @@ + +import os +from re import findall + + +class JobInputs(object): + """ + Abstractions over dynamic inputs created for a given job (namely the command to + execute and created configfiles). + + **Parameters** + + command_line : str + Local command to execute for this job. (To be rewritten.) + config_files : str + Config files created for this job. (To be rewritten.) + + + >>> import tempfile + >>> tf = tempfile.NamedTemporaryFile() + >>> def setup_inputs(tf): + ... open(tf.name, "w").write("world /path/to/input the rest") + ... inputs = JobInputs("hello /path/to/input", [tf.name]) + ... return inputs + >>> inputs = setup_inputs(tf) + >>> inputs.rewrite_paths("/path/to/input", 'C:\\input') + >>> inputs.rewritten_command_line + 'hello C:\\\\input' + >>> inputs.rewritten_config_files[tf.name] + 'world C:\\\\input the rest' + >>> tf.close() + >>> tf = tempfile.NamedTemporaryFile() + >>> inputs = setup_inputs(tf) + >>> inputs.find_referenced_subfiles('/path/to') + ['/path/to/input'] + >>> inputs.path_referenced('/path/to') + True + >>> inputs.path_referenced('/path/to/input') + True + >>> inputs.path_referenced('/path/to/notinput') + False + >>> tf.close() + """ + + def __init__(self, command_line, config_files): + self.rewritten_command_line = command_line + self.rewritten_config_files = {} + for config_file in config_files or []: + config_contents = _read(config_file) + self.rewritten_config_files[config_file] = config_contents + + def find_referenced_subfiles(self, directory): + """ + Return list of files below specified `directory` in job inputs. Could + use more sophisticated logic (match quotes to handle spaces, handle + subdirectories, etc...). + + **Parameters** + + directory : str + Full path to directory to search. + + """ + pattern = r"(%s%s\S+)" % (directory, os.sep) + referenced_files = set() + for input_contents in self.__items(): + referenced_files.update(findall(pattern, input_contents)) + return list(referenced_files) + + def path_referenced(self, path): + pattern = r"%s" % path + found = False + for input_contents in self.__items(): + if findall(pattern, input_contents): + found = True + break + return found + + def rewrite_paths(self, local_path, remote_path): + """ + Rewrite references to `local_path` with `remote_path` in job inputs. + """ + self.__rewrite_command_line(local_path, remote_path) + self.__rewrite_config_files(local_path, remote_path) + + def __rewrite_command_line(self, local_path, remote_path): + self.rewritten_command_line = self.rewritten_command_line.replace(local_path, remote_path) + + def __rewrite_config_files(self, local_path, remote_path): + for config_file, rewritten_contents in self.rewritten_config_files.iteritems(): + self.rewritten_config_files[config_file] = rewritten_contents.replace(local_path, remote_path) + + def __items(self): + items = [self.rewritten_command_line] + items.extend(self.rewritten_config_files.values()) + return items + + +class FileStager(object): + """ + Objects of the FileStager class interact with an LWR client object to + stage the files required to run jobs on a remote LWR server. + + **Parameters** + + client : Client + LWR client object. + command_line : str + The local command line to execute, this will be rewritten for the remote server. + config_files : list + List of Galaxy 'configfile's produced for this job. These will be rewritten and sent to remote server. + input_files : list + List of input files used by job. These will be transferred and references rewritten. + output_files : list + List of output_files produced by job. + tool_dir : str + Directory containing tool to execute (if a wrapper is used, it will be transferred to remote server). + working_directory : str + Local path created by Galaxy for running this job. + + """ + + def __init__(self, client, tool, command_line, config_files, input_files, output_files, working_directory): + """ + """ + self.client = client + self.command_line = command_line + self.config_files = config_files + self.input_files = input_files + self.output_files = output_files + self.tool_id = tool.id + self.tool_version = tool.version + self.tool_dir = os.path.abspath(tool.tool_dir) + self.working_directory = working_directory + + # Setup job inputs, these will need to be rewritten before + # shipping off to remote LWR server. + self.job_inputs = JobInputs(self.command_line, self.config_files) + + self.file_renames = {} + + self.__handle_setup() + self.__initialize_referenced_tool_files() + self.__upload_tool_files() + self.__upload_input_files() + self.__upload_working_directory_files() + self.__initialize_output_file_renames() + self.__initialize_task_output_file_renames() + self.__initialize_config_file_renames() + self.__handle_rewrites() + self.__upload_rewritten_config_files() + + def __handle_setup(self): + job_config = self.client.setup(self.tool_id, self.tool_version) + + self.new_working_directory = job_config['working_directory'] + self.new_outputs_directory = job_config['outputs_directory'] + self.remote_path_separator = job_config['path_separator'] + # If remote LWR server assigned job id, use that otherwise + # just use local job_id assigned. + galaxy_job_id = self.client.job_id + self.job_id = job_config.get('job_id', galaxy_job_id) + if self.job_id != galaxy_job_id: + # Remote LWR server assigned an id different than the + # Galaxy job id, update client to reflect this. + self.client.job_id = self.job_id + + def __initialize_referenced_tool_files(self): + self.referenced_tool_files = self.job_inputs.find_referenced_subfiles(self.tool_dir) + + def __upload_tool_files(self): + for referenced_tool_file in self.referenced_tool_files: + tool_upload_response = self.client.upload_tool_file(referenced_tool_file) + self.file_renames[referenced_tool_file] = tool_upload_response['path'] + + def __upload_input_files(self): + for input_file in self.input_files: + self.__upload_input_file(input_file) + self.__upload_input_extra_files(input_file) + + def __upload_input_file(self, input_file): + if self.job_inputs.path_referenced(input_file): + input_upload_response = self.client.upload_input(input_file) + self.file_renames[input_file] = input_upload_response['path'] + + def __upload_input_extra_files(self, input_file): + # TODO: Determine if this is object store safe and what needs to be + # done if it is not. + files_path = "%s_files" % input_file[0:-len(".dat")] + if os.path.exists(files_path) and self.job_inputs.path_referenced(files_path): + for extra_file in os.listdir(files_path): + extra_file_path = os.path.join(files_path, extra_file) + relative_path = os.path.basename(files_path) + extra_file_relative_path = os.path.join(relative_path, extra_file) + response = self.client.upload_extra_input(extra_file_path, extra_file_relative_path) + self.file_renames[extra_file_path] = response['path'] + + def __upload_working_directory_files(self): + # Task manager stages files into working directory, these need to be + # uploaded if present. + for working_directory_file in os.listdir(self.working_directory): + path = os.path.join(self.working_directory, working_directory_file) + working_file_response = self.client.upload_working_directory_file(path) + self.file_renames[path] = working_file_response['path'] + + def __initialize_output_file_renames(self): + for output_file in self.output_files: + self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, + self.remote_path_separator, + os.path.basename(output_file)) + + def __initialize_task_output_file_renames(self): + for output_file in self.output_files: + name = os.path.basename(output_file) + self.file_renames[os.path.join(self.working_directory, name)] = r'%s%s%s' % (self.new_working_directory, + self.remote_path_separator, + name) + + def __initialize_config_file_renames(self): + for config_file in self.config_files: + self.file_renames[config_file] = r'%s%s%s' % (self.new_working_directory, + self.remote_path_separator, + os.path.basename(config_file)) + + def __rewrite_paths(self, contents): + new_contents = contents + for local_path, remote_path in self.file_renames.iteritems(): + new_contents = new_contents.replace(local_path, remote_path) + return new_contents + + def __handle_rewrites(self): + for local_path, remote_path in self.file_renames.iteritems(): + self.job_inputs.rewrite_paths(local_path, remote_path) + + def __upload_rewritten_config_files(self): + for config_file, new_config_contents in self.job_inputs.rewritten_config_files.iteritems(): + self.client.upload_config_file(config_file, new_config_contents) + + def get_rewritten_command_line(self): + """ + Returns the rewritten version of the command line to execute suitable + for remote host. + """ + return self.job_inputs.rewritten_command_line + + +def _read(path): + """ + Utility method to quickly read small files (config files and tool + wrappers) into memory as strings. + """ + input = open(path, "r") + try: + return input.read() + finally: + input.close() https://bitbucket.org/galaxy/galaxy-central/commits/89fa5f5873e4/ changeset: 89fa5f5873e4 user: jmchilton date: 2013-03-10 06:51:59 summary: Update job_conf.xml.sample_advanced with LWR usage examples. affected #: 1 file diff -r 547d6844325ad305cc5d713365e3d66d75bbb5c1 -r 89fa5f5873e45f4e1ef5eabbf226d1dd528ff4d1 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -7,6 +7,7 @@ <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/><plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/><plugin id="gridengine" type="runner" load="galaxy.jobs.runners.drmaa:DRMAARunner"/> + <plugin id="lwr" type="runner" load="galaxy.jobs.runners.lwr.LwrJobRunner" /></plugins><handlers default="handlers"> + <param id="private_token">123456789changeme</param> + </destination></destinations><tools><!-- Tools can be configured to use specific destinations or handlers, https://bitbucket.org/galaxy/galaxy-central/commits/d0dd203bdaaf/ changeset: d0dd203bdaaf user: jmchilton date: 2013-03-10 06:51:59 summary: Small pbs runner fixes. affected #: 1 file diff -r 89fa5f5873e45f4e1ef5eabbf226d1dd528ff4d1 -r d0dd203bdaafd5507998241cdd096430e4f21f1f lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -173,7 +173,9 @@ return JobDestination(runner='pbs', params=params) def parse_destination_params(self, params): - """A wrapper method around __args_to_attrs() that allow administrators to define PBS params as either command-line options (as in ``qsub(1B)``) or more human-readable "long" args (as in ``pbs_submit(3B)``). + """A wrapper method around __args_to_attrs() that allow administrators to define PBS + params as either command-line options (as in ``qsub(1B)``) or more human-readable "long" + args (as in ``pbs_submit(3B)``). :returns: list of dicts -- The dicts map directly to pbs attropl structs (see ``pbs_submit(3B)``) """ @@ -185,7 +187,7 @@ arg = arg.lstrip('-') args[arg] = value except: - log.warning('Unrecognized long argument in destination params: %s' % k) + log.warning('Unrecognized long argument in destination params: %s' % arg) return self.__args_to_attrs(args) # Internal stuff https://bitbucket.org/galaxy/galaxy-central/commits/4e0659495eb2/ changeset: 4e0659495eb2 user: jmchilton date: 2013-03-10 06:51:59 summary: Allow child param elements to appear in plugin elements of job_conf.xml. Pass these as keyword arguments into job runner constructor. affected #: 1 file diff -r d0dd203bdaafd5507998241cdd096430e4f21f1f -r 4e0659495eb2ad674bcc0a08cc1a9d211f691104 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -126,7 +126,12 @@ for plugin in self.__findall_with_required(plugins, 'plugin', ('id', 'type', 'load')): if plugin.get('type') == 'runner': workers = plugin.get('workers', plugins.get('workers', JobConfiguration.DEFAULT_NWORKERS)) - self.runner_plugins.append(dict(id=plugin.get('id'), load=plugin.get('load'), workers=int(workers))) + runner_kwds = self.__get_params(plugin) + runner_info = dict(id=plugin.get('id'), + load=plugin.get('load'), + workers=int(workers), + kwds=runner_kwds) + self.runner_plugins.append(runner_info) else: log.error('Unknown plugin type: %s' % plugin.get('type')) # Load tasks if configured @@ -480,7 +485,7 @@ log.warning("Job runner classes must be subclassed from BaseJobRunner, %s has bases: %s" % (id, runner_class.__bases__)) continue try: - rval[id] = runner_class( self.app, runner['workers'] ) + rval[id] = runner_class( self.app, runner['workers'], **runner['kwds'] ) except TypeError: log.warning( "Job runner '%s:%s' has not been converted to a new-style runner" % ( module_name, class_name ) ) rval[id] = runner_class( self.app ) https://bitbucket.org/galaxy/galaxy-central/commits/71da862d92ab/ changeset: 71da862d92ab user: jmchilton date: 2013-03-10 06:51:59 summary: Use new plugin param passing from previous changeset to provide a much cleaner mechanism for specifing LWR transport type. To enable pycurl based transport for the LWR client, now one just needs to add <param id="transport">curl</param> to the plugin definition in job_conf.xml. Updates LWR client through LWR changeset: https://bitbucket.org/jmchilton/lwr/commits/b09da65bd2ffe12b28cf6c545c7d052…. affected #: 4 files Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/3b6c209d2d07/ changeset: 3b6c209d2d07 user: jmchilton date: 2013-03-17 18:39:17 summary: Task job runner fixes. affected #: 2 files Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/67b37b0c11e7/ changeset: 67b37b0c11e7 user: jmchilton date: 2013-03-17 20:14:22 summary: Fix for job runner configuration dicts without new kwds pair present. affected #: 1 file Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/7a4dd13dac9b/ changeset: 7a4dd13dac9b user: natefoo date: 2013-03-18 16:21:22 summary: Merged in jmchilton/galaxy-central-lwr (pull request #138) LWR Updates and Other Small Job Destination Tweaks affected #: 10 files Diff not available. 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: 0 new changesets
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

0 new commits in galaxy-central: 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: greg: Rename community_wsgi.ini.sample to be tool_shed_wsgi.ini.sample, run_community.sh to run_tool_shed.sh, and fix references to these files in the code.
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/da3aece419ca/ changeset: da3aece419ca user: greg date: 2013-03-18 15:24:03 summary: Rename community_wsgi.ini.sample to be tool_shed_wsgi.ini.sample, run_community.sh to run_tool_shed.sh, and fix references to these files in the code. affected #: 8 files diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b community_wsgi.ini.sample --- a/community_wsgi.ini.sample +++ /dev/null @@ -1,98 +0,0 @@ -# ---- HTTP Server ---------------------------------------------------------- - -[server:main] - -use = egg:Paste#http -port = 9009 - -# The address on which to listen. By default, only listen to localhost (the tool shed will not -# be accessible over the network). Use '0.0.0.0' to listen on all available network interfaces. -#host = 0.0.0.0 -host = 127.0.0.1 - -use_threadpool = true -threadpool_workers = 10 - -# ---- Galaxy Webapps Community Interface ------------------------------------------------- - -[app:main] - -# Specifies the factory for the universe WSGI application -paste.app_factory = galaxy.webapps.tool_shed.buildapp:app_factory -log_level = DEBUG - -# Database connection -database_file = database/community.sqlite -# You may use a SQLAlchemy connection string to specify an external database instead -#database_connection = postgres:///community_test?host=/var/run/postgresql - -# Where the hgweb.config file is stored. The default is the Galaxy installation directory. -#hgweb_config_dir = None - -# Where dataset files are saved -file_path = database/community_files -# Temporary storage for additional datasets, this should be shared through the cluster -new_file_path = database/tmp - -# Session support (beaker) -use_beaker_session = True -session_type = memory -session_data_dir = %(here)s/database/beaker_sessions -session_key = galaxysessions -session_secret = changethisinproduction - -# -- Users and Security - -# Galaxy encodes various internal values when these values will be output in -# some format (for example, in a URL or cookie). You should set a key to be -# used by the algorithm that encodes and decodes these values. It can be any -# string. If left unchanged, anyone could construct a cookie that would grant -# them access to others' sessions. -id_secret = changethisinproductiontoo - -# User authentication can be delegated to an upstream proxy server (usually -# Apache). The upstream proxy should set a REMOTE_USER header in the request. -# Enabling remote user disables regular logins. For more information, see: -# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy -#use_remote_user = False - -# Configuration for debugging middleware -debug = true -use_lint = false - -# NEVER enable this on a public site (even test or QA) -# use_interactive = true - -# this should be a comma-separated list of valid Galaxy users -#admin_users = user1@example.org,user2@example.org - -# Force everyone to log in (disable anonymous access) -require_login = False - -# path to sendmail -sendmail_path = /usr/sbin/sendmail - -# For use by email messages sent from the tool shed -#smtp_server = smtp.your_tool_shed_server -#email_from = your_tool_shed_email@server - -# The URL linked by the "Support" link in the "Help" menu. -#support_url = http://wiki.g2.bx.psu.edu/Support - -# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) -## use_heartbeat = True - -# Profiling middleware (cProfile based) -## use_profile = True - -# Use the new iframe / javascript based layout -use_new_layout = true - -# Serving static files (needed if running standalone) -static_enabled = True -static_cache_time = 360 -static_dir = %(here)s/static/ -static_images_dir = %(here)s/static/images -static_favicon_dir = %(here)s/static/favicon.ico -static_scripts_dir = %(here)s/static/scripts/ -static_style_dir = %(here)s/static/june_2007_style/blue diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b run_community.sh --- a/run_community.sh +++ /dev/null @@ -1,37 +0,0 @@ -#!/bin/sh - -cd `dirname $0` - -SAMPLES=" - community_wsgi.ini.sample - datatypes_conf.xml.sample - external_service_types_conf.xml.sample - migrated_tools_conf.xml.sample - reports_wsgi.ini.sample - shed_tool_conf.xml.sample - tool_conf.xml.sample - shed_tool_data_table_conf.xml.sample - tool_data_table_conf.xml.sample - tool_sheds_conf.xml.sample - openid_conf.xml.sample - universe_wsgi.ini.sample - tool-data/shared/ncbi/builds.txt.sample - tool-data/shared/ensembl/builds.txt.sample - tool-data/shared/ucsc/builds.txt.sample - tool-data/shared/ucsc/publicbuilds.txt.sample - tool-data/shared/igv/igv_build_sites.txt.sample - tool-data/shared/rviewer/rviewer_build_sites.txt.sample - tool-data/*.sample - static/welcome.html.sample -" - -# Create any missing config/location files -for sample in $SAMPLES; do - file=`echo $sample | sed -e 's/\.sample$//'` - if [ ! -f "$file" -a -f "$sample" ]; then - echo "Initializing $file from `basename $sample`" - cp $sample $file - fi -done - -python ./scripts/paster.py serve community_wsgi.ini --pid-file=community_webapp.pid --log-file=community_webapp.log $@ diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b run_tool_shed.sh --- /dev/null +++ b/run_tool_shed.sh @@ -0,0 +1,37 @@ +#!/bin/sh + +cd `dirname $0` + +SAMPLES=" + tool_shed_wsgi.ini.sample + datatypes_conf.xml.sample + external_service_types_conf.xml.sample + migrated_tools_conf.xml.sample + reports_wsgi.ini.sample + shed_tool_conf.xml.sample + tool_conf.xml.sample + shed_tool_data_table_conf.xml.sample + tool_data_table_conf.xml.sample + tool_sheds_conf.xml.sample + openid_conf.xml.sample + universe_wsgi.ini.sample + tool-data/shared/ncbi/builds.txt.sample + tool-data/shared/ensembl/builds.txt.sample + tool-data/shared/ucsc/builds.txt.sample + tool-data/shared/ucsc/publicbuilds.txt.sample + tool-data/shared/igv/igv_build_sites.txt.sample + tool-data/shared/rviewer/rviewer_build_sites.txt.sample + tool-data/*.sample + static/welcome.html.sample +" + +# Create any missing config/location files +for sample in $SAMPLES; do + file=`echo $sample | sed -e 's/\.sample$//'` + if [ ! -f "$file" -a -f "$sample" ]; then + echo "Initializing $file from `basename $sample`" + cp $sample $file + fi +done + +python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_webapp.pid --log-file=tool_shed_webapp.log $@ diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b scripts/db_shell.py --- a/scripts/db_shell.py +++ b/scripts/db_shell.py @@ -30,7 +30,7 @@ # Need to pop the last arg so the command line args will be correct # for sqlalchemy-migrate webapp = sys.argv.pop() - config_file = 'community_wsgi.ini' + config_file = 'tool_shed_wsgi.ini' repo = 'lib/galaxy/webapps/tool_shed/model/migrate' else: # Poor man's optparse diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b scripts/manage_db.py --- a/scripts/manage_db.py +++ b/scripts/manage_db.py @@ -18,7 +18,7 @@ # Need to pop the last arg so the command line args will be correct # for sqlalchemy-migrate webapp = sys.argv.pop() - config_file = 'community_wsgi.ini' + config_file = 'tool_shed_wsgi.ini' repo = 'lib/galaxy/webapps/tool_shed/model/migrate' else: # Poor man's optparse diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b scripts/tool_shed/migrate_tools_to_repositories.py --- a/scripts/tool_shed/migrate_tools_to_repositories.py +++ b/scripts/tool_shed/migrate_tools_to_repositories.py @@ -10,7 +10,7 @@ 0. This script must be run on a repo updated to changeset: 5621:4618be57481b -1. Before running this script, make sure the following config setting is set in community_wsgi.ini +1. Before running this script, make sure the following config setting is set in tool_shed_wsgi.ini # Enable next-gen tool shed features enable_next_gen_tool_shed = True @@ -262,7 +262,7 @@ print " " print "##########################################" print "%s - Migrating current tool archives to new tool repositories" % now - # community_wsgi.ini file + # tool_shed_wsgi.ini file ini_file = sys.argv[1] conf_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} ) conf_parser.read( ini_file ) diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -175,7 +175,7 @@ os.environ[ 'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file # ---- Build Tool Shed Application -------------------------------------------------- toolshedapp = None - global_conf = { '__file__' : 'community_wsgi.ini.sample' } + global_conf = { '__file__' : 'tool_shed_wsgi.ini.sample' } # if not toolshed_database_connection.startswith( 'sqlite://' ): # kwargs[ 'database_engine_option_max_overflow' ] = '20' if tool_dependency_dir is not None: diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b tool_shed_wsgi.ini.sample --- /dev/null +++ b/tool_shed_wsgi.ini.sample @@ -0,0 +1,98 @@ +# ---- HTTP Server ---------------------------------------------------------- + +[server:main] + +use = egg:Paste#http +port = 9009 + +# The address on which to listen. By default, only listen to localhost (the tool shed will not +# be accessible over the network). Use '0.0.0.0' to listen on all available network interfaces. +#host = 0.0.0.0 +host = 127.0.0.1 + +use_threadpool = true +threadpool_workers = 10 + +# ---- Galaxy Webapps Community Interface ------------------------------------------------- + +[app:main] + +# Specifies the factory for the universe WSGI application +paste.app_factory = galaxy.webapps.tool_shed.buildapp:app_factory +log_level = DEBUG + +# Database connection +database_file = database/community.sqlite +# You may use a SQLAlchemy connection string to specify an external database instead +#database_connection = postgres:///community_test?host=/var/run/postgresql + +# Where the hgweb.config file is stored. The default is the Galaxy installation directory. +#hgweb_config_dir = None + +# Where dataset files are saved +file_path = database/community_files +# Temporary storage for additional datasets, this should be shared through the cluster +new_file_path = database/tmp + +# Session support (beaker) +use_beaker_session = True +session_type = memory +session_data_dir = %(here)s/database/beaker_sessions +session_key = galaxysessions +session_secret = changethisinproduction + +# -- Users and Security + +# Galaxy encodes various internal values when these values will be output in +# some format (for example, in a URL or cookie). You should set a key to be +# used by the algorithm that encodes and decodes these values. It can be any +# string. If left unchanged, anyone could construct a cookie that would grant +# them access to others' sessions. +id_secret = changethisinproductiontoo + +# User authentication can be delegated to an upstream proxy server (usually +# Apache). The upstream proxy should set a REMOTE_USER header in the request. +# Enabling remote user disables regular logins. For more information, see: +# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy +#use_remote_user = False + +# Configuration for debugging middleware +debug = true +use_lint = false + +# NEVER enable this on a public site (even test or QA) +# use_interactive = true + +# this should be a comma-separated list of valid Galaxy users +#admin_users = user1@example.org,user2@example.org + +# Force everyone to log in (disable anonymous access) +require_login = False + +# path to sendmail +sendmail_path = /usr/sbin/sendmail + +# For use by email messages sent from the tool shed +#smtp_server = smtp.your_tool_shed_server +#email_from = your_tool_shed_email@server + +# The URL linked by the "Support" link in the "Help" menu. +#support_url = http://wiki.g2.bx.psu.edu/Support + +# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) +## use_heartbeat = True + +# Profiling middleware (cProfile based) +## use_profile = True + +# Use the new iframe / javascript based layout +use_new_layout = true + +# Serving static files (needed if running standalone) +static_enabled = True +static_cache_time = 360 +static_dir = %(here)s/static/ +static_images_dir = %(here)s/static/images +static_favicon_dir = %(here)s/static/favicon.ico +static_scripts_dir = %(here)s/static/scripts/ +static_style_dir = %(here)s/static/june_2007_style/blue Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Import clean up and documentation for compute tool.
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6be1fed44bf6/ changeset: 6be1fed44bf6 user: jgoecks date: 2013-03-18 15:09:43 summary: Import clean up and documentation for compute tool. affected #: 1 file diff -r 0ddc03509b24d4d4e9024902546025df185c6a18 -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 tools/stats/column_maker.py --- a/tools/stats/column_maker.py +++ b/tools/stats/column_maker.py @@ -1,13 +1,13 @@ #!/usr/bin/env python # This tool takes a tab-delimited textfile as input and creates another column in the file which is the result of # a computation performed on every row in the original file. The tool will skip over invalid lines within the file, -# informing the user about the number of lines skipped. -import sys, re, os.path -from galaxy import eggs -from galaxy.tools import validation -from galaxy.datatypes import metadata +# informing the user about the number of lines skipped. + +import sys, re +# These functions may be used in compute expression: from math import log,exp,sqrt,ceil,floor + assert sys.version_info[:2] >= ( 2, 4 ) def stop_err( msg ): 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: greg: Eliminate a duplicate method from shed_util_common and add missing documentation to several utility methods.
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0ddc03509b24/ changeset: 0ddc03509b24 user: greg date: 2013-03-18 14:55:28 summary: Eliminate a duplicate method from shed_util_common and add missing documentation to several utility methods. affected #: 6 files diff -r 92275794f6efe2f2e17c2d3785061e88f2f23f84 -r 0ddc03509b24d4d4e9024902546025df185c6a18 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -184,7 +184,7 @@ params = util.Params( kwd ) repository_id = params.get( 'id', None ) repository = suc.get_installed_tool_shed_repository( trans, repository_id ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) url = suc.url_join( tool_shed_url, 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ ( web.url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) ) @@ -314,7 +314,7 @@ need it so that we can derive the tool shed from which it was installed. """ repository = suc.get_installed_tool_shed_repository( trans, repository_id ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) url = suc.url_join( tool_shed_url, 'repository/get_repository_dependencies?name=%s&owner=%s&changeset_revision=%s' % \ ( repository_name, repository_owner, changeset_revision ) ) @@ -337,7 +337,7 @@ it so that we can derive the tool shed from which it was installed. """ repository = suc.get_installed_tool_shed_repository( trans, repository_id ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) url = suc.url_join( tool_shed_url, 'repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s' % \ ( repository_name, repository_owner, changeset_revision ) ) @@ -359,7 +359,7 @@ uninstalled tool shed repository. """ repository = suc.get_installed_tool_shed_repository( trans, repository_id ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) url = suc.url_join( tool_shed_url, 'repository/get_updated_repository_information?name=%s&owner=%s&changeset_revision=%s' % \ ( repository_name, repository_owner, changeset_revision ) ) @@ -654,7 +654,7 @@ suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed ) url = suc.url_join( tool_shed_url, '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) ) @@ -711,7 +711,7 @@ repository = suc.get_installed_tool_shed_repository( trans, repository_id ) if not repository: return trans.show_error_message( 'Invalid repository specified.' ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) if repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING ]: tool_shed_repository_ids = [ repository_id ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', @@ -1172,7 +1172,7 @@ clone_dir = os.path.join( tool_path, suc.generate_tool_shed_repository_install_dir( repository_clone_url, tool_shed_repository.installed_changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed ) tool_section = None tool_panel_section = kwd.get( 'tool_panel_section', '' ) new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) @@ -1317,7 +1317,7 @@ tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) metadata = tool_shed_repository.metadata - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed ) tool_path, relative_install_dir = tool_shed_repository.get_tool_relative_path( trans.app ) if latest_changeset_revision and latest_ctx_rev: # There are updates available in the tool shed for the repository, so use the receieved dependency information which was retrieved from @@ -1481,7 +1481,7 @@ def reset_repository_metadata( self, trans, id ): """Reset all metadata on a single installed tool shed repository.""" repository = suc.get_installed_tool_shed_repository( trans, id ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: @@ -1560,7 +1560,7 @@ metadata for the repository's revision in the Galaxy database. """ repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) url = suc.url_join( tool_shed_url, 'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ ( repository.name, repository.owner, repository.changeset_revision ) ) diff -r 92275794f6efe2f2e17c2d3785061e88f2f23f84 -r 0ddc03509b24d4d4e9024902546025df185c6a18 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -279,7 +279,7 @@ if self.__isinstalled( clone_dir ): print "Skipping automatic install of repository '", name, "' because it has already been installed in location ", clone_dir else: - tool_shed_url = self.__get_url_from_tool_shed( self.tool_shed ) + tool_shed_url = suc.get_url_from_tool_shed( self.app, self.tool_shed ) repository_clone_url = os.path.join( tool_shed_url, 'repos', self.repository_owner, name ) relative_install_dir = os.path.join( relative_clone_dir, name ) install_dir = os.path.join( clone_dir, name ) @@ -351,16 +351,6 @@ @property def non_shed_tool_panel_configs( self ): return common_util.get_non_shed_tool_panel_configs( self.app ) - def __get_url_from_tool_shed( self, tool_shed ): - # The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is something like: - # http://toolshed.g2.bx.psu.edu/ - for shed_name, shed_url in self.app.tool_shed_registry.tool_sheds.items(): - if shed_url.find( tool_shed ) >= 0: - if shed_url.endswith( '/' ): - shed_url = shed_url.rstrip( '/' ) - return shed_url - # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml. - return None def __isinstalled( self, clone_dir ): full_path = os.path.abspath( clone_dir ) if os.path.exists( full_path ): diff -r 92275794f6efe2f2e17c2d3785061e88f2f23f84 -r 0ddc03509b24d4d4e9024902546025df185c6a18 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -77,7 +77,7 @@ def get_update_to_changeset_revision_and_ctx_rev( trans, repository ): """Return the changeset revision hash to which the repository can be updated.""" changeset_revision_dict = {} - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) url = suc.url_join( tool_shed_url, 'repository/get_changeset_revision_and_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % \ ( repository.name, repository.owner, repository.installed_changeset_revision ) ) try: diff -r 92275794f6efe2f2e17c2d3785061e88f2f23f84 -r 0ddc03509b24d4d4e9024902546025df185c6a18 lib/tool_shed/galaxy_install/update_manager.py --- a/lib/tool_shed/galaxy_install/update_manager.py +++ b/lib/tool_shed/galaxy_install/update_manager.py @@ -34,7 +34,7 @@ self.sleeper.sleep( self.seconds_to_sleep ) log.info( 'Transfer job restarter shutting down...' ) def check_for_update( self, repository ): - tool_shed_url = suc.get_url_from_repository_tool_shed( self.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( self.app, repository.tool_shed ) url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&from_update_manager=True' % \ ( tool_shed_url, repository.name, repository.owner, repository.changeset_revision ) try: diff -r 92275794f6efe2f2e17c2d3785061e88f2f23f84 -r 0ddc03509b24d4d4e9024902546025df185c6a18 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1432,7 +1432,7 @@ def reset_all_metadata_on_installed_repository( trans, id ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" repository = suc.get_installed_tool_shed_repository( trans, id ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: diff -r 92275794f6efe2f2e17c2d3785061e88f2f23f84 -r 0ddc03509b24d4d4e9024902546025df185c6a18 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -160,7 +160,7 @@ return False, error_message def config_elems_to_xml_file( app, config_elems, config_filename, tool_path ): - # Persist the current in-memory list of config_elems to a file named by the value of config_filename. + """Persist the current in-memory list of config_elems to a file named by the value of config_filename.""" fd, filename = tempfile.mkstemp() os.write( fd, '<?xml version="1.0"?>\n' ) os.write( fd, '<toolbox tool_path="%s">\n' % str( tool_path ) ) @@ -242,7 +242,7 @@ def generate_clone_url_for_installed_repository( app, repository ): """Generate the URL for cloning a repository that has been installed into a Galaxy instance.""" - tool_shed_url = get_url_from_repository_tool_shed( app, repository ) + tool_shed_url = get_url_from_tool_shed( app, repository.tool_shed ) return url_join( tool_shed_url, 'repos', repository.owner, repository.name ) def generate_clone_url_for_repository_in_tool_shed( trans, repository ): @@ -469,7 +469,7 @@ return None def get_installed_tool_shed_repository( trans, id ): - """Get a repository on the Galaxy side from the database via id""" + """Get a tool shed repository record from the Galaxy database defined by the id.""" return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) def get_named_tmpfile_from_ctx( ctx, filename, dir ): @@ -516,6 +516,11 @@ return None def get_or_create_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision ): + """ + Return a tool shed repository database record defined by the combination of tool shed, repository name, repository owner and changeset_revision + or installed_changeset_revision. A new tool shed repository record will be created if one is not located. + """ + # This method is used only in Galaxy, not the tool shed. repository = get_repository_for_dependency_relationship( trans.app, tool_shed, name, owner, changeset_revision ) if not repository: tool_shed_url = get_url_from_tool_shed( trans.app, tool_shed ) @@ -572,7 +577,7 @@ previous_changeset_revision = changeset_revision def get_repo_info_tuple_contents( repo_info_tuple ): - # Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced. + """Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced.""" if len( repo_info_tuple ) == 6: description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple repository_dependencies = None @@ -613,6 +618,8 @@ return None def get_repository_for_dependency_relationship( app, tool_shed, name, owner, changeset_revision ): + """Return a tool shed repository database record that is defined by either the current changeset revision or the installed_changeset_revision.""" + # This method is used only in Galaxy, not the tool shed. repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app=app, tool_shed=tool_shed, name=name, @@ -627,6 +634,7 @@ return repository def get_repository_file_contents( file_path ): + """Return the display-safe contents of a repository file.""" if checkers.is_gzip( file_path ): safe_str = to_safe_string( '\ngzip compressed file\n' ) elif checkers.is_bz2( file_path ): @@ -646,6 +654,7 @@ return safe_str def get_repository_files( trans, folder_path ): + """Return the file hierarchy of a tool shed repository.""" contents = [] for item in os.listdir( folder_path ): # Skip .hg directories @@ -684,6 +693,7 @@ return None def get_repository_owner( cleaned_repository_url ): + """Gvien a "cleaned" repository clone URL, return the owner of the repository.""" items = cleaned_repository_url.split( '/repos/' ) repo_path = items[ 1 ] if repo_path.startswith( '/' ): @@ -691,11 +701,13 @@ return repo_path.lstrip( '/' ).split( '/' )[ 0 ] def get_repository_owner_from_clone_url( repository_clone_url ): + """Given a repository clone URL, return the owner of the repository.""" tmp_url = clean_repository_clone_url( repository_clone_url ) tool_shed = tmp_url.split( '/repos/' )[ 0 ].rstrip( '/' ) return get_repository_owner( tmp_url ) def get_repository_tools_tups( app, metadata_dict ): + """Return a list of tuples of the form (relative_path, guid, tool) for each tool defined in the received tool shed repository metadata.""" repository_tools_tups = [] index, shed_conf_dict = get_shed_tool_conf_dict( app, metadata_dict.get( 'shed_config_filename' ) ) if 'tools' in metadata_dict: @@ -713,6 +725,7 @@ return repository_tools_tups def get_reversed_changelog_changesets( repo ): + """Return a list of changesets in reverse order from that provided by the repository manifest.""" reversed_changelog = [] for changeset in repo.changelog: reversed_changelog.insert( 0, changeset ) @@ -728,6 +741,7 @@ return "-1:%s" % changeset_revision def get_rev_label_from_changeset_revision( repo, changeset_revision ): + """Given a changeset revision hash, return two strings, the changeset rev and the changeset revision hash.""" ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: rev = '%04d' % ctx.rev() @@ -748,8 +762,10 @@ return index, shed_tool_conf_dict def get_tool_panel_config_tool_path_install_dir( app, repository ): - # Return shed-related tool panel config, the tool_path configured in it, and the relative path to the directory where the - # repository is installed. This method assumes all repository tools are defined in a single shed-related tool panel config. + """ + Return shed-related tool panel config, the tool_path configured in it, and the relative path to the directory where the repository is installed. + This method assumes all repository tools are defined in a single shed-related tool panel config. + """ tool_shed = clean_tool_shed_url( repository.tool_shed ) partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.installed_changeset_revision ) # Get the relative tool installation paths from each of the shed tool configs. @@ -782,11 +798,14 @@ return None def get_tool_shed_repository_by_id( trans, repository_id ): + """Return a tool shed repository database record defined by the id.""" + # This method is used only in Galaxy, not the tool shed. return trans.sa_session.query( trans.model.ToolShedRepository ) \ .filter( trans.model.ToolShedRepository.table.c.id == trans.security.decode_id( repository_id ) ) \ .first() def get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ): + """Return a tool shed repository database record defined by the combination of a tool_shed, repository name, repository owner and current changeet_revision.""" # This method is used only in Galaxy, not the tool shed. sa_session = app.model.context.current if tool_shed.find( '//' ) > 0: @@ -800,6 +819,7 @@ .first() def get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app, tool_shed, name, owner, installed_changeset_revision ): + """Return a tool shed repository database record defined by the combination of a tool_shed, repository name, repository owner and installed_changeet_revision.""" # This method is used only in Galaxy, not the tool shed. sa_session = app.model.context.current if tool_shed.find( '//' ) > 0: @@ -816,23 +836,12 @@ tmp_url = clean_repository_clone_url( repository_clone_url ) return tmp_url.split( '/repos/' )[ 0 ].rstrip( '/' ) -def get_url_from_repository_tool_shed( app, repository ): +def get_url_from_tool_shed( app, tool_shed ): """ - The stored value of repository.tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is - something like: http://toolshed.g2.bx.psu.edu/. + The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is something like: + http://toolshed.g2.bx.psu.edu/ """ for shed_name, shed_url in app.tool_shed_registry.tool_sheds.items(): - if shed_url.find( repository.tool_shed ) >= 0: - if shed_url.endswith( '/' ): - shed_url = shed_url.rstrip( '/' ) - return shed_url - # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml. - return None - -def get_url_from_tool_shed( app, tool_shed ): - # The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is something like: - # http://toolshed.g2.bx.psu.edu/ - for shed_name, shed_url in app.tool_shed_registry.tool_sheds.items(): if shed_url.find( tool_shed ) >= 0: if shed_url.endswith( '/' ): shed_url = shed_url.rstrip( '/' ) @@ -856,26 +865,28 @@ return None def handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=False, admin_only=False ): - # There are 2 complementary features that enable a tool shed user to receive email notification: - # 1. Within User Preferences, they can elect to receive email when the first (or first valid) - # change set is produced for a new repository. - # 2. When viewing or managing a repository, they can check the box labeled "Receive email alerts" - # which caused them to receive email alerts when updates to the repository occur. This same feature - # is available on a per-repository basis on the repository grid within the tool shed. - # - # There are currently 4 scenarios for sending email notification when a change is made to a repository: - # 1. An admin user elects to receive email when the first change set is produced for a new repository - # from User Preferences. The change set does not have to include any valid content. This allows for - # the capture of inappropriate content being uploaded to new repositories. - # 2. A regular user elects to receive email when the first valid change set is produced for a new repository - # from User Preferences. This differs from 1 above in that the user will not receive email until a - # change set tha tincludes valid content is produced. - # 3. An admin user checks the "Receive email alerts" check box on the manage repository page. Since the - # user is an admin user, the email will include information about both HTML and image content that was - # included in the change set. - # 4. A regular user checks the "Receive email alerts" check box on the manage repository page. Since the - # user is not an admin user, the email will not include any information about both HTML and image content - # that was included in the change set. + """ + There are 2 complementary features that enable a tool shed user to receive email notification: + 1. Within User Preferences, they can elect to receive email when the first (or first valid) + change set is produced for a new repository. + 2. When viewing or managing a repository, they can check the box labeled "Receive email alerts" + which caused them to receive email alerts when updates to the repository occur. This same feature + is available on a per-repository basis on the repository grid within the tool shed. + + There are currently 4 scenarios for sending email notification when a change is made to a repository: + 1. An admin user elects to receive email when the first change set is produced for a new repository + from User Preferences. The change set does not have to include any valid content. This allows for + the capture of inappropriate content being uploaded to new repositories. + 2. A regular user elects to receive email when the first valid change set is produced for a new repository + from User Preferences. This differs from 1 above in that the user will not receive email until a + change set tha tincludes valid content is produced. + 3. An admin user checks the "Receive email alerts" check box on the manage repository page. Since the + user is an admin user, the email will include information about both HTML and image content that was + included in the change set. + 4. A regular user checks the "Receive email alerts" check box on the manage repository page. Since the + user is not an admin user, the email will not include any information about both HTML and image content + that was included in the change set. + """ repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) sharable_link = generate_sharable_link_for_repository_in_tool_shed( trans, repository, changeset_revision=None ) @@ -948,6 +959,7 @@ log.exception( "An error occurred sending a tool shed repository update alert by email." ) def open_repository_files_folder( trans, folder_path ): + """Return a list of dictionaries, each of which contains information for a file or directory contained within a directory in a repository file hierarchy.""" try: files_list = get_repository_files( trans, folder_path ) except OSError, e: @@ -957,19 +969,20 @@ folder_contents = [] for filename in files_list: is_folder = False - if filename and filename[-1] == os.sep: + if filename and filename[ -1 ] == os.sep: is_folder = True if filename: full_path = os.path.join( folder_path, filename ) - node = { "title": filename, - "isFolder": is_folder, - "isLazy": is_folder, - "tooltip": full_path, - "key": full_path } + node = { "title" : filename, + "isFolder" : is_folder, + "isLazy" : is_folder, + "tooltip" : full_path, + "key" : full_path } folder_contents.append( node ) return folder_contents def remove_dir( dir ): + """Attempt to remove a directory from disk.""" if os.path.exists( dir ): try: shutil.rmtree( dir ) @@ -1029,9 +1042,11 @@ return reversed_changelog def reversed_upper_bounded_changelog( repo, included_upper_bounds_changeset_revision ): + """Return a reversed list of changesets in the repository changelog up to and including the included_upper_bounds_changeset_revision.""" return reversed_lower_upper_bounded_changelog( repo, INITIAL_CHANGELOG_HASH, included_upper_bounds_changeset_revision ) def strip_path( fpath ): + """Attempt to strip the path from a file name.""" if not fpath: return fpath try: @@ -1072,12 +1087,15 @@ return text def tool_shed_from_repository_clone_url( repository_clone_url ): + """Given a repository clone URL, return the tool shed that contains the repository.""" return clean_repository_clone_url( repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' ) def tool_shed_is_this_tool_shed( toolshed_base_url ): + """Determine if a tool shed is the current tool shed.""" return toolshed_base_url.rstrip( '/' ) == str( url_for( '/', qualified=True ) ).rstrip( '/' ) def translate_string( raw_text, to_html=True ): + """Return a subset of a string (up to MAX_CONTENT_SIZE) translated to a safe string for display in a browser.""" if raw_text: if len( raw_text ) <= MAX_CONTENT_SIZE: translated_string = to_safe_string( raw_text, to_html=to_html ) @@ -1141,12 +1159,14 @@ commands.update( get_configured_ui(), repo, rev=ctx_rev ) def update_tool_shed_repository_status( app, tool_shed_repository, status ): + """Update the status of a tool shed repository in the process of being installed into Galaxy.""" sa_session = app.model.context.current tool_shed_repository.status = status sa_session.add( tool_shed_repository ) sa_session.flush() def url_join( *args ): + """Return a valid URL produced by appending a base URL and a set of request parameters.""" parts = [] for arg in args: parts.append( arg.strip( '/' ) ) 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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galaxy-commits March 2013