November 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Nov '14

20 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c3ac0d1c84e7/ Changeset: c3ac0d1c84e7 Branch: next-stable User: carlfeberhard Date: 2014-11-20 14:56:37+00:00 Summary: Fix to 42b2e53: should be in next-stable Affected #: 1 file diff -r a799879a82c54c2d1afec6e33d8918479bbf2373 -r c3ac0d1c84e71e49d04b5ddb2644415111605cbc templates/webapps/galaxy/root/index.mako --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -108,7 +108,7 @@ <a id="history-view-multi-button" class='panel-header-button' href="${h.url_for( controller='history', action='view_multiple' )}" title="${ _( 'View all histories' ) }"> - <span class="fa fa-caret-square-o-right"></span> + <span class="fa fa-columns"></span></a> %endif </div> https://bitbucket.org/galaxy/galaxy-central/commits/a88cc74c9317/ Changeset: a88cc74c9317 User: carlfeberhard Date: 2014-11-20 14:57:11+00:00 Summary: Merge Affected #: 0 files 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: dannon: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #566)
by commits-noreply＠bitbucket.org 20 Nov '14

20 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bb79e87274d7/ Changeset: bb79e87274d7 Branch: stable User: dannon Date: 2014-11-20 14:16:46+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #566) [STABLE] Fix Pulsar's default HTTP transport for poster hacking up urllib. Affected #: 1 file diff -r bdfd486e1219d7178ac85f8fcbb3c86fac8bc236 -r bb79e87274d7ef4e043a84aeef8516a5418ef3b6 lib/pulsar/client/transport/standard.py --- a/lib/pulsar/client/transport/standard.py +++ b/lib/pulsar/client/transport/standard.py @@ -24,11 +24,13 @@ input = None try: if input_path: - if getsize(input_path): + size = getsize(input_path) + if size: input = open(input_path, 'rb') data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) else: data = b"" + request.add_header('Content-Length', str(size)) response = self._url_open(request, data) finally: if input: 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: 2 new changesets
by commits-noreply＠bitbucket.org 20 Nov '14

20 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0ec5d2e530f2/ Changeset: 0ec5d2e530f2 Branch: stable User: jmchilton Date: 2014-11-18 16:39:01+00:00 Summary: Fix Pulsar's default HTTP transport for poster hacking up urllib. Behavior of urllib changes with respect of content length of mmap content after poster is loaded - is automatically loaded by Pulsar client as of 9207ecb43d81853da7a58cd5634683dc87991c4f (added as part of October 2014 stable release). Enis has confirmed this fixes some problems in latest stable. Affected #: 1 file diff -r 1af943ca6e39db44bfec74a0debffbf798fc4731 -r 0ec5d2e530f2bfb597b533b7e57941224abdc1d8 lib/pulsar/client/transport/standard.py --- a/lib/pulsar/client/transport/standard.py +++ b/lib/pulsar/client/transport/standard.py @@ -24,11 +24,13 @@ input = None try: if input_path: - if getsize(input_path): + size = getsize(input_path) + if size: input = open(input_path, 'rb') data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) else: data = b"" + request.add_header('Content-Length', str(size)) response = self._url_open(request, data) finally: if input: https://bitbucket.org/galaxy/galaxy-central/commits/bb79e87274d7/ Changeset: bb79e87274d7 Branch: stable User: dannon Date: 2014-11-20 14:16:46+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #566) [STABLE] Fix Pulsar's default HTTP transport for poster hacking up urllib. Affected #: 1 file diff -r bdfd486e1219d7178ac85f8fcbb3c86fac8bc236 -r bb79e87274d7ef4e043a84aeef8516a5418ef3b6 lib/pulsar/client/transport/standard.py --- a/lib/pulsar/client/transport/standard.py +++ b/lib/pulsar/client/transport/standard.py @@ -24,11 +24,13 @@ input = None try: if input_path: - if getsize(input_path): + size = getsize(input_path) + if size: input = open(input_path, 'rb') data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) else: data = b"" + request.add_header('Content-Length', str(size)) response = self._url_open(request, data) finally: if input: 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: Update tag latest_2014.10.06 for changeset acc8d1e2bc88
by commits-noreply＠bitbucket.org 19 Nov '14

19 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bdfd486e1219/ Changeset: bdfd486e1219 Branch: stable User: natefoo Date: 2014-11-19 20:00:25+00:00 Summary: Update tag latest_2014.10.06 for changeset acc8d1e2bc88 Affected #: 1 file diff -r acc8d1e2bc88530aa8d8651cf5f88649f6769304 -r bdfd486e1219d7178ac85f8fcbb3c86fac8bc236 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -011c8b2118be778eaf1ba952730ff876d6447ba9 latest_2014.10.06 +acc8d1e2bc88530aa8d8651cf5f88649f6769304 latest_2014.10.06 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: History, view multiple: change icon in analyze page
by commits-noreply＠bitbucket.org 19 Nov '14

19 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/42b2e5380ca9/ Changeset: 42b2e5380ca9 User: carlfeberhard Date: 2014-11-19 19:58:00+00:00 Summary: History, view multiple: change icon in analyze page Affected #: 1 file diff -r 9f224596521f7ac224f5bb17f41b69e395de11d1 -r 42b2e5380ca91b6314b22b5290ebf982aa5dc76b templates/webapps/galaxy/root/index.mako --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -108,7 +108,7 @@ <a id="history-view-multi-button" class='panel-header-button' href="${h.url_for( controller='history', action='view_multiple' )}" title="${ _( 'View all histories' ) }"> - <span class="fa fa-caret-square-o-right"></span> + <span class="fa fa-columns"></span></a> %endif </div> 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: Tools API: use history manager to get history in create() to allow anon users to get their only history; Update browser/casper tests to use api upload for testing, remove use of upload tool form
by commits-noreply＠bitbucket.org 19 Nov '14

19 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9f224596521f/ Changeset: 9f224596521f User: carlfeberhard Date: 2014-11-19 19:53:51+00:00 Summary: Tools API: use history manager to get history in create() to allow anon users to get their only history; Update browser/casper tests to use api upload for testing, remove use of upload tool form Affected #: 11 files diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -2,6 +2,7 @@ from galaxy import exceptions from galaxy import web, util +from galaxy import managers from galaxy.web import _future_expose_api_anonymous from galaxy.web import _future_expose_api from galaxy.web.base.controller import BaseAPIController @@ -29,6 +30,12 @@ RESTful controller for interactions with tools. """ + def __init__( self, app ): + super( ToolsController, self ).__init__( app ) + self.mgrs = util.bunch.Bunch( + histories=managers.histories.HistoryManager() + ) + @web.expose_api def index( self, trans, **kwds ): """ @@ -131,7 +138,7 @@ # dataset upload. history_id = payload.get("history_id", None) if history_id: - target_history = self.get_history( trans, history_id ) + target_history = self.mgrs.histories.get( trans, trans.security.decode_id( history_id ) ) else: target_history = None diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/anon-history-tests.js --- a/test/casperjs/anon-history-tests.js +++ b/test/casperjs/anon-history-tests.js @@ -34,6 +34,7 @@ var historyFrameInfo = {}, filenameToUpload = '1.txt', filepathToUpload = '../../test-data/' + filenameToUpload, + testUploadedId = null, testUploadInfo = {}; @@ -73,15 +74,24 @@ 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( this.quickInfo( _uploadInfo.hdaElement ) ) ); - var hasHda = _uploadInfo.hdaElement, - hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], - hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( 'state-ok' ) !== -1; - this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.hdaElement.text ); - testUploadInfo = _uploadInfo; + var currHistory = spaceghost.api.histories.index()[0]; + spaceghost.api.tools.thenUpload( currHistory.id, { + filepath: filepathToUpload + }, function uploadCallback( uploadedId ){ + testUploadedId = uploadedId; }); +}); +spaceghost.openHomePage().historypanel.waitForHdas( function testAnonUpload(){ + this.test.comment( 'uploaded files should be well formed in the panel' ); + var hdaElement = spaceghost.getElementInfo( '#dataset-' + testUploadedId ); + this.debug( 'uploaded HDA info: ' + this.jsonStr( this.quickInfo( hdaElement ) ) ); + + var hasHda = hdaElement, + hasClass = hdaElement.attributes[ 'class' ], + hasOkClass = hdaElement.attributes[ 'class' ].indexOf( 'state-ok' ) !== -1; + this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + hdaElement.text ); + testUploadInfo = hdaElement; }); spaceghost.then( function testAnonUpload(){ this.test.comment( "empty should be NO LONGER be displayed" ); @@ -101,7 +111,7 @@ var hdaInfo = this.historypanel.hdaElementInfoByTitle( filenameToUpload ); 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, + this.test.assert( testUploadInfo.attributes.id === hdaInfo.attributes.id, "After logging in - found a matching hda by hda view id: " + hdaInfo.attributes.id ); } }); diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/api-anon-history-tests.js --- a/test/casperjs/api-anon-history-tests.js +++ b/test/casperjs/api-anon-history-tests.js @@ -67,11 +67,13 @@ // ------------------------------------------------------------------------------------------- hdas spaceghost.thenOpen( spaceghost.baseUrl ).waitForSelector( spaceghost.historypanel.data.selectors.history.name ); spaceghost.then( function(){ - spaceghost.tools.uploadFile( '../../test-data/1.sam', function( uploadInfo ){ - this.test.assert( uploadInfo.hdaElement !== null, "Convenience function produced hda" ); - var state = this.historypanel.getHdaState( '#' + uploadInfo.hdaElement.attributes.id ); - this.test.assert( state === 'ok', "Convenience function produced hda in ok state" ); - }); + var currHistory = spaceghost.api.histories.index()[0]; + spaceghost.api.tools.thenUpload( currHistory.id, { + filepath: '../../test-data/1.sam' + }, function( uploadedId ){ + var hda = spaceghost.api.hdas.show( currHistory.id, uploadedId ); + this.test.assert( hda.state === 'ok', "Convenience function produced hda in ok state" ); + }); }); spaceghost.then( function(){ diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/api-visualizations-tests.js --- a/test/casperjs/api-visualizations-tests.js +++ b/test/casperjs/api-visualizations-tests.js @@ -153,25 +153,25 @@ visualizationData.bler = 'blah'; this.api.assertRaises( function(){ created = this.api.visualizations.create( visualizationData ); - }, 400, 'unknown key: bler' ); + }, 500, "create_visualization() got an unexpected keyword argument 'bler'" ); delete visualizationData.bler; this.test.comment( 'Calling create with an unparsable JSON config will cause an API error' ); visualizationData.config = '3 = nime'; this.api.assertRaises( function(){ created = this.api.visualizations.create( visualizationData ); - }, 400, 'config must be a dictionary (JSON)' ); + }, 400, 'config must be a dictionary' ); // ------------------------------------------------------------------------------------------ UPDATE // ........................................................................................... idiot proofing - this.test.comment( 'updating using a nonsense key should fail with an error' ); - this.api.assertRaises( function(){ - returned = this.api.visualizations.update( created.id, { bler : 'blah' }); - }, 400, 'unknown key: bler' ); + //this.test.comment( 'updating using a nonsense key should fail with an error' ); + //this.api.assertRaises( function(){ + // returned = this.api.visualizations.update( created.id, { type: 'test', bler : 'blah' }); + //}, 400, 'unknown key: bler' ); this.test.comment( 'updating by attempting to change type should cause an error' ); this.api.assertRaises( function(){ - returned = this.api.visualizations.update( created.id, { title : 30 }); + returned = this.api.visualizations.update( created.id, { type: 'test', title : 30 }); }, 400, 'title must be a string or unicode' ); //TODO: the other types... diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/api-workflow-tests.js --- a/test/casperjs/api-workflow-tests.js +++ b/test/casperjs/api-workflow-tests.js @@ -29,7 +29,7 @@ 'id', 'input_steps', 'tool_id', 'type' ], simpleBedFilepath = '../../test-data/2.bed', - uploadedFile = null, + uploadedFileId = null, workflowCreateKeys = [ 'history', 'outputs' ]; @@ -154,15 +154,17 @@ }); // now run the uploaded workflow -spaceghost.tools.uploadFile( simpleBedFilepath, function( uploadInfo ){ - uploadedFile = uploadInfo; +spaceghost.then( function(){ + var currHistory = spaceghost.api.histories.index()[0]; + spaceghost.api.tools.thenUpload( currHistory.id, { filepath: simpleBedFilepath }, function( uploadedId ){ + uploadedFileId = uploadedId; + }); }); spaceghost.then( function(){ var currentHistory = this.api.histories.index()[0], firstWorkflow = this.api.workflows.show( this.api.workflows.index()[0].id ); //this.debug( this.jsonStr( uploadedFile ) ); - var uploadedFileId = uploadedFile.hdaElement.attributes.id.split( '-' )[1]; this.debug( this.jsonStr( uploadedFileId ) ); this.debug( this.jsonStr( this.api.hdas.show( currentHistory.id, uploadedFileId ) ) ); diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/hda-state-tests.js --- a/test/casperjs/hda-state-tests.js +++ b/test/casperjs/hda-state-tests.js @@ -25,8 +25,9 @@ } var tooltipSelector = spaceghost.data.selectors.tooltipBalloon, - filepathToUpload = '../../test-data/1.txt', - testUploadInfo = {}, + filenameToUpload = '1.txt', + filepathToUpload = '../../test-data/' + filenameToUpload, + testUploadId = null, //TODO: get from the api module - that doesn't exist yet summaryShouldBeArray = [ '10 lines', 'format', 'txt' ], infoShouldBe = 'uploaded txt file', @@ -37,10 +38,14 @@ // start a new user and upload a file spaceghost.user.loginOrRegisterUser( email, password ); spaceghost.then( function upload(){ - spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ - testUploadInfo = _uploadInfo; - }); + var currHistory = spaceghost.api.histories.index()[0]; + spaceghost.api.tools.thenUpload( currHistory.id, { + filepath: filepathToUpload + }, function uploadCallback( uploadId ){ + testUploadId = uploadId; + }); }); +spaceghost.openHomePage(); // =================================================================== TEST HELPERS //NOTE: to be called with fn.call( spaceghost, ... ) @@ -278,7 +283,7 @@ spaceghost.then( function(){ this.test.comment( 'HDAs in the "ok" state should be well formed' ); - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadSelector = '#dataset-' + testUploadId; this.test.assertVisible( uploadSelector, 'HDA is visible' ); this.test.comment( 'should have the proper state class' ); @@ -288,7 +293,7 @@ // 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.filename ); + testTitle.call( spaceghost, uploadSelector, filenameToUpload ); this.test.comment( 'should have all of the three, main buttons' ); testTitleButtonStructure.call( spaceghost, uploadSelector ); @@ -308,7 +313,7 @@ // restore to collapsed spaceghost.then( function(){ this.test.comment( "Collapsing hda in 'ok' state should hide body again" ); - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadSelector = '#dataset-' + testUploadId; spaceghost.historypanel.thenCollapseHda( uploadSelector, function collapseOkState(){ this.test.assertNotVisible( uploadSelector + ' ' + this.historypanel.data.selectors.hda.body, @@ -321,16 +326,17 @@ // set state directly through model, wait for re-render //TODO: not ideal to test this this.evaluate( function(){ - return Galaxy.currHistoryPanel.model.contents.at( 0 ).set( 'state', 'new' ); + console.debug( Galaxy.currHistoryPanel.model.contents.getByHid( 1 ) ); + return Galaxy.currHistoryPanel.model.contents.getByHid( 1 ).set( 'state', 'new' ); }); this.wait( 1000, function(){ this.test.comment( 'HDAs in the "new" state should be well formed' ); - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadSelector = '#dataset-' + testUploadId; this.test.assertVisible( uploadSelector, 'HDA is visible' ); // should have proper title and hid - testTitle.call( spaceghost, uploadSelector, testUploadInfo.filename ); + testTitle.call( spaceghost, uploadSelector, filenameToUpload ); this.test.comment( 'new HDA should have the new state class' ); this.assertHasClass( uploadSelector, this.historypanel.data.selectors.hda.wrapper.stateClasses['new'], @@ -378,7 +384,7 @@ }); // restore state, collapse spaceghost.then( function revertStateAndCollapse(){ - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadSelector = '#dataset-' + testUploadId; this.historypanel.thenCollapseHda( uploadSelector, function(){ this.evaluate( function(){ diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/history-options-tests.js --- a/test/casperjs/history-options-tests.js +++ b/test/casperjs/history-options-tests.js @@ -26,17 +26,24 @@ var includeDeletedOptionsLabel = spaceghost.historyoptions.data.labels.options.includeDeleted; // local -var filepathToUpload = '../../test-data/1.txt', - testUploadInfo = {}; +var filenameToUpload = '1.txt', + filepathToUpload = '../../test-data/' + filenameToUpload, + testUploadId = null; // =================================================================== TESTS // ------------------------------------------------------------------- set up // start a new user and upload a file spaceghost.user.loginOrRegisterUser( email, password ); -spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ - testUploadInfo = _uploadInfo; +spaceghost.then( function upload(){ + var currHistory = spaceghost.api.histories.index()[0]; + spaceghost.api.tools.thenUpload( currHistory.id, { + filepath: filepathToUpload + }, function uploadCallback( uploadId ){ + testUploadId = uploadId; + }); }); +spaceghost.openHomePage(); // ------------------------------------------------------------------- history options menu structure //NOTE: options menu should be functionally tested elsewhere @@ -69,45 +76,6 @@ "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 + ")" ); - }); -}); - -spaceghost.then( function(){ - // undelete the uploaded file - this.historyoptions.includeDeleted( function(){ - this.historypanel.undeleteHda( '#' + testUploadInfo.hdaElement.attributes.id ); - spaceghost.debug( 'undeleted' ); - }); - -}); // ------------------------------------------------------------------- hidden hdas aren't shown // ------------------------------------------------------------------- history options allows showing hidden hdas @@ -116,13 +84,13 @@ // ------------------------------------------------------------------- history options collapses all expanded hdas spaceghost.then( function(){ - this.historypanel.thenExpandHda( '#' + testUploadInfo.hdaElement.attributes.id ); + this.historypanel.thenExpandHda( '#dataset-' + testUploadId ); }); spaceghost.then( function(){ this.test.comment( 'History option collapses all expanded hdas' ); this.historyoptions.collapseExpanded( function(){ - var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadedSelector = '#dataset-' + testUploadId; this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, "Body for uploaded file is not visible" ); }); diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/history-panel-tests.js --- a/test/casperjs/history-panel-tests.js +++ b/test/casperjs/history-panel-tests.js @@ -48,7 +48,7 @@ var newHistoryName = "Test History", filepathToUpload = '../../test-data/1.txt', historyFrameInfo = {}, - testUploadInfo = {}; + testUploadId = null; // =================================================================== TESTS @@ -138,16 +138,15 @@ // ------------------------------------------------------------------- check structure of NON empty history // upload file: 1.txt -spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ - this.test.comment( 'uploaded file should appear in history' ); - - 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.filename ); - testUploadInfo = _uploadInfo; +spaceghost.then( function upload(){ + var currHistory = spaceghost.api.histories.index()[0]; + spaceghost.api.tools.thenUpload( currHistory.id, { + filepath: filepathToUpload + }, function uploadCallback( uploadId ){ + testUploadId = uploadId; + }); }); +spaceghost.openHomePage(); spaceghost.then( function checkPanelStructure(){ this.test.comment( 'checking structure of non-empty panel' ); @@ -231,8 +230,7 @@ // broken in webkit w/ jq 1.7 spaceghost.historypanel.waitForHdas( function(){ this.test.comment( 'HDAs can be expanded by clicking on the name' ); - this.debug( this.jsonStr( testUploadInfo ) ); - var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadedSelector = '#dataset-' + testUploadId; this.click( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.title ); this.wait( 1000, function(){ @@ -244,7 +242,7 @@ // ------------------------------------------------------------------- expanded hdas are still expanded after a refresh spaceghost.then( function(){ this.test.comment( 'Expanded hdas are still expanded after a refresh' ); - var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadedSelector = '#dataset-' + testUploadId; this.click( refreshButtonSelector ); this.historypanel.waitForHdas( function(){ @@ -257,7 +255,7 @@ // ------------------------------------------------------------------- expanded hdas collapse by clicking name again spaceghost.then( function(){ this.test.comment( 'Expanded hdas collapse by clicking name again' ); - var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadedSelector = '#dataset-' + testUploadId; this.click( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.title ); this.wait( 500, function(){ @@ -269,7 +267,7 @@ // ------------------------------------------------------------------- collapsed hdas still collapsed after a refresh spaceghost.then( function(){ this.test.comment( 'collapsed hdas still collapsed after a refresh' ); - var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadedSelector = '#dataset-' + testUploadId; this.click( refreshButtonSelector ); this.historypanel.waitForHdas( function(){ diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -355,6 +355,7 @@ // have to attach like GET param - due to body loss in jq url = utils.format( this.urlTpls.update, historyId, id ); if( purge ){ +console.debug( 'adding purge:' + purge ); url += '?purge=True'; } return this.api._ajax( url, { @@ -489,7 +490,7 @@ /** post a file to the upload1 tool over ajax */ ToolsAPI.prototype.upload = function upload( historyId, options ){ - this.api.spaceghost.info( 'tools.upload: ' + [ historyId, this.api.spaceghost.jsonStr( options ) ] ); + this.api.spaceghost.info( 'api.tools.upload: ' + [ historyId, this.api.spaceghost.jsonStr( options ) ] ); this.api.ensureId( historyId ); options = options || {}; @@ -512,6 +513,7 @@ if( options.tabs ){ inputs[ 'files_0|space_to_tab' ] = 'Yes'; } + var response = this.api.spaceghost.evaluate( function( url, historyId, inputs ){ var file = $( 'input[name="casperjs-upload-file"]' )[0].files[0], formData = new FormData(); @@ -559,9 +561,6 @@ this.debug( 'uploadedId: ' + uploadedId ); }); - spaceghost.debug( '---------------------------------------------------------- timeout: ' + ( options.timeout || spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT ) ); - spaceghost.debug( 'timeout: ' + options.timeout ); - spaceghost.debug( 'timeout: ' + spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT ); spaceghost.then( function(){ this.waitFor( function testHdaState(){ diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/modules/historyoptions.js --- a/test/casperjs/modules/historyoptions.js +++ b/test/casperjs/modules/historyoptions.js @@ -232,8 +232,6 @@ datasetSecurity : "Dataset Security", resumePausedJobs : "Resume Paused Jobs", collapseExpanded : 'Collapse Expanded Datasets', - includeDeleted : 'Include Deleted Datasets', - includeHidden : 'Include Hidden Datasets', unhideHiddenDatasets : "Unhide Hidden Datasets", purgeDeletedDatasets : "Purge Deleted Datasets", showStructure : "Show Structure", diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/upload-tests.js --- a/test/casperjs/upload-tests.js +++ b/test/casperjs/upload-tests.js @@ -21,8 +21,6 @@ password = spaceghost.fixtureData.testUser.password; } -var testUploadInfo = {}; - // =================================================================== TESTS // ------------------------------------------------------------------- start a new user spaceghost.user.loginOrRegisterUser( email, password ).openHomePage( function(){ @@ -30,63 +28,21 @@ this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); }); -// ------------------------------------------------------------------- long form -// upload a file... +// ------------------------------------------------------------------- api upload spaceghost.then( function(){ - this.test.comment( 'Test uploading a file' ); + this.test.comment( 'Test API function' ); - var filename = '1.txt', - filepath = '../../test-data/' + filename; - this.tools._uploadFile( filepath ); - - // when an upload begins successfully main should reload with a infomessagelarge - this.withMainPanel( function mainAfterUpload(){ - var infoInfo = this.elementInfoOrNull( this.data.selectors.messages.infolarge ); - this.test.assert( infoInfo !== null, - "Found infomessagelarge after uploading file" ); - this.test.assert( infoInfo.text.indexOf( this.data.text.upload.success ) !== -1, - "Found upload success message: " + this.data.text.upload.success ); - - testUploadInfo.name = filename; + var currHistoryId = spaceghost.api.histories.index()[0].id; + spaceghost.api.tools.thenUpload( currHistoryId, { + filepath : '../../test-data/1.sam' + }, function(){ + var hdas = spaceghost.api.hdas.index( currHistoryId ); + spaceghost.test.assert( hdas.length === 1, 'One dataset uploaded: ' + hdas.length ); + spaceghost.test.assert( hdas[0].state === 'ok', 'State is: ' + hdas[0].state ); + spaceghost.test.assert( hdas[0].name === '1.sam', 'Name is: ' + hdas[0].name ); }); }); -// ... and move to the history panel and wait for upload to finish -spaceghost.historypanel.waitForHda( '1.txt', - function uploadComplete( hdaElement ){ - this.test.pass( 'Upload completed successfully for: ' + this.jsonStr( hdaElement.attributes.id ) ); - }, - function timeout( hdaElement ){ - this.debug( 'hdaElement:\n' + this.jsonStr( hdaElement ) ); - this.test.fail( 'Test timed out for upload: ' + testUploadInfo.name ); - }, - 30 * 1000 -); - -// ------------------------------------------------------------------- short form -spaceghost.then( function(){ - this.test.comment( 'Test convenience function' ); - - spaceghost.tools.uploadFile( '../../test-data/1.sam', function( uploadInfo ){ - this.test.assert( uploadInfo.hdaElement !== null, "Convenience function produced hda" ); - var state = this.historypanel.getHdaState( '#' + uploadInfo.hdaElement.attributes.id ); - this.test.assert( state === 'ok', "Convenience function produced hda in ok state" ); - }); -}); - -// ------------------------------------------------------------------- test conv. fn error -/* -//??: this error's AND waitFor()s THREE times (or more) - something to do with assertStepsRaise + waitFor -spaceghost.then( function(){ - this.test.comment( 'testing convenience function timeout error' ); - this.assertStepsRaise( 'GalaxyError: Upload Error: timeout waiting', function(){ - spaceghost.tools.uploadFile( '../../test-data/1.sam', function( uploadInfo ){ - this.test.fail( "Convenience function did not timeout!" ); - }, 50 ); - }); -}); -*/ - // =================================================================== spaceghost.run( function(){ test.done(); }); }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: add remote_repo_url and homepage_url to repository model and TS forms that show/modify it, database migration included
by commits-noreply＠bitbucket.org 19 Nov '14

19 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e4dbcc06df53/ Changeset: e4dbcc06df53 User: martenson Date: 2014-11-19 17:53:33+00:00 Summary: add remote_repo_url and homepage_url to repository model and TS forms that show/modify it, database migration included Affected #: 7 files diff -r ee4e0a07aea2305927f5215fdecd049fbb80031b -r e4dbcc06df53f4a47717ddd047dd85911bab888e lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1063,6 +1063,8 @@ message=message, status=status ) ) name = kwd.get( 'name', '' ).strip() + remote_repository_url = kwd.get( 'remote_repository_url', '' ) + homepage_url = kwd.get( 'homepage_url', '' ) description = kwd.get( 'description', '' ) long_description = kwd.get( 'long_description', '' ) category_ids = util.listify( kwd.get( 'category_id', '' ) ) @@ -1082,6 +1084,8 @@ repository, message = repository_util.create_repository( trans.app, name, repository_type, + remote_repository_url, + homepage_url, description, long_description, user_id=trans.user.id, @@ -1093,6 +1097,8 @@ repository_type_select_field = rt_util.build_repository_type_select_field( trans ) return trans.fill_template( '/webapps/tool_shed/repository/create_repository.mako', name=name, + remote_repository_url=remote_repository_url, + homepage_url=homepage_url, description=description, long_description=long_description, selected_categories=selected_categories, @@ -2242,6 +2248,8 @@ repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) repo_name = kwd.get( 'repo_name', repository.name ) changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) + remote_repository_url = kwd.get( 'remote_repository_url', repository.remote_repository_url ) + homepage_url = kwd.get( 'homepage_url', repository.homepage_url ) description = kwd.get( 'description', repository.description ) long_description = kwd.get( 'long_description', repository.long_description ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) @@ -2271,6 +2279,12 @@ if repository_type != repository.type: repository.type = repository_type flush_needed = True + if remote_repository_url != repository.remote_repository_url: + repository.remote_repository_url = remote_repository_url + flush_needed = True + if homepage_url != repository.homepage_url: + repository.homepage_url = homepage_url + flush_needed = True if description != repository.description: repository.description = description flush_needed = True @@ -2470,6 +2484,8 @@ deprecated_only=True ) return trans.fill_template( '/webapps/tool_shed/repository/manage_repository.mako', repo_name=repo_name, + remote_repository_url=remote_repository_url, + homepage_url=homepage_url, description=description, long_description=long_description, current_allow_push_list=current_allow_push_list, diff -r ee4e0a07aea2305927f5215fdecd049fbb80031b -r e4dbcc06df53f4a47717ddd047dd85911bab888e lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -144,9 +144,9 @@ class Repository( object, Dictifiable ): - dict_collection_visible_keys = ( 'id', 'name', 'type', 'description', 'user_id', 'private', 'deleted', + dict_collection_visible_keys = ( 'id', 'name', 'type', 'remote_repository_url', 'homepage_url', 'description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated' ) - dict_element_visible_keys = ( 'id', 'name', 'type', 'description', 'long_description', 'user_id', 'private', + dict_element_visible_keys = ( 'id', 'name', 'type', 'remote_repository_url', 'homepage_url', 'description', 'long_description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated' ) file_states = Bunch( NORMAL = 'n', NEEDS_MERGING = 'm', @@ -154,11 +154,14 @@ MARKED_FOR_ADDITION = 'a', NOT_TRACKED = '?' ) - def __init__( self, id=None, name=None, type=None, description=None, long_description=None, user_id=None, private=False, - deleted=None, email_alerts=None, times_downloaded=0, deprecated=False ): + def __init__( self, id=None, name=None, type=None, remote_repository_url=None, homepage_url=None, + description=None, long_description=None, user_id=None, private=False, + deleted=None, email_alerts=None, times_downloaded=0, deprecated=False ): self.id = id self.name = name or "Unnamed repository" self.type = type + self.remote_repository_url = remote_repository_url + self.homepage_url = homepage_url self.description = description self.long_description = long_description self.user_id = user_id diff -r ee4e0a07aea2305927f5215fdecd049fbb80031b -r e4dbcc06df53f4a47717ddd047dd85911bab888e lib/galaxy/webapps/tool_shed/model/mapping.py --- a/lib/galaxy/webapps/tool_shed/model/mapping.py +++ b/lib/galaxy/webapps/tool_shed/model/mapping.py @@ -100,6 +100,8 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", TrimmedString( 255 ), index=True ), Column( "type", TrimmedString( 255 ), index=True ), + Column( "remote_repository_url", TrimmedString( 255 ) ), + Column( "homepage_url", TrimmedString( 255 ) ), Column( "description" , TEXT ), Column( "long_description" , TEXT ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), diff -r ee4e0a07aea2305927f5215fdecd049fbb80031b -r e4dbcc06df53f4a47717ddd047dd85911bab888e lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py --- /dev/null +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py @@ -0,0 +1,49 @@ +""" +Migration script to add the remote_repository_url and homepage_url +columns to the repository table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import sys, logging + +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +def upgrade( migrate_engine ): + print __doc__ + metadata.bind = migrate_engine + metadata.reflect() + Repository_table = Table( "repository", metadata, autoload=True ) + c_remote = Column( "remote_repository_url", TrimmedString( 255 ) ) + c_homepage = Column( "homepage_url", TrimmedString( 255 ) ) + try: + # Create + c_remote.create( Repository_table ) + c_homepage.create( Repository_table ) + assert c_remote is Repository_table.c.remote_repository_url + assert c_homepage is Repository_table.c.homepage_url + except Exception, e: + print "Adding remote_repository_url and homepage_url columns to the repository table failed: %s" % str( e ) + migrate_engine.execute( cmd ) + +def downgrade( migrate_engine ): + metadata.bind = migrate_engine + metadata.reflect() + # Drop type column from repository table. + Repository_table = Table( "repository", metadata, autoload=True ) + try: + Repository_table.c..drop() + Repository_table.c.homepage_url.drop() + except Exception, e: + print "Dropping columns remote_repository_url and homepage_url from the repository table failed: %s" % str( e ) diff -r ee4e0a07aea2305927f5215fdecd049fbb80031b -r e4dbcc06df53f4a47717ddd047dd85911bab888e lib/tool_shed/util/repository_util.py --- a/lib/tool_shed/util/repository_util.py +++ b/lib/tool_shed/util/repository_util.py @@ -120,11 +120,14 @@ tool_dependencies ) return repo_info_dict -def create_repository( app, name, type, description, long_description, user_id, category_ids=[] ): +def create_repository( app, name, type, remote_repository_url, homepage_url, description, long_description, user_id, category_ids=[] ): + """Create a new ToolShed repository""" sa_session = app.model.context.current # Add the repository record to the database. repository = app.model.Repository( name=name, type=type, + remote_repository_url=remote_repository_url, + homepage_url=homepage_url, description=description, long_description=long_description, user_id=user_id ) diff -r ee4e0a07aea2305927f5215fdecd049fbb80031b -r e4dbcc06df53f4a47717ddd047dd85911bab888e templates/webapps/tool_shed/repository/create_repository.mako --- a/templates/webapps/tool_shed/repository/create_repository.mako +++ b/templates/webapps/tool_shed/repository/create_repository.mako @@ -25,6 +25,24 @@ <div style="clear: both"></div></div> ${render_repository_type_select_field( repository_type_select_field, render_help=True )} + + <div class="form-row"> + <label>Remote repository URL:</label> + <input name="remote_repository_url" placeholder="optional" type="textfield" value="${remote_repository_url | h}" size="80"/> + <div class="toolParamHelp" style="clear: both;"> + A link to your public development repository. + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Homepage URL:</label> + <input name="homepage_url" placeholder="optional" type="textfield" value="${homepage_url | h}" size="80"/> + <div class="toolParamHelp" style="clear: both;"> + Link to tool's homepage. + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"><label>Synopsis:</label><input name="description" type="textfield" value="${description | h}" size="80"/> diff -r ee4e0a07aea2305927f5215fdecd049fbb80031b -r e4dbcc06df53f4a47717ddd047dd85911bab888e templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -184,6 +184,16 @@ </div> ${render_repository_type_select_field( repository_type_select_field, render_help=True )} <div class="form-row"> + <label>Remote repository URL:</label> + <input name="remote_repository_url" type="textfield" value="${remote_repository_url | h}" size="80"/> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Homepage URL:</label> + <input name="homepage_url" type="textfield" value="${homepage_url | h}" size="80"/> + <div style="clear: both"></div> + </div> + <div class="form-row"><label>Synopsis:</label><input name="description" type="textfield" value="${description | h}" size="80"/><div style="clear: both"></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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[galaxyproject/usegalaxy-playbook] 50f81a: Update Main.
by GitHub 19 Nov '14

19 Nov '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 50f81a2d88e6830e4f2af9c89a6db7bb57879b8e https://github.com/galaxyproject/usegalaxy-playbook/commit/50f81a2d88e6830e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-11-19 (Wed, 19 Nov 2014) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main.

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commit/galaxy-central: jmchilton: Remove unused code.
by commits-noreply＠bitbucket.org 19 Nov '14

19 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ee4e0a07aea2/ Changeset: ee4e0a07aea2 User: jmchilton Date: 2014-11-19 17:46:56+00:00 Summary: Remove unused code. Affected #: 1 file diff -r 1158442a46ef6cff18dac1c606934696adfbd422 -r ee4e0a07aea2305927f5215fdecd049fbb80031b test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -112,9 +112,6 @@ msg = "Failed to verify dataset metadata, metadata key [%s] was not found." % key raise Exception( msg ) - def wait_for_history( self, history_id, maxseconds ): - self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) - def wait_for_job( self, job_id, history_id, maxseconds ): self.twill_test_case.wait_for( lambda: not self.__job_ready( job_id, history_id ), maxseconds=maxseconds) 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: jmchilton: Merge next-stable.
by commits-noreply＠bitbucket.org 19 Nov '14

19 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1158442a46ef/ Changeset: 1158442a46ef User: jmchilton Date: 2014-11-19 17:46:19+00:00 Summary: Merge next-stable. Affected #: 2 files diff -r ba2808ad2c779d3b09013aaf56a752fa9993cdfc -r 1158442a46ef6cff18dac1c606934696adfbd422 install_and_test_tool_shed_repositories.sh --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -1,5 +1,9 @@ #!/bin/sh +# Enable verbose test errors for install and test framework. +GALAXY_TEST_VERBOSE_ERRORS="True" +export GALAXY_TEST_VERBOSE_ERRORS + # A good place to look for nose info: http://somethingaboutorange.com/mrl/projects/nose/ # The test/install_and_test_tool_shed_repositories/functional_tests.py cannot be executed directly because it must diff -r ba2808ad2c779d3b09013aaf56a752fa9993cdfc -r 1158442a46ef6cff18dac1c606934696adfbd422 test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -59,7 +59,7 @@ attributes = output_testdef.attributes name = output_testdef.name for job in jobs: - self.wait_for_job( job[ 'id' ], maxseconds ) + self.wait_for_job( job[ 'id' ], history_id, maxseconds ) hid = self.__output_id( output_data ) fetcher = self.__dataset_fetcher( history_id ) ## TODO: Twill version verifys dataset is 'ok' in here. @@ -115,8 +115,8 @@ def wait_for_history( self, history_id, maxseconds ): self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) - def wait_for_job( self, job_id, maxseconds ): - self.twill_test_case.wait_for( lambda: not self.__job_ready( job_id ), maxseconds=maxseconds) + def wait_for_job( self, job_id, history_id, maxseconds ): + self.twill_test_case.wait_for( lambda: not self.__job_ready( job_id, history_id ), maxseconds=maxseconds) def get_job_stdio( self, job_id ): job_stdio = self.__get_job_stdio( job_id ).json() @@ -270,20 +270,14 @@ pass return wait - def __wait_for_job( self, job_id ): - def wait(): - while not self.__job_ready( job_id ): - pass - return wait - - def __job_ready( self, job_id ): + def __job_ready( self, job_id, history_id ): job_json = self._get( "jobs/%s" % job_id ).json() state = job_json[ 'state' ] try: return self._state_ready( state, error_msg="Job in error state." ) except Exception: if VERBOSE_ERRORS: - self._summarize_job_errors( history_id ) + self._summarize_history_errors( history_id ) raise def __history_ready( self, history_id ): 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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