galaxy-commits June 2013

galaxy-commits@lists.galaxyproject.org

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Jun '13

15 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/723bd4c7197a/ Changeset: 723bd4c7197a Branch: twobit_upload User: ghuls Date: 2013-05-27 15:02:06 Summary: Fix detection of 2bit files when uploading them. When 2bit files are uploaded, they were not detected as 2bit files: Example: test.2bit empty format: twobit, database: hg19 The uploaded binary file contains inappropriate content This issue is solved by registering the TwoBit file format in: ./lib/galaxy/datatypes/binary.py Affected #: 1 file diff -r 31714646a7b441f34a43748065278a1b08940c3c -r 723bd4c7197aec7ac42a20f07f48112cd5654a29 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -399,3 +399,5 @@ return dataset.peek except: return "Binary TwoBit format nucleotide file (%s)" % (data.nice_size(dataset.get_size())) + +Binary.register_sniffable_binary_format("twobit", "twobit", TwoBit) https://bitbucket.org/galaxy/galaxy-central/commits/eb910f78fa5b/ Changeset: eb910f78fa5b User: dannon Date: 2013-06-15 19:25:44 Summary: Merged in ghuls/galaxy-central/twobit_upload (pull request #170) Fix detection of 2bit files when uploading them. Affected #: 1 file diff -r b186609ec0cd60c8401b18b1c849745ce17ef0bd -r eb910f78fa5bb75eed2b967d1bdac69b2ae47894 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -399,3 +399,5 @@ return dataset.peek except: return "Binary TwoBit format nucleotide file (%s)" % (data.nice_size(dataset.get_size())) + +Binary.register_sniffable_binary_format("twobit", "twobit", TwoBit) 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 15 Jun '13

15 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b186609ec0cd/ Changeset: b186609ec0cd User: dannon Date: 2013-06-15 15:08:09 Summary: Fix reports import issue reported by Lance, https://trello.com/card/bug-in-reports-webapp-imports/506338ce32ae458f6d15e… Affected #: 1 file diff -r 12a45cc8c67f86f595f50bfcf2155892f5eafeb0 -r b186609ec0cd60c8401b18b1c849745ce17ef0bd lib/galaxy/webapps/reports/controllers/system.py --- a/lib/galaxy/webapps/reports/controllers/system.py +++ b/lib/galaxy/webapps/reports/controllers/system.py @@ -1,9 +1,9 @@ -import operator, os +import os +import logging from datetime import datetime, timedelta from galaxy.web.base.controller import BaseUIController, web from galaxy import model, util -from galaxy.model.orm import and_, not_, or_, desc -import logging +from galaxy.model.orm import and_, desc, eagerload log = logging.getLogger( __name__ ) class System( BaseUIController ): https://bitbucket.org/galaxy/galaxy-central/commits/f295092476c7/ Changeset: f295092476c7 Branch: stable User: dannon Date: 2013-06-15 15:08:09 Summary: Fix reports import issue reported by Lance, https://trello.com/card/bug-in-reports-webapp-imports/506338ce32ae458f6d15e… Affected #: 1 file diff -r 2efb1083676b56c4a2678e43600fd707756fca27 -r f295092476c781987d5a31e44e7a19a372a461aa lib/galaxy/webapps/reports/controllers/system.py --- a/lib/galaxy/webapps/reports/controllers/system.py +++ b/lib/galaxy/webapps/reports/controllers/system.py @@ -1,9 +1,9 @@ -import operator, os +import os +import logging from datetime import datetime, timedelta from galaxy.web.base.controller import BaseUIController, web from galaxy import model, util -from galaxy.model.orm import and_, not_, or_, desc -import logging +from galaxy.model.orm import and_, desc, eagerload log = logging.getLogger( __name__ ) class System( BaseUIController ): 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: Remove print statements from api/search, ctrl/visualization, ctrl/workflow
by commits-noreply＠bitbucket.org 14 Jun '13

14 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2efb1083676b/ Changeset: 2efb1083676b Branch: stable User: carlfeberhard Date: 2013-06-14 21:06:56 Summary: Remove print statements from api/search, ctrl/visualization, ctrl/workflow Affected #: 3 files diff -r 68c705bf0325a54d2424a7b8ed44232c57a3b506 -r 2efb1083676b56c4a2678e43600fd707756fca27 lib/galaxy/webapps/galaxy/api/search.py --- a/lib/galaxy/webapps/galaxy/api/search.py +++ b/lib/galaxy/webapps/galaxy/api/search.py @@ -30,7 +30,6 @@ current_user_roles = trans.get_current_user_roles() try: results = query.process(trans) - print results except Exception, e: return {'error' : str(e)} for item in results: diff -r 68c705bf0325a54d2424a7b8ed44232c57a3b506 -r 2efb1083676b56c4a2678e43600fd707756fca27 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -848,7 +848,6 @@ get the visualization with the given id; otherwise, create a new visualization using a given dataset and regions. """ - print 'sweepster:', id, hda_ldda, dataset_id, regions regions = regions or '{}' # Need to create history if necessary in order to create tool form. trans.get_history( create=True ) @@ -861,7 +860,6 @@ else: # Loading new visualization. dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) - print 'dataset:', dataset job = get_dataset_job( dataset ) viz_config = { 'dataset_id': dataset_id, diff -r 68c705bf0325a54d2424a7b8ed44232c57a3b506 -r 2efb1083676b56c4a2678e43600fd707756fca27 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -132,7 +132,6 @@ @web.expose def index( self, trans ): - print trans.request.host_url return self.list( trans ) @web.expose 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: Remove print statements from api/search, ctrl/visualization, ctrl/workflow
by commits-noreply＠bitbucket.org 14 Jun '13

14 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/12a45cc8c67f/ Changeset: 12a45cc8c67f User: carlfeberhard Date: 2013-06-14 21:01:12 Summary: Remove print statements from api/search, ctrl/visualization, ctrl/workflow Affected #: 3 files diff -r 48b7d75bbb339e27a6db906dd5b1b2a2dbbaaf71 -r 12a45cc8c67f86f595f50bfcf2155892f5eafeb0 lib/galaxy/webapps/galaxy/api/search.py --- a/lib/galaxy/webapps/galaxy/api/search.py +++ b/lib/galaxy/webapps/galaxy/api/search.py @@ -30,7 +30,6 @@ current_user_roles = trans.get_current_user_roles() try: results = query.process(trans) - print results except Exception, e: return {'error' : str(e)} for item in results: diff -r 48b7d75bbb339e27a6db906dd5b1b2a2dbbaaf71 -r 12a45cc8c67f86f595f50bfcf2155892f5eafeb0 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -848,7 +848,6 @@ get the visualization with the given id; otherwise, create a new visualization using a given dataset and regions. """ - print 'sweepster:', id, hda_ldda, dataset_id, regions regions = regions or '{}' # Need to create history if necessary in order to create tool form. trans.get_history( create=True ) @@ -861,7 +860,6 @@ else: # Loading new visualization. dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) - print 'dataset:', dataset job = get_dataset_job( dataset ) viz_config = { 'dataset_id': dataset_id, diff -r 48b7d75bbb339e27a6db906dd5b1b2a2dbbaaf71 -r 12a45cc8c67f86f595f50bfcf2155892f5eafeb0 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -132,7 +132,6 @@ @web.expose def index( self, trans ): - print trans.request.host_url return self.list( trans ) @web.expose 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: galaxy.base.js: Remove console.debug; pack scripts
by commits-noreply＠bitbucket.org 14 Jun '13

14 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/48b7d75bbb33/ Changeset: 48b7d75bbb33 User: carlfeberhard Date: 2013-06-14 20:51:49 Summary: galaxy.base.js: Remove console.debug; pack scripts Affected #: 2 files diff -r 07fb676b0a1d57f9352a0b9048bca9914b4095b6 -r 48b7d75bbb339e27a6db906dd5b1b2a2dbbaaf71 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -158,7 +158,6 @@ confirmtext = link_dom.getAttribute( "confirm" ), href = link_dom.getAttribute( "href" ), target = link_dom.getAttribute( "target" ); - console.debug( link.text(), href, target ); // no href - no function (gen. a label) if (!href) { diff -r 07fb676b0a1d57f9352a0b9048bca9914b4095b6 -r 48b7d75bbb339e27a6db906dd5b1b2a2dbbaaf71 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var 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c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!=="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tooltip){$(".tooltip").tooltip({placement:"top"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: Dave Bouvier: Add defaults to the tool shed's config.py for the toolbox dynamic filtering feature.
by commits-noreply＠bitbucket.org 14 Jun '13

14 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/07fb676b0a1d/ Changeset: 07fb676b0a1d User: Dave Bouvier Date: 2013-06-14 18:16:02 Summary: Add defaults to the tool shed's config.py for the toolbox dynamic filtering feature. Affected #: 1 file diff -r 3636ba2f4439b7b61f25425698f8e0be9f0f6f07 -r 07fb676b0a1d57f9352a0b9048bca9914b4095b6 lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -6,7 +6,7 @@ import logging, logging.config from optparse import OptionParser import ConfigParser -from galaxy.util import string_as_bool +from galaxy.util import string_as_bool, listify from galaxy import eggs import pkg_resources @@ -44,6 +44,9 @@ self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) # Tool stuff + self.tool_filters = listify( kwargs.get( "tool_filters", [] ) ) + self.tool_label_filters = listify( kwargs.get( "tool_label_filters", [] ) ) + self.tool_section_filters = listify( kwargs.get( "tool_section_filters", [] ) ) self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root ) self.tool_secret = kwargs.get( "tool_secret", "" ) self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "shed-tool-data" ), os.getcwd() ) 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 14 Jun '13

14 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d794e30fcd1a/ Changeset: d794e30fcd1a User: jmchilton Date: 2013-06-07 22:12:09 Summary: Refactor hardcoded references to static/welcome.html to a new welcome action on the root controller. Affected #: 4 files diff -r 30e8f84914bdd4ea66138f690c9df83e520d9572 -r d794e30fcd1ac28fa84c13d3f68c86c7de5df0d4 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -547,6 +547,10 @@ return trans.show_error_message( "<p>Failed to make secondary dataset primary.</p>" ) @web.expose + def welcome( self, trans ): + return trans.response.send_redirect( url_for( '/static/welcome.html' ) ) + + @web.expose def bucket_proxy( self, trans, bucket=None, **kwd): if bucket: trans.response.set_content_type( 'text/xml' ) diff -r 30e8f84914bdd4ea66138f690c9df83e520d9572 -r d794e30fcd1ac28fa84c13d3f68c86c7de5df0d4 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -52,7 +52,7 @@ def index(self, trans, tool_id=None, from_noframe=None, **kwd): # No tool id passed, redirect to main page if tool_id is None: - return trans.response.send_redirect( url_for( "/static/welcome.html" ) ) + return trans.response.send_redirect( url_for( controller="root", action="welcome" ) ) tool_version_select_field, tools, tool = self.__get_tool_components( tool_id, tool_version=None, get_loaded_tools_by_lineage=False, diff -r 30e8f84914bdd4ea66138f690c9df83e520d9572 -r d794e30fcd1ac28fa84c13d3f68c86c7de5df0d4 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -492,7 +492,7 @@ message = 'You are now logged in as %s.<br>You can <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \ ( user.email, redirect, url_for( '/' ) ) if trans.app.config.require_login: - message += ' <a target="_top" href="%s">Click here</a> to continue to the home page.' % web.url_for( '/static/welcome.html' ) + message += ' <a target="_top" href="%s">Click here</a> to continue to the home page.' % web.url_for( controller="root", action="welcome" ) success = True return ( message, status, user, success ) diff -r 30e8f84914bdd4ea66138f690c9df83e520d9572 -r d794e30fcd1ac28fa84c13d3f68c86c7de5df0d4 templates/webapps/galaxy/root/index.mako --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -149,7 +149,7 @@ elif m_c is not None: center_url = h.url_for( controller=m_c, action=m_a ) else: - center_url = h.url_for( '/static/welcome.html' ) + center_url = h.url_for( controller="root", action="welcome" ) %><div style="position: absolute; width: 100%; height: 100%"> https://bitbucket.org/galaxy/galaxy-central/commits/3636ba2f4439/ Changeset: 3636ba2f4439 User: jmchilton Date: 2013-06-08 00:35:36 Summary: Add config option 'welcome_url' to allow override of relative url to welcome file. Much like the tool filter request, the driving motivation here is allowing a single CloudMan packaged cloud image to host different Galaxys based on the supplied user data. More specifically, with this changset one can override the default welcome file to point to 'static/welcome_site1.html' when launching CloudMan by adding the option 'galaxy_universe_welcome_url: "/static/welcome_site1.html"' to the launch request's user data. Affected #: 2 files diff -r d794e30fcd1ac28fa84c13d3f68c86c7de5df0d4 -r 3636ba2f4439b7b61f25425698f8e0be9f0f6f07 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -166,6 +166,7 @@ self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) + self.welcome_url = kwargs.get( 'welcome_url', '/static/welcome.html' ) # Configuration for the message box directly below the masthead. self.message_box_visible = kwargs.get( 'message_box_visible', False ) self.message_box_content = kwargs.get( 'message_box_content', None ) diff -r d794e30fcd1ac28fa84c13d3f68c86c7de5df0d4 -r 3636ba2f4439b7b61f25425698f8e0be9f0f6f07 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -548,7 +548,8 @@ @web.expose def welcome( self, trans ): - return trans.response.send_redirect( url_for( '/static/welcome.html' ) ) + welcome_url = trans.app.config.welcome_url + return trans.response.send_redirect( url_for( welcome_url ) ) @web.expose def bucket_proxy( self, trans, bucket=None, **kwd): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 14 Jun '13

14 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/30e8f84914bd/ Changeset: 30e8f84914bd User: dannon Date: 2013-06-14 01:08:16 Summary: Fix toolshed migration 0017 to work with both postgres, postgresql dialect names Affected #: 1 file diff -r 827ff13a72914ed3ddacace717cc07af66af718e -r 30e8f84914bdd4ea66138f690c9df83e520d9572 lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py @@ -29,7 +29,7 @@ # Initialize. if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': default_false = "0" - elif migrate_engine.name == 'postgres': + elif migrate_engine.name in ['postgres', 'postgresql']: default_false = "false" # Create and initialize tools_functionally_correct, do_not_test, time_last_tested, and tool_test_errors columns in repository_metadata table. RepositoryMetadata_table = Table( "repository_metadata", metadata, autoload=True ) https://bitbucket.org/galaxy/galaxy-central/commits/68c705bf0325/ Changeset: 68c705bf0325 Branch: stable User: dannon Date: 2013-06-14 01:08:16 Summary: Fix toolshed migration 0017 to work with both postgres, postgresql dialect names Affected #: 1 file diff -r aea50b1c8d9178de429e58805ca6c12e7f0465ee -r 68c705bf0325a54d2424a7b8ed44232c57a3b506 lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py @@ -29,7 +29,7 @@ # Initialize. if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': default_false = "0" - elif migrate_engine.name == 'postgres': + elif migrate_engine.name in ['postgres', 'postgresql']: default_false = "false" # Create and initialize tools_functionally_correct, do_not_test, time_last_tested, and tool_test_errors columns in repository_metadata table. RepositoryMetadata_table = Table( "repository_metadata", metadata, autoload=True ) 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: Condor runner: Allow for per-destination ClassAd query params, don't delete the submit file if submission fails and cleanup_job != always.
by commits-noreply＠bitbucket.org 13 Jun '13

13 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/827ff13a7291/ Changeset: 827ff13a7291 User: natefoo Date: 2013-06-13 23:09:20 Summary: Condor runner: Allow for per-destination ClassAd query params, don't delete the submit file if submission fails and cleanup_job != always. Affected #: 2 files diff -r 6f9e73ec3e99d43f14e3d735ecfe7b66ea38472a -r 827ff13a72914ed3ddacace717cc07af66af718e job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -54,7 +54,15 @@ <param id="shell_hostname">foo.example.org</param><param id="Job_Execution_Time">24:00:00</param></destination> - <destination id="condor" runner="condor"/> + <destination id="condor" runner="condor"> +  + <param id="request_cpus">8</param> + </destination></destinations><tools><!-- Tools can be configured to use specific destinations or handlers, diff -r 6f9e73ec3e99d43f14e3d735ecfe7b66ea38472a -r 827ff13a72914ed3ddacace717cc07af66af718e lib/galaxy/jobs/runners/condor.py --- a/lib/galaxy/jobs/runners/condor.py +++ b/lib/galaxy/jobs/runners/condor.py @@ -32,6 +32,12 @@ %s """ +default_query_classad = dict( + universe = 'vanilla', + getenv = 'true', + notification = 'NEVER', +) + class CondorJobState( AsynchronousJobState ): def __init__( self, **kwargs ): """ @@ -71,6 +77,10 @@ # wrapper.get_id_tag() instead of job_id for compatibility with TaskWrappers. galaxy_id_tag = job_wrapper.get_id_tag() + # get destination params + query_params = default_query_classad.copy() + query_params.update( job_destination.params ) + # define job attributes cjs = CondorJobState( files_dir=self.app.config.cluster_files_directory, job_wrapper=job_wrapper ) cjs.user_log = os.path.join( self.app.config.cluster_files_directory, 'galaxy_%s.condor.log' % galaxy_id_tag ) @@ -78,13 +88,12 @@ submit_file = os.path.join( self.app.config.cluster_files_directory, 'galaxy_%s.condor.desc' % galaxy_id_tag ) executable = cjs.job_file submit_desc = [ ] - submit_desc.append( 'universe = vanilla' ) - submit_desc.append( 'getenv = true' ) + for k, v in query_params.items(): + submit_desc.append( '%s = %s' % ( k, v ) ) submit_desc.append( 'executable = ' + executable ) submit_desc.append( 'output = ' + cjs.output_file ) submit_desc.append( 'error = ' + cjs.error_file ) submit_desc.append( 'log = ' + cjs.user_log ) - submit_desc.append( 'notification = NEVER' ) submit_desc.append( 'queue' ) script = drm_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) @@ -138,15 +147,16 @@ # TODO Add extra except for OSError? s_out = str(e) - os.unlink( submit_file ) - if external_job_id is None: log.debug( "condor_submit failed for job %s: %s" % (job_wrapper.get_id_tag(), s_out) ) if self.app.config.cleanup_job == "always": + os.unlink( submit_file ) cjs.cleanup() job_wrapper.fail( "condor_submit failed", exception=True ) return + os.unlink( submit_file ) + log.info( "(%s) queued as %s" % ( galaxy_id_tag, external_job_id ) ) # store runner information for tracking if Galaxy restarts 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: 4 new changesets
by commits-noreply＠bitbucket.org 13 Jun '13

13 Jun '13

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/56b18b56417f/ Changeset: 56b18b56417f User: jmchilton Date: 2012-11-10 21:26:29 Summary: Refactor setting up valid extensions in DataToolParameter to eliminate code duplication, extra computation (multiple loading of same datatypes in unit tests for instance), and reduce code nesting. Affected #: 1 file diff -r 340438c62171578078323d39da398d5053b69d0a -r 56b18b56417f0c2613c79055b21170a3a92379ac lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1371,24 +1371,25 @@ # Add metadata validator if not string_as_bool( elem.get( 'no_validation', False ) ): self.validators.append( validation.MetadataValidator() ) + # Find datatypes_registry + if tool is None: + if trans: + # Must account for "Input Dataset" types, which while not a tool still need access to the real registry. + # A handle to the transaction (and thus app) will be given by the module. + datatypes_registry = trans.app.datatypes_registry + else: + #This occurs for things such as unit tests + import galaxy.datatypes.registry + datatypes_registry = galaxy.datatypes.registry.Registry() + datatypes_registry.load_datatypes() + else: + datatypes_registry = tool.app.datatypes_registry # Build tuple of classes for supported data formats formats = [] self.extensions = elem.get( 'format', 'data' ).split( "," ) for extension in self.extensions: extension = extension.strip() - if tool is None: - if trans: - # Must account for "Input Dataset" types, which while not a tool still need access to the real registry. - # A handle to the transaction (and thus app) will be given by the module. - formats.append( trans.app.datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) - else: - #This occurs for things such as unit tests - import galaxy.datatypes.registry - datatypes_registry = galaxy.datatypes.registry.Registry() - datatypes_registry.load_datatypes() - formats.append( datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) - else: - formats.append( tool.app.datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) + formats.append( datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) self.formats = tuple( formats ) self.multiple = string_as_bool( elem.get( 'multiple', False ) ) # TODO: Enhance dynamic options for DataToolParameters. Currently, https://bitbucket.org/galaxy/galaxy-central/commits/b999689a0130/ Changeset: b999689a0130 User: jmchilton Date: 2012-11-15 15:11:02 Summary: Centeralize logic for checking if a given galaxy datatype is any of the datatypes in a given iterator (tuple, list) (used when building up tool input options and evaluating tools, checking conversions, etc...). I think this is a solid (though slight) design improvement in its own right, but it will also ease the eventually merging of composite multifiles (https://bitbucket.org/galaxyp/galaxy-central-homogeneous-composite-datatypes) into galaxy-central or at least limit the divergence between galaxy-central and that fork long term. Affected #: 4 files diff -r 56b18b56417f0c2613c79055b21170a3a92379ac -r b999689a013025f2a009e313a3b6e6f65354e005 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -529,7 +529,13 @@ def has_resolution(self): return False - + def matches_any( self, target_datatypes ): + """ + Check if this datatype is of any of the target_datatypes or is + a subtype thereof. + """ + datatype_classes = tuple( [ datatype.__class__ for datatype in target_datatypes ] ) + return isinstance( self, datatype_classes ) def merge( split_files, output_file): """ diff -r 56b18b56417f0c2613c79055b21170a3a92379ac -r b999689a013025f2a009e313a3b6e6f65354e005 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -586,7 +586,7 @@ def find_conversion_destination_for_dataset_by_extensions( self, dataset, accepted_formats, converter_safe = True ): """Returns ( target_ext, existing converted dataset )""" for convert_ext in self.get_converters_by_datatype( dataset.ext ): - if isinstance( self.get_datatype_by_extension( convert_ext ), accepted_formats ): + if self.get_datatype_by_extension( convert_ext ).matches_any( accepted_formats ): converted_dataset = dataset.get_converted_files_by_type( convert_ext ) if converted_dataset: ret_data = converted_dataset diff -r 56b18b56417f0c2613c79055b21170a3a92379ac -r b999689a013025f2a009e313a3b6e6f65354e005 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -36,7 +36,7 @@ def process_dataset( data, formats = None ): if formats is None: formats = input.formats - if data and not isinstance( data.datatype, formats ): + if data and not data.datatype.matches_any( formats ): # Need to refresh in case this conversion just took place, i.e. input above in tool performed the same conversion trans.sa_session.refresh( data ) target_ext, converted_dataset = data.find_conversion_destination( formats ) @@ -66,7 +66,7 @@ conversions = [] for conversion_name, conversion_extensions, conversion_datatypes in input.conversions: new_data = process_dataset( input_datasets[ prefix + input.name + str( i + 1 ) ], conversion_datatypes ) - if not new_data or isinstance( new_data.datatype, conversion_datatypes ): + if not new_data or new_data.datatype.matches_any( conversion_datatypes ): input_datasets[ prefix + conversion_name + str( i + 1 ) ] = new_data conversions.append( ( conversion_name, new_data ) ) else: @@ -86,7 +86,7 @@ conversions = [] for conversion_name, conversion_extensions, conversion_datatypes in input.conversions: new_data = process_dataset( input_datasets[ prefix + input.name ], conversion_datatypes ) - if not new_data or isinstance( new_data.datatype, conversion_datatypes ): + if not new_data or new_data.datatype.matches_any( conversion_datatypes ): input_datasets[ prefix + conversion_name ] = new_data conversions.append( ( conversion_name, new_data ) ) else: @@ -261,7 +261,9 @@ ext = input_ext if output.format_source is not None and output.format_source in inp_data: try: - ext = inp_data[output.format_source].ext + input_dataset = inp_data[output.format_source] + input_extension = input_dataset.ext + ext = input_extension except Exception, e: pass diff -r 56b18b56417f0c2613c79055b21170a3a92379ac -r b999689a013025f2a009e313a3b6e6f65354e005 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -785,7 +785,7 @@ if isinstance( dep_value, RuntimeValue ): return True #dataset not ready yet - if hasattr( self, 'ref_input' ) and isinstance( dep_value, self.tool.app.model.HistoryDatasetAssociation ) and ( dep_value.is_pending or not isinstance( dep_value.datatype, self.ref_input.formats ) ): + if hasattr( self, 'ref_input' ) and isinstance( dep_value, self.tool.app.model.HistoryDatasetAssociation ) and ( dep_value.is_pending or not dep_value.datatype.matches_any( self.ref_input.formats ) ): return True # Dynamic, but all dependenceis are known and have values return False @@ -1037,7 +1037,7 @@ if not dataset.metadata.columns: # Only allow late validation if the dataset is not yet ready # (since we have reason to expect the metadata to be ready eventually) - if dataset.is_pending or not isinstance( dataset.datatype, self.ref_input.formats ): + if dataset.is_pending or not dataset.datatype.matches_any( self.ref_input.formats ): return True # No late validation return False @@ -1389,8 +1389,8 @@ self.extensions = elem.get( 'format', 'data' ).split( "," ) for extension in self.extensions: extension = extension.strip() - formats.append( datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) - self.formats = tuple( formats ) + formats.append( datatypes_registry.get_datatype_by_extension( extension.lower() ) ) + self.formats = formats self.multiple = string_as_bool( elem.get( 'multiple', False ) ) # TODO: Enhance dynamic options for DataToolParameters. Currently, # only the special case key='build' of type='data_meta' is @@ -1414,7 +1414,7 @@ conv_extensions = conv_elem.get( "type" ) #target datatype extension # FIXME: conv_extensions should be able to be an ordered list assert None not in [ name, type ], 'A name (%s) and type (%s) are required for explicit conversion' % ( name, type ) - conv_types = tool.app.datatypes_registry.get_datatype_by_extension( conv_extensions.lower() ).__class__ + conv_types = tool.app.datatypes_registry.get_datatype_by_extension( conv_extensions.lower() ) self.conversions.append( ( name, conv_extensions, conv_types ) ) def get_html_field( self, trans=None, value=None, other_values={} ): @@ -1452,7 +1452,7 @@ continue if self.options and self._options_filter_attribute( hda ) != filter_value: continue - if isinstance( hda.datatype, self.formats): + if hda.datatype.matches_any( self.formats ): selected = ( value and ( hda in value ) ) if hda.visible: hidden_text = "" @@ -1519,7 +1519,7 @@ for i, data in enumerate( datasets ): if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED]: is_valid = False - if isinstance( data.datatype, self.formats ): + if data.datatype.matches_any( self.formats ): is_valid = True else: target_ext, converted_dataset = data.find_conversion_destination( self.formats ) https://bitbucket.org/galaxy/galaxy-central/commits/c011bbda72b3/ Changeset: c011bbda72b3 User: jmchilton Date: 2012-11-15 15:23:15 Summary: Small refactoring of logic used to build up list of valid formats for an input data parameter. Affected #: 1 file diff -r b999689a013025f2a009e313a3b6e6f65354e005 -r c011bbda72b3e3fd974a759a53e4baef7b6121a2 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1387,9 +1387,9 @@ # Build tuple of classes for supported data formats formats = [] self.extensions = elem.get( 'format', 'data' ).split( "," ) - for extension in self.extensions: - extension = extension.strip() - formats.append( datatypes_registry.get_datatype_by_extension( extension.lower() ) ) + normalized_extensions = [extension.strip().lower() for extension in self.extensions] + for extension in normalized_extensions: + formats.append( datatypes_registry.get_datatype_by_extension( extension ) ) self.formats = formats self.multiple = string_as_bool( elem.get( 'multiple', False ) ) # TODO: Enhance dynamic options for DataToolParameters. Currently, https://bitbucket.org/galaxy/galaxy-central/commits/ada2dca97078/ Changeset: ada2dca97078 User: jmchilton Date: 2012-12-04 06:04:36 Summary: Leave process_dataset immediately if input data is `None` in collect_input_datasets of DefaultToolAction, simplifies code and eliminates some unneeded computation. Affected #: 1 file diff -r c011bbda72b3e3fd974a759a53e4baef7b6121a2 -r ada2dca97078b552d12b28e7da65d9667e28b125 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -34,9 +34,11 @@ input_datasets = dict() def visitor( prefix, input, value, parent = None ): def process_dataset( data, formats = None ): + if not data: + return data if formats is None: formats = input.formats - if data and not data.datatype.matches_any( formats ): + if not data.datatype.matches_any( formats ): # Need to refresh in case this conversion just took place, i.e. input above in tool performed the same conversion trans.sa_session.refresh( data ) target_ext, converted_dataset = data.find_conversion_destination( formats ) @@ -54,7 +56,7 @@ trans.sa_session.flush() data = new_data current_user_roles = trans.get_current_user_roles() - if data and not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): + if not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): raise "User does not have permission to use a dataset (%s) provided for input." % data.id return data if isinstance( input, DataToolParameter ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits June 2013