galaxy-commits June 2014

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 29 Jun '14

29 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c4519bae84d3/ Changeset: c4519bae84d3 Branch: stable User: guerler Date: 2014-06-30 02:04:28 Summary: Fix popovers Affected #: 2 files diff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 -r c4519bae84d32d638d8fe168c6fbcab40f4e8449 static/scripts/mvc/ui/ui-popover.js --- a/static/scripts/mvc/ui/ui-popover.js +++ b/static/scripts/mvc/ui/ui-popover.js @@ -140,7 +140,7 @@ // template _template: function(options) { - var tmpl = '<div class="popover-view popover fade ' + options.placement + ' in">' + + var tmpl = '<div class="ui-popover popover fade ' + options.placement + ' in">' + '<div class="arrow"></div>' + '<div class="popover-title">' + '<div class="popover-title-label">' + diff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 -r c4519bae84d32d638d8fe168c6fbcab40f4e8449 static/scripts/packed/mvc/ui/ui-popover.js --- a/static/scripts/packed/mvc/ui/ui-popover.js +++ b/static/scripts/packed/mvc/ui/ui-popover.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{with_close:true,container:"body",title:null,placement:"top"},visible:false,initialize:function(d){var c=this;this.options=_.defaults(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.parent().append(this.$el);if(this.options.with_close){this.$el.find("#close").on("click",function(){c.hide()})}this.uuid=a.uuid();var c=this;$("body").on("mousedown."+this.uuid,function(f){c._hide(f)})},title:function(c){if(c!==undefined){this.$el.find(".popover-title-label").html(c)}},show:function(){this.$el.show();this.visible=true;var c=this._get_placement(this.options.placement);this.$el.css(c)},_get_placement:function(h){var d=this._get_width(this.$el);var j=this.$el.height();var k=this.options.container;var c=this._get_width(k);var f=this._get_height(k);var g=k.position();var i=0;var e=0;if(h=="top"||h=="bottom"){e=g.left-d+(c+d)/2;if(h=="top"){i=g.top-j-5}else{i=g.top+f+5}}return{top:i,left:e}},_get_width:function(c){return c.width()+parseInt(c.css("padding-left"))+parseInt(c.css("padding-right"))},_get_height:function(c){return c.height()+parseInt(c.css("padding-top"))+parseInt(c.css("padding-bottom"))},hide:function(){this.$el.hide();this.visible=false},append:function(c){this.$el.find(".popover-content").append(c)},empty:function(c){this.$el.find(".popover-content").empty()},remove:function(){$("body").off("mousedown."+this.uuid);this.$el.remove()},_hide:function(c){if(!$(this.options.container).is(c.target)&&!$(this.el).is(c.target)&&$(this.el).has(c.target).length===0){this.hide()}},_template:function(d){var c='<div class="popover-view popover fade '+d.placement+' in"><div class="arrow"></div><div class="popover-title"><div class="popover-title-label">'+d.title+"</div>";if(d.with_close){c+='<div id="close" class="popover-close fa fa-times-circle"></div>'}c+='</div><div class="popover-content"></div></div>';return c}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{with_close:true,container:"body",title:null,placement:"top"},visible:false,initialize:function(d){var c=this;this.options=_.defaults(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.parent().append(this.$el);if(this.options.with_close){this.$el.find("#close").on("click",function(){c.hide()})}this.uuid=a.uuid();var c=this;$("body").on("mousedown."+this.uuid,function(f){c._hide(f)})},title:function(c){if(c!==undefined){this.$el.find(".popover-title-label").html(c)}},show:function(){this.$el.show();this.visible=true;var c=this._get_placement(this.options.placement);this.$el.css(c)},_get_placement:function(h){var d=this._get_width(this.$el);var j=this.$el.height();var k=this.options.container;var c=this._get_width(k);var f=this._get_height(k);var g=k.position();var i=0;var e=0;if(h=="top"||h=="bottom"){e=g.left-d+(c+d)/2;if(h=="top"){i=g.top-j-5}else{i=g.top+f+5}}return{top:i,left:e}},_get_width:function(c){return c.width()+parseInt(c.css("padding-left"))+parseInt(c.css("padding-right"))},_get_height:function(c){return c.height()+parseInt(c.css("padding-top"))+parseInt(c.css("padding-bottom"))},hide:function(){this.$el.hide();this.visible=false},append:function(c){this.$el.find(".popover-content").append(c)},empty:function(c){this.$el.find(".popover-content").empty()},remove:function(){$("body").off("mousedown."+this.uuid);this.$el.remove()},_hide:function(c){if(!$(this.options.container).is(c.target)&&!$(this.el).is(c.target)&&$(this.el).has(c.target).length===0){this.hide()}},_template:function(d){var c='<div class="ui-popover popover fade '+d.placement+' in"><div class="arrow"></div><div class="popover-title"><div class="popover-title-label">'+d.title+"</div>";if(d.with_close){c+='<div id="close" class="popover-close fa fa-times-circle"></div>'}c+='</div><div class="popover-content"></div></div>';return c}});return{View:b}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/2e1de0fc5a3c/ Changeset: 2e1de0fc5a3c User: guerler Date: 2014-06-30 02:05:17 Summary: Merge Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Merged in daniel_blanchard/galaxy-central/daniel_blanchard/update-drmaa-python-version-in-eggsini-t-1402925026891 (pull request #421)
by commits-noreply＠bitbucket.org 29 Jun '14

29 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dd77a9684c7b/ Changeset: dd77a9684c7b User: natefoo Date: 2014-06-29 22:03:46 Summary: Merged in daniel_blanchard/galaxy-central/daniel_blanchard/update-drmaa-python-version-in-eggsini-t-1402925026891 (pull request #421) Update DRMAA Python version in eggs.ini to 0.7.6. Affected #: 1 file diff -r 4de240e5a7819c768b8267c19e477530dab54370 -r dd77a9684c7b7430db1275c2e9bf30ab743cdc9f eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -38,7 +38,7 @@ boto = 2.27.0 decorator = 3.1.2 docutils = 0.7 -drmaa = 0.6 +drmaa = 0.7.6 elementtree = 1.2.6_20050316 Fabric = 1.7.0 GeneTrack = 2.0.0_beta_1 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 29 Jun '14

29 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6487537fba23/ Changeset: 6487537fba23 Branch: daniel_blanchard/update-drmaa-python-version-in-eggsini-t-1402925026891 User: daniel_blanchard Date: 2014-06-16 15:27:38 Summary: Update DRMAA Python version in eggs.ini to 0.7.6. This version has better string handling and supports Python 3. Affected #: 1 file diff -r d3a0b4b9da32927b5aab806f1a991594285475f7 -r 6487537fba23263b041b46ec6268c7c9cd3a8aa9 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -38,7 +38,7 @@ boto = 2.27.0 decorator = 3.1.2 docutils = 0.7 -drmaa = 0.6 +drmaa = 0.7.6 elementtree = 1.2.6_20050316 Fabric = 1.7.0 GeneTrack = 2.0.0_beta_1 https://bitbucket.org/galaxy/galaxy-central/commits/dd77a9684c7b/ Changeset: dd77a9684c7b User: natefoo Date: 2014-06-29 22:03:46 Summary: Merged in daniel_blanchard/galaxy-central/daniel_blanchard/update-drmaa-python-version-in-eggsini-t-1402925026891 (pull request #421) Update DRMAA Python version in eggs.ini to 0.7.6. Affected #: 1 file diff -r 4de240e5a7819c768b8267c19e477530dab54370 -r dd77a9684c7b7430db1275c2e9bf30ab743cdc9f eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -38,7 +38,7 @@ boto = 2.27.0 decorator = 3.1.2 docutils = 0.7 -drmaa = 0.6 +drmaa = 0.7.6 elementtree = 1.2.6_20050316 Fabric = 1.7.0 GeneTrack = 2.0.0_beta_1 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 29 Jun '14

29 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7094bb55cc8a/ Changeset: 7094bb55cc8a User: jmchilton Date: 2014-06-29 20:31:33 Summary: Spelling fix in method name. Affected #: 2 files diff -r 381a36069c14bf20c98955c01ab00e7838257943 -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2931,7 +2931,7 @@ Find any additional datasets generated by a tool and attach (for cases where number of outputs is not known in advance). """ - return output_collect.collect_primary_datatasets( self, output, job_working_directory ) + return output_collect.collect_primary_datasets( self, output, job_working_directory ) def to_dict( self, trans, link_details=False, io_details=False ): """ Returns dict of tool. """ diff -r 381a36069c14bf20c98955c01ab00e7838257943 -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c lib/galaxy/tools/parameters/output_collect.py --- a/lib/galaxy/tools/parameters/output_collect.py +++ b/lib/galaxy/tools/parameters/output_collect.py @@ -14,7 +14,7 @@ DEFAULT_EXTRA_FILENAME_PATTERN = r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?" -def collect_primary_datatasets( tool, output, job_working_directory ): +def collect_primary_datasets( tool, output, job_working_directory ): app = tool.app sa_session = tool.sa_session new_primary_datasets = {} https://bitbucket.org/galaxy/galaxy-central/commits/4de240e5a781/ Changeset: 4de240e5a781 User: jmchilton Date: 2014-06-29 20:31:33 Summary: Allow discovered datasets to use input data format in 'ext' definition. Affected #: 4 files diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r 4de240e5a7819c768b8267c19e477530dab54370 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1181,6 +1181,13 @@ out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] ) + input_ext = 'data' + for _, data in inp_data.items(): + # For loop odd, but sort simulating behavior in galaxy.tools.actions + if not data: + continue + input_ext = data.ext + param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] ) # why not re-use self.param_dict here? ##dunno...probably should, this causes tools.parameters.basic.UnvalidatedValue to be used in following methods instead of validated and transformed values during i.e. running workflows param_dict = self.tool.params_from_strings( param_dict, self.app ) # Check for and move associated_files @@ -1191,7 +1198,7 @@ # Create generated output children and primary datasets and add to param_dict collected_datasets = { 'children': self.tool.collect_child_datasets(out_data, self.working_directory), - 'primary': self.tool.collect_primary_datasets(out_data, self.working_directory) + 'primary': self.tool.collect_primary_datasets(out_data, self.working_directory, input_ext) } param_dict.update({'__collected_datasets__': collected_datasets}) # Certain tools require tasks to be completed after job execution diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r 4de240e5a7819c768b8267c19e477530dab54370 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2926,12 +2926,12 @@ self.sa_session.flush() return children - def collect_primary_datasets( self, output, job_working_directory ): + def collect_primary_datasets( self, output, job_working_directory, input_ext ): """ Find any additional datasets generated by a tool and attach (for cases where number of outputs is not known in advance). """ - return output_collect.collect_primary_datasets( self, output, job_working_directory ) + return output_collect.collect_primary_datasets( self, output, job_working_directory, input_ext ) def to_dict( self, trans, link_details=False, io_details=False ): """ Returns dict of tool. """ diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r 4de240e5a7819c768b8267c19e477530dab54370 lib/galaxy/tools/parameters/output_collect.py --- a/lib/galaxy/tools/parameters/output_collect.py +++ b/lib/galaxy/tools/parameters/output_collect.py @@ -14,7 +14,7 @@ DEFAULT_EXTRA_FILENAME_PATTERN = r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?" -def collect_primary_datasets( tool, output, job_working_directory ): +def collect_primary_datasets( tool, output, job_working_directory, input_ext ): app = tool.app sa_session = tool.sa_session new_primary_datasets = {} @@ -66,6 +66,8 @@ designation = fields_match.designation visible = fields_match.visible ext = fields_match.ext + if ext == "input": + ext = input_ext dbkey = fields_match.dbkey # Create new primary dataset primary_data = app.model.HistoryDatasetAssociation( extension=ext, diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r 4de240e5a7819c768b8267c19e477530dab54370 test/functional/tools/multi_output_configured.xml --- a/test/functional/tools/multi_output_configured.xml +++ b/test/functional/tools/multi_output_configured.xml @@ -8,19 +8,24 @@ echo "1" > subdir2/CUSTOM_1.txt; echo "2" > subdir2/CUSTOM_2.tabular; echo "3" > subdir2/CUSTOM_3.txt; + mkdir subdir3; + echo "Foo" > subdir3/Foo; </command><inputs> - <param name="input" type="integer" value="7" /> + <param name="num_param" type="integer" value="7" /> + <param name="input" type="data" /></inputs><outputs><data format="txt" name="report"><discover_datasets pattern="__designation_and_ext__" directory="subdir1" /><discover_datasets pattern="CUSTOM_(?P<designation>.+)\.(?P<ext>.+)" directory="subdir2" /> + <discover_datasets pattern="__designation__" directory="subdir3" ext="input" /></data></outputs><tests><test> - <param name="input" value="7" /> + <param name="num_param" value="7" /> + <param name="input" ftype="txt" value="simple_line.txt"/><output name="report"><assert_contents><has_line line="Hello" /> @@ -37,6 +42,9 @@ <discovered_dataset designation="2" ftype="tabular"><assert_contents><has_line line="2" /></assert_contents></discovered_dataset> + <discovered_dataset designation="Foo" ftype="txt"> + <assert_contents><has_line line="Foo" /></assert_contents> + </discovered_dataset></output></test></tests> 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 29 Jun '14

29 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/21b53ebad211/ Changeset: 21b53ebad211 Branch: stable User: jmchilton Date: 2014-06-29 20:24:32 Summary: Spelling fix in method name. Affected #: 2 files diff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 -r 21b53ebad2119dd9968c72f67b53d069ebc17902 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2874,7 +2874,7 @@ Find any additional datasets generated by a tool and attach (for cases where number of outputs is not known in advance). """ - return output_collect.collect_primary_datatasets( self, output, job_working_directory ) + return output_collect.collect_primary_datasets( self, output, job_working_directory ) def to_dict( self, trans, link_details=False, io_details=False ): """ Returns dict of tool. """ diff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 -r 21b53ebad2119dd9968c72f67b53d069ebc17902 lib/galaxy/tools/parameters/output_collect.py --- a/lib/galaxy/tools/parameters/output_collect.py +++ b/lib/galaxy/tools/parameters/output_collect.py @@ -14,7 +14,7 @@ DEFAULT_EXTRA_FILENAME_PATTERN = r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?" -def collect_primary_datatasets( tool, output, job_working_directory ): +def collect_primary_datasets( tool, output, job_working_directory ): app = tool.app sa_session = tool.sa_session new_primary_datasets = {} https://bitbucket.org/galaxy/galaxy-central/commits/c14bdcb9ae96/ Changeset: c14bdcb9ae96 Branch: stable User: jmchilton Date: 2014-06-29 20:24:32 Summary: Allow discovered datasets to use input data format in 'ext' definition. Affected #: 4 files diff -r 21b53ebad2119dd9968c72f67b53d069ebc17902 -r c14bdcb9ae9643525c0797090f293030ea899948 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1065,6 +1065,13 @@ out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] ) + input_ext = 'data' + for _, data in inp_data.items(): + # For loop odd, but sort simulating behavior in galaxy.tools.actions + if not data: + continue + input_ext = data.ext + param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] ) # why not re-use self.param_dict here? ##dunno...probably should, this causes tools.parameters.basic.UnvalidatedValue to be used in following methods instead of validated and transformed values during i.e. running workflows param_dict = self.tool.params_from_strings( param_dict, self.app ) # Check for and move associated_files @@ -1075,7 +1082,7 @@ # Create generated output children and primary datasets and add to param_dict collected_datasets = { 'children': self.tool.collect_child_datasets(out_data, self.working_directory), - 'primary': self.tool.collect_primary_datasets(out_data, self.working_directory) + 'primary': self.tool.collect_primary_datasets(out_data, self.working_directory, input_ext) } param_dict.update({'__collected_datasets__': collected_datasets}) # Certain tools require tasks to be completed after job execution diff -r 21b53ebad2119dd9968c72f67b53d069ebc17902 -r c14bdcb9ae9643525c0797090f293030ea899948 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2869,12 +2869,12 @@ self.sa_session.flush() return children - def collect_primary_datasets( self, output, job_working_directory ): + def collect_primary_datasets( self, output, job_working_directory, input_ext ): """ Find any additional datasets generated by a tool and attach (for cases where number of outputs is not known in advance). """ - return output_collect.collect_primary_datasets( self, output, job_working_directory ) + return output_collect.collect_primary_datasets( self, output, job_working_directory, input_ext ) def to_dict( self, trans, link_details=False, io_details=False ): """ Returns dict of tool. """ diff -r 21b53ebad2119dd9968c72f67b53d069ebc17902 -r c14bdcb9ae9643525c0797090f293030ea899948 lib/galaxy/tools/parameters/output_collect.py --- a/lib/galaxy/tools/parameters/output_collect.py +++ b/lib/galaxy/tools/parameters/output_collect.py @@ -14,7 +14,7 @@ DEFAULT_EXTRA_FILENAME_PATTERN = r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?" -def collect_primary_datasets( tool, output, job_working_directory ): +def collect_primary_datasets( tool, output, job_working_directory, input_ext ): app = tool.app sa_session = tool.sa_session new_primary_datasets = {} @@ -66,6 +66,8 @@ designation = fields_match.designation visible = fields_match.visible ext = fields_match.ext + if ext == "input": + ext = input_ext dbkey = fields_match.dbkey # Create new primary dataset primary_data = app.model.HistoryDatasetAssociation( extension=ext, diff -r 21b53ebad2119dd9968c72f67b53d069ebc17902 -r c14bdcb9ae9643525c0797090f293030ea899948 test/functional/tools/multi_output_configured.xml --- a/test/functional/tools/multi_output_configured.xml +++ b/test/functional/tools/multi_output_configured.xml @@ -8,19 +8,24 @@ echo "1" > subdir2/CUSTOM_1.txt; echo "2" > subdir2/CUSTOM_2.tabular; echo "3" > subdir2/CUSTOM_3.txt; + mkdir subdir3; + echo "Foo" > subdir3/Foo; </command><inputs> - <param name="input" type="integer" value="7" /> + <param name="num_param" type="integer" value="7" /> + <param name="input" type="data" /></inputs><outputs><data format="txt" name="report"><discover_datasets pattern="__designation_and_ext__" directory="subdir1" /><discover_datasets pattern="CUSTOM_(?P<designation>.+)\.(?P<ext>.+)" directory="subdir2" /> + <discover_datasets pattern="__designation__" directory="subdir3" ext="input" /></data></outputs><tests><test> - <param name="input" value="7" /> + <param name="num_param" value="7" /> + <param name="input" ftype="txt" value="simple_line.txt"/><output name="report"><assert_contents><has_line line="Hello" /> @@ -37,6 +42,9 @@ <discovered_dataset designation="2" ftype="tabular"><assert_contents><has_line line="2" /></assert_contents></discovered_dataset> + <discovered_dataset designation="Foo" ftype="txt"> + <assert_contents><has_line line="Foo" /></assert_contents> + </discovered_dataset></output></test></tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: davebgx: Close branch BjoernGruening/fix-some-spelling-mistake-and-hopefully--1404051898740
by commits-noreply＠bitbucket.org 29 Jun '14

29 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3b716a7ca813/ Changeset: 3b716a7ca813 Branch: BjoernGruening/fix-some-spelling-mistake-and-hopefully--1404051898740 User: davebgx Date: 2014-06-29 16:31:27 Summary: Close branch BjoernGruening/fix-some-spelling-mistake-and-hopefully--1404051898740 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: davebgx: Merged in BjoernGruening/galaxy-central-2/BjoernGruening/fix-some-spelling-mistake-and-hopefully--1404051898740 (pull request #430)
by commits-noreply＠bitbucket.org 29 Jun '14

29 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/381a36069c14/ Changeset: 381a36069c14 User: davebgx Date: 2014-06-29 16:30:21 Summary: Merged in BjoernGruening/galaxy-central-2/BjoernGruening/fix-some-spelling-mistake-and-hopefully--1404051898740 (pull request #430) Fix some spelling mistake and hopefully all of the install_*_environments. Affected #: 1 file diff -r 7b02c61a6c21d0ffe8b7160ba51a27ab1bbf2b01 -r 381a36069c14bf20c98955c01ab00e7838257943 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 @@ -44,8 +44,8 @@ def __init__( self, app ): self.app = app - self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environmnet', - 'setup_r_environmnet', 'setup_ruby_environmnet', 'shell_command' ] + self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environment', + 'setup_r_environment', 'setup_ruby_environment', 'shell_command' ] def format_traceback( self ): ex_type, ex, tb = sys.exc_info() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 29 Jun '14

29 Jun '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5606d3b0cbc7/ Changeset: 5606d3b0cbc7 Branch: BjoernGruening/fix-some-spelling-mistake-and-hopefully--1404051898740 User: BjoernGruening Date: 2014-06-29 16:25:44 Summary: Fix some spelling mistake and hopefully all of the install_*_environments. Affected #: 1 file diff -r 7b02c61a6c21d0ffe8b7160ba51a27ab1bbf2b01 -r 5606d3b0cbc768cff6581a5fd79d561a81d0dc36 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 @@ -44,8 +44,8 @@ def __init__( self, app ): self.app = app - self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environmnet', - 'setup_r_environmnet', 'setup_ruby_environmnet', 'shell_command' ] + self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environment', + 'setup_r_environment', 'setup_ruby_environent', 'shell_command' ] def format_traceback( self ): ex_type, ex, tb = sys.exc_info() https://bitbucket.org/galaxy/galaxy-central/commits/a78c3f818c01/ Changeset: a78c3f818c01 Branch: BjoernGruening/fix-some-spelling-mistake-and-hopefully--1404051898740 User: BjoernGruening Date: 2014-06-29 16:28:13 Summary: Fix some spelling mistake and hopefully all of the install_*_environments. Affected #: 1 file diff -r 5606d3b0cbc768cff6581a5fd79d561a81d0dc36 -r a78c3f818c01fbc9bd217c599052f9e6486c1fcf 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 @@ -45,7 +45,7 @@ def __init__( self, app ): self.app = app self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environment', - 'setup_r_environment', 'setup_ruby_environent', 'shell_command' ] + 'setup_r_environment', 'setup_ruby_environment', 'shell_command' ] def format_traceback( self ): ex_type, ex, tb = sys.exc_info() https://bitbucket.org/galaxy/galaxy-central/commits/381a36069c14/ Changeset: 381a36069c14 User: davebgx Date: 2014-06-29 16:30:21 Summary: Merged in BjoernGruening/galaxy-central-2/BjoernGruening/fix-some-spelling-mistake-and-hopefully--1404051898740 (pull request #430) Fix some spelling mistake and hopefully all of the install_*_environments. Affected #: 1 file diff -r 7b02c61a6c21d0ffe8b7160ba51a27ab1bbf2b01 -r 381a36069c14bf20c98955c01ab00e7838257943 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 @@ -44,8 +44,8 @@ def __init__( self, app ): self.app = app - self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environmnet', - 'setup_r_environmnet', 'setup_ruby_environmnet', 'shell_command' ] + self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environment', + 'setup_r_environment', 'setup_ruby_environment', 'shell_command' ] def format_traceback( self ): ex_type, ex, tb = sys.exc_info() 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: hackdna: Enable stopping jobs when history is deleted via the API.
by commits-noreply＠bitbucket.org 28 Jun '14

28 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7b02c61a6c21/ Changeset: 7b02c61a6c21 User: hackdna Date: 2014-06-28 23:57:06 Summary: Enable stopping jobs when history is deleted via the API. Affected #: 1 file diff -r 2577b386dbbe421e80c816abf7683359ab64fe1f -r 7b02c61a6c21d0ffe8b7160ba51a27ab1bbf2b01 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -235,6 +235,10 @@ for hda in history.datasets: if hda.purged: continue + if hda.creating_job_associations: + job = hda.creating_job_associations[0].job + job.mark_deleted( self.app.config.track_jobs_in_database ) + self.app.job_manager.job_stop_queue.put( job.id ) hda.purged = True trans.sa_session.add( hda ) trans.sa_session.flush() 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: dan: Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.
by commits-noreply＠bitbucket.org 27 Jun '14

27 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/65e5e5b72893/ Changeset: 65e5e5b72893 Branch: stable User: dan Date: 2014-06-27 20:44:55 Summary: Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0. Affected #: 9 files diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -7,7 +7,12 @@ <tool file="data_source/ebi_sra.xml" /><tool file="data_source/biomart.xml" /><tool file="data_source/gramene_mart.xml" /> + <tool file="data_source/flymine.xml" /><tool file="data_source/fly_modencode.xml" /> + <tool file="data_source/modmine.xml" /> + <tool file="data_source/mousemine.xml" /> + <tool file="data_source/ratmine.xml" /> + <tool file="data_source/yeastmine.xml" /><tool file="data_source/worm_modencode.xml" /><tool file="data_source/wormbase.xml" /><tool file="data_source/eupathdb.xml" /> diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -12,6 +12,13 @@ <tool file="data_source/cbi_rice_mart.xml" /><tool file="data_source/gramene_mart.xml" /><tool file="data_source/fly_modencode.xml" /> + <tool file="data_source/flymine.xml" /> + <tool file="data_source/flymine_test.xml" /> + <tool file="data_source/modmine.xml" /> + <tool file="data_source/mousemine.xml" /> + <tool file="data_source/ratmine.xml" /> + <tool file="data_source/yeastmine.xml" /> + <tool file="data_source/metabolicmine.xml" /><tool file="data_source/worm_modencode.xml" /><tool file="data_source/wormbase.xml" /><tool file="data_source/wormbase_test.xml" /> diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tools/data_source/flymine.xml --- /dev/null +++ b/tools/data_source/flymine.xml @@ -0,0 +1,35 @@ +<?xml version="1.0"?> + +<tool name="Flymine" id="flymine" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://www.flymine.org" check_values="false" method="get"> + <display>go to Flymine server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> + <request_param galaxy_name="URL" remote_name="URL" missing="" /> + <request_param galaxy_name="dbkey" remote_name="db" missing="?" /> + <request_param galaxy_name="organism" remote_name="organism" missing="" /> + <request_param galaxy_name="table" remote_name="table" missing="" /> + <request_param galaxy_name="description" remote_name="description" missing="" /> + <request_param galaxy_name="name" remote_name="name" missing="FlyMine query" /> + <request_param galaxy_name="info" remote_name="info" missing="" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" > + <value_translation> + <value galaxy_value="auto" remote_value="txt" /> + </value_translation> + </request_param> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> + diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tools/data_source/flymine_test.xml --- /dev/null +++ b/tools/data_source/flymine_test.xml @@ -0,0 +1,31 @@ +<?xml version="1.0"?> + +<tool name="Flymine test" id="flymine_test" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://preview.flymine.org/preview/begin.do" check_values="false" method="get"> + <display>go to Flymine server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> + <request_param galaxy_name="URL" remote_name="URL" missing="" /> + <request_param galaxy_name="dbkey" remote_name="db" missing="?" /> + <request_param galaxy_name="organism" remote_name="organism" missing="" /> + <request_param galaxy_name="table" remote_name="table" missing="" /> + <request_param galaxy_name="description" remote_name="description" missing="" /> + <request_param galaxy_name="name" remote_name="name" missing="FlyMine query" /> + <request_param galaxy_name="info" remote_name="info" missing="" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" /> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> + diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tools/data_source/metabolicmine.xml --- /dev/null +++ b/tools/data_source/metabolicmine.xml @@ -0,0 +1,13 @@ +<?xml version="1.0"?> +<tool name="metabolicMine" id="metabolicmine" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://www.metabolicmine.org/beta/begin.do" check_values="false" method="get"> + <display>go to metabolicMine server $GALAXY_URL</display> + </inputs> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tools/data_source/modmine.xml --- /dev/null +++ b/tools/data_source/modmine.xml @@ -0,0 +1,19 @@ +<?xml version="1.0"?> + +<tool name="modENCODE modMine" id="modmine" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://intermine.modencode.org/" check_values="false" method="get"> + <display>go to modENCODE modMine server $GALAXY_URL</display> + </inputs> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> + diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tools/data_source/mousemine.xml --- /dev/null +++ b/tools/data_source/mousemine.xml @@ -0,0 +1,35 @@ +<?xml version="1.0"?> + +<tool name="MouseMine" id="mousemine" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://www.mousemine.org/mousemine/begin.do" check_values="false" method="get"> + <display>go to MouseMine server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=mousemine" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> + <request_param galaxy_name="URL" remote_name="URL" missing="" /> + <request_param galaxy_name="dbkey" remote_name="db" missing="?" /> + <request_param galaxy_name="organism" remote_name="organism" missing="" /> + <request_param galaxy_name="table" remote_name="table" missing="" /> + <request_param galaxy_name="description" remote_name="description" missing="" /> + <request_param galaxy_name="name" remote_name="name" missing="MouseMine query" /> + <request_param galaxy_name="info" remote_name="info" missing="" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" > + <value_translation> + <value galaxy_value="auto" remote_value="txt" /> + </value_translation> + </request_param> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> + diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tools/data_source/ratmine.xml --- /dev/null +++ b/tools/data_source/ratmine.xml @@ -0,0 +1,34 @@ +<?xml version="1.0"?> + +<tool name="Ratmine" id="ratmine" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://ratmine.mcw.edu/ratmine/begin.do" check_values="false" method="get"> + <display>go to Ratmine server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=ratmine" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> + <request_param galaxy_name="URL" remote_name="URL" missing="" /> + <request_param galaxy_name="dbkey" remote_name="db" missing="?" /> + <request_param galaxy_name="organism" remote_name="organism" missing="" /> + <request_param galaxy_name="table" remote_name="table" missing="" /> + <request_param galaxy_name="description" remote_name="description" missing="" /> + <request_param galaxy_name="name" remote_name="name" missing="Ratmine query" /> + <request_param galaxy_name="info" remote_name="info" missing="" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" > + <value_translation> + <value galaxy_value="auto" remote_value="txt" /> + </value_translation> + </request_param> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tools/data_source/yeastmine.xml --- /dev/null +++ b/tools/data_source/yeastmine.xml @@ -0,0 +1,20 @@ +<?xml version="1.0"?> +<tool name="YeastMine" id="yeastmine" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://yeastmine.yeastgenome.org/yeastmine/begin.do" check_values="false" method="get"> + <display>go to yeastMine server $GALAXY_URL</display> + </inputs> + <request_param_translation> + <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" > + <value_translation> + <value galaxy_value="auto" remote_value="txt" /> + </value_translation> + </request_param> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits June 2014