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commit/galaxy-central: jgoecks: Fixes for Trackster and Circster, mostly around preference selection and usage.
by commits-noreply＠bitbucket.org 01 Jul '14

01 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7ecbf85f9181/ Changeset: 7ecbf85f9181 User: jgoecks Date: 2014-07-02 00:27:15 Summary: Fixes for Trackster and Circster, mostly around preference selection and usage. Affected #: 4 files diff -r b38a6f5e042bcad4beb40c3df51d4fe162258575 -r 7ecbf85f918180a1ed415629968c763441bb0869 static/scripts/utils/config.js --- a/static/scripts/utils/config.js +++ b/static/scripts/utils/config.js @@ -32,7 +32,7 @@ * Cast and set value. This should be instead of * setting.set('value', new_value) */ - set_value: function(value) { + set_value: function(value, options) { var type = this.get('type'); if (type === 'float') { @@ -43,7 +43,7 @@ } // TODO: handle casting from string to bool? - this.set('value', value); + this.set({value: value}, options); } }, { // This is a master list of default settings for known settings. @@ -101,10 +101,10 @@ /** * Set value for a setting. */ - set_value: function(key, value) { + set_value: function(key, value, options) { var s = this.get(key); if (s) { - return s.set_value(value); + return s.set_value(value, options); } return undefined; diff -r b38a6f5e042bcad4beb40c3df51d4fe162258575 -r 7ecbf85f918180a1ed415629968c763441bb0869 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -620,8 +620,13 @@ $.when(track.get('data_manager').get_genome_wide_data(this.genome)).then(function(genome_wide_data) { // Set bounds. self.data_bounds = self.get_data_bounds(genome_wide_data); - track.get('config').set_value('min_value', self.data_bounds[0]); - track.get('config').set_value('max_value', self.data_bounds[1]); + + // Set min, max value in config so that they can be adjusted. Make this silent + // because these attributes are watched for changes and the viz is updated + // accordingly (set up in initialize). Because we are setting up, we don't want + // the watch to trigger events here. + track.get('config').set_value('min_value', self.data_bounds[0], {silent: true}); + track.get('config').set_value('max_value', self.data_bounds[1], {silent: true}); // Merge chroms layout with data. layout_and_data = _.zip(chrom_arcs, genome_wide_data), diff -r b38a6f5e042bcad4beb40c3df51d4fe162258575 -r 7ecbf85f918180a1ed415629968c763441bb0869 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -994,7 +994,8 @@ }; })); }); - } + }, + minLength: 2 }); }); if (this.vis_id !== undefined) { diff -r b38a6f5e042bcad4beb40c3df51d4fe162258575 -r 7ecbf85f918180a1ed415629968c763441bb0869 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -894,7 +894,7 @@ // -- Set up config settings. -- var models = [ - { key: 'name', value: this.get('dataset').get('name') }, + { key: 'name', default_value: this.get('dataset').get('name') }, { key: 'color' }, { key: 'min_value', label: 'Min Value', type: 'float', default_value: 0 }, { key: 'max_value', label: 'Max Value', type: 'float', default_value: 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 01 Jul '14

01 Jul '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d6e0f352bfe/ Changeset: 1d6e0f352bfe User: jmchilton Date: 2014-07-01 14:07:09 Summary: Bugfix: Value error when specifying empty docker_volume param. Thanks Andrew Stewart! Affected #: 1 file diff -r 2e1de0fc5a3cacf0e7caf64963145fc59b239c7e -r 1d6e0f352bfe1db4b1e23ade889d72473054c73e lib/galaxy/tools/deps/containers.py --- a/lib/galaxy/tools/deps/containers.py +++ b/lib/galaxy/tools/deps/containers.py @@ -204,6 +204,9 @@ ) def __expand_str(self, value): + if not value: + return value + template = string.Template(value) variables = dict() https://bitbucket.org/galaxy/galaxy-central/commits/b38a6f5e042b/ Changeset: b38a6f5e042b User: jmchilton Date: 2014-07-01 14:07:09 Summary: Allow Docker destinations to use --volumes-from option. Enables certain kind of Docker-to-Docker job executions. Thanks to Andrew Stewart. Affected #: 3 files diff -r 1d6e0f352bfe1db4b1e23ade889d72473054c73e -r b38a6f5e042bcad4beb40c3df51d4fe162258575 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -154,6 +154,11 @@ are available to all jobs and $job_directory is also available for Pulsar jobs. --> +  +  diff -r 1d6e0f352bfe1db4b1e23ade889d72473054c73e -r b38a6f5e042bcad4beb40c3df51d4fe162258575 lib/galaxy/tools/deps/containers.py --- a/lib/galaxy/tools/deps/containers.py +++ b/lib/galaxy/tools/deps/containers.py @@ -190,10 +190,12 @@ volumes_raw = self.__expand_str(self.destination_info.get("docker_volumes", "$defaults")) # TODO: Remove redundant volumes... volumes = docker_util.DockerVolume.volumes_from_str(volumes_raw) + volumes_from = self.destination_info.get("docker_volumes_from", docker_util.DEFAULT_VOLUMES_FROM) return docker_util.build_docker_run_command( command, self.container_id, volumes=volumes, + volumes_from=volumes_from, env_directives=env_directives, working_directory=working_directory, docker_cmd=prop("cmd", docker_util.DEFAULT_DOCKER_COMMAND), diff -r 1d6e0f352bfe1db4b1e23ade889d72473054c73e -r b38a6f5e042bcad4beb40c3df51d4fe162258575 lib/galaxy/tools/deps/docker_util.py --- a/lib/galaxy/tools/deps/docker_util.py +++ b/lib/galaxy/tools/deps/docker_util.py @@ -7,6 +7,7 @@ DEFAULT_WORKING_DIRECTORY = None DEFAULT_NET = None DEFAULT_MEMORY = None +DEFAULT_VOLUMES_FROM = None class DockerVolume(object): @@ -55,6 +56,7 @@ tag=None, docker_cmd=DEFAULT_DOCKER_COMMAND, volumes=[], + volumes_from=DEFAULT_VOLUMES_FROM, memory=DEFAULT_MEMORY, env_directives=[], working_directory=DEFAULT_WORKING_DIRECTORY, @@ -75,6 +77,8 @@ command_parts.extend(["-e", env_directive]) for volume in volumes: command_parts.extend(["-v", str(volume)]) + if volumes_from: + command_parts.extend(["--volumes-from", str(volumes_from)]) if memory: command_parts.extend(["-m", memory]) if name: 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 30 Jun '14

30 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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