From 8e0be5089c63d94b841babfffcd70f2d8ab9b27c Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 30 Mar 2017 12:46:03 -0400 Subject: [PATCH 01/13] [17.01] Fix collection operations in workflows. Due to a couple bugs things weren't being delayed correctly for some of these tools in some workflows. --- lib/galaxy/model/__init__.py | 8 ++++ lib/galaxy/tools/__init__.py | 7 ++-- lib/galaxy/tools/actions/model_operations.py | 8 +++- lib/galaxy/tools/execute.py | 2 +- test/api/test_workflows.py | 44 ++++++++++++++++++++ 5 files changed, 63 insertions(+), 6 deletions(-) diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 99577bb40ff..8ebc8f07e08 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3485,6 +3485,14 @@ class DatasetCollectionElement( object, Dictifiable ): else: return element_object + @property + def dataset_instances( self ): + element_object = self.element_object + if isinstance( element_object, DatasetCollection ): + return element_object.dataset_instances + else: + return [element_object] + def copy_to_collection( self, collection, destination=None, element_destination=None ): element_object = self.element_object if element_destination: diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 325b1cbfa76..88fcf714ea5 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2384,9 +2384,10 @@ class DatabaseOperationTool( Tool ): for input_dataset in input_datasets.values(): check_dataset_instance( input_dataset ) - for input_dataset_collection in input_dataset_collections.values(): - if not input_dataset_collection.collection.populated: - raise ToolInputsNotReadyException() + for input_dataset_collection_pairs in input_dataset_collections.values(): + for input_dataset_collection, is_mapped in input_dataset_collection_pairs: + if not input_dataset_collection.collection.populated: + raise ToolInputsNotReadyException() map( check_dataset_instance, input_dataset_collection.dataset_instances ) diff --git a/lib/galaxy/tools/actions/model_operations.py b/lib/galaxy/tools/actions/model_operations.py index 2d421867a5f..eb10ae9959c 100644 --- a/lib/galaxy/tools/actions/model_operations.py +++ b/lib/galaxy/tools/actions/model_operations.py @@ -12,8 +12,12 @@ log = logging.getLogger( __name__ ) class ModelOperationToolAction( DefaultToolAction ): - def check_inputs_ready( self, tool, trans, incoming, history ): - history, inp_data, inp_dataset_collections = self._collect_inputs(tool, trans, incoming, history) + def check_inputs_ready( self, tool, trans, incoming, history, execution_cache=None ): + if execution_cache is None: + execution_cache = ToolExecutionCache(trans) + + current_user_roles = execution_cache.current_user_roles + history, inp_data, inp_dataset_collections = self._collect_inputs(tool, trans, incoming, history, current_user_roles) tool.check_inputs_ready( inp_data, inp_dataset_collections ) diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py index 45fd192162c..c131415b5ad 100644 --- a/lib/galaxy/tools/execute.py +++ b/lib/galaxy/tools/execute.py @@ -48,7 +48,7 @@ def execute( trans, tool, param_combinations, history, rerun_remap_job_id=None, burst_at = getattr( config, 'tool_submission_burst_at', 10 ) burst_threads = getattr( config, 'tool_submission_burst_threads', 1 ) - tool_action = tool.action + tool_action = tool.tool_action if hasattr( tool_action, "check_inputs_ready" ): for params in execution_tracker.param_combinations: # This will throw an exception if the tool is not ready. diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py index 1416e44678d..194534ce934 100644 --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -899,6 +899,50 @@ steps: content = self.dataset_populator.get_history_dataset_content( history_id ) self.assertEqual(content.strip(), "samp1\t10.0\nsamp2\t20.0\nsamp1\t20.0\nsamp2\t40.0") + def test_filter_failed_mapping( self ): + history_id = self.dataset_populator.new_history() + summary = self._run_jobs(""" +class: GalaxyWorkflow +inputs: + - type: collection + label: input_c +steps: + - label: mixed_collection + tool_id: exit_code_from_file + state: + input: + $link: input_c + + - label: filtered_collection + tool_id: "__FILTER_FAILED_DATASETS__" + state: + input: + $link: mixed_collection#out_file1 + + - tool_id: cat1 + state: + input1: + $link: filtered_collection +test_data: + input_c: + type: list + elements: + - identifier: i1 + content: "0" + - identifier: i2 + content: "1" +""", history_id=history_id, wait=True, assert_ok=False) + jobs = summary.jobs + + def filter_jobs_by_tool(tool_id): + return [j for j in summary.jobs if j["tool_id"] == tool_id] + + assert len(filter_jobs_by_tool("upload1")) == 2, jobs + assert len(filter_jobs_by_tool("exit_code_from_file")) == 2, jobs + assert len(filter_jobs_by_tool("__FILTER_FAILED_DATASETS__")) == 1, jobs + # Follow proves one job was filtered out of the result of cat1 + assert len(filter_jobs_by_tool("cat1")) == 1, jobs + def test_workflow_request( self ): workflow = self.workflow_populator.load_workflow( name="test_for_queue" ) workflow_request, history_id = self._setup_workflow_run( workflow ) From 9234420cd770661b58ee91051015e9580505ca47 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 5 Apr 2017 09:18:58 -0400 Subject: [PATCH 02/13] Fix multiple collection reductions on multiple data parameters. Was introduced in #805 but there was a small bug (maybe a last minute change before opening the PR) in the client code so this never was exposed to the users the way it was intended. This should largely negate the need for hacks such as in cuffmerge that allow multiple list collections in addition to main multiple data selector. xref galaxyproject/tools-iuc#1225. --- client/galaxy/scripts/mvc/ui/ui-select-content.js | 2 +- static/maps/mvc/ui/ui-select-content.js.map | 2 +- static/scripts/bundled/analysis.bundled.js | 2 +- static/scripts/bundled/analysis.bundled.js.map | 2 +- static/scripts/bundled/libs.bundled.js.map | 2 +- static/scripts/mvc/ui/ui-select-content.js | 2 +- test/qunit/tests/ui_tests.js | 4 ++-- 7 files changed, 8 insertions(+), 8 deletions(-) diff --git a/client/galaxy/scripts/mvc/ui/ui-select-content.js b/client/galaxy/scripts/mvc/ui/ui-select-content.js index 0d1c9112b89..eb393f5c24e 100644 --- a/client/galaxy/scripts/mvc/ui/ui-select-content.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-content.js @@ -11,7 +11,7 @@ var Configurations = { { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.LINKED } ], data_multiple: [ { src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.DISABLED }, - { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED } ], + { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collections', multiple: true, batch: Batch.DISABLED } ], data_collection: [ { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED } ], workflow_data: [ diff --git a/static/maps/mvc/ui/ui-select-content.js.map b/static/maps/mvc/ui/ui-select-content.js.map index 889b7c4dc62..55caa6063b1 100644 --- a/static/maps/mvc/ui/ui-select-content.js.map +++ b/static/maps/mvc/ui/ui-select-content.js.map @@ -1 +1 @@ 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").addClass("ui-options-menu")).append(this.$options=a(this._template())),this.all_button=null,this.model.get("multiple")&&(this.all_button=new t.ButtonCheck({onclick:function(){e.$("input").prop("checked",0!==e.all_button.value()),e.value(e._getValue()),e.trigger("change")}}),this.$menu.append(this.all_button.$el)),this._changeData(),this._changeWait(),this._changeVisible()},update:function(e){this.model.set("data",e)},_changeData:function(){var e=this;this.$options.empty(),this._templateOptions?this.$options.append(this._templateOptions(this.model.get("data"))):r.each(this.model.get("data"),function(t){e.$options.append(a(e._templateOption(t)).addClass("ui-option").tooltip({title:t.tooltip,placement:"bottom"}))});var e=this;this.$("input").on("change",function(){e.value(e._getValue()),e.trigger("change")}),this._changeValue(),this._changeWait()},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"]()},_changeWait:function(){this.model.get("wait")?0===this.length()&&(this._messageShow(this.model.get("wait_text"),"info"),this.$options.hide(),this.$menu.hide()):0===this.length()?(this._messageShow(this.model.get("error_text"),"danger"),this.$options.hide(),this.$menu.hide()):(this.$message.hide(),this.$options.css("display","inline-block"),this.$menu.show())},_changeValue:function(){this._setValue(this.model.get("value")),null!==this._getValue()||this.model.get("multiple")||this.model.get("optional")||this._setValue(this.first()),this.all_button&&this.all_button.value(a.isArray(this._getValue())?this._getValue().length:0,this.length())},value:function(e){return void 0!==e&&this.model.set("value",e),this._getValue()},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},length:function(){return this.$(".ui-option").length},_setValue:function(e){var t=this;if(void 0!==e&&(this.$("input").prop("checked",!1),null!==e)){var i=a.isArray(e)?e:[e];r.each(i,function(e){t.$('input[value="'+e+'"]').first().prop("checked",!0)})}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push(a(this).val())}),e.isEmpty(t)?null:this.model.get("multiple")?t:t[0]},_messageShow:function(e,t){this.$message.show().removeClass().addClass("ui-message alert alert-"+t).html(e)},_template:function(){return a("
").addClass("ui-options-list")}}),n=i.extend({_templateOption:function(t){var i=e.uid();return a("
").addClass("ui-option").append(a("").attr({id:i,type:this.model.get("type"),name:this.model.id,value:t.value})).append(a("