Merge branch 'release_18.09' into dev

client/galaxy/docs/bootstrap.md

@@ -135,8 +135,8 @@ Disabled
 
 ```
 <div>
-  <span class="badge badge-default">Default</span>
   <span class="badge badge-primary">Primary</span>
+  <span class="badge badge-secondary">Secondary</span>
   <span class="badge badge-success">Success</span>
   <span class="badge badge-warning">Warning</span>
   <span class="badge badge-danger">Danger</span>

client/galaxy/scripts/galaxy.pages.js

@@ -447,7 +447,11 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
                         // Get item ID and name.
                         var item_id = elt.val();
                         // Use ':first' because there are many labels in table; the first one is the item name.
-                        var item_name = elt.closest('td').next('td').find('label').text();
+                        var item_name = elt
+                            .closest("td")
+                            .next("td")
+                            .find("label")
+                            .text();
 
                         if (make_importable) make_item_importable(item_info.controller, item_id, item_info.singular);
 

client/galaxy/scripts/mvc/dataset/dataset-error.js

@@ -2,6 +2,12 @@ import _l from "utils/localization";
 import Utils from "utils/utils";
 import Ui from "mvc/ui/ui-misc";
 import Form from "mvc/form/form-view";
+import * as Backbone from "backbone";
+import * as _ from "underscore";
+
+/* global Galaxy */
+/* global $ */
+
 /** Dataset edit attributes view */
 var View = Backbone.View.extend({
     initialize: function() {
@@ -57,12 +63,23 @@ var View = Backbone.View.extend({
             <p>An error occured while running the tool <b>${job.tool_id}</b>.</p>
             <p>Tool execution generated the following messages:</p>
             <pre class="code">${_.escape(job.stderr)}</pre>
-            <h2>Report This Error</h2>
+
+            <h3>Troubleshoot This Error</h3>
             <p>
-                Usually the local Galaxy administrators regularly review errors that occur on the server
-                However, if you would like to provide additional information (such as what you were trying
-                to do when the error occurred) and a contact e-mail address, we will be better able to
-                investigate your problem and get back to you.
+                There are a number of help resources to self diagnose and
+                correct problems.
+                Start here: <a
+                href="https://galaxyproject.org/support/tool-error/"
+                target="_blank"> My job ended with an error. What can I do?</a>
+            </p>
+
+            <h3>Report This Error</h3>
+            <p>
+                Usually the local Galaxy administrators regularly review errors
+                that occur on the server However, if you would like to provide
+                additional information (such as what you were trying to do when
+                the error occurred) and a contact e-mail address, we will be
+                better able to investigate your problem and get back to you.
             </p>`);
         this.$el.append(this._getBugFormTemplate(dataset, job));
     },

client/galaxy/scripts/mvc/tool/tool-form-base.js

@@ -88,7 +88,7 @@ export default FormBase.extend({
         }
         options.tool_errors &&
             this.message.update({
-                status: 'danger',
+                status: "danger",
                 message: options.tool_errors,
                 persistent: true
             });

client/galaxy/scripts/mvc/tool/tool-form-composite.js

@@ -129,14 +129,14 @@ var View = Backbone.View.extend({
         this.wp_inputs = {};
 
         function _ensureWorkflowParameter(wp_name) {
-            return self.wp_inputs[wp_name] = self.wp_inputs[wp_name] || {
+            return (self.wp_inputs[wp_name] = self.wp_inputs[wp_name] || {
                 label: wp_name,
                 name: wp_name,
                 type: "text",
                 color: `hsl( ${++wp_count * 100}, 70%, 30% )`,
                 style: "ui-form-wp-source",
                 links: []
-            };
+            });
         }
 
         function _handleWorkflowParameter(value, callback) {

client/galaxy/scripts/mvc/tool/tools.js

@@ -828,7 +828,7 @@ var templates = {
             '<a class="<%- id %> tool-link" href="<%= link %>" target="<%- target %>" minsizehint="<%- min_width %>">',
             '<span class="labels">',
             "<% _.each( labels, function( label ){ %>",
-            '<span class="badge badge-default badge-<%- label %>">',
+            '<span class="badge badge-primary badge-<%- label %>">',
             "<%- label %>",
             "</span>",
             "<% }); %>",

client/galaxy/scripts/mvc/workflow/workflow-manager.js

@@ -278,7 +278,7 @@ class Workflow {
                 $.each(node.output_terminals, (ot_id, ot) => {
                     if (node.post_job_actions[`HideDatasetAction${ot.name}`] === undefined) {
                         node.addWorkflowOutput(ot.name);
-                        var callout = $(node.element).find(`.callout.${ot.name.replace(/(?=[()])/g, '\\')}`);
+                        var callout = $(node.element).find(`.callout.${ot.name.replace(/(?=[()])/g, "\\")}`);
                         callout.find("img").attr("src", `${Galaxy.root}static/images/fugue/asterisk-small.png`);
                         wf.has_changes = true;
                     }

client/galaxy/scripts/mvc/workflow/workflow-view.js

@@ -278,46 +278,51 @@ export default Backbone.View.extend({
             let workflow_versions = JSON.parse(
                 $.ajax({
                     url: `${Galaxy.root}api/workflows/${self.options.id}/versions`,
-                    async: false,
+                    async: false
                 }).responseText
             );
 
             for (let i = 0; i < workflow_versions.length; i++) {
                 let current_wf = workflow_versions[i];
-                let version_text = `Version ${current_wf['version']}, ${current_wf['steps']} steps`;
+                let version_text = `Version ${current_wf["version"]}, ${current_wf["steps"]} steps`;
                 let selected = false;
                 if (i == self.workflow.workflow_version) {
                     version_text = `${version_text} (active)`;
                     selected = true;
-                };
+                }
                 _workflow_version_dropdown[version_text] = {
                     version: i,
-                    selected: selected,
-                }
+                    selected: selected
+                };
             }
-            return _workflow_version_dropdown
-        }
+            return _workflow_version_dropdown;
+        };
 
         this.build_version_select = function() {
             let versions = this.get_workflow_versions();
             $("#workflow-version-switch").empty();
             $.each(versions, function(k, v) {
-                $('#workflow-version-switch').append($('<option></option>').html(k).val(v.version).selected(v.selected));
+                $("#workflow-version-switch").append(
+                    $("<option></option>")
+                        .html(k)
+                        .val(v.version)
+                        .selected(v.selected)
+                );
             });
-            $("#workflow-version-switch").on('change', function () {
-                $('#workflow-version-switch').unbind('change');
+            $("#workflow-version-switch").on("change", function() {
+                $("#workflow-version-switch").unbind("change");
                 if (this.value != self.workflow.workflow_version) {
                     if (self.workflow && self.workflow.has_changes) {
                         let r = confirm("There are unsaved changes to your workflow which will be lost. Continue ?");
                         if (r == false) {
                             // We rebuild the version select list, to reset the selected version
                             self.build_version_select();
-                            return
+                            return;
                         }
                     }
                     self.load_workflow(self.options.id, this.value);
                 }
-            })
+            });
         };
 
         this.load_workflow = function load_workflow(id, version) {
@@ -360,19 +365,21 @@ export default Backbone.View.extend({
                     self.showWorkflowParameters();
                 },
                 error: function(response) {
-                        window.show_modal("Loading workflow failed.", response.err_msg, { Ok: function( response ){
-                        window.onbeforeunload = undefined;
-                        window.document.location = workflow_index;
-}})
+                    window.show_modal("Loading workflow failed.", response.err_msg, {
+                        Ok: function(response) {
+                            window.onbeforeunload = undefined;
+                            window.document.location = workflow_index;
+                        }
+                    });
                 },
                 beforeSubmit: function(data) {
                     show_message("Loading workflow", "progress");
                 }
             });
-        }
+        };
 
         // Load workflow definition
-        this.load_workflow(self.options.id, self.options.version)
+        this.load_workflow(self.options.id, self.options.version);
         if (window.make_popupmenu) {
             make_popupmenu($("#workflow-options-button"), {
                 Save: save_current_workflow,

config/datatypes_conf.xml.sample

@@ -576,10 +576,10 @@
     <datatype extension="pdbqt" type="galaxy.datatypes.molecules:PDBQT" display_in_upload="true"/>
     <datatype extension="trr" type="galaxy.datatypes.binary:Trr" display_in_upload="true"/>
     <datatype extension="dcd" type="galaxy.datatypes.binary:Dcd" display_in_upload="true"/>
-    <datatype extension="top" type="galaxy.datatypes.text:Top" display_in_upload="true"/>
+    <datatype extension="top" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
     <datatype extension="xtc" type="galaxy.datatypes.binary:Xtc" display_in_upload="true"/>
     <datatype extension="cpt" type="galaxy.datatypes.binary:Cpt" display_in_upload="true"/>
-    <datatype extension="gro" type="galaxy.datatypes.tabular:Gro" display_in_upload="true"/>
+    <datatype extension="gro" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
     <datatype extension="vel" type="galaxy.datatypes.binary:Vel" display_in_upload="true"/>
     <datatype extension="grd" type="galaxy.datatypes.molecules:grd" display_in_upload="true"/>
     <datatype extension="grd.tgz" type="galaxy.datatypes.molecules:grdtgz" display_in_upload="true"/>

lib/galaxy/model/__init__.py

@@ -2599,7 +2599,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
             self.version = self.version + 1 if self.version else 1
             session.add(past_hda)
 
-    def copy(self, parent_id=None, copy_tags=None, force_flush=True, copy_hid=True):
+    def copy(self, parent_id=None, copy_tags=None, force_flush=True, copy_hid=True, new_name=None):
         """
         Create a copy of this HDA.
         """
@@ -2607,7 +2607,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
         if copy_hid:
             hid = self.hid
         hda = HistoryDatasetAssociation(hid=hid,
-                                        name=self.name,
+                                        name=new_name or self.name,
                                         info=self.info,
                                         blurb=self.blurb,
                                         peek=self.peek,
@@ -3451,6 +3451,17 @@ class DatasetCollection(Dictifiable, UsesAnnotations):
                 elements.append(element)
         return elements
 
+    @property
+    def first_dataset_element(self):
+        for element in self.elements:
+            if element.is_collection:
+                first_element = element.child_collection.first_dataset_element
+                if first_element:
+                    return first_element
+            else:
+                return element
+        return None
+
     @property
     def state(self):
         # TODO: DatasetCollection state handling...

lib/galaxy/tools/__init__.py

@@ -2481,14 +2481,15 @@ class ExtractDatasetCollectionTool(DatabaseOperationTool):
         assert collection_type in ["list", "paired"]
         how = incoming["which"]["which_dataset"]
         if how == "first":
-            extracted = collection.dataset_instances[0]
+            extracted_element = collection.first_dataset_element
         elif how == "by_identifier":
-            extracted = collection[incoming["which"]["identifier"]].element_object
+            extracted_element = collection[incoming["which"]["identifier"]]
         elif how == "by_index":
-            extracted = collection[int(incoming["which"]["index"])].element_object
+            extracted_element = collection[int(incoming["which"]["index"])]
         else:
             raise Exception("Invalid tool parameters.")
-        extracted_o = extracted.copy(copy_tags=tags)
+        extracted = extracted_element.element_object
+        extracted_o = extracted.copy(copy_tags=tags, new_name=extracted_element.element_identifier)
         self._add_datasets_to_history(history, [extracted_o])
 
         out_data["output"] = extracted_o

lib/galaxy/tools/extract_dataset.xml

@@ -50,7 +50,9 @@ This tool will create new history datasets from your collection but your quota u
           <element name="bar" value="simple_line_alternative.txt" />
         </collection>
       </param>
-      <output name="output" file="simple_line.txt" />
+      <output name="output" file="simple_line.txt">
+        <metadata name="name" value="foo" />
+      </output>
     </test>
     <test>
       <conditional name="which">
@@ -63,7 +65,9 @@ This tool will create new history datasets from your collection but your quota u
           <element name="bar" value="simple_line_alternative.txt" />
         </collection>
       </param>
-      <output name="output" file="simple_line_alternative.txt" />
+      <output name="output" file="simple_line_alternative.txt">
+        <metadata name="name" value="bar" />
+      </output>
     </test>
     <test>
       <conditional name="which">
@@ -76,7 +80,9 @@ This tool will create new history datasets from your collection but your quota u
           <element name="bar" value="simple_line_alternative.txt" />
         </collection>
       </param>
-      <output name="output" file="simple_line_alternative.txt" />
+      <output name="output" file="simple_line_alternative.txt">
+        <metadata name="name" value="bar" />
+      </output>
     </test>
   </tests>
 </tool>

lib/galaxy/tools/search/__init__.py

@@ -6,6 +6,7 @@ import logging
 import re
 import tempfile
 
+from bleach import clean
 from whoosh import analysis
 from whoosh.analysis import StandardAnalyzer
 from whoosh.fields import (
@@ -49,7 +50,7 @@ class ToolBoxSearch(object):
         self.storage, self.index = self._index_setup()
         # We keep track of how many times the tool index has been rebuilt.
         # We start at -1, so that after the first index the count is at 0,
-        # which is the same is the toolbox reload count. This way we can skip
+        # which is the same as the toolbox reload count. This way we can skip
         # reindexing if the index count is equal to the toolbox reload count.
         self.index_count = -1
 
@@ -105,7 +106,9 @@ class ToolBoxSearch(object):
             add_doc_kwds['labels'] = to_unicode(" ".join(tool.labels))
         if index_help and tool.help:
             try:
-                add_doc_kwds['help'] = to_unicode(tool.help.render(host_url="", static_path=""))
+                raw_html = tool.help.render(host_url="", static_path="")
+                cleantext = clean(raw_html, tags=[''], strip=True).replace('\n', ' ')
+                add_doc_kwds['help'] = to_unicode(cleantext)
             except Exception:
                 # Don't fail to build index just because a help message
                 # won't render.

test/api/test_tools.py

@@ -118,6 +118,27 @@ class ToolsTestCase(api.ApiTestCase):
             output_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output)
             assert output_details["file_ext"] == "bed"
 
+    @skip_without_tool("test_data_source")
+    def test_data_source_sniff_fastqsanger(self):
+        with self.dataset_populator.test_history() as history_id:
+            payload = self.dataset_populator.run_tool_payload(
+                tool_id="test_data_source",
+                inputs={
+                    "URL": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.fastqsanger.gz",
+                    "URL_method": "get",
+                },
+                history_id=history_id,
+            )
+            create_response = self._post("tools", data=payload)
+            self._assert_status_code_is(create_response, 200)
+            create_object = create_response.json()
+            self._assert_has_keys(create_object, "outputs")
+            assert len(create_object["outputs"]) == 1
+            output = create_object["outputs"][0]
+            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+            output_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output)
+            assert output_details["file_ext"] == "fastqsanger.gz", output_details
+
     @skip_without_tool("test_data_source")
     def test_data_sources_block_file_parameters(self):
         with self.dataset_populator.test_history() as history_id: