Merge pull request #2 from galaxyproject/release_19.09

Release 19.09

client/galaxy/scripts/components/Markdown/MarkdownEditor.vue

@@ -44,6 +44,6 @@ export default {
     padding: 20px;
 
     width: 100%;
-    height: 100%;
+    height: 95%; /* what now? this is needed or the editor overtakes workflow toolbar when too much text is added */
 }
 </style>

client/galaxy/scripts/components/ToolBox.vue

@@ -142,5 +142,6 @@ export default {
     display: flex;
     flex-flow: column;
     height: 100%;
+    overflow: auto;
 }
 </style>

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

@@ -240,7 +240,7 @@ class Workflow {
         // First pass, nodes
         var using_workflow_outputs = false;
         wf.workflow_version = data.version;
-        wf.report = data.report;
+        wf.report = data.report || {};
         const markdownEditorInstance = Vue.extend(MarkdownEditor);
         new markdownEditorInstance({
             propsData: {

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

@@ -20,6 +20,100 @@ import { make_popupmenu } from "ui/popupmenu";
 // TODO; tie into Galaxy state?
 window.workflow_globals = window.workflow_globals || {};
 
+const reportHelp = `
+<div>
+<h3>Overview</h3>
+
+<p>
+    This document Markdown document will be used to generate a report
+    for invocations of this workflow. This document should be Markdown
+    with embedded command for extracting and displaying parts of the workflow,
+    its invocation metadata, its inputs and outputs, etc.. For an overview
+    of standard Markdown visit the <a href="https://commonmark.org/help/tutorial/">commonmark.org
+    tutorial</a>.
+</p>
+
+<p>
+    The Galaxy extensions to Markdown are represented as code blocks, these blocks start
+    with the line <tt>\`\`\`galaxy</tt> and end with the line <tt>\`\`\`</tt> and have a
+    command with arguments that reference parts of the workflow in the middle.
+</p>
+
+<h3>Workflow Commands</h3>
+
+<p>
+    These commands to do not take any arguments and reference the whole workflow. For
+    instance, the following example would display a representation of the workflow in the
+    resulting report:
+</p>
+
+<pre>
+\`\`\`galaxy
+workflow_display()
+\`\`\`
+</pre>
+<dl>
+<dt><tt>workflow_display</tt></dt>
+<dd>Embed a description of the workflow itself in the resulting report.</dd>
+<dt><tt>invocation_inputs</tt></dt>
+<dd>Embed the labeled workflow inputs in the resulting report.</dd>
+<dt><tt>invocation_outputs</tt></dt>
+<dd>Embed the labeled workflow outputs in the resulting report.</dd>
+</dl>
+
+<h3>Step Commands</h3>
+
+<p>
+    These commands reference a workflow step label and refer to job corresponding
+    to that step. A current limitation is the report will break if these refer to
+    a collection mapping step, these must identify a single job. For instance, the
+    following example would show the job parameters the step labeled 'qc' was run
+    with:
+</p>
+
+<pre>
+\`\`\`galaxy
+job_parameters(step=qc)
+\`\`\`
+</pre>
+
+
+<dt><tt>tool_stderr</tt></dt>
+<dd>Embed the tool standard error stream for this step in the resulting report.</dd>
+<dt><tt>tool_stdout</tt></dt>
+<dd>Embed the tool standard output stream for this step in the resulting report.</dd>
+<dt><tt>job_metrics</tt></dt>
+<dd>Embed the job metrics for this step in the resulting report (if user has permission).</dd>
+<dt><tt>job_parameters</tt></dt>
+<dd>Embed the tool parameters for this step in the resulting report.</dd>
+
+<h3>Input/Output Commands</h3>
+
+<p>
+    These commands reference a workflow input or output by label. For instance, the
+    following example would display the dataset collection corresponding to output "Merged BAM":
+</p>
+
+<pre>
+\`\`\`galaxy
+history_dataset_collection_display(output="Merged Bam")
+\`\`\`
+</pre>
+
+<dt><tt>history_dataset_display</tt></dt>
+<dd>Embed a dataset description in the resulting report.</dd>
+<dt><tt>history_dataset_collection_display</tt></dt>
+<dd>Embed a dataset collection description in the resulting report.</dd>
+<dt><tt>history_dataset_as_image</tt></dt>
+<dd>Embed a dataset as an image in the resulting report - the dataset should be an image datatype.</dd>
+<dt><tt>history_dataset_peek</tt></dt>
+<dd>Embed Galaxy's metadata attribute 'peek' into the resulting report - this is datatype dependent metadata but usually this is a few lines from the start of a file.</dd>
+<dt><tt>history_dataset_info</tt></dt>
+<dd>Embed Galaxy's metadata attribute 'info' into the resulting report - this is datatype dependent metadata but usually this is the program output that generated the dataset.</dd>
+</dl>
+</div>
+`;
+
 // Reset tool search to start state.
 function reset_tool_search(initValue) {
     // Function may be called in top frame or in tool_menu_frame;
@@ -364,6 +458,7 @@ export default Backbone.View.extend({
             );
             $("#workflow-save-button").click(() => save_current_workflow());
             $("#workflow-report-button").click(() => edit_report());
+            $("#workflow-report-help-button").click(() => show_report_help());
             $("#workflow-canvas-button").click(() => edit_canvas());
             make_popupmenu($("#workflow-options-button"), {
                 "Save As": workflow_save_as,
@@ -428,6 +523,13 @@ export default Backbone.View.extend({
             $(".workflow-report-content").show();
         }
 
+        function show_report_help() {
+            const reportHelpBody = $(reportHelp);
+            show_modal("Workflow Invocation Report Help", reportHelpBody, {
+                Ok: hide_modal
+            });
+        }
+
         function edit_canvas() {
             $(".workflow-canvas-content").show();
             $(".workflow-report-content").hide();

config/plugins/visualizations/openlayers/package.json

@@ -8,6 +8,7 @@
     ],
     "license": "AFL-3.0",
     "dependencies": {
+        "axios": "^0.19.0",
         "babel-preset-env": "^1.6.1",
         "backbone": "^1.3.3",
         "bootstrap": "^3.3.7",
@@ -18,6 +19,7 @@
         "ol": "^5.3.3",
         "parcel-bundler": "^1.4.1",
         "proj4": "^2.5.0",
+        "shpjs": "^3.4.3",
         "underscore": "^1.8.3"
     },
     "scripts": {