From 828c37c6ff84115b4ae033a719aea66d894637ae Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 11 May 2020 11:53:40 -0400
Subject: [PATCH] [WIP] Simplified workflow run form.

Builds on refactoring the workflow run form landing and orchestration into Vue (#9147).

Implements #9111 - part of https://github.com/galaxyproject/galaxy/projects/15 and outlined in http://bit.ly/simplified-workflow-ui.

What is in the PR:

- Add new Galaxy configuration option - ``simplified_workflow_run_ui`` set to ``off`` by default (at least until batch parameters are hidden or implemented).
- If instead the admin has set this parameter to ``prefer``, on the workflow run page scan the workflow run request and if three conditions are met show a simplfied tool form. These conditions are:
  - No workflow "resource parameters" - pretty niche, not documented, I don't think anyone outside of Canada is using them and even them I'm not sure if they ever got to production.
  - No "open" tools (i.e. tools with disconnected runtime inputs).
  - No "replacement parameters" defined outside PJAs. I'm calling #{} inside PJA and ${} inside tool steps both "replacement parameters" because the user populates them the same way in the GUI. The API only handles them inside the context of the PJA - it seems the GUI is responsible for replacing them at runtime in the traditional form.
- The simplified workflow form:
   - Drops tool and subworkflow steps from rendering all together and instead just renders the inputs. These are not rendered as separate "steps" or forms - but as just different inputs the same clean, simple form (more the like tool GUI). Labels (or step indexes as a fallback) are used at the input name, step annotations are used as the input help text.
   - Simplify the workflow request made by the client - send only replacement parameters and inputs - do not serialize tool state for each module. I think this makes what we are tracking more structured and should be more performant as well. Prevents storing HDA IDs in unstructured JSON blobs in the database as well.
   - Drops history target option to simplify the UI (see TODO below for followup)
   - Drops job caching option to simplify the UI (see TODO below for followup)
   - Drops resource parameters - we've already verified there are none.

TODO:

- Handle batch parameters - either implement them or disable them in this context.
- Make history target in simplified mode configurable via galaxy.yml - simplified_workflow_run_ui_target_history in ['new', 'current', 'show_selection'].
- Make job caching option in simplified mode configurable via galaxy.yml - simplified_workflow_run_ui_cache in ['on', 'off'].
---
 .../components/Workflow/Run/WorkflowRun.vue   |  49 ++++++++
 .../Workflow/Run/WorkflowRunFormSimple.vue    | 109 ++++++++++++++++++
 .../scripts/components/Workflow/Run/model.js  |   9 +-
 .../scripts/entry/analysis/AnalysisRouter.js  |   5 +-
 lib/galaxy/managers/configuration.py          |   1 +
 lib/galaxy/webapps/galaxy/config_schema.yml   |  13 +++
 test/functional/tools/samples_tool_conf.xml   |   1 +
 7 files changed, 185 insertions(+), 2 deletions(-)
 create mode 100644 client/galaxy/scripts/components/Workflow/Run/WorkflowRunFormSimple.vue

diff --git a/client/galaxy/scripts/components/Workflow/Run/WorkflowRun.vue b/client/galaxy/scripts/components/Workflow/Run/WorkflowRun.vue
index a7d509ef30dd..850bc95a56ac 100644
--- a/client/galaxy/scripts/components/Workflow/Run/WorkflowRun.vue
+++ b/client/galaxy/scripts/components/Workflow/Run/WorkflowRun.vue
@@ -44,9 +44,20 @@
                 <workflow-run-form
                     ref="runform"
                     :model="model"
+                    v-if="!simpleForm"
                     :setRunButtonStatus="setRunButtonStatus"
                     @submissionSuccess="handleInvocations"
                 />
+                <div v-else>
+                    <workflow-run-form-simple
+                        ref="runform"
+                        :model="model"
+                        :setRunButtonStatus="setRunButtonStatus"
+                        @submissionSuccess="handleInvocations"
+                    />
+                    <!-- Options to default one way or the other, disable if admins want, etc.. -->
+                    <a href="#" @click="showAdvanced">Expand to full workflow form.</a>
+                </div>
             </div>
         </span>
     </span>
@@ -58,6 +69,7 @@ import WaitButton from "components/WaitButton";
 import LoadingSpan from "components/LoadingSpan";
 import WorkflowRunSuccess from "./WorkflowRunSuccess";
 import WorkflowRunForm from "./WorkflowRunForm";
+import WorkflowRunFormSimple from "./WorkflowRunFormSimple";
 import { WorkflowRunModel } from "./model.js";
 import { errorMessageAsString } from "utils/simple-error";
 
@@ -67,9 +79,14 @@ export default {
         WaitButton,
         WorkflowRunSuccess,
         WorkflowRunForm,
+        WorkflowRunFormSimple,
     },
     props: {
         workflowId: { type: String },
+        preferSimpleForm: {
+            type: Boolean,
+            default: false,
+        },
     },
     data() {
         return {
@@ -83,6 +100,7 @@ export default {
             runButtonWaitText: "",
             runButtonPercentage: -1,
             invocations: null,
+            simpleForm: null,
             model: null,
         };
     },
@@ -90,6 +108,33 @@ export default {
         getRunData(this.workflowId)
             .then((runData) => {
                 const model = new WorkflowRunModel(runData);
+                let simpleForm = this.preferSimpleForm;
+                if (simpleForm) {
+                    // These only work with PJA - the API doesn't evaluate them at
+                    // all outside that context currently. The main workflow form renders
+                    // these dynamically and takes care of all the validation and setup details
+                    // on the frontend. If these are implemented on the backend at some
+                    // point this restriction can be lifted.
+                    if (model.hasReplacementParametersInToolForm) {
+                        console.log("cannot render simple workflow form - has ${} values in tool steps");
+                        simpleForm = false;
+                    }
+                    // If there are required parameters in a tool form (a disconnected runtime
+                    // input), we have to render the tool form steps and cannot use the
+                    // simplified tool form.
+                    if (model.hasOpenToolSteps) {
+                        console.log(
+                            "cannot render simple workflow form - one or more tools have disconnected runtime inputs"
+                        );
+                    }
+                    // Just render the whole form for resource request parameters (kind of
+                    // niche - I'm not sure anyone is using these currently anyway).
+                    if (model.hasWorkflowResourceParameters) {
+                        console.log(`Cannot render simple workflow form - workflow resource parameters are configured`);
+                        simpleForm = false;
+                    }
+                }
+                this.simpleForm = simpleForm;
                 this.model = model;
                 this.hasUpgradeMessages = model.hasUpgradeMessages;
                 this.hasStepVersionChanges = model.hasStepVersionChanges;
@@ -97,6 +142,7 @@ export default {
                 this.loading = false;
             })
             .catch((response) => {
+                console.log(response);
                 this.error = errorMessageAsString(response);
             });
     },
@@ -112,6 +158,9 @@ export default {
         handleInvocations(invocations) {
             this.invocations = invocations;
         },
+        showAdvanced() {
+            this.simpleForm = false;
+        },
     },
 };
 </script>
diff --git a/client/galaxy/scripts/components/Workflow/Run/WorkflowRunFormSimple.vue b/client/galaxy/scripts/components/Workflow/Run/WorkflowRunFormSimple.vue
new file mode 100644
index 000000000000..1e70c2cc4eec
--- /dev/null
+++ b/client/galaxy/scripts/components/Workflow/Run/WorkflowRunFormSimple.vue
@@ -0,0 +1,109 @@
+<template>
+    <div ref="form"></div>
+</template>
+
+<script>
+import $ from "jquery";
+import _ from "underscore";
+
+import Form from "mvc/form/form-view";
+import { invokeWorkflow } from "./services";
+
+export default {
+    props: {
+        model: {
+            type: Object,
+            required: true,
+        },
+        setRunButtonStatus: {
+            type: Function,
+            required: true,
+        },
+    },
+    data() {
+        return {
+            form: null,
+            inputTypes: {},
+        };
+    },
+    computed: {},
+    created() {
+        this.form = new Form(this.formDefinition());
+        this.$nextTick(() => {
+            const el = this.$refs["form"];
+            $(el).append(this.form.$el);
+        });
+    },
+    methods: {
+        formDefinition() {
+            const inputs = [];
+
+            // Add workflow parameters.
+            _.each(this.model.wpInputs, (input, i) => {
+                // do we want to keep the color if we're not showing steps?
+                input["color"] = undefined;
+                inputs.push(input);
+                this.inputTypes[input.name] = "replacement_parameter";
+            });
+
+            // Add actual input modules.
+            _.each(this.model.steps, (step, i) => {
+                const is_input =
+                    ["data_input", "data_collection_input", "parameter_input"].indexOf(step.step_type) != -1;
+                if (!is_input) {
+                    return;
+                }
+
+                const stepName = new String(step.step_index);
+                const stepLabel = step.step_label || stepName;
+                const help = step.annotation;
+                const longFormInput = step.inputs[0];
+                const stepAsInput = Object.assign({}, longFormInput, { name: stepName, help: help, label: stepLabel });
+                inputs.push(stepAsInput);
+                this.inputTypes[stepName] = step.step_type;
+            });
+
+            const def = {
+                inputs: inputs,
+            };
+            return def;
+        },
+        execute() {
+            const replacementParams = {};
+            const inputs = {};
+            const formData = this.form.data.create();
+            for (const inputName in formData) {
+                const value = formData[inputName];
+                const inputType = this.inputTypes[inputName];
+                if (inputType == "replacement_parameter") {
+                    replacementParams[inputName] = value;
+                } else if (inputType == "data_input" || inputType == "data_collection_input") {
+                    const values = value["values"];
+                    if (values.length > 1) {
+                        console.error("batch values not yet implemented");
+                    } else if (values.length > 0) {
+                        inputs[inputName] = value["values"][0];
+                    }
+                } else {
+                    inputs[inputName] = value;
+                }
+            }
+            const data = {
+                replacement_dict: replacementParams,
+                inputs: inputs,
+                inputs_by: "step_index",
+            };
+            // Consider: copy_inputs_to_history, target_history
+            invokeWorkflow(this.model.workflowId, data)
+                .then((invocation) => {
+                    // emulate multi-invocation mode like other form for now.
+                    const invocations = [invocation];
+                    this.$emit("submissionSuccess", invocations);
+                })
+                .catch((error) => {
+                    console.log(error);
+                });
+        },
+    },
+};
+</script>
diff --git a/client/galaxy/scripts/components/Workflow/Run/model.js b/client/galaxy/scripts/components/Workflow/Run/model.js
index 1e5f2bdba14e..d1bfa3eb5bf5 100644
--- a/client/galaxy/scripts/components/Workflow/Run/model.js
+++ b/client/galaxy/scripts/components/Workflow/Run/model.js
@@ -10,16 +10,19 @@ export class WorkflowRunModel {
         this.runData = runData;
         this.name = runData.name;
         this.workflowResourceParameters = runData.workflow_resource_parameters;
+        this.hasWorkflowResourceParameters = !_.isEmpty(this.workflowResourceParameters);
         this.historyId = runData.history_id;
         this.workflowId = runData.id;
 
         this.hasUpgradeMessages = runData.has_upgrade_messages;
-        this.hasStepVersionChanges = runData.step_version_changes && runData.step_version_changes.length > 0;
+        this.hasStepVersionChanges = !_.isEmpty(runData.step_version_changes);
 
         this.steps = [];
         this.links = [];
         this.parms = [];
         this.wpInputs = {};
+        let hasOpenToolSteps = false;
+        let hasReplacementParametersInToolForm = false;
 
         _.each(runData.steps, (step, i) => {
             var icon = WorkflowIcons[step.step_type];
@@ -130,6 +133,7 @@ export class WorkflowRunModel {
         _.each(this.steps, (step, i) => {
             _.each(this.parms[i], (input, name) => {
                 _handleWorkflowParameter(input.value, (wp_input) => {
+                    hasReplacementParametersInToolForm = true;
                     wp_input.links.push(step);
                     input.wp_linked = true;
                     input.type = "text";
@@ -166,6 +170,7 @@ export class WorkflowRunModel {
                         (input.value && input.value.__class__ == "RuntimeValue" && !input.step_linked)
                     ) {
                         step.collapsed = false;
+                        hasOpenToolSteps = true;
                     }
                     if (is_runtime_value) {
                         input.value = null;
@@ -180,6 +185,8 @@ export class WorkflowRunModel {
                 });
             }
         });
+        this.hasOpenToolSteps = hasOpenToolSteps;
+        this.hasReplacementParametersInToolForm = hasReplacementParametersInToolForm;
     }
 }
 
diff --git a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
index c4a38eded3a7..0c3abddab952 100644
--- a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
+++ b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
@@ -386,6 +386,9 @@ export const getAnalysisRouter = (Galaxy) =>
         /** load workflow by its url in run mode */
         _loadWorkflow: function () {
             const workflowId = QueryStringParsing.get("id");
-            this._display_vue_helper(WorkflowRun, { workflowId: workflowId }, "workflow");
+            // const preferSimpleForm = (QueryStringParsing.get("simple") || "false").toLowerCase() == "true";
+            const Galaxy = getGalaxyInstance();
+            const preferSimpleForm = Galaxy.config.simplified_workflow_run_ui == "prefer";
+            this._display_vue_helper(WorkflowRun, { workflowId, preferSimpleForm }, "workflow");
         },
     });
diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index a34c21ccd518..48f3a22b9d51 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/lib/galaxy/managers/configuration.py
@@ -79,6 +79,7 @@ def _use_config(config, key, **context):
             'ga_code'                           : _use_config,
             'enable_unique_workflow_defaults'   : _use_config,
             'enable_beta_markdown_export'       : _use_config,
+            'simplified_workflow_run_ui'        : _use_config,
             'has_user_tool_filters'             : _defaults_to(False),
             # TODO: is there no 'correct' way to get an api url? controller='api', action='tools' is a hack
             # at any rate: the following works with path_prefix but is still brittle
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 204dd45b84d5..a66c59e3a77c 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -2412,6 +2412,19 @@ mapping:
           When false, the most recently added compatible item in the history will
           be used for each "Set at Runtime" input, independent of others in the workflow.
 
+      simplified_workflow_run_ui:
+        type: str
+        default: 'off'
+        required: false
+        desc: |
+          If set to 'off' by default, always use the traditional workflow form that renders
+          all steps in the GUI and serializes the tool state of all steps during
+          invocation. Set to 'prefer' to default to a simplified workflow UI that
+          only renders the inputs if possible (the workflow must have no disconnected
+          runtime inputs and not replacement parameters within tool steps). In the
+          future 'force' may be added an option for Galaskio-style servers that should
+          only render simplified workflows.
+
       myexperiment_target_url:
         type: str
         default: www.myexperiment.org:80
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index a7ae1aabffaf..bd42b438f091 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -191,6 +191,7 @@
   <tool file="for_workflows/count_list.xml" />
   <tool file="for_workflows/count_multi_file.xml" />
   <tool file="for_workflows/create_input_collection.xml" />
+  <tool file="for_workflows/randomlines.xml" />
 
   <section id="filter" name="For Tours">
     <tool file="for_tours/filtering.xml" />