From 0676fc323aa9e86574ed0433ff4280832e50678d Mon Sep 17 00:00:00 2001
From: yingfeng <yingfeng@iu.edu>
Date: Tue, 7 May 2024 16:44:49 -0400
Subject: [PATCH 1/2] AMP-3152: - fix item-search table row selection style -
 fix deliverable table row selection style - style.scss is added but not in
 use now. could be useful in the future

---
 public/css/style.css                         |  4 ++--
 src/App.vue                                  |  3 +++
 src/components/deliverables/Deliverables.vue |  4 ++--
 src/components/shared/Search.vue             | 11 ++++++++---
 src/styles/style.scss                        |  1 +
 5 files changed, 16 insertions(+), 7 deletions(-)
 create mode 100644 src/styles/style.scss

diff --git a/public/css/style.css b/public/css/style.css
index 6f1cce3b..aa47834c 100644
--- a/public/css/style.css
+++ b/public/css/style.css
@@ -658,8 +658,8 @@ svg.icon-user {
   height: 250px;
   overflow-y: scroll; }
 
-.highlight {
-  background: #F8ECB4; }
+/* .highlight {
+  background: #F8ECB4; } */
 
 .scrollDiv td, .scrollDiv th {
   text-align: left; }
diff --git a/src/App.vue b/src/App.vue
index 5487c8e7..fc8e05ab 100644
--- a/src/App.vue
+++ b/src/App.vue
@@ -62,3 +62,6 @@ export default {
 <style lang="css">
   @import './styles/style.css';
 </style>
+<style lang="scss">
+  @import './styles/style.scss';
+</style>
diff --git a/src/components/deliverables/Deliverables.vue b/src/components/deliverables/Deliverables.vue
index 3ac1efc0..52f2e783 100644
--- a/src/components/deliverables/Deliverables.vue
+++ b/src/components/deliverables/Deliverables.vue
@@ -164,8 +164,8 @@
                         v-on:keyup.down="onArrowDown"
                         v-on:keyup.up="onArrowUp"
                         v-on:click="rowClicked(index)"
-                        v-bind:class="{
-                          highlight: rowSelected(pfile.primaryfileId),
+                        :class="{
+                          'table-dark': rowSelected(pfile.primaryfileId),
                         }"
                       >
                         <td>{{ pfile.collectionName }}</td>
diff --git a/src/components/shared/Search.vue b/src/components/shared/Search.vue
index 5ec07b1d..9d3d6792 100644
--- a/src/components/shared/Search.vue
+++ b/src/components/shared/Search.vue
@@ -332,7 +332,7 @@
                   :class="
                     type === 'item-search'
                       ? source.id === selectedItemId
-                        ? 'item-cls trActive'
+                        ? 'item-cls table-dark'
                         : 'item-cls'
                       : ''
                   "
@@ -1086,9 +1086,14 @@ export default {
 </script>
 
 <style scoped>
+/*
 table tbody tr:nth-of-type(odd) {
   background-color: #f8ecb4;
 }
+.table-striped tbody tr:nth-of-type(odd) {
+  background-color: #f8ecb4;
+}
+*/
 .table td,
 .table th {
   padding: 0.75rem;
@@ -1124,10 +1129,10 @@ table tbody tr:nth-of-type(odd) {
 .item-cls {
   cursor: pointer;
 }
-.trActive {
+/* .trActive {
   background-color: #153c4d !important;
   color: #fff;
-}
+} */
 .trActive {
   animation-name: expandOpen;
   animation-duration: 0.3s;
diff --git a/src/styles/style.scss b/src/styles/style.scss
new file mode 100644
index 00000000..2a5ed915
--- /dev/null
+++ b/src/styles/style.scss
@@ -0,0 +1 @@
+/*$table-bg: #f8ecb4;*/
\ No newline at end of file

From 503b227360ec23fbbe17b27173b83356379995a0 Mon Sep 17 00:00:00 2001
From: yingfeng <yingfeng@iu.edu>
Date: Tue, 7 May 2024 19:06:45 -0400
Subject: [PATCH 2/2] AMP-3081: remove extra system params on WF nodes

---
 src/service/workflow-service.js | 33 ++++++++++++++++++++++-----------
 1 file changed, 22 insertions(+), 11 deletions(-)

diff --git a/src/service/workflow-service.js b/src/service/workflow-service.js
index d06868d7..58ccd3cc 100644
--- a/src/service/workflow-service.js
+++ b/src/service/workflow-service.js
@@ -119,17 +119,20 @@ export default class WorkflowService extends BaseService {
         var tempParams = [];
         return await super.get_auth('/workflows/' + id).then(response => {
             // Get the steps from the response
-            var data = response.data.steps;
+            var steps = response.data.steps;
 
             // If we didn't get an steps, return empty list
-            if (!response.data.steps) {
+            if (!steps) {
                 return tempParams;
             }
 
             // Get the node keys
-            var nodeKeys = Object.keys(data);
+            var nodeKeys = Object.keys(steps);
             for (var nodeKey in nodeKeys) {
-                var thisNode = data[nodeKey];
+                var thisNode = steps[nodeKey];
+
+                // skip input (non-MGM) nodes, which have null toolId and are of type "data_input"
+                if (!thisNode.toolId || thisNode.type == "data_input") continue;
 
                 // Create a new node object
                 var newNode = {
@@ -140,17 +143,23 @@ export default class WorkflowService extends BaseService {
                     params: []
                 };
 
-                // Iterate over the tool inputs and add appropriate
+                // Iterate over the tool inputs and add appropriate parameters
                 var toolInputKeys = Object.keys(thisNode.toolInputs);
                 for (var input = 0; input < toolInputKeys.length; input++) {
                     // Get the input
                     var toolInputKey = toolInputKeys[input];
                     var thisInput = thisNode.toolInputs[toolInputKey];
 
+                    // Note: below code commented out, as we do want to show all user parameters disregarding if the value is empty
                     // If we don't have an input, skip it
-                    if (!thisInput) continue;
-                    // __class__ as far as I can tell, is an indication it is not a parameter
-                    if (thisInput.__class__) continue;
+                    // if (!thisInput) continue;
+
+                    // skip Galaxy workflow system param such as __page__ and __rerun_remap_job_id__,
+                    // assuming no MGM parameter starts and ends with __
+                    if (toolInputKey.startsWith('__') && toolInputKey.endsWith('__')) continue;
+
+                    // skip input value "__class__": "RuntimeValue", which refers to data input of a tool, not a parameter.
+                    if (thisInput && thisInput.__class__) continue;
 
                     // Add the parameter
                     newNode.params.push({
@@ -160,10 +169,12 @@ export default class WorkflowService extends BaseService {
                     });
 
                 }
+                
+                // Note: below condition is commented out, as we do want to show all steps disregarding if it has any param
                 // If we had any params, add it to the list of nodes with params
-                if (newNode.params.length > 0) {
-                    tempParams.push(newNode);
-                }
+                // if (newNode.params.length > 0) {
+                tempParams.push(newNode);
+                // }
             }
             return { tempParams: tempParams, response: response.data };
         });