PIXI-157: Rename Patient-Derived Xenografts table to Patient-Derived …

…Tumors in the plugin settings (#21)
preclinical-imaging · Dec 19, 2024 · bcffb01 · bcffb01
1 parent 7ab7940
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diff --git a/CHANGELOG.MD b/CHANGELOG.MD
@@ -16,6 +16,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [PIXI-141]: A few internal changes to support XNAT 1.9 compatibility. The plugin is now works with XNAT 1.9.
 
+### Changed
+
+- [PIXI-157]: Rename Patient-Derived Xenografts table to Patient-Derived Tumors in the plugin settings. The table name
+              was misleading and did not reflect that we are storing tumor model data, not animal model data.
+
 ## [1.3.1] - 20204-11-19
 
 ### Added
@@ -144,4 +149,5 @@ plugins directory and restart XNAT.
 [PIXI-153]: https://radiologics.atlassian.net/browse/PIXI-153
 [PIXI-154]: https://radiologics.atlassian.net/browse/PIXI-154
 [PIXI-155]: https://radiologics.atlassian.net/browse/PIXI-155
-[PIXI-156]: https://radiologics.atlassian.net/browse/PIXI-156
+[PIXI-156]: https://radiologics.atlassian.net/browse/PIXI-156
+[PIXI-157]: https://radiologics.atlassian.net/browse/PIXI-157
diff --git a/src/main/resources/META-INF/resources/scripts/xnat/plugin/pixi/pixi-xenograft.js b/src/main/resources/META-INF/resources/scripts/xnat/plugin/pixi/pixi-xenograft.js
@@ -354,7 +354,7 @@ XNAT.plugin.pixi.pdxs = getObject(XNAT.plugin.pixi.pdxs || {});
 
     class PDXManager extends XenograftManager {
         constructor() {
-            super('PDX');
+            super('Patient-Derived Tumor');
         }
 
         getSpawnerElements() {
@@ -363,9 +363,9 @@ XNAT.plugin.pixi.pdxs = getObject(XNAT.plugin.pixi.pdxs || {});
             spawnerElements.push(
                 XNAT.ui.panel.input.text({
                 name: 'storage',
-                label: 'PDX Storage',
+                label: 'Storage',
                 id: 'storage',
-                description: 'Optional: PDX storage method.'
+                description: 'Optional: Storage method for this tumor model.'
             }).element)
 
             return spawnerElements;

diff --git a/.../resources/META-INF/resources/scripts/xnat/plugin/pixi/pixi-xenograftExperimentManager.js b/.../resources/META-INF/resources/scripts/xnat/plugin/pixi/pixi-xenograftExperimentManager.js
@@ -22,7 +22,7 @@ XNAT.plugin.pixi = pixi = getObject(XNAT.plugin.pixi || {});
     XNAT.plugin.pixi.pdxExperimentManager = class PdxExperimentManager extends XNAT.plugin.pixi.abstractExperimentManager {
 
         constructor() {
-            super("PIXI Patient-derived Tumor Engraftment Data Manager",
+            super("Patient-derived Tumor Engraftment Data Manager",
                   "Record and update patient-derived tumor tissue engraftments for small animal subjects within a project.",
                   "<div class='instructions action create whole'><ol>\n" +
                       "  <li>Select the project from the list of available projects in XNAT.</li>\n" +
@@ -80,7 +80,7 @@ XNAT.plugin.pixi = pixi = getObject(XNAT.plugin.pixi || {});
             let colHeaders = [
                 "Subject ID *",
                 "Experiment ID",
-                "PDX ID *",
+                "Patient-Derived Tumor ID *",
                 "Injection Date *",
                 "Injection Site",
                 "Injection Type",
@@ -90,7 +90,7 @@ XNAT.plugin.pixi = pixi = getObject(XNAT.plugin.pixi || {});
                 "Notes"
             ];
 
-            let colWidths = [150, 100, 150, 100, 150, 150, 150, 150, 115, 130];
+            let colWidths = [150, 100, 200, 100, 150, 150, 150, 150, 115, 130];
 
             const pdxs = await XNAT.plugin.pixi.pdxs.get()
                                    .then(pdxs => pdxs.sort(pixi.compareGenerator('sourceId')))
@@ -263,7 +263,7 @@ XNAT.plugin.pixi = pixi = getObject(XNAT.plugin.pixi || {});
     XNAT.plugin.pixi.cellLineExperimentManager = class CellLineExperimentManager extends XNAT.plugin.pixi.abstractExperimentManager {
 
         constructor() {
-            super("PIXI Cell Line Data Manager",
+            super("Cell Line Data Manager",
                   "Record and update cell line injections for small animal subjects within a project.",
                   "<div class='instructions action create whole'><ol>\n" +
                       "  <li>Select the project from the list of available projects in XNAT.</li>\n" +

diff --git a/src/main/resources/META-INF/resources/templates/screens/XDATScreen_edit_pixi_pdxData.vm b/src/main/resources/META-INF/resources/templates/screens/XDATScreen_edit_pixi_pdxData.vm
@@ -71,7 +71,7 @@ $page.setVlinkColor($ui.vlink)
                                     }
                                 </style>
                                 <tr>
-                                    #formLabelRequired("PDX ID")
+                                    #formLabelRequired("Patient-Derived Tumor ID")
                                     <td>
                                         <div class="choices__select__pixi form-control" id="pixi:pdxData/sourceId-select">
                                             <select name="pixi:pdxData/sourceId" id="pixi:pdxData/sourceId" required>
@@ -89,7 +89,7 @@ $page.setVlinkColor($ui.vlink)
                                             </select>
                                         </div>
                                     </td>
-                                    <td><button id="new-pdx-button" type="button" onclick="XNAT.plugin.pixi.pdxManager.dialog({}, true, updateChoices)">New PDX</button></td>
+                                    <td><button id="new-pdx-button" type="button" onclick="XNAT.plugin.pixi.pdxManager.dialog({}, true, updateChoices)">New Patient-Derived Tumor</button></td>
                                 </tr>
                                 <tr>
                                     #formLabelRequired("Injection Date")
@@ -167,7 +167,7 @@ $page.setVlinkColor($ui.vlink)
         const injectionYearEl = document.getElementsByName("pixi:pdxData/date.year")[0]
 
         let validateSourceId = XNAT.validate(sourceIdEl).reset().chain();
-        validateSourceId.required(true).failure("PDX ID is required.")
+        validateSourceId.required(true).failure("Patient-Derived Tumor ID is required.")
 
         let validateMonth = XNAT.validate(injectionMonthEl).reset().chain();
         validateMonth.is('integer').failure("Injection Date is required.")

diff --git a/src/main/resources/META-INF/resources/templates/screens/XDATScreen_report_pixi_pdxData.vm b/src/main/resources/META-INF/resources/templates/screens/XDATScreen_report_pixi_pdxData.vm
@@ -24,7 +24,7 @@ $page.setVlinkColor($ui.vlink)
 				<TR>
 					<TD valign="top">
 						<TABLE>
-							<TR><TD>PDX ID</TD><TD>$!item.getStringProperty("pixi:pdxData/sourceId")</TD></TR>
+							<TR><TD>Patient-Derived Tumor ID</TD><TD>$!item.getStringProperty("pixi:pdxData/sourceId")</TD></TR>
 							<TR><TD>Injection Date</TD><TD>$!item.getProperty("pixi:pdxData/date")</TD></TR>
 							<TR><TD>Injection Site</TD><TD>$!item.getStringProperty("pixi:pdxData/injectionSite")</TD></TR>
 							<TR><TD>Injection Type</TD><TD>$!item.getStringProperty("pixi:pdxData/injectionType")</TD></TR>

diff --git a/src/main/resources/META-INF/resources/templates/screens/pixi_pdxData_search.vm b/src/main/resources/META-INF/resources/templates/screens/pixi_pdxData_search.vm
@@ -24,7 +24,7 @@
             </tr>
             <tr>
                 <td>
-                    <h5>PDX ID:</h5>
+                    <h5>Patient-Derived Tumor ID:</h5>
                     #xdatSearchField($schemaElement $schemaElement.getDisplayField("SOURCEID"))
                 </td>
                 <td>

diff --git a/src/main/resources/META-INF/xnat/spawner/pixi/site-settings.yaml b/src/main/resources/META-INF/xnat/spawner/pixi/site-settings.yaml
@@ -106,7 +106,7 @@ animalEndpointsPanel:
 pdxPanel:
   kind: panel
   name: pdxPanel
-  label: Patient-Derived Xenografts
+  label: Patient-Derived Tumors
   contents:
     pdxPreferencesTable:
       tag: "div#pdx-manager"
@@ -212,10 +212,10 @@ siteSettings:
         ${speciesPreferencesPanel}
         ${vendorPreferencesPanel}
         ${animalEndpointsPanel}
-    xenograftSettingsTab:
+    tumorModelSettingsTab:
       kind: tab
-      name: xenograftSettingsTab
-      label: PDXs and Cell Lines
+      name: tumorModelSettingsTab
+      label: Tumor Models
       group: pixiTabGroup
       active: true
       contents:

diff --git a/src/main/resources/schemas/pixi/display/pixi_pdxData_display.xml b/src/main/resources/schemas/pixi/display/pixi_pdxData_display.xml
@@ -113,7 +113,7 @@
             <MappingColumn schemaField="pixi:pdxData.ID" queryField="expt_id"/>
         </MappingColumns>
     </DisplayField>
-    <DisplayField id="SOURCEID" header="PDX ID" visible="true" searchable="true">
+    <DisplayField id="SOURCEID" header="Patient-Derived Tumor ID" visible="true" searchable="true">
         <DisplayFieldElement name="Field1" schema-element="pixi:pdxData/sourceId"/>
     </DisplayField>
     <DisplayField id="INJECTIONSITE" header="Injection Site" visible="true" searchable="true">
-Original file line number
+Diff line change
@@ Expand Up / @@ -24,7 +24,7 @@ @@
                 </tr>
                 <tr>
                     <td>
-                        <h5>PDX ID:</h5>
+                        <h5>Patient-Derived Tumor ID:</h5>
                         #xdatSearchField($schemaElement $schemaElement.getDisplayField("SOURCEID"))
                     </td>
                     <td>
@@ Expand Down @@