From 5bad46929620d590c8a603ac204ce98f8a51d6aa Mon Sep 17 00:00:00 2001
From: Adam Rauch <adam@labkey.com>
Date: Sat, 13 Jul 2024 08:33:49 -0700
Subject: [PATCH 1/2] Migrate .view.xml files from deprecated <permissions>
 elements to <permissionClasses> (#298)

---
 OpenLdapSync/resources/views/ldapSettings.view.xml         | 6 +++---
 SequenceAnalysis/resources/views/importFasta.view.xml      | 6 +++---
 SequenceAnalysis/resources/views/importTracks.view.xml     | 6 +++---
 SequenceAnalysis/resources/views/sequenceDefaults.view.xml | 6 +++---
 SequenceAnalysis/resources/views/siteAdmin.view.xml        | 6 +++---
 blast/resources/views/settings.view.xml                    | 6 +++---
 jbrowse/resources/views/databaseDetails.view.xml           | 6 +++---
 jbrowse/resources/views/genotypeTable.view.xml             | 6 +++---
 jbrowse/resources/views/jbrowseSearch.view.xml             | 6 +++---
 jbrowse/src/client/entryPoints.js                          | 7 +++----
 10 files changed, 30 insertions(+), 31 deletions(-)

diff --git a/OpenLdapSync/resources/views/ldapSettings.view.xml b/OpenLdapSync/resources/views/ldapSettings.view.xml
index 9b9473d9f..b510de0ca 100644
--- a/OpenLdapSync/resources/views/ldapSettings.view.xml
+++ b/OpenLdapSync/resources/views/ldapSettings.view.xml
@@ -1,7 +1,7 @@
 <view xmlns="http://labkey.org/data/xml/view" title="LDAP Sync Settings">
-    <permissions>
-        <permission name="admin"/>
-    </permissions>
+    <permissionClasses>
+        <permissionClass name="org.labkey.api.security.permissions.AdminPermission"/>
+    </permissionClasses>
     <dependencies>
         <dependency path="clientapi"/>
         <dependency path="clientapi_core"/>
diff --git a/SequenceAnalysis/resources/views/importFasta.view.xml b/SequenceAnalysis/resources/views/importFasta.view.xml
index b6f2f7655..3b317b30f 100644
--- a/SequenceAnalysis/resources/views/importFasta.view.xml
+++ b/SequenceAnalysis/resources/views/importFasta.view.xml
@@ -1,7 +1,7 @@
 <view xmlns="http://labkey.org/data/xml/view" title="Import Sequence Data">
-    <permissions>
-        <permission name="insert"/>
-    </permissions>
+    <permissionClasses>
+        <permissionClass name="org.labkey.api.security.permissions.InsertPermission"/>
+    </permissionClasses>
     <dependencies>
         <dependency path="laboratory.context"/>
         <dependency path="SequenceAnalysis/sequenceAnalysis"/>
diff --git a/SequenceAnalysis/resources/views/importTracks.view.xml b/SequenceAnalysis/resources/views/importTracks.view.xml
index 4158cfcb8..8da8edb7a 100644
--- a/SequenceAnalysis/resources/views/importTracks.view.xml
+++ b/SequenceAnalysis/resources/views/importTracks.view.xml
@@ -1,7 +1,7 @@
 <view xmlns="http://labkey.org/data/xml/view" title="Import Tracks">
-    <permissions>
-        <permission name="insert"/>
-    </permissions>
+    <permissionClasses>
+        <permissionClass name="org.labkey.api.security.permissions.InsertPermission"/>
+    </permissionClasses>
     <dependencies>
         <dependency path="laboratory.context"/>
         <dependency path="SequenceAnalysis/sequenceAnalysis"/>
diff --git a/SequenceAnalysis/resources/views/sequenceDefaults.view.xml b/SequenceAnalysis/resources/views/sequenceDefaults.view.xml
index 7c6c756bd..1b574fcf9 100644
--- a/SequenceAnalysis/resources/views/sequenceDefaults.view.xml
+++ b/SequenceAnalysis/resources/views/sequenceDefaults.view.xml
@@ -1,7 +1,7 @@
 <view xmlns="http://labkey.org/data/xml/view" title="DISCVR-Seq Settings">
-    <permissions>
-        <permission name="admin"/>
-    </permissions>
+    <permissionClasses>
+        <permissionClass name="org.labkey.api.security.permissions.AdminPermission"/>
+    </permissionClasses>
     <dependencies>
         <dependency path="laboratory.context"/>
         <dependency path="SequenceAnalysis/sequenceAnalysis"/>
diff --git a/SequenceAnalysis/resources/views/siteAdmin.view.xml b/SequenceAnalysis/resources/views/siteAdmin.view.xml
index d13a756fe..eb5771bc0 100644
--- a/SequenceAnalysis/resources/views/siteAdmin.view.xml
+++ b/SequenceAnalysis/resources/views/siteAdmin.view.xml
@@ -1,7 +1,7 @@
 <view xmlns="http://labkey.org/data/xml/view" title="DISCVR-Seq Site Settings">
-    <permissions>
-        <permission name="admin"/>
-    </permissions>
+    <permissionClasses>
+        <permissionClass name="org.labkey.api.security.permissions.AdminPermission"/>
+    </permissionClasses>
     <dependencies>
         <dependency path="laboratory.context"/>
         <dependency path="SequenceAnalysis/sequenceAnalysis"/>
diff --git a/blast/resources/views/settings.view.xml b/blast/resources/views/settings.view.xml
index b2bab0e72..5ba49ad93 100644
--- a/blast/resources/views/settings.view.xml
+++ b/blast/resources/views/settings.view.xml
@@ -1,7 +1,7 @@
 <view xmlns="http://labkey.org/data/xml/view" title="BLAST Settings">
-    <permissions>
-        <permission name="admin"/>
-    </permissions>
+    <permissionClasses>
+        <permissionClass name="org.labkey.api.security.permissions.AdminPermission"/>
+    </permissionClasses>
     <dependencies>
         <dependency path="laboratory.context" />
     </dependencies>
diff --git a/jbrowse/resources/views/databaseDetails.view.xml b/jbrowse/resources/views/databaseDetails.view.xml
index d4ee31086..998b2b750 100644
--- a/jbrowse/resources/views/databaseDetails.view.xml
+++ b/jbrowse/resources/views/databaseDetails.view.xml
@@ -1,7 +1,7 @@
 <view xmlns="http://labkey.org/data/xml/view" title="JBrowse Session" frame="none">
-    <permissions>
-        <permission name="admin"/>
-    </permissions>
+    <permissionClasses>
+        <permissionClass name="org.labkey.api.security.permissions.AdminPermission"/>
+    </permissionClasses>
     <dependencies>
         <dependency path="laboratory.context" />
     </dependencies>
diff --git a/jbrowse/resources/views/genotypeTable.view.xml b/jbrowse/resources/views/genotypeTable.view.xml
index f7c07a79c..590ba906a 100644
--- a/jbrowse/resources/views/genotypeTable.view.xml
+++ b/jbrowse/resources/views/genotypeTable.view.xml
@@ -1,7 +1,7 @@
 <view xmlns="http://labkey.org/data/xml/view" title="Genotypes">
-    <permissions>
-        <permission name="read"/>
-    </permissions>
+    <permissionClasses>
+        <permissionClass name="org.labkey.api.security.permissions.ReadPermission"/>
+    </permissionClasses>
     <dependencies>
         <dependency path="laboratory.context" />
         <dependency path="internal/jQuery"/>
diff --git a/jbrowse/resources/views/jbrowseSearch.view.xml b/jbrowse/resources/views/jbrowseSearch.view.xml
index 91c3d19cd..9ade1f085 100644
--- a/jbrowse/resources/views/jbrowseSearch.view.xml
+++ b/jbrowse/resources/views/jbrowseSearch.view.xml
@@ -1,7 +1,7 @@
 <view xmlns="http://labkey.org/data/xml/view" title="JBrowse Search">
-    <permissions>
-        <permission name="read"/>
-    </permissions>
+    <permissionClasses>
+        <permissionClass name="org.labkey.api.security.permissions.ReadPermission"/>
+    </permissionClasses>
     <dependencies>
         <dependency path="gen/jbrowse2SearchWebpart.lib.xml"/>
         <dependency path="LDK.context"/>
diff --git a/jbrowse/src/client/entryPoints.js b/jbrowse/src/client/entryPoints.js
index 0696b39e4..4c5963301 100644
--- a/jbrowse/src/client/entryPoints.js
+++ b/jbrowse/src/client/entryPoints.js
@@ -7,24 +7,23 @@ module.exports = {
     apps: [{
         name: 'jbrowseBrowser',
         title: 'JBrowse Genome Browser',
-        permission: 'read',
+        permissionClasses: ['org.labkey.api.security.permissions.ReadPermission'],
         path: './src/client/JBrowse/Browser'
     },{
         name: 'jbrowse2SearchWebpart',
         title: 'JBrowse Search',
-        permission: 'read',
         template: 'app',
         generateLib: true,
         path: './src/client/JBrowse/Search/webpart'
     },{
         name: 'variantSearch',
         title: 'Variant Search',
-        permission: 'read',
+        permissionClasses: ['org.labkey.api.security.permissions.ReadPermission'],
         path: './src/client/JBrowse/VariantSearch'
     },{
         name: 'variantTable',
         title: 'Variant Table',
-        permission: 'read',
+        permissionClasses: ['org.labkey.api.security.permissions.ReadPermission'],
         path: './src/client/JBrowse/VariantTable'
     }]
 };

From 5feff7b476593d6457d7a35d975aabbab1591e2c Mon Sep 17 00:00:00 2001
From: Adam Rauch <adam@labkey.com>
Date: Wed, 24 Jul 2024 09:28:40 -0700
Subject: [PATCH 2/2] Remove empty <permissions> element (#302)

---
 cluster/resources/views/begin.view.xml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/cluster/resources/views/begin.view.xml b/cluster/resources/views/begin.view.xml
index 5da101db6..10ee8bcd7 100644
--- a/cluster/resources/views/begin.view.xml
+++ b/cluster/resources/views/begin.view.xml
@@ -1,7 +1,4 @@
 <view xmlns="http://labkey.org/data/xml/view" title="Cluster Module">
-    <permissions>
-
-    </permissions>
     <dependencies>
         <dependency path="Ext4ClientApi" />
     </dependencies>