Update version to 2.27.1 and rebuild docs

NCEAS · Dec 19, 2023 · 758ff8e · 758ff8e
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diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@ MetacatUI is an open source, community project.  We [welcome contributions](http
 
 Cite this software as:
 
-> Matthew B. Jones, Chris Jones, Lauren Walker, Robyn Thiessen-Bock, Ben Leinfelder, Peter Slaughter, Bryce Mecum, Rushiraj Nenuji, Hesham Elbashandy, Val Hendrix. 2022. MetacatUI: A client-side web interface for DataONE data repositories (version 2.27.0). Arctic Data Center. [doi:10.18739/A25M6282K](https://doi.org/10.18739/A25M6282K)
+> Matthew B. Jones, Chris Jones, Lauren Walker, Robyn Thiessen-Bock, Ben Leinfelder, Peter Slaughter, Bryce Mecum, Rushiraj Nenuji, Hesham Elbashandy, Val Hendrix. 2023. MetacatUI: A client-side web interface for DataONE data repositories (version 2.27.1). Arctic Data Center. [doi:10.18739/A25M6282K](https://doi.org/10.18739/A25M6282K)
 
 ## Screenshots
 

diff --git a/docs/_config.yml b/docs/_config.yml
@@ -1,3 +1,3 @@
 url: "/metacatui"
 highlighter: "rouge"
-version: "2.27.0"
+version: "2.27.1"
diff --git a/docs/docs/AccessPolicy.html b/docs/docs/AccessPolicy.html
@@ -564,7 +564,7 @@ <h4 class="name" id="getSubjectInfo">
 
     <dt class="tag-source">Source:</dt>
     <dd class="tag-source"><ul class="dummy"><li>
-        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line312">line 312</a>
+        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line311">line 311</a>
     </li></ul></dd>
 
 
@@ -659,7 +659,7 @@ <h4 class="name" id="hasOwner">
 
     <dt class="tag-source">Source:</dt>
     <dd class="tag-source"><ul class="dummy"><li>
-        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line339">line 339</a>
+        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line338">line 338</a>
     </li></ul></dd>
 
 
@@ -822,7 +822,7 @@ <h5>Parameters:</h5>
 
     <dt class="tag-source">Source:</dt>
     <dd class="tag-source"><ul class="dummy"><li>
-        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line248">line 248</a>
+        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line247">line 247</a>
     </li></ul></dd>
 
 
@@ -944,7 +944,7 @@ <h4 class="name" id="isAuthorizedUpdateSysMeta">
 
     <dt class="tag-source">Source:</dt>
     <dd class="tag-source"><ul class="dummy"><li>
-        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line288">line 288</a>
+        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line287">line 287</a>
     </li></ul></dd>
 
 
@@ -1057,7 +1057,7 @@ <h4 class="name" id="isPublic">
 
     <dt class="tag-source">Source:</dt>
     <dd class="tag-source"><ul class="dummy"><li>
-        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line222">line 222</a>
+        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line221">line 221</a>
     </li></ul></dd>
 
 
@@ -1170,7 +1170,7 @@ <h4 class="name" id="makePrivate">
 
     <dt class="tag-source">Source:</dt>
     <dd class="tag-source"><ul class="dummy"><li>
-        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line155">line 155</a>
+        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line154">line 154</a>
     </li></ul></dd>
 
 
@@ -1265,7 +1265,7 @@ <h4 class="name" id="makePublic">
 
     <dt class="tag-source">Source:</dt>
     <dd class="tag-source"><ul class="dummy"><li>
-        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line182">line 182</a>
+        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line181">line 181</a>
     </li></ul></dd>
 
 
@@ -1553,7 +1553,7 @@ <h5>Parameters:</h5>
 
     <dt class="tag-source">Source:</dt>
     <dd class="tag-source"><ul class="dummy"><li>
-        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line328">line 328</a>
+        <a href="src_js_collections_AccessPolicy.js.html">src/js/collections/AccessPolicy.js</a>, <a href="src_js_collections_AccessPolicy.js.html#line327">line 327</a>
     </li></ul></dd>
 
 
@@ -1594,7 +1594,7 @@ <h4 class="name" id="serialize">
         <svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="link" class="svg-inline--fa fa-link fa-w-16" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path fill="currentColor" d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"></path></svg>
 
       </a>
-      <span class="type-signature"></span>serialize<span class="signature">()</span><span class="type-signature"> &rarr; {string}</span>
+      <span class="type-signature"></span>serialize<span class="signature">()</span><span class="type-signature"> &rarr; {object}</span>
     </h4>
 
 
@@ -1677,7 +1677,7 @@ <h5>Returns:</h5>
 
 
 <div class="param-desc">
-    A string of the access policy XML
+    A XML object of the access policy or null if empty
 </div>
 
 
@@ -1688,7 +1688,7 @@ <h5>Returns:</h5>
     </dt>
     <dd>
 
-<span class="param-type">string</span>
+<span class="param-type">object</span>
 
 
     </dd>

diff --git a/docs/docs/AccessRule.html b/docs/docs/AccessRule.html
@@ -234,7 +234,7 @@ <h4 class="name" id=".getSubjectInfo">
 
     <dt class="tag-source">Source:</dt>
     <dd class="tag-source"><ul class="dummy"><li>
-        <a href="src_js_models_AccessRule.js.html">src/js/models/AccessRule.js</a>, <a href="src_js_models_AccessRule.js.html#line100">line 100</a>
+        <a href="src_js_models_AccessRule.js.html">src/js/models/AccessRule.js</a>, <a href="src_js_models_AccessRule.js.html#line124">line 124</a>
     </li></ul></dd>
 
 
@@ -328,7 +328,7 @@ <h4 class="name" id=".isGroup">
 
     <dt class="tag-source">Source:</dt>
     <dd class="tag-source"><ul class="dummy"><li>
-        <a href="src_js_models_AccessRule.js.html">src/js/models/AccessRule.js</a>, <a href="src_js_models_AccessRule.js.html#line206">line 206</a>
+        <a href="src_js_models_AccessRule.js.html">src/js/models/AccessRule.js</a>, <a href="src_js_models_AccessRule.js.html#line230">line 230</a>
     </li></ul></dd>
 
 
@@ -552,7 +552,7 @@ <h4 class="name" id=".serialize">
         <svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="link" class="svg-inline--fa fa-link fa-w-16" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path fill="currentColor" d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"></path></svg>
 
       </a>
-      <span class="type-signature"></span>serialize<span class="signature">()</span><span class="type-signature"> &rarr; {string}</span>
+      <span class="type-signature"></span>serialize<span class="signature">()</span><span class="type-signature"> &rarr; {object}</span>
     </h4>
 
 
@@ -606,7 +606,7 @@ <h4 class="name" id=".serialize">
 
     <dt class="tag-source">Source:</dt>
     <dd class="tag-source"><ul class="dummy"><li>
-        <a href="src_js_models_AccessRule.js.html">src/js/models/AccessRule.js</a>, <a href="src_js_models_AccessRule.js.html#line60">line 60</a>
+        <a href="src_js_models_AccessRule.js.html">src/js/models/AccessRule.js</a>, <a href="src_js_models_AccessRule.js.html#line89">line 89</a>
     </li></ul></dd>
 
 
@@ -635,7 +635,7 @@ <h5>Returns:</h5>
 
 
 <div class="param-desc">
-    The access rule XML string
+    The access rule XML object or null if not created
 </div>
 
 
@@ -646,7 +646,7 @@ <h5>Returns:</h5>
     </dt>
     <dd>
 
-<span class="param-type">string</span>
+<span class="param-type">object</span>
 
 
     </dd>

diff --git a/docs/docs/src_js_collections_AccessPolicy.js.html b/docs/docs/src_js_collections_AccessPolicy.js.html
@@ -170,28 +170,27 @@ <h1 class="page-title">Source: src/js/collections/AccessPolicy.js</h1>
           },
 
           /**
-          * Creates an access policy XML from the values set on the member
-          * AccessRule models.
-          * @return {string} A string of the access policy XML
-          */
-          serialize: function(){
-
-            if( this.length == 0 )
-              return "";
+           * Creates an access policy XML from the values set on the member
+           * AccessRule models.
+           * @returns {object} A XML object of the access policy or null if empty
+           */
+          serialize: function() {
+            if (this.length === 0) {
+                return null;
+            }
 
-            //Create the access policy node which will contain all the rules
-            var xml = "&lt;accessPolicy>\n";
+            // Create the access policy node which will contain all the rules
+            var accessPolicyElement = document.createElement('accesspolicy');
 
-            //Serialize each AccessRule member model and add to the policy DOM
-            this.each(function(accessRule){
-              xml += accessRule.serialize();
+            // Serialize each AccessRule member model and add to the policy DOM
+            this.each(function(accessRule) {
+                var accessRuleNode = accessRule.serialize();
+                if (accessRuleNode) {
+                    accessPolicyElement.appendChild(accessRuleNode);
+                }
             });
 
-            xml += "\n&lt;/accessPolicy>"
-
-            //Convert the access policy DOM to a string and return it
-            return xml;
-
+            return accessPolicyElement;
           },
 
           /**

diff --git a/docs/docs/src_js_models_AccessRule.js.html b/docs/docs/src_js_models_AccessRule.js.html
@@ -74,71 +74,95 @@ <h1 class="page-title">Source: src/js/models/AccessRule.js</h1>
 		},
 
 		/**
-		* Translates the access rule XML DOM into a JSON object to be set on the model.
-		* @param {Element} accessRuleXML An &lt;allow> DOM element that contains a single access rule
-		* @return {JSON} The Access Rule values to be set on this model
-		*/
-		parse: function( accessRuleXML ){
-			//If there is no access policy, do not attempt to parse anything
-			if( typeof accessRuleXML == "undefined" || !accessRuleXML)
-				return {};
-
-			accessRuleXML = $(accessRuleXML);
-
-			//Start an access rule object with the given subject
-			var parsedAccessRule = {
-						subject: accessRuleXML.find("subject").text()
-				  }
-
-			_.each( accessRuleXML.find("permission"), function( permissionNode ){
-				parsedAccessRule[ $(permissionNode).text() ] = true;
-			});
+     * Translates the access rule XML DOM into a JSON object to be set on the model.
+     * @param {Element} accessRuleXML An &lt;allow> DOM element that contains a single access rule
+     * @return {JSON} The Access Rule values to be set on this model
+     */
+    parse: function(accessRuleXML) {
+      // If there is no access policy, do not attempt to parse anything
+      if (typeof accessRuleXML === "undefined" || !accessRuleXML) {
+        return {};
+      }
 
-			return parsedAccessRule;
+      var accessRuleXMLObj = $(accessRuleXML);
 
-		},
+      // Start an access rule object with the given subject
+      var parsedAccessRule = {
+        subject: accessRuleXMLObj.find("subject").text()
+      };
 
-		/**
-		* Takes the values set on this model's attributes and creates an XML string
-		* to be inserted into a DataONEObject's system metadata access policy.
-		* @return {string} The access rule XML string
-		*/
-		serialize: function(){
+      _.each(accessRuleXMLObj.find("permission"), function(permissionNode, idx) {
+        let permissionText = $(permissionNode).text().trim();
 
-				var xml = "";
+        // Check if the permission text is not empty
+        if (permissionText.length) {
+          // Save the parsed permission
+          parsedAccessRule[permissionText] = true;
+        } else {
+          // This is added as a workaround for malformed permission XML
+          // introduced by Chromium 120.X
+          // See https://github.com/NCEAS/metacatui/issues/2235
 
-				//Serialize the allow rules
-				if( this.get("read") || this.get("write") || this.get("changePermission") ){
+          // Define the regular expression
+          let globalPermRegex = /&lt;permission>&lt;\/permission>(.*)/g;
+          // Define the regular expression
+          let permRegex = /&lt;permission>&lt;\/permission>(.*)/;
 
-					//Start the "allow" node
-					xml += '\t&lt;allow>\n';
+          let accessRoleStr = accessRuleXMLObj.html();
 
-					//Add the subject
-					xml += '\t\t&lt;subject>' + this.get("subject") + '&lt;/subject>\n';
+          let matches = accessRoleStr.match(globalPermRegex);
 
-					//Add the read permission
-					if( this.get("read") ){
-						xml += '\t\t&lt;permission>read&lt;/permission>\n';
-					}
+          // Check if matches exist and have a length
+          if (matches &amp;&amp; matches.length &amp;&amp; idx &lt; matches.length) {
+            let permMatch = matches[idx].match(permRegex);
 
-					//Add the write permission
-					if( this.get("write") ){
-						xml += '\t\t&lt;permission>write&lt;/permission>\n';
-					}
+            // Check if permMatch exists and has a length
+            if (permMatch &amp;&amp; permMatch.length) {
+              parsedAccessRule[permMatch[1]] = true;
+            }
+          }
+        }
+      });
 
-					//Add the changePermission permission
-					if( this.get("changePermission") ){
-						xml += '\t\t&lt;permission>changePermission&lt;/permission>\n';
-					}
+      return parsedAccessRule;
+    },
 
-					//Close the "allow" node
-					xml += '\t&lt;/allow>\n';
+		/**
+     * Takes the values set on this model's attributes and creates an XML string
+     * to be inserted into a DataONEObject's system metadata access policy.
+     * @returns {object} The access rule XML object or null if not created
+     */
+    serialize: function() {
+      // Serialize the allow rules
+      if (this.get("read") || this.get("write") || this.get("changePermission")) {
+          // Create the &lt;allow> element
+          var allowElement = document.createElement('allow');
+
+          // Create the &lt;subject> element and set its text content
+          var subjectElement = document.createElement('subject');
+          subjectElement.textContent = this.get("subject");
+
+          // Append the &lt;subject> and &lt;permission> elements to &lt;allow>
+          allowElement.appendChild(subjectElement);
+
+          // Create the &lt;permission> elements and set their text content
+          var permissions = ['read', 'write', 'changePermission'];
+          for (var i = 0; i &lt; permissions.length; i++) {
+              if (this.get(permissions[i])) {
+                  var permissionElement = document.createElement('permission');
+                  permissionElement.textContent = permissions[i];
+                  allowElement.appendChild(permissionElement);
+              }
+          }
 
-				}
+          // Return the &lt;allow> element
+          return allowElement;
+      }
 
-			return xml;
+      // If no access rule is created, return null
+      return null;
+    },
 
-		},
 
     /**
     * Gets and sets the subject info for the subjects in this access policy.

diff --git a/docs/index.md b/docs/index.md
@@ -22,7 +22,7 @@ MetacatUI is an open source, community project.  We [welcome contributions](http
 
 Cite this software as:
 
-> Matthew B. Jones, Chris Jones, Lauren Walker, Robyn Thiessen-Bock, Ben Leinfelder, Peter Slaughter, Bryce Mecum, Rushiraj Nenuji, Hesham Elbashandy, Val Hendrix. 2022. MetacatUI: A client-side web interface for DataONE data repositories (version 2.24.0). Arctic Data Center. [doi:10.18739/A25M6282K](https://doi.org/10.18739/A25M6282K)
+> Matthew B. Jones, Chris Jones, Lauren Walker, Robyn Thiessen-Bock, Ben Leinfelder, Peter Slaughter, Bryce Mecum, Rushiraj Nenuji, Hesham Elbashandy, Val Hendrix. 2023. MetacatUI: A client-side web interface for DataONE data repositories (version 2.27.1). Arctic Data Center. [doi:10.18739/A25M6282K](https://doi.org/10.18739/A25M6282K)
 
 ## Related Projects
 

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "metacatui",
-  "version": "2.27.0",
+  "version": "2.27.1",
   "description": "MetacatUI: A client-side web interface for DataONE data repositories",
   "main": "server.js",
   "dependencies": {

diff --git a/src/index.html b/src/index.html
@@ -44,7 +44,7 @@
 
     //Create the MetacatUI object
     var MetacatUI = {};
-    MetacatUI.metacatUIVersion = "2.27.0";
+    MetacatUI.metacatUIVersion = "2.27.1";
 
     //Catch errors when the config or loader file fails to load.
     // These are mainly helpful for developers/operators installing MetacatUI