From cd77289d5cdf950d45066215dda047aeaa76587f Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Mon, 27 Mar 2023 10:33:55 +0200
Subject: [PATCH 01/30] Improve input params handling (#92)

---
 .../mapred/api/v2/jobs/SubmitJob.java         | 15 +++---
 .../mapred/api/v2/jobs/SubmitJobTest.java     | 54 +++++++++++++------
 test-data/print-hidden-inputs.yaml            |  2 +-
 3 files changed, 47 insertions(+), 24 deletions(-)

diff --git a/src/main/java/cloudgene/mapred/api/v2/jobs/SubmitJob.java b/src/main/java/cloudgene/mapred/api/v2/jobs/SubmitJob.java
index d3c58a9c..550dc7f3 100644
--- a/src/main/java/cloudgene/mapred/api/v2/jobs/SubmitJob.java
+++ b/src/main/java/cloudgene/mapred/api/v2/jobs/SubmitJob.java
@@ -17,6 +17,7 @@
 import org.apache.commons.fileupload.disk.DiskFileItemFactory;
 import org.apache.commons.fileupload.util.Streams;
 import org.apache.commons.io.FileUtils;
+import org.apache.commons.lang.StringEscapeUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.restlet.ext.fileupload.RestletFileUpload;
@@ -168,23 +169,21 @@ private Map<String, String> parseAndUpdateInputParams(Representation entity, Wdl
 
 				FileItemStream item = iterator.next();
 
-				String name = item.getName();
+				String entryName = StringEscapeUtils.escapeHtml(item.getName());
 
-				if (name != null) {
+				if (entryName != null) {
 
 					File file = null;
 
 					try {
 						// file parameter
 						// write local file
-						String tmpFile = getSettings().getTempFilename(item.getName());
+						String tmpFile = getSettings().getTempFilename(entryName);
 						file = new File(tmpFile);
 
 						FileUtils.copyInputStreamToFile(item.openStream(), file);
 
-						// import into hdfs
-						String entryName = item.getName();
-
+	
 						// remove upload indentification!
 						String fieldName = item.getFieldName().replace("-upload", "").replace("input-", "");
 
@@ -260,11 +259,11 @@ private Map<String, String> parseAndUpdateInputParams(Representation entity, Wdl
 
 				} else {
 
-					String key = item.getFieldName();
+					String key = StringEscapeUtils.escapeHtml(item.getFieldName());
 					if (key.startsWith("input-")) {
 						key = key.replace("input-", "");
 					}
-					String value = Streams.asString(item.openStream());
+					String value = StringEscapeUtils.escapeHtml(Streams.asString(item.openStream()));
 					if (!props.containsKey(key)) {
 						// don't override uploaded files
 						props.put(key, value);
diff --git a/src/test/java/cloudgene/mapred/api/v2/jobs/SubmitJobTest.java b/src/test/java/cloudgene/mapred/api/v2/jobs/SubmitJobTest.java
index d2f653af..71af703a 100644
--- a/src/test/java/cloudgene/mapred/api/v2/jobs/SubmitJobTest.java
+++ b/src/test/java/cloudgene/mapred/api/v2/jobs/SubmitJobTest.java
@@ -271,12 +271,11 @@ public void testSubmitWithHiddenInputs() throws IOException, JSONException, Inte
 
 		FormDataSet form = new FormDataSet();
 		form.setMultipart(true);
-		//add visible checkbox
+		// add visible checkbox
 		form.getEntries().add(new FormData("input-checkbox1", "true"));
-		
+
 		// submit job
 		String id = submitJobPublic("print-hidden-inputs", form);
-		
 
 		// check feedback
 		waitForJob(id);
@@ -286,18 +285,18 @@ public void testSubmitWithHiddenInputs() throws IOException, JSONException, Inte
 		assertEquals(AbstractJob.STATE_SUCCESS, result.get("state"));
 
 		assertEquals(6, result.getJSONArray("steps").length());
-		assertEquals("text1: my-value\n",
-				result.getJSONArray("steps").getJSONObject(0).getJSONArray("logMessages").getJSONObject(0).get("message"));
-		assertEquals("checkbox1: true\n",
-				result.getJSONArray("steps").getJSONObject(1).getJSONArray("logMessages").getJSONObject(0).get("message"));
-		assertEquals("list1: value1\n",
-				result.getJSONArray("steps").getJSONObject(2).getJSONArray("logMessages").getJSONObject(0).get("message"));
-		assertEquals("text2: my-value\n",
-				result.getJSONArray("steps").getJSONObject(3).getJSONArray("logMessages").getJSONObject(0).get("message"));
-		assertEquals("checkbox2: true\n",
-				result.getJSONArray("steps").getJSONObject(4).getJSONArray("logMessages").getJSONObject(0).get("message"));
-		assertEquals("list2: value1\n",
-				result.getJSONArray("steps").getJSONObject(5).getJSONArray("logMessages").getJSONObject(0).get("message"));
+		assertEquals("text1: my-value\n", result.getJSONArray("steps").getJSONObject(0).getJSONArray("logMessages")
+				.getJSONObject(0).get("message"));
+		assertEquals("checkbox1: true\n", result.getJSONArray("steps").getJSONObject(1).getJSONArray("logMessages")
+				.getJSONObject(0).get("message"));
+		assertEquals("list1: value1\n", result.getJSONArray("steps").getJSONObject(2).getJSONArray("logMessages")
+				.getJSONObject(0).get("message"));
+		assertEquals("text2: my-value\n", result.getJSONArray("steps").getJSONObject(3).getJSONArray("logMessages")
+				.getJSONObject(0).get("message"));
+		assertEquals("checkbox2: true\n", result.getJSONArray("steps").getJSONObject(4).getJSONArray("logMessages")
+				.getJSONObject(0).get("message"));
+		assertEquals("list2: value1\n", result.getJSONArray("steps").getJSONObject(5).getJSONArray("logMessages")
+				.getJSONObject(0).get("message"));
 
 	}
 
@@ -342,4 +341,29 @@ public void testSubmitSftpUpload() throws IOException, JSONException, Interrupte
 
 	// TODO: wrong id
 
+	public void testSubmitHtmlInParams() throws IOException, JSONException, InterruptedException {
+
+		// form data
+
+		String html = "<script>console.log('Hey')<script>";
+
+		FormDataSet form = new FormDataSet();
+		form.setMultipart(true);
+		// add visible checkbox
+		form.getEntries().add(new FormData("text1", "value " + html));
+
+		// submit job
+		String id = submitJobPublic("print-hidden-inputs", form);
+
+		// check feedback
+		waitForJob(id);
+
+		JSONObject result = getJobDetails(id);
+		String message = result.getJSONArray("steps").getJSONObject(0).getJSONArray("logMessages").getJSONObject(0)
+				.get("message").toString();
+		System.out.println(message);
+		assertFalse(message.contains(html));
+
+	}
+
 }
diff --git a/test-data/print-hidden-inputs.yaml b/test-data/print-hidden-inputs.yaml
index e0d8da65..b6e27e84 100644
--- a/test-data/print-hidden-inputs.yaml
+++ b/test-data/print-hidden-inputs.yaml
@@ -5,7 +5,7 @@ workflow:
 
   steps:
     - name: text1
-      cmd: "/bin/echo text1: ${text1}"
+      cmd: "/bin/echo \"text1: ${text1}\""
       bash: true
       stdout: true
     - name: checkbox1

From 027ba6b8e0cb7ad7b0958846e468940d3e338e95 Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Mon, 27 Mar 2023 10:56:46 +0200
Subject: [PATCH 02/30] Prepare release 2.5.5

---
 pom.xml                                  | 2 +-
 src/main/html/webapp/package-lock.json   | 2 +-
 src/main/html/webapp/package.json        | 2 +-
 src/main/java/cloudgene/mapred/Main.java | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/pom.xml b/pom.xml
index 40d39ef9..c652233d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>cloudgene</groupId>
 	<artifactId>cloudgene</artifactId>
-	<version>2.5.4</version>
+	<version>2.5.5</version>
 
 	<name>Cloudgene</name>
 	<url>http://www.cloudgene.io</url>
diff --git a/src/main/html/webapp/package-lock.json b/src/main/html/webapp/package-lock.json
index 065b4011..639822e4 100644
--- a/src/main/html/webapp/package-lock.json
+++ b/src/main/html/webapp/package-lock.json
@@ -1,6 +1,6 @@
 {
   "name": "cloudgene",
-  "version": "2.5.4",
+  "version": "2.5.5",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
diff --git a/src/main/html/webapp/package.json b/src/main/html/webapp/package.json
index 8a1171f0..085a9442 100644
--- a/src/main/html/webapp/package.json
+++ b/src/main/html/webapp/package.json
@@ -1,6 +1,6 @@
 {
   "name": "cloudgene",
-  "version": "2.5.4",
+  "version": "2.5.5",
   "description": "Cloudgene web client",
   "homepage": "http://www.cloudgene.io",
   "author": "Lukas Forer <lukas.forer@i-med.ac.at (http://www.forer.it)",
diff --git a/src/main/java/cloudgene/mapred/Main.java b/src/main/java/cloudgene/mapred/Main.java
index fe7eb894..0a53d345 100644
--- a/src/main/java/cloudgene/mapred/Main.java
+++ b/src/main/java/cloudgene/mapred/Main.java
@@ -36,7 +36,7 @@
 
 public class Main {
 
-	public static final String VERSION = "2.5.4";
+	public static final String VERSION = "2.5.5";
 
 	private Database database;
 

From 6b539af3245e83324de5e70369ebd3d9adda1119 Mon Sep 17 00:00:00 2001
From: Sebastian Schoenherr <sebastian.schoenherr@i-med.ac.at>
Date: Tue, 4 Apr 2023 15:51:50 +0200
Subject: [PATCH 03/30] Remove url-based uploads (#94)

Co-authored-by: Lukas Forer <lukas.forer@i-med.ac.at>
---
 pom.xml                                       |  14 --
 .../core/job/submit/controls/folder.stache    |  23 --
 .../core/job/submit/dialogs/http.stache       |   6 -
 .../core/job/submit/dialogs/s3.stache         |   6 -
 .../core/job/submit/dialogs/sftp.stache       |  17 --
 .../components/core/job/submit/submit.js      | 207 +-----------------
 .../mapred/api/v2/data/ImporterFileList.java  |  71 +-----
 .../mapred/api/v2/jobs/SubmitJobTest.java     |  39 ----
 .../cloudgene/mapred/util/TestSFTPServer.java |  64 ------
 9 files changed, 6 insertions(+), 441 deletions(-)
 delete mode 100644 src/main/html/webapp/components/core/job/submit/dialogs/http.stache
 delete mode 100644 src/main/html/webapp/components/core/job/submit/dialogs/s3.stache
 delete mode 100644 src/main/html/webapp/components/core/job/submit/dialogs/sftp.stache
 delete mode 100644 src/test/java/cloudgene/mapred/util/TestSFTPServer.java

diff --git a/pom.xml b/pom.xml
index c652233d..466fb876 100644
--- a/pom.xml
+++ b/pom.xml
@@ -267,13 +267,6 @@
 			<version>1.6.2</version>
 		</dependency>
 
-
-		<dependency>
-			<groupId>com.jcraft</groupId>
-			<artifactId>jsch</artifactId>
-			<version>0.1.55</version>
-		</dependency>
-
 		<dependency>
 			<groupId>org.quartz-scheduler</groupId>
 			<artifactId>quartz</artifactId>
@@ -402,13 +395,6 @@
 			</exclusions>
 		</dependency>
 
-		<dependency>
-			<groupId>org.apache.sshd</groupId>
-			<artifactId>sshd-sftp</artifactId>
-			<version>0.9.0</version>
-			<scope>test</scope>
-		</dependency>
-
 	</dependencies>
 
 	<!-- **** Build **** -->
diff --git a/src/main/html/webapp/components/core/job/submit/controls/folder.stache b/src/main/html/webapp/components/core/job/submit/controls/folder.stache
index d2a6dfa8..82b853da 100644
--- a/src/main/html/webapp/components/core/job/submit/controls/folder.stache
+++ b/src/main/html/webapp/components/core/job/submit/controls/folder.stache
@@ -6,17 +6,10 @@
 </div>
 
 <div class="col-sm-7" {{data 'param'}} >
-  <select class="form-control folder-source" name="{{id}}-source">
-    <option value="upload" selected>File Upload</option>
-    <option value="http">URLs (HTTP)</option>
-    <option value="sftp">Secure File Transfer Protocol (SFTP)</option>
-		<option value="s3">S3 Bucket</option>
-  </select>
   <div class="form-control file-list-control">
     <ul class="fa-ul file-list">
     </ul>
   </div>
-  {{#is(source,'upload')}}
     <button id="select-files-btn" type="button" class="btn btn-sm btn-secondary"><i class="fa fa-folder-open"></i> Select Files</button>
     <button id="change-files-btn" type="button" class="btn btn-sm btn-secondary" style="display:none;"><i class="fa fa-folder-open"></i> Change</button>
     <button id="remove-all-files-btn" type="button" class="btn btn-sm btn-secondary" style="display:none;"><i class="fa fa-trash"></i> Remove All</button>
@@ -26,22 +19,6 @@
       style="display:none;" multiple
     >
     <small class="form-text text-muted">Multiple files can be selected by using the  <span class="badge badge-secondary">ctrl</span> /  <span class="badge badge-secondary">cmd</span> or  <span class="badge badge-secondary">shift</span> keys.</small>
-  {{/is}}
-  {{#is(source,'http')}}
-    <button id="add-urls-btn" type="button" class="btn btn-sm btn-secondary"><i class="fas fa-link"></i> Add URLs</button>
-    <input name="{{id}}" id="{{id}}" type ="text" style="display:none;" class="form-control hidden-parameter" {{#is(required, true)}}required{{/is}} value="{{value}}">
-  {{/is}}
-  {{#is(source,'sftp')}}
-    <button id="add-sftp-files-btn" type="button" class="btn btn-sm btn-secondary"><i class="fas fa-upload"></i> Import Files</button>
-    <input name="{{id}}" id="{{id}}" type ="text" style="display:none;" class="form-control hidden-parameter" {{#is(required, true)}}required{{/is}} value="{{value}}">
-  {{/is}}
-	{{#is(source,'s3')}}
-    <button id="add-s3-btn" type="button" class="btn btn-sm btn-secondary"><i class="fas fa-cloud"></i> Add S3 bucket</button>
-    <input name="{{id}}" id="{{id}}" type ="text" style="display:none;" class="form-control hidden-parameter" {{#is(required, true)}}required{{/is}} value="{{value}}">
-  {{/is}}
-	{{#if(details)}}
-    <small class="form-text text-muted">{{details}}</small>
-  {{/if}}
   <div class="invalid-feedback">
     Please choose one or more files.
   </div>
diff --git a/src/main/html/webapp/components/core/job/submit/dialogs/http.stache b/src/main/html/webapp/components/core/job/submit/dialogs/http.stache
deleted file mode 100644
index 70d23f8e..00000000
--- a/src/main/html/webapp/components/core/job/submit/dialogs/http.stache
+++ /dev/null
@@ -1,6 +0,0 @@
-<h4>Import data from public URLs</h4>
-<p>Please enter your URLs. </p>
-<form>
-    <textarea class="form-control" id="urls" placeholder="http://www.example.com/test-data.txt" rows="8" name="urls" width="30" height="20">{{value}}</textarea>
-    <small class="text-muted">To specify more than one url, separate the urls with a space or new line.</small>
-</form>
diff --git a/src/main/html/webapp/components/core/job/submit/dialogs/s3.stache b/src/main/html/webapp/components/core/job/submit/dialogs/s3.stache
deleted file mode 100644
index 570774a8..00000000
--- a/src/main/html/webapp/components/core/job/submit/dialogs/s3.stache
+++ /dev/null
@@ -1,6 +0,0 @@
-<h4>Import data from S3 bucket</h4>
-<p>Please enter the S3 bucket of your input folder. </p>
-<form>
-    <textarea class="form-control" id="buckets" placeholder="s3://my-bucket/input-folder" rows="8" name="buckets" width="30" height="20">{{value}}</textarea>
-    <small class="text-muted">Enter a the location of a s3 folder or file. To specify more than one file, separate the files with a space or new line.</small>
-</form>
diff --git a/src/main/html/webapp/components/core/job/submit/dialogs/sftp.stache b/src/main/html/webapp/components/core/job/submit/dialogs/sftp.stache
deleted file mode 100644
index 8d1e5556..00000000
--- a/src/main/html/webapp/components/core/job/submit/dialogs/sftp.stache
+++ /dev/null
@@ -1,17 +0,0 @@
-<h4>Secure File Transfer Protocol (SFTP)</h4>
-<p>Please enter your SFTP connection informations.</p>
-<form>
-    <div class="form-group">
-        <label>Username</label>
-        <input type="text" id="username" value="" class="form-control">
-    </div>
-    <div class="form-group">
-        <label>Password</label>
-        <input type="password" id="password" value="" class="form-control">
-    </div>
-    <div class="form-group">
-        <label>Files:</label>
-        <textarea class="form-control" id="path" placeholder="sftp://192.168.71.201/home/user/data/file.txt" rows="6" name="urls" width="30" height="20"></textarea>
-        <small class="text-muted">To specify more than one file, separate the files with a space or new line.</small>
-    </div>
-</form>
diff --git a/src/main/html/webapp/components/core/job/submit/submit.js b/src/main/html/webapp/components/core/job/submit/submit.js
index 9c52b925..fec385b2 100644
--- a/src/main/html/webapp/components/core/job/submit/submit.js
+++ b/src/main/html/webapp/components/core/job/submit/submit.js
@@ -9,9 +9,6 @@ import ErrorPage from 'helpers/error-page';
 import Application from 'models/application';
 
 import template from './submit.stache';
-import templateS3Dialog from './dialogs/s3.stache';
-import templateHttpDialog from './dialogs/http.stache';
-import templateSftpDialog from './dialogs/sftp.stache';
 import templateUploadingDialog from './dialogs/uploading.stache';
 import templateLabel from './controls/label.stache';
 import templateSelect from './controls/select.stache';
@@ -143,9 +140,9 @@ export default Control.extend({
 
   // custom file upload controls for single files
 
-'.select-control change': function(){
-  this.application.updateBinding();
-},
+  '.select-control change': function(){
+    this.application.updateBinding();
+  },
 
   '#select-single-file-btn click': function(button) {
     // trigger click to open file dialog
@@ -207,204 +204,6 @@ export default Control.extend({
     fileUpload.parent().find("#select-files").show();
     fileUpload.parent().find("#change-files").hide();
     fileUpload.parent().find("#remove-all-files").hide();
-  },
-
-  // custom handler for import urls
-
-  '.folder-source change': function(source) {
-
-    //delete filelist
-    var parent = $(source).parent();
-
-    var fileList = $(parent).find(".file-list");
-    fileList.empty();
-
-    //update parameter source
-    var param = domData.get.call($(parent)[0], 'param');
-    param.attr('source', $(source).val());
-  },
-
-  '#add-urls-btn click': function(button) {
-
-    var parent = $(button).parent();
-
-    var fileList = $(parent).find(".file-list");
-    //fileList.empty();
-
-    var paramInputField = $(parent).find(".hidden-parameter");
-
-
-    var urlDialog = bootbox.confirm(
-      templateHttpDialog({
-        value: paramInputField.val()
-      }),
-      function(result) {
-        if (result) {
-          var urls = $('#urls').val();
-          $.ajax({
-            url: "api/v2/importer/files",
-            type: "POST",
-            data: {
-              input: urls
-            },
-            success: function(data) {
-
-              var arr = $.parseJSON(data);
-              fileList.empty();
-              $.each(arr, function(index, value) {
-                fileList.append('<li><span class="fa-li"><i class="fas fa-file"></i></span>' + value["text"].toString() + '</li>');
-              });
-
-              //update value
-              if (arr.length > 0) {
-                paramInputField.val(urls);
-                urlDialog.modal('hide');
-              } else {
-                paramInputField.val("");
-                bootbox.alert("Error: No valid files found on the provided urls.");
-              }
-
-            },
-            error: function(message) {
-              bootbox.alert("Error: " + message.responseText);
-            }
-          });
-
-          return false;
-        }
-      });
-  },
-
-  '#add-s3-btn click': function(button) {
-
-    var parent = $(button).parent();
-
-    var fileList = $(parent).find(".file-list");
-    //fileList.empty();
-
-    var paramInputField = $(parent).find(".hidden-parameter");
-
-    var urlDialog = bootbox.confirm(
-      templateS3Dialog(),
-      function(result) {
-        if (result) {
-          var buckets = $('#buckets').val();
-
-          var waitingDialog = bootbox.dialog({
-            close: false,
-            message: '<p><i class="fa fa-spin fa-spinner"></i> Connecting...</p>',
-            show: false
-          });
-
-          waitingDialog.on('shown.bs.modal', function() {
-
-            $.ajax({
-              url: "api/v2/importer/files",
-              type: "POST",
-              data: {
-                input: buckets
-              },
-
-              success: function(data) {
-
-                waitingDialog.modal('hide');
-
-                var arr = $.parseJSON(data);
-                fileList.empty();
-                $.each(arr, function(index, value) {
-                  fileList.append('<li><span class="fa-li"><i class="fas fa-file"></i></span>' + value["text"].toString() + '</li>');
-                });
-
-                //update value
-                if (arr.length > 0) {
-                  paramInputField.val(buckets);
-                  urlDialog.modal('hide');
-                } else {
-                  paramInputField.val("");
-                  bootbox.alert('<p class="text-danger">Error: No valid files found on the provided urls. Please check your credentials and your file path.');
-                }
-
-              },
-              error: function(message) {
-                waitingDialog.modal('hide');
-                bootbox.alert('<p class="text-danger">Error: ' + message.responseText + '</p>');
-              }
-            });
-
-          });
-
-          waitingDialog.modal('show');
-
-          return false;
-        }
-      });
-  },
-
-  '#add-sftp-files-btn click': function(button) {
-
-    var parent = $(button).parent();
-
-    var fileList = $(parent).find(".file-list");
-    //fileList.empty();
-
-    var paramInputField = $(parent).find(".hidden-parameter");
-
-    var urlDialog = bootbox.confirm(
-      templateSftpDialog(),
-      function(result) {
-        if (result) {
-          var path = $('#path').val();
-          var username = $('#username').val();
-          var password = $('#password').val();
-
-          var waitingDialog = bootbox.dialog({
-            close: false,
-            message: '<p><i class="fa fa-spin fa-spinner"></i> Connecting...</p>',
-            show: false
-          });
-
-          waitingDialog.on('shown.bs.modal', function() {
-
-            $.ajax({
-              url: "api/v2/importer/files",
-              type: "POST",
-              data: {
-                input: path + ';' + username + ';' + password
-              },
-
-              success: function(data) {
-
-                waitingDialog.modal('hide');
-
-                var arr = $.parseJSON(data);
-                fileList.empty();
-                $.each(arr, function(index, value) {
-                  fileList.append('<li><span class="fa-li"><i class="fas fa-file"></i></span>' + value["text"].toString() + '</li>');
-                });
-
-                //update value
-                if (arr.length > 0) {
-                  paramInputField.val(path + ';' + username + ';' + password);
-                  urlDialog.modal('hide');
-                } else {
-                  paramInputField.val("");
-                  bootbox.alert('<p class="text-danger">Error: No valid files found on the provided urls. Please check your credentials and your file path.');
-                }
-
-              },
-              error: function(message) {
-                waitingDialog.modal('hide');
-                bootbox.alert('<p class="text-danger">Error: ' + message.responseText + '</p>');
-              }
-            });
-
-          });
-
-          waitingDialog.modal('show');
-
-          return false;
-        }
-      });
   }
 
 });
diff --git a/src/main/java/cloudgene/mapred/api/v2/data/ImporterFileList.java b/src/main/java/cloudgene/mapred/api/v2/data/ImporterFileList.java
index 12db3d65..3ba757b9 100644
--- a/src/main/java/cloudgene/mapred/api/v2/data/ImporterFileList.java
+++ b/src/main/java/cloudgene/mapred/api/v2/data/ImporterFileList.java
@@ -1,84 +1,19 @@
 package cloudgene.mapred.api.v2.data;
 
-import java.util.List;
-import java.util.Vector;
-
-import org.restlet.data.Form;
 import org.restlet.data.Status;
 import org.restlet.representation.Representation;
 import org.restlet.representation.StringRepresentation;
 import org.restlet.resource.Post;
 import org.restlet.resource.ServerResource;
 
-import genepi.hadoop.importer.FileItem;
-import genepi.hadoop.importer.IImporter;
-import genepi.hadoop.importer.ImporterFactory;
-import net.sf.json.JSONArray;
-
 public class ImporterFileList extends ServerResource {
 
 	@Post
 	public Representation validateImport(Representation entity) {
 
-		Form form = new Form(entity);
-
-		String input = form.getFirstValue("input").trim();
-
-		List<FileItem> results = new Vector<FileItem>();
-
-		try {
-
-			if (ImporterFactory.needsImport(input)) {
-
-				for (String url : ImporterFactory.parseImportString(input)) {
-
-					try {
-
-						IImporter importer = ImporterFactory.createImporter(
-								url, null);
-
-						if (importer != null) {
-
-							List<FileItem> items = importer.getFiles();
-
-							if (items != null) {
-
-								// add files to list
-								results.addAll(items);
-
-							} else {
-								setStatus(Status.CLIENT_ERROR_NOT_FOUND);
-								return new StringRepresentation(
-										importer.getErrorMessage());
-
-							}
-
-						} else {
-
-							setStatus(Status.CLIENT_ERROR_NOT_FOUND);
-							return new StringRepresentation(
-									"Protocol not supported");
-
-						}
-
-					} catch (Exception e) {
-						setStatus(Status.CLIENT_ERROR_NOT_FOUND);
-						return new StringRepresentation(e.toString());
-
-					}
-
-				}
-
-			}
-
-			JSONArray jsonArray = JSONArray.fromObject(results);
-
-			return new StringRepresentation(jsonArray.toString());
-
-		} catch (Exception e) {
-			setStatus(Status.SERVER_ERROR_INTERNAL);
-			return new StringRepresentation(e.toString());
-		}
+		setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
+		return new StringRepresentation(
+				"URL-based uploads are no longer supported. Please use direct file uploads instead.");
 
 	}
 
diff --git a/src/test/java/cloudgene/mapred/api/v2/jobs/SubmitJobTest.java b/src/test/java/cloudgene/mapred/api/v2/jobs/SubmitJobTest.java
index 71af703a..16a145ff 100644
--- a/src/test/java/cloudgene/mapred/api/v2/jobs/SubmitJobTest.java
+++ b/src/test/java/cloudgene/mapred/api/v2/jobs/SubmitJobTest.java
@@ -1,6 +1,5 @@
 package cloudgene.mapred.api.v2.jobs;
 
-import java.io.File;
 import java.io.IOException;
 
 import org.json.JSONArray;
@@ -15,7 +14,6 @@
 import cloudgene.mapred.jobs.AbstractJob;
 import cloudgene.mapred.util.JobsApiTestCase;
 import cloudgene.mapred.util.TestCluster;
-import cloudgene.mapred.util.TestSFTPServer;
 import cloudgene.mapred.util.TestServer;
 import cloudgene.sdk.internal.WorkflowContext;
 import genepi.io.FileUtil;
@@ -300,43 +298,6 @@ public void testSubmitWithHiddenInputs() throws IOException, JSONException, Inte
 
 	}
 
-	public void testSubmitSftpUpload() throws IOException, JSONException, InterruptedException {
-
-		TestSFTPServer sftp = new TestSFTPServer("test-data");
-
-		String url = "sftp://localhost:8001/" + new File("test-data/sftp-import.yaml").getAbsolutePath() + ";"
-				+ TestSFTPServer.USERNAME + ";" + TestSFTPServer.PASSWORD;
-
-		// form data
-
-		FormDataSet form = new FormDataSet();
-		form.setMultipart(true);
-		form.getEntries().add(new FormData("input-input", url));
-
-		// submit job
-		String id = submitJobPublic("sftp-import", form);
-
-		// get details to check *** bug
-		getJobDetails(id);
-
-		// check feedback
-		waitForJob(id);
-
-		JSONObject result = getJobDetails(id);
-
-		// check if no sftp url is in json
-		assertFalse(result.toString().contains(url));
-
-		// get log file
-
-		assertEquals(AbstractJob.STATE_SUCCESS, result.get("state"));
-
-		sftp.stop();
-
-		// check results!
-
-	}
-
 	// TODO: wrong permissions
 
 	// TODO: wrong id
diff --git a/src/test/java/cloudgene/mapred/util/TestSFTPServer.java b/src/test/java/cloudgene/mapred/util/TestSFTPServer.java
deleted file mode 100644
index dbc49222..00000000
--- a/src/test/java/cloudgene/mapred/util/TestSFTPServer.java
+++ /dev/null
@@ -1,64 +0,0 @@
-package cloudgene.mapred.util;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Arrays;
-
-import org.apache.commons.lang.StringUtils;
-import org.apache.sshd.SshServer;
-import org.apache.sshd.common.NamedFactory;
-import org.apache.sshd.common.Session;
-import org.apache.sshd.common.file.FileSystemView;
-import org.apache.sshd.common.file.nativefs.NativeFileSystemFactory;
-import org.apache.sshd.common.file.nativefs.NativeFileSystemView;
-import org.apache.sshd.server.Command;
-import org.apache.sshd.server.PasswordAuthenticator;
-import org.apache.sshd.server.command.ScpCommandFactory;
-import org.apache.sshd.server.keyprovider.SimpleGeneratorHostKeyProvider;
-import org.apache.sshd.server.session.ServerSession;
-import org.apache.sshd.sftp.subsystem.SftpSubsystem;
-
-public class TestSFTPServer {
-
-	private SshServer sshd;
-
-	public static final String USERNAME = "username";
-
-	public static final String PASSWORD = "password";
-
-	public TestSFTPServer(final String rootFolder) throws IOException {
-
-		sshd = SshServer.setUpDefaultServer();
-		sshd.setFileSystemFactory(new NativeFileSystemFactory() {
-			@Override
-			public FileSystemView createFileSystemView(final Session session) {
-				return new NativeFileSystemView(session.getUsername(), false) {
-					@Override
-					public String getVirtualUserDir() {
-						System.out.println("Virtual Root: " + new File(rootFolder).getAbsolutePath());
-						return new File(rootFolder).getAbsolutePath();
-					}
-
-				};
-			};
-		});
-		sshd.setPort(8001);
-		sshd.setSubsystemFactories(Arrays.<NamedFactory<Command>>asList(new SftpSubsystem.Factory()));
-		sshd.setCommandFactory(new ScpCommandFactory());
-		sshd.setKeyPairProvider(
-				new SimpleGeneratorHostKeyProvider(new File(rootFolder + "/hostkey.ser").getAbsolutePath()));
-		sshd.setPasswordAuthenticator(new PasswordAuthenticator() {
-			@Override
-			public boolean authenticate(final String username, final String password, final ServerSession session) {
-				return StringUtils.equals(username, USERNAME) && StringUtils.equals(password, PASSWORD);
-			}
-		});
-		sshd.start();
-
-	}
-
-	public void stop() throws InterruptedException {
-		sshd.stop();
-	}
-
-}

From ae8475deb05386b918ff79abcad9414c6cb3896d Mon Sep 17 00:00:00 2001
From: Snyk bot <github+bot@snyk.io>
Date: Tue, 4 Apr 2023 21:57:24 +0800
Subject: [PATCH 04/30] fix: pom.xml to reduce vulnerabilities (#93)

The following vulnerabilities are fixed with an upgrade:
- https://snyk.io/vuln/SNYK-JAVA-ORGTESTNG-3040285
---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 466fb876..58eaed71 100644
--- a/pom.xml
+++ b/pom.xml
@@ -190,7 +190,7 @@
 		<dependency>
 			<groupId>org.codehaus.groovy</groupId>
 			<artifactId>groovy-all</artifactId>
-			<version>3.0.9</version>
+			<version>3.0.17</version>
 			<type>pom</type>
 		</dependency>
 

From e8ee4b8710ee28f790093cc0016e2eaec3f79b1a Mon Sep 17 00:00:00 2001
From: Sebastian Schoenherr <sebastian.schoenherr@i-med.ac.at>
Date: Tue, 4 Apr 2023 16:05:06 +0200
Subject: [PATCH 05/30] Prepare release 2.5.6

---
 pom.xml                                | 2 +-
 src/main/html/webapp/package-lock.json | 2 +-
 src/main/html/webapp/package.json      | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pom.xml b/pom.xml
index 58eaed71..b8c97ef2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>cloudgene</groupId>
 	<artifactId>cloudgene</artifactId>
-	<version>2.5.5</version>
+	<version>2.5.6</version>
 
 	<name>Cloudgene</name>
 	<url>http://www.cloudgene.io</url>
diff --git a/src/main/html/webapp/package-lock.json b/src/main/html/webapp/package-lock.json
index 639822e4..69c9dcfc 100644
--- a/src/main/html/webapp/package-lock.json
+++ b/src/main/html/webapp/package-lock.json
@@ -1,6 +1,6 @@
 {
   "name": "cloudgene",
-  "version": "2.5.5",
+  "version": "2.5.6",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
diff --git a/src/main/html/webapp/package.json b/src/main/html/webapp/package.json
index 085a9442..91fef532 100644
--- a/src/main/html/webapp/package.json
+++ b/src/main/html/webapp/package.json
@@ -1,6 +1,6 @@
 {
   "name": "cloudgene",
-  "version": "2.5.5",
+  "version": "2.5.6",
   "description": "Cloudgene web client",
   "homepage": "http://www.cloudgene.io",
   "author": "Lukas Forer <lukas.forer@i-med.ac.at (http://www.forer.it)",

From 6153fdde9c8e14abee61c4db72b9e35301ca93b0 Mon Sep 17 00:00:00 2001
From: Sebastian Schoenherr <sebastian.schoenherr@i-med.ac.at>
Date: Tue, 4 Apr 2023 16:09:19 +0200
Subject: [PATCH 06/30] Prepare release 2.5.6

---
 src/main/java/cloudgene/mapred/Main.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/cloudgene/mapred/Main.java b/src/main/java/cloudgene/mapred/Main.java
index 0a53d345..4fd988f6 100644
--- a/src/main/java/cloudgene/mapred/Main.java
+++ b/src/main/java/cloudgene/mapred/Main.java
@@ -36,7 +36,7 @@
 
 public class Main {
 
-	public static final String VERSION = "2.5.5";
+	public static final String VERSION = "2.5.6";
 
 	private Database database;
 

From d8bad96c612cf06e00c5a04dfdc0ba1e0fb38702 Mon Sep 17 00:00:00 2001
From: Andy Boughton <abought@gmail.com>
Date: Tue, 11 Apr 2023 08:21:07 -0400
Subject: [PATCH 07/30] [v2.x][feature] Add logging of API endpoint usage (#95)

* Add authorization and admin logging statements to track API actions

* Log s3 download events

* Fix delete user resource

* Remove unnecessary sysout message

* Simplify log message in case no Hadoop Cluster is available.

---------

Co-authored-by: seppinho <sebastian.schoenherr@i-med.ac.at>
---
 .../components/core/user/profile/profile.js   | 69 ++++++++++---------
 src/main/html/webapp/models/user-profile.js   | 13 +++-
 .../mapred/api/v2/admin/ArchiveJob.java       |  7 ++
 .../mapred/api/v2/admin/ChangeGroup.java      |  8 +++
 .../mapred/api/v2/admin/ChangeRetireDate.java |  6 ++
 .../mapred/api/v2/admin/DeleteUser.java       |  9 +++
 .../mapred/api/v2/admin/ResetDownloads.java   |  6 ++
 .../mapred/api/v2/admin/RetireJobs.java       |  5 ++
 .../mapred/api/v2/jobs/CancelJob.java         | 10 +++
 .../mapred/api/v2/jobs/DownloadResults.java   | 10 ++-
 .../mapred/api/v2/jobs/GetJobDetails.java     | 10 +++
 .../cloudgene/mapred/api/v2/jobs/GetLogs.java | 10 +++
 .../mapred/api/v2/jobs/RestartJob.java        | 11 ++-
 .../mapred/api/v2/jobs/ShareResults.java      |  9 ++-
 .../mapred/api/v2/jobs/SubmitJob.java         |  9 ++-
 .../mapred/api/v2/users/ActivateUser.java     | 10 ++-
 .../mapred/api/v2/users/ApiTokens.java        |  7 ++
 .../mapred/api/v2/users/LoginUser.java        | 25 ++++++-
 .../mapred/api/v2/users/RegisterUser.java     |  4 ++
 .../mapred/api/v2/users/ResetPassword.java    |  5 +-
 .../mapred/api/v2/users/UpdatePassword.java   |  5 ++
 .../mapred/api/v2/users/UserProfile.java      | 16 ++++-
 .../cloudgene/mapred/cron/CleanUpTasks.java   |  2 +-
 .../cloudgene/mapred/util/BaseResource.java   |  9 +++
 .../cloudgene/mapred/util/JSONConverter.java  |  1 -
 .../mapred/api/v2/users/LoginUserTest.java    |  4 +-
 26 files changed, 229 insertions(+), 51 deletions(-)

diff --git a/src/main/html/webapp/components/core/user/profile/profile.js b/src/main/html/webapp/components/core/user/profile/profile.js
index 44ba2fa6..30b86669 100644
--- a/src/main/html/webapp/components/core/user/profile/profile.js
+++ b/src/main/html/webapp/components/core/user/profile/profile.js
@@ -170,41 +170,44 @@ export default Control.extend({
   '#delete_account click': function() {
 
 
-    var deleteAcountDialog = bootbox.dialog(templateDeleteDialog(), [
+    var deleteAcountDialog = bootbox.dialog({
+           message: templateDeleteDialog(),
+           buttons: {
+            cancel: {
+              label: "Cancel",
+              class: "btn-default",
+              callback: function() {}
+            },
+            ok: {
+               label: "Delete Account",
+               class: "btn-danger",
+               callback: function() {
+
+                 // get form parameters
+                 var form = deleteAcountDialog.find("form");
+                 var values = deparam(form.serialize());
+
+                 // create delete request
+                 var userProfile = new UserProfile();
+                 userProfile.attr('user', values['username']);
+                 userProfile.attr('username', values['username']);
+                 userProfile.attr('password', values['password']);
+                 userProfile.attr('id', 'id');
+                 userProfile.destroy(function() {
+                   bootbox.alert('<h4>Account deleted</h4>Your account is now deleted.');
+                   window.location.href = 'logout';
+                   return true;
+                 }, function(message) {
+                   var response = JSON.parse(message.responseText);
+                   bootbox.alert('<h4>Account not deleted</h4>Error: ' + response.message);
+                   return false;
+                 });
+               }
+             }
+          }
+       });
 
-      {
-        label: "Cancel",
-        class: "btn-default",
-        callback: function() {}
-      },
 
-      {
-        label: "Delete Account",
-        class: "btn-danger",
-        callback: function() {
-
-          // get form parameters
-          var form = deleteAcountDialog.find("form");
-          var values = deparam(form.serialize());
-
-          // create delete request
-          var userProfile = new UserProfile();
-          userProfile.attr('user', 'me');
-          userProfile.attr('username', values['username']);
-          userProfile.attr('password', values['password']);
-          userProfile.attr('id', 'id');
-          userProfile.destroy(function() {
-            bootbox.alert('<h4>Account deleted</h4>Your account is now deleted.');
-            window.location.href = 'logout';
-            return true;
-          }, function(message) {
-            var response = JSON.parse(message.responseText);
-            bootbox.alert('<h4>Account not deleted</h4>Error: ' + response.message);
-            return false;
-          });
-        }
-      }
-    ]);
   }
 
 });
diff --git a/src/main/html/webapp/models/user-profile.js b/src/main/html/webapp/models/user-profile.js
index 99aab08b..9a257131 100644
--- a/src/main/html/webapp/models/user-profile.js
+++ b/src/main/html/webapp/models/user-profile.js
@@ -1,7 +1,18 @@
 import Model from 'can-connect/can/model/model';
 
 export default Model.extend({
-  destroy: 'DELETE /api/v2/users/{user}/profile'
+    destroy: function(user) {
+
+        return $.ajax({
+            url: "/api/v2/users/" + user.username + "/profile",
+            type: "DELETE",
+            data: {
+                "username": user.username,
+                "password": user.password
+            }
+
+        })
+    }
 }, {
 
 });
diff --git a/src/main/java/cloudgene/mapred/api/v2/admin/ArchiveJob.java b/src/main/java/cloudgene/mapred/api/v2/admin/ArchiveJob.java
index 996dde72..b77aa627 100644
--- a/src/main/java/cloudgene/mapred/api/v2/admin/ArchiveJob.java
+++ b/src/main/java/cloudgene/mapred/api/v2/admin/ArchiveJob.java
@@ -1,5 +1,7 @@
 package cloudgene.mapred.api.v2.admin;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.restlet.data.Status;
 import org.restlet.representation.Representation;
 import org.restlet.representation.StringRepresentation;
@@ -17,6 +19,8 @@
 
 public class ArchiveJob extends BaseResource {
 
+	private static final Log log = LogFactory.getLog(ArchiveJob.class);
+
 	@Get
 	public Representation get() {
 
@@ -85,6 +89,9 @@ public Representation get() {
 					}
 				}
 
+				log.info(String.format("Job: Immediately retired job %s (by ADMIN user ID %s - email %s)",
+						job.getId(), user.getId(), user.getMail()));
+
 				return new StringRepresentation("Retired job " + jobId);
 
 			} catch (Exception e) {
diff --git a/src/main/java/cloudgene/mapred/api/v2/admin/ChangeGroup.java b/src/main/java/cloudgene/mapred/api/v2/admin/ChangeGroup.java
index d9d9f048..53017620 100644
--- a/src/main/java/cloudgene/mapred/api/v2/admin/ChangeGroup.java
+++ b/src/main/java/cloudgene/mapred/api/v2/admin/ChangeGroup.java
@@ -1,5 +1,7 @@
 package cloudgene.mapred.api.v2.admin;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.restlet.data.Form;
 import org.restlet.data.Status;
 import org.restlet.representation.Representation;
@@ -14,6 +16,8 @@
 
 public class ChangeGroup extends BaseResource {
 
+	private static final Log log = LogFactory.getLog(ChangeGroup.class);
+
 	@Post
 	public Representation post(Representation entity) {
 
@@ -59,6 +63,10 @@ public Representation post(Representation entity) {
 		user1.setRoles(role.split(User.ROLE_SEPARATOR));
 		dao.update(user1);
 
+		log.info(String.format("User: Changed group membership for %s (ID %s) to %s (by ADMIN user ID %s - email %s)",
+				user1.getUsername(), user1.getId(), String.join(",", user1.getRoles()),
+				user.getId(), user.getMail()));
+
 		JSONObject object = JSONConverter.convert(user1);
 		return new StringRepresentation(object.toString());
 
diff --git a/src/main/java/cloudgene/mapred/api/v2/admin/ChangeRetireDate.java b/src/main/java/cloudgene/mapred/api/v2/admin/ChangeRetireDate.java
index 88d24601..f81124af 100644
--- a/src/main/java/cloudgene/mapred/api/v2/admin/ChangeRetireDate.java
+++ b/src/main/java/cloudgene/mapred/api/v2/admin/ChangeRetireDate.java
@@ -1,5 +1,7 @@
 package cloudgene.mapred.api.v2.admin;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.restlet.data.Status;
 import org.restlet.representation.Representation;
 import org.restlet.representation.StringRepresentation;
@@ -12,6 +14,8 @@
 
 public class ChangeRetireDate extends BaseResource {
 
+	private static final Log log = LogFactory.getLog(ChangeRetireDate.class);
+
 	@Get
 	public Representation get() {
 
@@ -61,6 +65,8 @@ public Representation get() {
 
 				dao.update(job);
 
+				log.info(String.format("Job: Extended retire date for job %s (by ADMIN user ID %s - email %s)", job.getId(), user.getId(), user.getMail()));
+
 				return new StringRepresentation("Update delete on date for job " + job.getId() + ".");
 
 			} catch (Exception e) {
diff --git a/src/main/java/cloudgene/mapred/api/v2/admin/DeleteUser.java b/src/main/java/cloudgene/mapred/api/v2/admin/DeleteUser.java
index 02a7bb97..1eb214a6 100644
--- a/src/main/java/cloudgene/mapred/api/v2/admin/DeleteUser.java
+++ b/src/main/java/cloudgene/mapred/api/v2/admin/DeleteUser.java
@@ -1,5 +1,7 @@
 package cloudgene.mapred.api.v2.admin;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.restlet.data.Form;
 import org.restlet.data.Status;
 import org.restlet.representation.Representation;
@@ -13,6 +15,8 @@
 
 public class DeleteUser extends BaseResource {
 
+	private static final Log log = LogFactory.getLog(DeleteUser.class);
+
 	@Post
 	public Representation post(Representation entity) {
 
@@ -43,6 +47,11 @@ public Representation post(Representation entity) {
 			dao.delete(user1);
 
 			JSONObject object = JSONObject.fromObject(user1);
+
+			log.info(String.format("Job: Deleted user %s (ID %s) (by ADMIN user ID %s - email %s)",
+					user1.getUsername(), user1.getId(),
+					user.getId(), user.getMail()));
+
 			return new StringRepresentation(object.toString());
 		} else {
 			setStatus(Status.CLIENT_ERROR_NOT_FOUND);
diff --git a/src/main/java/cloudgene/mapred/api/v2/admin/ResetDownloads.java b/src/main/java/cloudgene/mapred/api/v2/admin/ResetDownloads.java
index 2f21734c..2bccbbf4 100644
--- a/src/main/java/cloudgene/mapred/api/v2/admin/ResetDownloads.java
+++ b/src/main/java/cloudgene/mapred/api/v2/admin/ResetDownloads.java
@@ -2,6 +2,8 @@
 
 import java.util.List;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.restlet.data.Status;
 import org.restlet.representation.Representation;
 import org.restlet.representation.StringRepresentation;
@@ -17,6 +19,8 @@
 
 public class ResetDownloads extends BaseResource {
 
+	private static final Log log = LogFactory.getLog(ResetDownloads.class);
+
 	@Get
 	public Representation get() {
 
@@ -72,6 +76,8 @@ public Representation get() {
 					}
 				}
 
+				log.info(String.format("Job: Resetting download counters for job %s (by ADMIN user ID %s - email %s)", job.getId(), user.getId(), user.getMail()));
+
 				return new StringRepresentation(
 						jobId + ": counter of " + count + " downloads reset to " + maxDownloads);
 
diff --git a/src/main/java/cloudgene/mapred/api/v2/admin/RetireJobs.java b/src/main/java/cloudgene/mapred/api/v2/admin/RetireJobs.java
index 7ff25661..122fc644 100644
--- a/src/main/java/cloudgene/mapred/api/v2/admin/RetireJobs.java
+++ b/src/main/java/cloudgene/mapred/api/v2/admin/RetireJobs.java
@@ -1,5 +1,7 @@
 package cloudgene.mapred.api.v2.admin;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.restlet.data.Status;
 import org.restlet.representation.Representation;
 import org.restlet.representation.StringRepresentation;
@@ -10,6 +12,7 @@
 import cloudgene.mapred.util.BaseResource;
 
 public class RetireJobs extends BaseResource {
+	private static final Log log = LogFactory.getLog(RetireJobs.class);
 
 	@Get
 	public Representation get() {
@@ -33,6 +36,8 @@ public Representation get() {
 		int notifications = CleanUpTasks.sendNotifications(getWebApp());
 		int retired = CleanUpTasks.executeRetire(getDatabase(), getSettings());
 
+		log.info(String.format("Job: Manually triggered retiring of all eligible jobs (by ADMIN user ID %s - email %s)", user.getId(), user.getMail()));
+
 		return new StringRepresentation("NotificationJob:\n" + notifications
 				+ " notifications sent." + "\n\nRetireJob:\n" + retired
 				+ " jobs retired.");
diff --git a/src/main/java/cloudgene/mapred/api/v2/jobs/CancelJob.java b/src/main/java/cloudgene/mapred/api/v2/jobs/CancelJob.java
index 74844b1f..34fe20c5 100644
--- a/src/main/java/cloudgene/mapred/api/v2/jobs/CancelJob.java
+++ b/src/main/java/cloudgene/mapred/api/v2/jobs/CancelJob.java
@@ -1,5 +1,7 @@
 package cloudgene.mapred.api.v2.jobs;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.restlet.representation.Representation;
 import org.restlet.representation.StringRepresentation;
 import org.restlet.resource.Get;
@@ -13,6 +15,8 @@
 
 public class CancelJob extends BaseResource {
 
+	private static final Log log = LogFactory.getLog(CancelJob.class);
+
 	@Get
 	public Representation get(Representation entity) {
 
@@ -40,6 +44,12 @@ public Representation get(Representation entity) {
 
 		getWorkflowEngine().cancel(job);
 
+		String message = String.format("Job: Canceled job ID %s", job.getId());
+		if (user.isAdmin()) {
+			message += String.format(" (by ADMIN user ID %s - email %s)", user.getId(), user.getMail());
+		}
+		log.info(message);
+
 		JSONObject object = JSONConverter.convert(job);
 
 		return new StringRepresentation(object.toString());
diff --git a/src/main/java/cloudgene/mapred/api/v2/jobs/DownloadResults.java b/src/main/java/cloudgene/mapred/api/v2/jobs/DownloadResults.java
index efe2f776..7c717da4 100644
--- a/src/main/java/cloudgene/mapred/api/v2/jobs/DownloadResults.java
+++ b/src/main/java/cloudgene/mapred/api/v2/jobs/DownloadResults.java
@@ -101,11 +101,19 @@ public Representation get() {
 				String resultFile = FileUtil.path(localWorkspace, download.getPath());
 				log.debug("Downloading file from local workspace " + resultFile);
 				MediaType mediaType = getMediaType(download.getPath());
+
+				User jobOwner = job.getUser();
+				String message  = String.format("Job: Downloading file '%s' for job %s - owner %s (ID %s - email %s)", filename, job.getId(), jobOwner.getUsername(), jobOwner.getId(), jobOwner.getMail());
+				if (user.isAdmin()) {
+					message += String.format(" (by ADMIN user ID %s - email %s)", user.getId(), user.getMail());
+				}
+				log.info(message);
+
 				return new FileRepresentation(resultFile, mediaType);
 			}
 
 		} catch (Exception e) {
-			log.error("Processing download failed.", e);
+			log.error("Job: Error while downloading file", e);
 			return error400("Processing download failed.");
 		}
 	}
diff --git a/src/main/java/cloudgene/mapred/api/v2/jobs/GetJobDetails.java b/src/main/java/cloudgene/mapred/api/v2/jobs/GetJobDetails.java
index 9afc0508..4b816b2e 100644
--- a/src/main/java/cloudgene/mapred/api/v2/jobs/GetJobDetails.java
+++ b/src/main/java/cloudgene/mapred/api/v2/jobs/GetJobDetails.java
@@ -3,6 +3,8 @@
 import java.util.List;
 import java.util.Vector;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.restlet.data.MediaType;
 import org.restlet.representation.Representation;
 import org.restlet.representation.StringRepresentation;
@@ -26,6 +28,8 @@
 
 public class GetJobDetails extends BaseResource {
 
+	private static final Log log = LogFactory.getLog(GetJobDetails.class);
+
 	private boolean publicMode = false;
 
 	@Get
@@ -159,6 +163,12 @@ public Representation deleteJob(Representation entity) {
 
 		JSONObject object = JSONConverter.convert(job);
 
+		String message = String.format("Job: Deleted job ID %s", job.getId());
+		if (user.isAdmin()) {
+			message += String.format(" (by ADMIN user ID %s - email %s)", user.getId(), user.getMail());
+		}
+		log.info(message);
+
 		return new StringRepresentation(object.toString());
 
 	}
diff --git a/src/main/java/cloudgene/mapred/api/v2/jobs/GetLogs.java b/src/main/java/cloudgene/mapred/api/v2/jobs/GetLogs.java
index fed84434..7aca6826 100644
--- a/src/main/java/cloudgene/mapred/api/v2/jobs/GetLogs.java
+++ b/src/main/java/cloudgene/mapred/api/v2/jobs/GetLogs.java
@@ -1,5 +1,7 @@
 package cloudgene.mapred.api.v2.jobs;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.restlet.representation.Representation;
 import org.restlet.representation.StringRepresentation;
 import org.restlet.resource.Get;
@@ -14,6 +16,8 @@
 
 public class GetLogs extends BaseResource {
 
+	private static final Log log = LogFactory.getLog(GetLogs.class);
+
 	@Get
 	public Representation get() {
 
@@ -67,6 +71,12 @@ public Representation get() {
 			buffer.append(outputContent);
 
 		}
+
+		String message = String.format("Job: viewing logs for job ID %s", job.getId());
+		if (user.isAdmin()) {
+			message += String.format(" (by ADMIN user ID %s - email %s)", user.getId(), user.getMail());
+		}
+		log.info(message);
 		//buffer.append("</code></pre>");
 		return new StringRepresentation(buffer.toString());
 
diff --git a/src/main/java/cloudgene/mapred/api/v2/jobs/RestartJob.java b/src/main/java/cloudgene/mapred/api/v2/jobs/RestartJob.java
index 949747b5..f3914afb 100644
--- a/src/main/java/cloudgene/mapred/api/v2/jobs/RestartJob.java
+++ b/src/main/java/cloudgene/mapred/api/v2/jobs/RestartJob.java
@@ -55,8 +55,8 @@ public Representation get(Representation entity) {
 			String hdfsWorkspace = "";			
 			try {
 				hdfsWorkspace = HdfsUtil.path(getSettings().getHdfsWorkspace(), id);
-			}catch (NoClassDefFoundError e) {
-				log.warn("Hadoop not found in classpath. Ignore HDFS Workspace.", e);
+			} catch (NoClassDefFoundError e) {
+				log.warn("Hadoop not found in classpath. Ignore HDFS Workspace.");
 			}
 			String localWorkspace = FileUtil.path(getSettings().getLocalWorkspace(), id);
 
@@ -84,6 +84,13 @@ public Representation get(Representation entity) {
 
 			Map<String, Object> params = new HashMap<String, Object>();
 			params.put("id", id);
+
+			String message = String.format("Job: Restarted job ID %s", job.getId());
+			if (user.isAdmin()) {
+				message += String.format(" (by ADMIN user ID %s - email %s)", user.getId(), user.getMail());
+			}
+			log.info(message);
+
 			return ok("Your job was successfully added to the job queue.", params);
 		} else {
 			return error400("Job " + id + " is not pending.");
diff --git a/src/main/java/cloudgene/mapred/api/v2/jobs/ShareResults.java b/src/main/java/cloudgene/mapred/api/v2/jobs/ShareResults.java
index 20ccff9a..3c06324f 100644
--- a/src/main/java/cloudgene/mapred/api/v2/jobs/ShareResults.java
+++ b/src/main/java/cloudgene/mapred/api/v2/jobs/ShareResults.java
@@ -16,12 +16,13 @@
 import genepi.io.FileUtil;
 
 public class ShareResults extends BaseResource {
-
+	// TODO: investigate the need for unauthenticated download feature. Whether exposed in UI or not, possibly a valid API endpoint
 	private static final Log log = LogFactory.getLog(ShareResults.class);
 
 	@Get
 	public Representation get() {
 
+		// FIXME: username is not actually checked
 		String username = (String) getRequest().getAttributes().get("username");
 		String hash = (String) getRequest().getAttributes().get("hash");
 		String filename = (String) getRequest().getAttributes().get("filename");
@@ -49,9 +50,10 @@ public Representation get() {
 
 		IExternalWorkspace externalWorkspace = ExternalWorkspaceFactory.get(download.getPath());
 		if (externalWorkspace != null) {
-			// external workspace found, use link method and create redirect response
+			// Example scenario: files are stored on an S3 bucket, and this is redirecting the user to a presigned download URL
 			String publicUrl = externalWorkspace.createPublicLink(download.getPath());
 			redirectTemporary(publicUrl);
+			log.info(String.format("Job: Anonymously downloading file '%s' (hash %s) associated with user %s", download.getName(), hash, download.getUsername()));
 			return new StringRepresentation(publicUrl);
 		} else {
 			// no external workspace found, use local workspace
@@ -59,6 +61,9 @@ public Representation get() {
 			String resultFile = FileUtil.path(localWorkspace, download.getPath());
 			log.debug("Downloading file from local workspace " + resultFile);
 			MediaType mediaType = DownloadResults.getMediaType(download.getPath());
+
+			log.info(String.format("Job: Anonymously downloading file '%s' (hash %s) associated with user %s", download.getName(), hash, download.getUsername()));
+
 			return new FileRepresentation(resultFile, mediaType);
 		}
 
diff --git a/src/main/java/cloudgene/mapred/api/v2/jobs/SubmitJob.java b/src/main/java/cloudgene/mapred/api/v2/jobs/SubmitJob.java
index 550dc7f3..dad86072 100644
--- a/src/main/java/cloudgene/mapred/api/v2/jobs/SubmitJob.java
+++ b/src/main/java/cloudgene/mapred/api/v2/jobs/SubmitJob.java
@@ -104,7 +104,7 @@ public Representation post(Representation entity) {
 		try {
 			hdfsWorkspace = HdfsUtil.path(getSettings().getHdfsWorkspace(), id);
 		} catch (NoClassDefFoundError e) {
-			log.warn("Hadoop not found in classpath. Ignore HDFS Workspace.", e);
+			log.warn("Hadoop not found in classpath. Ignore HDFS Workspace.");
 		}
 
 		String localWorkspace = FileUtil.path(getSettings().getLocalWorkspace(), id);
@@ -146,6 +146,13 @@ public Representation post(Representation entity) {
 
 		Map<String, Object> params = new HashMap<String, Object>();
 		params.put("id", id);
+
+		String message = String.format("Job: Created job ID %s for user %s (ID %s - email %s)", id, user.getUsername(), user.getId(), user.getMail());
+		if (this.isAccessedByApi()) {
+			message += " (via API token)";
+		}
+		log.info(message);
+
 		return ok("Your job was successfully added to the job queue.", params);
 
 	}
diff --git a/src/main/java/cloudgene/mapred/api/v2/users/ActivateUser.java b/src/main/java/cloudgene/mapred/api/v2/users/ActivateUser.java
index cb24f186..7ac5a165 100644
--- a/src/main/java/cloudgene/mapred/api/v2/users/ActivateUser.java
+++ b/src/main/java/cloudgene/mapred/api/v2/users/ActivateUser.java
@@ -1,5 +1,7 @@
 package cloudgene.mapred.api.v2.users;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.restlet.representation.Representation;
 import org.restlet.resource.Get;
 
@@ -9,6 +11,7 @@
 import cloudgene.mapred.util.BaseResource;
 
 public class ActivateUser extends BaseResource {
+	private static final Log log = LogFactory.getLog(ActivateUser.class);
 
 	@Get
 	public Representation get() {
@@ -26,15 +29,18 @@ public Representation get() {
 				user.setActive(true);
 				user.setActivationCode("");
 				dao.update(user);
+
+				log.info(String.format("User: activated user %s (ID %s - email %s)", user.getUsername(), user.getId(), user.getMail()));
+
 				return new JSONAnswer("User sucessfully activated.", true);
 
 			} else {
-
+				log.warn(String.format("User: code is either incorrect or has already been used for user %s (ID %s - email %s)", user.getUsername(), user.getId(), user.getMail()));
 				return new JSONAnswer("Wrong activation code.", false);
 
 			}
 		} else {
-
+			log.warn(String.format("User: used activation code for missing or unknown username '%s'", username));
 			return new JSONAnswer("Wrong username.", false);
 
 		}
diff --git a/src/main/java/cloudgene/mapred/api/v2/users/ApiTokens.java b/src/main/java/cloudgene/mapred/api/v2/users/ApiTokens.java
index 50c50cd1..2af1db2c 100644
--- a/src/main/java/cloudgene/mapred/api/v2/users/ApiTokens.java
+++ b/src/main/java/cloudgene/mapred/api/v2/users/ApiTokens.java
@@ -1,5 +1,7 @@
 package cloudgene.mapred.api.v2.users;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.json.JSONObject;
 import org.restlet.data.Status;
 import org.restlet.representation.Representation;
@@ -15,6 +17,7 @@
 import cloudgene.mapred.util.BaseResource;
 
 public class ApiTokens extends BaseResource {
+	private static final Log log = LogFactory.getLog(ApiTokens.class);
 
 	@Post
 	public Representation createApiKey(Representation entity) {
@@ -45,6 +48,8 @@ public Representation createApiKey(Representation entity) {
 			answer.put("message", "Creation successfull.");
 			answer.put("token", token);
 			answer.put("type", "plain");
+
+			log.info(String.format("User: generated API token for user %s (ID %s - email %s)", user.getUsername(), user.getId(), user.getMail()));
 			return new StringRepresentation(answer.toString());
 
 		} else {
@@ -102,6 +107,8 @@ public Representation revokeApiKey(Representation entity) {
 			answer.put("message", "Creation successfull.");
 			answer.put("token", "");
 			answer.put("type", "plain");
+
+			log.info(String.format("User: revoked API token for user %s (ID %s - email %s)", user.getUsername(), user.getId(), user.getMail()));
 			return new StringRepresentation(answer.toString());
 
 		} else {
diff --git a/src/main/java/cloudgene/mapred/api/v2/users/LoginUser.java b/src/main/java/cloudgene/mapred/api/v2/users/LoginUser.java
index 0fad6381..fa1e3c10 100644
--- a/src/main/java/cloudgene/mapred/api/v2/users/LoginUser.java
+++ b/src/main/java/cloudgene/mapred/api/v2/users/LoginUser.java
@@ -2,6 +2,8 @@
 
 import java.util.Date;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.json.JSONException;
 import org.json.JSONObject;
 import org.restlet.data.CookieSetting;
@@ -19,7 +21,9 @@
 
 public class LoginUser extends BaseResource {
 
-	public static final int MAX_LOGIN_ATTEMMPTS = 5;
+	private static final Log log = LogFactory.getLog(LoginUser.class);
+
+	public static final int MAX_LOGIN_ATTEMPTS = 5;
 
 	public static final int LOCKING_TIME_MIN = 30;
 
@@ -37,15 +41,18 @@ public Representation post(Representation entity) {
 		if (user != null) {
 
 			if (!user.isActive()) {
+				log.info(String.format("Authorization failure: User account is not activated for account %s (ID %s - email %s)", user.getUsername(), user.getId(), user.getMail()));
 				return new JSONAnswer("Login Failed! User account is not activated.", false);
 			}
 
-			if (user.getLoginAttempts() >= MAX_LOGIN_ATTEMMPTS) {
+			if (user.getLoginAttempts() >= MAX_LOGIN_ATTEMPTS) {
 				if (user.getLockedUntil() == null || user.getLockedUntil().after(new Date())) {
+					log.info(String.format("Authorization failure: login retries are currently locked for account %s (ID %s - email %s)", user.getUsername(), user.getId(), user.getMail()));
 					return new JSONAnswer("The user account is locked for " + LoginUser.LOCKING_TIME_MIN
 							+ " minutes. Too many failed logins.", false);
 				} else {
 					// penalty time is over. set to zero
+					log.info(String.format("Authorization: Account login lock has expired; releasing for account %s (ID %s - email %s)", user.getUsername(), user.getId(), user.getMail()));
 					user.setLoginAttempts(0);
 				}
 			}
@@ -77,9 +84,18 @@ public Representation post(Representation entity) {
 					answer.put("csrf", csrfToken);
 					answer.put("type", "plain");
 				} catch (JSONException e) {
+					log.error("Authorization: Unexpected error in serializing login tokens", e);
 					e.printStackTrace();
 				}
 
+
+				String message = String.format("Authorization success: user login %s (ID %s - email %s)", user.getUsername(), user.getId(), user.getMail());
+				if (user.isAdmin()) {
+					// Note: Admin user logins are called out explicitly, to aid log analysis in the event of a breach
+					message += " (ADMIN)";
+				}
+				log.info(message);
+
 				return new JsonRepresentation(answer);
 
 			} else {
@@ -90,14 +106,17 @@ public Representation post(Representation entity) {
 				user.setLoginAttempts(attempts);
 
 				// too many, lock user
-				if (attempts >= MAX_LOGIN_ATTEMMPTS) {
+				if (attempts >= MAX_LOGIN_ATTEMPTS) {
+					log.warn(String.format("Authorization failure: User account %s (ID %s - email %s) locked due to too many failed logins", user.getUsername(), user.getId(), user.getMail()));
 					user.setLockedUntil(new Date(System.currentTimeMillis() + (LOCKING_TIME_MIN * 60 * 1000)));
 				}
 				dao.update(user);
 
+				log.warn(String.format("Authorization failure: Invalid password for username: %s", username));
 				return new JSONAnswer("Login Failed! Wrong Username or Password.", false);
 			}
 		} else {
+			log.warn(String.format("Authorization failure: unknown username: %s", username));
 			return new JSONAnswer("Login Failed! Wrong Username or Password.", false);
 		}
 	}
diff --git a/src/main/java/cloudgene/mapred/api/v2/users/RegisterUser.java b/src/main/java/cloudgene/mapred/api/v2/users/RegisterUser.java
index 7c95d784..667e685e 100644
--- a/src/main/java/cloudgene/mapred/api/v2/users/RegisterUser.java
+++ b/src/main/java/cloudgene/mapred/api/v2/users/RegisterUser.java
@@ -1,5 +1,7 @@
 package cloudgene.mapred.api.v2.users;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.restlet.data.Form;
 import org.restlet.representation.Representation;
 import org.restlet.resource.Post;
@@ -13,6 +15,7 @@
 import cloudgene.mapred.util.Template;
 
 public class RegisterUser extends BaseResource {
+	private static final Log log = LogFactory.getLog(RegisterUser.class);
 
 	public static final String DEFAULT_ROLE = "User";
 
@@ -92,6 +95,7 @@ public Representation post(Representation entity) {
 
 			}
 
+			log.info(String.format("Registration: New user %s (ID %s - email %s)", newUser.getUsername(), newUser.getId(), newUser.getMail()));
 			MailUtil.notifySlack(getSettings(), "Hi! say hello to " + username + " (" + mail + ") :hugging_face:");
 
 			dao.insert(newUser);
diff --git a/src/main/java/cloudgene/mapred/api/v2/users/ResetPassword.java b/src/main/java/cloudgene/mapred/api/v2/users/ResetPassword.java
index e665541a..e89d6eef 100644
--- a/src/main/java/cloudgene/mapred/api/v2/users/ResetPassword.java
+++ b/src/main/java/cloudgene/mapred/api/v2/users/ResetPassword.java
@@ -1,5 +1,7 @@
 package cloudgene.mapred.api.v2.users;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.restlet.data.Form;
 import org.restlet.representation.Representation;
 import org.restlet.resource.Post;
@@ -13,6 +15,7 @@
 import cloudgene.mapred.util.Template;
 
 public class ResetPassword extends BaseResource {
+	private static final Log log = LogFactory.getLog(ResetPassword.class);
 
 	@Post
 	public Representation get(Representation entity) {
@@ -63,7 +66,7 @@ public Representation get(Representation entity) {
 			String body = getWebApp().getTemplate(Template.RECOVERY_MAIL, user.getFullName(), application, link);
 
 			try {
-
+				log.info(String.format("Password reset link requested for user '%s'", username));
 				MailUtil.notifySlack(getSettings(), "Hi! " + username + " asked for a new password :key:");
 
 				MailUtil.send(getSettings(), user.getMail(), subject, body);
diff --git a/src/main/java/cloudgene/mapred/api/v2/users/UpdatePassword.java b/src/main/java/cloudgene/mapred/api/v2/users/UpdatePassword.java
index f0ff9b3e..8b6f5d92 100644
--- a/src/main/java/cloudgene/mapred/api/v2/users/UpdatePassword.java
+++ b/src/main/java/cloudgene/mapred/api/v2/users/UpdatePassword.java
@@ -1,5 +1,7 @@
 package cloudgene.mapred.api.v2.users;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.restlet.data.Form;
 import org.restlet.representation.Representation;
 import org.restlet.resource.Post;
@@ -11,6 +13,7 @@
 import cloudgene.mapred.util.HashUtil;
 
 public class UpdatePassword extends BaseResource {
+	private static final Log log = LogFactory.getLog(UpdatePassword.class);
 
 	@Post
 	public Representation post(Representation entity) {
@@ -51,6 +54,8 @@ public Representation post(Representation entity) {
 		user.setActivationCode("");
 		dao.update(user);
 
+		log.info(String.format("User: changed password via account recovery mechanism for user %s (ID %s - email %s)", user.getUsername(), user.getId(), user.getMail()));
+
 		return new JSONAnswer("Password sucessfully updated.", true);
 
 	}
diff --git a/src/main/java/cloudgene/mapred/api/v2/users/UserProfile.java b/src/main/java/cloudgene/mapred/api/v2/users/UserProfile.java
index bad3c09d..30b182ea 100644
--- a/src/main/java/cloudgene/mapred/api/v2/users/UserProfile.java
+++ b/src/main/java/cloudgene/mapred/api/v2/users/UserProfile.java
@@ -1,5 +1,7 @@
 package cloudgene.mapred.api.v2.users;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.restlet.data.Form;
 import org.restlet.data.MediaType;
 import org.restlet.data.Status;
@@ -19,6 +21,7 @@
 import net.sf.json.JSONObject;
 
 public class UserProfile extends BaseResource {
+	private static final Log log = LogFactory.getLog(UserProfile.class);
 
 	@Get
 	public Representation get() {
@@ -75,6 +78,8 @@ public Representation post(Representation entity) {
 
 		// check if user is admin or it is his username
 		if (!user.getUsername().equals(username) && !user.isAdmin()) {
+			log.error(String.format("User: ID %s ('%s') attempted to change profile of a different user '%s'",
+					user.getId(), user.getUsername(), username));
 			return new JSONAnswer("You are not allowed to change this user profile.", false);
 		}
 
@@ -93,6 +98,11 @@ public Representation post(Representation entity) {
 		newUser.setFullName(fullname);
 		newUser.setMail(mail);
 
+		if (!user.getMail().equals(newUser.getMail())) {
+			log.info(String.format("User: changed email address for user %s (ID %s)", newUser.getUsername(),
+					newUser.getId()));
+		}
+
 		// update password only when it's not empty
 		if (newPassword != null && !newPassword.isEmpty()) {
 
@@ -103,6 +113,8 @@ public Representation post(Representation entity) {
 			}
 			newUser.setPassword(HashUtil.hashPassword(newPassword));
 
+			log.info(String.format("User: changed password for user %s (ID %s - email %s)", newUser.getUsername(),
+					newUser.getId(), newUser.getMail()));
 		}
 
 		dao.update(newUser);
@@ -126,13 +138,15 @@ public Representation delete(Representation entity) {
 		String password = form.getFirstValue("password");
 
 		// check if user is admin or it is his username
-		if (!user.getUsername().equals(username) && !user.isAdmin()) {
+		if (!user.getUsername().equals(username)) {
 			return error401("You are not allowed to delete this user profile.");
 		}
 
 		if (HashUtil.checkPassword(password, user.getPassword())) {
 
 			UserDao dao = new UserDao(getDatabase());
+			log.info(String.format("User: requested deletion of account %s (ID %s - email %s)", user.getUsername(),
+					user.getId(), user.getMail()));
 			boolean deleted = dao.delete(user);
 			if (deleted) {
 				return new JSONAnswer("User profile sucessfully delete.", true);
diff --git a/src/main/java/cloudgene/mapred/cron/CleanUpTasks.java b/src/main/java/cloudgene/mapred/cron/CleanUpTasks.java
index b405749c..caf21121 100644
--- a/src/main/java/cloudgene/mapred/cron/CleanUpTasks.java
+++ b/src/main/java/cloudgene/mapred/cron/CleanUpTasks.java
@@ -153,7 +153,7 @@ public static int sendNotifications(WebApp application) {
 
 		}
 
-		log.info(send + " notifications sent. " + otherJobs + " jobs marked without email ntofication.");
+		log.info(send + " notifications sent. " + otherJobs + " jobs marked without email notification.");
 
 		MailUtil.notifySlack(settings, "Hi! I sent " + send + " notifications :love_letter:");
 
diff --git a/src/main/java/cloudgene/mapred/util/BaseResource.java b/src/main/java/cloudgene/mapred/util/BaseResource.java
index ca0760c3..3ca3a437 100644
--- a/src/main/java/cloudgene/mapred/util/BaseResource.java
+++ b/src/main/java/cloudgene/mapred/util/BaseResource.java
@@ -4,6 +4,8 @@
 import java.util.Map;
 
 import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.json.JSONException;
 import org.json.JSONObject;
 import org.restlet.data.Status;
@@ -21,6 +23,7 @@
 import genepi.db.Database;
 
 public class BaseResource extends ServerResource {
+	private static final Log log = LogFactory.getLog(BaseResource.class);
 
 	private WebApp application;
 
@@ -61,12 +64,18 @@ public User getAuthUserAndAllowApiToken(boolean checkCsrf) {
 		User user = JWTUtil.getUserByRequest(getDatabase(), getRequest(), getSettings().getSecretKey(), checkCsrf);
 		if (user == null) {
 			user = JWTUtil.getUserByApiToken(getDatabase(), getRequest(), getSettings().getSecretKey());
+
+			if (user != null) {
+				log.info(String.format("User: API Token Authentication for user: %s (ID %s - email %s)", user.getUsername(), user.getId(), user.getMail()));
+			}
+
 			accessedByApi = true;
 		}
 		return user;
 	}
 	
 	public boolean isAccessedByApi() {
+		// TODO: Is this threadsafe?
 		return accessedByApi;
 	}
 
diff --git a/src/main/java/cloudgene/mapred/util/JSONConverter.java b/src/main/java/cloudgene/mapred/util/JSONConverter.java
index 02cca42f..d910b112 100644
--- a/src/main/java/cloudgene/mapred/util/JSONConverter.java
+++ b/src/main/java/cloudgene/mapred/util/JSONConverter.java
@@ -108,7 +108,6 @@ public static JSONObject convert(WdlParameterInput input, List<WdlApp> apps) {
 			String category = input.getValues().get("category");
 			String property = input.getValues().get("property");
 			String bind = input.getValues().get("bind");
-			System.out.println(property);
 			for (WdlApp app : apps) {
 				if (category != null && !category.isEmpty()) {
 					// filter by category
diff --git a/src/test/java/cloudgene/mapred/api/v2/users/LoginUserTest.java b/src/test/java/cloudgene/mapred/api/v2/users/LoginUserTest.java
index 2df8e98b..700bb6a0 100644
--- a/src/test/java/cloudgene/mapred/api/v2/users/LoginUserTest.java
+++ b/src/test/java/cloudgene/mapred/api/v2/users/LoginUserTest.java
@@ -102,7 +102,7 @@ public void testWrongPasswordAndLocking() throws JSONException, IOException {
 		int oldLoginAttempts = dao.findByUsername("lockeduser").getLoginAttempts();
 
 		// login should work xx times
-		for (int i = 1; i < LoginUser.MAX_LOGIN_ATTEMMPTS + 10; i++) {
+		for (int i = 1; i < LoginUser.MAX_LOGIN_ATTEMPTS + 10; i++) {
 			ClientResource resource = createClientResource("/login");
 			Form form = new Form();
 			form.set("loginUsername", "lockeduser");
@@ -114,7 +114,7 @@ public void testWrongPasswordAndLocking() throws JSONException, IOException {
 
 			int newLoginAttempts = dao.findByUsername("lockeduser").getLoginAttempts();
 
-			if (i <= LoginUser.MAX_LOGIN_ATTEMMPTS) {
+			if (i <= LoginUser.MAX_LOGIN_ATTEMPTS) {
 				// check login counter
 				assertEquals(oldLoginAttempts + 1, newLoginAttempts);
 				oldLoginAttempts = newLoginAttempts;

From 6f656f200964050fb1dfa41c17e394ad8eb6fe65 Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Thu, 27 Apr 2023 14:00:51 +0200
Subject: [PATCH 08/30] Return 400 when url-based upload is detected (#96)

* Return 400 when url-based upload is detected

* Fix issue with job-name parameter
---
 .../mapred/api/v2/jobs/SubmitJob.java         | 108 +++++++++++-------
 1 file changed, 64 insertions(+), 44 deletions(-)

diff --git a/src/main/java/cloudgene/mapred/api/v2/jobs/SubmitJob.java b/src/main/java/cloudgene/mapred/api/v2/jobs/SubmitJob.java
index dad86072..540fcbbe 100644
--- a/src/main/java/cloudgene/mapred/api/v2/jobs/SubmitJob.java
+++ b/src/main/java/cloudgene/mapred/api/v2/jobs/SubmitJob.java
@@ -37,11 +37,14 @@
 import cloudgene.mapred.wdl.WdlParameterInput;
 import cloudgene.mapred.wdl.WdlParameterInputType;
 import genepi.hadoop.HdfsUtil;
+import genepi.hadoop.importer.ImporterFactory;
 import genepi.io.FileUtil;
 
 public class SubmitJob extends BaseResource {
 
 	private static final Log log = LogFactory.getLog(SubmitJob.class);
+	
+	private static final String PARAM_JOB_NAME = "job-name";
 
 	@Post
 	public Representation post(Representation entity) {
@@ -116,6 +119,8 @@ public Representation post(Representation entity) {
 			inputParams = parseAndUpdateInputParams(entity, app, hdfsWorkspace, localWorkspace);
 		} catch (FileUploadIOException e) {
 			return error400("Upload limit reached.");
+		} catch (FileUploadException e) {
+			return error400(e.getMessage());
 		}
 
 		if (inputParams == null) {
@@ -124,8 +129,8 @@ public Representation post(Representation entity) {
 
 		String name = id;
 		if (!publicMode) {
-			if (inputParams.get("job-name") != null && !inputParams.get("job-name").trim().isEmpty()) {
-				name = inputParams.get("job-name");
+			if (inputParams.get(PARAM_JOB_NAME) != null && !inputParams.get(PARAM_JOB_NAME).trim().isEmpty()) {
+				name = inputParams.get(PARAM_JOB_NAME);
 			}
 		}
 
@@ -147,7 +152,8 @@ public Representation post(Representation entity) {
 		Map<String, Object> params = new HashMap<String, Object>();
 		params.put("id", id);
 
-		String message = String.format("Job: Created job ID %s for user %s (ID %s - email %s)", id, user.getUsername(), user.getId(), user.getMail());
+		String message = String.format("Job: Created job ID %s for user %s (ID %s - email %s)", id, user.getUsername(),
+				user.getId(), user.getMail());
 		if (this.isAccessedByApi()) {
 			message += " (via API token)";
 		}
@@ -158,7 +164,7 @@ public Representation post(Representation entity) {
 	}
 
 	private Map<String, String> parseAndUpdateInputParams(Representation entity, WdlApp app, String hdfsWorkspace,
-			String localWorkspace) throws FileUploadIOException {
+			String localWorkspace) throws FileUploadIOException, FileUploadException {
 		Map<String, String> props = new HashMap<String, String>();
 		Map<String, String> params = new HashMap<String, String>();
 
@@ -190,20 +196,14 @@ private Map<String, String> parseAndUpdateInputParams(Representation entity, Wdl
 
 						FileUtils.copyInputStreamToFile(item.openStream(), file);
 
-	
 						// remove upload indentification!
 						String fieldName = item.getFieldName().replace("-upload", "").replace("input-", "");
 
 						// boolean hdfs = false;
 						// boolean folder = false;
 
-						WdlParameterInput inputParam = null;
-						for (WdlParameterInput input : app.getWorkflow().getInputs()) {
-							if (input.getId().equals(fieldName)) {
-								inputParam = input;
-							}
-						}
-						
+						WdlParameterInput inputParam = getInputParamByName(app, fieldName);
+
 						if (inputParam == null) {
 							throw new Exception("Parameter '" + fieldName + "' not found.");
 						}
@@ -212,7 +212,7 @@ private Map<String, String> parseAndUpdateInputParams(Representation entity, Wdl
 
 							String targetPath = HdfsUtil.path(hdfsWorkspace, fieldName);
 
-							String cleandEntryName = new File(entryName).getName();							
+							String cleandEntryName = new File(entryName).getName();
 							String target = HdfsUtil.path(targetPath, cleandEntryName);
 
 							HdfsUtil.put(tmpFile, target);
@@ -222,8 +222,8 @@ private Map<String, String> parseAndUpdateInputParams(Representation entity, Wdl
 								props.put(fieldName, HdfsUtil.makeAbsolute(HdfsUtil.path(hdfsWorkspace, fieldName)));
 							} else {
 								// file
-								props.put(fieldName,
-										HdfsUtil.makeAbsolute(HdfsUtil.path(hdfsWorkspace, fieldName, cleandEntryName)));
+								props.put(fieldName, HdfsUtil
+										.makeAbsolute(HdfsUtil.path(hdfsWorkspace, fieldName, cleandEntryName)));
 							}
 
 						} else {
@@ -233,7 +233,7 @@ private Map<String, String> parseAndUpdateInputParams(Representation entity, Wdl
 
 							FileUtil.createDirectory(targetPath);
 
-							String cleandEntryName = new File(entryName).getName();							
+							String cleandEntryName = new File(entryName).getName();
 							String target = FileUtil.path(targetPath, cleandEntryName);
 
 							FileUtil.copy(tmpFile, target);
@@ -270,7 +270,20 @@ private Map<String, String> parseAndUpdateInputParams(Representation entity, Wdl
 					if (key.startsWith("input-")) {
 						key = key.replace("input-", "");
 					}
+
+					WdlParameterInput input = getInputParamByName(app, key);
+
+					if (!key.equals(PARAM_JOB_NAME) && input == null) {
+						throw new FileUploadException("Parameter '" + key + "' not found.");
+					}
+
 					String value = StringEscapeUtils.escapeHtml(Streams.asString(item.openStream()));
+
+					if (input != null && input.isFileOrFolder() && ImporterFactory.needsImport(value)) {
+						throw new FileUploadException("Parameter '" + input.getId()
+								+ "': URL-based uploads are no longer supported. Please use direct file uploads instead.");
+					}
+
 					if (!props.containsKey(key)) {
 						// don't override uploaded files
 						props.put(key, value);
@@ -281,47 +294,43 @@ private Map<String, String> parseAndUpdateInputParams(Representation entity, Wdl
 			}
 		} catch (FileUploadIOException e) {
 			throw e;
+		} catch (FileUploadException e) {
+			throw e;
 		} catch (Exception e) {
-			e.printStackTrace();
 			return null;
 
 		}
-		try {
-			for (WdlParameterInput input : app.getWorkflow().getInputs()) {
-				if (!params.containsKey(input.getId())) {
-					if (props.containsKey(input.getId())) {
-
-						if (input.isFolder() && input.getPattern() != null && !input.getPattern().isEmpty()) {
-							String pattern = props.get(input.getId() + "-pattern");
-							String value = props.get(input.getId());
-							if (!value.endsWith("/")) {
-								value = value + "/";
-							}
-							params.put(input.getId(), value + pattern);
-						} else {
 
-							if (input.getTypeAsEnum() == WdlParameterInputType.CHECKBOX) {
-								params.put(input.getId(), input.getValues().get("true"));
-							} else {
-								params.put(input.getId(), props.get(input.getId()));
-							}
+		for (WdlParameterInput input : app.getWorkflow().getInputs()) {
+			if (!params.containsKey(input.getId())) {
+				if (props.containsKey(input.getId())) {
+
+					if (input.isFolder() && input.getPattern() != null && !input.getPattern().isEmpty()) {
+						String pattern = props.get(input.getId() + "-pattern");
+						String value = props.get(input.getId());
+						if (!value.endsWith("/")) {
+							value = value + "/";
 						}
+						params.put(input.getId(), value + pattern);
 					} else {
-						// ignore invisible input parameters
-						if (input.getTypeAsEnum() == WdlParameterInputType.CHECKBOX && input.isVisible()) {
-							params.put(input.getId(), input.getValues().get("false"));
+
+						if (input.getTypeAsEnum() == WdlParameterInputType.CHECKBOX) {
+							params.put(input.getId(), input.getValues().get("true"));
+						} else {
+							params.put(input.getId(), props.get(input.getId()));
 						}
 					}
+				} else {
+					// ignore invisible input parameters
+					if (input.getTypeAsEnum() == WdlParameterInputType.CHECKBOX && input.isVisible()) {
+						params.put(input.getId(), input.getValues().get("false"));
+					}
 				}
 			}
+		}
 
-			params.put("job-name", props.get("job-name"));
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
+		params.put(PARAM_JOB_NAME, props.get(PARAM_JOB_NAME));
 
-		}
 		return params;
 	}
 
@@ -340,4 +349,15 @@ private FileItemIterator parseRequest(Representation entity) throws FileUploadEx
 		return upload.getItemIterator(entity);
 
 	}
+
+	private WdlParameterInput getInputParamByName(WdlApp app, String name) {
+
+		for (WdlParameterInput input : app.getWorkflow().getInputs()) {
+			if (input.getId().equals(name)) {
+				return input;
+			}
+		}
+		return null;
+	}
+
 }

From e738a40b0f9bcae3a56d65b4c369d269913849c6 Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Thu, 27 Apr 2023 14:03:04 +0200
Subject: [PATCH 09/30] Prepare release 2.5.7

---
 pom.xml                                  | 2 +-
 src/main/java/cloudgene/mapred/Main.java | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index b8c97ef2..04aea3da 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>cloudgene</groupId>
 	<artifactId>cloudgene</artifactId>
-	<version>2.5.6</version>
+	<version>2.5.7</version>
 
 	<name>Cloudgene</name>
 	<url>http://www.cloudgene.io</url>
diff --git a/src/main/java/cloudgene/mapred/Main.java b/src/main/java/cloudgene/mapred/Main.java
index 4fd988f6..186be2aa 100644
--- a/src/main/java/cloudgene/mapred/Main.java
+++ b/src/main/java/cloudgene/mapred/Main.java
@@ -36,7 +36,7 @@
 
 public class Main {
 
-	public static final String VERSION = "2.5.6";
+	public static final String VERSION = "2.5.7";
 
 	private Database database;
 

From 00a93ebdeadff15146e2d43744ea249836132d85 Mon Sep 17 00:00:00 2001
From: Sebastian Schoenherr <sebastian.schoenherr@i-med.ac.at>
Date: Fri, 2 Jun 2023 12:21:20 +0200
Subject: [PATCH 10/30] Delete cloudgene-daemon

---
 files/cloudgene-daemon | 235 -----------------------------------------
 1 file changed, 235 deletions(-)
 delete mode 100644 files/cloudgene-daemon

diff --git a/files/cloudgene-daemon b/files/cloudgene-daemon
deleted file mode 100644
index 7d5064d4..00000000
--- a/files/cloudgene-daemon
+++ /dev/null
@@ -1,235 +0,0 @@
-#! /bin/bash
-#  Cloudgene Daemon
-
-### BEGIN INIT INFO
-# Provides:          mydaemon
-# Required-Start:    $remote_fs $syslog
-# Required-Stop:     $remote_fs $syslog
-# Short-Description: Starts the MyDaemon service
-# Description:       This file is used to start the daemon
-#                    and should be placed in /etc/init.d
-### END INIT INFO
-
-# Author:   LF and SS
-# CREDITS to https://github.com/vbehar/bade/
-# Url:      cloudgene.uibk.ac.at
-# Date:     2015
-
-NAME="cloudgene"
-DESC="Cloudgene Webservice"
-
-# The path to jsvc
-EXEC=`which jsvc`
-
-# The path to the folder containing MyDaemon.jar
-FILE_PATH=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
-
-# Hadoop path with all jars
-HADOOP_CLASS_PATH=`hadoop classpath`
-
-# set JAVA PATH
-JAVA_HOME="/opt/jdk1.7.0_25/"
-
-# Our classpath including our jar file
-CLASS_PATH="$FILE_PATH/cloudgene.jar:$HADOOP_CLASS_PATH"
-
-# The fully qualified name of the class to execute
-CLASS="cloudgene.mapred.Main"
-
-# can also be set from command line
-user="hadoop"
-port="8082"
-
-
-# The file that will contain our process identification number (pid) for other scripts/programs that need to access it.
-PID="/var/run/$NAME.pid"
-
-# System.out writes to this file...
-LOG_OUT="$FILE_PATH/log/$NAME.out"
-
-# System.err writes to this file...
-LOG_ERR="$FILE_PATH/err/$NAME.err"
-
-
-# display the script usage
-function usage {
-  echo "Man Page - Cloudgene as a Daemon"
-  echo "built for with jsvc (Apache Commons Daemon) 1.0.15-dev"
-  echo "Available actions : start | stop | restart | status"
-  echo "Usage :"
-  echo "  $0 -a start [-u] [-j] [-d] [-h]"
-  echo "     start Cloudgene"
-  echo "  $0 -a stop [-u] [-j] [-d] [-h]"
-  echo "     stop Cloudgene"
-  echo "  $0 -a restart [-u] [-j] [-d] [-h]"
-  echo "     restart Cloudgene"
-  echo "  $0 -a status [-u] [-j] [-d] [-h]"
-  echo "     status of Cloudgene"
-  echo "Options : "
-  echo "   -u:  Hadoop user to start Cloudgene; default is hadoop"
-  echo "   -p:  Cloudgene port; default is 8082"
-  echo "   -j:  full java-path without bin (e.g. /opt/jdk1.7.0_25/); detected automatically if not set"
-  echo "   -d : debug mode: print anything and log everything on commandline"
-  echo "   -h : print this site"
-
-}
-
-# check if APP is running
-function is_app_running {
-  JSVC_PID_FILE="/var/run/$NAME.pid"
-  if [[ -s $JSVC_PID_FILE ]]; then
-    PID=`cat $JSVC_PID_FILE`
-    ps "$PID" > /dev/null
-    if [[ $? -eq 0 ]]; then
-      log "Cloudgene is running with pid $PID"
-      return 0
-    else
-      log "Cloudgene is not running"
-      rm -f $JSVC_PID_FILE
-      return 1
-    fi
-  else
-    log "Cloudgene is not running"
-    return 1    
-  fi
-}
-
-# some basic checks. improvement required
-function check_setup {
-  if [[ -z $JAVA_HOME ]]; then
-    log "Missing JAVA_HOME variable"
-    return 1
-  elif [[ -z $user ]]; then
-  log "No Cloudgene user set"
-  return 1
-  elif [[ -z $port ]]; then
-  log "No port set"
-  return 1
-  else
-   return 0
-  fi
-}
-
-# log (echo) the given message only if we are not in the "quiet" mode
-function log {
-  if [[ ! $QUIET && -n $1 ]]; then
-    if [[ $PRINT_TIME ]]; then
-      TIME=`date +%T.%2N`" "
-    else
-      TIME=""
-    fi
-    echo "$TIME$1"
-  fi
-}
-
-# main function
-# main function
-jsvc_exec() 
-{   
-    if ! check_setup; then
-  	log "Cloudgene not started!"
-   	return 1
-    elif [ $DEBUG ]
-    then
-        echo "DEBUG MODE"
-        $EXEC -cwd $FILE_PATH -nodetach -home $JAVA_HOME -cp $CLASS_PATH -debug -user $user -pidfile $PID $1 $CLASS --port $port 
-    else
-        echo "logging to" $LOG_OUT
-        $EXEC -cwd $FILE_PATH -home $JAVA_HOME -cp $CLASS_PATH -outfile $LOG_OUT -user $user -errfile $LOG_ERR -pidfile $PID $1 $CLASS --port $port
-    fi
-}
-
-
-while getopts ":a:u:j:p:dh" opt; do
-  case $opt in
- a)
-      ACTION=$OPTARG
-      ;;
-	u)
-       echo "starting Cloudgene with user: $OPTARG" >&2
-       user=$OPTARG
-      ;;
-	j)
-       echo "setting JAVA_HOME to : $OPTARG" >&2
-       JAVA_HOME=$OPTARG
-      ;;
-    d)
-       echo "starting daemon in debug mode" >&2
-	   DEBUG=YES
-      ;;
-    p)
-       echo "starting Cloudgene on port:: $OPTARG" >&2
-       port=$OPTARG
-      ;;
-	h)
-      usage
-      exit 0
-      ;;
-	\?)
-      echo "Invalid option: -$OPTARG" >&2
-      ;;
-	*)
-      echo "Option -$OPTARG requires an argument."
-      usage
-      exit 1
-      ;;
-	:)
-      echo "Option -$OPTARG requires an argument."
-      usage
-      exit 1
-      ;;
-  esac
-done
-
-case "$ACTION" in
-    start)
-       
- 		if is_app_running; then
-  			  log "Application is already running, not starting it"
-	
-		else
-			
-            echo "Starting the $DESC..."        
-            # Start the service
-            jsvc_exec
-        fi
-    ;;
-    stop)
-        if [ -f "$PID" ]; then
-            echo "Stopping the $DESC..."
-        
-            # Stop the service
-            jsvc_exec "-stop"       
-        
-            echo "The $DESC has been stopped."
-        else
-            echo "Cloudgene not running, no action taken"
-            exit 1
-        fi
-    ;;
-    restart)
-        if [ -f "$PID" ]; then
-            
-            echo "Restarting the $DESC..."
-            
-            # Stop the service
-            jsvc_exec "-stop"
-
-            # Start the service
-            jsvc_exec
-            
-            echo "The $DESC has been restarted."
-        else
-            echo "Daemon not running, no action taken"
-            exit 1
-        fi
-            ;;
- status) 
-    is_app_running
-    ;;
-	*)
-    usage
-    ;;
-esac
-
-exit $?
\ No newline at end of file

From 2906460140c8975db3306c2bbfc4ca817493e872 Mon Sep 17 00:00:00 2001
From: Sebastian Schoenherr <sebastian.schoenherr@i-med.ac.at>
Date: Sat, 3 Jun 2023 16:47:33 +0200
Subject: [PATCH 11/30] Store hash in database instead of API-token (#103)

Co-authored-by: Lukas Forer <lukas.forer@i-med.ac.at>
---
 .../core/user/profile/dialogs/new.stache      |  3 ++
 .../components/core/user/profile/profile.js   | 14 ++++--
 .../core/user/profile/profile.stache          | 13 +++---
 src/main/html/webapp/models/user-token.js     |  2 +-
 src/main/java/cloudgene/mapred/Main.java      |  2 +-
 .../mapred/api/v2/users/ApiTokens.java        | 34 +++++++++------
 .../mapred/api/v2/users/UserProfile.java      | 11 +----
 .../java/cloudgene/mapred/core/ApiToken.java  | 43 +++++++++++++++++++
 .../mapred/core/ApiTokenVerifier.java         |  7 +--
 .../java/cloudgene/mapred/core/JWTUtil.java   | 20 ++++++---
 src/main/java/cloudgene/mapred/core/User.java | 10 +++++
 .../cloudgene/mapred/database/UserDao.java    | 16 ++++---
 .../cloudgene/mapred/util/JSONConverter.java  | 30 ++++++++++---
 src/main/sql/updates.sql                      |  6 ++-
 14 files changed, 154 insertions(+), 57 deletions(-)
 create mode 100644 src/main/html/webapp/components/core/user/profile/dialogs/new.stache
 create mode 100644 src/main/java/cloudgene/mapred/core/ApiToken.java

diff --git a/src/main/html/webapp/components/core/user/profile/dialogs/new.stache b/src/main/html/webapp/components/core/user/profile/dialogs/new.stache
new file mode 100644
index 00000000..ca40e637
--- /dev/null
+++ b/src/main/html/webapp/components/core/user/profile/dialogs/new.stache
@@ -0,0 +1,3 @@
+<h4>API Token</h4>
+Make sure to copy your personal access token now. <b>You won’t be able to see it again</b>:<br><br>
+<textarea style="width:100%;height:100px;">{{token}}</textarea>
\ No newline at end of file
diff --git a/src/main/html/webapp/components/core/user/profile/profile.js b/src/main/html/webapp/components/core/user/profile/profile.js
index 30b86669..1e0c32b3 100644
--- a/src/main/html/webapp/components/core/user/profile/profile.js
+++ b/src/main/html/webapp/components/core/user/profile/profile.js
@@ -11,7 +11,7 @@ import UserProfile from 'models/user-profile';
 
 import template from './profile.stache';
 import templateDeleteDialog from './dialogs/delete.stache';
-
+import templateNewTokenDialog from './dialogs/new.stache'
 
 export default Control.extend({
 
@@ -99,17 +99,25 @@ export default Control.extend({
         callback: function(result) {
           if (result) {
 
+            var token_expiration = $('#token_expiration').val();
 
             var user = that.options.user;
 
             var userToken = new UserToken();
             userToken.attr('user', user.attr('username'));
+            userToken.attr('expiration', token_expiration);
 
             userToken.save(function(responseText) {
               user.attr('hasApiToken', true);
               user.attr('apiTokenValid', true);
               user.attr('apiTokenMessage', "");
-              bootbox.alert('<h4>API Token</h4>Your token for this service is:<br><textarea style="width:100%;height:100px;">' + responseText.token + '</textarea>');
+
+              bootbox.alert({
+                message: templateNewTokenDialog({
+                  token: responseText.token
+                })
+              });
+
             }, function(message) {
               bootbox.alert('<h4>API Token</h4>Error: ' + message);
             });
@@ -210,4 +218,4 @@ export default Control.extend({
 
   }
 
-});
+});
\ No newline at end of file
diff --git a/src/main/html/webapp/components/core/user/profile/profile.stache b/src/main/html/webapp/components/core/user/profile/profile.stache
index a268101d..e4a1ead0 100644
--- a/src/main/html/webapp/components/core/user/profile/profile.stache
+++ b/src/main/html/webapp/components/core/user/profile/profile.stache
@@ -50,18 +50,19 @@ Please fill out the form below to change your account settings or your password.
 <p>You need a access token to use the API. <a href="https://imputationbot.readthedocs.io/en/latest/getting-started/">Learn more</a>.</p>
 
 {{#user.hasApiToken}}
-
 	<div class="control-group">
 		<div class="controls">
-			<button class="btn btn-primary" id="show_token">Show API Token</button>
 			<button class="btn btn-danger" id="revoke_token">Revoke API Token</button>
 		</div>
 	</div>
   <small class="{{#is(../user.apiTokenValid, false)}}text-danger{{#is}}">{{../user.apiTokenMessage}}</small>
 	{{else}}
-		<button class="btn btn-primary" id="create_token">Create API Token
-	</button>
-
+		<button class="btn btn-primary" id="create_token">Create API Token</button>
+		Expires in 
+		<select  id="token_expiration">
+			<option value="30">30 days</option>
+			<option value="60">60 days</option>
+		</select>
 
 
 {{/user.hasApiToken}}
@@ -76,4 +77,4 @@ Please fill out the form below to change your account settings or your password.
 	<div class="controls">
 		<button class="btn btn-danger" id="delete_account">Delete Account</button>
 	</div>
-</div>
+</div>
\ No newline at end of file
diff --git a/src/main/html/webapp/models/user-token.js b/src/main/html/webapp/models/user-token.js
index a8500ba9..65328ed2 100644
--- a/src/main/html/webapp/models/user-token.js
+++ b/src/main/html/webapp/models/user-token.js
@@ -2,6 +2,6 @@ import Model from 'can-connect/can/model/model';
 
 export default Model.extend({
   findOne: 'GET /api/v2/users/{user}/api-token',
-  create: 'POST /api/v2/users/{user}/api-token',
+  create: 'POST /api/v2/users/{user}/api-token?expiration={expiration}',
   destroy: 'DELETE /api/v2/users/{user}/api-token',
 }, {});
diff --git a/src/main/java/cloudgene/mapred/Main.java b/src/main/java/cloudgene/mapred/Main.java
index 186be2aa..7d4e9808 100644
--- a/src/main/java/cloudgene/mapred/Main.java
+++ b/src/main/java/cloudgene/mapred/Main.java
@@ -36,7 +36,7 @@
 
 public class Main {
 
-	public static final String VERSION = "2.5.7";
+	public static final String VERSION = "2.6.0";
 
 	private Database database;
 
diff --git a/src/main/java/cloudgene/mapred/api/v2/users/ApiTokens.java b/src/main/java/cloudgene/mapred/api/v2/users/ApiTokens.java
index 2af1db2c..ebae7d65 100644
--- a/src/main/java/cloudgene/mapred/api/v2/users/ApiTokens.java
+++ b/src/main/java/cloudgene/mapred/api/v2/users/ApiTokens.java
@@ -10,6 +10,7 @@
 import org.restlet.resource.Get;
 import org.restlet.resource.Post;
 
+import cloudgene.mapred.core.ApiToken;
 import cloudgene.mapred.core.JWTUtil;
 import cloudgene.mapred.core.User;
 import cloudgene.mapred.database.UserDao;
@@ -19,6 +20,8 @@
 public class ApiTokens extends BaseResource {
 	private static final Log log = LogFactory.getLog(ApiTokens.class);
 
+	public static int DEFAULT_TOKEN_LIFETIME_API_SEC = 30 * 24 * 60 * 60;
+
 	@Post
 	public Representation createApiKey(Representation entity) {
 		User user = getAuthUser();
@@ -26,16 +29,23 @@ public Representation createApiKey(Representation entity) {
 		if (user == null) {
 
 			setStatus(Status.CLIENT_ERROR_UNAUTHORIZED);
-			return new StringRepresentation(
-					"The request requires user authentication.");
+			return new StringRepresentation("The request requires user authentication.");
 
 		}
 
+		String expirationValue = getQueryValue("expiration");
+
+		int expiration = DEFAULT_TOKEN_LIFETIME_API_SEC;
+		if (expirationValue != null) {
+			expiration = Integer.parseInt(expirationValue) * 24 * 60 * 60;
+		}
+
 		// create token
-		String token = JWTUtil.createApiToken(user,getSettings().getSecretKey());
+		ApiToken apiToken = JWTUtil.createApiToken(user, getSettings().getSecretKey(), expiration);
 
-		// update token
-		user.setApiToken(token);
+		// store random hash (not access token) in database to validate token
+		user.setApiToken(apiToken.getHash());
+		user.setApiTokenExpiresOn(apiToken.getExpiresOn());
 
 		UserDao userDao = new UserDao(getDatabase());
 		boolean successful = userDao.update(user);
@@ -46,10 +56,11 @@ public Representation createApiKey(Representation entity) {
 			JSONObject answer = new JSONObject();
 			answer.put("success", true);
 			answer.put("message", "Creation successfull.");
-			answer.put("token", token);
+			answer.put("token", apiToken.getAccessToken());
 			answer.put("type", "plain");
 
-			log.info(String.format("User: generated API token for user %s (ID %s - email %s)", user.getUsername(), user.getId(), user.getMail()));
+			log.info(String.format("User: generated API token for user %s (ID %s - email %s)", user.getUsername(),
+					user.getId(), user.getMail()));
 			return new StringRepresentation(answer.toString());
 
 		} else {
@@ -67,8 +78,7 @@ public Representation getApiKey(Representation entity) {
 		if (user == null) {
 
 			setStatus(Status.CLIENT_ERROR_UNAUTHORIZED);
-			return new StringRepresentation(
-					"The request requires user authentication.");
+			return new StringRepresentation("The request requires user authentication.");
 
 		}
 
@@ -88,8 +98,7 @@ public Representation revokeApiKey(Representation entity) {
 		if (user == null) {
 
 			setStatus(Status.CLIENT_ERROR_UNAUTHORIZED);
-			return new StringRepresentation(
-					"The request requires user authentication.");
+			return new StringRepresentation("The request requires user authentication.");
 
 		}
 
@@ -108,7 +117,8 @@ public Representation revokeApiKey(Representation entity) {
 			answer.put("token", "");
 			answer.put("type", "plain");
 
-			log.info(String.format("User: revoked API token for user %s (ID %s - email %s)", user.getUsername(), user.getId(), user.getMail()));
+			log.info(String.format("User: revoked API token for user %s (ID %s - email %s)", user.getUsername(),
+					user.getId(), user.getMail()));
 			return new StringRepresentation(answer.toString());
 
 		} else {
diff --git a/src/main/java/cloudgene/mapred/api/v2/users/UserProfile.java b/src/main/java/cloudgene/mapred/api/v2/users/UserProfile.java
index 30b182ea..a5b0cd62 100644
--- a/src/main/java/cloudgene/mapred/api/v2/users/UserProfile.java
+++ b/src/main/java/cloudgene/mapred/api/v2/users/UserProfile.java
@@ -37,16 +37,7 @@ public Representation get() {
 		User updatedUser = dao.findByUsername(user.getUsername());
 
 		JSONObject object = JSONConverter.convert(updatedUser);
-		try {
-			if (object.getBoolean("hasApiToken")) {
-				org.json.JSONObject result = ApiTokenVerifier.verify(user.getApiToken(), getSettings().getSecretKey(),
-						getDatabase());
-				object.put("apiTokenValid", result.get("valid"));
-				object.put("apiTokenMessage", result.get("message"));
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-		}
+
 		StringRepresentation representation = new StringRepresentation(object.toString(), MediaType.APPLICATION_JSON);
 
 		return representation;
diff --git a/src/main/java/cloudgene/mapred/core/ApiToken.java b/src/main/java/cloudgene/mapred/core/ApiToken.java
new file mode 100644
index 00000000..068d011f
--- /dev/null
+++ b/src/main/java/cloudgene/mapred/core/ApiToken.java
@@ -0,0 +1,43 @@
+package cloudgene.mapred.core;
+
+import java.util.Date;
+
+public class ApiToken {
+
+	private String accessToken;
+
+	private String hash;
+
+	private Date expiresOn;
+
+	public ApiToken(String accessToken, String hash, Date expiresOn) {
+		this.accessToken = accessToken;
+		this.hash = hash;
+		this.expiresOn = expiresOn;
+	}
+
+	public String getAccessToken() {
+		return accessToken;
+	}
+
+	public void setAccessToken(String accessToken) {
+		this.accessToken = accessToken;
+	}
+
+	public String getHash() {
+		return hash;
+	}
+
+	public void setHash(String hash) {
+		this.hash = hash;
+	}
+
+	public void setExpiresOn(Date expiresOn) {
+		this.expiresOn = expiresOn;
+	}
+
+	public Date getExpiresOn() {
+		return expiresOn;
+	}
+
+}
\ No newline at end of file
diff --git a/src/main/java/cloudgene/mapred/core/ApiTokenVerifier.java b/src/main/java/cloudgene/mapred/core/ApiTokenVerifier.java
index 56a255ac..a3ee2819 100644
--- a/src/main/java/cloudgene/mapred/core/ApiTokenVerifier.java
+++ b/src/main/java/cloudgene/mapred/core/ApiTokenVerifier.java
@@ -13,12 +13,13 @@
 import genepi.db.Database;
 
 public class ApiTokenVerifier {
-
+	
 	public static JSONObject verify(String token, String secretKey, Database database) {
 
 		if (token.isEmpty()) {
 			JSONObject result = new JSONObject();
 			result.put("valid", false);
+			result.put("message", "No token provided");
 			return result;
 		}
 
@@ -34,7 +35,7 @@ public static JSONObject verify(String token, String secretKey, Database databas
 				User user = getUser(database, payload);
 				if (user == null) {
 					payload.put("valid", false);
-					payload.put("message", "Invalid Usern mae in API Token.");
+					payload.put("message", "Invalid Username in API Token.");
 				} else {
 
 					Date expire = new Date((Long) payload.get("expire"));
@@ -42,7 +43,7 @@ public static JSONObject verify(String token, String secretKey, Database databas
 					if (((Long) payload.get("expire")) > System.currentTimeMillis()) {
 
 						// check if api key is on users whitelist
-						if (user.getApiToken().equals(token)) {
+						if (user.getApiToken().equals(payload.get(JWTUtil.ATTRIBUTE_API_HASH))) {
 							payload.put("valid", true);
 							payload.put("message", "API Token was created by " + user.getUsername()
 									+ " and is valid until " + expire + ".");
diff --git a/src/main/java/cloudgene/mapred/core/JWTUtil.java b/src/main/java/cloudgene/mapred/core/JWTUtil.java
index 94d2ae72..790d3c63 100644
--- a/src/main/java/cloudgene/mapred/core/JWTUtil.java
+++ b/src/main/java/cloudgene/mapred/core/JWTUtil.java
@@ -1,8 +1,10 @@
 package cloudgene.mapred.core;
 
+import java.util.Date;
 import java.util.HashMap;
 import java.util.Map;
 
+import org.apache.commons.lang.RandomStringUtils;
 import org.restlet.Request;
 import org.restlet.data.Parameter;
 import org.restlet.util.Series;
@@ -12,12 +14,12 @@
 
 public class JWTUtil {
 
+	public static String ATTRIBUTE_API_HASH = "api_hash";
+
 	public static final String COOKIE_NAME = "cloudgene-token";
 
 	public static long TOKEN_LIFETIME_MS = 24 * 60 * 60 * 1000;
 
-	public static long TOKEN_LIFETIME_API_MS = 30L * 24L * 60L * 60L * 1000L;
-
 	public JWTUtil() {
 	}
 
@@ -35,16 +37,22 @@ public static String createCookieToken(User user, String secretKey, String csrfT
 		return token;
 	}
 
-	public static String createApiToken(User user, String secretKey) {
+	public static ApiToken createApiToken(User user, String secretKey, int lifetime) {
+
+		String hash = RandomStringUtils.randomAlphanumeric(30);
 
 		Map<String, Object> playload = new HashMap<String, Object>();
 		playload.put("username", user.getUsername());
 		playload.put("name", user.getFullName());
 		playload.put("mail", user.getMail());
+		playload.put(ATTRIBUTE_API_HASH, hash);
 		playload.put("api", true);
-		String token = JWT.generate(playload, secretKey, TOKEN_LIFETIME_API_MS);
+		String token = JWT.generate(playload, secretKey, lifetime);
 
-		return token;
+		Date expiresOn = new Date(System.currentTimeMillis() + (lifetime * 1000L));
+
+		ApiToken apiToken = new ApiToken(token, hash, expiresOn);
+		return apiToken;
 	}
 
 	public static User getUser(Database database, Map<String, Object> payload) {
@@ -122,7 +130,7 @@ public static User getUserByApiToken(Database database, Request request, String
 			if (isApiToken(payload)) {
 				User user = getUser(database, payload);
 				// check if api key is on users whitelist
-				if (user != null && user.getApiToken().equals(payload.get("request-token").toString())) {
+				if (user != null && user.getApiToken().equals(payload.get(ATTRIBUTE_API_HASH))) {
 					return user;
 				} else {
 					return null;
diff --git a/src/main/java/cloudgene/mapred/core/User.java b/src/main/java/cloudgene/mapred/core/User.java
index 8fc5bc9e..20f9c4cb 100644
--- a/src/main/java/cloudgene/mapred/core/User.java
+++ b/src/main/java/cloudgene/mapred/core/User.java
@@ -29,6 +29,8 @@ public class User {
 
 	private int loginAttempts;
 
+	private Date apiTokenExpiresOn = null;
+	
 	public static final String ROLE_SEPARATOR = ",";
 
 	public static final String ROLE_ADMIN = "admin";
@@ -148,6 +150,14 @@ public void setLoginAttempts(int loginAttempts) {
 	public int getLoginAttempts() {
 		return loginAttempts;
 	}
+	
+	public void setApiTokenExpiresOn(Date apiTokenExpiresOn) {
+		this.apiTokenExpiresOn = apiTokenExpiresOn;
+	}
+	
+	public Date getApiTokenExpiresOn() {
+		return apiTokenExpiresOn;
+	}
 
 	public static String checkUsername(String username) {
 
diff --git a/src/main/java/cloudgene/mapred/database/UserDao.java b/src/main/java/cloudgene/mapred/database/UserDao.java
index 19675405..1cf7f0fc 100644
--- a/src/main/java/cloudgene/mapred/database/UserDao.java
+++ b/src/main/java/cloudgene/mapred/database/UserDao.java
@@ -25,12 +25,12 @@ public UserDao(Database database) {
 	public boolean insert(User user) {
 		StringBuilder sql = new StringBuilder();
 		sql.append(
-				"insert into `user` (username, password, full_name, aws_key, aws_secret_key, save_keys, export_to_s3, s3_bucket, mail, role, export_input_to_s3, activation_code, active,api_token, last_login, locked_until, login_attempts) ");
-		sql.append("values (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)");
+				"insert into `user` (username, password, full_name, aws_key, aws_secret_key, save_keys, export_to_s3, s3_bucket, mail, role, export_input_to_s3, activation_code, active,api_token, last_login, locked_until, login_attempts, api_token_expires_on) ");
+		sql.append("values (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)");
 
 		try {
 
-			Object[] params = new Object[17];
+			Object[] params = new Object[18];
 			params[0] = user.getUsername().toLowerCase();
 			params[1] = user.getPassword();
 			params[2] = user.getFullName();
@@ -41,7 +41,6 @@ public boolean insert(User user) {
 			params[7] = null;
 			params[8] = user.getMail();
 			params[9] = String.join(User.ROLE_SEPARATOR, user.getRoles());
-			;
 			params[10] = false;
 			params[11] = user.getActivationCode();
 			params[12] = user.isActive();
@@ -49,6 +48,7 @@ public boolean insert(User user) {
 			params[14] = user.getLastLogin();
 			params[15] = user.getLockedUntil();
 			params[16] = user.getLoginAttempts();
+			params[17] = user.getApiTokenExpiresOn();
 
 			int id = insert(sql.toString(), params);
 
@@ -67,12 +67,12 @@ public boolean insert(User user) {
 	public boolean update(User user) {
 		StringBuilder sql = new StringBuilder();
 		sql.append(
-				"update `user` set username = ?, password = ?, full_name = ?, aws_key = ?, aws_secret_key = ?, save_keys = ? , export_to_s3 = ?, s3_bucket = ?, mail = ?, role = ?, export_input_to_s3 = ?, active = ?, activation_code = ?, api_token = ?, last_login = ?, locked_until = ?, login_attempts = ? ");
+				"update `user` set username = ?, password = ?, full_name = ?, aws_key = ?, aws_secret_key = ?, save_keys = ? , export_to_s3 = ?, s3_bucket = ?, mail = ?, role = ?, export_input_to_s3 = ?, active = ?, activation_code = ?, api_token = ?, last_login = ?, locked_until = ?, login_attempts = ?, api_token_expires_on = ? ");
 		sql.append("where id = ?");
 
 		try {
 
-			Object[] params = new Object[18];
+			Object[] params = new Object[19];
 			params[0] = user.getUsername().toLowerCase();
 			params[1] = user.getPassword();
 			params[2] = user.getFullName();
@@ -90,7 +90,8 @@ public boolean update(User user) {
 			params[14] = user.getLastLogin();
 			params[15] = user.getLockedUntil();
 			params[16] = user.getLoginAttempts();
-			params[17] = user.getId();
+			params[17] = user.getApiTokenExpiresOn();
+			params[18] = user.getId();
 
 			update(sql.toString(), params);
 
@@ -317,6 +318,7 @@ public User mapRow(ResultSet rs, int row) throws SQLException {
 			user.setActivationCode(rs.getString("user.activation_code"));
 			user.setActive(rs.getBoolean("user.active"));
 			user.setApiToken(rs.getString("user.api_token"));
+			user.setApiTokenExpiresOn(rs.getTimestamp("user.api_token_expires_on"));
 			user.setLastLogin(rs.getTimestamp("user.last_login"));
 			user.setLockedUntil(rs.getTimestamp("user.locked_until"));
 			user.setLoginAttempts(rs.getInt("user.login_attempts"));
diff --git a/src/main/java/cloudgene/mapred/util/JSONConverter.java b/src/main/java/cloudgene/mapred/util/JSONConverter.java
index d910b112..4092af38 100644
--- a/src/main/java/cloudgene/mapred/util/JSONConverter.java
+++ b/src/main/java/cloudgene/mapred/util/JSONConverter.java
@@ -21,6 +21,10 @@
 
 public class JSONConverter {
 
+	public static final String MESSAGE_VALID_TOKEN = "API Token was created by %s and is valid until %s.";
+
+	public static final String MESSAGE_EXPIRED_TOKEN = "API Token was created by %s and expired on %s.";
+
 	public static JSONObject convert(AbstractJob job) {
 
 		JsonConfig config = new JsonConfig();
@@ -30,14 +34,14 @@ public static JSONObject convert(AbstractJob job) {
 				"logOutFile", "map", "reduce", "mapProgress", "reduceProgress", "jobId", "makeAbsolute", "mergeOutput",
 				"removeHeader", "value", "autoExport", "download", "tip", "apiToken", "parameterId", "count",
 				"username" });
-		
-		//create tree
-		for (CloudgeneParameterOutput param: job.getOutputParams()) {
+
+		// create tree
+		for (CloudgeneParameterOutput param : job.getOutputParams()) {
 			String hash = param.createHash();
 			param.setHash(hash);
 			param.setTree(JobResultsTreeUtil.createTree(param.getFiles()));
 		}
-		
+
 		return JSONObject.fromObject(job, config);
 	}
 
@@ -97,12 +101,11 @@ public static JSONObject convert(WdlParameterInput input, List<WdlApp> apps) {
 		if (input.isFolder()) {
 			object.put("source", "upload");
 		}
-		
+
 		if (input.getEmptySelection() != null) {
 			object.put("emptySelection", input.getEmptySelection());
 		}
 
-
 		if (input.getTypeAsEnum() == WdlParameterInputType.LIST && input.hasDataBindung()) {
 			JSONArray array = new JSONArray();
 			String category = input.getValues().get("category");
@@ -227,7 +230,20 @@ public static JSONObject convert(User user) {
 		object.put("role", String.join(User.ROLE_SEPARATOR, user.getRoles()).toLowerCase());
 		object.put("mail", user.getMail());
 		object.put("admin", user.isAdmin());
-		object.put("hasApiToken", user.getApiToken() != null && !user.getApiToken().isEmpty());
+		boolean hasApiToken = user.getApiToken() != null && !user.getApiToken().isEmpty();
+		object.put("hasApiToken", hasApiToken);
+		if (hasApiToken) {
+			if (user.getApiTokenExpiresOn().getTime() > System.currentTimeMillis()) {
+				object.put("apiTokenValid", true);
+				object.put("apiTokenMessage",
+						String.format(MESSAGE_VALID_TOKEN, user.getUsername(), user.getApiTokenExpiresOn()));
+			} else {
+				object.put("apiTokenValid", false);
+				object.put("apiTokenMessage",
+						String.format(MESSAGE_EXPIRED_TOKEN, user.getUsername(), user.getApiTokenExpiresOn()));
+			}
+		}
+
 		return object;
 
 	}
diff --git a/src/main/sql/updates.sql b/src/main/sql/updates.sql
index e288ede8..887a83d1 100644
--- a/src/main/sql/updates.sql
+++ b/src/main/sql/updates.sql
@@ -164,4 +164,8 @@ ALTER TABLE log_messages MODIFY COLUMN message VARCHAR (20000);
 ALTER TABLE html_snippets MODIFY COLUMN text VARCHAR (8000);
 
 -- 2.3.7
-alter table job add column user_agent VARCHAR (400);
\ No newline at end of file
+alter table job add column user_agent VARCHAR (400);
+
+
+-- 2.6.0
+alter table `user` add column api_token_expires_on timestamp null default null;
\ No newline at end of file

From 8c1da0623df4b21f14445032f8455dcad27f270c Mon Sep 17 00:00:00 2001
From: Sebastian Schoenherr <sebastian.schoenherr@i-med.ac.at>
Date: Sat, 3 Jun 2023 16:48:02 +0200
Subject: [PATCH 12/30] Optimize job list (#102)

---
 .../cloudgene/mapred/api/v2/admin/GetAllJobs.java   | 11 ++---------
 src/main/java/cloudgene/mapred/database/JobDao.java | 13 +++++++++----
 2 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/src/main/java/cloudgene/mapred/api/v2/admin/GetAllJobs.java b/src/main/java/cloudgene/mapred/api/v2/admin/GetAllJobs.java
index 52dfaf5d..f9d0f0e6 100644
--- a/src/main/java/cloudgene/mapred/api/v2/admin/GetAllJobs.java
+++ b/src/main/java/cloudgene/mapred/api/v2/admin/GetAllJobs.java
@@ -65,13 +65,6 @@ public Representation getJobs() {
 		case "current":
 
 			jobs = dao.findAllNotRetiredJobs();
-			List<AbstractJob> toRemove = new Vector<AbstractJob>();
-			for (AbstractJob job : jobs) {
-				if (engine.isInQueue(job)) {
-					toRemove.add(job);
-				}
-			}
-			jobs.removeAll(toRemove);
 			break;
 
 		case "retired":
@@ -99,7 +92,7 @@ public Representation getJobs() {
 		int running = 0;
 
 		for (AbstractJob job : jobs) {
-			
+
 			String workspace = getSettings().getLocalWorkspace();
 			String folder = FileUtil.path(workspace, job.getId());
 			File file = new File(folder);
@@ -107,7 +100,7 @@ public Representation getJobs() {
 				long size = FileUtils.sizeOfDirectory(file);
 				job.setWorkspaceSize(FileUtils.byteCountToDisplaySize(size));
 			}
-			
+
 			if (job.getState() == AbstractJob.STATE_EXPORTING || job.getState() == AbstractJob.STATE_RUNNING) {
 				running++;
 			}
diff --git a/src/main/java/cloudgene/mapred/database/JobDao.java b/src/main/java/cloudgene/mapred/database/JobDao.java
index efefca72..275deab4 100644
--- a/src/main/java/cloudgene/mapred/database/JobDao.java
+++ b/src/main/java/cloudgene/mapred/database/JobDao.java
@@ -267,14 +267,19 @@ public List<AbstractJob> findAllNotRetiredJobs() {
 		sql.append("select * ");
 		sql.append("from job ");
 		sql.append("join `user` on job.user_id = `user`.id ");
-		sql.append("where state != ? AND state != ? ");
+		sql.append("where state  not in (?,?,?,?,?,?,?) ");
 		sql.append("order by job.id desc ");
 
 		List<AbstractJob> result = new Vector<AbstractJob>();
 
-		Object[] params = new Object[2];
-		params[0] = AbstractJob.STATE_RETIRED;
-		params[1] = AbstractJob.STATE_DELETED;
+		Object[] params = new Object[7];
+		params[0] = AbstractJob.STATE_WAITING;
+		params[1] = AbstractJob.STATE_RUNNING;
+		params[2] = AbstractJob.STATE_EXPORTING;
+		params[3] = AbstractJob.STATE_RETIRED;
+		params[4] = AbstractJob.STATE_DELETED;
+		params[5] = AbstractJob.STATE_RETIRED;
+		params[6] = AbstractJob.STATE_DELETED;
 
 		try {
 

From 05893ad0bffdb8ca9255a1357d3a02073c0731ca Mon Sep 17 00:00:00 2001
From: seppinho <sebastian.schoenherr@i-med.ac.at>
Date: Sat, 3 Jun 2023 16:50:45 +0200
Subject: [PATCH 13/30] Prepare release 2.6.0

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 04aea3da..469d3f71 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>cloudgene</groupId>
 	<artifactId>cloudgene</artifactId>
-	<version>2.5.7</version>
+	<version>2.6.0</version>
 
 	<name>Cloudgene</name>
 	<url>http://www.cloudgene.io</url>

From d434b05d03ef049cf01d9a07de195b28f9733015 Mon Sep 17 00:00:00 2001
From: Sebastian Schoenherr <sebastian.schoenherr@i-med.ac.at>
Date: Wed, 7 Jun 2023 16:08:57 +0200
Subject: [PATCH 14/30] Handle missing expire date of API token

---
 src/main/java/cloudgene/mapred/util/JSONConverter.java | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/main/java/cloudgene/mapred/util/JSONConverter.java b/src/main/java/cloudgene/mapred/util/JSONConverter.java
index 4092af38..ded765e7 100644
--- a/src/main/java/cloudgene/mapred/util/JSONConverter.java
+++ b/src/main/java/cloudgene/mapred/util/JSONConverter.java
@@ -25,6 +25,8 @@ public class JSONConverter {
 
 	public static final String MESSAGE_EXPIRED_TOKEN = "API Token was created by %s and expired on %s.";
 
+	public static final String MESSAGE_INVALID_TOKEN = "API Token was created with a previous version and is therefore invalid. Please recreate.";
+
 	public static JSONObject convert(AbstractJob job) {
 
 		JsonConfig config = new JsonConfig();
@@ -233,7 +235,10 @@ public static JSONObject convert(User user) {
 		boolean hasApiToken = user.getApiToken() != null && !user.getApiToken().isEmpty();
 		object.put("hasApiToken", hasApiToken);
 		if (hasApiToken) {
-			if (user.getApiTokenExpiresOn().getTime() > System.currentTimeMillis()) {
+			if (user.getApiTokenExpiresOn() == null) {
+				object.put("apiTokenValid", false);
+				object.put("apiTokenMessage", MESSAGE_INVALID_TOKEN);
+			} else if (user.getApiTokenExpiresOn().getTime() > System.currentTimeMillis()) {
 				object.put("apiTokenValid", true);
 				object.put("apiTokenMessage",
 						String.format(MESSAGE_VALID_TOKEN, user.getUsername(), user.getApiTokenExpiresOn()));

From 16a195535a9fa0da4eb37a921703064a2470e835 Mon Sep 17 00:00:00 2001
From: Sebastian Schoenherr <sebastian.schoenherr@i-med.ac.at>
Date: Wed, 7 Jun 2023 16:11:37 +0200
Subject: [PATCH 15/30] Prepare release v2.6.1

---
 pom.xml                                  | 2 +-
 src/main/html/webapp/package-lock.json   | 2 +-
 src/main/html/webapp/package.json        | 2 +-
 src/main/java/cloudgene/mapred/Main.java | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/pom.xml b/pom.xml
index 469d3f71..d3c05daf 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>cloudgene</groupId>
 	<artifactId>cloudgene</artifactId>
-	<version>2.6.0</version>
+	<version>2.6.1</version>
 
 	<name>Cloudgene</name>
 	<url>http://www.cloudgene.io</url>
diff --git a/src/main/html/webapp/package-lock.json b/src/main/html/webapp/package-lock.json
index 69c9dcfc..632dc475 100644
--- a/src/main/html/webapp/package-lock.json
+++ b/src/main/html/webapp/package-lock.json
@@ -1,6 +1,6 @@
 {
   "name": "cloudgene",
-  "version": "2.5.6",
+  "version": "2.6.1",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
diff --git a/src/main/html/webapp/package.json b/src/main/html/webapp/package.json
index 91fef532..1d23bf7e 100644
--- a/src/main/html/webapp/package.json
+++ b/src/main/html/webapp/package.json
@@ -1,6 +1,6 @@
 {
   "name": "cloudgene",
-  "version": "2.5.6",
+  "version": "2.6.1",
   "description": "Cloudgene web client",
   "homepage": "http://www.cloudgene.io",
   "author": "Lukas Forer <lukas.forer@i-med.ac.at (http://www.forer.it)",
diff --git a/src/main/java/cloudgene/mapred/Main.java b/src/main/java/cloudgene/mapred/Main.java
index 7d4e9808..47dc0a2f 100644
--- a/src/main/java/cloudgene/mapred/Main.java
+++ b/src/main/java/cloudgene/mapred/Main.java
@@ -36,7 +36,7 @@
 
 public class Main {
 
-	public static final String VERSION = "2.6.0";
+	public static final String VERSION = "2.6.1";
 
 	private Database database;
 

From 2b6aebaad14ef6b9682b7f3e933c4537a88a0687 Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Tue, 20 Jun 2023 09:17:39 +0200
Subject: [PATCH 16/30] Fix expire date in new API keys

---
 src/main/java/cloudgene/mapred/core/JWTUtil.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/cloudgene/mapred/core/JWTUtil.java b/src/main/java/cloudgene/mapred/core/JWTUtil.java
index 790d3c63..071678bf 100644
--- a/src/main/java/cloudgene/mapred/core/JWTUtil.java
+++ b/src/main/java/cloudgene/mapred/core/JWTUtil.java
@@ -47,7 +47,7 @@ public static ApiToken createApiToken(User user, String secretKey, int lifetime)
 		playload.put("mail", user.getMail());
 		playload.put(ATTRIBUTE_API_HASH, hash);
 		playload.put("api", true);
-		String token = JWT.generate(playload, secretKey, lifetime);
+		String token = JWT.generate(playload, secretKey, lifetime * 1000L);
 
 		Date expiresOn = new Date(System.currentTimeMillis() + (lifetime * 1000L));
 

From 181973f79349bd877f7d84bd29a86e8c19cc69dc Mon Sep 17 00:00:00 2001
From: Sebastian Schoenherr <sebastian.schoenherr@i-med.ac.at>
Date: Tue, 20 Jun 2023 11:20:34 +0200
Subject: [PATCH 17/30] Prepeare release v2.6.2

---
 pom.xml                                  | 2 +-
 src/main/html/webapp/package-lock.json   | 2 +-
 src/main/html/webapp/package.json        | 2 +-
 src/main/java/cloudgene/mapred/Main.java | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/pom.xml b/pom.xml
index d3c05daf..4560c287 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>cloudgene</groupId>
 	<artifactId>cloudgene</artifactId>
-	<version>2.6.1</version>
+	<version>2.6.2</version>
 
 	<name>Cloudgene</name>
 	<url>http://www.cloudgene.io</url>
diff --git a/src/main/html/webapp/package-lock.json b/src/main/html/webapp/package-lock.json
index 632dc475..9892de69 100644
--- a/src/main/html/webapp/package-lock.json
+++ b/src/main/html/webapp/package-lock.json
@@ -1,6 +1,6 @@
 {
   "name": "cloudgene",
-  "version": "2.6.1",
+  "version": "2.6.2",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
diff --git a/src/main/html/webapp/package.json b/src/main/html/webapp/package.json
index 1d23bf7e..75fabc0e 100644
--- a/src/main/html/webapp/package.json
+++ b/src/main/html/webapp/package.json
@@ -1,6 +1,6 @@
 {
   "name": "cloudgene",
-  "version": "2.6.1",
+  "version": "2.6.2",
   "description": "Cloudgene web client",
   "homepage": "http://www.cloudgene.io",
   "author": "Lukas Forer <lukas.forer@i-med.ac.at (http://www.forer.it)",
diff --git a/src/main/java/cloudgene/mapred/Main.java b/src/main/java/cloudgene/mapred/Main.java
index 47dc0a2f..a289a3a4 100644
--- a/src/main/java/cloudgene/mapred/Main.java
+++ b/src/main/java/cloudgene/mapred/Main.java
@@ -36,7 +36,7 @@
 
 public class Main {
 
-	public static final String VERSION = "2.6.1";
+	public static final String VERSION = "2.6.2";
 
 	private Database database;
 

From deb795f654b5f6c39a3b01d35dd4919a3b2629cf Mon Sep 17 00:00:00 2001
From: Sebastian Schoenherr <sebastian.schoenherr@i-med.ac.at>
Date: Thu, 20 Jul 2023 13:23:40 +0200
Subject: [PATCH 18/30] Improve job handling (#109)

---
 .../cloudgene/mapred/jobs/WorkflowEngine.java | 22 +------------------
 1 file changed, 1 insertion(+), 21 deletions(-)

diff --git a/src/main/java/cloudgene/mapred/jobs/WorkflowEngine.java b/src/main/java/cloudgene/mapred/jobs/WorkflowEngine.java
index 3a530f10..8e8664c4 100644
--- a/src/main/java/cloudgene/mapred/jobs/WorkflowEngine.java
+++ b/src/main/java/cloudgene/mapred/jobs/WorkflowEngine.java
@@ -231,33 +231,13 @@ public List<AbstractJob> getAllJobsInShortTimeQueue() {
 
 		List<AbstractJob> jobs = shortTimeQueue.getAllJobs();
 
-		for (AbstractJob job : jobs) {
-
-			if (job instanceof CloudgeneJob) {
-
-				((CloudgeneJob) job).updateProgress();
-
-			}
-
-		}
-
-		return shortTimeQueue.getAllJobs();
+		return jobs;
 	}
 
 	public List<AbstractJob> getAllJobsInLongTimeQueue() {
 
 		List<AbstractJob> jobs = longTimeQueue.getAllJobs();
 
-		for (AbstractJob job : jobs) {
-
-			if (job instanceof CloudgeneJob) {
-
-				((CloudgeneJob) job).updateProgress();
-
-			}
-
-		}
-
 		return jobs;
 	}
 

From f195c0d53883179f6d48400a97b3493d1250f89c Mon Sep 17 00:00:00 2001
From: seppinho <sebastian.schoenherr@i-med.ac.at>
Date: Thu, 20 Jul 2023 13:30:17 +0200
Subject: [PATCH 19/30] Prepare release v2.6.3

---
 pom.xml                                  | 2 +-
 src/main/html/webapp/package-lock.json   | 2 +-
 src/main/html/webapp/package.json        | 2 +-
 src/main/java/cloudgene/mapred/Main.java | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/pom.xml b/pom.xml
index 4560c287..b7638509 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>cloudgene</groupId>
 	<artifactId>cloudgene</artifactId>
-	<version>2.6.2</version>
+	<version>2.6.3</version>
 
 	<name>Cloudgene</name>
 	<url>http://www.cloudgene.io</url>
diff --git a/src/main/html/webapp/package-lock.json b/src/main/html/webapp/package-lock.json
index 9892de69..0fa9640a 100644
--- a/src/main/html/webapp/package-lock.json
+++ b/src/main/html/webapp/package-lock.json
@@ -1,6 +1,6 @@
 {
   "name": "cloudgene",
-  "version": "2.6.2",
+  "version": "2.6.3",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
diff --git a/src/main/html/webapp/package.json b/src/main/html/webapp/package.json
index 75fabc0e..379f70d2 100644
--- a/src/main/html/webapp/package.json
+++ b/src/main/html/webapp/package.json
@@ -1,6 +1,6 @@
 {
   "name": "cloudgene",
-  "version": "2.6.2",
+  "version": "2.6.3",
   "description": "Cloudgene web client",
   "homepage": "http://www.cloudgene.io",
   "author": "Lukas Forer <lukas.forer@i-med.ac.at (http://www.forer.it)",
diff --git a/src/main/java/cloudgene/mapred/Main.java b/src/main/java/cloudgene/mapred/Main.java
index a289a3a4..9dbaafc4 100644
--- a/src/main/java/cloudgene/mapred/Main.java
+++ b/src/main/java/cloudgene/mapred/Main.java
@@ -36,7 +36,7 @@
 
 public class Main {
 
-	public static final String VERSION = "2.6.2";
+	public static final String VERSION = "2.6.3";
 
 	private Database database;
 

From 8cb03dbbbad21b75da06acc3421d824ec55434dd Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Fri, 1 Sep 2023 10:16:12 +0200
Subject: [PATCH 20/30] Update genepi maven repository (#111)

---
 pom.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pom.xml b/pom.xml
index b7638509..088ccc3a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -60,9 +60,9 @@
 		</repository>
 
 		<repository>
-			<id>jfrog-genepi-maven</id>
-			<name>jfrog-genepi-maven</name>
-			<url>https://genepi.jfrog.io/artifactory/maven/</url>
+			<id>genepi-maven</id>
+			<name>genepi-maven</name>
+			<url>https://genepi.i-med.ac.at/maven</url>
 		</repository>
 
 		<repository>

From 3f6a03d299308e7bccb82b71e2b4e5c539398f9c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sun, 24 Sep 2023 09:57:01 +0200
Subject: [PATCH 21/30] Bump junit from 4.8.1 to 4.13.1 (#47)

Bumps [junit](https://github.com/junit-team/junit4) from 4.8.1 to 4.13.1.
- [Release notes](https://github.com/junit-team/junit4/releases)
- [Changelog](https://github.com/junit-team/junit4/blob/main/doc/ReleaseNotes4.13.1.md)
- [Commits](https://github.com/junit-team/junit4/compare/r4.8.1...r4.13.1)

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Lukas Forer <lukas.forer@i-med.ac.at>
---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 088ccc3a..74d9187c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -374,7 +374,7 @@
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
-			<version>4.8.1</version>
+			<version>4.13.1</version>
 			<scope>test</scope>
 		</dependency>
 

From 12e6415c9efbf5457e2bfd7f67e05f5c93e1a2c7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sun, 24 Sep 2023 09:57:13 +0200
Subject: [PATCH 22/30] Bump com.google.guava:guava from 31.0.1-jre to
 32.0.0-jre (#121)

Bumps [com.google.guava:guava](https://github.com/google/guava) from 31.0.1-jre to 32.0.0-jre.
- [Release notes](https://github.com/google/guava/releases)
- [Commits](https://github.com/google/guava/commits)

---
updated-dependencies:
- dependency-name: com.google.guava:guava
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 74d9187c..d4aad35b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -300,7 +300,7 @@
 		<dependency>
 			<groupId>com.google.guava</groupId>
 			<artifactId>guava</artifactId>
-			<version>31.0.1-jre</version>
+			<version>32.0.0-jre</version>
 		</dependency>
 
 		<dependency>

From d26ecf6ba640edf3949ae6a6c6b25074323c1d3d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sun, 24 Sep 2023 09:57:33 +0200
Subject: [PATCH 23/30] Bump com.h2database:h2 from 2.1.210 to 2.2.220 (#120)

Bumps [com.h2database:h2](https://github.com/h2database/h2database) from 2.1.210 to 2.2.220.
- [Release notes](https://github.com/h2database/h2database/releases)
- [Commits](https://github.com/h2database/h2database/compare/version-2.1.210...version-2.2.220)

---
updated-dependencies:
- dependency-name: com.h2database:h2
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index d4aad35b..3d737c02 100644
--- a/pom.xml
+++ b/pom.xml
@@ -136,7 +136,7 @@
 		<dependency>
 			<groupId>com.h2database</groupId>
 			<artifactId>h2</artifactId>
-			<version>2.1.210</version>
+			<version>2.2.220</version>
 		</dependency>
 
 		<dependency>

From ada1bf04e80e964aab846f53d6770ba5a51f9a02 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sun, 24 Sep 2023 10:04:27 +0200
Subject: [PATCH 24/30] Bump org.apache.ivy:ivy from 2.5.1 to 2.5.2 (#122)

Bumps org.apache.ivy:ivy from 2.5.1 to 2.5.2.

---
updated-dependencies:
- dependency-name: org.apache.ivy:ivy
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 3d737c02..0f45a7f9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -197,7 +197,7 @@
 		<dependency>
 			<groupId>org.apache.ivy</groupId>
 			<artifactId>ivy</artifactId>
-			<version>2.5.1</version>
+			<version>2.5.2</version>
 		</dependency>
 
 		<!-- Logging -->

From 897343afcf5475a5d8a77e9d1e58fbd66c2f4395 Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Sun, 24 Sep 2023 11:29:47 +0200
Subject: [PATCH 25/30] Update bcprov-jdk15on to 1.70 (#123)

* Update bcprov-jdk15on to 1.67

* Update bcprov-jdk15on to 1.70
---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 0f45a7f9..7810afff 100644
--- a/pom.xml
+++ b/pom.xml
@@ -324,7 +324,7 @@
 		<dependency>
 			<groupId>org.bouncycastle</groupId>
 			<artifactId>bcprov-jdk15on</artifactId>
-			<version>1.58</version>
+			<version>1.70</version>
 			<scope>test</scope>
 		</dependency>
 

From aeeb7126b7525ffa3e2e332f20ccb757ddddd9d3 Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Wed, 27 Sep 2023 09:28:48 +0200
Subject: [PATCH 26/30] Update bootstrap to 4.6.2 (#124)

* Update boostrap to 4.6.3

* Update node and npm in maven plugin

* Update jquery to 3.5.0

* Update bootbox to 5.5.3 and update popper and jquery
---
 pom.xml                                |    4 +-
 src/main/html/webapp/package-lock.json | 6441 +++++++++++++-----------
 src/main/html/webapp/package.json      |    8 +-
 3 files changed, 3384 insertions(+), 3069 deletions(-)

diff --git a/pom.xml b/pom.xml
index 7810afff..edb2e85d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -33,8 +33,8 @@
 		<java.version>1.8</java.version>
 		<restlet.version>2.3.12</restlet.version>
 		<hadoop.version>2.6.0-cdh5.16.1</hadoop.version>
-		<node.version>v8.11.4</node.version>
-		<npm.version>6.4.1</npm.version>
+		<node.version>v18.17.1</node.version>
+		<npm.version>9.6.7</npm.version>
 		<webapp>${basedir}/src/main/html/webapp</webapp>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
diff --git a/src/main/html/webapp/package-lock.json b/src/main/html/webapp/package-lock.json
index 0fa9640a..288b51df 100644
--- a/src/main/html/webapp/package-lock.json
+++ b/src/main/html/webapp/package-lock.json
@@ -1,231 +1,364 @@
 {
   "name": "cloudgene",
   "version": "2.6.3",
-  "lockfileVersion": 1,
+  "lockfileVersion": 3,
   "requires": true,
-  "dependencies": {
-    "@fortawesome/fontawesome-free": {
+  "packages": {
+    "": {
+      "name": "cloudgene",
+      "version": "2.6.3",
+      "license": "AGPL-3.0",
+      "dependencies": {
+        "@fortawesome/fontawesome-free": "5.3.1",
+        "@popperjs/core": "^2.0.0",
+        "ansi_up": "4.0.4",
+        "bootbox": "5.5.3",
+        "bootstrap": "4.6.2",
+        "can-ajax": "1.1.4",
+        "can-connect": "1.5.18",
+        "can-control": "3.2.4",
+        "can-deparam": "1.0.3",
+        "can-list": "3.2.2",
+        "can-map": "3.4.2",
+        "can-map-define": "3.1.2",
+        "can-route": "3.3.4",
+        "can-stache": "3.14.22",
+        "can-util": "3.12.0",
+        "dateformat": "3.0.3",
+        "jquery": "3.5.1",
+        "jquery-form": "3.50.0",
+        "md5": "2.2.1",
+        "morris.js": "0.5.0",
+        "raphael": "2.2.7",
+        "steal": "^1.5.13"
+      },
+      "devDependencies": {
+        "steal-css": "^1.3.2",
+        "steal-less": "^1.3.1",
+        "steal-stache": "3.1.3",
+        "steal-tools": "^1.8.4"
+      }
+    },
+    "node_modules/@fortawesome/fontawesome-free": {
       "version": "5.3.1",
       "resolved": "https://registry.npmjs.org/@fortawesome/fontawesome-free/-/fontawesome-free-5.3.1.tgz",
-      "integrity": "sha512-jt6yi7iZVtkY9Jc6zFo+G2vqL4M81pb3IA3WmnnDt9ci7Asz+mPg4gbZL8pjx0nGFBsG0Bmd7BjU9IQkebqxFA=="
+      "integrity": "sha512-jt6yi7iZVtkY9Jc6zFo+G2vqL4M81pb3IA3WmnnDt9ci7Asz+mPg4gbZL8pjx0nGFBsG0Bmd7BjU9IQkebqxFA==",
+      "engines": {
+        "node": ">=6"
+      }
     },
-    "@mrmlnc/readdir-enhanced": {
+    "node_modules/@mrmlnc/readdir-enhanced": {
       "version": "2.2.1",
       "resolved": "https://registry.npmjs.org/@mrmlnc/readdir-enhanced/-/readdir-enhanced-2.2.1.tgz",
       "integrity": "sha512-bPHp6Ji8b41szTOcaP63VlnbbO5Ny6dwAATtY6JTjh5N2OLrb5Qk/Th5cRkRQhkWCt+EJsYrNB0MiL+Gpn6e3g==",
       "dev": true,
-      "requires": {
+      "dependencies": {
         "call-me-maybe": "^1.0.1",
         "glob-to-regexp": "^0.3.0"
+      },
+      "engines": {
+        "node": ">=4"
       }
     },
-    "@nodelib/fs.stat": {
-      "version": "1.1.2",
-      "resolved": "https://registry.npmjs.org/@nodelib/fs.stat/-/fs.stat-1.1.2.tgz",
-      "integrity": "sha512-yprFYuno9FtNsSHVlSWd+nRlmGoAbqbeCwOryP6sC/zoCjhpArcRMYp19EvpSUSizJAlsXEwJv+wcWS9XaXdMw==",
-      "dev": true
+    "node_modules/@nodelib/fs.stat": {
+      "version": "1.1.3",
+      "resolved": "https://registry.npmjs.org/@nodelib/fs.stat/-/fs.stat-1.1.3.tgz",
+      "integrity": "sha512-shAmDyaQC4H92APFoIaVDHCx5bStIocgvbwQyxPRrbUY20V1EYTbSDchWbuwlMG3V17cprZhA6+78JfB+3DTPw==",
+      "dev": true,
+      "engines": {
+        "node": ">= 6"
+      }
     },
-    "Base64": {
-      "version": "0.2.1",
-      "resolved": "https://registry.npmjs.org/Base64/-/Base64-0.2.1.tgz",
-      "integrity": "sha1-ujpCMHCOGGcFBl5mur3Uw1z2ACg="
+    "node_modules/@popperjs/core": {
+      "version": "2.11.8",
+      "resolved": "https://registry.npmjs.org/@popperjs/core/-/core-2.11.8.tgz",
+      "integrity": "sha512-P1st0aksCrn9sGZhp8GMYwBnQsbvAWsZAX44oXNNvLHGqAOcoVxmjZiohstwQ7SqKnbR47akdNi+uleWD8+g6A==",
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/popperjs"
+      }
+    },
+    "node_modules/ajv": {
+      "version": "6.12.6",
+      "resolved": "https://registry.npmjs.org/ajv/-/ajv-6.12.6.tgz",
+      "integrity": "sha512-j3fVLgvTo527anyYyJOGTYJbG+vnnQYvE0m5mmkc1TK+nxAppkCLMIL0aZ4dblVCNoGShhm+kzE4ZUykBoMg4g==",
+      "dev": true,
+      "optional": true,
+      "dependencies": {
+        "fast-deep-equal": "^3.1.1",
+        "fast-json-stable-stringify": "^2.0.0",
+        "json-schema-traverse": "^0.4.1",
+        "uri-js": "^4.2.2"
+      },
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/epoberezkin"
+      }
     },
-    "amdefine": {
+    "node_modules/amdefine": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/amdefine/-/amdefine-1.0.1.tgz",
-      "integrity": "sha1-SlKCrBZHKek2Gbz9OtFR+BfOkfU=",
-      "dev": true
-    },
-    "ansi-regex": {
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-      "integrity": "sha1-w7M6te42DYbg5ijwRorn7yfWVN8=",
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-    "ansi-styles": {
-      "version": "2.2.1",
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-      "integrity": "sha1-tDLdM1i2NM914eRmQ2gkBTPB3b4=",
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       "dev": true,
-      "optional": true
+      "engines": {
+        "node": ">=0.4.2"
+      }
     },
-    "ansi_up": {
+    "node_modules/ansi_up": {
       "version": "4.0.4",
       "resolved": "https://registry.npmjs.org/ansi_up/-/ansi_up-4.0.4.tgz",
-      "integrity": "sha512-vRxC8q6QY918MbehO869biJW4tiunJdjOhi5fpY6NLOliBQlZhOkKgABJKJqH+JZfb/WfjvjN1chLWI6tODerw=="
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+        "node": "*"
+      }
+    },
+    "node_modules/ansi-regex": {
+      "version": "3.0.1",
+      "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-3.0.1.tgz",
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+      "dev": true,
+      "engines": {
+        "node": ">=4"
+      }
     },
-    "anymatch": {
+    "node_modules/anymatch": {
       "version": "2.0.0",
       "resolved": "https://registry.npmjs.org/anymatch/-/anymatch-2.0.0.tgz",
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         "micromatch": "^3.1.4",
         "normalize-path": "^2.1.1"
       }
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       "version": "4.0.0",
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+    "node_modules/ws": {
+      "version": "5.2.3",
+      "resolved": "https://registry.npmjs.org/ws/-/ws-5.2.3.tgz",
+      "integrity": "sha512-jZArVERrMsKUatIdnLzqvcfydI85dvd/Fp1u/VOpfdDWQ4c9qWXe+VIeAbQ5FrDwciAkr+lzofXLz3Kuf26AOA==",
       "dev": true,
-      "requires": {
+      "dependencies": {
         "async-limiter": "~1.0.0"
       }
     },
-    "xtend": {
-      "version": "4.0.1",
-      "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.1.tgz",
-      "integrity": "sha1-pcbVMr5lbiPbgg77lDofBJmNY68=",
-      "dev": true
+    "node_modules/xtend": {
+      "version": "4.0.2",
+      "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz",
+      "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==",
+      "dev": true,
+      "engines": {
+        "node": ">=0.4"
+      }
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-    "y18n": {
-      "version": "3.2.1",
-      "resolved": "https://registry.npmjs.org/y18n/-/y18n-3.2.1.tgz",
-      "integrity": "sha1-bRX7qITAhnnA136I53WegR4H+kE=",
+    "node_modules/y18n": {
+      "version": "3.2.2",
+      "resolved": "https://registry.npmjs.org/y18n/-/y18n-3.2.2.tgz",
+      "integrity": "sha512-uGZHXkHnhF0XeeAPgnKfPv1bgKAYyVvmNL1xlKsPYZPaIHxGti2hHqvOCQv71XMsLxu1QjergkqogUnms5D3YQ==",
       "dev": true
     },
-    "yallist": {
-      "version": "2.1.2",
-      "resolved": "https://registry.npmjs.org/yallist/-/yallist-2.1.2.tgz",
-      "integrity": "sha1-HBH5IY8HYImkfdUS+TxmmaaoHVI=",
-      "dev": true
+    "node_modules/yargs": {
+      "version": "11.1.1",
+      "resolved": "https://registry.npmjs.org/yargs/-/yargs-11.1.1.tgz",
+      "integrity": "sha512-PRU7gJrJaXv3q3yQZ/+/X6KBswZiaQ+zOmdprZcouPYtQgvNU35i+68M4b1ZHLZtYFT5QObFLV+ZkmJYcwKdiw==",
+      "dev": true,
+      "dependencies": {
+        "cliui": "^4.0.0",
+        "decamelize": "^1.1.1",
+        "find-up": "^2.1.0",
+        "get-caller-file": "^1.0.1",
+        "os-locale": "^3.1.0",
+        "require-directory": "^2.1.1",
+        "require-main-filename": "^1.0.1",
+        "set-blocking": "^2.0.0",
+        "string-width": "^2.0.0",
+        "which-module": "^2.0.0",
+        "y18n": "^3.2.1",
+        "yargs-parser": "^9.0.2"
+      }
+    },
+    "node_modules/yargs-parser": {
+      "version": "9.0.2",
+      "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-9.0.2.tgz",
+      "integrity": "sha512-CswCfdOgCr4MMsT1GzbEJ7Z2uYudWyrGX8Bgh/0eyCzj/DXWdKq6a/ADufkzI1WAOIW6jYaXJvRyLhDO0kfqBw==",
+      "dev": true,
+      "dependencies": {
+        "camelcase": "^4.1.0"
+      }
     },
-    "zlib-browserify": {
+    "node_modules/zlib-browserify": {
       "version": "0.0.3",
       "resolved": "https://registry.npmjs.org/zlib-browserify/-/zlib-browserify-0.0.3.tgz",
-      "integrity": "sha1-JAzNv9AgP6hCsTDe77FBQSLIzFA=",
-      "requires": {
+      "integrity": "sha512-KW42YGoQKq7+oU46deeWMUsrPyBruEWV1DoObBTMfEC2LnTqQIrwKVKrPoz2mn5DXESW4Ca/lIP2MqGHrt/WFA==",
+      "dependencies": {
         "tape": "~0.2.2"
       }
     }
diff --git a/src/main/html/webapp/package.json b/src/main/html/webapp/package.json
index 379f70d2..5cd5dd4b 100644
--- a/src/main/html/webapp/package.json
+++ b/src/main/html/webapp/package.json
@@ -14,8 +14,8 @@
   },
   "dependencies": {
     "@fortawesome/fontawesome-free": "5.3.1",
-    "bootbox": "4.4.0",
-    "bootstrap": "4.1.3",
+    "bootbox": "5.5.3",
+    "bootstrap": "4.6.2",
     "can-ajax": "1.1.4",
     "can-map": "3.4.2",
     "can-map-define": "3.1.2",
@@ -27,11 +27,11 @@
     "can-util": "3.12.0",
     "can-list": "3.2.2",
     "dateformat": "3.0.3",
-    "jquery": "3.3.1",
+    "jquery": "3.5.1",
     "jquery-form": "3.50.0",
     "md5": "2.2.1",
     "morris.js": "0.5.0",
-    "popper.js": "1.14.3",
+	"@popperjs/core": "^2.0.0",
     "raphael": "2.2.7",
     "steal": "^1.5.13",
     "ansi_up": "4.0.4"

From c1c15d91f49d578fb36c65491bfbd32b27c530a4 Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Wed, 27 Sep 2023 10:09:57 +0200
Subject: [PATCH 27/30] Update ansi_up to 5.0.0 (#126)

---
 src/main/html/webapp/package-lock.json | 235 ++++++++-----------------
 src/main/html/webapp/package.json      |   4 +-
 2 files changed, 73 insertions(+), 166 deletions(-)

diff --git a/src/main/html/webapp/package-lock.json b/src/main/html/webapp/package-lock.json
index 288b51df..60a07a2e 100644
--- a/src/main/html/webapp/package-lock.json
+++ b/src/main/html/webapp/package-lock.json
@@ -11,7 +11,7 @@
       "dependencies": {
         "@fortawesome/fontawesome-free": "5.3.1",
         "@popperjs/core": "^2.0.0",
-        "ansi_up": "4.0.4",
+        "ansi_up": "5.0.0",
         "bootbox": "5.5.3",
         "bootstrap": "4.6.2",
         "can-ajax": "1.1.4",
@@ -105,9 +105,9 @@
       }
     },
     "node_modules/ansi_up": {
-      "version": "4.0.4",
-      "resolved": "https://registry.npmjs.org/ansi_up/-/ansi_up-4.0.4.tgz",
-      "integrity": "sha512-vRxC8q6QY918MbehO869biJW4tiunJdjOhi5fpY6NLOliBQlZhOkKgABJKJqH+JZfb/WfjvjN1chLWI6tODerw==",
+      "version": "5.0.0",
+      "resolved": "https://registry.npmjs.org/ansi_up/-/ansi_up-5.0.0.tgz",
+      "integrity": "sha512-RHw/w3Kb2U3k4XKfl8FXZW9ldxtTBbLNdKO0RboYeU4ReVwRP77M7b/OxiavMGZsBWcDxn/T0QiR+VtLf7mPYw==",
       "engines": {
         "node": "*"
       }
@@ -383,29 +383,6 @@
         "node": ">=0.10.0"
       }
     },
-    "node_modules/base/node_modules/define-property/node_modules/is-descriptor": {
-      "version": "1.0.2",
-      "resolved": "https://registry.npmjs.org/is-descriptor/-/is-descriptor-1.0.2.tgz",
-      "integrity": "sha512-2eis5WqQGV7peooDyLmNEPUrps9+SXX5c9pL3xEB+4e9HnGuDa7mB7kHxHw4CbqS9k1T2hOH3miL8n8WtiYVtg==",
-      "dev": true,
-      "dependencies": {
-        "is-accessor-descriptor": "^1.0.0",
-        "is-data-descriptor": "^1.0.0",
-        "kind-of": "^6.0.2"
-      },
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
-    "node_modules/base/node_modules/kind-of": {
-      "version": "6.0.3",
-      "resolved": "https://registry.npmjs.org/kind-of/-/kind-of-6.0.3.tgz",
-      "integrity": "sha512-dcS1ul+9tmeD95T+x28/ehLgd9mENa3LsvDTtzm3vyBEO7RPptvAD+t44WVXaUjTBRcrpFeFlC8WCruUR456hw==",
-      "dev": true,
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
     "node_modules/Base64": {
       "version": "0.2.1",
       "resolved": "https://registry.npmjs.org/Base64/-/Base64-0.2.1.tgz",
@@ -1719,29 +1696,6 @@
         "node": ">=0.10.0"
       }
     },
-    "node_modules/define-property/node_modules/is-descriptor": {
-      "version": "1.0.2",
-      "resolved": "https://registry.npmjs.org/is-descriptor/-/is-descriptor-1.0.2.tgz",
-      "integrity": "sha512-2eis5WqQGV7peooDyLmNEPUrps9+SXX5c9pL3xEB+4e9HnGuDa7mB7kHxHw4CbqS9k1T2hOH3miL8n8WtiYVtg==",
-      "dev": true,
-      "dependencies": {
-        "is-accessor-descriptor": "^1.0.0",
-        "is-data-descriptor": "^1.0.0",
-        "kind-of": "^6.0.2"
-      },
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
-    "node_modules/define-property/node_modules/kind-of": {
-      "version": "6.0.3",
-      "resolved": "https://registry.npmjs.org/kind-of/-/kind-of-6.0.3.tgz",
-      "integrity": "sha512-dcS1ul+9tmeD95T+x28/ehLgd9mENa3LsvDTtzm3vyBEO7RPptvAD+t44WVXaUjTBRcrpFeFlC8WCruUR456hw==",
-      "dev": true,
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
     "node_modules/defined": {
       "version": "0.0.0",
       "resolved": "https://registry.npmjs.org/defined/-/defined-0.0.0.tgz",
@@ -1905,6 +1859,19 @@
         "node": ">=4"
       }
     },
+    "node_modules/esprima-next": {
+      "version": "5.8.4",
+      "resolved": "https://registry.npmjs.org/esprima-next/-/esprima-next-5.8.4.tgz",
+      "integrity": "sha512-8nYVZ4ioIH4Msjb/XmhnBdz5WRRBaYqevKa1cv9nGJdCehMbzZCPNEEnqfLCZVetUVrUPEcb5IYyu1GG4hFqgg==",
+      "dev": true,
+      "bin": {
+        "esparse": "bin/esparse.js",
+        "esvalidate": "bin/esvalidate.js"
+      },
+      "engines": {
+        "node": ">=12"
+      }
+    },
     "node_modules/estemplate": {
       "version": "0.5.1",
       "resolved": "https://registry.npmjs.org/estemplate/-/estemplate-0.5.1.tgz",
@@ -2122,29 +2089,6 @@
         "node": ">=0.10.0"
       }
     },
-    "node_modules/extglob/node_modules/define-property/node_modules/is-descriptor": {
-      "version": "1.0.2",
-      "resolved": "https://registry.npmjs.org/is-descriptor/-/is-descriptor-1.0.2.tgz",
-      "integrity": "sha512-2eis5WqQGV7peooDyLmNEPUrps9+SXX5c9pL3xEB+4e9HnGuDa7mB7kHxHw4CbqS9k1T2hOH3miL8n8WtiYVtg==",
-      "dev": true,
-      "dependencies": {
-        "is-accessor-descriptor": "^1.0.0",
-        "is-data-descriptor": "^1.0.0",
-        "kind-of": "^6.0.2"
-      },
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
-    "node_modules/extglob/node_modules/kind-of": {
-      "version": "6.0.3",
-      "resolved": "https://registry.npmjs.org/kind-of/-/kind-of-6.0.3.tgz",
-      "integrity": "sha512-dcS1ul+9tmeD95T+x28/ehLgd9mENa3LsvDTtzm3vyBEO7RPptvAD+t44WVXaUjTBRcrpFeFlC8WCruUR456hw==",
-      "dev": true,
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
     "node_modules/extsprintf": {
       "version": "1.3.0",
       "resolved": "https://registry.npmjs.org/extsprintf/-/extsprintf-1.3.0.tgz",
@@ -2744,71 +2688,23 @@
       }
     },
     "node_modules/is-descriptor": {
-      "version": "0.1.6",
-      "resolved": "https://registry.npmjs.org/is-descriptor/-/is-descriptor-0.1.6.tgz",
-      "integrity": "sha512-avDYr0SB3DwO9zsMov0gKCESFYqCnE4hq/4z3TdUlukEy5t9C0YRq7HLrsN52NAcqXKaepeCD0n+B0arnVG3Hg==",
-      "dev": true,
-      "dependencies": {
-        "is-accessor-descriptor": "^0.1.6",
-        "is-data-descriptor": "^0.1.4",
-        "kind-of": "^5.0.0"
-      },
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
-    "node_modules/is-descriptor/node_modules/is-accessor-descriptor": {
-      "version": "0.1.6",
-      "resolved": "https://registry.npmjs.org/is-accessor-descriptor/-/is-accessor-descriptor-0.1.6.tgz",
-      "integrity": "sha512-e1BM1qnDbMRG3ll2U9dSK0UMHuWOs3pY3AtcFsmvwPtKL3MML/Q86i+GilLfvqEs4GW+ExB91tQ3Ig9noDIZ+A==",
-      "dev": true,
-      "dependencies": {
-        "kind-of": "^3.0.2"
-      },
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
-    "node_modules/is-descriptor/node_modules/is-accessor-descriptor/node_modules/kind-of": {
-      "version": "3.2.2",
-      "resolved": "https://registry.npmjs.org/kind-of/-/kind-of-3.2.2.tgz",
-      "integrity": "sha512-NOW9QQXMoZGg/oqnVNoNTTIFEIid1627WCffUBJEdMxYApq7mNE7CpzucIPc+ZQg25Phej7IJSmX3hO+oblOtQ==",
-      "dev": true,
-      "dependencies": {
-        "is-buffer": "^1.1.5"
-      },
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
-    "node_modules/is-descriptor/node_modules/is-data-descriptor": {
-      "version": "0.1.4",
-      "resolved": "https://registry.npmjs.org/is-data-descriptor/-/is-data-descriptor-0.1.4.tgz",
-      "integrity": "sha512-+w9D5ulSoBNlmw9OHn3U2v51SyoCd0he+bB3xMl62oijhrspxowjU+AIcDY0N3iEJbUEkB15IlMASQsxYigvXg==",
-      "dev": true,
-      "dependencies": {
-        "kind-of": "^3.0.2"
-      },
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
-    "node_modules/is-descriptor/node_modules/is-data-descriptor/node_modules/kind-of": {
-      "version": "3.2.2",
-      "resolved": "https://registry.npmjs.org/kind-of/-/kind-of-3.2.2.tgz",
-      "integrity": "sha512-NOW9QQXMoZGg/oqnVNoNTTIFEIid1627WCffUBJEdMxYApq7mNE7CpzucIPc+ZQg25Phej7IJSmX3hO+oblOtQ==",
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/is-descriptor/-/is-descriptor-1.0.2.tgz",
+      "integrity": "sha512-2eis5WqQGV7peooDyLmNEPUrps9+SXX5c9pL3xEB+4e9HnGuDa7mB7kHxHw4CbqS9k1T2hOH3miL8n8WtiYVtg==",
       "dev": true,
       "dependencies": {
-        "is-buffer": "^1.1.5"
+        "is-accessor-descriptor": "^1.0.0",
+        "is-data-descriptor": "^1.0.0",
+        "kind-of": "^6.0.2"
       },
       "engines": {
         "node": ">=0.10.0"
       }
     },
     "node_modules/is-descriptor/node_modules/kind-of": {
-      "version": "5.1.0",
-      "resolved": "https://registry.npmjs.org/kind-of/-/kind-of-5.1.0.tgz",
-      "integrity": "sha512-NGEErnH6F2vUuXDh+OlbcKW7/wOcfdRHaZ7VWtqCztfHri/++YKmP51OdWeGPuqCOba6kk2OTe5d02VmTB80Pw==",
+      "version": "6.0.3",
+      "resolved": "https://registry.npmjs.org/kind-of/-/kind-of-6.0.3.tgz",
+      "integrity": "sha512-dcS1ul+9tmeD95T+x28/ehLgd9mENa3LsvDTtzm3vyBEO7RPptvAD+t44WVXaUjTBRcrpFeFlC8WCruUR456hw==",
       "dev": true,
       "engines": {
         "node": ">=0.10.0"
@@ -4364,53 +4260,77 @@
         "node": ">=0.10.0"
       }
     },
-    "node_modules/snapdragon-node/node_modules/define-property/node_modules/is-descriptor": {
-      "version": "1.0.2",
-      "resolved": "https://registry.npmjs.org/is-descriptor/-/is-descriptor-1.0.2.tgz",
-      "integrity": "sha512-2eis5WqQGV7peooDyLmNEPUrps9+SXX5c9pL3xEB+4e9HnGuDa7mB7kHxHw4CbqS9k1T2hOH3miL8n8WtiYVtg==",
+    "node_modules/snapdragon-util": {
+      "version": "3.0.1",
+      "resolved": "https://registry.npmjs.org/snapdragon-util/-/snapdragon-util-3.0.1.tgz",
+      "integrity": "sha512-mbKkMdQKsjX4BAL4bRYTj21edOf8cN7XHdYUJEe+Zn99hVEYcMvKPct1IqNe7+AZPirn8BCDOQBHQZknqmKlZQ==",
       "dev": true,
       "dependencies": {
-        "is-accessor-descriptor": "^1.0.0",
-        "is-data-descriptor": "^1.0.0",
-        "kind-of": "^6.0.2"
+        "kind-of": "^3.2.0"
       },
       "engines": {
         "node": ">=0.10.0"
       }
     },
-    "node_modules/snapdragon-node/node_modules/kind-of": {
-      "version": "6.0.3",
-      "resolved": "https://registry.npmjs.org/kind-of/-/kind-of-6.0.3.tgz",
-      "integrity": "sha512-dcS1ul+9tmeD95T+x28/ehLgd9mENa3LsvDTtzm3vyBEO7RPptvAD+t44WVXaUjTBRcrpFeFlC8WCruUR456hw==",
+    "node_modules/snapdragon/node_modules/define-property": {
+      "version": "0.2.5",
+      "resolved": "https://registry.npmjs.org/define-property/-/define-property-0.2.5.tgz",
+      "integrity": "sha512-Rr7ADjQZenceVOAKop6ALkkRAmH1A4Gx9hV/7ZujPUN2rkATqFO0JZLZInbAjpZYoJ1gUx8MRMQVkYemcbMSTA==",
       "dev": true,
+      "dependencies": {
+        "is-descriptor": "^0.1.0"
+      },
       "engines": {
         "node": ">=0.10.0"
       }
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-    "node_modules/snapdragon-util": {
-      "version": "3.0.1",
-      "resolved": "https://registry.npmjs.org/snapdragon-util/-/snapdragon-util-3.0.1.tgz",
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+    "node_modules/snapdragon/node_modules/is-accessor-descriptor": {
+      "version": "0.1.6",
+      "resolved": "https://registry.npmjs.org/is-accessor-descriptor/-/is-accessor-descriptor-0.1.6.tgz",
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       "dev": true,
       "dependencies": {
-        "kind-of": "^3.2.0"
+        "kind-of": "^3.0.2"
       },
       "engines": {
         "node": ">=0.10.0"
       }
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-    "node_modules/snapdragon/node_modules/define-property": {
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-      "resolved": "https://registry.npmjs.org/define-property/-/define-property-0.2.5.tgz",
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+    "node_modules/snapdragon/node_modules/is-data-descriptor": {
+      "version": "0.1.4",
+      "resolved": "https://registry.npmjs.org/is-data-descriptor/-/is-data-descriptor-0.1.4.tgz",
+      "integrity": "sha512-+w9D5ulSoBNlmw9OHn3U2v51SyoCd0he+bB3xMl62oijhrspxowjU+AIcDY0N3iEJbUEkB15IlMASQsxYigvXg==",
       "dev": true,
       "dependencies": {
-        "is-descriptor": "^0.1.0"
+        "kind-of": "^3.0.2"
+      },
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/snapdragon/node_modules/is-descriptor": {
+      "version": "0.1.6",
+      "resolved": "https://registry.npmjs.org/is-descriptor/-/is-descriptor-0.1.6.tgz",
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+      "dev": true,
+      "dependencies": {
+        "is-accessor-descriptor": "^0.1.6",
+        "is-data-descriptor": "^0.1.4",
+        "kind-of": "^5.0.0"
       },
       "engines": {
         "node": ">=0.10.0"
       }
     },
+    "node_modules/snapdragon/node_modules/is-descriptor/node_modules/kind-of": {
+      "version": "5.1.0",
+      "resolved": "https://registry.npmjs.org/kind-of/-/kind-of-5.1.0.tgz",
+      "integrity": "sha512-NGEErnH6F2vUuXDh+OlbcKW7/wOcfdRHaZ7VWtqCztfHri/++YKmP51OdWeGPuqCOba6kk2OTe5d02VmTB80Pw==",
+      "dev": true,
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
     "node_modules/snapdragon/node_modules/source-map": {
       "version": "0.5.7",
       "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.5.7.tgz",
@@ -5017,19 +4937,6 @@
         "urix": "^0.1.0"
       }
     },
-    "node_modules/transpile/node_modules/esprima-next": {
-      "version": "5.8.4",
-      "resolved": "https://registry.npmjs.org/esprima-next/-/esprima-next-5.8.4.tgz",
-      "integrity": "sha512-8nYVZ4ioIH4Msjb/XmhnBdz5WRRBaYqevKa1cv9nGJdCehMbzZCPNEEnqfLCZVetUVrUPEcb5IYyu1GG4hFqgg==",
-      "dev": true,
-      "bin": {
-        "esparse": "bin/esparse.js",
-        "esvalidate": "bin/esvalidate.js"
-      },
-      "engines": {
-        "node": ">=12"
-      }
-    },
     "node_modules/transpile/node_modules/source-map": {
       "version": "0.1.43",
       "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.1.43.tgz",
diff --git a/src/main/html/webapp/package.json b/src/main/html/webapp/package.json
index 5cd5dd4b..d25d98b8 100644
--- a/src/main/html/webapp/package.json
+++ b/src/main/html/webapp/package.json
@@ -31,10 +31,10 @@
     "jquery-form": "3.50.0",
     "md5": "2.2.1",
     "morris.js": "0.5.0",
-	"@popperjs/core": "^2.0.0",
+    "@popperjs/core": "^2.0.0",
     "raphael": "2.2.7",
     "steal": "^1.5.13",
-    "ansi_up": "4.0.4"
+    "ansi_up": "5.0.0"
   },
   "scripts": {
     "build": "node build"

From a7c2a6d0ad9b0490cdb069f2c511f8269db5c318 Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Wed, 27 Sep 2023 12:41:23 +0200
Subject: [PATCH 28/30] Update velocity to 2.3 (#127)

---
 pom.xml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/pom.xml b/pom.xml
index edb2e85d..f089cebe 100644
--- a/pom.xml
+++ b/pom.xml
@@ -243,11 +243,12 @@
 		</dependency>
 
 		<dependency>
-			<groupId>org.apache.velocity</groupId>
-			<artifactId>velocity</artifactId>
-			<version>1.7</version>
+		    <groupId>org.apache.velocity</groupId>
+		    <artifactId>velocity-engine-core</artifactId>
+		    <version>2.3</version>
 		</dependency>
 
+
 		<dependency>
 			<groupId>com.nimbusds</groupId>
 			<artifactId>nimbus-jose-jwt</artifactId>

From c3c26fa4245019eac10f7e92c769f02b98991fba Mon Sep 17 00:00:00 2001
From: Andy Boughton <abought@gmail.com>
Date: Thu, 28 Sep 2023 10:45:01 -0400
Subject: [PATCH 29/30] Update Google analytics code to use new GA4 trackers
 (#118)

The old scripts stopped accepting user data as of July 2023.
---
 src/main/html/webapp/public/index.html | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/src/main/html/webapp/public/index.html b/src/main/html/webapp/public/index.html
index cd688082..c212b78d 100644
--- a/src/main/html/webapp/public/index.html
+++ b/src/main/html/webapp/public/index.html
@@ -26,18 +26,17 @@
     <script src="./dist/bundles/cloudgene/index.js"></script>
 
     <#if google_analytics??>
-      <!-- Google Analytics -->
+      <!-- Google tag (gtag.js) -->
+      <script async src="https://www.googletagmanager.com/gtag/js?id=${google_analytics}"></script>
       <script>
-      (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
-      (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
-      m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
-      })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
-
-      ga('create', ' ${google_analytics}', 'auto');
-      ga('send', 'pageview');
+        window.dataLayer = window.dataLayer || [];
+        function gtag(){dataLayer.push(arguments);}
+        gtag('js', new Date());
 
+        // Automatically sends a pageview with specified Tag ID
+        gtag('config', '${google_analytics}');
       </script>
-    	<!-- End Google Analytics -->
+      <!-- End Google Analytics -->
     </#if>
 
   </body>

From 4f9ba91932dab6fb8f7db9585eac3c95f91aa0a4 Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Tue, 3 Oct 2023 09:53:57 +0200
Subject: [PATCH 30/30] Update yamlbeans to 1.17 (#128)

---
 pom.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pom.xml b/pom.xml
index f089cebe..9062184d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -237,9 +237,9 @@
 		</dependency>
 
 		<dependency>
-			<groupId>com.esotericsoftware.yamlbeans</groupId>
-			<artifactId>yamlbeans</artifactId>
-			<version>1.15</version>
+		    <groupId>com.contrastsecurity</groupId>
+		    <artifactId>yamlbeans</artifactId>
+		    <version>1.17</version>
 		</dependency>
 
 		<dependency>