Merge branch 'master' of https://github.com/genepi/cloudgene into rel…

…ease-2.5.6-tis
statgen · Apr 6, 2023 · 368f031 · 368f031
2 parents f358107 + 6153fdd
commit 368f031
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Showing 14 changed files with 45 additions and 457 deletions.
diff --git 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>2.5.6</version>
 
 	<name>Cloudgene</name>
 	<url>http://www.cloudgene.io</url>
@@ -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>
 
@@ -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
@@ -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
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
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
diff --git 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/html/webapp/package-lock.json b/src/main/html/webapp/package-lock.json
diff --git 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": "2.5.6",
   "description": "Cloudgene web client",
   "homepage": "http://www.cloudgene.io",
   "author": "Lukas Forer <[email protected] (http://www.forer.it)",

diff --git 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 = "2.5.6";
 
 	private Database database;