Merge pull request #97 from genepi/micronaut-securtiy-updates

Update libraries and remove url based file upload

.classpath

@@ -11,7 +11,11 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" path="src/main/resources"/>
+	<classpathentry kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
@@ -24,7 +28,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
 		<attributes>
 			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>

.factorypath

@@ -29,5 +29,5 @@
     <factorypathentry kind="VARJAR" id="M2_REPO/io/micronaut/micronaut-websocket/3.3.4/micronaut-websocket-3.3.4.jar" enabled="true" runInBatchMode="false"/>
     <factorypathentry kind="VARJAR" id="M2_REPO/io/micronaut/micronaut-http/3.3.4/micronaut-http-3.3.4.jar" enabled="true" runInBatchMode="false"/>
     <factorypathentry kind="VARJAR" id="M2_REPO/io/micronaut/micronaut-http-client-core/3.3.4/micronaut-http-client-core-3.3.4.jar" enabled="true" runInBatchMode="false"/>
-    <factorypathentry kind="VARJAR" id="M2_REPO/io/micronaut/security/micronaut-security-annotations/3.3.0/micronaut-security-annotations-3.3.0.jar" enabled="true" runInBatchMode="false"/>
+    <factorypathentry kind="VARJAR" id="M2_REPO/io/micronaut/security/micronaut-security-annotations/3.11.0/micronaut-security-annotations-3.11.0.jar" enabled="true" runInBatchMode="false"/>
 </factorypath>

.github/workflows/create-release.yml

@@ -7,7 +7,7 @@ on:
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/maven-test.yml

@@ -8,7 +8,7 @@ on: [push, pull_request]
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@v2

.gitignore

@@ -18,3 +18,4 @@
 /src/main/html/webapp/node_modules
 /apps
 *.DS_Store
+/.apt_generated/

pom.xml

@@ -11,7 +11,7 @@
 		<relativePath>io.micronaut:micronaut-parent</relativePath>
 		<groupId>io.micronaut</groupId>
 		<artifactId>micronaut-parent</artifactId>
-		<version>3.4.3</version>
+		<version>3.9.1</version>
 	</parent>
 
 	<name>Cloudgene</name>
@@ -69,7 +69,7 @@
 		<repository>
 			<id>maven-restlet</id>
 			<name>Restlet Framework repository</name>
-			<url>https://maven.restlet.org</url>
+			<url>https://maven.restlet.talend.com</url>
 		</repository>
 
 		<repository>
@@ -214,7 +214,7 @@
 		<dependency>
 			<groupId>org.codehaus.groovy</groupId>
 			<artifactId>groovy-all</artifactId>
-			<version>3.0.9</version>
+			<version>3.0.17</version>
 			<type>pom</type>
 			<exclusions>
 				<exclusion>
@@ -227,7 +227,7 @@
 		<dependency>
 			<groupId>org.apache.ivy</groupId>
 			<artifactId>ivy</artifactId>
-			<version>2.5.0</version>
+			<version>2.5.1</version>
 		</dependency>
 
 		<!-- Logging -->
@@ -271,16 +271,11 @@
 		</dependency>
 
 
-		<dependency>
-			<groupId>com.jcraft</groupId>
-			<artifactId>jsch</artifactId>
-			<version>0.1.55</version>
-		</dependency>
 
 		<dependency>
 			<groupId>net.lingala.zip4j</groupId>
 			<artifactId>zip4j</artifactId>
-			<version>2.9.1</version>
+			<version>2.11.5</version>
 		</dependency>
 
 		<dependency>
@@ -302,7 +297,7 @@
 		<dependency>
 			<groupId>org.springframework.security</groupId>
 			<artifactId>spring-security-crypto</artifactId>
-			<version>5.6.3</version>
+			<version>5.8.3</version>
 		</dependency>
 
 		<!-- Test Dependencies -->
@@ -380,12 +375,6 @@
 			</exclusions>
 		</dependency>
 
-		<dependency>
-			<groupId>org.apache.sshd</groupId>
-			<artifactId>sshd-sftp</artifactId>
-			<version>0.9.0</version>
-			<scope>test</scope>
-		</dependency>
 
 
 		<!-- Micronaut -->

src/main/html/webapp/components/core/job/submit/controls/folder-pattern.stache

@@ -6,16 +6,11 @@
 </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="s3">S3 Bucket</option>
-  </select>
 	<small class="text-muted">Please define a <a href="https://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob" target="_blank">glob pattern</a> to filter or pair your files: </small> <input name="{{id}}-pattern" id="{{id}}-pattern" type ="text" class="form-control" required value="{{pattern}}" autocomplete="off">
   <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>
@@ -25,12 +20,8 @@
       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,'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)}}
+
+  {{#if(details)}}
     <small class="form-text text-muted">{{details}}</small>
   {{/if}}
   <div class="invalid-feedback">

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>