Update for Release 2020-09-11-1000

BEA#211 BEV Features: Toggle Tooltips BEA#212 BEV Features: Interpretation BEA#213 BEV Features: Capture Diagram (to PDF) BEA#214 BEV Features: PNG fit to width toggle BEA#215 BEI Update: for new BEV BEA#216 BEI Update: support discrete analysis BEA#217 BEI Update: support MutBatch analysis BEA#218 MBatchPipeline: update for BEI MutBatch BEA#223 Combined Release with BEI BEA#230 Image Deploy: docker-compose push and pull BEA#231 BEI Deployment Instructions Update BEA#238 BEV/SDB: download links STD#51 SDMW: Search STD#52 SDMW: Improved Error Handling STD#54 SDMW: GRC Assessment STD#55 SDMW: Release STD#63 MBatch HC/NGCHM: Number of Features 2000-5000 for Both STD#65 SDMW: Slow Load/Reload Projects STD#67 SDMW: Add Credit to MW.org STD#71 SMW: mapping metabolite names
MD-Anderson-Bioinformatics · Sep 18, 2020 · 2948c82 · 2948c82
1 parent 13cf8b5
commit 2948c82
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diff --git a/apps/BatchEffectsInterface/lib/BEVIndex.jar b/apps/BatchEffectsInterface/lib/BEVIndex.jar
diff --git a/apps/BatchEffectsInterface/lib/GDCAPI.jar b/apps/BatchEffectsInterface/lib/GDCAPI.jar
diff --git a/apps/BatchEffectsInterface/lib/commons-codec-1.14.jar b/apps/BatchEffectsInterface/lib/commons-codec-1.14.jar
diff --git a/apps/BatchEffectsInterface/lib/commons-compress-1.19.jar b/apps/BatchEffectsInterface/lib/commons-compress-1.19.jar
diff --git a/apps/BatchEffectsInterface/lib/commons-io-2.5.jar b/apps/BatchEffectsInterface/lib/commons-io-2.5.jar
diff --git a/apps/BatchEffectsInterface/lib/commons-io-2.6.jar b/apps/BatchEffectsInterface/lib/commons-io-2.6.jar
diff --git a/apps/BatchEffectsInterface/lib/gson-2.7.jar b/apps/BatchEffectsInterface/lib/gson-2.7.jar
diff --git a/apps/BatchEffectsInterface/lib/gson-2.8.6.jar b/apps/BatchEffectsInterface/lib/gson-2.8.6.jar
diff --git a/apps/BatchEffectsInterface/nbproject/ant-deploy.xml b/apps/BatchEffectsInterface/nbproject/ant-deploy.xml
@@ -1,42 +1,23 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
 
-Copyright (c) 2006, 2016 Oracle and/or its affiliates. All rights reserved.
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
 
-Oracle and Java are registered trademarks of Oracle and/or its affiliates.
-Other names may be trademarks of their respective owners.
+      http://www.apache.org/licenses/LICENSE-2.0
 
-The contents of this file are subject to the terms of either the GNU
-General Public License Version 2 only ("GPL") or the Common
-Development and Distribution License("CDDL") (collectively, the
-"License"). You may not use this file except in compliance with the
-License. You can obtain a copy of the License at
-http://www.netbeans.org/cddl-gplv2.html
-or nbbuild/licenses/CDDL-GPL-2-CP. See the License for the
-specific language governing permissions and limitations under the
-License.  When distributing the software, include this License Header
-Notice in each file and include the License file at
-nbbuild/licenses/CDDL-GPL-2-CP.  Oracle designates this
-particular file as subject to the "Classpath" exception as provided
-by Oracle in the GPL Version 2 section of the License file that
-accompanied this code. If applicable, add the following below the
-License Header, with the fields enclosed by brackets [] replaced by
-your own identifying information:
-"Portions Copyrighted [year] [name of copyright owner]"
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
 
-If you wish your version of this file to be governed by only the CDDL
-or only the GPL Version 2, indicate your decision by adding
-"[Contributor] elects to include this software in this distribution
-under the [CDDL or GPL Version 2] license." If you do not indicate a
-single choice of license, a recipient has the option to distribute
-your version of this file under either the CDDL, the GPL Version 2 or
-to extend the choice of license to its licensees as provided above.
-However, if you add GPL Version 2 code and therefore, elected the GPL
-Version 2 license, then the option applies only if the new code is
-made subject to such option by the copyright holder.
-
-Contributor(s):
 -->
 <project default="-deploy-ant" basedir=".">
     <target name="-init" if="deploy.ant.enabled">

diff --git a/apps/BatchEffectsInterface/nbproject/build-impl.xml b/apps/BatchEffectsInterface/nbproject/build-impl.xml
@@ -557,8 +557,7 @@ or ant -Dj2ee.platform.classpath=&lt;server_classpath&gt; (where no properties f
                     <formatter type="brief" usefile="false"/>
                     <formatter type="xml"/>
                     <jvmarg value="-ea"/>
-                    <jvmarg line="${debug-args-line}"/>
-                    <jvmarg value="-Xrunjdwp:transport=${debug-transport},address=${jpda.address}"/>
+                    <jvmarg value="-agentlib:jdwp=transport=${debug-transport},address=${jpda.address}"/>
                     <customize/>
                 </junit>
             </sequential>
@@ -590,8 +589,7 @@ or ant -Dj2ee.platform.classpath=&lt;server_classpath&gt; (where no properties f
                     <formatter type="xml"/>
                     <jvmarg value="-ea"/>
                     <jvmarg line="${run.jvmargs.ide}"/>
-                    <jvmarg line="${debug-args-line}"/>
-                    <jvmarg value="-Xrunjdwp:transport=${debug-transport},address=${jpda.address}"/>
+                    <jvmarg value="-agentlib:jdwp=transport=${debug-transport},address=${jpda.address}"/>
                     <customize/>
                 </junit>
             </sequential>
@@ -749,18 +747,6 @@ or ant -Dj2ee.platform.classpath=&lt;server_classpath&gt; (where no properties f
         </macrodef>
     </target>
     <target name="-init-debug-args">
-        <property name="version-output" value="java version &quot;${ant.java.version}"/>
-        <condition property="have-jdk-older-than-1.4">
-            <or>
-                <contains string="${version-output}" substring="java version &quot;1.0"/>
-                <contains string="${version-output}" substring="java version &quot;1.1"/>
-                <contains string="${version-output}" substring="java version &quot;1.2"/>
-                <contains string="${version-output}" substring="java version &quot;1.3"/>
-            </or>
-        </condition>
-        <condition else="-Xdebug" property="debug-args-line" value="-Xdebug -Xnoagent -Djava.compiler=none">
-            <istrue value="${have-jdk-older-than-1.4}"/>
-        </condition>
         <condition else="dt_socket" property="debug-transport-by-os" value="dt_shmem">
             <os family="windows"/>
         </condition>
@@ -777,8 +763,7 @@ or ant -Dj2ee.platform.classpath=&lt;server_classpath&gt; (where no properties f
             <sequential>
                 <java classname="@{classname}" fork="true">
                     <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
-                    <jvmarg line="${debug-args-line}"/>
-                    <jvmarg value="-Xrunjdwp:transport=${debug-transport},address=${jpda.address}"/>
+                    <jvmarg value="-agentlib:jdwp=transport=${debug-transport},address=${jpda.address}"/>
                     <jvmarg line="${runmain.jvmargs}"/>
                     <classpath>
                         <path path="@{classpath}"/>
@@ -853,17 +838,11 @@ exists or setup the property manually. For example like this:
                 COMPILATION SECTION
             -->
     <target depends="init" if="no.dist.ear.dir" name="deps-module-jar" unless="no.deps">
-        <ant antfile="${project.BEVIndex}/build.xml" inheritall="false" target="jar">
-            <property name="deploy.on.save" value="false"/>
-        </ant>
         <ant antfile="${project.SamplesValidation}/build.xml" inheritall="false" target="jar">
             <property name="deploy.on.save" value="false"/>
         </ant>
     </target>
     <target depends="init" if="dist.ear.dir" name="deps-ear-jar" unless="no.deps">
-        <ant antfile="${project.BEVIndex}/build.xml" inheritall="false" target="jar">
-            <property name="deploy.on.save" value="false"/>
-        </ant>
         <ant antfile="${project.SamplesValidation}/build.xml" inheritall="false" target="jar">
             <property name="deploy.on.save" value="false"/>
         </ant>
@@ -1011,22 +990,28 @@ exists or setup the property manually. For example like this:
     </target>
     <target depends="init,compile,compile-jsps,-pre-dist,-do-dist-with-manifest,-do-dist-without-manifest" name="do-dist"/>
     <target depends="init" if="dist.ear.dir" name="library-inclusion-in-manifest">
-        <copyfiles files="${file.reference.gson-2.7.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
+        <copyfiles files="${reference.SamplesValidation.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
         <copyfiles files="${file.reference.commons-lang3-3.4.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
-        <copyfiles files="${file.reference.commons-io-2.5.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
+        <copyfiles files="${file.reference.commons-codec-1.14.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
+        <copyfiles files="${file.reference.commons-compress-1.19.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
+        <copyfiles files="${file.reference.commons-io-2.6.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
+        <copyfiles files="${file.reference.gson-2.8.6.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
         <copyfiles files="${file.reference.javax.mail.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
-        <copyfiles files="${reference.SamplesValidation.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
-        <copyfiles files="${reference.BEVIndex.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
+        <copyfiles files="${file.reference.GDCAPI.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
+        <copyfiles files="${file.reference.BEVIndex.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
         <mkdir dir="${build.web.dir}/META-INF"/>
         <manifest file="${build.web.dir}/META-INF/MANIFEST.MF" mode="update"/>
     </target>
     <target depends="init" name="library-inclusion-in-archive" unless="dist.ear.dir">
-        <copyfiles files="${file.reference.gson-2.7.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
+        <copyfiles files="${reference.SamplesValidation.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
         <copyfiles files="${file.reference.commons-lang3-3.4.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
-        <copyfiles files="${file.reference.commons-io-2.5.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
+        <copyfiles files="${file.reference.commons-codec-1.14.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
+        <copyfiles files="${file.reference.commons-compress-1.19.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
+        <copyfiles files="${file.reference.commons-io-2.6.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
+        <copyfiles files="${file.reference.gson-2.8.6.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
         <copyfiles files="${file.reference.javax.mail.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
-        <copyfiles files="${reference.SamplesValidation.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
-        <copyfiles files="${reference.BEVIndex.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
+        <copyfiles files="${file.reference.GDCAPI.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
+        <copyfiles files="${file.reference.BEVIndex.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
     </target>
     <target depends="init" if="dist.ear.dir" name="-clean-webinf-lib">
         <delete dir="${build.web.dir}/WEB-INF/lib"/>
@@ -1440,7 +1425,6 @@ exists or setup the property manually. For example like this:
                 CLEANUP SECTION
             -->
     <target depends="init" name="deps-clean" unless="no.deps">
-        <ant antfile="${project.BEVIndex}/build.xml" inheritall="false" target="clean"/>
         <ant antfile="${project.SamplesValidation}/build.xml" inheritall="false" target="clean"/>
     </target>
     <target depends="init" name="do-clean">

diff --git a/apps/BatchEffectsInterface/nbproject/genfiles.properties b/apps/BatchEffectsInterface/nbproject/genfiles.properties
@@ -1,8 +1,8 @@
-build.xml.data.CRC32=b43ba9cd
+build.xml.data.CRC32=385f4cde
 build.xml.script.CRC32=ce51a6c1
-build.xml.stylesheet.CRC32=651128d4@1.77.1.1
+build.xml.stylesheet.CRC32=1707db4f@1.81.0.1
 # This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
 # Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
-nbproject/build-impl.xml.data.CRC32=b43ba9cd
-nbproject/build-impl.xml.script.CRC32=6b3bdfaf
-nbproject/build-impl.xml.stylesheet.CRC32=99ea4b56@1.77.1.1
+nbproject/build-impl.xml.data.CRC32=385f4cde
+nbproject/build-impl.xml.script.CRC32=2854ff96
+nbproject/build-impl.xml.stylesheet.CRC32=58472a1d@1.81.0.1
diff --git a/apps/BatchEffectsInterface/nbproject/project.properties b/apps/BatchEffectsInterface/nbproject/project.properties
@@ -10,7 +10,6 @@ auxiliary.org-netbeans-modules-css-prep.sass_2e_compiler_2e_options=
 auxiliary.org-netbeans-modules-css-prep.sass_2e_enabled=false
 auxiliary.org-netbeans-modules-css-prep.sass_2e_mappings=/scss:/css
 auxiliary.org-netbeans-modules-web-clientproject-api.js_2e_libs_2e_folder=js/libs
-auxiliary.org-netbeans-modules-whitelist.whitelist-oracle=false
 build.classes.dir=${build.web.dir}/WEB-INF/classes
 build.classes.excludes=**/*.java,**/*.form
 build.dir=build
@@ -34,27 +33,34 @@ dist.ear.war=${dist.dir}/${war.ear.name}
 dist.javadoc.dir=${dist.dir}/javadoc
 dist.war=${dist.dir}/${war.name}
 endorsed.classpath=\
-    ${libs.javaee-endorsed-api-6.0.classpath}
+    ${libs.javaee-endorsed-api-7.0.classpath}
 excludes=
-file.reference.commons-io-2.5.jar=lib/commons-io-2.5.jar
+file.reference.BEVIndex.jar=lib/BEVIndex.jar
+file.reference.commons-codec-1.14.jar=lib/commons-codec-1.14.jar
+file.reference.commons-compress-1.19.jar=lib/commons-compress-1.19.jar
+file.reference.commons-io-2.6.jar=lib/commons-io-2.6.jar
 file.reference.commons-lang3-3.4.jar=lib/commons-lang3-3.4.jar
-file.reference.gson-2.7.jar=lib/gson-2.7.jar
+file.reference.GDCAPI.jar=lib/GDCAPI.jar
+file.reference.gson-2.8.6.jar=lib/gson-2.8.6.jar
 file.reference.javax.mail.jar=lib/javax.mail.jar
 includes=**
-j2ee.compile.on.save=true
+j2ee.compile.on.save=false
 j2ee.copy.static.files.on.save=true
-j2ee.deploy.on.save=true
+j2ee.deploy.on.save=false
 j2ee.platform=1.7-web
-j2ee.platform.classpath=${j2ee.server.home}/lib/annotations-api.jar:${j2ee.server.home}/lib/catalina-ant.jar:${j2ee.server.home}/lib/catalina-ha.jar:${j2ee.server.home}/lib/catalina-storeconfig.jar:${j2ee.server.home}/lib/catalina-tribes.jar:${j2ee.server.home}/lib/catalina.jar:${j2ee.server.home}/lib/ecj-4.4.2.jar:${j2ee.server.home}/lib/el-api.jar:${j2ee.server.home}/lib/jasper-el.jar:${j2ee.server.home}/lib/jasper.jar:${j2ee.server.home}/lib/jsp-api.jar:${j2ee.server.home}/lib/servlet-api.jar:${j2ee.server.home}/lib/tomcat-api.jar:${j2ee.server.home}/lib/tomcat-coyote.jar:${j2ee.server.home}/lib/tomcat-dbcp.jar:${j2ee.server.home}/lib/tomcat-i18n-es.jar:${j2ee.server.home}/lib/tomcat-i18n-fr.jar:${j2ee.server.home}/lib/tomcat-i18n-ja.jar:${j2ee.server.home}/lib/tomcat-jdbc.jar:${j2ee.server.home}/lib/tomcat-jni.jar:${j2ee.server.home}/lib/tomcat-util-scan.jar:${j2ee.server.home}/lib/tomcat-util.jar:${j2ee.server.home}/lib/tomcat-websocket.jar:${j2ee.server.home}/lib/websocket-api.jar
+j2ee.platform.classpath=${j2ee.server.home}/lib/annotations-api.jar:${j2ee.server.home}/lib/catalina-ant.jar:${j2ee.server.home}/lib/catalina-ha.jar:${j2ee.server.home}/lib/catalina-storeconfig.jar:${j2ee.server.home}/lib/catalina-tribes.jar:${j2ee.server.home}/lib/catalina.jar:${j2ee.server.home}/lib/ecj-4.7.3a.jar:${j2ee.server.home}/lib/el-api.jar:${j2ee.server.home}/lib/jasper-el.jar:${j2ee.server.home}/lib/jasper.jar:${j2ee.server.home}/lib/jaspic-api.jar:${j2ee.server.home}/lib/jsp-api.jar:${j2ee.server.home}/lib/servlet-api.jar:${j2ee.server.home}/lib/tomcat-api.jar:${j2ee.server.home}/lib/tomcat-coyote.jar:${j2ee.server.home}/lib/tomcat-dbcp.jar:${j2ee.server.home}/lib/tomcat-i18n-es.jar:${j2ee.server.home}/lib/tomcat-i18n-fr.jar:${j2ee.server.home}/lib/tomcat-i18n-ja.jar:${j2ee.server.home}/lib/tomcat-i18n-ru.jar:${j2ee.server.home}/lib/tomcat-jdbc.jar:${j2ee.server.home}/lib/tomcat-jni.jar:${j2ee.server.home}/lib/tomcat-util-scan.jar:${j2ee.server.home}/lib/tomcat-util.jar:${j2ee.server.home}/lib/tomcat-websocket.jar:${j2ee.server.home}/lib/websocket-api.jar
 j2ee.server.type=Tomcat
 jar.compress=false
 javac.classpath=\
-    ${file.reference.gson-2.7.jar}:\
+    ${reference.SamplesValidation.jar}:\
     ${file.reference.commons-lang3-3.4.jar}:\
-    ${file.reference.commons-io-2.5.jar}:\
+    ${file.reference.commons-codec-1.14.jar}:\
+    ${file.reference.commons-compress-1.19.jar}:\
+    ${file.reference.commons-io-2.6.jar}:\
+    ${file.reference.gson-2.8.6.jar}:\
     ${file.reference.javax.mail.jar}:\
-    ${reference.SamplesValidation.jar}:\
-    ${reference.BEVIndex.jar}
+    ${file.reference.GDCAPI.jar}:\
+    ${file.reference.BEVIndex.jar}
 # Space-separated list of extra javac options
 javac.compilerargs=
 javac.debug=true
@@ -83,9 +89,7 @@ javadoc.windowtitle=
 lib.dir=${web.docbase.dir}/WEB-INF/lib
 persistence.xml.dir=${conf.dir}
 platform.active=default_platform
-project.BEVIndex=../../../BatchEffectsPackage/apps/BEVIndex
 project.SamplesValidation=../SamplesValidation
-reference.BEVIndex.jar=${project.BEVIndex}/dist/BEVIndex.jar
 reference.SamplesValidation.jar=${project.SamplesValidation}/dist/SamplesValidation.jar
 resource.dir=setup
 run.test.classpath=\

diff --git a/apps/BatchEffectsInterface/nbproject/project.xml b/apps/BatchEffectsInterface/nbproject/project.xml
@@ -7,27 +7,39 @@
             <minimum-ant-version>1.6.5</minimum-ant-version>
             <web-module-libraries>
                 <library dirs="200">
-                    <file>${file.reference.gson-2.7.jar}</file>
+                    <file>${reference.SamplesValidation.jar}</file>
                     <path-in-war>WEB-INF/lib</path-in-war>
                 </library>
                 <library dirs="200">
                     <file>${file.reference.commons-lang3-3.4.jar}</file>
                     <path-in-war>WEB-INF/lib</path-in-war>
                 </library>
                 <library dirs="200">
-                    <file>${file.reference.commons-io-2.5.jar}</file>
+                    <file>${file.reference.commons-codec-1.14.jar}</file>
+                    <path-in-war>WEB-INF/lib</path-in-war>
+                </library>
+                <library dirs="200">
+                    <file>${file.reference.commons-compress-1.19.jar}</file>
+                    <path-in-war>WEB-INF/lib</path-in-war>
+                </library>
+                <library dirs="200">
+                    <file>${file.reference.commons-io-2.6.jar}</file>
+                    <path-in-war>WEB-INF/lib</path-in-war>
+                </library>
+                <library dirs="200">
+                    <file>${file.reference.gson-2.8.6.jar}</file>
                     <path-in-war>WEB-INF/lib</path-in-war>
                 </library>
                 <library dirs="200">
                     <file>${file.reference.javax.mail.jar}</file>
                     <path-in-war>WEB-INF/lib</path-in-war>
                 </library>
                 <library dirs="200">
-                    <file>${reference.SamplesValidation.jar}</file>
+                    <file>${file.reference.GDCAPI.jar}</file>
                     <path-in-war>WEB-INF/lib</path-in-war>
                 </library>
                 <library dirs="200">
-                    <file>${reference.BEVIndex.jar}</file>
+                    <file>${file.reference.BEVIndex.jar}</file>
                     <path-in-war>WEB-INF/lib</path-in-war>
                 </library>
             </web-module-libraries>
@@ -39,15 +51,8 @@
                 <root id="test.src.dir"/>
             </test-roots>
         </data>
+        <libraries xmlns="http://www.netbeans.org/ns/cdnjs-libraries/1"/>
         <references xmlns="http://www.netbeans.org/ns/ant-project-references/1">
-            <reference>
-                <foreign-project>BEVIndex</foreign-project>
-                <artifact-type>jar</artifact-type>
-                <script>build.xml</script>
-                <target>jar</target>
-                <clean-target>clean</clean-target>
-                <id>jar</id>
-            </reference>
             <reference>
                 <foreign-project>SamplesValidation</foreign-project>
                 <artifact-type>jar</artifact-type>