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Merge pull request #3 from ipb-halle/jakarta/jdk17
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Support for JakartaEE & JDK17
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@fbroda
fbroda authored Apr 23, 2024
2 parents a6d0d68 + 0e07212 commit 0912a00
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152 changes: 71 additions & 81 deletions pom.xml
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Expand Up @@ -6,7 +6,7 @@

<groupId>de.ipb-halle</groupId>
<artifactId>molecularfaces</artifactId>
<version>0.5.0-SNAPSHOT</version>
<version>1.0.0</version>
<packaging>jar</packaging>

<name>MolecularFaces</name>
Expand All @@ -24,6 +24,12 @@
<organization>Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany</organization>
<organizationUrl>https://www.ipb-halle.de</organizationUrl>
</developer>
<developer>
<name>Frank Broda</name>
<email>[email protected]</email>
<organization>Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany</organization>
<organizationUrl>https://www.ipb-halle.de</organizationUrl>
</developer>
</developers>

<licenses>
Expand All @@ -40,25 +46,26 @@

<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<gpg.keyname>[email protected]</gpg.keyname>
<cdk.version>2.7.1</cdk.version>

<!-- OpenChemLib JS -->
<openchemlibjs.version>7.4.1</openchemlibjs.version>
<openchemlibjs.version>8.9.0</openchemlibjs.version>
<openchemlibjs.baseURL>https://cdn.jsdelivr.net/npm</openchemlibjs.baseURL>
<!-- This is the checksum from the package distributed via npm. -->
<openchemlibjs.sha256>e37439f6f4f397bdadaf0091109516916216db16ca8aa1bcbee3b7bfbad8869d</openchemlibjs.sha256>
<openchemlibjs.sha256>b596307ef53ac44f01e799a9ea2f7b790b7d4fbcc6f0ce47891cb4a994f250e8</openchemlibjs.sha256>

<!-- MolPaintJS -->
<molpaintjs.version>v0.3.5-alpha</molpaintjs.version>
<molpaintjs.sha256>580893aa3ad25abc2a78d3bee8ff14d2a9a4486e6d8df9291149f471e2c16791</molpaintjs.sha256>
<molpaintjs.version>v0.4.0</molpaintjs.version>
<molpaintjs.sha256>adfd98648b17e13614358dede520bf8bbf4a6095865b9af8fb003ea2514f50b7</molpaintjs.sha256>

<!-- openVectorEditor -->
<openVectorEditor.version>16.3.18</openVectorEditor.version>
<!-- 18.3.6 -->
<openVectorEditor.version>18.3.6</openVectorEditor.version>
<openVectorEditor.baseURL>https://cdn.jsdelivr.net/npm</openVectorEditor.baseURL>
<!-- These are the checksums from the package distributed via npm. -->
<openVectorEditor.min.js.sha256>88ec80b623069665051cca04bc29764df508656792e23acee7ca0060318edb78</openVectorEditor.min.js.sha256>
<openVectorEditor.main.css.sha256>7cc916424bf20811b989b6329acf2453c07be24d2a5477775282e72846beb604</openVectorEditor.main.css.sha256>
<!--<openVectorEditor.icons-16.1645f50f.woff.sha256>9700ae986c3357a771c7276c8eb30d1adc0c7b270bfd0bd56f6ea2df568cb88b</openVectorEditor.icons-16.1645f50f.woff.sha256>
<openVectorEditor.icons-16.2368f88a.eot.sha256>a8ef9e585479427f5f7fa35e4201caf851a748c5cdf7d89ecf5ba3bd84179eda</openVectorEditor.icons-16.2368f88a.eot.sha256>
<openVectorEditor.icons-16.13933033.ttf.sha256>3159a9b5dbf9c28ea27e925b24a468fc51298a49e16be06341fdf672efa19605</openVectorEditor.icons-16.13933033.ttf.sha256>-->
<openVectorEditor.min.js.sha256>f857f279e6719b8d960780facca0865228c7b6de747b938a054555ddc1a28b05</openVectorEditor.min.js.sha256>
<openVectorEditor.main.css.sha256>44e62c651698afa64bcaf36c65f500b3e25a10d70297c28bd1bbd51fb02d0d22</openVectorEditor.main.css.sha256>
</properties>

<distributionManagement>
Expand All @@ -79,8 +86,8 @@
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<source>17</source>
<target>17</target>
<encoding>${project.build.sourceEncoding}</encoding>
</configuration>
</plugin>
Expand Down Expand Up @@ -114,6 +121,12 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.2.0</version>
<configuration>
<author>Frank Lange</author>
<encoding>UTF-8</encoding>
<nohelp>true</nohelp>
<show>private</show>
</configuration>
<executions>
<execution>
<id>attach-javadocs</id>
Expand All @@ -123,6 +136,21 @@
</execution>
</executions>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>3.5.0</version>
</plugin>


<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>3.12.1</version>
</plugin>


<!-- 3rd party plugin downloads -->
<plugin>
<groupId>com.googlecode.maven-download-plugin</groupId>
Expand All @@ -138,7 +166,7 @@
</goals>
<configuration>
<!-- See https://github.com/cheminfo/openchemlib-js/issues/110#issuecomment-802697504 -->
<url>https://unpkg.com/openchemlib@${openchemlibjs.version}/dist/openchemlib-full.js</url>
<url>${openchemlibjs.baseURL}/openchemlib@${openchemlibjs.version}/dist/openchemlib-full.js</url>
<outputDirectory>${project.build.directory}/downloaded-resources/plugins/openchemlibjs/</outputDirectory>
<sha256>${openchemlibjs.sha256}</sha256>
<checkSignature>true</checkSignature>
Expand Down Expand Up @@ -168,7 +196,7 @@
<goal>wget</goal>
</goals>
<configuration>
<url>https://unpkg.com/open-vector-editor@${openVectorEditor.version}/umd/open-vector-editor.min.js</url>
<url>${openVectorEditor.baseURL}/open-vector-editor@${openVectorEditor.version}/umd/open-vector-editor.min.js</url>
<outputDirectory>${project.build.directory}/downloaded-resources/plugins/openVectorEditor/</outputDirectory>
<sha256>${openVectorEditor.min.js.sha256}</sha256>
<checkSignature>true</checkSignature>
Expand All @@ -181,51 +209,12 @@
<goal>wget</goal>
</goals>
<configuration>
<url>https://unpkg.com/open-vector-editor@${openVectorEditor.version}/umd/main.css</url>
<url>${openVectorEditor.baseURL}/open-vector-editor@${openVectorEditor.version}/umd/main.css</url>
<outputDirectory>${project.build.directory}/downloaded-resources/plugins/openVectorEditor/</outputDirectory>
<sha256>${openVectorEditor.main.css.sha256}</sha256>
<checkSignature>true</checkSignature>
</configuration>
</execution>
<!--<execution>
<id>download-openVectorEditor-icons-16.1645f50f.woff</id>
<phase>generate-resources</phase>
<goals>
<goal>wget</goal>
</goals>
<configuration>
<url>https://unpkg.com/open-vector-editor@${openVectorEditor.version}/umd/icons-16.1645f50f.woff</url>
<outputDirectory>${project.build.directory}/downloaded-resources/plugins/openVectorEditor/</outputDirectory>
<sha256>${openVectorEditor.icons-16.1645f50f.woff.sha256}</sha256>
<checkSignature>true</checkSignature>
</configuration>
</execution>
<execution>
<id>download-openVectorEditor-icons-16.2368f88a.eot</id>
<phase>generate-resources</phase>
<goals>
<goal>wget</goal>
</goals>
<configuration>
<url>https://unpkg.com/open-vector-editor@${openVectorEditor.version}/umd/icons-16.2368f88a.eot</url>
<outputDirectory>${project.build.directory}/downloaded-resources/plugins/openVectorEditor/</outputDirectory>
<sha256>${openVectorEditor.icons-16.2368f88a.eot.sha256}</sha256>
<checkSignature>true</checkSignature>
</configuration>
</execution>
<execution>
<id>download-openVectorEditor-icons-16.13933033.ttf</id>
<phase>generate-resources</phase>
<goals>
<goal>wget</goal>
</goals>
<configuration>
<url>https://unpkg.com/open-vector-editor@${openVectorEditor.version}/umd/icons-16.13933033.ttf</url>
<outputDirectory>${project.build.directory}/downloaded-resources/plugins/openVectorEditor/</outputDirectory>
<sha256>${openVectorEditor.icons-16.13933033.ttf.sha256}</sha256>
<checkSignature>true</checkSignature>
</configuration>
</execution>-->
</executions>
</plugin>
<plugin>
Expand Down Expand Up @@ -339,9 +328,9 @@
Runtime dependencies
-->
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-web-api</artifactId>
<version>7.0</version>
<groupId>jakarta.platform</groupId>
<artifactId>jakarta.jakartaee-web-api</artifactId>
<version>8.0.0</version>
<scope>provided</scope>
</dependency>
<!-- CDK is used during molfile validation and conversion. -->
Expand Down Expand Up @@ -379,44 +368,44 @@
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.11.0</version>
<version>2.16.1</version>
<scope>test</scope>
</dependency>
<!-- mocks for JSF classes -->
<!-- Source code: https://github.com/apache/myfaces-test/tree/master/test22 -->
<dependency>
<groupId>org.apache.myfaces.test</groupId>
<artifactId>myfaces-test22</artifactId>
<version>1.0.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.myfaces.core</groupId>
<artifactId>myfaces-impl</artifactId>
<version>2.2.14</version>
<scope>test</scope>
</dependency>
<!-- We need this dependency because org.apache.myfaces.core:myfaces-api does
not ship the javax.faces.LogStrings property files. -->
<dependency>
<groupId>com.sun.faces</groupId>
<artifactId>jsf-api</artifactId>
<version>2.2.20</version>
<artifactId>myfaces-bundle</artifactId>
<version>4.0.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.myfaces.core</groupId>
<artifactId>myfaces-api</artifactId>
<version>4.0.0</version>
<!-- <scope>provided</scope> -->
</dependency>

<dependency>
<groupId>org.apache.myfaces.core</groupId>
<artifactId>myfaces-test</artifactId>
<version>4.0.0</version>
<scope>test</scope>
</dependency>

<!-- The bean validation API is provided by the JavaEE container only
during runtime, but not during tests. Note: We are using JavaEE 7
with bean validation 1.1, thus the ancient version. -->
<dependency>
<groupId>org.hibernate</groupId>
<groupId>org.hibernate.validator</groupId>
<artifactId>hibernate-validator</artifactId>
<version>5.4.3.Final</version>
<scope>test</scope>
<version>8.0.0.Final</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.glassfish</groupId>
<artifactId>javax.el</artifactId>
<version>3.0.1-b12</version>
<artifactId>jakarta.el</artifactId>
<version>4.0.2</version>
<scope>test</scope>
</dependency>
<!-- used in verifications of molecules -->
Expand Down Expand Up @@ -456,6 +445,7 @@
<arg>--pinentry-mode</arg>
<arg>loopback</arg>
</gpgArguments>
<keyname>${gpg.keyname}</keyname>
</configuration>
<executions>
<execution>
Expand Down Expand Up @@ -493,4 +483,4 @@
</build>
</profile>
</profiles>
</project>
</project>
16 changes: 8 additions & 8 deletions src/main/java/de/ipb_halle/molecularfaces/component/molplugin/MarvinJSComponent.java
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Expand Up @@ -17,18 +17,18 @@
*/
package de.ipb_halle.molecularfaces.component.molplugin;

import javax.faces.component.FacesComponent;
import javax.faces.event.AbortProcessingException;
import javax.faces.event.ComponentSystemEvent;
import javax.faces.event.ComponentSystemEventListener;
import javax.faces.event.ListenerFor;
import javax.faces.event.PostAddToViewEvent;
import jakarta.faces.component.FacesComponent;
import jakarta.faces.event.AbortProcessingException;
import jakarta.faces.event.ComponentSystemEvent;
import jakarta.faces.event.ComponentSystemEventListener;
import jakarta.faces.event.ListenerFor;
import jakarta.faces.event.PostAddToViewEvent;

import de.ipb_halle.molecularfaces.util.WebXml;
import de.ipb_halle.molecularfaces.util.WebXmlImpl;

/**
* This {@link javax.faces.component.UIComponent} renders a chemical structure
* This {@link jakarta.faces.component.UIComponent} renders a chemical structure
* editor or viewer using the
* <a href="https://chemaxon.com/products/marvin-js">Marvin JS</a> JavaScript
* plugin.
Expand Down Expand Up @@ -106,4 +106,4 @@ private void processPostAddToViewEvent() {
getResourceLoader().addScriptExtToHead(baseDir + "/js/webservices.js");
}
}
}
}
12 changes: 6 additions & 6 deletions src/main/java/de/ipb_halle/molecularfaces/component/molplugin/MarvinJSRenderer.java
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Expand Up @@ -19,17 +19,17 @@

import java.io.IOException;
import java.util.Formatter;
import javax.faces.component.UIComponent;
import javax.faces.context.FacesContext;
import javax.faces.context.ResponseWriter;
import javax.faces.render.FacesRenderer;
import jakarta.faces.component.UIComponent;
import jakarta.faces.context.FacesContext;
import jakarta.faces.context.ResponseWriter;
import jakarta.faces.render.FacesRenderer;

import de.ipb_halle.molecularfaces.util.RendererUtils;
import de.ipb_halle.molecularfaces.util.WebXml;
import de.ipb_halle.molecularfaces.util.WebXmlImpl;

/**
* This {@link javax.faces.render.Renderer} renders a chemical structure editor or viewer using the
* This {@link jakarta.faces.render.Renderer} renders a chemical structure editor or viewer using the
* <a href="https://chemaxon.com/products/marvin-js">Marvin JS</a> Javascript
* plugin.
*
Expand Down Expand Up @@ -260,4 +260,4 @@ private void encodeEditorJS(FacesContext context, ResponseWriter writer, MolPlug
writer.writeText(sb, null);
writer.endElement("script");
}
}
}
6 changes: 3 additions & 3 deletions src/main/java/de/ipb_halle/molecularfaces/component/molplugin/MolPaintJSComponent.java
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Expand Up @@ -17,13 +17,13 @@
*/
package de.ipb_halle.molecularfaces.component.molplugin;

import javax.faces.component.FacesComponent;
import jakarta.faces.component.FacesComponent;

import de.ipb_halle.molecularfaces.util.WebXml;
import de.ipb_halle.molecularfaces.util.WebXmlImpl;

/**
* This {@link javax.faces.component.UIComponent} renders a chemical structure
* This {@link jakarta.faces.component.UIComponent} renders a chemical structure
* editor or viewer using the
* <a href="https://github.com/ipb-halle/MolPaintJS">MolPaintJS</a> JavaScript
* plugin.
Expand Down Expand Up @@ -55,4 +55,4 @@ public MolPaintJSComponent() {

setRendererType(DEFAULT_RENDERER);
}
}
}
12 changes: 6 additions & 6 deletions src/main/java/de/ipb_halle/molecularfaces/component/molplugin/MolPaintJSRenderer.java
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Expand Up @@ -19,15 +19,15 @@

import java.io.IOException;
import java.util.Formatter;
import javax.faces.component.UIComponent;
import javax.faces.context.FacesContext;
import javax.faces.context.ResponseWriter;
import javax.faces.render.FacesRenderer;
import jakarta.faces.component.UIComponent;
import jakarta.faces.context.FacesContext;
import jakarta.faces.context.ResponseWriter;
import jakarta.faces.render.FacesRenderer;

import de.ipb_halle.molecularfaces.util.RendererUtils;

/**
* This {@link javax.faces.render.Renderer} renders a chemical structure editor or viewer using the
* This {@link jakarta.faces.render.Renderer} renders a chemical structure editor or viewer using the
* <a href="https://github.com/ipb-halle/MolPaintJS">MolPaintJS</a> Javascript
* plugin.
*
Expand Down Expand Up @@ -241,4 +241,4 @@ private void encodeEditorJS(ResponseWriter writer, MolPluginCore plugin, String
writer.writeText(sb, null);
writer.endElement("script");
}
}
}
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