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Merge pull request #3 from ipb-halle/jakarta/jdk17
Support for JakartaEE & JDK17
2 parents a6d0d68 + 0e07212 commit 0912a00

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‎pom.xml

Lines changed: 71 additions & 81 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
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<groupId>de.ipb-halle</groupId>
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<artifactId>molecularfaces</artifactId>
9-
<version>0.5.0-SNAPSHOT</version>
9+
<version>1.0.0</version>
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<packaging>jar</packaging>
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<name>MolecularFaces</name>
@@ -24,6 +24,12 @@
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<organization>Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany</organization>
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<organizationUrl>https://www.ipb-halle.de</organizationUrl>
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</developer>
27+
<developer>
28+
<name>Frank Broda</name>
29+
<email>[email protected]</email>
30+
<organization>Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany</organization>
31+
<organizationUrl>https://www.ipb-halle.de</organizationUrl>
32+
</developer>
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</developers>
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<licenses>
@@ -40,25 +46,26 @@
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<properties>
4248
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
49+
<gpg.keyname>[email protected]</gpg.keyname>
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<cdk.version>2.7.1</cdk.version>
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<!-- OpenChemLib JS -->
46-
<openchemlibjs.version>7.4.1</openchemlibjs.version>
53+
<openchemlibjs.version>8.9.0</openchemlibjs.version>
54+
<openchemlibjs.baseURL>https://cdn.jsdelivr.net/npm</openchemlibjs.baseURL>
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<!-- This is the checksum from the package distributed via npm. -->
48-
<openchemlibjs.sha256>e37439f6f4f397bdadaf0091109516916216db16ca8aa1bcbee3b7bfbad8869d</openchemlibjs.sha256>
56+
<openchemlibjs.sha256>b596307ef53ac44f01e799a9ea2f7b790b7d4fbcc6f0ce47891cb4a994f250e8</openchemlibjs.sha256>
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<!-- MolPaintJS -->
51-
<molpaintjs.version>v0.3.5-alpha</molpaintjs.version>
52-
<molpaintjs.sha256>580893aa3ad25abc2a78d3bee8ff14d2a9a4486e6d8df9291149f471e2c16791</molpaintjs.sha256>
59+
<molpaintjs.version>v0.4.0</molpaintjs.version>
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<molpaintjs.sha256>adfd98648b17e13614358dede520bf8bbf4a6095865b9af8fb003ea2514f50b7</molpaintjs.sha256>
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<!-- openVectorEditor -->
55-
<openVectorEditor.version>16.3.18</openVectorEditor.version>
63+
<!-- 18.3.6 -->
64+
<openVectorEditor.version>18.3.6</openVectorEditor.version>
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<openVectorEditor.baseURL>https://cdn.jsdelivr.net/npm</openVectorEditor.baseURL>
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<!-- These are the checksums from the package distributed via npm. -->
57-
<openVectorEditor.min.js.sha256>88ec80b623069665051cca04bc29764df508656792e23acee7ca0060318edb78</openVectorEditor.min.js.sha256>
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<openVectorEditor.main.css.sha256>7cc916424bf20811b989b6329acf2453c07be24d2a5477775282e72846beb604</openVectorEditor.main.css.sha256>
59-
<!--<openVectorEditor.icons-16.1645f50f.woff.sha256>9700ae986c3357a771c7276c8eb30d1adc0c7b270bfd0bd56f6ea2df568cb88b</openVectorEditor.icons-16.1645f50f.woff.sha256>
60-
<openVectorEditor.icons-16.2368f88a.eot.sha256>a8ef9e585479427f5f7fa35e4201caf851a748c5cdf7d89ecf5ba3bd84179eda</openVectorEditor.icons-16.2368f88a.eot.sha256>
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<openVectorEditor.icons-16.13933033.ttf.sha256>3159a9b5dbf9c28ea27e925b24a468fc51298a49e16be06341fdf672efa19605</openVectorEditor.icons-16.13933033.ttf.sha256>-->
67+
<openVectorEditor.min.js.sha256>f857f279e6719b8d960780facca0865228c7b6de747b938a054555ddc1a28b05</openVectorEditor.min.js.sha256>
68+
<openVectorEditor.main.css.sha256>44e62c651698afa64bcaf36c65f500b3e25a10d70297c28bd1bbd51fb02d0d22</openVectorEditor.main.css.sha256>
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</properties>
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<distributionManagement>
@@ -79,8 +86,8 @@
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<artifactId>maven-compiler-plugin</artifactId>
8087
<version>3.1</version>
8188
<configuration>
82-
<source>1.8</source>
83-
<target>1.8</target>
89+
<source>17</source>
90+
<target>17</target>
8491
<encoding>${project.build.sourceEncoding}</encoding>
8592
</configuration>
8693
</plugin>
@@ -114,6 +121,12 @@
114121
<groupId>org.apache.maven.plugins</groupId>
115122
<artifactId>maven-javadoc-plugin</artifactId>
116123
<version>3.2.0</version>
124+
<configuration>
125+
<author>Frank Lange</author>
126+
<encoding>UTF-8</encoding>
127+
<nohelp>true</nohelp>
128+
<show>private</show>
129+
</configuration>
117130
<executions>
118131
<execution>
119132
<id>attach-javadocs</id>
@@ -123,6 +136,21 @@
123136
</execution>
124137
</executions>
125138
</plugin>
139+
140+
<plugin>
141+
<groupId>org.apache.maven.plugins</groupId>
142+
<artifactId>maven-project-info-reports-plugin</artifactId>
143+
<version>3.5.0</version>
144+
</plugin>
145+
146+
147+
<plugin>
148+
<groupId>org.apache.maven.plugins</groupId>
149+
<artifactId>maven-site-plugin</artifactId>
150+
<version>3.12.1</version>
151+
</plugin>
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153+
126154
<!-- 3rd party plugin downloads -->
127155
<plugin>
128156
<groupId>com.googlecode.maven-download-plugin</groupId>
@@ -138,7 +166,7 @@
138166
</goals>
139167
<configuration>
140168
<!-- See https://github.com/cheminfo/openchemlib-js/issues/110#issuecomment-802697504 -->
141-
<url>https://unpkg.com/openchemlib@${openchemlibjs.version}/dist/openchemlib-full.js</url>
169+
<url>${openchemlibjs.baseURL}/openchemlib@${openchemlibjs.version}/dist/openchemlib-full.js</url>
142170
<outputDirectory>${project.build.directory}/downloaded-resources/plugins/openchemlibjs/</outputDirectory>
143171
<sha256>${openchemlibjs.sha256}</sha256>
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<checkSignature>true</checkSignature>
@@ -168,7 +196,7 @@
168196
<goal>wget</goal>
169197
</goals>
170198
<configuration>
171-
<url>https://unpkg.com/open-vector-editor@${openVectorEditor.version}/umd/open-vector-editor.min.js</url>
199+
<url>${openVectorEditor.baseURL}/open-vector-editor@${openVectorEditor.version}/umd/open-vector-editor.min.js</url>
172200
<outputDirectory>${project.build.directory}/downloaded-resources/plugins/openVectorEditor/</outputDirectory>
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<sha256>${openVectorEditor.min.js.sha256}</sha256>
174202
<checkSignature>true</checkSignature>
@@ -181,51 +209,12 @@
181209
<goal>wget</goal>
182210
</goals>
183211
<configuration>
184-
<url>https://unpkg.com/open-vector-editor@${openVectorEditor.version}/umd/main.css</url>
212+
<url>${openVectorEditor.baseURL}/open-vector-editor@${openVectorEditor.version}/umd/main.css</url>
185213
<outputDirectory>${project.build.directory}/downloaded-resources/plugins/openVectorEditor/</outputDirectory>
186214
<sha256>${openVectorEditor.main.css.sha256}</sha256>
187215
<checkSignature>true</checkSignature>
188216
</configuration>
189217
</execution>
190-
<!--<execution>
191-
<id>download-openVectorEditor-icons-16.1645f50f.woff</id>
192-
<phase>generate-resources</phase>
193-
<goals>
194-
<goal>wget</goal>
195-
</goals>
196-
<configuration>
197-
<url>https://unpkg.com/open-vector-editor@${openVectorEditor.version}/umd/icons-16.1645f50f.woff</url>
198-
<outputDirectory>${project.build.directory}/downloaded-resources/plugins/openVectorEditor/</outputDirectory>
199-
<sha256>${openVectorEditor.icons-16.1645f50f.woff.sha256}</sha256>
200-
<checkSignature>true</checkSignature>
201-
</configuration>
202-
</execution>
203-
<execution>
204-
<id>download-openVectorEditor-icons-16.2368f88a.eot</id>
205-
<phase>generate-resources</phase>
206-
<goals>
207-
<goal>wget</goal>
208-
</goals>
209-
<configuration>
210-
<url>https://unpkg.com/open-vector-editor@${openVectorEditor.version}/umd/icons-16.2368f88a.eot</url>
211-
<outputDirectory>${project.build.directory}/downloaded-resources/plugins/openVectorEditor/</outputDirectory>
212-
<sha256>${openVectorEditor.icons-16.2368f88a.eot.sha256}</sha256>
213-
<checkSignature>true</checkSignature>
214-
</configuration>
215-
</execution>
216-
<execution>
217-
<id>download-openVectorEditor-icons-16.13933033.ttf</id>
218-
<phase>generate-resources</phase>
219-
<goals>
220-
<goal>wget</goal>
221-
</goals>
222-
<configuration>
223-
<url>https://unpkg.com/open-vector-editor@${openVectorEditor.version}/umd/icons-16.13933033.ttf</url>
224-
<outputDirectory>${project.build.directory}/downloaded-resources/plugins/openVectorEditor/</outputDirectory>
225-
<sha256>${openVectorEditor.icons-16.13933033.ttf.sha256}</sha256>
226-
<checkSignature>true</checkSignature>
227-
</configuration>
228-
</execution>-->
229218
</executions>
230219
</plugin>
231220
<plugin>
@@ -339,9 +328,9 @@
339328
Runtime dependencies
340329
-->
341330
<dependency>
342-
<groupId>javax</groupId>
343-
<artifactId>javaee-web-api</artifactId>
344-
<version>7.0</version>
331+
<groupId>jakarta.platform</groupId>
332+
<artifactId>jakarta.jakartaee-web-api</artifactId>
333+
<version>8.0.0</version>
345334
<scope>provided</scope>
346335
</dependency>
347336
<!-- CDK is used during molfile validation and conversion. -->
@@ -379,44 +368,44 @@
379368
<dependency>
380369
<groupId>commons-io</groupId>
381370
<artifactId>commons-io</artifactId>
382-
<version>2.11.0</version>
371+
<version>2.16.1</version>
383372
<scope>test</scope>
384373
</dependency>
385374
<!-- mocks for JSF classes -->
386375
<!-- Source code: https://github.com/apache/myfaces-test/tree/master/test22 -->
387-
<dependency>
388-
<groupId>org.apache.myfaces.test</groupId>
389-
<artifactId>myfaces-test22</artifactId>
390-
<version>1.0.8</version>
391-
<scope>test</scope>
392-
</dependency>
393376
<dependency>
394377
<groupId>org.apache.myfaces.core</groupId>
395-
<artifactId>myfaces-impl</artifactId>
396-
<version>2.2.14</version>
397-
<scope>test</scope>
398-
</dependency>
399-
<!-- We need this dependency because org.apache.myfaces.core:myfaces-api does
400-
not ship the javax.faces.LogStrings property files. -->
401-
<dependency>
402-
<groupId>com.sun.faces</groupId>
403-
<artifactId>jsf-api</artifactId>
404-
<version>2.2.20</version>
378+
<artifactId>myfaces-bundle</artifactId>
379+
<version>4.0.0</version>
405380
<scope>test</scope>
406381
</dependency>
382+
<dependency>
383+
<groupId>org.apache.myfaces.core</groupId>
384+
<artifactId>myfaces-api</artifactId>
385+
<version>4.0.0</version>
386+
<!-- <scope>provided</scope> -->
387+
</dependency>
388+
389+
<dependency>
390+
<groupId>org.apache.myfaces.core</groupId>
391+
<artifactId>myfaces-test</artifactId>
392+
<version>4.0.0</version>
393+
<scope>test</scope>
394+
</dependency>
395+
407396
<!-- The bean validation API is provided by the JavaEE container only
408397
during runtime, but not during tests. Note: We are using JavaEE 7
409398
with bean validation 1.1, thus the ancient version. -->
410399
<dependency>
411-
<groupId>org.hibernate</groupId>
400+
<groupId>org.hibernate.validator</groupId>
412401
<artifactId>hibernate-validator</artifactId>
413-
<version>5.4.3.Final</version>
414-
<scope>test</scope>
402+
<version>8.0.0.Final</version>
403+
<scope>provided</scope>
415404
</dependency>
416405
<dependency>
417406
<groupId>org.glassfish</groupId>
418-
<artifactId>javax.el</artifactId>
419-
<version>3.0.1-b12</version>
407+
<artifactId>jakarta.el</artifactId>
408+
<version>4.0.2</version>
420409
<scope>test</scope>
421410
</dependency>
422411
<!-- used in verifications of molecules -->
@@ -456,6 +445,7 @@
456445
<arg>--pinentry-mode</arg>
457446
<arg>loopback</arg>
458447
</gpgArguments>
448+
<keyname>${gpg.keyname}</keyname>
459449
</configuration>
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<executions>
461451
<execution>
@@ -493,4 +483,4 @@
493483
</build>
494484
</profile>
495485
</profiles>
496-
</project>
486+
</project>

‎src/main/java/de/ipb_halle/molecularfaces/component/molplugin/MarvinJSComponent.java

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*/
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package de.ipb_halle.molecularfaces.component.molplugin;
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20-
import javax.faces.component.FacesComponent;
21-
import javax.faces.event.AbortProcessingException;
22-
import javax.faces.event.ComponentSystemEvent;
23-
import javax.faces.event.ComponentSystemEventListener;
24-
import javax.faces.event.ListenerFor;
25-
import javax.faces.event.PostAddToViewEvent;
20+
import jakarta.faces.component.FacesComponent;
21+
import jakarta.faces.event.AbortProcessingException;
22+
import jakarta.faces.event.ComponentSystemEvent;
23+
import jakarta.faces.event.ComponentSystemEventListener;
24+
import jakarta.faces.event.ListenerFor;
25+
import jakarta.faces.event.PostAddToViewEvent;
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2727
import de.ipb_halle.molecularfaces.util.WebXml;
2828
import de.ipb_halle.molecularfaces.util.WebXmlImpl;
2929

3030
/**
31-
* This {@link javax.faces.component.UIComponent} renders a chemical structure
31+
* This {@link jakarta.faces.component.UIComponent} renders a chemical structure
3232
* editor or viewer using the
3333
* <a href="https://chemaxon.com/products/marvin-js">Marvin JS</a> JavaScript
3434
* plugin.
@@ -106,4 +106,4 @@ private void processPostAddToViewEvent() {
106106
getResourceLoader().addScriptExtToHead(baseDir + "/js/webservices.js");
107107
}
108108
}
109-
}
109+
}

‎src/main/java/de/ipb_halle/molecularfaces/component/molplugin/MarvinJSRenderer.java

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -19,17 +19,17 @@
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import java.io.IOException;
2121
import java.util.Formatter;
22-
import javax.faces.component.UIComponent;
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import javax.faces.context.FacesContext;
24-
import javax.faces.context.ResponseWriter;
25-
import javax.faces.render.FacesRenderer;
22+
import jakarta.faces.component.UIComponent;
23+
import jakarta.faces.context.FacesContext;
24+
import jakarta.faces.context.ResponseWriter;
25+
import jakarta.faces.render.FacesRenderer;
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2727
import de.ipb_halle.molecularfaces.util.RendererUtils;
2828
import de.ipb_halle.molecularfaces.util.WebXml;
2929
import de.ipb_halle.molecularfaces.util.WebXmlImpl;
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3131
/**
32-
* This {@link javax.faces.render.Renderer} renders a chemical structure editor or viewer using the
32+
* This {@link jakarta.faces.render.Renderer} renders a chemical structure editor or viewer using the
3333
* <a href="https://chemaxon.com/products/marvin-js">Marvin JS</a> Javascript
3434
* plugin.
3535
*
@@ -260,4 +260,4 @@ private void encodeEditorJS(FacesContext context, ResponseWriter writer, MolPlug
260260
writer.writeText(sb, null);
261261
writer.endElement("script");
262262
}
263-
}
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}

‎src/main/java/de/ipb_halle/molecularfaces/component/molplugin/MolPaintJSComponent.java

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -17,13 +17,13 @@
1717
*/
1818
package de.ipb_halle.molecularfaces.component.molplugin;
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import javax.faces.component.FacesComponent;
20+
import jakarta.faces.component.FacesComponent;
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import de.ipb_halle.molecularfaces.util.WebXml;
2323
import de.ipb_halle.molecularfaces.util.WebXmlImpl;
2424

2525
/**
26-
* This {@link javax.faces.component.UIComponent} renders a chemical structure
26+
* This {@link jakarta.faces.component.UIComponent} renders a chemical structure
2727
* editor or viewer using the
2828
* <a href="https://github.com/ipb-halle/MolPaintJS">MolPaintJS</a> JavaScript
2929
* plugin.
@@ -55,4 +55,4 @@ public MolPaintJSComponent() {
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5656
setRendererType(DEFAULT_RENDERER);
5757
}
58-
}
58+
}

‎src/main/java/de/ipb_halle/molecularfaces/component/molplugin/MolPaintJSRenderer.java

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -19,15 +19,15 @@
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2020
import java.io.IOException;
2121
import java.util.Formatter;
22-
import javax.faces.component.UIComponent;
23-
import javax.faces.context.FacesContext;
24-
import javax.faces.context.ResponseWriter;
25-
import javax.faces.render.FacesRenderer;
22+
import jakarta.faces.component.UIComponent;
23+
import jakarta.faces.context.FacesContext;
24+
import jakarta.faces.context.ResponseWriter;
25+
import jakarta.faces.render.FacesRenderer;
2626

2727
import de.ipb_halle.molecularfaces.util.RendererUtils;
2828

2929
/**
30-
* This {@link javax.faces.render.Renderer} renders a chemical structure editor or viewer using the
30+
* This {@link jakarta.faces.render.Renderer} renders a chemical structure editor or viewer using the
3131
* <a href="https://github.com/ipb-halle/MolPaintJS">MolPaintJS</a> Javascript
3232
* plugin.
3333
*
@@ -241,4 +241,4 @@ private void encodeEditorJS(ResponseWriter writer, MolPluginCore plugin, String
241241
writer.writeText(sb, null);
242242
writer.endElement("script");
243243
}
244-
}
244+
}

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