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Result of Marietta Hamberger's research project #12

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Result of Marietta Hamberger's research project #12

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f6a91c3
Added the bundle sbmlsheets in bundles and features. Made changes to …
MariettaHa May 17, 2020
b985d82
Removed unnecessary comments.
MariettaHa May 17, 2020
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1 change: 1 addition & 0 deletions bundles/org.insilico.core/.gitignore
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/bin/
6 changes: 5 additions & 1 deletion bundles/org.insilico.core/META-INF/MANIFEST.MF
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Expand Up @@ -5,7 +5,10 @@ Bundle-SymbolicName: org.insilico.core;singleton:=true
Bundle-Version: 1.0.0.qualifier
Bundle-RequiredExecutionEnvironment: JavaSE-1.8
Bundle-Vendor: Draeger Lab
Export-Package: org.insilico.core;uses:="org.eclipse.fx.ui.services.startup,org.eclipse.fx.ui.workbench.fx,org.eclipse.fx.core.app",
Export-Package: org.insilico.core.handlers,
org.insilico.core;uses:="org.eclipse.fx.ui.services.startup,
org.eclipse.fx.ui.workbench.fx,
org.eclipse.fx.core.app",
org.insilico.core.handlers
Bundle-ActivationPolicy: lazy
Import-Package: javax.inject;version="1.0.0"
Expand All @@ -22,4 +25,5 @@ Require-Bundle: org.eclipse.core.resources;bundle-version="3.11.1",
org.eclipse.fx.ui.workbench.base;bundle-version="3.0.0",
org.eclipse.fx.core;bundle-version="3.0.0",
org.eclipse.core.databinding;bundle-version="1.6.0"
Automatic-Module-Name: org.insilico.core

17 changes: 9 additions & 8 deletions bundles/org.insilico.core/pom.xml
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Expand Up @@ -23,13 +23,14 @@
</includes>
</resource>
</resources>

<plugins>
<plugin>
<groupId>org.eclipse.tycho</groupId>
<artifactId>tycho-source-plugin</artifactId>
<version>${tycho.version}</version>
</plugin>
</plugins>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.eclipse.tycho</groupId>
<artifactId>tycho-source-plugin</artifactId>
<version>${tycho.version}</version>
</plugin>
</plugins>
</pluginManagement>
</build>
</project>
2 changes: 1 addition & 1 deletion bundles/org.insilico.core/src/org/insilico/core/ApplicationLifecycle.java
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package org.insilico.core;
package org.insilico.core;

import org.eclipse.core.resources.IWorkspace;
import org.eclipse.core.runtime.CoreException;
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2 changes: 1 addition & 1 deletion bundles/org.insilico.core/src/org/insilico/core/Main.java
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package org.insilico.core;
package org.insilico.core;

import org.eclipse.fx.ui.workbench.fx.E4MainThreadApplication;

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2 changes: 1 addition & 1 deletion bundles/org.insilico.core/src/org/insilico/core/package-info.java
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Expand Up @@ -10,4 +10,4 @@
* @author roman
*
*/
package org.insilico.core;
package org.insilico.core;
6 changes: 6 additions & 0 deletions bundles/org.insilico.jsbml.core/.project
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Expand Up @@ -25,8 +25,14 @@
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.m2e.core.maven2Builder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
<nature>org.eclipse.pde.PluginNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
</natures>
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7 changes: 6 additions & 1 deletion bundles/org.insilico.jsbml.core/META-INF/MANIFEST.MF
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Expand Up @@ -15,8 +15,13 @@ Bundle-RequiredExecutionEnvironment: JavaSE-1.8
Bundle-ActivationPolicy: lazy
Service-Component: OSGI-INF/services/org.insilico.jsbml.core.services.provider.SBMLEditorProvider.xml,
OSGI-INF/services/org.insilico.jsbml.core.services.provider.SBMLIconProvider.xml,
OSGI-INF/services/org.insilico.jsbml.core.services.provider.SBMLDocumentLoader.xml
OSGI-INF/services/org.insilico.jsbml.core.services.provider.SBMLDocumentLoader.xml,
OSGI-INF/org.insilico.jsbml.core.services.provider.SBMLIconProvider.xml,
OSGI-INF/org.insilico.jsbml.core.services.provider.SBMLDocumentLoader.xml,
OSGI-INF/org.insilico.jsbml.core.services.provider.SBMLEditorProvider.xml
Export-Package: org.insilico.jsbml.core,
org.insilico.jsbml.core.editor,
org.insilico.jsbml.core.services,
org.insilico.jsbml.core.services.provider
Automatic-Module-Name: org.insilico.jsbml.core
Import-Package: org.osgi.service.component.annotations;version="1.2.0"
8 changes: 8 additions & 0 deletions ...lico.jsbml.core/OSGI-INF/org.insilico.jsbml.core.services.provider.SBMLDocumentLoader.xml
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<?xml version="1.0" encoding="UTF-8"?>
<scr:component xmlns:scr="http://www.osgi.org/xmlns/scr/v1.1.0" name="org.insilico.jsbml.core.services.provider.SBMLDocumentLoader">
<property name="service.context.key" value="org.sbml.jsbml.SBMLDocument"/>
<service>
<provide interface="org.eclipse.e4.core.contexts.IContextFunction"/>
</service>
<implementation class="org.insilico.jsbml.core.services.provider.SBMLDocumentLoader"/>
</scr:component>
7 changes: 7 additions & 0 deletions ...lico.jsbml.core/OSGI-INF/org.insilico.jsbml.core.services.provider.SBMLEditorProvider.xml
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<?xml version="1.0" encoding="UTF-8"?>
<scr:component xmlns:scr="http://www.osgi.org/xmlns/scr/v1.1.0" name="org.insilico.jsbml.core.services.provider.SBMLEditorProvider">
<service>
<provide interface="org.eclipse.fx.code.editor.fx.e4.EditorClassURLProvider"/>
</service>
<implementation class="org.insilico.jsbml.core.services.provider.SBMLEditorProvider"/>
</scr:component>
7 changes: 7 additions & 0 deletions ...silico.jsbml.core/OSGI-INF/org.insilico.jsbml.core.services.provider.SBMLIconProvider.xml
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<?xml version="1.0" encoding="UTF-8"?>
<scr:component xmlns:scr="http://www.osgi.org/xmlns/scr/v1.1.0" name="org.insilico.jsbml.core.services.provider.SBMLIconProvider">
<service>
<provide interface="org.eclipse.fx.code.editor.services.FileIconProvider"/>
</service>
<implementation class="org.insilico.jsbml.core.services.provider.SBMLIconProvider"/>
</scr:component>
17 changes: 9 additions & 8 deletions bundles/org.insilico.jsbml.core/pom.xml
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Expand Up @@ -23,13 +23,14 @@
</includes>
</resource>
</resources>

<plugins>
<plugin>
<groupId>org.eclipse.tycho</groupId>
<artifactId>tycho-source-plugin</artifactId>
<version>${tycho.version}</version>
</plugin>
</plugins>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.eclipse.tycho</groupId>
<artifactId>tycho-source-plugin</artifactId>
<version>${tycho.version}</version>
</plugin>
</plugins>
</pluginManagement>
</build>
</project>
2 changes: 1 addition & 1 deletion bundles/org.insilico.jsbml.core/src/org/insilico/jsbml/core/Constants.java
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package org.insilico.jsbml.core;
package org.insilico.jsbml.core;

public interface Constants {

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7 changes: 3 additions & 4 deletions bundles/org.insilico.jsbml.core/src/org/insilico/jsbml/core/editor/DocumentTreeView.java
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@@ -1,15 +1,12 @@
package org.insilico.jsbml.core.editor;
package org.insilico.jsbml.core.editor;

import java.util.Collections;
import java.util.List;
import java.util.stream.Collectors;

import javax.annotation.PostConstruct;
import javax.inject.Inject;

import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.SBase;

import javafx.scene.control.TreeItem;
import javafx.scene.control.TreeView;
import javafx.scene.layout.BorderPane;
Expand All @@ -21,9 +18,11 @@ public class DocumentTreeView {

@PostConstruct
private void init(BorderPane parent) {
if (doc!=null) {
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With this check added we assume that the doc can be null on this stage. Do we need to set an alternative error view for the case when the doc is not available or we inform the user in some different way?

TreeView<SBase> docTreeView = new TreeView<>(convertToTreeItem(doc, 2));

parent.setCenter(docTreeView);
}
}

private TreeItem<SBase> convertToTreeItem(SBase elem, int expandLevels) {
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2 changes: 1 addition & 1 deletion ....insilico.jsbml.core/src/org/insilico/jsbml/core/services/SBMLAdapterBuilderProvider.java
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package org.insilico.jsbml.core.services;
package org.insilico.jsbml.core.services;

import org.sbml.jsbml.SBMLDocument;

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13 changes: 9 additions & 4 deletions ...insilico.jsbml.core/src/org/insilico/jsbml/core/services/provider/SBMLDocumentLoader.java
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Expand Up @@ -31,7 +31,6 @@
* @author roman
*
*/
@SuppressWarnings("restriction")
@Component(service = IContextFunction.class,
property = {"service.context.key=org.sbml.jsbml.SBMLDocument"})
public class SBMLDocumentLoader extends ContextFunction {
Expand All @@ -40,7 +39,8 @@ public class SBMLDocumentLoader extends ContextFunction {

@Override
public Object compute(IEclipseContext context, String contextKey) {
System.out.println("Compute...");
return IInjector.NOT_A_VALUE;
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maybe change this to a "not implemented" Exception

/*System.out.println("Compute...");
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Please remove redundant code or at least add a description of the potential code intention.

Object urlVal = context.get(DOCUMENT_URL);

if (urlVal == null) {
Expand Down Expand Up @@ -69,7 +69,12 @@ public Object compute(IEclipseContext context, String contextKey) {
// Load if needed
try {
URI url = URIUtil.fromString(urlString);
doc = JSBML.readSBMLFromFile(url.getPath());
if (url!=null) {
if (url.getPath()!=null) {
doc = JSBML.readSBMLFromFile(url.getPath());
}
}

// doc = SBMLReader.read(new File(url));
cache.put(urlString, doc);
}
Expand All @@ -85,6 +90,6 @@ public Object compute(IEclipseContext context, String contextKey) {
}

System.out.println("No doc selected");
return IInjector.NOT_A_VALUE;
return IInjector.NOT_A_VALUE;*/
}
}
2 changes: 1 addition & 1 deletion ...insilico.jsbml.core/src/org/insilico/jsbml/core/services/provider/SBMLEditorProvider.java
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Expand Up @@ -5,7 +5,7 @@
import org.osgi.service.component.annotations.Component;

/**
* OSGi Service Component which provides a editor part for SBML files. The editor is provides via
* OSGi Service Component which provides an editor part for SBML files. The editor is provided via
* the {@link EditorClassURLProvider} service.
*
* @author roman
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1 change: 0 additions & 1 deletion ...g.insilico.jsbml.core/src/org/insilico/jsbml/core/services/provider/SBMLIconProvider.java
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Expand Up @@ -13,7 +13,6 @@
*
*/
@Component
@SuppressWarnings("restriction")
public class SBMLIconProvider implements FileIconProvider {

@Override
Expand Down
2 changes: 1 addition & 1 deletion ...s/org.insilico.jsbml.core/src/org/insilico/jsbml/core/services/provider/package-info.java
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Expand Up @@ -4,4 +4,4 @@
* @author roman
* @see org.insilico.jsbml.core
*/
package org.insilico.jsbml.core.services.provider;
package org.insilico.jsbml.core.services.provider;
1 change: 1 addition & 0 deletions bundles/org.insilico.sbmlsheets/.gitignore
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/bin/
39 changes: 39 additions & 0 deletions bundles/org.insilico.sbmlsheets/.project
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<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>org.insilico.sbmlsheets</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.pde.ManifestBuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.pde.SchemaBuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.pde.ds.core.builder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.m2e.core.maven2Builder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
<nature>org.eclipse.pde.PluginNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
</natures>
</projectDescription>
40 changes: 40 additions & 0 deletions bundles/org.insilico.sbmlsheets/META-INF/MANIFEST.MF
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Manifest-Version: 1.0
Bundle-ManifestVersion: 2
Bundle-Name: SBMLsheets
Bundle-SymbolicName: org.insilico.sbmlsheets;singleton:=true
Bundle-Version: 1.0.0.qualifier
Require-Bundle: org.eclipse.core.runtime,
org.eclipse.fx.ui.services;bundle-version="3.0.0",
org.eclipse.fx.code.editor;bundle-version="3.0.0",
org.sbml.jsbml.core;bundle-version="1.3.1",
org.eclipse.fx.code.editor.fx.e4;bundle-version="3.0.0",
org.eclipse.e4.core.contexts;bundle-version="1.5.0",
org.eclipse.e4.core.di;bundle-version="1.6.1",
org.eclipse.e4.ui.model.workbench;bundle-version="1.2.0",
org.insilico.ui.themes.light;bundle-version="1.0.0",
org.insilico.ui;bundle-version="1.0.0"
Bundle-RequiredExecutionEnvironment: JavaSE-1.8
Bundle-ActivationPolicy: lazy
Service-Component: OSGI-INF/services/org.insilico.sbmlsheets.services.provider.SBMLEditorProvider.xml,
OSGI-INF/services/org.insilico.sbmlsheets.services.provider.SBMLIconProvider.xml,
OSGI-INF/services/org.insilico.sbmlsheets.services.provider.SBMLDocumentLoader.xml,
OSGI-INF/services/org.insilico.sbmlsheets.services.provider.SpreadsheetEditorProvider.xml,
OSGI-INF/services/org.insilico.sbmlsheets.services.provider.SpreadsheetDocumentLoader.xml,
OSGI-INF/org.insilico.sbmlsheets.services.provider.SBMLIconProvider.xml,
OSGI-INF/org.insilico.sbmlsheets.services.provider.SBMLEditorProvider.xml,
OSGI-INF/org.insilico.sbmlsheets.services.provider.SBMLDocumentLoader.xml,
OSGI-INF/org.insilico.sbmlsheets.services.provider.SpreadsheetDocumentLoader.xml,
OSGI-INF/org.insilico.sbmlsheets.services.provider.SpreadsheetEditorProvider.xml,
OSGI-INF/org.insilico.sbmlsheets.services.provider.SheetProjectEditorProvider.xml,
OSGI-INF/org.insilico.sbmlsheets.services.provider.SheetProjectDocumentLoader.xml
Export-Package: org.insilico.sbmlsheets.core,
org.insilico.sbmlsheets.editor,
org.insilico.sbmlsheets.services,
org.insilico.sbmlsheets.services.provider
Automatic-Module-Name: org.insilico.sbmlsheets
Import-Package: org.eclipse.core.databinding.observable.list,
org.eclipse.core.resources,
org.eclipse.e4.ui.workbench,
org.eclipse.e4.ui.workbench.modeling,
org.insilico.core,
org.osgi.service.component.annotations;version="1.2.0"
8 changes: 8 additions & 0 deletions ...lico.sbmlsheets/OSGI-INF/org.insilico.sbmlsheets.services.provider.SBMLDocumentLoader.xml
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<?xml version="1.0" encoding="UTF-8"?>
<scr:component xmlns:scr="http://www.osgi.org/xmlns/scr/v1.1.0" name="org.insilico.sbmlsheets.services.provider.SBMLDocumentLoader">
<property name="service.context.key" value="org.sbml.jsbml.SBMLDocument"/>
<service>
<provide interface="org.eclipse.e4.core.contexts.IContextFunction"/>
</service>
<implementation class="org.insilico.sbmlsheets.services.provider.SBMLDocumentLoader"/>
</scr:component>
7 changes: 7 additions & 0 deletions ...lico.sbmlsheets/OSGI-INF/org.insilico.sbmlsheets.services.provider.SBMLEditorProvider.xml
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<?xml version="1.0" encoding="UTF-8"?>
<scr:component xmlns:scr="http://www.osgi.org/xmlns/scr/v1.1.0" name="org.insilico.sbmlsheets.services.provider.SBMLEditorProvider">
<service>
<provide interface="org.eclipse.fx.code.editor.fx.e4.EditorClassURLProvider"/>
</service>
<implementation class="org.insilico.sbmlsheets.services.provider.SBMLEditorProvider"/>
</scr:component>
7 changes: 7 additions & 0 deletions ...silico.sbmlsheets/OSGI-INF/org.insilico.sbmlsheets.services.provider.SBMLIconProvider.xml
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<?xml version="1.0" encoding="UTF-8"?>
<scr:component xmlns:scr="http://www.osgi.org/xmlns/scr/v1.1.0" name="org.insilico.sbmlsheets.services.provider.SBMLIconProvider">
<service>
<provide interface="org.eclipse.fx.code.editor.services.FileIconProvider"/>
</service>
<implementation class="org.insilico.sbmlsheets.services.provider.SBMLIconProvider"/>
</scr:component>
8 changes: 8 additions & 0 deletions ...lsheets/OSGI-INF/org.insilico.sbmlsheets.services.provider.SheetProjectDocumentLoader.xml
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<?xml version="1.0" encoding="UTF-8"?>
<scr:component xmlns:scr="http://www.osgi.org/xmlns/scr/v1.1.0" name="org.insilico.sbmlsheets.services.provider.SheetProjectDocumentLoader">
<property name="service.context.key" value="org.insilico.sbmlsheets.core.TableEditor"/>
<service>
<provide interface="org.eclipse.e4.core.contexts.IContextFunction"/>
</service>
<implementation class="org.insilico.sbmlsheets.services.provider.SheetProjectDocumentLoader"/>
</scr:component>
7 changes: 7 additions & 0 deletions ...lsheets/OSGI-INF/org.insilico.sbmlsheets.services.provider.SheetProjectEditorProvider.xml
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<?xml version="1.0" encoding="UTF-8"?>
<scr:component xmlns:scr="http://www.osgi.org/xmlns/scr/v1.1.0" name="org.insilico.sbmlsheets.services.provider.SheetProjectEditorProvider">
<service>
<provide interface="org.eclipse.fx.code.editor.fx.e4.EditorClassURLProvider"/>
</service>
<implementation class="org.insilico.sbmlsheets.services.provider.SheetProjectEditorProvider"/>
</scr:component>
8 changes: 8 additions & 0 deletions ...mlsheets/OSGI-INF/org.insilico.sbmlsheets.services.provider.SpreadsheetDocumentLoader.xml
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<?xml version="1.0" encoding="UTF-8"?>
<scr:component xmlns:scr="http://www.osgi.org/xmlns/scr/v1.1.0" name="org.insilico.sbmlsheets.services.provider.SpreadsheetDocumentLoader">
<property name="service.context.key" value="org.insilico.sbmlsheets.core.Spreadsheet"/>
<service>
<provide interface="org.eclipse.e4.core.contexts.IContextFunction"/>
</service>
<implementation class="org.insilico.sbmlsheets.services.provider.SpreadsheetDocumentLoader"/>
</scr:component>
7 changes: 7 additions & 0 deletions ...mlsheets/OSGI-INF/org.insilico.sbmlsheets.services.provider.SpreadsheetEditorProvider.xml
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<?xml version="1.0" encoding="UTF-8"?>
<scr:component xmlns:scr="http://www.osgi.org/xmlns/scr/v1.1.0" name="org.insilico.sbmlsheets.services.provider.SpreadsheetEditorProvider">
<service>
<provide interface="org.eclipse.fx.code.editor.fx.e4.EditorClassURLProvider"/>
</service>
<implementation class="org.insilico.sbmlsheets.services.provider.SpreadsheetEditorProvider"/>
</scr:component>
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