Help:Known problems

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===WikiPathways Editor Usage===
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The WikiPathways Editor is the PathVisio program.
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On this page you'll find some known problems with WikiPathways.  
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* If you have never edited or built a pathway model before, we would advise you to use our online learning tool [http://academy.wikipathways.org/ WikiPathways Academy] first.
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'''If your problem is not on this list''', please check our '''[http://www.bigcat.unimaas.nl/tracprojects/pathvisio bug tracker]''' or send an email to our  '''[http://groups.google.com/group/wikipathways-dev Google group]'''.
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* If you directly want to start editing, please download the [https://www.pathvisio.org/downloads/ local PathVisio installation] from the PathVisio website, and install the [https://www.pathvisio.org/plugin/wikipathways-plugin/ WikiPathways plugin] from within PathVisio.
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Please be aware that new users (starting in 2019) need to request access to use the WikiPathways plugin; which can be done [http://plugins.pathvisio.org/wp-client/request-webservice-access/ here] or through sending a message to our team on our [https://groups.google.com/forum/#!forum/wikipathways-discuss google discussion forum].
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* Save your pathway by clicking '''Plugins > WikiPathways > Update'''. You will be asked to describe your edits.
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* That's it!
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===Java Security Settings===
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To enable direct-launch of the WikiPathways editor on MacOS, it is necessary to add the Java Security exceptions for WikiPathways. To do this, go to '''System Preferences > Java > Security'''. In the '''Exceptions Site List''', add both https://www.wikipathways.org and https://wikipathways.org. [https://www.youtube.com/watch?v=uUH1JVgnkug This video] shows how to add security exceptions. More details on MacOS Java Security are available [https://www.java.com/en/download/help/jcp_security.xml here].
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===Ignorable Java Warnings===
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Even when your setup is configured properly, you may still see Java Security Warnings.  They look scary, but they are harmless. These are simply due to the fact that we refuse to pay Apple to authorize our free and open source software. We are pursuing a free alternative through a non-profit collaboration. But, ultimately, if the warning says, "Location: <nowiki>http://wikipathways.org</nowiki>" then you can click through it and get to our Java Applet editor. Here's a [https://www.youtube.com/watch?v=JyaLTAAn9SQ super short video] showing errors you can expect and safely ignore.
=== No Java installed ===
=== No Java installed ===
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You need to have [http://java.sun.com Java] installed to be able to edit pathways. If you only see a grey box when you click the edit button below the pathway image, please check if you have Java installed (version JSE 5 or above). You can download Java [http://java.sun.com/javase/downloads/?intcmp=1281 here].
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You need to have [http://java.sun.com Java] installed to be able to edit pathways. If you only see a grey box when you click the edit button below the pathway image, please check if you have Java installed (version JSE 5 or above). You can test if Java is working in your browser [http://www.java.com/en/download/testjava.jsp here] and download Java [http://java.sun.com/javase/downloads/?intcmp=1281 here].
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=== Javascipt disabled ===
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=== Javascript disabled ===
You need to have javascript enabled in your browser. [http://www.google.com/support/bin/answer.py?answer=23852 Click here] to see how to enable javascript for your browser.
You need to have javascript enabled in your browser. [http://www.google.com/support/bin/answer.py?answer=23852 Click here] to see how to enable javascript for your browser.
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=== Strange error while starting Java ===
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Sometimes a dialog with "NullPointerException" or "InvocationTargetException" appears when you try to start the edit applet. In this case it may help to clear the Java Applet Cache. In Windows XP, you do this as follows:
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# Go to '''Start -> Control Panel'''
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# (In Classic View) click on the icon Labeled '''Java'''
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# In the Java Control Panel dialog, in the general tab, under the heading '''Temporary Internet Files''' click on '''Settings'''
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# Click '''Delete Files'''. This will only delete temporary files that are safe to delete.
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# Close the browser completely, then try WikiPathways again.
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On a Mac:
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# Open /Applications/Utilities/Java Preferences
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# Click on Network tab
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# Click on '''Delete Files''' and click '''OK'''
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# Close the browser completely, then try WikiPathways again
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=== Editor does not load and you just see a black window ===
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In this case it might help to clear the Java Applet Cache. In Windows XP, you do this as follows:
 +
# Go to '''Start -> Control Panel'''
 +
# (In Classic View) click on the icon Labeled '''Java'''
 +
# In the Java Control Panel dialog, in the general tab, under the heading '''Temporary Internet Files''' click on '''Settings'''
 +
# Click '''Delete Files'''. This will only delete temporary files that are safe to delete.
 +
# Close the browser completely, then try WikiPathways again.
=== Wrong Java version on Ubuntu ===
=== Wrong Java version on Ubuntu ===
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By default the Ubuntu linux distribution comes with the gij (GNU libgcj) Java virtual machine. In order to make wikipathways work correctly, you will need to replace this with Sun's JVM. You can do this by installing the packages '''<code>sun-java5-jre</code>''' and '''<code>sun-java5-plugin</code>''' or '''<code>sun-java6-jre</code>''' and '''<code>sun-java6-plugin</code>'''.
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Older Ubuntu linux distribution came with the gij (GNU libgcj) Java virtual machine, while newer versions come with the icedtea plugins. In order to make WikiPathways work correctly, you will need to replace this with Oracle's JVM. Details on how to install this can be found [https://help.ubuntu.com/community/Java here].
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=== No SVG viewer in Internet Explorer ===
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===Application blocked by Security Setting===
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When you are using Internet Explorer you need to install an SVG viewer to view the pathway images at full size. Go to [http://www.adobe.com/svg/viewer/install/main.html Adobe SVG viewer] to download an SVG viewer for Internet Explorer.
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In the latest Java update the security settings for self-signed applications have been adapted (Java 7 Update 51). Self-Signed applications, like Pathvisio, are blocked on high security level.
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For details see [http://www.pathvisio.org/documentation/faqs/#SecurityError the Pathvisio FAQ]
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=== Other Problems ===
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'''If your problem is not on this list''', please check our '''[https://github.com/pathvisio/pathvisio/issues bug tracker]''' or send an email to our  '''[http://groups.google.com/group/wikipathways-discuss Google group]'''.
<p>[[:Help:Contents|Return to Help Contents]]</p>
<p>[[:Help:Contents|Return to Help Contents]]</p>
<p>[[:Help:Tutorial|Continue to Tutorials]]</p>
<p>[[:Help:Tutorial|Continue to Tutorials]]</p>

Current revision

Contents

WikiPathways Editor Usage

The WikiPathways Editor is the PathVisio program.

  • If you have never edited or built a pathway model before, we would advise you to use our online learning tool WikiPathways Academy first.

Please be aware that new users (starting in 2019) need to request access to use the WikiPathways plugin; which can be done here or through sending a message to our team on our google discussion forum.

  • Save your pathway by clicking Plugins > WikiPathways > Update. You will be asked to describe your edits.
  • That's it!

Java Security Settings

To enable direct-launch of the WikiPathways editor on MacOS, it is necessary to add the Java Security exceptions for WikiPathways. To do this, go to System Preferences > Java > Security. In the Exceptions Site List, add both https://www.wikipathways.org and https://wikipathways.org. This video shows how to add security exceptions. More details on MacOS Java Security are available here.

Ignorable Java Warnings

Even when your setup is configured properly, you may still see Java Security Warnings. They look scary, but they are harmless. These are simply due to the fact that we refuse to pay Apple to authorize our free and open source software. We are pursuing a free alternative through a non-profit collaboration. But, ultimately, if the warning says, "Location: http://wikipathways.org" then you can click through it and get to our Java Applet editor. Here's a super short video showing errors you can expect and safely ignore.

No Java installed

You need to have Java installed to be able to edit pathways. If you only see a grey box when you click the edit button below the pathway image, please check if you have Java installed (version JSE 5 or above). You can test if Java is working in your browser here and download Java here.

Javascript disabled

You need to have javascript enabled in your browser. Click here to see how to enable javascript for your browser.

Strange error while starting Java

Sometimes a dialog with "NullPointerException" or "InvocationTargetException" appears when you try to start the edit applet. In this case it may help to clear the Java Applet Cache. In Windows XP, you do this as follows:

  1. Go to Start -> Control Panel
  2. (In Classic View) click on the icon Labeled Java
  3. In the Java Control Panel dialog, in the general tab, under the heading Temporary Internet Files click on Settings
  4. Click Delete Files. This will only delete temporary files that are safe to delete.
  5. Close the browser completely, then try WikiPathways again.

On a Mac:

  1. Open /Applications/Utilities/Java Preferences
  2. Click on Network tab
  3. Click on Delete Files and click OK
  4. Close the browser completely, then try WikiPathways again

Editor does not load and you just see a black window

In this case it might help to clear the Java Applet Cache. In Windows XP, you do this as follows:

  1. Go to Start -> Control Panel
  2. (In Classic View) click on the icon Labeled Java
  3. In the Java Control Panel dialog, in the general tab, under the heading Temporary Internet Files click on Settings
  4. Click Delete Files. This will only delete temporary files that are safe to delete.
  5. Close the browser completely, then try WikiPathways again.

Wrong Java version on Ubuntu

Older Ubuntu linux distribution came with the gij (GNU libgcj) Java virtual machine, while newer versions come with the icedtea plugins. In order to make WikiPathways work correctly, you will need to replace this with Oracle's JVM. Details on how to install this can be found here.

Application blocked by Security Setting

In the latest Java update the security settings for self-signed applications have been adapted (Java 7 Update 51). Self-Signed applications, like Pathvisio, are blocked on high security level. For details see the Pathvisio FAQ

Other Problems

If your problem is not on this list, please check our bug tracker or send an email to our Google group.

Return to Help Contents

Continue to Tutorials

Retrieved from "https://classic.wikipathways.org/index.php/Help:Known_problems"
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