Bug importing file and when starting iBioSim

[PhysicsTeacher13]

WARNING: Some external components are missing or have problems. You may continue but with some loss of functionality. GeneNet not functional (3). WARN (XMLNodeReader.java:261) - The type of String '' on the element constraint (Constraint) is unknown! Some data might be lost. javax.xml.stream.XMLStreamException: JSBML could not properly read file G:\Backup_2024_2025\Genetics\Eco1C1G1T1_collection.xml. Please check if it contains valid SBML. If you think it is valid, please submit a bug report to the bug tracker of JSBML. at org.sbml.jsbml.xml.stax.SBMLReader.readSBML(SBMLReader.java:325) at org.sbml.jsbml.SBMLReader.readSBML(SBMLReader.java:116) at org.sbml.jsbml.SBMLReader.read(SBMLReader.java:105) at org.sbml.jsbml.SBMLReader.read(SBMLReader.java:92) at edu.utah.ece.async.ibiosim.dataModels.biomodel.util.SBMLutilities.readSBML(SBMLutilities.java:5766) at edu.utah.ece.async.ibiosim.gui.Gui.importCombineArchive(Gui.java:4247) at edu.utah.ece.async.ibiosim.gui.Gui.importArchive(Gui.java:4412) at edu.utah.ece.async.ibiosim.gui.Gui.actionPerformed(Gui.java:2370) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:374) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1029) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1073) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398) at java.desktop/java.awt.Component.processEvent(Component.java:6386) at java.desktop/java.awt.Container.processEvent(Container.java:2266) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90) ERROR (SBMLDocument.java:561) - There was an error accessing the sbml online validator! ERROR (SBMLDocument.java:561) - There was an error accessing the sbml online validator! WARN (XMLNodeReader.java:261) - The type of String '' on the element constraint (Constraint) is unknown! Some data might be lost. javax.xml.stream.XMLStreamException: JSBML could not properly read file G:\Backup_2024_2025\Genetics\Eco1C1G1T1_collection.xml. Please check if it contains valid SBML. If you think it is valid, please submit a bug report to the bug tracker of JSBML. at org.sbml.jsbml.xml.stax.SBMLReader.readSBML(SBMLReader.java:325) at org.sbml.jsbml.SBMLReader.readSBML(SBMLReader.java:116) at org.sbml.jsbml.SBMLReader.read(SBMLReader.java:105) at org.sbml.jsbml.SBMLReader.read(SBMLReader.java:92) at edu.utah.ece.async.ibiosim.dataModels.biomodel.util.SBMLutilities.readSBML(SBMLutilities.java:5766) at edu.utah.ece.async.ibiosim.gui.Gui.importSBMLFile(Gui.java:3712) at edu.utah.ece.async.ibiosim.gui.Gui.importCombineArchive(Gui.java:4266) at edu.utah.ece.async.ibiosim.gui.Gui.importArchive(Gui.java:4412) at edu.utah.ece.async.ibiosim.gui.Gui.actionPerformed(Gui.java:2370) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:374) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1029) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1073) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398) at java.desktop/java.awt.Component.processEvent(Component.java:6386) at java.desktop/java.awt.Container.processEvent(Container.java:2266) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90) ERROR (SBMLDocument.java:561) - There was an error accessing the sbml online validator! ERROR (SBMLDocument.java:561) - There was an error accessing the sbml online validator!

[cjmyers]

You can ignore the GeneNet error message. As far as the other error message, can you provide more details about what you were doing when you received this error?

[PhysicsTeacher13]

Importing week2 assignment. I noticed one time I downloaded the file it was two different sizes one was 107KB and then the same file was 10 KB maybe there was an issue with the file on Coursera Also I can’t connect to the sysbiohub so I had to download each part separately. Is there network permissions I need besides my account login?

On Wed, Sep 25, 2024 at 10:50 AM cjmyers @.***> wrote:

You can ignore the GeneNet error message. As far as the other error message, can you provide more details about what you were doing when you received this error?

— Reply to this email directly, view it on GitHub https://github.com/MyersResearchGroup/iBioSim/issues/634#issuecomment-2374320923, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFMZPTXP7OSVO7K7XQGGPCDZYLETRAVCNFSM6AAAAABO2LSAV6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZUGMZDAOJSGM . You are receiving this because you authored the thread.Message ID: @.***>

[PhysicsTeacher13]

I am getting a message when trying to use synbiohub for parts. Javax.net.ssl. SSL Handshake Exception: PKIX path build failed: sun.security.provider.certpath. SunCertPathBuilderException: unable to find valid certification path to requested target

On Wed, Sep 25, 2024 at 12:59 PM Wilfred Henry @.***> wrote:

Importing week2 assignment. I noticed one time I downloaded the file it was two different sizes one was 107KB and then the same file was 10 KB maybe there was an issue with the file on Coursera Also I can’t connect to the sysbiohub so I had to download each part separately. Is there network permissions I need besides my account login?

On Wed, Sep 25, 2024 at 10:50 AM cjmyers @.***> wrote:

You can ignore the GeneNet error message. As far as the other error message, can you provide more details about what you were doing when you received this error?

— Reply to this email directly, view it on GitHub https://github.com/MyersResearchGroup/iBioSim/issues/634#issuecomment-2374320923, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFMZPTXP7OSVO7K7XQGGPCDZYLETRAVCNFSM6AAAAABO2LSAV6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZUGMZDAOJSGM . You are receiving this because you authored the thread.Message ID: @.***>

[cjmyers]

Sorry for your issues with SynBioHub. It is possible that SynBioHub was either down or in the process of a restart when you had these issues. Please try logging out of SynBioHub, logging in again, and trying to download parts again.

[PhysicsTeacher13]

No luck.

I ended up downloading the collection and then adding it to iBioSim as a local collection

On Thu, Sep 26, 2024 at 10:58 AM cjmyers @.***> wrote:

Sorry for your issues with SynBioHub. It is possible that SynBioHub was either down or in the process of a restart when you had these issues. Please try logging out of SynBioHub, logging in again, and trying to download parts again.

— Reply to this email directly, view it on GitHub https://github.com/MyersResearchGroup/iBioSim/issues/634#issuecomment-2377217558, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFMZPTS4QVR7AMEECATO7MTZYQOIVAVCNFSM6AAAAABO2LSAV6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZXGIYTONJVHA . You are receiving this because you authored the thread.Message ID: @.***>

[cjmyers]

Glad you found a workaround. Sorry for the trouble.