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Error opening project: caused by null

Ramon Joly
Greenhorn

Joined: May 07, 2013
Posts: 5
Dear all,
In a program which is based on java I got this error. I'm not programmer and waiting for your help. Here is a part of log file:

05/07/13 at 4:49:45 PM, JST INFO [AWT-EventQueue-0] - admin : logged in successfully...
05/07/13 at 4:49:48 PM, JST DEBUG [AWT-EventQueue-0] - Received OpenProjectCommand.
05/07/13 at 4:49:54 PM, JST ERROR [Thread-5] - Error while opening project: ATI
com.apldbio.csa.DataStore.DataAccessException: Error opening project: ATI caused by null
at com.apldbio.csa.DataStore.DataManager.openProject(DataManager.java:1142)
at com.apldbio.csa.Managers.ProjectManager.ProjectManager.openProject(ProjectManager.java:1364)
at com.apldbio.csa.Managers.ProjectManager.ProjectManager$2.run(ProjectManager.java:1331)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.IllegalArgumentException
at com.apldbio.gacomponents.datamodel.biology.ElectropherogramSequenceMapping.<init>(ElectropherogramSequenceMapping.java:51)
at com.apldbio.csa.DataStore.CSASampleFileIO.getElectropherogramSequenceMapping(CSASampleFileIO.java:1700)
at com.apldbio.csa.DataStore.DataManager.refreshPLOC(DataManager.java:2824)
at com.apldbio.csa.DataStore.DataManager.openProject(DataManager.java:1072)
... 3 more
Joe Ess
Bartender

Joined: Oct 29, 2001
Posts: 8997
    
    9

Welcome to the JavaRanch.
How did you come to run this program if you are not a programmer? Was the program working and something changed? Given that the exception takes place in an AWT queue, what makes you think this is a Struts problem (AWT is for desktop applications, Struts is for web applications).
Any information you can give us is helpful. The complete error message, for instance. The better question you ask, the more help we can be.


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Ramon Joly
Greenhorn

Joined: May 07, 2013
Posts: 5
Joe Ess wrote:Welcome to the JavaRanch.
How did you come to run this program if you are not a programmer? Was the program working and something changed? Given that the exception takes place in an AWT queue, what makes you think this is a Struts problem (AWT is for desktop applications, Struts is for web applications).
Any information you can give us is helpful. The complete error message, for instance. The better question you ask, the more help we can be.


Thank you very much for your help.
The program itself is a GUI windows desktop application and working. I have made projects on this program but when I try to open some project it gives this error. Each project is a sequence alignment.
Here is screenshot of error message.



Here is complete log file.
webpage

BTW, sorry! I open thread in wrong place. Moderators may move to right section.
Paul Clapham
Bartender

Joined: Oct 14, 2005
Posts: 18991
    
    8

I moved the thread to the forum about Swing and its relatives.

And to make it easier for others to help, let me just say that the linked image is just a dialog box which says "Error while opening project tRALS. Please see the SeqScape log file for details."

Basically, the error message is straightforward. It tells you to look in the log file. But if you aren't the programmer of the application, then you can't be expected to debug problems it's having. I suggest you track down the person who is the programmer, or the person who is supposed to provide support for it, or some other person with that sort of responsibility, and ask them for help.

Edit: Oh, wait a minute, I didn't notice you also posted a link to the data from the log file. It would have been much easier if you had just copied and pasted the data here. Anyway... is that XML file with the "knownInsertionStylm" element your doing? If so then my guess is that its name is actually supposed to be "knownInsertionStyle". Probably there's an end tag for "knownInsertionStyle" which doesn't match the start tag for "knownInsertionStylm".

If you don't have any control over that XML then again I suggest you track down somebody who does.
Ramon Joly
Greenhorn

Joined: May 07, 2013
Posts: 5
Paul Clapham wrote:I moved the thread to the forum about Swing and its relatives.

And to make it easier for others to help, let me just say that the linked image is just a dialog box which says "Error while opening project tRALS. Please see the SeqScape log file for details."

Basically, the error message is straightforward. It tells you to look in the log file. But if you aren't the programmer of the application, then you can't be expected to debug problems it's having. I suggest you track down the person who is the programmer, or the person who is supposed to provide support for it, or some other person with that sort of responsibility, and ask them for help.

Edit: Oh, wait a minute, I didn't notice you also posted a link to the data from the log file. It would have been much easier if you had just copied and pasted the data here. Anyway... is that XML file with the "knownInsertionStylm" element your doing? If so then my guess is that its name is actually supposed to be "knownInsertionStyle". Probably there's an end tag for "knownInsertionStyle" which doesn't match the start tag for "knownInsertionStylm".

If you don't have any control over that XML then again I suggest you track down somebody who does.

Thank you for support.
The "ITS_Dalbergia.xml" is corresponds to another project file which I'm missing from the list for unknown reason. The project which I'm not able to open is tRALS. Each projects have its own .xml file, a kind of reference.
Paul Clapham
Bartender

Joined: Oct 14, 2005
Posts: 18991
    
    8

Here's a copy of the logs from that paste place:



SeqScape 05/08/13 at 10:45:44 AM, JST DEBUG [Thread-1] - Log4J configured!
SeqScape.MESSAGEMEDIATOR 05/08/13 at 10:45:44 AM, JST DEBUG [Thread-1] - Starting up server socket!
SeqScape 05/08/13 at 10:45:45 AM, JST ERROR [main] - Error reading 'D:\AppliedBiosystems\New folder (2)\data\DataStore\master\projects\ITS_Dalbergia.xml': The file does not conform to CSA Document Type Definition.Error: org.xml.sax.SAXParseException; lineNumber: 2; columnNumber: 4420; The element type "knownInsertionStylm" must be terminated by the matching end-tag "</knownInsertionStylm>".
SeqScape 05/08/13 at 10:45:45 AM, JST ERROR [main] - Unable to load Project file D:\AppliedBiosystems\New folder (2)\data\DataStore\master\projects\ITS_Dalbergia.xml
com.apldbio.csa.DataStore.DataAccessException: null caused by Error reading 'D:\AppliedBiosystems\New folder (2)\data\DataStore\master\projects\ITS_Dalbergia.xml': The file does not conform to CSA Document Type Definition.Error: The element type "knownInsertionStylm" must be terminated by the matching end-tag "</knownInsertionStylm>".
at com.apldbio.csa.DataStore.CSAXMLReader.getProject(CSAXMLReader.java:365)
at com.apldbio.csa.DataStore.CSAXMLReader.getProjects(CSAXMLReader.java:382)
at com.apldbio.csa.DataStore.DataManager.getProjects(DataManager.java:999)
at com.apldbio.csa.DataStore.DataManager.getInstance(DataManager.java:282)
at com.apldbio.csa.Managers.AccessManager.AccessManager.<init>(AccessManager.java:181)
at com.apldbio.csa.Managers.AccessManager.AccessManager.getInstance(AccessManager.java:53)
at com.apldbio.csa.CSA.<init>(CSA.java:270)
at com.apldbio.csa.CSA.main(CSA.java:463)
Caused by: com.apldbio.csa.DataStore.DataAccessException: Error reading 'D:\AppliedBiosystems\New folder (2)\data\DataStore\master\projects\ITS_Dalbergia.xml': The file does not conform to CSA Document Type Definition.Error: The element type "knownInsertionStylm" must be terminated by the matching end-tag "</knownInsertionStylm>".
at com.apldbio.csa.DataStore.CSAXMLReader.parse(CSAXMLReader.java:4230)
at com.apldbio.csa.DataStore.CSAXMLReader.getRootNode(CSAXMLReader.java:4245)
at com.apldbio.csa.DataStore.CSAXMLReader.getProject(CSAXMLReader.java:361)
... 7 more
SeqScape 05/08/13 at 10:45:46 AM, JST DEBUG [main] - Succeeded in getting all Feature's Access Level
SeqScape 05/08/13 at 10:45:46 AM, JST DEBUG [main] - Access Manager instantiated
SeqScape 05/08/13 at 10:45:46 AM, JST DEBUG [main] - Succeeded on getting Audit List
SeqScape 05/08/13 at 10:45:46 AM, JST DEBUG [main] - AuditManager Instatiated
SeqScape 05/08/13 at 10:45:49 AM, JST INFO [AWT-EventQueue-0] - seqscape : logged in successfully...
SeqScape 05/08/13 at 10:45:53 AM, JST DEBUG [AWT-EventQueue-0] - Received OpenProjectCommand.
SeqScape 05/08/13 at 10:45:59 AM, JST ERROR [Thread-5] - Error while opening project: tRALS
com.apldbio.csa.DataStore.DataAccessException: Error opening project: tRALS caused by null
at com.apldbio.csa.DataStore.DataManager.openProject(DataManager.java:1142)
at com.apldbio.csa.Managers.ProjectManager.ProjectManager.openProject(ProjectManager.java:1364)
at com.apldbio.csa.Managers.ProjectManager.ProjectManager$2.run(ProjectManager.java:1331)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.IllegalArgumentException
at com.apldbio.gacomponents.datamodel.biology.ElectropherogramSequenceMapping.<init>(ElectropherogramSequenceMapping.java:51)
at com.apldbio.csa.DataStore.CSASampleFileIO.getElectropherogramSequenceMapping(CSASampleFileIO.java:1700)
at com.apldbio.csa.DataStore.DataManager.refreshPLOC(DataManager.java:2824)
at com.apldbio.csa.DataStore.DataManager.openProject(DataManager.java:1072)
... 3 more


Paul Clapham
Bartender

Joined: Oct 14, 2005
Posts: 18991
    
    8

Then maybe the error is here:

Caused by: java.lang.IllegalArgumentException
at com.apldbio.gacomponents.datamodel.biology.ElectropherogramSequenceMapping.<init>(ElectropherogramSequenceMapping.java:51)

Ramon Joly
Greenhorn

Joined: May 07, 2013
Posts: 5
Paul Clapham wrote:Then maybe the error is here:

Caused by: java.lang.IllegalArgumentException
at com.apldbio.gacomponents.datamodel.biology.ElectropherogramSequenceMapping.<init>(ElectropherogramSequenceMapping.java:51)


What this is mean? :(
Paul Clapham
Bartender

Joined: Oct 14, 2005
Posts: 18991
    
    8

You're not the programmer, right?

So there's no point in telling you what it means, because you wouldn't be able to do anything about it.

Follow my earlier advice about finding somebody who supports that product.
Ramon Joly
Greenhorn

Joined: May 07, 2013
Posts: 5
Paul Clapham wrote:You're not the programmer, right?

So there's no point in telling you what it means, because you wouldn't be able to do anything about it.

Follow my earlier advice about finding somebody who supports that product.


Right. I'll try to find someone to ask. Meanwhile here is xml file for the project. It may have some clue.
Campbell Ritchie
Sheriff

Joined: Oct 13, 2005
Posts: 40052
    
  28
Ramon Joly wrote: . . . xml file for the project. It may have some clue. . . .
Not unless you divide it into lines and indent it and keep the lines shorter than 120 characters. Nobody can read that unformatted XML.
 
I agree. Here's the link: http://aspose.com/file-tools
 
subject: Error opening project: caused by null