structure table contains newer data version

I have everything working again with postgresql 9.1.  Now back to the original problem that I was trying to solve,
but remains after upgrading postgresql and jchem.   I am trying to access the database through the:
.../JChem/examples/db_search program you provided.  See the error messages below.  Any ideas.  I searched 
the forum for similar questions and did not find any.  Forgive me (and point me to the posting) if someone 
submitted this topic before.

Thanks for your help,
Dick


JChem version : 5.5.1.0

JVM : Sun Microsystems Inc. 1.6.0_31

OS  : i386 Linux 2.6.32-42-generic





Stack trace:

------------





chemaxon.jchem.db.DatabaseSearchException: The structure table contains newer data version that this program version can handle. Please use a later version.

	at chemaxon.jchem.db.JChemSearch.initTable(JChemSearch.java:2622)

	at chemaxon.jchem.db.JChemSearch.init(JChemSearch.java:3479)

	at chemaxon.jchem.db.JChemSearch.search1(JChemSearch.java:1979)

	at chemaxon.jchem.db.JChemSearch.search(JChemSearch.java:1879)

	at chemaxon.jchem.db.JChemSearch.access$2800(JChemSearch.java:121)

	at chemaxon.jchem.db.JChemSearch$SearchThread.run(JChemSearch.java:853)

You have created the table with a newer JChem version (JChemManager), than the version you are trying to use in your web application (5.5.1,0, pretty old).

Please make sure the versions are the same.

Best regards,

Szilard

Thanks for the suggestion.  I completely purged the system of all postresql files and JChem files, and reinstalled.  I think part of my problem was files hanging around from old versions.

Now I have a different problem, the search seems to go alright, but when it tries to load the molecules into the viewer I get the following error:

 

JChem version : 5.10.2

JVM : Sun Microsystems Inc. 1.6.0_31

OS  : i386 Linux 2.6.32-42-generic





Stack trace:

------------





chemaxon.formats.MolFormatException: Could not read molecule from byte array.

	at chemaxon.jchem.db.JChemSearch.getMolecule(JChemSearch.java:6350)

	at chemaxon.jchem.db.JChemSearch.fetchHitsAsMolecules(JChemSearch.java:3547)

	at chemaxon.jchem.db.JChemSearch.getHitsAsHitDisplayTool(JChemSearch.java:3389)

	at chemaxon.jchem.db.JChemSearch.getHitsAsMolecules(JChemSearch.java:3315)

	at org.apache.jsp.examples.db_005fsearch.searchresults_jsp._jspService(searchresults_jsp.java:1005)

	at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)

	at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

	at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:377)

	at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)

	at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)

	at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)

	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

	at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:646)

	at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:436)

	at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:374)

	at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:302)

	at org.apache.jasper.runtime.PageContextImpl.doForward(PageContextImpl.java:706)

	at org.apache.jasper.runtime.PageContextImpl.forward(PageContextImpl.java:677)

	at org.apache.jsp.examples.db_005fsearch.searching_jsp._jspService(searching_jsp.java:558)

	at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)

	at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

	at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:377)

	at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)

	at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)

	at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)

	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)

	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)

	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)

	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)

	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)

	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)

	at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)

	at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)

	at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)

	at java.lang.Thread.run(Thread.java:662)

Caused by: chemaxon.formats.MolFormatException: Cannot create record reader for the "chime" format

	at chemaxon.marvin.io.MRecordImporter.(MRecordImporter.java:278)

	at chemaxon.formats.MolImporter.init(MolImporter.java:583)

	at chemaxon.formats.MolImporter.(MolImporter.java:138)

	at chemaxon.util.MolHandler.importMol(MolHandler.java:658)

	at chemaxon.util.MolHandler.setMolecule(MolHandler.java:178)

	at chemaxon.util.MolHandler.(MolHandler.java:111)

	at chemaxon.jchem.db.JChemSearch.getMolecule(JChemSearch.java:6348)

	... 37 more

Hi,

It seems like a structure source you have imported / inserted into the database is not recognized properly as an individual record.

This may be either a bug or incorrect usage.

- How did you import the structures ? E.g. did you use JChem Manager, or did you do it programmatically via Updatehandler , etc ?

- Can you reproduce this with a new table? Could you send us the structures and necessary steps to reproduce ?

I suggest to zip the structures before sending.

If the structures are confidential please send it to our support e-mail addres referencing this topic.

In case too big for e-mail we can provide alternitve means to upload - ask on our support e-mail.

Best regards,

Szilard

Thanks, Szilard.

I am probably doing something grosly wrong - haveing no luck.  I presume a smiles file should also work (according to the documentation).  I would like to get the rest of the data in the file into the db, but will settle for the structure and identifier (ddd_name).  I have tried cutting out all columns except smiles and ddd_name.  That did not work either.

Thanks again for you patience and help.

Dick

Dick,

I'm afraid we cannot help you more unless you provide the answers and data requested above.

Thank you,

Szilard