Errors with setup of non-AWS Bio4j v0.9

[Alexander Stoddard]

 

Hello, 

I am naively attempting to get a non-AWS, i.e. entirely locally installed on a physical server, instance of Bio4j 0.9 up and running following the instructions,starting from point 6 at:

https://github.com/bio4j/Bio4j/wiki/Importing-bio4j

The documentation implies java 1.6 is used but this appears out of date,  with version number of 51 on the class files in the ExecuteBio4jTool.jar requiring java 1.7.

Executing the jar file with java1.7 as below produces the following errors:

java -d64 -Xmx30G -jar ExecuteBio4jTool.jar executionsBio4j.xml

Oct 21, 2013 12:40:58 PM org.openide.util.Exceptions printStackTrace

SEVERE: null

java.io.FileNotFoundException: neo4j.properties (No such file or directory)

at java.io.FileInputStream.open(Native Method)

at java.io.FileInputStream.<init>(FileInputStream.java:138)

at org.neo4j.helpers.collection.MapUtil.load(MapUtil.java:214)

at com.era7.bioinfo.bio4j.tools.GetNodeAndRelsStatistics.main(GetNodeAndRelsStatistics.java:106)

at com.era7.bioinfo.bio4j.tools.GetNodeAndRelsStatistics.execute(GetNodeAndRelsStatistics.java:86)

at com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile.main(ExecuteFromFile.java:66)

at com.era7.bioinfo.bio4j.tools.ExecuteBio4jTool.main(ExecuteBio4jTool.java:28)

Oct 21, 2013 12:40:58 PM com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile main

SEVERE: null

java.lang.NullPointerException

at com.era7.bioinfo.bio4j.tools.GetNodeAndRelsStatistics.main(GetNodeAndRelsStatistics.java:304)

at com.era7.bioinfo.bio4j.tools.GetNodeAndRelsStatistics.execute(GetNodeAndRelsStatistics.java:86)

at com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile.main(ExecuteFromFile.java:66)

at com.era7.bioinfo.bio4j.tools.ExecuteBio4jTool.main(ExecuteBio4jTool.java:28)

Is the ExecuteBio4jTool.jar file entirely self contained or do I need a neo4j installation set up and configured separately?

Why does the documentation have the ExecuteBio4jTool.jar running with sudo? 

Thank you for your help,

Alex

[Pablo Pareja Tobes]

Hi Alex,

Thanks for your interest in Bio4j project ;)

You're right, some of the information provided in the Importing Bio4j section was out of date. I just updated it so that it reflects the current situation, getting rid of the references to both Java 1.6 and the sudo command (that command is not really necessary as long as you have write permissions in the folder where you want to import the database).

Regarding the issue you were getting, the reason is simply that all executions were commented out but the last one which is a statistics retrieving program that needs and extra configuration file called neo4j.properties. I just updated the file in github https://github.com/bio4j/Bio4j/blob/master/executionsBio4j.xml so that now all executions are uncommented but this last one which is not really necessary to import the data.

> Is the ExecuteBio4jTool.jar file entirely self contained or do I need a neo4j installation set up and configured separately?

Yeah it should be entirely self contained, there's no need to have a neo4j installation set up.

> Why does the documentation have the ExecuteBio4jTool.jar running with sudo? 

As I mentioned before that's not really necessary, it comes from copy-pasting the command I normally use with the default configuration we have in EC2.

Hope this helps.

Cheers,

Pablo

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[Sandeep Shantharam]

Hi,

I am getting the same error as the above on a Non-AWS server build;

Feb 21, 2014 1:53:24 PM com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile main

SEVERE: null

java.lang.ClassNotFoundException: com.ohnosequences.bio4j.neo4j.programs.InitBio4jDB

        at java.net.URLClassLoader$1.run(URLClassLoader.java:366)

        at java.net.URLClassLoader$1.run(URLClassLoader.java:355)

        at java.security.AccessController.doPrivileged(Native Method)

        at java.net.URLClassLoader.findClass(URLClassLoader.java:354)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:425)

        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:358)

        at java.lang.Class.forName0(Native Method)

        at java.lang.Class.forName(Class.java:190)

        at com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile.main(ExecuteFromFile.java:50)

        at com.era7.bioinfo.bio4j.tools.ExecuteBio4jTool.main(ExecuteBio4jTool.java:28)

I am using Java 1.7 Build, and running the command - " java -d64 -Xmx23G -jar ExecuteBio4jTool.jar executionsBio4j.xml"

I have both "executionsBio4j.xml" and "uniprotData.xml" file in the same folder that I am running the command from. Seems like the github resources is all scattered and am unable to properly understand everything.

Could you let me know, the Jar file and ExecutionsBIo4j file to use to build NEO4j Database.

Thank you,

Sandeep

[Pablo Pareja Tobes]

Hi Sandeep,

I apologize for the inconveniences but we're carrying out a major reorganization of Bio4j platform (including repository changes, documentation updates, code refactoring, a more robust release system, and much more...)

Bio4j is growing quite fast and we needed to do all this before everything got out of hand.

Unfortunately all this is taking us a bit longer than we expected but as soon as things are sorted out (it shouldn't take more than a week) I will let you all know.

Please bear with us till then. 

Cheers ;)

Pablo

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[Sandeep Shantharam]

Hi,

Thank you Pablo, waiting for the final result - done with literature review for my class project..Waiting for Bio4j :)

[Sandeep Shantharam]

Hi, 

Any Update on this, it would be good - if you could just provide the JAR file for importing the data into the NeO4J Db - While trying to build from the .sbt files; there are files missing.

Thank you,

Sandeep