cPath 0.7 - Initializing cPath Database error

[Fong Chun Chan]

Hello,

I am not sure whether this is a big issue or not, but I have
downloaded the latest stable release 0.7 and when initalizing the
cPath database I get the following error:

ERROR 1406 (22001) at line 68: Data too long for column 'DESC' at row
1
Importing MySQL File: reference.sql

I just wanted to point that out. The program should still run.

[Ethan Cerami]

have you re-run init.db to re-create the tables required for release
0.7? Perhaps, that will fix the problem.

Ethan

Fong Chun Chan wrote:

--
Ethan Cerami
Computational Biology Center
Memorial Sloan-Kettering Cancer Center
http://cbio.mskcc.org
Email: cer...@cbio.mskcc.org
Direct phone: (646) 888-2625

[Fong Chun Chan]

Hi,

I was acutally running the initDb.pl file and that's what caused the
error.

Additionally, I was trying to import the meta file and I keep getting
the

"Exception in thread "main" java.lang.NoClassDefFoundError: and"

I am not exactly sure what is it trying to do

Any suggestions?

On Mar 26, 12:20 pm, Ethan Cerami <cer...@cbio.mskcc.org> wrote:
> have you re-run init.db to re-create the tables required for release
> 0.7? Perhaps, that will fix the problem.
>
> Ethan
>
>
>
> Fong Chun Chan wrote:
> >Hello,
>
> >I am not sure whether this is a big issue or not, but I have
> >downloaded the latest stable release 0.7 and when initalizing the
> >cPath database I get the following error:
>
> >ERROR 1406 (22001) at line 68: Data too long for column 'DESC' at row
> >1
> >Importing MySQL File: reference.sql
>
> >I just wanted to point that out. The program should still run.
>
> --
> Ethan Cerami
> Computational Biology Center

> Memorial Sloan-Kettering Cancer Centerhttp://cbio.mskcc.org

[Ethan Cerami]

Fong,

I am not able to recreate your error over here.  What version of MySQL are you using?

The NoClassDefFoundError sounds like the code has not (yet) been compiled.  Perhaps, just re-run:  ant ?

If it's easier, we can also talk by phone.  My contact info is here:  http://cbio.mskcc.org/people/info/ethan_cerami.html

[Fong Chun Chan]

Hi,

I am running MySQL 5.0.

I already ran ant...I am really not sure why I keep getting this error.  I am going to try to do the installation process all over again and see if that helps.

Fong

--
Fong Chun Chan

Fraser Valley Regional Health Promotion Chair,
School of Computing Science
School of Molecular Biology and Biochemistry
Simon Fraser University
Email: f...@sfu.ca

[Ethan Cerami]

ok, sounds good.  feel free to call me with any further questions...

[Fong Chun Chan]

Hey Ethan,

I found the problem.  At first, it was because I had spaces in the my CPATH_HOME, and didn't have quotes around it.  So I put quotes and ran the admin.pl file and then I got errors;

Exception in thread "main" java.lang.NoClassDefFoundError: net/sf/ehcache/CacheManager
        at org.mskcc.pathdb.util.cache.EhCache.shutDownCache(EhCache.java:70)
        at org.mskcc.pathdb.tool.Admin.main(Admin.java:212)

It wasn't taking the lib files and putting them onto the class path.  I figured it was my CPATH_HOME acting funny again.  So this time I just took it and placed it into D drive.  Reset the path to D:\cPath.  And ran the script and it worked.

Also, I can't seem to the find the dbData/externalDb/biopax/db.info file that is stated in the tutorial.

[Ethan Cerami]

Fong:

I'm glad you figured out the problem.   I do all my development work on a Mac, so this looks to be a Windows specific issue.

If you can find any additional details about the problem, I will be happy to include your info in the admin manual.

As to db.info, the admin manual has a typo (which I will now fix).  The correct path should be:

testData/biopax/db.info

[Fong Chun Chan]

All right...more problems.

I tried to import a biopax file.  I chose the Apoptosis.file from the Rectome database just like the tutorial.  The problem was when I tried to import it I kept getting duplication errors.  So I went into mySQL and cleared all my tables.

That solved the duplications errors.  When I run the script again, I get the same error I had with the initDb.pl file:

-----------------------------
Reading in file:  Apoptosis.owl
XML Type:  BIO_PAX
Reading in meta-data from:  db.info
Data source is:  Reactome
Reading in file content...
Processing file...
Validating BioPAX File with RDF Validator...
   --->  BioPAX RDF is Valid
Categorizing BioPAX Resources...
Validating All External References
..............................

..........................
Percentage Complete:  23%
Mem Allocated:  11.922 MB, Mem used:  7.647 MB, Mem free
........................................................
Percentage Complete:  47%
Mem Allocated:  11.922 MB, Mem used:  7.753 MB, Mem free
........................................................
Percentage Complete:  70%
Mem Allocated:  11.922 MB, Mem used:  6.976 MB, Mem free
........................................................
Percentage Complete:  93%
Mem Allocated:  11.922 MB, Mem used:  7.049 MB, Mem free
..............................
Storing Pathway Records to Database:
................................
Storing Interaction Records to Database:
........................................................
Storing Physical Entity Records to Database:
......
-----------------------------------------
Fatal Error:  Data too long for column 'DESC' at row 1
-----------------------------------------

It seems that mySQL 5.0 is causing a lot of problems.

Fong

[Ethan Cerami]

Fong,

Today, I switched over to MySQL 5.0 on Mac OS X, and unfortunately, I am not able to recreate your problem.  The sample Apoptosis pathway loads fine.  Were you able to track down any other details?

Ethan,