Hi ,
I am trying to import an entire directory of biopax files to my
instance of cpath using the command "./admin.pl -f directoryName
import" and the program tests the validity of all the files in the
directory but doesn't actually import any of them The last file it
looks at is the db.info to which it says it is not valid RDF but it
ends normally (there are no exceptions listed) with Time of execution
but nothing ends up in the db.
I have written a shell script to interate through all the files and
call the admin.pl for each file separately and that works fine,
everything gets imported into the db. Is the admin.pl supposed to
work with a directory?
Thanks,
Ruth
Which is what it should do, then it ends with something ike....
Import Summary: -----------------------------------------------------
# of Pathways saved to database: 0
-> # of Existing Pathways found in db: 1
# of Interactions saved to database: 0
-> # of Existing Interactions found in db: 74
# of Physical Entities saved to database: 0
-> # of Existing Physical Entities found in db: 54
-----------------------------------------------------
File Import Complete
That said, if any of the files in your directory are invalid, admin.pl will not import any of them. Perhaps that is what's happening?
Try running with the -d flag, to see if you might be getting any extra warning / stack track messages.
Ruth wrote:
> Hi ,
> I am trying to import an entire directory of biopax files to my
> instance of cpath using the command "./admin.pl -f directoryName
> import" and the program tests the validity of all the files in the
> directory but doesn't actually import any of them The last file it
> looks at is the db.info to which it says it is not valid RDF but it
> ends normally (there are no exceptions listed) with Time of execution
> but nothing ends up in the db.
> I have written a shell script to interate through all the files and
> call the admin.pl for each file separately and that works fine,
> everything gets imported into the db. Is the admin.pl supposed to
> work with a directory?
> Thanks,
> Ruth
-- Ethan Cerami
Computational Biology Center
Memorial Sloan-Kettering Cancer Center
http://cbio.mskcc.org
Hi Ethan,
Thanks. They weren't loading because one or two of the files were
invalid. Is there any way to tell admin.pl to skip invalid files?
Thanks,
Ruth
On Jul 2, 3:25 pm, Ethan Cerami <cer...@cbio.mskcc.org> wrote:
> Which is what it should do, then it ends with something ike....
> Import Summary:
> -----------------------------------------------------
> # of Pathways saved to database: 0
> -> # of Existing Pathways found in db: 1
> # of Interactions saved to database: 0
> -> # of Existing Interactions found in db: 74
> # of Physical Entities saved to database: 0
> -> # of Existing Physical Entities found in db: 54
> -----------------------------------------------------
> File Import Complete
> That said, if any of the files in your directory are invalid, admin.pl
> will not import any of them. Perhaps that is what's happening?
> Try running with the -d flag, to see if you might be getting any extra
> warning / stack track messages.
> Ethan
> Ruth wrote:
> > Hi ,
> > I am trying to import an entire directory of biopax files to my
> > instance of cpath using the command "./admin.pl -f directoryName
> > import" and the program tests the validity of all the files in the
> > directory but doesn't actually import any of them The last file it
> > looks at is the db.info to which it says it is not valid RDF but it
> > ends normally (there are no exceptions listed) with Time of execution
> > but nothing ends up in the db.
> > I have written a shell script to interate through all the files and
> > call the admin.pl for each file separately and that works fine,
> > everything gets imported into the db. Is the admin.pl supposed to
> > work with a directory?
> > Thanks,
> > Ruth
> --
> Ethan Cerami
> Computational Biology Center
> Memorial Sloan-Kettering Cancer Centerhttp://cbio.mskcc.org
No, there's no way to skip invalid files within a directory. It's actually intentionally meant to be "all or nothing" to cut down on inadvertently missing invalid files during large imports.
Ruth wrote:
> Hi Ethan,
> Thanks. They weren't loading because one or two of the files were
> invalid. Is there any way to tell admin.pl to skip invalid files?
> Thanks,
> Ruth
> On Jul 2, 3:25 pm, Ethan Cerami <cer...@cbio.mskcc.org> wrote:
>> Yes, admin.pl loads all files within a directory.
>> I just tried it out, and it seemed to work ok. When it gets to db.info,
>> it says:
>> Which is what it should do, then it ends with something ike....
>> Import Summary:
>> -----------------------------------------------------
>> # of Pathways saved to database: 0
>> -> # of Existing Pathways found in db: 1
>> # of Interactions saved to database: 0
>> -> # of Existing Interactions found in db: 74
>> # of Physical Entities saved to database: 0
>> -> # of Existing Physical Entities found in db: 54
>> -----------------------------------------------------
>> File Import Complete
>> That said, if any of the files in your directory are invalid, admin.pl
>> will not import any of them. Perhaps that is what's happening?
>> Try running with the -d flag, to see if you might be getting any extra
>> warning / stack track messages.
>> Ethan
>> Ruth wrote:
>>> Hi ,
>>> I am trying to import an entire directory of biopax files to my
>>> instance of cpath using the command "./admin.pl -f directoryName
>>> import" and the program tests the validity of all the files in the
>>> directory but doesn't actually import any of them The last file it
>>> looks at is the db.info to which it says it is not valid RDF but it
>>> ends normally (there are no exceptions listed) with Time of execution
>>> but nothing ends up in the db.
>>> I have written a shell script to interate through all the files and
>>> call the admin.pl for each file separately and that works fine,
>>> everything gets imported into the db. Is the admin.pl supposed to
>>> work with a directory?
>>> Thanks,
>>> Ruth
>> --
>> Ethan Cerami
>> Computational Biology Center
>> Memorial Sloan-Kettering Cancer Centerhttp://cbio.mskcc.org
