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

> 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:

>  >  Loading File:  /Users/ceramie/Desktop/temp/db.info
> Cannot determine file type.  Skipping...

> 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

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:

>>  >  Loading File:  /Users/ceramie/Desktop/temp/db.info
>> Cannot determine file type.  Skipping...

>> 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