[EMBOSS] Handling of local file input in Jemboss

[Rozenbaum, Daniel (Biocceleration Inc)]

Mahmut, please disregard my previous email - I must have made a mistake in my rebuild. After rebuilding more carefully again, the problem seems to have disappeared. My apologies for the confusion.
________________________________________
From: Rozenbaum, Daniel (Biocceleration Inc)
Sent: Monday, September 24, 2012 12:13 PM
To: Mahmut Uludag
Cc: emboss at lists.open-bio.org
Subject: RE: [EMBOSS] Handling of local file input in Jemboss

Hi Mahmut,

After re-building with the latest versions of gui/form/BuildJembossForm.java (1.116) and server/JembossServer.java (1.47) I'm running into a problem with adding ":sequence_name" to local files. It is reproducible in my environment using the following steps:

1. Run makeprotseq to generate say 10 sequences

2. Call up seqret and drag-and-drop the file "makeseq.fasta" generated at the previous step from the File Manager window to the "Sequence Filename" field of seqret.

3. Append ":EMBOSS_003". So the full string in the "Sequence Filename" field looks like

/path/emboss/results/username/makeprotseq_Mon_Sep_24_12_04_32_EDT_2012_51429/makeseq.fasta:EMBOSS_003

4. Execute seqret. Everything works as expected.

5. Drag-and-drop the file "makeseq.fasta" to a local folder

6. Drag-and-drop the file from the Local pane to seqret input, and add the same sequence id. So the full string in the "Sequence Filename" field in my case (a Windows client) looks something like

H:\tmp\makeseq.fasta:EMBOSS_003

7. When seqret is run, the following error message appears:

Error: Failed to open filename 'H'
Error: Unable to read sequence 'H:\tmp\makeseq.fasta:EMBOSS_003'
Died: seqret terminated: Bad value for '-sequence' with -auto defined


Would you be able to look into this?

Many thanks,
Daniel







________________________________________
From: Mahmut Uludag [uludag at ebi.ac.uk]
Sent: Friday, September 21, 2012 10:58 AM
To: Rozenbaum, Daniel (Biocceleration Inc)
Cc: emboss at lists.open-bio.org
Subject: Re: [EMBOSS] Handling of local file input in Jemboss

Hi Daniel,

> server side directories for Jemboss jobs on the
> server now appear to be created under the path that is a
> concatenation of paths "results.home" and "embossBin"

I have checked in a fix for this problem in JembossServer class.

In Soaplab and jdispatcher projects we don't hide the full path of the
program executed. While working on the previous problem I thought we can
do the same in Jemboss. Although I was not quite sure with it I just
made that change. Obviously I didn't made it in the correct way. I now
have undone it but we can add this feature properly if it is desirable.

I have also checked in a fix in BuildJembossForm class as the recent fix
did also broke the inputs through copy/paste form.

Mahmut