Re: [EMBOSS] Handling of local file input in Jemboss
Hi Mahmut, Thank you for being able to find the kernel of reason in my continued attempts to confuse this discussion :-) I rebuilt everything again with today's fix in BuildJembossForm, and everything seems to be working fine. With best regards, Daniel From: Mahmut Uludag [ulu...@ebi.ac.uk] Sent: Monday, September 24, 2012 4:17 PM To: Rozenbaum, Daniel (Biocceleration Inc) Cc: emboss@lists.open-bio.org Subject: Re: [EMBOSS] Handling of local file input in Jemboss > 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. Confused again. I was able to reproduce the problem following the steps you described and just checked in a fix in BuildJembossForm class. Have you tried updating from CVS before your last rebuild? Since your email is about 4 minutes later than I checked in above change to CVS. Mahmut ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Handling of local file input in Jemboss
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. Confused again. I was able to reproduce the problem following the steps you described and just checked in a fix in BuildJembossForm class. Have you tried updating from CVS before your last rebuild? Since your email is about 4 minutes later than I checked in above change to CVS. Mahmut ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Handling of local file input in Jemboss
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@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 [ulu...@ebi.ac.uk] Sent: Friday, September 21, 2012 10:58 AM To: Rozenbaum, Daniel (Biocceleration Inc) Cc: emboss@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 ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
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 [ulu...@ebi.ac.uk] Sent: Friday, September 21, 2012 10:58 AM To: Rozenbaum, Daniel (Biocceleration Inc) Cc: emboss@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 ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
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 ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
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" in jemboss.properties. I just checked that I have the same problem in my Jemboss jobs folder. this should be easy to fix. I will return soon. Mahmut ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Handling of local file input in Jemboss
Hi Mahmut, I just noticed that the most recent changes might have introduced the following glitch: 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" in jemboss.properties. In other words if results.home is /path/to/emboss_results/ and embossBin is /usr/local/emboss/6.4.0/bin/ , I'm now getting Jemboss job directories created under /path/to/emboss_results/usr/local/emboss/6.4.0/bin/ . Could you please let me know if you're able to repdocude this? Many thanks, Daniel From: Mahmut Uludag [ulu...@ebi.ac.uk] Sent: Friday, September 21, 2012 7:07 AM To: Rozenbaum, Daniel (Biocceleration Inc) Cc: emboss@lists.open-bio.org Subject: Re: [EMBOSS] Handling of local file input in Jemboss Hi Daniel, > supplying a remote file as input no longer works, and neither > does using list files (either local or remote). > > When I try to use a local list file, the file does make it to server > side, but the command line appearing in .desc doesn't have the '@' > before the file name, and that seems to be the reason for the job > failure. > > When I try to use a remote file, the generated command line doesn't > contain a reference to the input file at all, and the resultant error > message reads "Error: Unable to read sequence '' ". > > Can you reproduce these, or did I mess something up during my attempt > to apply the patch and reinstall? It was my mistake, apologies. When I initially looked to the problem I noticed possible changes may include/interfere-with handling of list-files and remote-files but in my last look I just forgot this point. I now have tried fixing it but this has required some changes on the server side as well. Can you download latest versions of the following two files and test again. http://code.open-bio.org/emboss/emboss/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java?view=log http://code.open-bio.org/emboss/emboss/jemboss/org/emboss/jemboss/server/JembossServer.java?view=log (These 2 files has not changed much recently, as far as i can see they are happy to work as part of 6.4.0) Regards, Mahmut ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Handling of local file input in Jemboss
Hi Daniel, Thanks for the update. Good to hear that changes working as expected. Mahmut ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Handling of local file input in Jemboss
Hi Mahmut, No apologies necessary, and your prompt response is sincerely appreciated! I have rebuilt Jemboss.jar with these two new versions and everything seems to be working as expected. Many thanks, Daniel From: Mahmut Uludag [ulu...@ebi.ac.uk] Sent: Friday, September 21, 2012 7:07 AM To: Rozenbaum, Daniel (Biocceleration Inc) Cc: emboss@lists.open-bio.org Subject: Re: [EMBOSS] Handling of local file input in Jemboss Hi Daniel, > supplying a remote file as input no longer works, and neither > does using list files (either local or remote). > > When I try to use a local list file, the file does make it to server > side, but the command line appearing in .desc doesn't have the '@' > before the file name, and that seems to be the reason for the job > failure. > > When I try to use a remote file, the generated command line doesn't > contain a reference to the input file at all, and the resultant error > message reads "Error: Unable to read sequence '' ". > > Can you reproduce these, or did I mess something up during my attempt > to apply the patch and reinstall? It was my mistake, apologies. When I initially looked to the problem I noticed possible changes may include/interfere-with handling of list-files and remote-files but in my last look I just forgot this point. I now have tried fixing it but this has required some changes on the server side as well. Can you download latest versions of the following two files and test again. http://code.open-bio.org/emboss/emboss/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java?view=log http://code.open-bio.org/emboss/emboss/jemboss/org/emboss/jemboss/server/JembossServer.java?view=log (These 2 files has not changed much recently, as far as i can see they are happy to work as part of 6.4.0) Regards, Mahmut ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Handling of local file input in Jemboss
Hi Daniel, supplying a remote file as input no longer works, and neither does using list files (either local or remote). When I try to use a local list file, the file does make it to server side, but the command line appearing in .desc doesn't have the '@' before the file name, and that seems to be the reason for the job failure. When I try to use a remote file, the generated command line doesn't contain a reference to the input file at all, and the resultant error message reads "Error: Unable to read sequence '' ". Can you reproduce these, or did I mess something up during my attempt to apply the patch and reinstall? It was my mistake, apologies. When I initially looked to the problem I noticed possible changes may include/interfere-with handling of list-files and remote-files but in my last look I just forgot this point. I now have tried fixing it but this has required some changes on the server side as well. Can you download latest versions of the following two files and test again. http://code.open-bio.org/emboss/emboss/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java?view=log http://code.open-bio.org/emboss/emboss/jemboss/org/emboss/jemboss/server/JembossServer.java?view=log (These 2 files has not changed much recently, as far as i can see they are happy to work as part of 6.4.0) Regards, Mahmut ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Handling of local file input in Jemboss
Hi Mahmut,
I've applied the patch you suggested and it seems to have fixed the problem
with supplying local sequence files. However, now it appears that supplying a
remote file as input no longer works, and neither does using list files (either
local or remote).
When I try to use a local list file, the file does make it to server side, but
the command line appearing in .desc doesn't have the '@' before the file name,
and that seems to be the reason for the job failure.
When I try to use a remote file, the generated command line doesn't contain a
reference to the input file at all, and the resultant error message reads
"Error: Unable to read sequence '' ".
Can you reproduce these, or did I mess something up during my attempt to apply
the patch and reinstall?
Many thanks in advance,
Daniel
From: Mahmut Uludag [ulu...@ebi.ac.uk]
Sent: Thursday, September 20, 2012 6:00 PM
To: Rozenbaum, Daniel (Biocceleration Inc)
Cc: emboss@lists.open-bio.org
Subject: Re: [EMBOSS] Handling of local file input in Jemboss
Hi Daniel,
When we were implementing the array representation of command lines we
mistakenly added the input sequence file names to the command line array
prepared on the client side. As you showed in your example these inputs
are added to the command line on the server side using their final file
names.
It looks following changes fixes the problem in my 6.4.0 test server and
current CVS code base client.
Index: org/emboss/jemboss/gui/form/BuildJembossForm.java
===
RCS file:
/home/repository/emboss/emboss/emboss/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java,v
retrieving revision 1.113
diff -u -r1.113 BuildJembossForm.java
--- org/emboss/jemboss/gui/form/BuildJembossForm.java29 Jun 2011
14:12:48 -1.113
+++ org/emboss/jemboss/gui/form/BuildJembossForm.java20 Sep 2012
21:28:14 -
@@ -1113,12 +1113,11 @@
fn = fn.trim();
- optionsA.add("-" + val);
- optionsA.add(fn);
-
if(withSoap)
options = filesForSoap(fn,options,val,filesToMove);
else {
+optionsA.add("-" + val);
+optionsA.add(fn);
fn = addQuote(fn);
options = options.concat(" -" + val + " " + fn);
}
Can you please try applying the above change to your 6.4.0 installation.
In 6.4.0 deleted optionsA.add() lines are the lines 1116 and 1117.
Since jemboss has relatively complex installation mechanism, it might be
easier if you apply this change to a freshly extracted tar ball and make
a new installation. Make sure jawa web start doesn't use the cached
version of the jemboss client but uses the updated version.
Regards,
Mahmut
> 2. Open "seqret" in Jemboss, and use the "Browse files" option to select
> "C:\TEMP\sequences.fasta" as input.
>
> 3. Run seqret interactively. The Saved Results window that opens contains the
> following error messages:
> Error: Failed to open filename 'C'
> Error: Unable to read sequence 'C:\TEMP\sequences.fasta'
> Died: seqret terminated: Bad value for '-sequence' with -auto defined
> Looking in the subdirectory created for this job on the server side, it does
> contain a file "C__TEMP__sequences.fasta" with the correct contents. But the
> ".desc" file in that directory reads the following:
> EMBOSS run details
>
> Application: seqret
> -nofeature -sequence C:\TEMP\sequences.fasta -nofirstonly -auto
> C__TEMP_sequences.fasta
> Started at Thu Sep 20 11_15_22 EDT 2012
>
> Input files:
> /usr/local/emboss/results/username/seqret_Thu_Sep_20_11_15_22_EDT_2012_1234/C__TEMP_sequences.fasta
> It appears therefore that the command line, instead of using the path to the
> server-side copy of the input file, still uses the path to the file on the
> client.
>
___
EMBOSS mailing list
EMBOSS@lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Handling of local file input in Jemboss
Hi Daniel,
When we were implementing the array representation of command lines we
mistakenly added the input sequence file names to the command line array
prepared on the client side. As you showed in your example these inputs
are added to the command line on the server side using their final file
names.
It looks following changes fixes the problem in my 6.4.0 test server and
current CVS code base client.
Index: org/emboss/jemboss/gui/form/BuildJembossForm.java
===
RCS file:
/home/repository/emboss/emboss/emboss/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java,v
retrieving revision 1.113
diff -u -r1.113 BuildJembossForm.java
--- org/emboss/jemboss/gui/form/BuildJembossForm.java29 Jun 2011
14:12:48 -1.113
+++ org/emboss/jemboss/gui/form/BuildJembossForm.java20 Sep 2012
21:28:14 -
@@ -1113,12 +1113,11 @@
fn = fn.trim();
- optionsA.add("-" + val);
- optionsA.add(fn);
-
if(withSoap)
options = filesForSoap(fn,options,val,filesToMove);
else {
+optionsA.add("-" + val);
+optionsA.add(fn);
fn = addQuote(fn);
options = options.concat(" -" + val + " " + fn);
}
Can you please try applying the above change to your 6.4.0 installation.
In 6.4.0 deleted optionsA.add() lines are the lines 1116 and 1117.
Since jemboss has relatively complex installation mechanism, it might be
easier if you apply this change to a freshly extracted tar ball and make
a new installation. Make sure jawa web start doesn't use the cached
version of the jemboss client but uses the updated version.
Regards,
Mahmut
2. Open "seqret" in Jemboss, and use the "Browse files" option to select
"C:\TEMP\sequences.fasta" as input.
3. Run seqret interactively. The Saved Results window that opens contains the
following error messages:
Error: Failed to open filename 'C'
Error: Unable to read sequence 'C:\TEMP\sequences.fasta'
Died: seqret terminated: Bad value for '-sequence' with -auto defined
Looking in the subdirectory created for this job on the server side, it does contain a file
"C__TEMP__sequences.fasta" with the correct contents. But the ".desc" file in
that directory reads the following:
EMBOSS run details
Application: seqret
-nofeature -sequence C:\TEMP\sequences.fasta -nofirstonly -auto
C__TEMP_sequences.fasta
Started at Thu Sep 20 11_15_22 EDT 2012
Input files:
/usr/local/emboss/results/username/seqret_Thu_Sep_20_11_15_22_EDT_2012_1234/C__TEMP_sequences.fasta
It appears therefore that the command line, instead of using the path to the
server-side copy of the input file, still uses the path to the file on the
client.
___
EMBOSS mailing list
EMBOSS@lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss
