Re: [galaxy-dev] Error download composite dataset from history
Hi Ross Thanks a million, I hg-pull'ed it solved the problem!! Please push it to galaxy-dist? ;) I ran in another little bug though, but nothing serious, you might even have already spotted it by now: In lib/galaxy/web/framework/__init__.py the line 873 made the whole thing crash due to a wrong arguments number, so I changed it from: self._ensure_logged_in_user( environ ) to: self._ensure_logged_in_user( environ, session_cookie ) and it works fine now! Best, L-A Le 19/01/2012 02:13, Ross a écrit : Hi, L-A Thanks for reporting this - I just pushed a fix in galaxy-central 6556:ab1a5ab063ce Please let us know if that resolves the problem? 2012/1/19 Louise-Amélie Schmittlouise-amelie.schm...@embl.de: Hello! I'm running into an error when trying to download a composite dataset from the history with the floppy disk icon. Here is the error message in the logs: galaxy.web.controllers.dataset ERROR 2012-01-18 16:32:10,324 Unable to remove temporary library download archive and directory Traceback (most recent call last): File /g/funcgen/galaxy-dev/lib/galaxy/web/controllers/dataset.py, line 285, in archive_composite_dataset os.rmdir( tmpd ) OSError: [Errno 39] Directory not empty: './database/tmp/tmpkRv28I' Then I tried replacing the os.rmdir by a shutil.rmtree to see if it would solve the issue, and here is what I got: galaxy.web.controllers.dataset ERROR 2012-01-18 16:34:30,239 Unable to remove temporary library download archive and directory Traceback (most recent call last): File /g/funcgen/galaxy-dev/lib/galaxy/web/controllers/dataset.py, line 286, in archive_composite_dataset shutil.rmtree( tmpd ) File /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/shutil.py, line 221, in rmtree onerror(os.remove, fullname, sys.exc_info()) File /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/shutil.py, line 219, in rmtree os.remove(fullname) OSError: [Errno 16] Device or resource busy: './database/tmp/tmpwpsShD/.nfs0289ccea0138' But when I check the contents of the direcory, there is no hidden .nfs-something file. Does anyone have an idea why this could occur? Both our testing instance and our production instance have the same issue, the first being on galaxy-central and the second on galaxy-dist. Thanks, L-A ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Error download composite dataset from history
Hi, L-A, 2012/1/19 Louise-Amélie Schmitt louise-amelie.schm...@embl.de: Hi Ross Thanks a million, I hg-pull'ed it solved the problem!! Please push it to galaxy-dist? ;) Glad to hear it works - thanks for reporting back. I ran in another little bug though, but nothing serious, you might even have already spotted it by now: In lib/galaxy/web/framework/__init__.py the line 873 made the whole thing crash due to a wrong arguments number, so I changed it from: self._ensure_logged_in_user( environ ) to: self._ensure_logged_in_user( environ, session_cookie ) and it works fine now! No, I hadn't encountered that - AFAIK, the function definition and call are correct in the current tip of galaxy-central @ https://bitbucket.org/galaxy/galaxy-central/src/ab1a5ab063ce/lib/galaxy/web/framework/__init__.py The tip of galaxy-dist on bitbucket currently looks consistent - neither definition nor call have the session_cookie parameter - so I'm not sure where the error you saw at line 873 comes from - in https://bitbucket.org/galaxy/galaxy-dist/src/b258de1e6cea/lib/galaxy/web/framework/__init__.py the call is at line 860...perhaps you were working with an older revision or one that's been merged with central at some stage? Best, L-A Le 19/01/2012 02:13, Ross a écrit : Hi, L-A Thanks for reporting this - I just pushed a fix in galaxy-central 6556:ab1a5ab063ce Please let us know if that resolves the problem? 2012/1/19 Louise-Amélie Schmittlouise-amelie.schm...@embl.de: Hello! I'm running into an error when trying to download a composite dataset from the history with the floppy disk icon. Here is the error message in the logs: galaxy.web.controllers.dataset ERROR 2012-01-18 16:32:10,324 Unable to remove temporary library download archive and directory Traceback (most recent call last): File /g/funcgen/galaxy-dev/lib/galaxy/web/controllers/dataset.py, line 285, in archive_composite_dataset os.rmdir( tmpd ) OSError: [Errno 39] Directory not empty: './database/tmp/tmpkRv28I' Then I tried replacing the os.rmdir by a shutil.rmtree to see if it would solve the issue, and here is what I got: galaxy.web.controllers.dataset ERROR 2012-01-18 16:34:30,239 Unable to remove temporary library download archive and directory Traceback (most recent call last): File /g/funcgen/galaxy-dev/lib/galaxy/web/controllers/dataset.py, line 286, in archive_composite_dataset shutil.rmtree( tmpd ) File /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/shutil.py, line 221, in rmtree onerror(os.remove, fullname, sys.exc_info()) File /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/shutil.py, line 219, in rmtree os.remove(fullname) OSError: [Errno 16] Device or resource busy: './database/tmp/tmpwpsShD/.nfs0289ccea0138' But when I check the contents of the direcory, there is no hidden .nfs-something file. Does anyone have an idea why this could occur? Both our testing instance and our production instance have the same issue, the first being on galaxy-central and the second on galaxy-dist. Thanks, L-A ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Error download composite dataset from history
Hello! I'm running into an error when trying to download a composite dataset from the history with the floppy disk icon. Here is the error message in the logs: galaxy.web.controllers.dataset ERROR 2012-01-18 16:32:10,324 Unable to remove temporary library download archive and directory Traceback (most recent call last): File /g/funcgen/galaxy-dev/lib/galaxy/web/controllers/dataset.py, line 285, in archive_composite_dataset os.rmdir( tmpd ) OSError: [Errno 39] Directory not empty: './database/tmp/tmpkRv28I' Then I tried replacing the os.rmdir by a shutil.rmtree to see if it would solve the issue, and here is what I got: galaxy.web.controllers.dataset ERROR 2012-01-18 16:34:30,239 Unable to remove temporary library download archive and directory Traceback (most recent call last): File /g/funcgen/galaxy-dev/lib/galaxy/web/controllers/dataset.py, line 286, in archive_composite_dataset shutil.rmtree( tmpd ) File /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/shutil.py, line 221, in rmtree onerror(os.remove, fullname, sys.exc_info()) File /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/shutil.py, line 219, in rmtree os.remove(fullname) OSError: [Errno 16] Device or resource busy: './database/tmp/tmpwpsShD/.nfs0289ccea0138' But when I check the contents of the direcory, there is no hidden .nfs-something file. Does anyone have an idea why this could occur? Both our testing instance and our production instance have the same issue, the first being on galaxy-central and the second on galaxy-dist. Thanks, L-A ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Error download composite dataset from history
Hi, L-A Thanks for reporting this - I just pushed a fix in galaxy-central 6556:ab1a5ab063ce Please let us know if that resolves the problem? 2012/1/19 Louise-Amélie Schmitt louise-amelie.schm...@embl.de: Hello! I'm running into an error when trying to download a composite dataset from the history with the floppy disk icon. Here is the error message in the logs: galaxy.web.controllers.dataset ERROR 2012-01-18 16:32:10,324 Unable to remove temporary library download archive and directory Traceback (most recent call last): File /g/funcgen/galaxy-dev/lib/galaxy/web/controllers/dataset.py, line 285, in archive_composite_dataset os.rmdir( tmpd ) OSError: [Errno 39] Directory not empty: './database/tmp/tmpkRv28I' Then I tried replacing the os.rmdir by a shutil.rmtree to see if it would solve the issue, and here is what I got: galaxy.web.controllers.dataset ERROR 2012-01-18 16:34:30,239 Unable to remove temporary library download archive and directory Traceback (most recent call last): File /g/funcgen/galaxy-dev/lib/galaxy/web/controllers/dataset.py, line 286, in archive_composite_dataset shutil.rmtree( tmpd ) File /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/shutil.py, line 221, in rmtree onerror(os.remove, fullname, sys.exc_info()) File /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/shutil.py, line 219, in rmtree os.remove(fullname) OSError: [Errno 16] Device or resource busy: './database/tmp/tmpwpsShD/.nfs0289ccea0138' But when I check the contents of the direcory, there is no hidden .nfs-something file. Does anyone have an idea why this could occur? Both our testing instance and our production instance have the same issue, the first being on galaxy-central and the second on galaxy-dist. Thanks, L-A ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
