uploading files from local directory strangeness
Hi, I'm trying to implement the data upload from a directory as per here: http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles And all seems to be working, in that I can import the datasets into my current history. The problem is that I shouldn't be able to! I set the upload to not copy the files into Galaxy and then I deleted the softlinks and renamed the original files. However, I'm still able to import the files to my current history? How's that possible? I've checked that the files don't exist under <galaxy>/database/files/. Anyone have any suggestions? Thanks, Chris
Just had another look at this and it is working as expected now. Although, the deleted files show up in the current history (incl. peek info), trying to view them results in an error. I don't I checked whether the files could be viewed every time, previously. The problem was me, it seems ;) On 05/01/10 14:43, Chris Cole wrote:
Hi,
I'm trying to implement the data upload from a directory as per here: http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles
And all seems to be working, in that I can import the datasets into my current history. The problem is that I shouldn't be able to!
I set the upload to not copy the files into Galaxy and then I deleted the softlinks and renamed the original files. However, I'm still able to import the files to my current history? How's that possible? I've checked that the files don't exist under <galaxy>/database/files/.
Anyone have any suggestions? Thanks,
Chris _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Chris, I was just about to start working on this. I'm glad to hear it's not a bug! Galaxy doesn't check to see if the disk files actually exist, although this is probably a feature that should be added. Thanks, --nate Chris Cole wrote:
Just had another look at this and it is working as expected now. Although, the deleted files show up in the current history (incl. peek info), trying to view them results in an error. I don't I checked whether the files could be viewed every time, previously.
The problem was me, it seems ;)
On 05/01/10 14:43, Chris Cole wrote:
Hi,
I'm trying to implement the data upload from a directory as per here: http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles
And all seems to be working, in that I can import the datasets into my current history. The problem is that I shouldn't be able to!
I set the upload to not copy the files into Galaxy and then I deleted the softlinks and renamed the original files. However, I'm still able to import the files to my current history? How's that possible? I've checked that the files don't exist under <galaxy>/database/files/.
Anyone have any suggestions? Thanks,
Chris _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Nate, Yes, it would be useful. The dataset showing up as green in the history is confusing. If Galaxy checked during import into your history and showed the dataset as red if the file no longer existed would be handy. Cheers, Chris On 08/01/10 17:30, Nate Coraor wrote:
Hi Chris,
I was just about to start working on this. I'm glad to hear it's not a bug! Galaxy doesn't check to see if the disk files actually exist, although this is probably a feature that should be added.
Thanks, --nate
Chris Cole wrote:
Just had another look at this and it is working as expected now. Although, the deleted files show up in the current history (incl. peek info), trying to view them results in an error. I don't I checked whether the files could be viewed every time, previously.
The problem was me, it seems ;)
On 05/01/10 14:43, Chris Cole wrote:
Hi,
I'm trying to implement the data upload from a directory as per here: http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles
And all seems to be working, in that I can import the datasets into my current history. The problem is that I shouldn't be able to!
I set the upload to not copy the files into Galaxy and then I deleted the softlinks and renamed the original files. However, I'm still able to import the files to my current history? How's that possible? I've checked that the files don't exist under <galaxy>/database/files/.
Anyone have any suggestions? Thanks,
Chris
I've put the enhancement request in bitbucket here: http://bitbucket.org/galaxy/galaxy-central/issue/274/display-some-form-of-no... --nate Chris Cole wrote:
Hi Nate,
Yes, it would be useful. The dataset showing up as green in the history is confusing. If Galaxy checked during import into your history and showed the dataset as red if the file no longer existed would be handy. Cheers,
Chris
On 08/01/10 17:30, Nate Coraor wrote:
Hi Chris,
I was just about to start working on this. I'm glad to hear it's not a bug! Galaxy doesn't check to see if the disk files actually exist, although this is probably a feature that should be added.
Thanks, --nate
Chris Cole wrote:
Just had another look at this and it is working as expected now. Although, the deleted files show up in the current history (incl. peek info), trying to view them results in an error. I don't I checked whether the files could be viewed every time, previously.
The problem was me, it seems ;)
On 05/01/10 14:43, Chris Cole wrote:
Hi,
I'm trying to implement the data upload from a directory as per here: http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles
And all seems to be working, in that I can import the datasets into my current history. The problem is that I shouldn't be able to!
I set the upload to not copy the files into Galaxy and then I deleted the softlinks and renamed the original files. However, I'm still able to import the files to my current history? How's that possible? I've checked that the files don't exist under <galaxy>/database/files/.
Anyone have any suggestions? Thanks,
Chris
participants (2)
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Chris Cole -
Nate Coraor