sort list of ftp uploaded files
Dear all Is there a way to sort the list of files that a user has uploaded via FTP? Currently they appear on the form of the tool 'Upload File' in random order it seems. There is not much documentation on the <param type="ftpfile" /> tag unfortunately. If the user just selects all files they end up in his/her history in the same random order, which causes a slight inconvenience when using these files as paired multiple input for a workflow. The obvious work-around is to put the files into the history one pair at a time, but this becomes a bit onerous for larger number of files. Thanks a lot for your help. Cheers Ulf ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
If Galaxy just sorted these files alphabetically before display/import would that fix your problem? Or do your users need to be able to modify the order? -John On Mon, Dec 16, 2013 at 9:19 AM, Ulf Schaefer <Ulf.Schaefer@phe.gov.uk> wrote:
Dear all
Is there a way to sort the list of files that a user has uploaded via FTP? Currently they appear on the form of the tool 'Upload File' in random order it seems. There is not much documentation on the <param type="ftpfile" /> tag unfortunately.
If the user just selects all files they end up in his/her history in the same random order, which causes a slight inconvenience when using these files as paired multiple input for a workflow.
The obvious work-around is to put the files into the history one pair at a time, but this becomes a bit onerous for larger number of files.
Thanks a lot for your help.
Cheers Ulf
************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
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John, I can't speak for Ulf, but a more general solution would be to allow sorting by a standard unix SORT set keys. That would allow things like - sort by the sample ID after the 3rd dash, then by the read direction. -t - -k1,1n -k2,2r # http://unixhelp.ed.ac.uk/CGI/man-cgi?sort Regards, Curtis PS - granted simple filename sort is a good place to start and a lot better than nothing. Date sort is often useful, too. -----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of John Chilton Sent: Tuesday, December 17, 2013 4:03 PM To: Ulf Schaefer Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] sort list of ftp uploaded files If Galaxy just sorted these files alphabetically before display/import would that fix your problem? Or do your users need to be able to modify the order? -John On Mon, Dec 16, 2013 at 9:19 AM, Ulf Schaefer <Ulf.Schaefer@phe.gov.uk> wrote:
Dear all
Is there a way to sort the list of files that a user has uploaded via FTP? Currently they appear on the form of the tool 'Upload File' in random order it seems. There is not much documentation on the <param type="ftpfile" /> tag unfortunately.
If the user just selects all files they end up in his/her history in the same random order, which causes a slight inconvenience when using these files as paired multiple input for a workflow.
The obvious work-around is to put the files into the history one pair at a time, but this becomes a bit onerous for larger number of files.
Thanks a lot for your help.
Cheers Ulf
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Dear John, dear Curtis, and all all that is required to fix my current issue is that the files show up in the 'Upload File' tool form in alphabetical order. I assume that at some point an 'ls' command is done on the users' ftp home folder. The result of that could possibly be stored in a hash of some sort, which could explain why the order is randomised when the files come back out to go on the form. But I might be wrong. Of course a better but more involved solution would be if the 'Files uploaded via FTP' table was sortable, e.g. by clicking on the table headers. Any idea where I might find the code that populates this table? Thanks a lot for your help. Cheers Ulf On 17/12/13 22:31, Curtis Hendrickson (Campus) wrote:
John,
I can't speak for Ulf, but a more general solution would be to allow sorting by a standard unix SORT set keys. That would allow things like - sort by the sample ID after the 3rd dash, then by the read direction. -t - -k1,1n -k2,2r # http://unixhelp.ed.ac.uk/CGI/man-cgi?sort
Regards, Curtis
PS - granted simple filename sort is a good place to start and a lot better than nothing. Date sort is often useful, too.
-----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of John Chilton Sent: Tuesday, December 17, 2013 4:03 PM To: Ulf Schaefer Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] sort list of ftp uploaded files
If Galaxy just sorted these files alphabetically before display/import would that fix your problem? Or do your users need to be able to modify the order?
-John
On Mon, Dec 16, 2013 at 9:19 AM, Ulf Schaefer <Ulf.Schaefer@phe.gov.uk> wrote:
Dear all
Is there a way to sort the list of files that a user has uploaded via FTP? Currently they appear on the form of the tool 'Upload File' in random order it seems. There is not much documentation on the <param type="ftpfile" /> tag unfortunately.
If the user just selects all files they end up in his/her history in the same random order, which causes a slight inconvenience when using these files as paired multiple input for a workflow.
The obvious work-around is to put the files into the history one pair at a time, but this becomes a bit onerous for larger number of files.
Thanks a lot for your help.
Cheers Ulf
********************************************************************** **** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ********************************************************************** ****
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************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
Couple things... I just pushed a commit to galaxy-central to sort those files by default - that is a clear improvement: https://bitbucket.org/galaxy/galaxy-central/commits/ce186eb5fefcb7ff332c73bd... Clearly not enough though - it would be nice to have for more advanced sorting options though so I have created a Trello card - https://trello.com/c/0hgUrW4H If you really wanted to dig into this there are many files that may be relevant - templates/embed_base.mako lib/galaxy/web/form_builder.py lib/galaxy/tools/parameters/basic.py lib/galaxy/web/framework/helpers/grids.py Hopefully this helps. Also just as a heads up, coming from a different direction me and Martin are actively working building abstractions for pairs of data and that will have to include a nice UI for building these pairs - our plan is to start with library imports but we will try to architect the creation widget to be able to target history items as well. This would largely negate the need to import them in any particular order. This will likely not be in the next release, but hopefully the following one (I can build pairs via the API now, but I want to be able to do useful stuff with them before committing :) ). -John On Wed, Dec 18, 2013 at 2:37 AM, Ulf Schaefer <Ulf.Schaefer@phe.gov.uk> wrote:
Dear John, dear Curtis, and all
all that is required to fix my current issue is that the files show up in the 'Upload File' tool form in alphabetical order.
I assume that at some point an 'ls' command is done on the users' ftp home folder. The result of that could possibly be stored in a hash of some sort, which could explain why the order is randomised when the files come back out to go on the form. But I might be wrong.
Of course a better but more involved solution would be if the 'Files uploaded via FTP' table was sortable, e.g. by clicking on the table headers.
Any idea where I might find the code that populates this table?
Thanks a lot for your help.
Cheers Ulf
On 17/12/13 22:31, Curtis Hendrickson (Campus) wrote:
John,
I can't speak for Ulf, but a more general solution would be to allow sorting by a standard unix SORT set keys. That would allow things like - sort by the sample ID after the 3rd dash, then by the read direction. -t - -k1,1n -k2,2r # http://unixhelp.ed.ac.uk/CGI/man-cgi?sort
Regards, Curtis
PS - granted simple filename sort is a good place to start and a lot better than nothing. Date sort is often useful, too.
-----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of John Chilton Sent: Tuesday, December 17, 2013 4:03 PM To: Ulf Schaefer Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] sort list of ftp uploaded files
If Galaxy just sorted these files alphabetically before display/import would that fix your problem? Or do your users need to be able to modify the order?
-John
On Mon, Dec 16, 2013 at 9:19 AM, Ulf Schaefer <Ulf.Schaefer@phe.gov.uk> wrote:
Dear all
Is there a way to sort the list of files that a user has uploaded via FTP? Currently they appear on the form of the tool 'Upload File' in random order it seems. There is not much documentation on the <param type="ftpfile" /> tag unfortunately.
If the user just selects all files they end up in his/her history in the same random order, which causes a slight inconvenience when using these files as paired multiple input for a workflow.
The obvious work-around is to put the files into the history one pair at a time, but this becomes a bit onerous for larger number of files.
Thanks a lot for your help.
Cheers Ulf
********************************************************************** **** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ********************************************************************** ****
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************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
Dear John Thanks very much. This is the perfect (minimal) solution that I need right now. I am looking forward to your work on pairs of data. It sounds like it will be exceptionally useful for us. Thanks again and best wishes Ulf On 18/12/13 14:29, John Chilton wrote:
Couple things...
I just pushed a commit to galaxy-central to sort those files by default - that is a clear improvement:
https://bitbucket.org/galaxy/galaxy-central/commits/ce186eb5fefcb7ff332c73bd...
Clearly not enough though - it would be nice to have for more advanced sorting options though so I have created a Trello card -
If you really wanted to dig into this there are many files that may be relevant -
templates/embed_base.mako lib/galaxy/web/form_builder.py lib/galaxy/tools/parameters/basic.py lib/galaxy/web/framework/helpers/grids.py
Hopefully this helps.
Also just as a heads up, coming from a different direction me and Martin are actively working building abstractions for pairs of data and that will have to include a nice UI for building these pairs - our plan is to start with library imports but we will try to architect the creation widget to be able to target history items as well. This would largely negate the need to import them in any particular order.
This will likely not be in the next release, but hopefully the following one (I can build pairs via the API now, but I want to be able to do useful stuff with them before committing :) ).
-John
On Wed, Dec 18, 2013 at 2:37 AM, Ulf Schaefer <Ulf.Schaefer@phe.gov.uk> wrote:
Dear John, dear Curtis, and all
all that is required to fix my current issue is that the files show up in the 'Upload File' tool form in alphabetical order.
I assume that at some point an 'ls' command is done on the users' ftp home folder. The result of that could possibly be stored in a hash of some sort, which could explain why the order is randomised when the files come back out to go on the form. But I might be wrong.
Of course a better but more involved solution would be if the 'Files uploaded via FTP' table was sortable, e.g. by clicking on the table headers.
Any idea where I might find the code that populates this table?
Thanks a lot for your help.
Cheers Ulf
On 17/12/13 22:31, Curtis Hendrickson (Campus) wrote:
John,
I can't speak for Ulf, but a more general solution would be to allow sorting by a standard unix SORT set keys. That would allow things like - sort by the sample ID after the 3rd dash, then by the read direction. -t - -k1,1n -k2,2r # http://unixhelp.ed.ac.uk/CGI/man-cgi?sort
Regards, Curtis
PS - granted simple filename sort is a good place to start and a lot better than nothing. Date sort is often useful, too.
-----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of John Chilton Sent: Tuesday, December 17, 2013 4:03 PM To: Ulf Schaefer Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] sort list of ftp uploaded files
If Galaxy just sorted these files alphabetically before display/import would that fix your problem? Or do your users need to be able to modify the order?
-John
On Mon, Dec 16, 2013 at 9:19 AM, Ulf Schaefer <Ulf.Schaefer@phe.gov.uk> wrote:
Dear all
Is there a way to sort the list of files that a user has uploaded via FTP? Currently they appear on the form of the tool 'Upload File' in random order it seems. There is not much documentation on the <param type="ftpfile" /> tag unfortunately.
If the user just selects all files they end up in his/her history in the same random order, which causes a slight inconvenience when using these files as paired multiple input for a workflow.
The obvious work-around is to put the files into the history one pair at a time, but this becomes a bit onerous for larger number of files.
Thanks a lot for your help.
Cheers Ulf
********************************************************************** **** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ********************************************************************** ****
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************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
participants (3)
-
Curtis Hendrickson (Campus) -
John Chilton -
Ulf Schaefer