Using synchronous method to upload multiple files
Hi all, I've set up a simple tool using the synchronous method to upload a file on galaxy. I'm able to visit the external link, select and upload a file by the list. The script that I use is data_source.py and the 'command' part in the xml configuration is the same as the ucsc xml config (ucsc_tablebrowser.xml). But my purpose is to import multiple files. Have you any idea how I can set a way to import/upload multiple files by using the synchronous method? Thank in advance, Best regards Daniele
There was some work last summer to allow something that at least vaguely sounds like what you are trying to accomplish - though I was not involved so I probably am unable to help out much. The Trello card that was tracking progress on this can be found here - https://trello.com/c/YlADVbkI - and seems to provide some good details. I am not sure if there is more formal documentation anywhere though. Hope this helps, -John On Fri, Mar 27, 2015 at 7:34 AM, Daniele P Colobraro <d.colobraro@gmail.com> wrote:
Hi all,
I've set up a simple tool using the synchronous method to upload a file on galaxy. I'm able to visit the external link, select and upload a file by the list. The script that I use is data_source.py and the 'command' part in the xml configuration is the same as the ucsc xml config (ucsc_tablebrowser.xml). But my purpose is to import multiple files.
Have you any idea how I can set a way to import/upload multiple files by using the synchronous method?
Thank in advance, Best regards Daniele
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Thanks John for your help, if I get it will I set just a external view of my files? My idea is to provide multiple files in the galaxy history. I tried to rewrite the 'galaxy.joson' file but without results. So far, I have made up just the tool below: upload3.py $report1 $report1.id $__new_file_path__ #if (len(str($url_paste).split(','))>1): #for $i in $url_paste: $i #end for #else: $url_paste #end if </command> <inputs action="link to" check_values="false" method="post"> </inputs> <request_param_translation> <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> <request_param galaxy_name="URL" remote_name="URL" missing="" /> <request_param galaxy_name="url_paste" remote_name="mclfile[]" missing="txt" /> </request_param_translation> <outputs> <data format="txt" name="report1" /> </outputs> Using this config file I'm able to import multiple files in the galaxy history. But I can't set a name to distinguish them. I am not sure how to proceed. If you or anyone have other suggestions I will be grateful. thanks again Daniele 2015-03-30 2:57 GMT+02:00 John Chilton <jmchilton@gmail.com>:
There was some work last summer to allow something that at least vaguely sounds like what you are trying to accomplish - though I was not involved so I probably am unable to help out much. The Trello card that was tracking progress on this can be found here - https://trello.com/c/YlADVbkI - and seems to provide some good details. I am not sure if there is more formal documentation anywhere though.
Hope this helps,
-John
Hi all,
I've set up a simple tool using the synchronous method to upload a file on galaxy. I'm able to visit the external link, select and upload a file by the
On Fri, Mar 27, 2015 at 7:34 AM, Daniele P Colobraro <d.colobraro@gmail.com> wrote: list.
The script that I use is data_source.py and the 'command' part in the xml configuration is the same as the ucsc xml config (ucsc_tablebrowser.xml). But my purpose is to import multiple files.
Have you any idea how I can set a way to import/upload multiple files by using the synchronous method?
Thank in advance, Best regards Daniele
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Yeah - I am not very familiar with data source tools at all - sorry. Are you creating a galaxy.json file in upload3.py? If you are creating that file but cannot distinguish between the files - I would try adding "name" or "designation" fields to the JSON lines in that file - I would think one of those should work. -John On Wed, Apr 1, 2015 at 9:07 AM, Daniele P Colobraro <d.colobraro@gmail.com> wrote:
Thanks John for your help, if I get it will I set just a external view of my files? My idea is to provide multiple files in the galaxy history. I tried to rewrite the 'galaxy.joson' file but without results. So far, I have made up just the tool below:
upload3.py $report1 $report1.id $__new_file_path__ #if (len(str($url_paste).split(','))>1): #for $i in $url_paste: $i #end for #else: $url_paste #end if </command> <inputs action="link to" check_values="false" method="post"> </inputs> <request_param_translation> <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> <request_param galaxy_name="URL" remote_name="URL" missing="" /> <request_param galaxy_name="url_paste" remote_name="mclfile[]" missing="txt" /> </request_param_translation> <outputs> <data format="txt" name="report1" /> </outputs>
Using this config file I'm able to import multiple files in the galaxy history. But I can't set a name to distinguish them. I am not sure how to proceed.
If you or anyone have other suggestions I will be grateful.
thanks again Daniele
2015-03-30 2:57 GMT+02:00 John Chilton <jmchilton@gmail.com>:
There was some work last summer to allow something that at least vaguely sounds like what you are trying to accomplish - though I was not involved so I probably am unable to help out much. The Trello card that was tracking progress on this can be found here - https://trello.com/c/YlADVbkI - and seems to provide some good details. I am not sure if there is more formal documentation anywhere though.
Hope this helps,
-John
On Fri, Mar 27, 2015 at 7:34 AM, Daniele P Colobraro <d.colobraro@gmail.com> wrote:
Hi all,
I've set up a simple tool using the synchronous method to upload a file on galaxy. I'm able to visit the external link, select and upload a file by the list. The script that I use is data_source.py and the 'command' part in the xml configuration is the same as the ucsc xml config (ucsc_tablebrowser.xml). But my purpose is to import multiple files.
Have you any idea how I can set a way to import/upload multiple files by using the synchronous method?
Thank in advance, Best regards Daniele
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Daniele, I would suggest having a look at the tools/genomespace/genomespace_importer.py/xml tool, particularly the ‘download_from_genomespace_importer’ method, it uses a comma-separated list of URLs and downloads an adds multiple files to Galaxy, with history names of “GenomeSpace importer on FILENAME”. If you don’t need to sniff datatypes, etc, you can ignore those parts. Thanks for using Galaxy, Dan On Apr 16, 2015, at 9:23 AM, John Chilton <jmchilton@gmail.com> wrote:
Yeah - I am not very familiar with data source tools at all - sorry. Are you creating a galaxy.json file in upload3.py? If you are creating that file but cannot distinguish between the files - I would try adding "name" or "designation" fields to the JSON lines in that file - I would think one of those should work.
-John
On Wed, Apr 1, 2015 at 9:07 AM, Daniele P Colobraro <d.colobraro@gmail.com> wrote:
Thanks John for your help, if I get it will I set just a external view of my files? My idea is to provide multiple files in the galaxy history. I tried to rewrite the 'galaxy.joson' file but without results. So far, I have made up just the tool below:
upload3.py $report1 $report1.id $__new_file_path__ #if (len(str($url_paste).split(','))>1): #for $i in $url_paste: $i #end for #else: $url_paste #end if </command> <inputs action="link to" check_values="false" method="post"> </inputs> <request_param_translation> <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> <request_param galaxy_name="URL" remote_name="URL" missing="" /> <request_param galaxy_name="url_paste" remote_name="mclfile[]" missing="txt" /> </request_param_translation> <outputs> <data format="txt" name="report1" /> </outputs>
Using this config file I'm able to import multiple files in the galaxy history. But I can't set a name to distinguish them. I am not sure how to proceed.
If you or anyone have other suggestions I will be grateful.
thanks again Daniele
2015-03-30 2:57 GMT+02:00 John Chilton <jmchilton@gmail.com>:
There was some work last summer to allow something that at least vaguely sounds like what you are trying to accomplish - though I was not involved so I probably am unable to help out much. The Trello card that was tracking progress on this can be found here - https://trello.com/c/YlADVbkI - and seems to provide some good details. I am not sure if there is more formal documentation anywhere though.
Hope this helps,
-John
On Fri, Mar 27, 2015 at 7:34 AM, Daniele P Colobraro <d.colobraro@gmail.com> wrote:
Hi all,
I've set up a simple tool using the synchronous method to upload a file on galaxy. I'm able to visit the external link, select and upload a file by the list. The script that I use is data_source.py and the 'command' part in the xml configuration is the same as the ucsc xml config (ucsc_tablebrowser.xml). But my purpose is to import multiple files.
Have you any idea how I can set a way to import/upload multiple files by using the synchronous method?
Thank in advance, Best regards Daniele
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
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Hi Daniel and John, thanks a lot for your replies. I have tried creating a galaxy.json file, but I haven't had much time, so I gave up that. But I am interested to use your suggestions. For my solution, I followed the explanations in: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files https://bitbucket.org/galaxy/galaxy-central/src/default/test/functional/tool... So, I am able to visit my remote web page, select which items I want (with a check-box form) and upload them to galaxy. As advised in multi_output_configured.xml, I create the subdir in my python script by using os.mkdir('subdir1'). But I am going to create a more elegant solution. Thanks again for your replies, I'll exploit them soon. Daniele 2015-04-16 16:01 GMT+02:00 Daniel Blankenberg <dan@bx.psu.edu>:
Hi Daniele,
I would suggest having a look at the tools/genomespace/ genomespace_importer.py/xml tool, particularly the ‘ download_from_genomespace_importer’ method, it uses a comma-separated list of URLs and downloads an adds multiple files to Galaxy, with history names of “GenomeSpace importer on FILENAME”.
If you don’t need to sniff datatypes, etc, you can ignore those parts.
Thanks for using Galaxy,
Dan
On Apr 16, 2015, at 9:23 AM, John Chilton <jmchilton@gmail.com> wrote:
Yeah - I am not very familiar with data source tools at all - sorry. Are you creating a galaxy.json file in upload3.py? If you are creating that file but cannot distinguish between the files - I would try adding "name" or "designation" fields to the JSON lines in that file - I would think one of those should work.
-John
On Wed, Apr 1, 2015 at 9:07 AM, Daniele P Colobraro <d.colobraro@gmail.com> wrote:
Thanks John for your help, if I get it will I set just a external view of my files? My idea is to provide multiple files in the galaxy history. I tried to rewrite the 'galaxy.joson' file but without results. So far, I have made up just the tool below:
upload3.py $report1 $report1.id $__new_file_path__ #if (len(str($url_paste).split(','))>1): #for $i in $url_paste: $i #end for #else: $url_paste #end if </command> <inputs action="link to" check_values="false" method="post"> </inputs> <request_param_translation> <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> <request_param galaxy_name="URL" remote_name="URL" missing="" /> <request_param galaxy_name="url_paste" remote_name="mclfile[]" missing="txt" /> </request_param_translation> <outputs> <data format="txt" name="report1" /> </outputs>
Using this config file I'm able to import multiple files in the galaxy history. But I can't set a name to distinguish them. I am not sure how to proceed.
If you or anyone have other suggestions I will be grateful.
thanks again Daniele
2015-03-30 2:57 GMT+02:00 John Chilton <jmchilton@gmail.com>:
There was some work last summer to allow something that at least vaguely sounds like what you are trying to accomplish - though I was not involved so I probably am unable to help out much. The Trello card that was tracking progress on this can be found here - https://trello.com/c/YlADVbkI - and seems to provide some good details. I am not sure if there is more formal documentation anywhere though.
Hope this helps,
-John
On Fri, Mar 27, 2015 at 7:34 AM, Daniele P Colobraro <d.colobraro@gmail.com> wrote:
Hi all,
I've set up a simple tool using the synchronous method to upload a file on galaxy. I'm able to visit the external link, select and upload a file by the list. The script that I use is data_source.py and the 'command' part in the xml configuration is the same as the ucsc xml config (ucsc_tablebrowser.xml). But my purpose is to import multiple files.
Have you any idea how I can set a way to import/upload multiple files by using the synchronous method?
Thank in advance, Best regards Daniele
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
-
Daniel Blankenberg -
Daniele P Colobraro -
John Chilton