On Tue, Oct 22, 2013 at 1:38 AM, John Chilton chilton@msi.umn.edu wrote:

This question is vaguely related to the following pull request put together by Gert Hulselmans.

https://bitbucket.org/galaxy/galaxy-central/pull-request/171/avoid-corruptio...

I think it makes sense to add this option. But I also I think the upload form is getting quite complicated and it only promises to get more complicated (looking ahead to things like advanced handling of compressed datasets or dataset collections). So I have the outline of a plan that could potentially address some of this that I would be interested in feedback on:

1. We merge this pull request.

2. Rename (or re-describe I guess): "Upload File from your computer"

to "Advanced Upload Tool" (still with id upload1 to keep things as simple as possible).

3. We then create several news tools, which would appear before

"Advanced Upload Tool" in the "Get Data" section:

"Upload file from your computer" "Import files from the web via URLs" "Import FTP uploaded files" "Paste file contents"

Each of these has just the form element they need (upload box, textbox, or FTP selector) as well for genome selection box. They also have a checkbox conditional for advanced options for "Convert tabs to spaces", the new "Posix lines", and perhaps "File format" (we could default to *auto* and make specification an advanced option).

More thought should be given to what is considered a advanced option in each of these cases. If you are pasting content, you do not need the new "posix lines" option, but replace spaces with tabs might be a very common option. Whereas for uploaded files the inverse is sort of true.

As long as these import data tools appear as just another tool in the left hand pane, this seems more consistent than the multi-tab interface James mentioned.

If however, importing data becomes a special action, then we do have prior examples of a tabbed interface (e.g. editing the attributes of a history dataset).

I understand there is already special case code for the upload tool in workflows, so removing it as a traditional tool does have upsides.

4. To further streamline things, we could replace "Your history is

empty. Click 'Get Data' on the left pane to start" in the empty history section with something with links: "Your history is empty. To get started, import data from [your computer], [web links], [your clipboard], [FTP], or by choosing an external data source from the 'Get Data' section in the left panel".

I kind of find the big upload form daunting and I consider myself something of a Galaxy expert, I assume new users must find it even more so. I have no data to back this however, so let me know if you think I am way off base here. I would be really interested for perspectives from people who work closely with new users.

Also it is potentially confusing that to upload data via URLs for instance you click a link that says "Upload File from your computer". This could simplify that as well.

Thoughts?

5) Deprecate the upload1 tool to keep the interface clean (i.e. keep it in the tool_conf.xml but hide it, so that it can be used for legacy purposes only).

6) Rework the test framework to use "Upload file from your computer" instead (or more radically to point at test-data files in situ?).

Peter