DataTables load using AJAX, Search by metadata on studies page

[squirrelo]

This pull request lays the groundwork for selections by study on the study listing page. The following changes have happened:

• New Study.get_info() function to get all information for a given list of studies and, optionally, columns. This allows for orders of magnitude faster loading of study data for the listings tables.
• New SearchStudiesAJAX handler and page, for getting the DataTables json information to build the tables.
• Merged the public and user studies tables and pages into a single table that can be sorted by status, and allows for a single listing page that can be searched over.
• DataTables are now loaded from AJAX-derived json, meaning the page no longer has a wait logo and can reload the table as metadata searches are performed.
• Minor DB changes - Renaming the description and title columns on study satellite tables to allow for easier joins.

[squirrelo]

SciPy build is failing, causing the tests to register as failed. Not sure what to do.

 Command "/home/travis/miniconda3/envs/env_name/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip-build-baUMF0/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-t4sETC-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-baUMF0/scipy

[coveralls]

Changes Unknown when pulling 1872555 on squirrelo:cart into * on biocore:master*.

[ElDeveloper]

Can you add a docstring?

[squirrelo]

done

[squirrelo]

This is failing because of qiime install issues, but is ready for review.

[josenavas]

Since I've already faced 2 database merge conflicts on my previous PR #900 please, review that one and merge that one first...

[squirrelo]

Single list for now, Issue #1019 opened for later multi-table support.

[josenavas]

Thanks @squirrelo, baby steps works, so PR are smaller. Assigned to you and to alpha.

[coveralls]

Coverage decreased (-0.05%) to 79.05% when pulling 3a12f87 on squirrelo:cart into 54f63e9 on biocore:master.

[josenavas]

BTW, this PR is not modifying the DB schema files neither the html. See this section on the contributing.md file for making database changes.

[coveralls]

Coverage decreased (-0.05%) to 79.05% when pulling 25ae8f2 on squirrelo:cart into 54f63e9 on biocore:master.

[squirrelo]

Ready for review/merge

[antgonza]

Some comments on code.

The GUI looks soooo much better, thanks! Anyway, when I try to search the button gets grayed out but nothing happens, not even python or JS errors, and never comes back. Also, not sure what the left checkbox column is for, there is no button to add or anything like that.

[squirrelo]

Checkbox is a placeholder for sample selection, which will be added once all the initial bits are in place. Doesn't harm anything, and means there is less to change to get full functionality.

I'll take a look at the JS, sounds like browser compatibility issue.

[antgonza]

What about adding the button(s) that will interact with the studies selected but when you click them you get a simple message like: "Not yet implemented" so we can review the distribution of the GUI.

BTW I'm using Chrome Version 41.0.2272.104 (64-bit)

[squirrelo]

I'd rather wait and add the button when it works, that way we don't ever give the impression of being able to select studies on the page until you actually can. I don't want to confuse users.

[squirrelo]

Also, if all goes well, there won't be a button. It will ajax-select the samples as the things rea clicked and unclicked.

[antgonza]

That will be nice but note that having the checkboxes already gives the wrong impression. What about removing or commenting that section in the code so they do not get created and mislead users? Other option is to have that functionality part of this PR but I can see the benefits of having this already deployed.

[squirrelo]

I guess I can comment out the code and just return a blank line for those cells.

[antgonza]

Thanks, that works for me.

[squirrelo]

Changes made, ready for merge.

[antgonza]

Thanks. Tested and works fine except that if I search for the example: env_matter includes soil AND (ph < 4 OR ph > 8) I get no results but if I go to the metaanalysis page and do the same search I get results, any ideas?

[squirrelo]

Just tested and I get the same results on both pages. Not sure how you're getting no results as it's all the same search object setup.

[antgonza]

Thanks for checking. Figured it out, when you search the "Narrow search results by column data (Title, abstract, PI, etc):" field doesn't get cleaned so it seems that there are no results but there are ... could you clean on click?

[squirrelo]

The checkboxes are too embedded in the code to safely hide them and re-add later. The textbox is cleared on search now though.

[coveralls]

Coverage decreased (-0.05%) to 79.13% when pulling e01e224 on squirrelo:cart into e1c7a7c on biocore:master.