A requested functionality is to have contextual presets, i.e "Order Status" should be the default preset for "Pending" projects list.

TODO

• Implement logic
• Map preset --> list

We need a better way to handle uncaught exceptions, db, authorization issues etc.. Should consider to (at least) catch more exceptions and possibly also to log them.

Take a look at tornado.log:
http://tornado.readthedocs.org/en/branch3.2/log.html

ref: #91

Would be awesome if you could make a column preset called “Order status” that should be applied to the list of pending projects.
Do you think it would be possible to set different preset defaults for the different lists?

Project
Project Name
Application
Type
Portal ID
User Project Reference
Project Coordinator
Order Received
Plates Sent
Contract Sent
Contract Received
Sample Information Received
Samples Received
Latest Running Note

Note! Changed order of the dates!

On Project View --> Project details --> Wet Lab --> Custor Primier, that should be Custom Primer

On the Q30 page - the plot has a bunch of filters, and it’s missing one of the more recent run modes: RapidHighOutput mode

Make the User Project Reference in the project list a link to the portal using the Portal ID. (Same as in the heading on the project view pages)

The Portal ID column could then be removed from the Order Status preset, which would save some needed horizontal real estate, and save us quite a few clicks.

Hej,

The caliper images are always retrieved eventhough the checkbox is not checked. This is causing the API call https://genomics-status.scilifelab.se/api/v1/project/ to be extremely slow for projects with lots of samples (see attached screenshot).

@Galithil I would suggest an implementation like the one for Zendesk tickets: To load the caliper images under request. Even more, given the slowness of the retrieval, I would suggest that checking the "Caliper images" checkbox enables a button in the sample row to download the corresponding caliper images.

What do you think?

Some statuses are represented as P/F others as PASSED/FAILED, unify them!

Some of the JS code we've moved out from the template and to separate files, it would be nice if they didn't get cached by the browsers when we add/change some code.

Maybe it would be possible to add the commit id's of the current files in the templates, thusly

<script type="text/javascript" src="somescript.js?{latest git commit id}"></script>

As suggested by @ewels in the the discussion here: #100

From the word of Chuan, caliper images for library validation is not supported properly in LIMS. As such it should be removed (at least not be displayed) in genstat.

The images that are displaying now are wrong and is confusing to the users.

The fields displayed in the project-sample screen of genomic status is governed by the gs-users DB. In order to display the new fields, namely, the caliper images, this database needs to be updated.

Proposed changes :
user : genstat_default

New key : sample_columns . INITIAL_QC_COLUMNS . Initial QC Caliper Image
Value : caliper_image

New key : sample_columns . LIBRARY_VALIDATION_COLUMNS . Library Validation Caliper Image
Value : caliper_image

Details: https://trello.com/c/5zJ92mC8/39-url-to-select-a-list-of-projects-in-project-list-view-information-management

Modify run_dir/static/js/project_samples.js @867 so that when clicking the run of a sample the URL is flowcells_ont instead of flowcells if the value matches an ONT run pattern.

And remove from Sample Details column the fields: Extraction method, Passed Initial QC and Progress, they should be in Undefined/Extra

"Genomics Status" is the title for all pages. Change it according to the context, i.e PXXX, Reception Control, Flowcells, etc...

Details: https://trello.com/c/TwYxpqBk/49-anonymous-page-titles-information-management

Whenever someone submits a new suggestion, the suggestion box page freezes: Users cannot scroll up or down, and the form is not cleaned up.

The bigger problem is that they actually can click "Submit Suggestions" again, and as they don't get any feedback when submitting it, they think that it has not been submitted, and therefore they click again, and again... so we end up with a lot of repeated suggestions in Trello.

The behaviour should be:

1. Once the user clicks in "Send Suggestiong" some feedback (pop-up, whatever) tells the user that everything is fine
2. The form is wiped out after the Suggestion is submitted

Study the possibility, and eventually implement, the deletion of already existing running notes.

https://trello.com/c/Rrd9CMdQ/53-delete-running-notes-information-management

Currently, this is all what we see when a page is not found:

Traceback (most recent call last):
  File "/home/genomics.www/anaconda/envs/web/lib/python2.7/site-packages/tornado-4.0.2-py2.7-linux-x86_64.egg/tornado/web.py", line 1309, in _execute
    result = self.prepare()
  File "/home/genomics.www/anaconda/envs/web/lib/python2.7/site-packages/tornado-4.0.2-py2.7-linux-x86_64.egg/tornado/web.py", line 1998, in prepare
    raise HTTPError(self._status_code)
HTTPError: HTTP 404: Not Found

Handle this situation to show a nicer message...

When checking or unchecking checkboxes from different columns, if the checkboxes have the same ID, will load the firs one, even if the intention is to load the one from another column.

For example, both BASIC_COLUMNS and LIBRARY_VALIDATION_COLUMNS have a checkbox with ID well_location. When loading the "Library Validation" preset, it will check the one from "Basic" instead of the one from "Library Validation".

The title tag should be updated depending on what page is viewed: e.g. when viewing "Reception control projects" the title in the tab/window should say "Reception control projects / Genomics Status" making it easier to find the right tab if more than one is opened.

So for example if we take project in genomics-status, the date for "All samples sequenced" is 2014-05-16, but if we go to the same project in the LIMS, in project summary, the date is 2014-07-21

Whyyy?

and there is no field in which I could add a date of my own. This should be a relatively easy fix?

Joel discovered that any HTML you write in running notes is dumped straight out in the browser. Whilst quite handy for people wanting to write links and stuff, we should probably limit which HTML tags we allow (and maybe strip attributes).

Can probably strip everything simply with $("<p>").html(running_note).text(); - though we may want to make it slightly more complex so that we can keep links etc. May be easier to do this server side.

When issue #171 is fixed, clean up repeated suggestions in the database