U19-GUI

This repository contains the sourcecode of the MATLAB GUI of the animal and behavioral database. This is a brief documentation of

• Startup
• Code use
• Code structure
• Work to do
• Known issues
• Health checks done (can be removed once we are happy).

Startup

First, start matlab. Them add

• U19-pipeline-matlab
• U19-GUI to the search patch.

General use

The AnimalDatabase allows for programmatic access and update of the contained data. In your code, you should first create an instance of the database to interact with:

  dbase     = AnimalDatabase();                       % keep this object around for communications
  dbase.gui();                                        % user interface from which one can add/view animals

There are a series of "pull" functions to retrive info at various levels:

  [people, templates] = dbase.pullOverview();
  animals   = dbase.pullAnimalList();                 % all researchers
  animals   = dbase.pullAnimalList('sakoay');         % a single researcher with ID = sakoay
  logs      = dbase.pullDailyLogs('sakoay');          % all animals for sakoay
  logs      = dbase.pullDailyLogs('sakoay','K62');    % a particular animal ID for sakoay

To write data to the database, use the following "push*" functions:

  db.pushAnimalInfo('testuser', 'testuser_T01', 'initWeight', 23.5)
  db.pushDailyInfo( 'testuser', 'testuser_T01', 'received', 1.3, 'weight', 22.5);

And of course, you can also use all low-level datajoint functions.

Code documentation

Code structure

Some general comments about architecture of the GUI.

All reading from the database is done via the functions

• pullAnimalList
• pullOverview
• pullDailyLogs
• And of course all dj-queries (e.g. for templates)

All writing into the database happens in the functions

• pushDailyInfo
• pushAnimaInfo
• writeTrainingDataToDatabase.m (uses pullAnimalList and pushDailyInfo of the animalDatabase)

The notification system is called periodically and the GUI sends out eMails and messages. This happens via the files

• checkActionItems.m
• checkCageReturn.m
• checkMouseWeighing.m

I also added a set of helper function that make the use of dj simpler:

• getResearcherDJ to return researcher structure from researcherID
• getTemplateDJ to return template structure
• getAnimalDJ to return animal structure of a given researcherID

Known issues/features

• Adding a new mouse-line for a mouse will throw an error. This is on purpose to avoid typos and enforce standards in gene/line naming. To do this more cracefully: should we add a dialog to add new line?

Work to do

This is sorted by importance:

1. Do health checks, i.e. play with db.gui('testuser'). In the GUI, I checked adding mouse, dead mouse, add action items, body weight, lines... This seemed fine. Try adding and removing animals from/to the graveyard. Make sure notification systems works etc. (DOING)
2. Add additional feature (per LAR request): If animal reaches endpoint via 1910 protocol. Automatically and immediately send emails to people specified in a list (new dj table). (DONE)
3. In the GUI, either remove the delete mouse button, or update the notification with a message that it "only works if you have the required user rights". (DONE)
4. In the GUI, remove the check in/out button. Nobody is using it. (DONE)
5. Write either a new GUI to add a new user, or alternatively add a "new user" button and form to existing GUI, so that new users don't have to be entered with SequelPro. (DONE)
6. Clean up code. This repo started as a branch of tankmousevr. The only relevant stuff for the GUI should be in /database/. AnimalDatabase.m should be ok, but we should go through the other code as well. I have also tried to remove all google-stuff, but there might be dead wood left. Can this be cleaned effectively?