dejesus2010 / cen3031project Goto Github PK

If you update a project with an empty description, it will show the box in red but still allow you to submit. The project description field does not get updated.

If you enter a string instead of a number in the ID field of the forms that create new customers and species the form will highlight green like the date is good, but it will generate a bad request with no feedback to the user. We need to update the form validation logic.

In project.server.model.test, I am testing the retrieval of a project and populating the 'species' field with the Specie object corresponding to the specified objectID(). For some reason, the population of the species field never occurs. Note: for the 'customer' field, population does occur. I believe the species field not being populated may be due to the conflicting namespace issue?? Refer to commit 85f4aa0 where the tests are added.

The number will update when plates are added/removed from the user's worklist.

As a lab tech, I'd like to automatically generate three e-mails:

1. a Plate Layout Request e-mail (See #22 )
2. a Reminder e-mail to gently remind the client that they need to send their plate layout file
3. a Summary e-mail, to hand to the customer after the samples have begun processing. This will contain a picture as well.

I think that we should make the project due date required, it doesn't make any sense to me to just have it set to Date.now() if it's not specified. Any objections?

https://github.com/dejesus2010/CEN3031Project/blob/master/mean/app/models/project.server.model.js#L19

When you type in a username and hit enter, nothing happens. Inspecting the console logs shows...
"Failed to load resource: the server responded with a status of 500 (Internal Server Error) http://127.0.0.1:3000/auth/forgot"

It seems like an express route is broken somewhere.

I think we should move datepicker controller logic into a service, because the datepicker logic may be logic that multiple controllers may want to use.

As a user, I'd like to be able to choose between open / closed / all project tabs; open is to be the default.
This would be on the Project Listing Page.

Sessions enable the lab techs to log in and stay logged in. Take for example when a tech signs in and performs the next step of a plate, performing the next step will log the user who performed the step using the sessions data.

We should have, in addition to what we already have:
Number of Samples in the Project
Sequencing Method

Maybe more?

If a user tries to add an unassigned plate to their work list from the "All" tab, you'll notice that something weird happens. Screen shots provided

Selecting unassigned plate:

After clicking "Add Plate":

Notice how the "Unassigned" and "All" tabs are both selected. What I expect to happen after adding a plate from the All tab is to remain in the All tab and for the plates in the All tab to update the new state of assigned plates to me.

Such as this:

As a lab tech or admin, I want to be able to view the overall status of a project and see links to each plate.

In the places were we return a user object, such as in the listPlates route the assignee objects are being returned with alot of info: email, hashed password, salt, etc... that shouldn't be making it.

I need to add unit tests to plate generation and upload of filled out plate layout functionality

Using the application previously written for RAPiD Genomics, generate a plate layout via Node.

As a lab tech or administrator, I want to be able to view a list of all open projects.

They should have their own collection

They should be stored in their own collection

If a user adds plates x, y, z from project 1 to their work list then deletes project 1 before completing the plates, plates x, y, z still remain in the work list. I think these plates should be removed from the work list.

Change this confusing naming convention.

As a lab tech, I'd like to access a calculator for various master mix calculations.

Encountered an error when trying to create plate layout for RDJ_020501 using:
java -jar app/bin/PrepareSummarySpreadsheet.jar RDJ_020501 app/tmp/plate_layouts "Future of farming sperm" 67
Exception in thread "main" java.lang.NullPointerException
at com.rapidgenomics.PrepareSpreadsheetWriter.checkProjectNameAvailable(PrepareSpreadsheetWriter.java:64)
at com.rapidgenomics.PrepareSpreadsheetWriter.(PrepareSpreadsheetWriter.java:40)
at com.rapidgenomics.GUIPrepareSpreadsheetWriter.runCommandLineUtil(GUIPrepareSpreadsheetWriter.java:140)
at com.rapidgenomics.GUIPrepareSpreadsheetWriter.main(GUIPrepareSpreadsheetWriter.java:60)

Error: Command failed: Exception in thread "main" java.lang.NullPointerException
at com.rapidgenomics.PrepareSpreadsheetWriter.checkProjectNameAvailable(PrepareSpreadsheetWriter.java:64)
at com.rapidgenomics.PrepareSpreadsheetWriter.(PrepareSpreadsheetWriter.java:40)
at com.rapidgenomics.GUIPrepareSpreadsheetWriter.runCommandLineUtil(GUIPrepareSpreadsheetWriter.java:140)
at com.rapidgenomics.GUIPrepareSpreadsheetWriter.main(GUIPrepareSpreadsheetWriter.java:60)

As a lab tech, I'd like to enter the number of samples, and automatically generate a Plate Layout .xlsx file. This file would then we send to the client via e-mail.

Specifically if I enter rdj@gmail and press enter, an error notification is presented to me, but the input box does not turn red as I would expect it to.

When you hover over the Projects dropdown on /#!/projects it displays the wierd icon of when your hovering over text in a document. It should display the regular cursor arrow, or some other icon indicating that this dropdown is selectable.

On the project listing page if you try to click on the little up/down arrows to change the sort of that column, it will fail. This feels buggy and is not what a user would expect to happen. We need to toggle the sort regardless of where you click in the column header.

As a lab tech, I'd like to be able to upload a filled out Plate_Layout.xlsx file, and have this populate the plates / samples within the project with it's information.

As an Admin, I'd like to see a log users who have made changes to a project chronologically.

In the project schema there are two keys at the bottom just kinda hanging around in there: speciesId + customerId. Joe, should we put those into a normal object like the rest of the file or is there a reason why they're just in there?

https://github.com/dejesus2010/CEN3031Project/blob/master/mean/app/models/project.server.model.js#L56

Whenever you navigate to the new project page, if you check out the developer console there will be a Uncaught TypeError: Cannot read property 'getToggleElement' of null. I checked before I last pushed--the issue was already existing. I'm not sure what triggers it.

We need a customer e-mail address field in the schema

In the customer creation page, the user should only be able to input 3 capital letter for the 'Code' field.

As a lab tech I would like to be able to sort the list of all open projects by due date, species, and project code.

Although the plate is removed from the back end, the removed selected plate still persists in the front end array of selected plates to be sent to perform stage.

Recreating bug:

• Have chrome dev tools opened to the console tab
• Select more than 1 plate in a stage to be performed.
• Remove one of those plates from the work list by pressing the remove button
• Press the Perform selected button
• Notice how all plates are passed to perform the step

My propose fix:
Put the removal of a plate from the work list into the myWorklistPlate directive. Doing this allows us to create an isolated function that when the remove button is clicked on it will be called. In this isolated function which is defined in post: function(scope, element, attrs), we have access to the DOM element. Because we have access to the DOM element, I believe we may be able to call element.deleteRow(0).

As a lab tech or administrator, I want to log in with a username and password.

Doing so creates a session #3, #2

Going to the page gives:

TypeError: boolean is not a function
at http://localhost:3000/lib/angular/angular.js:10848:15
at Scope.isolateScope.(anonymous function) as dateDisabled
at http://localhost:3000/lib/angular/angular.js:10847:21
at Scope.isolateScope.(anonymous function) as dateDisabled
at isDisabled (http://localhost:3000/lib/angular-bootstrap/ui-bootstrap-tpls.js:1079:160)
at createDateObject (http://localhost:3000/lib/angular-bootstrap/ui-bootstrap-tpls.js:1073:22)
at ctrl._refreshView (http://localhost:3000/lib/angular-bootstrap/ui-bootstrap-tpls.js:1221:41)
at refreshView (http://localhost:3000/lib/angular-bootstrap/ui-bootstrap-tpls.js:1060:12)
at render (http://localhost:3000/lib/angular-bootstrap/ui-bootstrap-tpls.js:1055:10)
at ngModelCtrl.$render (http://localhost:3000/lib/angular-bootstrap/ui-bootstrap-tpls.js:1039:12)

And neither the description nor the date are updated properly when you try to submit.

Current idea: One column of the project list view will have a colored bar broken into X boxes where X is the number of stages. Each box will have a number, the number of plates completed (or to do) in that stage and the box will be colored so that it is red if not much progress has been made and then it shifts to green as all the plates get past that stage.

We should add functions later on to the mongoose schemes to verify our database inputs, such as what constitutes a valid customer code, project code, etc.