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onyx's Introduction

Onyx Build Status

Web-based application that manages participant baseline interviews at biobanks assessment centres or clinics.

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License

OBiBa software are open source and made available under the GPL3 licence. OBiBa software are free of charge.

OBiBa acknowledgments

If you are using OBiBa software, please cite our work in your code, websites, publications or reports.

"The work presented herein was made possible using the OBiBa suite (www.obiba.org), a software suite developed by Maelstrom Research (www.maelstrom-research.org)"

onyx's People

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apruden avatar bkhezry avatar firone avatar inglis-dl avatar kazoompa avatar meek0 avatar obiba-ci avatar plaflamme avatar programmax avatar rima-b avatar tonydebat avatar ymarcon avatar

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onyx's Issues

ONYX-40: edit participant info

Jira issue originally created by user vferrett:

1- in the participant reception page, replace text in the edit button by "Edit Participant Info".

2- Edition of the apartment number doesn't work. Edited values are not displayed in the participant reception page
There is an inconsistency in the analysis document that might explain this. In the excel file, there is no apartment number column, i.e the apartment number is expected to appear at the end of the street field
In the view page and the participant reception page, there is a specific field for apartment.

ONYX-16: stage table

Jira issue originally created by user vferrett:

as a user, I want to see the stage table in the participant interview page as specified in the analysis document.
No action View for this milestone

The view link in the comment column opens the comment pop-up window

ONYX-15: cancelling an interview

Jira issue originally created by user vferrett:

As a participant manager or a interviewer, I want to be able to cancel an interview from the participant interview page. See and follow specification in the analysis document

ONYX-41: Search participant according to enrollment Id

Jira issue originally created by user vferrett:

In the participant list page, i should be able to find a participant if i enter his enrollment id in the ID text box.
This box should accept both the participant Id and the enrollment id

ONYX-22: update personnal information on participant

Jira issue originally created by user vferrett:

as a participant manager or interviewer, I want to be able to edit the personal information of a participant at the reception step.
From the participant reception page, clicking on edit button will open a pop-up window containing fields to edit.
Save, cancel button.
Fields are
appointment code
first name
last name
sex
birth date
street
city
Province (predefined list)
country
postal code
phone

ONYX-13: view details for a participant

Jira issue originally created by user vferrett:

As a participant manager, I want to be able to see in a pop-up window the detailed personal information about a participant.
This is obtained by clicking on the view link in each row of the participant list table in the participant list page.
The pop-up windows must be as specified in the analysis document.

ONYX-49: real user name

Jira issue originally created by user vferrett:

for the demo, would be nice to have a real name for the user instead of the ONYX administrator.
I would rename also the site by Test site instead of ONYX test site.
This is really a detail, I admit

the name would be Vincent Ferretti
pwd: www

ONYX-5: Participant Page

Jira issue originally created by user vferrett:

From the home page, the user obtains the participant page.
To be displayed:

Participant code (if any), letter code (if any), personal info (name, sex, birth date),
The interview box (appointment, start, stop, status),
receive participant link, cancel interview link.

The stage table with 3 stages in the following order: dummy stage 1 (DMS1), dummy stage 2 (DMS2), instrument stage 1 (IS1).

NOTE: Create stages such as IS1 is conditional to DS2 which is conditional to DS1.

ONYX-27: Editing personal user profile

Jira issue originally created by user nlambert:

As a user, I want to be able to modify my language preference and my password.
Note: Implements the "Profile" link in task bar - See screen 17 in ONYXScreenShot.ppt

ONYX-4: Participant Reception

Jira issue originally created by user vferrett:

From the home page or from the participant page, a user is able to receive a participant.
This means
1- get the participant reception page
2- fill the form which include to assign a new code to the participant (the participant code).

Once done, the user is redirected to the previous page but refreshed with the new participant status.

NOTE: Participant code must be unique. No editing of personal information for now, No "EAV" data for now, No address, just name, sex and birth date

ONYX-42: comment at reception

Jira issue originally created by user vferrett:

Comments taken during the reception step are not persisted and cannot be viewed on the participant interview page

ONYX-12: participant List/search page

Jira issue originally created by user vferrett:

As a user (all 3 roles), I want to see the participant list / search page as exactly specified in the analysis document. I want to see a list of 100 participants using the table pager (50 participants by page).

ONYX-14: update appointment list

Jira issue originally created by user vferrett:

As a participant manager, I want to be able to update the appointment list according to specifications described in the analysis document

ONYX-11: Code review for changeset 523

Jira issue originally created by user mboulang:

Added participant reception page.

MenuBuilder.java: Removed menu when not logged in.
HomePage.java: Removed link "receive participants", will be accessible via participant search page instead.
ParticipantSearchPage.java: Added link to reception page.
ParticipantReceptionPage.java, AssignCodeToParticipantPanel.java: Participant reception page.
ParticipantService.java: Added a service which assign a barcode to a participant.

ONYX-46: add event in comment

Jira issue originally created by user vferrett:

Yannick was right. We should have the event name in addition of the stage name in the comment window.

e.g.
Stage: participant consent
Event: start

ONYX-45: add cancellation reason to the interview page

Jira issue originally created by user vferrett:

go to the interview page
click on cancel interview
select a reason
submit

the reason should appear bellow the status

Cancellation reason:

We should do the same for interruption
Interruption reason:

ONYX-43: page header during a stage

Jira issue originally created by user vferrett:

start the consent stage
the header should display the name of the stage and not it's abbreviation (CON in this case).
Add the Participant ID.

So we should have
Participant consent: 788888: John Baker: 0ct 5, 1967

The format of the dates should be consistent in the whole application

ONYX-26: menu bar during stage execution

Jira issue originally created by user vferrett:

Add stage name and participant information on the menu bar during stage execution as specified in the analysis document

ONYX-39: ActiveInterviewService holds a stale Participant entity

Jira issue originally created by user @plaflamme:

The implementation of ActiveInterviewService holds an instance of Participant. This instance is detached from the Hibernate session that instanciated it.

If one uses this instance elsewhere, the TransientObjectException will most probably be thrown at one point...

The current fix in obiba-wicket is inappropriate (using instanceof to test for IEntity)

ONYX-2: Search Page

Jira issue originally created by user vferrett:

The advanced search page displays by default the list of the appointment of the day.

Display all links but no effect on Print, Excel, Enroll Volounteer, advanced search.

Columns must be sortable

ONYX-8: Interview Page

Jira issue originally created by user @ymarcon:

As an operator,

I want to access as directly as possible to participant interview page:

  • from the home page, which provides simply a textfield for participant's barcode,
  • participant's interview page offers access to available stages (not the completed ones and not the dependent ones).

ONYX-47: display reasons along with the status of a stage

Jira issue originally created by user vferrett:

skip or interrupt a stage and select a reason for such event.
The reason must then be displayed next to the status in the stage table of the interview page.
See screen shot in the analysis document

ONYX-33: Participant search -- problem

Jira issue originally created by user nemond:

In participant search, when I put trem in name I got one record, it's ok. When I put blay in name I got no record and when I put Michel in name I got no record too!!!

So, I think, we have a problem OR I don't understand the scope!!!

After talking with Vincent, we want a search on first name last name and % % with like.

ONYX-31: Code review ONYX-27

Jira issue originally created by user acarey:

J'aimerais que tu fasses un peu de code-review pour la classe ChangePasswordPanel

ONYX-3: Simple Participant Searches

Jira issue originally created by user vferrett:

From the home page, the user is able to search by name, by codes (participant and letter code).
Able to obtain the appointments of the day as well as the currently interviewed participants

ONYX-1: Login Page

Jira issue originally created by user vferrett:

On the login page, the user is able to enter his user name and password. He is also able to select other language versions of the software from a drop down list obtained by mouse over a tag at the top of the page.

We consider only the administrator role for now.

ONYX-9: Homepage

Jira issue originally created by user mboulang:

Participant serial number scan

ONYX-38: Fix parent pom dependencies

Jira issue originally created by user @ymarcon:

It seems like that all dependencies declared in the parent pom are said to be dependencies of child pom.
This is a problem as we found wicket jars in generated JNLP package...

ONYX-21: user list

Jira issue originally created by user vferrett:

As a administrator, I want to see a list of user as specified in the analysis document.

ONYX-36: 2 buttons cancel but it is not clear what is the difference

Jira issue originally created by user nemond:

If you go to the height measurement, at the instrument selction (for example), you have 2 buttons cancel. One in the top and another one just beside Finish...What is the difference? Both are talking about the cancellation of the stage....

ONYX-7: wizard for initial configuration

Jira issue originally created by user nemond:

When the application is launched for the first time after installation, an configuration page is displayed instead of the normal home page. This configuration page allows specifying site-specific data:

  • Study Name (default is Cart@Gene)
  • Site Name and unique ID
  • Administrator email and password

ONYX-10: Code review for changeset 503

Jira issue originally created by user mboulang:

Added login page (LoginPage.java LoginPanel.java) and password encyption.

BasePage.java: Removed page header if not logged in.
HeaderPanel.java: Added current user logged in logout action.
OnyxApplication.java, OnyxAuthenticatedSession.java: Added authenticated session.
TestDatabaseSeed.java, User.java: Encrypt password when seeding users.

ONYX-30: Lost of the participant search result

Jira issue originally created by user vferrett:

Go to participant search.
Select current interviews
go to the interview page of richard desjardins
click back button
Bug: the participant table is empty i.e. it doesn't display anymore the current interviews

ONYX-52: sorting arrow for appointment of the day in partipant list page

Jira issue originally created by user vferrett:

in the participant list page, by default the appointment of the day are displayed.
But there is no arrow in any column indicating in which order the list is sorted.
(This should be by appointment date)

Idem when one clicks on the Appointments of the Day button.

The two other buttons display the sorting arrow

ONYX-37: Correcting spelling errors

Jira issue originally created by user nlambert:

Login: Username -> User Name

Home page: code à barre -> code-barres
démarrer -> commencer
Code barre -> Code-barres
"its" interview -> "the" interview (avoids issues with the feminists)

Participant Search page: Since the search is carried out only on the last name of the participant, label the search "Last Name"

Participant reception: Instructions:toujours en anglais.
Ask participant and ID card with photo -> Ask participant for an ID card...
Suggestions pour le français:
Demander au participant de vous présenter une carte d'identité avec photo
Valider l'information personnelle du participant
Lire un code de participant

Interview page: En français: Status -> Statut (2 endroits dans la page)
dates toujours en français (2 fois)

Dans tous les pop-ups avec commentaires: Commentaire additionnels -> Commentaire Additionnel
Raisons et Reasons-> Raison et Reason (il me semble que ça devrait être au singulier - on ne peut sélectionner qu'une raison.)
In French, the reasons are in English

Start pop-up: Instead of: "Please give some comments before starting this stage." it would be better to say "You may enter a comment before starting the stage."

Consent: Je consent -> Je consens

Dans tous les instruments, Code barre -> Code-Barres

ONYX-18: general comments on a participant

Jira issue originally created by user vferrett:

As a user, I want to be able to add and read comments on participant from reception step and from the participant interview page at any time. See document analysis for precise specification

ONYX-23: Displaying the list of users

Jira issue originally created by user nlambert:

As an administrator, I want to be able to see the list of users as per the User Profile management screen mock-up

ONYX-48: wrong page after editing profile

Jira issue originally created by user vferrett:

go to the participant list page
click on profile
click on cancel
the home page is displayed instead of the previous page i.e. the participant list page

ONYX-6: Execute stages

Jira issue originally created by user vferrett:

The user must be able to start, interrupt, resume, stop, and cancel stages following the analysis document specifications

NOTE: No "change user" feature. No comments
DS1 requires a password, DS2 does not.

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