nfdi4chem / nmrxiv Goto Github PK

perform php unit test of features before deploying code to the server.

As a developer, I want to notify the admin to explicitly change the default password for super-admin.

As a developer, I want to add the default option for the Role dropdown in the Filter section.

As a developer, I want to create a workflow in GitHub Action for the Continous Deployment pipeline to GKE.

As a user I should be able to perform the below task in the nmrXiv platform:

1. register and create my account on the website.
2. login to the website with my existing ID.
3. should be able to confirm my account (via email).
4. reset my password(forgot password).
5. able to delete my account if required.
6. update my profile(email,name,Photo)

As a user I should be able to perform single sing-on in nmrXiv platform using anyone of the my below Ids.

1. GitHub.
2. Twitter.
3. ORCHID.

Describe the bug
When trying to upload picture to my profile, its getting failed.

To Reproduce
Steps to reproduce the behavior:

1. Go to Profile.
2. Click on Select a New Photo.

Expected behavior
It should allow uploading the photo and reflect as a profile picture.

As a developer, I want to conditionally render the single sign-on buttons on the basis of the Client ID in .env file.

Global

• super-admins - roles, read/write all data, stats on the platform
• curators - read/write, stats (UI)
• community-curators - read, stats
• advisor - read, stats
• developer - read (API), r/w owned studies

Team / Project

• owner - read/write
• collaborator - comment (private)
• reviewer - read only (optional)

As a developer, I want to change the default README.md file in the repo and add the nmrXiv logo and details about the project.

Describe the bug
When we accept the team invitation, success notification is being hidden behind the side bar

To Reproduce
Steps to reproduce the behavior:

1. Add a new team member to the team
2. Team member creates account and clicks on the accept invitation in the email
3. Success notification is displayed but hidden behind the side bar

Expected behavior
Notification bar should be on top of all the elements on the page

Screenshots

Desktop (please complete the following information):

• Browser [chrome]
• Version [Version 96.0.4664.55 (Official Build) (x86_64)]
• OS - MacOS Monterey 12.0.1

Right now nmrXiv-doc and app are deployed in GKE in two separate clusters.
As a developer, I want to merge them into a single cluster and create Ingress in order to route the request.

Description: Ability to

• Version study based on parent/child relationship of the models
• Metadata needs to be copied
• Original files must be symlinked while new files/file updated must have real links (backups)
• DOI versioning

As a developer, I want to provide a cancel button option when the super-admin tries to edit the User's information.
Console --> Users --> Edit.

As a developer, I want to integrate Minio with the nmrXiv application and perform testing of file uploads.

Add audit trails to any models (projects, studied, users etc.)

Description: Implement the following options in the study details view

• Ability to select a colour for the study
• Star the study, so they are easily retrievable
• Option to archive study in the study settings page (Option will be provided only for the project)
• #510
• #509

Description: Studies view to be rendered as cards instead of the list by default

• Render cards
• Use the header image (study_photo_path) or placeholder if not provided

Model generation documentation: https://laravel.com/docs/8.x/eloquent#generating-model-classes

Describe the bug
The common search tab is not working.

To Reproduce
Steps to reproduce the behavior:

1. log in to nmrXiv.
2. Use the search option.
3. No result gets displayed.

Expected behavior
It should have highlighted the options searched for.

Describe the bug
Single Sign-On not working for ORCID.

To Reproduce
Steps to reproduce the behavior:

1. Go to nmrXiv
2. Click on login
3. Click on Login via ORCID
4. Routing to unauthorized page

Expected behavior
The link should allow user to login via ORCID.

Upgrade DB from MySQL to PostgreSQL.

As a developer, I want the bootstrap the basic CRUD Laravel project for nmrXiv.

As a developer, I want to create a workflow in GitHub Actions for Continuous Integration, which needs to be passed first in order to get deployed.

Ability to:

• #785
• Trigger download

As a developer, I want to change the theme color of the application and all pages wherever applicable to a more professional color.
Options:

• #33B0C9

Describe the bug
Not able to delete the project when logged in via single sign-on option.

To Reproduce
Steps to reproduce the behavior:

1. Click on Login button.
2. Sign in via any of the single sign-on option.
3. Create a new project
4. Go to Project setting
5. Click on Delete Project button.
6. Ask for password to delete.

Expected behavior
The user should have a password to provide in order to delete. But when you log in via single sing-on you don't have a password.

Description: To be able to delete study from the study settings page

• Password confirmation before delete
• Move study to a dormant stage
• #422
• Ability to restore back to the normal state within this cool-off period
• Delete all backups / Indexes or reindex
• #423

Adding tests: https://laravel.com/docs/8.x/testing#running-tests-in-parallel

Ability to

• Deploy Meili search node
• Update the env and config search parameters, create indexes
• Make study / projects searchable
• Define hidden fields
• Cast model properties
• Implement UI search functionality
• Highlight the matched content
• Reindex triggers
• Export indexes (backups)

Description:
Enable users to create one or more studies within a project. Studies associated with a project are all accessible to the team members. The study owner should also be able to provide explicit study access to an external user who is not a member of the project.

• Add basic study model, migration, controller, UI to enable CRUD operation
• Associate study with user/team
• Audit tracking / Activity
• #44
• #43
• #45
• #46
• #47
• #48
• #49
• #50
• #51
• #52
• #53

As a developer, I want to create cluster and deplyment environment for staging in GKE, accessible via the below URL.
https://staging.nmrxiv.org/
This environment will be purely used only by developers to test their features.

Seeder / Factory : https://laravel.com/docs/8.x/seeding#writing-seeders

Generating migrations: https://laravel.com/docs/8.x/migrations#generating-migrations
DB Schemas column types: https://laravel.com/docs/8.x/migrations#available-column-types

Describe the bug

On dev.nmrxiv.org the cookie banner has links:
for https://dev.nmrxiv.org/privacy-policy there is a stub,
for https://dev.nmrxiv.org/terms I get a 404

Yours,
Steffen

Description:

• Deploy minio to the cluster (VM)
• #81
• #82
  - [x] Use Laravel Vapor.js to upload files
  - [ ] Direct file copy from S3 compatible buckets
  - [ ] API end points to retrieve files list
  - [ ] UI rendering
• Backups
• BagIt implementation
  - [ ] Generate file checksums
  - [ ] Meta data files
• Sanitise tmp folders
• Activity logging (Audit)

Description: Add ability to

• Provide an email of the user to whom the study needs to be transferred (user must be preregistered)
• Move the study to a different project within the user teams
• Audit the ownership transfer
• Email the study owners ~ associated project owners

Description:

• Public status - generate a unique URL with study slug
• Private - offered with 2 options
• Restricted - only users in the team and users with explicit study access can access it (URL - with random string ~ should not be guessable)
• Link - Generate a unique link ~ grant either "Readonly", "Commentable", "Edit"

Describe the bug
Learn more about sharing link not working in View details tab.

To Reproduce
Steps to reproduce the behavior:

1. Login
2. Go to any particular study.
3. Click on the View Details option in the top.
4. Click on Learn more about sharing link.
5. Not clickable.

Expected behavior
It should route to the proper link.

As a developer, I want to perform basic deployment of the project to GKE and complete the setup development enviroment accessible via the below URL.
https://dev.nmrxiv.org/

As a developer, I want to develop a banner(environment-specific) on the home page where any quick information/warning can be conveyed to the user.

Description: Add image upload option to the study details view (study_photo_path field is already provided)

Description:
Users with a specific role(s) should be able to access an announcements page in the console and create an announcement to be active from a start date to an end date. A scheduled task should check the time interval and set it as active or inactive (admins should also be able to override the start date). When an active announcement is available the information is then passed on to the front end (App layout) to be displayed on all pages. The user should be able to dismiss the announcement (tracked via local storage) and then the announcement is not shown for the user.

Implementation steps

• #66
• #67
• #68
• #69
• #70
• #71
• #72
• #73
• #96
• #27

Add controller: https://laravel.com/docs/8.x/controllers
Inertia / Jetstream: https://jetstream.laravel.com/2.x/stacks/inertia.html

Description: Ability to add a user who is not part of the team owning the study/project to a particular study

• Define user - studies relationship
• Send an invitation email
• Add the study to their shared list / own workspace or add the parent project to the workspace

Description: Ability to

• Download metadata files
• Zip any raw files and download
• #784

As a developer, I want to create a workflow in GitHub Action for the Continous Deployment pipeline to GKE.