The projects service adds pathogens, projects and user management to the Overture studies workflow.
docker-compose up --builddocker exec -it app bashflask db init
flask db migrate -m "Run migrations"
flask db upgradeShould be accessible on http://localhost:5000
Currently the ability to edit and manage projects and pathogens is defined in config.py with the values:
PROJECT_GROUP = 'ego_group_id'
PATHOGEN_GROUP = 'ego_group_id'Use a .env file to control config variables.
The Projects Service requires a valid EGO generated JWT token.
GET /api/pathogens
Returns all pathogens
GET /api/pathogens/<string:id>
Returns a single pathogen
POST /api/pathogens
Creates a new pathogens
PUT /api/pathogens/<string:id>
Edits a pathogen
DELETE /api/pathogens/<string:id>
Soft deletes a pathogen
Pathogens are only used in this projects service and does not currently use any external Overture endpoints apart from optionally referencing a Song schema.
A newly created pathogen in the projects service db will have:
id: A uuid string
common_name: The common name
scientific_name: The scientific name
schema: An associated Song metadata schema name
schema_version: The schema version
created_at: Date created
updated_at: Date updated
delete_at: Date soft deletedGET /api/projects
Gets all the projects
GET /api/projects/<string:id>
Gets a project by uuid
POST /api/projects
Add a new project
POST /api/projects/<string:id>/users/<string:user_id>
Add a user to the project admin group
PUT /api/projects/<string:id>
Edits a project
DELETE /api/projects/<string:id>
soft deletes a project
DELETE /api/projects/<string:id>/users/<string:user_id>
Removes a user from project admin group
When creating a project, the projects service will:
- Create a new project in the projects service db
- Create an Ego group for project administrators
- Create and Ego policy for project administration
- Add the current user to the group
Newly created projects in the projects service db will have:
id: A uuid string
common_namtitlee: A project title
pid: A short, unique identifier
pathogen_id: The related pathogen uuid
admin_group: The Ego admin group uuid
description: A project description
owner: The Ego uuid of the user who created the project
created_at: Date created
updated_at: Date updated
delete_at: Date soft deleted
GET /api/studies
Returns all studies
GET /api/studies/<string:study_id>
Returns a single study
POST /api/studies/<string:study_id>/users/<string:user_id>/admin
POST /api/studies/<string:study_id>/users/<string:user_id>/member
Adds a user to a study. Role can be either admin or member
DELETE /api/studies/<string:study_id>/users/<string:user_id>/
Removes a user from a study group
DELETE /api/studies/<string:study_id>
soft deletes a study in the projects service db
Studies are added to a project by project administrators. When adding a new project projects service will:
- Create a new study in Song
- Create a new project in the projects service db
- Create a new Ego group for study administrators
- Create a new Ego grou for study members
- Create new Ego policies
- Add the current user to the administrators group
A new study in the projects service db will have:
id: A uuid string
study: The Song study name
project_id: The related project uuid
admin_group: The Ego admin group uuid
member_group: The Ego member group uuid
created_at: Date created
updated_at: Date updated
delete_at: Date soft deleted
Please read the Swagger docs here: http://localhost:5000/swagger.
API documentation may be incomplete.
Test are in /app/tests/ and can be run with pytest app/tests/