SciCat Backend Next

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This repository contains the source code of the next version of the SciCat backend, which is under development. The current version of the backend is located in SciCatProject/backend.

Get started

1. git clone https://github.com/SciCatProject/scicat-backend-next.git
2. npm install
3. Add .env file to project root folder. See Environment variables.
4. Optional Add functionalAccounts.json file to project root folder. If not set up, the functional accounts in functionalAccounts.json.example will be created automatically.
5. npm run start:dev
6. Go to http://localhost:3000/explorer-next to get an overview of available endpoints and database schemas.
7. To be able to run the e2e tests with the same setup as in the Github actions you will need to run npm run prepare:local and after that run npm run start:dev. This will start all needed containers and copy some configuration to the right place.

Develop in a container using the docker-compose.dev file

1. git clone https://github.com/SciCatProject/scicat-backend-next.git
2. docker-compose -f docker-compose.dev.yaml up -d
3. Optional Mount functionalAccounts.json file to a volume in the container. If not set up, the functional accounts in functionalAccounts.json.example will be created automatically.
4. Optional change the container env variables
5. Attach to the container
6. npm run start:dev
7. Go to http://localhost:3000/explorer-next to get an overview of available endpoints and database schemas.

Test the app

1. Running the unit tests: npm run test
2. Running the e2e(api) tests:

• First of all run npm run prepare:local to prepare the local environment for starting
• After that run npm run test:api which will start the backend locally and run both jest and mocha e2e(api) tests.
• [Optional] If you want to run only the mocha tests you will need to start the backend locally with npm run start and then use npm run test:api:mocha
• [Optional] If you want to run only the jest tests you can use npm run test:api:jest

Configuration

There are multiple ways to configure your SciCat instance.

In order to configure a SciCat instance run on barebone OS, there are three options:

1. Edit directly the file src/config/configuration.ts
2. Create a .env file with your local value of the variables listed in the next session. Only the variables that are required by your installation should be defined. To create your .env file, you can copy and edit the sample .env.example provided with in code
3. Define in your environment all the necessary variables (list provided below), prior running SciCat.

If SciCat runs in a containeraized environment, like docker or kubernetes, you can run the release image and specify your configuration using one of the following two methods:

1. create .env and mount it directly in your container.
2. define the necessary environment variables directly in your container.

More information are provided in the official documentation.

Environment variables

Valid environment variables for the .env file. See .env.example for examples value formats.

• ACCESS_GROUPS_STATIC_VALUES [string] Optional Comma separated list of access groups automatically assigned to all users. Example: "scicat,user"
• ACCESS_GROUPS_SERVICE_TOKEN [string] Optional Authentication token used if access groups are obtained from a third party service. This value is not used by the vanilla installation, but only if the instance is customized to use an external service to provide user groups, like the ESS example
• ACCESS_GROUP_SERVICE_API_URL [string] Optional URL of the service providing the users' access groups. This value is not used by the vanilla installation, but only if the instance is customized to use an external service to provide user groups, like the ESS example
• DOI_PREFIX [string] The facility DOI prefix, with trailing slash.
• EXPRESS_SESSION_SECRET [string] Optional Secret used to set up express session.
• HTTP_MAX_REDIRECTS [number] Optional Max redirects for http requests. Defaults to 5.
• HTTP_TIMEOUT [number] Optional Timeout from http requests in ms. Defaults to 5000.
• JWT_SECRET [string] The secret for your JWT token, used for authorization.
• JWT_EXPIRES_IN [number] Optional How long, in seconds, the JWT token is valid. Defaults to 3600.
• LDAP_URL [string] Optional The URL to your LDAP server.
• LDAP_BIND_DN [string] Optional Bind_DN for your LDAP server.
• LDAP_BIND_CREDENTIALS [string] Optional Credentials for your LDAP server.
• LDAP_SEARCH_BASE [string] Optional Search base for your LDAP server.
• LDAP_SEARCH_FILTER [string] Optional Search filter for you LDAP server.
• OIDC_ISSUER [string] Optional URL of the oidc server providing the authentication service. Example: https://identity.esss.dk/realm/ess.
• OIDC_CLIENT_ID [string] Optional Identity of the client that we want to use to obtain the user token. Example: scicat
• OIDC_CLIENT_SECRET [string] Optional Secret to provide to the oidc service to obtain the user token. Example: Aa1JIw3kv3mQlGFWhRrE3gOdkH6xreAwro
• OIDC_CALLBACK_URL [string] Optional SciCat callback URL that we want th eoidc service to redirect to, in case of successful login. Example: http://myscicat/api/v3/oidc/callback
• OIDC_SCOPE [string] Optional Space separated list of the info returned by the oidc service. Example: "openid profile email"
• OIDC_SUCCESS_URL [string] Optional SciCat URL. It is still unclear the functionality of this URL
• OIDC_ACCESS_GROUPS [string] Optional Functionality is still unclear.
• LOGBOOK_ENABLED [string] Optional Flag to enable/disable the Logbook endpoints. Values "yes" or "no". Defaults to "no".
• LOGBOOK_BASE_URL [string] Optional The base URL to the Logbook API. Only required if Logbook is enabled.
• LOGBOOK_USERNAME [string] Optional The username used to authenticate to the Logbook API. Only required if Logbook is enabled.
• LOGBOOK_PASSWORD [string] Optional The password used to authenticate to the Logbook API. Only required if Logbook is enabled.
• METADATA_KEYS_RETURN_LIMIT [number] Optional The return limit for the /Datasets/metadataKeys endpoint.
• METADATA_PARENT_INSTANCES_RETURN_LIMIT Optional The return limit of Datasets to extract metadata keys from for the /Datasets/metadataKeys endpoint.
• MONGODB_URI [string] The URI for your MongoDB instance.
• OAI_PROVIDER_ROUTE [string] Optional URI to OAI provider, used for the /publisheddata/:id/resync endpoint.
• PID_PREFIX [string] The facility PID prefix, with trailing slash.
• PUBLIC_URL_PREFIX [string] The base URL to the facility Landing Page.
• PORT [number] Optional The port on which you want to access the app. Defaults to 3000.
• RABBITMQ_ENABLED [string] Optional Flag to enable/disable RabbitMQ consumer. Values "yes" or "no". Defaults to "no".
• RABBITMQ_HOSTNAME [string] Optional The hostname of the RabbitMQ message broker. Only required if RabbitMQ is enabled.
• RABBITMQ_USERNAME [string] Optional The username used to authenticate to the RabbitMQ message broker. Only required if RabbitMQ is enabled.
• RABBITMQ_PASSWORD [string] Optional The password used to authenticate to the RabbitMQ message broker. Only required if RabbitMQ is enabled.
• REGISTER_DOI_URI [string] URI to the organization that registers the facilities DOI's.
• REGISTER_METADATA_URI [string] URI to the organization that registers the facilities published data metadata.
• SITE [string] The name of your site.
• SMTP_HOST [string] Optional Host of SMTP server.
• SMTP_MESSAGE_FROM [string] Optional Email address that emails should be sent from.
• SMTP_PORT [string] Optional Port of SMTP server.
• SMTP_SECURE [string] Optional Secure of SMTP server.
• POLICY_PUBLICATION_SHIFT [integer] Optional Embargo period expressed in years. Default value: 3 years
• POLICY_RETENTION_SHIFT [integer] Optional Retention period (aka how long the facility will hold on to data) expressed in years. Default value: -1 (data will be hold indefinitely)

Migrating from the old SciCat Backend

Where the current SciCat Backend accepts id fields in the database named pid, doi, or similar, this implementation requires there to be an id field of the form _id on every document. It is therefore necessary to run a database migration script towards MongoDB instance from a place where you have access to it and can install migrate-mongo package.

All database migration scripts located in the migrations folder. To start the migration use:

npm run migrate:db:up

For down migration use:

npm run migrate:db:down

For listing applied DB migrations:

npm run migrate:db:status

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For the full documentation please go to the SciCat home page and follow the documentation link

Migration documentation and NestJs resources

Following are the post that I found useful working on the migration:

• Schema and DTOs: https://betterprogramming.pub/how-to-use-data-transfer-objects-dto-for-validation-in-nest-js-7ff95309f650
• Validation:
  • Official documentation
  • Custom validation with datasbase in NestJs
  • Validating nested objects with class-validator in NestJs
  • Validating numeric query parameters in NestJS
  • Injecting request object to a custom validation class in NestJS
• Swagger and OpenAPI:
  • https://docs.nestjs.com/openapi/introduction
  • https://docs.nestjs.com/openapi/types-and-parameters
  • https://docs.nestjs.com/openapi/decorators

License

This project is licensed under the GPL License - see the LICENSE file for details

Acknowledgments

Scicat is developed at PSI, ESS and MAXIV with in-kind funding from ESS and from the European Union Framework Programme for Research and Innovation Horizon 2020, under grant agreement 676548, “BrightnESS”.