SciCat Backend

Version: v4.x

NestJS implementation

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IMPORTANT!!!!

As of 2023/06/15, this repository holds the official version of SciCat backend This is the only version that is officially supported. It is commonly referred to as backend, BE, v4.x or a combination of them.

You can find the old backend (v3.x, loopback implementation) at (https://github.com/SciCatProject/backend). The repo for backend v3.x is archived and read-only

If you have any questions, please feel free to contact any member of the development team, or the SciCat team at ESS.

Contributing

If you're planning to contribute to this project by adding new functionality, we encourage you to discuss it first in the Discussions tab. This helps ensure that your proposed changes align with the project's goals and prevents duplicate efforts. Here's how you can initiate a discussion:

1. Go to the Discussions tab.
2. Start a new discussion thread outlining your proposed changes.
3. Wait for feedback and consensus before proceeding with creating a pull request.

Thank you for your interest in contributing to our project!

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 to create local users.
5. Optional Add loggers.json file to the root folder and configure multiple loggers.
6. npm run start:dev
7. Go to http://localhost:3000/explorer to get an overview of available endpoints and database schemas.
8. 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 to create local users.
4. Optional Mount loggers.json file to a volume in the container to configure multiple loggers.
5. Optional change the container env variables
6. Attach to the container
7. npm run start:dev
8. Go to http://localhost:3000/explorer 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.

Local User Accounts

Providing a file called functionalAccounts.json at the root of the project, locally or in the container, will automatically create the specified accounts on startup. If this file is not provided, no local users will be created.

Follow the structure of functionalAccounts.json.minimal.example to create your own functionalAccounts.json file.

Loggers configuration

Providing a file called loggers.json at the root of the project, locally or in the container, and create an external logger class in the src/loggers/loggingProviders/directory will automatically create specified one or multiple loggers instances.

The loggers.json.example file in the root directory showcases the example of configuration structure for the one or multiple loggers. logger.service.ts file contains the configuration handling process logic, and src/loggers/loggingProviders/grayLogger.ts includes actual usecase of grayLogger.

Environment variables

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

Environment Variable	Type	Optional	Description	Default Value
ADMIN_GROUPS	string	Yes	Comma-separated list of admin groups with admin permission assigned to the listed users. Example: "admin, ingestor". For more details check: Scicat Documentation
CREATE_DATASET_GROUPS	string	Yes	Comma-separated list of create dataset groups. Users belong to the listed groups can create dataset with/without PID. Example: "group1, group2". For more details check: Scicat Documentation
CREATE_DATASET_WITH_PID_GROUPS	string	Yes	Comma-separated list of create dataset with pid groups. Users belong to the listed groups can create dataset with PID. Example: "group1, group2". For more details check: Scicat Documentation
DELETE_GROUPS	string	Yes	Comma-separated list of delete groups. Users belong to the listed groups can delete any dataset, origDatablocks, datablocks, etc. For more details check: Scicat Documentation
DATASET_CREATION_VALIDATION_ENABLED	boolean		Flag to enable/disable dataset validation to validate if requested new dataset is valid with given regular expression. Preconfigure DATASET_CREATION_VALIDATION_REGEX variable is required.	false
DATASET_CREATION_VALIDATION_REGEX	string		Regular expression validation for new dataset request.	""
PROPOSAL_GROUPS	string	Yes	Comma-separated list of proposal groups with permission to create any proposals. Example: "proposaladmin, proposalingestor". For more details check: Scicat Documentation
SAMPLE_GROUPS	string	Yes	Comma-separated list of sample groups with permission to create any samples. Example: "sampleadmin, sampleingestor". For more details check: Scicat Documentation
ACCESS_GROUPS_GRAPHQL_ENABLED	string	Yes	Flag to enable/disable the GraphQL service to get access groups. Requires configuration of ACCESS_GROUP_SERVICE_TOKEN, ACCESS_GROUP_SERVICE_API_URL, and ACCESS_GROUP_SERVICE_HANDLER.	true
ACCESS_GROUPS_SERVICE_TOKEN	string	Yes	Authentication token used if access groups are obtained from a third-party service. 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	Yes	URL of the service providing the users' access groups. 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_HANDLER	string	Yes	Configuration property that points to the source of a module. This module provides a specific responseProcessor function for handling GraphQL responses and a query template for making GraphQL requests.
ACCESS_GROUPS_STATIC_ENABLED	string	Yes	Flag to enable/disable automatic assignment of predefined access groups to all users.	true
ACCESS_GROUPS_STATIC_VALUES	string	Yes	Comma-separated list of access groups automatically assigned to all users. Example: "scicat, user".
ACCESS_GROUPS_OIDCPAYLOAD_ENABLED	string	Yes	Flag to enable/disable fetching access groups directly from OIDC response. Requires specifying a field via OIDC_ACCESS_GROUPS_PROPERTY to extract access groups.	false
DOI_PREFIX	string		The facility DOI prefix, with trailing slash.
EXPRESS_SESSION_SECRET	string	Yes	Secret used to set up express session.
HTTP_MAX_REDIRECTS	number	Yes	Max redirects for HTTP requests.	5
HTTP_TIMEOUT	number	Yes	Timeout for HTTP requests in ms.	5000
JWT_SECRET	string		The secret for your JWT token, used for authorization.
JWT_EXPIRES_IN	number	Yes	How long, in seconds, the JWT token is valid.	3600
LDAP_URL	string	Yes	The URL to your LDAP server.
LDAP_BIND_DN	string	Yes	Bind_DN for your LDAP server.
LDAP_BIND_CREDENTIALS	string	Yes	Credentials for your LDAP server.
LDAP_SEARCH_BASE	string	Yes	Search base for your LDAP server.
LDAP_SEARCH_FILTER	string	Yes	Search filter for your LDAP server.
OIDC_ISSUER	string	Yes	URL of the OIDC server providing the authentication service. Example: https://identity.esss.dk/realm/ess.
OIDC_CLIENT_ID	string	Yes	Identity of the client used to obtain the user token. Example: scicat.
OIDC_CLIENT_SECRET	string	Yes	Secret to provide to the OIDC service to obtain the user token. Example: Aa1JIw3kv3mQlGFWhRrE3gOdkH6xreAwro.
OIDC_CALLBACK_URL	string	Yes	SciCat callback URL to redirect to after a successful login. Example: http://myscicat/api/v3/oidc/callback.
OIDC_SCOPE	string	Yes	Space-separated list of info returned by the OIDC service. Example: "openid profile email".
OIDC_SUCCESS_URL	string	Yes	SciCat Frontend auth-callback URL. Required to pass user credentials to SciCat Frontend after OIDC login. Example: https://myscicatfrontend/auth-callback.
OIDC_ACCESS_GROUPS	string	Yes	Functionality is still unclear.
OIDC_ACCESS_GROUPS_PROPERTY	string	Yes	Target field to get the access groups value from OIDC response.
OIDC_USERINFO_MAPPING_FIELD_USERNAME	string	Yes	Comma-separated list of fields from the OIDC response to use as the user's profile username. Example: OIDC_USERINFO_MAPPING_FIELD_USERNAME="iss, sub".	"preferred_username" || "name"
OIDC_USERINFO_MAPPING_FIELD_DISPLAYNAME	string	Yes	Field from the OIDC response to use as the user's profile display name. Example: OIDC_USERINFO_MAPPING_FIELD_DISPLAYNAME="preferred_username".	"name"
OIDC_USERINFO_MAPPING_FIELD_EMAIL	string	Yes	Field from the OIDC response to use as the user's profile email.	"email"
OIDC_USERINFO_MAPPING_FIELD_FAMILYNAME	string	Yes	Field from the OIDC response to use as the user's profile family name.	"family_name"
OIDC_USERINFO_MAPPING_FIELD_ID	string	Yes	Field from the OIDC response to use as the user's profile ID.	"sub" || "user_id"
OIDC_USERINFO_MAPPING_FIELD_THUMBNAILPHOTO	string	Yes	Field from the OIDC response to use as the user's profile thumbnail photo.	"thumbnailPhoto"
OIDC_USERINFO_MAPPING_FIELD_PROVIDER	string	Yes	Field from the OIDC response to use as the user's profile provider.	"iss"
OIDC_USERINFO_MAPPING_FIELD_GROUP	string	Yes	Field from the OIDC response to use as the user's profile group.	"groups"
OIDC_USERQUERY_OPERATOR	string	Yes	Specifies the operator ("or" or "and") for UserModel.findOne queries, determining the logic used to match fields like "username" or "email". Example: UserModel.findOne({$or: {"username":"testUser", "email":"test@test.com"}}).	"or"
OIDC_USERQUERY_FILTER	string	Yes	Defines key-value pairs for UserModel.findOne queries, using a "key:value" format. Example: OIDC_USERQUERY_FILTER="username:sub, email:email".	"username:username, email:email"
LOGBOOK_ENABLED	string	Yes	Flag to enable/disable the Logbook endpoints. Values "yes" or "no".	"no"
LOGBOOK_BASE_URL	string	Yes	The base URL to the Logbook API. Only required if Logbook is enabled.
METADATA_KEYS_RETURN_LIMIT	number	Yes	The return limit for the /Datasets/metadataKeys endpoint.
METADATA_PARENT_INSTANCES_RETURN_LIMIT	number	Yes	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	Yes	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	Yes	The port on which you want to access the app.	3000
RABBITMQ_ENABLED	string	Yes	Flag to enable/disable RabbitMQ consumer. Values "yes" or "no".	"no"
RABBITMQ_HOSTNAME	string	Yes	The hostname of the RabbitMQ message broker. Only required if RabbitMQ is enabled.
RABBITMQ_USERNAME	string	Yes	The username used to authenticate to the RabbitMQ message broker. Only required if RabbitMQ is enabled.
RABBITMQ_PASSWORD	string	Yes	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 facility's DOIs.
REGISTER_METADATA_URI	string		URI to the organization that registers the facility's published data metadata.
SITE	string		The name of your site.
SMTP_HOST	string	Yes	Host of SMTP server.
SMTP_MESSAGE_FROM	string	Yes	Email address that emails should be sent from.
SMTP_PORT	string	Yes	Port of SMTP server.
SMTP_SECURE	string	Yes	Secure of SMTP server.
POLICY_PUBLICATION_SHIFT	integer	Yes	Embargo period expressed in years.	3 years
POLICY_RETENTION_SHIFT	integer	Yes	Retention period (how long the facility will hold on to data) expressed in years.	-1 (indefinitely)
ELASTICSEARCH_ENABLED	string		Flag to enable/disable the Elasticsearch endpoints. Values "yes" or "no".	"no"
ES_HOST	string		Host of Elasticsearch server instance.
ES_USERNAME	string	Yes	Elasticsearch username.	"elastic"
ES_PASSWORD	string		Elasticsearch password.
MONGODB_COLLECTION	string		Collection name to be mapped into specified Elasticsearch index. Used for data synchronization between MongoDB and Elasticsearch index.
ES_MAX_RESULT	number		Maximum records that can be indexed into Elasticsearch.	10000
ES_FIELDS_LIMIT	number		The total number of fields in an index.	1000
ES_REFRESH	string		If set to wait_for, Elasticsearch will wait till data is inserted into the specified index before returning a response.	false
LOGGERS_CONFIG_FILE	string		The file name for loggers configuration, located in the project root directory.	"loggers.json"
SWAGGER_PATH	string	Yes	swaggerPath is the path where the swagger UI will be available	"explorer"

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”.