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.

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 start or npm run start:dev for starting the backend locally
• And in the end start the e2e/api tests with running npm run test:e2e:mocha

Environment variables

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

• 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.
• 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.

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 in your MongoDB instance before you can connect this backend to it.

The scripts migrateIdFields.js and migrateIdFields.sh are located in the /scripts folder. Copy these to a location were you can access your MongoDB instance, then modify the shell script to run the script on your MongoDB instance. Once modified, start the migration by running

sh ./migrateIdFields.sh

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

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”.