Configuration
SciCat Frontend
This is the configuration file for the frontend client. The configuration file allows the systems administrator to configure every aspect of the client including switching on/off almost all non essential features. The configuration file can either be served from the backend, via the /client/config.json endpoint or mounted into the docker container at the following path /usr/share/nginx/html/assets/config.json.
An example is shown below
frontend/src/assets/config.json:
{
"accessTokenPrefix": "", // Set the backend token prefix. Should be empty string for current backend or "Bearer " if using scicat-backend-next.
"addDatasetEnabled": true, // Show/hide the "Create Dataset" button in the Datasets Dashboard.
"archiveWorkflowEnabled": true, // Enable/disable the archive/retrieve workflow.
"datasetReduceEnabled": true, // Enable/disable the automatic Dataset reduction/analysis workflow.
"editDatasetSampleEnabled": true, // Enable/disable editing of which Sample a Dataset belongs to.
"editMetadataEnabled": true, // Enable/disable editing of Scientific Metadata.
"editPublishedData": true, // Enable/disable editing of Published Data.
"editSampleEnabled": true, // Enable/disable editing of Samples.
"externalAuthEndpoint": "/auth/msad", // Endpoint used for third party authentication, e.g, LDAP.
"facility": "ESS", // Facility running the SciCat instance.
"fileColorEnabled": true, // Enable/disable file size color representation in the Datasets Dashboard.
"fileDownloadEnabled": true, // Enable/disable download workflow for Dataset datafiles.
"gettingStarted": null, // URL to Getting Started guide for SciCat, displayed on the Help page.
"ingestManual": null, // URL to Ingest Manual for SciCat, displayed on the Help page.
"jobsEnabled": true, // Enable/disable Job workflow.
"jsonMetadataEnabled": true, // Show/hide the "Show Metadata" button on the details pages, allowing users to see the JSON represantion of the current document.
"jupyterHubUrl": "https://jupyterhub.esss.lu.se/", // URL to Jupyter Hub instance used for data analysis.
"landingPage": "doi2.psi.ch/detail/", // URL to the facility's Landing Page for Published Data.
"lbBaseURL": "http://127.0.0.1:3000", // URL to the SciCat Backend.
"localColumns": [ // Default columns to be displayed in the table on the Datasets Dashboard.
{
"name": "select",
"order": 0,
"type": "standard",
"enabled": true
},
{
"name": "datasetName",
"order": 1,
"type": "standard",
"enabled": true
},
{
"name": "runNumber",
"order": 2,
"type": "standard",
"enabled": true
},
{
"name": "sourceFolder",
"order": 3,
"type": "standard",
"enabled": true
},
{
"name": "size",
"order": 4,
"type": "standard",
"enabled": true
},
{
"name": "creationTime",
"order": 5,
"type": "standard",
"enabled": true
},
{
"name": "type",
"order": 6,
"type": "standard",
"enabled": true
},
{
"name": "image",
"order": 7,
"type": "standard",
"enabled": true
},
{
"name": "metadata",
"order": 8,
"type": "standard",
"enabled": true
},
{
"name": "proposalId",
"order": 9,
"type": "standard",
"enabled": true
},
{
"name": "ownerGroup",
"order": 10,
"type": "standard",
"enabled": false
},
{
"name": "dataStatus",
"order": 11,
"type": "standard",
"enabled": false
}
],
"logbookEnabled": true, // Enable/disable SciChat Logbook integration.
"loginFormEnabled": true, // Enable/disable the local Login form. Should be disabled if using oAuth2 for authentication.
"maxDirectDownloadSize": 5000000000, // Set a maximum allowed file size for downloading datafiles over HTTP.
"metadataPreviewEnabled": true, // Enable/disable Scientific Metadata preview on the Datasets Dashboard.
"metadataStructure": "tree", // Allow tree structure for Scientific Metadata. Set to empty string for flat structure.
"multipleDownloadAction": "http://localhost:3012/zip", // URL to service handling direct download of datafiles.
"multipleDownloadEnabled": true, // Enable/disable ability to download multiple datafiles.
"oAuth2Endpoints": [], // List of endpoints used for oAuth2 authentication.
"policiesEnabled": true, // Enable/disable Dataset Policies workflow.
"retrieveDestinations": [], // List of destinations for Dataset retrievals.
"riotBaseUrl": "http://scitest.esss.lu.se/riot", // URL to SciChat client.
"scienceSearchEnabled": true, // Enable/disable filtering documents on Scientific Metadata.
"scienceSearchUnitsEnabled": true, // Enable/disable filtering documents on Scientific Metadata using units.
"searchPublicDataEnabled": true, // Enable/disable filtering Datasets on public or non-public data.
"searchSamples": true, // Enable/disable searching Samples on Samples Dashboard.
"sftpHost": "login.esss.dk", // URL to SFTP service used for downloading files exceeding maximum allowed file size.
"shareEnabled": true, // Enable/disable workflow for sharing Datasets with other users using their email address.
"shoppingCartEnabled": true, // Enable/disable the Dataset cart used for bulk actions.
"shoppingCartOnHeader": true, // Toggle Dataset cart placement, either on header or to the left on the Datasets Dashboard.
"tableSciDataEnabled": true // Enable/disable Scientific Metadata table view on details pages. If disabled, Scientific Metadata is displayed as raw JSON.
}
SciCat Backend
Dotenv config
This is the configuration file for the backend. This file allows the systems administrator to configure connected services, like authentication services and message queues, and also switching on/off almost all non essential features. The configuration file is a dotenv file and is read by the backend at runtime.
An example is shown below
backend/.env
ACCESS_GROUPS_STATIC_VALUES="group1,group2,group3,..." // List of groups assigned by default as access groups to all users. Used in the vanilla implementation. Facilities customization might not use this
ACCESS_GROUP_SERVICE_TOKEN="90f126864824ede0e22f7b4407aa1a5cd8158e6cabbce39aaf091937589f1750" // Token needed to access the API specified in ACCESS_GROUP_SERVICE_API_URL
ACCESS_GROUP_SERVICE_API_URL="https://my.access.group/service/api/url" // Url of the service API which is used to provide access groups. At the moment only one value is allowed
DOI_PREFIX="<DOI_PREFIX>" // The facility DOI prefix, with trailing slash.
EXPRESS_SESSION_SECRET="<EXPRESS_SESSION_SECRET>" // *Optional* Secret used to set up express session.
HTTP_MAX_REDIRECTS=5 // *Optional* Max redirects for http requests. Defaults to 5.
HTTP_TIMEOUT=5000 // *Optional* Timeout from http requests in ms. Defaults to 5000.
JWT_SECRET=<JWT_SECRET> // The secret for your JWT token, used for authorization.
JWT_EXPIRES_IN=3600 // *Optional* How long, in seconds, the JWT token is valid. Defaults to `3600`.
LDAP_URL="ldaps://ldap.server.com:636/" // *Optional* The URL (and port) to your LDAP server.
LDAP_BIND_DN="<USERNAME>@server.com" // *Optional* Bind_DN for your LDAP server.
LDAP_BIND_CREDENTIALS=<PASSWORD> // *Optional* Credentials for your LDAP server.
LDAP_SEARCH_BASE=<SEARCH_BASE> // *Optional* Search base for your LDAP server.
LDAP_SEARCH_FILTER="(LDAPUsername={{username}})" // *Optional* Search filter for you LDAP server.
OIDC_ISSUER="https://identity.your.facility/your/realm" // Full URL of the identity provider
OIDC_CLIENT_ID= "scicat" // Client id used to convert OIDC code to OIDC token. This is assigned in the OIDC service when the token is generated
OIDC_CLIENT_SECRET="90f126864824ede0e22f7b4407aa1a5cd8158e6cabbce39aaf091937589f1750" // Token used to convert OIDC code to OIDC token. This is assigned in the OIDC service when the token is generated
OIDC_CALLBACK_URL="http://localhost:3000/api/v3/oidc/callback" // URL of the endpoint that is called when the authentication has been executed with the OIDC service.
OIDC_SCOPE="openid profile email" // Information returned by the OIDC service together with token"
OIDC_SUCCESS_URL="http://localhost:3000/explorer" // URL of the endpoint that is called after a successful authentication. IT is not used in the vanilla implementaation.
OIDC_ACCESS_GROUPS="access_groups" // field used to retrieve access groups from the OIDC service. It is not used in the vanilla implementation.
LOGBOOK_ENABLED=<"yes"|"no"> // *Optional* Flag to enable/disable the Logbook endpoints. Values "yes" or "no". Defaults to "no".
LOGBOOK_BASE_URL="http://localhost:3030/scichatapi" // *Optional* The base URL to the SciChat wrapper API. Only required if Logbook is enabled.
LOGBOOK_USERNAME="<LOGBOOK_USERNAME>" // *Optional* The username used to authenticate to the SciChat wrapper API. Only required if Logbook is enabled.
LOGBOOK_PASSWORD="<LOGBOOK_PASSWORD>" // *Optional* The password used to authenticate to the SciChat wrapper API. Only required if Logbook is enabled.
METADATA_KEYS_RETURN_LIMIT=100 // *Optional* The return limit for the `/Datasets/metadataKeys` endpoint.
METADATA_PARENT_INSTANCES_RETURN_LIMIT=100 // *Optional* The return limit of Datasets to extract metadata keys from for the `/Datasets/metadataKeys` endpoint.
MONGODB_URI="mongodb://<USERNAME>:<PASSWORD>@<HOST>:27017/<DB_NAME>" // The URI for your MongoDB instance.
OAI_PROVIDER_ROUTE="<OAI_PROVIDER_ROUTE>" // *Optional* URI to OAI provider, used for the `/publisheddata/:id/resync` endpoint.
PID_PREFIX="<PID_PREFIX>" // The facility PID prefix, with trailing slash.
PUBLIC_URL_PREFIX="https://doi.ess.eu/detail/" // The base URL to the facility Landing Page.
PORT=3000 // *Optional* The port on which you want to access the app. Defaults to `3000`.
RABBITMQ_ENABLED=<"yes"|"no"> *Optional* Flag to enable/disable RabbitMQ consumer. Values "yes" or "no". Defaults to "no".
RABBITMQ_HOSTNAME="localhost" // *Optional* The hostname of the RabbitMQ message broker. Only required if RabbitMQ is enabled.
RABBITMQ_USERNAME="rabbitmq" // *Optional* The username used to authenticate to the RabbitMQ message broker. Only required if RabbitMQ is enabled.
RABBITMQ_PASSWORD="rabbitmq" // *Optional* The password used to authenticate to the RabbitMQ message broker. Only required if RabbitMQ is enabled.
REGISTER_DOI_URI="https://mds.test.datacite.org/doi" // URI to the organization that registers the facilities DOIs.
REGISTER_METADATA_URI="https://mds.test.datacite.org/metadata" // URI to the organization that registers the facilities published data metadata.
SITE=<SITE> // The name of your site.
SMTP_HOST=<SMTP_HOST> // Host of SMTP server.
SMTP_MESSAGE_FROM=<SMTP_MESSAGE_FROM> // Email address that emails should be sent from.
SMTP_PORT=<SMTP_PORT> // Port of SMTP server.
SMTP_SECURE=<SMTP_SECURE> // Secure of SMTP server.
DOI Config
This config file contains the username and password for authenicating against your DOI provider, e.g., DataCite, which is used when registering the DOI and metadata of your published data.
backend/src/config/doiconfig.local.json
{
"username": "<DOI_CONFIG_USERNAME>",
"password": "<DOI_CONFIG_PASSWORD>"
}