Configuration¶
When running a SampleDB installation, you can set environment variables to configure it. The following sections will describe groups of such variables and their effects.
E-Mail¶
Variable Name |
Description |
|---|---|
SAMPLEDB_CONTACT_EMAIL |
An email address for users to contact |
SAMPLEDB_MAIL_SENDER |
The email address used for outbound emails |
SAMPLEDB_MAIL_SERVER |
The mail server used for outbound emails |
SAMPLEDB_MAIL_PORT |
The port to use for connections to the mail server (default: |
SAMPLEDB_MAIL_USE_TLS / SAMPLEDB_MAIL_USE_SSL |
Whether to use TLS or SSL for connections to the mail server (default: |
SAMPLEDB_MAIL_USERNAME |
The username sent to the mail server |
SAMPLEDB_MAIL_PASSWORD |
The password sent to the mail server |
While the SAMPLEDB_CONTACT_EMAIL, SAMPLEDB_MAIL_SENDER and SAMPLEDB_MAIL_SERVER variables are required, you may need to set one or more of the other variables to connect to your mail server, depending on its configuration.
LDAP¶
Variable Name |
Description |
|---|---|
SAMPLEDB_LDAP_NAME |
The name of the LDAP server shown to the users |
SAMPLEDB_LDAP_SERVER |
The ldaps-URL of the LDAP server, or a comma separated list of ldaps-URLs to use more than one LDAP server |
SAMPLEDB_LDAP_CONNECT_TIMEOUT |
The timeout to use for connecting to the LDAP server(s) |
SAMPLEDB_LDAP_USER_BASE_DN |
The LDAP base DN to search users with |
SAMPLEDB_LDAP_UID_FILTER |
The filter to use for identifying a user in LDAP as python template, e.g. |
SAMPLEDB_LDAP_NAME_ATTRIBUTE |
The name of the attribute containing a user’s name in LDAP, e.g. |
SAMPLEDB_LDAP_MAIL_ATTRIBUTE |
The name of the attribute containing a user’s email address in LDAP, e.g. |
SAMPLEDB_LDAP_OBJECT_DEF |
The object def to use for looking up user attributes, e.g. inetOrgPerson |
SAMPLEDB_LDAP_USER_DN |
The DN of an LDAP user to use when searching for other users |
SAMPLEDB_LDAP_PASSWORD |
The password for the user identified by SAMPLEDB_LDAP_USER_DN |
SAMPLEDB_TESTING_LDAP_LOGIN |
The uid of an LDAP user (only used during tests) |
SAMPLEDB_TESTING_LDAP_PW |
The password for the ldap user identified by SAMPLEDB_TESTING_LDAP_LOGIN (only used during tests) |
If you use LDAP for user management, you can use these variables to configure how SampleDB should connect to your LDAP server.
Customization¶
Variable Name |
Description |
|---|---|
SAMPLEDB_SERVICE_NAME |
The name of the service |
SAMPLEDB_SERVICE_DESCRIPTION |
A short description of the service |
SAMPLEDB_SERVICE_LEGAL_NOTICE or SAMPLEDB_SERVICE_IMPRINT |
The URL to use for the legal notice link |
SAMPLEDB_SERVICE_PRIVACY_POLICY |
The URL to use for the privacy policy link |
SAMPLEDB_SERVICE_ACCESSIBILITY |
The URL to use for the accessibility link |
SAMPLEDB_PDFEXPORT_LOGO_URL |
A file, http or https URL for a PNG or JPEG logo to be included in object export PDF documents |
SAMPLEDB_PDFEXPORT_LOGO_ALIGNMENT |
The alignment (left, center or right) of the logo, if SAMPLEDB_PDFEXPORT_LOGO_URL is set (default: right) |
SAMPLEDB_HELP_URL |
The URL to use for the help link |
You can use these variables to customize how your SampleDB instance is called, described and which links are included in the footer. The logo at the given PDFEXPORT_LOGO_URL will be fetched when SampleDB is started and cached afterwards. To refresh the logo, you will need to restart SampleDB.
JupyterHub Support¶
Variable Name |
Description |
|---|---|
SAMPLEDB_JUPYTERHUB_NAME |
The name of your JupyterHub server (default: |
SAMPLEDB_JUPYTERHUB_URL |
The base URL of your JupyterHub server |
SAMPLEDB_JUPYTERHUB_TEMPLATES_URL |
The URL of a Jupyter notebook templating server (default: SAMPLEDB_JUPYTERHUB_URL + |
For more information on JupyterHub support and Jupyter notebook templates, see JupyterHub Support.
Dataverse Export¶
Variable Name |
Description |
|---|---|
SAMPLEDB_DATAVERSE_NAME |
The name of the Dataverse server (default: |
SAMPLEDB_DATAVERSE_URL |
The base URL of the Dataverse server |
SAMPLEDB_DATAVERSE_ROOT_IDS |
A comma seperated list of IDs of Dataverses, which objects may be exported to (default: |
For more information on the Dataverse export, see Dataverse Export.
SciCat Export¶
Variable Name |
Description |
|---|---|
SAMPLEDB_SCICAT_NAME |
The name of the SciCat instance (default: |
SAMPLEDB_SCICAT_API_URL |
The base URL of the SciCat API server |
SAMPLEDB_SCICAT_FRONTEND_URL |
The base URL of the SciCat frontend server |
SCICAT_EXTRA_PID_PREFIX |
An additional prefix to use for generating persistent identifiers in combination with a UUID |
For more information on the SciCat export, see SciCat Export.
Download Service¶
Variable Name |
Description |
|---|---|
DOWNLOAD_SERVICE_URL |
The base URL of the Download Service |
DOWNLOAD_SERVICE_SECRET |
The shared secret |
DOWNLOAD_SERVICE_WHITELIST |
Whitelist in form of a json dict. Example: {“/normally/restricted/path/”: [userID, userID2]} |
DOWNLOAD_SERVICE_TIME_LIMIT |
Time the created download link is valid. In seconds. Default are 24h. |
For more information on the Download Service, see Download Service.
Administrator Account¶
Variable Name |
Description |
|---|---|
SAMPLEDB_ADMIN_PASSWORD |
The password for the admin account. |
SAMPLEDB_ADMIN_USERNAME |
The username for the admin account (default: |
SAMPLEDB_ADMIN_EMAIL |
The email address for the admin account (default: SAMPLEDB_CONTACT_EMAIL) |
If no users exist yet and the SAMPLEDB_ADMIN_PASSWORD variable is set, a new user will be created with this password. This user will be a SampleDB admin. The username for this user will be set to value of SAMPLEDB_ADMIN_USERNAME and the email address for this user will be set to the value of SAMPLEDB_ADMIN_EMAIL.
If another user already exists, these variables will have no effect. It is meant for creating an administrator account as part of the initial setup.
Federation¶
Variable Name |
Description |
|---|---|
SAMPLEDB_FEDERATION_UUID |
This instance’s federation UUID. See Federation for details |
SAMPLEDB_ALLOW_HTTP |
If set, insecure communication to other databases via HTTP will be allowed. |
SAMPLEDB_VALID_TIME_DELTA |
Valid time delta between SampleDB instances in a federation in seconds (default: |
SAMPLEDB_ENABLE_DEFAULT_USER_ALIASES |
If set, users will have aliases using their profile information by default (default: False). This will not apply to bot users or imported users. |
SAMPLEDB_ENABLE_FEDERATION_DISCOVERABILITY |
If set, this instance will be discoverable by other databases in the same federation. (default: True). |
Monitoring Dashboard¶
Variable Name |
Description |
|---|---|
SAMPLEDB_ENABLE_MONITORINGDASHBOARD |
If set, the monitoring dashboard will be enabled. |
SAMPLEDB_MONITORINGDASHBOARD_DATABASE |
The database URL for the monitoring dashboard (default: |
Miscellaneous¶
Variable Name |
Description |
|---|---|
SAMPLEDB_FILE_STORAGE_PATH |
A path to the directory that uploaded files should be stored in |
SAMPLEDB_SERVER_NAME |
The server name for Flask. See: https://flask.palletsprojects.com/en/1.1.x/config/#SERVER_NAME |
SAMPLEDB_SQLALCHEMY_DATABASE_URI |
The database URI for SQLAlchemy. See: https://flask-sqlalchemy.palletsprojects.com/en/2.x/config/ |
SAMPLEDB_SECRET_KEY |
The secret key for Flask and Flask extensions. See: https://flask.palletsprojects.com/en/1.1.x/config/#SECRET_KEY |
SAMPLEDB_WTF_CSRF_TIME_LIMIT |
The time limit for WTForms CSRF tokens in seconds. See: https://flask-wtf.readthedocs.io/en/stable/config.html |
SAMPLEDB_INVITATION_TIME_LIMIT |
The time limit for invitation links in seconds. |
SAMPLEDB_ONLY_ADMINS_CAN_MANAGE_LOCATIONS |
If set, only administrators will be able to create and edit locations. |
SAMPLEDB_ONLY_ADMINS_CAN_CREATE_GROUPS |
If set, only administrators will be able to create basic groups. |
SAMPLEDB_ONLY_ADMINS_CAN_DELETE_GROUPS |
If set, only administrators will be able to delete non-empty basic groups. |
SAMPLEDB_ONLY_ADMINS_CAN_CREATE_PROJECTS |
If set, only administrators will be able to create project groups. |
SAMPLEDB_DISABLE_USE_IN_MEASUREMENT |
If set, the “Use in Measurement” button will not be shown. |
SAMPLEDB_DISABLE_SUBPROJECTS |
If set, project groups cannot have child project groups assigned to them. |
SAMPLEDB_ENFORCE_SPLIT_NAMES |
If set, force names to be entered as “surname, given names”. Note: this will prevent users with a mononym from setting their name correctly! |
SAMPLEDB_PYBABEL_PATH |
The path to the pybabel executable (default: |
SAMPLEDB_EXTRA_USER_FIELDS |
A JSON-encoded dict containing extra user fields, e.g. |
SAMPLEDB_SHOW_PREVIEW_WARNING |
If set, a warning will be shown indicating that the instance is a preview installation and that data will be deleted. |
SAMPLEDB_DISABLE_INLINE_EDIT |
If set, the inline edit mode will be disabled and users will not be able to edit individual fields. |
SAMPLEDB_SHOW_OBJECT_TITLE |
If set, object schema titles will be shown when viewing metadata by default. Users may override this setting in their preferences. |
SAMPLEDB_FULL_WIDTH_OBJECTS_TABLE |
If set, the table of objects will be the full width of the browser. Users may override this setting in their preferences. (default: True) |
SAMPLEDB_HIDE_OBJECT_TYPE_AND_ID_ON_OBJECT_PAGE |
If set, the object type and id, e.g. “Sample #4” will not be shown on the object page. |
SAMPLEDB_MAX_BATCH_SIZE |
Maximum number of objects that can be created in one batch (default: 100) |
SAMPLEDB_ENABLE_BACKGROUND_TASKS |
If set, some potentially time consuming tasks such as sending emails will be performed in the background to reduce frontend latency or timeouts. |
SAMPLEDB_TIMEZONE |
If set, the given timezone will be used for all users instead of using their browser timezone or the one set in their preferences. |
SAMPLEDB_USE_TYPEAHEAD_FOR_OBJECTS |
Experimental: If set, a text field with typeahead.js based suggestions will be used for object references instead of a dropdown/select field. |
SAMPLEDB_TYPEAHEAD_OBJECT_LIMIT |
If SAMPLEDB_USE_TYPEAHEAD_FOR_OBJECTS is set, this value can set an upper limit for the number of object suggestions shown. Not set by default. |
SAMPLEDB_ENABLE_ANONYMOUS_USERS |
If set, objects may be set to be readable by anonymous users, without requiring them to sign in. |
SAMPLEDB_SHOW_UNHANDLED_OBJECT_RESPONSIBILITY_ASSIGNMENTS |
If set, any unhandled object responsibility assignment will be shown as an urgent notification on non-object pages (default: True). |
SAMPLEDB_SHOW_LAST_PROFILE_UPDATE |
If set, show the date and time of the last user information update in each user profile (default: True). Updates by an administrator will be shown regardless of this configuration value. |
SAMPLEDB_ONLY_ADMINS_CAN_MANAGE_GROUP_CATEGORIES |
If set, only administrators will be able to manage group categories (default: True). |
SAMPLEDB_DISABLE_INSTRUMENTS |
If set, features related to instruments will be disabled (default: False). |
SAMPLEDB_ENABLE_FUNCTION_CACHES |
If set, some functions with results that cannot change will use caches (default: True). |
SAMPLEDB_TEMPORARY_FILE_TIME_LIMIT |
Time that temporary files uploaded when editing an object are stored, in seconds (default: 604800 seconds / 7 days). |
SAMPLEDB_ENABLE_ELN_FILE_IMPORT |
If set, .eln files can be imported by users (default: False). Importing .eln files is currently experimental and not recommended for production systems, as the file format is still a work in progress. |
SAMPLEDB_ENABLE_WEBHOOKS_FOR_USERS |
If set, “normal” users can register webhooks (default: False). If this option is not set or set to |
SAMPLEDB_WEBHOOKS_ALLOW_HTTP |
If set, using webhook targets that do not support https is allowed (default: False). |
There are other configuration values related to packages used by SampleDB. For more information on those, see the documentation of the corresponding packages.
