.env.example

# rename this file to .env and change the values to match your settings

# ########################################################################## #
# ########################## General Settings ############################## #
# ########################################################################## #

## The following variable defines whether the file finding will be "exclusive",
## meaning that records will only include files for which NexusLIMS has an explicit
## metadata extractor defined (see https://datasophos.github.io/NexusLIMS/stable/),
## or "inclusive", meaning that records will include all files, with basic
## metadata defined for files without a NexusLIMS extractor. The variable should
## be either the string 'exclusive' or 'inclusive'. If no value (or a value other than
## those two) is given, the default 'exclusive' strategy will be used.

NX_FILE_STRATEGY='exclusive'
# NX_FILE_STRATEGY='inclusive'

## The following variable defines patterns that will be ignored when searching
## for files that are part of an Experiment. This value can be tailored to
## exclude files that may not be of interest depending on what instruments
## are producing data. The values should be in a string representing a JSON array,
## meaning it is surrounded by single apostrophe (') characters, and each
## individual pattern is surrounded by quotation mark (") characters, separated
## by commas. The patterns should follow the same syntax as the '-name' argument
## to the GNU find command (see https://manpages.org/find)

NX_IGNORE_PATTERNS='["*.mib","*.db","*.emi","*.hdr"]'

## The following value is used to authenticate to the
## CDCS API for uploading built records to the
## front-end record repository (see https://github.com/datasophos/NexusLIMS-CDCS).
## Obtain this token from the CDCS admin panel or via the API token endpoint.

NX_CDCS_TOKEN='your-api-token-here'

## The following value should be set to the root URL of the NexusLIMS CDCS
## front-end (the one installed using https://github.com/datasophos/NexusLIMS-CDCS).
## This will be the target for record uploads using the NX_CDCS_TOKEN above
## (should include the trailing slash)

NX_CDCS_URL='https://nexuslims.domain.com/'

## Per-user record ownership in CDCS (optional)
## When true, NexusLIMS looks up or creates a CDCS user account matching the
## NEMO session user and assigns record ownership accordingly. Requires the
## NX_CDCS_TOKEN to belong to a superuser account. Default: false.

# NX_CDCS_USER_OWNED_RECORDS='false'

## When true (default), uploaded records are assigned to the global public
## workspace so all users can browse them. Set false only in combination with
## NX_CDCS_USER_OWNED_RECORDS=true to keep records in the user's private space.

# NX_CDCS_ASSIGN_TO_PUBLIC_WORKSPACE='true'

## LabArchives API configuration (optional)
## If configured, records will also be exported to LabArchives in addition to CDCS.
## If not configured, LabArchives export will be disabled.

# NX_LABARCHIVES_ACCESS_KEY_ID='your-access-key-id-here'
# NX_LABARCHIVES_ACCESS_PASSWORD='your-access-password-here'
# NX_LABARCHIVES_USER_ID='your-user-id-uid-here'
# NX_LABARCHIVES_URL='https://api.labarchives.com/api'  # default for cloud LabArchives
# NX_LABARCHIVES_NOTEBOOK_ID=''  # Optional: target notebook ID (nbid)

## The following value (for development) should be set to the root URL of a
## NexusLIMS CDCS instance to use for testing. If defined, this URL will be
## used for the CDCS tests rather than the "actual" URL defined above. If not
## defined, the CDCS tests will be skipped so the tests do not impact the production
## deployment.

# NX_EXPORT_STRATEGY='all'

## If you need a custom SSL certificate CA bundle to verify requests to the
## "NX_CDCS_URL" or NEMO URLs, provide the path to that bundle here and uncomment
## the variable. Any certificates provided in this bundle will be appended to
## the existing system certificates.

# NX_CERT_BUNDLE_FILE='/path/to/bundle.pem'

## Alternatively, you can provide the entire certificate bundle as a single
# string (this can be useful for CI/CD pipelines). Lines should be separated
# by a single '\n' character If defined, this value will take precedence over
# NX_CERT_BUNDLE_FILE

# NX_CERT_BUNDLE='-----BEGIN CERTIFICATE-----\nMIIFBTCCAu2gAwIBAgIQdRxyg4+

## WARNING: Do NOT enable in production. Disables SSL certificate verification
## for all outgoing HTTPS requests. Only useful during local development with
## self-signed certificates where providing every CA via NX_CERT_BUNDLE_FILE is
## impractical.

# NX_DISABLE_SSL_VERIFY=false

## NX_INSTRUMENT_DATA_PATH should be the path to the centralized file store for instrument
## data (i.e. the root of the paths specified for each instrument in the
## NexusLIMS DB ``filestore_path`` column). The expectation is that this path
## is mounted read-only to ensure data preservation

NX_INSTRUMENT_DATA_PATH='/path/to/instrument/data'

## NX_DATA_PATH should be a writable path that will be a parallel directory
## structure to "NX_INSTRUMENT_DATA_PATH", which is where extracted metadata will be
## and generated preview images will be written. This path must be made
## available to the frontend NexusLIMS CDCS instance for proper record display
## and metadata/preview image download

NX_DATA_PATH='/path/to/nexusLIMS/data'

## NX_DB_PATH should be the writable path to the NexusLIMS SQLite
## database that is used to get information about instruments and sessions that
## are built into records

NX_DB_PATH='/path/to/nexuslims_db.sqlite'

## NX_FILE_DELAY_DAYS controls the maximum delay between observing a
## session ending and when the files are expected to be present. For the number
## of days set below (can be a fraction of a day, if desired), record building
## will not fail if no files are found, and the builder will search again until
## the delay has passed. So if the value is "2", and a session ended Monday at
## 5PM, the record builder will continue to try looking for files until
## Wednesday at 5PM.

NX_FILE_DELAY_DAYS=2

## NX_CLUSTERING_SENSITIVITY (optional) controls the sensitivity of file clustering
## into Acquisition Activities. Higher values (e.g., 2.0) make clustering more
## sensitive to time gaps, resulting in more activities. Lower values (e.g., 0.5)
## make clustering less sensitive, resulting in fewer activities. Set to 0 to
## disable clustering entirely and group all files into a single activity.
## Default is 1.0 (no change to automatic clustering).

NX_CLUSTERING_SENSITIVITY=1.0

## NX_LOG_PATH (optional) sets the directory for application logs. If not specified,
## defaults to NX_DATA_PATH/logs/. Logs are organized by date in subdirectories:
## logs/YYYY/MM/DD/YYYYMMDD-HHMM.log

# NX_LOG_PATH='/var/log/nexuslims'

## NX_RECORDS_PATH (optional) sets the directory for generated XML records. If not
## specified, defaults to NX_DATA_PATH/records/. Successfully uploaded records are
## moved to a 'uploaded' subdirectory within this path.

# NX_RECORDS_PATH='/data/nexuslims/records'

## NX_LOCAL_PROFILES_PATH (optional) sets the directory for site-specific instrument
## profiles. These profiles customize metadata extraction for instruments unique to
## your deployment without modifying the core NexusLIMS codebase. Profile files
## should be Python modules that register InstrumentProfile objects. If not specified,
## only built-in profiles will be loaded.

# NX_LOCAL_PROFILES_PATH='/opt/nexuslims/local_profiles'

# ########################################################################## #
# ############## Email Notification Settings (Optional) #################### #
# ########################################################################## #

# These settings control email notifications for the process_records CLI.
# If not configured, email notifications will be disabled.
# Email notifications are sent when errors are detected in the record builder logs.

# SMTP server hostname (required)
# NX_EMAIL_SMTP_HOST='smtp.gmail.com'

# SMTP server port (optional, default: 587 for STARTTLS)
# NX_EMAIL_SMTP_PORT=587

# SMTP username for authentication (optional, required for authenticated SMTP)
# NX_EMAIL_SMTP_USERNAME='your-email@gmail.com'

# SMTP password for authentication (optional, required for authenticated SMTP)
# NX_EMAIL_SMTP_PASSWORD='your-app-password'

# Use TLS encryption (optional, default: true)
# NX_EMAIL_USE_TLS=true

# Email address to send from (required)
# NX_EMAIL_SENDER='nexuslims@yourdomain.com'

# Address(es) to email when an error is detected (required, comma-separated)
# NX_EMAIL_RECIPIENTS='admin@yourdomain.com,team@yourdomain.com'

# ########################################################################## #
# #################### Settings for NEMO Harvesters  ####################### #
# ########################################################################## #

## One or more NEMO Harvesters can be enabled by setting at least one of
## NX_NEMO_ADDRESS_1 and NX_NEMO_TOKEN_1 (and optionally NX_NEMO_STRFTIME_FMT_1,
## NX_NEMO_STRPTIME_FMT_1, and NX_NEMO_TZ_1). To enable multiple harvesters, duplicate
## the same environment variables, but with a different suffix (e.g.
## NX_NEMO_ADDRESS_2, NX_NEMO_TOKEN_2, etc.). For specifics of what each variable does
## and the expected values, see below. To enable the NEMO harvesting, uncomment
## and fill out the values starting with "NX_NEMO..."

## NX_NEMO_ADDRESS_1 should be the full path to the root of the API, with the
## trailing slash included, as shown in the example value below

# NX_NEMO_ADDRESS_1="https://nemo.address.com/api/"

## NX_NEMO_TOKEN_1 authenticates the application to the NEMO server.
## The token can be obtained from the "detailed administration" page of the NEMO
## installation,

# NX_NEMO_TOKEN_1="xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"

## The following strftime_fmt, strptime_fmt, and tz options are optional, and
## control how dates/times are sent to (strftime) and interpreted from
## (strptime) the API. If "strftime_fmt" or "strptime_fmt" are not provided, the
## standard ISO 8601 format for datetime representation will be used (which
## should work with the default NEMO settings). These options are configurable
## to allow for support of non-default date format settings on a NEMO server.
## The formats should be provided using the standard datetime library syntax for
## encoding date and time information (see
## https://docs.python.org/3/library/datetime.html#strftime-and-strptime-format-codes)

# format to send to filter API responses
# NX_NEMO_STRFTIME_FMT_1="%Y-%m-%dT%H:%M:%S%z"

# format to expect back from API
# NX_NEMO_STRPTIME_FMT_1="%Y-%m-%dT%H:%M:%S%z"

## If the following "tz" option is provided, the datetime strings received from
## the API will be coerced into the given timezone. The timezone should be
## specified using the IANA "tz database" name (see
## https://en.wikipedia.org/wiki/List_of_tz_database_time_zones). This option
## should not be supplied for NEMO servers that return time zone information in
## their API response, since it will override the timezone of the returned data.
## It is mostly useful for servers that return reservation/usage event times
## without any timezone information. Providing it here helps properly map file
## creation times to usage event times

# NX_NEMO_TZ_1="America/Denver"

# ########################################################################## #
# If needed, uncomment and change these to enable additional NEMO harvesters #
# ########################################################################## #

# NX_NEMO_ADDRESS_2="https://nemo.address.com/api/"
# NX_NEMO_TOKEN_2="xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"
# NX_NEMO_STRFTIME_FMT_2="%Y-%m-%dT%H:%M:%S%z"
# NX_NEMO_STRPTIME_FMT_2="%m-%d-%Y %H:%M:%S"
# NX_NEMO_TZ_2="America/New_York"

# ########################################################################## #
# ################## eLabFTW Export Configuration (Optional) ############### #
# ########################################################################## #

## eLabFTW is an electronic lab notebook that can receive NexusLIMS records
## as experiments. If configured, NexusLIMS will automatically export session
## records to eLabFTW alongside (or instead of) CDCS uploads.

## NX_ELABFTW_API_KEY is the API authentication key. Obtain this from your
## eLabFTW user panel (typically under "API keys" in user settings).
## Format: {id}-{key} (e.g., "1-abc123...")

# NX_ELABFTW_API_KEY='your-elabftw-api-key'

## NX_ELABFTW_URL is the root URL of your eLabFTW instance.
## Should NOT include /api/ or any path - just the domain.
## Examples: 'https://elabftw.example.com' or 'http://localhost:3148'

# NX_ELABFTW_URL='https://elabftw.example.com'

## NX_ELABFTW_EXPERIMENT_CATEGORY (optional) sets the default category ID
## for created experiments. If not specified, eLabFTW uses its default category.
## Find category IDs in the eLabFTW admin panel under Categories.

# NX_ELABFTW_EXPERIMENT_CATEGORY=1

## NX_ELABFTW_EXPERIMENT_STATUS (optional) sets the default status ID
## for created experiments. If not specified, eLabFTW uses its default status.
## Find status IDs in the eLabFTW admin panel under Status.

# NX_ELABFTW_EXPERIMENT_STATUS=1