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Configuration

Introduction

Many aspects of NOMAD and its operation can be modified through configuration. Most configuration items have reasonable defaults and typically only a small subset has to be overwritten.

Configuration items get their value in the following order:

  1. The item is read from the environment. This has the highest priority and will overwrite values in a nomad.yaml file or the NOMAD source-code.
  2. The value is given in a nomad.yaml configuration file.
  3. There is no custom value, and the value hard-coded in the NOMAD sources will be used.

Configuration items are structured. The configuration is hierarchical and items are aggregated in potentially nested section. For example the configuration item services.api_host denotes the attribute api_host in the configuration section services.

Setting values from the environment

NOMAD services will look at the environment. All environment variables starting with NOMAD_ are considered. The rest of the name is interpreted as a configuration item. Sections and attributes are concatenated with a _. For example, the environment variable NOMAD_SERVICES_API_HOST will set the value for the api_host attribute in the services section.

Setting values from a nomad.yaml

NOMAD services will look for a nomad.yaml file. By default, they will look in the current working directory. This location can be overwritten with the NOMAD_CONFIG environment variable.

The configuration sections and attributes can be denoted with YAML objects and attributes. Here is an example nomad.yaml file:

services:
  api_host: 'localhost'
  api_base_path: '/nomad-oasis'

oasis:
  is_oasis: true
  uses_central_user_management: true

north:
  jupyterhub_crypt_key: '978bfb2e13a8448a253c629d8dd84ff89587f30e635b753153960930cad9d36d'

meta:
  deployment: 'oasis'
  deployment_url: 'https://my-oasis.org/api'
  maintainer_email: 'me@my-oasis.org'

logtransfer:
  enabled: false

mongo:
    db_name: nomad_oasis_v1

elastic:
    entries_index: nomad_oasis_entries_v1
    materials_index: nomad_oasis_materials_v1

When overwriting an object in the configuration, the new value will be merged with the default value. The new merged object will have all of the attributes of the new object in addition to any old attributes that were not overwritten. This allows you to simply change an individual setting without having to provide the entire structure again, which simplifies customization that happens deep in the configuration hierarchy. When overwriting anything else (numbers, strings, lists etc.) the new value completely replaces the old one.

User interface customization

Many of the UI options use a data model that contains the following three fields: include, exclude and options. This structure allows you to easily disable, enable, reorder and modify the UI layout with minimal config rewrite. Here are examples of common customization tasks using the search columns as an example:

Disable item:

ui:
  apps:
    options:
      entries:
        columns:
          exclude: ['upload_create_time']

Explicitly select the shown items and their order

ui:
  apps:
    options:
      entries:
        columns:
          include: ['entry_id', 'upload_create_time']

Modify existing option

ui:
  apps:
    options:
      entries:
        columns:
          options:
            upload_create_time:
              label: "Uploaded"

Add a new item that does not yet exist in options. Note that by default all options are shown in the order they have been declared unless the order is explicitly given in include.

ui:
  apps:
    options:
      entries:
        columns:
          options:
            upload_id:
              label: "Upload ID"

The following is a reference of all configuration sections and attributes.

Services

services

Contains basic configuration of the NOMAD services (app, worker, north).

name type
console_log_level Union[int, str] The log level that controls console logging for all NOMAD services (app, worker, north). The level is given in Python logging log level numbers.
default: 30
api_host str The external hostname that clients can use to reach this NOMAD installation.
default: localhost
api_port int The port used to expose the NOMAD app and api to clients.
default: 8000
api_base_path str The base path prefix for the NOMAD app and api.
default: /fairdi/nomad/latest
api_secret str A secret that is used to issue download and other tokens.
default: defaultApiSecret
api_timeout int If the NOMAD app is run with gunicorn as process manager, this timeout (in s) is passed and worker processes will be restarted, if they do not respond in time.
default: 600
https int Set to True, if external clients are using SSL to connect to this installation. Requires to setup a reverse-proxy (e.g. the one used in the docker-compose based installation) that handles the SSL encryption.
default: False
https_upload int Set to True, if upload curl commands should suggest the use of SSL for file uploads. This can be configured independently of https to suggest large file via regular HTTP.
default: False
admin_user_id str The admin user user_id. All users are treated the same; there are no particular authorization information attached to user accounts. However, the API will grant the user with the given user_id more rights, e.g. using the admin owner setting in accessing data.
default: 00000000-0000-0000-0000-000000000000
encyclopedia_base str This enables links to the given encyclopedia installation in the UI.
default: https://nomad-lab.eu/prod/rae/encyclopedia/#
aitoolkit_enabled int If true, the UI will show a menu with links to the AI Toolkit notebooks on nomad-lab.eu.
default: False
optimade_enabled int If true, the app will serve the optimade API.
default: True
dcat_enabled int If true the app will serve the DCAT API.
default: True
h5grove_enabled int If true the app will serve the h5grove API.
default: True
upload_limit int The maximum allowed unpublished uploads per user. If a user exceeds this amount, the user cannot add more uploads.
default: 10
force_raw_file_decoding int By default, text raw-files are interpreted with utf-8 encoding. If this fails, the actual encoding is guessed. With this setting, we force to assume iso-8859-1 encoding, if a file is not decodable with utf-8.
default: False
max_entry_download int There is an inherent limit in page-based pagination with Elasticsearch. If you increased this limit with your Elasticsearch, you can also adopt this setting accordingly, changing the maximum amount of entries that can be paginated with page-base pagination.
Page-after-value-based pagination is independent and can be used without limitations.
default: 50000
unavailable_value str Value that is used in results section Enum fields (e.g. system type, spacegroup, etc.) to indicate that the value could not be determined.
default: unavailable
app_token_max_expires_in int Maximum expiration time for an app token in seconds. Requests with a higher value will be declined.
default: 2592000
html_resource_http_max_age int Used for the max_age cache-control directive on statically served html, js, css resources.
default: 60
image_resource_http_max_age int Used for the max_age cache-control directive on statically served image resources.
default: 2592000

meta

Metadata about the deployment and how it is presented to clients.

name type
deployment_url str The NOMAD deployment's url. If not explicitly set, will default to the (api url) read from the configuration.
label str An additional log-stash data key-value pair added to all logs. Can be used to differentiate deployments when analyzing logs.
beta dict Additional data that describes how the deployment is labeled as a beta-version in the UI.
default: Complex object, default value not displayed.
version str The NOMAD version string.
default: 1.3.3.dev66+g230bcffd7
commit str The source-code commit that this installation's NOMAD version is build from.
default: ""
deployment str Human-friendly name of this nomad deployment.
default: devel
service str Name for the service that is added to all logs. Depending on how NOMAD is installed, services get a name (app, worker, north) automatically.
default: unknown nomad service
name str Web-site title for the NOMAD UI.
default: NOMAD
deprecated
homepage str Provider homepage.
default: https://nomad-lab.eu
deprecated
source_url str URL of the NOMAD source-code repository.
default: https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR
deprecated
maintainer_email str Email of the NOMAD deployment maintainer.
default: markus.scheidgen@physik.hu-berlin.de

oasis

Settings related to the configuration of a NOMAD Oasis deployment.

name type
allowed_users str A list of usernames or user account emails. These represent a white-list of allowed users. With this, users will need to login right-away and only the listed users might use this deployment. All API requests must have authentication information as well.
is_oasis int Set to True to indicate that this deployment is a NOMAD Oasis.
default: False
uses_central_user_management int Set to True to use the central user-management. Typically the NOMAD backend is using the configured keycloak to access user data. With this, the backend will use the API of the central NOMAD (central_nomad_deployment_url) instead.
default: False
central_nomad_deployment_url str The URL of the API of the NOMAD deployment that is considered the central NOMAD.
default: https://nomad-lab.eu/prod/v1/api

north

Settings related to the operation of the NOMAD remote tools hub service north.

name type
enabled int Enables or disables the NORTH API and UI views. This is independent of whether you run a jupyter hub or not.
default: True
hub_connect_ip str Overwrites the default hostname that can be used from within a north container to reach the host system.
Typically has to be set for non Linux hosts. Set this to host.docker.internal on windows/macos.
hub_connect_url str This setting is forwarded to jupyterhub; refer to the jupyterhub documentation.
docker_network str This setting is forwarded to jupyterhub; refer to the jupyterhub documentation.
jupyterhub_crypt_key str This setting is forwarded to jupyterhub; refer to the jupyterhub documentation.
nomad_host str The NOMAD app host name that spawned containers use.
nomad_access_token_expiry_time int All tools are run with an access token for the NOMAD api in the NOMAD_CLIENT_ACCESS_TOKEN environment variable. This token will be automatically used by the nomad-lab Python package, e.g. if you use the ArchiveQuery to access data. This option sets the amount of seconds that this token is valid for.
default: 86400
tools NORTHTools The available north tools. Either the tools definitions as dict or a path to a .json file.
default: Complex object, default value not displayed.
hub_service_api_token str A secret token shared between NOMAD and the NORTH jupyterhub. This needs to be the token of an admin service.
default: secret-token
hub_ip str This setting is forwarded to jupyterhub; refer to the jupyterhub documentation.
default: 0.0.0.0
hub_host str The internal host name that NOMAD services use to connect to the jupyterhub API.
default: localhost
hub_port int The internal port that NOMAD services use to connect to the jupyterhub API.
default: 9000
windows int Enable windows OS hacks.
default: True

NORTHTools

name type
include List[str] List of included options. If not explicitly defined, all of the options will be included by default.
exclude List[str] List of excluded options. Has higher precedence than include.
options Dict[str, NORTHTool] The available plugin.
default: Complex object, default value not displayed.

NORTHTool

name type
short_description str A short description of the tool, e.g. shown in the NOMAD GUI.
description str A description of the tool, e.g. shown in the NOMAD GUI.
image str The docker image (incl. tags) to use for the tool.
cmd str The container cmd that is passed to the spawner.
image_pull_policy str The image pull policy used in k8s deployments.
default: Always
privileged int Whether the tool needs to run in privileged mode.
default: False
path_prefix str An optional path prefix that is added to the container URL to reach the tool, e.g. "lab/tree" for jupyterlab.
with_path int Whether the tool supports a path to a file or directory. This also enables tools to be launched from files in the NOMAD UI.
default: False
file_extensions List[str] The file extensions of files that this tool should be launchable for.
default: []
mount_path str The path in the container where uploads and work directories will be mounted, e.g. /home/jovyan for Jupyter containers.
icon str A URL to an icon that is used to represent the tool in the NOMAD UI.
maintainer List[NORTHToolMaintainer] The maintainers of the tool.
default: []
external_mounts List[NORTHExternalMount] Additional mounts to be added to tool containers.
default: []

NORTHToolMaintainer

name type
name str
email str

NORTHExternalMount

name type
host_path str
bind str
mode str default: ro
options:
- ro
- rw

Files, databases, external services

rabbitmq

Configures how NOMAD is connecting to RabbitMQ.

name type
host str The name of the host that runs RabbitMQ.
default: localhost
user str The RabbitMQ user that is used to connect.
default: rabbitmq
password str The password that is used to connect.
default: rabbitmq

fs

name type
staging_external str
public_external str
north_home_external str
archive_version_suffix Union[str, List[str]] This allows to add an additional segment to the names of archive files and thereby allows different NOMAD installations to work with the same storage directories and raw files, but with separate archives.
If this is a list, the first string is used. If the file with the first string does not exist on read, the system will look for the file with the next string, etc.
default: ['v1.2', 'v1']
external_working_directory str
tmp str default: .volumes/fs/tmp
staging str default: .volumes/fs/staging
public str default: .volumes/fs/public
north_home str default: .volumes/fs/north/users
local_tmp str default: /tmp
prefix_size int default: 2
working_directory str default: /app

elastic

name type
username str
password str
host str default: localhost
port int default: 9200
timeout int default: 60
bulk_timeout int default: 600
bulk_size int default: 1000
entries_per_material_cap int default: 1000
entries_index str default: nomad_entries_v1
materials_index str default: nomad_materials_v1

keycloak

name type
public_server_url str
client_secret str
server_url str default: https://nomad-lab.eu/fairdi/keycloak/auth/
realm_name str default: fairdi_nomad_prod
username str default: admin
password str default: password
client_id str default: nomad_public

mongo

Connection and usage settings for MongoDB.

name type
host str The name of the host that runs mongodb.
default: localhost
port int The port to connect with mongodb.
default: 27017
db_name str The used mongodb database name.
default: nomad_v1
username str
password str

logstash

name type
level Union[int, str] default: 10
enabled int default: False
host str default: localhost
tcp_port str default: 5000

mail

name type
cc_address str
enabled int default: False
with_login int default: False
host str default: ""
port int default: 8995
user str default: ""
password str default: ""
from_address str default: support@nomad-lab.eu

datacite

name type
mds_host str default: https://mds.datacite.org
enabled int default: False
prefix str default: 10.17172
user str default: *
password str default: *

rfc3161_timestamp

name type
cert str Path to the optional rfc3161ng timestamping server certificate.
username str
password str
server str The rfc3161ng timestamping host.
default: http://zeitstempel.dfn.de
hash_algorithm str Hash algorithm used by the rfc3161ng timestamping server.
default: sha256

Processing

celery

name type
max_memory float default: 64000000.0
timeout int default: 1800
acks_late int default: False
routing str default: queue
priorities dict default: Complex object, default value not displayed.

normalize

name type
normalizers Options default: Complex object, default value not displayed.
springer_db_path str default: /usr/local/lib/python3.9/site-packages/nomad/config/models/normalizing/data/springer.msg
system_classification_with_clusters_threshold int The system size limit for running the dimensionality analysis. For very large systems the dimensionality analysis will get too expensive.
default: 64
clustering_size_limit int The system size limit for running the system clustering. For very large systems the clustering will get too expensive.
default: 600
symmetry_tolerance float Symmetry tolerance controls the precision used by spglib in order to find symmetries. The atoms are allowed to move this much from their symmetry positions in order for spglib to still detect symmetries. The unit is angstroms. The value of 0.1 is used e.g. by Materials Project according to https://pymatgen.org/pymatgen.symmetry.html#pymatgen.symmetry.analyzer.SpacegroupAnalyzer
default: 0.1
prototype_symmetry_tolerance float The symmetry tolerance used in aflow prototype matching. Should only be changed before re-running the prototype detection.
default: 0.1
max_2d_single_cell_size int Maximum number of atoms in the single cell of a 2D material for it to be considered valid.
default: 7
cluster_threshold float The distance tolerance between atoms for grouping them into the same cluster. Used in detecting system type.
default: 2.5
angle_rounding float Defines the "bin size" for rounding cell angles for the material hash in degree.
default: 10.0
flat_dim_threshold float The threshold for a system to be considered "flat". Used e.g. when determining if a 2D structure is purely 2-dimensional to allow extra rigid transformations that are improper in 3D but proper in 2D.
default: 0.1
k_space_precision float The threshold for point equality in k-space. Unit: 1/m.
default: 150000000.0
band_structure_energy_tolerance float The energy threshold for how much a band can be on top or below the fermi level in order to still detect a gap. Unit: Joule.
default: 8.01088e-21

Options

Common configuration class used for enabling/disabling certain elements and defining the configuration of each element.

name type
include List[str] List of included options. If not explicitly defined, all of the options will be included by default.
exclude List[str] List of excluded options. Has higher precedence than include.
options Dict[str, typing.Any] Contains the available options.
default: Complex object, default value not displayed.

process

name type
redirect_stdouts int True will redirect lines to stdout (e.g. print output) that occur during processing (e.g. created by parsers or normalizers) as log entries.
default: False
store_package_definition_in_mongo int Configures whether to store the corresponding package definition in mongodb.
default: False
add_definition_id_to_reference int Configures whether to attach definition id to m_def, note it is different from m_def_id. The m_def_id will be exported with the with_def_id=True via m_to_dict.
default: False
write_definition_id_to_archive int Write m_def_id to the archive.
default: False
index_materials int default: True
reuse_parser int default: True
metadata_file_name str default: nomad
metadata_file_extensions tuple default: ('json', 'yaml', 'yml')
auxfile_cutoff int default: 100
parser_matching_size int default: 12000
max_upload_size int default: 34359738368
use_empty_parsers int default: False
rfc3161_skip_published int default: False

reprocess

Configures standard behaviour when reprocessing. Note, the settings only matter for published uploads and entries. For uploads in staging, we always reparse, add newfound entries, and delete unmatched entries.

name type
rematch_published int default: True
reprocess_existing_entries int default: True
use_original_parser int default: False
add_matched_entries_to_published int default: True
delete_unmatched_published_entries int default: False
index_individual_entries int default: False

bundle_export

Controls behaviour related to exporting bundles.

name type
default_cli_bundle_export_path str Default path used when exporting bundles using the CLI command.
default: ./bundles
default_settings BundleExportSettings General default settings.
default: Complex object, default value not displayed.
default_settings_cli BundleExportSettings Additional default settings, applied when exporting using the CLI. This allows to override some of the settings specified in the general default settings above.

BundleExportSettings

name type
include_raw_files int If the raw files should be included in the export
default: True
include_archive_files int If the parsed archive files should be included in the export
default: True
include_datasets int If the datasets should be included in the export
default: True

bundle_import

Controls behaviour related to importing bundles.

name type
required_nomad_version str Minimum NOMAD version of bundles required for import.
default: 1.1.2
default_cli_bundle_import_path str Default path used when importing bundles using the CLI command.
default: ./bundles
allow_bundles_from_oasis int If oasis admins can "push" bundles to this NOMAD deployment.
default: False
allow_unpublished_bundles_from_oasis int If oasis admins can "push" bundles of unpublished uploads.
default: False
default_settings BundleImportSettings General default settings.
default: Complex object, default value not displayed.
default_settings_cli BundleImportSettings Additional default settings, applied when importing using the CLI. This allows to override some of the settings specified in the general default settings above.
default: Complex object, default value not displayed.

BundleImportSettings

name type
include_raw_files int If the raw files should be included in the import
default: True
include_archive_files int If the parsed archive files should be included in the import
default: True
include_datasets int If the datasets should be included in the import
default: True
include_bundle_info int If the bundle_info.json file should be kept (not necessary but may be nice to have.
default: True
keep_original_timestamps int If all timestamps (create time, publish time etc) should be imported from the bundle.
default: False
set_from_oasis int If the from_oasis flag and oasis_deployment_url should be set.
default: True
delete_upload_on_fail int If False, it is just removed from the ES index on failure.
default: False
delete_bundle_on_fail int Deletes the source bundle if the import fails.
default: True
delete_bundle_on_success int Deletes the source bundle if the import succeeds.
default: True
delete_bundle_include_parent_folder int When deleting the bundle, also include parent folder, if empty.
default: True
trigger_processing int If the upload should be processed when the import is done (not recommended).
default: False
process_settings Reprocess When trigger_processing is set to True, these settings control the reprocessing behaviour (see the config for reprocess for more info). NOTE: reprocessing is no longer the recommended method to import bundles.
default: Complex object, default value not displayed.

Reprocess

Configures standard behaviour when reprocessing. Note, the settings only matter for published uploads and entries. For uploads in staging, we always reparse, add newfound entries, and delete unmatched entries.

name type
rematch_published int default: True
reprocess_existing_entries int default: True
use_original_parser int default: False
add_matched_entries_to_published int default: True
delete_unmatched_published_entries int default: False
index_individual_entries int default: False

archive

name type
block_size int In case of using blocked TOC, this is the size of each block.
default: 1048576
read_buffer_size int GPFS needs at least 256K to achieve decent performance.
default: 1048576
copy_chunk_size int The chunk size of every read of binary data. It is used to copy data from one file to another. A small value will result in more syscalls, a large value will result in higher peak memory usage.
default: 16777216
toc_depth int Depths of table of contents in the archive.
default: 10
use_new_writer int default: True
small_obj_optimization_threshold int For any child of lists/dicts whose encoded size is smaller than this value, no TOC will be generated.
default: 1048576
fast_loading int When enabled, this flag determines whether to read the whole dict/list at once when a certain mount of children has been visited. This reduces the number of syscalls although data may be repeatedly read. Otherwise, always read children one by one. This may slow down the loading as more syscalls are needed.
default: True
fast_loading_threshold float If the fraction of children that have been visited is less than this threshold, fast loading will be used.
default: 0.6
trivial_size int To identify numerical lists.
default: 20

User Interface

These settings affect the behaviour of the user interface. Note that the preferred way for creating custom apps is by using app plugin entry points.

ui

Used to customize the user interface.

name type
app_base str This is automatically set.
north_base str This is automatically set.
theme Theme Controls the site theme and identity.
unit_systems UnitSystems Controls the available unit systems.
entry Entry Controls the entry visualization.
apps Apps Contains the App definitions.
north NORTHUI NORTH (NOMAD Remote Tools Hub) UI configuration.
default: Complex object, default value not displayed.
example_uploads ExampleUploads Controls the available example uploads.
default: Complex object, default value not displayed.

NORTHUI

NORTH (NOMAD Remote Tools Hub) UI configuration.

name type
enabled int Whether the NORTH tools are available in the UI. The default value is read from the root-level NORTH configuration.
default: True

Entry

Controls the entry visualization.

name type
cards Cards Controls the cards that are displayed on the entry overview page.

Cards

Contains the overview page card definitions and controls their visibility.

name type
include List[str] List of included options. If not explicitly defined, all of the options will be included by default.
exclude List[str] List of excluded options. Has higher precedence than include.
options Dict[str, Card] Contains the available card options.

Card

Definition for a card shown in the entry overview page.

name type
error str The error message to show if an error is encountered within the card.

ExampleUploads

Controls the availability of example uploads.

name type
include List[str] List of included options. If not explicitly defined, all of the options will be included by default.
exclude List[str] List of excluded options. Has higher precedence than include.

Apps

Contains App definitions and controls their availability.

name type
include List[str] List of included options. If not explicitly defined, all of the options will be included by default.
exclude List[str] List of excluded options. Has higher precedence than include.
options Dict[str, App] Contains the available app options.

Theme

Theme and identity settings.

name type
title str Site name in the browser tab.

UnitSystems

Controls the available unit systems.

name type
include List[str] List of included options. If not explicitly defined, all of the options will be included by default.
exclude List[str] List of excluded options. Has higher precedence than include.
options Dict[str, UnitSystem] Contains the available unit systems.
selected str Selected option.

UnitSystem

name type
label str Short, descriptive label used for this unit system.
units Dict[str, UnitSystemUnit] Contains a mapping from each dimension to a unit. If a unit is not specified for a dimension, the SI equivalent will be used by default. The following dimensions are available: - dimensionless - length - mass - time - current - temperature - luminosity - luminous_flux - substance - angle - information - force - energy - power - pressure - charge - resistance - conductance - inductance - magnetic_flux - magnetic_field - frequency - luminance - illuminance - electric_potential - capacitance - activity

UnitSystemUnit

name type
definition str The unit definition. Can be a mathematical expression that combines several units, e.g. (kg * m) / s^2. You should only use units that are registered in the NOMAD unit registry (nomad.units.ureg).
locked int Whether the unit is locked in the unit system it is defined in.
default: False

Others

logtransfer

Configuration of logtransfer and statistics service.

When enabled (enabled) an additional logger will write logs to a log file (log_file). At regular intervals (transfer_interval) a celery task is scheduled. It will log a set of statistics. It will copy the log file (transfer_log_files). Transfer the contents of the copy to the central NOMAD (oasis.central_nomad_deployment_url) and delete the copy. The transfer is only done if the the log file has a certain size (transfer_threshold). Only a maximum amount of logs are transferred (transfer_capacity). Only logs with a certain level (level) are considered. The files will be stored in fs.tmp.

name type
enabled int If enabled this starts process that frequently generates logs with statistics.
default: False
transfer_threshold int The minimum size in bytes of stored logs before logs are transferred. 0 means transfer at every transfer interval.
default: 0
transfer_capacity int The maximum number of bytes of stored logs that are transferred. Excess is dropped.
default: 1000000
transfer_interval int Time interval in seconds after which stored logs are potentially transferred.
default: 600
level Union[int, str] The min log level for logs to be transferred.
default: 20
log_file str The log file that is used to store logs for transfer.
default: nomad.log
transfer_log_file str The log file that is used to copy logs for transfer.
default: .transfer.log
file_rollover_wait_time float Time in seconds to wait after log file was "rolled over" for transfer.
default: 1

tests

name type
assume_auth_for_username str Will assume that all API calls with no authentication have authentication for the user with the given username.
default_timeout int default: 60

resources

name type
enabled int default: False
db_name str default: nomad_v1_resources
max_time_in_mongo float Maxmimum time a resource is stored in mongodb before being updated.
default: 31536000.0
download_retries int Number of retries when downloading resources.
default: 2
download_retry_delay int Delay between retries in seconds
default: 10
max_connections int Maximum simultaneous connections used to download resources.
default: 10

client

name type
user str
password str
access_token str
url str default: http://nomad-lab.eu/prod/v1/api

gitlab

name type
private_token str default: not set

plugins

name type
entry_points EntryPoints Used to control plugin entry points.
plugin_packages Dict[str, PluginPackage] Contains the installed installed plugin packages with the package name used as a key. This is autogenerated and should not be modified.

PluginPackage

name type
name str Name of the plugin Python package, read from pyproject.toml.
description str Package description, read from pyproject.toml.
version str Plugin package version, read from pyproject.toml.
homepage str Link to the plugin package homepage, read from pyproject.toml.
documentation str Link to the plugin package documentation page, read from pyproject.toml.
repository str Link to the plugin package source code repository, read from pyproject.toml.
entry_points List[str] List of entry point ids contained in this package, read form pyproject.toml

EntryPoints

name type
include List[str] List of included options. If not explicitly defined, all of the options will be included by default.
exclude List[str] List of excluded options. Has higher precedence than include.
options Dict[str, Union[Schema, Normalizer, Parser, SchemaPackageEntryPoint, ParserEntryPoint, NormalizerEntryPoint, AppEntryPoint]] The available plugin entry points.
default: Complex object, default value not displayed.

Parser

A Parser describes a NOMAD parser that can be loaded as a plugin.

The parser itself is referenced via python_name. For Parser instances python_name must refer to a Python class that has a parse function. The other properties are used to create a MatchingParserInterface. This comprises general metadata that allows users to understand what the parser is, and metadata used to decide if a given file "matches" the parser.

name type
plugin_type Literal[parser] The type of the plugin. This has to be the string parser for parser plugins.
default: parser
id str The unique identifier for this plugin.
name str A short descriptive human readable name for the plugin.
description str A human readable description of the plugin.
plugin_documentation_url str The URL to the plugins main documentation page.
plugin_source_code_url str The URL of the plugins main source code repository.
python_package str Name of the python package that contains the plugin code and a plugin metadata file called nomad_plugin.yaml.
parser_class_name str The fully qualified name of the Python class that implements the parser. This class must have a function def parse(self, mainfile, archive, logger).
parser_as_interface int By default the parser metadata from this config (and the loaded nomad_plugin.yaml) is used to instantiate a parser interface that is lazy loading the actual parser and performs the mainfile matching. If the parser interface matching based on parser metadata is not sufficient and you implemented your own is_mainfile parser method, this setting can be used to use the given parser class directly for parsing and matching.
default: False
mainfile_contents_re str A regular expression that is applied the content of a potential mainfile. If this expression is given, the parser is only considered for a file, if the expression matches.
mainfile_name_re str A regular expression that is applied the name of a potential mainfile. If this expression is given, the parser is only considered for a file, if the expression matches.
default: .*
mainfile_mime_re str A regular expression that is applied the mime type of a potential mainfile. If this expression is given, the parser is only considered for a file, if the expression matches.
default: text/.*
mainfile_binary_header bytes Matches a binary file if the given bytes are included in the file.
mainfile_binary_header_re bytes Matches a binary file if the given binary regular expression bytes matches the file contents.
mainfile_alternative int If True, the parser only matches a file, if no other file in the same directory matches a parser.
default: False
mainfile_contents_dict dict Is used to match structured data files like JSON or HDF5.
supported_compressions List[str] Files compressed with the given formats (e.g. xz, gz) are uncompressed and matched like normal files.
default: []
domain str The domain value dft will apply all normalizers for atomistic codes. Deprecated.
default: dft
level int The order by which the parser is executed with respect to other parsers.
default: 0
code_name str
code_homepage str
code_category str
metadata dict Metadata passed to the UI. Deprecated.

Schema

A Schema describes a NOMAD Python schema that can be loaded as a plugin.

name type
plugin_type Literal[schema] The type of the plugin. This has to be the string schema for schema plugins.
default: schema
id str The unique identifier for this plugin.
name str A short descriptive human readable name for the plugin.
description str A human readable description of the plugin.
plugin_documentation_url str The URL to the plugins main documentation page.
plugin_source_code_url str The URL of the plugins main source code repository.
python_package str Name of the python package that contains the plugin code and a plugin metadata file called nomad_plugin.yaml.
package_path str Path of the plugin package. Will be determined using python_package if not explicitly defined.
key str Key used to identify this plugin.

AppEntryPoint

Base model for a app plugin entry points.

name type
id str Unique identifier corresponding to the entry point name. Automatically set to the plugin entry point name in pyproject.toml.
entry_point_type Literal[app] Determines the entry point type.
default: app
name str Name of the plugin entry point.
description str A human readable description of the plugin entry point.
plugin_package str The plugin package from which this entry points comes from.
app App The app configuration.

NormalizerEntryPoint

Base model for normalizer plugin entry points.

name type
id str Unique identifier corresponding to the entry point name. Automatically set to the plugin entry point name in pyproject.toml.
entry_point_type Literal[normalizer] Determines the entry point type.
default: normalizer
name str Name of the plugin entry point.
description str A human readable description of the plugin entry point.
plugin_package str The plugin package from which this entry points comes from.
level int Integer that determines the execution order of this normalizer. Normalizers are run in order from lowest level to highest level.
default: 0

SchemaPackageEntryPoint

Base model for schema package plugin entry points.

name type
id str Unique identifier corresponding to the entry point name. Automatically set to the plugin entry point name in pyproject.toml.
entry_point_type Literal[schema_package] Specifies the entry point type.
default: schema_package
name str Name of the plugin entry point.
description str A human readable description of the plugin entry point.
plugin_package str The plugin package from which this entry points comes from.

Normalizer

A Normalizer describes a NOMAD normalizer that can be loaded as a plugin.

name type
plugin_type Literal[normalizer] The type of the plugin. This has to be the string normalizer for normalizer plugins.
default: normalizer
id str The unique identifier for this plugin.
name str A short descriptive human readable name for the plugin.
description str A human readable description of the plugin.
plugin_documentation_url str The URL to the plugins main documentation page.
plugin_source_code_url str The URL of the plugins main source code repository.
python_package str Name of the python package that contains the plugin code and a plugin metadata file called nomad_plugin.yaml.
normalizer_class_name str The fully qualified name of the Python class that implements the normalizer. This class must have a function def normalize(self, logger).

ParserEntryPoint

Base model for parser plugin entry points.

name type
id str Unique identifier corresponding to the entry point name. Automatically set to the plugin entry point name in pyproject.toml.
entry_point_type Literal[parser] Determines the entry point type.
default: parser
name str Name of the plugin entry point.
description str A human readable description of the plugin entry point.
plugin_package str The plugin package from which this entry points comes from.
level int Integer that determines the execution order of this parser. Parser with lowest level will attempt to match raw files first.
default: 0
mainfile_contents_re str A regular expression that is applied the content of a potential mainfile. If this expression is given, the parser is only considered for a file, if the expression matches.
mainfile_name_re str A regular expression that is applied the name of a potential mainfile. If this expression is given, the parser is only considered for a file, if the expression matches.
default: .*
mainfile_mime_re str A regular expression that is applied the mime type of a potential mainfile. If this expression is given, the parser is only considered for a file, if the expression matches.
default: .*
mainfile_binary_header bytes Matches a binary file if the given bytes are included in the file.
mainfile_binary_header_re bytes Matches a binary file if the given binary regular expression bytes matches the file contents.
mainfile_alternative int If True, the parser only matches a file, if no other file in the same directory matches a parser.
default: False
mainfile_contents_dict dict Is used to match structured data files like JSON or HDF5.
supported_compressions List[str] Files compressed with the given formats (e.g. xz, gz) are uncompressed and matched like normal files.
default: []