How to write an app¶

Apps provide customized views of data in the GUI, making it easier for the users to navigate and understand the data related to a specific domain. This typically means that certain domain-specific properties are highlighted, different units may be used for physical properties, and specialized dashboards may be presented. This becomes crucial for NOMAD installations to be able to scale with data that contains a mixture of experiments and simulations, different techniques, and physical properties spanning different time and length scales.

Apps only affect the way data is displayed for the user: if you wish to affect the underlying data structure, you will need to write a Python schema package or a YAML schema package.

This documentation shows you how to write an plugin entry point for an app. You should read the documentation on getting started with plugins to have a basic understanding of how plugins and plugin entry points work in the NOMAD ecosystem.

Getting started¶

You can use our template repository to create an initial structure for a plugin containing an app. The relevant part of the repository layout will look something like this:

nomad-example
   ├── src
   │   ├── nomad_example
   │   │   ├── apps
   │   │   │   ├── __init__.py
   ├── LICENSE.txt
   ├── README.md
   └── pyproject.toml

See the documentation on plugin development guidelines for more details on the best development practices for plugins, including linting, testing and documenting.

App entry point¶

The entry point defines basic information about your app and is used to automatically load the app into a NOMAD distribution. It is an instance of an AppEntryPoint and unlike many other plugin entry points, it does not have a separate resource that needs to be lazy-loaded as the entire app is defined in the configuration as an instance of nomad.config.models.ui.App. You will learn more about the App class in the next sections. The entry point should be defined in */apps/__init__.py like this:

from nomad.config.models.plugins import AppEntryPoint

myapp = MyAppEntryPoint(
    name = 'MyApp',
    description = 'My custom app.',
    app = App(...)
)

Here we have instantiated an object myapp in which you specify the default parameterization and other details about the app. In the reference you can see all of the available configuration options for an AppEntryPoint.

The entry point instance should then be added to the [project.entry-points.'nomad.plugin'] table in pyproject.toml in order for the app to be automatically detected:

[project.entry-points.'nomad.plugin']
myapp = "nomad_example.apps:myapp"

`App` class¶

The definition fo the actual app is given as an instance of the App class specified as part of the entry point. A full breakdown of the model is given below in the app reference, but here is a small example:

from nomad.config.models.plugins import AppEntryPoint
from nomad.config.models.ui import App, Column, Columns, FilterMenu, FilterMenus, Filters


myapp = AppEntryPoint(
    name='MyApp',
    description='App defined using the new plugin mechanism.',
    app = App(
        # Label of the App
        label='My App',
        # Path used in the URL, must be unique
        path='myapp',
        # Used to categorize apps in the explore menu
        category='Theory',
        # Brief description used in the app menu
        description='An app customized for me.',
        # Longer description that can also use markdown
        readme='Here is a much longer description of this app.',
        # Controls the available search filters. If you want to filter by
        # quantities in a schema package, you need to load the schema package
        # explicitly here. Note that you can use a glob syntax to load the
        # entire package, or just a single schema from a package.
        filters=Filters(
            include=['*#nomad_example.schema_packages.mypackage.MySchema'],
        ),
        # Controls which columns are shown in the results table
        columns=Columns(
            selected=[
                'entry_id'
                'data.mysection.myquantity#nomad_example.schema_packages.mypackage.MySchema'
            ],
            options={
                'entry_id': Column(),
                'upload_create_time': Column(),
                'data.mysection.myquantity#nomad_example.schema_packages.mypackage.MySchema': Column(),
            }
        ),
        # Dictionary of search filters that are always enabled for queries made
        # within this app. This is especially important to narrow down the
        # results to the wanted subset. Any available search filter can be
        # targeted here. This example makes sure that only entries that use
        # MySchema are included.
        filters_locked={
            "section_defs.definition_qualified_name:all": [
                "nomad_example.schema_packages.mypackage.MySchema"
            ]
        },
        # Controls the filter menus shown on the left
        filter_menus=FilterMenus(
            options={
                'material': FilterMenu(label="Material"),
            }
        ),
        # Controls the default dashboard shown in the search interface
        dashboard={
            'widgets': [
                {
                    'type': 'histogram',
                    'showinput': False,
                    'autorange': True,
                    'nbins': 30,
                    'scale': 'linear',
                    'quantity': 'data.mysection.myquantity#nomad_example.schema_packages.mypackage.MySchema',
                    'layout': {
                        'lg': {
                            'minH': 3,
                            'minW': 3,
                            'h': 4,
                            'w': 12,
                            'y': 0,
                            'x': 0
                        }
                    }
                }
            ]
        }
    )
)

Tip

If you want to load an app definition from a YAML file, this can be easily done with the pydantic parse_obj function:

    import yaml
    from nomad.config.models.plugins import AppEntryPoint
    from nomad.config.models.ui import App

    yaml_data = """
        label: My App
        path: myapp
        category: Theory
    """
    myapp = AppEntryPoint(
        name='MyApp',
        description='App defined using the new plugin mechanism.',
        app=App.parse_obj(
            yaml.safe_load(yaml_data)
        ),
    )

Loading custom quantity definitions into an app¶

By default, none of the quantities from custom schemas are available in an app, and they need to be explicitly added. Each app may define additional filters that should be enabled in it. Filters have a special meaning in the app context: filters are pieces of (meta)info that can be queried in the search interface of the app, but also targeted in the rest of the app configuration as explained below in.

Note

Note that not all of the quantities from a custom schema can be exposed as filters. At the moment we only support targeting scalar quantities from custom schemas.

Each schema has a unique name within the NOMAD ecosystem, which is needed to target them in the configuration. The name depends on the resource in which the schema is defined in:

Python schemas are identified by the python path for the class that inherits from Schema. For example, if you have a python package called nomad_example, which has a subpackage called schema_packages, containing a module called mypackage.py, which contains the class MySchema, then the schema name will be nomad_example.schema_packages.mypackage.MySchema.
YAML schemas are identified by the entry id of the schema file together with the name of the section defined in the YAML schema. For example if you have uploaded a schema YAML file containing a section definition called MySchema, and it has been assigned an entry_id, the schema name will be entry_id:<entry_id>.MySchema.

The quantities from schemas may be included or excluded as filter by using the filters field in the app config. This option supports a wildcard/glob syntax for including/excluding certain filters. For example, to include all filters from the Python schema defined in the class nomad_example.schema_packages.mypackage.MySchema, you could use:

filters=Filters(
    include=['*#nomad_example.schema_packages.mypackage.MySchema']
)

The same thing for a YAML schema could be achieved with:

filters=Filters(
    include=['*#entry_id:<entry_id>.MySchema']
)

Once quantities from a schema are included in an app as filters, they can be targeted in the rest of the app. The app configuration often refers to specific filters to configure parts of the user interface. For example, one could configure the results table to show a new column using one of the schema quantities with:

columns=Columns(
    selected=[
        'entry_id'
        'data.mysection.myquantity#nomad_example.schema_packages.mypackage.MySchema'
    ],
    options={
        'entry_id': Column(),
        'upload_create_time': Column(),
        'data.mysection.myquantity#nomad_example.schema_packages.mypackage.MySchema': Column(),
    }
)

The syntax for targeting quantities depends on the resource:

For python schemas, you need to provide the path and the python schema name separated by a hashtag (#), for example data.mysection.myquantity#nomad_example.schema_packages.mypackage.MySchema.
For YAML schemas, you need to provide the path and the YAML schema name separated by a hashtag (#), for example data.mysection.myquantity#entry_id:<entry_id>.MySchema.
Quantities that are common for all NOMAD entries can be targeted by using only the path without the need for specifying a schema, e.g. results.material.symmetry.space_group.

App reference¶

App¶

Defines the layout and functionality for an App.

name	type
label	`str`	Name of the App.
path	`str`	Path used in the browser address bar.
resource	`str`	Targeted resource. default: `entries` options: - `entries` - `materials`
breadcrumb	`str`	Name displayed in the breadcrumb, by default the label will be used.
category	`str`	Category used to organize Apps in the explore menu.
description	`str`	Short description of the App.
readme	`str`	Longer description of the App that can also use markdown.
pagination	`Pagination`	Default result pagination. default: Complex object, default value not displayed.
columns	`Columns`	Controls the columns shown in the results table.
rows	`Rows`	Controls the display of entry rows in the results table. default: Complex object, default value not displayed.
filter_menus	`FilterMenus`	Filter menus displayed on the left side of the screen.
filters	`Filters`	Controls the filters that are available in this app. default: Complex object, default value not displayed.
dashboard	`Dashboard`	Default dashboard layout.
filters_locked	`dict`	Fixed query object that is applied for this search context. This filter will always be active for this context and will not be displayed to the user by default.
search_syntaxes	`SearchSyntaxes`	Controls which types of search syntax are available.

Filters¶

Controls the availability of filters in the app. Filters are pieces of (meta)info than can be queried in the search interface of the app, but also targeted in the rest of the app configuration. The include and exlude attributes can use glob syntax to target metainfo, e.g. results.* or *.#myschema.schema.MySchema.

name	type
include	`List[str]`	List of included options. Supports glob/wildcard syntax.
exclude	`List[str]`	List of excluded options. Supports glob/wildcard syntax. Has higher precedence than include.

SearchSyntaxes¶

Controls the availability of different search syntaxes. These syntaxes determine how raw user input in e.g. the search bar is parsed into queries supported by the API.

Currently you can only exclude items. By default, the following options are included:

existence: Used to query for the existence of a specific metainfo field in the data.
equality: Used to query for a specific value with exact match.
range_bounded: Queries values that are between two numerical limits, inclusive or exclusive.
range_half_bounded: Queries values that are above/below a numerical limit, inclusive or exclusive.
free_text: For inexact, free-text queries. Requires that a set of keywords has been filled in the entry.

name	type
exclude	`List[str]`	List of excluded options.

Rows¶

Controls the visualization of rows in the search results.

name	type
actions	`RowActions`
details	`RowDetails`
selection	`RowSelection`

RowActions¶

Controls the visualization of row actions that are shown at the end of each row.

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, RowActionURL]`	All available row actions.
enabled	`int`	Whether to enable row actions. default: `True`

RowActionURL¶

Action that will open an external link read from the archive.

name	type
description	`str`	Description of the action shown to the user.
type	`str`	Set as `url` to get this widget type. default: `url`
path	`str`	JMESPath pointing to a path in the archive that contains the URL.

RowSelection¶

Controls the selection of rows. If enabled, rows can be selected and additional actions performed on them.

name	type
enabled	`int`	Whether to show the row selection. default: `True`

RowDetails¶

Controls the visualization of row details that are shown upon pressing the row and contain basic details about the entry.

name	type
enabled	`int`	Whether to show row details. default: `True`

Dashboard¶

Dashboard configuration.

name	type
widgets	`List[Union[WidgetTerms, WidgetHistogram, WidgetScatterPlot, WidgetPeriodicTable]]`	List of widgets contained in the dashboard.

WidgetTerms¶

Terms widget configuration.

name	type
title	`str`	Custom widget title. If not specified, a widget-specific default title is used.
type	`str`	Set as `terms` to get this widget type. default: `terms`
layout	`Dict[str, Layout]`	Defines widget size and grid positioning for different breakpoints. The following breakpoints are supported: `sm`, `md`, `lg`, `xl` and `xxl`.
quantity	`str`	Targeted quantity.
scale	`str`	Statistics scaling. options: - `linear` - `1/2` - `1/4` - `1/8`
showinput	`int`	Whether to show text input field. default: `True`

Layout¶

Defines widget size and grid positioning for different breakpoints.

name	type
h	`int`	Height in grid units
w	`int`	Width in grid units.
x	`int`	Horizontal start location in the grid.
y	`int`	Vertical start location in the grid.
minH	`int`	Minimum height in grid units. default: `3`
minW	`int`	Minimum width in grid units. default: `3`

WidgetScatterPlot¶

Scatter plot widget configuration.

name	type
title	`str`	Custom widget title. If not specified, a widget-specific default title is used.
type	`str`	Set as `scatterplot` to get this widget type. default: `scatterplot`
layout	`Dict[str, Layout]`	Defines widget size and grid positioning for different breakpoints. The following breakpoints are supported: `sm`, `md`, `lg`, `xl` and `xxl`.
x	`Union[Axis, str]`	Configures the information source and display options for the x-axis.
y	`Union[Axis, str]`	Configures the information source and display options for the y-axis.
markers	`Markers`	Configures the information source and display options for the markers.
color	`str`	Quantity used for coloring points. Note that this field is deprecated and `markers` should be used instead.
size	`int`	Maximum number of entries to fetch. Notice that the actual number may be more of less, depending on how many entries exist and how many of the requested values each entry contains. default: `1000`
autorange	`int`	Whether to automatically set the range according to the data limits. default: `True`

Axis¶

Configuration for a plot axis.

name	type
title	`str`	Custom title to show for the axis.
unit	`str`	Custom unit used for displaying the values.
quantity	`str`	Path of the targeted quantity. Note that you can most of the features JMESPath syntax here to further specify a selection of values. This becomes especially useful when dealing with repeated sections or statistical values.

Markers¶

Configuration for plot markers.

name	type
color	`Axis`	Configures the information source and display options for the marker colors.

WidgetHistogram¶

Histogram widget configuration.

name	type
title	`str`	Custom widget title. If not specified, a widget-specific default title is used.
type	`str`	Set as `histogram` to get this widget type. default: `histogram`
layout	`Dict[str, Layout]`	Defines widget size and grid positioning for different breakpoints. The following breakpoints are supported: `sm`, `md`, `lg`, `xl` and `xxl`.
quantity	`str`	Targeted quantity. Note that this field is deprecated and `x` should be used instead.
x	`Union[Axis, str]`	Configures the information source and display options for the x-axis.
scale	`str`	Statistics scaling. options: - `linear` - `1/2` - `1/4` - `1/8`
autorange	`int`	Whether to automatically set the range according to the data limits. default: `True`
showinput	`int`	Whether to show input text fields for minimum and maximum value. default: `True`
nbins	`int`	Maximum number of histogram bins. Notice that the actual number of bins may be smaller if there are fewer data items available.

WidgetPeriodicTable¶

Periodic table widget configuration.

name	type
title	`str`	Custom widget title. If not specified, a widget-specific default title is used.
type	`str`	Set as `periodictable` to get this widget type. default: `periodictable`
layout	`Dict[str, Layout]`	Defines widget size and grid positioning for different breakpoints. The following breakpoints are supported: `sm`, `md`, `lg`, `xl` and `xxl`.
quantity	`str`	Targeted quantity.
scale	`str`	Statistics scaling. options: - `linear` - `1/2` - `1/4` - `1/8`

FilterMenus¶

Contains filter menu 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, FilterMenu]`	Contains the available filter menu options.

FilterMenu¶

Defines the layout and functionality for a filter menu.

name	type
label	`str`	Menu label to show in the UI.
level	`int`	Indentation level of the menu. default: `0`
size	`str`	Width of the menu. default: `s` options: - `s` - `m` - `l` - `xl`
actions	`FilterMenuActions`

FilterMenuActions¶

Contains filter menu action 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, FilterMenuActionCheckbox]`	Contains options for filter menu actions.

FilterMenuActionCheckbox¶

Contains definition for checkbox action in the filter menu.

name	type
type	`str`	Action type. options: - `checkbox`
label	`str`	Label to show.
quantity	`str`	Targeted quantity

Pagination¶

name	type
order_by	`str`	Field used for sorting. default: `upload_create_time`
order	`str`	Sorting order. default: `desc`
page_size	`int`	Number of results on each page. default: `20`

Columns¶

Contains column definitions, controls their availability and specifies the default selection.

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, Column]`	All available column options. Note here that the key must correspond to a quantity path that exists in the metadata.
selected	`List[str]`	Selected options.

Column¶

Option for a column show in the search results.

name	type
label	`str`	Label shown in the header. Defaults to the quantity name.
align	`str`	Alignment in the table. default: `left` options: - `left` - `right` - `center`
unit	`str`	Unit to convert to when displaying. If not given will be displayed in using the default unit in the active unit system.
format	`Format`	Controls the formatting of the values.

Format¶

Value formatting options.

name	type
decimals	`int`	Number of decimals to show for numbers. default: `3`
mode	`str`	Display mode for numbers. default: `standard` options: - `standard` - `scientific` - `separators` - `date` - `time`