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‎docs/tutorial/customization/custom_schemas.md‎

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@@ -6,18 +6,17 @@ Custom schemas in NOMAD define how data is structured, stored, and displayed, al
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- Define data structures that dictate how information is organized and presented.
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- Enable ELN functionality for manual data input and structured documentation.
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- Extract structured data from files using parsers, which allow NOMAD to read data from raw files.
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- Transform and enrich data post-upload using normalizers, ensuring compatibility with schema requirements and enhancing metadata consistency.
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- Transform and enrich data, post-upload, using [normalizers](../../reference/glossary.md#normalizer), ensuring compatibility with schema requirements and enhancing metadata consistency.
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There are two primary approaches to creating custom schemas:
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- **Python schemas**: These offer highest possible level of customization by allowing the integration of **custom parsers** and **normalizers**, enabling maximum automation.
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- **Serialized schemas (YAML/JSON)**: Human-readable and easier to write and manage, ideal for defining customized ELNs without coding skills. However, they do not support normalizers.
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- **Python schemas**: These offer highest possible level of customization by allowing the integration of [parsers](../../reference/glossary.md#parser) and [normalizers](../../reference/glossary.md#normalizer), enabling maximum automation.
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- **Serialized schemas (YAML/JSON)**: Human-readable and easier to write and manage, ideal for defining customized ELNs without coding skills. They can be used on both the central NOMAD and any Oasis instance without requiring configuration changes, making them especially convenient for quick customization.
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This part of the tutorial covers the following topics:
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- [YAML schemas](custom_yaml.md): Defining structured YAML schemas for NOMAD.
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- [Custom ELN with YAML](custom_eln.md): Creating an ELN schema to enable structured metadata entry.
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- [Tabular parser in YAML](custom_tabular.md): Utilizing the built-in tabular parser to process spreadsheet data.
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- [Python schemas](custom_python.md): Exploring Python schemas and their advanced capabilities.
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- [Normalizers](custom_normalizer.md): Implementing normalizers to automate data processing.
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- [Tabular parser in YAML](custom_tabular.md): Utilizing the built-in tabular parser to process spreadsheet data.

‎docs/tutorial/customization/custom_yaml.md‎

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## Guidelines for building a custom schema
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NOMAD YAML schema files must have the `.archive.yaml` extension for NOMAD to recognize them as schema files. Below are six main guidelines for creating a custom YAML schema file.
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To define custom YAML schemas in NOMAD, you need to create a YAML file with the `.archive.yaml` extension. These files represent a [schema package](../../reference/glossary.md#schema-package), which can include one or more section and quantity definitions.. Below are six main guidelines for creating a custom YAML schema file.
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??? info "1. NOMAD's `archive.yaml` files start with the `definitions:` keyword, and must have a `name:`, and can have a `description:`."
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NOMAD syntax:
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```yaml
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definitions:
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name:
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description:
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name: ...
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description: ...
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```
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Example:
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```yaml
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definitions:
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name:
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description:
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name: ...
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description: ...
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sections:
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My_first_section:
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My_second_section:
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My_third_section:
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MyFirstSection: ...
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MySecondSection: ...
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MyThirdSection: ...
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```
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description: This is a custom schema that includes several sections.
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sections:
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My_first_section:
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MyFirstSection:
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base_sections:
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- nomad.datamodel.data.EntryData
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- nomad.datamodel.metainfo.eln.Sample
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- nomad.datamodel.metainfo.eln.ELNSample
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My_second_section:
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My_third_section:
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MySecondSection: ...
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MyThirdSection: ...
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```
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or alternatively in the form of a Python list:
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```yaml
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definitions:
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name: My NOMAD ELN
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name: My NOMAD Custom Schema
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description: This is a custom schema that includes several sections.
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sections:
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My_first_section:
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base_sections: ['nomad.datamodel.data.EntryData', 'nomad.datamodel.metainfo.eln.Sample']
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MyFirstSection:
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base_sections: ['nomad.datamodel.data.EntryData', 'nomad.datamodel.metainfo.eln.ELNSample']
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My_second_section:
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My_third_section:
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MySecondSection: ...
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MyThirdSection: ...
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```
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??? info "4. Each section can contain quantities, other sections, and subsections."
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```yaml
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definitions:
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name: My NOMAD ELN
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name: My NOMAD Custom Schema
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description: This is a custom schema that includes several sections.
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sections:
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My_first_section:
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MyFirstSection:
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base_sections:
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- nomad.datamodel.data.EntryData
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- nomad.datamodel.metainfo.eln.Sample
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quantities:
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- nomad.datamodel.metainfo.eln.ELNSample
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quantities:
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first_quantity:
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type: str # Uses python type notation like: int, np.float64, etc.
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sub_sections:
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My_first_subsection:
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section:
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My_second_subsection:
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section:
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My_second_section:
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My_third_section:
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my_first_subsection:
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section: ...
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my_second_subsection:
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section: ...
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MySecondSection: ...
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MyThirdSection: ...
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```
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```yaml
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definitions:
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name: My NOMAD ELN
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name: My NOMAD Custom Schema
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description: This is a custom schema that includes several sections.
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sections:
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My_first_section:
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MyFirstSection:
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base_sections:
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- nomad.datamodel.data.EntryData
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- nomad.datamodel.metainfo.eln.Sample
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- nomad.datamodel.metainfo.eln.ELNSample
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quantities:
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first_quantity:
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- type: #For example, str or np.float64
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- shape: #For example scalar or list (['*'])
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- unit: #For example, meters, amperes, or seconds
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type: #For example, str or np.float64
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shape: #For example scalar or list (['*'])
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unit: #For example, meters, amperes, or seconds
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sub_sections:
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My_first_subsection:
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section:
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My_second_subsection:
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section:
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My_third_subsection:
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section:
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My_second_section:
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My_third_section:
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my_first_subsection:
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section: ...
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my_second_subsection:
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section: ...
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my_third_subsection:
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section: ...
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MySecondSection: ...
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MyThirdSection: ...
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```
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??? info "6. Sections and quantities can have annotations"
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Annotations provide additional information that NOMAD can use to alter its behavior around these definitions and how users can interact with them. The keyword for annotations is `m_annotations:`.
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Among the various functionalities that annotations provide, they enable the transformation of schema sections, subsections, and quantities into ELN components that users can edit directly within the GUI.
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```yaml
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definitions:
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name: My NOMAD ELN
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name: My NOMAD Custom Schema
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description: This is an electronic lab notebook schema that includes several sections.
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sections:
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My_first_section:
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MyFirst_Section:
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base_sections:
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- nomad.datamodel.metainfo.eln.Sample
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- nomad.datamodel.metainfo.eln.ELNSample
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key1: value1
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sub_section:
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section:
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section:
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section:
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My_second_section:
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My_third_section:
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sub_sections:
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my_first_subsection:
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section: ...
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my_second_subsection:
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section: ...
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my_third_subsection:
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section: ...
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MySecondSection: ...
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MyThirdSection: ...
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```

‎mkdocs.yml‎

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- YAML schemas: tutorial/customization/custom_yaml.md
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- Custom ELN with YAML: tutorial/customization/custom_eln.md
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- Tabular parser in YAML: tutorial/customization/custom_tabular.md
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- Python schemas: tutorial/customization/custom_python.md
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- Normalizers: tutorial/customization/custom_normalizer.md
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- Developing a NOMAD plugin: tutorial/develop_plugin.md
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- How-to guides:
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- Overview: howto/overview.md

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