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Excellent Source of Schemas and Examples (ESSE) for Digital Materials R&D","maintainers":[{"name":"exabyte-io","email":"info@exabyte.io"}],"readme":"[![PyPI version](https://badge.fury.io/py/mat3ra-esse.svg)](https://badge.fury.io/py/mat3ra-esse)\n[![npm version](https://badge.fury.io/js/@mat3ra%2Fesse.svg)](https://badge.fury.io/js/@mat3ra%2Fesse)\n[![License: Apache](https://img.shields.io/badge/License-Apache-blue.svg)](https://www.apache.org/licenses/LICENSE-2.0)\n\n# ESSE\n\nEssential Source of Schemas and Examples (ESSE) contains data format definitions (schemas) and examples for common entities used in digital materials science (see refs. [^1], [^2] below).\n\nAlthough the schemas are used to facilitate the operations of [mat3ra.com](https://mat3ra.com), they are designed to be generic and can be used in other applications. The open-source packages developed by Mat3ra.com use the schemas available in this repository.\n\nThe latest variants of schemas and examples are available at [schemas.mat3ra.com](https://schemas.mat3ra.com/), which has three surfaces:\n\n- **[Documentation](https://schemas.mat3ra.com/docs/)** — how ESSE is put together and why: the schema layering, entity anatomy, categorization, conventions and the build pipeline. Start here if you are new.\n- **[Explorer](https://schemas.mat3ra.com/)** — a file browser over every resolved schema and example.\n- **[Ontology](https://schemas.mat3ra.com/map/)** — an interactive map of the ontology: every entity type and every relationship the schemas declare between them (`extends`, `contains`, `variant`), laid out by architectural layer — primitives at the centre, root entities around them, catalogues on the rim. Search for a schema, fly to it, and follow what it extends, contains and is used by.\n\nThe map is built from `graph.json`, an extracted reference graph that is also published at [schemas.mat3ra.com/graph.json](https://schemas.mat3ra.com/graph.json) and doubles as a lint over the corpus.\n\nESSE has a dual-nature as both a Python and a Node.js package.\n\n## 1. Installation\n\n### 1.1. Python\n\nESSE is compatible with Python 3.8+.\n\n#### 1.1.1. PyPI\n\n```bash\npip install mat3ra-esse\n```\n\n#### 1.1.2. Repository\n\n```bash\nvirtualenv .venv\nsource .venv/bin/activate\npip install -e PATH_TO_ESSE_REPOSITORY\n```\n\n### 1.2. Node\n\n#### 1.2.1. NPM\n\n```bash\nnpm install @mat3ra/esse\n```\n\n## 2. Usage\n\nESSE contains separate but equivalent interfaces for Python and Javascript.\nThe package provides `ESSE` class that can be initialized and used as below.\n\n### 2.1. Usage in Python\n\n```python\nfrom mat3ra.esse import ESSE\n\nhelper = ESSE()\nschema = helper.get_schema_by_id(\"material\")\n\n# standalone schema validation and cleaning\nfrom mat3ra.esse import validate_and_clean\n\ndata = {\"a\": \"x\", \"b\": 1, \"c\": \"drop\"}\nschema = {\n    \"type\": \"object\",\n    \"properties\": {\n        \"a\": {\"type\": \"string\"},\n        \"b\": {\"type\": \"integer\"}\n    }\n}\n\nvalidate_and_clean(data, schema)\nprint(data) # {\"a\": \"x\", \"b\": 1}\n\n# alternative: schema-aware cleaning via generated pydantic models\n# also see how it is used in ade: https://github.com/mat3ra/ade/blob/main/src/py/mat3ra/ade/application.py\nfrom pydantic import ConfigDict\nfrom mat3ra.esse.models.software.application import ApplicationSchemaBase\n\n\nclass Application(ApplicationSchemaBase):\n    # drop keys the schema doesn't declare at construction time\n    model_config = ConfigDict(extra=\"ignore\")\n\n\nconfig = {\"name\": \"espresso\", \"version\": \"6.3\", \"buildConfig\": {\"moduleName\": \"6.3-gnu\"}}\napp = Application(**config)\nprint(app.model_dump(exclude_none=True)) # {\"name\": \"espresso\", \"version\": \"6.3\", ...}\n```\n\n### 2.2. Usage in Node/JS/TS\n\n```javascript\nconst { ESSE } = require(\"@mat3ra/esse/lib/js/esse\");\n\nconst helper = new ESSE();\nconst schema = helper.getSchemaById(\"material\");\n\n# schema validation and cleaning\nconst { validateAndClean } = require(\"@mat3ra/esse/lib/js/esse\");\n\nconst data = {\"a\": \"x\", \"b\": 1, \"c\": \"drop\"};\nconst schema = {\n    \"type\": \"object\",\n    \"properties\": {\n        \"a\": {\"type\": \"string\"},\n        \"b\": {\"type\": \"integer\"}\n    }\n}\n\nconst result = validateAndClean(data, schema);\nconsole.log(result); // {\"a\": \"x\", \"b\": 1}\n```\n\n## 3. Directory Structure\n\nESSE contains 3 main directories, [schema](schema), [example](example) and [src](src) outlined below, plus [docs](docs) (documentation sources) and [plan](plan) (design documents).\n\n### 3.1. Schema\n\nThe schema directory contains the schemas specifying the rules to structure data. A set of core schemas, outlined below, are defined to facilitate the schema modularity.\n\n- [Primitive](schema/core/primitive) directory contains a set of custom primitives that extends default standard primitive types allowed by schema, such as String and Number.\nPrimitives are solely defined by the default primitives and can not be re-constructed from each other.\n- [Abstract](schema/core/abstract) directory contains unit-less schemas that are constructed from default and custom primitives.\n- [Reusable](schema/core/reusable) directory contains the schemas that are widely used in other schemas to avoid duplication, constructed from the abstract and primitive schemas.\n- [Reference](schema/core/reference) directory contains the schemas defining the rules to structure the references to data sources.\n\n### 3.2. Example\n\nThis directory contains the examples formed according to the schemas and implements the same directory structure as the schema directory.\n\n### 3.3. src\n\nThis directory contains Python and Javascript interfaces implementing the functionality to access and validate schemas and examples.\n\n### 3.4. docs\n\nMarkdown sources for the [concept documentation](https://schemas.mat3ra.com/docs/), rendered to HTML at deploy time. Pages may embed generated fragments (`<!-- generated:name -->`) that are expanded from the entity graph, so counts and relationship listings cannot drift from the schemas.\n\n### 3.5. plan\n\nDesign documents, filed by status (`upcoming/`, `review/`, `implemented/`, `context/`) per the convention in [mat3ra/agents](https://github.com/mat3ra/agents/blob/main/AGENTS.md). See [plan/README.md](plan/README.md).\n\n## 4. Conventions\n\n### 4.1. Generative vs Non-generative keys\n\nGenerative keys are the fields which allow for user input prior to calculation of the final property values. A flag is included in the schema comments on the fields in [property schemas](schema/properties_directory): `isGenerative:true` marks which fields to use as subschemas in the generation of a user input schema. On properties allowing user inputs, additional fields may be tagged, as in [the `file_content` property](schema/properties_directory/non-scalar/file_content.json)\n\n## 5. Development\n\nThe schemas and examples are stored as JSON assets. The JSON assets are used to generate JS/TS and PY modules that can be used to access the schemas and examples in the corresponding runtimes. The modules are generated using the [build_schemas.py](./build_schemas.py) and [build_schema.js](./build_schema.js) scripts. The JS modules are generated during the transpilation step of the npm. The PY modules are generated during the development and distributed within the pip package.\n\nThe following outlines the development process workflow:\n\n1. Setup: clone the repository and install the dependencies for both JS and PY (as explained below).\n2. Edit code and commit changes.\n3. Pre commit is used to regenerate the modules.\n4. Push the changes to GitHub.\n5. GH workflow is used to generate the fully resolved file (without \"$ref\"s and \"$allOf\" etc.) and examples, render the documentation and the ontology map, and publish them to [schemas.mat3ra.com](http://schemas.mat3ra.com/). The site is assembled in a gitignored `site/` staging directory; internal links are checked before it deploys.\n6. Publish the new version of the package to PyPI and npm.\n\nThe [pre-commit](.husky/pre-commit) is using both JS and PY runtime(s) to regenerate the schemas and examples.\n\n[//]: # (TODO: consider reusing JS runtime and schemas build script for PY modules for consistency)\nNOTE: The PY and JS modules are built from the same JSON sources, but using different runtimes (scripts) and thus may still be different. Only for JS the fully resolved schemas (with merged \"$allOf\") are created. They are used for the docs website.\n\n### 5.1. Development in Python\n\nWhen developing in python the following should be taken into account:\n\n1. The modules containing the schemas and examples are generated using the [build-schemas.py](./build_schemas.py) script. There is a setup for it to be run automatically on every commit, but it is recommended to run it manually before committing to make sure that the changes are reflected in the modules. This can be done with `pre-commit run --all-files`. The pre-commit package can be installed with `pip install pre-commit`. To rebuild schemas manually, run (note `-e` in install):\n\n    ```bash\n    python -m venv .venv\n    source .venv/bin/activate\n    pip install -e \".[tests]\"\n    pip install pre-commit\n    pre-commit --install\n    git config --unset-all core.hooksPath\n    python build_schemas.py\n    ```\n\n2. Tests can be run using the following commands:\n\n    ```bash\n    python -m venv .venv\n    source .venv/bin/activate\n    pip install \".[tests]\"\n    python -m unittest discover --verbose --catch --start-directory tests/py/esse/\n    ```\n\n### 5.2. Development in Javascript/Typescript\n\nSee [package.json](package.json) for the list of available npm commands. The JS modules are generated using the [build_schema.js](./build_schema.js) script. There is a setup for it to be run automatically when the package is installed (see \"transpile\" directive). To rebuild schemas manually, run:\n\n```bash\nnpm install\nnpm run transpile\n```\n\n### 5.3. General Dev Suggestions\n\nThis repository is an [open-source](LICENSE.md) work-in-progress and we welcome contributions. We suggest forking this repository and introducing the adjustments there, the changes in the fork can further be considered for merging into this repository as it is commonly done on GitHub (see [^3] below).\n\nOther suggestions:\n\n- Use unique IDs for schemas\n- Do not use circular references in the schemas, instead leave the type as object and add explanation to description.\n\nThe schema lint (`npm run lint-entity-graph`, also part of `npm test`) enforces both of the above along with `$id` conventions, JSON-pointer targets and manifest references. [Contributing a schema](https://schemas.mat3ra.com/docs/contributing-a-schema.html) walks through adding one end to end.\n\n## Links\n\n[^1]: [Data-centric online ecosystem for digital materials science](https://arxiv.org/pdf/1902.10838.pdf)\n[^2]: [CateCom: A Practical Data-Centric Approach to Categorization of Computational Models](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.2c00112)\n[^3]: [GitHub Standard Fork & Pull Request Workflow](https://gist.github.com/Chaser324/ce0505fbed06b947d962)\n","readmeFilename":"README.md"}