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ivan-aksamentovivan-aksamentov
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feat: add pathogen.json example of schema usage
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‎.gitignore

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*.bak
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*.log
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*.pyc
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/build/
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/data_dev*/
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/data_local*

‎packages/nextclade-schemas/README.md

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## Example: Python
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This is a simple example which demonstrates how to use Nextclade JSON schemas to generate Python dataclasses and how to use them to read Nextclade JSON files in a type-safe way. Note that Python language is duck typed, so it's probably not the best choice if you want to build something type-safe. We demonstrate with Python here only because its omnipresence in bioinformatics.
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First you need to obtain JSON schema definitions. Depending on your needs and tools you use you could:
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- run `nextclade schemas write -o nextclade-schemas/`
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pip3 install dacite datamodel-code-generator pydantic
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mkdir -p examples/python/lib/
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# Generate Python classes
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datamodel-codegen --input-file-type "jsonschema" --output-model-type "dataclasses.dataclass" --enum-field-as-literal=all --input "output-json.schema.yaml" --output "examples/python/nextclade_output_json.py"
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datamodel-codegen --input-file-type "jsonschema" --output-model-type "dataclasses.dataclass" --enum-field-as-literal=all --input "output-json.schema.yaml" --output "examples/python/lib/nextclade_output_json.py"
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datamodel-codegen --input-file-type "jsonschema" --output-model-type "dataclasses.dataclass" --enum-field-as-literal=all --input "input-pathogen-json.schema.yaml" --output "examples/python/lib/nextclade_input_pathogen_json.py"
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cd examples python/
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# Run the example which is using the generated Python classes
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# See packages/nextclade-schemas/examples/python/example.py
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python3 examples/python/example.py path/to/your/nextclade.json
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# Run the output JSON example which is using the generated Python classes.
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# See packages/nextclade-schemas/examples/python/example_output_json.py
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python3 examples/python/example_output_json.py $path_to_your_output_nextclade_json
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# Run the input pathogen JSON example which is using the generated Python classes.
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# See packages/nextclade-schemas/examples/python/example_pathogen_json.py
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python3 examples/python/example_pathogen_json.py $path_to_your_pathogen_json
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```
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In this example the generated file `nextclade_output_json.py` will contain the Python dataclasses derived from `output-json.schema.yaml`. The example program in `examples/python/example.py` reads the Nextclade output JSON file (produced separately with `nextclade run --output-json ...`) and casts the resulting dict to the generated dataclasses (recursively) types using `dacite` library. You can then access to the data in a convenient and type-safe manner, and most text editors should also provide code completions. This is especially true for type-safe, compiled languages.
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In this example the generated file `nextclade_output_json.py` will contain the Python dataclasses derived from `output-json.schema.yaml`. The example program in `examples/python/example.py` reads the Nextclade output JSON file (produced separately with `nextclade run --output-json ...`) and casts the resulting dict to the generated dataclasses (recursively) types using `dacite` library. You can then access to the data in a convenient and type-safe manner, and most text editors should also provide code completions. This approach with dataclasses can be somewhat slow for big inputs, because it requires converting Python dicts into dataclasses. You might find another, better solution which fits your use-case better - there are many tools which can understand JSON schema.
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## Other languages and tools
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‎packages/nextclade-schemas/examples/python/example.py renamed to ‎packages/nextclade-schemas/examples/python/example_output_json.py

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"""
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Example demonstrating how to read JSON using Python classes generated from JSON schema.
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Example demonstrating how to read Nextclade output JSON using Python classes generated from JSON schema.
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See README.md in the parent directory for instructions.
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```
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"""
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import sys
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import json
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from dacite import from_dict
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from nextclade_output_json import ResultsJson
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from lib.nextclade_output_json import ResultsJson
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def read_nextclade_output_json(filepath: str | None = None) -> ResultsJson:

‎packages/nextclade-schemas/examples/python/example_pathogen_json.py

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"""
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Example demonstrating how to read Nextclade pathogen JSON using Python classes generated from JSON schema.
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See README.md in the parent directory for instructions.
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"""
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import sys
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import json
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from pathlib import Path
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from dacite import from_dict
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from lib.nextclade_input_pathogen_json import PathogenJson
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def read_nextclade_pathogen_json(filepath: str | None = None) -> PathogenJson:
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source = sys.stdin if filepath is None else open(filepath)
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with source as f:
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json_data = json.load(f)
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return from_dict(PathogenJson, json_data)
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def dict_get(d: dict, key: str, default=None):
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return d[key] if key in d else default
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if __name__ == "__main__":
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filepath = sys.argv[1] if len(sys.argv) > 1 else None
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data = read_nextclade_pathogen_json(filepath)
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name = dict_get(data.attributes or {}, "name", "unknown")
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ref_name = dict_get(data.attributes or {}, "reference name", "unknown")
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ref_accession = dict_get(data.attributes or {}, "reference accession", "unknown")
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print(f"Dataset name: {name}")
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if data.shortcuts:
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print(f"aka: {', '.join(data.shortcuts)}")
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print(f"Reference name: {ref_name}")
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print(f"Reference accession: {ref_accession}")
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if data.files:
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print("\nDataset files:")
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dataset_dir = Path(filepath).parent if filepath else Path.cwd()
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for file_type, filename in vars(data.files).items():
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if filename:
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absolute_path = dataset_dir / filename
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print(f" {file_type}: {absolute_path}")
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if data.alignmentParams:
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print("\nAlignment parameters:")
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params_dict = {k: v for k, v in vars(data.alignmentParams).items() if v is not None}
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print(json.dumps(params_dict, indent=2, default=str))

‎packages/nextclade-schemas/examples/python/lib/.gitkeep

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‎packages/nextclade-schemas/input-pathogen-json.schema.json

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},
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"attributes": {
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"type": "object",
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"additionalProperties": {
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"$ref": "#/definitions/AnyType"
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}
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"additionalProperties": true
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},
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"shortcuts": {
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"type": "array",
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}
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},
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"definitions": {
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"AnyType": {
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"description": "Any type that can be represented in JSON",
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"anyOf": [
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{
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"title": "string",
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"type": "string"
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},
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{
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"title": "int",
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"type": "integer",
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},
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"type": "number",
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"format": "double"
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},
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{
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"title": "bool",
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"type": "boolean"
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},
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"items": {
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"$ref": "#/definitions/AnyType"
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}
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},
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{
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"title": "object",
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"additionalProperties": {
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},
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"title": "null",
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}
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]
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},
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"DatasetMeta": {
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"properties": {
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"minimum": 0.0
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},
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"maxIndel": {
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"description": "REMOVED",
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"anyOf": [
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{
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"$ref": "#/definitions/AnyType"
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},
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{
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"description": "REMOVED"
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},
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"seedLength": {
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"description": "REMOVED"
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"mismatchesAllowed": {
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"anyOf": [
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"$ref": "#/definitions/AnyType"
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"description": "REMOVED"
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"minSeeds": {
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"anyOf": [
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"description": "REMOVED"
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"minMatchRate": {
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}
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"AaMotifsDesc": {

‎packages/nextclade-schemas/input-pathogen-json.schema.yaml

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type: string
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attributes:
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additionalProperties:
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$ref: '#/definitions/AnyType'
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additionalProperties: true
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shortcuts:
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definitions:
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AnyType:
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description: Any type that can be represented in JSON
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anyOf:
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- title: string
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type: string
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- title: int
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type: integer
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format: int
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type: number
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format: double
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items:
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additionalProperties:
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anyOf:
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seedLength:
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AlignmentPreset:
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AaMotifsDesc:
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description: Describes motifs in amino acid sequences, such as glycosylation sites, disulfide bonds, etc.
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examples:

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