init

.github/workflows/validate.yaml

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+name: '[validate] json schema validation'
+on:
+  push:
+    branches: ["main"]
+  workflow_dispatch:
+    inputs:
+      use-cfg:
+        description: "branch of siibra-configuration to be checkout"
+        required: false
+        type: string
+        default: 'expmt_attr'
+jobs:
+  validate:
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    - uses: actions/checkout@v4
+    - uses: actions/checkout@v4
+      with:
+        repository: FZJ-INM1-BDA/siibra-configurations
+        path:  siibra-configurations
+        fetch-depth: 1
+        clean: True
+        ref: ${{ inputs.use-cfg }}
+    - run: |
+        pip install -r requirements.txt
+    - run: |
+        python code/validate.py ./siibra-configurations/features/

.gitignore

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+venv

code/validate.py

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+import sys
+import os
+from pathlib import Path
+from logging import getLogger, DEBUG, INFO, StreamHandler
+from jsonschema import ValidationError, Draft202012Validator
+import referencing
+import json
+from enum import Enum
+
+
+class ValidationResult(Enum):
+    SKIPPED = "SKIPPED"
+    PASSED = "PASSED"
+    FAILED = "FAILED"
+
+logger = getLogger(__name__)
+logger.setLevel(INFO)
+logger.addHandler(StreamHandler())
+
+ROOT_DIR = os.path.abspath(f"{os.path.dirname(os.path.realpath(__file__))}/..")
+
+skip_path = ("venv", )
+
+skip_types = (
+    "siibra/feature/timeseries/activity/v0.1",
+    "siibra/feature/connectivitymatrix/v0.3",
+)
+
+def populate_jsonschema_reg():
+    registry = referencing.Registry()
+    walk_path = Path(ROOT_DIR) / "siibra"
+    for dirpath, dirnames, filenames in os.walk(walk_path):
+        for filename in filenames:
+            if not filename.endswith(".json"):
+                continue
+
+            filepath = Path(dirpath) / filename
+            with open(filepath, "r") as fp:
+                uri = f"urn:siibra-local:{str(filepath.relative_to(ROOT_DIR))}"
+                resource = referencing.Resource.from_contents(json.load(fp=fp))
+                registry = registry.with_resource(uri=uri, resource=resource)
+
+    return registry
+
+def validate_json(path_to_json, registry, fail_fast=False):
+    if any([path_fragment in path_to_json for path_fragment in skip_path]):
+        return (
+            path_to_json,
+            ValidationResult.SKIPPED,
+            None,
+        )
+    with open(path_to_json, "r") as fp:
+        json_obj = json.load(fp)
+
+    # skip list
+    if isinstance(json_obj, list):
+        return (path_to_json, ValidationResult.SKIPPED, None)
+    _type = json_obj.get("@type", None)
+    if not _type:
+        # TODO consolidate how error are raied
+        if fail_fast:
+            raise ValidationError(f"type does not exist: {path_to_json}")
+        return (path_to_json, ValidationResult.FAILED, None)
+
+    # assert _schema is None
+    if not _type or not _type.startswith("siibra"):
+        return (path_to_json, ValidationResult.SKIPPED, None)
+    if _type in skip_types:
+        return (path_to_json, ValidationResult.SKIPPED, None)
+    abspath = os.path.join(ROOT_DIR, (_type + ".json"))
+    path_to_schema = os.path.abspath(abspath)
+    with open(path_to_schema, "r") as fp:
+        schema = json.load(fp)
+    try:
+        validator = Draft202012Validator(schema, registry=registry)
+        validator.validate(json_obj)
+    except ValidationError as e:
+        if fail_fast:
+            # TODO consolidate how error are raied
+            raise e from e
+        return (path_to_json, ValidationResult.FAILED, e)
+    return (path_to_json, ValidationResult.PASSED, None)
+
+def main(dir_to_validate: str=None, *args, debug=False):
+
+    if debug:
+        logger.setLevel(DEBUG)
+
+    jsonschema_reg = populate_jsonschema_reg()
+    # resolver = jsonschema_reg.resolver()
+
+    if dir_to_validate is None:
+        raise RuntimeError(f"pass the directory that needs to validated")
+
+    result = []
+    for dirpath, dirnames, filenames in os.walk(dir_to_validate):
+        for filename in filenames:
+            if not filename.endswith(".json"):
+                logger.debug(f"Skipping {path_to_file} because it does not end in .json")
+                continue
+            path_to_file = Path(dirpath) / filename
+            logger.debug(f"Processing {path_to_file}")
+            result.append(
+                validate_json(str(path_to_file), jsonschema_reg, fail_fast=False)
+            )
+
+    passed = [r for r in result if r[1] == ValidationResult.PASSED]
+    failed = [r for r in result if r[1] == ValidationResult.FAILED]
+    skipped = [r for r in result if r[1] == ValidationResult.SKIPPED]
+    print(
+        f"Validation results: PASSED: {len(passed)} SKIPPED: {len(skipped)} FAILED: {len(failed)}"
+    )
+
+    if len(failed) > 0:
+        print(failed)
+        # TODO consolidate how error are raied
+        raise ValidationError(
+            message="\n-----\n".join([f"{f[0]}: {str(f[2])}" for f in failed])
+        )
+
+
+
+if __name__ == "__main__":
+    main(*sys.argv[1:])

requirements.txt

@@ -0,0 +1 @@
+jsonschema

siibra/attr/data/image/v0.1.json

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+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "type": "object",
+    "properties": {
+        "@type": {
+            "const": "siibra/attr/data/image/v0.1"
+        },
+        "format": {
+            "$ref": "#/definitions/format"
+        },
+        "fetcher": {
+            "type": "string"
+        },
+        "key": {
+            "type": "string"
+        }
+    },
+    "required": [
+        "@type",
+        "format",
+        "fetcher"
+    ],
+    "definitions": {
+        "format": {
+            "oneOf": [
+                {
+                    "const": "neuroglancer/precomputed"
+                },
+                {
+                    "const": "nii"
+                }
+            ]
+        }
+    },
+    "additionalProperties": false
+}

siibra/attr/data/tabular/v0.1.json

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+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "type": "object",
+    "properties": {
+        "@type": {
+            "const": "siibra/attr/data/tabular/v0.1"
+        },
+        "format": {
+            "$ref": "#/definitions/format"
+        },
+        "parse_options": {
+            "$ref": "#/definitions/parse_options"
+        },
+        "plot_options": {
+            "$ref": "#/definitions/plot_options"
+        }
+    },
+    "required": [
+        "@type",
+        "format"
+    ],
+    "definitions": {
+        "format": {
+            "anyOf": [
+                {
+                    "const": "csv"
+                }
+            ]
+        },
+        "parse_options": {
+            "type": "object",
+            "description": "Passed directly to [pandas.read_csv](https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.read_csv.html) as keyword arguments"
+        },
+        "plot_options": {
+            "type": "object",
+            "description": "Passed directly to [pandas.DataFrame.plot](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.plot.html) as keyword arguments"
+        }
+    }
+}

siibra/attr/data/v0.1.json

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+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "oneOf": [
+        {
+            "$ref": "urn:siibra-local:siibra/attr/data/image/v0.1.json"
+        },
+        {
+            "$ref": "urn:siibra-local:siibra/attr/data/tabular/v0.1.json"
+        }
+    ]
+}

siibra/attr/desc/ebrains/v0.1.json

@@ -0,0 +1,21 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "type": "object",
+    "properties": {
+        "@type": {
+            "const": "siibra/attr/desc/ebrains/v0.1"
+        },
+        "ids": {
+            "type": "object",
+            "patternProperties": {
+                "^.+$": {
+                    "type": "string"
+                }
+            }
+        }
+    },
+    "required": [
+        "ids",
+        "@type"
+    ]
+}

siibra/attr/desc/modality/v0.1.json

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+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "type": "object",
+    "allOf": [
+        {
+            "$ref": "urn:siibra-local:siibra/attr/util/humanreadable/v0.1.json"
+        }
+    ],
+    "properties": {
+        "@type": {
+            "const": "siibra/attr/desc/modality/v0.1"
+        }
+    },
+    "required": ["@type"]
+}

siibra/attr/desc/name/v0.1.json

@@ -0,0 +1,15 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "type": "object",
+    "allOf": [
+        {
+            "$ref": "urn:siibra-local:siibra/attr/util/humanreadable/v0.1.json"
+        }
+    ],
+    "properties": {
+        "@type": {
+            "const": "siibra/attr/desc/name/v0.1"
+        }
+    },
+    "required": ["@type"]
+}

siibra/attr/desc/regionspec/v0.1.json

@@ -0,0 +1,15 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "type": "object",
+    "allOf": [
+        {
+            "$ref": "urn:siibra-local:siibra/attr/util/humanreadable/v0.1.json"
+        }
+    ],
+    "properties": {
+        "@type": {
+            "const": "siibra/attr/desc/regionspec/v0.1"
+        }
+    },
+    "required": ["@type"]
+}

siibra/attr/desc/speciesspec/v0.1.json

@@ -0,0 +1,15 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "type": "object",
+    "allOf": [
+        {
+            "$ref": "urn:siibra-local:siibra/attr/util/humanreadable/v0.1.json"
+        }
+    ],
+    "properties": {
+        "@type": {
+            "const": "siibra/attr/desc/speciesspec/v0.1"
+        }
+    },
+    "required": ["@type"]
+}

siibra/attr/desc/v0.1.json

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+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "oneOf": [
+        {
+            "$ref": "urn:siibra-local:siibra/attr/desc/ebrains/v0.1.json"
+        },
+        {
+            "$ref": "urn:siibra-local:siibra/attr/desc/modality/v0.1.json"
+        },
+        {
+            "$ref": "urn:siibra-local:siibra/attr/desc/name/v0.1.json"
+        },
+        {
+            "$ref": "urn:siibra-local:siibra/attr/desc/regionspec/v0.1.json"
+        },
+        {
+            "$ref": "urn:siibra-local:siibra/attr/desc/speciesspec/v0.1.json"
+        }
+    ]
+}

siibra/attr/extra/v0.1.json

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+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "type": "object",
+    "description": "Experimental attributes",
+    "properties": {
+        "@type": {
+            "type": "string",
+            "pattern": "^x-"
+        }
+    }
+}

siibra/attr/loc/layerboundary/v0.1.json

@@ -0,0 +1,12 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "type": "object",
+    "properties": {
+        "@type": {
+            "const": "siibra/attr/loc/layerboundary/v0.1"
+        },
+        "url": {
+            "type": "string"
+        }
+    }
+}