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remove jsonschema version constrain #287

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merged 5 commits into from
Nov 12, 2024
Merged

remove jsonschema version constrain #287

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14c2352
remove jsonschema version constrain
sameeul Oct 17, 2024
5553fbf
Use referencing library
sameeul Nov 10, 2024
7d6ca99
Fix lint
sameeul Nov 10, 2024
2e26d0d
Fix lint
sameeul Nov 10, 2024
bf24452
update schema validatoin code
sameeul Nov 10, 2024
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5 changes: 3 additions & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ dependencies = [
# This 'graphviz' is equivalent to `conda install python-graphviz` or
# `sudo apt install python3-graphviz` ONLY.
"graphviz",
"jsonschema<4.18", # temporarily downgrade due to severe performance regression
"jsonschema",
"pyyaml",
"requests",
"mergedeep",
Expand All @@ -42,7 +42,8 @@ dependencies = [
"toil[cwl]",
"fastapi",
"python-jose",
"uvicorn"
"uvicorn",
"referencing"
]

[project.readme]
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13 changes: 9 additions & 4 deletions src/sophios/schemas/wic_schema.py
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Expand Up @@ -5,7 +5,9 @@

import networkx as nx
import graphviz
from jsonschema import RefResolver, Draft202012Validator
from jsonschema import Draft202012Validator
from referencing import Registry, Resource
from referencing.jsonschema import DRAFT202012
import yaml

import sophios
Expand Down Expand Up @@ -680,7 +682,6 @@ def get_validator(tools_cwl: Tools, yml_stems: List[str], schema_store: Dict[str

schema = wic_main_schema(tools_cwl, yml_stems, schema_store, hypothesis)
schema_store[schema['$id']] = schema
schema_store['wic_tag'] = wic_tag_schema(hypothesis)
if write_to_disk:
with open('autogenerated/schemas/wic.json', mode='w', encoding='utf-8') as f:
f.write(json.dumps(schema, indent=2))
Expand All @@ -696,7 +697,11 @@ def get_validator(tools_cwl: Tools, yml_stems: List[str], schema_store: Dict[str
# The $ref tag refers to URIs defined in $id tags, NOT relative paths on
# the local filesystem! We need to create a global mapping between ids and schemas
# i.e. schema_store.
resolver = RefResolver.from_schema(schema, store=schema_store)
schema_store_resource: Resource = Resource(contents=schema_store, specification=DRAFT202012) # type: ignore
registry: Registry = Registry().with_resource(uri="wic_schema_store", resource=schema_store_resource)
wic_tag_schema_resource: Resource = Resource(contents=wic_tag_schema(
hypothesis), specification=DRAFT202012) # type: ignore
registry = registry.with_resource(uri="wic_tag", resource=wic_tag_schema_resource)
""" Use check_schema to 'first verify that the provided schema is
itself valid, since not doing so can lead to less obvious error
messages and fail in less obvious or consistent ways.'
Expand All @@ -707,5 +712,5 @@ def get_validator(tools_cwl: Tools, yml_stems: List[str], schema_store: Dict[str
# try temporarily commenting this line out to generate the schema anyway.
# Then, in any yml file, the very first line should show a "schema stack trace"
Draft202012Validator.check_schema(schema)
validator = Draft202012Validator(schema, resolver=resolver)
validator = Draft202012Validator(schema, registry=registry)
return validator
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