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adjust for modified 'schema' of input objects with 'plugins(ICT)' #273

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merged 1 commit into from
Sep 18, 2024
Merged

adjust for modified 'schema' of input objects with 'plugins(ICT)' #273

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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -141,7 +141,7 @@ namespaces = true

[tool.setuptools.package-data]
"*" = ["*.txt"]
"sophios" = ["*.json"]
"sophios" = ["**/*.json"]

[tool.aliases]
test = "pytest --workers 8"
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156 changes: 29 additions & 127 deletions src/sophios/api/utils/converter.py
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Original file line number Diff line number Diff line change
@@ -1,130 +1,17 @@
import copy
from pathlib import Path
from typing import Any, Dict, List
import json
import yaml
from jsonschema import Draft202012Validator
from sophios.utils_yaml import wic_loader

from sophios.wic_types import Json, Cwl

SCHEMA: Json = {
"$schema": "http://json-schema.org/draft-07/schema#",
"definitions": {
"Link": {
"properties": {
"id": {
"type": "number"
},
"inletIndex": {
"type": "number"
},
"outletIndex": {
"type": "number"
},
"sourceId": {
"type": "number"
},
"targetId": {
"type": "number"
},
"x1": {
"type": "number"
},
"x2": {
"type": "number"
},
"y1": {
"type": "number"
},
"y2": {
"type": "number"
}
},
"type": "object",
"required": ["id", "sourceId", "targetId"]
},
"NodeSettings": {
"properties": {
"inputs": {
"additionalProperties": {
"$ref": "#/definitions/T"
},
"type": "object"
},
"outputs": {
"additionalProperties": {
"$ref": "#/definitions/T"
},
"type": "object"
}
},
"type": "object"
},
"NodeX": {
"properties": {
"expanded": {
"type": "boolean"
},
"height": {
"type": "number"
},
"id": {
"type": "number"
},
"internal": {
"type": "boolean"
},
"name": {
"type": "string"
},
"pluginId": {
"type": "string"
},
"settings": {
"$ref": "#/definitions/NodeSettings"
},
"width": {
"type": "number"
},
"x": {
"type": "number"
},
"y": {
"type": "number"
},
"z": {
"type": "number"
},
},
"type": "object",
"required": ["id", "name", "pluginId", "settings", "internal"]
},
"T": {
"type": "object"
}
},
"properties": {
"links": {
"items": {
"$ref": "#/definitions/Link"
},
"type": "array"
},
"nodes": {
"items": {
"$ref": "#/definitions/NodeX"
},
"type": "array"
},
"selection": {
"items": {
"type": "number"
},
"type": "array"
}
},
"type": "object",
"required": ["links", "nodes"]
}
SCHEMA_FILE = Path(__file__).parent / "input_object_schema.json"
SCHEMA: Json = {}
with open(SCHEMA_FILE, 'r', encoding='utf-8') as f:
SCHEMA = json.load(f)


def del_irrelevant_keys(ldict: List[Dict[Any, Any]], relevant_keys: List[Any]) -> None:
Expand All @@ -137,20 +24,36 @@ def del_irrelevant_keys(ldict: List[Dict[Any, Any]], relevant_keys: List[Any]) -
elem.pop(ek, None)


def validate_schema_and_object(schema: Json, jobj: Json) -> None:
def validate_schema_and_object(schema: Json, jobj: Json) -> bool:
"""Validate schema object"""
Draft202012Validator.check_schema(schema)
df2012 = Draft202012Validator(schema)
df2012.is_valid(jobj)
return df2012.is_valid(jobj)


def extract_state(inp: Json) -> Json:
"""Extract only the state information from the incoming wfb object.
It includes converting "ICT" nodes to "CLT" using "plugins" tag of the object.
"""
inp_restrict: Json = {}
if not inp.get('plugins'):
inp_restrict = copy.deepcopy(inp['state'])
else:
inp_inter = copy.deepcopy(inp)
# Here goes the ICT to CLT extraction logic
inp_restrict = inp_inter['state']
return inp_restrict


def raw_wfb_to_lean_wfb(inp: Json) -> Json:
"""drop all the unnecessary info from incoming wfb object"""
inp_restrict = copy.deepcopy(inp)
keys = list(inp.keys())
"""Drop all the unnecessary info from incoming wfb object"""
if validate_schema_and_object(SCHEMA, inp):
print('incoming object is valid against input object schema')
inp_restrict = extract_state(inp)
keys = list(inp_restrict.keys())
# To avoid deserialization
# required attributes from schema
prop_req = SCHEMA['required']
prop_req = SCHEMA['definitions']['State']['required']
nodes_req = SCHEMA['definitions']['NodeX']['required']
links_req = SCHEMA['definitions']['Link']['required']
do_not_rem_nodes_prop = ['cwlScript', 'run']
Expand All @@ -170,12 +73,11 @@ def raw_wfb_to_lean_wfb(inp: Json) -> Json:
else:
pass

validate_schema_and_object(SCHEMA, inp_restrict)
return inp_restrict


def wfb_to_wic(inp: Json) -> Cwl:
"""convert lean wfb json to compliant wic"""
"""Convert lean wfb json to compliant wic"""
# non-schema preserving changes
inp_restrict = copy.deepcopy(inp)

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