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70 validation error in config.yaml for empty fields #71

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merged 2 commits into from
Nov 14, 2024
Merged

70 validation error in config.yaml for empty fields #71

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c7ea946
ensure optional typing for optional fields
yaseminbridges Nov 14, 2024
86adaa0
bump version for release
yaseminbridges Nov 14, 2024
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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
@@ -1,6 +1,6 @@
[tool.poetry]
name = "pheval_exomiser"
version = "0.2.5"
version = "0.2.6"
description = ""
authors = ["Yasemin Bridges <y.bridges@qmul.ac.uk>",
"Julius Jacobsen <j.jacobsen@qmul.ac.uk>",
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26 changes: 13 additions & 13 deletions src/pheval_exomiser/prepare/tool_specific_configuration_options.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
from pathlib import Path
from typing import List
from typing import List, Optional

from pydantic import BaseModel, Field

Expand All @@ -20,17 +20,17 @@ class ApplicationProperties(BaseModel):
cache_caffeine_spec (int): Cache limit
"""

remm_version: str = Field(None)
cadd_version: str = Field(None)
hg19_data_version: str = Field(None)
hg19_local_frequency_path: Path = Field(None)
hg19_whitelist_path: Path = Field(None)
hg38_data_version: str = Field(None)
hg38_local_frequency_path: Path = Field(None)
hg38_whitelist_path: Path = Field(None)
phenotype_data_version: str = Field(None)
cache_type: str = Field(None)
cache_caffeine_spec: int = Field(None)
remm_version: Optional[str] = Field(None)
cadd_version: Optional[str] = Field(None)
hg19_data_version: Optional[str] = Field(None)
hg19_local_frequency_path: Optional[Path] = Field(None)
hg19_whitelist_path: Optional[Path] = Field(None)
hg38_data_version: Optional[str] = Field(None)
hg38_local_frequency_path: Optional[Path] = Field(None)
hg38_whitelist_path: Optional[Path] = Field(None)
phenotype_data_version: Optional[str] = Field(None)
cache_type: Optional[str] = Field(None)
cache_caffeine_spec: Optional[int] = Field(None)


class PostProcessing(BaseModel):
Expand Down Expand Up @@ -64,5 +64,5 @@ class ExomiserConfigurations(BaseModel):
analysis_configuration_file: Path = Field(...)
max_jobs: int = Field(...)
application_properties: ApplicationProperties = Field(...)
output_formats: List[str] = Field(None)
output_formats: Optional[List[str]] = Field(None)
post_process: PostProcessing = Field(...)
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