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fix: Adding default values for optional fields #19

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merged 1 commit into from
Mar 1, 2024
Merged

fix: Adding default values for optional fields #19

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10 changes: 7 additions & 3 deletions ingestion_tools/dataset_configs/template.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -117,16 +117,20 @@ tomograms:
standardization_config:
destination_prefix: '99999'
source_prefix: path/to/source
run_glob: frames/*
run_regex: /TS_\d\d$
run_name_regex: (.*)
frames_glob: frames/{run_name}_*.tif
frames_name_regex: (.*)
gain_glob: frames/CountRef.dm4
rawtlt_files:
- metadata/{run_name}.rawtlt
- metadata/{run_name}.xf
- metadata/mdocs_modified/{run_name}.mdoc
tiltseries_glob: metadata/{run_name}.st
ts_name_regex: (.*)\.rec
tomo_format: mrc
tomo_glob: tomograms/*.rec
tomo_regex: (.*)\.mrc
tomo_voxel_size: '13.48'
run_glob: frames/*
run_regex: /TS_\d\d$
run_name_regex: (.*)
tomo_key_photo_glob: .*\.jpg
28 changes: 14 additions & 14 deletions ingestion_tools/scripts/common/config.py
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Expand Up @@ -36,22 +36,22 @@ class DataImportConfig:
run_regex: re.Pattern[str]
tomo_glob: str
tomo_format: str
tomo_regex: re.Pattern[str] | None
tomo_key_photo_glob: str | None
tomo_regex: re.Pattern[str] | None = None
tomo_key_photo_glob: str | None = None
tomo_voxel_size: str
ts_name_regex: re.Pattern[str] | None
ts_name_regex: re.Pattern[str] | None = None
run_name_regex: re.Pattern[str]
frames_name_regex: re.Pattern[str]
frames_name_regex: re.Pattern[str] | None = None
frames_glob: str
tiltseries_glob: str | None
run_to_tomo_map_file: str | None
run_to_tomo_map: dict[str, str] | None
run_to_frame_map_csv: str | None
run_to_frame_map: dict[str, str] | None
run_to_ts_map_csv: str | None
run_to_ts_map: dict[str, str] | None
tiltseries_glob: str | None = None
run_to_tomo_map_file: str | None = None
run_to_tomo_map: dict[str, str] | None = None
run_to_frame_map_csv: str | None = None
run_to_frame_map: dict[str, str] | None = None
run_to_ts_map_csv: str | None = None
run_to_ts_map: dict[str, str] | None = None
gain_glob: str
rawtlt_files: list[str] | None
rawtlt_files: list[str] | None = None
# metadata templates
dataset_template: dict[str, Any]
run_template: dict[str, Any]
Expand All @@ -60,9 +60,9 @@ class DataImportConfig:
annotation_template: dict[str, Any]
output_prefix: str
input_prefix: str
overrides_by_run: list[RunOverride] | None
overrides_by_run: list[RunOverride] | None = None
run_data_map: dict[str, Any]
run_data_map_file: str | None
run_data_map_file: str | None = None

def __init__(self, fs: FileSystemApi, config_path: str, output_prefix: str, input_bucket: str):
self.output_prefix = output_prefix
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