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Model correction #351

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merged 2 commits into from
Jan 18, 2024
Merged

Model correction #351

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beeaebf
correctly parse model object
MattWellie Jan 17, 2024
4932adf
tweak tweak
MattWellie Jan 17, 2024
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7 changes: 3 additions & 4 deletions reanalysis/query_panelapp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -273,9 +273,7 @@ def overwrite_new_status(gene_dict: PanelApp, new_genes: set[str]):

for gene, gene_data in gene_dict.genes.items():
if gene in new_genes:
gene_data.new = [panel_id]
else:
gene_data.new = []
gene_data.new = {panel_id}


@click.command()
Expand Down Expand Up @@ -343,7 +341,7 @@ def main(panels: str | None, out_path: str, dataset: str | None = None):

# store the list of genes currently on the core panel
if twelve_months:
twelve_months = set(gene_dict['genes'])
twelve_months = set(gene_dict.genes)

# if participant panels were provided, add each of those to the gene data
panel_list = set()
Expand Down Expand Up @@ -394,6 +392,7 @@ def main(panels: str | None, out_path: str, dataset: str | None = None):
with to_path(out_path).open('w') as out_file:
out_file.write(PanelApp.model_validate(gene_dict).model_dump_json(indent=4))

# Only save here if we have a historic location in config
save_new_historic(old_data, dataset=dataset, prefix='panel_')


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3 changes: 3 additions & 0 deletions reanalysis/utils.py
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Expand Up @@ -886,6 +886,9 @@ def save_new_historic(
"""

directory = get_cohort_seq_type_conf(dataset).get('historic_results')
if directory is None:
get_logger().info('No historic data folder, no saving')
return

new_file = to_path(directory) / f'{prefix}{TODAY}.json'
with new_file.open('w') as handle:
Expand Down