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refact(utils): support new Katsu private overview response format #79

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merged 2 commits into from
Apr 12, 2024
Merged

refact(utils): support new Katsu private overview response format #79

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3a7491d
refact(utils): support new Katsu private overview response format
davidlougheed Apr 11, 2024
40f4e60
fix(utils): correctly handle katsu experiment stats
davidlougheed Apr 12, 2024
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11 changes: 7 additions & 4 deletions bento_beacon/utils/beacon_response.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,12 +43,15 @@ def add_overview_stats_to_response():


def package_biosample_and_experiment_stats(stats):
biosamples = stats.get("biosamples", {})
experiments = stats.get("experiments", {})
phenopacket_dts_stats = stats.get("phenopacket", {}).get("data_type_specific", {})
experiment_stats = stats.get("experiment", {}).get("data_type_specific", {}).get("experiments", {})

biosamples = phenopacket_dts_stats.get("biosamples", {})
biosamples_count = biosamples.get("count", 0)
experiments_count = experiments.get("count", 0)
sampled_tissue = biosamples.get("sampled_tissue", {})
experiment_type = experiments.get("experiment_type", {})

experiments_count = experiment_stats.get("count", 0)
experiment_type = experiment_stats.get("experiment_type", {})

# convert to bento_public response format
sampled_tissue_data = [{"label": key, "value": value} for key, value in sampled_tissue.items()]
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2 changes: 1 addition & 1 deletion bento_beacon/utils/katsu_utils.py
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Expand Up @@ -270,7 +270,7 @@ def search_summary_statistics(ids):


def overview_statistics():
return katsu_get(current_app.config["KATSU_PRIVATE_OVERVIEW"]).get("data_type_specific", {})
return katsu_get(current_app.config["KATSU_PRIVATE_OVERVIEW"])


def katsu_censorship_settings() -> tuple[int | None, int | None]:
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