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Misc BDC fixes #36

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merged 3 commits into from
Sep 25, 2024
Merged

Misc BDC fixes #36

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6aaed7b
[ALS-7382] - counts that are -1 should be shown as N/A
Sep 24, 2024
8d80556
[ALS-7384] Fix consent null check
Sep 24, 2024
187f011
[CHORE] switch additional info link to study link for BDC hack
Sep 24, 2024
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24 changes: 18 additions & 6 deletions src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardRepository.java
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Original file line number Diff line number Diff line change
Expand Up @@ -55,22 +55,34 @@ public List<Map<String, String>> getHackyBDCRows() {
SELECT
dataset.abbreviation AS abbreviation,
dataset.full_name AS name,
consent.variable_count AS clinvars,
consent.participant_count AS participants,
consent.sample_count AS samples,
CASE
WHEN consent.consent_code <> NULL THEN concat(study_accession_meta.value, '.', consent.consent_code)
WHEN consent.variable_count > -1 THEN consent.variable_count
ELSE 'N/A'
END
AS clinvars,
CASE
WHEN consent.participant_count > -1 THEN consent.participant_count
ELSE 'N/A'
END
AS participants,
CASE
WHEN consent.sample_count > -1 THEN consent.sample_count
ELSE 'N/A'
END
AS samples,
CASE
WHEN consent.consent_code IS NOT NULL THEN concat(study_accession_meta.value, '.', consent.consent_code)
ELSE study_accession_meta.value
END
AS accession,
AS accession,
study_focus_meta.value AS study_focus,
additional_info_meta.value AS additional_info_link
FROM
dataset
LEFT JOIN consent ON consent.dataset_id = dataset.dataset_id
LEFT JOIN dataset_meta AS study_focus_meta ON study_focus_meta.dataset_id = dataset.dataset_id AND study_focus_meta.KEY = 'study_focus'
LEFT JOIN dataset_meta AS study_accession_meta ON study_accession_meta.dataset_id = dataset.dataset_id AND study_accession_meta.KEY = 'study_accession'
LEFT JOIN dataset_meta AS additional_info_meta ON additional_info_meta.dataset_id = dataset.dataset_id AND additional_info_meta.KEY = 'additional_info_link'
LEFT JOIN dataset_meta AS additional_info_meta ON additional_info_meta.dataset_id = dataset.dataset_id AND additional_info_meta.KEY = 'study_link'
ORDER BY name ASC, abbreviation ASC
""";
return template.query(sql, new ListMapExtractor());
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