From 44909f6c0e823ac695a1dca38f5e48e079a4f740 Mon Sep 17 00:00:00 2001 From: Jonathan Crabtree Date: Wed, 21 Sep 2022 11:21:04 -0400 Subject: [PATCH] Remove reference(s) to biosample.assay_type. See #7. --- c2m2_assessment/rubrics/NCE.py | 20 -------------------- c2m2_assessment/rubrics/amanda2022.py | 3 +-- 2 files changed, 1 insertion(+), 22 deletions(-) diff --git a/c2m2_assessment/rubrics/NCE.py b/c2m2_assessment/rubrics/NCE.py index 73e6c4a..404189e 100644 --- a/c2m2_assessment/rubrics/NCE.py +++ b/c2m2_assessment/rubrics/NCE.py @@ -301,26 +301,6 @@ def m_cfde_fair_11(CFDE, full=False, **kwargs): 'denominator': total_biosamples(CFDE), } -#%% -@rubric.metric({ - '@id': 'cfde_fair:12', - 'name': 'biosamples with assay', - 'description': 'What ratio of biosamples are associated with an assay', -}) -def m_cfde_fair_12(CFDE, full=False, **kwargs): - total_biosamples_associated_with_assay = CFDE.tables['assay_type'] \ - .link(CFDE.tables['biosample'], on=( - CFDE.tables['biosample'].assay_type == CFDE.tables['assay_type'].id - )) \ - .groupby(CFDE.tables['biosample'].id_namespace, CFDE.tables['biosample'].local_id) \ - .count() - value = (total_biosamples_associated_with_assay / total_biosamples(CFDE)) if total_biosamples(CFDE) else None - return { - 'value': value, - 'numerator': total_biosamples_associated_with_assay, - 'denominator': total_biosamples(CFDE), - } - #%% @rubric.metric({ '@id': 'cfde_fair:13', diff --git a/c2m2_assessment/rubrics/amanda2022.py b/c2m2_assessment/rubrics/amanda2022.py index 3cb8a8f..6941800 100644 --- a/c2m2_assessment/rubrics/amanda2022.py +++ b/c2m2_assessment/rubrics/amanda2022.py @@ -12,7 +12,6 @@ rubric.metric('c2m2_assessment.rubrics.NCE.m_cfde_fair_9') rubric.metric('c2m2_assessment.rubrics.NCE.m_cfde_fair_10') rubric.metric('c2m2_assessment.rubrics.NCE.m_cfde_fair_11') -rubric.metric('c2m2_assessment.rubrics.NCE.m_cfde_fair_12') rubric.metric('c2m2_assessment.rubrics.NCE.m_cfde_fair_13') rubric.metric('c2m2_assessment.rubrics.NCE.m_cfde_fair_14') rubric.metric('c2m2_assessment.rubrics.NCE.m_cfde_fair_15') @@ -36,4 +35,4 @@ rubric.metric('c2m2_assessment.rubrics.FAIR_2022_q4.m_cfde_fair_41') rubric.metric('c2m2_assessment.rubrics.FAIR_2022_q4.m_cfde_fair_42') rubric.metric('c2m2_assessment.rubrics.FAIR_2022_q4.m_cfde_fair_43') -rubric.metric('c2m2_assessment.rubrics.FAIR_2022_q4.m_cfde_fair_44') \ No newline at end of file +rubric.metric('c2m2_assessment.rubrics.FAIR_2022_q4.m_cfde_fair_44')