Remove reference(s) to biosample.assay_type. See #7.

nih-cfde · Sep 21, 2022 · 44909f6 · 44909f6
1 parent 9d0fb66
commit 44909f6
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Showing 2 changed files with 1 addition and 22 deletions.
diff --git 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
@@ -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')
+rubric.metric('c2m2_assessment.rubrics.FAIR_2022_q4.m_cfde_fair_44')