Add clinical event sample SQL code

clinical_event_counts.sql

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+-- This is example code to get Clinical Event counts using pure SQL
+-- Could replace JAVA code tied to the /api/clinical-event-type-counts/fetch endpoint
+-- Authors: Robert Sheridan, Matthijs Pon
+
+WITH select_all_events_from_studies AS -- Keeps this table IN memory, saves overhead?
+(
+    SELECT
+        sample.stable_id AS stableId,
+        clinical_event.event_type AS eventType,
+        patient.stable_id AS patientId,
+        cancer_study.cancer_study_identifier AS cancerStudyId
+    FROM
+        sample
+    Inner Join patient ON sample.patient_id = patient.internal_id
+    Inner join clinical_event ON clinical_event.patient_id = patient.internal_id
+    Inner Join cancer_study ON cancer_study.cancer_study_id = patient.cancer_study_id
+    WHERE cancer_study.cancer_study_identifier IN ('brca_akt1_genie_2019','erbb2_genie_public','crc_public_genie_bpc',
+                                                   'nsclc_public_genie_bpc','mbc_genie_2020')
+),
+    studyViewFilter AS -- TEMP representation of full studyviewfilter, this is only the clinical event part
+(
+SELECT
+    DISTINCT stableId AS uniqueSampleKey,
+    patientId AS uniquePatientKey
+FROM
+    select_all_events_from_studies WHERE eventType IN ('Treatment', 'LAB_TEST') -- OR
+INTERSECT -- AND
+SELECT
+    DISTINCT stableId AS UniqueSampleKey,
+    patientId AS uniquePatientKey
+FROM
+    select_all_events_from_studies WHERE eventType IN ('Pathology') -- OR
+)
+SELECT
+    eventType,
+    count(DISTINCT patientId) AS count  -- Counts are on patient level
+FROM
+    select_all_events_from_studies
+WHERE
+    stableId IN (SELECT uniqueSampleKey FROM studyViewFilter)
+GROUP BY eventType
+ORDER BY count DESC;

clinical_event_studyviewfilter.sql

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+-- This is example code to filter a sample list using clinical event filters
+-- Should become part of a bigger 'StudyViewFilter' SQL statement, which performs the full filtering.
+-- Authors: Robert Sheridan, Matthijs Pon
+
+WITH select_all_events_from_study as -- Keeps this table in memory, saves overhead?
+(
+    SELECT
+        sample.stable_id as stableId,
+        clinical_event.event_type as eventType,
+        patient.stable_id as patientId,
+        cancer_study.cancer_study_identifier as cancerStudyId
+    FROM
+        sample
+    Inner Join patient on sample.patient_id = patient.internal_id
+    Inner join clinical_event on clinical_event.patient_id = patient.internal_id
+    Inner Join cancer_study on cancer_study.cancer_study_id = patient.cancer_study_id
+    WHERE cancer_study.cancer_study_identifier in ('brca_akt1_genie_2019','erbb2_genie_public','crc_public_genie_bpc',
+                                                   'nsclc_public_genie_bpc','mbc_genie_2020')
+)
+SELECT
+    DISTINCT stableId as uniqueSampleKey,
+    patientId as uniquePatientKey,
+    cancerStudyId
+FROM
+    select_all_events_from_study WHERE eventType in ('Treatment', 'LAB_TEST') -- OR filter
+INTERSECT -- AND filter
+SELECT
+    DISTINCT stableId as UniqueSampleKey,
+    patientId as uniquePatientKey,
+    cancerStudyId
+FROM
+    select_all_events_from_study WHERE eventType in ('Pathology'); -- OR filter