1+ -- ============================================================
2+ -- COVID_LAB_DATAMART Post-Processing Stored Procedure
3+ -- Happy path unit test for sp_covid_lab_datamart_postprocessing
4+ -- - assumes all entities are present in nrt tables
5+ -- - skips code branch to populate AOE columns
6+ -- ============================================================
7+
8+ USE [RDB_Modern];
9+
10+ -- ------------------------------------------------------------
11+ -- UIDs
12+ -- ------------------------------------------------------------
13+ DECLARE @patient_uid BIGINT = 90001001 ;
14+ DECLARE @org_uid_perform BIGINT = 90002001 ; -- Testing lab
15+ DECLARE @org_uid_author BIGINT = 90002002 ; -- Reporting facility
16+ DECLARE @org_uid_order BIGINT = 90002003 ; -- Ordering facility
17+ DECLARE @provider_uid BIGINT = 90003001 ;
18+ DECLARE @material_id BIGINT = 90004001 ;
19+ DECLARE @phc_uid BIGINT = 90005001 ;
20+ DECLARE @obs_uid_order BIGINT = 90006001 ;
21+ DECLARE @obs_uid_result BIGINT = 90006002 ;
22+
23+ -- ------------------------------------------------------------
24+ -- Reference / SRTE tables
25+ -- ------------------------------------------------------------
26+
27+ -- Add condition mapping for Covid LOINCs
28+ INSERT INTO dbo .nrt_srte_Loinc_condition (loinc_cd, condition_cd)
29+ SELECT ' 94500-6'' 11065'
30+ WHERE NOT EXISTS (SELECT 1 FROM dbo .nrt_srte_Loinc_condition WHERE loinc_cd = ' 94500-6'AND condition_cd = ' 11065'
31+
32+ INSERT INTO dbo .nrt_srte_Loinc_condition (loinc_cd, condition_cd)
33+ SELECT ' 94309-2'' 11065'
34+ WHERE NOT EXISTS (SELECT 1 FROM dbo .nrt_srte_Loinc_condition WHERE loinc_cd = ' 94309-2'AND condition_cd = ' 11065'
35+
36+ -- Ensure our LOINC values don't have invalid details
37+ DELETE FROM dbo .nrt_srte_Loinc_code
38+ WHERE loinc_cd IN (' 94500-6'' 94309-2'AND time_aspect = ' Pt'AND system_cd = ' ^Patient'
39+
40+ -- ------------------------------------------------------------
41+ -- Patient
42+ -- ------------------------------------------------------------
43+ INSERT INTO dbo .nrt_patient
44+ (patient_uid, local_id, last_name, middle_name, first_name, curr_sex_cd,
45+ age_reported, age_reported_unit_cd, dob, phone_home,
46+ street_address_1, city, state_code, zip, county_code, county,
47+ race_calculated, ethnic_group_ind)
48+ VALUES
49+ (@patient_uid, ' PSN-TEST-'+ CAST (@patient_uid AS VARCHAR ), ' Smith'' A'' John'' M'
50+ ' 45'' a'' 1979-03-15'' 4045550100'
51+ ' 123 Main St'' Atlanta'' 13'' 30301'' 063'' Fulton'
52+ ' White'' N'
53+
54+ INSERT INTO dbo .nrt_patient_key (patient_uid)
55+ VALUES (@patient_uid);
56+
57+ -- ------------------------------------------------------------
58+ -- Organizations
59+ -- ------------------------------------------------------------
60+ INSERT INTO dbo .nrt_organization
61+ (organization_uid, organization_name, street_address_1, city, state_code, state , zip, county_code, county, country_code, facility_id, phone_work, phone_ext_work)
62+ VALUES
63+ (@org_uid_perform, ' State Reference Lab'' 456 Lab Blvd'' Atlanta'' 13'' Georgia'' 30302'' 063'' Fulton'' US'' 10D2289533'' 4045550200'' '
64+ (@org_uid_author, ' Emory University Hospital'' 789 Clifton Rd'' Atlanta'' 13'' Georgia'' 30322'' 063'' Fulton'' US'' 10D0123456'' 4045550300'' '
65+ (@org_uid_order, ' Peachtree Urgent Care'' 321 Peachtree St'' Atlanta'' 13'' Georgia'' 30303'' 063'' Fulton'' US'' 10D9876543'' 4045550400'' '
66+
67+ -- ------------------------------------------------------------
68+ -- Provider
69+ -- ------------------------------------------------------------
70+ INSERT INTO dbo .nrt_provider
71+ (provider_uid, first_name, last_name, street_address_1, city, state_code, zip, county_code, county, country_code, phone_work_phone, phone_ext_work_phone, provider_npi)
72+ VALUES
73+ (@provider_uid, ' Jane'' Doe'' 555 Provider Ave'' Atlanta'' 13'' 30308'' 063'' Fulton'' US'' 4045550500'' '' 1234567890'
74+
75+ -- ------------------------------------------------------------
76+ -- Observation material (specimen)
77+ -- ------------------------------------------------------------
78+ INSERT INTO dbo .nrt_observation_material (act_uid, material_id, material_cd, material_desc, material_details)
79+ VALUES (@obs_uid_order, @material_id, ' NP'' Nasopharyngeal Swab'' Combined Naso/Oropharyngeal Swab'
80+
81+ -- ------------------------------------------------------------
82+ -- Investigation
83+ -- ------------------------------------------------------------
84+ INSERT INTO dbo .nrt_investigation (public_health_case_uid, local_id)
85+ VALUES (@phc_uid, ' CAS-TEST-'+ CAST (@phc_uid AS VARCHAR ));
86+
87+ -- ------------------------------------------------------------
88+ -- Observations (order and result)
89+ -- ------------------------------------------------------------
90+ INSERT INTO dbo .nrt_observation
91+ (observation_uid, local_id, record_status_cd, cd, cd_desc_txt, cd_system_cd,
92+ electronic_ind, version_ctrl_nbr, prog_area_cd, jurisdiction_cd,
93+ activity_to_time, rpt_to_state_time, activity_from_time, effective_from_time,
94+ target_site_cd, target_site_desc_txt, status_cd,
95+ accession_number, add_time, last_chg_time,
96+ result_observation_uid, obs_domain_cd_st_1,
97+ material_id, patient_id,
98+ performing_organization_id, author_organization_id, ordering_organization_id,
99+ ordering_person_id, associated_phc_uids, batch_id,
100+ method_cd, method_desc_txt, device_instance_id_1, device_instance_id_2,
101+ interpretation_cd, interpretation_desc_txt)
102+ VALUES
103+ -- ORDER row
104+ (@obs_uid_order, ' LAB-TEST-'+ CAST (@obs_uid_order AS VARCHAR ), ' ACTIVE'' 94500-6'' SARS-CoV-2 RNA panel'' LN'
105+ ' Y'1 , ' STD'' 130001'
106+ ' 2021-01-10 12:00:00'' 2021-01-10 14:00:00'' 2021-01-09 09:00:00'' 2021-01-09 09:00:00'
107+ ' NP'' Nasopharynx'' D'
108+ ' ACC-2021-001'' 2021-01-10 08:00:00'' 2021-01-10 15:00:00'
109+ CAST (@obs_uid_result AS NVARCHAR (MAX )), ' Order'
110+ @material_id, @patient_uid,
111+ @org_uid_perform, @org_uid_author, @org_uid_order,
112+ CAST (@provider_uid AS NVARCHAR (MAX )), CAST (@phc_uid AS NVARCHAR (MAX )), 1 ,
113+ NULL , NULL , NULL , NULL , NULL , NULL ),
114+
115+ -- RESULT row
116+ (@obs_uid_result, ' LAB-TEST-'+ CAST (@obs_uid_result AS VARCHAR ), ' ACTIVE'' 94309-2'' SARS-CoV-2 RNA Ql NAA+probe'' LN'
117+ ' Y'1 , ' STD'' GA'
118+ ' 2021-01-10 12:00:00'NULL , NULL , NULL ,
119+ NULL , NULL , ' D'
120+ NULL , ' 2021-01-10 08:00:00'' 2021-01-10 15:00:00'
121+ NULL , ' Result'
122+ NULL , @patient_uid,
123+ @org_uid_perform, @org_uid_author, @org_uid_order,
124+ CAST (@provider_uid AS NVARCHAR (MAX )), CAST (@phc_uid AS NVARCHAR (MAX )), 1 ,
125+ ' EUA001'' RT-PCR'' DEVICE-SERIAL-001'NULL ,
126+ ' POS'' Positive'
127+
128+ -- ------------------------------------------------------------
129+ -- Observation results
130+ -- ------------------------------------------------------------
131+
132+ -- Coded result — "Detected"
133+ INSERT INTO dbo .nrt_observation_coded (observation_uid, ovc_code, ovc_code_system_cd, ovc_display_name)
134+ VALUES (@obs_uid_result, ' 260373001'' SCT'' Detected'
135+
136+ -- Text result (type 'O') and comment (type 'N')
137+ INSERT INTO dbo .nrt_observation_txt (observation_uid, ovt_seq, ovt_txt_type_cd, ovt_value_txt)
138+ VALUES
139+ (@obs_uid_result, 1 , ' O'' SARS-CoV-2 RNA Detected'
140+ (@obs_uid_result, 2 , ' N'' Specimen received in good condition.'
141+
142+ -- ------------------------------------------------------------
143+ -- Execute the stored procedure
144+ -- ------------------------------------------------------------
145+ DECLARE @obs_id_list NVARCHAR (MAX ) = CAST (@obs_uid_order AS NVARCHAR (MAX ));
146+
147+ EXEC dbo .sp_covid_lab_datamart_postprocessing
148+ @observation_id_list = @obs_id_list,
149+ @debug = ' false'
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