removing SQL files

src/sql/basic-observation.sql

@@ -1,83 +0,0 @@
-SELECT person.person_id,sex_at_birth,birth_date, race,zip,city,state, gender
-FROM 
-  (SELECT DISTINCT person_id from deid_tmp.observation order by person_id) as person
-FULL JOIN (
-  SELECT 
-    person_id,MAX(value_as_string) as race 
-  FROM deid_tmp.observation   
-  WHERE REGEXP_CONTAINS(observation_source_value,'Race_WhatRace')  and value_as_string IS NOT NULL
-  
-  GROUP BY person_id
-  order by person_id
-) as lang
-ON lang.person_id = person.person_id
-
-FULL JOIN (
- SELECT 
-    person_id,MAX(value_as_string) as zip 
-  FROM deid_tmp.observation   
-  WHERE REGEXP_CONTAINS(observation_source_value,'PIIZIP')  and value_as_string IS NOT NULL
-  GROUP BY person_id
-  order by person_id
-) as work_add
-ON work_add.person_id = person.person_id
-
-
-
-FULL JOIN (
- SELECT 
-    person_id,max(value_as_string) as city 
-  FROM deid_tmp.observation   
-  WHERE REGEXP_CONTAINS(observation_source_value,'PIICity')  and value_as_string IS NOT NULL
-  GROUP BY person_id
-  order by person_id
-) as u_city
-ON u_city.person_id = person.person_id
-
-FULL JOIN (
-  SELECT
-    person_id,max(value_as_string) as state 
-  FROM deid_tmp.observation   
-  WHERE REGEXP_CONTAINS(observation_source_value,'PIIState')  and value_as_string IS NOT NULL
-  GROUP BY person_id
-  order by person_id
-
-) as p_addr_o
-ON p_addr_o.person_id = person.person_id
-
-FULL JOIN (
-  SELECT
-    person_id,max(value_as_string) as gender
-  FROM deid_tmp.observation   
-  WHERE REGEXP_CONTAINS(observation_source_value,'Gender_GenderIdentity')  and value_as_string IS NOT NULL
-  GROUP BY person_id
-  order by person_id
-
-) as p_gender
-ON p_gender.person_id = person.person_id
-
-FULL JOIN (
-  SELECT
-    person_id,max(value_as_string) as birth_date
-  FROM deid_tmp.observation   
-  WHERE REGEXP_CONTAINS(observation_source_value,'PIIBirthInformation_BirthDate')  and value_as_string IS NOT NULL
-  GROUP BY person_id
-  order by person_id
-
-) as p_birth
-ON p_birth.person_id = person.person_id
-
-FULL JOIN (
-  SELECT
-    person_id,max(value_as_string) as sex_at_birth
-  FROM deid_tmp.observation   
-  WHERE REGEXP_CONTAINS(observation_source_value,'BiologicalSexAtBirth_SexAtBirth')  and value_as_string IS NOT NULL
-  GROUP BY person_id
-  order by person_id
-
-) as p_sex
-ON p_sex.person_id = person.person_id
-
-
-ORDER BY person.person_id
-

src/sql/observation-registered.sql

@@ -1,376 +0,0 @@
-SELECT * 
-FROM (
-    SELECT person.person_id,first_name,last_name,birth_date,city,family_history_aware,current_hyper_tension,sex_at_birth, race,state, gender,ethnicity,birth_place,orientation,education,employment_status,
-    marital_status,language,home_owner,sd_bloodbank, nhpi, living_situation,income,death_cause, death_date,  active_duty_status,
-    gender_identity, insurance_type, work_address_state,consent_18_years_age,person_one_state,person_two_state,sc_site,
-    health_abroad_6_months,travel_abroad_6_months
-    FROM 
-    (SELECT DISTINCT person_id from deid_tmp.observation order by person_id) as person
-
-    
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as travel_abroad_6_months
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'OutsideTravel6Month_OutsideTravel6MonthWhere')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as te_
-    ON te_.person_id = person.person_id
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as health_abroad_6_months
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'OverallHealth_OutsideTravel6Month')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as he_
-    ON he_.person_id = person.person_id
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as active_duty_status
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'ActiveDuty_AvtiveDutyServeStatus')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as mil_
-    ON mil_.person_id = person.person_id
-    
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as sc_site
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'SouthCarolinaSitePairing_EauClaireAppointment')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as sc_
-    ON sc_.person_id = person.person_id
-
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as person_one_state
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'PersonOneAddress_PersonOneAddressState')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as p1_
-    ON p1_.person_id = person.person_id
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as person_two_state
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'SecondContactsAddress_SecondContactState')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as p2_
-    ON p2_.person_id = person.person_id
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_as_string) as work_address_state
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'EmploymentWorkAddress_State')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as ws_
-    ON ws_.person_id = person.person_id
-
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as consent_18_years_age
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'ExtraConsent_18YearsofAge')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as c18_
-    ON c18_.person_id = person.person_id
-
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as gender_identity
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'Gender_GenderIdentity')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as gi_
-    ON gi_.person_id = person.person_id
-
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as income
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'Income_AnnualIncome')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as income_
-    ON income_.person_id = person.person_id
-
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as living_situation
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'LivingSituation_CurrentLiving')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as living_
-    ON living_.person_id = person.person_id
-
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as nhpi
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'NHPI_NHPISpecific')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as nhpi_
-    ON nhpi_.person_id = person.person_id
-
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_as_string) as sd_bloodbank
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'SanDiegoBloodBank')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as sd
-    ON sd.person_id = person.person_id
-
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as education
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'EducationLevel_HighestGrade')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as edu
-    ON edu.person_id = person.person_id
-
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as home_owner 
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'HomeOwn_CurrentHomeOwn')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as h_owner
-    ON h_owner.person_id = person.person_id
-
-
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as employment_status
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'Employment_EmploymentStatus')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as empl
-    ON empl.person_id = person.person_id
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as marital_status
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'MaritalStatus_CurrentMaritalStatus')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as marital
-    ON marital.person_id = person.person_id
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as language
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'Language_SpokenWrittenLanguage')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as lang_
-    ON lang_.person_id = person.person_id
-
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as race 
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'Race_WhatRace')  and value_source_value IS NOT NULL
-    
-    GROUP BY person_id
-    order by person_id
-    ) as lang
-    ON lang.person_id = person.person_id
-    FULL JOIN (
-        SELECT 
-        person_id,MAX(value_source_value) as ethnicity
-        FROM deid_tmp.observation   
-        WHERE REGEXP_CONTAINS(observation_source_value,'Race_WhatRaceEthnicity')  and value_source_value IS NOT NULL
-    
-    GROUP BY person_id
-    order by person_id
-    ) as ethnic 
-    ON ethnic.person_id = person.person_id
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as birth_place
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'TheBasics_Birthplace')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as birthp
-    ON birthp.person_id = person.person_id
-
-    FULL JOIN (
-    SELECT 
-        person_id,MAX(value_source_value) as orientation
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'TheBasics_SexualOrientation')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-    ) as sexo
-    ON sexo.person_id = person.person_id
-
-
-    FULL JOIN (
-    SELECT
-        person_id,max(value_source_value) as state 
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'PIIState')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-
-    ) as p_addr_o
-    ON p_addr_o.person_id = person.person_id
-
-    FULL JOIN (
-    SELECT
-        person_id,max(value_source_value) as gender
-    FROM deid_tmp.observation  
-    WHERE REGEXP_CONTAINS(observation_source_value,'Gender_GenderIdentity')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-
-    ) as p_gender
-    ON p_gender.person_id = person.person_id
-
-    FULL JOIN (
-    SELECT
-        person_id,max(value_source_value) as sex_at_birth
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'_SexAtBirth')  --and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-
-    ) as p_sex
-    ON p_sex.person_id = person.person_id
-
-    FULL JOIN (
-    SELECT
-        person_id,max(value_source_value) as insurance_type
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'HealthInsurance_HealthInsuranceType')  and value_source_value IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-
-    ) as ins_
-    ON ins_.person_id = person.person_id
-
-    FULL JOIN (
-    SELECT
-        person_id,max(value_as_string) as last_name
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'PIIName_Last')  and value_as_string IS NOT NULL
-    GROUP BY person_id
-    order by person_id
-
-    ) as ln_
-    ON ln_.person_id = person.person_id
-
-
-    FULL JOIN (
-    SELECT
-        person_id,max(value_as_string) as first_name
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'PIIName_First') 
-    GROUP BY person_id
-    order by person_id
-
-    ) as fn_
-    ON fn_.person_id = person.person_id
-
-    FULL JOIN (
-    SELECT
-        person_id,max(value_as_string) as current_hyper_tension
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'Circulatory_HypertensionCurrently') 
-    GROUP BY person_id
-    order by person_id
-
-    ) as cht_
-    ON cht_.person_id = person.person_id
-
-    FULL JOIN (
-    SELECT
-        person_id,max( cast(value_as_string as DATE)) as birth_date
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'PIIBirthInformation_BirthDate') 
-    GROUP BY person_id
-    order by person_id
-
-    ) as bd_
-    ON bd_.person_id = person.person_id
-
-
-    FULL JOIN (
-    SELECT
-        person_id,max(value_as_string) as city
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'StreetAddress_PIICity') 
-    GROUP BY person_id
-    order by person_id
-
-    ) as city_
-    ON city_.person_id = person.person_id
-
-    FULL JOIN (
-    SELECT
-        person_id,max(value_as_string) as family_history_aware
-    FROM deid_tmp.observation   
-    WHERE REGEXP_CONTAINS(observation_source_value,'FamilyHistory_FamilyMedicalHistoryAware') 
-    GROUP BY person_id
-    order by person_id
-
-    ) as bro_
-    ON bro_.person_id = person.person_id
-    FULL JOIN (
-        SELECT person_id, max(death_date) AS death_date
-        FROM deid_tmp.death
-        GROUP BY person_id
-        order BY person_id
-
-    ) as death_
-    ON death_.person_id = person.person_id
-
-    FULL JOIN (
-        SELECT person_id, max(cause_source_value) as death_cause
-        FROM deid_tmp.death
-        GROUP BY person_id
-        order BY person_id
-
-
-    ) as death_c ON death_c.person_id = person.person_id
-    ORDER BY person.person_id
-) as frame
-