From 0456a77beb1721a6ce7b5da534590d070cca368b Mon Sep 17 00:00:00 2001 From: Steve Nyemba Date: Tue, 5 Mar 2019 11:09:21 -0600 Subject: [PATCH] removing SQL files --- src/sql/basic-observation.sql | 83 ------- src/sql/observation-registered.sql | 376 ----------------------------- 2 files changed, 459 deletions(-) delete mode 100644 src/sql/basic-observation.sql delete mode 100644 src/sql/observation-registered.sql diff --git a/src/sql/basic-observation.sql b/src/sql/basic-observation.sql deleted file mode 100644 index 96b7067..0000000 --- a/src/sql/basic-observation.sql +++ /dev/null @@ -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 - diff --git a/src/sql/observation-registered.sql b/src/sql/observation-registered.sql deleted file mode 100644 index abfb249..0000000 --- a/src/sql/observation-registered.sql +++ /dev/null @@ -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 - --- WHERE first_name is not NULL