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Commit 76643a9a authored by Lorenz Kapsner's avatar Lorenz Kapsner
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removed distinct from SQLs due to strange error

parent 2918570e
master add_dataelements adjusted_Markdown change_from_.rmd_to_.qmd development fhir_gw_sqls_patch latest mdrfix omop trino v3.1.0 v3.0.0 v2.1.2 v2.1.1 v2.1.0 v2.0.8 v2.0.7 v2.0.6 v2.0.5 v2.0.4 v2.0.3 v2.0.2 v2.0.1 v2.0.0 v1.3.2.9010
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+69 -69
inst/application/_utilities/SQL/SQL_i2b2.JSON
+ 15
- 15
View file @ 76643a9a
......@@ -4,19 +4,19 @@
"dt.zipcode_target": ["SELECT\n patient_num AS \"patient_identifier_value\",\n zip_cd AS \"patient_address_postalCode\"\nFROM\n\ti2b2miracum.patient_dimension\nORDER BY\n\tpatient_num;"],
"dt.birthdate_target": ["SELECT\n patient_num AS \"patient_identifier_value\",\n birth_date::date AS \"patient_birthDate\"\nFROM\n\ti2b2miracum.patient_dimension\nORDER BY\n\tpatient_num;"],
"dt.encounter_target": ["SELECT\n\tpatient_num AS \"encounter_subject_patient_identifier_value\",\n encounter_num AS \"encounter_identifier_value\"\nFROM\n i2b2miracum.visit_dimension\nORDER BY\n patient_num;"],
"dt.encounterstart_target": ["SELECT\n DISTINCT b.encounter_num AS \"encounter_identifier_value\",\n a.start_date::date AS \"EpisodeOfCare_period_start\"\nFROM\n i2b2miracum.encounter_mapping AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, start_date\nFROM\n i2b2miracum.visit_dimension) AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.encounterend_target": ["SELECT\n DISTINCT b.encounter_num AS \"encounter_identifier_value\",\n a.end_date::date AS \"EpisodeOfCare_period_end\"\nFROM\n i2b2miracum.encounter_mapping AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, end_date\nFROM\n i2b2miracum.visit_dimension) AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.ageindays_target": ["SELECT\n DISTINCT b.encounter_num AS \"encounter_identifier_value\",\n a.nval_num AS \"encounter_subject_patient_age_days\"\nFROM\n i2b2miracum.encounter_mapping AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, nval_num\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'FALL:AITAA') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.ageinyears_target": ["SELECT\n DISTINCT b.encounter_num AS \"encounter_identifier_value\",\n a.nval_num AS \"encounter_subject_patient_age_years\"\nFROM\n i2b2miracum.encounter_mapping AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, nval_num\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'FALL:AIJAA') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.admission_target": ["SELECT\n DISTINCT b.encounter_num AS \"encounter_identifier_value\",\n a.concept_cd AS \"encounter_hospitalization_admitSource\"\nFROM\n i2b2miracum.encounter_mapping AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, concept_cd\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'AUFNAN%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.hospitalization_target": ["SELECT\n DISTINCT b.encounter_num AS \"encounter_identifier_value\",\n a.concept_cd AS \"encounter_hospitalization_class\"\nFROM\n i2b2miracum.encounter_mapping AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, concept_cd\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'AUFNGR%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.discharge_target": ["SELECT\n DISTINCT b.encounter_num AS \"encounter_identifier_value\",\n a.concept_cd AS \"encounter_hospitalization_dischargeDisposition\"\nFROM\n i2b2miracum.encounter_mapping AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, concept_cd\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'ENTLGR%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.ventilation_target": ["SELECT\n DISTINCT b.encounter_num AS \"procedure_encounter_identifier_value\",\n a.nval_num AS \"procedure_code_coding_code_40617009\"\nFROM\n i2b2miracum.encounter_mapping AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, nval_num\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'FALL:BEATMST') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.condition_target": ["SELECT\n DISTINCT b.encounter_num AS \"condition_encounter_identifier_value\",\n a.concept_cd AS \"condition_code_coding_code\"\nFROM\n i2b2miracum.encounter_mapping AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, concept_cd\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'ICD%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.conditioncategory_target": ["SELECT\n DISTINCT b.encounter_num AS \"condition_encounter_identifier_value\",\n a.modifier_cd AS \"condition_category_encounter_diagnosis\"\nFROM\n i2b2miracum.encounter_mapping AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, modifier_cd\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'ICD%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.procedure_target": ["SELECT\n DISTINCT b.encounter_num AS \"procedure_encounter_identifier_value\",\n a.concept_cd AS \"procedure_code_coding_code\"\nFROM\n i2b2miracum.encounter_mapping AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, concept_cd\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'OPS%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.proceduredate_target": ["SELECT\n DISTINCT b.encounter_num AS \"procedure_encounter_identifier_value\",\n a.start_date::date AS \"procedure_performedDateTime\"\nFROM\n i2b2miracum.encounter_mapping AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, start_date\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'OPS%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.provider_target": ["SELECT\n DISTINCT b.encounter_num AS \"encounter_identifier_value\",\n a.tval_char AS \"encounter_serviceProvider_type_Organization_name\"\nFROM\n i2b2miracum.encounter_mapping AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, tval_char\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'FACHABT%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.providerstart_target": ["SELECT\n DISTINCT b.encounter_num AS \"encounter_identifier_value\",\n a.start_date::date AS \"encounter_period_start\"\nFROM\n i2b2miracum.encounter_mapping AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, start_date\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'FACHABT%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.providerend_target": ["SELECT\n DISTINCT b.encounter_num AS \"encounter_identifier_value\",\n a.end_date::date AS \"encounter_period_end\"\nFROM\n i2b2miracum.encounter_mapping AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, end_date\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'FACHABT%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"]
"dt.encounterstart_target": ["SELECT\n b.encounter_num AS \"encounter_identifier_value\",\n a.start_date::date AS \"EpisodeOfCare_period_start\"\nFROM\n i2b2miracum.visit_dimension AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, start_date\nFROM\n i2b2miracum.visit_dimension) AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.encounterend_target": ["SELECT\n b.encounter_num AS \"encounter_identifier_value\",\n a.end_date::date AS \"EpisodeOfCare_period_end\"\nFROM\n i2b2miracum.visit_dimension AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, end_date\nFROM\n i2b2miracum.visit_dimension) AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.ageindays_target": ["SELECT\n b.encounter_num AS \"encounter_identifier_value\",\n a.nval_num AS \"encounter_subject_patient_age_days\"\nFROM\n i2b2miracum.visit_dimension AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, nval_num\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'FALL:AITAA') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.ageinyears_target": ["SELECT\n b.encounter_num AS \"encounter_identifier_value\",\n a.nval_num AS \"encounter_subject_patient_age_years\"\nFROM\n i2b2miracum.visit_dimension AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, nval_num\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'FALL:AIJAA') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.admission_target": ["SELECT\n b.encounter_num AS \"encounter_identifier_value\",\n a.concept_cd AS \"encounter_hospitalization_admitSource\"\nFROM\n i2b2miracum.visit_dimension AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, concept_cd\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'AUFNAN%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.hospitalization_target": ["SELECT\n b.encounter_num AS \"encounter_identifier_value\",\n a.concept_cd AS \"encounter_hospitalization_class\"\nFROM\n i2b2miracum.visit_dimension AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, concept_cd\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'AUFNGR%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.discharge_target": ["SELECT\n b.encounter_num AS \"encounter_identifier_value\",\n a.concept_cd AS \"encounter_hospitalization_dischargeDisposition\"\nFROM\n i2b2miracum.visit_dimension AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, concept_cd\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'ENTLGR%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.ventilation_target": ["SELECT\n b.encounter_num AS \"procedure_encounter_identifier_value\",\n a.nval_num AS \"procedure_code_coding_code_40617009\"\nFROM\n i2b2miracum.visit_dimension AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, nval_num\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'FALL:BEATMST') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.condition_target": ["SELECT\n b.encounter_num AS \"condition_encounter_identifier_value\",\n a.concept_cd AS \"condition_code_coding_code\"\nFROM\n i2b2miracum.visit_dimension AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, concept_cd\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'ICD%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.conditioncategory_target": ["SELECT\n b.encounter_num AS \"condition_encounter_identifier_value\",\n a.modifier_cd AS \"condition_category_encounter_diagnosis\"\nFROM\n i2b2miracum.visit_dimension AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, modifier_cd\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'ICD%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.procedure_target": ["SELECT\n b.encounter_num AS \"procedure_encounter_identifier_value\",\n a.concept_cd AS \"procedure_code_coding_code\"\nFROM\n i2b2miracum.visit_dimension AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, concept_cd\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'OPS%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.proceduredate_target": ["SELECT\n b.encounter_num AS \"procedure_encounter_identifier_value\",\n a.start_date::date AS \"procedure_performedDateTime\"\nFROM\n i2b2miracum.visit_dimension AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, start_date\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'OPS%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.provider_target": ["SELECT\n b.encounter_num AS \"encounter_identifier_value\",\n a.tval_char AS \"encounter_serviceProvider_type_Organization_name\"\nFROM\n i2b2miracum.visit_dimension AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, tval_char\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'FACHABT%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.providerstart_target": ["SELECT\n b.encounter_num AS \"encounter_identifier_value\",\n a.start_date::date AS \"encounter_period_start\"\nFROM\n i2b2miracum.visit_dimension AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, start_date\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'FACHABT%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"],
"dt.providerend_target": ["SELECT\n b.encounter_num AS \"encounter_identifier_value\",\n a.end_date::date AS \"encounter_period_end\"\nFROM\n i2b2miracum.visit_dimension AS b\nLEFT OUTER JOIN (\nSELECT\n encounter_num, end_date\nFROM\n i2b2miracum.observation_fact\nWHERE\n concept_cd LIKE 'FACHABT%') AS a ON\n a.encounter_num = b.encounter_num\nORDER BY\n b.encounter_num;"]
}
inst/application/_utilities/SQL/SQL_omop.JSON
+ 15
- 15
View file @ 76643a9a
......@@ -4,19 +4,19 @@
"dt.zipcode_target": ["SELECT\n per.person_id AS \"patient_identifier_value\",\n loc.zip AS \"patient_address_postalCode\"\nFROM\n\tp21_cdm.person AS per\nLEFT OUTER JOIN\n p21_cdm.location AS loc ON\n per.location_id = loc.location_id\nORDER BY\n\tperson_id;"],
"dt.birthdate_target": ["SELECT\n person_id AS \"patient_identifier_value\",\n year_of_birth AS \"patient_birthDate\"\nFROM\n\tp21_cdm.person\nORDER BY\n\tperson_id;"],
"dt.encounter_target": ["SELECT\n\tperson_id AS \"encounter_subject_patient_identifier_value\",\n visit_occurrence_id AS \"encounter_identifier_value\"\nFROM\n p21_cdm.visit_occurrence\nORDER BY\n person_id;"],
"dt.encounterstart_target": ["SELECT\n DISTINCT b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.visit_start_date AS \"EpisodeOfCare_period_start\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, visit_start_date\nFROM\n p21_cdm.visit_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.encounterend_target": ["SELECT\n DISTINCT b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.visit_end_date AS \"EpisodeOfCare_period_end\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, visit_end_date\nFROM\n p21_cdm.visit_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.ageindays_target": ["SELECT\n DISTINCT b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.observation_source_value::numeric AS \"encounter_subject_patient_age_days\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, observation_source_value\nFROM\n p21_cdm.observation\nWHERE\n observation_concept_id = 4265453 AND unit_concept_id = 8512) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.ageinyears_target": ["SELECT\n DISTINCT b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.observation_source_value::numeric AS \"encounter_subject_patient_age_years\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, observation_source_value\nFROM\n p21_cdm.observation\nWHERE\n observation_concept_id = 4265453 AND unit_concept_id = 9448) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.admission_target": ["SELECT\n DISTINCT b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.observation_source_value AS \"encounter_hospitalization_admitSource\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, observation_source_value\nFROM\n p21_cdm.observation\nWHERE\n observation_type_concept_id = 43542355 AND observation_concept_id IN (4164916, 4194310, 4138807, 4216316, 4079617, 4146925, 4123917)) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.hospitalization_target": ["SELECT\n DISTINCT b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.observation_source_value AS \"encounter_hospitalization_class\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, observation_source_value\nFROM\n p21_cdm.observation\nWHERE\n observation_type_concept_id = 43542355 AND observation_concept_id NOT IN (4164916, 4194310, 4138807, 4079617, 4146925, 4123917)) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.discharge_target": ["SELECT\n DISTINCT b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.observation_source_value AS \"encounter_hospitalization_dischargeDisposition\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, observation_source_value\nFROM\n p21_cdm.observation\nWHERE\n observation_concept_id IN (433128, 4021968, 4049607, 4052193, 4053230, 4082735, 4084500, 4084686, 4127600, 4139566, 4143443, 4147710, 4185328, 4185329, 4186037, 4203130, 4213258, 4216643, 4274958, 45878214)) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.ventilation_target": ["SELECT\n DISTINCT b.visit_occurrence_id AS \"procedure_encounter_identifier_value\",\n a.observation_source_value::numeric AS \"procedure_code_coding_code_40617009\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, observation_source_value\nFROM\n p21_cdm.observation\nWHERE\n observation_concept_id = 4108449) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.condition_target": ["SELECT\n DISTINCT b.visit_occurrence_id AS \"condition_encounter_identifier_value\",\n a.condition_source_value AS \"condition_code_coding_code\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, condition_source_value\nFROM\n p21_cdm.condition_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.conditioncategory_target": ["SELECT\n DISTINCT b.visit_occurrence_id AS \"condition_encounter_identifier_value\",\n a.condition_type_concept_id AS \"condition_category_encounter_diagnosis\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, condition_type_concept_id\nFROM\n p21_cdm.condition_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.procedure_target": ["SELECT\n DISTINCT b.visit_occurrence_id AS \"procedure_encounter_identifier_value\",\n a.procedure_source_value AS \"procedure_code_coding_code\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, procedure_source_value\nFROM\n p21_cdm.procedure_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.proceduredate_target": ["SELECT\n DISTINCT b.visit_occurrence_id AS \"procedure_encounter_identifier_value\",\n a.procedure_date AS \"procedure_performedDateTime\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, procedure_date\nFROM\n p21_cdm.procedure_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.provider_target": ["SELECT\n DISTINCT b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.care_site_id AS \"encounter_serviceProvider_type_Organization_name\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, care_site_id\nFROM\n p21_cdm.visit_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.providerstart_target": ["SELECT\n DISTINCT b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.visit_start_date AS \"encounter_period_start\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, visit_start_date\nFROM\n p21_cdm.visit_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.providerend_target": ["SELECT\n DISTINCT b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.visit_end_date AS \"encounter_period_end\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, visit_end_date\nFROM\n p21_cdm.visit_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"]
"dt.encounterstart_target": ["SELECT\n b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.visit_start_date AS \"EpisodeOfCare_period_start\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, visit_start_date\nFROM\n p21_cdm.visit_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.encounterend_target": ["SELECT\n b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.visit_end_date AS \"EpisodeOfCare_period_end\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, visit_end_date\nFROM\n p21_cdm.visit_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.ageindays_target": ["SELECT\n b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.observation_source_value::numeric AS \"encounter_subject_patient_age_days\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, observation_source_value\nFROM\n p21_cdm.observation\nWHERE\n observation_concept_id = 4265453 AND unit_concept_id = 8512) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.ageinyears_target": ["SELECT\n b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.observation_source_value::numeric AS \"encounter_subject_patient_age_years\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, observation_source_value\nFROM\n p21_cdm.observation\nWHERE\n observation_concept_id = 4265453 AND unit_concept_id = 9448) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.admission_target": ["SELECT\n b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.observation_source_value AS \"encounter_hospitalization_admitSource\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, observation_source_value\nFROM\n p21_cdm.observation\nWHERE\n observation_type_concept_id = 43542355 AND observation_concept_id IN (4164916, 4194310, 4138807, 4216316, 4079617, 4146925, 4123917)) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.hospitalization_target": ["SELECT\n b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.observation_source_value AS \"encounter_hospitalization_class\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, observation_source_value\nFROM\n p21_cdm.observation\nWHERE\n observation_type_concept_id = 43542355 AND observation_concept_id NOT IN (4164916, 4194310, 4138807, 4079617, 4146925, 4123917)) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.discharge_target": ["SELECT\n b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.observation_source_value AS \"encounter_hospitalization_dischargeDisposition\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, observation_source_value\nFROM\n p21_cdm.observation\nWHERE\n observation_concept_id IN (433128, 4021968, 4049607, 4052193, 4053230, 4082735, 4084500, 4084686, 4127600, 4139566, 4143443, 4147710, 4185328, 4185329, 4186037, 4203130, 4213258, 4216643, 4274958, 45878214)) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.ventilation_target": ["SELECT\n b.visit_occurrence_id AS \"procedure_encounter_identifier_value\",\n a.observation_source_value::numeric AS \"procedure_code_coding_code_40617009\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, observation_source_value\nFROM\n p21_cdm.observation\nWHERE\n observation_concept_id = 4108449) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.condition_target": ["SELECT\n b.visit_occurrence_id AS \"condition_encounter_identifier_value\",\n a.condition_source_value AS \"condition_code_coding_code\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, condition_source_value\nFROM\n p21_cdm.condition_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.conditioncategory_target": ["SELECT\n b.visit_occurrence_id AS \"condition_encounter_identifier_value\",\n a.condition_type_concept_id AS \"condition_category_encounter_diagnosis\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, condition_type_concept_id\nFROM\n p21_cdm.condition_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.procedure_target": ["SELECT\n b.visit_occurrence_id AS \"procedure_encounter_identifier_value\",\n a.procedure_source_value AS \"procedure_code_coding_code\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, procedure_source_value\nFROM\n p21_cdm.procedure_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.proceduredate_target": ["SELECT\n b.visit_occurrence_id AS \"procedure_encounter_identifier_value\",\n a.procedure_date AS \"procedure_performedDateTime\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, procedure_date\nFROM\n p21_cdm.procedure_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.provider_target": ["SELECT\n b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.care_site_id AS \"encounter_serviceProvider_type_Organization_name\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, care_site_id\nFROM\n p21_cdm.visit_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.providerstart_target": ["SELECT\n b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.visit_start_date AS \"encounter_period_start\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, visit_start_date\nFROM\n p21_cdm.visit_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"],
"dt.providerend_target": ["SELECT\n b.visit_occurrence_id AS \"encounter_identifier_value\",\n a.visit_end_date AS \"encounter_period_end\"\nFROM\n p21_cdm.visit_occurrence AS b\nLEFT OUTER JOIN (\nSELECT\n visit_occurrence_id, visit_end_date\nFROM\n p21_cdm.visit_occurrence) AS a ON\n a.visit_occurrence_id = b.visit_occurrence_id\nORDER BY\n b.visit_occurrence_id;"]
}
inst/application/_utilities/SQL/create_i2b2.R
+ 6
- 6
View file @ 76643a9a
......@@ -96,10 +96,10 @@ for (i in names(looplist)){
assign(i, paste0(
"SELECT
DISTINCT b.", looplist[[i]]$var1, " AS \"", mdr.use[source_variable_name==looplist[[i]]$var1,variable_name], "\",
b.", looplist[[i]]$var1, " AS \"", mdr.use[source_variable_name==looplist[[i]]$var1,variable_name], "\",
a.", looplist[[i]]$var2, "::date AS \"", mdr.use[source_variable_name==looplist[[i]]$var2,variable_name], "\"
FROM
i2b2miracum.encounter_mapping AS b
i2b2miracum.visit_dimension AS b
LEFT OUTER JOIN (
SELECT
", looplist[[i]]$var1, ", ", looplist[[i]]$var2, "
......@@ -131,10 +131,10 @@ for (i in names(looplist)){
assign(i, paste0(
"SELECT
DISTINCT b.", looplist[[i]]$var1, " AS \"", mdr.use[source_variable_name==looplist[[i]]$var1,variable_name], "\",
b.", looplist[[i]]$var1, " AS \"", mdr.use[source_variable_name==looplist[[i]]$var1,variable_name], "\",
a.", looplist[[i]]$var2, " AS \"", mdr.use[source_variable_name==looplist[[i]]$var2,variable_name], "\"
FROM
i2b2miracum.encounter_mapping AS b
i2b2miracum.visit_dimension AS b
LEFT OUTER JOIN (
SELECT
", looplist[[i]]$var1, ", ", looplist[[i]]$var2, "
......@@ -161,10 +161,10 @@ for (i in names(looplist)){
assign(i, paste0(
"SELECT
DISTINCT b.", looplist[[i]]$var1, " AS \"", mdr.use[source_variable_name==looplist[[i]]$var1,variable_name], "\",
b.", looplist[[i]]$var1, " AS \"", mdr.use[source_variable_name==looplist[[i]]$var1,variable_name], "\",
a.", looplist[[i]]$var2, "::date AS \"", mdr.use[source_variable_name==looplist[[i]]$var2,variable_name], "\"
FROM
i2b2miracum.encounter_mapping AS b
i2b2miracum.visit_dimension AS b
LEFT OUTER JOIN (
SELECT
", looplist[[i]]$var1, ", ", looplist[[i]]$var2, "
......
inst/application/_utilities/SQL/create_omop.R
+ 3
- 3
View file @ 76643a9a
......@@ -105,7 +105,7 @@ for (i in names(looplist)){
assign(i, paste0(
"SELECT
DISTINCT b.", looplist[[i]]$var1, " AS \"", mdr.use[source_variable_name==looplist[[i]]$var1,variable_name], "\",
b.", looplist[[i]]$var1, " AS \"", mdr.use[source_variable_name==looplist[[i]]$var1,variable_name], "\",
a.", looplist[[i]]$var2, " AS \"", mdr.use[source_variable_name==looplist[[i]]$var2,variable_name], "\"
FROM
p21_cdm.visit_occurrence AS b
......@@ -133,7 +133,7 @@ for (i in names(looplist)){
assign(i, paste0(
"SELECT
DISTINCT b.", looplist[[i]]$var1, " AS \"", mdr.use[source_variable_name==looplist[[i]]$var1,variable_name], "\",
b.", looplist[[i]]$var1, " AS \"", mdr.use[source_variable_name==looplist[[i]]$var1,variable_name], "\",
a.", looplist[[i]]$var2, " AS \"", mdr.use[source_variable_name==looplist[[i]]$var2,variable_name], "\"
FROM
p21_cdm.visit_occurrence AS b
......@@ -163,7 +163,7 @@ for (i in names(looplist)){
assign(i, paste0(
"SELECT
DISTINCT b.", looplist[[i]]$var1, " AS \"", mdr.use[source_variable_name==looplist[[i]]$var1,variable_name], "\",
b.", looplist[[i]]$var1, " AS \"", mdr.use[source_variable_name==looplist[[i]]$var1,variable_name], "\",
a.", looplist[[i]]$var2, "::numeric AS \"", mdr.use[source_variable_name==looplist[[i]]$var2,variable_name], "\"
FROM
p21_cdm.visit_occurrence AS b
......
tests/testthat/test-sql-i2b2.R
+ 15
- 15
View file @ 76643a9a
......@@ -14,26 +14,26 @@ test_that("correct sql statments",{
expect_type(rv$sql_target, "list")
# Loop over target_keys and check for hash and type
known_hashes <- list("dt.admission_target" = "5571137f21",
known_hashes <- list("dt.admission_target" = "8198d80cde",
"dt.gender_target" = "556e9b677c",
"dt.birthdate_target" = "0ea256fecc",
"dt.zipcode_target" = "2b9cb2ad54",
"dt.encounterstart_target" = "8c13d331c0",
"dt.encounterend_target" = "af1053ed66",
"dt.conditioncategory_target" = "f4785f44ca",
"dt.proceduredate_target" = "f1181e508e",
"dt.providerstart_target" = "19a51d5640",
"dt.providerend_target" = "8cab3454b0",
"dt.ageindays_target" = "975c9c4903",
"dt.ageinyears_target" = "9efcac17ab",
"dt.condition_target" = "5aae54afbd",
"dt.discharge_target" = "5dbf555825",
"dt.encounterstart_target" = "221bd12034",
"dt.encounterend_target" = "21940b328f",
"dt.conditioncategory_target" = "1a3049afbc",
"dt.proceduredate_target" = "0b9933c396",
"dt.providerstart_target" = "0e49175b01",
"dt.providerend_target" = "9dc46cd975",
"dt.ageindays_target" = "e1647fc283",
"dt.ageinyears_target" = "e25fd4fabb",
"dt.condition_target" = "d32784c9f6",
"dt.discharge_target" = "e4ec9539b8",
"dt.encounter_target" = "e04436ffae",
"dt.hospitalization_target" = "49a8b3c6cc",
"dt.hospitalization_target" = "fd77171844",
"dt.patient_target" = "3ed7ad8ce2",
"dt.procedure_target" = "7b7644fc5d",
"dt.provider_target" = "768a26127c",
"dt.ventilation_target" = "0af5b3ba0f")
"dt.procedure_target" = "50e04be749",
"dt.provider_target" = "51541f137f",
"dt.ventilation_target" = "2c7f68e3ec")
for (i in names(known_hashes)){
expect_type(rv$sql_target[[i]], "character")
expect_known_hash(rv$sql_target[[i]], known_hashes[[i]])
......
tests/testthat/test-sql-omop.R
+ 15
- 15
View file @ 76643a9a
......@@ -14,26 +14,26 @@ test_that("correct sql statments",{
expect_type(rv$sql_target, "list")
# Loop over target_keys and check for hash and type
known_hashes <- list("dt.admission_target" = "6691b03cbb",
known_hashes <- list("dt.admission_target" = "82e83232ef",
"dt.gender_target" = "f0b8920d07",
"dt.birthdate_target" = "d7f4bbda37",
"dt.zipcode_target" = "6947bb9e94",
"dt.encounterstart_target" = "b4334f895c",
"dt.encounterend_target" = "3cfac97baa",
"dt.conditioncategory_target" = "f4785f44ca",
"dt.proceduredate_target" = "1ec2cded6a",
"dt.providerstart_target" = "c066f495fb",
"dt.providerend_target" = "21cddcb740",
"dt.ageindays_target" = "a003c23e2f",
"dt.ageinyears_target" = "c3e2577917",
"dt.condition_target" = "5aae54afbd",
"dt.discharge_target" = "6fe2d76111",
"dt.encounterstart_target" = "a5bc51524f",
"dt.encounterend_target" = "2ccf876bd4",
"dt.conditioncategory_target" = "311c1ccfd7",
"dt.proceduredate_target" = "363684fbdb",
"dt.providerstart_target" = "b7b3a86a30",
"dt.providerend_target" = "c770cf3e88",
"dt.ageindays_target" = "90c488d63e",
"dt.ageinyears_target" = "c9ef48e00c",
"dt.condition_target" = "0963cbebc1",
"dt.discharge_target" = "b4d691dbb4",
"dt.encounter_target" = "ee4fc87b05",
"dt.hospitalization_target" = "62c0b350b7",
"dt.hospitalization_target" = "5bdf8b4549",
"dt.patient_target" = "2dc2a0de0b",
"dt.procedure_target" = "7b7644fc5d",
"dt.provider_target" = "768a26127c",
"dt.ventilation_target" = "c2a32c0b96")
"dt.procedure_target" = "e028bc6936",
"dt.provider_target" = "06a54ef21c",
"dt.ventilation_target" = "7f713cc6ef")
for (i in names(known_hashes)){
expect_type(rv$sql_target[[i]], "character")
expect_known_hash(rv$sql_target[[i]], known_hashes[[i]])
......
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