mz-health/OMOP
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OMOP
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Merge pull request #68 from tomwhite/impala-atlas 

Change empty 'invalid_reason' field to null for compatibility with Atlas cohort generation
This commit is contained in:
clairblacketer 2017-07-12 15:41:20 -04:00 committed by GitHub
parent 55d15a6a2e de8c1d0f23
commit 14826eeea9
2 changed files with 8 additions and 8 deletions
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8
Impala/OMOP_Parquet.sql
View File

@ -15,7 +15,7 @@ SELECT
concept_code,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_start_date AS STRING), 1, 4), SUBSTR(CAST(valid_start_date AS STRING), 5, 2), SUBSTR(CAST(valid_start_date AS STRING), 7, 2)), 'UTC') AS valid_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_end_date AS STRING), 1, 4), SUBSTR(CAST(valid_end_date AS STRING), 5, 2), SUBSTR(CAST(valid_end_date AS STRING), 7, 2)), 'UTC') AS valid_end_date,
invalid_reason
nullif(invalid_reason, '') AS invalid_reason
FROM omop_cdm.concept;
CREATE TABLE omop_cdm_parquet.vocabulary
@ -42,7 +42,7 @@ SELECT
relationship_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_start_date AS STRING), 1, 4), SUBSTR(CAST(valid_start_date AS STRING), 5, 2), SUBSTR(CAST(valid_start_date AS STRING), 7, 2)), 'UTC') AS valid_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_end_date AS STRING), 1, 4), SUBSTR(CAST(valid_end_date AS STRING), 5, 2), SUBSTR(CAST(valid_end_date AS STRING), 7, 2)), 'UTC') AS valid_end_date,
invalid_reason
nullif(invalid_reason, '') AS invalid_reason
FROM omop_cdm.concept_relationship;
CREATE TABLE omop_cdm_parquet.relationship
@ -72,7 +72,7 @@ SELECT
target_vocabulary_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_start_date AS STRING), 1, 4), SUBSTR(CAST(valid_start_date AS STRING), 5, 2), SUBSTR(CAST(valid_start_date AS STRING), 7, 2)), 'UTC') AS valid_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_end_date AS STRING), 1, 4), SUBSTR(CAST(valid_end_date AS STRING), 5, 2), SUBSTR(CAST(valid_end_date AS STRING), 7, 2)), 'UTC') AS valid_end_date,
invalid_reason
nullif(invalid_reason, '') AS invalid_reason
FROM omop_cdm.source_to_concept_map;
CREATE TABLE omop_cdm_parquet.drug_strength
@ -90,7 +90,7 @@ SELECT
box_size,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_start_date AS STRING), 1, 4), SUBSTR(CAST(valid_start_date AS STRING), 5, 2), SUBSTR(CAST(valid_start_date AS STRING), 7, 2)), 'UTC') AS valid_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_end_date AS STRING), 1, 4), SUBSTR(CAST(valid_end_date AS STRING), 5, 2), SUBSTR(CAST(valid_end_date AS STRING), 7, 2)), 'UTC') AS valid_end_date,
invalid_reason
nullif(invalid_reason, '') AS invalid_reason
FROM omop_cdm.drug_strength;
CREATE TABLE omop_cdm_parquet.cohort_definition

8
Impala/OMOP_Parquet_v5.1.sql
View File

@ -15,7 +15,7 @@ SELECT
concept_code,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_start_date AS STRING), 1, 4), SUBSTR(CAST(valid_start_date AS STRING), 5, 2), SUBSTR(CAST(valid_start_date AS STRING), 7, 2)), 'UTC') AS valid_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_end_date AS STRING), 1, 4), SUBSTR(CAST(valid_end_date AS STRING), 5, 2), SUBSTR(CAST(valid_end_date AS STRING), 7, 2)), 'UTC') AS valid_end_date,
invalid_reason
nullif(invalid_reason, '') AS invalid_reason
FROM omop_cdm.concept;
CREATE TABLE omop_cdm_parquet.vocabulary
@ -42,7 +42,7 @@ SELECT
relationship_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_start_date AS STRING), 1, 4), SUBSTR(CAST(valid_start_date AS STRING), 5, 2), SUBSTR(CAST(valid_start_date AS STRING), 7, 2)), 'UTC') AS valid_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_end_date AS STRING), 1, 4), SUBSTR(CAST(valid_end_date AS STRING), 5, 2), SUBSTR(CAST(valid_end_date AS STRING), 7, 2)), 'UTC') AS valid_end_date,
invalid_reason
nullif(invalid_reason, '') AS invalid_reason
FROM omop_cdm.concept_relationship;
CREATE TABLE omop_cdm_parquet.relationship
@ -72,7 +72,7 @@ SELECT
target_vocabulary_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_start_date AS STRING), 1, 4), SUBSTR(CAST(valid_start_date AS STRING), 5, 2), SUBSTR(CAST(valid_start_date AS STRING), 7, 2)), 'UTC') AS valid_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_end_date AS STRING), 1, 4), SUBSTR(CAST(valid_end_date AS STRING), 5, 2), SUBSTR(CAST(valid_end_date AS STRING), 7, 2)), 'UTC') AS valid_end_date,
invalid_reason
nullif(invalid_reason, '') AS invalid_reason
FROM omop_cdm.source_to_concept_map;
CREATE TABLE omop_cdm_parquet.drug_strength
@ -90,7 +90,7 @@ SELECT
box_size,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_start_date AS STRING), 1, 4), SUBSTR(CAST(valid_start_date AS STRING), 5, 2), SUBSTR(CAST(valid_start_date AS STRING), 7, 2)), 'UTC') AS valid_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_end_date AS STRING), 1, 4), SUBSTR(CAST(valid_end_date AS STRING), 5, 2), SUBSTR(CAST(valid_end_date AS STRING), 7, 2)), 'UTC') AS valid_end_date,
invalid_reason
nullif(invalid_reason, '') AS invalid_reason
FROM omop_cdm.drug_strength;
CREATE TABLE omop_cdm_parquet.cohort_definition