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updated source/index dataset names for sd-vumc-tanagra-test env #550

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updated source/index dataset names for sd-vumc-tanagra-test env #550

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14 changes: 7 additions & 7 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sdd_refresh0323.json
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Expand Up @@ -3,17 +3,17 @@
"dataPointers": [
{ "type": "BQ_DATASET",
"name": "omop_dataset",
"projectId": "victr-tanagra-test",
"dataflowRegion" : "us-east1",
"projectId": "sd-vumc-tanagra-test",
"dataflowRegion" : "us-central1",
"datasetId": "sd_20230328"
},
{ "type": "BQ_DATASET",
"name": "index_dataset",
"projectId": "victr-tanagra-deploytest",
"datasetId": "sd_20230328_indexes",
"dataflowServiceAccountEmail": "victr-tanagra-deploytest@appspot.gserviceaccount.com",
"dataflowTempLocation": "gs://dataflow-indexing-victr-tanagra-deploytest/temp/",
"dataflowRegion": "us-east1",
"projectId": "sd-vumc-tanagra-test",
"datasetId": "indexed_sd_20230328",
"dataflowServiceAccountEmail": "[email protected].gserviceaccount.com",
"dataflowTempLocation": "gs://dataflow-indexing-sd-test-tanagra/temp/",
"dataflowRegion": "us-central1",
"dataflowWorkerMachineType" : "n1-standard-4",
"dataflowUsePublicIps": false
}
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2 changes: 1 addition & 1 deletion service/src/main/resources/config/vumc/sdd_refresh0323/sql/brand_all.sql
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@@ -1,5 +1,5 @@
SELECT *
FROM `victr-tanagra-test.sd_20230328.concept`
FROM `sd-vumc-tanagra-test.sd_20230328.concept`
WHERE
domain_id = 'Drug' AND concept_class_id = 'Brand Name'
AND vocabulary_id IN ('RxNorm', 'RxNorm Extension')
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4 changes: 2 additions & 2 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sql/brand_ingredients.sql
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Expand Up @@ -11,7 +11,7 @@
*/
SELECT cr.*
FROM
`victr-tanagra-test.sd_20230328.concept_relationship` cr,
`victr-tanagra-test.sd_20230328.concept` c2
`sd-vumc-tanagra-test.sd_20230328.concept_relationship` cr,
`sd-vumc-tanagra-test.sd_20230328.concept` c2
WHERE
cr.concept_id_2 = c2.concept_id AND c2.concept_class_id = 'Ingredient'
8 changes: 4 additions & 4 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sql/brand_textSearch.sql
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Expand Up @@ -2,22 +2,22 @@ SELECT textsearch.id, textsearch.text FROM (

SELECT
c.concept_id AS id, c.concept_name AS text
FROM `victr-tanagra-test.sd_20230328.concept` c
FROM `sd-vumc-tanagra-test.sd_20230328.concept` c

UNION ALL

SELECT
c.concept_id AS id, CAST(c.concept_id AS STRING) AS text
FROM `victr-tanagra-test.sd_20230328.concept` c
FROM `sd-vumc-tanagra-test.sd_20230328.concept` c

UNION ALL

SELECT
c.concept_id AS id, c.concept_code AS text
FROM `victr-tanagra-test.sd_20230328.concept` c
FROM `sd-vumc-tanagra-test.sd_20230328.concept` c
) AS textsearch

JOIN `victr-tanagra-test.sd_20230328.concept` c
JOIN `sd-vumc-tanagra-test.sd_20230328.concept` c
ON c.concept_id = textsearch.id

WHERE c.domain_id = 'Drug'
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6 changes: 3 additions & 3 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sql/condition_occurrence_all.sql
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Expand Up @@ -5,10 +5,10 @@ SELECT
CAST(FLOOR(TIMESTAMP_DIFF(co.condition_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence,
co.visit_occurrence_id, vo.visit_concept_id

FROM `victr-tanagra-test.sd_20230328.condition_occurrence` AS co
FROM `sd-vumc-tanagra-test.sd_20230328.condition_occurrence` AS co

JOIN `victr-tanagra-test.sd_20230328.person` AS p
JOIN `sd-vumc-tanagra-test.sd_20230328.person` AS p
ON p.person_id = co.person_id

LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo
LEFT JOIN `sd-vumc-tanagra-test.sd_20230328.visit_occurrence` AS vo
ON vo.visit_occurrence_id = co.visit_occurrence_id
6 changes: 3 additions & 3 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sql/condition_parentChild.sql
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@@ -1,9 +1,9 @@
SELECT
cr.concept_id_1 AS parent,
cr.concept_id_2 AS child,
FROM `victr-tanagra-test.sd_20230328.concept_relationship` cr
JOIN `victr-tanagra-test.sd_20230328.concept` c1 ON c1.concept_id = cr.concept_id_1
JOIN `victr-tanagra-test.sd_20230328.concept` c2 ON c2.concept_id = cr.concept_id_2
FROM `sd-vumc-tanagra-test.sd_20230328.concept_relationship` cr
JOIN `sd-vumc-tanagra-test.sd_20230328.concept` c1 ON c1.concept_id = cr.concept_id_1
JOIN `sd-vumc-tanagra-test.sd_20230328.concept` c2 ON c2.concept_id = cr.concept_id_2
WHERE
cr.relationship_id = 'Subsumes'
AND c1.domain_id = c2.domain_id
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8 changes: 4 additions & 4 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sql/condition_textSearch.sql
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Expand Up @@ -2,22 +2,22 @@ SELECT textsearch.id, textsearch.text FROM (

SELECT
c.concept_id AS id, c.concept_name AS text
FROM `victr-tanagra-test.sd_20230328.concept` c
FROM `sd-vumc-tanagra-test.sd_20230328.concept` c

UNION ALL

SELECT
c.concept_id AS id, CAST(c.concept_id AS STRING) AS text
FROM `victr-tanagra-test.sd_20230328.concept` c
FROM `sd-vumc-tanagra-test.sd_20230328.concept` c

UNION ALL

SELECT
c.concept_id AS id, c.concept_code AS text
FROM `victr-tanagra-test.sd_20230328.concept` c
FROM `sd-vumc-tanagra-test.sd_20230328.concept` c
) AS textsearch

JOIN `victr-tanagra-test.sd_20230328.concept` c
JOIN `sd-vumc-tanagra-test.sd_20230328.concept` c
ON c.concept_id = textsearch.id

WHERE c.domain_id = 'Condition'
4 changes: 2 additions & 2 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sql/cpt4_all.sql
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Expand Up @@ -5,9 +5,9 @@ SELECT
pc.type, pc.is_standard, pc.code,
CASE WHEN pc.code IS NULL THEN pc.name ELSE CONCAT(pc.code, ' ', pc.name) END AS label

FROM `victr-tanagra-test.aou_static_prep.prep_cpt` pc
FROM `sd-vumc-tanagra-test.aou_static_prep.prep_cpt` pc

LEFT JOIN `victr-tanagra-test.sd_20230328.concept` c
LEFT JOIN `sd-vumc-tanagra-test.sd_20230328.concept` c
ON c.concept_id = pc.concept_id
AND c.vocabulary_id = pc.type

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4 changes: 2 additions & 2 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sql/cpt4_ingredientOccurrence.sql
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@@ -1,7 +1,7 @@
SELECT io.drug_exposure_id, pc.id AS cpt4_id
FROM `victr-tanagra-test.sd_20230328.drug_exposure` AS io
FROM `sd-vumc-tanagra-test.sd_20230328.drug_exposure` AS io

JOIN `victr-tanagra-test.aou_static_prep.prep_cpt` AS pc
JOIN `sd-vumc-tanagra-test.aou_static_prep.prep_cpt` AS pc
ON pc.concept_id = io.drug_source_concept_id

WHERE pc.type = 'CPT4'
4 changes: 2 additions & 2 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sql/cpt4_measurementOccurrence.sql
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@@ -1,7 +1,7 @@
SELECT mo.measurement_id, pc.id AS cpt4_id
FROM `victr-tanagra-test.sd_20230328.measurement` AS mo
FROM `sd-vumc-tanagra-test.sd_20230328.measurement` AS mo

JOIN `victr-tanagra-test.aou_static_prep.prep_cpt` AS pc
JOIN `sd-vumc-tanagra-test.aou_static_prep.prep_cpt` AS pc
ON pc.concept_id = mo.measurement_source_concept_id

WHERE pc.type = 'CPT4'
4 changes: 2 additions & 2 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sql/cpt4_observationOccurrence.sql
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@@ -1,7 +1,7 @@
SELECT oo.observation_id, pc.id AS cpt4_id
FROM `victr-tanagra-test.sd_20230328.observation` AS oo
FROM `sd-vumc-tanagra-test.sd_20230328.observation` AS oo

JOIN `victr-tanagra-test.aou_static_prep.prep_cpt` AS pc
JOIN `sd-vumc-tanagra-test.aou_static_prep.prep_cpt` AS pc
ON pc.concept_id = oo.observation_source_concept_id

WHERE pc.type = 'CPT4'
2 changes: 1 addition & 1 deletion service/src/main/resources/config/vumc/sdd_refresh0323/sql/cpt4_parentChild.sql
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Expand Up @@ -2,7 +2,7 @@ SELECT
pc.id AS child,
pc.parent_id AS parent

FROM `victr-tanagra-test.aou_static_prep.prep_cpt` pc
FROM `sd-vumc-tanagra-test.aou_static_prep.prep_cpt` pc

WHERE pc.type = 'CPT4'
AND pc.parent_id != 0
16 changes: 8 additions & 8 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sql/cpt4_person.sql
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@@ -1,37 +1,37 @@
SELECT po.person_id, pc.id AS cpt4_id
FROM `victr-tanagra-test.sd_20230328.procedure_occurrence` AS po
FROM `sd-vumc-tanagra-test.sd_20230328.procedure_occurrence` AS po

JOIN `victr-tanagra-test.aou_static_prep.prep_cpt` AS pc
JOIN `sd-vumc-tanagra-test.aou_static_prep.prep_cpt` AS pc
ON pc.concept_id = po.procedure_source_concept_id

WHERE pc.type = 'CPT4'

UNION ALL

SELECT mo.person_id, pc.id AS cpt4_id
FROM `victr-tanagra-test.sd_20230328.measurement` AS mo
FROM `sd-vumc-tanagra-test.sd_20230328.measurement` AS mo

JOIN `victr-tanagra-test.aou_static_prep.prep_cpt` AS pc
JOIN `sd-vumc-tanagra-test.aou_static_prep.prep_cpt` AS pc
ON pc.concept_id = mo.measurement_source_concept_id

WHERE pc.type = 'CPT4'

UNION ALL

SELECT oo.person_id, pc.id AS cpt4_id
FROM `victr-tanagra-test.sd_20230328.observation` AS oo
FROM `sd-vumc-tanagra-test.sd_20230328.observation` AS oo

JOIN `victr-tanagra-test.aou_static_prep.prep_cpt` AS pc
JOIN `sd-vumc-tanagra-test.aou_static_prep.prep_cpt` AS pc
ON pc.concept_id = oo.observation_source_concept_id

WHERE pc.type = 'CPT4'

UNION ALL

SELECT io.person_id, pc.id AS cpt4_id
FROM `victr-tanagra-test.sd_20230328.drug_exposure` AS io
FROM `sd-vumc-tanagra-test.sd_20230328.drug_exposure` AS io

JOIN `victr-tanagra-test.aou_static_prep.prep_cpt` AS pc
JOIN `sd-vumc-tanagra-test.aou_static_prep.prep_cpt` AS pc
ON pc.concept_id = io.drug_source_concept_id

WHERE pc.type = 'CPT4'
4 changes: 2 additions & 2 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sql/cpt4_procedureOccurrence.sql
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@@ -1,7 +1,7 @@
SELECT po.procedure_occurrence_id, pc.id AS cpt4_id
FROM `victr-tanagra-test.sd_20230328.procedure_occurrence` AS po
FROM `sd-vumc-tanagra-test.sd_20230328.procedure_occurrence` AS po

JOIN `victr-tanagra-test.aou_static_prep.prep_cpt` AS pc
JOIN `sd-vumc-tanagra-test.aou_static_prep.prep_cpt` AS pc
ON pc.concept_id = po.procedure_source_concept_id

WHERE pc.type = 'CPT4'
2 changes: 1 addition & 1 deletion service/src/main/resources/config/vumc/sdd_refresh0323/sql/cpt4_rootNodesFilter.sql
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@@ -1,5 +1,5 @@
SELECT pc.id

FROM `victr-tanagra-test.aou_static_prep.prep_cpt` pc
FROM `sd-vumc-tanagra-test.aou_static_prep.prep_cpt` pc

WHERE pc.type = 'CPT4' AND pc.parent_id = 0
6 changes: 3 additions & 3 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sql/device_occurrence_all.sql
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Expand Up @@ -5,10 +5,10 @@ SELECT
CAST(FLOOR(TIMESTAMP_DIFF(de.device_exposure_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence,
de.visit_occurrence_id, vo.visit_concept_id

FROM `victr-tanagra-test.sd_20230328.device_exposure` AS de
FROM `sd-vumc-tanagra-test.sd_20230328.device_exposure` AS de

JOIN `victr-tanagra-test.sd_20230328.person` AS p
JOIN `sd-vumc-tanagra-test.sd_20230328.person` AS p
ON p.person_id = de.person_id

LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo
LEFT JOIN `sd-vumc-tanagra-test.sd_20230328.visit_occurrence` AS vo
ON vo.visit_occurrence_id = de.visit_occurrence_id
8 changes: 4 additions & 4 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sql/device_textSearch.sql
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Expand Up @@ -2,22 +2,22 @@ SELECT textsearch.id, textsearch.text FROM (

SELECT
c.concept_id AS id, c.concept_name AS text
FROM `victr-tanagra-test.sd_20230328.concept` c
FROM `sd-vumc-tanagra-test.sd_20230328.concept` c

UNION ALL

SELECT
c.concept_id AS id, CAST(c.concept_id AS STRING) AS text
FROM `victr-tanagra-test.sd_20230328.concept` c
FROM `sd-vumc-tanagra-test.sd_20230328.concept` c

UNION ALL

SELECT
c.concept_id AS id, c.concept_code AS text
FROM `victr-tanagra-test.sd_20230328.concept` c
FROM `sd-vumc-tanagra-test.sd_20230328.concept` c
) AS textsearch

JOIN `victr-tanagra-test.sd_20230328.concept` c
JOIN `sd-vumc-tanagra-test.sd_20230328.concept` c
ON c.concept_id = textsearch.id

WHERE c.domain_id = 'Device'
Expand Down
2 changes: 1 addition & 1 deletion service/src/main/resources/config/vumc/sdd_refresh0323/sql/genotype_result.sql
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Expand Up @@ -3,4 +3,4 @@
Currently indexing doesn't handle floats properly, so change column to INTEGER.
*/
SELECT genotype_result_id AS genotype_result_id, person_id, CAST(platform_id as INT64) as platform_id
FROM `victr-tanagra-test.sd_20230328.x_genotype_result`
FROM `sd-vumc-tanagra-test.sd_20230328.x_genotype_result`
2 changes: 1 addition & 1 deletion service/src/main/resources/config/vumc/sdd_refresh0323/sql/genotyping_all.sql
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Expand Up @@ -3,7 +3,7 @@
Currently indexing doesn't handle floats properly, so change column to INTEGER.
*/
SELECT CAST(platform_id as INT64) AS platform_id, assay_name as assay_name
FROM `victr-tanagra-test.sd_20230328.platform`
FROM `sd-vumc-tanagra-test.sd_20230328.platform`
UNION ALL
/*
Add some rows to get hierarchy to work. Parent ids are defined in
Expand Down
2 changes: 1 addition & 1 deletion service/src/main/resources/config/vumc/sdd_refresh0323/sql/genotyping_parentChild.sql
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Expand Up @@ -2,5 +2,5 @@ SELECT
/* Use parent ids defined in platform.sql */
parent_seq + 100 AS parent,
CAST(platform_id as INT64) AS child
FROM `victr-tanagra-test.sd_20230328.genotype_criteria` g, `victr-tanagra-test.sd_20230328.platform` p
FROM `sd-vumc-tanagra-test.sd_20230328.genotype_criteria` g, `sd-vumc-tanagra-test.sd_20230328.platform` p
WHERE g.name = p.assay_name
4 changes: 2 additions & 2 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sql/icd10cm_all.sql
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@@ -1,6 +1,6 @@
SELECT concept_id, concept_name, vocabulary_id, standard_concept, concept_code,
CASE WHEN concept_code IS NULL THEN concept_name ELSE CONCAT(concept_code, ' ', concept_name) END AS label
FROM `victr-tanagra-test.sd_20230328.concept`
FROM `sd-vumc-tanagra-test.sd_20230328.concept`
WHERE
vocabulary_id = 'ICD10CM'
AND DATE_DIFF(CAST(valid_end_date AS DATE), CURRENT_DATE(), DAY) > 0
Expand All @@ -9,7 +9,7 @@ UNION ALL

SELECT concept_id, concept_name, vocabulary_id, standard_concept, concept_code,
CASE WHEN concept_code IS NULL THEN concept_name ELSE CONCAT(concept_code, ' ', concept_name) END AS label
FROM `victr-tanagra-test.aou_static_prep.prep_concept`
FROM `sd-vumc-tanagra-test.aou_static_prep.prep_concept`
WHERE
vocabulary_id = 'ICD10CM'
AND DATE_DIFF(CAST(valid_end_date AS DATE), CURRENT_DATE(), DAY) > 0
16 changes: 8 additions & 8 deletions service/src/main/resources/config/vumc/sdd_refresh0323/sql/icd10cm_parentChild.sql
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Expand Up @@ -4,9 +4,9 @@ Relationships between levels 1 and 2, which includes the AoU/VUMC-defined organi
SELECT
cr.concept_id_1 AS parent,
cr.concept_id_2 AS child,
FROM `victr-tanagra-test.aou_static_prep.prep_concept_relationship` cr
JOIN `victr-tanagra-test.aou_static_prep.prep_concept` c1 ON c1.concept_id = cr.concept_id_1
JOIN `victr-tanagra-test.aou_static_prep.prep_concept` c2 ON c2.concept_id = cr.concept_id_2
FROM `sd-vumc-tanagra-test.aou_static_prep.prep_concept_relationship` cr
JOIN `sd-vumc-tanagra-test.aou_static_prep.prep_concept` c1 ON c1.concept_id = cr.concept_id_1
JOIN `sd-vumc-tanagra-test.aou_static_prep.prep_concept` c2 ON c2.concept_id = cr.concept_id_2
WHERE
cr.relationship_id = 'Subsumes'
AND c1.vocabulary_id = c2.vocabulary_id
Expand All @@ -20,8 +20,8 @@ Relationships between levels 2 and 3, which is the link between the standard ICD
SELECT
p.concept_id AS parent,
c.concept_id AS child
FROM `victr-tanagra-test.aou_static_prep.prep_concept` p
LEFT JOIN `victr-tanagra-test.sd_20230328.concept` AS c
FROM `sd-vumc-tanagra-test.aou_static_prep.prep_concept` p
LEFT JOIN `sd-vumc-tanagra-test.sd_20230328.concept` AS c
ON c.vocabulary_id = p.vocabulary_id
AND UPPER(c.concept_code) >= UPPER(REGEXP_EXTRACT(p.concept_code, r'^([a-zA-Z0-9]+)-'))
AND UPPER(c.concept_code) <= UPPER(REGEXP_EXTRACT(p.concept_code, r'-([a-zA-Z0-9]+)$'))
Expand All @@ -36,9 +36,9 @@ Relationships between levels 3+, which includes the standard ICD-10-CM defined c
SELECT
cr.concept_id_1 AS parent,
cr.concept_id_2 AS child,
FROM `victr-tanagra-test.sd_20230328.concept_relationship` cr
JOIN `victr-tanagra-test.sd_20230328.concept` c1 ON c1.concept_id = cr.concept_id_1
JOIN `victr-tanagra-test.sd_20230328.concept` c2 ON c2.concept_id = cr.concept_id_2
FROM `sd-vumc-tanagra-test.sd_20230328.concept_relationship` cr
JOIN `sd-vumc-tanagra-test.sd_20230328.concept` c1 ON c1.concept_id = cr.concept_id_1
JOIN `sd-vumc-tanagra-test.sd_20230328.concept` c2 ON c2.concept_id = cr.concept_id_2
WHERE
cr.relationship_id = 'Subsumes'
AND c1.vocabulary_id = c2.vocabulary_id
Expand Down
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