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Ensure queries and documentation are up to date #186

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Feb 23, 2024
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Ensure queries and documentation are up to date #186

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850e7d0
Update instructions
burrowse Feb 23, 2024
6e5ade8
Update measurement and procedure logic
burrowse Feb 23, 2024
d024c41
Update payer plan period logic
burrowse Feb 23, 2024
c8bc144
Ensure documentation is up to date
burrowse Feb 23, 2024
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5 changes: 3 additions & 2 deletions README.md
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Expand Up @@ -15,7 +15,8 @@ Follow the steps on the [synthea wiki](https://github.com/synthetichealth/synthe
# The ETLSyntheaBuilder package leverages the OHDSI/CommonDataModel package for CDM creation.
# Valid CDM versions are determined by executing CommonDataModel::listSupportedVersions().
# The strings representing supported CDM versions are currently "5.3" and "5.4".
# The Synthea version we use in this example is 2.7.0. However, at this time we also support 3.0.0, 3.1.0 and 3.2.0.
# The Synthea version we use in this example is 2.7.0.
# However, at this time we also support 3.0.0, 3.1.0 and 3.2.0.
# Please note that Synthea's MASTER branch is always active and this package will be updated to support
# future versions as possible.
# The schema to load the Synthea tables is called "native".
Expand Down Expand Up @@ -52,7 +53,7 @@ ETLSyntheaBuilder::LoadVocabFromCsv(connectionDetails = cd, cdmSchema = cdmSchem
ETLSyntheaBuilder::CreateMapAndRollupTables(connectionDetails = cd, cdmSchema = cdmSchema, syntheaSchema = syntheaSchema, cdmVersion = cdmVersion, syntheaVersion = syntheaVersion)

## Optional Step to create extra indices
ETLSyntheaBuilder::CreateExtraIndices(connectionDetails = cd, cdmSchema = cdmSchema, syntheaSchema = syntheaSchema, cdmVersion = cdmVersion, syntheaVersion = syntheaVersion)
ETLSyntheaBuilder::CreateExtraIndices(connectionDetails = cd, cdmSchema = cdmSchema, syntheaSchema = syntheaSchema, syntheaVersion = syntheaVersion)

ETLSyntheaBuilder::LoadEventTables(connectionDetails = cd, cdmSchema = cdmSchema, syntheaSchema = syntheaSchema, cdmVersion = cdmVersion, syntheaVersion = syntheaVersion)
```
Expand Down
5 changes: 3 additions & 2 deletions docs/index.html
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2 changes: 1 addition & 1 deletion docs/pkgdown.yml
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Expand Up @@ -18,5 +18,5 @@ articles:
provider: provider.html
visit_detail: visit_detail.html
visit_occurrence: visit_occurrence.html
last_built: 2024-02-06T20:39Z
last_built: 2024-02-23T16:59Z

2 changes: 1 addition & 1 deletion docs/reference/CreateCDMIndices.html
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2 changes: 1 addition & 1 deletion docs/reference/CreateCDMTables.html
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2 changes: 1 addition & 1 deletion inst/sql/sql_server/cdm_version/v531/insert_measurement.sql
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Expand Up @@ -53,7 +53,7 @@ select
pr.date measurement_time,
}

{@synthea_version == "3.0.0"} ? {
{@synthea_version == "3.0.0" | @synthea_version == "3.1.0" | @synthea_version == "3.2.0" } ? {
pr.start measurement_date,
pr.start measurement_datetime,
pr.start measurement_time,
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75 changes: 38 additions & 37 deletions inst/sql/sql_server/cdm_version/v531/insert_payer_plan_period.sql
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@@ -1,4 +1,3 @@

insert into @cdm_schema.payer_plan_period (
payer_plan_period_id,
person_id,
Expand All @@ -19,42 +18,44 @@ insert into @cdm_schema.payer_plan_period (
stop_reason_source_concept_id
)

select ROW_NUMBER()OVER(ORDER BY pat.id, pt.start_year) payer_plan_period_id,
select ROW_NUMBER()OVER(ORDER BY person_id, payer_plan_period_start_date) payer_plan_period_id,
*
from (select
per.person_id person_id,

{@synthea_version == "2.7.0"} ? {
CAST(CONCAT('01-JAN-',CAST(pt.start_year AS VARCHAR)) AS DATE) payer_plan_period_start_date,
CAST(CONCAT('31-DEC-',CAST(pt.end_year AS VARCHAR)) AS DATE) payer_plan_period_end_date,
}

{@synthea_version == "3.0.0"} ? {
CAST(pt.start_year AS DATE) payer_plan_period_start_date,
CAST(pt.end_year AS DATE) payer_plan_period_end_date,
}
{@synthea_version == "2.7.0"} ? {
CAST(CONCAT('01-JAN-',CAST(pt.start_year AS VARCHAR)) AS DATE) payer_plan_period_start_date,
CAST(CONCAT('31-DEC-',CAST(pt.end_year AS VARCHAR)) AS DATE) payer_plan_period_end_date,
}

{@synthea_version == "3.0.0"} ? {
CAST(pt.start_year AS DATE) payer_plan_period_start_date,
CAST(pt.end_year AS DATE) payer_plan_period_end_date,
}

{@synthea_version == "3.1.0" | @synthea_version == "3.2.0" } ? {
CAST(pt.start_date AS DATE) payer_plan_period_start_date,
CAST(pt.end_date AS DATE) payer_plan_period_end_date,
}

{@synthea_version == "3.1.0" | @synthea_version == "3.2.0" } ? {
CAST(pt.start_date AS DATE) payer_plan_period_start_date,
CAST(pt.end_date AS DATE) payer_plan_period_end_date,
}

0 payer_concept_id,
pt.payer payer_source_value,
0 payer_source_concept_id,
0 plan_concept_id,
pay.name plan_source_value,
0 plan_source_concept_id,
0 sponsor_concept_id,
CAST(NULL AS VARCHAR) sponsor_source_value,
0 sponsor_source_concept_id,
CAST(NULL AS VARCHAR) family_source_value,
0 stop_reason_concept_id,
CAST(NULL AS VARCHAR) stop_reason_source_value,
0 stop_reason_source_concept_id
from @synthea_schema.payers pay
join @synthea_schema.payer_transitions pt
on pay.id = pt.payer
join @synthea_schema.patients pat
on pt.patient = pat.id
join @cdm_schema.person per
on pat.id = per.person_source_value
;
0 payer_concept_id,
pt.payer payer_source_value,
0 payer_source_concept_id,
0 plan_concept_id,
pay.name plan_source_value,
0 plan_source_concept_id,
0 sponsor_concept_id,
CAST(NULL AS VARCHAR) sponsor_source_value,
0 sponsor_source_concept_id,
CAST(NULL AS VARCHAR) family_source_value,
0 stop_reason_concept_id,
CAST(NULL AS VARCHAR) stop_reason_source_value,
0 stop_reason_source_concept_id
from @synthea_schema.payers pay
join @synthea_schema.payer_transitions pt
on pay.id = pt.payer
join @synthea_schema.patients pat
on pt.patient = pat.id
join @cdm_schema.person per
on pat.id = per.person_source_value) person_payer_windows
;
2 changes: 1 addition & 1 deletion inst/sql/sql_server/cdm_version/v531/insert_procedure_occurrence.sql
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Expand Up @@ -25,7 +25,7 @@ pr.date procedure_date,
pr.date procedure_datetime,
}

{@synthea_version == "3.0.0"} ? {
{@synthea_version == "3.0.0" | @synthea_version == "3.1.0" | @synthea_version == "3.2.0" } ? {
pr.start procedure_date,
pr.start procedure_datetime,
}
Expand Down
2 changes: 1 addition & 1 deletion inst/sql/sql_server/cdm_version/v540/insert_measurement.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ select
pr.date measurement_time,
}

{@synthea_version == "3.0.0"} ? {
{@synthea_version == "3.0.0" | @synthea_version == "3.1.0" | @synthea_version == "3.2.0" } ? {
pr.start measurement_date,
pr.start measurement_datetime,
pr.start measurement_time,
Expand Down
72 changes: 37 additions & 35 deletions inst/sql/sql_server/cdm_version/v540/insert_payer_plan_period.sql
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Expand Up @@ -19,42 +19,44 @@ insert into @cdm_schema.payer_plan_period (
stop_reason_source_concept_id
)

select ROW_NUMBER()OVER(ORDER BY pat.id, pt.start_year) payer_plan_period_id,
select ROW_NUMBER()OVER(ORDER BY person_id, payer_plan_period_start_date) payer_plan_period_id,
*
from (select
per.person_id person_id,

{@synthea_version == "2.7.0"} ? {
CAST(CONCAT('01-JAN-',CAST(pt.start_year AS VARCHAR)) AS DATE) payer_plan_period_start_date,
CAST(CONCAT('31-DEC-',CAST(pt.end_year AS VARCHAR)) AS DATE) payer_plan_period_end_date,
}

{@synthea_version == "3.0.0"} ? {
CAST(pt.start_year AS DATE) payer_plan_period_start_date,
CAST(pt.end_year AS DATE) payer_plan_period_end_date,
}
{@synthea_version == "2.7.0"} ? {
CAST(CONCAT('01-JAN-',CAST(pt.start_year AS VARCHAR)) AS DATE) payer_plan_period_start_date,
CAST(CONCAT('31-DEC-',CAST(pt.end_year AS VARCHAR)) AS DATE) payer_plan_period_end_date,
}

{@synthea_version == "3.0.0"} ? {
CAST(pt.start_year AS DATE) payer_plan_period_start_date,
CAST(pt.end_year AS DATE) payer_plan_period_end_date,
}

{@synthea_version == "3.1.0" | @synthea_version == "3.2.0" } ? {
CAST(pt.start_date AS DATE) payer_plan_period_start_date,
CAST(pt.end_date AS DATE) payer_plan_period_end_date,
}
0 payer_concept_id,
pt.payer payer_source_value,
0 payer_source_concept_id,
0 plan_concept_id,
pay.name plan_source_value,
0 plan_source_concept_id,
0 sponsor_concept_id,
CAST(NULL AS VARCHAR) sponsor_source_value,
0 sponsor_source_concept_id,
CAST(NULL AS VARCHAR) family_source_value,
0 stop_reason_concept_id,
CAST(NULL AS VARCHAR) stop_reason_source_value,
0 stop_reason_source_concept_id
from @synthea_schema.payers pay
join @synthea_schema.payer_transitions pt
on pay.id = pt.payer
join @synthea_schema.patients pat
on pt.patient = pat.id
join @cdm_schema.person per
on pat.id = per.person_source_value
;
CAST(pt.start_date AS DATE) payer_plan_period_start_date,
CAST(pt.end_date AS DATE) payer_plan_period_end_date,
}

0 payer_concept_id,
pt.payer payer_source_value,
0 payer_source_concept_id,
0 plan_concept_id,
pay.name plan_source_value,
0 plan_source_concept_id,
0 sponsor_concept_id,
CAST(NULL AS VARCHAR) sponsor_source_value,
0 sponsor_source_concept_id,
CAST(NULL AS VARCHAR) family_source_value,
0 stop_reason_concept_id,
CAST(NULL AS VARCHAR) stop_reason_source_value,
0 stop_reason_source_concept_id
from @synthea_schema.payers pay
join @synthea_schema.payer_transitions pt
on pay.id = pt.payer
join @synthea_schema.patients pat
on pt.patient = pat.id
join @cdm_schema.person per
on pat.id = per.person_source_value) person_payer_windows
;
2 changes: 1 addition & 1 deletion inst/sql/sql_server/cdm_version/v540/insert_procedure_occurrence.sql
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Expand Up @@ -29,7 +29,7 @@ pr.date procedure_end_date,
pr.date procedure_end_datetime,
}

{@synthea_version == "3.0.0"} ? {
{@synthea_version == "3.0.0" | @synthea_version == "3.1.0" | @synthea_version == "3.2.0" } ? {
pr.start procedure_date,
pr.start procedure_datetime,
pr.stop procedure_end_date,
Expand Down
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