diff --git a/README.md b/README.md index 58b603b..0ceb7d2 100644 --- a/README.md +++ b/README.md @@ -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". @@ -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) ``` diff --git a/docs/index.html b/docs/index.html index 9f8607b..44768c3 100644 --- a/docs/index.html +++ b/docs/index.html @@ -137,7 +137,8 @@

Step by Step Example# 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". @@ -174,7 +175,7 @@

Step by Step ExampleETLSyntheaBuilder::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) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index c9afe35..4cb1989 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -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 diff --git a/docs/reference/CreateCDMIndices.html b/docs/reference/CreateCDMIndices.html index 649193b..477df74 100644 --- a/docs/reference/CreateCDMIndices.html +++ b/docs/reference/CreateCDMIndices.html @@ -138,7 +138,7 @@

Arguments

Details

This function creates the indices specified by the function CommonDataModel::writeIndex(). Supported CDM versions and db dialects are determined by CommonDataModel::listSupportedVersions() - and CommonDataModel::listSupportedDialects(), respectively.

+ and CommonDataModel::listSupportedDialects(), respectively.

diff --git a/docs/reference/CreateCDMTables.html b/docs/reference/CreateCDMTables.html index 057829f..e623e12 100644 --- a/docs/reference/CreateCDMTables.html +++ b/docs/reference/CreateCDMTables.html @@ -144,7 +144,7 @@

Details

This function creates all the tables in a CDM by calling CommonDataModel::executeDdl(). Indices, if created, come from CommonDataModel::writeIndex(). Supported CDM versions and db dialects are determined by CommonDataModel::listSupportedVersions() - and CommonDataModel::listSupportedDialects(), respectively.

+ and CommonDataModel::listSupportedDialects(), respectively.

diff --git a/inst/sql/sql_server/cdm_version/v531/insert_measurement.sql b/inst/sql/sql_server/cdm_version/v531/insert_measurement.sql index 40718b5..fac11f5 100644 --- a/inst/sql/sql_server/cdm_version/v531/insert_measurement.sql +++ b/inst/sql/sql_server/cdm_version/v531/insert_measurement.sql @@ -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, diff --git a/inst/sql/sql_server/cdm_version/v531/insert_payer_plan_period.sql b/inst/sql/sql_server/cdm_version/v531/insert_payer_plan_period.sql index bf95ea9..286f3d1 100644 --- a/inst/sql/sql_server/cdm_version/v531/insert_payer_plan_period.sql +++ b/inst/sql/sql_server/cdm_version/v531/insert_payer_plan_period.sql @@ -1,4 +1,3 @@ - insert into @cdm_schema.payer_plan_period ( payer_plan_period_id, person_id, @@ -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 -; \ No newline at end of file + 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 +; diff --git a/inst/sql/sql_server/cdm_version/v531/insert_procedure_occurrence.sql b/inst/sql/sql_server/cdm_version/v531/insert_procedure_occurrence.sql index 82abb4e..0954208 100644 --- a/inst/sql/sql_server/cdm_version/v531/insert_procedure_occurrence.sql +++ b/inst/sql/sql_server/cdm_version/v531/insert_procedure_occurrence.sql @@ -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, } diff --git a/inst/sql/sql_server/cdm_version/v540/insert_measurement.sql b/inst/sql/sql_server/cdm_version/v540/insert_measurement.sql index 1b80ee4..32893f0 100644 --- a/inst/sql/sql_server/cdm_version/v540/insert_measurement.sql +++ b/inst/sql/sql_server/cdm_version/v540/insert_measurement.sql @@ -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, diff --git a/inst/sql/sql_server/cdm_version/v540/insert_payer_plan_period.sql b/inst/sql/sql_server/cdm_version/v540/insert_payer_plan_period.sql index 06812e0..e5ccaa8 100644 --- a/inst/sql/sql_server/cdm_version/v540/insert_payer_plan_period.sql +++ b/inst/sql/sql_server/cdm_version/v540/insert_payer_plan_period.sql @@ -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 -; \ No newline at end of file + 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 +; diff --git a/inst/sql/sql_server/cdm_version/v540/insert_procedure_occurrence.sql b/inst/sql/sql_server/cdm_version/v540/insert_procedure_occurrence.sql index 344888a..224a8ab 100644 --- a/inst/sql/sql_server/cdm_version/v540/insert_procedure_occurrence.sql +++ b/inst/sql/sql_server/cdm_version/v540/insert_procedure_occurrence.sql @@ -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,