OMOP_CDM_TABLES/script_inserting_data.R at master · cidacslab/OMOP_CDM_TABLES · GitHub

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# inserting previously mapped data into the OMOP tables -- SINASC --

# getting mapped tables

care_site <- read.csv('MOCK_DATA/care_site.csv')
condition_occurrence <- read.csv('MOCK_DATA/condition_occurrence.csv')
location <- read.csv('MOCK_DATA/location.csv')
measurement <- read.csv('MOCK_DATA/measurement.csv')
observation_period <- read.csv('MOCK_DATA/observation_period.csv')
observation <- read.csv('MOCK_DATA/observation.csv')
person <- read.csv('MOCK_DATA/person.csv')
procedure_occurrence <- read.csv('MOCK_DATA/procedure_occurrence.csv')
visit_occurrence <- read.csv('MOCK_DATA/visit_occurrence.csv')


insertTable(connection = connection,
            databaseSchema = 'main',
            tableName = 'care_site',
            data = care_site,
            dropTableIfExists = TRUE,
            createTable = TRUE,
            tempTable = FALSE)

insertTable(connection = connection,
            databaseSchema = 'main',
            tableName = 'condition_occurrence',
            data = condition_occurrence,
            dropTableIfExists = TRUE,
            createTable = TRUE,
            tempTable = FALSE)

insertTable(connection = connection,
            databaseSchema = 'main',
            tableName = 'location',
            data = location,
            dropTableIfExists = TRUE,
            createTable = TRUE,
            tempTable = FALSE)

insertTable(connection = connection,
            databaseSchema = 'main',
            tableName = 'measurement',
            data = measurement,
            dropTableIfExists = TRUE,
            createTable = TRUE,
            tempTable = FALSE)

insertTable(connection = connection,
            databaseSchema = 'main',
            tableName = 'observation_period',
            data = observation_period,
            dropTableIfExists = TRUE,
            createTable = TRUE,
            tempTable = FALSE)

insertTable(connection = connection,
            databaseSchema = 'main',
            tableName = 'observation',
            data = observation,
            dropTableIfExists = TRUE,
            createTable = TRUE,
            tempTable = FALSE)

insertTable(connection = connection,
            databaseSchema = 'main',
            tableName = 'person',
            data = person,
            dropTableIfExists = TRUE,
            createTable = TRUE,
            tempTable = FALSE)

insertTable(connection = connection,
            databaseSchema = 'main',
            tableName = 'procedure_occurrence',
            data = procedure_occurrence,
            dropTableIfExists = TRUE,
            createTable = TRUE,
            tempTable = FALSE)

insertTable(connection = connection,
            databaseSchema = 'main',
            tableName = 'visit_occurrence',
            data = visit_occurrence,
            dropTableIfExists = TRUE,
            createTable = TRUE,
            tempTable = FALSE)


write.csv(care_site, 'EUNOMIA_CSV_TABLES/care_site.csv', row.names=FALSE)
write.csv(condition_occurrence, 'EUNOMIA_CSV_TABLES/condition_occurrence.csv', row.names=FALSE)
write.csv(location, 'EUNOMIA_CSV_TABLES/location.csv', row.names=FALSE)
write.csv(measurement, 'EUNOMIA_CSV_TABLES/measurement.csv', row.names=FALSE)
write.csv(observation_period, 'EUNOMIA_CSV_TABLES/observation_period.csv', row.names=FALSE)
write.csv(observation, 'EUNOMIA_CSV_TABLES/observation.csv', row.names=FALSE)
write.csv(procedure_occurrence, 'EUNOMIA_CSV_TABLES/procedure_occurence.csv', row.names =FALSE)
write.csv(visit_occurrence,'EUNOMIA_CSV_TABLES/visit_occurrence.csv', row.names=FALSE)