Error during LoadEventTables into PostreSQL

[guybartal]

Hi,

I've generated 10 person CSV files with Synthea v2.7.0, and get the following error when running ETLSyntheaBuilder::LoadEventTables on CDM v5.3 in PostgreSQL:

> ETLSyntheaBuilder::LoadEventTables(connectionDetails,cdmDatabaseSchema,syntheaSchema,cdmVersion,syntheaVersion)
Connecting using PostgreSQL driver
Running: create_source_to_standard_vocab_map.sql
  |=======================================================================================================================| 100%
Executing SQL took 60 secs
Running: create_source_to_source_vocab_map.sql
  |=======================================================================================================================| 100%
Executing SQL took 47.8 secs
Connecting using PostgreSQL driver
Running: AllVisitTable.sql
  |=======================================================================================================================| 100%
Executing SQL took 0.0722 secs
Running: AAVITable.sql
  |=======================================================================================================================| 100%
Executing SQL took 0.0181 secs
Running: final_visit_ids.sql
  |=======================================================================================================================| 100%
Executing SQL took 0.0163 secs
Connecting using PostgreSQL driver
Running: insert_person.sql
  |=======================================================================================================================| 100%
Executing SQL took 0.00905 secs
Running: insert_observation_period.sql
  |=======================================================================================================================| 100%
Executing SQL took 0.00759 secs
Running: insert_provider.sql
  |=======================================================================================================================| 100%
Executing SQL took 0.00793 secs
Running: insert_visit_occurrence.sql
  |=======================================================================================================================| 100%
Executing SQL took 0.011 secs
Running: insert_visit_detail.sql
  |=======================================================================================================================| 100%
Executing SQL took 0.0109 secs
Running: insert_condition_occurrence.sql
  |=======================================================================================================================| 100%
Executing SQL took 14.4 secs
Running: insert_observation.sql
  |=======================================================================================================================| 100%
Executing SQL took 0.113 secs
Running: insert_measurement.sql
  |=======================================================================================================================| 100%
Executing SQL took 42.6 secs
Running: insert_procedure_occurrence.sql
  |=======================================================================================================================| 100%
Executing SQL took 0.0341 secs
Running: insert_drug_exposure.sql
  |=======================================================================================================================| 100%
Executing SQL took 0.0575 secs
Running: insert_condition_era.sql
  |=======================================================================================================================| 100%
Executing SQL took 0.0176 secs
Running: insert_drug_era.sql
  |=======================================================================================================================| 100%
Executing SQL took 10.2 secs
Running: insert_cdm_source.sql
  |=======================================================================================================================| 100%
Executing SQL took 0.00696 secs
Running: insert_device_exposure.sql
  |                                                                                                                       |   0%Error in `.createErrorReport()`:
! Error executing SQL:
org.postgresql.util.PSQLException: ERROR: value too long for type character varying(50)
An error report has been created at  /home/ohdsi/errorReportSql.txt
Run `rlang::last_error()` to see where the error occurred.

[dsasson48]

I'm also encountering the same bug with a sample synthea dataset and PostgreSQL. LoadEventTables is frozen and crashes my R session due to the same warning. Thanks in advance for figuring out a solution

[burrowse]

Thanks for letting us know @dsasson48! We are currently working on a solution. What version of synthea is the sample dataset you are using?

[dsasson48]

Sounds good! The dataset was from the latest version from the Synthea repo after running ./run_synthea -p 10 --exporter.csv.export=true

extraSettings <- "integratedSecurity=false;encrypt=false;trustServerCertificate=true;sslProtocol=TLSv1"

cd <- DatabaseConnector::createConnectionDetails(
  dbms     = "postgresql", 
  server = 'localhost/normal',
  user     = "postgres",
  password = "my_password",
  port     = 5432, 
  pathToDriver = "/Desktop/", 
  extraSettings = extraSettings
)

cdmSchema      <- "cdm_synthea10"
cdmVersion     <- "5.4"
syntheaVersion <- "3.0.0"
syntheaSchema  <- "native"

ETLSyntheaBuilder::LoadEventTables(connectionDetails = cd, 
                                   cdmSchema = cdmSchema, 
                                   syntheaSchema = syntheaSchema, 
                                   cdmVersion = cdmVersion, 
                                   syntheaVersion = syntheaVersion)