OHDSI Home | Forums | Wiki | Github

Achilles and Docker Setup

Implementers
#21

I restarted Achilles and I got:

library(Achilles)
Loading required package: DatabaseConnector
Sys.setenv(“DATABASECONNECTOR_JAR_FOLDER” = “/application/jdbcDrivers”)
downloadJdbcDrivers(“postgresql”)
trying URL ‘https://ohdsi.github.io/DatabaseConnectorJars/postgresqlV42.2.18.zip’
Content type ‘application/zip’ length 931791 bytes (909 KB)
==================================================
downloaded 909 KB

DatabaseConnector JDBC drivers downloaded to ‘/application/jdbcDrivers’.

connectionDetails ← createConnectionDetails(

  • dbms=“postgresql”,
  • server=“hsc-ctsc-achilles.health.unm.edu/truven”,
  • user=“usr4atlas”,
  • password=’*******************’,
  • port=“5432”)

achilles(connectionDetails,

  • cdmDatabaseSchema = “mdcr2003_2016”,
  • resultsDatabaseSchema = “atlas_results”,
  • scratchDatabaseSchema = “achilles_scratch”,
  • vocabDatabaseSchema = “mdcr2003_2016”,
  • numThreads = 1,
  • sourceName = “AchilesAtlas”,
  • cdmVersion = “5.3.0”,
  • runHeel = TRUE,
  • runCostAnalysis = TRUE)
    Connecting using PostgreSQL driver
    2021-09-16 18:04:47 Beginning single-threaded execution
    Connecting using PostgreSQL driver
    |======================================================================| 100%
    Executing SQL took 0.215 secs
    2021-09-16 18:04:50 warning: The ‘oracleTempSchema’ argument is deprecated. Use ‘tempEmulationSchema’ instead.
    This warning is displayed once every 8 hours.

2021-09-16 18:04:50 warning: Temp table name ‘#s_tmpach_Drug_rawCost’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.

2021-09-16 18:04:50 warning: Temp table name ‘#s_tmpach_Drug_cost_raw’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.

2021-09-16 18:04:50 warning: Temp table name ‘#s_tmpach_Procedure_cost_raw’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.

2021-09-16 18:04:50 warning: Temp table name ‘#s_tmpach_Procedure_rawCost’ is too long. Temp table names should be shorter than 22 characters to prevent Oracle from crashing.

2021-09-16 18:04:50 [Raw Cost] [START] 15000
|========== | 14%

Why I got the oracle warnings if I am using postgres?

#22

I have the feeling Achilles is stuck… How to be sure? The only screen I can see is:

2021-09-16 23:18:31 [Cost Analysis] [START] 1502
|======================================================================| 100% Executing SQL took 1.83 days
2021-09-18 19:07:57 [Cost Analysis] [COMPLETE] 1502 (1.826005 days)
2021-09-18 19:07:57 [Cost Analysis] [START] 1503
|======================================================================| 100%
Executing SQL took 17.1 hours
2021-09-19 12:14:24 [Cost Analysis] [COMPLETE] 1503 (17.107274 hours)
2021-09-19 12:14:24 [Cost Analysis] [START] 1504
|======================================================================| 100%
Executing SQL took 11.2 hours
2021-09-19 23:28:03 [Cost Analysis] [COMPLETE] 1504 (11.227541 hours)
2021-09-19 23:28:03 [Cost Analysis] [START] 1505
|==================== | 29%

#23

those oracle warnings are shown regardless if you’re using oracle or not. it’s to try to get OHDSI developers to use table names that won’t cause issues in oracle

#24

I think checking in pgAdmin the health of the queries executing can help show if it’s stuck or better still, what’s happening with it.

#25

Is there a version of this which doesn’t have password protection? The password thing is messing with my orchestration.

#26

On closer inspection of this thread, I should be asking @Konstantin_Yaroshove.

#27

If you mean the password I mentioned then I can only say that password is needed to “plug” to the database.

#28

If you are asking about Docker Hub image, then yes.

Simply set the environmental variable DISABLE_AUTH=true, e.g.

docker run -d \
--name=rstudio-ohdsi \
-p 8787:8787 \
-e DISABLE_AUTH=true \
odysseusinc/rstudio-ohdsi:latest
1 Like
t