Achilles Run issues - Oracle

Implementers
1

Hi Team,

I am running Achilles and am getting the below error. I was able to create the tables in the Results schema, from the WebAPI/ddl/results location. and then I ran Achilles.

Here are the steps I followed with reference to Achilles:

  1. Installed R
  2. Installed Achilles by following the documentation
  3. Ran Achilles as below:

library(Achilles)
connectionDetails ← createConnectionDetails(
dbms=“oracle”,
server=“server/sid”,
user=“username”,
password=‘password’,
port=“1521”)

achilles(connectionDetails,
cdmDatabaseSchema = “c#cdm”,
resultsDatabaseSchema=“c##results”,
vocabDatabaseSchema = “c#cdm”,
numThreads = 1,
sourceName = “My Cdm”,
cdmVersion = “5.3.1”,
runHeel = TRUE,
runCostAnalysis = FALSE)

When I gave TRUE for cost analysis, it gave me some other error, hence I wanted to first test with out cost analysis. The screenshot with error is attached.

Not sure if I am missing something. Appreciate any help on this.

achilles_error_03Apr19
achilles_error_03Apr191379×620 14 KB

For now, i am trying to run it in Single Thread mode

2

Is this really your schema name? With ## in it?

3

@Chris_Knoll,

That’s correct Chris! I think thats the policy/standard here at UT-SBMI. Any user/schema will have the prefix ‘c##’. And my username is: c##smanikonda.

Do you think that is causing the issues I am facing?

4

@Ajit_Londhe @Chris_Knoll,

I ran Achilles again and I still get similar error. The tables names are prefixed with ‘#.’ , which is causing the issues. Any help on how to fix this issue.

I have installed Atlas, but not able to see any of my CDM table data as I am not able to run Achilles.

achilles_issue_04Apr19
achilles_issue_04Apr19975×607 62.6 KB

5

What version of Oracle?

6

Hi @smanikonda,

I think I found the issue, but I can’t test since I don’t have Oracle. Essentially, I have been setting tempOracleSchema to scratchDatabaseSchema in every SqlRender translate call, which is making the temp tables become named “#.tablename”, which is invalid.

Can you uninstall Achilles completely and try installing the oraclefixes branch by using this command:

devtools::install_github("OHDSI/Achilles", ref = "oraclefixes")

7

HI @Ajit_Londhe,
Thanks a lot for your quick response. We have:
Oracle Database 12c Enterprise Edition Release 12.2.0.1.0 - 64bit Production

Could you please let me know how I can uninstall Achilles completely. I tried to look for any documentation, but could not find. Can you please help.

I will run the command you mentioned after Uninstalling Achilles.

8

Restart R, then run remove.packages("Achilles")

9

Thanks a lot @Ajit_Londhe

I don’t have permissions to remove the packages. And I got the error (attached) when I try to do it. Logged a ticket for my sysadmins. Will work on it tomorrow and update you.

I really appreciate your help.

achilles_error_04Apr19
achilles_error_04Apr19804×179 6.98 KB

10

@Ajit_Londhe,
I got the permissions finally and followed the below steps:

  • Uninstalled Achilles

  • Reinstalled using the option you provided (i.e. with this command
    devtools::install_github(“OHDSI/Achilles”, ref = “oraclefixes”)

  • When I run it. I got the error shown in the attached file. Earlier i was able to connect, but this time it is not able to connect to Oracle i think.

Can you please help me in resolving this issue.

achilles_issue_09Apr19
achilles_issue_09Apr192000×339 85 KB

11

Hi Sarath,

Which version of Java do you have installed?

-Dave Barman

12

@Dave.Barman ,

This is what I have:

java version "1.6.0_41"
OpenJDK Runtime Environment (IcedTea6 1.13.13) (rhel-1.13.13.1.el7_3-x86_64)
OpenJDK 64-Bit Server VM (build 23.41-b41, mixed mode)

13

@Ajit_Londhe, @Dave.Barman

What version of Java is required. We have upgraded our Java and tried. But still getting the same error.

achilles_issue_09Apr19_2
achilles_issue_09Apr19_22000×559 171 KB

14

I did not have the best luck with the OpenJDK. I ended up having success with Oracle Java JDK version 11. Make sure your JAVA_HOME environment variable is set to the correct directly

15

Hi @Ajit_Londhe, @Chris_Knoll

I need your help. I was able to Oracle JDK version 11 installed today and when I run it, i get the below error. Looks like the build was made for SQL Server. Appreciate if you can help me with the correct one.

Thanks and Regards

Sarath M

achilles_error_10Apr19
achilles_error_10Apr19997×319 9.97 KB

16

use a lowercase ‘O’ in ‘oracle’ in your dbms paramater.

1 Like
17

Yep, and please re-install from the oraclefixes branch of Achilles. I pushed some fixes today that should help with ensuring the tempOracleSchema is used properly.

18

I changed the O in oracle to lower case. This time its the Java error again. We have installed Java 11, but I am still getting the ‘…major.minor version 52.0 error’.

Could you please suggest the version of Java that we need to have installed for Achilles to work. Thanks a lot for all your help. I feel like I am almost there, but not there yet. :slight_smile:

achilles_error_10Apr19_2
achilles_error_10Apr19_2927×773 35.2 KB

19

Looks like you will need to run under JDK 8:

The issue is because of Java version mismatch. Referring to the Wikipedia Java Class Reference:

  • Java SE 12 = 56 (0x38 hex)
  • Java SE 11 = 55 (0x37 hex)
  • Java SE 10 = 54
  • Java SE 9 = 53
  • Java SE 8 = 52
  • Java SE 7 = 51
  • Java SE 6.0 = 50
  • Java SE 5.0 = 49
  • JDK 1.4 = 48
  • JDK 1.3 = 47
  • JDK 1.2 = 46
  • JDK 1.1 = 45

The version 52 is referring to JDK 8.

I’m surprised that 11 is not working for you, but the problem is definitely related to the version of the JDK.

20

This may help you:

If you execute:

library(rJava)
.jinit()
.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")

in R, what output does it give you?