Running Achilles package successfully, but not all the tables are generated

Implementers
1

Dear @Ajit_Londhe and @Chris_Knoll,

I am running Achilles scripts by following the documents list here, it runs successfully, but in my results schema, only the following 5 tables are created:

  • ACHILLES_analysis
  • achilles_results
  • achilles_results_dist
  • cohort
  • cohort_definition

There should be a lot more tables created. Also, when I go to the Dashboard under my data source, lots of the reports are showing “error load report”. @Ajit_Londhe or @Chris_Knoll, could you please kindly let me know what could be the possible reason?

Also, would running the following help to generate all the missing tables?

https://yourserver/WebAPI/ddl/results?dialect=yourDBFlavor&schema=results&vocabSchema=yourVocabSchema&tempSchema=your_atlas_temp&initConceptHierarchy=true

Running the above gives me back lots of SQL statements… should we run these statements on our CDM server, so we can see the missing table under results schema?

Thank you in advance!

2

Hello @liyang,

Yes, that should help. This service endpoint generates the necessary SQL queries for you based on the provided parameter values, but it doesn’t run them against your CDM database — you’ll have to to it separately.

3

thank you @rookie_crewkie for the help! let me fully understand this:

so I should:

  1. run this,
    https://yourserver/WebAPI/ddl/results?dialect=yourDBFlavor&schema=results&vocabSchema=yourVocabSchema&tempSchema=your_atlas_temp&initConceptHierarchy=true
    which gives me a lots of SQL queries

  2. run these SQL queries on CDM server side manually

  3. run the achilles package, as described here

is the above the right order to do this? my goal is to be able to see all the dashboard reports on Atlas for a given data source.

Thanks for the help!

4

@liyang,

It’s basically like this:

  • A. run Achilles analysis;
  • B. create additional tables for Atlas, in two sequential steps:
    • get generated SQL from WebAPI endpoint;
    • run it on CDM server manually.

Steps A and B are independent and can be done in any order, but both are required for proper Atlas operation. Achilles does most of the job and calculates all statistics for your dataset — this’d be the actual content of the ‘Data Sources’ reports in Atlas (including dashboard).
Step B usually takes much less time than Achilles, by the way.

1 Like
5

@rookie_crewkie - thank you! this is very clear and will be my main goal for today. Thank you again!

6

Sorry for the delay @liyang. Thanks for providing the answer @rookie_crewkie!

7

@Ajit_Londhe no problem, I know you are busy. Thank you @rookie_crewkie again for the help, all is good now on my side.

8

Hello @rookie_crewkie @Ajit_Londhe,

I was running Achilles heel and reviewing the rules. Have a quick questions on couple of rules and Achilles web

q1) May I check what does the below rule mean?

“Number of drug exposure recorded by drug exposure start month, there’s a 100% change in monthly count of events”

I am not able to understand this rule (could be due to my limitation with english language).

Can help me understand what does the above rule mean?

Let’s say 10 drug exposure records for 2 patients in my db

5 drug exposure records for 1 person started on Jan, Feb, Mar, Apr and May 2005 and another 5 drug exposure records for another person started on May, Jun, July, Aug, Sep 2007.

So what does change in monthly count of events mean? and in which cases would this info be useful to know. If my example is not applicable for this scenario, can help with any other example?

q2) I also didn’t understand what does GeneralPopulationOnly mean here? Can help me with the below rule as well?

“[GeneralPopulationOnly] Not all deciles represented at first observation”

q3) I tried launching achilles web using the below command

http://C:/Users/abcde/Downloads/AchillesWeb-master/AchillesWeb-master/data/datasources.json

http:///C:/Users/abcde/Downloads/AchillesWeb-master/AchillesWeb-master/data/datasources.json

file:///C:/Users/abcde/Downloads/AchillesWeb-master/AchillesWeb-master/index.html#/loading.../conditions

The first 2 links with 2 slashes and 3 slashes doesn’t return anything. I get page cannot be displayed error message.

The 3 rd link with file:/// shows the UI layout but doesn’t show any data or respond properly to clicks

As per github instructions, I have created data folder Achilles-web-master as you can see above. Inside data folder, I have another folder called SAMPLE. but datasources.json file is under data folder and not under SAMPLE folder. Guess that’s how it should be.

Can help me on how can I launch Achilles Web? So, is the problem with index.html file or with my exported json files?.

q4) When we run Achilles Heel (R-shiny), I see Associated analysis SQL and Achilles Heel Analysis SQL. What is the difference between these two? and Why is Achilless Analysis SQL NA for some Heel output