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Running Athena Locally

Developers
#1

Hi All,

We are trying to set up Athena locally.

Is there any documentation or steps available to create and load the DB from scratch, and bring up Athena connecting to it?

Thanks,
Chandan

#2

Hi @Chandan_PR , quick question: what is your use case for setting up Athena locally? Do you just want to browse standardized vocabularies or also custom (local) ones? Do you also want to distribute vocabularies to your local network?
Thanks - Mik

#3

@mik Is there a way to view licensed vocabularies in Athena? That would be a reason I have thought of a local Athena instance.

#4

Yes, once you obtain the license, the vocabulary is visible in search.

#5

And on a second note, local Athena instance might be needed if someone has a CDM based on some stable vocabulary version and they want to continue mapping their data on that (alredy historic) version of the vocabuary, while the OMOP vocabularies got updated.

#6

Hi @mik,
We would like to run Athena locally to use it for our historic vocabulary, internally.
We don’t have any plans for distribution.

#7

Hi All,

Any reference documents or links for this?

@mik,
Any place where I can look for useful documentation?

#8
#9

Hi @Dymshyts ,

I don’t see documentation on setting up the DB and Athena application locally in the GitHub repo.

I have set up the project locally and now after setting up the DB and application parameters, the unit tests are failing.

Thought if anyone running Athena locally or if there is some documentation available, that might cut down the efforts on what would be a spike otherwise.

#10

Hi @Chandan_PR
there is to my knowledge no one running Athena locally, as use cases for this are rather academic if existent at all… Mostly they would not justify the effort for setting it up as there is the Athena server freely available, as long as you have access to the internet…
What would you do with it, having your historic vocabularies in it?

I would assume there is at least one table missing, besides all the regular OMOP vocabulary tables: '“vocabulary_conversion” as referenced here.
I think the below would be the DDL to create it:
CREATE TABLE [put your schema here].vocabulary_conversion (
vocabulary_id_v4 int4 NOT NULL,
vocabulary_id_v5 varchar(20) NULL,
omop_req varchar(1) NULL,
click_default varchar(1) NULL,
available varchar(25) NULL,
url varchar(256) NULL,
click_disabled varchar(1) NULL,
latest_update date NULL,
CONSTRAINT vocabulary_conversion_pkey PRIMARY KEY (vocabulary_id_v4)
);

Only… content for this table is filled during the release process from vocabulary server to Athena. You would have to duplicate the ids from your vocabulary table for the v5 column and copy the respective v4 ids (numbers) from the Athena download page… omop_req gets a Y for all vocabularies that you got but weren’t able to select in the download process.

So, again, I would not invest too much time into this, unless you have a crystal clear use case that justifies the investment. And: I am afraid I would not be able to help you any further, as I have exhausted my knowledge… So, if you cannot get it to run with the above information, weigh your options carefully and decide if you want to pursue.

Cheers - mik

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