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Hi
I have downloaded omop standard vocabularies into my laptop.
When I opened the files in notepad, I see that the values are separated by tabs rather than commas.
And I am not able to import the table into postgresql thorough pgadmin 4. It gives an error message- “import failed exit code1”
What can do about it?
Can anyone please guide me how to import the vocabulary files into postgresql database?
Thanks
We’ve developed a package to upload OMOP voca to the SQL DB, OmopVocaManager.
Could you try to upload vocabulary to DB by using this package?
thanks for the reply.
I tried it.
But I’m getting an error
“Error: Failed to install ‘OmopVocaManager’ from GitHub:
(converted from warning) installation of package ‘C:/Users/draru/AppData/Local/Temp/Rtmpacor9y/file297c43fd6640/OmopVocaManager_0.9.5.tar.gz’ had non-zero exit status”
Hi,
I’ve just tried to install OmopVocaManager, and it worked.
In my experience, the error showed up when there’s no dependencies or previous version of the package(or other dependencies) was installed.
Is there any massages before your error like “Try removing ‘C:/Users/…/<package name>’”(The message may not start with ‘Try removing’)? If there is, you can follow the direction.
20.03.10 +) I updated latest version of OmopVocaManager. Please use latest version 
I’m using postgres 12 and have been using /COPY to read the csv/tsv files in. It ran fine until I hit the VOCABULARY table, where the vocabulary_version colum has null values. The file has consecutive tabs there. The table has a not-null for all of its columns. I got the data loaded by slipping a space in between the tab characters. I’ll find out shortly how good an idea that was, but I wonder what the intent is here and what a better fix might be.
thanks
-Chris
Hi @CRoeder and @drarunbabu02,
has the issue been resolved with a later vocabulary download or does it persist? For which vocabularies did you find a NULL in the vocabulary version column?
Thanks ~ Mik