My experiences using the unm-improvements branch - Apr 14 about etl-cms HOT 6 CLOSED

Hi Sean,

Thanks for the feedback, and glad it was helpful. Let me respond to your feedback:

• We will look into the confusing message
• The script get_synpuf_files.py used to be in python3 -- in our branch, we converted it to 2.7 for just the reason you mentioned -- consistency. Are you sure you retrieved the unm-improvements branch? The change to 2.7 is documented in the header.
• We didn't know how to get that file either, so we overhauled the program to directly read the OMOP vocabulary files as they come out of the box. Again, are you sure you retrieved the right branch? I can't even find a reference to that file in our branch.
• We did not provide instructions on how to create the OMOP CDM v5 database, as we hadn't got there yet, but I agree it would be helpful to have the full soup-to-nuts instructions.
• Great idea to have a script to run it all.
• I would like to do release the results of running the ETL as a zip file as well. It will be quite large -- any suggestions where?

Thanks!

Christophe

from etl-cms.

Christophe, if you made a version of the dataset using your ETL, the
coordinating center can host it on our amazon instance, and we can expose
it via the OHDSI website. Lee Evans can help with those logistics. Thanks
for your contribution, this is great!

On Thu, Apr 14, 2016 at 7:18 PM, Christophe Lambert <
[email protected]> wrote:

Hi Sean,

Thanks for the feedback, and glad it was helpful. Let me respond to your
feedback:

• We will look into the confusing message
• The script get_synpuf_files.py used to be in python3 -- in our
  branch, we converted it to 2.7 for just the reason you mentioned --
  consistency. Are you sure you retrieved the unm-improvements branch? The
  change to 2.7 is documented in the header.
• We didn't know how to get that file either, so we overhauled the
  program to directly read the OMOP vocabulary files as they come out of the
  box. Again, are you sure you retrieved the right branch? I can't even find
  a reference to that file in our branch.
• We did not provide instructions on how to create the OMOP CDM v5
  database, as we hadn't got there yet, but I agree it would be helpful to
  have the full soup-to-nuts instructions.
• Great idea to have a script to run it all.
• I would like to do release the results of running the ETL as a zip
  file as well. It will be quite large -- any suggestions where?

Thanks!

Christophe

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#18 (comment)

from etl-cms.

Hey @ChristopheLambert, well false alarm. I was on 94540d0 from master, thinking I was on unm-improvements. No wonder you were so confused, oops! :)

Looks like there's a lead as to where to put the output, excellent. I'll close the issue as most else what I said doesn't seem to apply. Thanks!

from etl-cms.

Patrick, we will be sure to do that.

Sean, glad you reached out anyways. Let us know how it works out!

from etl-cms.

Hi @ChristopheLambert how big is the SYNPUF CDMV5 dataset that you would like to share?

Do you have a preferred way to transfer it? ftp server? I can setup a temporary AWS S3 bucket for you to upload the dataset if needed.

You can send me a direct message on the OHDSI forum, or connect and message me on linkedIn to share the transfer connection details.

Thanks.

from etl-cms.

Hi @leeevans, we are not finished yet, but estimate it will be 110GB uncompressed, and about 18GB compressed. SFTP would be fine.

from etl-cms.