Eliminating "_DATA_TABLE" from names of .csv files about mimic-code

[tompollard]

I was thinking the same thing recently when creating the bash script for our data export (login needed - https://github.com/MIT-LCP/mimic-iii-building/tree/master/data_export).

The "_DATA_TABLE" is added by default when dumping CSV files using the Oracle GUI, but as we now export the data via custom scripts there's no reason to include it.

We'll go ahead with this change sometime soonish...

[tompollard]

Rename csvs with:

rename 's/_DATA_TABLE*//' *.csv

[tompollard]

CSV files and checksums have been updated on PhysioNet and testing servers.

[tompollard]

"_DATA_TABLE" has been removed from the filename in the data and associated scripts. Closing issue...

[alistairewj]

Can do this in Windows powershell as follows:

get-childItem *_DATA_TABLE.csv | rename-item -newname { $_.name -replace '_DATA_TABLE','' }

[tompollard]

Closed issue Alistair, closed issue. If _DATA_TABLE is in the filename, it's time to upgrade to the current version!

[alistairewj]

Just downloaded ADMISSIONS and CALLOUT from Physionet and while the .csv.gz
don't have DATA_TABLE in the name, when I extract them the final .csv does.

On Sat, Jan 23, 2016 at 2:07 PM, Tom Pollard [email protected]
wrote:

Closed issue Alistair, closed issue. If _DATA_TABLE is in the filename,
it's time to upgrade to the current version!

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#43 (comment).

[tompollard]

Oh, what...I'll sort that out.

[tompollard]

I just downloaded the ADMISSIONS and CALLOUT tables (+ a couple of others) from Physionet and decompressed using gzip -d *.gz. The decompressed files do not contain DATA_TABLE in the name:

-rw-r--r-- 1 name group 12738420 Jan 24 10:58 ADMISSIONS.csv
-rw-r--r-- 1 name group 6397862 Jan 24 10:58 CALLOUT.csv
-rw-r--r-- 1 name group 43532 Jan 24 10:56 D_LABITEMS.csv

Something weird going on here. Possible that you're somehow downloading an older version? Or some form of caching related to the two PhysioNet servers?

[alistairewj]

I used 7zip on Windows 7. Not sure if that changes things..
On 24 Jan 2016 11:02, "Tom Pollard" [email protected] wrote:

I just downloaded the ADMISSIONS and CALLOUT tables (+ a couple of others)
from Physionet and decompressed using gzip -d *.gz. The decompressed files
do not contain DATA_TABLE in the name:

-rw-r--r-- 1 name group 12738420 Jan 24 10:58 ADMISSIONS.csv
-rw-r--r-- 1 name group 6397862 Jan 24 10:58 CALLOUT.csv
-rw-r--r-- 1 name group 43532 Jan 24 10:56 D_LABITEMS.csv

Something weird going on here. Possible that you're somehow downloading an
older version? Or some form of caching related to the two PhysioNet servers?

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Reply to this email directly or view it on GitHub
#43 (comment).

[alistairewj]

https://physionet.org/works/MIMICIIIClinicalDatabase/files/version_1_3/ADMISSIONS.csv.gz

Opening this on 7zip:

[tompollard]

Oh, that's annoying, I see what's happened. I'll update the export scripts and we can include the new filename in the next release.

[tompollard]

https://github.com/MIT-LCP/mimic-iii-building/commit/496ae0db006dae6427c8c6f726c4b62e7cb03767

[alistairewj]

Fixed with release of v1.4.