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MIMIC repo code consolidation #1034

Merged
merged 307 commits into from
May 18, 2021
Merged

MIMIC repo code consolidation #1034

merged 307 commits into from
May 18, 2021

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briangow
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This pull request addresses the code consolidation for #910 . In particular it addresses:

  1. Move all of the mimic-code files under a mimic-iii folder
  2. Merge the mimic-iv files into the mimic-code directory under a mimic-iv folder
  3. Repeat step 7 for the mimic-cxr repository in place of the mimic-iv repository

The issues from the mimic-iv and mimic-cxr repos were transferred prior to this as outlined in #910 .

Some initial clean-up of the README files was also done. The issue template was updated to request that users add at least one mimic label when creating a new issue. The .travis.yml path was updated with the path to the mimic-iii tests.

closes #910

alistairewj and others added 30 commits November 5, 2019 18:14
@alistairewj
init comparison of negbio+chexpert using chexpert phrases
7961e7a
@alistairewj
outputting to tex files
4d4bdab
@alistairewj
add outputs
fe9750d
@alistairewj
add notebooks used to generate results in preprint
9a36da0
@alistairewj
add tex/csv/csvgz to ignore
f87e00c
@alistairewj
Initial commit
cc39fed
@alistairewj
init vent settings and durations
0694d57
@alistairewj
fix: remove debug filter to a few stays
77db577
@alistairewj
AP vs PA chest x-ray image
3190146
@alistairewj
add website theme as submodule
0f6ce85
@alistairewj
add mimic-theme as submodule
df66670
@alistairewj
migrate website from mimic-iv-website repo
797ae42
@alistairewj
update website to use docsy
adc506c
@alistairewj
tidy up content
f6a3635
@alistairewj
tidy content a bit more
5b74d84
@alistairewj
remove mimic-theme submodule
3d7b7cf
@alistairewj
continue to tidy up the docs content
5e5d677
@alistairewj
crop unused part of image
232c17c
@alistairewj
simpler language on community page
fab6062
@alistairewj
add npm package files
61b0524
@alistairewj
restore package jsons to original content
de7c31f
@alistairewj
remove example about page
779f73d
@alistairewj
change weight
c128e74
@alistairewj
fix query in bq tutorial
3eb2807
@alistairewj
fix links
2aa57eb
@alistairewj
update v0.4 change notes
def04ac
@ajb5d
Update bigquery.md
06db39d 
Fixed broken link
@alistairewj
Merge pull request #2 from ajb5d/patch-1
6b94122 
Update bigquery.md
@ajb5d
First pass of porting MIMIC-III first-day views to MIMIC-IV
01c255b
@SichengH
test
4b8d311
alistairewj and others added 25 commits March 16, 2021 19:51
@alistairewj
Merge pull request #109 from MIT-LCP/v1.0_updates
37c7702 
V1.0 updates
@alistairewj
Merge pull request #104 from arielhasidim/patch-1
8042146 
Update whatsnew.md
@alistairewj
fix typos, remove order by for bq, add los precision
403018a
@alistairewj
Merge pull request #92 from Hans0124SG/patch-2
f3c0ebf 
Create icustay_detail.sql
@alistairewj
add stay_id description
756f271
@alistairewj
fix date of v1.0 release
f37c62b
@alistairewj
add compatibility with bashv3.2
35ae66d
@alistairewj
fix itemid and overhaul query
03da086
@alistairewj
change interval to datetime_add (bq syntax)
bc9e41d
@alistairewj
add comorbidity/organfailure/sepsis subfolders
f07b281
@alistairewj
fix video links, closes #89
d6c4585
@alistairewj
Merge pull request #113 from MIT-LCP/fix_v1_concepts
41b2ede 
Fix creation of concepts
@alldefector
Update postgres create.sql for v1 data release
bfce63b
@alistairewj
add constraint
82a9eac
@alistairewj
Merge pull request #116 from alldefector/v1_psql_create_fix
9c89acc 
Update postgres create.sql for v1 data release
@alistairewj
add chartdate to hcpcs/proc_icd to match v1.0 schema
da03393
@briangow
Move mimic-code files under mimic-iii subfolder
7c4dc30
@briangow
Merge in mimic-iv repo. resolve conflicts in .gitignore/LICENSE/READM…
40cb3c3 
…E.md
@briangow
Move mimic-iv files under a mimic-iv subfolder
4f62c00
@briangow
Merge in mimic-cxr repo. resolve conflicts in .gitignore/LICENSE/READ…
58b2987 
…ME.md. remove .gitmodules
@briangow
Move mimic-cxr files into a mimic-cxr subfolder
47463f6
@briangow
Update README files
9ab7540
@briangow
Update ISSUE_TEMPLATE.md to request adding mimic labels to new issues
0edeb78
@briangow
Add path to MIMIC-III tests to .travis.yml
7721bae
@tompollard
update path to build script. fix test.
6a64145
@tompollard
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Thanks for all of your work on this Brian. Looks good to me! We should coordinate this merge with our switch to the updated website, and also make sure that URL rewrites are in place for the MIMIC-IV and MIMIC-CXR domains.

@briangow
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Thanks for the review and help here @tompollard ! @elfeto will help us setup the redirects as soon as we build the new site.

@tompollard tompollard merged commit 52d7df5 into main May 18, 2021
@tompollard
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The consolidated website (MIMIC-III, MIMIC-IV, MIMIC-CXR) is at: https://mimic.mit.edu/

@tompollard tompollard deleted the new_consol branch May 18, 2021 23:43
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MIMIC repository consolidation