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FINNGEN
/
ETL
second version for the ETL of the detailed longitudinal data to the OMOP-CDM
https://finngen.github.io/ETL/
MIT License
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icdo3 added
#150
javier-gracia-tabuenca-tuni
closed
1 year ago
0
Main update docu
#149
javier-gracia-tabuenca-tuni
closed
1 year ago
0
Change finngenid_info table name to minimum_extended
#148
shanmukhasampath
opened
1 year ago
0
Achilles now has table with RC, DRC, PC and DPC
#147
shanmukhasampath
closed
1 year ago
0
Made changes to unittest add_finngenid function to check BIOBANK visits
#146
shanmukhasampath
closed
1 year ago
0
Changed R version to 4.3.0 in Dockerfile
#145
shanmukhasampath
closed
1 year ago
0
Update dockerfile to R 4.3
#144
shanmukhasampath
closed
1 year ago
0
ETL now maps BMI, Height and Smoking codes. All unit tests PASS.
#143
shanmukhasampath
closed
1 year ago
2
Update README.md
#142
javier-gracia-tabuenca-tuni
closed
1 year ago
0
updated readme
#141
javier-gracia-tabuenca-tuni
closed
1 year ago
0
Update home.md
#140
javier-gracia-tabuenca-tuni
closed
1 year ago
0
updated documentation
#139
javier-gracia-tabuenca-tuni
closed
1 year ago
0
My single change
#138
javier-gracia-tabuenca-tuni
closed
1 year ago
0
added doc
#137
javier-gracia-tabuenca-tuni
closed
1 year ago
0
Create jekyll-gh-pages.yml
#136
javier-gracia-tabuenca-tuni
closed
1 year ago
0
Defined all input parameters for birth mother unit test.
#135
shanmukhasampath
closed
1 year ago
0
Updated documentation and RabbitInaHat json file
#134
shanmukhasampath
closed
1 year ago
5
Smoking
#133
shanmukhasampath
closed
1 year ago
0
BMI
#132
shanmukhasampath
closed
1 year ago
0
fg codes info table creation copied from atlasdevelopment
#131
shanmukhasampath
opened
1 year ago
0
Add ETL documentation
#130
shanmukhasampath
closed
1 year ago
0
execute the new ETL in Sandbox and access it with a dockerise Atlas
#129
shanmukhasampath
closed
1 year ago
2
Fixed Python virtual environment name in renv.lock file
#128
shanmukhasampath
closed
1 year ago
0
ETL birth mother registry is done. All tests PASS.
#127
shanmukhasampath
closed
1 year ago
6
Investigate: Atlas is not showing person counts for the non-standard codes
#126
javier-gracia-tabuenca-tuni
closed
1 month ago
2
updated renv
#125
javier-gracia-tabuenca-tuni
closed
1 year ago
0
123 update r to 430
#124
javier-gracia-tabuenca-tuni
closed
1 year ago
0
Update R to 4.3.0
#123
javier-gracia-tabuenca-tuni
closed
1 year ago
1
Updated CDM schema from github CommonDataModel repo commit.
#122
shanmukhasampath
closed
1 year ago
0
era tables date fields with datetime
#121
shanmukhasampath
closed
1 year ago
0
write ETL script to add mothers table to to cdm
#120
javier-gracia-tabuenca-tuni
closed
1 year ago
2
create a dummy data for the mothers table in the birth registry
#119
javier-gracia-tabuenca-tuni
closed
1 year ago
1
create a table in BQ atals develpment, keep files , https://github.com/FINNGEN/AtlasDevelopment,
#118
javier-gracia-tabuenca-tuni
closed
1 year ago
0
STEPS: Adding birth register data to the cdm
#117
javier-gracia-tabuenca-tuni
closed
1 year ago
0
birth register data
#116
shanmukhasampath
closed
1 year ago
1
Fixed NULL in observation source value by changing stem SQL
#115
shanmukhasampath
closed
1 year ago
0
Updated DQD to v2.1.2. DQD works.
#114
shanmukhasampath
closed
1 year ago
0
DQD conformace tests wrongly tells that some fileds should be NULL
#113
javier-gracia-tabuenca-tuni
closed
1 year ago
0
observation source value as null
#112
shanmukhasampath
closed
1 year ago
0
Fixed the correct domain for measurement ETL
#111
shanmukhasampath
closed
1 year ago
0
measurement with correct domain
#110
shanmukhasampath
closed
1 year ago
0
Fixed an error in ERA tables that gives huge gap values in drug era
#109
shanmukhasampath
closed
1 year ago
0
Fixed missing zero measurement concept id.
#108
shanmukhasampath
closed
1 year ago
0
error in measurement standard concept.
#107
shanmukhasampath
closed
1 year ago
0
completenes errors in DQD that may show some other issues
#106
javier-gracia-tabuenca-tuni
closed
1 year ago
3
One test fail in **DRUG_EXPOSURE** table because there is a single drug concept id **43163536** which is no longer a standard concept and is invalid.
#105
javier-gracia-tabuenca-tuni
closed
1 year ago
1
The first two fail tests in `Conformance` category is about a single concept id **200047** not present in **CONCEPT** table of `schema_vocab`
#104
javier-gracia-tabuenca-tuni
closed
1 year ago
1
error in era tables
#103
shanmukhasampath
closed
1 year ago
3
Fixed Device Exposure source concept id SQL code
#102
shanmukhasampath
closed
1 year ago
0
device exposure wrong code
#101
shanmukhasampath
closed
1 year ago
2
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