mz-health/OMOP
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OMOP
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35 Commits

Author SHA1 Message Date
Clair Blacketer 15f5fb1ed5 Update OMOP_CDMv5.4_Field_Level.csv 
Fixing PK issue in cohort and cohort definition
 2021-12-21 10:07:32 -05:00
Clair Blacketer 9e4b5978c8 Bugfix to cdm v6.0 
VISIT_DETAIL.admitting_source_value and admitting_souce_concept_id were renamed to admitted_from_concept_id and admitted_from_source_value.
 2021-09-23 15:26:59 -04:00
Clair Blacketer 4c8f054784 Fix to CDM v6.0 to add back cohort table 2021-09-23 10:52:05 -04:00
Clair Blacketer 5927b49a53 Multiple fixes 
Fixed issue in CDM v5.3 field level csv, formatted rmd files, fixed documentation of the buildReleaseZip() function.
 2021-09-23 10:42:24 -04:00
Clair Blacketer 46da3238af Documentation updates to support CDM v5.4 2021-09-22 15:39:44 -04:00
Clair Blacketer 041291eb27 Foreign key fixes 2021-08-19 15:52:33 -04:00
Clair Blacketer c1a4422dd1 Changed bigint to integer for consistency 2021-08-19 14:54:44 -04:00
Clair Blacketer 7067be34ac Hack-a-thon updates 
Closes #81, #387, #239, #412, #391, #330, #408, #365, #306, #264
 2021-08-19 14:42:18 -04:00
Alan Andryc d73a0f426d
Merge branch 'v5.4' into v5.4 2021-08-19 13:30:50 -04:00
Andryc 7036b0e0f3 resolving merge issue on field level csv 2021-08-19 13:14:23 -04:00
Clair Blacketer c9463d0cf1 Adding EPISODE and EPISODE event tables 2021-08-19 12:58:41 -04:00
Clair Blacketer a2812b85e5 Added EPISODE and EPISODE_EVENT tables to table_level_5.4 
Also update the oncology extension documents to align with the table level file for v5.4
 2021-08-19 12:45:44 -04:00
Adam Black 19462d322d
Add tests, github actions, and executeDdl function (#425) 
* Add github actions workflow to build package and run tests.

* update Description file

* rename .Rproj file.

* Consolidate 'create' functions into one file.

* Add tests for create functions.

* update description

* removed spaces in file and folder names. Regenerated ddl output. Tried to fix Field_Level.csv file.

* consolidate write functions into one file. Add execute function.

* update docs

* add tests for write and execute functions

* update documentation

* Add windows and linux runners in github actions.

* update github actions

* download drivers before running tests

* fix small error in setup test file.

* debug github actions

* debug github actions

* debug github actions

* debug github actions

* fix tiny bug

* comment out execute ddl test

* fix bug in test

* Add execute test back in

* revert accidental change in description

* add print statement for debugging schema error on github actions.

* Fix schema environment variable name

* Add comment to github actions workflow file.

* remove placeholder text in function documentation.

* Rename createdDdl.R to createDdl.R

Co-authored-by: Adam Black <adam.black@odysseusinc.com>
 2021-08-19 11:49:36 -04:00
Frank DeFalco 918b57bcca Merge branch 'v5.4' into v5.4_cleanup 2021-08-18 16:06:08 -04:00
Frank DeFalco a4bfeccf83 function naming & additional cleanup 
made create and write functions consistent
fixed render issue that was not including dialect name in generated files
added loop to codeToRun to generate all scripts.
 2021-08-18 15:30:04 -04:00
clairblacketer ea0fc0f80b
Merge branch 'v5.4' into v5.4 2021-08-18 15:05:14 -04:00
unknown b4661f637d Issue #149 saved fix for nullables in vocabulary table (vocabulary_reference and vocabulary_version both have isRequired=No) 2021-08-18 14:37:43 -04:00
unknown 543893d406 Issue #149 fix for nullables in vocabulary table (vocabulary_reference isRequired=Yes vocabulary_version isRequired=No) 2021-08-18 14:23:54 -04:00
clairblacketer b17ca8a856
Merge branch 'v5.4' into v5.4 2021-08-18 13:52:15 -04:00
clairblacketer efc286e738
Merge branch 'v5.4' into v5.4 2021-08-18 13:47:13 -04:00
Andryc 3e17ee1715 Merge branch 'v5.4' of https://github.com/aandryc/CommonDataModel 
Updating local branch to reflect changes made by team.
 2021-08-18 13:36:21 -04:00
Alan Andryc 73a62ce122
Merge branch 'OHDSI:v5.4' into v5.4 2021-08-18 13:36:01 -04:00
clairblacketer 3dc0ad43ae
Merge pull request #420 from lizb101/v5.4 
V5.4
 2021-08-18 13:27:59 -04:00
unknown 826f6a923f Issue #149 fix for nullables in vocabulary table (vocabulary_reference and vocabulary_version both have isRequired=No) 2021-08-18 12:55:26 -04:00
Lisa Schilling 8dc0432f02
Update OMOP_CDMv5.4_Field_Level.csv 
Addresses #418
 2021-08-18 10:40:04 -06:00
Elizabeth Betts 7bc145ca0c Update OMOP_CDMv5.4_Field_Level.csv 2021-08-18 17:39:38 +01:00
Elizabeth Betts 0f4f17f937 Update OMOP_CDMv5.4_Field_Level.csv 
Issue #382
 2021-08-18 17:22:52 +01:00
stephanieshong 4f1a5af4ae issue 193 - Added value_source_value column to the Observation Table. 2021-08-18 12:21:52 -04:00
Andryc 2c3c42fb1c update to metadata table - issue 202 2021-08-18 12:19:04 -04:00
Lisa Schilling 26018caea2
Update OMOP_CDMv5.4_Field_Level.csv 
Addresses #386
 2021-08-18 10:07:58 -06:00
unknown 0941a0783c Issue #259 [measurement table] added unit_source_concept_id 2021-08-18 11:55:08 -04:00
Andryc 41bda9c907 Issue 329 updated visit_detail_parent_id 2021-08-18 11:27:56 -04:00
Clair Blacketer b49077f9cd Added v5.4 table level file 2021-08-18 11:18:20 -04:00
Clair Blacketer 0f1d9333dd Adding v5.4 field level file 2021-07-20 13:59:23 -04:00
Clair Blacketer f892dac55d Moved R project from CdmDdlBase 
This commit pulls the R project over from the CdmDdlBase repository. This will be the jumping-off code for the new OMOP CDM repo.
 2021-06-08 20:19:01 -04:00