mz-health/OMOP
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OMOP
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427 Commits

Author SHA1 Message Date
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 27522b0896
Merge pull request #423 from OHDSI/v5.4_cleanup 
various
 2021-08-18 16:07:09 -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 5dd9850088
Merge pull request #414 from NACHC-CAD/v5.4 
Issue #259 [measurement table] added unit_source_concept_id
 2021-08-18 15:05:21 -04:00
clairblacketer ea0fc0f80b
Merge branch 'v5.4' into v5.4 2021-08-18 15:05:14 -04:00
clairblacketer 577cad1cc5
Merge pull request #413 from aandryc/v5.4 
Added CDM v5.4 menu item
 2021-08-18 14:56:29 -04:00
clairblacketer 915d7595bb
Merge branch 'v5.4' into v5.4 2021-08-18 14:56:07 -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
Frank DeFalco be7ea44fba various 
fixed writePrimary use of fk function
removed old/unnecessary files - reviewed with CB
added listSupportedVersions function - explicitly not including 6.0
 2021-08-18 14:24:45 -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
Frank DeFalco 25ac31bee4
Merge pull request #421 from OHDSI/sql-creates-refactor 
Refactor create and write SQL functions
 2021-08-18 13:55:26 -04:00
clairblacketer be95ab5260
Merge pull request #417 from stephanieshong/v5.4 
issue 193 - Added value_source_value column to the Observation Table.
 2021-08-18 13:52:24 -04:00
clairblacketer b17ca8a856
Merge branch 'v5.4' into v5.4 2021-08-18 13:52:15 -04:00
clairblacketer a83cf75580
Merge pull request #419 from schillil/v5.4 
Fixes Admitting_Source_xx to Admitted_From_xx in Visit_Detail and Visit_Occurrence Tables
 2021-08-18 13:47:30 -04:00
Maxim Moinat 12e5fb3467 add new ddl folder with generated sql 2021-08-18 19:47:13 +02:00
clairblacketer efc286e738
Merge branch 'v5.4' into v5.4 2021-08-18 13:47:13 -04:00
Maxim Moinat 8d29222563 refactor index creation and cleanup codeToRun 2021-08-18 19:42:01 +02:00
Alan Andryc 73a62ce122
Merge branch 'OHDSI:v5.4' into v5.4 2021-08-18 13:36:01 -04:00
Maxim Moinat 5d9887a356 refactor create and write sql for foreign key and primary key 2021-08-18 19:28:21 +02:00
clairblacketer 3dc0ad43ae
Merge pull request #420 from lizb101/v5.4 
V5.4
 2021-08-18 13:27:59 -04:00
Maxim Moinat f8cd93d159 refactoring of create and write DDL 2021-08-18 19:02:22 +02:00
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
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
Andryc 066b872ee1 Added CDM v5.4 menu item 2021-08-17 15:26:11 -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
Clair Blacketer 482b1f0388 Updated front page 2021-06-03 10:57:22 -04:00
Clair Blacketer 4c4c012d83 Merge branch 'master' of https://github.com/OHDSI/CommonDataModel 2021-06-03 10:45:28 -04:00
Clair Blacketer 6b12abb349 Add refresh cycle info 
Added information about the CDM refresh cycle and notes about CDM v6.0
 2021-06-03 10:45:05 -04:00
clairblacketer 91304762f7
Added note about CDM v5.3 vs CDM v6.0 2021-06-03 09:28:05 -04:00
Clair Blacketer 35d53c9f5a Fixes to documentation 
Closes #380, #379, #350, #334, #316, #129
 2021-02-18 21:37:32 -05:00
clairblacketer 7bb9cf23a0 FAQ numbering fix 
closes #344
 2021-01-06 10:52:57 -05:00
clairblacketer 371917f138 Merge branch 'master' of https://github.com/OHDSI/CommonDataModel 2020-12-10 12:44:09 -05:00
clairblacketer e2f43de8bf Closes #371 2020-12-10 12:43:21 -05:00
clairblacketer d14b83cfaa
Merge pull request #370 from wibeasley/master 
correct spelling of "vocabulary"
 2020-11-12 15:35:33 -05:00
clairblacketer aa360f9014 Update to DEATH table documentation 2020-10-22 13:07:38 -04:00
Will Beasley 181849343d correct spelling of "vocabulary" 2020-10-21 23:12:22 -05:00
clairblacketer ccea723163 Added article on how to download the ddls. 2020-10-16 15:26:46 -04:00
clairblacketer 32d0cb9a0a Clarification to drug dose calculations 2020-10-06 11:46:48 -04:00
clairblacketer ed105b1e55 Updates to website 2020-10-06 11:11:13 -04:00
clairblacketer 58f01a2a69 Added skype link for meeting on third Tuesday of the month 2020-08-17 22:32:41 -04:00
clairblacketer f07cf54bd5 Small fix for drug_era documentation 2020-05-26 21:02:26 -04:00