mz-health/OMOP
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OMOP
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543 Commits

Author SHA1 Message Date
Adam Black f7a42d5482 replace outputpath with outputfolder for consitent argument names in the package. 2021-08-20 11:06:23 -04:00
Adam Black 57d40c2a7d Allow user to specify output location in buildRelease 2021-08-20 11:05:46 -04:00
Clair Blacketer 39213577c3 Trying again to remove .DS_Store, adding to gitignore 2021-08-20 09:34:21 -04:00
Clair Blacketer 83d6a30376 Removing unnecessary file 2021-08-20 08:52:52 -04:00
Clair Blacketer 02d03b4a60 Resolving conflicts 2021-08-20 08:50:18 -04:00
Adam Black 532be98c0c
Add unit tests for all databases and DDLs (#431) 
* 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

* Hack-a-thon updates

Closes #81, #387, #239, #412, #391, #330, #408, #365, #306, #264

* Changed bigint to integer for consistency

* Updated DDLs

* Add tests for redshift. Clean up test setup file.

* Foreign key fixes

* Add imports and update docs.

* Fix bug in setup test script.

* update setup file

* Add tests for oracle and sql server. Move setup.R file.

* fix bug in setup

* debug tests on github

* debug github actions

* debug actions.

* debug actions

* debug actions.

* Add missing secrets to yaml!!

* debug actions

* test connection on all platforms

* add ddl execution

* add windows and linux runners

Co-authored-by: Adam Black <adam.black@odysseusinc.com>
Co-authored-by: Clair Blacketer <mblacke@its.jnj.com>
 2021-08-20 07:59:29 -04:00
Adam Black d1186aacbe add windows and linux runners 2021-08-20 00:10:41 -04:00
Adam Black c98e171ebc add ddl execution 2021-08-19 23:58:18 -04:00
Adam Black ec02071b64 test connection on all platforms 2021-08-19 23:42:04 -04:00
Adam Black 8fc2ae6e4e debug actions 2021-08-19 23:38:29 -04:00
Adam Black 1f994c7eb4 Add missing secrets to yaml!! 2021-08-19 23:30:12 -04:00
Adam Black 2a9fa71612 debug actions. 2021-08-19 23:12:55 -04:00
Adam Black 3af7fdbe69 debug actions 2021-08-19 23:05:43 -04:00
Adam Black 94ffcba404 debug actions. 2021-08-19 22:59:07 -04:00
Adam Black 1610328836 debug github actions 2021-08-19 22:46:33 -04:00
Adam Black e68cb43854 debug tests on github 2021-08-19 22:45:23 -04:00
Adam Black d6d213c7f6 fix bug in setup 2021-08-19 22:31:06 -04:00
Adam Black cedf334df6 Add tests for oracle and sql server. Move setup.R file. 2021-08-19 22:23:39 -04:00
Adam Black 2b0acc8d53 update setup file 2021-08-19 18:49:15 -04:00
Adam Black ff4f8337f8 Fix bug in setup test script. 2021-08-19 16:28:21 -04:00
Adam Black 7e08fa1737 Merge Claire's DDL updates 2021-08-19 16:24:06 -04:00
Adam Black eb3d27926f Add imports and update docs. 2021-08-19 16:22:08 -04:00
Adam Black 63ba979509 Merge in Maxims changes. update documentation 2021-08-19 16:00:24 -04:00
Clair Blacketer 041291eb27 Foreign key fixes 2021-08-19 15:52:33 -04:00
Maxim Moinat b3fddfbb85
Function to Build Release Zips (#429) 
* buildRelease and buildReleaseZip

* add buildRelease
 2021-08-19 15:43:34 -04:00
Adam Black ed5fb2d428 Add tests for redshift. Clean up test setup file. 2021-08-19 15:17:01 -04:00
Clair Blacketer 690c9edf40 Updated DDLs 2021-08-19 15:04:43 -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
Andryc 6414b42f6b prepping for pull request 2021-08-19 12:46:40 -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
Andryc 4be728e9d8 Updates to yml and cdm531.Rmd 2021-08-19 12:20:49 -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
Adam Black 05e9b801e0 Rename createdDdl.R to createDdl.R 2021-08-19 11:47:56 -04:00
Adam Black 948a78c09f remove placeholder text in function documentation. 2021-08-19 11:46:01 -04:00
Adam Black 35ce18ce81 Add comment to github actions workflow file. 2021-08-19 09:23:11 -04:00
Adam Black 618f35fe02 Fix schema environment variable name 2021-08-19 09:13:04 -04:00
Adam Black 66a892d87c add print statement for debugging schema error on github actions. 2021-08-19 09:11:02 -04:00
Adam Black fb950dedf8 revert accidental change in description 2021-08-19 08:58:34 -04:00
Adam Black c2717409d3 Add execute test back in 2021-08-19 08:33:24 -04:00
Adam Black cea09cf273 fix bug in test 2021-08-19 08:23:41 -04:00
Adam Black 7ecd0a5410 comment out execute ddl test 2021-08-19 08:13:03 -04:00
Adam Black c85759800e fix tiny bug 2021-08-19 07:47:49 -04:00
Adam Black bce8bc5edc debug github actions 2021-08-19 07:45:18 -04:00
Adam Black 639d6a9d0a debug github actions 2021-08-19 07:35:41 -04:00
Adam Black 7a59d0350f debug github actions 2021-08-19 00:25:02 -04:00
Adam Black b54b1947dd debug github actions 2021-08-19 00:18:54 -04:00