Commit Graph

577 Commits

Author SHA1 Message Date
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 b89ce618c5 Formatting to front page 2021-09-23 10:06:07 -04:00
Clair Blacketer 794be47b0b Formatting Update to index.rmd 2021-09-23 09:34:28 -04:00
Clair Blacketer ea933efe86 Updated html
Updated html with changes to rmarkdown files
2021-09-23 09:26:43 -04:00
Clair Blacketer 542a76e6a1 Update README.md
Updated function call in the readme to use buildRelease()
2021-09-23 09:23:21 -04:00
Clair Blacketer b5b79fbfa5 Update README.md
Added link to bugfix description
2021-09-23 09:21:16 -04:00
Clair Blacketer 568246ec60 Update cdm60.Rmd
Updated links to cdm v5.4
2021-09-23 09:12:58 -04:00
Clair Blacketer fb9dcab5be Merge branch 'master' of https://github.com/OHDSI/CommonDataModel 2021-09-23 09:09:15 -04:00
Clair Blacketer 2103e95087 Update index.Rmd
Adding more detail on the model and vocabulary with links to athena and hades.
2021-09-23 09:09:10 -04:00
clairblacketer 3338dcfa7c
Update README.md 2021-09-22 16:08:01 -04:00
Clair Blacketer bb36513f6c Updated ReadMe with images 2021-09-22 16:07:07 -04:00
clairblacketer fd0703ae4c
Merge pull request #448 from OHDSI/v5.4
CDM V5.4
2021-09-22 15:56:34 -04:00
Clair Blacketer 8d7d0199af Regenerate DDLs for CDM 5.4 2021-09-22 15:50:21 -04:00
Clair Blacketer 46da3238af Documentation updates to support CDM v5.4 2021-09-22 15:39:44 -04:00
Clair Blacketer a87f9d149a Update .gitignore
added CodeToRun.R to gitignore
2021-09-09 15:45:55 -04:00
Clair Blacketer df96c30bf4 Merge branch 'v5.4' of https://github.com/OHDSI/CommonDataModel into v5.4 2021-09-09 15:39:21 -04:00
Clair Blacketer 2f7da6ab09 Delete .DS_Store 2021-09-09 15:39:11 -04:00
clairblacketer a611aec18a
Merge pull request #438 from OHDSI/vocabulary-doc-update
Update vocabulary.Rmd
2021-09-08 16:42:46 -04:00
clairblacketer 9779c07b72
Merge pull request #437 from OHDSI/v5.4_unittest
Add more unit tests
2021-08-31 13:48:45 -04:00
Maxim Moinat f13f657d7c update vocabulary doc html 2021-08-24 14:11:11 +02:00
Maxim Moinat 15bb11df2d
Update vocabulary.Rmd 2021-08-24 13:48:11 +02:00
Adam Black 3949b9e395 Merge branch 'v5.4_unittest' of github.com:OHDSI/CommonDataModel into v5.4_unittest 2021-08-20 14:19:44 -04:00
Adam Black 63e2979481
V5.4 (#435)
* 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

* Resolving conflicts

* Removing unnecessary file

* Trying again to remove .DS_Store, adding to gitignore

* Allow user to specify output location in buildRelease

* replace outputpath with outputfolder for consitent argument names in the package.

* Add test for buildRelease.

* replace outputpath with outputfolder for consistency. update documentation.

* move ddl folder to inst so it is accessible from tests

* update documentation

* Add OMOP header genearator function

Co-authored-by: Adam Black <adam.black@odysseusinc.com>
Co-authored-by: Clair Blacketer <mblacke@its.jnj.com>
Co-authored-by: clairblacketer <clairblacketer@users.noreply.github.com>
2021-08-20 13:30:34 -04:00
Adam Black d84141b5d8
add changes to v5.4 (#433)
* 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

* Resolving conflicts

* Removing unnecessary file

* Trying again to remove .DS_Store, adding to gitignore

* Allow user to specify output location in buildRelease

* replace outputpath with outputfolder for consitent argument names in the package.

* Add test for buildRelease.

* replace outputpath with outputfolder for consistency. update documentation.

* move ddl folder to inst so it is accessible from tests

* update documentation

* Add OMOP header genearator function

Co-authored-by: Adam Black <adam.black@odysseusinc.com>
Co-authored-by: Clair Blacketer <mblacke@its.jnj.com>
Co-authored-by: clairblacketer <clairblacketer@users.noreply.github.com>
2021-08-20 13:00:03 -04:00
Adam Black b7a651d5a1 Merge branch 'v5.4' of github.com:OHDSI/CommonDataModel into v5.4 2021-08-20 12:58:03 -04:00
Adam Black 17a0b8c8b5 Merge branch 'v5.4_unittest' of github.com:OHDSI/CommonDataModel into v5.4 2021-08-20 12:53:57 -04:00
Adam Black fabf605543 Add OMOP header genearator function 2021-08-20 12:52:08 -04:00
clairblacketer 5a27d02ead
Merge pull request #430 from OHDSI/v5.4_cb_updates
Hack-a-thon updates
2021-08-20 12:50:35 -04:00
Adam Black 40e26982d4
Add test for buildRelease (#432)
* 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

* Allow user to specify output location in buildRelease

* replace outputpath with outputfolder for consitent argument names in the package.

* Add test for buildRelease.

* replace outputpath with outputfolder for consistency. update documentation.

* move ddl folder to inst so it is accessible from tests

* update documentation

Co-authored-by: Adam Black <adam.black@odysseusinc.com>
Co-authored-by: Clair Blacketer <mblacke@its.jnj.com>
2021-08-20 12:32:46 -04:00
Adam Black 4e0f815228 Merge branch 'v5.4_unittest' of github.com:OHDSI/CommonDataModel into v5.4 2021-08-20 12:23:33 -04:00
Adam Black 13c6fc4cf3 update documentation 2021-08-20 12:10:41 -04:00
Adam Black d17a4c3e2e move ddl folder to inst so it is accessible from tests 2021-08-20 12:05:15 -04:00
Adam Black de1c577b6b replace outputpath with outputfolder for consistency. update documentation. 2021-08-20 11:25:10 -04:00
Adam Black b8425920ff Add test for buildRelease. 2021-08-20 11:06:47 -04:00
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