Commit Graph

584 Commits

Author SHA1 Message Date
Clair Blacketer c768fa7e91 Fix to visit_detail change doc v5.4 discharge_to_source_value 2021-09-28 09:18:00 -04:00
Clair Blacketer 57cb8127cb Fix to discharged_to_source_value change doc 2021-09-28 09:04:23 -04:00
Clair Blacketer dd85c0d30b Adding titles to webpages 2021-09-24 21:02:39 -04:00
Clair Blacketer 02af0bc317 Reintroducing a v5.3.1 html page to alleviate confusion 2021-09-24 12:24:55 -04:00
Clair Blacketer 8dfc4835a7 Corresponding fixes to html for v5.3 and v6.0 2021-09-23 15:34:17 -04:00
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 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