Commit Graph

550 Commits

Author SHA1 Message Date
clairblacketer 805553cdb2
Merge pull request #462 from na399/master
Fix broken links: v5.4.0
2022-01-14 11:38:06 -05:00
clairblacketer 5de46c92b6
Merge pull request #473 from OHDSI/Jan2022_fixes
Jan2022 fixes
2022-01-14 10:59:52 -05:00
Clair Blacketer f006431a5e Bug fixes and updates from Nov 2021 - Jan 2022 2022-01-13 13:59:03 -05:00
Clair Blacketer 09fe23fd44 Fixes mismatches in data types (removes bigints)
closes #453
2022-01-13 12:34:30 -05:00
Clair Blacketer 4d77b93fe7 Makes sure ingredients pulled are standard concepts
closes #454
2022-01-13 12:28:44 -05:00
clairblacketer 80eebce2b6
Merge pull request #472 from OHDSI/master
Rebase Jan2022_fixes branch
2022-01-13 12:19:58 -05:00
clairblacketer 7e092bc44e
Merge pull request #460 from flying-burrito/era-dates
Update v5.3 / v5.4 docs for Era tables: use date type for *_date fields
2022-01-13 12:15:43 -05:00
Clair Blacketer 4aee003f5d Clean up readMe
closes #461
2022-01-13 12:11:00 -05:00
Clair Blacketer 247a1fe0c1 Adds version queries for the cdm and vocab
closes #463
2022-01-13 11:49:47 -05:00
Clair Blacketer 6b53641c83 Clarifies CARE_SITE_ID description
closes #468
2022-01-13 11:09:21 -05:00
Clair Blacketer c66a27e3db Add link to vocab wiki about type concepts
closes #470
2022-01-13 11:07:21 -05:00
Clair Blacketer ed3a4a49a3 Adds link directly to DDLs
Closes #471
2022-01-13 11:01:36 -05:00
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 125ac08c77 Add CDM R package demo to website 2021-11-19 09:22:53 -05:00
Max Natthawut Adulyanukosol c4b593c35f Fix broken links: v5.4.0 2021-11-18 11:49:33 +07:00
flying-burrito f5841f55e4 upd: v5.3 / v5.4 docs for Era tables, use date type for *_date fields 2021-11-17 16:51:11 +01:00
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