Commit Graph

551 Commits

Author SHA1 Message Date
Clair Blacketer 7821578b10 Updating symbols
This commit changes the symbols used in the support table so that they can be recognized without colors
2022-01-17 13:29:26 -05:00
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