Commit Graph

37 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 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
Adam Black d17a4c3e2e move ddl folder to inst so it is accessible from tests 2021-08-20 12:05:15 -04:00
Clair Blacketer 041291eb27 Foreign key fixes 2021-08-19 15:52:33 -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
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
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
Frank DeFalco 918b57bcca Merge branch 'v5.4' into v5.4_cleanup 2021-08-18 16:06:08 -04:00
Frank DeFalco a4bfeccf83 function naming & additional cleanup
made create and write functions consistent
fixed render issue that was not including dialect name in generated files
added loop to codeToRun to generate all scripts.
2021-08-18 15:30:04 -04:00
clairblacketer ea0fc0f80b
Merge branch 'v5.4' into v5.4 2021-08-18 15:05:14 -04:00
unknown b4661f637d Issue #149 saved fix for nullables in vocabulary table (vocabulary_reference and vocabulary_version both have isRequired=No) 2021-08-18 14:37:43 -04:00
Frank DeFalco be7ea44fba various
fixed writePrimary use of fk function
removed old/unnecessary files - reviewed with CB
added listSupportedVersions function - explicitly not including 6.0
2021-08-18 14:24:45 -04:00
unknown 543893d406 Issue #149 fix for nullables in vocabulary table (vocabulary_reference isRequired=Yes vocabulary_version isRequired=No) 2021-08-18 14:23:54 -04:00
Frank DeFalco 25ac31bee4
Merge pull request #421 from OHDSI/sql-creates-refactor
Refactor create and write SQL functions
2021-08-18 13:55:26 -04:00
clairblacketer b17ca8a856
Merge branch 'v5.4' into v5.4 2021-08-18 13:52:15 -04:00
clairblacketer efc286e738
Merge branch 'v5.4' into v5.4 2021-08-18 13:47:13 -04:00
Maxim Moinat 8d29222563 refactor index creation and cleanup codeToRun 2021-08-18 19:42:01 +02:00
Andryc 3e17ee1715 Merge branch 'v5.4' of https://github.com/aandryc/CommonDataModel
Updating local branch to reflect changes made by team.
2021-08-18 13:36:21 -04:00
Alan Andryc 73a62ce122
Merge branch 'OHDSI:v5.4' into v5.4 2021-08-18 13:36:01 -04:00
clairblacketer 3dc0ad43ae
Merge pull request #420 from lizb101/v5.4
V5.4
2021-08-18 13:27:59 -04:00
unknown 826f6a923f Issue #149 fix for nullables in vocabulary table (vocabulary_reference and vocabulary_version both have isRequired=No) 2021-08-18 12:55:26 -04:00
Lisa Schilling 8dc0432f02
Update OMOP_CDMv5.4_Field_Level.csv
Addresses #418
2021-08-18 10:40:04 -06:00
Elizabeth Betts 7bc145ca0c Update OMOP_CDMv5.4_Field_Level.csv 2021-08-18 17:39:38 +01:00
Elizabeth Betts 0f4f17f937 Update OMOP_CDMv5.4_Field_Level.csv
Issue #382
2021-08-18 17:22:52 +01:00
stephanieshong 4f1a5af4ae issue 193 - Added value_source_value column to the Observation Table. 2021-08-18 12:21:52 -04:00
Andryc 2c3c42fb1c update to metadata table - issue 202 2021-08-18 12:19:04 -04:00
Lisa Schilling 26018caea2
Update OMOP_CDMv5.4_Field_Level.csv
Addresses #386
2021-08-18 10:07:58 -06:00
unknown 0941a0783c Issue #259 [measurement table] added unit_source_concept_id 2021-08-18 11:55:08 -04:00
Andryc 41bda9c907 Issue 329 updated visit_detail_parent_id 2021-08-18 11:27:56 -04:00
Clair Blacketer b49077f9cd Added v5.4 table level file 2021-08-18 11:18:20 -04:00
Clair Blacketer 0f1d9333dd Adding v5.4 field level file 2021-07-20 13:59:23 -04:00
Clair Blacketer f892dac55d Moved R project from CdmDdlBase
This commit pulls the R project over from the CdmDdlBase repository. This will be the jumping-off code for the new OMOP CDM repo.
2021-06-08 20:19:01 -04:00