mz-health/OMOP
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OMOP
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59 Commits

Author SHA1 Message Date
Kyle Zollo-Venecek 7bb073b18a Implement note_nlp changes 2023-06-08 12:55:54 -04:00
Clair Blacketer 4432382693 Minor updates to package 
This release has some minor bugfixes and updates to the rmd files
 2023-02-08 15:04:22 -05:00
alex-odysseus eab766eab8 Merge remote-tracking branch 'remotes/origin/snowflake_support' into synapse 2022-09-23 16:40:49 +02:00
alex-odysseus b0685e98c7 Merge remote-tracking branch 'remotes/upstream/main' into snowflake 2022-09-23 16:32:59 +02:00
ssuvorov-fls 27e1924b1b added azure synapse support 2022-05-23 09:41:37 +03:00
ssuvorov-fls b4b8df34a5 added schema variable to ddl 2022-05-17 09:19:45 +03:00
Clair Blacketer 3b5f6819a5 Fixing an issue in PROCEDURE_OCCURRENCE documentation 2022-04-22 15:25:25 -04:00
ssuvorov-fls 0c13595972 restored some columns due to changes in omop cdm 2022-04-01 09:08:50 +03:00
ssuvorov-fls e1e010a3df added snowflake support 2022-03-30 10:53:52 +03:00
Clair Blacketer 477fb8a191 Fixes to CDM v5.4 constraints 
Removed an incorrect linkage of person.person_id as a foreign key to payer_plan_period.payer_plan_period_id
 2022-01-21 15:32:48 -05:00
Clair Blacketer 8fecffb215 Fix to CDM v5.3 Constraints 
Removed constraint linking person.person_id as a foreign key to payer_plan_period.payer_plan_period_id
 2022-01-21 15:30:53 -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
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 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 15f5fb1ed5 Update OMOP_CDMv5.4_Field_Level.csv 
Fixing PK issue in cohort and cohort definition
 2021-12-21 10:07:32 -05:00
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 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 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