mz-health/OMOP
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OMOP
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64 Commits

Author SHA1 Message Date
Clair Blacketer 8971ed2f66 Update gender_source_concept_id text 
closes #631
 2024-04-12 11:55:22 -04:00
Clair Blacketer 611e810dbe Update gender_source_value text 
closes #632
 2024-04-12 11:53:36 -04:00
Clair Blacketer c6fbdd6077 care site table description update 
closes #633
 2024-04-12 11:51:23 -04:00
Yaroslav Halchenko dceb3a182b [DATALAD RUNCMD] run codespell throughout fixing typos automagically 
=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
 2024-03-28 15:31:24 -04:00
Clair Blacketer 8b74e16ce0 closes #546 2024-03-28 15:28:11 -04:00
Clair Blacketer 8ed7a3908e closes #550 2024-03-28 15:25:28 -04:00
Clair Blacketer 22fe755ae0 Fixing typos 2024-03-28 14:37:46 -04:00
Clair Blacketer 4145f5bd97 closes #625 2024-03-28 13:41:01 -04:00
Clair Blacketer f1d1c3a23d closes #604 2024-03-28 13:39:03 -04:00
Clair Blacketer 47eced44c9 closes #617 2024-03-28 13:26:52 -04:00
Clair Blacketer 6333928fe0 Closes #587 2024-03-28 13:16:30 -04:00
Clair Blacketer 03ce1d5260 Closes OHDSI/Themis 77 2024-03-28 13:09:11 -04:00
Clair Blacketer 4e90a3529e closes #595 2024-03-28 12:54:26 -04:00
Clair Blacketer d9dfaff735 Merge branch 'main' of https://github.com/OHDSI/CommonDataModel 2024-03-28 12:44:12 -04:00
Clair Blacketer 7be2cd2a84 closes #599 2024-03-28 12:38:20 -04:00
Clair Blacketer 95fef98c90 Closes #603 2024-03-28 12:34:04 -04:00
Maxim Moinat 46e13a1a3c
update days supply convention to v5.3 and v6.0 2023-12-09 10:57:32 +01:00
Maxim Moinat 4a764dcca1
Update days_supply description and convention 2023-10-06 21:19:43 +02:00
Frank DeFalco f39870c7d5 correct build of new files 
includes consistent case for table names
proper directory structure
 2023-09-06 13:22:41 -04:00
Clair Blacketer 3b5f6819a5 Fixing an issue in PROCEDURE_OCCURRENCE documentation 2022-04-22 15:25:25 -04:00
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 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 46da3238af Documentation updates to support CDM v5.4 2021-09-22 15:39:44 -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
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
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
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