80eebce2b6
Merge pull request #472 from OHDSI/master
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Rebase Jan2022_fixes branch
2022-01-13 12:19:58 -05:00
7e092bc44e
Merge pull request #460 from flying-burrito/era-dates
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Update v5.3 / v5.4 docs for Era tables: use date type for *_date fields
2022-01-13 12:15:43 -05:00
247a1fe0c1
Adds version queries for the cdm and vocab
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closes #463
2022-01-13 11:49:47 -05:00
6b53641c83
Clarifies CARE_SITE_ID description
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closes #468
2022-01-13 11:09:21 -05:00
c66a27e3db
Add link to vocab wiki about type concepts
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closes #470
2022-01-13 11:07:21 -05:00
15f5fb1ed5
Update OMOP_CDMv5.4_Field_Level.csv
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Fixing PK issue in cohort and cohort definition
2021-12-21 10:07:32 -05:00
f5841f55e4
upd: v5.3 / v5.4 docs for Era tables, use date type for *_date fields
2021-11-17 16:51:11 +01:00
9e4b5978c8
Bugfix to cdm v6.0
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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
4c8f054784
Fix to CDM v6.0 to add back cohort table
2021-09-23 10:52:05 -04:00
5927b49a53
Multiple fixes
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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
46da3238af
Documentation updates to support CDM v5.4
2021-09-22 15:39:44 -04:00
041291eb27
Foreign key fixes
2021-08-19 15:52:33 -04:00
c1a4422dd1
Changed bigint to integer for consistency
2021-08-19 14:54:44 -04:00
7067be34ac
Hack-a-thon updates
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Closes #81 , #387 , #239 , #412 , #391 , #330 , #408 , #365 , #306 , #264
2021-08-19 14:42:18 -04:00
d73a0f426d
Merge branch 'v5.4' into v5.4
2021-08-19 13:30:50 -04:00
7036b0e0f3
resolving merge issue on field level csv
2021-08-19 13:14:23 -04:00
c9463d0cf1
Adding EPISODE and EPISODE event tables
2021-08-19 12:58:41 -04:00
a2812b85e5
Added EPISODE and EPISODE_EVENT tables to table_level_5.4
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Also update the oncology extension documents to align with the table level file for v5.4
2021-08-19 12:45:44 -04:00
19462d322d
Add tests, github actions, and executeDdl function ( #425 )
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* 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
918b57bcca
Merge branch 'v5.4' into v5.4_cleanup
2021-08-18 16:06:08 -04:00
a4bfeccf83
function naming & additional cleanup
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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
ea0fc0f80b
Merge branch 'v5.4' into v5.4
2021-08-18 15:05:14 -04:00
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
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
b17ca8a856
Merge branch 'v5.4' into v5.4
2021-08-18 13:52:15 -04:00
efc286e738
Merge branch 'v5.4' into v5.4
2021-08-18 13:47:13 -04:00
3e17ee1715
Merge branch 'v5.4' of https://github.com/aandryc/CommonDataModel
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Updating local branch to reflect changes made by team.
2021-08-18 13:36:21 -04:00
73a62ce122
Merge branch 'OHDSI:v5.4' into v5.4
2021-08-18 13:36:01 -04:00
3dc0ad43ae
Merge pull request #420 from lizb101/v5.4
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V5.4
2021-08-18 13:27:59 -04:00
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
8dc0432f02
Update OMOP_CDMv5.4_Field_Level.csv
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Addresses #418
2021-08-18 10:40:04 -06:00
7bc145ca0c
Update OMOP_CDMv5.4_Field_Level.csv
2021-08-18 17:39:38 +01:00
0f4f17f937
Update OMOP_CDMv5.4_Field_Level.csv
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Issue #382
2021-08-18 17:22:52 +01:00
4f1a5af4ae
issue 193 - Added value_source_value column to the Observation Table.
2021-08-18 12:21:52 -04:00
2c3c42fb1c
update to metadata table - issue 202
2021-08-18 12:19:04 -04:00
26018caea2
Update OMOP_CDMv5.4_Field_Level.csv
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Addresses #386
2021-08-18 10:07:58 -06:00
0941a0783c
Issue #259 [measurement table] added unit_source_concept_id
2021-08-18 11:55:08 -04:00
41bda9c907
Issue 329 updated visit_detail_parent_id
2021-08-18 11:27:56 -04:00
b49077f9cd
Added v5.4 table level file
2021-08-18 11:18:20 -04:00
0f1d9333dd
Adding v5.4 field level file
2021-07-20 13:59:23 -04:00
f892dac55d
Moved R project from CdmDdlBase
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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
clairblacketer
Clair Blacketer
flying-burrito
Alan Andryc
Andryc
Adam Black
Frank DeFalco
unknown
Lisa Schilling
Elizabeth Betts
stephanieshong