46e13a1a3c
update days supply convention to v5.3 and v6.0
2023-12-09 10:57:32 +01:00
4a764dcca1
Update days_supply description and convention
2023-10-06 21:19:43 +02:00
f39870c7d5
correct build of new files
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includes consistent case for table names
proper directory structure
2023-09-06 13:22:41 -04:00
a029324c48
updating for recent SqlRender supported dialects
2023-08-23 12:28:00 -04:00
4432382693
Minor updates to package
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This release has some minor bugfixes and updates to the rmd files
2023-02-08 15:04:22 -05:00
eab766eab8
Merge remote-tracking branch 'remotes/origin/snowflake_support' into synapse
2022-09-23 16:40:49 +02:00
b0685e98c7
Merge remote-tracking branch 'remotes/upstream/main' into snowflake
2022-09-23 16:32:59 +02:00
27e1924b1b
added azure synapse support
2022-05-23 09:41:37 +03:00
b4b8df34a5
added schema variable to ddl
2022-05-17 09:19:45 +03:00
3b5f6819a5
Fixing an issue in PROCEDURE_OCCURRENCE documentation
2022-04-22 15:25:25 -04:00
0c13595972
restored some columns due to changes in omop cdm
2022-04-01 09:08:50 +03:00
e1e010a3df
added snowflake support
2022-03-30 10:53:52 +03:00
477fb8a191
Fixes to CDM v5.4 constraints
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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
8fecffb215
Fix to CDM v5.3 Constraints
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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
f006431a5e
Bug fixes and updates from Nov 2021 - Jan 2022
2022-01-13 13:59:03 -05:00
09fe23fd44
Fixes mismatches in data types (removes bigints)
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closes #453
2022-01-13 12:34:30 -05:00
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
8d7d0199af
Regenerate DDLs for CDM 5.4
2021-09-22 15:50:21 -04:00
46da3238af
Documentation updates to support CDM v5.4
2021-09-22 15:39:44 -04:00
d17a4c3e2e
move ddl folder to inst so it is accessible from tests
2021-08-20 12:05:15 -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
be7ea44fba
various
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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
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
25ac31bee4
Merge pull request #421 from OHDSI/sql-creates-refactor
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Refactor create and write SQL functions
2021-08-18 13:55:26 -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
8d29222563
refactor index creation and cleanup codeToRun
2021-08-18 19:42:01 +02:00
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
Maxim Moinat
Frank DeFalco
Clair Blacketer
alex-odysseus
ssuvorov-fls
clairblacketer
flying-burrito
Adam Black
Alan Andryc
Andryc
Adam Black
Frank DeFalco
unknown
Maxim Moinat