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required column (modifier_concept_id) - seems strange #330

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vojtechhuser opened this issue Feb 10, 2020 · 4 comments
Closed

required column (modifier_concept_id) - seems strange #330

vojtechhuser opened this issue Feb 10, 2020 · 4 comments
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@clairblacketer

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@vojtechhuser
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vojtechhuser commented Feb 10, 2020 •
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  • in v6 - modifier_concept_id in procedure_occurrece is required (in wiki and in DDL SQL )

But there are many procedures where no modifier is used.

https://github.com/OHDSI/CommonDataModel/wiki/PROCEDURE_OCCURRENCE

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@clairblacketer
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@vojtechhuser almost all of the standard concepts were made required in v6 based on a THEMIS recommendation that standard concepts should not be null. Instead if a value does not exist then the representing concept_id should be set to 0.

@MaximMoinat
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MaximMoinat commented Dec 20, 2020 •
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Maybe a bit late to the discussion, but I agree with @vojtechhuser. A 0 ('No matching concep') means that the information from the source could not be mapped to a standard concept. For modifiers, as Vojtech points out, there might nog be a source value to map. The modifier is empty and also the modifier_source_value will be empty.

So the modifier (just like value_concept_id, operator_concept_id, etc. but also race_concept_id and ethnicity_concept_id) should not be mandatory. There might just not be a value in the source contaning that information.

@clairblacketer Is this still something that is possible to be changed in v6. If you think it is not worth the effort, that is okay too. Then I will conform :).

@cgreich
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cgreich commented Dec 20, 2020

@MaximMoinat:

I agree with you. However, we want to clean up the modifiers. Right now they are a hogepodge of things following the arbitrary US claims codes. Let us get this sorted out first. We may do away with the modifier_concept_id.

@clairblacketer
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clairblacketer commented Jan 6, 2021 •
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I want to bring this back up at a CDM meeting. CDM v6.1 gives us the opportunity to revisit the required concept choice. Currently this is on the calendar for Feb 2, 2020

@clairblacketer clairblacketer self-assigned this Aug 17, 2021
clairblacketer pushed a commit that referenced this issue Aug 19, 2021
Hack-a-thon updates
7067be3 
Closes #81, #387, #239, #412, #391, #330, #408, #365, #306, #264
@clairblacketer clairblacketer mentioned this issue Aug 19, 2021
Merged
ablack3 added a commit that referenced this issue Aug 20, 2021
@ablack3
Add unit tests for all databases and DDLs (#431)
532be98 
* 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

* Hack-a-thon updates

Closes #81, #387, #239, #412, #391, #330, #408, #365, #306, #264

* Changed bigint to integer for consistency

* Updated DDLs

* Add tests for redshift. Clean up test setup file.

* Foreign key fixes

* Add imports and update docs.

* Fix bug in setup test script.

* update setup file

* Add tests for oracle and sql server. Move setup.R file.

* fix bug in setup

* debug tests on github

* debug github actions

* debug actions.

* debug actions

* debug actions.

* Add missing secrets to yaml!!

* debug actions

* test connection on all platforms

* add ddl execution

* add windows and linux runners

Co-authored-by: Adam Black <adam.black@odysseusinc.com>
Co-authored-by: Clair Blacketer <mblacke@its.jnj.com>
ablack3 added a commit that referenced this issue Aug 20, 2021
@ablack3
Add test for buildRelease (#432)
40e2698 
* 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

* Hack-a-thon updates

Closes #81, #387, #239, #412, #391, #330, #408, #365, #306, #264

* Changed bigint to integer for consistency

* Updated DDLs

* Add tests for redshift. Clean up test setup file.

* Foreign key fixes

* Add imports and update docs.

* Fix bug in setup test script.

* update setup file

* Add tests for oracle and sql server. Move setup.R file.

* fix bug in setup

* debug tests on github

* debug github actions

* debug actions.

* debug actions

* debug actions.

* Add missing secrets to yaml!!

* debug actions

* test connection on all platforms

* add ddl execution

* add windows and linux runners

* Allow user to specify output location in buildRelease

* replace outputpath with outputfolder for consitent argument names in the package.

* Add test for buildRelease.

* replace outputpath with outputfolder for consistency. update documentation.

* move ddl folder to inst so it is accessible from tests

* update documentation

Co-authored-by: Adam Black <adam.black@odysseusinc.com>
Co-authored-by: Clair Blacketer <mblacke@its.jnj.com>
ablack3 added a commit that referenced this issue Aug 20, 2021
@ablack3 @clairblacketer
add changes to v5.4 (#433)
d84141b 
* 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

* Hack-a-thon updates

Closes #81, #387, #239, #412, #391, #330, #408, #365, #306, #264

* Changed bigint to integer for consistency

* Updated DDLs

* Add tests for redshift. Clean up test setup file.

* Foreign key fixes

* Add imports and update docs.

* Fix bug in setup test script.

* update setup file

* Add tests for oracle and sql server. Move setup.R file.

* fix bug in setup

* debug tests on github

* debug github actions

* debug actions.

* debug actions

* debug actions.

* Add missing secrets to yaml!!

* debug actions

* test connection on all platforms

* add ddl execution

* add windows and linux runners

* Resolving conflicts

* Removing unnecessary file

* Trying again to remove .DS_Store, adding to gitignore

* Allow user to specify output location in buildRelease

* replace outputpath with outputfolder for consitent argument names in the package.

* Add test for buildRelease.

* replace outputpath with outputfolder for consistency. update documentation.

* move ddl folder to inst so it is accessible from tests

* update documentation

* Add OMOP header genearator function

Co-authored-by: Adam Black <adam.black@odysseusinc.com>
Co-authored-by: Clair Blacketer <mblacke@its.jnj.com>
Co-authored-by: clairblacketer <clairblacketer@users.noreply.github.com>
ablack3 added a commit that referenced this issue Aug 20, 2021
@ablack3 @clairblacketer
V5.4 (#435)
63e2979 
* 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

* Hack-a-thon updates

Closes #81, #387, #239, #412, #391, #330, #408, #365, #306, #264

* Changed bigint to integer for consistency

* Updated DDLs

* Add tests for redshift. Clean up test setup file.

* Foreign key fixes

* Add imports and update docs.

* Fix bug in setup test script.

* update setup file

* Add tests for oracle and sql server. Move setup.R file.

* fix bug in setup

* debug tests on github

* debug github actions

* debug actions.

* debug actions

* debug actions.

* Add missing secrets to yaml!!

* debug actions

* test connection on all platforms

* add ddl execution

* add windows and linux runners

* Resolving conflicts

* Removing unnecessary file

* Trying again to remove .DS_Store, adding to gitignore

* Allow user to specify output location in buildRelease

* replace outputpath with outputfolder for consitent argument names in the package.

* Add test for buildRelease.

* replace outputpath with outputfolder for consistency. update documentation.

* move ddl folder to inst so it is accessible from tests

* update documentation

* Add OMOP header genearator function

Co-authored-by: Adam Black <adam.black@odysseusinc.com>
Co-authored-by: Clair Blacketer <mblacke@its.jnj.com>
Co-authored-by: clairblacketer <clairblacketer@users.noreply.github.com>
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@cgreich @vojtechhuser @clairblacketer @MaximMoinat