CDM V5.4 #448
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CDM V5.4 #448
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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.
Addresses #386
Addresses #418
…e and vocabulary_version both have isRequired=No)
Updating local branch to reflect changes made by team.
Fixes Admitting_Source_xx to Admitted_From_xx in Visit_Detail and Visit_Occurrence Tables
issue 193 - Added value_source_value column to the Observation Table.
Refactor create and write SQL functions
…e isRequired=Yes vocabulary_version isRequired=No)
…ference and vocabulary_version both have isRequired=No)
Added CDM v5.4 menu item
* 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>
* 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>
Hack-a-thon updates
* 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>
* 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>
Add more unit tests
Update vocabulary.Rmd
added CodeToRun.R to gitignore
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