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Tag New Release of 0.5.0 (#76)
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* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Updated changelog for new release

* Beginning draft of submission

* Creating header affiliations

* Autogenerated or compiled files

* Ruby routine for generating header.tex

* Removed Memoization dependency for user flexibility

* Added dispatches to render SQL; found bug in GetPatientAgeGroup

* Added get function for ethnicity

* Cherry picking some files to resolve conflicts

* Initial Tests for Getters, Filters, and Executors (#24)

* Version 0.1.0 Release (#4)

* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Added todo action to automatically create todos

* Added todos for issues in getters

* Removed dependency on HealthSampleData and compat entries

* Added todosfor multiple tests that need to be created

* Uncommented test sets for running and added todo for Generators

* Created test for GetPatientVisits()

* Created Test for ExecuteAudit()

* Created test for GetMostRecentVisit

* updated tests

* started creating test for GetVisitCondition

* Changed GetVisitCondition Test

* created test for VisitFilterPersonIDs

* Added test for filters.jl

* Finished tests for filters

* Added a test step for code coverage

* Removed VSCode configurations

* Bumped compat entry for HealthSampleData

* Removed todos and fixed GenderFilterPersonIDs test

* Removed unnecessary comments

* For allowing HealthSampleData to always download sample data

* Test with adding latest codecoverage version

* Added code coverage badge icon

Co-authored-by: TheCedarPrince <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Simplify Age Calculations (#27)

* Added SQL generation for filter statements

* Removed option for internal DB calculation

* Fixed GetPatientAgeGroup and added GetDatabaseYearRange and updated docstrings

* Updated test suite

* Removed old tests for GetPatientAgeGroup

* Updated tests for helper functions

* Added Additional Test Coverage for Getters and Helpers (#28)

* Updated docstrings for SQL rendering

* Updated docstrings, formatting, and enforced String returns for SQL dispatches

* Updated test explanation

* Added test suite for GetMostRecentConditions and formatted

* Fix to Docs Deployment (#29)

* Testing fix for docs deployment

* Expected the OMOPCDMCohortCreator package to be available

* Added push preview information and the edit link

* Fixed deprecation warning

* Final layout fixes to collapselevel

* Final fix

* Update to Beginner Tutorial and Minor Refactor of Tutorials Layout (#30)

* Configured nesting of tutorial

* Updated landing page description

* Broke up tutorial pages

* Added revamped beginner tutorial

* Overhaul of Docs (#31)

* Moved beginner tutorial

* Added tutorial for R usage

* Updated index of tutorials

* Fixed up tutorials index

* Renamed R tutorial

* Clarified links for tutorials

* Julia on the brain

* Added contributing guide

* Added contributing guide

* Updated API exports

* Revamped overview of package

* Added the most necessary of all things: emojis :sparkles:

* Fixed up emojis

* Fixed up API table of contents

* Fixed emojis

* Updated main features of package

* Removed emoji

* Updated and fixed Citation file (#32)

* Expanded CI to test on Windows & OSX and Julia Versions 1, Nightly, and LTS (#35)

* Tag New Release v2.0.0 (#33)

* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Updated changelog for new release

* Beginning draft of submission

* Creating header affiliations

* Autogenerated or compiled files

* Ruby routine for generating header.tex

* Removed Memoization dependency for user flexibility

* Added dispatches to render SQL; found bug in GetPatientAgeGroup

* Added get function for ethnicity

* Cherry picking some files to resolve conflicts

* Initial Tests for Getters, Filters, and Executors (#24)

* Version 0.1.0 Release (#4)

* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Added todo action to automatically create todos

* Added todos for issues in getters

* Removed dependency on HealthSampleData and compat entries

* Added todosfor multiple tests that need to be created

* Uncommented test sets for running and added todo for Generators

* Created test for GetPatientVisits()

* Created Test for ExecuteAudit()

* Created test for GetMostRecentVisit

* updated tests

* started creating test for GetVisitCondition

* Changed GetVisitCondition Test

* created test for VisitFilterPersonIDs

* Added test for filters.jl

* Finished tests for filters

* Added a test step for code coverage

* Removed VSCode configurations

* Bumped compat entry for HealthSampleData

* Removed todos and fixed GenderFilterPersonIDs test

* Removed unnecessary comments

* For allowing HealthSampleData to always download sample data

* Test with adding latest codecoverage version

* Added code coverage badge icon

Co-authored-by: TheCedarPrince <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Simplify Age Calculations (#27)

* Added SQL generation for filter statements

* Removed option for internal DB calculation

* Fixed GetPatientAgeGroup and added GetDatabaseYearRange and updated docstrings

* Updated test suite

* Removed old tests for GetPatientAgeGroup

* Updated tests for helper functions

* Added Additional Test Coverage for Getters and Helpers (#28)

* Updated docstrings for SQL rendering

* Updated docstrings, formatting, and enforced String returns for SQL dispatches

* Updated test explanation

* Added test suite for GetMostRecentConditions and formatted

* Fix to Docs Deployment (#29)

* Testing fix for docs deployment

* Expected the OMOPCDMCohortCreator package to be available

* Added push preview information and the edit link

* Fixed deprecation warning

* Final layout fixes to collapselevel

* Final fix

* Update to Beginner Tutorial and Minor Refactor of Tutorials Layout (#30)

* Configured nesting of tutorial

* Updated landing page description

* Broke up tutorial pages

* Added revamped beginner tutorial

* Overhaul of Docs (#31)

* Moved beginner tutorial

* Added tutorial for R usage

* Updated index of tutorials

* Fixed up tutorials index

* Renamed R tutorial

* Clarified links for tutorials

* Julia on the brain

* Added contributing guide

* Added contributing guide

* Updated API exports

* Revamped overview of package

* Added the most necessary of all things: emojis :sparkles:

* Fixed up emojis

* Fixed up API table of contents

* Fixed emojis

* Updated main features of package

* Removed emoji

* Updated and fixed Citation file (#32)

* Tagged new release

* Revamped README details about package

* Added docstring to ExecuteAudit

Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Moved paper document to its own branch while in progress

* Quickfix to R tutorial on strep_patients

* Expanded CI to test on windows, OSX, and 1.6

* Attempt at making CI process more reasonable

* Removed paper directory again

* Bumped for minor patch release

Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Added function to get place of service information (#39)

Added GetVisitPlaceOfService getter

* Added GetVisitConcept getter function (#41)

* issue #44 add GetVisitDate (#45)

* added a function GetVisitDate and its tests. Also fixed test for GetVisitConcept

* Removed SQLite dep

* Added and updated docstrings

---------

Co-authored-by: Varshini Chinta <[email protected]>
Co-authored-by: TheCedarPrince <[email protected]>

* Adding the column name (#43)

* Tag Release of v0.2.1 (#37)

* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Updated changelog for new release

* Beginning draft of submission

* Creating header affiliations

* Autogenerated or compiled files

* Ruby routine for generating header.tex

* Removed Memoization dependency for user flexibility

* Added dispatches to render SQL; found bug in GetPatientAgeGroup

* Added get function for ethnicity

* Cherry picking some files to resolve conflicts

* Initial Tests for Getters, Filters, and Executors (#24)

* Version 0.1.0 Release (#4)

* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Added todo action to automatically create todos

* Added todos for issues in getters

* Removed dependency on HealthSampleData and compat entries

* Added todosfor multiple tests that need to be created

* Uncommented test sets for running and added todo for Generators

* Created test for GetPatientVisits()

* Created Test for ExecuteAudit()

* Created test for GetMostRecentVisit

* updated tests

* started creating test for GetVisitCondition

* Changed GetVisitCondition Test

* created test for VisitFilterPersonIDs

* Added test for filters.jl

* Finished tests for filters

* Added a test step for code coverage

* Removed VSCode configurations

* Bumped compat entry for HealthSampleData

* Removed todos and fixed GenderFilterPersonIDs test

* Removed unnecessary comments

* For allowing HealthSampleData to always download sample data

* Test with adding latest codecoverage version

* Added code coverage badge icon

Co-authored-by: TheCedarPrince <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Simplify Age Calculations (#27)

* Added SQL generation for filter statements

* Removed option for internal DB calculation

* Fixed GetPatientAgeGroup and added GetDatabaseYearRange and updated docstrings

* Updated test suite

* Removed old tests for GetPatientAgeGroup

* Updated tests for helper functions

* Added Additional Test Coverage for Getters and Helpers (#28)

* Updated docstrings for SQL rendering

* Updated docstrings, formatting, and enforced String returns for SQL dispatches

* Updated test explanation

* Added test suite for GetMostRecentConditions and formatted

* Fix to Docs Deployment (#29)

* Testing fix for docs deployment

* Expected the OMOPCDMCohortCreator package to be available

* Added push preview information and the edit link

* Fixed deprecation warning

* Final layout fixes to collapselevel

* Final fix

* Update to Beginner Tutorial and Minor Refactor of Tutorials Layout (#30)

* Configured nesting of tutorial

* Updated landing page description

* Broke up tutorial pages

* Added revamped beginner tutorial

* Overhaul of Docs (#31)

* Moved beginner tutorial

* Added tutorial for R usage

* Updated index of tutorials

* Fixed up tutorials index

* Renamed R tutorial

* Clarified links for tutorials

* Julia on the brain

* Added contributing guide

* Added contributing guide

* Updated API exports

* Revamped overview of package

* Added the most necessary of all things: emojis :sparkles:

* Fixed up emojis

* Fixed up API table of contents

* Fixed emojis

* Updated main features of package

* Removed emoji

* Updated and fixed Citation file (#32)

* Expanded CI to test on Windows & OSX and Julia Versions 1, Nightly, and LTS (#35)

* Tag New Release v2.0.0 (#33)

* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Updated changelog for new release

* Beginning draft of submission

* Creating header affiliations

* Autogenerated or compiled files

* Ruby routine for generating header.tex

* Removed Memoization dependency for user flexibility

* Added dispatches to render SQL; found bug in GetPatientAgeGroup

* Added get function for ethnicity

* Cherry picking some files to resolve conflicts

* Initial Tests for Getters, Filters, and Executors (#24)

* Version 0.1.0 Release (#4)

* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Added todo action to automatically create todos

* Added todos for issues in getters

* Removed dependency on HealthSampleData and compat entries

* Added todosfor multiple tests that need to be created

* Uncommented test sets for running and added todo for Generators

* Created test for GetPatientVisits()

* Created Test for ExecuteAudit()

* Created test for GetMostRecentVisit

* updated tests

* started creating test for GetVisitCondition

* Changed GetVisitCondition Test

* created test for VisitFilterPersonIDs

* Added test for filters.jl

* Finished tests for filters

* Added a test step for code coverage

* Removed VSCode configurations

* Bumped compat entry for HealthSampleData

* Removed todos and fixed GenderFilterPersonIDs test

* Removed unnecessary comments

* For allowing HealthSampleData to always download sample data

* Test with adding latest codecoverage version

* Added code coverage badge icon

Co-authored-by: TheCedarPrince <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Simplify Age Calculations (#27)

* Added SQL generation for filter statements

* Removed option for internal DB calculation

* Fixed GetPatientAgeGroup and added GetDatabaseYearRange and updated docstrings

* Updated test suite

* Removed old tests for GetPatientAgeGroup

* Updated tests for helper functions

* Added Additional Test Coverage for Getters and Helpers (#28)

* Updated docstrings for SQL rendering

* Updated docstrings, formatting, and enforced String returns for SQL dispatches

* Updated test explanation

* Added test suite for GetMostRecentConditions and formatted

* Fix to Docs Deployment (#29)

* Testing fix for docs deployment

* Expected the OMOPCDMCohortCreator package to be available

* Added push preview information and the edit link

* Fixed deprecation warning

* Final layout fixes to collapselevel

* Final fix

* Update to Beginner Tutorial and Minor Refactor of Tutorials Layout (#30)

* Configured nesting of tutorial

* Updated landing page description

* Broke up tutorial pages

* Added revamped beginner tutorial

* Overhaul of Docs (#31)

* Moved beginner tutorial

* Added tutorial for R usage

* Updated index of tutorials

* Fixed up tutorials index

* Renamed R tutorial

* Clarified links for tutorials

* Julia on the brain

* Added contributing guide

* Added contributing guide

* Updated API exports

* Revamped overview of package

* Added the most necessary of all things: emojis :sparkles:

* Fixed up emojis

* Fixed up API table of contents

* Fixed emojis

* Updated main features of package

* Removed emoji

* Updated and fixed Citation file (#32)

* Tagged new release

* Revamped README details about package

* Added docstring to ExecuteAudit

Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Moved paper document to its own branch while in progress

* Quickfix to R tutorial on strep_patients

* Expanded CI to test on windows, OSX, and 1.6

* Attempt at making CI process more reasonable

* Removed paper directory again

* Bumped for minor patch release

Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>

Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Adding the column name

---------

Co-authored-by: Jacob S. Zelko <[email protected]>
Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Bumped compat and release version

* Updated CHANGELOG for new release

* Bumped release version

* Added GetVisitProcedure associated with someones visit (#59)

* Tag Release of v0.2.2 (#46)

* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Updated changelog for new release

* Beginning draft of submission

* Creating header affiliations

* Autogenerated or compiled files

* Ruby routine for generating header.tex

* Removed Memoization dependency for user flexibility

* Added dispatches to render SQL; found bug in GetPatientAgeGroup

* Added get function for ethnicity

* Cherry picking some files to resolve conflicts

* Initial Tests for Getters, Filters, and Executors (#24)

* Version 0.1.0 Release (#4)

* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Added todo action to automatically create todos

* Added todos for issues in getters

* Removed dependency on HealthSampleData and compat entries

* Added todosfor multiple tests that need to be created

* Uncommented test sets for running and added todo for Generators

* Created test for GetPatientVisits()

* Created Test for ExecuteAudit()

* Created test for GetMostRecentVisit

* updated tests

* started creating test for GetVisitCondition

* Changed GetVisitCondition Test

* created test for VisitFilterPersonIDs

* Added test for filters.jl

* Finished tests for filters

* Added a test step for code coverage

* Removed VSCode configurations

* Bumped compat entry for HealthSampleData

* Removed todos and fixed GenderFilterPersonIDs test

* Removed unnecessary comments

* For allowing HealthSampleData to always download sample data

* Test with adding latest codecoverage version

* Added code coverage badge icon

Co-authored-by: TheCedarPrince <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Simplify Age Calculations (#27)

* Added SQL generation for filter statements

* Removed option for internal DB calculation

* Fixed GetPatientAgeGroup and added GetDatabaseYearRange and updated docstrings

* Updated test suite

* Removed old tests for GetPatientAgeGroup

* Updated tests for helper functions

* Added Additional Test Coverage for Getters and Helpers (#28)

* Updated docstrings for SQL rendering

* Updated docstrings, formatting, and enforced String returns for SQL dispatches

* Updated test explanation

* Added test suite for GetMostRecentConditions and formatted

* Fix to Docs Deployment (#29)

* Testing fix for docs deployment

* Expected the OMOPCDMCohortCreator package to be available

* Added push preview information and the edit link

* Fixed deprecation warning

* Final layout fixes to collapselevel

* Final fix

* Update to Beginner Tutorial and Minor Refactor of Tutorials Layout (#30)

* Configured nesting of tutorial

* Updated landing page description

* Broke up tutorial pages

* Added revamped beginner tutorial

* Overhaul of Docs (#31)

* Moved beginner tutorial

* Added tutorial for R usage

* Updated index of tutorials

* Fixed up tutorials index

* Renamed R tutorial

* Clarified links for tutorials

* Julia on the brain

* Added contributing guide

* Added contributing guide

* Updated API exports

* Revamped overview of package

* Added the most necessary of all things: emojis :sparkles:

* Fixed up emojis

* Fixed up API table of contents

* Fixed emojis

* Updated main features of package

* Removed emoji

* Updated and fixed Citation file (#32)

* Expanded CI to test on Windows & OSX and Julia Versions 1, Nightly, and LTS (#35)

* Tag New Release v2.0.0 (#33)

* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Updated changelog for new release

* Beginning draft of submission

* Creating header affiliations

* Autogenerated or compiled files

* Ruby routine for generating header.tex

* Removed Memoization dependency for user flexibility

* Added dispatches to render SQL; found bug in GetPatientAgeGroup

* Added get function for ethnicity

* Cherry picking some files to resolve conflicts

* Initial Tests for Getters, Filters, and Executors (#24)

* Version 0.1.0 Release (#4)

* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Added todo action to automatically create todos

* Added todos for issues in getters

* Removed dependency on HealthSampleData and compat entries

* Added todosfor multiple tests that need to be created

* Uncommented test sets for running and added todo for Generators

* Created test for GetPatientVisits()

* Created Test for ExecuteAudit()

* Created test for GetMostRecentVisit

* updated tests

* started creating test for GetVisitCondition

* Changed GetVisitCondition Test

* created test for VisitFilterPersonIDs

* Added test for filters.jl

* Finished tests for filters

* Added a test step for code coverage

* Removed VSCode configurations

* Bumped compat entry for HealthSampleData

* Removed todos and fixed GenderFilterPersonIDs test

* Removed unnecessary comments

* For allowing HealthSampleData to always download sample data

* Test with adding latest codecoverage version

* Added code coverage badge icon

Co-authored-by: TheCedarPrince <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Simplify Age Calculations (#27)

* Added SQL generation for filter statements

* Removed option for internal DB calculation

* Fixed GetPatientAgeGroup and added GetDatabaseYearRange and updated docstrings

* Updated test suite

* Removed old tests for GetPatientAgeGroup

* Updated tests for helper functions

* Added Additional Test Coverage for Getters and Helpers (#28)

* Updated docstrings for SQL rendering

* Updated docstrings, formatting, and enforced String returns for SQL dispatches

* Updated test explanation

* Added test suite for GetMostRecentConditions and formatted

* Fix to Docs Deployment (#29)

* Testing fix for docs deployment

* Expected the OMOPCDMCohortCreator package to be available

* Added push preview information and the edit link

* Fixed deprecation warning

* Final layout fixes to collapselevel

* Final fix

* Update to Beginner Tutorial and Minor Refactor of Tutorials Layout (#30)

* Configured nesting of tutorial

* Updated landing page description

* Broke up tutorial pages

* Added revamped beginner tutorial

* Overhaul of Docs (#31)

* Moved beginner tutorial

* Added tutorial for R usage

* Updated index of tutorials

* Fixed up tutorials index

* Renamed R tutorial

* Clarified links for tutorials

* Julia on the brain

* Added contributing guide

* Added contributing guide

* Updated API exports

* Revamped overview of package

* Added the most necessary of all things: emojis :sparkles:

* Fixed up emojis

* Fixed up API table of contents

* Fixed emojis

* Updated main features of package

* Removed emoji

* Updated and fixed Citation file (#32)

* Tagged new release

* Revamped README details about package

* Added docstring to ExecuteAudit

Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Moved paper document to its own branch while in progress

* Quickfix to R tutorial on strep_patients

* Expanded CI to test on windows, OSX, and 1.6

* Attempt at making CI process more reasonable

* Removed paper directory again

* Bumped for minor patch release

Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Added function to get place of service information (#39)

Added GetVisitPlaceOfService getter

* Added GetVisitConcept getter function (#41)

* issue #44 add GetVisitDate (#45)

* added a function GetVisitDate and its tests. Also fixed test for GetVisitConcept

* Removed SQLite dep

* Added and updated docstrings

---------

Co-authored-by: Varshini Chinta <[email protected]>
Co-authored-by: TheCedarPrince <[email protected]>

* Adding the column name (#43)

* Tag Release of v0.2.1 (#37)

* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Updated changelog for new release

* Beginning draft of submission

* Creating header affiliations

* Autogenerated or compiled files

* Ruby routine for generating header.tex

* Removed Memoization dependency for user flexibility

* Added dispatches to render SQL; found bug in GetPatientAgeGroup

* Added get function for ethnicity

* Cherry picking some files to resolve conflicts

* Initial Tests for Getters, Filters, and Executors (#24)

* Version 0.1.0 Release (#4)

* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Added todo action to automatically create todos

* Added todos for issues in getters

* Removed dependency on HealthSampleData and compat entries

* Added todosfor multiple tests that need to be created

* Uncommented test sets for running and added todo for Generators

* Created test for GetPatientVisits()

* Created Test for ExecuteAudit()

* Created test for GetMostRecentVisit

* updated tests

* started creating test for GetVisitCondition

* Changed GetVisitCondition Test

* created test for VisitFilterPersonIDs

* Added test for filters.jl

* Finished tests for filters

* Added a test step for code coverage

* Removed VSCode configurations

* Bumped compat entry for HealthSampleData

* Removed todos and fixed GenderFilterPersonIDs test

* Removed unnecessary comments

* For allowing HealthSampleData to always download sample data

* Test with adding latest codecoverage version

* Added code coverage badge icon

Co-authored-by: TheCedarPrince <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Simplify Age Calculations (#27)

* Added SQL generation for filter statements

* Removed option for internal DB calculation

* Fixed GetPatientAgeGroup and added GetDatabaseYearRange and updated docstrings

* Updated test suite

* Removed old tests for GetPatientAgeGroup

* Updated tests for helper functions

* Added Additional Test Coverage for Getters and Helpers (#28)

* Updated docstrings for SQL rendering

* Updated docstrings, formatting, and enforced String returns for SQL dispatches

* Updated test explanation

* Added test suite for GetMostRecentConditions and formatted

* Fix to Docs Deployment (#29)

* Testing fix for docs deployment

* Expected the OMOPCDMCohortCreator package to be available

* Added push preview information and the edit link

* Fixed deprecation warning

* Final layout fixes to collapselevel

* Final fix

* Update to Beginner Tutorial and Minor Refactor of Tutorials Layout (#30)

* Configured nesting of tutorial

* Updated landing page description

* Broke up tutorial pages

* Added revamped beginner tutorial

* Overhaul of Docs (#31)

* Moved beginner tutorial

* Added tutorial for R usage

* Updated index of tutorials

* Fixed up tutorials index

* Renamed R tutorial

* Clarified links for tutorials

* Julia on the brain

* Added contributing guide

* Added contributing guide

* Updated API exports

* Revamped overview of package

* Added the most necessary of all things: emojis :sparkles:

* Fixed up emojis

* Fixed up API table of contents

* Fixed emojis

* Updated main features of package

* Removed emoji

* Updated and fixed Citation file (#32)

* Expanded CI to test on Windows & OSX and Julia Versions 1, Nightly, and LTS (#35)

* Tag New Release v2.0.0 (#33)

* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Updated changelog for new release

* Beginning draft of submission

* Creating header affiliations

* Autogenerated or compiled files

* Ruby routine for generating header.tex

* Removed Memoization dependency for user flexibility

* Added dispatches to render SQL; found bug in GetPatientAgeGroup

* Added get function for ethnicity

* Cherry picking some files to resolve conflicts

* Initial Tests for Getters, Filters, and Executors (#24)

* Version 0.1.0 Release (#4)

* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

* Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this

* Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits

* Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

* Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Added todo action to automatically create todos

* Added todos for issues in getters

* Removed dependency on HealthSampleData and compat entries

* Added todosfor multiple tests that need to be created

* Uncommented test sets for running and added todo for Generators

* Created test for GetPatientVisits()

* Created Test for ExecuteAudit()

* Created test for GetMostRecentVisit

* updated tests

* started creating test for GetVisitCondition

* Changed GetVisitCondition Test

* created test for VisitFilterPersonIDs

* Added test for filters.jl

* Finished tests for filters

* Added a test step for code coverage

* Removed VSCode configurations

* Bumped compat entry for HealthSampleData

* Removed todos and fixed GenderFilterPersonIDs test

* Removed unnecessary comments

* For allowing HealthSampleData to always download sample data

* Test with adding latest codecoverage version

* Added code coverage badge icon

Co-authored-by: TheCedarPrince <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Simplify Age Calculations (#27)

* Added SQL generation for filter statements

* Removed option for internal DB calculation

* Fixed GetPatientAgeGroup and added GetDatabaseYearRange and updated docstrings

* Updated test suite

* Removed old tests for GetPatientAgeGroup

* Updated tests for helper functions

* Added Additional Test Coverage for Getters and Helpers (#28)

* Updated docstrings for SQL rendering

* Updated docstrings, formatting, and enforced String returns for SQL dispatches

* Updated test explanation

* Added test suite for GetMostRecentConditions and formatted

* Fix to Docs Deployment (#29)

* Testing fix for docs deployment

* Expected the OMOPCDMCohortCreator package to be available

* Added push preview information and the edit link

* Fixed deprecation warning

* Final layout fixes to collapselevel

* Final fix

* Update to Beginner Tutorial and Minor Refactor of Tutorials Layout (#30)

* Configured nesting of tutorial

* Updated landing page description

* Broke up tutorial pages

* Added revamped beginner tutorial

* Overhaul of Docs (#31)

* Moved beginner tutorial

* Added tutorial for R usage

* Updated index of tutorials

* Fixed up tutorials index

* Renamed R tutorial

* Clarified links for tutorials

* Julia on the brain

* Added contributing guide

* Added contributing guide

* Updated API exports

* Revamped overview of package

* Added the most necessary of all things: emojis :sparkles:

* Fixed up emojis

* Fixed up API table of contents

* Fixed emojis

* Updated main features of package

* Removed emoji

* Updated and fixed Citation file (#32)

* Tagged new release

* Revamped README details about package

* Added docstring to ExecuteAudit

Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Moved paper document to its own branch while in progress

* Quickfix to R tutorial on strep_patients

* Expanded CI to test on windows, OSX, and 1.6

* Attempt at making CI process more reasonable

* Removed paper directory again

* Bumped for minor patch release

Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>

Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Adding the column name

---------

Co-authored-by: Jacob S. Zelko <[email protected]>
Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>

* Bumped compat and release version

* Updated CHANGELOG for new release

* Bumped release version

---------

Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>
Co-authored-by: Farreeda <[email protected]>

* fixing issues (#54)

* fixing issues

* removing useless packages

* change variable name to df

* Adding documenting comments to explain multiple dispatch

* docs and tests

Tests need some check for GetAmounts

* issue #55

* Re-enabled pull request workflows

* fixing test errors and tutorial changes

* increasing code coverage

* maybe it needs space before @testset

---------

Co-authored-by: Farreeda <[email protected]>
Co-authored-by: TheCedarPrince <[email protected]>

* Tagging for 0.3.0 release

* added Getter

* add to api.md

* added test cases

* moved to getters

* reverts

* test cases updated

* Adding a few more tests and satisfying CodeCov

* resolved

* resolved

* added some final test cases

* corrected the test cases

---------

Co-authored-by: Jacob S. Zelko <[email protected]>
Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>
Co-authored-by: Farreeda <[email protected]>
Co-authored-by: Farreeda <[email protected]>

* Resolving `ExecuteAudit` function getting Breaked Easily  (#60)

* updated executaors.jl

* fixed doc

* added the test cases

* renamed to GetDrugExposureIDs (#63)

* renamed to GetDrugExposureIDs

* Updated changelog for new changes

* Updated docstring for Drug Exposures

---------

Co-authored-by: TheCedarPrince <[email protected]>

* Creating Queries That Return Cohort Information (#61)

* added GetCohortSubjects

* updated runtests.jl

* Added additional test dependencies

* Fixed up imports and generating initial cohort

* Added test cohort definition asset

* added tests for GetCohortSubjects

* corrected

* added GetCohortSubjectStartDate

* test suite for GetCohortSubjectStartDate

* added a dispatch for GetDatabaseCohorts

* added GetCohortSubjectEndDate

* Added notes and fixed a docstring error

* requested changes made

* added requested changes

* added requested changes

* Small fix to return unique IDs and doc updates

* Fixed export signature

---------

Co-authored-by: TheCedarPrince <[email protected]>

* Added GetDrugExposureEndDate function (#71)

* added GetDrugExposureEndDate

* added

* api.md

* Added GetDrugExposureStartDate function (#72)

* GetDrugExposureStartDate added

* Itty bitty typo fix

* similar typo fixed

---------

Co-authored-by: Jacob S. Zelko <[email protected]>

* Added a…
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19 changes: 19 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,25 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/)
and this project adheres to [Semantic Versioning](http://semver.org/).


## [0.5.0] - February 23rd, 2024

Patch release to add in some new features and fixes

### Added

- Added Getters for Drug Exposures

* GetDrugExposureStartDate

* GetDrugExposureEndDate

- Misc

* Minor fixes in GetPatientAgeGroup Function

- Extensive test suite for new features


## [0.4.0] - December 1st, 2023

Patch release to add in some new features and fixes
Expand Down
6 changes: 3 additions & 3 deletions CITATION.cff
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ authors:
given-names: Fareeda
- family-names: Sanjay
given-names: Jay
title: "OMOPCDMCohortCreator 0.4.0"
version: 0.4.0
title: "OMOPCDMCohortCreator 0.5.0"
version: 0.5.0
doi: 10.5281/zenodo.7052105
date-released: 2023-12-01
date-released: 2024-02-23
2 changes: 1 addition & 1 deletion Project.toml
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "OMOPCDMCohortCreator"
uuid = "f525a15e-a73f-4eef-870f-f901257eae22"
authors = ["Jacob Zelko <[email protected]>", "Fareeda Abdelazeez", "Varshini Chinta", "Jay Sanjay <[email protected]>"]
version = "0.4.0"
version = "0.5.0"

[deps]
DBInterface = "a10d1c49-ce27-4219-8d33-6db1a4562965"
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2 changes: 2 additions & 0 deletions docs/src/api.md
Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,8 @@ GetCohortSubjects
GetCohortSubjectStartDate
GetCohortSubjectEndDate
GetVisitProcedure
GetDrugExposureEndDate
GetDrugExposureStartDate
```

## Filters
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198 changes: 189 additions & 9 deletions src/getters.jl
Original file line number Diff line number Diff line change
Expand Up @@ -432,6 +432,7 @@ GetPatientAgeGroup(
[80, 89],
],
tab = person,
ungrouped_label = "Unspecified"
)
Finds all individuals in age groups as specified by `age_groupings`.
Expand All @@ -451,6 +452,8 @@ Finds all individuals in age groups as specified by `age_groupings`.
- any year provided by a user as long as it is an `Integer` (such as 2022, 1998, etc.)
- `tab` - the `SQLTable` representing the Person table; default `person`
- `ungrouped_label` - the label to assign persons who do not fit to a provided matching age group; default label "Unspecified"
# Returns
Expand Down Expand Up @@ -483,10 +486,11 @@ function GetPatientAgeGroup(
[70, 79],
[80, 89],
],
tab=person
tab=person,
ungrouped_label = "Unspecified"
)

df = DBInterface.execute(conn, GetPatientAgeGroup(ids; minuend=minuend, age_groupings=age_groupings, tab=tab)) |> DataFrame
df = DBInterface.execute(conn, GetPatientAgeGroup(ids; minuend=minuend, age_groupings=age_groupings, tab=tab, ungrouped_label=ungrouped_label)) |> DataFrame

return df

Expand All @@ -504,7 +508,9 @@ age_groupings=[
[60, 69],
[70, 79],
[80, 89],
], tab = person)
],
tab = person,
ungrouped_label = "Unspecified")
Given a `DataFrame` with a `:person_id` column, return the `DataFrame` with an associated `:ageGroup` for each person in the `DataFrame`
Expand All @@ -515,13 +521,13 @@ function GetPatientAgeGroup(
df::DataFrame,
conn;
minuend=:now,
tab=person
tab=person,
ungrouped_label = "Unspecified"
)

df_ids= df[:,"person_id"]


return outerjoin(GetPatientAgeGroup(df_ids, conn; minuend=minuend, tab=tab), df, on = :person_id)
return outerjoin(GetPatientAgeGroup(df_ids, conn; minuend=minuend, tab=tab, ungrouped_label=ungrouped_label), df, on = :person_id)
end

"""
Expand All @@ -540,6 +546,7 @@ GetPatientAgeGroup(
[80, 89],
],
tab = person,
ungrouped_label = "Unspecified"
)
Return SQL statement that assigns an age group to each patient in a given patient list.
Expand All @@ -559,6 +566,8 @@ Customized age groupings can be provided as a list.
- `tab` - the `SQLTable` representing the Person table; default `person`
- `ungrouped_label` - the label to assign persons who do not fit to a provided matching age group; default label "Unspecified"
# Returns
- `df::DataFrame` - a two column `DataFrame` comprised of columns: `:person_id` and `:age_group`
Expand Down Expand Up @@ -589,7 +598,8 @@ function GetPatientAgeGroup(
[70, 79],
[80, 89],
],
tab=person
tab=person,
ungrouped_label = "Unspecified"
)

minuend = _determine_calculated_year(minuend)
Expand All @@ -603,7 +613,7 @@ function GetPatientAgeGroup(
sql = From(tab) |>
Where(Fun.in(Get.person_id, ids...)) |>
Select(Get.person_id, :age => minuend .- Get.year_of_birth) |>
Define(:age_group => Fun.case(age_arr...)) |>
Define(:age_group => Fun.case(age_arr..., ungrouped_label)) |>
Select(Get.person_id, Get.age_group) |>
q -> render(q, dialect=dialect)

Expand Down Expand Up @@ -1885,4 +1895,174 @@ function GetDatabaseCohorts(

end

export GetDatabasePersonIDs, GetPatientState, GetPatientGender, GetPatientRace, GetPatientAgeGroup, GetPatientVisits, GetMostRecentConditions, GetMostRecentVisit, GetVisitCondition, GetPatientEthnicity, GetDatabaseYearRange, GetVisitPlaceOfService, GetVisitConcept, GetVisitDate, GetDrugExposures, GetDrugConceptIDs, GetDrugAmounts, GetVisitProcedure, GetDatabaseCohorts, GetCohortSubjects, GetCohortSubjectStartDate, GetCohortSubjectEndDate, GetDrugExposureIDs
"""
function GetDrugExposureEndDate(drug_exposure_ids, conn; tab = drug_exposure)
Given a list of drug_exposure IDs, find their exposure end dates.
# Arguments:
- `drug_exposure_ids` - list of `drug_exposure_id`'s; each ID must be of subtype `Float64`
- `conn` - database connection using DBInterface
# Keyword Arguments:
- `tab` - the `SQLTable` representing the Drug Exposure table; default `drug_exposure`
# Returns
- `df::DataFrame` - a two column `DataFrame` comprised of columns: `:drug_exposure_id` and `:drug_exposure_end_date`
"""

function GetDrugExposureEndDate(
drug_exposure_ids,
conn;
tab = drug_exposure
)

df = DBInterface.execute(conn, GetDrugExposureEndDate(drug_exposure_ids; tab=tab)) |> DataFrame

return df
end

"""
function GetDrugExposureEndDate(df:DataFrame, conn; tab = drug_exposure)
Given a DataFrame with a :drug_exposure_id column, return the DataFrame with an associated :drug_exposure_end_date corresponding to a given drug_exposure_id in the DataFrame.
Multiple dispatch that accepts all other arguments like in ` GetDrugExposureEndDate(ids, conn; tab = drug_exposure)`
"""

function GetDrugExposureEndDate(
df::DataFrame,
conn;
tab = drug_exposure
)

df_ids = df[:,"drug_exposure_id"]

return outerjoin(GetDrugExposureEndDate(df_ids, conn; tab=tab), df, on = :drug_exposure_id)

end

"""
function GetDrugExposureEndDate(drug_exposure_ids; tab = drug_exposure)
Given a list of drug_exposure IDs, find their corresponding drug_exposure_end_date ID.
# Arguments:
- `drug_exposure_ids` - list of `drug_exposure_id`'s; each ID must be of subtype `Float64`
# Keyword Arguments:
- `tab` - the `SQLTable` representing the Drug Exposure table; default `drug_exposure`
# Returns
- SQL statement comprised of: `:drug_exposure_id` and `:drug_exposure_end_date`
"""
function GetDrugExposureEndDate(
drug_exposure_ids;
tab = drug_exposure
)

sql =
From(tab) |>
Where(Fun.in(Get.drug_exposure_id, drug_exposure_ids...)) |>
Select(Get.drug_exposure_id, Get.drug_exposure_end_date) |>
q -> render(q, dialect=dialect)

return String(sql)

end

"""
function GetDrugExposureStartDate(drug_exposure_ids, conn; tab = drug_exposure)
Given a list of drug_exposure IDs, find their exposure start dates.
# Arguments:
- `drug_exposure_ids` - list of `drug_exposure_id`'s; each ID must be of subtype `Float64`
- `conn` - database connection using DBInterface
# Keyword Arguments:
- `tab` - the `SQLTable` representing the Drug Exposure table; default `drug_exposure`
# Returns
- `df::DataFrame` - a two column `DataFrame` comprised of columns: `:drug_exposure_id` and `:drug_exposure_start_date`
"""

function GetDrugExposureStartDate(
drug_exposure_ids,
conn;
tab = drug_exposure
)

df = DBInterface.execute(conn, GetDrugExposureStartDate(drug_exposure_ids; tab=tab)) |> DataFrame

return df
end

"""
function GetDrugExposureStartDate(df:DataFrame, conn; tab = drug_exposure)
Given a DataFrame with a :drug_exposure_id column, return the DataFrame with an associated :drug_exposure_start_date corresponding to a given drug_exposure_id in the DataFrame.
Multiple dispatch that accepts all other arguments like in ` GetDrugExposureStartDate(ids, conn; tab = drug_exposure)`
"""
function GetDrugExposureStartDate(
df::DataFrame,
conn;
tab = drug_exposure
)

df_ids = df[:,"drug_exposure_id"]

return outerjoin(GetDrugExposureStartDate(df_ids, conn; tab=tab), df, on = :drug_exposure_id)

end

"""
function GetDrugExposureStartDate(drug_exposure_ids; tab = drug_exposure)
Given a list of drug_exposure IDs, find their corresponding drug_exposure_start_date ID.
# Arguments:
- `drug_exposure_ids` - list of `drug_exposure_id`'s; each ID must be of subtype `Float64`
# Keyword Arguments:
- `tab` - the `SQLTable` representing the Drug Exposure table; default `drug_exposure`
# Returns
- SQL statement comprised of: `:drug_exposure_id` and `:drug_exposure_start_date`
"""
function GetDrugExposureStartDate(
drug_exposure_ids;
tab = drug_exposure
)

sql =
From(tab) |>
Where(Fun.in(Get.drug_exposure_id, drug_exposure_ids...)) |>
Select(Get.drug_exposure_id, Get.drug_exposure_start_date) |>
q -> render(q, dialect=dialect)

return String(sql)

end

export GetDatabasePersonIDs, GetPatientState, GetPatientGender, GetPatientRace, GetPatientAgeGroup, GetPatientVisits, GetMostRecentConditions, GetMostRecentVisit, GetVisitCondition, GetPatientEthnicity, GetDatabaseYearRange, GetVisitPlaceOfService, GetVisitConcept, GetVisitDate, GetDrugExposures, GetDrugConceptIDs, GetDrugAmounts, GetVisitProcedure, GetDatabaseCohorts, GetCohortSubjects, GetCohortSubjectStartDate, GetCohortSubjectEndDate, GetDrugExposureIDs, GetDrugExposureEndDate, GetDrugExposureStartDate
40 changes: 37 additions & 3 deletions test/sqlite/getters.jl
Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ end
push!(age_groups, default_age_grouping_values[idx])
break
elseif ismissing(grouping)
push!(age_groups, missing)
push!(age_groups, "Unspecified")
end
end
end
Expand All @@ -74,7 +74,7 @@ end
default_test = default_test[!, [:person_id, :age_group]]
default_test.age_group = convert(Vector{Union{Missing,String}}, default_test.age_group)

minuend_now_test = DataFrame(:person_id => [6.0, 123.0, 129.0, 16.0, 65.0, 74.0, 42.0, 187.0, 18.0, 111.0], :age_group => ["55 - 59", "70 - 74", "45 - 49", "50 - 54", "55 - 59", "50 - 54", missing, "75 - 79", "55 - 59", "45 - 49"])
minuend_now_test = DataFrame(:person_id => [6.0, 123.0, 129.0, 16.0, 65.0, 74.0, 42.0, 187.0, 18.0, 111.0], :age_group => ["55 - 59", "70 - 74", "45 - 49", "50 - 54", "55 - 59", "50 - 54", "Unspecified", "75 - 79", "55 - 59", "45 - 49"])

@test isequal(default_test, GetPatientAgeGroup(test_ids, sqlite_conn; minuend=default_minuend, age_groupings=default_age_grouping))
@test isequal(minuend_now_test, GetPatientAgeGroup(test_ids, sqlite_conn; minuend=minuend_now, age_groupings=test_age_grouping_2))
Expand Down Expand Up @@ -341,7 +341,7 @@ end
push!(age_groups, default_age_grouping_values[idx])
break
elseif ismissing(grouping)
push!(age_groups, missing)
push!(age_groups, "Unspecified")
end
end
end
Expand Down Expand Up @@ -526,6 +526,40 @@ end
@test test_ids == new[1:1]
end

@testset "GetDrugExposureEndDate" begin

test_drug_exposure_ids = [1.0, 2.0, 3.0, 4.0, 5.0]

test_drug_exposure_end_date_ids = [-364953600, 31449600, -532483200, -80006400, 1330387200]

res = sort(GetDrugExposureEndDate(test_drug_exposure_ids, sqlite_conn))
test_df1 = DataFrame(drug_exposure_id = test_drug_exposure_ids, drug_exposure_end_date = res.drug_exposure_end_date[1:5])

new = GetDrugExposureEndDate(test_df1[:,"drug_exposure_id"], sqlite_conn)

@test test_drug_exposure_end_date_ids == res.drug_exposure_end_date[1:5]
@test new.drug_exposure_end_date[1:5] == test_df1.drug_exposure_end_date[1:5]
@test isa(GetDrugExposureEndDate(test_drug_exposure_ids, sqlite_conn), DataFrame)

end

@testset "GetDrugExposureStartDate" begin

test_drug_exposure_ids = [1.0, 2.0, 3.0, 4.0, 5.0]

test_drug_exposure_start_date_ids = [-3.727296e8, 2.90304e7, -5.333472e8, -8.18208e7, 1.3291776e9]

res = sort(GetDrugExposureStartDate(test_drug_exposure_ids, sqlite_conn))
test_df1 = DataFrame(drug_exposure_id = test_drug_exposure_ids, drug_exposure_start_date = res.drug_exposure_start_date[1:5])

new = GetDrugExposureStartDate(test_df1[:,"drug_exposure_id"], sqlite_conn)

@test test_drug_exposure_start_date_ids == res.drug_exposure_start_date[1:5]
@test new.drug_exposure_start_date[1:5] == test_df1.drug_exposure_start_date[1:5]
@test isa(GetDrugExposureStartDate(test_drug_exposure_ids, sqlite_conn), DataFrame)

end

@testset "GetVisitProcedure Tests" begin
test_visit_occurrence_ids = [22951.0, 23670.0, 26205.0, 26759.0, 27401.0, 28537.0, 29330.0, 30237.0, 31282.0, 32616.0]

Expand Down

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