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Tag New Release of 0.4.0 (#66)
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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]>

* updated for new release

---------

Co-authored-by: TheCedarPrince <[email protected]>
Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>
Co-authored-by: Farreeda <[email protected]>
Co-authored-by: Farreeda <fareedaabdel…
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26 changes: 26 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,32 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](http://keepachangelog.com/)
and this project adheres to [Semantic Versioning](http://semver.org/).


## [0.4.0] - December 1st, 2023

Patch release to add in some new features and fixes

### Added

- Added Getters that return Cohort information

* GetDatabaseCohorts

* GetCohortSubjects

* GetCohortSubjectEndDate

* GetCohortSubjectStartDate

- Misc

* Changed GetDrugExposures to GetDrugExposureIDs

* Added GetVisitProcedure in getters

- Extensive test suite for new features


## [0.3.0] - August 25th, 2023

New minor release to introduce some new functionalities and novel extensions of the API
Expand Down
8 changes: 5 additions & 3 deletions CITATION.cff
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,9 @@ authors:
given-names: Varshini
- family-names: Abdelazeez
given-names: Fareeda
title: "OMOPCDMCohortCreator 0.3.0"
version: 0.3.0
- family-names: Sanjay
given-names: Jay
title: "OMOPCDMCohortCreator 0.4.0"
version: 0.4.0
doi: 10.5281/zenodo.7052105
date-released: 2023-08-25
date-released: 2023-12-01
4 changes: 2 additions & 2 deletions 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"]
version = "0.3.0"
authors = ["Jacob Zelko <[email protected]>", "Fareeda Abdelazeez", "Varshini Chinta", "Jay Sanjay <[email protected]>"]
version = "0.4.0"

[deps]
DBInterface = "a10d1c49-ce27-4219-8d33-6db1a4562965"
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7 changes: 6 additions & 1 deletion docs/src/api.md
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Expand Up @@ -24,9 +24,14 @@ GetMostRecentConditions
GetMostRecentVisit
GetVisitCondition
GetDatabaseYearRange
GetDrugExposure
GetDrugExposureIDs
GetDrugConceptIDs
GetDrugAmounts
GetDatabaseCohorts
GetCohortSubjects
GetCohortSubjectStartDate
GetCohortSubjectEndDate
GetVisitProcedure
```

## Filters
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2 changes: 1 addition & 1 deletion docs/src/tutorials/beginner_tutorial.md
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Expand Up @@ -108,7 +108,7 @@ For the patients who have strep throat diagnoses, find their race.
Suggested solution:

```julia
strep_patients_race = occ.GetPatientRace(strep_patients, conn)
strep_patients_race = occ.GetPatientRace(strep_patients.person_id, conn)
```

### Task: Find the Gender of Patients with Strep Throat
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4 changes: 3 additions & 1 deletion src/executors.jl
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Expand Up @@ -11,11 +11,13 @@ Function that executes an audit on a dataframe that must contain a `count` colum
- `hitech::Bool` - a boolean that enforces HITECH standards for privacy preserving methods.
- `target_column::Symbol` - the name of the column to target for auditing (default set to :count).
# Returns
- `df` - a `DataFrame` that is appropriately audited per a given standard
"""
function ExecuteAudit(data::DataFrame; hitech = true)
function ExecuteAudit(data::DataFrame; hitech = true, target_column = :count)
df = hitech && filter(row -> row.count >= 11, data)

return df
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2 changes: 1 addition & 1 deletion src/filters.jl
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Expand Up @@ -282,4 +282,4 @@ function StateFilterPersonIDs(states; tab = location, join_tab = person)

end

export VisitFilterPersonIDs, ConditionFilterPersonIDs, RaceFilterPersonIDs, GenderFilterPersonIDs, StateFilterPersonIDs
export VisitFilterPersonIDs, ConditionFilterPersonIDs, RaceFilterPersonIDs, GenderFilterPersonIDs, StateFilterPersonIDs
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