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[FEATURE] Add Function GetVisitDate #44

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TheCedarPrince opened this issue Feb 19, 2023 · 2 comments
Closed

[FEATURE] Add Function GetVisitDate #44

TheCedarPrince opened this issue Feb 19, 2023 · 2 comments
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documentation Improvements or additions to documentation enhancement New feature or request good for beginners tests Testing of functions or features

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@TheCedarPrince
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I was tinkering with the Mental Health Equity study code today, and realized in creating one of our cohorts, we need a function called GetVisitDate that does the following:

  1. Accepts either a single visit_occurrence_id or a list of visit_occurrence_id's
  2. Contains a kwarg to query either for the visit_start_date or visit_end_date (I would do something like: interval = :start for visit_start_date and interval=:end for visit_end_date)
  3. Queries a given database for each visit_occurrence_id given to the function and finds its associated interval in the visit occurrence.
  4. Returns a dataframe that has two columns for the visit_occurrence_id and the requested date for the second column named either visit_start_dateorvisit_end_date`
  5. Add tests for this

Could you get to this asap @VarshC ? Thanks! 😄

@TheCedarPrince TheCedarPrince added documentation Improvements or additions to documentation enhancement New feature or request tests Testing of functions or features good for beginners labels Feb 19, 2023
@TheCedarPrince
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Here's a very loose description of the function's docstring:

"""
GetVisitDate(visit_occurrence_id; interval::Symbol = :start, tab = visit_occurrence)

This function queries a database for the start or end date of the visit occurrence associated with the given `visit_occurrence_id` or list of `visit_occurrence_id`'s.

# Arguments:
- `visit_occurrence_id`: A single `visit_occurrence_id` or a vector of `visit_occurrence_id`'s to query for.
- `interval`: A keyword argument that determines whether to query for the visit start date (`interval=:start`) or the visit end date (`interval=:end`). Default value is `interval=:start`.

# Returns:
A dataframe with two columns: `visit_occurrence_id` and either `visit_start_date` or `visit_end_date`, depending on the value of the `interval` argument.

TheCedarPrince added a commit that referenced this issue Feb 22, 2023
* added a function GetVisitDate and its tests. Also fixed test for GetVisitConcept

* Removed SQLite dep

* Added and updated docstrings

---------

Co-authored-by: Varshini Chinta <vchinta6@icl.gtri.org>
Co-authored-by: TheCedarPrince <jacobszelko@gmail.com>
@TheCedarPrince
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Thanks @VarshC for adding this feature!

TheCedarPrince added a commit that referenced this issue Feb 28, 2023
* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 ✨

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 ✨

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <vchinta6@icl.gtri.org>
Co-authored-by: TheCedarPrince <jacobszelko@gmail.com>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 ✨

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 ✨

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* Adding the column name

---------

Co-authored-by: Jacob S. Zelko <jacobszelko@gmail.com>
Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* Bumped compat and release version

* Updated CHANGELOG for new release

* Bumped release version

---------

Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>
Co-authored-by: Farreeda <94711213+Farreeda@users.noreply.github.com>
TheCedarPrince added a commit that referenced this issue Oct 26, 2023
* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 ✨

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 ✨

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <vchinta6@icl.gtri.org>
Co-authored-by: TheCedarPrince <jacobszelko@gmail.com>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 ✨

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 ✨

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* Adding the column name

---------

Co-authored-by: Jacob S. Zelko <jacobszelko@gmail.com>
Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* Bumped compat and release version

* Updated CHANGELOG for new release

* Bumped release version

---------

Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>
Co-authored-by: Farreeda <94711213+Farreeda@users.noreply.github.com>

* 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 <fareedaabdelazeez@gmail.com>
Co-authored-by: TheCedarPrince <jacobszelko@gmail.com>

* 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 <jacobszelko@gmail.com>
Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>
Co-authored-by: Farreeda <94711213+Farreeda@users.noreply.github.com>
Co-authored-by: Farreeda <fareedaabdelazeez@gmail.com>
TheCedarPrince added a commit that referenced this issue Nov 30, 2023
* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <vchinta6@icl.gtri.org>
Co-authored-by: TheCedarPrince <jacobszelko@gmail.com>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* Adding the column name

---------

Co-authored-by: Jacob S. Zelko <jacobszelko@gmail.com>
Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <vchinta6@icl.gtri.org>
Co-authored-by: TheCedarPrince <jacobszelko@gmail.com>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* Adding the column name

---------

Co-authored-by: Jacob S. Zelko <jacobszelko@gmail.com>
Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* Bumped compat and release version

* Updated CHANGELOG for new release

* Bumped release version

---------

Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>
Co-authored-by: Farreeda <94711213+Farreeda@users.noreply.github.com>

* 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 <fareedaabdelazeez@gmail.com>
Co-authored-by: TheCedarPrince <jacobszelko@gmail.com>

* 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 <jacobszelko@gmail.com>
Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>
Co-authored-by: Farreeda <94711213+Farreeda@users.noreply.github.com>
Co-authored-by: Farreeda <fareedaabdelazeez@gmail.com>

* 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 <jacobszelko@gmail.com>

* 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 <jacobszelko@gmail.com>

* updated for new release

---------

Co-authored-by: TheCedarPrince <jacobszelko@gmail.com>
Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>
Co-authored-by: Farreeda <94711213+Farreeda@users.noreply.github.com>
Co-authored-by: Farreeda <fareedaabdel…
TheCedarPrince added a commit that referenced this issue Feb 22, 2024
* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <vchinta6@icl.gtri.org>
Co-authored-by: TheCedarPrince <jacobszelko@gmail.com>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* Adding the column name

---------

Co-authored-by: Jacob S. Zelko <jacobszelko@gmail.com>
Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <vchinta6@icl.gtri.org>
Co-authored-by: TheCedarPrince <jacobszelko@gmail.com>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <jacobszelko@gmail.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* 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 <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* Adding the column name

---------

Co-authored-by: Jacob S. Zelko <jacobszelko@gmail.com>
Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>

* Bumped compat and release version

* Updated CHANGELOG for new release

* Bumped release version

---------

Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>
Co-authored-by: Farreeda <94711213+Farreeda@users.noreply.github.com>

* 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 <fareedaabdelazeez@gmail.com>
Co-authored-by: TheCedarPrince <jacobszelko@gmail.com>

* 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 <jacobszelko@gmail.com>
Co-authored-by: VarshC <49307186+VarshC@users.noreply.github.com>
Co-authored-by: Chinta <vchinta6@icl.gtri.org>
Co-authored-by: Farreeda <94711213+Farreeda@users.noreply.github.com>
Co-authored-by: Farreeda <fareedaabdelazeez@gmail.com>

* 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 <jacobszelko@gmail.com>

* 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 <jacobszelko@gmail.com>

* 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 <jacobszelko@gmail.com>

* Added a…
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