Skip to content

Commit

Permalink
Tag Release of v0.2.2 (#46)
Browse files Browse the repository at this point in the history
* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

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

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

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

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

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

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Updated changelog for new release

* Beginning draft of submission

* Creating header affiliations

* Autogenerated or compiled files

* Ruby routine for generating header.tex

* Removed Memoization dependency for user flexibility

* Added dispatches to render SQL; found bug in GetPatientAgeGroup

* Added get function for ethnicity

* Cherry picking some files to resolve conflicts

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

* Version 0.1.0 Release (#4)

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

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

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

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

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

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

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

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Added todo action to automatically create todos

* Added todos for issues in getters

* Removed dependency on HealthSampleData and compat entries

* Added todosfor multiple tests that need to be created

* Uncommented test sets for running and added todo for Generators

* Created test for GetPatientVisits()

* Created Test for ExecuteAudit()

* Created test for GetMostRecentVisit

* updated tests

* started creating test for GetVisitCondition

* Changed GetVisitCondition Test

* created test for VisitFilterPersonIDs

* Added test for filters.jl

* Finished tests for filters

* Added a test step for code coverage

* Removed VSCode configurations

* Bumped compat entry for HealthSampleData

* Removed todos and fixed GenderFilterPersonIDs test

* Removed unnecessary comments

* For allowing HealthSampleData to always download sample data

* Test with adding latest codecoverage version

* Added code coverage badge icon

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

* Simplify Age Calculations (#27)

* Added SQL generation for filter statements

* Removed option for internal DB calculation

* Fixed GetPatientAgeGroup and added GetDatabaseYearRange and updated docstrings

* Updated test suite

* Removed old tests for GetPatientAgeGroup

* Updated tests for helper functions

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

* Updated docstrings for SQL rendering

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

* Updated test explanation

* Added test suite for GetMostRecentConditions and formatted

* Fix to Docs Deployment (#29)

* Testing fix for docs deployment

* Expected the OMOPCDMCohortCreator package to be available

* Added push preview information and the edit link

* Fixed deprecation warning

* Final layout fixes to collapselevel

* Final fix

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

* Configured nesting of tutorial

* Updated landing page description

* Broke up tutorial pages

* Added revamped beginner tutorial

* Overhaul of Docs (#31)

* Moved beginner tutorial

* Added tutorial for R usage

* Updated index of tutorials

* Fixed up tutorials index

* Renamed R tutorial

* Clarified links for tutorials

* Julia on the brain

* Added contributing guide

* Added contributing guide

* Updated API exports

* Revamped overview of package

* Added the most necessary of all things: emojis ✨

* Fixed up emojis

* Fixed up API table of contents

* Fixed emojis

* Updated main features of package

* Removed emoji

* Updated and fixed Citation file (#32)

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

* Tag New Release v2.0.0 (#33)

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

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

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

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

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

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

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

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Updated changelog for new release

* Beginning draft of submission

* Creating header affiliations

* Autogenerated or compiled files

* Ruby routine for generating header.tex

* Removed Memoization dependency for user flexibility

* Added dispatches to render SQL; found bug in GetPatientAgeGroup

* Added get function for ethnicity

* Cherry picking some files to resolve conflicts

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

* Version 0.1.0 Release (#4)

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

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

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

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

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

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

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

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Added todo action to automatically create todos

* Added todos for issues in getters

* Removed dependency on HealthSampleData and compat entries

* Added todosfor multiple tests that need to be created

* Uncommented test sets for running and added todo for Generators

* Created test for GetPatientVisits()

* Created Test for ExecuteAudit()

* Created test for GetMostRecentVisit

* updated tests

* started creating test for GetVisitCondition

* Changed GetVisitCondition Test

* created test for VisitFilterPersonIDs

* Added test for filters.jl

* Finished tests for filters

* Added a test step for code coverage

* Removed VSCode configurations

* Bumped compat entry for HealthSampleData

* Removed todos and fixed GenderFilterPersonIDs test

* Removed unnecessary comments

* For allowing HealthSampleData to always download sample data

* Test with adding latest codecoverage version

* Added code coverage badge icon

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

* Simplify Age Calculations (#27)

* Added SQL generation for filter statements

* Removed option for internal DB calculation

* Fixed GetPatientAgeGroup and added GetDatabaseYearRange and updated docstrings

* Updated test suite

* Removed old tests for GetPatientAgeGroup

* Updated tests for helper functions

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

* Updated docstrings for SQL rendering

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

* Updated test explanation

* Added test suite for GetMostRecentConditions and formatted

* Fix to Docs Deployment (#29)

* Testing fix for docs deployment

* Expected the OMOPCDMCohortCreator package to be available

* Added push preview information and the edit link

* Fixed deprecation warning

* Final layout fixes to collapselevel

* Final fix

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

* Configured nesting of tutorial

* Updated landing page description

* Broke up tutorial pages

* Added revamped beginner tutorial

* Overhaul of Docs (#31)

* Moved beginner tutorial

* Added tutorial for R usage

* Updated index of tutorials

* Fixed up tutorials index

* Renamed R tutorial

* Clarified links for tutorials

* Julia on the brain

* Added contributing guide

* Added contributing guide

* Updated API exports

* Revamped overview of package

* Added the most necessary of all things: emojis ✨

* Fixed up emojis

* Fixed up API table of contents

* Fixed emojis

* Updated main features of package

* Removed emoji

* Updated and fixed Citation file (#32)

* Tagged new release

* Revamped README details about package

* Added docstring to ExecuteAudit

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

* Moved paper document to its own branch while in progress

* Quickfix to R tutorial on strep_patients

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

* Attempt at making CI process more reasonable

* Removed paper directory again

* Bumped for minor patch release

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

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

Added GetVisitPlaceOfService getter

* Added GetVisitConcept getter function (#41)

* issue #44 add GetVisitDate (#45)

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

* Removed SQLite dep

* Added and updated docstrings

---------

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

* Adding the column name (#43)

* Tag Release of v0.2.1 (#37)

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

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

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

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

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

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

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

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Updated changelog for new release

* Beginning draft of submission

* Creating header affiliations

* Autogenerated or compiled files

* Ruby routine for generating header.tex

* Removed Memoization dependency for user flexibility

* Added dispatches to render SQL; found bug in GetPatientAgeGroup

* Added get function for ethnicity

* Cherry picking some files to resolve conflicts

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

* Version 0.1.0 Release (#4)

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

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

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

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

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

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

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

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Added todo action to automatically create todos

* Added todos for issues in getters

* Removed dependency on HealthSampleData and compat entries

* Added todosfor multiple tests that need to be created

* Uncommented test sets for running and added todo for Generators

* Created test for GetPatientVisits()

* Created Test for ExecuteAudit()

* Created test for GetMostRecentVisit

* updated tests

* started creating test for GetVisitCondition

* Changed GetVisitCondition Test

* created test for VisitFilterPersonIDs

* Added test for filters.jl

* Finished tests for filters

* Added a test step for code coverage

* Removed VSCode configurations

* Bumped compat entry for HealthSampleData

* Removed todos and fixed GenderFilterPersonIDs test

* Removed unnecessary comments

* For allowing HealthSampleData to always download sample data

* Test with adding latest codecoverage version

* Added code coverage badge icon

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

* Simplify Age Calculations (#27)

* Added SQL generation for filter statements

* Removed option for internal DB calculation

* Fixed GetPatientAgeGroup and added GetDatabaseYearRange and updated docstrings

* Updated test suite

* Removed old tests for GetPatientAgeGroup

* Updated tests for helper functions

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

* Updated docstrings for SQL rendering

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

* Updated test explanation

* Added test suite for GetMostRecentConditions and formatted

* Fix to Docs Deployment (#29)

* Testing fix for docs deployment

* Expected the OMOPCDMCohortCreator package to be available

* Added push preview information and the edit link

* Fixed deprecation warning

* Final layout fixes to collapselevel

* Final fix

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

* Configured nesting of tutorial

* Updated landing page description

* Broke up tutorial pages

* Added revamped beginner tutorial

* Overhaul of Docs (#31)

* Moved beginner tutorial

* Added tutorial for R usage

* Updated index of tutorials

* Fixed up tutorials index

* Renamed R tutorial

* Clarified links for tutorials

* Julia on the brain

* Added contributing guide

* Added contributing guide

* Updated API exports

* Revamped overview of package

* Added the most necessary of all things: emojis ✨

* Fixed up emojis

* Fixed up API table of contents

* Fixed emojis

* Updated main features of package

* Removed emoji

* Updated and fixed Citation file (#32)

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

* Tag New Release v2.0.0 (#33)

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

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

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

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

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

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

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

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Updated changelog for new release

* Beginning draft of submission

* Creating header affiliations

* Autogenerated or compiled files

* Ruby routine for generating header.tex

* Removed Memoization dependency for user flexibility

* Added dispatches to render SQL; found bug in GetPatientAgeGroup

* Added get function for ethnicity

* Cherry picking some files to resolve conflicts

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

* Version 0.1.0 Release (#4)

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

* Added TODO's for what tests to write

* Removed type signatures and added TODO for futures

* Removed type signatures

* Removed type signatures

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

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

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

* Added and updated CHANGELOG

* Bumped project version numbers for new release

* Removed as it was an early testing prototype file

* Began revising tutorial documentation

* Removed Manifest file for package

* Added Dates and TimeZones deps for managing age groups

* Disallowed some exports and created new function for generating defaults

* Added new deps Dates and TimeZones for time management

* Began refactoring of GetPatientAgeGroup

* Refactored GetPatientAgeGroup to correctly get age group of patients

* Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings

* Added SampleData compat and dependency

* Renamed files and fixed docs

* Fixed documentation and fixed methods for calculating age

* Added helper function to determine year

* Started adding first batch of tests

* Added helpers file

* Removed entry for SampleHealthData until merge of package occurs

* Converted this function to internal helper function

* Added new tests and dependencies

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

* Added ignore for various Julia artifacts

* Initial drafting of full tutorial

* Finished initial beginner tutorial

* Updated README with badges and documentation link

* Modified footer

* Updated landing page

* Reordered pages on sidebar

* Added todo action to automatically create todos

* Added todos for issues in getters

* Removed dependency on HealthSampleData and compat entries

* Added todosfor multiple tests that need to be created

* Uncommented test sets for running and added todo for Generators

* Created test for GetPatientVisits()

* Created Test for ExecuteAudit()

* Created test for GetMostRecentVisit

* updated tests

* started creating test for GetVisitCondition

* Changed GetVisitCondition Test

* created test for VisitFilterPersonIDs

* Added test for filters.jl

* Finished tests for filters

* Added a test step for code coverage

* Removed VSCode configurations

* Bumped compat entry for HealthSampleData

* Removed todos and fixed GenderFilterPersonIDs test

* Removed unnecessary comments

* For allowing HealthSampleData to always download sample data

* Test with adding latest codecoverage version

* Added code coverage badge icon

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

* Simplify Age Calculations (#27)

* Added SQL generation for filter statements

* Removed option for internal DB calculation

* Fixed GetPatientAgeGroup and added GetDatabaseYearRange and updated docstrings

* Updated test suite

* Removed old tests for GetPatientAgeGroup

* Updated tests for helper functions

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

* Updated docstrings for SQL rendering

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

* Updated test explanation

* Added test suite for GetMostRecentConditions and formatted

* Fix to Docs Deployment (#29)

* Testing fix for docs deployment

* Expected the OMOPCDMCohortCreator package to be available

* Added push preview information and the edit link

* Fixed deprecation warning

* Final layout fixes to collapselevel

* Final fix

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

* Configured nesting of tutorial

* Updated landing page description

* Broke up tutorial pages

* Added revamped beginner tutorial

* Overhaul of Docs (#31)

* Moved beginner tutorial

* Added tutorial for R usage

* Updated index of tutorials

* Fixed up tutorials index

* Renamed R tutorial

* Clarified links for tutorials

* Julia on the brain

* Added contributing guide

* Added contributing guide

* Updated API exports

* Revamped overview of package

* Added the most necessary of all things: emojis ✨

* Fixed up emojis

* Fixed up API table of contents

* Fixed emojis

* Updated main features of package

* Removed emoji

* Updated and fixed Citation file (#32)

* Tagged new release

* Revamped README details about package

* Added docstring to ExecuteAudit

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

* Moved paper document to its own branch while in progress

* Quickfix to R tutorial on strep_patients

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

* Attempt at making CI process more reasonable

* Removed paper directory again

* Bumped for minor patch release

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

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

* Adding the column name

---------

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

* Bumped compat and release version

* Updated CHANGELOG for new release

* Bumped release version

---------

Co-authored-by: VarshC <[email protected]>
Co-authored-by: Chinta <[email protected]>
Co-authored-by: Farreeda <[email protected]>
  • Loading branch information
4 people authored Feb 28, 2023
1 parent 335bf2f commit 77126d0
Show file tree
Hide file tree
Showing 6 changed files with 260 additions and 8 deletions.
13 changes: 13 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,19 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](http://keepachangelog.com/)
and this project adheres to [Semantic Versioning](http://semver.org/).

## [0.2.2] - February 28th, 2023

Patch release to add in some new features and fixes

### Added

- Added Getter for visit dates
- Upated and added tests

### Changed

- Small fix to Julia beginner tutorial

## [0.2.1] - November 5th, 2022

Minor patch release that adjusted CI test coverage and fixed some documentation errors.
Expand Down
6 changes: 3 additions & 3 deletions CITATION.cff
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ authors:
orcid: https://orcid.org/0000-0003-4531-1614
- family-names: Chinta
given-names: Varshini
title: "OMOPCDMCohortCreator 0.2.1"
version: 0.2.1
title: "OMOPCDMCohortCreator 0.2.2"
version: 0.2.2
doi: 10.5281/zenodo.7052105
date-released: 2022-11-05
date-released: 2023-02-28
4 changes: 2 additions & 2 deletions Project.toml
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "OMOPCDMCohortCreator"
uuid = "f525a15e-a73f-4eef-870f-f901257eae22"
authors = ["Jacob Zelko <[email protected]>"]
version = "0.2.1"
version = "0.2.2"

[deps]
DBInterface = "a10d1c49-ce27-4219-8d33-6db1a4562965"
Expand All @@ -13,6 +13,6 @@ TimeZones = "f269a46b-ccf7-5d73-abea-4c690281aa53"
[compat]
DBInterface = "2.5"
DataFrames = "1.3"
FunSQL = "0.10"
FunSQL = "0.10, 0.11"
TimeZones = "1.9"
julia = "1.6"
4 changes: 2 additions & 2 deletions docs/src/tutorials/beginner_tutorial.md
Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,7 @@ For the patients who have strep throat diagnoses, find their race.
Suggested solution:

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

### Task: Find the Gender of Patients with Strep Throat
Expand All @@ -112,7 +112,7 @@ For the patients who have strep throat diagnoses, find their gender.
Suggested solution:

```julia
strep_patients_gender = occ.GetPatientGender(strep_patients, conn)
strep_patients_gender = occ.GetPatientGender(strep_patients.person_id, conn)
```

### Task: Create Age Groupings of Patients with Strep Throat
Expand Down
217 changes: 216 additions & 1 deletion src/getters.jl
Original file line number Diff line number Diff line change
Expand Up @@ -774,4 +774,219 @@ function GetVisitCondition(

end

export GetDatabasePersonIDs, GetPatientState, GetPatientGender, GetPatientRace, GetPatientAgeGroup, GetPatientVisits, GetMostRecentConditions, GetMostRecentVisit, GetVisitCondition, GetPatientEthnicity, GetDatabaseYearRange
#= TODO: Write tests for GetVisitPlaceOfService
Only needs one or two tests; may be difficult to test as I do not think Eunomia has anything other than missing
labels: tests, good first issue
assignees: VarshC
=#

"""
GetVisitPlaceOfService(visit_ids, conn; tab = visit_occurrence, join_tab = care_site)
Given a list of visit IDs, find their place of service
# Arguments:
- `visit_ids` - list of `visit_id`'s; each ID must be of subtype `Integer`
- `conn` - database connection using DBInterface
# Keyword Arguments:
- `tab` - the `SQLTable` representing the Condition Occurrence table; default `visit_occurrence`
- `join_tab` - the `SQLTable` representing the Person table; default `care_site`
# Returns
- `df::DataFrame` - a two column `DataFrame` comprised of columns: `:visit_occurrence_id` and `:condition_concept_id`
"""
function GetVisitPlaceOfService(
visit_ids,
conn;
tab=visit_occurrence,
join_tab=care_site
)

df = DBInterface.execute(conn, GetVisitPlaceOfService(visit_ids; tab=tab, join_tab=join_tab)) |> DataFrame

return df

end

"""
GetVisitPlaceOfService(visit_ids; tab = visit_occurrence, join_tab = care_site)
Produces SQL statement that, given a list of visit IDs, find their place of service
# Arguments:
- `visit_ids` - list of `visit_id`'s; each ID must be of subtype `Integer`
# Keyword Arguments:
- `tab` - the `SQLTable` representing the Condition Occurrence table; default `visit_occurrence`
- `join_tab` - the `SQLTable` representing the Person table; default `care_site`
# Returns
- `sql::String` - Prepared SQL statement as a `String`
"""
function GetVisitPlaceOfService(
visit_ids;
tab=visit_occurrence,
join_tab=care_site
)

sql =
From(tab) |>
Where(Fun.in(Get.visit_occurrence_id, visit_ids...)) |>
Select(Get.visit_occurrence_id, Get.care_site_id) |>
Join(:join => join_tab, Get.care_site_id .== Get.join.care_site_id) |>
Select(Get.visit_occurrence_id, Get.join.place_of_service_concept_id) |>
q -> render(q, dialect=dialect)

return String(sql)

end

#= TODO: Write tests for GetVisitConcept
Only needs one or two tests; should have everything that is required in Eunomia to run!
labels: tests, good first issue
assignees: VarshC
=#
"""
GetVisitConcept(visit_ids, conn; tab = visit_occurrence)
Given a list of visit IDs, find their corresponding visit_concept_id's.
# Arguments:
- `visit_ids` - list of `visit_id`'s; each ID must be of subtype `Integer`
- `conn` - database connection using DBInterface
# Keyword Arguments:
- `tab` - the `SQLTable` representing the Condition Occurrence table; default `visit_occurrence`
# Returns
- `df::DataFrame` - a two column `DataFrame` comprised of columns: `:visit_occurrence_id` and `:visit_concept_id`
"""
function GetVisitConcept(
visit_ids,
conn;
tab=visit_occurrence
)

df = DBInterface.execute(conn, GetVisitConcept(visit_ids; tab=tab)) |> DataFrame

return df

end

"""
GetVisitConcept(visit_ids; tab = visit_occurrence)
Produces SQL statement that, given a list of visit IDs, find their corresponding visit_concept_id's.
# Arguments:
- `visit_ids` - list of `visit_id`'s; each ID must be of subtype `Integer`
# Keyword Arguments:
- `tab` - the `SQLTable` representing the Condition Occurrence table; default `visit_occurrence`
# Returns
- `sql::String` - Prepared SQL statement as a `String`
"""
function GetVisitConcept(
visit_ids;
tab=visit_occurrence
)

sql =
From(tab) |>
Where(Fun.in(Get.visit_occurrence_id, visit_ids...)) |>
Select(Get.visit_occurrence_id, Get.visit_concept_id) |>
q -> render(q, dialect=dialect)

return String(sql)

end

"""
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.
- `conn` - database connection using DBInterface
# Keyword Arguments
- `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.
"""
function GetVisitDate(
visit_occurrence_ids,
conn;
interval::Symbol = :start,
tab=visit_occurrence
)
df = DBInterface.execute(conn, GetVisitDate(visit_occurrence_ids; interval, tab=tab)) |> DataFrame
return df
end

"""
GetVisitDate(visit_occurrence_id; interval::Symbol = :start, tab = visit_occurrence)
Produces SQL statement that, given a list of visit IDs, finds the visit start or end date.
# Arguments:
- `visit_occurrence_id`: A single `visit_occurrence_id` or a vector of `visit_occurrence_id`'s to query for.
# Keyword Arguments
- `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.
"""
function GetVisitDate(
visit_occurrence_id;
interval::Symbol = :start,
tab=visit_occurrence
)
if (interval == :start)
sql =
From(tab) |>
Where(Fun.in(Get.visit_occurrence_id, visit_occurrence_id...)) |>
Select(Get.visit_occurrence_id, Get.visit_start_date) |>
q -> render(q, dialect=dialect)
return String(sql)
elseif (interval == :end)
sql =
From(tab) |>
Where(Fun.in(Get.visit_occurrence_id, visit_occurrence_id...)) |>
Select(Get.visit_occurrence_id, Get.visit_end_date) |>
q -> render(q, dialect=dialect)
return String(sql)
else
return "NA"
end

end


export GetDatabasePersonIDs, GetPatientState, GetPatientGender, GetPatientRace, GetPatientAgeGroup, GetPatientVisits, GetMostRecentConditions, GetMostRecentVisit, GetVisitCondition, GetPatientEthnicity, GetDatabaseYearRange, GetVisitPlaceOfService, GetVisitConcept, GetVisitDate
24 changes: 24 additions & 0 deletions test/sqlite/getters.jl
Original file line number Diff line number Diff line change
Expand Up @@ -131,6 +131,13 @@ end
@test recent_visit == evaluated_visit.visit_occurrence_id
end

@testset "GetVisitConcept Tests" begin
test_ids = From(OMOPCDMCohortCreator.visit_occurrence) |> Select(Get.visit_occurrence_id) |> Limit(20) |> q -> render(q, dialect=OMOPCDMCohortCreator.dialect) |> q -> DBInterface.execute(sqlite_conn, q) |> DataFrame |> Array
test_concept_ids = From(OMOPCDMCohortCreator.visit_occurrence) |> Select(Get.visit_occurrence_id, Get.visit_concept_id) |> Where(Fun.in(Get.visit_occurrence_id, test_ids...)) |> q -> render(q, dialect=OMOPCDMCohortCreator.dialect) |> q -> DBInterface.execute(sqlite_conn, q) |> DataFrame

@test test_concept_ids == GetVisitConcept(test_ids, sqlite_conn)
end

@testset "GetVisitCondition Tests" begin

#test for 3 visit ids with only 1 condition each
Expand Down Expand Up @@ -158,3 +165,20 @@ end

@test ethnicities == GetPatientEthnicity(test_ids, sqlite_conn)
end

@testset "GetVisitDate Tests" begin

#test with interval = start
test_visit_ids= [65475.0, 14930.0, 25743.0, 14888.0]
test_start_dates = [840585600.0, 575510400.0, 1336953600.0, 1063497600.0]
test_df_start = DataFrame(visit_occurrence_id=test_visit_ids, visit_start_date=test_start_dates)

@test test_df_start == GetVisitDate(test_visit_ids, sqlite_conn, interval=Symbol("start"))

#test with interval = end
test_end_dates = [840672000.0, 575596800.0, 1337040000.0, 1063584000.0]
test_df_end = DataFrame(visit_occurrence_id=test_visit_ids, visit_end_date=test_end_dates)

@test test_df_end == GetVisitDate(test_visit_ids, sqlite_conn, interval=Symbol("end"))

end

0 comments on commit 77126d0

Please sign in to comment.