Resolving ExecuteAudit function getting Breaked Easily
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## dev #60 +/- ##
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+ Coverage 73.36% 73.81% +0.45%
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Files 6 6
Lines 199 275 +76
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+ Hits 146 203 +57
- Misses 53 72 +19
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Jay-sanjay
changed the title
ExecuteAudit function getting Breaked Easily
|
Hey @Jay-sanjay ! Thanks for working on this! The functionality looks perfect -- could you just add in one test testing the auditing of a DataFrame by passing a value to the kwarg? Once you add the test, this should be set for merging! 😄 Great work! |
TheCedarPrince
requested changes
Oct 26, 2023
TheCedarPrince
approved these changes
Oct 26, 2023
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LGTM -- let's merge it! Great work and thanks @Jay-sanjay ! 😄
|
Thanks !! again |
TheCedarPrince
added a commit
that referenced
this pull request
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…
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* Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM * Added TODO's for what tests to write * Removed type signatures and added TODO for futures * Removed type signatures * Removed type signatures * Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this * Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits * Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports * Added and updated CHANGELOG * Bumped project version numbers for new release * Removed as it was an early testing prototype file * Began revising tutorial documentation * Removed Manifest file for package * Added Dates and TimeZones deps for managing age groups * Disallowed some exports and created new function for generating defaults * Added new deps Dates and TimeZones for time management * Began refactoring of GetPatientAgeGroup * Refactored GetPatientAgeGroup to correctly get age group of patients * Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings * Added SampleData compat and dependency * Renamed files and fixed docs * Fixed documentation and fixed methods for calculating age * Added helper function to determine year * Started adding first batch of tests * Added helpers file * Removed entry for SampleHealthData until merge of package occurs * Converted this function to internal helper function * Added new tests and dependencies * Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs * Added ignore for various Julia artifacts * Initial drafting of full tutorial * Finished initial beginner tutorial * Updated README with badges and documentation link * Modified footer * Updated landing page * Reordered pages on sidebar * Updated changelog for new release * Beginning draft of submission * Creating header affiliations * Autogenerated or compiled files * Ruby routine for generating header.tex * Removed Memoization dependency for user flexibility * Added dispatches to render SQL; found bug in GetPatientAgeGroup * Added get function for ethnicity * Cherry picking some files to resolve conflicts * Initial Tests for Getters, Filters, and Executors (#24) * Version 0.1.0 Release (#4) * Removed type signatures + fixed docstrings; lowercased table names and columns in prep for OMOPCDM * Added TODO's for what tests to write * Removed type signatures and added TODO for futures * Removed type signatures * Removed type signatures * Raised proposal to CDM maintainers and am awaiting feedback before moving forward on this * Removed type signatures and fixed bug with GetPatientVisits to correctly return patient visits * Changed docstring in StateFilterPersonIDs and enforced uppercasing for state abbreviations; added exports * Added and updated CHANGELOG * Bumped project version numbers for new release * Removed as it was an early testing prototype file * Began revising tutorial documentation * Removed Manifest file for package * Added Dates and TimeZones deps for managing age groups * Disallowed some exports and created new function for generating defaults * Added new deps Dates and TimeZones for time management * Began refactoring of GetPatientAgeGroup * Refactored GetPatientAgeGroup to correctly get age group of patients * Removed AgeGroupFilter in favor of supporting GetPatientAgeGroup and fixed docstrings * Added SampleData compat and dependency * Renamed files and fixed docs * Fixed documentation and fixed methods for calculating age * Added helper function to determine year * Started adding first batch of tests * Added helpers file * Removed entry for SampleHealthData until merge of package occurs * Converted this function to internal helper function * Added new tests and dependencies * Added tests for GetPatientGender, GetPatientAgeGroup, GetPatientRace, and GetDatabasePersonIDs * Added ignore for various Julia artifacts * Initial drafting of full tutorial * Finished initial beginner tutorial * Updated README with badges and documentation link * Modified footer * Updated landing page * Reordered pages on sidebar * Added todo action to automatically create todos * Added todos for issues in getters * Removed dependency on HealthSampleData and compat entries * Added todosfor multiple tests that need to be created * Uncommented test sets for running and added todo for Generators * Created test for GetPatientVisits() * Created Test for ExecuteAudit() * Created test for GetMostRecentVisit * updated tests * started creating test for GetVisitCondition * Changed GetVisitCondition Test * created test for VisitFilterPersonIDs * Added test for filters.jl * Finished tests for filters * Added a test step for code coverage * Removed VSCode configurations * Bumped compat entry for HealthSampleData * Removed todos and fixed GenderFilterPersonIDs test * Removed unnecessary comments * For allowing HealthSampleData to always download sample data * Test with adding latest codecoverage version * Added code coverage badge icon Co-authored-by: TheCedarPrince <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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* Tag New Release of 0.5.0 (#76) * 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 …
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fixing #48