Tag New Release of 0.5.0

CHANGELOG.md

@@ -6,6 +6,25 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
 
+## [0.5.0] - February 23rd, 2024
+
+Patch release to add in some new features and fixes 
+
+### Added 
+
+- Added Getters for Drug Exposures
+
+  *  GetDrugExposureStartDate
+
+  *  GetDrugExposureEndDate
+
+- Misc
+
+  * Minor fixes in  GetPatientAgeGroup Function
+
+- Extensive test suite for new features
+
+
 ## [0.4.0] - December 1st, 2023
 
 Patch release to add in some new features and fixes 

CITATION.cff

@@ -10,7 +10,7 @@ authors:
     given-names: Fareeda
   - family-names: Sanjay
     given-names: Jay
-title: "OMOPCDMCohortCreator 0.4.0"
-version: 0.4.0
+title: "OMOPCDMCohortCreator 0.5.0"
+version: 0.5.0
 doi: 10.5281/zenodo.7052105
-date-released: 2023-12-01
+date-released: 2024-02-23

Project.toml

@@ -1,7 +1,7 @@
 name = "OMOPCDMCohortCreator"
 uuid = "f525a15e-a73f-4eef-870f-f901257eae22"
 authors = ["Jacob Zelko <[email protected]>", "Fareeda Abdelazeez", "Varshini Chinta", "Jay Sanjay <[email protected]>"]
-version = "0.4.0"
+version = "0.5.0"
 
 [deps]
 DBInterface = "a10d1c49-ce27-4219-8d33-6db1a4562965"

docs/src/api.md

@@ -32,6 +32,8 @@ GetCohortSubjects
 GetCohortSubjectStartDate
 GetCohortSubjectEndDate
 GetVisitProcedure
+GetDrugExposureEndDate
+GetDrugExposureStartDate
 ```
 
 ## Filters

src/getters.jl

@@ -432,6 +432,7 @@
         [80, 89],
     ],
     tab = person,
+    ungrouped_label = "Unspecified"
 )
 
 Finds all individuals in age groups as specified by `age_groupings`.
@@ -451,6 +452,8 @@
     - any year provided by a user as long as it is an `Integer` (such as 2022, 1998, etc.)
 
 - `tab` - the `SQLTable` representing the Person table; default `person`
+
+- `ungrouped_label` - the label to assign persons who do not fit to a provided matching age group; default label "Unspecified"
 
 # Returns
 
@@ -483,10 +486,11 @@
         [70, 79],
         [80, 89],
     ],
-    tab=person
+    tab=person,
+    ungrouped_label = "Unspecified"
 )
 
-    df = DBInterface.execute(conn, GetPatientAgeGroup(ids; minuend=minuend, age_groupings=age_groupings, tab=tab)) |> DataFrame
+    df = DBInterface.execute(conn, GetPatientAgeGroup(ids; minuend=minuend, age_groupings=age_groupings, tab=tab, ungrouped_label=ungrouped_label)) |> DataFrame
 
     return df
 
@@ -504,7 +508,9 @@
     [60, 69],
     [70, 79],
     [80, 89],
-], tab = person)
+], 
+tab = person,
+ungrouped_label = "Unspecified")
 
 Given a `DataFrame` with a `:person_id` column, return the `DataFrame` with an associated `:ageGroup` for each person in the `DataFrame`
 
@@ -515,13 +521,13 @@
     df::DataFrame,
     conn;
     minuend=:now,
-    tab=person
+    tab=person,
+    ungrouped_label = "Unspecified"
     )
 
     df_ids= df[:,"person_id"]
 
-
-    return outerjoin(GetPatientAgeGroup(df_ids, conn; minuend=minuend, tab=tab), df, on = :person_id)
+    return outerjoin(GetPatientAgeGroup(df_ids, conn; minuend=minuend, tab=tab, ungrouped_label=ungrouped_label), df, on = :person_id)
 end
 
 """
@@ -540,6 +546,7 @@
         [80, 89],
     ],
     tab = person,
+    ungrouped_label = "Unspecified"
 )
 
 Return SQL statement that assigns an age group to each patient in a given patient list. 
@@ -559,6 +566,8 @@
 
 - `tab` - the `SQLTable` representing the Person table; default `person`
 
+- `ungrouped_label` - the label to assign persons who do not fit to a provided matching age group; default label "Unspecified"
+
 # Returns
 
 - `df::DataFrame` - a two column `DataFrame` comprised of columns: `:person_id` and `:age_group`
@@ -589,7 +598,8 @@
         [70, 79],
         [80, 89],
     ],
-    tab=person
+    tab=person,
+    ungrouped_label = "Unspecified"
 )
 
     minuend = _determine_calculated_year(minuend)
@@ -603,7 +613,7 @@
     sql = From(tab) |>
           Where(Fun.in(Get.person_id, ids...)) |>
           Select(Get.person_id, :age => minuend .- Get.year_of_birth) |>
-          Define(:age_group => Fun.case(age_arr...)) |>
+          Define(:age_group => Fun.case(age_arr..., ungrouped_label)) |>
           Select(Get.person_id, Get.age_group) |>
           q -> render(q, dialect=dialect)
 
@@ -1885,4 +1895,174 @@
 
 end
 
-export GetDatabasePersonIDs, GetPatientState, GetPatientGender, GetPatientRace, GetPatientAgeGroup, GetPatientVisits, GetMostRecentConditions, GetMostRecentVisit, GetVisitCondition, GetPatientEthnicity, GetDatabaseYearRange, GetVisitPlaceOfService, GetVisitConcept, GetVisitDate, GetDrugExposures, GetDrugConceptIDs, GetDrugAmounts, GetVisitProcedure, GetDatabaseCohorts, GetCohortSubjects, GetCohortSubjectStartDate, GetCohortSubjectEndDate, GetDrugExposureIDs
+"""
+function GetDrugExposureEndDate(drug_exposure_ids, conn; tab = drug_exposure)
+
+Given a list of drug_exposure IDs, find their exposure end dates.
+
+# Arguments:
+
+- `drug_exposure_ids` - list of `drug_exposure_id`'s; each ID must be of subtype `Float64`
+
+- `conn` - database connection using DBInterface
+
+
+# Keyword Arguments:
+
+- `tab` - the `SQLTable` representing the Drug Exposure table; default `drug_exposure`
+
+# Returns
+
+- `df::DataFrame` - a two column `DataFrame` comprised of columns: `:drug_exposure_id` and `:drug_exposure_end_date`
+"""
+
+function GetDrugExposureEndDate(
+    drug_exposure_ids,
+    conn;
+    tab = drug_exposure 
+)
+
+    df = DBInterface.execute(conn, GetDrugExposureEndDate(drug_exposure_ids; tab=tab)) |> DataFrame
+
+    return df
+end
+
+"""
+function GetDrugExposureEndDate(df:DataFrame, conn; tab = drug_exposure)
+
+Given a DataFrame with a :drug_exposure_id column, return the DataFrame with an associated :drug_exposure_end_date corresponding to a given drug_exposure_id in the DataFrame.
+
+Multiple dispatch that accepts all other arguments like in ` GetDrugExposureEndDate(ids, conn; tab = drug_exposure)`
+"""
+
+function GetDrugExposureEndDate(
+    df::DataFrame,
+    conn;
+    tab = drug_exposure
+)
+
+    df_ids = df[:,"drug_exposure_id"]
+
+    return outerjoin(GetDrugExposureEndDate(df_ids, conn; tab=tab), df, on = :drug_exposure_id)
+
+end
+
+"""
+function GetDrugExposureEndDate(drug_exposure_ids; tab = drug_exposure)
+
+Given a list of drug_exposure IDs, find their corresponding drug_exposure_end_date ID.
+
+# Arguments:
+
+- `drug_exposure_ids` - list of `drug_exposure_id`'s; each ID must be of subtype `Float64`
+
+
+# Keyword Arguments:
+
+- `tab` - the `SQLTable` representing the Drug Exposure table; default `drug_exposure`
+
+# Returns
+
+- SQL statement comprised of: `:drug_exposure_id` and `:drug_exposure_end_date`
+"""
+function GetDrugExposureEndDate(
+    drug_exposure_ids;
+    tab = drug_exposure
+)
+
+    sql =
+        From(tab) |>
+        Where(Fun.in(Get.drug_exposure_id, drug_exposure_ids...)) |>
+        Select(Get.drug_exposure_id, Get.drug_exposure_end_date) |>
+        q -> render(q, dialect=dialect)
+
+    return String(sql)
+
+end
+
+"""
+function GetDrugExposureStartDate(drug_exposure_ids, conn; tab = drug_exposure)
+
+Given a list of drug_exposure IDs, find their exposure start dates.
+
+# Arguments:
+
+- `drug_exposure_ids` - list of `drug_exposure_id`'s; each ID must be of subtype `Float64`
+
+- `conn` - database connection using DBInterface
+
+
+# Keyword Arguments:
+
+- `tab` - the `SQLTable` representing the Drug Exposure table; default `drug_exposure`
+
+# Returns
+
+- `df::DataFrame` - a two column `DataFrame` comprised of columns: `:drug_exposure_id` and `:drug_exposure_start_date`
+"""
+
+function GetDrugExposureStartDate(
+    drug_exposure_ids,
+    conn;
+    tab = drug_exposure 
+)
+
+    df = DBInterface.execute(conn, GetDrugExposureStartDate(drug_exposure_ids; tab=tab)) |> DataFrame
+
+    return df
+end
+
+"""
+function GetDrugExposureStartDate(df:DataFrame, conn; tab = drug_exposure)
+
+Given a DataFrame with a :drug_exposure_id column, return the DataFrame with an associated :drug_exposure_start_date corresponding to a given drug_exposure_id in the DataFrame.
+
+Multiple dispatch that accepts all other arguments like in ` GetDrugExposureStartDate(ids, conn; tab = drug_exposure)`
+"""
+function GetDrugExposureStartDate(
+    df::DataFrame,
+    conn;
+    tab = drug_exposure
+)
+
+    df_ids = df[:,"drug_exposure_id"]
+
+    return outerjoin(GetDrugExposureStartDate(df_ids, conn; tab=tab), df, on = :drug_exposure_id)
+
+end
+
+"""
+function GetDrugExposureStartDate(drug_exposure_ids; tab = drug_exposure)
+
+
+    Given a list of drug_exposure IDs, find their corresponding drug_exposure_start_date ID.
+
+    # Arguments:
+
+    - `drug_exposure_ids` - list of `drug_exposure_id`'s; each ID must be of subtype `Float64`
+
+
+    # Keyword Arguments:
+
+    - `tab` - the `SQLTable` representing the Drug Exposure table; default `drug_exposure`
+
+    # Returns
+
+    - SQL statement comprised of: `:drug_exposure_id` and `:drug_exposure_start_date`
+"""
+function GetDrugExposureStartDate(
+    drug_exposure_ids;
+    tab = drug_exposure
+)
+
+    sql =
+        From(tab) |>
+        Where(Fun.in(Get.drug_exposure_id, drug_exposure_ids...)) |>
+        Select(Get.drug_exposure_id, Get.drug_exposure_start_date) |>
+        q -> render(q, dialect=dialect)
+
+    return String(sql)
+
+end
+
+export GetDatabasePersonIDs, GetPatientState, GetPatientGender, GetPatientRace, GetPatientAgeGroup, GetPatientVisits, GetMostRecentConditions, GetMostRecentVisit, GetVisitCondition, GetPatientEthnicity, GetDatabaseYearRange, GetVisitPlaceOfService, GetVisitConcept, GetVisitDate, GetDrugExposures, GetDrugConceptIDs, GetDrugAmounts, GetVisitProcedure, GetDatabaseCohorts, GetCohortSubjects, GetCohortSubjectStartDate, GetCohortSubjectEndDate, GetDrugExposureIDs, GetDrugExposureEndDate, GetDrugExposureStartDate

test/sqlite/getters.jl

@@ -65,7 +65,7 @@ end
                 push!(age_groups, default_age_grouping_values[idx])
                 break
             elseif ismissing(grouping)
-                push!(age_groups, missing)
+                push!(age_groups, "Unspecified")
             end
         end
     end
@@ -74,7 +74,7 @@ end
     default_test = default_test[!, [:person_id, :age_group]]
     default_test.age_group = convert(Vector{Union{Missing,String}}, default_test.age_group)
 
-    minuend_now_test = DataFrame(:person_id => [6.0, 123.0, 129.0, 16.0, 65.0, 74.0, 42.0, 187.0, 18.0, 111.0], :age_group => ["55 - 59", "70 - 74", "45 - 49", "50 - 54", "55 - 59", "50 - 54", missing, "75 - 79", "55 - 59", "45 - 49"])
+    minuend_now_test = DataFrame(:person_id => [6.0, 123.0, 129.0, 16.0, 65.0, 74.0, 42.0, 187.0, 18.0, 111.0], :age_group => ["55 - 59", "70 - 74", "45 - 49", "50 - 54", "55 - 59", "50 - 54", "Unspecified", "75 - 79", "55 - 59", "45 - 49"])
 
     @test isequal(default_test, GetPatientAgeGroup(test_ids, sqlite_conn; minuend=default_minuend, age_groupings=default_age_grouping))
     @test isequal(minuend_now_test, GetPatientAgeGroup(test_ids, sqlite_conn; minuend=minuend_now, age_groupings=test_age_grouping_2))
@@ -341,7 +341,7 @@ end
                 push!(age_groups, default_age_grouping_values[idx])
                 break
             elseif ismissing(grouping)
-                push!(age_groups, missing)
+                push!(age_groups, "Unspecified")
             end
         end
     end
@@ -526,6 +526,40 @@ end
     @test test_ids == new[1:1]
 end
 
+@testset "GetDrugExposureEndDate" begin
+
+    test_drug_exposure_ids = [1.0, 2.0, 3.0, 4.0, 5.0]
+
+    test_drug_exposure_end_date_ids = [-364953600, 31449600, -532483200, -80006400, 1330387200]
+
+    res = sort(GetDrugExposureEndDate(test_drug_exposure_ids, sqlite_conn))
+    test_df1 = DataFrame(drug_exposure_id = test_drug_exposure_ids, drug_exposure_end_date = res.drug_exposure_end_date[1:5])
+
+    new = GetDrugExposureEndDate(test_df1[:,"drug_exposure_id"], sqlite_conn)
+
+    @test test_drug_exposure_end_date_ids == res.drug_exposure_end_date[1:5]
+    @test new.drug_exposure_end_date[1:5] == test_df1.drug_exposure_end_date[1:5]
+    @test isa(GetDrugExposureEndDate(test_drug_exposure_ids, sqlite_conn), DataFrame)
+
+end
+
+@testset "GetDrugExposureStartDate" begin
+
+    test_drug_exposure_ids = [1.0, 2.0, 3.0, 4.0, 5.0]
+
+    test_drug_exposure_start_date_ids = [-3.727296e8, 2.90304e7, -5.333472e8, -8.18208e7, 1.3291776e9]
+
+    res = sort(GetDrugExposureStartDate(test_drug_exposure_ids, sqlite_conn))
+    test_df1 = DataFrame(drug_exposure_id = test_drug_exposure_ids, drug_exposure_start_date = res.drug_exposure_start_date[1:5])
+
+    new = GetDrugExposureStartDate(test_df1[:,"drug_exposure_id"], sqlite_conn)
+
+    @test test_drug_exposure_start_date_ids == res.drug_exposure_start_date[1:5]
+    @test new.drug_exposure_start_date[1:5] == test_df1.drug_exposure_start_date[1:5]
+    @test isa(GetDrugExposureStartDate(test_drug_exposure_ids, sqlite_conn), DataFrame)
+
+end
+
 @testset "GetVisitProcedure Tests" begin
     test_visit_occurrence_ids = [22951.0, 23670.0, 26205.0, 26759.0, 27401.0, 28537.0, 29330.0, 30237.0, 31282.0, 32616.0]