Merge pull request #216 from RECETOX/wverastegui/issue185

Implemented unit test for the function load.lcms.R

.github/workflows/r-conda.yml

@@ -28,10 +28,10 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Create conda environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: recetox-aplcms-dev
           auto-update-conda: true

CHANGELOG.md

@@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [dev] - unreleased
 ### Added
+- added tests for mzdata and mzxml formats [#216](https://github.com/RECETOX/recetox-aplcms/pull/216)
 ### Changed
 ### Removed
 

conda/environment-build.yaml

@@ -7,4 +7,4 @@ dependencies:
   - anaconda-client
   - conda-build
   - conda-verify
-  - r-base =4.2
+  - r-base

conda/environment-dev.yaml

@@ -4,11 +4,11 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - r-base =4.2
+  - r-base
   - icu <=70.1
   - r-mass
   - r-rgl
-  - bioconductor-mzR
+  - bioconductor-mzR ==2.28.0
   - r-splines2
   - r-doparallel
   - r-foreach

conda/environment.yaml

@@ -4,10 +4,10 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - r-base =4.2
+  - r-base
   - r-mass
   - r-rgl
-  - bioconductor-mzR
+  - bioconductor-mzR ==2.28.0
   - r-splines2
   - r-doparallel
   - r-foreach

conda/meta.yaml

@@ -21,10 +21,10 @@ build:
 
 requirements:
   host:
-    - r-base =4.2
+    - r-base
     - r-mass
     - r-rgl
-    - bioconductor-mzR
+    - bioconductor-mzR ==2.28.0
     - r-splines2
     - r-doparallel
     - r-foreach
@@ -37,10 +37,10 @@ requirements:
     - r-tibble
 
   run:
-    - r-base =4.2
+    - r-base
     - r-mass
     - r-rgl
-    - bioconductor-mzR
+    - bioconductor-mzR ==2.28.0
     - r-splines2
     - r-doparallel
     - r-foreach

tests/remote-files/input.txt

@@ -4,4 +4,6 @@ https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/
 https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/RCX_06_shortened.mzML
 https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/RCX_07_shortened.mzML
 https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/RCX_08_shortened.mzML
-https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/single_eic.mzml
+https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/single_eic.mzml
+https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/alg3.mzdata
+https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/test_file.mzXML

tests/testthat/test-load.lcms.R

@@ -0,0 +1,39 @@
+create_test_case <- function(filename, mz_length, rt_length, intensities_length) {
+  list(
+    filename = filename,
+    expected_type = "list",
+    expected_lengths = c(mz = mz_length, rt = rt_length, intensities = intensities_length),
+    expected_num_na = c(mz = 0, rt = 0, intensities = 0)
+  )
+}
+
+patrick::with_parameters_test_that(
+  "test load.lcms reads different file types",
+  {
+    # Arrange: Set up test inputs
+    testdata <- file.path("..", "testdata")
+    input_path <- file.path(testdata, "input", filename)
+
+    # Act: Execute the function with the test inputs
+    data <- load.lcms(input_path)
+
+    # Assert: Verify the function output matches expected results
+    # Check that the function returns an object of the expected type
+    actual_type <- data
+    testthat::expect_type(actual_type, expected_type)
+
+    # Check the lengths of the vectors in the list
+    actual_lengths <- lengths(data)
+    testthat::expect_equal(actual_lengths, expected_lengths)
+
+    # Check the number of NA values in each vector
+    actual_num_na <- sapply(data, function(x) sum(is.na(x)))
+    testthat::expect_equal(actual_num_na, expected_num_na)
+  },
+
+  patrick::cases(
+    test_case_1 = create_test_case("RCX_06_shortened.mzML", 879476, 879476, 879476),
+    test_case_2 = create_test_case("test_file.mzXML", 9647575, 9647575, 9647575),
+    test_case_3 = create_test_case("alg3.mzdata", 543894, 543894, 543894)
+  )
+)