Merge pull request #84 from taxonomicallyinformedannotation/refactor-rt

adding example retention time library (addition to #76, #83)

inst/paths.yaml

@@ -74,6 +74,9 @@ data:
       set: data/source/benchmark/ALL_GNPS_210125_matchms_pubchem_cleaned_v2.msp
     libraries:
       path: data/source/libraries
+      rt:
+        path: data/source/libraries/rt
+        example_mini: data/source/libraries/rt/example_lib_mini_rt.tsv
       sop:
         path: data/source/libraries/sop
         closed: ../lotus-processor/data/processed/230224_closed_metadata.csv.gz
@@ -184,6 +187,8 @@ urls:
   benchmarking_set: https://zenodo.org/record/5186176/files/ALL_GNPS_210125_matchms_pubchem_cleaned_v2.msp?download=1
   examples:
     features: https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_features.csv
+    lib_mini:
+      rt: https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_lib_mini_rt.tsv
     metadata: https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_metadata.tsv
     sirius: https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_sirius.zip
     spectra: https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_spectra.mgf

tests/testthat/test_functions.R

@@ -93,6 +93,11 @@ testthat::test_that("Whole process", {
     url = paths$urls$examples$spectral_lib_mini$with_rt,
     export = paths$data$source$libraries$spectra$exp$with_rt
   )
+  ### Temporal library
+  get_file(
+    url = paths$urls$examples$lib_mini$rt,
+    export = paths$data$source$libraries$rt$example_mini
+  )
 
   #### SIRIUS
   ## mini version for tests
@@ -255,8 +260,15 @@ testthat::test_that("Whole process", {
     mgf_exp = list(
       "neg" = "data/interim/libraries/spectra/exp/internal_neg.rds",
       "pos" = "data/interim/libraries/spectra/exp/internal_pos.rds"
-    )
+    ),
+    mgf_is = list(
+      "neg" = "data/interim/libraries/spectra/exp/internal_neg.rds",
+      "pos" = "data/interim/libraries/spectra/exp/internal_pos.rds"
+    ),
+    temp_exp = paths$data$source$libraries$rt$example_mini,
+    temp_is = paths$data$source$libraries$rt$example_mini
   )
+  prepare_libraries_rt()
 
   ### Features
   step <- "prepare_features_tables"