fix tests

R/prepare_libraries_spectra.R

@@ -161,6 +161,24 @@ prepare_libraries_spectra <-
  }
  )
  rm(spectra_extracted)
+
+ log_debug("Extracting structures for the SOP library.")
+ sop <- bind_rows(
+ spectra_harmonized_pos |>
+ bind_rows(),
+ spectra_harmonized_neg |>
+ bind_rows()
+ ) |>
+ distinct(
+ structure_inchikey = inchikey,
+ structure_smiles = smiles,
+ structure_smiles_no_stereo = smiles_no_stereo
+ ) |>
+ mutate(
+ structure_inchikey_no_stereo = structure_inchikey |>
+ gsub(pattern = "-.*", replacement = ""),
+ organism_name = NA_character_
+ )
  } else {
  log_debug("Your input file does not exist, returning empty lib instead.")
  spectra_harmonized_pos <- list(
@@ -191,22 +209,14 @@ prepare_libraries_spectra <-
  )
  )
  spectra_harmonized_neg <- spectra_harmonized_pos
- }
- log_debug("Extracting structures for the SOP library.")
- sop <- bind_rows(
- spectra_harmonized_pos |>
- bind_rows(),
- spectra_harmonized_neg |> bind_rows()
- ) |>
- distinct(
- structure_inchikey = inchikey,
- structure_smiles = smiles,
- structure_smiles_no_stereo = smiles_no_stereo
- ) |>
- mutate(
- structure_inchikey_no_stereo = stri_sub(str = structure_inchikey, from = 1, to = 14),
- organism_name = NA_character_
+ sop <- tidytable(
+ "structure_inchikey" = NA_character_,
+ "structure_smiles" = NA_character_,
+ "structure_smiles_no_stereo" = NA_character_,
+ "structure_inchikey_no_stereo" = NA_character_,
+ "organism_name" = NA_character_
  )
+ }
  log_debug("Exporting")
  export_output(sop, file = output_sop)
  mapply(

codemeta.json

@@ -644,7 +644,7 @@
  "SystemRequirements": null
  },
  "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
- "fileSize": "3192.028KB",
+ "fileSize": "3192.363KB",
  "citation": [
  {
  "@type": "ScholarlyArticle",