diff --git a/DESCRIPTION b/DESCRIPTION index 405c6018..2a7ea486 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: MotrpacBicQC Type: Package Title: QC/QA functions for the MoTrPAC community -Version: 0.9.1 -Date: 2024-02-02 +Version: 0.9.2 +Date: 2024-03-04 Author: MoTrPAC Bioinformatics Center Maintainer: David Jimenez-Morales Description: R Package for the analysis of MoTrPAC datasets. diff --git a/NEWS.md b/NEWS.md index efb7d374..409af1b7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,11 @@ +# MotrpacBicQC 0.9.2 (2024-03-04) + +* Critical Update: Resolved an issue where the validation of refmet names was +compromised due to updates to the Metabolomics Workbench REST service. +This version introduces adjustments to ensure accurate validation of +refmet names. + + # MotrpacBicQC 0.9.1 (2024-02-02) * New assays: `PROT_OX` diff --git a/R/metabolomics_data_dictionary.R b/R/metabolomics_data_dictionary.R index f863c4aa..907d4b77 100644 --- a/R/metabolomics_data_dictionary.R +++ b/R/metabolomics_data_dictionary.R @@ -97,7 +97,7 @@ validate_refmetname <- function(dataf, verbose){ search_api <- paste0("https://www.metabolomicsworkbench.org/rest/refmet/match/",URLencode(rn),"/name/") here <- jsonlite::fromJSON(search_api) - if(length(here) == 0){ + if(here$refmet_name == "-"){ if(verbose) message(paste0(" (-) `refmet_name` [`", rn, "`] not available in RefMet. Please, contact MW/BIC (Error RN1)")) irm <- irm + 1 idna <- idna + 1 diff --git a/docs/404.html b/docs/404.html index 415e0f95..dfd3d83f 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index b442cdc3..f925ab46 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/articles/index.html b/docs/articles/index.html index a6a47917..f4a6ee48 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/articles/other_functions.html b/docs/articles/other_functions.html index 9ba58453..a8f94462 100644 --- a/docs/articles/other_functions.html +++ b/docs/articles/other_functions.html @@ -4,7 +4,7 @@ - + MotrpacBicQC: Other Functions @@ -123,7 +123,7 @@

MotrpacBicQC: Other Functions

-

2024-02-02

+

2024-03-04

diff --git a/docs/articles/qc_metabolomics.html b/docs/articles/qc_metabolomics.html index 029052c4..3c765882 100644 --- a/docs/articles/qc_metabolomics.html +++ b/docs/articles/qc_metabolomics.html @@ -4,7 +4,7 @@ - + MotrpacBicQC: Metabolomics QC @@ -126,7 +126,7 @@

MotrpacBicQC: Metabolomics QC

-

2024-02-02

+

2024-03-04

diff --git a/docs/articles/qc_olink.html b/docs/articles/qc_olink.html index eb130979..e4c72e91 100644 --- a/docs/articles/qc_olink.html +++ b/docs/articles/qc_olink.html @@ -4,7 +4,7 @@ - + MotrpacBicQC: OLINK QC @@ -125,7 +125,7 @@

MotrpacBicQC: OLINK QC

-

2024-02-02

+

2024-03-04

diff --git a/docs/articles/qc_proteomics.html b/docs/articles/qc_proteomics.html index 07a77926..010e9670 100644 --- a/docs/articles/qc_proteomics.html +++ b/docs/articles/qc_proteomics.html @@ -4,7 +4,7 @@ - + MotrpacBicQC: Proteomics QC @@ -125,7 +125,7 @@

MotrpacBicQC: Proteomics QC

-

2024-02-02

+

2024-03-04

diff --git a/docs/authors.html b/docs/authors.html index 894d6914..f92b7063 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 @@ -82,13 +82,13 @@

Citation

Center MB (2024). MotrpacBicQC: QC/QA functions for the MoTrPAC community. -R package version 0.9.1, https://github.com/MoTrPAC/MotrpacBicQC. +R package version 0.9.2, https://github.com/MoTrPAC/MotrpacBicQC. 

@Manual{,
   title = {MotrpacBicQC: QC/QA functions for the MoTrPAC community},
   author = {MoTrPAC Bioinformatics Center},
   year = {2024},
-  note = {R package version 0.9.1},
+  note = {R package version 0.9.2},
   url = {https://github.com/MoTrPAC/MotrpacBicQC},
 }
diff --git a/docs/index.html b/docs/index.html index 371cb0db..03c479ea 100644 --- a/docs/index.html +++ b/docs/index.html @@ -41,7 +41,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/news/index.html b/docs/news/index.html index aac84032..dd1cbf52 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 @@ -66,6 +66,10 @@

Changelog

Source: NEWS.md +
+

MotrpacBicQC 0.9.2 (2024-03-04)

+

MotrpacBicQC 0.9.1 (2024-02-02)

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 4f8161e7..afc87589 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -6,5 +6,5 @@ articles: qc_metabolomics: qc_metabolomics.html qc_olink: qc_olink.html qc_proteomics: qc_proteomics.html -last_built: 2024-02-02T17:56Z +last_built: 2024-03-04T17:46Z diff --git a/docs/reference/assay_abbr.html b/docs/reference/assay_abbr.html index 74ba1eb1..59f4cc26 100644 --- a/docs/reference/assay_abbr.html +++ b/docs/reference/assay_abbr.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/assay_codes.html b/docs/reference/assay_codes.html index b657261e..dc97e62e 100644 --- a/docs/reference/assay_codes.html +++ b/docs/reference/assay_codes.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/assay_order.html b/docs/reference/assay_order.html index fbe10742..d578f6ae 100644 --- a/docs/reference/assay_order.html +++ b/docs/reference/assay_order.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/bic_animal_tissue_code.html b/docs/reference/bic_animal_tissue_code.html index 252788fe..e238f9b5 100644 --- a/docs/reference/bic_animal_tissue_code.html +++ b/docs/reference/bic_animal_tissue_code.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/check_crossfile_olink_validation.html b/docs/reference/check_crossfile_olink_validation.html index 4d5a69b4..426c5dc5 100644 --- a/docs/reference/check_crossfile_olink_validation.html +++ b/docs/reference/check_crossfile_olink_validation.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/check_failedsamples.html b/docs/reference/check_failedsamples.html index fa591f0e..33e3a12e 100644 --- a/docs/reference/check_failedsamples.html +++ b/docs/reference/check_failedsamples.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/check_manifest_rawdata.html b/docs/reference/check_manifest_rawdata.html index abbcada0..16764508 100644 --- a/docs/reference/check_manifest_rawdata.html +++ b/docs/reference/check_manifest_rawdata.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/check_metadata_metabolites.html b/docs/reference/check_metadata_metabolites.html index 3b7dbf8f..d3436748 100644 --- a/docs/reference/check_metadata_metabolites.html +++ b/docs/reference/check_metadata_metabolites.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/check_metadata_phase_file.html b/docs/reference/check_metadata_phase_file.html index 15182268..969fda01 100644 --- a/docs/reference/check_metadata_phase_file.html +++ b/docs/reference/check_metadata_phase_file.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/check_metadata_proteins.html b/docs/reference/check_metadata_proteins.html index c5be8d49..5dcbdc56 100644 --- a/docs/reference/check_metadata_proteins.html +++ b/docs/reference/check_metadata_proteins.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/check_metadata_samples.html b/docs/reference/check_metadata_samples.html index 3cbc620a..55494169 100644 --- a/docs/reference/check_metadata_samples.html +++ b/docs/reference/check_metadata_samples.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/check_metadata_samples_olink.html b/docs/reference/check_metadata_samples_olink.html index 93de5fa2..f9cae71b 100644 --- a/docs/reference/check_metadata_samples_olink.html +++ b/docs/reference/check_metadata_samples_olink.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/check_missing_values.html b/docs/reference/check_missing_values.html index 86683837..bd150649 100644 --- a/docs/reference/check_missing_values.html +++ b/docs/reference/check_missing_values.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/check_ratio_proteomics.html b/docs/reference/check_ratio_proteomics.html index 2abda10f..871fbae5 100644 --- a/docs/reference/check_ratio_proteomics.html +++ b/docs/reference/check_ratio_proteomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/check_results.html b/docs/reference/check_results.html index 0c87adde..9caf1853 100644 --- a/docs/reference/check_results.html +++ b/docs/reference/check_results.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/check_results_olink.html b/docs/reference/check_results_olink.html index e902613d..6070e572 100644 --- a/docs/reference/check_results_olink.html +++ b/docs/reference/check_results_olink.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/check_rii_proteomics.html b/docs/reference/check_rii_proteomics.html index 0c3ba799..6f58ba3a 100644 --- a/docs/reference/check_rii_proteomics.html +++ b/docs/reference/check_rii_proteomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/check_vial_metadata_proteomics.html b/docs/reference/check_vial_metadata_proteomics.html index 966ac50a..c4be6ef3 100644 --- a/docs/reference/check_vial_metadata_proteomics.html +++ b/docs/reference/check_vial_metadata_proteomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/check_viallabel_dmaqc.html b/docs/reference/check_viallabel_dmaqc.html index fd9939f4..8cdcc743 100644 --- a/docs/reference/check_viallabel_dmaqc.html +++ b/docs/reference/check_viallabel_dmaqc.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/combine_metabolomics_batch.html b/docs/reference/combine_metabolomics_batch.html index 30a6577d..cffe1ffa 100644 --- a/docs/reference/combine_metabolomics_batch.html +++ b/docs/reference/combine_metabolomics_batch.html @@ -19,7 +19,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/create_folder.html b/docs/reference/create_folder.html index cfedc793..dc2a85e7 100644 --- a/docs/reference/create_folder.html +++ b/docs/reference/create_folder.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/dl_read_gcp.html b/docs/reference/dl_read_gcp.html index d462e42b..962c2558 100644 --- a/docs/reference/dl_read_gcp.html +++ b/docs/reference/dl_read_gcp.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/filter_required_columns.html b/docs/reference/filter_required_columns.html index 5c6f53ae..3589f215 100644 --- a/docs/reference/filter_required_columns.html +++ b/docs/reference/filter_required_columns.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/generate_phase_details.html b/docs/reference/generate_phase_details.html index a7d20b89..53db82a9 100644 --- a/docs/reference/generate_phase_details.html +++ b/docs/reference/generate_phase_details.html @@ -21,7 +21,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/get_and_validate_mdd.html b/docs/reference/get_and_validate_mdd.html index e99d8232..480c437f 100644 --- a/docs/reference/get_and_validate_mdd.html +++ b/docs/reference/get_and_validate_mdd.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/get_full_path2batch.html b/docs/reference/get_full_path2batch.html index 0f69574d..a61ea6cb 100644 --- a/docs/reference/get_full_path2batch.html +++ b/docs/reference/get_full_path2batch.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/group_abbr.html b/docs/reference/group_abbr.html index f3331ee0..222b3c4a 100644 --- a/docs/reference/group_abbr.html +++ b/docs/reference/group_abbr.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/group_cols.html b/docs/reference/group_cols.html index 3069a058..92fe3a77 100644 --- a/docs/reference/group_cols.html +++ b/docs/reference/group_cols.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/index.html b/docs/reference/index.html index 75de9407..c58bd71c 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/load_metabolomics_batch.html b/docs/reference/load_metabolomics_batch.html index 2e6ffe27..40c722f2 100644 --- a/docs/reference/load_metabolomics_batch.html +++ b/docs/reference/load_metabolomics_batch.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/load_olink_batch.html b/docs/reference/load_olink_batch.html index 4bd3a422..d4cf1b7e 100644 --- a/docs/reference/load_olink_batch.html +++ b/docs/reference/load_olink_batch.html @@ -21,7 +21,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/load_proteomics.html b/docs/reference/load_proteomics.html index 3d2fd910..2096e472 100644 --- a/docs/reference/load_proteomics.html +++ b/docs/reference/load_proteomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/merge_all_metabolomics.html b/docs/reference/merge_all_metabolomics.html index 6ee306e8..63dd6c09 100644 --- a/docs/reference/merge_all_metabolomics.html +++ b/docs/reference/merge_all_metabolomics.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/merge_metabolomics_metadata.html b/docs/reference/merge_metabolomics_metadata.html index 6b2e6c99..e7ffcd0a 100644 --- a/docs/reference/merge_metabolomics_metadata.html +++ b/docs/reference/merge_metabolomics_metadata.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/merge_phenotype_metabolomics.html b/docs/reference/merge_phenotype_metabolomics.html index aa901bbe..5f375aeb 100644 --- a/docs/reference/merge_phenotype_metabolomics.html +++ b/docs/reference/merge_phenotype_metabolomics.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/metabolomics_data_dictionary.html b/docs/reference/metabolomics_data_dictionary.html index bf1f5069..2a876bff 100644 --- a/docs/reference/metabolomics_data_dictionary.html +++ b/docs/reference/metabolomics_data_dictionary.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/metadata_metabolites_named.html b/docs/reference/metadata_metabolites_named.html index f8c16abd..5364eaa1 100644 --- a/docs/reference/metadata_metabolites_named.html +++ b/docs/reference/metadata_metabolites_named.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/metadata_metabolites_unnamed.html b/docs/reference/metadata_metabolites_unnamed.html index 3da459f2..6185ee22 100644 --- a/docs/reference/metadata_metabolites_unnamed.html +++ b/docs/reference/metadata_metabolites_unnamed.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/metadata_sample_named.html b/docs/reference/metadata_sample_named.html index c4b61b5a..00b93bfa 100644 --- a/docs/reference/metadata_sample_named.html +++ b/docs/reference/metadata_sample_named.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/metadata_sample_unnamed.html b/docs/reference/metadata_sample_unnamed.html index 51bb5615..80d1a4c3 100644 --- a/docs/reference/metadata_sample_unnamed.html +++ b/docs/reference/metadata_sample_unnamed.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/open_file.html b/docs/reference/open_file.html index a72a2aa3..ece8aaf3 100644 --- a/docs/reference/open_file.html +++ b/docs/reference/open_file.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/phenotypes_pass1a06_short.html b/docs/reference/phenotypes_pass1a06_short.html index 436273e8..243a0573 100644 --- a/docs/reference/phenotypes_pass1a06_short.html +++ b/docs/reference/phenotypes_pass1a06_short.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/plot_basic_metabolomics_qc.html b/docs/reference/plot_basic_metabolomics_qc.html index 74e16e87..22eced76 100644 --- a/docs/reference/plot_basic_metabolomics_qc.html +++ b/docs/reference/plot_basic_metabolomics_qc.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/plot_basic_olink_qc.html b/docs/reference/plot_basic_olink_qc.html index e773a14e..17117c4a 100644 --- a/docs/reference/plot_basic_olink_qc.html +++ b/docs/reference/plot_basic_olink_qc.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/proteomics_plots_rii.html b/docs/reference/proteomics_plots_rii.html index d493f652..07eddbcf 100644 --- a/docs/reference/proteomics_plots_rii.html +++ b/docs/reference/proteomics_plots_rii.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/remove_empty_columns.html b/docs/reference/remove_empty_columns.html index feddb96a..6cf666d5 100644 --- a/docs/reference/remove_empty_columns.html +++ b/docs/reference/remove_empty_columns.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/remove_empty_rows.html b/docs/reference/remove_empty_rows.html index 663a354c..e4f0a7e3 100644 --- a/docs/reference/remove_empty_rows.html +++ b/docs/reference/remove_empty_rows.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/results_named.html b/docs/reference/results_named.html index 4207a30c..5bdffcf1 100644 --- a/docs/reference/results_named.html +++ b/docs/reference/results_named.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/results_unnamed.html b/docs/reference/results_unnamed.html index 3c901b9e..953f78a4 100644 --- a/docs/reference/results_unnamed.html +++ b/docs/reference/results_unnamed.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/set_phase.html b/docs/reference/set_phase.html index 5ad6834e..2c65b33c 100644 --- a/docs/reference/set_phase.html +++ b/docs/reference/set_phase.html @@ -27,7 +27,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/sex_abbr.html b/docs/reference/sex_abbr.html index b6f6dfca..c824a9d1 100644 --- a/docs/reference/sex_abbr.html +++ b/docs/reference/sex_abbr.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/sex_cols.html b/docs/reference/sex_cols.html index 3a14764d..db3abbbf 100644 --- a/docs/reference/sex_cols.html +++ b/docs/reference/sex_cols.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/tissue_abbr.html b/docs/reference/tissue_abbr.html index acaefdf6..df52a9cd 100644 --- a/docs/reference/tissue_abbr.html +++ b/docs/reference/tissue_abbr.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/tissue_cols.html b/docs/reference/tissue_cols.html index 675965dd..70205b44 100644 --- a/docs/reference/tissue_cols.html +++ b/docs/reference/tissue_cols.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/tissue_order.html b/docs/reference/tissue_order.html index db5d4ff4..6dd064c3 100644 --- a/docs/reference/tissue_order.html +++ b/docs/reference/tissue_order.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_assay.html b/docs/reference/validate_assay.html index 18361ea3..c847aea2 100644 --- a/docs/reference/validate_assay.html +++ b/docs/reference/validate_assay.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_batch.html b/docs/reference/validate_batch.html index 3f0c0d16..2a063b11 100644 --- a/docs/reference/validate_batch.html +++ b/docs/reference/validate_batch.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_cas.html b/docs/reference/validate_cas.html index 4cf4e66e..9e0454c8 100644 --- a/docs/reference/validate_cas.html +++ b/docs/reference/validate_cas.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_dates_times.html b/docs/reference/validate_dates_times.html index 9b2b91f2..947901ba 100644 --- a/docs/reference/validate_dates_times.html +++ b/docs/reference/validate_dates_times.html @@ -19,7 +19,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_lc_column_id.html b/docs/reference/validate_lc_column_id.html index c4ae2206..b216d4d7 100644 --- a/docs/reference/validate_lc_column_id.html +++ b/docs/reference/validate_lc_column_id.html @@ -19,7 +19,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_metabolomics.html b/docs/reference/validate_metabolomics.html index 84a7dead..cb7969b5 100644 --- a/docs/reference/validate_metabolomics.html +++ b/docs/reference/validate_metabolomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_na_empty.html b/docs/reference/validate_na_empty.html index 9eba2dd7..b2824d5b 100644 --- a/docs/reference/validate_na_empty.html +++ b/docs/reference/validate_na_empty.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_olink.html b/docs/reference/validate_olink.html index c14c9d5f..7b929971 100644 --- a/docs/reference/validate_olink.html +++ b/docs/reference/validate_olink.html @@ -20,7 +20,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_phase.html b/docs/reference/validate_phase.html index 7d7c64d0..db77628d 100644 --- a/docs/reference/validate_phase.html +++ b/docs/reference/validate_phase.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_processFolder.html b/docs/reference/validate_processFolder.html index a7057731..7ad21968 100644 --- a/docs/reference/validate_processFolder.html +++ b/docs/reference/validate_processFolder.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_proteomics.html b/docs/reference/validate_proteomics.html index 6566229d..18ed0892 100644 --- a/docs/reference/validate_proteomics.html +++ b/docs/reference/validate_proteomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_refmetname.html b/docs/reference/validate_refmetname.html index 8b6967c8..10d0b090 100644 --- a/docs/reference/validate_refmetname.html +++ b/docs/reference/validate_refmetname.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_tissue.html b/docs/reference/validate_tissue.html index fb6fa1f3..6f9495a5 100644 --- a/docs/reference/validate_tissue.html +++ b/docs/reference/validate_tissue.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_two_phases.html b/docs/reference/validate_two_phases.html index 4aa29c90..9b1eb982 100644 --- a/docs/reference/validate_two_phases.html +++ b/docs/reference/validate_two_phases.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_uniprot_ids_with_uniprot.html b/docs/reference/validate_uniprot_ids_with_uniprot.html index 1bef597f..75bf97e3 100644 --- a/docs/reference/validate_uniprot_ids_with_uniprot.html +++ b/docs/reference/validate_uniprot_ids_with_uniprot.html @@ -21,7 +21,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/validate_yyyymmdd_dates.html b/docs/reference/validate_yyyymmdd_dates.html index e93b6e24..4bc05780 100644 --- a/docs/reference/validate_yyyymmdd_dates.html +++ b/docs/reference/validate_yyyymmdd_dates.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/write_metabolomics_releases.html b/docs/reference/write_metabolomics_releases.html index 9fb28ad3..cdc8f16c 100644 --- a/docs/reference/write_metabolomics_releases.html +++ b/docs/reference/write_metabolomics_releases.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/write_olink_releases.html b/docs/reference/write_olink_releases.html index 431b04bb..e254216a 100644 --- a/docs/reference/write_olink_releases.html +++ b/docs/reference/write_olink_releases.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/docs/reference/write_proteomics_releases.html b/docs/reference/write_proteomics_releases.html index 4320f824..a84e16f4 100644 --- a/docs/reference/write_proteomics_releases.html +++ b/docs/reference/write_proteomics_releases.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.1 + 0.9.2 diff --git a/tests/testthat/test-refmet.R b/tests/testthat/test-refmet.R new file mode 100644 index 00000000..017a05c1 --- /dev/null +++ b/tests/testthat/test-refmet.R @@ -0,0 +1,39 @@ +context("Testing validate_refmetname function") + +test_that("validate_refmetname handles known refmet_name correctly", { + # Example test data + test_data <- data.frame( + refmet_name = c("1-Methyl nicotinamide", "11-Deoxycortisol", "This Should Fail", "I hope this as well---", "-"), + stringsAsFactors = FALSE + ) + + # Call the function with verbose = FALSE to suppress messages during test + actual_missed_ids <- validate_refmetname(test_data, verbose = FALSE) + + # Check if the actual missed IDs match the expected outcome + expect_equal(actual_missed_ids, 3) +}) + + +test_that("Successful API call returns correctly structured list with no additional elements", { + # Known good refmet_name that will return a successful response + test_refmet_name <- "11-Deoxycortisol" + + # Expected elements in the response + expected_elements <- c("refmet_name", "formula", "exactmass", "super_class", "main_class", "sub_class") + + search_api <- paste0("https://www.metabolomicsworkbench.org/rest/refmet/match/",URLencode(test_refmet_name),"/name/") + response <- jsonlite::fromJSON(search_api) + + # Check that the response has all the expected elements + expect_true(all(expected_elements %in% names(response)), "Response is missing expected elements.") + + # Check for no additional elements + expect_equal(length(names(response)), length(expected_elements), + info = "Response contains additional unexpected elements.") + + unexpected_elements <- setdiff(names(response), expected_elements) + expect_equal(unexpected_elements, character(0), + info = paste("Unexpected elements in response:", paste(unexpected_elements, collapse = ", "))) +}) +