Merge pull request #230 from MoTrPAC/develop

MotrpacBicQC 0.9.2: critical update of refmet name validation
MoTrPAC · Mar 4, 2024 · f6242f9 · f6242f9
2 parents 82244f3 + 61f15d2
commit f6242f9
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diff --git 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 <davidjm@stanford.edu>
 Description: R Package for the analysis of MoTrPAC datasets. 

diff --git 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
@@ -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
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/other_functions.html b/docs/articles/other_functions.html
@@ -4,7 +4,7 @@
 <meta charset="utf-8">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="generator" content="pandoc">
-<meta name="date" content="2024-02-02">
+<meta name="date" content="2024-03-04">
 <title>MotrpacBicQC: Other Functions</title>
 <script src="other_functions_files/header-attrs-2.25/header-attrs.js"></script><script src="other_functions_files/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1">
 <link href="other_functions_files/bootstrap-3.3.7/css/bootstrap.min.css" rel="stylesheet">
@@ -123,7 +123,7 @@ <h1 class="title">MotrpacBicQC: Other Functions</h1>
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-02-02</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-03-04</p>
 
 
 

diff --git a/docs/articles/qc_metabolomics.html b/docs/articles/qc_metabolomics.html
@@ -4,7 +4,7 @@
 <meta charset="utf-8">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="generator" content="pandoc">
-<meta name="date" content="2024-02-02">
+<meta name="date" content="2024-03-04">
 <title>MotrpacBicQC: Metabolomics QC</title>
 <script src="qc_metabolomics_files/header-attrs-2.25/header-attrs.js"></script><script src="qc_metabolomics_files/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1">
 <link href="qc_metabolomics_files/bootstrap-3.3.7/css/bootstrap.min.css" rel="stylesheet">
@@ -126,7 +126,7 @@ <h1 class="title">MotrpacBicQC: Metabolomics QC</h1>
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-02-02</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-03-04</p>
 
 
 

diff --git a/docs/articles/qc_olink.html b/docs/articles/qc_olink.html
@@ -4,7 +4,7 @@
 <meta charset="utf-8">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="generator" content="pandoc">
-<meta name="date" content="2024-02-02">
+<meta name="date" content="2024-03-04">
 <title>MotrpacBicQC: OLINK QC</title>
 <script src="qc_olink_files/header-attrs-2.25/header-attrs.js"></script><script src="qc_olink_files/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1">
 <link href="qc_olink_files/bootstrap-3.3.7/css/bootstrap.min.css" rel="stylesheet">
@@ -125,7 +125,7 @@ <h1 class="title">MotrpacBicQC: OLINK QC</h1>
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-02-02</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-03-04</p>
 
 
 

diff --git a/docs/articles/qc_proteomics.html b/docs/articles/qc_proteomics.html
@@ -4,7 +4,7 @@
 <meta charset="utf-8">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="generator" content="pandoc">
-<meta name="date" content="2024-02-02">
+<meta name="date" content="2024-03-04">
 <title>MotrpacBicQC: Proteomics QC</title>
 <script src="qc_proteomics_files/header-attrs-2.25/header-attrs.js"></script><script src="qc_proteomics_files/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1">
 <link href="qc_proteomics_files/bootstrap-3.3.7/css/bootstrap.min.css" rel="stylesheet">
@@ -125,7 +125,7 @@ <h1 class="title">MotrpacBicQC: Proteomics QC</h1>
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-02-02</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-03-04</p>
 
 
 

diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/notes_developers.html b/docs/notes_developers.html
diff --git 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
diff --git a/docs/reference/assay_codes.html b/docs/reference/assay_codes.html
diff --git a/docs/reference/assay_order.html b/docs/reference/assay_order.html
diff --git a/docs/reference/bic_animal_tissue_code.html b/docs/reference/bic_animal_tissue_code.html
diff --git a/docs/reference/check_crossfile_olink_validation.html b/docs/reference/check_crossfile_olink_validation.html
diff --git a/docs/reference/check_failedsamples.html b/docs/reference/check_failedsamples.html
diff --git a/docs/reference/check_manifest_rawdata.html b/docs/reference/check_manifest_rawdata.html
diff --git a/docs/reference/check_metadata_metabolites.html b/docs/reference/check_metadata_metabolites.html
diff --git a/docs/reference/check_metadata_phase_file.html b/docs/reference/check_metadata_phase_file.html
diff --git a/docs/reference/check_metadata_proteins.html b/docs/reference/check_metadata_proteins.html
diff --git a/docs/reference/check_metadata_samples.html b/docs/reference/check_metadata_samples.html
diff --git a/docs/reference/check_metadata_samples_olink.html b/docs/reference/check_metadata_samples_olink.html
diff --git a/docs/reference/check_missing_values.html b/docs/reference/check_missing_values.html
diff --git a/docs/reference/check_ratio_proteomics.html b/docs/reference/check_ratio_proteomics.html
diff --git a/docs/reference/check_results.html b/docs/reference/check_results.html
diff --git a/docs/reference/check_results_olink.html b/docs/reference/check_results_olink.html
diff --git a/docs/reference/check_rii_proteomics.html b/docs/reference/check_rii_proteomics.html
diff --git a/docs/reference/check_vial_metadata_proteomics.html b/docs/reference/check_vial_metadata_proteomics.html
diff --git a/docs/reference/check_viallabel_dmaqc.html b/docs/reference/check_viallabel_dmaqc.html
diff --git a/docs/reference/combine_metabolomics_batch.html b/docs/reference/combine_metabolomics_batch.html
diff --git a/docs/reference/create_folder.html b/docs/reference/create_folder.html
diff --git a/docs/reference/dl_read_gcp.html b/docs/reference/dl_read_gcp.html