v0.5.6: Bug fix

Bug fix affecting manifest file check
MoTrPAC · Jul 23, 2021 · 9599da1 · 9599da1
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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: 0.5.5
-Date: 2021-07-21
+Version: 0.5.6
+Date: 2021-07-22
 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 +1,7 @@
+# MotrpacBicQC 0.5.6 (2021-07-22)
+
+* Bug fix
+
 # MotrpacBicQC 0.5.5 (2021-07-21)
 
 * Update: add human tissue codes

diff --git a/R/metabolomics_qc.R b/R/metabolomics_qc.R
@@ -830,7 +830,7 @@ validate_metabolomics <- function(input_results_folder,
       manifest$file_base <- basename(manifest$file_name)
 
       if(f_mmn){
-        metadata_metabolites_named_file <- basename(manifest$file_name[grepl(".*etadata_metabolit.*_named", manifest$file_name)])
+        metadata_metabolites_named_file <- basename(manifest$file_name[grepl(".*etadata_metabolit.*_named", manifest$file_name)])[1]
         tocheck <- basename(m_m_n_f)
         if( tocheck == metadata_metabolites_named_file){
           if(verbose) message("   + (+) metadata_metabolites_named_file included in manifest: OK")
@@ -841,7 +841,7 @@ validate_metabolomics <- function(input_results_folder,
       }
 
       if(f_msn){
-        metadata_samples_named_file <- basename(manifest$file_name[grepl(".*etadata_samp.*_named", manifest$file_name)])
+        metadata_samples_named_file <- basename(manifest$file_name[grepl(".*etadata_samp.*_named", manifest$file_name)])[1]
         tocheck <- basename(m_s_n_f)
         if( tocheck == metadata_samples_named_file ){
           if(verbose) message("   + (+) metadata_sample_named_file included in manifest: OK")
@@ -865,7 +865,7 @@ validate_metabolomics <- function(input_results_folder,
       } # f_msn
 
       if(f_rmn){
-        results_metabolites_named_file <- basename(manifest$file_name[grepl(".*esults_metabolit.*_named", manifest$file_name)])
+        results_metabolites_named_file <- basename(manifest$file_name[grepl(".*esults_metabolit.*_named", manifest$file_name)])[1]
         tocheck <- basename(r_m_n_f)
         if( tocheck == results_metabolites_named_file ){
           if(verbose) message("   + (+) results_metabolites_named_file included in manifest: OK")
@@ -880,7 +880,8 @@ validate_metabolomics <- function(input_results_folder,
       if( any(grepl(processfolder, experimentalDetails_file)) ){
         if(verbose) message("   + (+) experimentalDetails_file included in manifest: OK")
         full_path_edf <- file.path(normalizePath(batch_folder) , experimentalDetails_file )
-        if( file.exists(full_path_edf)  ){
+        full_path_edf <- sort(full_path_edf, decreasing = TRUE)
+        if( file.exists(full_path_edf[1])  ){
           if(verbose) message("   + (+) experimentalDetails_file exists: OK")
         }else{
           if(verbose) message("      - (-) experimentalDetails_file cannot be found: FAIL")
@@ -895,7 +896,7 @@ validate_metabolomics <- function(input_results_folder,
       if(untargeted){
 
         if(f_mmu){
-          metadata_metabolites_unnamed_file <- basename(manifest$file_name[grepl(".*etadata_metabolit.*_unnamed", manifest$file_name)])
+          metadata_metabolites_unnamed_file <- basename(manifest$file_name[grepl(".*etadata_metabolit.*_unnamed", manifest$file_name)])[1]
           tocheck <- basename(m_m_u_f)
           if( tocheck == metadata_metabolites_unnamed_file ){
             if(verbose) message("   + (+) results_metabolites_unnamed_file included in manifest: OK")
@@ -906,7 +907,7 @@ validate_metabolomics <- function(input_results_folder,
         }
 
         if(f_msu){
-          metadata_samples_unnamed_file <- basename(manifest$file_name[grepl(".*etadata_sam.*_unnamed", manifest$file_name)])
+          metadata_samples_unnamed_file <- basename(manifest$file_name[grepl(".*etadata_sam.*_unnamed", manifest$file_name)])[1]
           tocheck <- basename(m_s_u_f)
           if( tocheck == metadata_samples_unnamed_file ){
             if(verbose) message("   + (+) metadata_sample_unnamed_file included in manifest: OK")
@@ -931,7 +932,7 @@ validate_metabolomics <- function(input_results_folder,
         }
 
         if(f_rmu){
-          results_metabolites_unnamed_file <- basename(manifest$file_name[grepl(".*esults_metabolit.*_unnamed", manifest$file_name)])
+          results_metabolites_unnamed_file <- basename(manifest$file_name[grepl(".*esults_metabolit.*_unnamed", manifest$file_name)])[1]
 
           tocheck <- basename(r_m_u_f)
           if( tocheck == results_metabolites_unnamed_file ){
@@ -947,7 +948,8 @@ validate_metabolomics <- function(input_results_folder,
         if( any(grepl(processfolder, experimentalDetails_file)) ){
           if(verbose) message("   + (+) experimentalDetails_file included in manifest: OK")
           full_path_edf <- file.path(normalizePath(batch_folder) , experimentalDetails_file )
-          if( file.exists(full_path_edf)  ){
+          full_path_edf <- sort(full_path_edf, decreasing = TRUE)
+          if( file.exists(full_path_edf)[1]  ){
             if(verbose) message("   + (+) experimentalDetails_file exists: OK")
           }else{
             if(verbose) message("      - (-) experimentalDetails_file cannot be found: FAIL")

diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@ Currently supports both Metabolomics and Proteomics datasets.
 
 ## Package Updates
 
-This package is frequently updated. Please, check the file [NEWS.md](https://github.com/MoTrPAC/MotrpacBicQC/blob/master/NEWS.md) to find out more about the changes affecting every version
+This package is frequently updated. Please, check the file [NEWS.md](https://motrpac.github.io/MotrpacBicQC/news/index.html) to find out more about the changes affecting every version
 
 ## Installation
 

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="2021-07-21">
+<meta name="date" content="2021-07-22">
 <title>MotrpacBicQC: Other Functions</title>
 <script src="other_functions_files/header-attrs-2.9/header-attrs.js"></script><script src="other_functions_files/jquery-1.11.3/jquery.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="hasAnchor">
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2021-07-21</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2021-07-22</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="2021-07-21">
+<meta name="date" content="2021-07-22">
 <title>MotrpacBicQC: Metabolomics QC</title>
 <script src="qc_metabolomics_files/header-attrs-2.9/header-attrs.js"></script><script src="qc_metabolomics_files/jquery-1.11.3/jquery.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">
@@ -191,7 +191,7 @@ <h1 class="hasAnchor">
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2021-07-21</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2021-07-22</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="2021-07-21">
+<meta name="date" content="2021-07-22">
 <title>MotrpacBicQC: Proteomics QC</title>
 <script src="qc_proteomics_files/header-attrs-2.9/header-attrs.js"></script><script src="qc_proteomics_files/jquery-1.11.3/jquery.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">
@@ -191,7 +191,7 @@ <h1 class="hasAnchor">
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2021-07-21</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2021-07-22</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
@@ -5,5 +5,5 @@ articles:
   other_functions: other_functions.html
   qc_metabolomics: qc_metabolomics.html
   qc_proteomics: qc_proteomics.html
-last_built: 2021-07-21T16:48Z
+last_built: 2021-07-23T02:37Z
 
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_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_samples.html b/docs/reference/check_metadata_samples.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_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/filter_required_columns.html b/docs/reference/filter_required_columns.html
diff --git a/docs/reference/get_and_validate_mdd.html b/docs/reference/get_and_validate_mdd.html