Merge pull request #212 from MoTrPAC/develop

MotrpacBicQC 0.8.9: process BICRESULTS and more
MoTrPAC · Jul 7, 2023 · 5113b9b · 5113b9b
2 parents 1969b8c + 1aefbd4
commit 5113b9b
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Showing 80 changed files with 107 additions and 91 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: MotrpacBicQC
 Type: Package
 Title: QC/QA functions for the MoTrPAC community
-Version: 0.8.8
-Date: 2023-06-15
+Version: 0.8.9
+Date: 2023-07-07
 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 +1,10 @@
+
+# MotrpacBicQC 0.8.9 (2023-07-07)
+
+* Fix bug preventing the processing of BICRESULTS folders (proteomics)
+* Make clear that the metadata_phase.txt file is required
+* Other enhancements
+
 # MotrpacBicQC 0.8.8 (2023-06-15)
 
 * Add 24 hours time support for the `acquisition_date` (`MM/DD/YYYY HH:MM:SS`)

diff --git a/R/misc.R b/R/misc.R
@@ -420,7 +420,7 @@ set_phase <- function(input_results_folder,
   if ( !(purrr::is_empty(file_phase)) ){
     phase_details <- readr::read_lines(file_phase, n_max = 1)
     if ( !(is.na(phase_details) || phase_details == '') ){
-      if(verbose) message("+ Motrpac phase reported: ", phase_details, " (info from metadata_phase.txt available)")
+      if(verbose) message("+ Motrpac phase reported: ", phase_details, " (info from metadata_phase.txt available): OK")
 
       if( grepl("\\|", phase_details) ){
         validate_two_phases(phase_details = phase_details, verbose = FALSE)
@@ -431,13 +431,13 @@ set_phase <- function(input_results_folder,
         dmaqc_phase2validate <- phase_details
       }
     }else{
-      if(verbose) message("+ Motrpac phase: ", phase, " (metadata_phase.txt available but EMPTY)")
+      if(verbose) message("+ Motrpac phase: ", phase, " (metadata_phase.txt available but EMPTY): FAIL")
       if( isFALSE(dmaqc_phase2validate) ){
         dmaqc_phase2validate <- phase
       }
     }
   }else{
-    if(verbose) message("+ Motrpac phase: ", phase, " (metadata_phase.txt file NOT available)")
+    if(verbose) message("+ Motrpac phase: ", phase, " (metadata_phase.txt file NOT available): FAIL")
     if( isFALSE(dmaqc_phase2validate) ){
       dmaqc_phase2validate <- phase
     }

diff --git a/R/proteomics_qc.R b/R/proteomics_qc.R
@@ -1330,7 +1330,7 @@ validate_proteomics <- function(input_results_folder,
 
 
   # PRINT OUT RESULTS-----
-  batchversion <- stringr::str_extract(string = input_results_folder, pattern = "BATCH.*_[0-9]+/RESULTS_[0-9]+")
+  batchversion <- stringr::str_extract(string = input_results_folder, pattern = "BATCH.*_([0-9]+/(RESULTS|BICRESULTS)_[0-9]+)")
 
   qc_date <- Sys.time()
   qc_date <- gsub("-", "", qc_date)

diff --git a/R/validations.R b/R/validations.R
@@ -218,7 +218,7 @@ check_viallabel_dmaqc <- function(vl_submitted,
 validate_assay <- function(input_results_folder){
 
   assay <- stringr::str_extract(string = input_results_folder,
-                                pattern = "(IONPNEG|RPNEG|RPPOS|HILICPOS|LRPPOS|LRPNEG|3HIB|AA|AC_DUKE|ACOA|BAIBA|CER_DUKE|CONV|KA|NUC|OA|SPHM|OXYLIPNEG|ETAMIDPOS|AC_MAYO|AMINES|CER_MAYO|TCA|IMM_CRT|IMM_GLC|IMM_INS|PROT_PH|PROT_PR|PROT_AC|PROT_UB)")
+                                pattern = "(?<=T\\d{2}/)(IONPNEG|RPNEG|RPPOS|HILICPOS|LRPPOS|LRPNEG|3HIB|AA|AC_DUKE|ACOA|BAIBA|CER_DUKE|CONV|KA|NUC|OA|SPHM|OXYLIPNEG|ETAMIDPOS|AC_MAYO|AMINES|CER_MAYO|TCA|IMM_CRT|IMM_GLC|IMM_INS|PROT_PH|PROT_PR|PROT_AC|PROT_UB)")
   if(is.na(assay)){
     stop("ASSAY not found in the folder structure")
   }else{

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="2023-06-15">
+<meta name="date" content="2023-07-07">
 <title>MotrpacBicQC: Other Functions</title>
 <script src="other_functions_files/header-attrs-2.21/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> 2023-06-15</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2023-07-07</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="2023-06-15">
+<meta name="date" content="2023-07-07">
 <title>MotrpacBicQC: Metabolomics QC</title>
 <script src="qc_metabolomics_files/header-attrs-2.21/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> 2023-06-15</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2023-07-07</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="2023-06-15">
+<meta name="date" content="2023-07-07">
 <title>MotrpacBicQC: Proteomics QC</title>
 <script src="qc_proteomics_files/header-attrs-2.21/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> 2023-06-15</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2023-07-07</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: 2023-06-15T22:43Z
+last_built: 2023-07-07T18:20Z
 
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_phase_file.html b/docs/reference/check_metadata_phase_file.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/create_folder.html b/docs/reference/create_folder.html