Merge pull request #207 from MoTrPAC/develop

v0.8.8: 24 hours time support
MoTrPAC · Jun 15, 2023 · 1969b8c · 1969b8c
2 parents cc75061 + 92b1763
commit 1969b8c
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Showing 79 changed files with 100 additions and 93 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: MotrpacBicQC
 Type: Package
 Title: QC/QA functions for the MoTrPAC community
-Version: 0.8.7
-Date: 2023-05-22
+Version: 0.8.8
+Date: 2023-06-15
 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 0.8.8 (2023-06-15)
+
+* Add 24 hours time support for the `acquisition_date` (`MM/DD/YYYY HH:MM:SS`)
+
 # MotrpacBicQC 0.8.7 (2023-05-22)
 
 * Add QC for the new required batching variables

diff --git a/R/misc.R b/R/misc.R
@@ -136,7 +136,7 @@ dl_read_gcp <- function(path,
     dt <- data.table::fread(new_path, sep=sep, header=header,...)
     return(dt)
   }else{
-    stop("- Problems loading the file")
+    stop("- Problems loading the file. Possible reason: the file does not exist in the bucket anymore. Please, validate the address. Re-run this command again with `verbose = TRUE`)")
   }
 }
 

diff --git a/R/validations.R b/R/validations.R
@@ -311,8 +311,10 @@ validate_dates_times <- function(df, column_name, verbose = TRUE) {
   parsed_datetimes <- lubridate::parse_date_time(datetime_values, 
                                                  orders = c("mdy HM", 
                                                             "mdy HMp", 
+                                                            "mdy H:M:S",
                                                             "m/d/y h:M:s a", 
-                                                            "m/d/y h:M a"), 
+                                                            "m/d/y h:M a",
+                                                            "mdY h:M:S p"), 
                                                  quiet = TRUE)
 
   # Detect incorrect format

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="2023-05-22">
+<meta name="date" content="2023-06-15">
 <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> 2023-05-22</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2023-06-15</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="2023-05-22">
+<meta name="date" content="2023-06-15">
 <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> 2023-05-22</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2023-06-15</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="2023-05-22">
+<meta name="date" content="2023-06-15">
 <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> 2023-05-22</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2023-06-15</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
@@ -1,9 +1,9 @@
-pandoc: 2.19.2
+pandoc: 3.1.1
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   other_functions: other_functions.html
   qc_metabolomics: qc_metabolomics.html
   qc_proteomics: qc_proteomics.html
-last_built: 2023-05-22T16:25Z
+last_built: 2023-06-15T22:43Z
 
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
diff --git a/docs/reference/dl_read_gcp.html b/docs/reference/dl_read_gcp.html
diff --git a/docs/reference/filter_required_columns.html b/docs/reference/filter_required_columns.html
diff --git a/docs/reference/generate_phase_details.html b/docs/reference/generate_phase_details.html