MotrpacBicQC 0.9.3: critical update of refmet name additional validation

MoTrPAC · Mar 25, 2024 · f523ef1 · f523ef1
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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: 0.9.2
-Date: 2024-03-04
+Version: 0.9.3
+Date: 2024-03-25
 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 +1,15 @@
+# MotrpacBicQC 0.9.3 (2024-03-25)
+
+* Critical update `validate_refmetname`: ensure checking the refmet standarized name. Update refmet tests
+* Update `get_and_validate_mdd()`
+  + Update REST service url
+  + Update Documentation
+  + Remove dependency on data.table
+* Enhance: only one `metadata_phase` file allowed
+* Enhance `dl_read_gcp`: replace data table by read_delim
+* Enhance `open_file`: accept only tab delimited files
+
+
 # MotrpacBicQC 0.9.2 (2024-03-04)
 
 * Critical Update: Resolved an issue where the validation of refmet names was 

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="2024-03-04">
+<meta name="date" content="2024-03-25">
 <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> 2024-03-04</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-03-25</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="2024-03-04">
+<meta name="date" content="2024-03-25">
 <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> 2024-03-04</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-03-25</p>
 
 
 
@@ -203,7 +203,11 @@ <h2 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a>
 <pre><code><span><span class="co">##   + (+) `metabolite_name` OK</span></span></code></pre>
 <pre><code><span><span class="co">##   + (+) `refmet_name` unique values: OK</span></span></code></pre>
 <pre><code><span><span class="co">##   + Validating `refmet_name` (it might take some time)</span></span></code></pre>
-<pre><code><span><span class="co">##   + (+) `refmet_name` ids found in refmet: OK</span></span></code></pre>
+<pre><code><span><span class="co">##       (-) `refmet_name` [`Leucine/Isoleucine`] must be modified to the RefMet Standarized name: "Leucine" (Error RN2)</span></span></code></pre>
+<pre><code><span><span class="co">##       (-) `refmet_name` [`Oxoglutaric acid`] must be modified to the RefMet Standarized name: "2-Oxoglutaric acid" (Error RN2)</span></span></code></pre>
+<pre><code><span><span class="co">##       (-) `refmet_name` [`Citric acid/Isocitric acid`] must be modified to the RefMet Standarized name: "Citric acid" (Error RN2)</span></span></code></pre>
+<pre><code><span><span class="co">##       (-) Total number of missed ids on MW: 3</span></span></code></pre>
+<pre><code><span><span class="co">##    - (-) SUMMARY: 3 `refmet_name` not found in RefMet Metabolomics Data Dictionary: FAIL</span></span></code></pre>
 <pre><code><span><span class="co">##   + (+) {rt} all numeric: OK</span></span></code></pre>
 <pre><code><span><span class="co">##   + (+) {mz} all numeric: OK</span></span></code></pre>
 <pre><code><span><span class="co">##   + (+) {`neutral_mass`} all numeric values OK</span></span></code></pre>

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="2024-03-04">
+<meta name="date" content="2024-03-25">
 <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> 2024-03-04</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-03-25</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="2024-03-04">
+<meta name="date" content="2024-03-25">
 <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> 2024-03-04</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2024-03-25</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: 2024-03-04T17:46Z
+last_built: 2024-03-25T18:31Z
 
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
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diff --git a/docs/reference/check_vial_metadata_proteomics.html b/docs/reference/check_vial_metadata_proteomics.html