Fix typo in property description, rerender affected docs

BioLockJ-Dev-Team · Jan 18, 2021 · 99d1279 · 99d1279
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diff --git a/docs/GENERATED/General-Properties/index.html b/docs/GENERATED/General-Properties/index.html
@@ -693,11 +693,7 @@ <h3 id="r"><a href="../R/">r</a><a class="headerlink" href="#r" title="Permanent
 </tr>
 <tr>
 <td align="left"><em>r.timeout</em></td>
-<td align="left"><em>integer</em> <br>defines the number of minutes before R script fails due to</td>
-</tr>
-<tr>
-<td align="left">* timeout. If set to 0, an estimate is used.<br><em>default:</em>  0</td>
-<td align="left"></td>
+<td align="left"><em>integer</em> <br>defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used.<br><em>default:</em>  0</td>
 </tr>
 <tr>
 <td align="left"><em>r.useUniqueColors</em></td>

diff --git a/docs/GENERATED/R/index.html b/docs/GENERATED/R/index.html
@@ -287,11 +287,7 @@ <h1 id="r-properties">r properties<a class="headerlink" href="#r-properties" tit
 </tr>
 <tr>
 <td align="left"><em>r.timeout</em></td>
-<td align="left"><em>integer</em> <br>defines the number of minutes before R script fails due to</td>
-</tr>
-<tr>
-<td align="left">* timeout. If set to 0, an estimate is used.<br><em>default:</em>  0</td>
-<td align="left"></td>
+<td align="left"><em>integer</em> <br>defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used.<br><em>default:</em>  0</td>
 </tr>
 <tr>
 <td align="left"><em>r.useUniqueColors</em></td>

diff --git a/docs/GENERATED/biolockj.module.report.r/R_CalculateStats/index.html b/docs/GENERATED/biolockj.module.report.r/R_CalculateStats/index.html
@@ -298,11 +298,7 @@ <h3 id="general-properties-applicable-to-this-module">General properties applica
 </tr>
 <tr>
 <td align="left"><em>r.timeout</em></td>
-<td align="left"><em>integer</em> <br>defines the number of minutes before R script fails due to</td>
-</tr>
-<tr>
-<td align="left">* timeout. If set to 0, an estimate is used.<br><em>default:</em>  0</td>
-<td align="left"></td>
+<td align="left"><em>integer</em> <br>defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used.<br><em>default:</em>  0</td>
 </tr>
 <tr>
 <td align="left"><em>script.defaultHeader</em></td>

diff --git a/docs/GENERATED/biolockj.module.report.r/R_PlotEffectSize/index.html b/docs/GENERATED/biolockj.module.report.r/R_PlotEffectSize/index.html
@@ -318,11 +318,7 @@ <h3 id="general-properties-applicable-to-this-module">General properties applica
 </tr>
 <tr>
 <td align="left"><em>r.timeout</em></td>
-<td align="left"><em>integer</em> <br>defines the number of minutes before R script fails due to</td>
-</tr>
-<tr>
-<td align="left">* timeout. If set to 0, an estimate is used.<br><em>default:</em>  0</td>
-<td align="left"></td>
+<td align="left"><em>integer</em> <br>defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used.<br><em>default:</em>  0</td>
 </tr>
 <tr>
 <td align="left"><em>script.defaultHeader</em></td>

diff --git a/docs/GENERATED/biolockj.module.report.r/R_PlotMds/index.html b/docs/GENERATED/biolockj.module.report.r/R_PlotMds/index.html
@@ -314,11 +314,7 @@ <h3 id="general-properties-applicable-to-this-module">General properties applica
 </tr>
 <tr>
 <td align="left"><em>r.timeout</em></td>
-<td align="left"><em>integer</em> <br>defines the number of minutes before R script fails due to</td>
-</tr>
-<tr>
-<td align="left">* timeout. If set to 0, an estimate is used.<br><em>default:</em>  0</td>
-<td align="left"></td>
+<td align="left"><em>integer</em> <br>defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used.<br><em>default:</em>  0</td>
 </tr>
 <tr>
 <td align="left"><em>r_PlotMds.reportFields</em></td>

diff --git a/docs/GENERATED/biolockj.module.report.r/R_PlotOtus/index.html b/docs/GENERATED/biolockj.module.report.r/R_PlotOtus/index.html
@@ -314,11 +314,7 @@ <h3 id="general-properties-applicable-to-this-module">General properties applica
 </tr>
 <tr>
 <td align="left"><em>r.timeout</em></td>
-<td align="left"><em>integer</em> <br>defines the number of minutes before R script fails due to</td>
-</tr>
-<tr>
-<td align="left">* timeout. If set to 0, an estimate is used.<br><em>default:</em>  0</td>
-<td align="left"></td>
+<td align="left"><em>integer</em> <br>defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used.<br><em>default:</em>  0</td>
 </tr>
 <tr>
 <td align="left"><em>script.defaultHeader</em></td>

diff --git a/docs/GENERATED/biolockj.module.report.r/R_PlotPvalHistograms/index.html b/docs/GENERATED/biolockj.module.report.r/R_PlotPvalHistograms/index.html
@@ -290,11 +290,7 @@ <h3 id="general-properties-applicable-to-this-module">General properties applica
 </tr>
 <tr>
 <td align="left"><em>r.timeout</em></td>
-<td align="left"><em>integer</em> <br>defines the number of minutes before R script fails due to</td>
-</tr>
-<tr>
-<td align="left">* timeout. If set to 0, an estimate is used.<br><em>default:</em>  0</td>
-<td align="left"></td>
+<td align="left"><em>integer</em> <br>defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used.<br><em>default:</em>  0</td>
 </tr>
 <tr>
 <td align="left"><em>script.defaultHeader</em></td>

diff --git a/docs/javadocs/biolockj/module/report/r/R_CalculateStats.html b/docs/javadocs/biolockj/module/report/r/R_CalculateStats.html
@@ -2,7 +2,7 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_211) on Sun Jan 17 19:03:28 EST 2021 -->
+<!-- Generated by javadoc (1.8.0_211) on Sun Jan 17 23:26:44 EST 2021 -->
 <title>R_CalculateStats</title>
 <meta name="date" content="2021-01-17">
 <link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">

diff --git a/docs/javadocs/biolockj/module/report/r/R_PlotEffectSize.html b/docs/javadocs/biolockj/module/report/r/R_PlotEffectSize.html
@@ -2,7 +2,7 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_211) on Sun Jan 17 19:03:28 EST 2021 -->
+<!-- Generated by javadoc (1.8.0_211) on Sun Jan 17 23:26:44 EST 2021 -->
 <title>R_PlotEffectSize</title>
 <meta name="date" content="2021-01-17">
 <link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">

diff --git a/docs/javadocs/biolockj/module/report/r/R_PlotMds.html b/docs/javadocs/biolockj/module/report/r/R_PlotMds.html
@@ -2,7 +2,7 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_211) on Sun Jan 17 19:03:28 EST 2021 -->
+<!-- Generated by javadoc (1.8.0_211) on Sun Jan 17 23:26:44 EST 2021 -->
 <title>R_PlotMds</title>
 <meta name="date" content="2021-01-17">
 <link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">

diff --git a/docs/javadocs/biolockj/module/report/r/R_PlotOtus.html b/docs/javadocs/biolockj/module/report/r/R_PlotOtus.html
@@ -2,7 +2,7 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_211) on Sun Jan 17 19:03:28 EST 2021 -->
+<!-- Generated by javadoc (1.8.0_211) on Sun Jan 17 23:26:44 EST 2021 -->
 <title>R_PlotOtus</title>
 <meta name="date" content="2021-01-17">
 <link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">

diff --git a/docs/javadocs/biolockj/module/report/r/R_PlotPvalHistograms.html b/docs/javadocs/biolockj/module/report/r/R_PlotPvalHistograms.html
@@ -2,7 +2,7 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_211) on Sun Jan 17 19:03:28 EST 2021 -->
+<!-- Generated by javadoc (1.8.0_211) on Sun Jan 17 23:26:44 EST 2021 -->
 <title>R_PlotPvalHistograms</title>
 <meta name="date" content="2021-01-17">
 <link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">

diff --git a/mkdocs/user-guide/docs/GENERATED/General-Properties.md b/mkdocs/user-guide/docs/GENERATED/General-Properties.md
@@ -120,8 +120,7 @@
 | *r.rareOtuThreshold* | _numeric_ <br>If >=1, R will filter OTUs found in fewer than this many samples. If <1, R will interperate the value as a percentage and discard OTUs not found in at least that percentage of samples<br>*default:*  1 |
 | *r.reportFields* | _list_ <br>Metadata fields to include in reports; Fields listed here must exist in the metadata file. R reports must contain at least one valid field.<br>*default:*  *null* |
 | *r.saveRData* | _boolean_ <br>If Y, all R script generating BioModules will save R Session data to the module output directory to a file using the extension ".RData"<br>*default:*  *null* |
-| *r.timeout* | _integer_ <br>defines the number of minutes before R script fails due to
-	 * timeout. If set to 0, an estimate is used.<br>*default:*  0 |
+| *r.timeout* | _integer_ <br>defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used.<br>*default:*  0 |
 | *r.useUniqueColors* | _boolean_ <br>force to use a unique color for every value in every field plotted; only recommended for low numbers of metadata columns/values.<br>*default:*  *null* |
 
 ### r_PlotMds                   

diff --git a/mkdocs/user-guide/docs/GENERATED/R.md b/mkdocs/user-guide/docs/GENERATED/R.md
@@ -18,8 +18,7 @@ These properties are directed to R modules.
 | *r.rareOtuThreshold* | _numeric_ <br>If >=1, R will filter OTUs found in fewer than this many samples. If <1, R will interperate the value as a percentage and discard OTUs not found in at least that percentage of samples<br>*default:*  1 |
 | *r.reportFields* | _list_ <br>Metadata fields to include in reports; Fields listed here must exist in the metadata file. R reports must contain at least one valid field.<br>*default:*  *null* |
 | *r.saveRData* | _boolean_ <br>If Y, all R script generating BioModules will save R Session data to the module output directory to a file using the extension ".RData"<br>*default:*  *null* |
-| *r.timeout* | _integer_ <br>defines the number of minutes before R script fails due to
-	 * timeout. If set to 0, an estimate is used.<br>*default:*  0 |
+| *r.timeout* | _integer_ <br>defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used.<br>*default:*  0 |
 | *r.useUniqueColors* | _boolean_ <br>force to use a unique color for every value in every field plotted; only recommended for low numbers of metadata columns/values.<br>*default:*  *null* |
                    
 Several plotting options are available.                   
diff --git a/mkdocs/user-guide/docs/GENERATED/biolockj.module.report.r/R_CalculateStats.md b/mkdocs/user-guide/docs/GENERATED/biolockj.module.report.r/R_CalculateStats.md
@@ -31,8 +31,7 @@ Generate a summary statistics table with [adjusted and unadjusted] [parameteric
 | *r.debug* | _boolean_ <br>Options: Y/N. If Y, will generate R Script log files<br>*default:*  Y |
 | *r.rareOtuThreshold* | _numeric_ <br>If >=1, R will filter OTUs found in fewer than this many samples. If <1, R will interperate the value as a percentage and discard OTUs not found in at least that percentage of samples<br>*default:*  1 |
 | *r.saveRData* | _boolean_ <br>If Y, all R script generating BioModules will save R Session data to the module output directory to a file using the extension ".RData"<br>*default:*  *null* |
-| *r.timeout* | _integer_ <br>defines the number of minutes before R script fails due to
-	 * timeout. If set to 0, an estimate is used.<br>*default:*  0 |
+| *r.timeout* | _integer_ <br>defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used.<br>*default:*  0 |
 | *script.defaultHeader* | _string_ <br>Store default script header for MAIN script and locally run WORKER scripts.<br>*default:*  #!/bin/bash |
 | *script.numThreads* | _integer_ <br>Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter.<br>*default:*  8 |
 | *script.numWorkers* | _integer_ <br>Set number of samples to process per script (if parallel processing)<br>*default:*  1 |

diff --git a/mkdocs/user-guide/docs/GENERATED/biolockj.module.report.r/R_PlotEffectSize.md b/mkdocs/user-guide/docs/GENERATED/biolockj.module.report.r/R_PlotEffectSize.md
@@ -36,8 +36,7 @@ Generate horizontal barplot representing effect size (Cohen's d, r<sup>2</sup>,
 | *r.colorFile* | _file path_ <br>path to a tab-delimited file giving the color to use for each value of each metadata field plotted.<br>*default:*  *null* |
 | *r.debug* | _boolean_ <br>Options: Y/N. If Y, will generate R Script log files<br>*default:*  Y |
 | *r.saveRData* | _boolean_ <br>If Y, all R script generating BioModules will save R Session data to the module output directory to a file using the extension ".RData"<br>*default:*  *null* |
-| *r.timeout* | _integer_ <br>defines the number of minutes before R script fails due to
-	 * timeout. If set to 0, an estimate is used.<br>*default:*  0 |
+| *r.timeout* | _integer_ <br>defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used.<br>*default:*  0 |
 | *script.defaultHeader* | _string_ <br>Store default script header for MAIN script and locally run WORKER scripts.<br>*default:*  #!/bin/bash |
 | *script.numThreads* | _integer_ <br>Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter.<br>*default:*  8 |
 | *script.numWorkers* | _integer_ <br>Set number of samples to process per script (if parallel processing)<br>*default:*  1 |

diff --git a/mkdocs/user-guide/docs/GENERATED/biolockj.module.report.r/R_PlotMds.md b/mkdocs/user-guide/docs/GENERATED/biolockj.module.report.r/R_PlotMds.md
@@ -35,8 +35,7 @@ Generate sets of multidimensional scaling plots showing 2 axes at a time (up to
 | *r.debug* | _boolean_ <br>Options: Y/N. If Y, will generate R Script log files<br>*default:*  Y |
 | *r.pch* | _integer_ <br>Sets R plot pch parameter for PDF report<br>*default:*  21 |
 | *r.saveRData* | _boolean_ <br>If Y, all R script generating BioModules will save R Session data to the module output directory to a file using the extension ".RData"<br>*default:*  *null* |
-| *r.timeout* | _integer_ <br>defines the number of minutes before R script fails due to
-	 * timeout. If set to 0, an estimate is used.<br>*default:*  0 |
+| *r.timeout* | _integer_ <br>defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used.<br>*default:*  0 |
 | *r_PlotMds.reportFields* | _list_ <br>Override field used to explicitly list metadata columns to build MDS plots. If left undefined, all columns are reported<br>*default:*  *null* |
 | *script.defaultHeader* | _string_ <br>Store default script header for MAIN script and locally run WORKER scripts.<br>*default:*  #!/bin/bash |
 | *script.numThreads* | _integer_ <br>Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter.<br>*default:*  8 |

diff --git a/mkdocs/user-guide/docs/GENERATED/biolockj.module.report.r/R_PlotOtus.md b/mkdocs/user-guide/docs/GENERATED/biolockj.module.report.r/R_PlotOtus.md
@@ -35,8 +35,7 @@ Generate OTU-metadata box-plots and scatter-plots for each reportable metadata f
 | *r.pch* | _integer_ <br>Sets R plot pch parameter for PDF report<br>*default:*  21 |
 | *r.rareOtuThreshold* | _numeric_ <br>If >=1, R will filter OTUs found in fewer than this many samples. If <1, R will interperate the value as a percentage and discard OTUs not found in at least that percentage of samples<br>*default:*  1 |
 | *r.saveRData* | _boolean_ <br>If Y, all R script generating BioModules will save R Session data to the module output directory to a file using the extension ".RData"<br>*default:*  *null* |
-| *r.timeout* | _integer_ <br>defines the number of minutes before R script fails due to
-	 * timeout. If set to 0, an estimate is used.<br>*default:*  0 |
+| *r.timeout* | _integer_ <br>defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used.<br>*default:*  0 |
 | *script.defaultHeader* | _string_ <br>Store default script header for MAIN script and locally run WORKER scripts.<br>*default:*  #!/bin/bash |
 | *script.numThreads* | _integer_ <br>Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter.<br>*default:*  8 |
 | *script.numWorkers* | _integer_ <br>Set number of samples to process per script (if parallel processing)<br>*default:*  1 |

diff --git a/mkdocs/user-guide/docs/GENERATED/biolockj.module.report.r/R_PlotPvalHistograms.md b/mkdocs/user-guide/docs/GENERATED/biolockj.module.report.r/R_PlotPvalHistograms.md
@@ -29,8 +29,7 @@ Generate p-value histograms for each reportable metadata field and each *report.
 | *r.debug* | _boolean_ <br>Options: Y/N. If Y, will generate R Script log files<br>*default:*  Y |
 | *r.pvalCutoff* | _numeric_ <br>p-value cutoff used to assign label _r.colorHighlight_<br>*default:*  0.05 |
 | *r.saveRData* | _boolean_ <br>If Y, all R script generating BioModules will save R Session data to the module output directory to a file using the extension ".RData"<br>*default:*  *null* |
-| *r.timeout* | _integer_ <br>defines the number of minutes before R script fails due to
-	 * timeout. If set to 0, an estimate is used.<br>*default:*  0 |
+| *r.timeout* | _integer_ <br>defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used.<br>*default:*  0 |
 | *script.defaultHeader* | _string_ <br>Store default script header for MAIN script and locally run WORKER scripts.<br>*default:*  #!/bin/bash |
 | *script.numThreads* | _integer_ <br>Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter.<br>*default:*  8 |
 | *script.numWorkers* | _integer_ <br>Set number of samples to process per script (if parallel processing)<br>*default:*  1 |

diff --git a/src/biolockj/Constants.java b/src/biolockj/Constants.java
@@ -856,8 +856,7 @@ static final void registerProps() throws API_Exception {
 	 * {@link biolockj.Config} property {@value #R_TIMEOUT}: {@value #R_TIMEOUT_DESC} 
 	 */
 	public static final String R_TIMEOUT = "r.timeout";
-	private static final String R_TIMEOUT_DESC = "defines the number of minutes before R script fails due to\n" + 
-		"	 * timeout. If set to 0, an estimate is used.";
+	private static final String R_TIMEOUT_DESC = "defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used.";
 
 	/**
 	 * {@link biolockj.Config} Boolean property to signal R scripts to build HumanN2 reports