Added support for related reports. Fixes #17.

Nozzle.R1/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: Nozzle.R1
 Type: Package
 Title: Nozzle Reports
-Version: 1.2-0
-Date: 2012-05-21
+Version: 1.3-0
+Date: 2012-06-23
 Author: Nils Gehlenborg <nils@hms.harvard.edu>
 Maintainer: Nils Gehlenborg <nils@hms.harvard.edu>
 Description: The Nozzle package provides an API to generate HTML reports with

Nozzle.R1/NAMESPACE

@@ -1,3 +1,4 @@
+export(addRelatedReport)
 export(addTo)
 export(addToInput)
 export(addToIntroduction)

Nozzle.R1/NEWS

@@ -1,3 +1,10 @@
+Release R1-1.3-0 / 23 June 2013
+
+- Added support to add and display of "related reports", e.g. the reports that
+  correspond to the same analysis but were applied to different inputs.
+
+-----------------
+
 Release R1-1.2-0 / 21 May 2013
 
 - Added folding sections for maintainer and citation information.
@@ -6,12 +13,14 @@ Release R1-1.2-0 / 21 May 2013
   version. This is useful for reports that are part of a larger set of reports
   that are being generated together.
 
+-----------------
 
 Release R1-1.1-1 / 15 May 2013
 
 - Fixed problem with subtitle if reports generated with Nozzle versions older than
   R1-1.1-0 were rendered with R1-1.1-0.
 
+-----------------
 
 Release R1-1.1-0 / 14 May 2013
 
@@ -30,7 +39,6 @@ Release R1-1.1-0 / 14 May 2013
 
 -----------------
 
-
 Release R1-1.0-0 / 8 January 2013
 
 - Fully documented API.

Nozzle.R1/R/nozzle.R

@@ -14,8 +14,8 @@
 #' \tabular{ll}{
 #' Package: \tab Nozzle.R1\cr
 #' Type: \tab Package\cr
-#' Version: \tab 1.2-0\cr
-#' Date: \tab 2013-05-15\cr
+#' Version: \tab 1.3-0\cr
+#' Date: \tab 2013-06-23\cr
 #' License: \tab LGPL (>= 2)\cr
 #' LazyLoad: \tab yes\cr
 #' }
@@ -42,7 +42,7 @@ NULL
 
 .nozzleEnv <- new.env();
 
-.PACKAGE.VERSION <- "1.2-0";
+.PACKAGE.VERSION <- "1.3-0";
 
 .ELEMENT.REPORT <- "_report_";
 .ELEMENT.SECTION <- "_section_";
@@ -730,7 +730,7 @@ newReport <- function( ..., version=0 )
 	references$domId <- "references";
 
 	meta <- newSection( "Meta Information", class="meta" )
-	meta$domId <- "meta";		
+	meta$domId <- "meta";
 
 	# If a new predefined section is added here a ".hasPredefinedXXXSection" function needs to be added below as well as an an "addToXXX" function.
 
@@ -862,6 +862,9 @@ newCustomReport <- function( ..., version=0 )
 
 	element$navigation$previousUrl <- NA;
 	element$navigation$previousName <- NA;
+
+	# report navigation: related reports matrix (name: STRING, url: STRING, significant findings: BOOLEAN)
+	element$relatedReports <- matrix( NA, nrow=0, ncol=3 );	
 
 	return ( element );
 }
@@ -933,6 +936,29 @@ setParentReport <- function( report, url, ... )
 }
 
 
+#' Add the URL, title, and signficance status of a related report, e.g. one summarizing the same type of analysis but on a different input set. 
+#' @param report Report object.
+#' @param name Name of the related report.
+#' @param url URL of the related report (may be relative).
+#' @param isSignificant Flag indicating whether the related report contains significant findings.
+#' @export
+#' @return Updated report element.
+#' 
+#' @author nils
+addRelatedReport <- function( report, name, url, isSignificant=FALSE )
+{	
+	if ( is.null( report$relatedReports ) )
+	{
+		report$relatedReports <- matrix( NA, nrow=0, ncol=3 );
+	}
+
+	report$relatedReports = rbind( report$relatedReports, c( name=name, url=url, isSignificant=isSignificant ) )
+
+	return ( report );
+}
+
+
+
 #' Get the title of \code{report}.
 #' @param report Report element.
 #' @export
@@ -4017,6 +4043,14 @@ writeReport <- function( report, filename=DEFAULT.REPORT.FILENAME, debug=FALSE,
 	.write( "<script type=\"text/javascript\">", file );
 	.writeJsonElement( "nozzleMeta", report$meta, file );
 	.writeJsonElement( "nozzleNavigation", report$navigation, file );
+	if ( !is.null( report$relatedReports ) )
+	{
+		.writeJsonMatrix( "nozzleRelatedReports", report$relatedReports, file );		
+	}
+	else
+	{
+		.writeJsonMatrix( "nozzleRelatedReports", matrix( NA, nrow=0, ncol=3 ), file );				
+	}
 	.write( "</script>", file );	
 
 	# === REPORT META END ===	
@@ -4299,6 +4333,58 @@ writeReport <- function( report, filename=DEFAULT.REPORT.FILENAME, debug=FALSE,
 }
 
 
+# write rows of matrix as an array of objects, using column header as field names
+.writeJsonMatrix <- function( jsVariable, element, file )
+{	
+	.write( "var ", jsVariable, " = [", file );
+
+	if ( dim( element )[1] > 0 && dim( element )[2] > 0 )
+	{
+		for ( r in 1:dim( element )[1] )
+		{
+			.write( "   { ", file, nobreak=T );			
+
+			for ( c in 1:dim( element )[2] )
+			{
+				.write( "\"", colnames(element)[c], "\"", ": ", file, nobreak=T );
+
+				if ( is.numeric( element[r,c] ) )
+				{
+					.write( element[r,c], file, nobreak=T )
+				}
+				else if ( element[r,c] == "TRUE" )
+				{
+					.write( "true", file, nobreak=T )
+				}
+				else if ( element[r,c] == "FALSE" )
+				{
+					.write( "false", file, nobreak=T )
+				}
+				else 
+				{
+					.write( "\"", element[r,c], "\"", file, nobreak=T )				
+				}
+
+				if ( c < dim( element )[2] )
+				{
+					.write( ", ", file, nobreak=T );							
+				}				
+			}
+
+			.write( " }", file, nobreak=T );
+
+			if ( r < dim( element )[1] )
+			{
+				.write( ",", file );							
+			}
+		}			
+	}	
+	.write( "", file );
+	.write( "];", file );			
+}
+
+
+
 .writeJsonNumeric <- function( name, value, file, indent=0 )
 {
 	if ( length( value ) == 1 )

Nozzle.R1/inst/css/nozzle.css

@@ -37,7 +37,6 @@ li p {
 	text-transform: uppercase;	
 }
 
-
 .menuitem {
 	display: inline-block;
 	padding-left: 5px;
@@ -52,6 +51,62 @@ li p {
 	background-color: #eeeeee;
 }
 
+ul.submenu {
+	display: inline;
+	margin-left: 0;
+	padding-left: 0;
+}
+
+ul.submenu, ul.submenu li, ul.submenu ul {
+	list-style: none;	
+}
+
+ul.submenu ul {
+	visibility: hidden;
+	position: absolute;
+	top: 1.75em;
+	z-index: 598;
+	padding-right: 5px;
+	padding-left: 5px;
+	margin-left: -6px; 
+	border: 1px solid #ccc;
+	//border-top: none;
+	color: #666666;	
+	cursor: pointer;
+	border-bottom-left-radius: 0.55ex;
+	border-bottom-right-radius: 0.55ex;
+	background-color: #efefef;
+	-webkit-box-shadow: 0px 2px 4px black;
+	-moz-box-shadow: 0px 2px 4px black;
+	-opera-box-shadow: 0px 2px 4px black;
+	box-shadow: 0px 2px 4px black;		
+}
+
+ul.submenu ul li {
+	float: none;
+	text-transform: none;
+	line-height: 2em;	
+}
+
+ul.submenu ul li:hover {
+	text-decoration: underline;
+}
+
+ul.submenu .submenuhead:hover {
+	/*
+	-webkit-box-shadow: 0px 0px 0px black;
+	-moz-box-shadow: 0px 0px 0px black;
+	-opera-box-shadow: 0px 0px 0px black;
+	box-shadow: 0px 0px 0px black;
+	*/
+	z-index: -600;
+	border-bottom-left-radius: 0ex;		
+}
+
+ul.submenu .submenuhead:hover > ul {
+	visibility: visible;	
+}
+
 .menuitem a {
 	text-decoration: none;
 	color: #666666;
@@ -595,6 +650,15 @@ div.significant {
 }
 
 
+span.summary-small {
+	width: 6px;
+	height: 6px;
+	display: inline-block;
+	position: relative;
+	border-radius: 15ex;
+	top: -1px;
+}
+
 span.summary {
 	color: #919191;
 	cursor: default;

Nozzle.R1/inst/js/nozzle.js

@@ -387,6 +387,29 @@ function applyFilePrefixPostfix( prefix, postfix )
 			menu += "<div class=\"menuitem deactivated\">&gt;</div>";
 		}
 
+		if ( nozzleRelatedReports != null && nozzleRelatedReports.length > 0 ) {
+			menu += "<ul class=\"submenu\"><li id=\"menu_related_reports_button\" class=\"menuitem submenuhead\">" + nozzleRelatedReports.length + " Related Reports"; 
+
+			menu += "<ul id=\"menu_related_reports_list\">";
+			for ( var i = 0; i < nozzleRelatedReports.length; ++i ) {
+				menu += "<li class=\"submenuitem\"><a href=\"" + nozzleRelatedReports[i].url + "\">" + nozzleRelatedReports[i].name + "</a>"
+
+				if ( nozzleRelatedReports[i].isSignificant ) {
+					menu += "&nbsp;<span class=\"summary-small significant\" title=\"Report contains findings that crossed a significance threshold.\"></span>";
+				} 				
+
+				menu += "</li>" ;
+
+			}
+			menu += "</ul>"; // submenu			
+
+			menu += "</li></ul>"; // submenuhead
+
+		}
+		else {
+			// there are no related reports, ignore
+		}
+
 		menu += "<div class=\"menuitem separator\"></div>";
 
 		menu += "<div class=\"menuitem\" id=\"menu_expand_all\">Expand All</div>\
@@ -411,6 +434,12 @@ function applyFilePrefixPostfix( prefix, postfix )
 		menu += "</div></div>";
 
 		getFrame().prepend( menu );
+
+		/*
+		$( "#menu_related_reports_button" ).hover( function() {
+			$( "#menu_related_reports_list" ).show();	
+		});
+		*/
 
 		$( "#menu_expand_all" ).click( function() {
 			toggleAllContents( true, ToggleMode.SHOW );