comparison createHTML.sh @ 4:363cd315d0e9 draft

Uploaded

3:945e72d0e723

gbcount=0

##
## Create Cover Page
##
function makeIntroPage  ( ){
	echo "Creating Intro Page"
	title="$1"
	coverimage=$2
	link=$3

		<b><font size=\"15\"> iReport: ${title} </font></b><br/>
		<br/>
		<br/>
		<a href=\"$link\">  Click image to view report	</a> <br/><br/>
		<a href=\"$link\"> <img src="$coverimage" width=\"50%\" alt=\"loading image..\"/> </a><br/><br/>		
		<a href=\"$zipireport\">  Click here to download a copy of this iReport </a> <br/><br/>
		</center>
	</body>
</html>" > $htmlout

}

	tab=$1			# name of current tab
	itemslist=$2	# list of all items
	tracklist=$3	# genome browser tracks info
	contentline=""  # HTML code for tab
	imgcount=0		# keep track of the number of images on the current tab
	iframecount=0
	
	for item in $itemslist
	do
		## Parse items lists
		item=${item/::/:emptycol:}
		declare -a myarr=(`echo $item |sed 's/:/ /g'`)

				else
					widthstring="width=\"${zoomlevel}\""
				fi
				
				if [[ ${zoomlevel} -eq 0 || ${zoomenable} == "N" ]]
				then
					contentline="${contentline}<span id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
				else				
					contentline="${contentline}<span class=\"zoomme\" id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
				fi
				
			fi

				tsvfile="tablehead.tsv"
				fname=`basename ${tsvfile_orig}`
				fname=${fname%.*}
				fancy=${myarr[4]}
				makelinks=${myarr[5]}
				iframeid="iframe"$iframecount
				#echo "\nmakelinks: $makelinks fancy: $fancy <br>"
				
				#TODO client side database for large files. For now only display first section of file and add download link
				numlines=`wc -l ${tsvfile_orig} |cut -d" " -f1`
								

					minw=${myarr[6]}
					minh=${myarr[7]}
					cp ${tsvfile} ${tsvfile}2
				fi
				
				iframecount=$[$iframecount+1]
				if [ $fancy == "Y" ]
				then
					perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
					contentline="${contentline}\n<iframe class=\"invisibleframe fancyiframe\" id=\"$iframeid\" src=\"htmltable_${fname}.html\" width=\"100%\" style=\"height: 760px; min-height: ${minh}px !important; overflow-y: hidden; overflow-x: scroll\" ></iframe>"
					iframecount=$[$iframecount+1]
				else
					perl ${repositorypath}/tsv2html_simple.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
					contentline="${contentline}\n<iframe class=\"unfancyiframe invisibleframe\" id=\"$iframeid\" src=\"htmltable_${fname}.html\" scrolling=\"no\" style=\"min-width: ${minw}px; min-height: ${minh}px !important; max-width: 100%; vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>"
					iframecount=$[$iframecount+1]
				fi
				
				if [[ $numlines -gt ${maxlines} ]]
				then
					tablename=`basename ${tsvfile_orig}`

							samtools index "${galaxypath}/${newgbfilename}"
							
							userTracks="${userTracks},
								{name:                 '${gbfilelabel}',
								 bamURI:                  '${servername}/datasets/${apiid}/display/${newgbfilename}'}
							"
						
						fi
						
						if [[ $ftype == "bedtabix" ]]

			fi		
		fi
	done
	
	echo "${contentline}"
}

##
## Create HTML content for iReport
##
createMainPage (){
	page=$1
	tabtitles=$2	# comma-separated list of tab titles
	tabitems=$3		# colon-sparated list of tabs specifications
	iframecount=1	# keep track of number of iFrames so that they can be referenced by ID
	minwidth=$4		# width of page
	gbtracks=$5		# genome browser track information
	
	echo "createMainPage: tabitems: $tabitems. tabtitles: $tabtitles. gbtracks: $gbtracks"
	# create correct number of tabs

4:363cd315d0e9

gbcount=0

##
## Create Cover Page
##
#<a href=\"$zipireport\">  Click here to download a copy of this iReport </a> <br/><br/>
function makeIntroPage  ( ){
	echo "Creating Intro Page"
	title="$1"
	coverimage=$2
	link=$3

		<b><font size=\"15\"> iReport: ${title} </font></b><br/>
		<br/>
		<br/>
		<a href=\"$link\">  Click image to view report	</a> <br/><br/>
		<a href=\"$link\"> <img src="$coverimage" width=\"50%\" alt=\"loading image..\"/> </a><br/><br/>		
		</center>
	</body>
</html>" > $htmlout

}

	tab=$1			# name of current tab
	itemslist=$2	# list of all items
	tracklist=$3	# genome browser tracks info
	contentline=""  # HTML code for tab
	imgcount=0		# keep track of the number of images on the current tab
	iframename=`head -n 1 < /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 8 | head -n 1`
	#iframename="test"
	for item in $itemslist
	do
		## Parse items lists
		item=${item/::/:emptycol:}
		declare -a myarr=(`echo $item |sed 's/:/ /g'`)

				else
					widthstring="width=\"${zoomlevel}\""
				fi
				
				if [[ ${zoomlevel} -eq 0 || ${zoomenable} == "N" ]]
				then                                    
					contentline="${contentline}<span id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"                                    
				else				
					contentline="${contentline}<span class=\"zoomme\" id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
				fi
				
			fi

				tsvfile="tablehead.tsv"
				fname=`basename ${tsvfile_orig}`
				fname=${fname%.*}
				fancy=${myarr[4]}
				makelinks=${myarr[5]}
				#iframeid="iframe$giframecount"
				iframeid="iframe-$iframename"
				
				#echo "\nmakelinks: $makelinks fancy: $fancy <br>"
				
				#TODO client side database for large files. For now only display first section of file and add download link
				numlines=`wc -l ${tsvfile_orig} |cut -d" " -f1`
								

					minw=${myarr[6]}
					minh=${myarr[7]}
					cp ${tsvfile} ${tsvfile}2
				fi
				
				#iframecount=$[$iframecount+1]
				
				if [ $fancy == "Y" ]
				then
					perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
					contentline="${contentline}\n<iframe class=\"invisibleframe fancyiframe\" id=\"$iframeid\" src=\"htmltable_${fname}.html\" width=\"100%\" style=\"height: 350px; min-height: ${minh}px !important; overflow-y: hidden; overflow-x: scroll\" onClick=resizeIframe(\"$iframeid\")></iframe>"
					
				else
					perl ${repositorypath}/tsv2html_simple.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
					contentline="${contentline}\n<iframe class=\"unfancyiframe invisibleframe\" id=\"$iframeid\" src=\"htmltable_${fname}.html\" scrolling=\"no\" style=\"min-width: ${minw}px; min-height: ${minh}px !important; max-width: 100%; vertical-align: top;\" onClick=resizeIframe(\"$iframeid\") ></iframe>"
					
				fi
				
				if [[ $numlines -gt ${maxlines} ]]
				then
					tablename=`basename ${tsvfile_orig}`

							samtools index "${galaxypath}/${newgbfilename}"
							
							userTracks="${userTracks},
								{name:                 '${gbfilelabel}',
								 bamURI:                  '${servername}/datasets/${apiid}/display/${newgbfilename}'}
							"
						
						fi
						
						if [[ $ftype == "bigbed" ]]
						then
							newgbfilename="${fname}.bigbed"
							
							cp ${gbfilename} "${galaxypath}/${newgbfilename}"
							#bgzip "${galaxypath}/${newgbfilename}"
							#tabix -f -p bed "${galaxypath}/${newgbfilename}.gz"
							
							userTracks="${userTracks},
								{name:                 '${gbfilelabel}',
								bwgURI:                  '${servername}/datasets/${apiid}/display/${newgbfilename}'}
							"
						
						fi
						
						if [[ $ftype == "bedtabix" ]]

			fi		
		fi
	done
	
	echo "${contentline}"
	
	
}

##
## Create HTML content for iReport
##
createMainPage (){
        #export IFRAMECNT=1
	page=$1
	tabtitles=$2	# comma-separated list of tab titles
	tabitems=$3		# colon-sparated list of tabs specifications
	#giframecount=1	# keep track of number of iFrames so that they can be referenced by ID
	minwidth=$4		# width of page
	gbtracks=$5		# genome browser track information
	
	echo "createMainPage: tabitems: $tabitems. tabtitles: $tabtitles. gbtracks: $gbtracks"
	# create correct number of tabs