Mercurial > repos > saskia-hiltemann > ireport
diff createHTML.sh @ 0:ac5f9272033b draft
first upload
| author | saskia-hiltemann |
|---|---|
| date | Tue, 01 Jul 2014 11:42:23 -0400 |
| parents | |
| children | 440f4aa3db97 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/createHTML.sh Tue Jul 01 11:42:23 2014 -0400 @@ -0,0 +1,558 @@ +function makeIntroPage ( ){ + echo "Creating Intro Page" + title="$1" + coverimage=$2 + link=$3 + htmlout=$4 + + echo -e "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01//EN\" \"http://www.w3.org/TR/html4/strict.dtd\"> +<html> + <head> + </head> + <body> + <!-- dummy intro page, since first page will not have any javascript/css features enabled unless specified in universe_wsgi.ini file, but subsequent pages will --> + <br/> + <br/> + <center> + <b><font size=\"15\"> iReport: ${title} </font></b><br/> + <br/> + <br/> + <a href=\"$link\"> Click here to view report </a> <br/><br/> + <a href=\"$link\"> <img src="$coverimage" width=\"50%\" alt=\"loading image..\"/> </a><br/><br/> + </center> + </body> +</html>" > $htmlout + +} + + +function makeTabContent ( ){ + tab=$1 #name of current tab + itemslist=$2 #list of all items + contentline="<br/>" + imgcount=0 + #echo -e "\n Creating items. itemslist: $itemslist" + + for item in $itemslist + do + #echo -e "\n -> item : $item" + item=${item/::/:emptycol:} + declare -a myarr=(`echo $item |sed 's/:/ /g'`) + #echo "break: ${myarr[3]}" + if [ ${myarr[0]} == $tab ] + then + + ## add contents of text field to page#### + if [ ${myarr[1]} == "text" ] + then + text=${myarr[2]} + ## allow some html formatting tags + text=${text//==lt==strong==gt==/<strong>} # search for strong tags + text=${text//==lt====slash==strong==gt==/<\/strong>} # search for strong tags + text=${text//==lt==em==gt==/<em>} # search for strong tags + text=${text//==lt====slash==em==gt==/<\/em>} # search for strong tags + + text=${text//==lt==b==gt==/<strong>} # search for strong tags + text=${text//==lt====slash==b==gt==/<\/strong>} # search for strong tags + text=${text//==lt==i==gt==/<em>} # search for strong tags + text=${text//==lt====slash==i==gt==/<\/em>} # search for strong tags + + text=${text//==lt==br==gt==/<br\/>} # search for strong tags + text=${text//==lt====br==slash==gt==/<br\/>} # search for strong tags + text=${text//==lt==h1==gt==/<h1>} # search for h1-h6 tags + text=${text//==lt==h2==gt==/<h2>} # search for h1-h6 tags + text=${text//==lt==h3==gt==/<h3>} # search for h1-h6 tags + text=${text//==lt==h4==gt==/<h4>} # search for h1-h6 tags + text=${text//==lt==h5==gt==/<h5>} # search for h1-h6 tags + text=${text//==lt==h6==gt==/<h6>} # search for h1-h6 tags + text=${text//==lt====slash==h1==gt==/<\/h1>} # search for h1-h6 closing tags + text=${text//==lt====slash==h2==gt==/<\/h2>} # search for h1-h6 closing tags + text=${text//==lt====slash==h3==gt==/<\/h3>} # search for h1-h6 closing tags + text=${text//==lt====slash==h4==gt==/<\/h4>} # search for h1-h6 closing tags + text=${text//==lt====slash==h5==gt==/<\/h5>} # search for h1-h6 closing tags + text=${text//==lt====slaxh==h6==gt==/<\/h6>} # search for h1-h6 closing tags + + ## display everything else verbatim + text=${text//==space==/ } + text=${text//==colon==/:} + text=${text//==comma==/,} + text=${text//==slash==/\/} + text=${text//==lt==/<} + text=${text//==gt==/>} + text=${text//==apos==/'} + text=${text//==quote==/"} + text=${text//&&/&} + text=${text//\\n/<br/>} + text=${text//\\t/ } + text=${text//\&r\&n/<br/>} + text=${text//\&r/<br/>} + text=${text//\&n/<br/>} + text=${text//\&c/:} + contentline="${contentline}${text}" + fi + + ## add contents of a text file to page + if [ ${myarr[1]} == "textfile" ] + then + tfile=${myarr[2]} + fname=`basename ${tfile}` + fname=${fname%.*} + fname="${fname}.txt" + cp ${tfile} "${galaxypath}/${fname}" + + #estimate height for iframe based on number oflines in the file + numlines=`wc -l ${tfile} | cut -d" " -f1` + minheight=$[$numlines*17] + + contentline="${contentline}<iframe class=\"invisibleframe\" src=\"${fname}\" width=\"100%\" height=\"$minheight\"> </iframe>" + fi + + ## add image file to page + if [ ${myarr[1]} == "image" ] + then + imgcount=$[$imgcount+1] + #restore file suffix for html + ftype=`file ${myarr[2]}` + zoomlevel=${myarr[4]} + zoomenable=${myarr[5]} + align=${myarr[6]} + #####echo "zoomenable:${zoomenable}, align:${align}" + if [[ $ftype == *JPEG* ]] + then + suffix=".jpg" + fi + if [[ $ftype == *SVG* ]] + then + suffix=".svg" + fi + if [[ $ftype == *PNG* ]] + then + suffix=".png" + fi + + image=`basename ${myarr[2]}` + image=${image%.dat} + image="${image}${suffix}" + cp ${myarr[2]} ${galaxypath}/${image} + + if [[ ${align} == "none" ]] + then + alignstring="" + alignstring2="" + else + alignstring="<div float=\"${align}\">" + alignstring2="</div>" + + alignstring="align=\"${align}\"" + alignstring2="" + fi + + + if [[ ${zoomlevel} -eq 0 ]] + then + widthstring="" + else + widthstring="width=\"${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 + if [ ${myarr[1]} == "table" ] + then + maxlines=50000 + tsvfile_orig=${myarr[2]} + tsvfile="tablehead.tsv" + fname=`basename ${tsvfile_orig}` + fname=${fname%.*} + fancy=${myarr[4]} + makelinks=${myarr[5]} + #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 ${tsvfile_orig} |cut -d" " -f1` + + head -${maxlines} ${tsvfile_orig} > tsvtmpfile + + #remove any empty or header lines (lines starting with #, unless vcf file, then keep #CHROM line) + awk 'BEGIN{ + FS="\t" + OFS="\t" + }{ + if((index($0,"#")==1 && index($0,"#CHROM")!=1) || $0==""){ + headerlines++ + } + else print $0 + + }END{}' tsvtmpfile > ${tsvfile} + + if [[ $makelinks == "Y" ]] + then + col=${myarr[6]} + prefix=${myarr[7]} + suffix=${myarr[8]} + suffix=${suffix/emptycol/} + suffix=${suffix/==quote==/&} + prefix=${prefix/emptycol/} + prefix=${prefix/==quote==/&} + prefix=${prefix/==colon==/:} + #echo "prefix: $prefix" + + #edit the table to include links + awk 'BEGIN{ + FS="\t" + OFS="\t" + url="'"$prefix"'" + url2="'"$suffix"'" + prefix="<a href=\42" + suffix="\42>" + col="'"$col"'" + end="</a>" + }{ + if(FNR==1) + print $0 + else{ + $col=prefix""url""$col""url2""suffix""$col""end + print $0 + } + }END{}' ${tsvfile} > ${tsvfile}2 + #echo "converted file: " + #cat ${tsvfile}2 + else + cp ${tsvfile} ${tsvfile}2 + fi + + if [ $fancy == "Y" ] + then + perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html + #contentline="${contentline}\n<div class=\"resizable\" id=\"iframe${iframecount}\"><iframe src=\"htmltable_${fname}.html\" style=\"max-width: 100%;vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe></div>" + #contentline="${contentline}\n<iframe class=\"resizable\" id=\"iframe${iframecount}\" src=\"htmltable_${fname}.html\" style=\"max-width: 100%;vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>" + contentline="${contentline}\n<iframe class=\"invisibleframe fancyiframe\" src=\"htmltable_${fname}.html\" width=\"100%\" style=\"min-height: 300px; overflow-y: hidden; overflow-x: scroll\" ></iframe>" + + iframecount=$[$iframecount+1] + else + perl ${repositorypath}/tsv2html_simple.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html + #contentline="${contentline}\n<iframe class=\"invisibleframe\" id=\"iframe${iframecount}\" style=\"max-width: 100%; vertical-align: top;\" src=\"htmltable_${fname}.html\" onload=\"resizeIframe(this)\"></iframe>" + contentline="${contentline}\n<iframe class=\"unfancyiframe invisibleframe\" src=\"htmltable_${fname}.html\" scrolling=\"no\" style=\"max-width: 100%; vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>" + iframecount=$[$iframecount+1] + fi + + if [[ $numlines -gt ${maxlines} ]] + then + tablename=`basename ${tsvfile_orig}` + cp ${tsvfile_orig} ${galaxypath}/$tablename + contentline="${contentline}<br/>\nLarge tables will be supported soon. The first ${maxlines} lines are shown here, and you can download the full file <a href=\"${tablename}\">here</a>." + fi + fi + + if [[ ${myarr[1]} == "pdf" ]] + then + pdffile=${myarr[2]} + fname=`basename ${pdffile}` + fname=${fname%.dat} + pdfname="${fname}.pdf" + cp ${pdffile} "${galaxypath}/${pdfname}" + + width=1000 + height=800 + #contentline="${contentline}<object data=\"${fname}\" type=\"application/pdf\" width=\"1000\" height=\"1000\"><p>It appears you have no PDF plugin for your browser. No biggie... you can <a href=\"${fname}\">click here to download the PDF file.</a></p></object>" + echo -e "<html><body><object data=\"${pdfname}\" type=\"application/pdf\" width=\"$width\" height=\"$height\"><embed src=\"${pdfname}\" type=\"application/pdf\" /><p>It appears you have no PDF plugin for your browser. No biggie... you can <a href=\"${pdfname}\">click here to download the PDF file.</a></p></object></body></html>" > "${galaxypath}/${fname}.html" + width=$[$width+10] + height=$[$height+10] + contentline="${contentline}<iframe src=\"${fname}.html\" width=\"${width}\" height=\"${height}\"></iframe>\n" + + fi + ## link to a location on the web, open in new window + if [ ${myarr[1]} == "weblink" ] + then + url=${myarr[2]} + linktext=${myarr[4]} + url=${url/==colon==/:} + url=${url/==quote==/&} + + contentline="${contentline}<a href=\"${url}\" target=\"_blank\">${linktext}</a>" + fi + + ## link to a file in the history + if [ ${myarr[1]} == "link" ] + then + linkfile=${myarr[2]} + apiid=${myarr[4]} + isireport=${myarr[5]} + linkfilename=`basename ${linkfile}` + linktext=${myarr[6]} + + + #check for some basic filetypes + ftype=`file $linkfile` + if [[ $ftype == *HTML* ]] + then + linkfilename=${linkfilename%.dat} + linkfilename=${linkfilename}.html + fi + if [[ $ftype == *PNG* ]] + then + linkfilename=${linkfilename%.dat} + linkfilename=${linkfilename}.png + fi + if [[ $ftype == *SVG* ]] + then + linkfilename=${linkfilename%.dat} + linkfilename=${linkfilename}.svg + fi + if [[ $ftype == *JPEG* ]] + then + linkfilename=${linkfilename%.dat} + linkfilename=${linkfilename}.jpg + fi + + + if [[ ${isireport} == "Y" ]] + then + linkfilename="/datasets/${apiid}/display/" + else + cp ${linkfile} "${galaxypath}/${linkfilename}" + fi + + contentline="${contentline}<a href=\"${linkfilename}\">${linktext}</a>" + fi + + ## link to files in an archive in the history item + if [[ ${myarr[1]} == "links" ]] + then + #echo "making links:" + archive=${myarr[2]} + fname=`basename ${archive}` + fname=${fname%.dat} + ftype=`file $archive` + mkdir ${galaxypath}/archive_${fname}/ + + #echo "archive type: `file $archive`" + # decompress archive + if [[ $ftype == *Zip* ]] + then + #echo "detected zip file" + cp $archive ${galaxypath}/archive_${fname}/${fname}.zip + wd=`pwd` + cd ${galaxypath}/archive_${fname}/ + unzip -q ${fname}.zip + rm ${fname}.zip + cd $wd + fi + if [[ $ftype == *tar* ]] + then + cp $archive ${galaxypath}/archive_${fname}/${fname}.tar + wd=`pwd` + cd ${galaxypath}/archive_${fname}/ + tar xf ${fname}.tar + rm ${fname}.tar + cd $wd + fi + if [[ $ftype == *gzip* ]] + then + cp $archive ${galaxypath}/archive_${fname}/${fname}.gz + gunzip ${galaxypath}/archive_${fname}/${fname}.gz + #ls ${galaxypath}/archive_${fname}/ + + # check for tar.gz + ftype=`file ${galaxypath}/archive_${fname}/${fname}` + if [[ $ftype == *tar* ]] + then + # turns out it was tar.gz + rm -Rf ${galaxypath}/archive_${fname}/* + ls ${galaxypath}/archive_${fname}/ + cp $archive ${galaxypath}/archive_${fname}/${fname}.tar.gz + + wd=`pwd` + cd ${galaxypath}/archive_${fname}/ + tar xzf ${fname}.tar.gz + cd $wd + fi + wait + rm -f ${galaxypath}/archive_${fname}/*.tar + rm -f ${galaxypath}/archive_${fname}/*.tar.gz + fi + if [[ $ftype == *bzip2* ]] + then + cp $archive ${galaxypath}/archive_${fname}/${fname}.gz + gunzip2 ${galaxypath}/archive_${fname}/${fname}.gz + fi + + + + # add links to webpage + # separate line for each folder, files within folder on same line + for linkfile in `ls ${galaxypath}/archive_${fname}/ |sort -V` + do + #echo "<br/> ->making link to file: $linkfile " + if [ -d ${galaxypath}/archive_${fname}/$linkfile ] # if directory, add break, and list all contained files, max level 1 deep + then + #echo "<br/> ->is directory, entering: $linkfile " + #ls ${galaxypath}/archive_${fname}/$linkfile + contentline="${contentline}" + for linkfile2 in `ls ${galaxypath}/archive_${fname}/$linkfile | sort -V` + do + #echo "<br/> ->making link to file: ${galaxypath}/archive_${fname}/$linkfile2" + if [ -f ${galaxypath}/archive_${fname}/$linkfile/$linkfile2 ] # if directory, add break, and list all contained files, max level 1 deep + then + #echo "<br/> ->is file, making link: $linkfile " + label=`basename $linkfile2` + label=${label%.*} + contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}/${linkfile2}\">${label}</a> \n " + fi + done + elif [ -f ${galaxypath}/archive_${fname}/$linkfile ] + then + label=`basename ${galaxypath}/archive_${fname}/$linkfile` + label=${label%.*} + contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}\">$label</a> \n" + fi + done + + + fi + + if [[ ${myarr[3]} == "Y" ]] + then + contentline="${contentline}<br/>" + fi + fi + done + + echo "${contentline}" +} + + +createMainPage (){ + page=$1 + tabtitles=$2 #comma-separated list of tab titles + tabitems=$3 + iframecount=1 + minwidth=$4 + + echo "createMainPage: tabitems: $tabitems. tabtitles: $tabtitles" + # create correct number of tabs + count=0 + + tabtitles=${tabtitles//,/ } + tabtitles=${tabtitles//==colon==/:} + tabslist="<ul>\n" + mytabs="" + for title in $tabtitles + do + #create list of tabs + + count=$[count+1] + title2=${title//_s_/ } + tabslist="${tabslist} <li><a href=\"#tabs-${count}\">${title2}</a></li>\n" + + #create tabs with content + tabcontent=$(makeTabContent $title "$tabitems") + mytabs="${mytabs}\n<div id=\"tabs-${count}\">\n" + mytabs="${mytabs}${tabcontent}" + mytabs="${mytabs}\n</div>\n" + done + tabslist="${tabslist}</ul>" + + #output the webpage + echo -e "<!doctype html> +<head> + <meta charset=\"utf-8\"> + <title>jQuery UI Tabs - Default functionality</title> + + + <link rel=\"stylesheet\" href=\"//code.jquery.com/ui/1.10.4/themes/smoothness/jquery-ui.css\"> + <link rel=\"stylesheet\" href=\"/resources/demos/style.css\"> + + <script src=\"//code.jquery.com/jquery-1.10.2.js\"></script> + <script src=\"//code.jquery.com/ui/1.10.4/jquery-ui.js\"></script> + <script type=\"text/javascript\" src=\"iframe-resizer/src/iframeResizer.js\"></script> + <script type=\"text/javascript\" src=\"jquery.zoom.js\"></script> + <script> + \$(function() { + \$( \"#tabs\" ).tabs(); + }); + + \$(function() { + \$( \".resizable\" ).resizable(); + }); + + \$(document).ready(function(){ + \$('.zoomme').zoom(); + \$('#ex2').zoom({ on:'grab' }); + \$('#ex3').zoom({ on:'click' }); + \$('#ex4').zoom({ on:'toggle' }); + \$('.fancyiframe').iFrameResize({ + heightCalculationMethod: 'max', + minHeight: 250, + scrolling: true, + checkOrigin: false, + bodyMargin: 15 + }); + \$('.unfancyiframe').iFrameResize({ + heightCalculationMethod: 'max', + scrolling: false, + checkOrigin: false + }); + }); + + </script> + + + <script language=\"javascript\" type=\"text/javascript\"> + function resizeIframe(obj) { + oldheight=obj.style.height + oldwidth=obj.style.width + obj.style.height = obj.contentWindow.document.body.scrollHeight + 4 + 'px'; + obj.style.width = obj.contentWindow.document.body.scrollWidth + 4 + 'px'; + + if(obj.style.height < 50){ + obj.style.height=oldheight + } + } + </script> +<style type=\"text/css\"> + body { + min-width: ${minwidth}px; + width: ${minwidth}px; + min-height: 100%; + } + .invisibleframe{ + border: 0px; + overflow: hidden + } + .mylinks{ + color: blue !important; + } + .mylinks:visited { + color: #551A8B !important; + } +</style> + <style > + .zoomme { + display: inline-block; + } +</style> + + +</head> +<body> + +<div id=\"tabs\" style=\"display:inline-block; min-height:100%; min-width:${minwidth}px\"> +$tabslist + +$mytabs +</div> + + +</body> +</html>" > $page + + + +} \ No newline at end of file