Mercurial > repos > saskia-hiltemann > ireport_devel
diff createHTML.sh @ 0:3c160414da2e
initial upload
| author | shiltemann |
|---|---|
| date | Thu, 26 Feb 2015 14:05:23 +0100 |
| parents | |
| children | d582e2cd3e13 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/createHTML.sh Thu Feb 26 14:05:23 2015 +0100 @@ -0,0 +1,825 @@ +gbcount=0 + +## +## Create Cover Page +## +function makeIntroPage ( ){ + echo "Creating Intro Page" + title="$1" + coverimage=$2 + link=$3 + htmlout=$4 + zipireport=$5 + + echo -e "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01//EN\" \"http://www.w3.org/TR/html4/strict.dtd\"> +<html> + <head> + </head> + <body> + <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/> + <a href=\"$zipireport\"> Click here to download a copy of this iReport </a> <br/><br/> + </center> + </body> +</html>" > $htmlout + +} + +## +## Decompress archive fiels +## -> will detect archive formats: zip, tar, gzip, tar.gz, bzip2 +## -> input: path to archive +## -> files will be located in ${galaxypath}/archive_${fname}/ +## +function decompressArchive (){ + archive=$1 + + fname=`basename ${archive}` + fname=${fname%.dat} + ftype=`file $archive` + + if [[ ! -d ${galaxypath}/archive_${fname}/ ]] + then + 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 + fi +} + +## +## Create HTML content for the tabs specified by user +## +function makeTabContent ( ){ + 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'`) + + ## Create the tab contents HTML code + if [ ${myarr[0]} == $tab ] + then + + ## + ## Text Field + ## + if [ ${myarr[1]} == "text" ] + then + text=${myarr[2]} + md=${myarr[4]} + + # if markdown, convert to html + if [ $md == "Y" ] + then + ## resubstitute sanitized charachters + text=${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//==backtick==/\`} + text=${text//==dollar==/$} + text=${text//==bar==/|} + text=${text//&&/&} + text=${text//\\n/\\n} + text=${text//\\t/\\t} + text=${text//\&r\&n/\\n} + text=${text//\&r/\\n} + text=${text//\&n/\\n} + text=${text//\&c/:} + + + ## convert markdown in textfield to html + echo -e "$text" > mytext.md + + if [ -z `type -p pandoc` ] + then + # pandoc missing + ${repositorypath}/Markdown/markdown2.py mytext.md > mytext.html + + else + # pandoc exists + pandoc -f markdown -o mytext.html mytext.md + pandoc -f markdown -o standalone.html -s mytext.md + + #get css generated by pandoc and add as scoped attribute (HTML5) + pandocstyle=`sed -n '/<style/,/style>/p' standalone.html` + fi + + markdowntext=$(cat mytext.html) + contentline="${contentline}\n<div class=\"markdown-body\">${pandocstyle} ${markdowntext}</div>\n" + + else # If not markdown, print verbatim (with exception of few html tags) + + ## allow some html formatting tags + text=${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/:} + text=${text//==backtick==/`} + text=${text//==dollar==/$} + text=${text//==bar==/|} + contentline="${contentline}\n${text}\n" + fi + + + fi + + ## + ## Text File + ## + if [ ${myarr[1]} == "textfile" ] + then + tfile=${myarr[2]} + md=${myarr[4]} + 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] + + # if markdown, convert to html + if [ $md == "Y" ] + then + + if [ -z `type -p pandoc` ] + then + # pandoc missing + ${repositorypath}/Markdown/markdown2.py ${tfile} > mytext.html + + else + # pandoc exists + pandoc -o mytext.html ${tfile} + pandoc -o standalone.html -s ${tfile} + + # get css generated by pandoc and add as scoped attribute (HTML5) + pandocstyle=`sed -n '/<style/,/style>/p' standalone.html` + + fi + + markdowntext=$(cat mytext.html) + contentline="${contentline}\n<div class=\"markdown-body\">${pandocstyle} ${markdowntext}</div>\n" + else + contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${fname}\" width=\"100%\" height=\"$minheight\"> </iframe>\n" + fi + fi + + ## + ## Image + ## + 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 + + ## + ## Table + ## + 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]} + 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 ${tsvfile_orig} |cut -d" " -f1` + + head -${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]} + urlitems=${myarr[9]} + minw=${myarr[10]} + suffix=${suffix/emptycol/} + suffix=${suffix/==quote==/&} + prefix=${prefix/emptycol/} + prefix=${prefix/==quote==/&} + prefix=${prefix/==colon==/:} + + # unpack archive of files to link to if present + if [[ ${urlitems} != None ]] + then + oldfname=$fname + decompressArchive ${urlitems} + prefix=archive_${fname}/${prefix} + fname=$oldfname + fi + + + #edit the table to include links + awk 'BEGIN{ + FS="\t" + OFS="\t" + url="'"$prefix"'" + url2="'"$suffix"'" + iframeid="'"$iframeid"'" + prefix="<a href=\42" + suffix="\42 onclick=\42resizeIframe("iframeid")\42>" + col="'"$col"'" + end="</a>" + }{ + if(FNR==1) + print $0 + else{ + $col=prefix""url""$col""url2""suffix""$col""end + print $0 + } + }END{}' ${tsvfile} > ${tsvfile}2 + + else + minw=${myarr[6]} + 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_${fname}.html\" width=\"100%\" style=\"height: 760px; min-height: 525px; overflow-y: hidden; overflow-x: scroll\" ></iframe>" + iframecount=$[$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: ${minw}px; max-width: 100%; vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>" + iframecount=$[$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 + + ## + ## PDF + ## + if [[ ${myarr[1]} == "pdf" ]] + then + pdffile=${myarr[2]} + fname=`basename ${pdffile}` + fname=${fname%.dat} + pdfname="${fname}.pdf" + cp ${pdffile} "${galaxypath}/${pdfname}" + + width=1000 + height=800 + echo -e "<html><body><object data=\"${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="${contentline}\n<iframe src=\"${fname}.html\" width=\"${width}\" height=\"${height}\"></iframe>\n" + + fi + + ## + ## HTML + ## + if [[ ${myarr[1]} == "htmlfile" ]] + then + htmlfile=${myarr[2]} + height=${myarr[4]} + fname=`basename ${htmlfile}` + fname=${fname%.dat} + htmlname="${fname}.html" + cp ${htmlfile} "${galaxypath}/${htmlname}" + + contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${htmlname}\" width=\"100%\" height=\"${height}px\"></iframe>\n" + fi + + + if [[ ${myarr[1]} == "htmlpage" ]] + then + url=${myarr[2]} + url=${url//==colon==/:} + url=${url//==fslash==//} + height=${myarr[4]} + + contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${url}\" width=\"100%\" height=\"${height}px\"></iframe>\n" + fi + + ## + ## Web Link + ## + 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 + + + ## + ## Genome Browser + ## + if [ ${myarr[1]} == "genomebrowser" ] + then + # parse inputs + + apiid=${myarr[4]} + servername=${myarr[5]} + buildver=${myarr[2]} + + #TODO + ftype="vcf" + + servername=${servername/==colon==/:} + + ## parse and prepare all tracks + gbcount=$[$gbcount+1] + gbfilelist=${tracklist} + userTracks="" + #IFS=',' read -a gbfilearray <<< ${gbfilelist} + gbfilearray=(${gbfilelist//,/ }) + for gbfile in "${gbfilearray[@]}" + do + # gbfile is in format "browsernum:file" + #IFS=':' read -a gbfileinfo <<< ${gbfile} + gbfileinfo=(${gbfile//:/ }) + if [[ ${gbfileinfo[0]} == $gbcount ]] + then + + ftype=${gbfileinfo[3]} + if [ $ftype == "vcf" ] + then + gbfilename=${gbfileinfo[1]} + gbfilelabel=${gbfileinfo[2]} + gbfilelabel=${gbfilelabel//==space==/ } + fname=`basename ${gbfilename}` + fname=${fname%.dat} + newgbfilename="${fname}.vcf" + + + cp ${gbfilename} "${galaxypath}/${newgbfilename}" + bgzip "${galaxypath}/${newgbfilename}" + tabix -p vcf "${galaxypath}/${newgbfilename}.gz" + + userTracks="${userTracks}, + {name: '${gbfilelabel}', + uri: '${servername}/datasets/${apiid}/display/${newgbfilename}.gz', + tier_type: 'tabix', + payload: 'vcf'} + " + fi + + if [ $ftype == "bam" ] + then + gbfilename=${gbfileinfo[1]} + gbfilelabel=${gbfileinfo[2]} + gbfilelabel=${gbfilelabel//==space==/ } + fname=`basename ${gbfilename}` + fname=${fname%.dat} + newgbfilename="${fname}.bam" + + # link to bam instead of copying + ln -s ${gbfilename} "${galaxypath}/${newgbfilename}" + samtools index "${galaxypath}/${newgbfilename}" + + userTracks="${userTracks}, + {name: '${gbfilelabel}', + bamURI: '${servername}/datasets/${apiid}/display/${newgbfilename}'} + " + + fi + fi + done + + + + if [ ${buildver} == "hg18" ] + then + coordSystem="coordSystem: { + speciesName: 'Human', + taxon: 9606, + auth: 'NCBI', + version: '36', + ucscName: 'hg18' + }," + + chains="chains: { + hg19ToHg18: new Chainset('https://www.biodalliance.org/das/hg19ToHg18/', 'GRCh37', 'NCBI36', + { + speciesName: 'Human', + taxon: 9606, + auth: 'GRCh', + version: 37 + }) + }," + + genesTrack="{name: 'Genes', + desc: 'Gene structures from Ensembl 54', + uri: 'https://www.biodalliance.org/das/hsa_54_36p/', + collapseSuperGroups: true, + provides_karyotype: true, + provides_search: true, + provides_entrypoints: true, + maxbins: false}, " + + repeatsTrack="{name: 'Repeats', + desc: 'Repeat annotation from Ensembl 59', + bwgURI: 'https://www.biodalliance.org/datasets/repeats.bb', + stylesheet_uri: 'https://www.biodalliance.org/stylesheets/bb-repeats.xml'}" + + + # default is hg19 + else + coordSystem="coordSystem: { + speciesName: 'Human', + taxon: 9606, + auth: 'NCBI', + version: '37', + ucscName: 'hg19' + }," + + chains="" + + genesTrack="{name: 'Genes', + desc: 'Gene structures from GENCODE 19', + bwgURI: 'https://www.biodalliance.org/datasets/gencode.bb', + stylesheet_uri: 'https://www.biodalliance.org/stylesheets/gencode.xml', + collapseSuperGroups: true, + trixURI: 'https://www.biodalliance.org/datasets/geneIndex.ix'}," + + repeatsTrack="{name: 'Repeats', + desc: 'Repeat annotation from Ensembl 59', + bwgURI: 'https://www.biodalliance.org/datasets/repeats.bb', + stylesheet_uri: 'https://www.biodalliance.org/stylesheets/bb-repeats.xml'}," + + fi + + contentline="${contentline} +<script language=\"javascript\" src=\"https://www.biodalliance.org/release-0.13/dalliance-compiled.js\"></script> +<script language=\"javascript\"> + new Browser({ + chr: '1', + viewStart: 0, + viewEnd: 100000, + cookieKey: 'human', + + ${coordSystem} + + ${chains} + sources: [{name: 'Genome', + twoBitURI: 'https://www.biodalliance.org/datasets/${buildver}.2bit', + tier_type: 'sequence'}, + ${genesTrack}, + ${repeatsTrack}, + {name: 'Conservation', + desc: 'Conservation', + bwgURI: 'https://www.biodalliance.org/datasets/phastCons46way.bw', + noDownsample: true} + ${userTracks} + ], + + + + + browserLinks: { + Ensembl: 'http://www.ensembl.org/Homo_sapiens/Location/View?r=${chr}:${start}-${end}', + UCSC: 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=${buildver}&position=chr${chr}:${start}-${end}', + Sequence: 'http://www.derkholm.net:8080/das/${buildver}comp/sequence?segment=${chr}:${start},${end}' + } + + }); +</script> + +<div id=\"svgHolder\"></div> +" + fi + + ## + ## Link to Dataset + ## + 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 + + ## + ## Links to Archive Contents + ## + if [[ ${myarr[1]} == "links" ]] + then + archive=${myarr[2]} + decompressArchive $archive + + # 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/>\n" + 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: $gbtracks" + # create correct number of tabs + count=0 + + tabtitles=${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" "$gbtracks") + mytabs="${mytabs}\n<div id=\"tabs-${count}\">\n" + mytabs="${mytabs}${tabcontent}" + mytabs="${mytabs}\n</div>\n" + done + tabslist="${tabslist}</ul>" + + ## Output the webpage + echo -e "<!doctype html> + <head> + <meta charset=\"utf-8\"> + <title>iReport</title> + <link rel=\"stylesheet\" href=\"jquery-ui.css\"> + <link rel=\"stylesheet\" href=\"ireport_css.css\"> + <link rel=\"stylesheet\" href=\"md.css\"> + <script type=\"text/javascript\" src=\"jquery-1.10.2.js\"></script> + <script type=\"text/javascript\" src=\"jquery-ui.js\"></script> + <script type=\"text/javascript\" src=\"iframe-resizer/src/iframeResizer.js\"></script> + <script type=\"text/javascript\" src=\"jquery.zoom.js\"></script> + <script type=\"text/javascript\" src=\"ireport_jquery.js\"></script> + <script type=\"text/javascript\" src=\"ireport_javascript.js\"></script> + </head> + <body> + <div id=\"tabs\" style=\"display:inline-block; min-height:100%; min-width:${minwidth}px\"> + $tabslist + + $mytabs + </div> + </body> +</html>" > $page +}