Mercurial > repos > saskia-hiltemann > ireport
view createHTML.sh @ 5:4e21ce709269 draft
Uploaded
| author | saskia-hiltemann |
|---|---|
| date | Tue, 07 Oct 2014 08:49:14 -0400 |
| parents | a4813532bbc6 |
| children | 42076db43d42 |
line wrap: on
line source
## ## 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 } ## ## Create HTML content for the tabs specified by user ## function makeTabContent ( ){ tab=$1 # name of current tab itemslist=$2 # list of all items contentline="" # HTML code for tab imgcount=0 # keep track of the number of images on the current tab 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 ${repositorypath}/Markdown/markdown2.py mytext.md > mytext.html else # pandoc exists echo "pandoc exists" pandoc -o mytext.html mytext.md pandoc -o standalone.html -s mytext.md #get css generated by pandoc and add as scoped attribute (HTML5) pandocstyle=`sed -n '/<style/,/style>/p' standalone.html` fi markdowntext=$(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]} #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 else cp ${tsvfile} ${tsvfile}2 fi if [ $fancy == "Y" ] then perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html contentline="${contentline}\n<iframe class=\"invisibleframe fancyiframe\" src=\"htmltable_${fname}.html\" width=\"100%\" style=\"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="${contentline}\n<iframe class=\"unfancyiframe invisibleframe\" src=\"htmltable_${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 ## ## 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 ## ## 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 ## ## 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 [[ ${myarr[1]} == "links" ]] then #echo "making links:" archive=${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/>\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 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>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 }