Mercurial > repos > saskia-hiltemann > ireport
view createHTML.sh @ 9:7300ed4c1481 draft default tip
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| author | saskia-hiltemann |
|---|---|
| date | Mon, 04 Sep 2017 10:49:00 -0400 |
| parents | 42076db43d42 |
| children |
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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 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 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 } ## ## 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 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'`) ## 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=${text//==braceopen==/(} text=${text//==braceclose==/)} text=${text//==cbraceopen==/{} text=${text//==cbraceclose==/}} 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==/|} text=${text//==braceopen==/(} text=${text//==braceclose==/)} text=${text//==cbraceopen==/{} text=${text//==cbraceclose==/}} 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]} typestring="" #####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 if [[ $ftype == *TIFF* ]] then suffix=".tiff" typestring="type=\"image/tiff\"" 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$giframecount" iframeid="iframe-$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 ${tsvfile_orig} |cut -d" " -f1` head -${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]} minh=${myarr[11]} suffix=${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]} 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}` 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}/${htmlname}" apiid=${myarr[5]} isireport=${myarr[6]} localhost=${myarr[7]} proxy=${myarr[8]} localhost=${localhost//==colon==/:} localhost=${localhost//==fslash==/\/} if [[ ${isireport} == "Y" ]] then #cp ${localhost}/datasets/${apiid}/* "${galaxypath}/tst" htmlname="/${proxy}/datasets/${apiid}/display/" fi contentline="${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=${myarr[4]} echo -n "$url" > tmpfileb64 url=`base64 -d tmpfileb64` echo -n "$linktext" > tmpfileb64 linktext=`base64 -d tmpfileb64` if [[ -z $linktext ]] then linktext=$url fi 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]} region=${myarr[6]} echo -n "$region" > tmpfileb64 region=`base64 -d tmpfileb64` initialchrom=${region%:*} initialrange=${region#*:} initialstart=${initialrange%-*} initialend=${initialrange#*-} #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]} gbfilename=${gbfileinfo[1]} gbfilelabel=${gbfileinfo[2]} gbfilelabel=${gbfilelabel//==space==/ } gbfilelabel=${gbfilelabel//==bopen==/(} gbfilelabel=${gbfilelabel//==bclose==/)} fname=`basename ${gbfilename}` fname=${fname%.dat} if [[ $ftype == "vcftabix" ]] then newgbfilename="${fname}.vcf" cp ${gbfilename} "${galaxypath}/${newgbfilename}" bgzip "${galaxypath}/${newgbfilename}" tabix -f -p vcf "${galaxypath}/${newgbfilename}.gz" userTracks="${userTracks}, {name: '${gbfilelabel}', uri: '${servername}/datasets/${apiid}/display/${newgbfilename}.gz', tier_type: 'tabix', payload: 'vcf'} " fi if [[ $ftype == "vcfmemstore" ]] then newgbfilename="${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}', tier_type: 'memstore', payload: 'vcf'} " fi if [[ $ftype == "bam" ]] then newgbfilename="${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 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 [[ $ftype == "bedtabix" ]] then newgbfilename="${fname}.bed" cp ${gbfilename} "${galaxypath}/${newgbfilename}" bgzip "${galaxypath}/${newgbfilename}" tabix -f -p bed "${galaxypath}/${newgbfilename}.gz" userTracks="${userTracks}, {name: '${gbfilelabel}', uri: '${servername}/datasets/${apiid}/display/${newgbfilename}.gz', tier_type: 'tabix', payload: 'bed'} " fi if [[ $ftype == "bedmemstore" ]] then newgbfilename="${fname}.bed" cp ${gbfilename} "${galaxypath}/${newgbfilename}" #bgzip "${galaxypath}/${newgbfilename}" #tabix -p bed "${galaxypath}/${newgbfilename}.gz" userTracks="${userTracks}, {name: '${gbfilelabel}', uri: '${servername}/datasets/${apiid}/display/${newgbfilename}', tier_type: 'memstore', payload: 'bed'} " 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: '$initialchrom', viewStart: $initialstart, viewEnd: $initialend, cookieKey: 'human', pageName: 'svgHolder${gbcount}', ${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${gbcount}\"></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]} localhost=${myarr[7]} proxy=${myarr[8]} localhost=${localhost//==colon==/:} localhost=${localhost//==fslash==/\/} #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 [[ ${isireport} == "Y" ]] then linkfilename="/${proxy}/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 (){ #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: $gbtracks" # create correct number of tabs count=0 tabtitles=${tabtitles/,/} tabtitles=${tabtitles//,/ } echo $tabtitles tabcount=0 for tabt in $tabtitles do echo -n $tabt > tmpfileb64 thistabtitle=`base64 -d tmpfileb64` newtabtitles+=" $thistabtitle" tabcount=$[tabcount+1] done echo $newtabtitles tabslist="<ul>\n" mytabs="" for title in $newtabtitles do # Create list of tabs count=$[count+1] title2=${title//==space==/ } title2=${title2//==dollar==/$} title2=${title2//==colon==/} 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 }