Mercurial > repos > saskia-hiltemann > ireport_devel
comparison createHTML.sh @ 6:e3cb63c2b7c1 draft
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| author | saskia-hiltemann |
|---|---|
| date | Mon, 16 Nov 2015 10:06:52 -0500 |
| parents | |
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| 5:a89dd3328d2c | 6:e3cb63c2b7c1 |
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| 1 gbcount=0 | |
| 2 | |
| 3 ## | |
| 4 ## Create Cover Page | |
| 5 ## | |
| 6 #<a href=\"$zipireport\"> Click here to download a copy of this iReport </a> <br/><br/> | |
| 7 function makeIntroPage ( ){ | |
| 8 echo "Creating Intro Page" | |
| 9 title="$1" | |
| 10 coverimage=$2 | |
| 11 link=$3 | |
| 12 htmlout=$4 | |
| 13 zipireport=$5 | |
| 14 | |
| 15 echo -e "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01//EN\" \"http://www.w3.org/TR/html4/strict.dtd\"> | |
| 16 <html> | |
| 17 <head> | |
| 18 </head> | |
| 19 <body> | |
| 20 <br/> | |
| 21 <br/> | |
| 22 <center> | |
| 23 <b><font size=\"15\"> iReport: ${title} </font></b><br/> | |
| 24 <br/> | |
| 25 <br/> | |
| 26 <a href=\"$link\"> Click image to view report </a> <br/><br/> | |
| 27 <a href=\"$link\"> <img src="$coverimage" width=\"50%\" alt=\"loading image..\"/> </a><br/><br/> | |
| 28 </center> | |
| 29 </body> | |
| 30 </html>" > $htmlout | |
| 31 | |
| 32 } | |
| 33 | |
| 34 ## | |
| 35 ## Decompress archive fiels | |
| 36 ## -> will detect archive formats: zip, tar, gzip, tar.gz, bzip2 | |
| 37 ## -> input: path to archive | |
| 38 ## -> files will be located in ${galaxypath}/archive_${fname}/ | |
| 39 ## | |
| 40 function decompressArchive (){ | |
| 41 archive=$1 | |
| 42 | |
| 43 fname=`basename ${archive}` | |
| 44 fname=${fname%.dat} | |
| 45 ftype=`file $archive` | |
| 46 | |
| 47 if [[ ! -d ${galaxypath}/archive_${fname}/ ]] | |
| 48 then | |
| 49 mkdir ${galaxypath}/archive_${fname}/ | |
| 50 | |
| 51 #echo "archive type: `file $archive`" | |
| 52 # decompress archive | |
| 53 if [[ $ftype == *Zip* ]] | |
| 54 then | |
| 55 #echo "detected zip file" | |
| 56 cp $archive ${galaxypath}/archive_${fname}/${fname}.zip | |
| 57 wd=`pwd` | |
| 58 cd ${galaxypath}/archive_${fname}/ | |
| 59 unzip -q ${fname}.zip | |
| 60 rm ${fname}.zip | |
| 61 cd $wd | |
| 62 fi | |
| 63 if [[ $ftype == *tar* ]] | |
| 64 then | |
| 65 cp $archive ${galaxypath}/archive_${fname}/${fname}.tar | |
| 66 wd=`pwd` | |
| 67 cd ${galaxypath}/archive_${fname}/ | |
| 68 tar xf ${fname}.tar | |
| 69 rm ${fname}.tar | |
| 70 cd $wd | |
| 71 fi | |
| 72 if [[ $ftype == *gzip* ]] | |
| 73 then | |
| 74 cp $archive ${galaxypath}/archive_${fname}/${fname}.gz | |
| 75 gunzip ${galaxypath}/archive_${fname}/${fname}.gz | |
| 76 #ls ${galaxypath}/archive_${fname}/ | |
| 77 | |
| 78 # check for tar.gz | |
| 79 ftype=`file ${galaxypath}/archive_${fname}/${fname}` | |
| 80 if [[ $ftype == *tar* ]] | |
| 81 then | |
| 82 # turns out it was tar.gz | |
| 83 rm -Rf ${galaxypath}/archive_${fname}/* | |
| 84 ls ${galaxypath}/archive_${fname}/ | |
| 85 cp $archive ${galaxypath}/archive_${fname}/${fname}.tar.gz | |
| 86 | |
| 87 wd=`pwd` | |
| 88 cd ${galaxypath}/archive_${fname}/ | |
| 89 tar xzf ${fname}.tar.gz | |
| 90 cd $wd | |
| 91 fi | |
| 92 wait | |
| 93 rm -f ${galaxypath}/archive_${fname}/*.tar | |
| 94 rm -f ${galaxypath}/archive_${fname}/*.tar.gz | |
| 95 fi | |
| 96 if [[ $ftype == *bzip2* ]] | |
| 97 then | |
| 98 cp $archive ${galaxypath}/archive_${fname}/${fname}.gz | |
| 99 gunzip2 ${galaxypath}/archive_${fname}/${fname}.gz | |
| 100 fi | |
| 101 fi | |
| 102 } | |
| 103 | |
| 104 ## | |
| 105 ## Create HTML content for the tabs specified by user | |
| 106 ## | |
| 107 function makeTabContent ( ){ | |
| 108 tab=$1 # name of current tab | |
| 109 itemslist=$2 # list of all items | |
| 110 tracklist=$3 # genome browser tracks info | |
| 111 contentline="" # HTML code for tab | |
| 112 imgcount=0 # keep track of the number of images on the current tab | |
| 113 iframename=`head -n 1 < /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 8 | head -n 1` | |
| 114 #iframename="test" | |
| 115 for item in $itemslist | |
| 116 do | |
| 117 ## Parse items lists | |
| 118 item=${item/::/:emptycol:} | |
| 119 declare -a myarr=(`echo $item |sed 's/:/ /g'`) | |
| 120 | |
| 121 ## Create the tab contents HTML code | |
| 122 if [ ${myarr[0]} == $tab ] | |
| 123 then | |
| 124 | |
| 125 ## | |
| 126 ## Text Field | |
| 127 ## | |
| 128 if [ ${myarr[1]} == "text" ] | |
| 129 then | |
| 130 text=${myarr[2]} | |
| 131 md=${myarr[4]} | |
| 132 | |
| 133 # if markdown, convert to html | |
| 134 if [ $md == "Y" ] | |
| 135 then | |
| 136 ## resubstitute sanitized charachters | |
| 137 text=${text//==space==/ } | |
| 138 text=${text//==colon==/:} | |
| 139 text=${text//==comma==/,} | |
| 140 | |
| 141 text=${text//==braceopen==/(} | |
| 142 text=${text//==braceclose==/)} | |
| 143 text=${text//==cbraceopen==/{} | |
| 144 text=${text//==cbraceclose==/}} | |
| 145 | |
| 146 text=${text//==slash==/\/} | |
| 147 text=${text//==lt==/<} | |
| 148 text=${text//==gt==/>} | |
| 149 text=${text//==apos==/\'} | |
| 150 text=${text//==quote==/\"} | |
| 151 text=${text//==backtick==/\`} | |
| 152 text=${text//==dollar==/$} | |
| 153 text=${text//==bar==/|} | |
| 154 text=${text//&&/&} | |
| 155 text=${text//\\n/\\n} | |
| 156 text=${text//\\t/\\t} | |
| 157 text=${text//\&r\&n/\\n} | |
| 158 text=${text//\&r/\\n} | |
| 159 text=${text//\&n/\\n} | |
| 160 text=${text//\&c/:} | |
| 161 | |
| 162 | |
| 163 ## convert markdown in textfield to html | |
| 164 echo -e "$text" > mytext.md | |
| 165 | |
| 166 if [ -z `type -p pandoc` ] | |
| 167 then | |
| 168 # pandoc missing | |
| 169 ${repositorypath}/Markdown/markdown2.py mytext.md > mytext.html | |
| 170 | |
| 171 else | |
| 172 # pandoc exists | |
| 173 pandoc -f markdown -o mytext.html mytext.md | |
| 174 pandoc -f markdown -o standalone.html -s mytext.md | |
| 175 | |
| 176 #get css generated by pandoc and add as scoped attribute (HTML5) | |
| 177 pandocstyle=`sed -n '/<style/,/style>/p' standalone.html` | |
| 178 fi | |
| 179 | |
| 180 markdowntext=$(cat mytext.html) | |
| 181 contentline="${contentline}\n<div class=\"markdown-body\">${pandocstyle} ${markdowntext}</div>\n" | |
| 182 | |
| 183 else # If not markdown, print verbatim (with exception of few html tags) | |
| 184 | |
| 185 ## allow some html formatting tags | |
| 186 text=${text//==lt==strong==gt==/<strong>} # search for strong tags | |
| 187 text=${text//==lt====slash==strong==gt==/<\/strong>} # search for strong tags | |
| 188 text=${text//==lt==em==gt==/<em>} # search for strong tags | |
| 189 text=${text//==lt====slash==em==gt==/<\/em>} # search for strong tags | |
| 190 | |
| 191 text=${text//==lt==b==gt==/<strong>} # search for strong tags | |
| 192 text=${text//==lt====slash==b==gt==/<\/strong>} # search for strong tags | |
| 193 text=${text//==lt==i==gt==/<em>} # search for strong tags | |
| 194 text=${text//==lt====slash==i==gt==/<\/em>} # search for strong tags | |
| 195 | |
| 196 text=${text//==lt==br==gt==/<br\/>} # search for strong tags | |
| 197 text=${text//==lt====br==slash==gt==/<br\/>} # search for strong tags | |
| 198 text=${text//==lt==h1==gt==/<h1>} # search for h1-h6 tags | |
| 199 text=${text//==lt==h2==gt==/<h2>} # search for h1-h6 tags | |
| 200 text=${text//==lt==h3==gt==/<h3>} # search for h1-h6 tags | |
| 201 text=${text//==lt==h4==gt==/<h4>} # search for h1-h6 tags | |
| 202 text=${text//==lt==h5==gt==/<h5>} # search for h1-h6 tags | |
| 203 text=${text//==lt==h6==gt==/<h6>} # search for h1-h6 tags | |
| 204 text=${text//==lt====slash==h1==gt==/<\/h1>} # search for h1-h6 closing tags | |
| 205 text=${text//==lt====slash==h2==gt==/<\/h2>} # search for h1-h6 closing tags | |
| 206 text=${text//==lt====slash==h3==gt==/<\/h3>} # search for h1-h6 closing tags | |
| 207 text=${text//==lt====slash==h4==gt==/<\/h4>} # search for h1-h6 closing tags | |
| 208 text=${text//==lt====slash==h5==gt==/<\/h5>} # search for h1-h6 closing tags | |
| 209 text=${text//==lt====slaxh==h6==gt==/<\/h6>} # search for h1-h6 closing tags | |
| 210 | |
| 211 ## display everything else verbatim | |
| 212 text=${text//==space==/ } | |
| 213 text=${text//==colon==/:} | |
| 214 text=${text//==comma==/,} | |
| 215 text=${text//==slash==/\/} | |
| 216 text=${text//==lt==/<} | |
| 217 text=${text//==gt==/>} | |
| 218 text=${text//==apos==/'} | |
| 219 text=${text//==quote==/"} | |
| 220 text=${text//&&/&} | |
| 221 text=${text//\\n/<br/>} | |
| 222 text=${text//\\t/ } | |
| 223 text=${text//\&r\&n/<br/>} | |
| 224 text=${text//\&r/<br/>} | |
| 225 text=${text//\&n/<br/>} | |
| 226 text=${text//\&c/:} | |
| 227 text=${text//==backtick==/`} | |
| 228 text=${text//==dollar==/$} | |
| 229 text=${text//==bar==/|} | |
| 230 text=${text//==braceopen==/(} | |
| 231 text=${text//==braceclose==/)} | |
| 232 text=${text//==cbraceopen==/{} | |
| 233 text=${text//==cbraceclose==/}} | |
| 234 contentline="${contentline}\n${text}\n" | |
| 235 fi | |
| 236 | |
| 237 | |
| 238 fi | |
| 239 | |
| 240 ## | |
| 241 ## Text File | |
| 242 ## | |
| 243 if [ ${myarr[1]} == "textfile" ] | |
| 244 then | |
| 245 tfile=${myarr[2]} | |
| 246 md=${myarr[4]} | |
| 247 fname=`basename ${tfile}` | |
| 248 fname=${fname%.*} | |
| 249 fname="${fname}.txt" | |
| 250 cp ${tfile} "${galaxypath}/${fname}" | |
| 251 | |
| 252 #estimate height for iframe based on number oflines in the file | |
| 253 numlines=`wc -l ${tfile} | cut -d" " -f1` | |
| 254 minheight=$[$numlines*17] | |
| 255 | |
| 256 # if markdown, convert to html | |
| 257 if [ $md == "Y" ] | |
| 258 then | |
| 259 | |
| 260 if [ -z `type -p pandoc` ] | |
| 261 then | |
| 262 # pandoc missing | |
| 263 ${repositorypath}/Markdown/markdown2.py ${tfile} > mytext.html | |
| 264 | |
| 265 else | |
| 266 # pandoc exists | |
| 267 pandoc -o mytext.html ${tfile} | |
| 268 pandoc -o standalone.html -s ${tfile} | |
| 269 | |
| 270 # get css generated by pandoc and add as scoped attribute (HTML5) | |
| 271 pandocstyle=`sed -n '/<style/,/style>/p' standalone.html` | |
| 272 | |
| 273 fi | |
| 274 | |
| 275 markdowntext=$(cat mytext.html) | |
| 276 contentline="${contentline}\n<div class=\"markdown-body\">${pandocstyle} ${markdowntext}</div>\n" | |
| 277 else | |
| 278 contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${fname}\" width=\"100%\" height=\"$minheight\"> </iframe>\n" | |
| 279 fi | |
| 280 fi | |
| 281 | |
| 282 ## | |
| 283 ## Image | |
| 284 ## | |
| 285 if [ ${myarr[1]} == "image" ] | |
| 286 | |
| 287 then | |
| 288 imgcount=$[$imgcount+1] | |
| 289 #restore file suffix for html | |
| 290 ftype=`file ${myarr[2]}` | |
| 291 zoomlevel=${myarr[4]} | |
| 292 zoomenable=${myarr[5]} | |
| 293 align=${myarr[6]} | |
| 294 typestring="" | |
| 295 #####echo "zoomenable:${zoomenable}, align:${align}" | |
| 296 if [[ $ftype == *JPEG* ]] | |
| 297 then | |
| 298 suffix=".jpg" | |
| 299 fi | |
| 300 if [[ $ftype == *SVG* ]] | |
| 301 then | |
| 302 suffix=".svg" | |
| 303 fi | |
| 304 if [[ $ftype == *PNG* ]] | |
| 305 then | |
| 306 suffix=".png" | |
| 307 fi | |
| 308 if [[ $ftype == *TIFF* ]] | |
| 309 then | |
| 310 suffix=".tiff" | |
| 311 typestring="type=\"image/tiff\"" | |
| 312 fi | |
| 313 | |
| 314 image=`basename ${myarr[2]}` | |
| 315 image=${image%.dat} | |
| 316 image="${image}${suffix}" | |
| 317 cp ${myarr[2]} ${galaxypath}/${image} | |
| 318 | |
| 319 if [[ ${align} == "none" ]] | |
| 320 then | |
| 321 alignstring="" | |
| 322 alignstring2="" | |
| 323 else | |
| 324 alignstring="<div float=\"${align}\">" | |
| 325 alignstring2="</div>" | |
| 326 | |
| 327 alignstring="align=\"${align}\"" | |
| 328 alignstring2="" | |
| 329 fi | |
| 330 | |
| 331 | |
| 332 if [[ ${zoomlevel} -eq 0 ]] | |
| 333 then | |
| 334 widthstring="" | |
| 335 else | |
| 336 widthstring="width=\"${zoomlevel}\"" | |
| 337 fi | |
| 338 | |
| 339 if [[ ${zoomlevel} -eq 0 || ${zoomenable} == "N" ]] | |
| 340 then | |
| 341 contentline="${contentline}<span id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>" | |
| 342 else | |
| 343 contentline="${contentline}<span class=\"zoomme\" id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>" | |
| 344 fi | |
| 345 | |
| 346 fi | |
| 347 | |
| 348 ## | |
| 349 ## Table | |
| 350 ## | |
| 351 if [ ${myarr[1]} == "table" ] | |
| 352 then | |
| 353 | |
| 354 maxlines=50000 | |
| 355 tsvfile_orig=${myarr[2]} | |
| 356 tsvfile="tablehead.tsv" | |
| 357 fname=`basename ${tsvfile_orig}` | |
| 358 fname=${fname%.*} | |
| 359 fancy=${myarr[4]} | |
| 360 makelinks=${myarr[5]} | |
| 361 #iframeid="iframe$giframecount" | |
| 362 iframeid="iframe-$iframename" | |
| 363 | |
| 364 #echo "\nmakelinks: $makelinks fancy: $fancy <br>" | |
| 365 | |
| 366 #TODO client side database for large files. For now only display first section of file and add download link | |
| 367 numlines=`wc -l ${tsvfile_orig} |cut -d" " -f1` | |
| 368 | |
| 369 head -${maxlines} ${tsvfile_orig} > tsvtmpfile | |
| 370 | |
| 371 #remove any empty or header lines (lines starting with #, unless vcf file, then keep #CHROM line) | |
| 372 awk 'BEGIN{ | |
| 373 FS="\t" | |
| 374 OFS="\t" | |
| 375 }{ | |
| 376 if((index($0,"#")==1 && index($0,"#CHROM")!=1) || $0==""){ | |
| 377 headerlines++ | |
| 378 } | |
| 379 else print $0 | |
| 380 | |
| 381 }END{}' tsvtmpfile > ${tsvfile} | |
| 382 | |
| 383 if [[ $makelinks == "Y" ]] | |
| 384 then | |
| 385 col=${myarr[6]} | |
| 386 prefix=${myarr[7]} | |
| 387 suffix=${myarr[8]} | |
| 388 urlitems=${myarr[9]} | |
| 389 minw=${myarr[10]} | |
| 390 minh=${myarr[11]} | |
| 391 suffix=${suffix/emptycol/} | |
| 392 suffix=${suffix/==quote==/&} | |
| 393 prefix=${prefix/emptycol/} | |
| 394 prefix=${prefix/==quote==/&} | |
| 395 prefix=${prefix/==colon==/:} | |
| 396 | |
| 397 # unpack archive of files to link to if present | |
| 398 if [[ ${urlitems} != None ]] | |
| 399 then | |
| 400 oldfname=$fname | |
| 401 decompressArchive ${urlitems} | |
| 402 prefix=archive_${fname}/${prefix} | |
| 403 fname=$oldfname | |
| 404 fi | |
| 405 | |
| 406 | |
| 407 #edit the table to include links | |
| 408 awk 'BEGIN{ | |
| 409 FS="\t" | |
| 410 OFS="\t" | |
| 411 url="'"$prefix"'" | |
| 412 url2="'"$suffix"'" | |
| 413 iframeid="'"$iframeid"'" | |
| 414 prefix="<a href=\42" | |
| 415 suffix="\42 onclick=\42resizeIframe("iframeid")\42>" | |
| 416 col="'"$col"'" | |
| 417 end="</a>" | |
| 418 }{ | |
| 419 if(FNR==1) | |
| 420 print $0 | |
| 421 else{ | |
| 422 $col=prefix""url""$col""url2""suffix""$col""end | |
| 423 print $0 | |
| 424 } | |
| 425 }END{}' ${tsvfile} > ${tsvfile}2 | |
| 426 | |
| 427 else | |
| 428 minw=${myarr[6]} | |
| 429 minh=${myarr[7]} | |
| 430 cp ${tsvfile} ${tsvfile}2 | |
| 431 fi | |
| 432 | |
| 433 #iframecount=$[$iframecount+1] | |
| 434 | |
| 435 if [ $fancy == "Y" ] | |
| 436 then | |
| 437 perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html | |
| 438 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>" | |
| 439 | |
| 440 else | |
| 441 perl ${repositorypath}/tsv2html_simple.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html | |
| 442 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>" | |
| 443 | |
| 444 fi | |
| 445 | |
| 446 if [[ $numlines -gt ${maxlines} ]] | |
| 447 then | |
| 448 tablename=`basename ${tsvfile_orig}` | |
| 449 cp ${tsvfile_orig} ${galaxypath}/$tablename | |
| 450 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>." | |
| 451 fi | |
| 452 fi | |
| 453 | |
| 454 ## | |
| 455 ## PDF | |
| 456 ## | |
| 457 if [[ ${myarr[1]} == "pdf" ]] | |
| 458 then | |
| 459 pdffile=${myarr[2]} | |
| 460 fname=`basename ${pdffile}` | |
| 461 fname=${fname%.dat} | |
| 462 pdfname="${fname}.pdf" | |
| 463 cp ${pdffile} "${galaxypath}/${pdfname}" | |
| 464 | |
| 465 width=1000 | |
| 466 height=800 | |
| 467 echo -e "<html><body><object data=\"${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" | |
| 468 width=$[$width+10] | |
| 469 height=$[$height+10] | |
| 470 contentline="${contentline}\n<iframe src=\"${fname}.html\" width=\"${width}\" height=\"${height}\"></iframe>\n" | |
| 471 | |
| 472 fi | |
| 473 | |
| 474 ## | |
| 475 ## HTML | |
| 476 ## | |
| 477 if [[ ${myarr[1]} == "htmlfile" ]] | |
| 478 then | |
| 479 htmlfile=${myarr[2]} | |
| 480 height=${myarr[4]} | |
| 481 fname=`basename ${htmlfile}` | |
| 482 fname=${fname%.dat} | |
| 483 htmlname="${fname}.html" | |
| 484 cp ${htmlfile} "${galaxypath}/${htmlname}" | |
| 485 | |
| 486 apiid=${myarr[5]} | |
| 487 isireport=${myarr[6]} | |
| 488 localhost=${myarr[7]} | |
| 489 proxy=${myarr[8]} | |
| 490 localhost=${localhost//==colon==/:} | |
| 491 localhost=${localhost//==fslash==/\/} | |
| 492 if [[ ${isireport} == "Y" ]] | |
| 493 then | |
| 494 #cp ${localhost}/datasets/${apiid}/* "${galaxypath}/tst" | |
| 495 htmlname="/${proxy}/datasets/${apiid}/display/" | |
| 496 fi | |
| 497 | |
| 498 contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${htmlname}\" width=\"100%\" height=\"${height}px\"></iframe>\n" | |
| 499 fi | |
| 500 | |
| 501 | |
| 502 if [[ ${myarr[1]} == "htmlpage" ]] | |
| 503 then | |
| 504 url=${myarr[2]} | |
| 505 url=${url//==colon==/:} | |
| 506 url=${url//==fslash==//} | |
| 507 height=${myarr[4]} | |
| 508 contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${url}\" width=\"100%\" height=\"${height}px\"></iframe>\n" | |
| 509 fi | |
| 510 | |
| 511 ## | |
| 512 ## Web Link | |
| 513 ## | |
| 514 if [ ${myarr[1]} == "weblink" ] | |
| 515 then | |
| 516 url=${myarr[2]} | |
| 517 linktext=${myarr[4]} | |
| 518 | |
| 519 echo -n "$url" > tmpfileb64 | |
| 520 url=`base64 -d tmpfileb64` | |
| 521 | |
| 522 echo -n "$linktext" > tmpfileb64 | |
| 523 linktext=`base64 -d tmpfileb64` | |
| 524 | |
| 525 if [[ -z $linktext ]] | |
| 526 then | |
| 527 linktext=$url | |
| 528 fi | |
| 529 contentline="${contentline}<a href=\"${url}\" target=\"_blank\">${linktext}</a>" | |
| 530 fi | |
| 531 | |
| 532 | |
| 533 ## | |
| 534 ## Genome Browser | |
| 535 ## | |
| 536 if [ ${myarr[1]} == "genomebrowser" ] | |
| 537 then | |
| 538 | |
| 539 # parse inputs | |
| 540 | |
| 541 apiid=${myarr[4]} | |
| 542 servername=${myarr[5]} | |
| 543 buildver=${myarr[2]} | |
| 544 | |
| 545 | |
| 546 region=${myarr[6]} | |
| 547 | |
| 548 | |
| 549 echo -n "$region" > tmpfileb64 | |
| 550 region=`base64 -d tmpfileb64` | |
| 551 | |
| 552 | |
| 553 initialchrom=${region%:*} | |
| 554 initialrange=${region#*:} | |
| 555 | |
| 556 initialstart=${initialrange%-*} | |
| 557 initialend=${initialrange#*-} | |
| 558 | |
| 559 | |
| 560 #TODO | |
| 561 ftype="vcf" | |
| 562 | |
| 563 servername=${servername/==colon==/:} | |
| 564 | |
| 565 ## parse and prepare all tracks | |
| 566 gbcount=$[$gbcount+1] | |
| 567 gbfilelist=${tracklist} | |
| 568 userTracks="" | |
| 569 #IFS=',' read -a gbfilearray <<< ${gbfilelist} | |
| 570 gbfilearray=(${gbfilelist//,/ }) | |
| 571 for gbfile in "${gbfilearray[@]}" | |
| 572 do | |
| 573 # gbfile is in format "browsernum:file" | |
| 574 #IFS=':' read -a gbfileinfo <<< ${gbfile} | |
| 575 gbfileinfo=(${gbfile//:/ }) | |
| 576 if [[ ${gbfileinfo[0]} == $gbcount ]] | |
| 577 then | |
| 578 | |
| 579 ftype=${gbfileinfo[3]} | |
| 580 | |
| 581 gbfilename=${gbfileinfo[1]} | |
| 582 gbfilelabel=${gbfileinfo[2]} | |
| 583 gbfilelabel=${gbfilelabel//==space==/ } | |
| 584 gbfilelabel=${gbfilelabel//==bopen==/(} | |
| 585 gbfilelabel=${gbfilelabel//==bclose==/)} | |
| 586 fname=`basename ${gbfilename}` | |
| 587 fname=${fname%.dat} | |
| 588 | |
| 589 if [[ $ftype == "vcftabix" ]] | |
| 590 then | |
| 591 newgbfilename="${fname}.vcf" | |
| 592 | |
| 593 | |
| 594 cp ${gbfilename} "${galaxypath}/${newgbfilename}" | |
| 595 bgzip "${galaxypath}/${newgbfilename}" | |
| 596 tabix -f -p vcf "${galaxypath}/${newgbfilename}.gz" | |
| 597 | |
| 598 userTracks="${userTracks}, | |
| 599 {name: '${gbfilelabel}', | |
| 600 uri: '${servername}/datasets/${apiid}/display/${newgbfilename}.gz', | |
| 601 tier_type: 'tabix', | |
| 602 payload: 'vcf'} | |
| 603 " | |
| 604 fi | |
| 605 | |
| 606 if [[ $ftype == "vcfmemstore" ]] | |
| 607 then | |
| 608 newgbfilename="${fname}.vcf" | |
| 609 | |
| 610 | |
| 611 cp ${gbfilename} "${galaxypath}/${newgbfilename}" | |
| 612 #bgzip "${galaxypath}/${newgbfilename}" | |
| 613 #tabix -p vcf "${galaxypath}/${newgbfilename}.gz" | |
| 614 | |
| 615 userTracks="${userTracks}, | |
| 616 {name: '${gbfilelabel}', | |
| 617 uri: '${servername}/datasets/${apiid}/display/${newgbfilename}', | |
| 618 tier_type: 'memstore', | |
| 619 payload: 'vcf'} | |
| 620 " | |
| 621 fi | |
| 622 | |
| 623 if [[ $ftype == "bam" ]] | |
| 624 then | |
| 625 newgbfilename="${fname}.bam" | |
| 626 | |
| 627 # link to bam instead of copying | |
| 628 ln -s ${gbfilename} "${galaxypath}/${newgbfilename}" | |
| 629 samtools index "${galaxypath}/${newgbfilename}" | |
| 630 | |
| 631 userTracks="${userTracks}, | |
| 632 {name: '${gbfilelabel}', | |
| 633 bamURI: '${servername}/datasets/${apiid}/display/${newgbfilename}'} | |
| 634 " | |
| 635 | |
| 636 fi | |
| 637 | |
| 638 if [[ $ftype == "bigbed" ]] | |
| 639 then | |
| 640 newgbfilename="${fname}.bigbed" | |
| 641 | |
| 642 cp ${gbfilename} "${galaxypath}/${newgbfilename}" | |
| 643 #bgzip "${galaxypath}/${newgbfilename}" | |
| 644 #tabix -f -p bed "${galaxypath}/${newgbfilename}.gz" | |
| 645 | |
| 646 userTracks="${userTracks}, | |
| 647 {name: '${gbfilelabel}', | |
| 648 bwgURI: '${servername}/datasets/${apiid}/display/${newgbfilename}'} | |
| 649 " | |
| 650 | |
| 651 fi | |
| 652 | |
| 653 if [[ $ftype == "bedtabix" ]] | |
| 654 then | |
| 655 newgbfilename="${fname}.bed" | |
| 656 | |
| 657 cp ${gbfilename} "${galaxypath}/${newgbfilename}" | |
| 658 bgzip "${galaxypath}/${newgbfilename}" | |
| 659 tabix -f -p bed "${galaxypath}/${newgbfilename}.gz" | |
| 660 | |
| 661 userTracks="${userTracks}, | |
| 662 {name: '${gbfilelabel}', | |
| 663 uri: '${servername}/datasets/${apiid}/display/${newgbfilename}.gz', | |
| 664 tier_type: 'tabix', | |
| 665 payload: 'bed'} | |
| 666 " | |
| 667 | |
| 668 fi | |
| 669 | |
| 670 if [[ $ftype == "bedmemstore" ]] | |
| 671 then | |
| 672 newgbfilename="${fname}.bed" | |
| 673 | |
| 674 cp ${gbfilename} "${galaxypath}/${newgbfilename}" | |
| 675 #bgzip "${galaxypath}/${newgbfilename}" | |
| 676 #tabix -p bed "${galaxypath}/${newgbfilename}.gz" | |
| 677 | |
| 678 userTracks="${userTracks}, | |
| 679 {name: '${gbfilelabel}', | |
| 680 uri: '${servername}/datasets/${apiid}/display/${newgbfilename}', | |
| 681 tier_type: 'memstore', | |
| 682 payload: 'bed'} | |
| 683 " | |
| 684 | |
| 685 fi | |
| 686 fi | |
| 687 done | |
| 688 | |
| 689 | |
| 690 | |
| 691 if [ ${buildver} == "hg18" ] | |
| 692 then | |
| 693 coordSystem="coordSystem: { | |
| 694 speciesName: 'Human', | |
| 695 taxon: 9606, | |
| 696 auth: 'NCBI', | |
| 697 version: '36', | |
| 698 ucscName: 'hg18' | |
| 699 }," | |
| 700 | |
| 701 chains="chains: { | |
| 702 hg19ToHg18: new Chainset('https://www.biodalliance.org/das/hg19ToHg18/', 'GRCh37', 'NCBI36', | |
| 703 { | |
| 704 speciesName: 'Human', | |
| 705 taxon: 9606, | |
| 706 auth: 'GRCh', | |
| 707 version: 37 | |
| 708 }) | |
| 709 }," | |
| 710 | |
| 711 genesTrack="{name: 'Genes', | |
| 712 desc: 'Gene structures from Ensembl 54', | |
| 713 uri: 'https://www.biodalliance.org/das/hsa_54_36p/', | |
| 714 collapseSuperGroups: true, | |
| 715 provides_karyotype: true, | |
| 716 provides_search: true, | |
| 717 provides_entrypoints: true, | |
| 718 maxbins: false}, " | |
| 719 | |
| 720 repeatsTrack="{name: 'Repeats', | |
| 721 desc: 'Repeat annotation from Ensembl 59', | |
| 722 bwgURI: 'https://www.biodalliance.org/datasets/repeats.bb', | |
| 723 stylesheet_uri: 'https://www.biodalliance.org/stylesheets/bb-repeats.xml'}" | |
| 724 | |
| 725 | |
| 726 # default is hg19 | |
| 727 else | |
| 728 coordSystem="coordSystem: { | |
| 729 speciesName: 'Human', | |
| 730 taxon: 9606, | |
| 731 auth: 'NCBI', | |
| 732 version: '37', | |
| 733 ucscName: 'hg19' | |
| 734 }," | |
| 735 | |
| 736 chains="" | |
| 737 | |
| 738 genesTrack="{name: 'Genes', | |
| 739 desc: 'Gene structures from GENCODE 19', | |
| 740 bwgURI: 'https://www.biodalliance.org/datasets/gencode.bb', | |
| 741 stylesheet_uri: 'https://www.biodalliance.org/stylesheets/gencode.xml', | |
| 742 collapseSuperGroups: true, | |
| 743 trixURI: 'https://www.biodalliance.org/datasets/geneIndex.ix'}," | |
| 744 | |
| 745 repeatsTrack="{name: 'Repeats', | |
| 746 desc: 'Repeat annotation from Ensembl 59', | |
| 747 bwgURI: 'https://www.biodalliance.org/datasets/repeats.bb', | |
| 748 stylesheet_uri: 'https://www.biodalliance.org/stylesheets/bb-repeats.xml'}," | |
| 749 | |
| 750 fi | |
| 751 | |
| 752 contentline="${contentline} | |
| 753 <script language=\"javascript\" src=\"https://www.biodalliance.org/release-0.13/dalliance-compiled.js\"></script> | |
| 754 <script language=\"javascript\"> | |
| 755 new Browser({ | |
| 756 chr: '$initialchrom', | |
| 757 viewStart: $initialstart, | |
| 758 viewEnd: $initialend, | |
| 759 cookieKey: 'human', | |
| 760 pageName: 'svgHolder${gbcount}', | |
| 761 ${coordSystem} | |
| 762 | |
| 763 ${chains} | |
| 764 sources: [{name: 'Genome', | |
| 765 twoBitURI: 'https://www.biodalliance.org/datasets/${buildver}.2bit', | |
| 766 tier_type: 'sequence'}, | |
| 767 ${genesTrack}, | |
| 768 ${repeatsTrack}, | |
| 769 {name: 'Conservation', | |
| 770 desc: 'Conservation', | |
| 771 bwgURI: 'https://www.biodalliance.org/datasets/phastCons46way.bw', | |
| 772 noDownsample: true} | |
| 773 ${userTracks} | |
| 774 ], | |
| 775 | |
| 776 | |
| 777 | |
| 778 | |
| 779 browserLinks: { | |
| 780 Ensembl: 'http://www.ensembl.org/Homo_sapiens/Location/View?r=${chr}:${start}-${end}', | |
| 781 UCSC: 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=${buildver}&position=chr${chr}:${start}-${end}', | |
| 782 Sequence: 'http://www.derkholm.net:8080/das/${buildver}comp/sequence?segment=${chr}:${start},${end}' | |
| 783 } | |
| 784 | |
| 785 }); | |
| 786 </script> | |
| 787 | |
| 788 <div id=\"svgHolder${gbcount}\"></div> | |
| 789 " | |
| 790 fi | |
| 791 | |
| 792 ## | |
| 793 ## Link to Dataset | |
| 794 ## | |
| 795 if [ ${myarr[1]} == "link" ] | |
| 796 then | |
| 797 linkfile=${myarr[2]} | |
| 798 apiid=${myarr[4]} | |
| 799 isireport=${myarr[5]} | |
| 800 linkfilename=`basename ${linkfile}` | |
| 801 linktext=${myarr[6]} | |
| 802 | |
| 803 localhost=${myarr[7]} | |
| 804 proxy=${myarr[8]} | |
| 805 localhost=${localhost//==colon==/:} | |
| 806 localhost=${localhost//==fslash==/\/} | |
| 807 | |
| 808 #check for some basic filetypes | |
| 809 ftype=`file $linkfile` | |
| 810 if [[ $ftype == *HTML* ]] | |
| 811 then | |
| 812 linkfilename=${linkfilename%.dat} | |
| 813 linkfilename=${linkfilename}.html | |
| 814 fi | |
| 815 if [[ $ftype == *PNG* ]] | |
| 816 then | |
| 817 linkfilename=${linkfilename%.dat} | |
| 818 linkfilename=${linkfilename}.png | |
| 819 fi | |
| 820 if [[ $ftype == *SVG* ]] | |
| 821 then | |
| 822 linkfilename=${linkfilename%.dat} | |
| 823 linkfilename=${linkfilename}.svg | |
| 824 fi | |
| 825 if [[ $ftype == *JPEG* ]] | |
| 826 then | |
| 827 linkfilename=${linkfilename%.dat} | |
| 828 linkfilename=${linkfilename}.jpg | |
| 829 fi | |
| 830 | |
| 831 | |
| 832 if [[ ${isireport} == "Y" ]] | |
| 833 then | |
| 834 linkfilename="/${proxy}/datasets/${apiid}/display/" | |
| 835 else | |
| 836 cp ${linkfile} "${galaxypath}/${linkfilename}" | |
| 837 fi | |
| 838 | |
| 839 contentline="${contentline}<a href=\"${linkfilename}\">${linktext}</a>" | |
| 840 fi | |
| 841 | |
| 842 ## | |
| 843 ## Links to Archive Contents | |
| 844 ## | |
| 845 if [[ ${myarr[1]} == "links" ]] | |
| 846 then | |
| 847 archive=${myarr[2]} | |
| 848 decompressArchive $archive | |
| 849 | |
| 850 # add links to webpage | |
| 851 # separate line for each folder, files within folder on same line | |
| 852 for linkfile in `ls ${galaxypath}/archive_${fname}/ |sort -V` | |
| 853 do | |
| 854 #echo "<br/> ->making link to file: $linkfile " | |
| 855 if [ -d ${galaxypath}/archive_${fname}/$linkfile ] # if directory, add break, and list all contained files, max level 1 deep | |
| 856 then | |
| 857 #echo "<br/> ->is directory, entering: $linkfile " | |
| 858 #ls ${galaxypath}/archive_${fname}/$linkfile | |
| 859 contentline="${contentline}" | |
| 860 for linkfile2 in `ls ${galaxypath}/archive_${fname}/$linkfile | sort -V` | |
| 861 do | |
| 862 #echo "<br/> ->making link to file: ${galaxypath}/archive_${fname}/$linkfile2" | |
| 863 if [ -f ${galaxypath}/archive_${fname}/$linkfile/$linkfile2 ] # if directory, add break, and list all contained files, max level 1 deep | |
| 864 then | |
| 865 #echo "<br/> ->is file, making link: $linkfile " | |
| 866 label=`basename $linkfile2` | |
| 867 label=${label%.*} | |
| 868 contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}/${linkfile2}\">${label}</a> \n " | |
| 869 fi | |
| 870 done | |
| 871 elif [ -f ${galaxypath}/archive_${fname}/$linkfile ] | |
| 872 then | |
| 873 label=`basename ${galaxypath}/archive_${fname}/$linkfile` | |
| 874 label=${label%.*} | |
| 875 contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}\">$label</a> \n" | |
| 876 fi | |
| 877 done | |
| 878 | |
| 879 | |
| 880 fi | |
| 881 | |
| 882 if [[ ${myarr[3]} == "Y" ]] | |
| 883 then | |
| 884 contentline="${contentline}<br/>\n" | |
| 885 fi | |
| 886 fi | |
| 887 done | |
| 888 | |
| 889 echo "${contentline}" | |
| 890 | |
| 891 | |
| 892 } | |
| 893 | |
| 894 ## | |
| 895 ## Create HTML content for iReport | |
| 896 ## | |
| 897 createMainPage (){ | |
| 898 #export IFRAMECNT=1 | |
| 899 page=$1 | |
| 900 tabtitles=$2 # comma-separated list of tab titles | |
| 901 tabitems=$3 # colon-sparated list of tabs specifications | |
| 902 #giframecount=1 # keep track of number of iFrames so that they can be referenced by ID | |
| 903 minwidth=$4 # width of page | |
| 904 gbtracks=$5 # genome browser track information | |
| 905 | |
| 906 echo "createMainPage: tabitems: $tabitems. tabtitles: $tabtitles. gbtracks: $gbtracks" | |
| 907 # create correct number of tabs | |
| 908 count=0 | |
| 909 | |
| 910 tabtitles=${tabtitles/,/} | |
| 911 tabtitles=${tabtitles//,/ } | |
| 912 echo $tabtitles | |
| 913 | |
| 914 tabcount=0 | |
| 915 for tabt in $tabtitles | |
| 916 do | |
| 917 echo -n $tabt > tmpfileb64 | |
| 918 thistabtitle=`base64 -d tmpfileb64` | |
| 919 newtabtitles+=" $thistabtitle" | |
| 920 tabcount=$[tabcount+1] | |
| 921 done | |
| 922 | |
| 923 echo $newtabtitles | |
| 924 | |
| 925 tabslist="<ul>\n" | |
| 926 mytabs="" | |
| 927 | |
| 928 for title in $newtabtitles | |
| 929 do | |
| 930 # Create list of tabs | |
| 931 count=$[count+1] | |
| 932 title2=${title//==space==/ } | |
| 933 title2=${title2//==dollar==/$} | |
| 934 title2=${title2//==colon==/} | |
| 935 tabslist="${tabslist} <li><a href=\"#tabs-${count}\">${title2}</a></li>\n" | |
| 936 | |
| 937 # Create tabs with content | |
| 938 tabcontent=$(makeTabContent $title "$tabitems" "$gbtracks") | |
| 939 mytabs="${mytabs}\n<div id=\"tabs-${count}\">\n" | |
| 940 mytabs="${mytabs}${tabcontent}" | |
| 941 mytabs="${mytabs}\n</div>\n" | |
| 942 done | |
| 943 tabslist="${tabslist}</ul>" | |
| 944 | |
| 945 ## Output the webpage | |
| 946 echo -e "<!doctype html> | |
| 947 <head> | |
| 948 <meta charset=\"utf-8\"> | |
| 949 <title>iReport</title> | |
| 950 <link rel=\"stylesheet\" href=\"jquery-ui.css\"> | |
| 951 <link rel=\"stylesheet\" href=\"ireport_css.css\"> | |
| 952 <link rel=\"stylesheet\" href=\"md.css\"> | |
| 953 <script type=\"text/javascript\" src=\"jquery-1.10.2.js\"></script> | |
| 954 <script type=\"text/javascript\" src=\"jquery-ui.js\"></script> | |
| 955 <script type=\"text/javascript\" src=\"iframe-resizer/src/iframeResizer.js\"></script> | |
| 956 <script type=\"text/javascript\" src=\"jquery.zoom.js\"></script> | |
| 957 <script type=\"text/javascript\" src=\"ireport_jquery.js\"></script> | |
| 958 <script type=\"text/javascript\" src=\"ireport_javascript.js\"></script> | |
| 959 </head> | |
| 960 <body> | |
| 961 <div id=\"tabs\" style=\"display:inline-block; min-height:100%; min-width:${minwidth}px\"> | |
| 962 $tabslist | |
| 963 | |
| 964 $mytabs | |
| 965 </div> | |
| 966 </body> | |
| 967 </html>" > $page | |
| 968 } |