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Fixed auto resizing plus various other minor bugs
author saskia-hiltemann
date Mon, 16 Nov 2015 08:56:22 -0500
parents a4813532bbc6
children
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5:4e21ce709269 6:42076db43d42
1 gbcount=0
2
1 ## 3 ##
2 ## Create Cover Page 4 ## Create Cover Page
3 ## 5 ##
6 #<a href=\"$zipireport\"> Click here to download a copy of this iReport </a> <br/><br/>
4 function makeIntroPage ( ){ 7 function makeIntroPage ( ){
5 echo "Creating Intro Page" 8 echo "Creating Intro Page"
6 title="$1" 9 title="$1"
7 coverimage=$2 10 coverimage=$2
8 link=$3 11 link=$3
18 <br/> 21 <br/>
19 <center> 22 <center>
20 <b><font size=\"15\"> iReport: ${title} </font></b><br/> 23 <b><font size=\"15\"> iReport: ${title} </font></b><br/>
21 <br/> 24 <br/>
22 <br/> 25 <br/>
23 <a href=\"$link\"> Click here to view report </a> <br/><br/> 26 <a href=\"$link\"> Click image to view report </a> <br/><br/>
24 <a href=\"$link\"> <img src="$coverimage" width=\"50%\" alt=\"loading image..\"/> </a><br/><br/> 27 <a href=\"$link\"> <img src="$coverimage" width=\"50%\" alt=\"loading image..\"/> </a><br/><br/>
25 <a href=\"$zipireport\"> Click here to download a copy of this iReport </a> <br/><br/>
26 </center> 28 </center>
27 </body> 29 </body>
28 </html>" > $htmlout 30 </html>" > $htmlout
29 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
30 } 102 }
31 103
32 ## 104 ##
33 ## Create HTML content for the tabs specified by user 105 ## Create HTML content for the tabs specified by user
34 ## 106 ##
35 function makeTabContent ( ){ 107 function makeTabContent ( ){
36 tab=$1 # name of current tab 108 tab=$1 # name of current tab
37 itemslist=$2 # list of all items 109 itemslist=$2 # list of all items
110 tracklist=$3 # genome browser tracks info
38 contentline="" # HTML code for tab 111 contentline="" # HTML code for tab
39 imgcount=0 # keep track of the number of images on the current tab 112 imgcount=0 # keep track of the number of images on the current tab
40 113 iframename=`head -n 1 < /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 8 | head -n 1`
114 #iframename="test"
41 for item in $itemslist 115 for item in $itemslist
42 do 116 do
43 ## Parse items lists 117 ## Parse items lists
44 item=${item/::/:emptycol:} 118 item=${item/::/:emptycol:}
45 declare -a myarr=(`echo $item |sed 's/:/ /g'`) 119 declare -a myarr=(`echo $item |sed 's/:/ /g'`)
61 then 135 then
62 ## resubstitute sanitized charachters 136 ## resubstitute sanitized charachters
63 text=${text//==space==/ } 137 text=${text//==space==/ }
64 text=${text//==colon==/:} 138 text=${text//==colon==/:}
65 text=${text//==comma==/,} 139 text=${text//==comma==/,}
140
141 text=${text//==braceopen==/(}
142 text=${text//==braceclose==/)}
143 text=${text//==cbraceopen==/{}
144 text=${text//==cbraceclose==/&#125;}
145
66 text=${text//==slash==/\/} 146 text=${text//==slash==/\/}
67 text=${text//==lt==/<} 147 text=${text//==lt==/<}
68 text=${text//==gt==/>} 148 text=${text//==gt==/>}
69 text=${text//==apos==/\'} 149 text=${text//==apos==/\'}
70 text=${text//==quote==/\"} 150 text=${text//==quote==/\"}
76 text=${text//\\t/\\t} 156 text=${text//\\t/\\t}
77 text=${text//\&r\&n/\\n} 157 text=${text//\&r\&n/\\n}
78 text=${text//\&r/\\n} 158 text=${text//\&r/\\n}
79 text=${text//\&n/\\n} 159 text=${text//\&n/\\n}
80 text=${text//\&c/:} 160 text=${text//\&c/:}
81 161
82 162
83 ## convert markdown in textfield to html 163 ## convert markdown in textfield to html
84 echo -e "$text" > mytext.md 164 echo -e "$text" > mytext.md
85 165
86 if [ -z `type -p pandoc` ] 166 if [ -z `type -p pandoc` ]
87 then 167 then
88 # pandoc missing 168 # pandoc missing
89 ${repositorypath}/Markdown/markdown2.py mytext.md > mytext.html 169 ${repositorypath}/Markdown/markdown2.py mytext.md > mytext.html
90 170
91 else 171 else
92 # pandoc exists 172 # pandoc exists
93 echo "pandoc exists" 173 pandoc -f markdown -o mytext.html mytext.md
94 pandoc -o mytext.html mytext.md 174 pandoc -f markdown -o standalone.html -s mytext.md
95 pandoc -o standalone.html -s mytext.md
96 175
97 #get css generated by pandoc and add as scoped attribute (HTML5) 176 #get css generated by pandoc and add as scoped attribute (HTML5)
98 pandocstyle=`sed -n '/<style/,/style>/p' standalone.html` 177 pandocstyle=`sed -n '/<style/,/style>/p' standalone.html`
99 fi 178 fi
100 179
146 text=${text//\&n/<br/>} 225 text=${text//\&n/<br/>}
147 text=${text//\&c/:} 226 text=${text//\&c/:}
148 text=${text//==backtick==/&#96;} 227 text=${text//==backtick==/&#96;}
149 text=${text//==dollar==/$} 228 text=${text//==dollar==/$}
150 text=${text//==bar==/|} 229 text=${text//==bar==/|}
230 text=${text//==braceopen==/(}
231 text=${text//==braceclose==/)}
232 text=${text//==cbraceopen==/{}
233 text=${text//==cbraceclose==/&#125;}
151 contentline="${contentline}\n${text}\n" 234 contentline="${contentline}\n${text}\n"
152 fi 235 fi
153 236
154 237
155 fi 238 fi
206 #restore file suffix for html 289 #restore file suffix for html
207 ftype=`file ${myarr[2]}` 290 ftype=`file ${myarr[2]}`
208 zoomlevel=${myarr[4]} 291 zoomlevel=${myarr[4]}
209 zoomenable=${myarr[5]} 292 zoomenable=${myarr[5]}
210 align=${myarr[6]} 293 align=${myarr[6]}
294 typestring=""
211 #####echo "zoomenable:${zoomenable}, align:${align}" 295 #####echo "zoomenable:${zoomenable}, align:${align}"
212 if [[ $ftype == *JPEG* ]] 296 if [[ $ftype == *JPEG* ]]
213 then 297 then
214 suffix=".jpg" 298 suffix=".jpg"
215 fi 299 fi
218 suffix=".svg" 302 suffix=".svg"
219 fi 303 fi
220 if [[ $ftype == *PNG* ]] 304 if [[ $ftype == *PNG* ]]
221 then 305 then
222 suffix=".png" 306 suffix=".png"
307 fi
308 if [[ $ftype == *TIFF* ]]
309 then
310 suffix=".tiff"
311 typestring="type=\"image/tiff\""
223 fi 312 fi
224 313
225 image=`basename ${myarr[2]}` 314 image=`basename ${myarr[2]}`
226 image=${image%.dat} 315 image=${image%.dat}
227 image="${image}${suffix}" 316 image="${image}${suffix}"
246 else 335 else
247 widthstring="width=\"${zoomlevel}\"" 336 widthstring="width=\"${zoomlevel}\""
248 fi 337 fi
249 338
250 if [[ ${zoomlevel} -eq 0 || ${zoomenable} == "N" ]] 339 if [[ ${zoomlevel} -eq 0 || ${zoomenable} == "N" ]]
251 then 340 then
252 contentline="${contentline}<span id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>" 341 contentline="${contentline}<span id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
253 else 342 else
254 contentline="${contentline}<span class=\"zoomme\" id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>" 343 contentline="${contentline}<span class=\"zoomme\" id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
255 fi 344 fi
256 345
257 fi 346 fi
259 ## 348 ##
260 ## Table 349 ## Table
261 ## 350 ##
262 if [ ${myarr[1]} == "table" ] 351 if [ ${myarr[1]} == "table" ]
263 then 352 then
353
264 maxlines=50000 354 maxlines=50000
265 tsvfile_orig=${myarr[2]} 355 tsvfile_orig=${myarr[2]}
266 tsvfile="tablehead.tsv" 356 tsvfile="tablehead.tsv"
267 fname=`basename ${tsvfile_orig}` 357 fname=`basename ${tsvfile_orig}`
268 fname=${fname%.*} 358 fname=${fname%.*}
269 fancy=${myarr[4]} 359 fancy=${myarr[4]}
270 makelinks=${myarr[5]} 360 makelinks=${myarr[5]}
361 #iframeid="iframe$giframecount"
362 iframeid="iframe-$iframename"
363
271 #echo "\nmakelinks: $makelinks fancy: $fancy <br>" 364 #echo "\nmakelinks: $makelinks fancy: $fancy <br>"
272 365
273 #TODO client side database for large files. For now only display first section of file and add download link 366 #TODO client side database for large files. For now only display first section of file and add download link
274 numlines=`wc -l ${tsvfile_orig} |cut -d" " -f1` 367 numlines=`wc -l ${tsvfile_orig} |cut -d" " -f1`
275 368
289 382
290 if [[ $makelinks == "Y" ]] 383 if [[ $makelinks == "Y" ]]
291 then 384 then
292 col=${myarr[6]} 385 col=${myarr[6]}
293 prefix=${myarr[7]} 386 prefix=${myarr[7]}
294 suffix=${myarr[8]} 387 suffix=${myarr[8]}
388 urlitems=${myarr[9]}
389 minw=${myarr[10]}
390 minh=${myarr[11]}
295 suffix=${suffix/emptycol/} 391 suffix=${suffix/emptycol/}
296 suffix=${suffix/==quote==/&} 392 suffix=${suffix/==quote==/&}
297 prefix=${prefix/emptycol/} 393 prefix=${prefix/emptycol/}
298 prefix=${prefix/==quote==/&} 394 prefix=${prefix/==quote==/&}
299 prefix=${prefix/==colon==/:} 395 prefix=${prefix/==colon==/:}
300 #echo "prefix: $prefix" 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
301 406
302 #edit the table to include links 407 #edit the table to include links
303 awk 'BEGIN{ 408 awk 'BEGIN{
304 FS="\t" 409 FS="\t"
305 OFS="\t" 410 OFS="\t"
306 url="'"$prefix"'" 411 url="'"$prefix"'"
307 url2="'"$suffix"'" 412 url2="'"$suffix"'"
413 iframeid="'"$iframeid"'"
308 prefix="<a href=\42" 414 prefix="<a href=\42"
309 suffix="\42>" 415 suffix="\42 onclick=\42resizeIframe("iframeid")\42>"
310 col="'"$col"'" 416 col="'"$col"'"
311 end="</a>" 417 end="</a>"
312 }{ 418 }{
313 if(FNR==1) 419 if(FNR==1)
314 print $0 420 print $0
315 else{ 421 else{
316 $col=prefix""url""$col""url2""suffix""$col""end 422 $col=prefix""url""$col""url2""suffix""$col""end
317 print $0 423 print $0
318 } 424 }
319 }END{}' ${tsvfile} > ${tsvfile}2 425 }END{}' ${tsvfile} > ${tsvfile}2
320 426
321 else 427 else
428 minw=${myarr[6]}
429 minh=${myarr[7]}
322 cp ${tsvfile} ${tsvfile}2 430 cp ${tsvfile} ${tsvfile}2
323 fi 431 fi
324 432
433 #iframecount=$[$iframecount+1]
434
325 if [ $fancy == "Y" ] 435 if [ $fancy == "Y" ]
326 then 436 then
327 perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html 437 perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
328 contentline="${contentline}\n<iframe class=\"invisibleframe fancyiframe\" src=\"htmltable_${fname}.html\" width=\"100%\" style=\"min-height: 525px; overflow-y: hidden; overflow-x: scroll\" ></iframe>" 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>"
329 iframecount=$[$iframecount+1] 439
330 else 440 else
331 perl ${repositorypath}/tsv2html_simple.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html 441 perl ${repositorypath}/tsv2html_simple.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
332 contentline="${contentline}\n<iframe class=\"unfancyiframe invisibleframe\" src=\"htmltable_${fname}.html\" scrolling=\"no\" style=\"max-width: 100%; vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>" 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>"
333 iframecount=$[$iframecount+1] 443
334 fi 444 fi
335 445
336 if [[ $numlines -gt ${maxlines} ]] 446 if [[ $numlines -gt ${maxlines} ]]
337 then 447 then
338 tablename=`basename ${tsvfile_orig}` 448 tablename=`basename ${tsvfile_orig}`
371 fname=`basename ${htmlfile}` 481 fname=`basename ${htmlfile}`
372 fname=${fname%.dat} 482 fname=${fname%.dat}
373 htmlname="${fname}.html" 483 htmlname="${fname}.html"
374 cp ${htmlfile} "${galaxypath}/${htmlname}" 484 cp ${htmlfile} "${galaxypath}/${htmlname}"
375 485
376 contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${htmlname}\" width=\"100%\" height=\"${height}px\"></iframe>\n" 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"
377 fi 509 fi
378 510
379 ## 511 ##
380 ## Web Link 512 ## Web Link
381 ## 513 ##
382 if [ ${myarr[1]} == "weblink" ] 514 if [ ${myarr[1]} == "weblink" ]
383 then 515 then
384 url=${myarr[2]} 516 url=${myarr[2]}
385 linktext=${myarr[4]} 517 linktext=${myarr[4]}
386 url=${url/==colon==/:} 518
387 url=${url/==quote==/&} 519 echo -n "$url" > tmpfileb64
388 520 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
389 contentline="${contentline}<a href=\"${url}\" target=\"_blank\">${linktext}</a>" 529 contentline="${contentline}<a href=\"${url}\" target=\"_blank\">${linktext}</a>"
390 fi 530 fi
391 531
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
392 ## 792 ##
393 ## Link to Dataset 793 ## Link to Dataset
394 ## 794 ##
395 if [ ${myarr[1]} == "link" ] 795 if [ ${myarr[1]} == "link" ]
396 then 796 then
398 apiid=${myarr[4]} 798 apiid=${myarr[4]}
399 isireport=${myarr[5]} 799 isireport=${myarr[5]}
400 linkfilename=`basename ${linkfile}` 800 linkfilename=`basename ${linkfile}`
401 linktext=${myarr[6]} 801 linktext=${myarr[6]}
402 802
803 localhost=${myarr[7]}
804 proxy=${myarr[8]}
805 localhost=${localhost//==colon==/:}
806 localhost=${localhost//==fslash==/\/}
403 807
404 #check for some basic filetypes 808 #check for some basic filetypes
405 ftype=`file $linkfile` 809 ftype=`file $linkfile`
406 if [[ $ftype == *HTML* ]] 810 if [[ $ftype == *HTML* ]]
407 then 811 then
425 fi 829 fi
426 830
427 831
428 if [[ ${isireport} == "Y" ]] 832 if [[ ${isireport} == "Y" ]]
429 then 833 then
430 linkfilename="/datasets/${apiid}/display/" 834 linkfilename="/${proxy}/datasets/${apiid}/display/"
431 else 835 else
432 cp ${linkfile} "${galaxypath}/${linkfilename}" 836 cp ${linkfile} "${galaxypath}/${linkfilename}"
433 fi 837 fi
434 838
435 contentline="${contentline}<a href=\"${linkfilename}\">${linktext}</a>" 839 contentline="${contentline}<a href=\"${linkfilename}\">${linktext}</a>"
437 841
438 ## 842 ##
439 ## Links to Archive Contents 843 ## Links to Archive Contents
440 ## 844 ##
441 if [[ ${myarr[1]} == "links" ]] 845 if [[ ${myarr[1]} == "links" ]]
442 then 846 then
443 #echo "making links:"
444 archive=${myarr[2]} 847 archive=${myarr[2]}
445 fname=`basename ${archive}` 848 decompressArchive $archive
446 fname=${fname%.dat} 849
447 ftype=`file $archive`
448 mkdir ${galaxypath}/archive_${fname}/
449
450 #echo "archive type: `file $archive`"
451 # decompress archive
452 if [[ $ftype == *Zip* ]]
453 then
454 #echo "detected zip file"
455 cp $archive ${galaxypath}/archive_${fname}/${fname}.zip
456 wd=`pwd`
457 cd ${galaxypath}/archive_${fname}/
458 unzip -q ${fname}.zip
459 rm ${fname}.zip
460 cd $wd
461 fi
462 if [[ $ftype == *tar* ]]
463 then
464 cp $archive ${galaxypath}/archive_${fname}/${fname}.tar
465 wd=`pwd`
466 cd ${galaxypath}/archive_${fname}/
467 tar xf ${fname}.tar
468 rm ${fname}.tar
469 cd $wd
470 fi
471 if [[ $ftype == *gzip* ]]
472 then
473 cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
474 gunzip ${galaxypath}/archive_${fname}/${fname}.gz
475 #ls ${galaxypath}/archive_${fname}/
476
477 # check for tar.gz
478 ftype=`file ${galaxypath}/archive_${fname}/${fname}`
479 if [[ $ftype == *tar* ]]
480 then
481 # turns out it was tar.gz
482 rm -Rf ${galaxypath}/archive_${fname}/*
483 ls ${galaxypath}/archive_${fname}/
484 cp $archive ${galaxypath}/archive_${fname}/${fname}.tar.gz
485
486 wd=`pwd`
487 cd ${galaxypath}/archive_${fname}/
488 tar xzf ${fname}.tar.gz
489 cd $wd
490 fi
491 wait
492 rm -f ${galaxypath}/archive_${fname}/*.tar
493 rm -f ${galaxypath}/archive_${fname}/*.tar.gz
494 fi
495 if [[ $ftype == *bzip2* ]]
496 then
497 cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
498 gunzip2 ${galaxypath}/archive_${fname}/${fname}.gz
499 fi
500
501
502
503 # add links to webpage 850 # add links to webpage
504 # separate line for each folder, files within folder on same line 851 # separate line for each folder, files within folder on same line
505 for linkfile in `ls ${galaxypath}/archive_${fname}/ |sort -V` 852 for linkfile in `ls ${galaxypath}/archive_${fname}/ |sort -V`
506 do 853 do
507 #echo "<br/> ->making link to file: $linkfile " 854 #echo "<br/> ->making link to file: $linkfile "
538 fi 885 fi
539 fi 886 fi
540 done 887 done
541 888
542 echo "${contentline}" 889 echo "${contentline}"
890
891
543 } 892 }
544 893
545 ## 894 ##
546 ## Create HTML content for iReport 895 ## Create HTML content for iReport
547 ## 896 ##
548 createMainPage (){ 897 createMainPage (){
898 #export IFRAMECNT=1
549 page=$1 899 page=$1
550 tabtitles=$2 # comma-separated list of tab titles 900 tabtitles=$2 # comma-separated list of tab titles
551 tabitems=$3 # colon-sparated list of tabs specifications 901 tabitems=$3 # colon-sparated list of tabs specifications
552 iframecount=1 # keep track of number of iFrames so that they can be referenced by ID 902 #giframecount=1 # keep track of number of iFrames so that they can be referenced by ID
553 minwidth=$4 # width of page 903 minwidth=$4 # width of page
554 904 gbtracks=$5 # genome browser track information
555 echo "createMainPage: tabitems: $tabitems. tabtitles: $tabtitles" 905
906 echo "createMainPage: tabitems: $tabitems. tabtitles: $tabtitles. gbtracks: $gbtracks"
556 # create correct number of tabs 907 # create correct number of tabs
557 count=0 908 count=0
558 909
910 tabtitles=${tabtitles/,/}
559 tabtitles=${tabtitles//,/ } 911 tabtitles=${tabtitles//,/ }
560 tabtitles=${tabtitles//==colon==/:} 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
561 tabslist="<ul>\n" 925 tabslist="<ul>\n"
562 mytabs="" 926 mytabs=""
563 927
564 for title in $tabtitles 928 for title in $newtabtitles
565 do 929 do
566 # Create list of tabs 930 # Create list of tabs
567 count=$[count+1] 931 count=$[count+1]
568 title2=${title//_s_/ } 932 title2=${title//==space==/ }
933 title2=${title2//==dollar==/$}
934 title2=${title2//==colon==/}
569 tabslist="${tabslist} <li><a href=\"#tabs-${count}\">${title2}</a></li>\n" 935 tabslist="${tabslist} <li><a href=\"#tabs-${count}\">${title2}</a></li>\n"
570 936
571 # Create tabs with content 937 # Create tabs with content
572 tabcontent=$(makeTabContent $title "$tabitems") 938 tabcontent=$(makeTabContent $title "$tabitems" "$gbtracks")
573 mytabs="${mytabs}\n<div id=\"tabs-${count}\">\n" 939 mytabs="${mytabs}\n<div id=\"tabs-${count}\">\n"
574 mytabs="${mytabs}${tabcontent}" 940 mytabs="${mytabs}${tabcontent}"
575 mytabs="${mytabs}\n</div>\n" 941 mytabs="${mytabs}\n</div>\n"
576 done 942 done
577 tabslist="${tabslist}</ul>" 943 tabslist="${tabslist}</ul>"