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comparison createHTML.sh @ 0:c73753f1606f draft

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author saskia-hiltemann
date Mon, 06 Oct 2014 08:13:54 -0400
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children bda1cc8041bf
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-1:000000000000 0:c73753f1606f
1 function makeIntroPage ( ){
2 echo "Creating Intro Page"
3 title="$1"
4 coverimage=$2
5 link=$3
6 htmlout=$4
7 zipireport=$5
8
9 echo -e "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01//EN\" \"http://www.w3.org/TR/html4/strict.dtd\">
10 <html>
11 <head>
12 </head>
13 <body>
14 <!-- dummy intro page, since first page will not have any javascript/css features enabled unless specified in universe_wsgi.ini file, but subsequent pages will -->
15 <br/>
16 <br/>
17 <center>
18 <b><font size=\"15\"> iReport: ${title} </font></b><br/>
19 <br/>
20 <br/>
21 <a href=\"$link\"> Click here to view report </a> <br/><br/>
22 <a href=\"$link\"> <img src="$coverimage" width=\"50%\" alt=\"loading image..\"/> </a><br/><br/>
23 <a href=\"$zipireport\"> Click here to download a copy of this iReport </a> <br/><br/>
24 </center>
25 </body>
26 </html>" > $htmlout
27
28 }
29
30
31 function makeTabContent ( ){
32 tab=$1 #name of current tab
33 itemslist=$2 #list of all items
34 contentline="<br/>"
35 imgcount=0
36 #echo -e "\n Creating items. itemslist: $itemslist"
37
38 for item in $itemslist
39 do
40 #echo -e "\n -> item : $item"
41 item=${item/::/:emptycol:}
42 declare -a myarr=(`echo $item |sed 's/:/ /g'`)
43 #echo "break: ${myarr[3]}"
44 if [ ${myarr[0]} == $tab ]
45 then
46
47 ## add contents of text field to page####
48 if [ ${myarr[1]} == "text" ]
49 then
50 text=${myarr[2]}
51 ## allow some html formatting tags
52 text=${text//==lt==strong==gt==/<strong>} # search for strong tags
53 text=${text//==lt====slash==strong==gt==/<\/strong>} # search for strong tags
54 text=${text//==lt==em==gt==/<em>} # search for strong tags
55 text=${text//==lt====slash==em==gt==/<\/em>} # search for strong tags
56
57 text=${text//==lt==b==gt==/<strong>} # search for strong tags
58 text=${text//==lt====slash==b==gt==/<\/strong>} # search for strong tags
59 text=${text//==lt==i==gt==/<em>} # search for strong tags
60 text=${text//==lt====slash==i==gt==/<\/em>} # search for strong tags
61
62 text=${text//==lt==br==gt==/<br\/>} # search for strong tags
63 text=${text//==lt====br==slash==gt==/<br\/>} # search for strong tags
64 text=${text//==lt==h1==gt==/<h1>} # search for h1-h6 tags
65 text=${text//==lt==h2==gt==/<h2>} # search for h1-h6 tags
66 text=${text//==lt==h3==gt==/<h3>} # search for h1-h6 tags
67 text=${text//==lt==h4==gt==/<h4>} # search for h1-h6 tags
68 text=${text//==lt==h5==gt==/<h5>} # search for h1-h6 tags
69 text=${text//==lt==h6==gt==/<h6>} # search for h1-h6 tags
70 text=${text//==lt====slash==h1==gt==/<\/h1>} # search for h1-h6 closing tags
71 text=${text//==lt====slash==h2==gt==/<\/h2>} # search for h1-h6 closing tags
72 text=${text//==lt====slash==h3==gt==/<\/h3>} # search for h1-h6 closing tags
73 text=${text//==lt====slash==h4==gt==/<\/h4>} # search for h1-h6 closing tags
74 text=${text//==lt====slash==h5==gt==/<\/h5>} # search for h1-h6 closing tags
75 text=${text//==lt====slaxh==h6==gt==/<\/h6>} # search for h1-h6 closing tags
76
77 ## display everything else verbatim
78 text=${text//==space==/ }
79 text=${text//==colon==/:}
80 text=${text//==comma==/,}
81 text=${text//==slash==/\/}
82 text=${text//==lt==/&lt;}
83 text=${text//==gt==/&gt;}
84 text=${text//==apos==/&apos;}
85 text=${text//==quote==/&quot;}
86 text=${text//&&/&amp;}
87 text=${text//\\n/<br/>}
88 text=${text//\\t/&emsp;}
89 text=${text//\&r\&n/<br/>}
90 text=${text//\&r/<br/>}
91 text=${text//\&n/<br/>}
92 text=${text//\&c/:}
93 contentline="${contentline}${text}"
94 fi
95
96 ## add contents of a text file to page
97 if [ ${myarr[1]} == "textfile" ]
98 then
99 tfile=${myarr[2]}
100 fname=`basename ${tfile}`
101 fname=${fname%.*}
102 fname="${fname}.txt"
103 cp ${tfile} "${galaxypath}/${fname}"
104
105 #estimate height for iframe based on number oflines in the file
106 numlines=`wc -l ${tfile} | cut -d" " -f1`
107 minheight=$[$numlines*17]
108
109 contentline="${contentline}<iframe class=\"invisibleframe\" src=\"${fname}\" width=\"100%\" height=\"$minheight\"> </iframe>"
110 fi
111
112 ## add image file to page
113 if [ ${myarr[1]} == "image" ]
114 then
115 imgcount=$[$imgcount+1]
116 #restore file suffix for html
117 ftype=`file ${myarr[2]}`
118 zoomlevel=${myarr[4]}
119 zoomenable=${myarr[5]}
120 align=${myarr[6]}
121 #####echo "zoomenable:${zoomenable}, align:${align}"
122 if [[ $ftype == *JPEG* ]]
123 then
124 suffix=".jpg"
125 fi
126 if [[ $ftype == *SVG* ]]
127 then
128 suffix=".svg"
129 fi
130 if [[ $ftype == *PNG* ]]
131 then
132 suffix=".png"
133 fi
134
135 image=`basename ${myarr[2]}`
136 image=${image%.dat}
137 image="${image}${suffix}"
138 cp ${myarr[2]} ${galaxypath}/${image}
139
140 if [[ ${align} == "none" ]]
141 then
142 alignstring=""
143 alignstring2=""
144 else
145 alignstring="<div float=\"${align}\">"
146 alignstring2="</div>"
147
148 alignstring="align=\"${align}\""
149 alignstring2=""
150 fi
151
152
153 if [[ ${zoomlevel} -eq 0 ]]
154 then
155 widthstring=""
156 else
157 widthstring="width=\"${zoomlevel}\""
158 fi
159
160 if [[ ${zoomlevel} -eq 0 || ${zoomenable} == "N" ]]
161 then
162 contentline="${contentline}<span id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
163 else
164 contentline="${contentline}<span class=\"zoomme\" id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
165 fi
166
167 fi
168 if [ ${myarr[1]} == "table" ]
169 then
170 maxlines=50000
171 tsvfile_orig=${myarr[2]}
172 tsvfile="tablehead.tsv"
173 fname=`basename ${tsvfile_orig}`
174 fname=${fname%.*}
175 fancy=${myarr[4]}
176 makelinks=${myarr[5]}
177 #echo "\nmakelinks: $makelinks fancy: $fancy <br>"
178
179 #TODO client side database for large files. For now only display first section of file and add download link
180 numlines=`wc -l ${tsvfile_orig} |cut -d" " -f1`
181
182 head -${maxlines} ${tsvfile_orig} > tsvtmpfile
183
184 #remove any empty or header lines (lines starting with #, unless vcf file, then keep #CHROM line)
185 awk 'BEGIN{
186 FS="\t"
187 OFS="\t"
188 }{
189 if((index($0,"#")==1 && index($0,"#CHROM")!=1) || $0==""){
190 headerlines++
191 }
192 else print $0
193
194 }END{}' tsvtmpfile > ${tsvfile}
195
196 if [[ $makelinks == "Y" ]]
197 then
198 col=${myarr[6]}
199 prefix=${myarr[7]}
200 suffix=${myarr[8]}
201 suffix=${suffix/emptycol/}
202 suffix=${suffix/==quote==/&}
203 prefix=${prefix/emptycol/}
204 prefix=${prefix/==quote==/&}
205 prefix=${prefix/==colon==/:}
206 #echo "prefix: $prefix"
207
208 #edit the table to include links
209 awk 'BEGIN{
210 FS="\t"
211 OFS="\t"
212 url="'"$prefix"'"
213 url2="'"$suffix"'"
214 prefix="<a href=\42"
215 suffix="\42>"
216 col="'"$col"'"
217 end="</a>"
218 }{
219 if(FNR==1)
220 print $0
221 else{
222 $col=prefix""url""$col""url2""suffix""$col""end
223 print $0
224 }
225 }END{}' ${tsvfile} > ${tsvfile}2
226 #echo "converted file: "
227 #cat ${tsvfile}2
228 else
229 cp ${tsvfile} ${tsvfile}2
230 fi
231
232 if [ $fancy == "Y" ]
233 then
234 perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
235 #contentline="${contentline}\n<div class=\"resizable\" id=\"iframe${iframecount}\"><iframe src=\"htmltable_${fname}.html\" style=\"max-width: 100%;vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe></div>"
236 #contentline="${contentline}\n<iframe class=\"resizable\" id=\"iframe${iframecount}\" src=\"htmltable_${fname}.html\" style=\"max-width: 100%;vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>"
237 contentline="${contentline}\n<iframe class=\"invisibleframe fancyiframe\" src=\"htmltable_${fname}.html\" width=\"100%\" style=\"min-height: 300px; overflow-y: hidden; overflow-x: scroll\" ></iframe>"
238
239 iframecount=$[$iframecount+1]
240 else
241 perl ${repositorypath}/tsv2html_simple.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
242 #contentline="${contentline}\n<iframe class=\"invisibleframe\" id=\"iframe${iframecount}\" style=\"max-width: 100%; vertical-align: top;\" src=\"htmltable_${fname}.html\" onload=\"resizeIframe(this)\"></iframe>"
243 contentline="${contentline}\n<iframe class=\"unfancyiframe invisibleframe\" src=\"htmltable_${fname}.html\" scrolling=\"no\" style=\"max-width: 100%; vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>"
244 iframecount=$[$iframecount+1]
245 fi
246
247 if [[ $numlines -gt ${maxlines} ]]
248 then
249 tablename=`basename ${tsvfile_orig}`
250 cp ${tsvfile_orig} ${galaxypath}/$tablename
251 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>."
252 fi
253 fi
254
255 if [[ ${myarr[1]} == "pdf" ]]
256 then
257 pdffile=${myarr[2]}
258 fname=`basename ${pdffile}`
259 fname=${fname%.dat}
260 pdfname="${fname}.pdf"
261 cp ${pdffile} "${galaxypath}/${pdfname}"
262
263 width=1000
264 height=800
265 #contentline="${contentline}<object data=\"${fname}\" type=\"application/pdf\" width=\"1000\" height=\"1000\"><p>It appears you have no PDF plugin for your browser. No biggie... you can <a href=\"${fname}\">click here to download the PDF file.</a></p></object>"
266 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}/${fname}.html"
267 width=$[$width+10]
268 height=$[$height+10]
269 contentline="${contentline}<iframe src=\"${fname}.html\" width=\"${width}\" height=\"${height}\"></iframe>\n"
270
271 fi
272 ## link to a location on the web, open in new window
273 if [ ${myarr[1]} == "weblink" ]
274 then
275 url=${myarr[2]}
276 linktext=${myarr[4]}
277 url=${url/==colon==/:}
278 url=${url/==quote==/&}
279
280 contentline="${contentline}<a href=\"${url}\" target=\"_blank\">${linktext}</a>"
281 fi
282
283 ## link to a file in the history
284 if [ ${myarr[1]} == "link" ]
285 then
286 linkfile=${myarr[2]}
287 apiid=${myarr[4]}
288 isireport=${myarr[5]}
289 linkfilename=`basename ${linkfile}`
290 linktext=${myarr[6]}
291
292
293 #check for some basic filetypes
294 ftype=`file $linkfile`
295 if [[ $ftype == *HTML* ]]
296 then
297 linkfilename=${linkfilename%.dat}
298 linkfilename=${linkfilename}.html
299 fi
300 if [[ $ftype == *PNG* ]]
301 then
302 linkfilename=${linkfilename%.dat}
303 linkfilename=${linkfilename}.png
304 fi
305 if [[ $ftype == *SVG* ]]
306 then
307 linkfilename=${linkfilename%.dat}
308 linkfilename=${linkfilename}.svg
309 fi
310 if [[ $ftype == *JPEG* ]]
311 then
312 linkfilename=${linkfilename%.dat}
313 linkfilename=${linkfilename}.jpg
314 fi
315
316
317 if [[ ${isireport} == "Y" ]]
318 then
319 linkfilename="/datasets/${apiid}/display/"
320 else
321 cp ${linkfile} "${galaxypath}/${linkfilename}"
322 fi
323
324 contentline="${contentline}<a href=\"${linkfilename}\">${linktext}</a>"
325 fi
326
327 ## link to files in an archive in the history item
328 if [[ ${myarr[1]} == "links" ]]
329 then
330 #echo "making links:"
331 archive=${myarr[2]}
332 fname=`basename ${archive}`
333 fname=${fname%.dat}
334 ftype=`file $archive`
335 mkdir ${galaxypath}/archive_${fname}/
336
337 #echo "archive type: `file $archive`"
338 # decompress archive
339 if [[ $ftype == *Zip* ]]
340 then
341 #echo "detected zip file"
342 cp $archive ${galaxypath}/archive_${fname}/${fname}.zip
343 wd=`pwd`
344 cd ${galaxypath}/archive_${fname}/
345 unzip -q ${fname}.zip
346 rm ${fname}.zip
347 cd $wd
348 fi
349 if [[ $ftype == *tar* ]]
350 then
351 cp $archive ${galaxypath}/archive_${fname}/${fname}.tar
352 wd=`pwd`
353 cd ${galaxypath}/archive_${fname}/
354 tar xf ${fname}.tar
355 rm ${fname}.tar
356 cd $wd
357 fi
358 if [[ $ftype == *gzip* ]]
359 then
360 cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
361 gunzip ${galaxypath}/archive_${fname}/${fname}.gz
362 #ls ${galaxypath}/archive_${fname}/
363
364 # check for tar.gz
365 ftype=`file ${galaxypath}/archive_${fname}/${fname}`
366 if [[ $ftype == *tar* ]]
367 then
368 # turns out it was tar.gz
369 rm -Rf ${galaxypath}/archive_${fname}/*
370 ls ${galaxypath}/archive_${fname}/
371 cp $archive ${galaxypath}/archive_${fname}/${fname}.tar.gz
372
373 wd=`pwd`
374 cd ${galaxypath}/archive_${fname}/
375 tar xzf ${fname}.tar.gz
376 cd $wd
377 fi
378 wait
379 rm -f ${galaxypath}/archive_${fname}/*.tar
380 rm -f ${galaxypath}/archive_${fname}/*.tar.gz
381 fi
382 if [[ $ftype == *bzip2* ]]
383 then
384 cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
385 gunzip2 ${galaxypath}/archive_${fname}/${fname}.gz
386 fi
387
388
389
390 # add links to webpage
391 # separate line for each folder, files within folder on same line
392 for linkfile in `ls ${galaxypath}/archive_${fname}/ |sort -V`
393 do
394 #echo "<br/> ->making link to file: $linkfile "
395 if [ -d ${galaxypath}/archive_${fname}/$linkfile ] # if directory, add break, and list all contained files, max level 1 deep
396 then
397 #echo "<br/> ->is directory, entering: $linkfile "
398 #ls ${galaxypath}/archive_${fname}/$linkfile
399 contentline="${contentline}"
400 for linkfile2 in `ls ${galaxypath}/archive_${fname}/$linkfile | sort -V`
401 do
402 #echo "<br/> ->making link to file: ${galaxypath}/archive_${fname}/$linkfile2"
403 if [ -f ${galaxypath}/archive_${fname}/$linkfile/$linkfile2 ] # if directory, add break, and list all contained files, max level 1 deep
404 then
405 #echo "<br/> ->is file, making link: $linkfile "
406 label=`basename $linkfile2`
407 label=${label%.*}
408 contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}/${linkfile2}\">${label}</a>&nbsp;\n "
409 fi
410 done
411 elif [ -f ${galaxypath}/archive_${fname}/$linkfile ]
412 then
413 label=`basename ${galaxypath}/archive_${fname}/$linkfile`
414 label=${label%.*}
415 contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}\">$label</a>&nbsp;\n"
416 fi
417 done
418
419
420 fi
421
422 if [[ ${myarr[3]} == "Y" ]]
423 then
424 contentline="${contentline}<br/>"
425 fi
426 fi
427 done
428
429 echo "${contentline}"
430 }
431
432
433 createMainPage (){
434 page=$1
435 tabtitles=$2 #comma-separated list of tab titles
436 tabitems=$3
437 iframecount=1
438 minwidth=$4
439
440 echo "createMainPage: tabitems: $tabitems. tabtitles: $tabtitles"
441 # create correct number of tabs
442 count=0
443
444 tabtitles=${tabtitles//,/ }
445 tabtitles=${tabtitles//==colon==/:}
446 tabslist="<ul>\n"
447 mytabs=""
448 for title in $tabtitles
449 do
450 #create list of tabs
451
452 count=$[count+1]
453 title2=${title//_s_/ }
454 tabslist="${tabslist} <li><a href=\"#tabs-${count}\">${title2}</a></li>\n"
455
456 #create tabs with content
457 tabcontent=$(makeTabContent $title "$tabitems")
458 mytabs="${mytabs}\n<div id=\"tabs-${count}\">\n"
459 mytabs="${mytabs}${tabcontent}"
460 mytabs="${mytabs}\n</div>\n"
461 done
462 tabslist="${tabslist}</ul>"
463
464 #output the webpage
465 echo -e "<!doctype html>
466 <head>
467 <meta charset=\"utf-8\">
468 <title>jQuery UI Tabs - Default functionality</title>
469
470
471 <link rel=\"stylesheet\" href=\"jquery-ui.css\">
472 <script src=\"jquery-1.10.2.js\"></script>
473 <script src=\"jquery-ui.js\"></script>
474 <script type=\"text/javascript\" src=\"iframe-resizer/src/iframeResizer.js\"></script>
475 <script type=\"text/javascript\" src=\"jquery.zoom.js\"></script>
476
477 <script>
478 \$(function() {
479 \$( \"#tabs\" ).tabs();
480 });
481
482 \$(function() {
483 \$( \".resizable\" ).resizable();
484 });
485
486 \$(document).ready(function(){
487 \$('.zoomme').zoom();
488 \$('#ex2').zoom({ on:'grab' });
489 \$('#ex3').zoom({ on:'click' });
490 \$('#ex4').zoom({ on:'toggle' });
491 \$('.fancyiframe').iFrameResize({
492 heightCalculationMethod: 'max',
493 minHeight: 250,
494 scrolling: true,
495 checkOrigin: false,
496 bodyMargin: 15
497 });
498 \$('.unfancyiframe').iFrameResize({
499 heightCalculationMethod: 'max',
500 scrolling: false,
501 checkOrigin: false
502 });
503 });
504
505 </script>
506
507
508 <script language=\"javascript\" type=\"text/javascript\">
509 function resizeIframe(obj) {
510 oldheight=obj.style.height
511 oldwidth=obj.style.width
512 obj.style.height = obj.contentWindow.document.body.scrollHeight + 4 + 'px';
513 obj.style.width = obj.contentWindow.document.body.scrollWidth + 4 + 'px';
514
515 if(obj.style.height < 50){
516 obj.style.height=oldheight
517 }
518 }
519 </script>
520 <style type=\"text/css\">
521 body {
522 min-width: ${minwidth}px;
523 width: ${minwidth}px;
524 min-height: 100%;
525 }
526 .invisibleframe{
527 border: 0px;
528 overflow: hidden
529 }
530 .mylinks{
531 color: blue !important;
532 }
533 .mylinks:visited {
534 color: #551A8B !important;
535 }
536 </style>
537 <style >
538 .zoomme {
539 display: inline-block;
540 }
541 </style>
542
543
544 </head>
545 <body>
546
547 <div id=\"tabs\" style=\"display:inline-block; min-height:100%; min-width:${minwidth}px\">
548 $tabslist
549
550 $mytabs
551 </div>
552
553
554 </body>
555 </html>" > $page
556
557
558
559 }