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42
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1
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2 class tooloutHTMLifyer(self):
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3
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4 def compressPDF(self,inpdf=None,thumbformat='png'):
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5 """need absolute path to pdf
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6 note that GS gets confoozled if no $TMP or $TEMP
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7 so we set it
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8 """
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9 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
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10 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
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11 sto = open(hlog,'a')
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12 our_env = os.environ.copy()
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13 our_tmp = our_env.get('TMP',None)
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14 if not our_tmp:
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15 our_tmp = our_env.get('TEMP',None)
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16 if not (our_tmp and os.path.exists(our_tmp)):
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17 newtmp = os.path.join(self.opts.output_dir,'tmp')
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18 try:
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19 os.mkdir(newtmp)
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20 except:
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21 sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
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22 our_env['TEMP'] = newtmp
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23 if not self.temp_warned:
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24 sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
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25 self.temp_warned = True
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26 outpdf = '%s_compressed' % inpdf
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27 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
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28 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
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29 retval1 = x.wait()
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30 sto.close()
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31 if retval1 == 0:
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32 os.unlink(inpdf)
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33 shutil.move(outpdf,inpdf)
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34 os.unlink(hlog)
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35 hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
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36 sto = open(hlog,'w')
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37 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
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38 if self.useGM:
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39 cl2 = ['gm', 'convert', inpdf, outpng]
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40 else: # assume imagemagick
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41 cl2 = ['convert', inpdf, outpng]
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42 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
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43 retval2 = x.wait()
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44 sto.close()
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45 if retval2 == 0:
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46 os.unlink(hlog)
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47 retval = retval1 or retval2
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48 return retval
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49
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50
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51 def getfSize(self,fpath,outpath):
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52 """
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53 format a nice file size string
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54 """
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55 size = ''
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56 fp = os.path.join(outpath,fpath)
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57 if os.path.isfile(fp):
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58 size = '0 B'
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59 n = float(os.path.getsize(fp))
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60 if n > 2**20:
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61 size = '%1.1f MB' % (n/2**20)
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62 elif n > 2**10:
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63 size = '%1.1f KB' % (n/2**10)
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64 elif n > 0:
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65 size = '%d B' % (int(n))
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66 return size
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67
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68 def makeHtml(self):
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69 """ Create an HTML file content to list all the artifacts found in the output_dir
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70 """
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71
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72 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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73 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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74 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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75 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
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76 <title></title>
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77 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
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78 </head>
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79 <body>
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80 <div class="toolFormBody">
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81 """
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82 galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>"""
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83 galhtmlpostfix = """</div></body></html>\n"""
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84
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85 flist = os.listdir(self.opts.output_dir)
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86 flist = [x for x in flist if x != 'Rplots.pdf']
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87 flist.sort()
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88 html = []
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89 html.append(galhtmlprefix % progname)
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90 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
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91 fhtml = []
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92 if len(flist) > 0:
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93 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
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94 logfiles.sort()
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95 logfiles = [x for x in logfiles if os.path.abspath(x) != os.path.abspath(self.tlog)]
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96 logfiles.append(os.path.abspath(self.tlog)) # make it the last one
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97 pdflist = []
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98 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
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99 for rownum,fname in enumerate(flist):
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100 dname,e = os.path.splitext(fname)
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101 sfsize = self.getfSize(fname,self.opts.output_dir)
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102 if e.lower() == '.pdf' : # compress and make a thumbnail
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103 thumb = '%s.%s' % (dname,self.thumbformat)
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104 pdff = os.path.join(self.opts.output_dir,fname)
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105 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
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106 if retval == 0:
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107 pdflist.append((fname,thumb))
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108 else:
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109 pdflist.append((fname,fname))
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110 if (rownum+1) % 2 == 0:
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111 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
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112 else:
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113 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
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114 for logfname in logfiles: # expect at least tlog - if more
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115 if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
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116 sectionname = 'All tool run'
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117 if (len(logfiles) > 1):
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118 sectionname = 'Other'
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119 ourpdfs = pdflist
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120 else:
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121 realname = os.path.basename(logfname)
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122 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
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123 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
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124 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] != sectionname] # remove
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125 nacross = 1
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126 npdf = len(ourpdfs)
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127
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128 if npdf > 0:
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129 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
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130 if int(nacross)**2 != npdf:
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131 nacross += 1
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132 nacross = int(nacross)
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133 width = min(400,int(1200/nacross))
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134 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
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135 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
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136 ntogo = nacross # counter for table row padding with empty cells
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137 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
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138 for i,paths in enumerate(ourpdfs):
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139 fname,thumb = paths
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140 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
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141 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
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142 if ((i+1) % nacross == 0):
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143 s += '</tr>\n'
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144 ntogo = 0
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145 if i < (npdf - 1): # more to come
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146 s += '<tr>'
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147 ntogo = nacross
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148 else:
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149 ntogo -= 1
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150 html.append(s)
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151 if html[-1].strip().endswith('</tr>'):
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152 html.append('</table></div>\n')
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153 else:
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154 if ntogo > 0: # pad
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155 html.append('<td> </td>'*ntogo)
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156 html.append('</tr></table></div>\n')
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157 logt = open(logfname,'r').readlines()
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158 logtext = [x for x in logt if x.strip() > '']
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159 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
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160 if len(logtext) > 1:
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161 html.append('\n<pre>\n')
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162 html += logtext
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163 html.append('\n</pre>\n')
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164 else:
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165 html.append('%s is empty<br/>' % logfname)
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166 if len(fhtml) > 0:
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167 fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
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168 fhtml.append('</table></div><br/>')
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169 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
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170 html += fhtml # add all non-pdf files to the end of the display
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171 else:
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172 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
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173 html.append(galhtmlpostfix)
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174 htmlf = file(self.opts.output_html,'w')
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175 htmlf.write('\n'.join(html))
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176 htmlf.write('\n')
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177 htmlf.close()
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178 self.html = html
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179
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180
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