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1 function makeIntroPage ( ){
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2 echo "Creating Intro Page"
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3 title="$1"
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4 coverimage=$2
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5 link=$3
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6 htmlout=$4
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7
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8 echo -e "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01//EN\" \"http://www.w3.org/TR/html4/strict.dtd\">
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9 <html>
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10 <head>
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11 </head>
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12 <body>
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13 <!-- 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 -->
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14 <br/>
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15 <br/>
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16 <center>
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17 <b><font size=\"15\"> iReport: ${title} </font></b><br/>
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18 <br/>
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19 <br/>
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20 <a href=\"$link\"> Click here to view report </a> <br/><br/>
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21 <a href=\"$link\"> <img src="$coverimage" width=\"50%\" alt=\"loading image..\"/> </a><br/><br/>
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22 </center>
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23 </body>
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24 </html>" > $htmlout
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25
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26 }
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27
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28
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29 function makeTabContent ( ){
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30 tab=$1 #name of current tab
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31 itemslist=$2 #list of all items
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32 contentline="<br/>"
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33 imgcount=0
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34 #echo -e "\n Creating items. itemslist: $itemslist"
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35
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36 for item in $itemslist
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37 do
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38 #echo -e "\n -> item : $item"
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39 item=${item/::/:emptycol:}
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40 declare -a myarr=(`echo $item |sed 's/:/ /g'`)
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41 #echo "break: ${myarr[3]}"
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42 if [ ${myarr[0]} == $tab ]
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43 then
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44
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45 ## add contents of text field to page####
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46 if [ ${myarr[1]} == "text" ]
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47 then
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48 text=${myarr[2]}
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49 ## allow some html formatting tags
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50 text=${text//==lt==strong==gt==/<strong>} # search for strong tags
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51 text=${text//==lt====slash==strong==gt==/<\/strong>} # search for strong tags
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52 text=${text//==lt==em==gt==/<em>} # search for strong tags
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53 text=${text//==lt====slash==em==gt==/<\/em>} # search for strong tags
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54
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55 text=${text//==lt==b==gt==/<strong>} # search for strong tags
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56 text=${text//==lt====slash==b==gt==/<\/strong>} # search for strong tags
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57 text=${text//==lt==i==gt==/<em>} # search for strong tags
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58 text=${text//==lt====slash==i==gt==/<\/em>} # search for strong tags
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59
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60 text=${text//==lt==br==gt==/<br\/>} # search for strong tags
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61 text=${text//==lt====br==slash==gt==/<br\/>} # search for strong tags
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62 text=${text//==lt==h1==gt==/<h1>} # search for h1-h6 tags
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63 text=${text//==lt==h2==gt==/<h2>} # search for h1-h6 tags
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64 text=${text//==lt==h3==gt==/<h3>} # search for h1-h6 tags
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65 text=${text//==lt==h4==gt==/<h4>} # search for h1-h6 tags
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66 text=${text//==lt==h5==gt==/<h5>} # search for h1-h6 tags
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67 text=${text//==lt==h6==gt==/<h6>} # search for h1-h6 tags
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68 text=${text//==lt====slash==h1==gt==/<\/h1>} # search for h1-h6 closing tags
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69 text=${text//==lt====slash==h2==gt==/<\/h2>} # search for h1-h6 closing tags
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70 text=${text//==lt====slash==h3==gt==/<\/h3>} # search for h1-h6 closing tags
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71 text=${text//==lt====slash==h4==gt==/<\/h4>} # search for h1-h6 closing tags
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72 text=${text//==lt====slash==h5==gt==/<\/h5>} # search for h1-h6 closing tags
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73 text=${text//==lt====slaxh==h6==gt==/<\/h6>} # search for h1-h6 closing tags
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74
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75 ## display everything else verbatim
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76 text=${text//==space==/ }
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77 text=${text//==colon==/:}
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78 text=${text//==comma==/,}
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79 text=${text//==slash==/\/}
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80 text=${text//==lt==/<}
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81 text=${text//==gt==/>}
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82 text=${text//==apos==/'}
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83 text=${text//==quote==/"}
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84 text=${text//&&/&}
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85 text=${text//\\n/<br/>}
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86 text=${text//\\t/ }
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87 text=${text//\&r\&n/<br/>}
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88 text=${text//\&r/<br/>}
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89 text=${text//\&n/<br/>}
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90 text=${text//\&c/:}
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91 contentline="${contentline}${text}"
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92 fi
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93
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94 ## add contents of a text file to page
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95 if [ ${myarr[1]} == "textfile" ]
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96 then
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97 tfile=${myarr[2]}
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98 fname=`basename ${tfile}`
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99 fname=${fname%.*}
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100 fname="${fname}.txt"
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101 cp ${tfile} "${galaxypath}/${fname}"
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102
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103 #estimate height for iframe based on number oflines in the file
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104 numlines=`wc -l ${tfile} | cut -d" " -f1`
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105 minheight=$[$numlines*17]
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106
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107 contentline="${contentline}<iframe class=\"invisibleframe\" src=\"${fname}\" width=\"100%\" height=\"$minheight\"> </iframe>"
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108 fi
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109
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110 ## add image file to page
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111 if [ ${myarr[1]} == "image" ]
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112 then
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113 imgcount=$[$imgcount+1]
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114 #restore file suffix for html
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115 ftype=`file ${myarr[2]}`
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116 zoomlevel=${myarr[4]}
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117 zoomenable=${myarr[5]}
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118 align=${myarr[6]}
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119 #####echo "zoomenable:${zoomenable}, align:${align}"
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120 if [[ $ftype == *JPEG* ]]
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121 then
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122 suffix=".jpg"
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123 fi
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124 if [[ $ftype == *SVG* ]]
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125 then
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126 suffix=".svg"
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127 fi
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128 if [[ $ftype == *PNG* ]]
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129 then
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130 suffix=".png"
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131 fi
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132
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133 image=`basename ${myarr[2]}`
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134 image=${image%.dat}
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135 image="${image}${suffix}"
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136 cp ${myarr[2]} ${galaxypath}/${image}
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137
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138 if [[ ${align} == "none" ]]
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139 then
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140 alignstring=""
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141 alignstring2=""
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142 else
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143 alignstring="<div float=\"${align}\">"
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144 alignstring2="</div>"
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145
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146 alignstring="align=\"${align}\""
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147 alignstring2=""
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148 fi
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149
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150
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151 if [[ ${zoomlevel} -eq 0 ]]
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152 then
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153 widthstring=""
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154 else
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155 widthstring="width=\"${zoomlevel}\""
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156 fi
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157
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158 if [[ ${zoomlevel} -eq 0 || ${zoomenable} == "N" ]]
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159 then
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160 contentline="${contentline}<span id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
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161 else
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162 contentline="${contentline}<span class=\"zoomme\" id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
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163 fi
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164
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165 fi
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166 if [ ${myarr[1]} == "table" ]
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167 then
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168 maxlines=50000
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169 tsvfile_orig=${myarr[2]}
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170 tsvfile="tablehead.tsv"
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171 fname=`basename ${tsvfile_orig}`
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172 fname=${fname%.*}
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173 fancy=${myarr[4]}
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174 makelinks=${myarr[5]}
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175 #echo "\nmakelinks: $makelinks fancy: $fancy <br>"
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176
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177 #TODO client side database for large files. For now only display first section of file and add download link
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178 numlines=`wc -l ${tsvfile_orig} |cut -d" " -f1`
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179
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180 head -${maxlines} ${tsvfile_orig} > tsvtmpfile
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181
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182 #remove any empty or header lines (lines starting with #, unless vcf file, then keep #CHROM line)
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183 awk 'BEGIN{
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184 FS="\t"
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185 OFS="\t"
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186 }{
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187 if((index($0,"#")==1 && index($0,"#CHROM")!=1) || $0==""){
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188 headerlines++
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189 }
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190 else print $0
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191
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192 }END{}' tsvtmpfile > ${tsvfile}
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193
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194 if [[ $makelinks == "Y" ]]
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195 then
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196 col=${myarr[6]}
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197 prefix=${myarr[7]}
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198 suffix=${myarr[8]}
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199 suffix=${suffix/emptycol/}
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200 suffix=${suffix/==quote==/&}
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201 prefix=${prefix/emptycol/}
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202 prefix=${prefix/==quote==/&}
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203 prefix=${prefix/==colon==/:}
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204 #echo "prefix: $prefix"
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205
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206 #edit the table to include links
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207 awk 'BEGIN{
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208 FS="\t"
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209 OFS="\t"
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210 url="'"$prefix"'"
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211 url2="'"$suffix"'"
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212 prefix="<a href=\42"
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213 suffix="\42>"
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214 col="'"$col"'"
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215 end="</a>"
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216 }{
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217 if(FNR==1)
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218 print $0
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219 else{
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220 $col=prefix""url""$col""url2""suffix""$col""end
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221 print $0
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222 }
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223 }END{}' ${tsvfile} > ${tsvfile}2
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224 #echo "converted file: "
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225 #cat ${tsvfile}2
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226 else
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227 cp ${tsvfile} ${tsvfile}2
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228 fi
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229
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230 if [ $fancy == "Y" ]
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231 then
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232 perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
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233 #contentline="${contentline}\n<div class=\"resizable\" id=\"iframe${iframecount}\"><iframe src=\"htmltable_${fname}.html\" style=\"max-width: 100%;vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe></div>"
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234 #contentline="${contentline}\n<iframe class=\"resizable\" id=\"iframe${iframecount}\" src=\"htmltable_${fname}.html\" style=\"max-width: 100%;vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>"
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235 contentline="${contentline}\n<iframe class=\"invisibleframe fancyiframe\" src=\"htmltable_${fname}.html\" width=\"100%\" style=\"min-height: 300px; overflow-y: hidden; overflow-x: scroll\" ></iframe>"
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236
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237 iframecount=$[$iframecount+1]
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238 else
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239 perl ${repositorypath}/tsv2html_simple.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
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240 #contentline="${contentline}\n<iframe class=\"invisibleframe\" id=\"iframe${iframecount}\" style=\"max-width: 100%; vertical-align: top;\" src=\"htmltable_${fname}.html\" onload=\"resizeIframe(this)\"></iframe>"
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241 contentline="${contentline}\n<iframe class=\"unfancyiframe invisibleframe\" src=\"htmltable_${fname}.html\" scrolling=\"no\" style=\"max-width: 100%; vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>"
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242 iframecount=$[$iframecount+1]
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243 fi
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244
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245 if [[ $numlines -gt ${maxlines} ]]
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246 then
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247 tablename=`basename ${tsvfile_orig}`
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248 cp ${tsvfile_orig} ${galaxypath}/$tablename
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249 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>."
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250 fi
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251 fi
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252
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253 if [[ ${myarr[1]} == "pdf" ]]
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254 then
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255 pdffile=${myarr[2]}
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256 fname=`basename ${pdffile}`
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257 fname=${fname%.dat}
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258 pdfname="${fname}.pdf"
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259 cp ${pdffile} "${galaxypath}/${pdfname}"
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260
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261 width=1000
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262 height=800
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263 #contentline="${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>"
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264 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}/${fname}.html"
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265 width=$[$width+10]
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266 height=$[$height+10]
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267 contentline="${contentline}<iframe src=\"${fname}.html\" width=\"${width}\" height=\"${height}\"></iframe>\n"
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268
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269 fi
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270 ## link to a location on the web, open in new window
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271 if [ ${myarr[1]} == "weblink" ]
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272 then
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273 url=${myarr[2]}
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274 linktext=${myarr[4]}
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275 url=${url/==colon==/:}
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276 url=${url/==quote==/&}
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277
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278 contentline="${contentline}<a href=\"${url}\" target=\"_blank\">${linktext}</a>"
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279 fi
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280
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281 ## link to a file in the history
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282 if [ ${myarr[1]} == "link" ]
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283 then
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284 linkfile=${myarr[2]}
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285 apiid=${myarr[4]}
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286 isireport=${myarr[5]}
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287 linkfilename=`basename ${linkfile}`
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288 linktext=${myarr[6]}
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289
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290
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291 #check for some basic filetypes
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292 ftype=`file $linkfile`
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293 if [[ $ftype == *HTML* ]]
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294 then
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295 linkfilename=${linkfilename%.dat}
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296 linkfilename=${linkfilename}.html
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297 fi
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298 if [[ $ftype == *PNG* ]]
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299 then
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300 linkfilename=${linkfilename%.dat}
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301 linkfilename=${linkfilename}.png
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302 fi
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303 if [[ $ftype == *SVG* ]]
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304 then
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305 linkfilename=${linkfilename%.dat}
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306 linkfilename=${linkfilename}.svg
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307 fi
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308 if [[ $ftype == *JPEG* ]]
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309 then
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310 linkfilename=${linkfilename%.dat}
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311 linkfilename=${linkfilename}.jpg
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312 fi
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313
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314
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315 if [[ ${isireport} == "Y" ]]
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316 then
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317 linkfilename="/datasets/${apiid}/display/"
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318 else
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319 cp ${linkfile} "${galaxypath}/${linkfilename}"
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320 fi
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321
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322 contentline="${contentline}<a href=\"${linkfilename}\">${linktext}</a>"
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323 fi
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324
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325 ## link to files in an archive in the history item
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326 if [[ ${myarr[1]} == "links" ]]
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327 then
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328 #echo "making links:"
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329 archive=${myarr[2]}
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330 fname=`basename ${archive}`
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331 fname=${fname%.dat}
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332 ftype=`file $archive`
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333 mkdir ${galaxypath}/archive_${fname}/
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334
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335 #echo "archive type: `file $archive`"
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336 # decompress archive
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337 if [[ $ftype == *Zip* ]]
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338 then
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339 #echo "detected zip file"
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340 cp $archive ${galaxypath}/archive_${fname}/${fname}.zip
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341 wd=`pwd`
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342 cd ${galaxypath}/archive_${fname}/
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343 unzip -q ${fname}.zip
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344 rm ${fname}.zip
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345 cd $wd
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346 fi
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347 if [[ $ftype == *tar* ]]
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348 then
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349 cp $archive ${galaxypath}/archive_${fname}/${fname}.tar
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350 wd=`pwd`
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351 cd ${galaxypath}/archive_${fname}/
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352 tar xf ${fname}.tar
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353 rm ${fname}.tar
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354 cd $wd
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355 fi
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356 if [[ $ftype == *gzip* ]]
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357 then
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358 cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
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359 gunzip ${galaxypath}/archive_${fname}/${fname}.gz
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360 #ls ${galaxypath}/archive_${fname}/
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361
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362 # check for tar.gz
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363 ftype=`file ${galaxypath}/archive_${fname}/${fname}`
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364 if [[ $ftype == *tar* ]]
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365 then
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366 # turns out it was tar.gz
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367 rm -Rf ${galaxypath}/archive_${fname}/*
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368 ls ${galaxypath}/archive_${fname}/
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369 cp $archive ${galaxypath}/archive_${fname}/${fname}.tar.gz
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370
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371 wd=`pwd`
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372 cd ${galaxypath}/archive_${fname}/
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373 tar xzf ${fname}.tar.gz
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374 cd $wd
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375 fi
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376 wait
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377 rm -f ${galaxypath}/archive_${fname}/*.tar
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378 rm -f ${galaxypath}/archive_${fname}/*.tar.gz
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379 fi
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380 if [[ $ftype == *bzip2* ]]
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381 then
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382 cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
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383 gunzip2 ${galaxypath}/archive_${fname}/${fname}.gz
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384 fi
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385
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386
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387
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388 # add links to webpage
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389 # separate line for each folder, files within folder on same line
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390 for linkfile in `ls ${galaxypath}/archive_${fname}/ |sort -V`
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391 do
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392 #echo "<br/> ->making link to file: $linkfile "
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393 if [ -d ${galaxypath}/archive_${fname}/$linkfile ] # if directory, add break, and list all contained files, max level 1 deep
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394 then
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395 #echo "<br/> ->is directory, entering: $linkfile "
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396 #ls ${galaxypath}/archive_${fname}/$linkfile
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397 contentline="${contentline}"
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398 for linkfile2 in `ls ${galaxypath}/archive_${fname}/$linkfile | sort -V`
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399 do
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400 #echo "<br/> ->making link to file: ${galaxypath}/archive_${fname}/$linkfile2"
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401 if [ -f ${galaxypath}/archive_${fname}/$linkfile/$linkfile2 ] # if directory, add break, and list all contained files, max level 1 deep
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402 then
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403 #echo "<br/> ->is file, making link: $linkfile "
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404 label=`basename $linkfile2`
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405 label=${label%.*}
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406 contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}/${linkfile2}\">${label}</a> \n "
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407 fi
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408 done
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409 elif [ -f ${galaxypath}/archive_${fname}/$linkfile ]
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410 then
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411 label=`basename ${galaxypath}/archive_${fname}/$linkfile`
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412 label=${label%.*}
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|
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413 contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}\">$label</a> \n"
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|
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414 fi
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|
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415 done
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|
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416
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417
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418 fi
|
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419
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|
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420 if [[ ${myarr[3]} == "Y" ]]
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|
|
421 then
|
|
|
422 contentline="${contentline}<br/>"
|
|
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423 fi
|
|
|
424 fi
|
|
|
425 done
|
|
|
426
|
|
|
427 echo "${contentline}"
|
|
|
428 }
|
|
|
429
|
|
|
430
|
|
|
431 createMainPage (){
|
|
|
432 page=$1
|
|
|
433 tabtitles=$2 #comma-separated list of tab titles
|
|
|
434 tabitems=$3
|
|
|
435 iframecount=1
|
|
|
436 minwidth=$4
|
|
|
437
|
|
|
438 echo "createMainPage: tabitems: $tabitems. tabtitles: $tabtitles"
|
|
|
439 # create correct number of tabs
|
|
|
440 count=0
|
|
|
441
|
|
|
442 tabtitles=${tabtitles//,/ }
|
|
|
443 tabtitles=${tabtitles//==colon==/:}
|
|
|
444 tabslist="<ul>\n"
|
|
|
445 mytabs=""
|
|
|
446 for title in $tabtitles
|
|
|
447 do
|
|
|
448 #create list of tabs
|
|
|
449
|
|
|
450 count=$[count+1]
|
|
|
451 title2=${title//_s_/ }
|
|
|
452 tabslist="${tabslist} <li><a href=\"#tabs-${count}\">${title2}</a></li>\n"
|
|
|
453
|
|
|
454 #create tabs with content
|
|
|
455 tabcontent=$(makeTabContent $title "$tabitems")
|
|
|
456 mytabs="${mytabs}\n<div id=\"tabs-${count}\">\n"
|
|
|
457 mytabs="${mytabs}${tabcontent}"
|
|
|
458 mytabs="${mytabs}\n</div>\n"
|
|
|
459 done
|
|
|
460 tabslist="${tabslist}</ul>"
|
|
|
461
|
|
|
462 #output the webpage
|
|
|
463 echo -e "<!doctype html>
|
|
|
464 <head>
|
|
|
465 <meta charset=\"utf-8\">
|
|
|
466 <title>jQuery UI Tabs - Default functionality</title>
|
|
|
467
|
|
|
468
|
|
|
469 <link rel=\"stylesheet\" href=\"//code.jquery.com/ui/1.10.4/themes/smoothness/jquery-ui.css\">
|
|
|
470 <link rel=\"stylesheet\" href=\"/resources/demos/style.css\">
|
|
|
471
|
|
|
472 <script src=\"//code.jquery.com/jquery-1.10.2.js\"></script>
|
|
|
473 <script src=\"//code.jquery.com/ui/1.10.4/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 <script>
|
|
|
477 \$(function() {
|
|
|
478 \$( \"#tabs\" ).tabs();
|
|
|
479 });
|
|
|
480
|
|
|
481 \$(function() {
|
|
|
482 \$( \".resizable\" ).resizable();
|
|
|
483 });
|
|
|
484
|
|
|
485 \$(document).ready(function(){
|
|
|
486 \$('.zoomme').zoom();
|
|
|
487 \$('#ex2').zoom({ on:'grab' });
|
|
|
488 \$('#ex3').zoom({ on:'click' });
|
|
|
489 \$('#ex4').zoom({ on:'toggle' });
|
|
|
490 \$('.fancyiframe').iFrameResize({
|
|
|
491 heightCalculationMethod: 'max',
|
|
|
492 minHeight: 250,
|
|
|
493 scrolling: true,
|
|
|
494 checkOrigin: false,
|
|
|
495 bodyMargin: 15
|
|
|
496 });
|
|
|
497 \$('.unfancyiframe').iFrameResize({
|
|
|
498 heightCalculationMethod: 'max',
|
|
|
499 scrolling: false,
|
|
|
500 checkOrigin: false
|
|
|
501 });
|
|
|
502 });
|
|
|
503
|
|
|
504 </script>
|
|
|
505
|
|
|
506
|
|
|
507 <script language=\"javascript\" type=\"text/javascript\">
|
|
|
508 function resizeIframe(obj) {
|
|
|
509 oldheight=obj.style.height
|
|
|
510 oldwidth=obj.style.width
|
|
|
511 obj.style.height = obj.contentWindow.document.body.scrollHeight + 4 + 'px';
|
|
|
512 obj.style.width = obj.contentWindow.document.body.scrollWidth + 4 + 'px';
|
|
|
513
|
|
|
514 if(obj.style.height < 50){
|
|
|
515 obj.style.height=oldheight
|
|
|
516 }
|
|
|
517 }
|
|
|
518 </script>
|
|
|
519 <style type=\"text/css\">
|
|
|
520 body {
|
|
|
521 min-width: ${minwidth}px;
|
|
|
522 width: ${minwidth}px;
|
|
|
523 min-height: 100%;
|
|
|
524 }
|
|
|
525 .invisibleframe{
|
|
|
526 border: 0px;
|
|
|
527 overflow: hidden
|
|
|
528 }
|
|
|
529 .mylinks{
|
|
|
530 color: blue !important;
|
|
|
531 }
|
|
|
532 .mylinks:visited {
|
|
|
533 color: #551A8B !important;
|
|
|
534 }
|
|
|
535 </style>
|
|
|
536 <style >
|
|
|
537 .zoomme {
|
|
|
538 display: inline-block;
|
|
|
539 }
|
|
|
540 </style>
|
|
|
541
|
|
|
542
|
|
|
543 </head>
|
|
|
544 <body>
|
|
|
545
|
|
|
546 <div id=\"tabs\" style=\"display:inline-block; min-height:100%; min-width:${minwidth}px\">
|
|
|
547 $tabslist
|
|
|
548
|
|
|
549 $mytabs
|
|
|
550 </div>
|
|
|
551
|
|
|
552
|
|
|
553 </body>
|
|
|
554 </html>" > $page
|
|
|
555
|
|
|
556
|
|
|
557
|
|
|
558 } |
