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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 zipireport=$5
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8
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9 echo -e "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01//EN\" \"http://www.w3.org/TR/html4/strict.dtd\">
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10 <html>
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11 <head>
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12 </head>
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13 <body>
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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 -->
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15 <br/>
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16 <br/>
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17 <center>
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18 <b><font size=\"15\"> iReport: ${title} </font></b><br/>
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19 <br/>
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20 <br/>
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21 <a href=\"$link\"> Click here to view report </a> <br/><br/>
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22 <a href=\"$link\"> <img src="$coverimage" width=\"50%\" alt=\"loading image..\"/> </a><br/><br/>
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23 <a href=\"$zipireport\"> Click here to download a copy of this iReport </a> <br/><br/>
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24 </center>
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25 </body>
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26 </html>" > $htmlout
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27
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28 }
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29
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30
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31 function makeTabContent ( ){
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32 tab=$1 #name of current tab
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33 itemslist=$2 #list of all items
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34 contentline="<br/>"
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35 imgcount=0
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36 #echo -e "\n Creating items. itemslist: $itemslist"
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37
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38 for item in $itemslist
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39 do
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40 #echo -e "\n -> item : $item"
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41 item=${item/::/:emptycol:}
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42 declare -a myarr=(`echo $item |sed 's/:/ /g'`)
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43 #echo "break: ${myarr[3]}"
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44 if [ ${myarr[0]} == $tab ]
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45 then
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46
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47 ## add contents of text field to page####
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48 if [ ${myarr[1]} == "text" ]
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49 then
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50 text=${myarr[2]}
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51 ## allow some html formatting tags
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52 text=${text//==lt==strong==gt==/<strong>} # search for strong tags
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53 text=${text//==lt====slash==strong==gt==/<\/strong>} # search for strong tags
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54 text=${text//==lt==em==gt==/<em>} # search for strong tags
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55 text=${text//==lt====slash==em==gt==/<\/em>} # search for strong tags
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56
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57 text=${text//==lt==b==gt==/<strong>} # search for strong tags
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58 text=${text//==lt====slash==b==gt==/<\/strong>} # search for strong tags
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59 text=${text//==lt==i==gt==/<em>} # search for strong tags
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60 text=${text//==lt====slash==i==gt==/<\/em>} # search for strong tags
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61
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62 text=${text//==lt==br==gt==/<br\/>} # search for strong tags
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63 text=${text//==lt====br==slash==gt==/<br\/>} # search for strong tags
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64 text=${text//==lt==h1==gt==/<h1>} # search for h1-h6 tags
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65 text=${text//==lt==h2==gt==/<h2>} # search for h1-h6 tags
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66 text=${text//==lt==h3==gt==/<h3>} # search for h1-h6 tags
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67 text=${text//==lt==h4==gt==/<h4>} # search for h1-h6 tags
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68 text=${text//==lt==h5==gt==/<h5>} # search for h1-h6 tags
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69 text=${text//==lt==h6==gt==/<h6>} # search for h1-h6 tags
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70 text=${text//==lt====slash==h1==gt==/<\/h1>} # search for h1-h6 closing tags
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71 text=${text//==lt====slash==h2==gt==/<\/h2>} # search for h1-h6 closing tags
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72 text=${text//==lt====slash==h3==gt==/<\/h3>} # search for h1-h6 closing tags
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73 text=${text//==lt====slash==h4==gt==/<\/h4>} # search for h1-h6 closing tags
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74 text=${text//==lt====slash==h5==gt==/<\/h5>} # search for h1-h6 closing tags
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75 text=${text//==lt====slaxh==h6==gt==/<\/h6>} # search for h1-h6 closing tags
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76
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77 ## display everything else verbatim
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78 text=${text//==space==/ }
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79 text=${text//==colon==/:}
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80 text=${text//==comma==/,}
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81 text=${text//==slash==/\/}
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82 text=${text//==lt==/<}
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83 text=${text//==gt==/>}
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84 text=${text//==apos==/'}
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85 text=${text//==quote==/"}
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86 text=${text//&&/&}
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87 text=${text//\\n/<br/>}
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88 text=${text//\\t/ }
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89 text=${text//\&r\&n/<br/>}
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90 text=${text//\&r/<br/>}
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91 text=${text//\&n/<br/>}
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92 text=${text//\&c/:}
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93 contentline="${contentline}${text}"
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94 fi
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95
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96 ## add contents of a text file to page
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97 if [ ${myarr[1]} == "textfile" ]
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98 then
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99 tfile=${myarr[2]}
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100 fname=`basename ${tfile}`
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101 fname=${fname%.*}
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102 fname="${fname}.txt"
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103 cp ${tfile} "${galaxypath}/${fname}"
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104
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105 #estimate height for iframe based on number oflines in the file
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106 numlines=`wc -l ${tfile} | cut -d" " -f1`
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107 minheight=$[$numlines*17]
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108
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109 contentline="${contentline}<iframe class=\"invisibleframe\" src=\"${fname}\" width=\"100%\" height=\"$minheight\"> </iframe>"
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110 fi
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111
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112 ## add image file to page
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113 if [ ${myarr[1]} == "image" ]
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114 then
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115 imgcount=$[$imgcount+1]
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116 #restore file suffix for html
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117 ftype=`file ${myarr[2]}`
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118 zoomlevel=${myarr[4]}
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119 zoomenable=${myarr[5]}
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120 align=${myarr[6]}
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121 #####echo "zoomenable:${zoomenable}, align:${align}"
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122 if [[ $ftype == *JPEG* ]]
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123 then
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124 suffix=".jpg"
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125 fi
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126 if [[ $ftype == *SVG* ]]
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127 then
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128 suffix=".svg"
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129 fi
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130 if [[ $ftype == *PNG* ]]
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131 then
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132 suffix=".png"
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133 fi
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134
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135 image=`basename ${myarr[2]}`
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136 image=${image%.dat}
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137 image="${image}${suffix}"
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138 cp ${myarr[2]} ${galaxypath}/${image}
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139
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140 if [[ ${align} == "none" ]]
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141 then
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142 alignstring=""
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143 alignstring2=""
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144 else
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145 alignstring="<div float=\"${align}\">"
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146 alignstring2="</div>"
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147
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148 alignstring="align=\"${align}\""
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149 alignstring2=""
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150 fi
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151
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152
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153 if [[ ${zoomlevel} -eq 0 ]]
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154 then
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155 widthstring=""
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156 else
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157 widthstring="width=\"${zoomlevel}\""
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158 fi
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159
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160 if [[ ${zoomlevel} -eq 0 || ${zoomenable} == "N" ]]
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161 then
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162 contentline="${contentline}<span id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
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163 else
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164 contentline="${contentline}<span class=\"zoomme\" id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
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165 fi
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166
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167 fi
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168 if [ ${myarr[1]} == "table" ]
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169 then
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170 maxlines=50000
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171 tsvfile_orig=${myarr[2]}
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172 tsvfile="tablehead.tsv"
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173 fname=`basename ${tsvfile_orig}`
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174 fname=${fname%.*}
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175 fancy=${myarr[4]}
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176 makelinks=${myarr[5]}
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177 #echo "\nmakelinks: $makelinks fancy: $fancy <br>"
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178
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179 #TODO client side database for large files. For now only display first section of file and add download link
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180 numlines=`wc -l ${tsvfile_orig} |cut -d" " -f1`
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181
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182 head -${maxlines} ${tsvfile_orig} > tsvtmpfile
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183
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184 #remove any empty or header lines (lines starting with #, unless vcf file, then keep #CHROM line)
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185 awk 'BEGIN{
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186 FS="\t"
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187 OFS="\t"
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188 }{
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189 if((index($0,"#")==1 && index($0,"#CHROM")!=1) || $0==""){
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190 headerlines++
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191 }
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192 else print $0
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193
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194 }END{}' tsvtmpfile > ${tsvfile}
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195
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196 if [[ $makelinks == "Y" ]]
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197 then
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198 col=${myarr[6]}
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199 prefix=${myarr[7]}
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200 suffix=${myarr[8]}
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201 suffix=${suffix/emptycol/}
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202 suffix=${suffix/==quote==/&}
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203 prefix=${prefix/emptycol/}
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204 prefix=${prefix/==quote==/&}
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205 prefix=${prefix/==colon==/:}
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206 #echo "prefix: $prefix"
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207
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208 #edit the table to include links
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209 awk 'BEGIN{
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210 FS="\t"
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211 OFS="\t"
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212 url="'"$prefix"'"
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213 url2="'"$suffix"'"
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214 prefix="<a href=\42"
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215 suffix="\42>"
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216 col="'"$col"'"
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217 end="</a>"
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218 }{
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219 if(FNR==1)
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220 print $0
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221 else{
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222 $col=prefix""url""$col""url2""suffix""$col""end
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223 print $0
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224 }
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225 }END{}' ${tsvfile} > ${tsvfile}2
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226 #echo "converted file: "
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227 #cat ${tsvfile}2
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228 else
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229 cp ${tsvfile} ${tsvfile}2
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230 fi
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231
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232 if [ $fancy == "Y" ]
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233 then
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234 perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
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235 #contentline="${contentline}\n<div class=\"resizable\" id=\"iframe${iframecount}\"><iframe src=\"htmltable_${fname}.html\" style=\"max-width: 100%;vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe></div>"
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236 #contentline="${contentline}\n<iframe class=\"resizable\" id=\"iframe${iframecount}\" src=\"htmltable_${fname}.html\" style=\"max-width: 100%;vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>"
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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>"
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238
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239 iframecount=$[$iframecount+1]
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240 else
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241 perl ${repositorypath}/tsv2html_simple.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
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242 #contentline="${contentline}\n<iframe class=\"invisibleframe\" id=\"iframe${iframecount}\" style=\"max-width: 100%; vertical-align: top;\" src=\"htmltable_${fname}.html\" onload=\"resizeIframe(this)\"></iframe>"
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243 contentline="${contentline}\n<iframe class=\"unfancyiframe invisibleframe\" src=\"htmltable_${fname}.html\" scrolling=\"no\" style=\"max-width: 100%; vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>"
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244 iframecount=$[$iframecount+1]
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245 fi
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246
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247 if [[ $numlines -gt ${maxlines} ]]
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248 then
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249 tablename=`basename ${tsvfile_orig}`
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250 cp ${tsvfile_orig} ${galaxypath}/$tablename
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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>."
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252 fi
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253 fi
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254
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255 if [[ ${myarr[1]} == "pdf" ]]
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256 then
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257 pdffile=${myarr[2]}
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258 fname=`basename ${pdffile}`
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259 fname=${fname%.dat}
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260 pdfname="${fname}.pdf"
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261 cp ${pdffile} "${galaxypath}/${pdfname}"
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262
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263 width=1000
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264 height=800
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265 #contentline="${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>"
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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}/${fname}.html"
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267 width=$[$width+10]
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268 height=$[$height+10]
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269 contentline="${contentline}<iframe src=\"${fname}.html\" width=\"${width}\" height=\"${height}\"></iframe>\n"
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270
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271 fi
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272 ## link to a location on the web, open in new window
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273 if [ ${myarr[1]} == "weblink" ]
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274 then
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275 url=${myarr[2]}
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276 linktext=${myarr[4]}
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277 url=${url/==colon==/:}
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278 url=${url/==quote==/&}
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279
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280 contentline="${contentline}<a href=\"${url}\" target=\"_blank\">${linktext}</a>"
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281 fi
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282
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283 ## link to a file in the history
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284 if [ ${myarr[1]} == "link" ]
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285 then
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286 linkfile=${myarr[2]}
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287 apiid=${myarr[4]}
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288 isireport=${myarr[5]}
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289 linkfilename=`basename ${linkfile}`
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290 linktext=${myarr[6]}
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291
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292
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293 #check for some basic filetypes
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294 ftype=`file $linkfile`
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295 if [[ $ftype == *HTML* ]]
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296 then
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297 linkfilename=${linkfilename%.dat}
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298 linkfilename=${linkfilename}.html
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299 fi
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300 if [[ $ftype == *PNG* ]]
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301 then
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302 linkfilename=${linkfilename%.dat}
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303 linkfilename=${linkfilename}.png
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304 fi
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305 if [[ $ftype == *SVG* ]]
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306 then
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307 linkfilename=${linkfilename%.dat}
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308 linkfilename=${linkfilename}.svg
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309 fi
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310 if [[ $ftype == *JPEG* ]]
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311 then
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312 linkfilename=${linkfilename%.dat}
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313 linkfilename=${linkfilename}.jpg
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314 fi
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315
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316
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317 if [[ ${isireport} == "Y" ]]
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318 then
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319 linkfilename="/datasets/${apiid}/display/"
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320 else
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321 cp ${linkfile} "${galaxypath}/${linkfilename}"
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322 fi
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323
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324 contentline="${contentline}<a href=\"${linkfilename}\">${linktext}</a>"
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325 fi
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326
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327 ## link to files in an archive in the history item
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328 if [[ ${myarr[1]} == "links" ]]
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329 then
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330 #echo "making links:"
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331 archive=${myarr[2]}
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332 fname=`basename ${archive}`
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333 fname=${fname%.dat}
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334 ftype=`file $archive`
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335 mkdir ${galaxypath}/archive_${fname}/
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336
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337 #echo "archive type: `file $archive`"
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338 # decompress archive
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339 if [[ $ftype == *Zip* ]]
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340 then
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341 #echo "detected zip file"
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342 cp $archive ${galaxypath}/archive_${fname}/${fname}.zip
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343 wd=`pwd`
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344 cd ${galaxypath}/archive_${fname}/
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345 unzip -q ${fname}.zip
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346 rm ${fname}.zip
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347 cd $wd
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348 fi
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349 if [[ $ftype == *tar* ]]
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350 then
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351 cp $archive ${galaxypath}/archive_${fname}/${fname}.tar
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352 wd=`pwd`
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353 cd ${galaxypath}/archive_${fname}/
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354 tar xf ${fname}.tar
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355 rm ${fname}.tar
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356 cd $wd
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357 fi
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358 if [[ $ftype == *gzip* ]]
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359 then
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360 cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
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361 gunzip ${galaxypath}/archive_${fname}/${fname}.gz
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362 #ls ${galaxypath}/archive_${fname}/
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363
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364 # check for tar.gz
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365 ftype=`file ${galaxypath}/archive_${fname}/${fname}`
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366 if [[ $ftype == *tar* ]]
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367 then
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368 # turns out it was tar.gz
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369 rm -Rf ${galaxypath}/archive_${fname}/*
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370 ls ${galaxypath}/archive_${fname}/
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371 cp $archive ${galaxypath}/archive_${fname}/${fname}.tar.gz
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372
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373 wd=`pwd`
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374 cd ${galaxypath}/archive_${fname}/
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375 tar xzf ${fname}.tar.gz
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376 cd $wd
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377 fi
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378 wait
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379 rm -f ${galaxypath}/archive_${fname}/*.tar
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380 rm -f ${galaxypath}/archive_${fname}/*.tar.gz
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381 fi
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382 if [[ $ftype == *bzip2* ]]
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383 then
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384 cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
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385 gunzip2 ${galaxypath}/archive_${fname}/${fname}.gz
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386 fi
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387
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388
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389
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390 # add links to webpage
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391 # separate line for each folder, files within folder on same line
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392 for linkfile in `ls ${galaxypath}/archive_${fname}/ |sort -V`
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393 do
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394 #echo "<br/> ->making link to file: $linkfile "
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395 if [ -d ${galaxypath}/archive_${fname}/$linkfile ] # if directory, add break, and list all contained files, max level 1 deep
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396 then
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397 #echo "<br/> ->is directory, entering: $linkfile "
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398 #ls ${galaxypath}/archive_${fname}/$linkfile
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399 contentline="${contentline}"
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400 for linkfile2 in `ls ${galaxypath}/archive_${fname}/$linkfile | sort -V`
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401 do
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402 #echo "<br/> ->making link to file: ${galaxypath}/archive_${fname}/$linkfile2"
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403 if [ -f ${galaxypath}/archive_${fname}/$linkfile/$linkfile2 ] # if directory, add break, and list all contained files, max level 1 deep
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404 then
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405 #echo "<br/> ->is file, making link: $linkfile "
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406 label=`basename $linkfile2`
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407 label=${label%.*}
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408 contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}/${linkfile2}\">${label}</a> \n "
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409 fi
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410 done
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411 elif [ -f ${galaxypath}/archive_${fname}/$linkfile ]
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412 then
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413 label=`basename ${galaxypath}/archive_${fname}/$linkfile`
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|
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414 label=${label%.*}
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|
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415 contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}\">$label</a> \n"
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|
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416 fi
|
|
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417 done
|
|
|
418
|
|
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419
|
|
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420 fi
|
|
|
421
|
|
|
422 if [[ ${myarr[3]} == "Y" ]]
|
|
|
423 then
|
|
|
424 contentline="${contentline}<br/>"
|
|
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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
|
|
1
|
471 <link rel=\"stylesheet\" href=\"jquery-ui.css\">
|
|
|
472 <script src=\"jquery-1.10.2.js\"></script>
|
|
|
473 <script src=\"jquery-ui.js\"></script>
|
|
0
|
474 <script type=\"text/javascript\" src=\"iframe-resizer/src/iframeResizer.js\"></script>
|
|
|
475 <script type=\"text/javascript\" src=\"jquery.zoom.js\"></script>
|
|
1
|
476
|
|
0
|
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 } |
