File: fis-privacy-breach.patch

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gff2aplot 2.0-14
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file content (208 lines) | stat: -rw-r--r-- 11,741 bytes parent folder | download | duplicates (4) 
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Description: Fix privacy issues by linking to local images, js and css locally
Author: Andreas Tille <tille@debian.org>
Last-Update Sat, 20 Oct 2018 14:15:43 +0200

--- a/examples/mhcregion/index.html
+++ b/examples/mhcregion/index.html
@@ -9,12 +9,12 @@
   <META NAME="description" CONTENT="GFF2APLOT HOWTOs: Analyzing SIM output for a syntenic sequences pair.">
  <TITLE>GFF2APLOT HOWTOs: SIM output for a syntenic sequences pair.</TITLE>
 <!-- <BASE HREF="http://genome.imim.es/software/gfftools/gff2aplot_docs/mhcregion/"> -->
-<link rel=stylesheet type="text/css" href="http://genome.imim.es/Genome.css" title="Genome">
-<link rel=stylesheet type="text/css" href="http://genome.imim.es/software/gfftools/gff2aplot_docs/HowTo.css" title="Genome">
+<link rel=stylesheet type="text/css" href="../imgs/Genome.css" title="Genome">
+<link rel=stylesheet type="text/css" href="../imgs/HowTo.css" title="Genome">
 <STYLE type="text/css">
- @import url(http://genome.imim.es/Genome_forms_mozilla.css);
+ @import url(file:///usr/share/doc/gff2aplot/examples/imgs/Genome_forms_mozilla.css);
 </STYLE>
-<SCRIPT type="text/javascript" src="http://genome.imim.es/Genome.js"></SCRIPT>
+<SCRIPT type="text/javascript" src="../imgs/Genome.js"></SCRIPT>
 </head>
 
 <body onResize="init();" MARGINWIDTH="2" MARGINHEIGHT="0">
@@ -81,39 +81,39 @@
 <a href="http://www.imim.es/"
  onMouseover="window.status='Institut Municipal d\'Investigaci&oacute; M&egrave;dica';">IMIM</a>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <a href="http://www.upf.es/"
  onMouseover="window.status='Universitat Pompeu Fabra';">UPF</a>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <a href="http://www.crg.es/"
  onMouseover="window.status='Centre de Regulaci&oacute; Gen&ograve;mica';">CRG</a>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <a href="http://www.imim.es/grib/eng/default.htm"
  onMouseover="window.status='Grup de Recerca en Informtica Biom&egrave;dica';">GRIB</a>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <A HREF="http://genome.imim.es/index.html" onMouseover="window.status='Genome Informatics Research Laboratory HOME PAGE: You are Welcome!!!'">
-<IMG SRC="http://genome.imim.es/g_icons/lhr.gif" ALT="HOME" HEIGHT=10 WIDTH=36 BORDER=0>
+<IMG SRC="../imgs/lhr.gif" ALT="HOME" HEIGHT=10 WIDTH=36 BORDER=0>
 </A>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <a href="http://genome.imim.es/main/software.html"
   onMouseover="window.status='Software';">SOFTWARE</a>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <a href="http://genome.imim.es/software/gfftools/GFF2APLOT.html#TOP"
  onMouseover="window.status='This is the main page for GFF2APLOT.';">gff2aplot</a>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <a href="http://genome.imim.es/software/gfftools/GFF2APLOT.html#HOWTOS"
  onMouseover="window.status='GFF2APLOT Tutorials...';">HowTo</a>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <a href="http://genome.imim.es/software/gfftools/gff2aplot_docs/mhcregion/index.html#TOP"
  onMouseover="window.status='An Alignment from WU-BLAST';">SIM Data</a>
@@ -164,7 +164,7 @@ Bitmaps for the examples were generated
 <TD class="section" width=20% ALIGN=RIGHT>
 <a href="index.html#TOP"
  onMouseover="window.status='TOP of the PAGE';">
-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
 </TD></TR>
 </TABLE>
 <P> <BR class="hh">
@@ -188,7 +188,7 @@ $BIN/ali2gff -x "X87344"             \
 <TD class="section" width=20% ALIGN=RIGHT>
 <a href="index.html#TOP"
  onMouseover="window.status='TOP of the PAGE';">
-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
 </TD></TR>
 </TABLE>
 <P> <BR class="hh">
@@ -240,7 +240,7 @@ gff2aplot.pl
 <TD class="section" width=20% ALIGN=RIGHT>
 <a href="index.html#TOP"
  onMouseover="window.status='TOP of the PAGE';">
-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
 </TD></TR>
 </TABLE>
 <P> <BR class="hh">
@@ -275,7 +275,7 @@ gff2aplot.pl
 <TD class="section" width=20% ALIGN=RIGHT>
 <a href="index.html#TOP"
  onMouseover="window.status='TOP of the PAGE';">
-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
 </TD></TR>
 </TABLE>
 <P> <BR class="hh">
--- a/examples/wublast/index.html
+++ b/examples/wublast/index.html
@@ -9,12 +9,12 @@
   <META NAME="description" CONTENT="GFF2APLOT HOWTOs: Analizing data from WU-BLAST alignment output.">
  <TITLE>GFF2APLOT HOWTOs: Plotting WU-BLAST Results.</TITLE>
 <!-- <BASE HREF="http://genome.imim.es/software/gfftools/gff2aplot_docs/wublast/"> -->
-<link rel=stylesheet type="text/css" href="http://genome.imim.es/Genome.css" title="Genome">
-<link rel=stylesheet type="text/css" href="http://genome.imim.es/software/gfftools/gff2aplot_docs/HowTo.css" title="Genome">
+<link rel=stylesheet type="text/css" href="../imgs/Genome.css" title="Genome">
+<link rel=stylesheet type="text/css" href="../imgs/HowTo.css" title="Genome">
 <STYLE type="text/css">
- @import url(http://genome.imim.es/Genome_forms_mozilla.css);
+ @import url(file:///usr/share/doc/gff2aplot/examples/imgs/Genome_forms_mozilla.css);
 </STYLE>
-<SCRIPT type="text/javascript" src="http://genome.imim.es/Genome.js"></SCRIPT>
+<SCRIPT type="text/javascript" src="../imgs/Genome.js"></SCRIPT>
 </head>
 
 <body onResize="init();" MARGINWIDTH="2" MARGINHEIGHT="0">
@@ -81,39 +81,39 @@
 <a href="http://www.imim.es/"
  onMouseover="window.status='Institut Municipal d\'Investigaci&oacute; M&egrave;dica';">IMIM</a>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <a href="http://www.upf.es/"
  onMouseover="window.status='Universitat Pompeu Fabra';">UPF</a>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <a href="http://www.crg.es/"
  onMouseover="window.status='Centre de Regulaci&oacute; Gen&ograve;mica';">CRG</a>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <a href="http://www.imim.es/grib/eng/default.htm"
  onMouseover="window.status='Grup de Recerca en Informtica Biom&egrave;dica';">GRIB</a>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <A HREF="http://genome.imim.es/index.html" onMouseover="window.status='Genome Informatics Research Laboratory HOME PAGE: You are Welcome!!!'">
-<IMG SRC="http://genome.imim.es/g_icons/lhr.gif" ALT="HOME" HEIGHT=10 WIDTH=36 BORDER=0>
+<IMG SRC="../imgs/lhr.gif" ALT="HOME" HEIGHT=10 WIDTH=36 BORDER=0>
 </A>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <a href="http://genome.imim.es/main/software.html"
   onMouseover="window.status='Software';">SOFTWARE</a>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <a href="http://genome.imim.es/software/gfftools/GFF2APLOT.html#TOP"
  onMouseover="window.status='This is the main page for GFF2APLOT.';">gff2aplot</a>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <a href="http://genome.imim.es/software/gfftools/GFF2APLOT.html#HOWTOS"
  onMouseover="window.status='GFF2APLOT Tutorials...';">HowTo</a>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
  </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
 <a href="http://genome.imim.es/software/gfftools/gff2aplot_docs/wublast/index.html#TOP"
  onMouseover="window.status='An Alignment from WU-BLAST';">WU-BLAST Data</a>
@@ -163,7 +163,7 @@ Bitmaps for the examples were generated
 <TD class="section" width=20% ALIGN=RIGHT>
 <a href="index.html#TOP"
  onMouseover="window.status='TOP of the PAGE';">
-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
 </TD></TR>
 </TABLE>
 <P> <BR class="hh">
@@ -212,7 +212,7 @@ $BIN/parseblast.pl --verbose --no-frame
 <TD class="section" width=20% ALIGN=RIGHT>
 <a href="index.html#TOP"
  onMouseover="window.status='TOP of the PAGE';">
-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
 </TD></TR>
 </TABLE>
 <P> <BR class="hh">
@@ -263,7 +263,7 @@ gff2aplot.pl
 <TD class="section" width=20% ALIGN=RIGHT>
 <a href="index.html#TOP"
  onMouseover="window.status='TOP of the PAGE';">
-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
 </TD></TR>
 </TABLE>
 <P> <BR class="hh">
@@ -313,7 +313,7 @@ gff2aplot.pl
 <TD class="section" width=20% ALIGN=RIGHT>
 <a href="index.html#TOP"
  onMouseover="window.status='TOP of the PAGE';">
-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
 </TD></TR>
 </TABLE>
 <P> <BR class="hh">