Mercurial > repos > jankanis > blast2html

changeset 27:4e6ac737ba17

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improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy
author Jan Kanis <jan.code@jankanis.nl>
date Thu, 15 May 2014 16:46:09 +0200
parents eee23a36c582
children 8a8c0c71b5d1
files blast2html.html.jinja blast2html.py
diffstat 2 files changed, 15 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/blast2html.html.jinja	Thu May 15 12:44:44 2014 +0200
+++ b/blast2html.html.jinja	Thu May 15 16:46:09 2014 +0200
@@ -371,8 +371,16 @@
 
   
   <body>
-    <div id="strip_html_warning" style="border: 3px solid red; color: red">
-      This html seems to have been stripped by Galaxy. Disable Galaxy's html sanitization feature to view the full page, or download this page instead of viewing it in Galaxy.
+    
+    <div id="strip_html_warning">
+      <!-- This div should be hidden by the header css block. Galaxy
+      strips all css, breaking this page but making this warning
+      visible. This warning contains some ugly old skool tabular html
+      layout that is not stripped. -->
+      <table bgcolor="#FFE5C9"><tr><td><font color="red"><b>
+                <font size=5><center>This html page seems to have been stripped by Galaxy.</center></font>
+                Disable Galaxy's html sanitization feature to view the full page (see <font face=monospace>sanitize_all_html</font> in your galaxy's universe_wsgi.ini), or download this page instead of viewing it in Galaxy.
+      </b></font></td></tr></table>
     </div>
     
     <div id=content>
--- a/blast2html.py	Thu May 15 12:44:44 2014 +0200
+++ b/blast2html.py	Thu May 15 16:46:09 2014 +0200
@@ -1,4 +1,5 @@
 #!/usr/bin/env python3
+# Actually runs under either python 2 or 3
 
 # Copyright The Hyve B.V. 2014
 # License: GPL version 3 or higher
@@ -273,8 +274,10 @@
                        ident = "{:.0%}".format(float(min(hsp.Hsp_identity / blastxml_len(hsp) for hsp in hsps))),
                        accession = hit.Hit_accession)
 
+
 def main():
-
+    default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja')
+    
     parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",
                                      usage="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0]))
     input_group = parser.add_mutually_exclusive_group(required=True)
@@ -289,7 +292,7 @@
     # handle the errors. This introduces a small race condition when
     # jinja later tries to re-open the template file, but we don't
     # care too much.
-    parser.add_argument('--template', type=argparse.FileType(mode='r'), default='blast2html.html.jinja',
+    parser.add_argument('--template', type=argparse.FileType(mode='r'), default=default_template,
                         help='The template file to use. Defaults to blast_html.html.jinja')
 
     args = parser.parse_args()