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Viewing changes to debian/patches/fix_path_for_support_files

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-06-17 18:28:26 UTC
  • mfrom: (9.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20130617182826-376az5ad080a0sfe
Tags: 1.7.0+dfsg-1
Upload preparations done for BioLinux to Debian

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debian/patches/fix_path_for_support_files
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Get QIIME to look in the right directory for support_files.
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The default location is relative to the script which is
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in a different location depending on the python version.
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Author: Tim Booth <tbooth@ceh.ac.uk>
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---
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The information above should follow the Patch Tagging Guidelines, please
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checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
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are templates for supplementary fields that you might want to add:
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Origin: <vendor|upstream|other>, <url of original patch>
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Bug: <url in upstream bugtracker>
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Bug-Debian: http://bugs.debian.org/<bugnumber>
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Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
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Forwarded: <no|not-needed|url proving that it has been forwarded>
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Reviewed-By: <name and email of someone who approved the patch>
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Last-Update: <YYYY-MM-DD>
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--- qiime-1.5.0+repack.orig/scripts/plot_taxa_summary.py
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+++ qiime-1.5.0+repack/scripts/plot_taxa_summary.py
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@@ -219,8 +219,7 @@ def main():
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         pass
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     # move javascript file to javascript output directory
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-    shutil.copyfile(os.path.join(qiime_dir,'qiime','support_files',\
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-                    'js/overlib.js'),\
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+    shutil.copyfile('/usr/lib/qiime/support_files/js/overlib.js',\
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                     os.path.join(javascript_path,'overlib.js'))
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     #make css output directory
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@@ -231,8 +230,7 @@ def main():
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         pass
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     # move css file to css output directory
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-    shutil.copyfile(os.path.join(qiime_dir,'qiime','support_files',\
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-                    'css/qiime_style.css'),\
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+    shutil.copyfile('/usr/lib/qiime/support_files/css/qiime_style.css',\
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                     os.path.join(css_path,'qiime_style.css'))
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     # verify all parameters are valid
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--- qiime-1.5.0+repack.orig/scripts/make_otu_heatmap_html.py
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+++ qiime-1.5.0+repack/scripts/make_otu_heatmap_html.py
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@@ -137,7 +137,8 @@ def main():
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     qiime_dir=get_qiime_project_dir()
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-    js_path=os.path.join(qiime_dir,'qiime/support_files/js')
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+    #js_path=os.path.join(qiime_dir,'qiime/support_files/js')
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+    js_path='/usr/lib/qiime/support_files/js'
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     shutil.copyfile(os.path.join(js_path,'overlib.js'), os.path.join(js_dir_path,'overlib.js'))
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     shutil.copyfile(os.path.join(js_path,'otu_count_display.js'), os.path.join(js_dir_path,'otu_count_display.js'))
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--- qiime-1.5.0+repack.orig/scripts/compare_3d_plots.py
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+++ qiime-1.5.0+repack/scripts/compare_3d_plots.py
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@@ -143,7 +143,8 @@ def main():
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     qiime_dir=get_qiime_project_dir()
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-    jar_path=os.path.join(qiime_dir,'qiime/support_files/jar/')
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+    #jar_path=os.path.join(qiime_dir,'qiime/support_files/jar/')
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+    jar_path='/usr/lib/qiime/support_files/jar/'
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     data_dir_path = get_random_directory_name(output_dir=dir_path,
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                                               return_absolute_path=False)    
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--- qiime-1.5.0+repack.orig/scripts/make_distance_histograms.py
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+++ qiime-1.5.0+repack/scripts/make_distance_histograms.py
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@@ -142,7 +142,8 @@ def main():
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     for color_info in groups_and_colors:
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         field_to_colors[color_info[0]]=color_info[1:]
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-    qiime_dir = get_qiime_project_dir()+'/qiime/support_files/'
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+    #qiime_dir = get_qiime_project_dir()+'/qiime/support_files/'
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+    qiime_dir='/usr/lib/qiime/support_files/'
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     fields = opts.fields
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     if fields is not None:
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--- qiime-1.5.0+repack.orig/scripts/make_2d_plots.py
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+++ qiime-1.5.0+repack/scripts/make_2d_plots.py
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@@ -148,7 +148,8 @@ def main():
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     qiime_dir=get_qiime_project_dir()
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-    js_path=os.path.join(qiime_dir,'qiime','support_files','js')
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+    #js_path=os.path.join(qiime_dir,'qiime','support_files','js')
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+    js_path='/usr/lib/qiime/support_files/js'
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     if opts.output_dir:
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         if os.path.exists(opts.output_dir):
 
1
This may be a much simpler fix than patching every single mention
 
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of support_files, but I'm not sure what else this function is used
 
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to find?
 
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--- a/qiime/util.py
 
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+++ b/qiime/util.py
 
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@@ -301,8 +301,9 @@
 
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     # Get the directory containing util.py
 
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     current_dir_path = dirname(current_file_path)
 
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     # Return the directory containing the directory containing util.py
 
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-    return dirname(current_dir_path)
 
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-    
 
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+    # In Debian what we actually want is /usr/lib/[qiime]
 
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+    return "/usr/lib"
 
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+
 
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 def get_qiime_scripts_dir():
 
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     """ Returns the QIIME scripts directory 
 
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