From greg@bx.psu.edu Wed Mar 24 15:04:47 2010
From: Greg Von Kuster <greg@bx.psu.edu>
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] [hg] galaxy 3550: Assume plink is on the executing	node
 path for...
Date: Wed, 24 Mar 2010 15:04:43 -0400
Message-ID:
 <hg.8938319bf173.1269457483.-3662315834786559821@scofield.bx.psu.edu>
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details:   http://www.bx.psu.edu/hg/galaxy/rev/8938319bf173
changeset: 3550:8938319bf173
user:      fubar: ross Lazarus at gmail period com
date:      Mon Mar 22 12:32:14 2010 -0400
description:
Assume plink is on the executing node path for converters
Add a non-specific exception catcher to archive creation code in library_comm=
on

diffstat:

 lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml |  2 +-
 lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml |  2 +-
 lib/galaxy/datatypes/genetics.py                           |  5 ++++-
 lib/galaxy/web/controllers/dataset.py                      |  2 +-
 lib/galaxy/web/controllers/library_common.py               |  5 +++++
 5 files changed, 12 insertions(+), 4 deletions(-)

diffs (66 lines):

diff -r 7120c4848270 -r 8938319bf173 lib/galaxy/datatypes/converters/lped_to_=
pbed_converter.xml
--- a/lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml	Mon Mar 22 1=
1:06:40 2010 -0400
+++ b/lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml	Mon Mar 22 1=
2:32:14 2010 -0400
@@ -3,7 +3,7 @@
   <!-- Used on the metadata edit page. -->
   <command interpreter=3D"python">
    lped_to_pbed_converter.py '$input1.extra_files_path/$input1.metadata.base=
_name'
-   '$output1' '$output1.files_path' '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink'
+   '$output1' '$output1.files_path' 'plink'
   </command>
   <inputs>
     <param format=3D"lped" name=3D"input1" type=3D"data" label=3D"Choose lin=
kage pedigree file"/>
diff -r 7120c4848270 -r 8938319bf173 lib/galaxy/datatypes/converters/pbed_to_=
lped_converter.xml
--- a/lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml	Mon Mar 22 1=
1:06:40 2010 -0400
+++ b/lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml	Mon Mar 22 1=
2:32:14 2010 -0400
@@ -3,7 +3,7 @@
   <!-- Used on the metadata edit page. -->
   <command interpreter=3D"python">
    pbed_to_lped_converter.py '$input1.extra_files_path/$input1.metadata.base=
_name'
-   '$output1' '$output1.files_path' '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink'
+   '$output1' '$output1.files_path' 'plink'
   </command>
   <inputs>
     <param format=3D"pbed" name=3D"input1" type=3D"data" label=3D"Choose com=
pressed Plink binary format genotype file"/>
diff -r 7120c4848270 -r 8938319bf173 lib/galaxy/datatypes/genetics.py
--- a/lib/galaxy/datatypes/genetics.py	Mon Mar 22 11:06:40 2010 -0400
+++ b/lib/galaxy/datatypes/genetics.py	Mon Mar 22 12:32:14 2010 -0400
@@ -114,7 +114,10 @@
         npeek =3D 5
         out =3D ['<table cellspacing=3D"0" cellpadding=3D"3">']
         f =3D open(dataset.file_name,'r')
-        d =3D [f.next() for x in range(npeek)]
+        d =3D f.readlines()[:5]
+        if len(d) =3D=3D 0:
+	    out =3D "Cannot find anything to parse in %s" % dataset.name
+	    return out
         hasheader =3D 0
         try:
             test =3D ['%f' % x for x in d[0][1:]] # first is name - see if s=
tarts all numerics
diff -r 7120c4848270 -r 8938319bf173 lib/galaxy/web/controllers/dataset.py
--- a/lib/galaxy/web/controllers/dataset.py	Mon Mar 22 11:06:40 2010 -0400
+++ b/lib/galaxy/web/controllers/dataset.py	Mon Mar 22 12:32:14 2010 -0400
@@ -332,7 +332,7 @@
                     trans.response.set_content_type( mime )
                     return open( file_path )
                 else:
-                    return "Could not find '%s' on the extra files path." % =
filename
+                    return "Could not find '%s' on the extra files path %s."=
 % (filename,file_path)
            =20
             mime =3D trans.app.datatypes_registry.get_mimetype_by_extension(=
 data.extension.lower() )
             trans.response.set_content_type(mime)
diff -r 7120c4848270 -r 8938319bf173 lib/galaxy/web/controllers/library_commo=
n.py
--- a/lib/galaxy/web/controllers/library_common.py	Mon Mar 22 11:06:40 2010 -=
0400
+++ b/lib/galaxy/web/controllers/library_common.py	Mon Mar 22 12:32:14 2010 -=
0400
@@ -1334,6 +1334,11 @@
                     log.exception( "Unable to create archive for download" )
                     msg =3D "Unable to create archive for download, please r=
eport this error"
                     messagetype =3D 'error'
+                except:
+                     error =3D True
+         	     log.exception( "Unexpected error %s in create archive for dow=
nload" % sys.exc_info()[0])
+                     msg =3D "Unable to create archive for download, please =
report - %s" % sys.exc_info()[0]
+                     messagetype =3D 'error'
                 if not error:
                     composite_extensions =3D trans.app.datatypes_registry.ge=
t_composite_extensions( )
                     seen =3D []

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