[hg] galaxy 3768: Add mimetypes to snp/wga datatypes in genetics.py

20 May 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/8470f5588775
changeset: 3768:8470f5588775
user:      fubar/ross period lazarus at gmail d0t com
date:      Tue May 11 11:51:49 2010 -0400
description:
Add mimetypes to snp/wga datatypes in genetics.py
Fix edit_attributes to snp/wga composite files in tests

diffstat:

 lib/galaxy/datatypes/genetics.py |  19 ++++++++++++++++++-
 lib/galaxy/tools/__init__.py     |   2 +-
 test/functional/test_toolbox.py  |   6 ++++--
 tools/rgenetics/rgCaCo.xml       |   1 +
 tools/rgenetics/rgClean.xml      |   1 +
 tools/rgenetics/rgEigPCA.xml     |   1 +
 tools/rgenetics/rgGLM.xml        |   2 ++
 tools/rgenetics/rgGRR.xml        |   1 +
 tools/rgenetics/rgHaploView.xml  |   1 +
 tools/rgenetics/rgLDIndep.xml    |   1 +
 tools/rgenetics/rgPedSub.xml     |   1 +
 tools/rgenetics/rgQC.xml         |   1 +
 tools/rgenetics/rgTDT.xml        |   1 +
 13 files changed, 34 insertions(+), 4 deletions(-)

diffs (200 lines):

diff -r 39268be26944 -r 8470f5588775 lib/galaxy/datatypes/genetics.py

--- a/lib/galaxy/datatypes/genetics.py	Mon May 10 20:59:41 2010 -0400
+++ b/lib/galaxy/datatypes/genetics.py	Tue May 11 11:51:49 2010 -0400
@@ -173,6 +173,10 @@
                 return false
         return true
 
+    def get_mime(self):
+        """Returns the mime type of the datatype"""
+        return 'application/vnd.ms-excel'
+
 
 class rgTabList(Tabular):
     """ 
@@ -211,6 +215,10 @@
             out = "Can't create peek %s" % exc
         return out
 
+    def get_mime(self):
+        """Returns the mime type of the datatype"""
+        return 'text/html'
+
 
 class rgSampleList(rgTabList):
     """ 
@@ -262,7 +270,7 @@
     stored in extra files path
     """
    
-    MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", 
+    MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default='RgeneticsData',
     readonly=True, set_in_upload=True)
     
     composite_type = 'auto_primary_file'
@@ -302,6 +310,11 @@
         f.write('\n')
         f.close()
 
+    def get_mime(self):
+        """Returns the mime type of the datatype"""
+        return 'text/html'
+
+
     def set_meta( self, dataset, **kwd ):
 
         """
@@ -506,6 +519,10 @@
         cannot rename the datasets here - they come with the default unfortunately
         """
         return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>'
+
+    def get_mime(self):
+        """Returns the mime type of the datatype"""
+        return 'text/html'
     
     def get_phecols(self, phenolist=[], maxConc=20):
         """
diff -r 39268be26944 -r 8470f5588775 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py	Mon May 10 20:59:41 2010 -0400
+++ b/lib/galaxy/tools/__init__.py	Tue May 11 11:51:49 2010 -0400
@@ -541,7 +541,7 @@
                                 attrib['composite_data'].append( child )
                                 if composite_data_name is None:
                                     #generate a unique name; each test uses a fresh history
-                                    composite_data_name = '_COMPOSITE_RENAMED %i_' % ( composite_data_names_counter )
+                                    composite_data_name = '_COMPOSITE_RENAMED_%i_' % ( composite_data_names_counter )
                                     composite_data_names_counter += 1
                             elif child.tag == 'metadata':
                                 attrib['metadata'].append( child )
diff -r 39268be26944 -r 8470f5588775 test/functional/test_toolbox.py
--- a/test/functional/test_toolbox.py	Mon May 10 20:59:41 2010 -0400
+++ b/test/functional/test_toolbox.py	Tue May 11 11:51:49 2010 -0400
@@ -45,8 +45,10 @@
                     new_name = edit_att.get( 'value', None )
                     assert new_name, 'You must supply the new dataset name as the value tag of the edit_attributes tag'
                     hda_id = self.get_history_as_data_list()[-1].get( 'id' )
-                    self.edit_hda_attribute_info( hda_id, new_name = new_name )
-                    print "Renamed uploaded file to:", new_name
+                    try:
+                        self.edit_hda_attribute_info( hda_id = str(hda_id), new_name = new_name )
+                    except:
+                        print "### call to edit_hda failed for hda_id",hda_id,"new_name=",new_name
                 else:
                     raise Exception( 'edit_attributes type (%s) is unimplemented' % edit_att.get( 'type', None ) )
         # We need to handle the case where we've uploaded a valid compressed file since the upload
diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgCaCo.xml
--- a/tools/rgenetics/rgCaCo.xml	Mon May 10 20:59:41 2010 -0400
+++ b/tools/rgenetics/rgCaCo.xml	Tue May 11 11:51:49 2010 -0400
@@ -28,6 +28,7 @@
    <composite_data value='tinywga.bim' />
    <composite_data value='tinywga.bed' />
    <composite_data value='tinywga.fam' />
+   <edit_attributes type='name' value='tinywga' /> 
  </param>
  <param name='name' value='rgCaCotest1' />
  <output name='out_file1' file='rgCaCotest1_CaCo.xls' ftype='tabular' compare='diff' />
diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgClean.xml
--- a/tools/rgenetics/rgClean.xml	Mon May 10 20:59:41 2010 -0400
+++ b/tools/rgenetics/rgClean.xml	Tue May 11 11:51:49 2010 -0400
@@ -57,6 +57,7 @@
     <composite_data value='tinywga.bim' />
     <composite_data value='tinywga.bed' />
     <composite_data value='tinywga.fam' />
+    <edit_attributes type='name' value='tinywga' /> 
     </param>
     <param name='title' value='rgCleantest1' />
     <param name="geno" value="1" />
diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgEigPCA.xml
--- a/tools/rgenetics/rgEigPCA.xml	Mon May 10 20:59:41 2010 -0400
+++ b/tools/rgenetics/rgEigPCA.xml	Tue May 11 11:51:49 2010 -0400
@@ -40,6 +40,7 @@
    <composite_data value='tinywga.bim' />
    <composite_data value='tinywga.bed' />
    <composite_data value='tinywga.fam' />
+   <edit_attributes type='name' value='tinywga' /> 
    </param>
     <param name='title' value='rgEigPCAtest1' />
     <param name="k" value="4" />
diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgGLM.xml
--- a/tools/rgenetics/rgGLM.xml	Mon May 10 20:59:41 2010 -0400
+++ b/tools/rgenetics/rgGLM.xml	Tue May 11 11:51:49 2010 -0400
@@ -52,10 +52,12 @@
    <composite_data value='tinywga.bim' />
    <composite_data value='tinywga.bed' />
    <composite_data value='tinywga.fam' />
+   <edit_attributes type='name' value='tinywga' /> 
  </param>
  <param name='phef' value='tinywga' ftype='pphe' >
    <metadata name='base_name' value='tinywga' />
    <composite_data value='tinywga.pphe' />
+   <edit_attributes type='name' value='tinywga' /> 
  </param>
  <param name='title1' value='rgGLMtest1' />
  <param name='predvar' value='c1' />
diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgGRR.xml
--- a/tools/rgenetics/rgGRR.xml	Mon May 10 20:59:41 2010 -0400
+++ b/tools/rgenetics/rgGRR.xml	Tue May 11 11:51:49 2010 -0400
@@ -27,6 +27,7 @@
     <composite_data value='tinywga.bim' />
     <composite_data value='tinywga.bed' />       
     <composite_data value='tinywga.fam' />
+    <edit_attributes type='name' value='tinywga' /> 
     </param>
   <param name='title1' value='rgGRRtest1' />
   <param name='n' value='100' />
diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgHaploView.xml
--- a/tools/rgenetics/rgHaploView.xml	Mon May 10 20:59:41 2010 -0400
+++ b/tools/rgenetics/rgHaploView.xml	Tue May 11 11:51:49 2010 -0400
@@ -88,6 +88,7 @@
    <metadata name='base_name' value='tinywga' />
    <composite_data value='tinywga.ped' />
    <composite_data value='tinywga.map' />
+   <edit_attributes type='name' value='tinywga' /> 
   </param>
  <param name='ucsc_region' value='' />
  <param name='title' value='rgHaploViewtest1' />
diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgLDIndep.xml
--- a/tools/rgenetics/rgLDIndep.xml	Mon May 10 20:59:41 2010 -0400
+++ b/tools/rgenetics/rgLDIndep.xml	Tue May 11 11:51:49 2010 -0400
@@ -41,6 +41,7 @@
     <composite_data value='tinywga.bim' />
     <composite_data value='tinywga.bed' />
     <composite_data value='tinywga.fam' />
+    <edit_attributes type='name' value='tinywga' /> 
     </param>
     <param name='title1' value='rgLDIndeptest1' />
     <param name="mind" value="1" />
diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgPedSub.xml
--- a/tools/rgenetics/rgPedSub.xml	Mon May 10 20:59:41 2010 -0400
+++ b/tools/rgenetics/rgPedSub.xml	Tue May 11 11:51:49 2010 -0400
@@ -73,6 +73,7 @@
     <metadata name='base_name' value='tinywga' />
     <composite_data value='tinywga.ped' />
     <composite_data value='tinywga.map' />
+    <edit_attributes type='name' value='tinywga' /> 
     </param>
     <param name='title' value='rgPedSubtest1' />
     <param name="region" value="" />
diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgQC.xml
--- a/tools/rgenetics/rgQC.xml	Mon May 10 20:59:41 2010 -0400
+++ b/tools/rgenetics/rgQC.xml	Tue May 11 11:51:49 2010 -0400
@@ -25,6 +25,7 @@
     <composite_data value='tinywga.bim' />
     <composite_data value='tinywga.bed' />
     <composite_data value='tinywga.fam' />
+    <edit_attributes type='name' value='tinywga' /> 
     </param>
     <param name='out_prefix' value='rgQCtest1' />
     <output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='280'>
diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgTDT.xml
--- a/tools/rgenetics/rgTDT.xml	Mon May 10 20:59:41 2010 -0400
+++ b/tools/rgenetics/rgTDT.xml	Tue May 11 11:51:49 2010 -0400
@@ -27,6 +27,7 @@
    <composite_data value='tinywga.bim' />
    <composite_data value='tinywga.bed' />
    <composite_data value='tinywga.fam' />
+   <edit_attributes type='name' value='tinywga' /> 
  </param>
  <param name='title1' value='rgTDTtest1' />
  <output name='out_file1' file='rgTDTtest1_TDT.xls' ftype='tabular' compare="diff"/>

    

Nate Coraor

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