From 8c5787f21dc188dd271e140c99ce9338df1d151e Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 20 May 2008 19:54:12 +0000
Subject: [PATCH] Fix Errors reported by Cathy regarding the GMAJ tool.

With these notes:

User's can now specify the warnings that they which to report ('nowarns').  There are likely more options but they are unknown.

Using Firefox 1.5.0.12 on Ubuntu with no extensions/addons installed gives me no issues with loading the applet while Javascript is enabled or disabled (works for me).
---
 lib/galaxy/tools/actions/__init__.py |  4 +--
 lib/galaxy/tools/parameters/basic.py | 18 +++++++---
 lib/galaxy/web/controllers/root.py   | 15 ++++----
 tools/visualization/GMAJ.xml         | 51 ++++++++++++++++++----------
 4 files changed, 55 insertions(+), 33 deletions(-)

diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 3617c9e1246..3c90fd320f1 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -32,7 +32,7 @@ class DefaultToolAction( object ):
                         if target_ext in data.get_converter_types():
                             assoc = data.get_associated_files_by_type( "CONVERTED_%s" % target_ext )
                             if assoc: data = assoc[0].dataset
-                            else:
+                            elif not tool.config_files:
                                 #run converter here
                                 assoc = trans.app.model.DatasetAssociatedFile( parent_id = data.id, file_type = "CONVERTED_%s" % target_ext, metadata_safe = False )
                                 new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0]
@@ -40,7 +40,7 @@ class DefaultToolAction( object ):
                                 new_data.name = data.name
                                 assoc.dataset_id = new_data.id
                                 data = new_data
-                            break
+                                break
                 return data
             if isinstance( input, DataToolParameter ):
                 if isinstance( value, list ):
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index beb459958db..79516257280 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1049,6 +1049,8 @@ class DataToolParameter( ToolParameter ):
                                 assoc = data.get_associated_files_by_type( "CONVERTED_%s" % target_ext )
                                 if assoc:
                                     data = assoc[0].dataset
+                                elif self.tool.config_files:
+                                    continue #dataset conversion and configuration files currently only work with datasets that have already been converted
                                 selected = ( value and ( data in value ) )
                                 field.add_option( "%s: (as %s) %s" % ( hid, target_ext, data.name[:30] ), data.id, selected )
                                 break #we only report the first valid converter, assume self.extensions is a priority list
@@ -1065,7 +1067,10 @@ class DataToolParameter( ToolParameter ):
                 else:
                     field.options[-1] = a, b, True
         if self.optional:
-            field.add_option( "Selection is Optional", 'None', True )
+            if not value:
+                field.add_option( "Selection is Optional", 'None', True )
+            else:
+                field.add_option( "Selection is Optional", 'None', False )
         return field
 
     def get_initial_value( self, trans, context ):
@@ -1079,14 +1084,21 @@ class DataToolParameter( ToolParameter ):
         assert trans is not None, "DataToolParameter requires a trans"
         history = trans.history
         assert history is not None, "DataToolParameter requires a history"
+        if self.optional:
+            return None
         history = trans.history
         most_recent_dataset = [None]
         filter_key = filter_value = None
         if self.options:
             filter_key, filter_value = self.options.get_options( trans, context )
         def dataset_collector( datasets ):
+            def is_convertable( dataset ):
+                for target_ext in self.extensions:
+                    if target_ext in data.get_converter_types():
+                        return True
+                return False
             for i, data in enumerate( datasets ):
-                if isinstance( data.datatype, self.formats) and not data.deleted and data.state not in [data.states.ERROR]:
+                if data.visible and not data.deleted and data.state not in [data.states.ERROR] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ):
                     if self.options and filter_key == 'build' and data.get_dbkey() != filter_value:
                         continue
                     most_recent_dataset[0] = data
@@ -1096,8 +1108,6 @@ class DataToolParameter( ToolParameter ):
         most_recent_dataset = most_recent_dataset.pop()
         if most_recent_dataset is not None:
             return most_recent_dataset
-        elif self.optional:
-            return None
         else:
             return ''
 
diff --git a/lib/galaxy/web/controllers/root.py b/lib/galaxy/web/controllers/root.py
index 1ed2742308d..f32b1563db2 100644
--- a/lib/galaxy/web/controllers/root.py
+++ b/lib/galaxy/web/controllers/root.py
@@ -530,20 +530,17 @@ class RootController( BaseController ):
         """Adds a POSTed file to a History"""
         try:
             history = trans.app.model.History.get( history_id )
-            data = trans.app.model.Dataset()
-            data.name = name
-            data.extension = ext
-            data.dbkey = dbkey
-            data.info = info
+            data = trans.app.model.Dataset( name = name, info = info, extension = ext, dbkey = dbkey )
             data.flush()
-            data_file = open(data.file_name, "w")
-            file_data.file.seek(0)
-            data_file.writelines(file_data.file.readlines())
+            data_file = open( data.file_name, "wb" )
+            file_data.file.seek( 0 )
+            data_file.write( file_data.file.read() )
             data_file.close()
             data.state = data.states.OK
             data.init_meta()
+            data.set_meta()
             data.flush()
-            history.add_dataset( data)
+            history.add_dataset( data )
             history.flush()
             data.set_peek()
             data.set_size()
diff --git a/tools/visualization/GMAJ.xml b/tools/visualization/GMAJ.xml
index 09510fbb38e..293aa853b3c 100644
--- a/tools/visualization/GMAJ.xml
+++ b/tools/visualization/GMAJ.xml
@@ -3,6 +3,18 @@
   <command interpreter="python">GMAJ.py $out_file1 $maf_input $gmaj_file $filenames_file</command>
   <inputs>
       <param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/>
+      <param name="nowarn" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true" label="Choose Warnings to suppress" separator=" ">
+        <options>    
+          <option name="All" value="all" selected="True">
+            <option name="seqname_mismatch" value="seqname_mismatch"/>
+            <option name="bed_blocks" value="bed_blocks"/>
+            <option name="bed_thick" value="bed_thick"/>
+            <option name="bed_name" value="bed_name"/>
+            <option name="repeat_type_missing" value="repeat_type_missing"/>
+            <option name="bed_name_prefix" value="bed_name_prefix"/>
+          </option>
+        </options>
+      </param>
       <repeat name="annotations" title="Annotations">
         <param name="species" type="select" label="Species of Annotation" multiple="False">
           <options>
@@ -10,11 +22,11 @@
           </options>
         </param>
         <param name="chromosome" label="Chromosome" value="" type="text"/>
-        <param name="exons_file" type="data" format="bed" label="Exons File" optional="True"/>
-        <param name="highlights_file" type="data" format="bed" label="Highlights File" optional="True"/>
-        <param name="underlays_file" type="data" format="bed" label="Underlays File" optional="True"/>
-        <param name="repeats_file" type="data" format="bed" label="Repeats File" optional="True"/>
-        <param name="links_file" type="data" format="bed" label="Links File" optional="True"/>
+        <param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/>
+        <param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/>
+        <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/>
+        <param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/>
+        <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/>
         <param name="offset" label="Offset" value="0" type="integer"/>
       </repeat>
   </inputs>
@@ -24,29 +36,32 @@
 title = "Galaxy: $maf_input.name"
 alignfile = input.maf
 refseq = any
-tabext = .bed
+tabext = .bed .gff .gtf
+#if $nowarn.value:
+nowarn = $nowarn
+#end if
 
 #for $seq_count, $annotation in $enumerate( $annotations ):
 seq ${seq_count}:
-#if $annotation['chromosome']:
+#if $annotation['chromosome'].value:
 seqname = $annotation['species'].$annotation['chromosome']
 #else:
 seqname = $annotation['species']
 #end if
 #if $annotation['exons_file'].value:
-exons = ${seq_count}.exons.bed
+exons = ${seq_count}.exons.${annotation['exons_file'].extension}
 #end if
 #if $annotation['repeats_file'].value:
-exons = ${seq_count}.repeats.bed
+repeats = ${seq_count}.repeats.${annotation['repeats_file'].extension}
 #end if
 #if $annotation['links_file'].value:
-exons = ${seq_count}.links.bed
+links = ${seq_count}.links.${annotation['links_file'].extension}
 #end if
 #if $annotation['underlays_file'].value:
-exons = ${seq_count}.underlays.bed
+underlays = ${seq_count}.underlays.${annotation['underlays_file'].extension}
 #end if
 #if $annotation['highlights_file'].value:
-exons = ${seq_count}.highlights.bed
+highlights = ${seq_count}.highlights.${annotation['highlights_file'].extension}
 #end if
 offset = $annotation['offset']
 
@@ -55,19 +70,19 @@ offset = $annotation['offset']
     <configfile name="filenames_file">
 #for $seq_count, $annotation in $enumerate( $annotations ):
 #if $annotation['exons_file'].value:
-$annotation['exons_file'] = ${seq_count}.exons.bed
+$annotation['exons_file'] = ${seq_count}.exons.${annotation['exons_file'].extension}
 #end if
 #if $annotation['repeats_file'].value:
-$annotation['repeats_file'] = ${seq_count}.repeats.bed
+$annotation['repeats_file'] = ${seq_count}.repeats.${annotation['repeats_file'].extension}
 #end if
 #if $annotation['links_file'].value:
-$annotation['links_file'] = ${seq_count}.links.bed
+$annotation['links_file'] = ${seq_count}.links.${annotation['links_file'].extension}
 #end if
 #if $annotation['underlays_file'].value:
-$annotation['underlays_file'] = ${seq_count}.underlays.bed
+$annotation['underlays_file'] = ${seq_count}.underlays.${annotation['underlays_file'].extension}
 #end if
 #if $annotation['highlights_file'].value:
-$annotation['highlights_file'] = ${seq_count}.highlights.bed
+$annotation['highlights_file'] = ${seq_count}.highlights.${annotation['highlights_file'].extension}
 #end if
 #end for
 </configfile>
@@ -76,7 +91,7 @@ $annotation['highlights_file'] = ${seq_count}.highlights.bed
     <data name="out_file1" format="gmaj.zip"/>
   </outputs>
 <help>
-You can use this tool to view a set of MAF alignments.  You may also include optional additional information about the primary organism in the BED format.
+You can use this tool to view a set of MAF alignments.  You may also include optional annotation data for one or more of the organisms.
 
 For detailed information on GMAJ, click here_.