From bb7c69f247247edbefb3b6f4372da52bcee389cb Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sun, 3 Jun 2012 12:19:30 -0400
Subject: [PATCH] More support for genomes as first-class objects: (a) add
 genomes API; (b) fix bugs in providing genome data.

---
 lib/galaxy/visualization/genomes.py  |  7 +++++--
 lib/galaxy/web/api/genomes.py        | 25 +++++++++++++++++++++++++
 lib/galaxy/web/buildapp.py           |  1 +
 lib/galaxy/web/controllers/tracks.py |  6 +++---
 4 files changed, 34 insertions(+), 5 deletions(-)
 create mode 100644 lib/galaxy/web/api/genomes.py

diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index 37ba53b44ce..1bf642d8506 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -107,6 +107,8 @@ class Genomes( object ):
         #
         # Get len file.
         #
+        
+        # Look first in user's custom builds.
         len_file = None
         len_ds = None
         user_keys = {}
@@ -121,10 +123,11 @@ class Genomes( object ):
                 elif 'len' in dbkey_attributes:
                     len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[ dbkey ][ 'len' ] ).file_name
 
+        # Look in system builds.
         if not len_file:
             len_ds = trans.db_dataset_for( dbkey )
             if not len_ds:
-                len_file = os.path.join( trans.app.config.len_file_path, "%s.len" % dbkey )
+                len_file = self.genomes[ dbkey ].len_file
             else:
                 len_file = len_ds.file_name
             
@@ -203,7 +206,7 @@ class Genomes( object ):
         dbkey_owner is needed to determine if there is reference data.
         """
         # Look for key in built-in builds.
-        if dbkey in self.available_genomes:
+        if dbkey in self.genomes and self.genomes[ dbkey ].twobit_file:
             # There is built-in reference data.
             return True
 
diff --git a/lib/galaxy/web/api/genomes.py b/lib/galaxy/web/api/genomes.py
new file mode 100644
index 00000000000..480e281b3f3
--- /dev/null
+++ b/lib/galaxy/web/api/genomes.py
@@ -0,0 +1,25 @@
+from galaxy import config, tools, web, util
+from galaxy.web.base.controller import BaseController, BaseAPIController
+from galaxy.util.bunch import Bunch
+
+class GenomesController( BaseAPIController ):
+    """
+    RESTful controller for interactions with genome data.
+    """
+    
+    @web.expose_api
+    def index( self, trans, **kwds ):
+        """
+        GET /api/genomes: returns a list of installed genomes
+        """        
+        
+        return []
+
+    @web.json
+    def show( self, trans, id, num=None, chrom=None, low=None ):
+        """
+        GET /api/genomes/{id}
+        
+        Returns information about build <id>
+        """
+        return self.app.genomes.chroms( trans, dbkey=id, num=num, chrom=chrom, low=low )
\ No newline at end of file
diff --git a/lib/galaxy/web/buildapp.py b/lib/galaxy/web/buildapp.py
index e3138dc542e..c032349d219 100644
--- a/lib/galaxy/web/buildapp.py
+++ b/lib/galaxy/web/buildapp.py
@@ -132,6 +132,7 @@ def app_factory( global_conf, **kwargs ):
     webapp.api_mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' )
     webapp.api_mapper.resource( 'tool', 'tools', path_prefix='/api' )
     webapp.api_mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' )
+    webapp.api_mapper.resource( 'genome', 'genomes', path_prefix='/api' )
     webapp.api_mapper.resource( 'visualization', 'visualizations', path_prefix='/api' )
     webapp.api_mapper.resource( 'workflow', 'workflows', path_prefix='/api' )
     webapp.api_mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' )
diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index bd3a8680a84..e96ca4047fd 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -268,11 +268,11 @@ class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryMix
 
     @web.json
     def chroms( self, trans, dbkey=None, num=None, chrom=None, low=None ):
-        return self.genomes.chroms( trans, dbkey=dbkey, num=num, chrom=chrom, low=low )
+        return self.app.genomes.chroms( trans, dbkey=dbkey, num=num, chrom=chrom, low=low )
         
     @web.json
     def reference( self, trans, dbkey, chrom, low, high, **kwargs ):
-        return self.genomes.reference( trans, dbkey, chrom, low, high, **kwargs )
+        return self.app.genomes.reference( trans, dbkey, chrom, low, high, **kwargs )
         
     @web.json
     def raw_data( self, trans, dataset_id, chrom, low, high, **kwargs ):
@@ -771,7 +771,7 @@ class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryMix
 
         # Get genome info.
         dbkey = dataset.dbkey
-        chroms_info = self.genomes.chroms( trans, dbkey=dbkey )
+        chroms_info = self.app.genomes.chroms( trans, dbkey=dbkey )
         genome = { 'dbkey': dbkey, 'chroms_info': chroms_info }
 
         # Get summary tree data for dataset.