Remove hardcoded path to builds.txt from util, fix unit test that relies on this.

lib/galaxy/tools/parameters/basic.py

@@ -1002,7 +1002,7 @@ class GenomeBuildParameter( SelectToolParameter ):
 
     >>> # Create a mock transaction with 'hg17' as the current build
     >>> from galaxy.util.bunch import Bunch
-    >>> trans = Bunch( history=Bunch( genome_build='hg17' ), db_builds=util.dbnames )
+    >>> trans = Bunch( history=Bunch( genome_build='hg17' ), db_builds=util.read_dbnames( None ) )
 
     >>> p = GenomeBuildParameter( None, XML(
     ... '''
@@ -1071,7 +1071,7 @@ class GenomeBuildParameter( SelectToolParameter ):
     def _get_dbkey_names( self, trans=None ):
         if not self.tool:
             # Hack for unit tests, since we have no tool
-            return util.dbnames
+            return util.read_dbnames( None )
         return self.tool.app.genome_builds.get_genome_build_names( trans=trans )
 
 

lib/galaxy/util/__init__.py

@@ -796,6 +796,9 @@ def read_dbnames(filename):
         ucsc_builds = {}
         man_builds = []  # assume these are integers
         name_to_db_base = {}
+        if filename is None:
+            # Should only be happening with the galaxy.tools.parameters.basic:GenomeBuildParameter docstring unit test
+            filename = os.path.join( 'tool-data', 'shared', 'ucsc', 'builds.txt.sample' )
         for line in open(filename):
             try:
                 if line[0:1] == "#":
@@ -1126,8 +1129,6 @@ def safe_str_cmp(a, b):
 
 galaxy_root_path = os.path.join(__path__[0], "..", "..", "..")
 
-# The dbnames list is used in edit attributes and the upload tool
-dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "builds.txt" ) )
 ucsc_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "ucsc_build_sites.txt" ) )
 gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "gbrowse", "gbrowse_build_sites.txt" ) )
 

lib/galaxy/util/dbkeys.py

@@ -2,7 +2,7 @@
 Functionality for dealing with dbkeys.
 """
 #dbkeys read from disk using builds.txt
-from galaxy.util import dbnames
+from galaxy.util import read_dbnames
 from galaxy.util.json import from_json_string
 import os.path
 
@@ -17,7 +17,7 @@ class GenomeBuilds( object ):
         self._static_chrom_info_path = app.config.len_file_path
         # A dbkey can be listed multiple times, but with different names, so we can't use dictionaries for lookups
         if load_old_style:
-            self._static_dbkeys = list( dbnames )
+            self._static_dbkeys = list( read_dbnames( app.config.builds_file_path ) )
         else:
             self._static_dbkeys = []
 

test/unit/tools_support.py

@@ -99,6 +99,7 @@ class MockApp( object ):
             root=os.path.join(test_directory, "galaxy"),
             admin_users="mary@example.com",
             len_file_path=os.path.join( 'tool-data', 'shared', 'ucsc', 'chrom' ),
+            builds_file_path=os.path.join( 'tool-data', 'shared', 'ucsc', 'builds.txt.sample' ),
         )
 
         # Setup some attributes for downstream extension by specific tests.

universe_wsgi.ini.sample

@@ -180,6 +180,9 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 #   https://wiki.galaxyproject.org/Admin/DataIntegration
 #tool_data_path = tool-data
 
+# File containing old-style genome builds
+#builds_file_path = tool-data/shared/ucsc/builds.txt
+
 # Directory where chrom len files are kept, currently mainly used by trackster
 #len_file_path = tool-data/shared/ucsc/chrom