Correctly use the initialized test_environment dict when running the tool shed's install and test framework and additional code cleanup for the framework.

lib/tool_shed/scripts/check_repositories_for_functional_tests.py

@@ -4,7 +4,7 @@ import os
 import sys
 
 new_path = [ os.path.join( os.getcwd(), "lib" ),
-            os.path.join( os.getcwd(), "test" ) ]
+             os.path.join( os.getcwd(), "test" ) ]
 new_path.extend( sys.path[ 1: ] )
 sys.path = new_path
 
@@ -21,8 +21,8 @@ import shutil
 import tempfile
 import time
 
-from base.util import get_database_version
-from base.util import get_repository_current_revision
+from install_and_test_tool_shed_repositories.base.util import get_database_version
+from install_and_test_tool_shed_repositories.base.util import get_repository_current_revision
 from galaxy.model.orm import and_
 from galaxy.model.orm import not_
 from galaxy.model.orm import select

lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py

@@ -25,9 +25,8 @@ from mercurial import __version__
 import galaxy.webapps.tool_shed.config as tool_shed_config
 import galaxy.webapps.tool_shed.model.mapping
 
-from base.util import get_database_version
-from base.util import get_repository_current_revision
-from base.util import get_test_environment
+from install_and_test_tool_shed_repositories.base.util import get_database_version
+from install_and_test_tool_shed_repositories.base.util import get_repository_current_revision
 from galaxy.model.orm import and_
 from galaxy.model.orm import not_
 from galaxy.model.orm import select

scripts/functional_tests.py

@@ -13,7 +13,7 @@ new_path = [ os.path.join( cwd, "lib" ), os.path.join( cwd, "test" ) ]
 new_path.extend( sys.path[1:] )
 sys.path = new_path
 
-from base.util import parse_tool_panel_config
+from base.tool_shed_util import parse_tool_panel_config
 
 from galaxy import eggs
 

test/base/tool_shed_util.py

@@ -1,6 +1,5 @@
 import logging
 import os
-import platform
 import sys
 
 cwd = os.getcwd()
@@ -13,32 +12,9 @@ if new_path not in sys.path:
     sys.path = new_path
 
 from galaxy.util import parse_xml
-from galaxy import eggs
-
-eggs.require( 'mercurial' )
-
-from mercurial import hg
-from mercurial import ui
 
 log = logging.getLogger(__name__)
 
-def get_database_version( app ):
-    '''
-    This method returns the value of the version column from the migrate_version table, using the provided app's SQLAlchemy session to determine
-    which table to get that from. This way, it's provided with an instance of a Galaxy UniverseApplication, it will return the Galaxy instance's
-    database migration version. If a tool shed UniverseApplication is provided, it returns the tool shed's database migration version.
-    '''
-    sa_session = app.model.context.current
-    result = sa_session.execute( 'SELECT version FROM migrate_version LIMIT 1' )
-    # This query will return the following structure:
-    # row = [ column 0, column 1, ..., column n ]
-    # rows = [ row 0, row 1, ..., row n ]
-    # The first column in the first row is the version number we want.
-    for row in result:
-        version = row[ 0 ]
-        break
-    return version
-
 def get_installed_repository_info( elem, last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision, tool_path ):
     """
     Return the GALAXY_TEST_FILE_DIR, the containing repository name and the change set revision for the tool elem.
@@ -55,39 +31,13 @@ def get_installed_repository_info( elem, last_galaxy_test_file_dir, last_tested_
         # Locate the test-data directory.
         installed_tool_path = os.path.join( installed_tool_path_items[ 0 ], 'repos', repository_owner, repository_name, changeset_revision )
         for root, dirs, files in os.walk( os.path.join(tool_path, installed_tool_path )):
-            if '.hg' in dirs:
+            if '.' in dirs:
                 dirs.remove( '.hg' )
             if 'test-data' in dirs:
                 return os.path.join( root, 'test-data' ), repository_name, changeset_revision
         return None, repository_name, changeset_revision
     return last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision
 
-def get_repository_current_revision( repo_path ):
-    '''
-    This method uses the python mercurial API to get the current working directory's mercurial changeset hash. Note that if the author of mercurial
-    changes the API, this method will have to be updated or replaced.
-    '''
-    # Initialize a mercurial repo object from the provided path.
-    repo = hg.repository( ui.ui(), repo_path )
-    # Get the working directory's change context.
-    ctx = repo[ None ]
-    # Extract the changeset hash of the first parent of that change context (the most recent changeset to which the working directory was updated).
-    changectx = ctx.parents()[ 0 ]
-    # Also get the numeric revision, so we can return the customary id:hash changeset identifiers.
-    ctx_rev = changectx.rev()
-    hg_id = '%d:%s' % ( ctx_rev, str( changectx ) )
-    return hg_id
-
-def get_test_environment( current_environment=None ):
-    if current_environment is None:
-        current_environment = {}
-    rval = current_environment
-    rval[ 'python_version' ] = platform.python_version()
-    rval[ 'architecture' ] = platform.machine()
-    os, hostname, os_version, uname, arch, processor = platform.uname()
-    rval[ 'system' ] = '%s %s' % ( os, os_version )
-    return rval
-
 def parse_tool_panel_config( config, shed_tools_dict ):
     """
     Parse a shed-related tool panel config to generate the shed_tools_dict. This only happens when testing tools installed from the tool shed.

test/install_and_test_tool_shed_repositories/base/util.py

@@ -0,0 +1,54 @@
+import logging
+import os
+import sys
+
+cwd = os.getcwd()
+if cwd not in sys.path:
+    sys.path.append( cwd )
+
+new_path = [ os.path.join( cwd, "lib" ) ]
+if new_path not in sys.path:
+    new_path.extend( sys.path )
+    sys.path = new_path
+
+from galaxy import eggs
+
+eggs.require( 'mercurial' )
+
+from mercurial import hg
+from mercurial import ui
+
+log = logging.getLogger(__name__)
+
+def get_database_version( app ):
+    '''
+    This method returns the value of the version column from the migrate_version table, using the provided app's SQLAlchemy session to determine
+    which table to get that from. This way, it's provided with an instance of a Galaxy UniverseApplication, it will return the Galaxy instance's
+    database migration version. If a tool shed UniverseApplication is provided, it returns the tool shed's database migration version.
+    '''
+    sa_session = app.model.context.current
+    result = sa_session.execute( 'SELECT version FROM migrate_version LIMIT 1' )
+    # This query will return the following structure:
+    # row = [ column 0, column 1, ..., column n ]
+    # rows = [ row 0, row 1, ..., row n ]
+    # The first column in the first row is the version number we want.
+    for row in result:
+        version = row[ 0 ]
+        break
+    return version
+
+def get_repository_current_revision( repo_path ):
+    '''
+    This method uses the python mercurial API to get the current working directory's mercurial changeset hash. Note that if the author of mercurial
+    changes the API, this method will have to be updated or replaced.
+    '''
+    # Initialize a mercurial repo object from the provided path.
+    repo = hg.repository( ui.ui(), repo_path )
+    # Get the working directory's change context.
+    ctx = repo[ None ]
+    # Extract the changeset hash of the first parent of that change context (the most recent changeset to which the working directory was updated).
+    changectx = ctx.parents()[ 0 ]
+    # Also get the numeric revision, so we can return the customary id:hash changeset identifiers.
+    ctx_rev = changectx.rev()
+    hg_id = '%d:%s' % ( ctx_rev, str( changectx ) )
+    return hg_id

test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py

@@ -1,6 +1,8 @@
-import new, logging
+import logging
+import new
 import install_and_test_tool_shed_repositories.base.test_db_util as test_db_util
 from install_and_test_tool_shed_repositories.base.twilltestcase import InstallTestRepository
+
 log = logging.getLogger(__name__)
 
 
@@ -80,4 +82,3 @@ def generate_deactivate_or_uninstall_method( repository_dict=None, deactivate=Fa
     # from baseclasses (which should be a tuple of classes) and with namespace dict.
     new_class_obj = new.classobj( str( name ), baseclasses, namespace )
     G[ name ] = new_class_obj
-    

test/install_and_test_tool_shed_repositories/functional_tests.py

@@ -10,9 +10,9 @@ import sys
 cwd = os.getcwd()
 sys.path.append( cwd )
 new_path = [ os.path.join( cwd, "scripts" ),
-            os.path.join( cwd, "lib" ),
-            os.path.join( cwd, 'test' ),
-            os.path.join( cwd, 'scripts', 'api' ) ]
+             os.path.join( cwd, "lib" ),
+             os.path.join( cwd, 'test' ),
+             os.path.join( cwd, 'scripts', 'api' ) ]
 new_path.extend( sys.path )
 sys.path = new_path
 
@@ -30,6 +30,7 @@ import install_and_test_tool_shed_repositories.base.test_db_util as test_db_util
 import install_and_test_tool_shed_repositories.functional.test_install_repositories as test_install_repositories
 import logging
 import nose
+import platform
 import random
 import re
 import shutil
@@ -41,10 +42,9 @@ import threading
 import tool_shed.util.shed_util_common as suc
 import urllib
 
-from base.util import get_database_version
-from base.util import get_repository_current_revision
-from base.util import get_test_environment
-from base.util import parse_tool_panel_config
+from base.tool_shed_util import parse_tool_panel_config
+from install_and_test_tool_shed_repositories.base.util import get_database_version
+from install_and_test_tool_shed_repositories.base.util import get_repository_current_revision
 from common import update
 from datetime import datetime
 from galaxy.app import UniverseApplication
@@ -614,31 +614,38 @@ def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool
         owner = str( repository_dict[ 'owner' ] )
         changeset_revision = str( repository_dict[ 'changeset_revision' ] )
         log.debug( "Processing revision %s of repository %s owned by %s..." % ( changeset_revision, name, owner ) )
-        # Populate the tool_test_results_dict.
+        # Retrieve the stored list of tool_test_results_dicts.
         tool_test_results_dicts, error_message = get_tool_test_results_dicts( galaxy_tool_shed_url, encoded_repository_metadata_id )
         if error_message:
             log.debug( error_message )
         else:
-            # The preparation script ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered
-            # information in the 'test_environment' and possibly the 'missing_test_components' entries of the first
-            # tool_test_results_dict in the list of tool_test_results_dicts. We need to be careful to not lose this
-            # information.
-            try:
-                tool_test_results_dict = tool_test_results_dicts.pop( 0 )
-            except Exception, e:
-                log.exception( "Invalid list of tool_test_results_dicts %s: %s" % ( str( tool_test_results_dicts ), str( e ) ) )
-                continue
+            if tool_test_results_dicts:
+                # Inspect the tool_test_results_dict for the last test run to make sure it contains only a test_environment
+                # entry.  If it contains more entries, then the script ~/tool_shed/api/check_repositories_for_functional_tests.py
+                # was not executed in preparation for this script's execution, so we'll just create an empty dictionary.
+                tool_test_results_dict = tool_test_results_dicts[ 0 ]
+                if len( tool_test_results_dict ) <= 1:
+                    # We can re-use the mostly empty tool_test_results_dict for this run because it is either empty or it contains only
+                    # a test_environment entry.  If we use it we need to temporarily eliminate it from the list of tool_test_results_dicts
+                    # since it will be re-inserted later.
+                    tool_test_results_dict = tool_test_results_dicts.pop( 0 )
+                else:
+                    # The latest tool_test_results_dict has been populated with the results of a test run, so it cannot be used.
+                    tool_test_results_dict = {}
+            else:
+                # Create a new dictionary for this test test run, 
+                tool_test_results_dict = {}
             # See if this repository should be skipped for any reason.
-            this_repository_is_in_the_exclude_lost = False
+            this_repository_is_in_the_exclude_list = False
             skip_reason = None
             for exclude_dict in exclude_list:
                 reason = exclude_dict[ 'reason' ]
                 exclude_repositories = exclude_dict[ 'repositories' ]
                 if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories:
-                    this_repository_is_in_the_exclude_lost = True
+                    this_repository_is_in_the_exclude_list = True
                     skip_reason = reason
                     break
-            if this_repository_is_in_the_exclude_lost:
+            if this_repository_is_in_the_exclude_list:
                 tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason )
                 params = dict( tools_functionally_correct=False,
                                do_not_test=False )
@@ -647,19 +654,32 @@ def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool
                 log.debug( "Not testing revision %s of repository %s owned by %s because it is in the exclude list for this test run." % \
                            ( changeset_revision, name, owner ) )
             else:
-                test_environment_dict = tool_test_results_dict.get( 'test_environment', None )
-                test_environment_dict = get_test_environment( test_environment_dict )
+                test_environment_dict = tool_test_results_dict.get( 'test_environment', {} )
+                if len( test_environment_dict ) == 0:
+                    # Set information about the tool shed to nothing since we cannot currently determine it from here.
+                    # We could eventually add an API method...
+                    test_environment_dict = dict( tool_shed_database_version='',
+                                                  tool_shed_mercurial_version='',
+                                                  tool_shed_revision='' )
                 # Add the current time as the approximate time that this test run occurs.  A similar value will also be
                 # set to the repository_metadata.time_last_tested column, but we also store it here because the Tool Shed
                 # may be configured to store multiple test run results, so each must be associated with a time stamp.
                 now = time.strftime( "%Y-%m-%d %H:%M:%S" )
+                # Add information about the current platform.
                 test_environment_dict[ 'time_tested' ] = now
+                test_environment_dict[ 'python_version' ] = platform.python_version()
+                test_environment_dict[ 'architecture' ] = platform.machine()
+                operating_system, hostname, operating_system_version, uname, arch, processor = platform.uname()
+                test_environment_dict[ 'system' ] = '%s %s' % ( operating_system, operating_system_version )
+                # Add information about the current Galaxy environment.
                 test_environment_dict[ 'galaxy_database_version' ] = get_database_version( app )
                 test_environment_dict[ 'galaxy_revision' ] = get_repository_current_revision( os.getcwd() )
+                # Initialize and populate the tool_test_results_dict.
                 tool_test_results_dict[ 'test_environment' ] = test_environment_dict
                 tool_test_results_dict[ 'passed_tests' ] = []
                 tool_test_results_dict[ 'failed_tests' ] = []
                 tool_test_results_dict[ 'installation_errors' ] = dict( current_repository=[], repository_dependencies=[], tool_dependencies=[] )
+                # Proceed with installing repositories and testing contained tools.
                 repository, error_message = install_repository( app, repository_dict )
                 if error_message:
                     tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message