[galaxy-commits] commit/galaxy-central: inithello: Tool shed functional tests for installation order with complex repository dependencies. Modified tests 0100 and 1100 to be less ambiguous regarding which repository contains what.

22 Apr 2013

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/1037ab5b4f76/
Changeset:   1037ab5b4f76
User:        inithello
Date:        2013-04-22 18:53:43
Summary:     Tool shed functional tests for installation order with complex repository dependencies. Modified tests 0100 and 1100 to be less ambiguous regarding which repository contains what.
Affected #:  8 files

diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/base/twilltestcase.py

--- a/test/tool_shed/base/twilltestcase.py
+++ b/test/tool_shed/base/twilltestcase.py
@@ -800,8 +800,12 @@
         self.check_for_strings( strings_displayed, strings_not_displayed )
         # This section is tricky, due to the way twill handles form submission. The tool dependency checkbox needs to 
         # be hacked in through tc.browser, putting the form field in kwd doesn't work.
+        form = tc.browser.get_form( 'select_tool_panel_section' )
+        submit_button = 'select_tool_panel_section_button'
+        if form is None:
+            form = tc.browser.get_form( 'select_shed_tool_panel_config' )
+            submit_button = 'select_shed_tool_panel_config_button'
         if 'install_tool_dependencies' in self.last_page():
-            form = tc.browser.get_form( 'select_tool_panel_section' )
             checkbox = form.find_control( id="install_tool_dependencies" )
             checkbox.disabled = False
             if install_tool_dependencies:
@@ -816,14 +820,10 @@
             kwd[ 'shed_tool_conf' ] = self.shed_tool_conf
         if new_tool_panel_section:
             kwd[ 'new_tool_panel_section' ] =  new_tool_panel_section
-        if includes_tools_for_display_in_tool_panel:
-            self.submit_form( 1, 'select_tool_panel_section_button', **kwd )
-            self.check_for_strings( post_submit_strings_displayed, strings_not_displayed )
-        else:
-            self.check_for_strings( strings_displayed=[ 'Choose the configuration file whose tool_path setting will be used for installing repositories' ] )
-            args = dict( shed_tool_conf=self.shed_tool_conf )
-            self.submit_form( 1, 'select_shed_tool_panel_config_button', **args )
-            self.check_for_strings( post_submit_strings_displayed, strings_not_displayed )
+        if not includes_tools_for_display_in_tool_panel:
+            self.check_for_strings( strings_displayed=[ 'Choose the configuration file' ] )
+        self.submit_form( 1, submit_button, **kwd )
+        self.check_for_strings( post_submit_strings_displayed, strings_not_displayed )
         repository_ids = self.initiate_installation_process( new_tool_panel_section=new_tool_panel_section )
         self.wait_for_repository_installation( repository_ids )
         

diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/functional/test_0100_complex_repository_dependencies.py
--- a/test/tool_shed/functional/test_0100_complex_repository_dependencies.py
+++ b/test/tool_shed/functional/test_0100_complex_repository_dependencies.py
@@ -6,11 +6,11 @@
 
 bwa_base_repository_name = 'bwa_base_repository_0100'
 bwa_base_repository_description = "BWA Base"
-bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at bwa_tool_repository_0100"
+bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at package_bwa_0_5_9_0100"
 
-bwa_tool_repository_name = 'bwa_tool_repository_0100'
-bwa_tool_repository_description = "BWA Tool"
-bwa_tool_repository_long_description = "BWA repository with a package tool dependency defined for BWA 0.5.9."
+bwa_package_repository_name = 'package_bwa_0_5_9_0100'
+bwa_package_repository_description = "BWA Tool"
+bwa_package_repository_long_description = "BWA repository with a package tool dependency defined for BWA 0.5.9."
 
 category_name = 'Test 0100 Complex Repository Dependencies'
 category_description = 'Test 0100 Complex Repository Dependencies'
@@ -32,15 +32,15 @@
         assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
         admin_user_private_role = test_db_util.get_private_role( admin_user )
 
-    def test_0005_create_bwa_tool_repository( self ):
-        '''Create and populate bwa_tool_repository_0100.'''
+    def test_0005_create_bwa_package_repository( self ):
+        '''Create and populate package_bwa_0_5_9_0100.'''
         category = self.create_category( name=category_name, description=category_description )
         self.logout()
         self.login( email=common.test_user_1_email, username=common.test_user_1_name )
-        # Create a repository named bwa_tool_repository_0100 owned by user1.
-        repository = self.get_or_create_repository( name=bwa_tool_repository_name, 
-                                                    description=bwa_tool_repository_description, 
-                                                    long_description=bwa_tool_repository_long_description, 
+        # Create a repository named package_bwa_0_5_9_0100 owned by user1.
+        repository = self.get_or_create_repository( name=bwa_package_repository_name, 
+                                                    description=bwa_package_repository_description, 
+                                                    long_description=bwa_package_repository_long_description, 
                                                     owner=common.test_user_1_name,
                                                     category_id=self.security.encode_id( category.id ), 
                                                     strings_displayed=[] )
@@ -53,7 +53,7 @@
                           commit_message='Uploaded tool_dependencies.xml.',
                           strings_displayed=[ 'The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool' ], 
                           strings_not_displayed=[] )
-        # Visit the manage repository page for bwa_tool_repository_0100.
+        # Visit the manage repository page for package_bwa_0_5_9_0100.
         self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] )
 
     def test_0010_create_bwa_base_repository( self ):
@@ -85,10 +85,10 @@
         xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
         # The repository named bwa_base_repository_0100 is the dependent repository.
         base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
-        # The tool_repository named bwa_tool_repository_0100 is the required repository.
-        tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
+        # The repository named package_bwa_0_5_9_0100 is the required repository.
+        tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
         url = 'http://http://this is not an url!'
-        name = 'bwa_tool_repository_0100'
+        name = 'package_bwa_0_5_9_0100'
         owner = 'user1'
         changeset_revision = self.get_repository_tip( tool_repository )
         strings_displayed = [ 'Repository dependencies are currently supported only within the same tool shed' ] 
@@ -108,14 +108,14 @@
         xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
         # The base_repository named bwa_base_repository_0100 is the dependent repository.
         base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
-        # The tool_repository named bwa_tool_repository_0100 is the required repository.
-        tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
+        # The repository named package_bwa_0_5_9_0100 is the required repository.
+        tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
         url = self.url
         name = 'invalid_repository!?'
         owner = 'user1'
         changeset_revision = self.get_repository_tip( tool_repository )
         strings_displayed = [ 'because the name is invalid' ]
-        # Populate the dependent base_repository named bwa_tool_repository_0100 with an invalid tool_dependencies.xml file.
+        # Populate the dependent base_repository named package_bwa_0_5_9_0100 with an invalid tool_dependencies.xml file.
         repository_tuple = ( url, name, owner, changeset_revision )
         self.create_repository_dependency( repository=base_repository, 
                                            filepath=dependency_path, 
@@ -131,10 +131,10 @@
         xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
         # The base_repository named bwa_base_repository_0100 is the dependent repository.
         base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
-        # The tool_repository named bwa_tool_repository_0100 is the required repository.
-        tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
+        # The repository named package_bwa_0_5_9_0100 is the required repository.
+        tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
         url = self.url
-        name = 'bwa_tool_repository_0100'
+        name = 'package_bwa_0_5_9_0100'
         owner = 'invalid_owner!?'
         changeset_revision = self.get_repository_tip( tool_repository )
         strings_displayed = [ 'because the owner is invalid.' ] 
@@ -153,10 +153,10 @@
         xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
         # The base_repository named bwa_base_repository_0100 is the dependent repository.
         base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
-        # The tool_repository named bwa_tool_repository_0100 is the required repository.
-        tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
+        # The repository named package_bwa_0_5_9_0100 is the required repository.
+        tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
         url = self.url
-        name = 'bwa_tool_repository_0100'
+        name = 'package_bwa_0_5_9_0100'
         owner = 'user1'
         changeset_revision = '1234abcd'
         strings_displayed = [ 'because the changeset revision is invalid.' ] 
@@ -170,14 +170,14 @@
                                            version='0.5.9' )
  
     def test_0035_generate_complex_repository_dependency( self ):
-        '''Generate and upload a valid tool_dependencies.xml file that specifies bwa_tool_repository_0100.'''
+        '''Generate and upload a valid tool_dependencies.xml file that specifies package_bwa_0_5_9_0100.'''
         # The base_repository named bwa_base_repository_0100 is the dependent repository.
         base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
-        # The tool_repository named bwa_tool_repository_0100 is the required repository.
-        tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
+        # The repository named package_bwa_0_5_9_0100 is the required repository.
+        tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
         dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex' ] )
         url = self.url
-        name = 'bwa_tool_repository_0100'
+        name = 'package_bwa_0_5_9_0100'
         owner = 'user1'
         changeset_revision = self.get_repository_tip( tool_repository )
         repository_tuple = ( url, name, owner, changeset_revision )
@@ -194,8 +194,8 @@
         '''Generate and upload a new tool_dependencies.xml file that specifies an arbitrary file on the filesystem, and verify that bwa_base depends on the new changeset revision.'''
         # The base_repository named bwa_base_repository_0100 is the dependent repository.
         base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
-        # The tool_repository named bwa_tool_repository_0100 is the required repository.
-        tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
+        # The repository named package_bwa_0_5_9_0100 is the required repository.
+        tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
         previous_changeset = self.get_repository_tip( tool_repository )
         old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) )
         new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] )
@@ -220,12 +220,12 @@
         self.display_manage_repository_page( tool_repository, 
                                              strings_displayed=strings_displayed,
                                              strings_not_displayed=strings_not_displayed )
-        # Visit the manage page of the bwa_tool_repository_0100 to confirm the valid tool dependency definition.
+        # Visit the manage page of the package_bwa_0_5_9_0100 to confirm the valid tool dependency definition.
         self.display_manage_repository_page( tool_repository, 
                                              strings_displayed=strings_displayed,
                                              strings_not_displayed=strings_not_displayed )
         # Visit the manage page of the bwa_base_repository_0100 to confirm the valid tool dependency definition
-        # and the updated changeset revision (updated tip) of the bwa_tool_repository_0100 repository is displayed
+        # and the updated changeset revision (updated tip) of the package_bwa_0_5_9_0100 repository is displayed
         # as the required repository revision.  The original revision defined in the previously uploaded
         # tool_dependencies.xml file will be updated.
         self.display_manage_repository_page( base_repository, 

diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/functional/test_0170_complex_prior_installation_required.py
--- /dev/null
+++ b/test/tool_shed/functional/test_0170_complex_prior_installation_required.py
@@ -0,0 +1,137 @@
+from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
+import tool_shed.base.test_db_util as test_db_util
+
+matplotlib_repository_name = 'package_matplotlib_1_2_0170'
+matplotlib_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.2.x of the the python matplotlib package."
+matplotlib_repository_long_description = "This repository is intended to be defined as a complex repository dependency within a separate repository."
+
+numpy_repository_name = 'package_numpy_1_7_0170'
+numpy_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package."
+numpy_repository_long_description = "This repository is intended to be defined as a complex repository dependency within a separate repository."
+
+category_name = 'Test 0170 Prior Installation Complex Dependencies'
+category_description = 'Test 0170 Prior Installation Complex Dependencies'
+
+'''
+1. Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170.
+2. Create a complex repository dependency on package_numpy_1_7_0170, and upload this to package_matplotlib_1_2_0170.
+3. Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool dependency displays correctly.
+'''
+
+
+class TestComplexPriorInstallation( ShedTwillTestCase ):
+    '''Test features related to datatype converters.'''
+    
+    def test_0000_initiate_users( self ):
+        """Create necessary user accounts."""
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        test_user_1 = test_db_util.get_user( common.test_user_1_email )
+        assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email
+        test_user_1_private_role = test_db_util.get_private_role( test_user_1 )
+        self.logout()
+        self.login( email=common.admin_email, username=common.admin_username )
+        admin_user = test_db_util.get_user( common.admin_email )
+        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
+        admin_user_private_role = test_db_util.get_private_role( admin_user )
+        
+    def test_0005_create_matplotlib_repository( self ):
+        '''Create and populate the package_matplotlib_1_2_0170 repository.'''
+        '''
+        This is step 1 - Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170.
+        '''
+        category = self.create_category( name=category_name, description=category_description )
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        repository = self.get_or_create_repository( name=matplotlib_repository_name, 
+                                                    description=matplotlib_repository_description, 
+                                                    long_description=matplotlib_repository_long_description, 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category.id ), 
+                                                    strings_displayed=[] )
+        self.upload_file( repository, 
+                          filename='package_matplotlib/package_matplotlib_1_2.tar', 
+                          filepath=None,
+                          valid_tools_only=False,
+                          uncompress_file=True,
+                          remove_repo_files_not_in_tar=False, 
+                          commit_message='Uploaded matplotlib tool dependency tarball.',
+                          strings_displayed=['orphan'], 
+                          strings_not_displayed=[] )
+    
+    def test_0010_create_numpy_repository( self ):
+        '''Create and populate the package_numpy_1_7_0170 repository.'''
+        '''
+        This is step 1 - Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170.
+        '''
+        category = self.create_category( name=category_name, description=category_description )
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        repository = self.get_or_create_repository( name=numpy_repository_name, 
+                                                    description=numpy_repository_description, 
+                                                    long_description=numpy_repository_long_description, 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category.id ), 
+                                                    strings_displayed=[] )
+        self.upload_file( repository, 
+                          filename='package_numpy/package_numpy_1_7.tar', 
+                          filepath=None,
+                          valid_tools_only=False,
+                          uncompress_file=True,
+                          remove_repo_files_not_in_tar=False, 
+                          commit_message='Uploaded numpy tool dependency tarball.',
+                          strings_displayed=['orphan'], 
+                          strings_not_displayed=[] )
+        
+    def test_0015_create_complex_repository_dependency( self ):
+        '''Create a dependency on package_numpy_1_7_0170.'''
+        '''
+        This is step 2 - Create a complex repository dependency on package_numpy_1_7_0170, and upload this to package_matplotlib_1_2_0170.
+        package_matplotlib_1_2_0170 should depend on package_numpy_1_7_0170, with prior_installation_required
+        set to True. When matplotlib is selected for installation, the result should be that numpy is compiled
+        and installed first.
+        '''
+        numpy_repository = test_db_util.get_repository_by_name_and_owner( numpy_repository_name, common.test_user_1_name )
+        matplotlib_repository = test_db_util.get_repository_by_name_and_owner( matplotlib_repository_name, common.test_user_1_name )
+        # Generate the new dependency XML. Normally, the create_repository_dependency method would be used for this, but
+        # it replaces any existing tool or repository dependency XML file with the generated contents. This is undesirable
+        # in this case, because matplotlib already has an additional tool dependency definition that we don't want to
+        # overwrite.
+        new_xml = '    <package name="numpy" version="1.7">\n'
+        new_xml += '        <repository toolshed="%s" name="%s" owner="%s" changeset_revision="%s" prior_installation_required="True" />\n'
+        new_xml += '    </package>\n'
+        url = self.url
+        name = numpy_repository.name
+        owner = numpy_repository.user.username
+        changeset_revision = self.get_repository_tip( numpy_repository )
+        processed_xml = new_xml % ( url, name, owner, changeset_revision )
+        original_xml = file( self.get_filename( 'package_matplotlib/tool_dependencies.xml' ), 'r' ).read()
+        dependency_xml_path = self.generate_temp_path( 'test_0170', additional_paths=[ 'matplotlib' ] )
+        new_xml_file = os.path.join( dependency_xml_path, 'tool_dependencies.xml' )
+        file( new_xml_file, 'w' ).write( original_xml.replace( '<!--NUMPY-->', processed_xml ) )
+        # Upload the generated complex repository dependency XML to the matplotlib repository.
+        self.upload_file( matplotlib_repository, 
+                          filename='tool_dependencies.xml', 
+                          filepath=dependency_xml_path,
+                          valid_tools_only=True,
+                          uncompress_file=True,
+                          remove_repo_files_not_in_tar=False, 
+                          commit_message='Uploaded complex repository dependency on numpy 1.7.',
+                          strings_displayed=[], 
+                          strings_not_displayed=[] )
+        
+    def test_0020_verify_generated_dependency( self ):
+        '''Verify that matplotlib now has a package tool dependency and a complex repository dependency.'''
+        '''
+        This is step 3 - Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool
+                         dependency displays correctly.
+        'Inhherited' in this case means that matplotlib should show a package tool dependency on numpy version 1.7, and a repository
+        dependency on the latest revision of package_numpy_1_7_0170.
+        '''
+        numpy_repository = test_db_util.get_repository_by_name_and_owner( numpy_repository_name, common.test_user_1_name )
+        matplotlib_repository = test_db_util.get_repository_by_name_and_owner( matplotlib_repository_name, common.test_user_1_name )
+        changeset_revision = self.get_repository_tip( numpy_repository )
+        self.check_repository_dependency( matplotlib_repository, depends_on_repository=numpy_repository )
+        self.display_manage_repository_page( matplotlib_repository, strings_displayed=[ 'numpy', '1.7', 'package', changeset_revision ] )
+
+        
\ No newline at end of file

diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py
--- a/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py
+++ b/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py
@@ -3,11 +3,11 @@
 
 bwa_base_repository_name = 'bwa_base_repository_0100'
 bwa_base_repository_description = "BWA Base"
-bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at bwa_tool_repository_0100"
+bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at package_bwa_0_5_9_0100"
 
-bwa_tool_repository_name = 'bwa_tool_repository_0100'
-bwa_tool_repository_description = "BWA Tool"
-bwa_tool_repository_long_description = "BWA repository with a package tool dependency defined for BWA 0.5.9."
+bwa_package_repository_name = 'package_bwa_0_5_9_0100'
+bwa_package_repository_description = "BWA Tool"
+bwa_package_repository_long_description = "BWA repository with a package tool dependency defined to compile and install BWA 0.5.9."
 
 category_name = 'Test 0100 Complex Repository Dependencies'
 category_description = 'Test 0100 Complex Repository Dependencies'
@@ -30,15 +30,15 @@
         assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
         admin_user_private_role = test_db_util.get_private_role( admin_user )
 
-    def test_0005_create_bwa_tool_repository( self ):
+    def test_0005_create_bwa_package_repository( self ):
         '''Create and populate bwa_tool_0100.'''
         global running_standalone
         category = self.create_category( name=category_name, description=category_description )
         self.logout()
         self.login( email=common.test_user_1_email, username=common.test_user_1_name )
-        repository = self.get_or_create_repository( name=bwa_tool_repository_name, 
-                                                    description=bwa_tool_repository_description, 
-                                                    long_description=bwa_tool_repository_long_description, 
+        repository = self.get_or_create_repository( name=bwa_package_repository_name, 
+                                                    description=bwa_package_repository_description, 
+                                                    long_description=bwa_package_repository_long_description, 
                                                     owner=common.test_user_1_name,
                                                     category_id=self.security.encode_id( category.id ), 
                                                     strings_displayed=[] )
@@ -73,7 +73,7 @@
                                                         owner=common.test_user_1_name,
                                                         category_id=self.security.encode_id( category.id ), 
                                                         strings_displayed=[] )
-            tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
+            tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
             self.upload_file( repository, 
                               filename='bwa/complex/bwa_base.tar',
                               filepath=None,
@@ -91,7 +91,7 @@
             dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] )
             xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
             base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
-            tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
+            tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
             url = 'http://http://this is not an url!'
             name = tool_repository.name
             owner = tool_repository.user.username
@@ -113,7 +113,7 @@
             dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] )
             xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
             base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
-            tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
+            tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
             url = self.url
             name = 'invalid_repository!?'
             owner = tool_repository.user.username
@@ -135,7 +135,7 @@
             dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] )
             xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
             base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
-            tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
+            tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
             url = self.url
             name = tool_repository.name
             owner = 'invalid_owner!?'
@@ -157,7 +157,7 @@
             dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] )
             xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
             base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
-            tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
+            tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
             url = self.url
             name = tool_repository.name
             owner = tool_repository.user.username
@@ -173,11 +173,11 @@
                                                version='0.5.9' )
   
     def test_0035_generate_valid_complex_repository_dependency( self ):
-        '''Generate and upload a valid tool_dependencies.xml file that specifies bwa_tool_repository_0100.'''
+        '''Generate and upload a valid tool_dependencies.xml file that specifies package_bwa_0_5_9_0100.'''
         global running_standalone
         if running_standalone:
             base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
-            tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
+            tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
             dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex' ] )
             xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
             url = self.url
@@ -199,7 +199,7 @@
         global running_standalone
         if running_standalone:
             base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
-            tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
+            tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
             previous_changeset = self.get_repository_tip( tool_repository )
             old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) )
             new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] )
@@ -225,7 +225,7 @@
         self.galaxy_logout()
         self.galaxy_login( email=common.admin_email, username=common.admin_username )
         base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
-        tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
+        tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
         preview_strings_displayed = [ tool_repository.name, self.get_repository_tip( tool_repository ) ]
         self.install_repository( bwa_base_repository_name, 
                                  common.test_user_1_name, 
@@ -238,19 +238,19 @@
     def test_0050_verify_installed_repositories( self ):
         '''Verify that the installed repositories are displayed properly.'''
         base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name )
-        tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_tool_repository_name, common.test_user_1_name )
+        tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_package_repository_name, common.test_user_1_name )
         strings_displayed = [ 'bwa_base_repository_0100', 'user1', base_repository.installed_changeset_revision ]
-        strings_displayed.extend( [ 'bwa_tool_repository_0100', 'user1', tool_repository.installed_changeset_revision ] )
+        strings_displayed.extend( [ 'package_bwa_0_5_9_0100', 'user1', tool_repository.installed_changeset_revision ] )
         strings_displayed.append( self.url.replace( 'http://', '' ) )
         self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=[] )
-        strings_displayed = [ 'bwa_tool_repository_0100', 'user1', tool_repository.installed_changeset_revision ]
+        strings_displayed = [ 'package_bwa_0_5_9_0100', 'user1', tool_repository.installed_changeset_revision ]
         strings_not_displayed = [ 'Missing tool dependencies' ]
         self.display_installed_repository_manage_page( tool_repository, 
                                                        strings_displayed=strings_displayed, 
                                                        strings_not_displayed=strings_not_displayed )
         strings_displayed = [ 'bwa_base_repository_0100',
                               'user1', 
-                              'bwa_tool_repository_0100', 
+                              'package_bwa_0_5_9_0100', 
                               base_repository.installed_changeset_revision, 
                               tool_repository.installed_changeset_revision ]
         strings_not_displayed = [ 'Missing tool dependencies' ]
@@ -261,7 +261,7 @@
     def test_0055_verify_complex_tool_dependency( self ):
         '''Verify that the generated env.sh contains the right data.'''
         base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name )
-        tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_tool_repository_name, common.test_user_1_name )
+        tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_package_repository_name, common.test_user_1_name )
         env_sh_path = os.path.join( self.galaxy_tool_dependency_dir, 
                                     'bwa', 
                                     '0.5.9', 
@@ -274,17 +274,17 @@
         if tool_repository.installed_changeset_revision not in contents:
             raise AssertionError( 'Installed changeset revision %s not found in env.sh.\nContents of env.sh: %s' % \
                                   ( tool_repository.installed_changeset_revision, contents ) )
-        if 'bwa_tool_repository_0100' not in contents:
-            raise AssertionError( 'Repository name bwa_tool_repository_0100 not found in env.sh.\nContents of env.sh: %s' % contents )
+        if 'package_bwa_0_5_9_0100' not in contents:
+            raise AssertionError( 'Repository name package_bwa_0_5_9_0100 not found in env.sh.\nContents of env.sh: %s' % contents )
         
     def test_0060_verify_tool_dependency_uninstallation( self ):
-        '''Uninstall the bwa_tool_repository_0100 repository.'''
+        '''Uninstall the package_bwa_0_5_9_0100 repository.'''
         '''
         Uninstall the repository that defines an orphan tool dependency on BWA 0.5.9, and verify
         that this results in the compiled binary package also being removed.
         '''
         base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name )
-        tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_tool_repository_name, common.test_user_1_name )
+        tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_package_repository_name, common.test_user_1_name )
         self.uninstall_repository( tool_repository, remove_from_disk=True )
         env_sh_path = os.path.join( self.galaxy_tool_dependency_dir, 
                                     'bwa', 

diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/functional/test_1170_complex_prior_installation_required.py
--- /dev/null
+++ b/test/tool_shed/functional/test_1170_complex_prior_installation_required.py
@@ -0,0 +1,181 @@
+from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
+import tool_shed.base.test_db_util as test_db_util
+
+matplotlib_repository_name = 'package_matplotlib_1_2_0170'
+matplotlib_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.2.x of the the python matplotlib package."
+matplotlib_repository_long_description = "This repository is intended to be defined as a complex repository dependency within a separate repository."
+
+numpy_repository_name = 'package_numpy_1_7_0170'
+numpy_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package."
+numpy_repository_long_description = "This repository is intended to be defined as a complex repository dependency within a separate repository."
+
+category_name = 'Test 0170 Prior Installation Complex Dependencies'
+category_description = 'Test 0170 Prior Installation Complex Dependencies'
+
+'''
+1. Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170.
+2. Create a complex repository dependency on package_numpy_1_7_0170, and upload this to package_matplotlib_1_2_0170.
+3. Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool dependency displays correctly.
+4. Install package_matplotlib_1_2_0170 with repository dependencies.
+5. Verify that the prior_installation_required attribute resulted in package_numpy_1_7_0170 being installed first.
+'''
+
+running_standalone = False
+
+
+class TestComplexPriorInstallation( ShedTwillTestCase ):
+    '''Test features related to datatype converters.'''
+    
+    def test_0000_initiate_users( self ):
+        """Create necessary user accounts."""
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        test_user_1 = test_db_util.get_user( common.test_user_1_email )
+        assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email
+        test_user_1_private_role = test_db_util.get_private_role( test_user_1 )
+        self.logout()
+        self.login( email=common.admin_email, username=common.admin_username )
+        admin_user = test_db_util.get_user( common.admin_email )
+        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
+        admin_user_private_role = test_db_util.get_private_role( admin_user )
+        
+    def test_0005_create_matplotlib_repository( self ):
+        '''Create and populate the package_matplotlib_1_2_0170 repository.'''
+        '''
+        This is step 1 - Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170.
+        '''
+        global running_standalone
+        category = self.create_category( name=category_name, description=category_description )
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        repository = self.get_or_create_repository( name=matplotlib_repository_name, 
+                                                    description=matplotlib_repository_description, 
+                                                    long_description=matplotlib_repository_long_description, 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category.id ), 
+                                                    strings_displayed=[] )
+        if self.repository_is_new( repository ):
+            running_standalone = True
+            self.upload_file( repository, 
+                              filename='package_matplotlib/package_matplotlib_1_2.tar', 
+                              filepath=None,
+                              valid_tools_only=False,
+                              uncompress_file=True,
+                              remove_repo_files_not_in_tar=False, 
+                              commit_message='Uploaded matplotlib tool dependency tarball.',
+                              strings_displayed=['orphan'], 
+                              strings_not_displayed=[] )
+    
+    def test_0010_create_numpy_repository( self ):
+        '''Create and populate the package_numpy_1_7_0170 repository.'''
+        '''
+        This is step 1 - Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170.
+        '''
+        global running_standalone
+        category = self.create_category( name=category_name, description=category_description )
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        if running_standalone:
+            repository = self.get_or_create_repository( name=numpy_repository_name, 
+                                                        description=numpy_repository_description, 
+                                                        long_description=numpy_repository_long_description, 
+                                                        owner=common.test_user_1_name,
+                                                        category_id=self.security.encode_id( category.id ), 
+                                                        strings_displayed=[] )
+            self.upload_file( repository, 
+                              filename='package_numpy/package_numpy_1_7.tar', 
+                              filepath=None,
+                              valid_tools_only=False,
+                              uncompress_file=True,
+                              remove_repo_files_not_in_tar=False, 
+                              commit_message='Uploaded numpy tool dependency tarball.',
+                              strings_displayed=['orphan'], 
+                              strings_not_displayed=[] )
+        
+    def test_0015_create_complex_repository_dependency( self ):
+        '''Create a dependency on package_numpy_1_7_0170.'''
+        '''
+        This is step 2 - Create a complex repository dependency on package_numpy_1_7_0170, and upload this to package_matplotlib_1_2_0170.
+        package_matplotlib_1_2_0170 should depend on package_numpy_1_7_0170, with prior_installation_required
+        set to True. When matplotlib is selected for installation, the result should be that numpy is compiled
+        and installed first.
+        '''
+        global running_standalone
+        numpy_repository = test_db_util.get_repository_by_name_and_owner( numpy_repository_name, common.test_user_1_name )
+        matplotlib_repository = test_db_util.get_repository_by_name_and_owner( matplotlib_repository_name, common.test_user_1_name )
+        # Generate the new dependency XML. Normally, the create_repository_dependency method would be used for this, but
+        # it replaces any existing tool or repository dependency XML file with the generated contents. This is undesirable
+        # in this case, because matplotlib already has an additional tool dependency definition that we don't want to
+        # overwrite.
+        new_xml = '    <package name="numpy" version="1.7">\n'
+        new_xml += '        <repository toolshed="%s" name="%s" owner="%s" changeset_revision="%s" prior_installation_required="True" />\n'
+        new_xml += '    </package>\n'
+        url = self.url
+        name = numpy_repository.name
+        owner = numpy_repository.user.username
+        if running_standalone:
+            changeset_revision = self.get_repository_tip( numpy_repository )
+            processed_xml = new_xml % ( url, name, owner, changeset_revision )
+            original_xml = file( self.get_filename( 'package_matplotlib/tool_dependencies.xml' ), 'r' ).read()
+            dependency_xml_path = self.generate_temp_path( 'test_0170', additional_paths=[ 'matplotlib' ] )
+            new_xml_file = os.path.join( dependency_xml_path, 'tool_dependencies.xml' )
+            file( new_xml_file, 'w' ).write( original_xml.replace( '<!--NUMPY-->', processed_xml ) )
+            # Upload the generated complex repository dependency XML to the matplotlib repository.
+            self.upload_file( matplotlib_repository, 
+                              filename='tool_dependencies.xml', 
+                              filepath=dependency_xml_path,
+                              valid_tools_only=True,
+                              uncompress_file=True,
+                              remove_repo_files_not_in_tar=False, 
+                              commit_message='Uploaded complex repository dependency on numpy 1.7.',
+                              strings_displayed=[], 
+                              strings_not_displayed=[] )
+        
+    def test_0020_verify_generated_dependency( self ):
+        '''Verify that matplotlib now has a package tool dependency and a complex repository dependency.'''
+        '''
+        This is step 3 - Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool
+                         dependency displays correctly.
+        'Inhherited' in this case means that matplotlib should show a package tool dependency on numpy version 1.7, and a repository
+        dependency on the latest revision of package_numpy_1_7_0170.
+        '''
+        numpy_repository = test_db_util.get_repository_by_name_and_owner( numpy_repository_name, common.test_user_1_name )
+        matplotlib_repository = test_db_util.get_repository_by_name_and_owner( matplotlib_repository_name, common.test_user_1_name )
+        changeset_revision = self.get_repository_tip( numpy_repository )
+        self.check_repository_dependency( matplotlib_repository, depends_on_repository=numpy_repository )
+        self.display_manage_repository_page( matplotlib_repository, strings_displayed=[ 'numpy', '1.7', 'package', changeset_revision ] )
+
+    def test_0025_install_matplotlib_repository( self ):
+        '''Install the package_matplotlib_1_2_0170 repository.'''
+        '''
+        This is step 4 - Install package_matplotlib_1_2_0170 with repository dependencies.
+        '''
+        self.galaxy_logout()
+        self.galaxy_login( email=common.admin_email, username=common.admin_username )
+        matplotlib_repository = test_db_util.get_repository_by_name_and_owner( matplotlib_repository_name, common.test_user_1_name )
+        preview_strings_displayed = [ 'package_matplotlib_1_2_0170', self.get_repository_tip( matplotlib_repository ) ]
+        strings_displayed = [ 'Choose the tool panel section' ]
+        self.install_repository( matplotlib_repository_name, 
+                                 common.test_user_1_name, 
+                                 category_name,
+                                 install_tool_dependencies=False, 
+                                 install_repository_dependencies=True,
+                                 preview_strings_displayed=preview_strings_displayed,
+                                 strings_displayed=[],
+                                 strings_not_displayed=[],
+                                 post_submit_strings_displayed=[ 'package_matplotlib_1_2_0170', 'new' ],
+                                 includes_tools_for_display_in_tool_panel=False )
+        
+    def test_0030_verify_installation_order( self ):
+        '''Verify that the numpy repository was installed before the matplotlib repository.'''
+        '''
+        This is step 5 - Verify that the prior_installation_required attribute resulted in package_numpy_1_7_0170 being installed first.
+        In the previous step, package_matplotlib_1_2_0170 was selected for installation, but package_numpy_1_7_0170 had the 
+        prior_installation_required attribute set. Confirm that this resulted in package_numpy_1_7_0170 being installed before 
+        package_matplotlib_1_2_0170.
+        '''
+        matplotlib_repository = test_db_util.get_installed_repository_by_name_owner( matplotlib_repository_name, common.test_user_1_name )
+        numpy_repository = test_db_util.get_installed_repository_by_name_owner( numpy_repository_name, common.test_user_1_name )
+        assert matplotlib_repository.update_time > numpy_repository.update_time, \
+            'Error: package_numpy_1_7_0170 shows a later update time than package_matplotlib_1_2_0170'
+        
\ No newline at end of file

diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar
Binary file test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar has changed

diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml
--- /dev/null
+++ b/test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml
@@ -0,0 +1,25 @@
+<tool_dependency>
+<!--NUMPY-->
+    <package name="matplotlib" version="1.2.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.2.1/matplotlib-1.2.1.tar.gz</action>
+                <action type="shell_command">wget http://downloads.sourceforge.net/project/freetype/freetype2/2.4.11/freetype-2.4.11.tar.bz2</action>
+                <action type="shell_command">tar xfvj freetype-2.4.11.tar.bz2 && 
+                    cd freetype-2.4.11 && 
+                    ./configure --prefix=$INSTALL_DIR/freetype/build &&
+                    make && 
+                    make install</action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && 
+                    export CPLUS_INCLUDE_PATH=$INSTALL_DIR/freetype/build/include:$INSTALL_DIR/freetype/build/include/freetype2/ && 
+                    export LIBRARY_PATH=$INSTALL_DIR/freetype/build/lib/ && 
+                    python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
+                <action type="set_environment">
+                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Compiling matplotlib requires a C compiler (typically gcc), freetype2, numpy and libpng.</readme>
+    </package>
+</tool_dependency>

diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar
Binary file test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar has changed

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[galaxy-commits] commit/galaxy-central: inithello: Tool shed functional tests for installation order with complex repository dependencies. Modified tests 0100 and 1100 to be less ambiguous regarding which repository contains what.

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