def test_0065_reinstall_column_repository(self):
'''Reinstall column_maker without repository dependencies, verify both convert_chars and column_maker are installed.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
installed_column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
self.reinstall_repository(installed_column_repository,
install_repository_dependencies=False)
strings_displayed = [
installed_column_repository.name,
installed_column_repository.description,
installed_column_repository.tool_shed,
installed_column_repository.installed_changeset_revision,
installed_convert_repository.name,
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies'
]
self.display_installed_repository_manage_page(
installed_column_repository, strings_displayed=strings_displayed)
strings_displayed = [
installed_convert_repository.name,
installed_convert_repository.description,
installed_convert_repository.tool_shed,
installed_convert_repository.installed_changeset_revision,
installed_column_repository.name,
installed_column_repository.installed_changeset_revision,
'Installed repository dependencies'
]
self.display_installed_repository_manage_page(
installed_convert_repository, strings_displayed=strings_displayed)
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)
strings_displayed = [
base_repository.name, base_repository.owner,
base_repository.installed_changeset_revision
]
strings_displayed.extend([
tool_repository.name, tool_repository.owner,
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=[])
checks = [(tool_repository, [
tool_repository.name, tool_repository.owner,
tool_repository.installed_changeset_revision
], ['Missing tool dependencies']),
(base_repository, [
base_repository.name, base_repository.owner,
base_repository.installed_changeset_revision,
tool_repository.name, tool_repository.owner,
tool_repository.installed_changeset_revision
], ['Missing tool dependencies'])]
for repository, strings_displayed, strings_not_displayed in checks:
self.display_installed_repository_manage_page(
repository,
strings_displayed=strings_displayed,
strings_not_displayed=strings_not_displayed)
def test_0020_install_convert_repository(self):
'''Install convert_chars without repository dependencies into convert_chars tool panel section.'''
self.galaxy_logout()
self.galaxy_login(email=common.admin_email,
username=common.admin_username)
self.install_repository(convert_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
install_repository_dependencies=False,
new_tool_panel_section='convert_chars')
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
installed_column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
browse_strings_displayed = [
installed_convert_repository.name,
installed_convert_repository.description,
installed_convert_repository.tool_shed,
installed_convert_repository.installed_changeset_revision
]
strings_displayed = [
installed_convert_repository.name,
installed_convert_repository.description,
installed_convert_repository.tool_shed,
installed_convert_repository.installed_changeset_revision,
installed_column_repository.name,
installed_column_repository.installed_changeset_revision,
'Missing repository dependencies'
]
self.display_galaxy_browse_repositories_page(
strings_displayed=browse_strings_displayed)
self.display_installed_repository_manage_page(
installed_convert_repository, strings_displayed=strings_displayed)
def test_0055_reactivate_convert_repository(self):
'''Activate convert_chars. Both convert_chars and column_maker should now show as installed.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
installed_column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
self.reactivate_repository(installed_convert_repository)
strings_displayed = [
installed_column_repository.name,
installed_column_repository.description,
installed_column_repository.tool_shed,
installed_column_repository.installed_changeset_revision,
installed_convert_repository.name,
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies'
]
self.display_installed_repository_manage_page(
installed_column_repository, strings_displayed=strings_displayed)
strings_displayed = [
installed_convert_repository.name,
installed_convert_repository.description,
installed_convert_repository.tool_shed,
installed_convert_repository.installed_changeset_revision,
installed_column_repository.name,
installed_column_repository.installed_changeset_revision,
'Installed repository dependencies'
]
self.display_installed_repository_manage_page(
installed_convert_repository, strings_displayed=strings_displayed)
def test_0020_install_convert_repository( self ):
'''Install convert_chars without repository dependencies into convert_chars tool panel section.'''
self.galaxy_logout()
self.galaxy_login( email=common.admin_email, username=common.admin_username )
self.install_repository( convert_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
install_repository_dependencies=False,
new_tool_panel_section='convert_chars' )
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name,
common.test_user_1_name )
installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name,
common.test_user_1_name )
browse_strings_displayed = [ 'convert_chars_0080',
'Convert delimiters',
self.url.replace( 'http://', '' ),
installed_convert_repository.installed_changeset_revision ]
strings_displayed = [ 'convert_chars_0080',
'Convert delimiters',
self.url.replace( 'http://', '' ),
installed_convert_repository.installed_changeset_revision,
'column_maker_0080',
installed_column_repository.installed_changeset_revision,
'Missing repository dependencies' ]
self.display_galaxy_browse_repositories_page( strings_displayed=browse_strings_displayed )
self.display_installed_repository_manage_page( installed_convert_repository,
strings_displayed=strings_displayed )
def test_0080_reinstall_convert_repository( self ):
'''Reinstall convert_chars with repository dependencies, verify that this installs both convert_chars and column_maker.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name,
common.test_user_1_name )
installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name,
common.test_user_1_name )
self.reinstall_repository( installed_convert_repository,
install_repository_dependencies=True,
no_changes=False,
new_tool_panel_section='convert_maker' )
strings_displayed = [ installed_column_repository.name,
installed_column_repository.description,
installed_column_repository.tool_shed,
installed_column_repository.installed_changeset_revision,
installed_convert_repository.name,
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies' ]
self.display_installed_repository_manage_page( installed_column_repository,
strings_displayed=strings_displayed )
strings_displayed = [ installed_convert_repository.name,
installed_convert_repository.description,
installed_convert_repository.tool_shed,
installed_convert_repository.installed_changeset_revision,
installed_column_repository.name,
installed_column_repository.installed_changeset_revision,
'Installed repository dependencies' ]
self.display_installed_repository_manage_page( installed_convert_repository,
strings_displayed=strings_displayed )
def test_0065_reinstall_column_repository( self ):
'''Reinstall column_maker without repository dependencies, verify both convert_chars and column_maker are installed.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name,
common.test_user_1_name )
installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name,
common.test_user_1_name )
self.reinstall_repository( installed_column_repository, install_repository_dependencies=False )
strings_displayed = [ installed_column_repository.name,
installed_column_repository.description,
installed_column_repository.tool_shed,
installed_column_repository.installed_changeset_revision,
installed_convert_repository.name,
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies' ]
self.display_installed_repository_manage_page( installed_column_repository,
strings_displayed=strings_displayed )
strings_displayed = [ installed_convert_repository.name,
installed_convert_repository.description,
installed_convert_repository.tool_shed,
installed_convert_repository.installed_changeset_revision,
installed_column_repository.name,
installed_column_repository.installed_changeset_revision,
'Installed repository dependencies' ]
self.display_installed_repository_manage_page( installed_convert_repository,
strings_displayed=strings_displayed )
def test_0055_reactivate_convert_repository( self ):
'''Activate convert_chars. Both convert_chars and column_maker should now show as installed.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name,
common.test_user_1_name )
installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name,
common.test_user_1_name )
self.reactivate_repository( installed_convert_repository )
strings_displayed = [ installed_column_repository.name,
installed_column_repository.description,
installed_column_repository.tool_shed,
installed_column_repository.installed_changeset_revision,
installed_convert_repository.name,
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies' ]
self.display_installed_repository_manage_page( installed_column_repository,
strings_displayed=strings_displayed )
strings_displayed = [ installed_convert_repository.name,
installed_convert_repository.description,
installed_convert_repository.tool_shed,
installed_convert_repository.installed_changeset_revision,
installed_column_repository.name,
installed_column_repository.installed_changeset_revision,
'Installed repository dependencies' ]
self.display_installed_repository_manage_page( installed_convert_repository,
strings_displayed=strings_displayed )
def test_0025_install_column_repository( self ):
'''Install column maker with repository dependencies into column_maker tool panel section.'''
self.install_repository( column_repository_name,
common.test_user_1_name,
category_name,
install_repository_dependencies=True,
new_tool_panel_section='column_maker',
strings_displayed=[ 'install_repository_dependencies' ] )
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name,
common.test_user_1_name )
installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name,
common.test_user_1_name )
browse_strings_displayed = [ 'convert_chars_0080',
'Convert delimiters',
self.url.replace( 'http://', '' ),
installed_convert_repository.installed_changeset_revision,
'column_maker_0080',
'Add column',
installed_column_repository.installed_changeset_revision ]
strings_displayed = [ 'column_maker_0080',
'Add column',
self.url.replace( 'http://', '' ),
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies' ]
self.display_galaxy_browse_repositories_page( strings_displayed=browse_strings_displayed )
self.display_installed_repository_manage_page( installed_column_repository,
strings_displayed=strings_displayed )
def test_0050_verify_repository_installation(self):
'''Verify installation of blastxml_to_top_descr_0120 and blast_datatypes_0120.'''
'''
We are at step 1a, Galaxy side.
Check that the blastxml_to_top_descr_0120 and blast_datatypes_0120 repositories installed correctly, and that there
are now new datatypes in the registry matching the ones defined in blast_datatypes_0120. Also check that
blast_datatypes_0120 is labeled as an installed repository dependency of blastxml_to_top_descr_0120.
'''
global repository_datatypes_count
global base_datatypes_count
tool_repository = test_db_util.get_installed_repository_by_name_owner(
tool_repository_name, common.test_user_1_name)
datatypes_repository = test_db_util.get_installed_repository_by_name_owner(
datatypes_repository_name, common.test_user_2_name)
current_datatypes = int(self.get_datatypes_count())
expected_count = base_datatypes_count + repository_datatypes_count
assert current_datatypes == expected_count, 'Installing %s did not add new datatypes. Expected: %d. Found: %d' % \
( 'blastxml_to_top_descr_0120', expected_count, current_datatypes )
strings_displayed = [
'Installed repository dependencies', 'user1',
'blast_datatypes_0120'
]
strings_displayed.extend([
'Valid tools', 'BLAST top hit', 'Make a table',
datatypes_repository.installed_changeset_revision
])
self.display_installed_repository_manage_page(
tool_repository, strings_displayed=strings_displayed)
strings_displayed = [
'Datatypes', 'blastxml', 'blastdbp', 'blastdbn', 'BlastXml',
'BlastNucDb', 'BlastProtDb'
]
strings_displayed.extend(['application/xml', 'text/html'])
self.display_installed_repository_manage_page(
datatypes_repository, strings_displayed=strings_displayed)
def test_0055_reactivate_convert_repository(self):
'''Activate convert_chars. Both convert_chars and column_maker should now show as installed.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
installed_column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
self.reactivate_repository(installed_convert_repository)
strings_displayed = [
'column_maker_0080', 'Add column',
self.url.replace('http://', ''),
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies'
]
self.display_installed_repository_manage_page(
installed_column_repository, strings_displayed=strings_displayed)
strings_displayed = [
'convert_chars_0080', 'Convert delimiters',
self.url.replace('http://', ''),
installed_convert_repository.installed_changeset_revision,
'column_maker_0080',
installed_column_repository.installed_changeset_revision,
'Installed repository dependencies'
]
self.display_installed_repository_manage_page(
installed_convert_repository, strings_displayed=strings_displayed)
def test_0080_reinstall_convert_repository(self):
'''Reinstall convert_chars with repository dependencies, verify that this installs both convert_chars and column_maker.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
installed_column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
self.reinstall_repository(installed_convert_repository,
install_repository_dependencies=True,
no_changes=False,
new_tool_panel_section='convert_maker')
strings_displayed = [
'column_maker_0080', 'Add column',
self.url.replace('http://', ''),
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies'
]
self.display_installed_repository_manage_page(
installed_column_repository, strings_displayed=strings_displayed)
strings_displayed = [
'convert_chars_0080', 'Convert delimiters',
self.url.replace('http://', ''),
installed_convert_repository.installed_changeset_revision,
'column_maker_0080',
installed_column_repository.installed_changeset_revision,
'Installed repository dependencies'
]
self.display_installed_repository_manage_page(
installed_convert_repository, strings_displayed=strings_displayed)
def test_0055_reactivate_convert_repository( self ):
'''Activate convert_chars. Both convert_chars and column_maker should now show as installed.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name,
common.test_user_1_name )
installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name,
common.test_user_1_name )
self.reactivate_repository( installed_convert_repository )
strings_displayed = [ 'column_maker_0080',
'Add column',
self.url.replace( 'http://', '' ),
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies' ]
self.display_installed_repository_manage_page( installed_column_repository,
strings_displayed=strings_displayed )
strings_displayed = [ 'convert_chars_0080',
'Convert delimiters',
self.url.replace( 'http://', '' ),
installed_convert_repository.installed_changeset_revision,
'column_maker_0080',
installed_column_repository.installed_changeset_revision,
'Installed repository dependencies' ]
self.display_installed_repository_manage_page( installed_convert_repository,
strings_displayed=strings_displayed )
def test_0025_install_column_repository(self):
'''Install column maker with repository dependencies into column_maker tool panel section.'''
self.install_repository(
column_repository_name,
common.test_user_1_name,
category_name,
install_repository_dependencies=True,
new_tool_panel_section='column_maker',
strings_displayed=['install_repository_dependencies'])
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
installed_column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
browse_strings_displayed = [
'convert_chars_0080', 'Convert delimiters',
self.url.replace('http://', ''),
installed_convert_repository.installed_changeset_revision,
'column_maker_0080', 'Add column',
installed_column_repository.installed_changeset_revision
]
strings_displayed = [
'column_maker_0080', 'Add column',
self.url.replace('http://', ''),
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies'
]
self.display_galaxy_browse_repositories_page(
strings_displayed=browse_strings_displayed)
self.display_installed_repository_manage_page(
installed_column_repository, strings_displayed=strings_displayed)
def test_0080_reinstall_convert_repository(self):
'''Reinstall convert_chars with repository dependencies, verify that this installs both convert_chars and column_maker.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
installed_column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
self.reinstall_repository(installed_convert_repository,
install_repository_dependencies=True,
no_changes=False,
new_tool_panel_section='convert_maker')
strings_displayed = [
installed_column_repository.name,
installed_column_repository.description,
installed_column_repository.tool_shed,
installed_column_repository.installed_changeset_revision,
installed_convert_repository.name,
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies'
]
self.display_installed_repository_manage_page(
installed_column_repository, strings_displayed=strings_displayed)
strings_displayed = [
installed_convert_repository.name,
installed_convert_repository.description,
installed_convert_repository.tool_shed,
installed_convert_repository.installed_changeset_revision,
installed_column_repository.name,
installed_column_repository.installed_changeset_revision,
'Installed repository dependencies'
]
self.display_installed_repository_manage_page(
installed_convert_repository, strings_displayed=strings_displayed)
def test_0025_install_column_repository(self):
'''Install column maker with repository dependencies into column_maker tool panel section.'''
self.install_repository(
column_repository_name,
common.test_user_1_name,
category_name,
install_repository_dependencies=True,
new_tool_panel_section='column_maker',
strings_displayed=['install_repository_dependencies'])
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
installed_column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
browse_strings_displayed = [
installed_convert_repository.name,
installed_convert_repository.description,
installed_convert_repository.tool_shed,
installed_convert_repository.installed_changeset_revision,
installed_column_repository.name,
installed_column_repository.description,
installed_column_repository.installed_changeset_revision
]
strings_displayed = [
installed_column_repository.name,
installed_column_repository.description,
installed_column_repository.tool_shed,
installed_column_repository.installed_changeset_revision,
installed_convert_repository.name,
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies'
]
self.display_galaxy_browse_repositories_page(
strings_displayed=browse_strings_displayed)
self.display_installed_repository_manage_page(
installed_column_repository, strings_displayed=strings_displayed)
def test_0020_install_repositories( self ):
'''Install column_maker into column_maker tool panel section and install repository dependencies.'''
self.galaxy_logout()
self.galaxy_login( email=common.admin_email, username=common.admin_username )
self.install_repository( column_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
install_repository_dependencies=True,
new_tool_panel_section='column_maker',
strings_displayed=[ 'install_repository_dependencies' ] )
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name,
common.test_user_1_name )
installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name,
common.test_user_1_name )
browse_strings_displayed = [ installed_convert_repository.name,
installed_convert_repository.description,
installed_convert_repository.tool_shed,
installed_convert_repository.installed_changeset_revision,
installed_column_repository.name,
installed_column_repository.description,
installed_column_repository.installed_changeset_revision ]
strings_displayed = [ installed_convert_repository.name,
installed_convert_repository.description,
installed_convert_repository.tool_shed,
installed_convert_repository.installed_changeset_revision,
installed_column_repository.name,
installed_column_repository.installed_changeset_revision,
'Installed repository dependencies' ]
self.display_galaxy_browse_repositories_page( strings_displayed=browse_strings_displayed )
self.display_installed_repository_manage_page( installed_convert_repository,
strings_displayed=strings_displayed )
def test_0080_reinstall_convert_repository( self ):
'''Reinstall convert_chars with repository dependencies, verify that this installs both convert_chars and column_maker.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name,
common.test_user_1_name )
installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name,
common.test_user_1_name )
self.reinstall_repository( installed_convert_repository,
install_repository_dependencies=True,
no_changes=False,
new_tool_panel_section='convert_maker' )
strings_displayed = [ 'column_maker_0080',
'Add column',
self.url.replace( 'http://', '' ),
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision,
'Installed repository dependencies' ]
self.display_installed_repository_manage_page( installed_column_repository,
strings_displayed=strings_displayed )
strings_displayed = [ 'convert_chars_0080',
'Convert delimiters',
self.url.replace( 'http://', '' ),
installed_convert_repository.installed_changeset_revision,
'column_maker_0080',
installed_column_repository.installed_changeset_revision,
'Installed repository dependencies' ]
self.display_installed_repository_manage_page( installed_convert_repository,
strings_displayed=strings_displayed )
def test_0075_install_freebayes_repository( self ):
'''Install freebayes with repository dependencies. This should also automatically reactivate emboss_datatypes and reinstall emboss_5.'''
original_datatypes = self.get_datatypes_count()
strings_displayed = [ 'Handle', 'tool dependencies', 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18' ]
self.install_repository( freebayes_repository_name,
common.test_user_1_name,
category_name,
strings_displayed=strings_displayed,
install_tool_dependencies=False,
install_repository_dependencies=True,
new_tool_panel_section='freebayes' )
assert original_datatypes < self.get_datatypes_count(), 'Installing a repository that depends on emboss_datatypes did not add datatypes.'
emboss_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name )
datatypes_repository = test_db_util.get_installed_repository_by_name_owner( emboss_datatypes_repository_name, common.test_user_1_name )
strings_displayed = [ 'emboss_0050',
'emboss_datatypes_0050',
emboss_repository.installed_changeset_revision,
datatypes_repository.installed_changeset_revision ]
self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
# Installing freebayes should automatically reinstall emboss and reactivate emboss_datatypes.
# Now column_maker, convert_chars, emboss, emboss_datatypes, freebayes, and bismark should be installed.
installed_repositories = [ ( column_repository_name, common.test_user_1_name ),
( emboss_datatypes_repository_name, common.test_user_1_name ),
( emboss_repository_name, common.test_user_1_name ),
( freebayes_repository_name, common.test_user_1_name ),
( convert_repository_name, common.test_user_1_name ),
( bismark_repository_name, common.test_user_1_name ) ]
strings_displayed = [ 'emboss_0050', 'emboss_datatypes_0050', 'column_maker_0050', 'convert_chars_0050', 'bismark_0050', 'freebayes_0050' ]
strings_not_displayed = [ 'filtering_0050' ]
self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed )
self.verify_installed_repositories( installed_repositories )
def test_0050_verify_reinstallation_order( self ):
'''Verify that convert_chars_0160 and column_maker_0160 were reinstalled before filtering_0160.'''
filter_repository = test_db_util.get_installed_repository_by_name_owner( filter_repository_name, common.test_user_1_name )
column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name )
convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name )
# Filtering was selected for reinstallation, so convert chars and column maker should have been installed first.
assert filter_repository.update_time > convert_repository.update_time, 'Error: convert_chars_0160 shows a later update time than filtering_0160'
assert filter_repository.update_time > column_repository.update_time, 'Error: column_maker_0160 shows a later update time than filtering_0160'
def test_0030_verify_installation_order(self):
'''Verify that convert_chars_0150 was installed before column_maker_0150.'''
column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
# Column maker was selected for installation, so convert chars should have been installed first, as reflected by the update_time field.
assert column_repository.update_time > convert_repository.update_time, 'Error: column_maker_0150 shows an earlier update time than convert_chars_0150'
def test_0040_uninstall_all_repositories( self ):
'''Uninstall convert_chars_0160, column_maker_0160, and filtering_0160.'''
filter_repository = test_db_util.get_installed_repository_by_name_owner( filter_repository_name, common.test_user_1_name )
column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name )
convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name )
self.uninstall_repository( filter_repository, remove_from_disk=True )
self.uninstall_repository( column_repository, remove_from_disk=True )
self.uninstall_repository( convert_repository, remove_from_disk=True )
def test_0040_uninstall_filtering_repository( self ):
'''Uninstall filtering, verify tool panel section.'''
installed_filtering_repository = test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name )
installed_freebayes_repository = test_db_util.get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name )
self.uninstall_repository( installed_filtering_repository, remove_from_disk=True )
test_db_util.ga_refresh( installed_filtering_repository )
self.check_galaxy_repository_tool_panel_section( installed_filtering_repository, '' )
strings_displayed = [ 'Missing repository', 'filtering' ]
self.display_installed_repository_manage_page( installed_freebayes_repository, strings_displayed=strings_displayed )
self.check_galaxy_repository_db_status( filtering_repository_name,
common.test_user_1_name,
'Uninstalled' )
def test_0045_uninstall_freebayes_repository( self ):
'''Uninstall freebayes, verify tool panel section and missing repository dependency.'''
installed_freebayes_repository = test_db_util.get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name )
installed_filtering_repository = test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name )
self.uninstall_repository( installed_freebayes_repository, remove_from_disk=True )
test_db_util.ga_refresh( installed_freebayes_repository )
self.check_galaxy_repository_tool_panel_section( installed_freebayes_repository, 'freebayes' )
strings_displayed = [ 'Missing repository', 'freebayes', 'filtering_0040', 'user1', "Galaxy's filtering tool for test 0040" ]
self.display_installed_repository_manage_page( installed_filtering_repository, strings_displayed=strings_displayed )
self.check_galaxy_repository_db_status( 'freebayes_0040',
'user1',
'Uninstalled' )
def test_0085_uninstall_all_repositories( self ):
'''Uninstall convert_chars and column_maker to verify that they are in the right tool panel sections.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name,
common.test_user_1_name )
installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name,
common.test_user_1_name )
self.uninstall_repository( installed_column_repository, remove_from_disk=True )
self.uninstall_repository( installed_convert_repository, remove_from_disk=True )
test_db_util.ga_refresh( installed_column_repository )
test_db_util.ga_refresh( installed_convert_repository )
self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'convert_maker' )
self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'convert_maker' )
def test_0045_deactivate_convert_repository( self ):
'''Deactivate convert_chars, verify that both convert_chars and column_maker are deactivated.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name,
common.test_user_1_name )
installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name,
common.test_user_1_name )
self.uninstall_repository( installed_convert_repository, remove_from_disk=False )
strings_not_displayed = [ 'column_maker_0080',
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision ]
self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed )
def test_0045_uninstall_and_verify_tool_panel_sections( self ):
'''uninstall both and verify tool panel sections'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name,
common.test_user_1_name )
installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name,
common.test_user_1_name )
self.uninstall_repository( installed_column_repository, remove_from_disk=True )
self.uninstall_repository( installed_convert_repository, remove_from_disk=True )
test_db_util.ga_refresh( installed_convert_repository )
test_db_util.ga_refresh( installed_column_repository )
self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'new_column_maker' )
self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'new_convert_chars' )
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'
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_package_repository_name, common.test_user_1_name )
env_sh_path = self.get_env_sh_path( tool_dependency_name='bwa',
tool_dependency_version='0.5.9',
repository=base_repository )
assert os.path.exists( env_sh_path ), 'env.sh was not generated in %s for this dependency.' % env_sh_path
contents = file( env_sh_path, 'r' ).read()
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 '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_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'
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 )
env_sh_path = os.path.join( self.galaxy_tool_dependency_dir,
'bwa',
'0.5.9',
base_repository.owner,
base_repository.name,
base_repository.installed_changeset_revision,
'env.sh' )
assert os.path.exists( env_sh_path ), 'env.sh was not generated in %s for this dependency.' % env_sh_path
contents = file( env_sh_path, 'r' ).read()
if tool_repository.installed_changeset_revision not in contents or tool_repository.name not in contents:
raise AssertionError( 'The env.sh file was not correctly generated. Contents: %s' % contents )
def test_0065_deactivate_datatypes_repository(self):
'''Deactivate emboss_datatypes and verify that the datatypes count is reduced.'''
original_datatypes = self.get_datatypes_count()
repository = test_db_util.get_installed_repository_by_name_owner(
emboss_datatypes_repository_name, common.test_user_1_name)
self.uninstall_repository(repository, remove_from_disk=False)
assert original_datatypes > self.get_datatypes_count(
), 'Deactivating emboss_datatypes did not remove datatypes.'
# Now we have emboss, bismark, column_maker, and convert_chars installed, filtering and freebayes never installed, and emboss_datatypes deactivated.
installed_repositories = [
(column_repository_name, common.test_user_1_name),
(emboss_repository_name, common.test_user_1_name),
(convert_repository_name, common.test_user_1_name),
(bismark_repository_name, common.test_user_1_name)
]
uninstalled_repositories = [
(emboss_datatypes_repository_name, common.test_user_1_name),
(filtering_repository_name, common.test_user_1_name),
(freebayes_repository_name, common.test_user_1_name)
]
self.verify_installed_uninstalled_repositories(
installed_repositories=installed_repositories,
uninstalled_repositories=uninstalled_repositories)
strings_not_displayed = [
repository.name, repository.installed_changeset_revision
]
self.display_galaxy_browse_repositories_page(
strings_not_displayed=strings_not_displayed)
def test_0015_install_emboss_repository( self ):
'''Install the emboss repository without installing tool dependencies.'''
global repository_datatypes_count
global base_datatypes_count
strings_displayed = [ 'Handle', 'Never installed', 'tool dependencies', 'emboss', '5.0.0', 'package' ]
self.install_repository( 'emboss_0020',
common.test_user_1_name,
'Test 0020 Basic Repository Dependencies',
strings_displayed=strings_displayed,
install_tool_dependencies=False,
new_tool_panel_section='test_1020' )
installed_repository = test_db_util.get_installed_repository_by_name_owner( 'emboss_0020', common.test_user_1_name )
strings_displayed = [ 'emboss_0020',
'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020',
'user1',
self.url.replace( 'http://', '' ),
installed_repository.installed_changeset_revision ]
self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
strings_displayed.extend( [ 'Installed tool shed repository', 'Valid tools', 'antigenic' ] )
self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed )
strings_displayed = [ 'emboss', '5.0.0', 'package' ]
self.check_installed_repository_tool_dependencies( installed_repository, strings_displayed=strings_displayed, dependencies_installed=False )
self.verify_tool_metadata_for_installed_repository( installed_repository )
current_datatypes = int( self.get_datatypes_count() )
assert current_datatypes > base_datatypes_count, 'Installing emboss did not add new datatypes. Expected: %d. Found: %d' % \
( base_datatypes_count + repository_datatypes_count, current_datatypes )
def test_0035_reactivate_convert_repository(self):
'''Reactivate convert_chars, both convert_chars and column_maker should now show as installed.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
installed_column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
self.reactivate_repository(installed_convert_repository)
strings_displayed = [
'convert_chars_0080', 'Compute', 'an expression on every row',
'1.1.0', 'column_maker_0080', 'Installed repository dependencies',
self.url.replace('http://', ''),
installed_column_repository.installed_changeset_revision,
installed_convert_repository.installed_changeset_revision
]
self.display_installed_repository_manage_page(
installed_column_repository, strings_displayed=strings_displayed)
def test_0030_repair_column_repository( self ):
'''Repair the column_1430 repository.'''
'''
This is step 3 - Repair the column_1430 repository.
'''
column_repository = test_db_util.get_installed_repository_by_name_owner( 'column_1430', common.test_user_1_name )
self.repair_installed_repository( column_repository )
def test_0045_uninstall_and_verify_tool_panel_sections(self):
'''uninstall both and verify tool panel sections'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
installed_column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
self.uninstall_repository(installed_column_repository,
remove_from_disk=True)
self.uninstall_repository(installed_convert_repository,
remove_from_disk=True)
test_db_util.ga_refresh(installed_convert_repository)
test_db_util.ga_refresh(installed_column_repository)
self.check_galaxy_repository_tool_panel_section(
installed_column_repository, 'new_column_maker')
self.check_galaxy_repository_tool_panel_section(
installed_convert_repository, 'new_convert_chars')
def test_0045_install_repository_with_invalid_repository_dependency(self):
'''Install the repository and verify that galaxy detects invalid repository dependencies.'''
self.galaxy_logout()
self.galaxy_login(email=common.admin_email,
username=common.admin_username)
repository = test_db_util.get_repository_by_name_and_owner(
emboss_repository_name, common.test_user_1_name)
preview_strings_displayed = [
'emboss_0110',
self.get_repository_tip(repository),
'Ignoring repository dependency definition'
]
self.install_repository(
emboss_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
install_repository_dependencies=True,
preview_strings_displayed=preview_strings_displayed,
post_submit_strings_displayed=[
repository.name, repository.name, 'new'
],
includes_tools_for_display_in_tool_panel=True)
repository = test_db_util.get_installed_repository_by_name_owner(
emboss_repository_name, common.test_user_1_name)
self.display_installed_repository_manage_page(
repository, strings_not_displayed=['Repository dependencies'])
def test_0010_install_filtering_repository(self):
'''Install the filtering_1410 repository.'''
'''
We are at step 2 - Install filtering_1410 to Galaxy.
Install the filtering repository to Galaxy.
'''
self.galaxy_logout()
self.galaxy_login(email=common.admin_email,
username=common.admin_username)
self.install_repository('filtering_1410',
common.test_user_1_name,
category_name,
new_tool_panel_section='test_1410')
installed_repository = test_db_util.get_installed_repository_by_name_owner(
'filtering_1410', common.test_user_1_name)
strings_displayed = [
'filtering_1410', "Galaxy's filtering tool", 'user1',
self.url.replace('http://', ''),
installed_repository.installed_changeset_revision
]
self.display_galaxy_browse_repositories_page(
strings_displayed=strings_displayed)
strings_displayed.extend(
['Installed tool shed repository', 'Valid tools', 'Filter1'])
self.display_installed_repository_manage_page(
installed_repository, strings_displayed=strings_displayed)
self.verify_tool_metadata_for_installed_repository(
installed_repository)
def test_0025_uninstall_column_repository( self ):
'''uninstall column_maker, verify same section'''
installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name,
common.test_user_1_name )
self.uninstall_repository( installed_column_repository, remove_from_disk=True )
test_db_util.ga_refresh( installed_column_repository )
self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'column_maker' )
def test_0015_install_freebayes_repository(self):
'''Install the freebayes repository without installing tool dependencies.'''
strings_displayed = [
'Never installed', 'dependencies can be automatically handled',
'Handle', 'tool dependencies'
]
strings_displayed.extend(
['freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18'])
self.install_repository(repository_name,
common.test_user_1_name,
category_name,
strings_displayed=strings_displayed,
install_tool_dependencies=False,
new_tool_panel_section='test_1010')
installed_repository = test_db_util.get_installed_repository_by_name_owner(
repository_name, common.test_user_1_name)
strings_displayed = [
installed_repository.name, installed_repository.description,
installed_repository.owner, installed_repository.tool_shed,
installed_repository.installed_changeset_revision
]
self.display_galaxy_browse_repositories_page(
strings_displayed=strings_displayed)
self.display_installed_repository_manage_page(
installed_repository,
strings_displayed=[
'Installed tool shed repository', 'Valid tools', 'FreeBayes'
])
self.check_installed_repository_tool_dependencies(
installed_repository, dependencies_installed=False)
self.verify_tool_metadata_for_installed_repository(
installed_repository)
def test_0010_install_emboss_repository( self ):
'''Install the emboss repository into the Galaxy instance.'''
global repository_datatypes_count
global base_datatypes_count
self.galaxy_logout()
self.galaxy_login( email=common.admin_email, username=common.admin_username )
base_datatypes_count = int( self.get_datatypes_count() )
strings_displayed = [ 'Handle', 'Never installed', 'tool dependencies', 'emboss', '5.0.0', 'package' ]
self.install_repository( emboss_repository_name,
common.test_user_1_name,
'Test 0020 Basic Repository Dependencies',
strings_displayed=strings_displayed,
new_tool_panel_section='test_1210' )
installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name )
strings_displayed = [ installed_repository.name,
installed_repository.description,
installed_repository.owner,
installed_repository.tool_shed,
installed_repository.installed_changeset_revision ]
self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
current_datatypes = int( self.get_datatypes_count() )
# If we are running this test by itself, installing the emboss repository should also install the emboss_datatypes
# repository, and this should add datatypes to the datatypes registry. If that is the case, verify that datatypes
# have been added, otherwise verify that the count is unchanged.
if running_standalone:
assert current_datatypes == base_datatypes_count + repository_datatypes_count, 'Installing emboss did not add new datatypes.'
else:
assert current_datatypes == base_datatypes_count, 'Installing emboss added new datatypes.'
def test_0015_install_emboss_repository( self ):
'''Install the emboss repository without installing tool dependencies.'''
global repository_datatypes_count
global base_datatypes_count
global running_standalone
base_datatypes_count = int( self.get_datatypes_count() )
strings_displayed = [ 'Handle', 'Never installed', 'tool dependencies', 'emboss', '5.0.0', 'package' ]
self.install_repository( 'emboss_0030',
common.test_user_1_name,
'Test 0030 Repository Dependency Revisions',
strings_displayed=strings_displayed,
install_tool_dependencies=False,
new_tool_panel_section='test_1030' )
installed_repository = test_db_util.get_installed_repository_by_name_owner( 'emboss_0030', common.test_user_1_name )
strings_displayed = [ installed_repository.name,
installed_repository.description,
installed_repository.owner,
installed_repository.tool_shed,
installed_repository.installed_changeset_revision ]
self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
self.display_installed_repository_manage_page( installed_repository,
strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'antigenic' ] )
self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False )
self.verify_tool_metadata_for_installed_repository( installed_repository )
self.update_installed_repository( installed_repository, strings_displayed=[ "there are no updates available" ] )
current_datatypes = int( self.get_datatypes_count() )
if running_standalone:
assert current_datatypes == base_datatypes_count + repository_datatypes_count, 'Installing emboss did not add new datatypes.'
else:
assert current_datatypes == base_datatypes_count, 'Installing emboss added new datatypes.'
def test_0050_install_deactivate_filtering_repository( self ):
'''Install and deactivate filtering.'''
global running_standalone
original_datatypes = self.get_datatypes_count()
# After this test, the repositories should be in the following states:
# Installed: freebayes
# Deactivated: filtering
# Never installed: emboss, emboss_datatypes, bwa_color, bwa_base
self.install_repository( filtering_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
install_repository_dependencies=False,
new_tool_panel_section='filtering_1090' )
installed_repositories = [ ( filtering_repository_name, common.test_user_1_name ),
( freebayes_repository_name, common.test_user_1_name ) ]
strings_displayed = [ 'filtering_0090', 'freebayes_0090' ]
strings_not_displayed = [ 'emboss_0090', 'emboss_datatypes_0090', 'bwa_color_0090', 'bwa_base_0090' ]
self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed )
self.verify_installed_repositories( installed_repositories )
filtering_repository = test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name )
self.uninstall_repository( filtering_repository, remove_from_disk=False )
strings_displayed = [ 'freebayes_0090' ]
strings_not_displayed = [ 'filtering_0090', 'emboss_0090', 'emboss_datatypes_0090', 'bwa_color_0090', 'bwa_base_0090' ]
self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed )
def test_0010_install_emboss_repository(self):
'''Install the emboss repository into the Galaxy instance.'''
global repository_datatypes_count
global base_datatypes_count
global running_standalone
self.galaxy_logout()
self.galaxy_login(email=common.admin_email,
username=common.admin_username)
base_datatypes_count = int(self.get_datatypes_count())
strings_displayed = [
'Handle', 'Never installed', 'tool dependencies', 'emboss',
'5.0.0', 'package'
]
self.install_repository(emboss_repository_name,
common.test_user_1_name,
'Test 0030 Repository Dependency Revisions',
strings_displayed=strings_displayed,
new_tool_panel_section='test_1210')
installed_repository = test_db_util.get_installed_repository_by_name_owner(
emboss_repository_name, common.test_user_1_name)
strings_displayed = [
installed_repository.name, installed_repository.description,
installed_repository.owner, installed_repository.tool_shed,
installed_repository.installed_changeset_revision
]
self.display_galaxy_browse_repositories_page(
strings_displayed=strings_displayed)
current_datatypes = int(self.get_datatypes_count())
# If we are running this test by itself, installing the emboss repository should also install the emboss_datatypes
# repository, and this should add datatypes to the datatypes registry. If that is the case, verify that datatypes
# have been added, otherwise verify that the count is unchanged.
if running_standalone:
assert current_datatypes == base_datatypes_count + repository_datatypes_count, 'Installing emboss did not add new datatypes.'
else:
assert current_datatypes == base_datatypes_count, 'Installing emboss added new datatypes.'
def test_0055_install_uninstall_datatypes_repository( self ):
'''Install and uninstall emboss_datatypes.'''
# After this test, the repositories should be in the following states:
# Installed: freebayes
# Deactivated: filtering
# Uninstalled: emboss_datatypes
# Never installed: emboss, bwa_color, bwa_base
self.install_repository( emboss_datatypes_repository_name,
common.test_user_1_name,
category_name,
includes_tools_for_display_in_tool_panel=False )
installed_repositories = [ ( emboss_datatypes_repository_name, common.test_user_1_name ),
( freebayes_repository_name, common.test_user_1_name ) ]
uninstalled_repositories = [ ( emboss_repository_name, common.test_user_1_name ),
( filtering_repository_name, common.test_user_1_name ),
( bwa_color_repository_name, common.test_user_1_name ),
( bwa_base_repository_name, common.test_user_1_name ) ]
strings_displayed = [ 'emboss_datatypes_0090', 'freebayes_0090' ]
strings_not_displayed = [ 'filtering_0090', 'emboss_0090', 'bwa_color_0090', 'bwa_base_0090' ]
self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed )
self.verify_installed_repositories( installed_repositories )
datatypes_repository = test_db_util.get_installed_repository_by_name_owner( emboss_datatypes_repository_name, common.test_user_1_name )
self.uninstall_repository( datatypes_repository, remove_from_disk=True )
strings_displayed = [ 'freebayes_0090' ]
strings_not_displayed = [ 'emboss_datatypes_0090', 'filtering_0090', 'emboss_0090', 'bwa_color_0090', 'bwa_base_0090' ]
self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed )
def test_0070_uninstall_emboss_repository(self):
'''Uninstall the emboss_5 repository.'''
repository = test_db_util.get_installed_repository_by_name_owner(
emboss_repository_name, common.test_user_1_name)
self.uninstall_repository(repository, remove_from_disk=True)
strings_not_displayed = [
repository.name, repository.installed_changeset_revision
]
self.display_galaxy_browse_repositories_page(
strings_not_displayed=strings_not_displayed)
test_db_util.ga_refresh(repository)
self.check_galaxy_repository_tool_panel_section(
repository, 'emboss_5_0050')
# Now we have bismark, column_maker, and convert_chars installed, filtering and freebayes never installed, emboss_datatypes deactivated,
# and emboss uninstalled.
installed_repositories = [
(column_repository_name, common.test_user_1_name),
(convert_repository_name, common.test_user_1_name),
(bismark_repository_name, common.test_user_1_name)
]
uninstalled_repositories = [
(emboss_datatypes_repository_name, common.test_user_1_name),
(emboss_repository_name, common.test_user_1_name),
(filtering_repository_name, common.test_user_1_name),
(freebayes_repository_name, common.test_user_1_name)
]
self.verify_installed_uninstalled_repositories(
installed_repositories=installed_repositories,
uninstalled_repositories=uninstalled_repositories)
def test_0025_uninstall_datatypes_repository( self ):
'''Uninstall the emboss_datatypes repository.'''
global base_datatypes_count
installed_repository = test_db_util.get_installed_repository_by_name_owner( datatypes_repository_name, common.test_user_1_name )
self.uninstall_repository( installed_repository, remove_from_disk=True )
current_datatypes = int( self.get_datatypes_count() )
assert current_datatypes == base_datatypes_count, 'Uninstalling emboss did not remove datatypes.'
def test_0085_uninstall_all_repositories(self):
'''Uninstall convert_chars and column_maker to verify that they are in the right tool panel sections.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
installed_column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
self.uninstall_repository(installed_column_repository,
remove_from_disk=True)
self.uninstall_repository(installed_convert_repository,
remove_from_disk=True)
test_db_util.ga_refresh(installed_column_repository)
test_db_util.ga_refresh(installed_convert_repository)
self.check_galaxy_repository_tool_panel_section(
installed_column_repository, 'convert_maker')
self.check_galaxy_repository_tool_panel_section(
installed_convert_repository, 'convert_maker')
def test_0025_deactivate_emboss_repository( self ):
'''Deactivate the emboss repository without removing it from disk.'''
installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name )
self.uninstall_repository( installed_repository, remove_from_disk=False )
strings_not_displayed = [ installed_repository.name,
installed_repository.installed_changeset_revision ]
self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed )
def test_0045_deactivate_convert_repository(self):
'''Deactivate convert_chars, verify that both convert_chars and column_maker are deactivated.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
installed_column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
self.uninstall_repository(installed_convert_repository,
remove_from_disk=False)
strings_not_displayed = [
installed_column_repository.name,
installed_column_repository.installed_changeset_revision,
installed_convert_repository.name,
installed_convert_repository.installed_changeset_revision
]
self.display_galaxy_browse_repositories_page(
strings_not_displayed=strings_not_displayed)
def test_0040_reactivate_datatypes_repository( self ):
'''Reactivate the datatypes repository and verify that the datatypes are again present.'''
global repository_datatypes_count
global base_datatypes_count
installed_repository = test_db_util.get_installed_repository_by_name_owner( datatypes_repository_name, common.test_user_1_name )
self.reactivate_repository( installed_repository )
current_datatypes = int( self.get_datatypes_count() )
assert current_datatypes > base_datatypes_count, 'Reactivating emboss did not add new datatypes.'
def test_0075_install_freebayes_repository(self):
'''Install freebayes with repository dependencies. This should also automatically reactivate emboss_datatypes and reinstall emboss_5.'''
original_datatypes = self.get_datatypes_count()
strings_displayed = [
'Handle', 'tool dependencies', 'freebayes', '0.9.4_9696d0ce8a9',
'samtools', '0.1.18'
]
self.install_repository(freebayes_repository_name,
common.test_user_1_name,
category_name,
strings_displayed=strings_displayed,
install_tool_dependencies=False,
install_repository_dependencies=True,
new_tool_panel_section='freebayes')
assert original_datatypes < self.get_datatypes_count(
), 'Installing a repository that depends on emboss_datatypes did not add datatypes.'
emboss_repository = test_db_util.get_installed_repository_by_name_owner(
emboss_repository_name, common.test_user_1_name)
datatypes_repository = test_db_util.get_installed_repository_by_name_owner(
emboss_datatypes_repository_name, common.test_user_1_name)
strings_displayed = [
'emboss_0050', 'emboss_datatypes_0050',
emboss_repository.installed_changeset_revision,
datatypes_repository.installed_changeset_revision
]
self.display_galaxy_browse_repositories_page(
strings_displayed=strings_displayed)
# Installing freebayes should automatically reinstall emboss and reactivate emboss_datatypes.
# Now column_maker, convert_chars, emboss, emboss_datatypes, freebayes, and bismark should be installed.
installed_repositories = [
(column_repository_name, common.test_user_1_name),
(emboss_datatypes_repository_name, common.test_user_1_name),
(emboss_repository_name, common.test_user_1_name),
(freebayes_repository_name, common.test_user_1_name),
(convert_repository_name, common.test_user_1_name),
(bismark_repository_name, common.test_user_1_name)
]
strings_displayed = [
'emboss_0050', 'emboss_datatypes_0050', 'column_maker_0050',
'convert_chars_0050', 'bismark_0050', 'freebayes_0050'
]
strings_not_displayed = ['filtering_0050']
self.display_galaxy_browse_repositories_page(
strings_displayed=strings_displayed,
strings_not_displayed=strings_not_displayed)
self.verify_installed_repositories(installed_repositories)
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 )
strings_displayed = [ base_repository.name, base_repository.owner, base_repository.installed_changeset_revision ]
strings_displayed.extend( [ tool_repository.name, tool_repository.owner, 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=[] )
checks = [ ( tool_repository,
[ tool_repository.name, tool_repository.owner, tool_repository.installed_changeset_revision ],
[ 'Missing tool dependencies' ] ),
( base_repository,
[ base_repository.name, base_repository.owner, base_repository.installed_changeset_revision, tool_repository.name,
tool_repository.owner, tool_repository.installed_changeset_revision ],
[ 'Missing tool dependencies' ] ) ]
for repository, strings_displayed, strings_not_displayed in checks:
self.display_installed_repository_manage_page( repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed )
def test_0050_reactivate_column_repository(self):
'''Reactivate column_maker. This should not automatically reactivate convert_chars, so column_maker should be displayed as installed but missing repository dependencies.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
installed_column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
self.reactivate_repository(installed_column_repository)
strings_displayed = [
'column_maker_0080', 'Add column',
self.url.replace('http://', ''),
installed_column_repository.installed_changeset_revision,
'convert_chars_0080',
installed_convert_repository.installed_changeset_revision,
'Missing repository dependencies', 'Deactivated'
]
self.display_installed_repository_manage_page(
installed_column_repository, strings_displayed=strings_displayed)
