2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/8990b28bb0e7/
changeset: 8990b28bb0e7
user: inithello
date: 2012-12-21 16:32:45
summary: Fix handling of repository tools and tool dependencies. Fix issue with
functional tests altering the integrated tool panel.
affected #: 2 files
diff -r 5c9971aba1b4f4062e27dcbdd9262e3e81c88ddf -r
8990b28bb0e77dbf06a83e47e0f76045c28968f3 lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -75,8 +75,9 @@
# Replace the old list of in-memory config_elems with the new list for this
shed_tool_conf_dict.
shed_tool_conf_dict[ 'config_elems' ] = config_elems
app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict
- # Write the current in-memory version of the integrated_tool_panel.xml file to disk.
- app.toolbox.write_integrated_tool_panel_config_file()
+ if app.config.update_integrated_tool_panel:
+ # Write the current in-memory version of the integrated_tool_panel.xml file to
disk.
+ app.toolbox.write_integrated_tool_panel_config_file()
app.toolbox_search = ToolBoxSearch( app.toolbox )
def alter_config_and_load_prorietary_datatypes( app, datatypes_config,
relative_install_dir, deactivate=False, override=True ):
"""
@@ -1055,7 +1056,7 @@
shed_tool_conf_dict[ 'config_elems' ] = config_elems
trans.app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict
trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox )
- if uninstall:
+ if uninstall and trans.app.config.update_integrated_tool_panel:
# Write the current in-memory version of the integrated_tool_panel.xml file to
disk.
trans.app.toolbox.write_integrated_tool_panel_config_file()
def remove_tool_dependency( trans, tool_dependency ):
diff -r 5c9971aba1b4f4062e27dcbdd9262e3e81c88ddf -r
8990b28bb0e77dbf06a83e47e0f76045c28968f3
lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1088,14 +1088,16 @@
if ( not includes_tools and not includes_repository_dependencies ) or \
( ( includes_tools or includes_repository_dependencies ) and kwd.get(
'select_tool_panel_section_button', False ) ):
install_repository_dependencies = CheckboxField.is_checked(
install_repository_dependencies )
- if includes_tool_dependencies:
- install_tool_dependencies = CheckboxField.is_checked(
install_tool_dependencies )
+ if includes_tools:
shed_tool_conf = kwd[ 'shed_tool_conf' ]
else:
- install_tool_dependencies = False
# If installing a repository that includes no tools, get the relative
tool_path from the file to which the migrated_tools_config
# setting points.
shed_tool_conf = trans.app.config.migrated_tools_config
+ if includes_tool_dependencies:
+ install_tool_dependencies = CheckboxField.is_checked(
install_tool_dependencies )
+ else:
+ install_tool_dependencies = False
tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans,
shed_tool_conf )
created_or_updated_tool_shed_repositories, repo_info_dicts,
filtered_repo_info_dicts, message = \
shed_util.create_repository_dependency_objects( trans, tool_path,
tool_shed_url, repo_info_dicts, reinstalling=False )
https://bitbucket.org/galaxy/galaxy-central/changeset/5e60f799a868/
changeset: 5e60f799a868
user: inithello
date: 2012-12-21 16:33:18
summary: Make functional tests explicitly specify which shed tool config to use.
affected #: 2 files
diff -r 8990b28bb0e77dbf06a83e47e0f76045c28968f3 -r
5e60f799a8687d92fb41dd8a764d434623837772 test/tool_shed/base/twilltestcase.py
--- a/test/tool_shed/base/twilltestcase.py
+++ b/test/tool_shed/base/twilltestcase.py
@@ -28,6 +28,7 @@
self.file_dir = os.environ.get( 'TOOL_SHED_TEST_FILE_DIR', None )
self.tool_shed_test_file = None
self.tool_data_path = os.environ.get( 'GALAXY_TEST_TOOL_DATA_PATH' )
+ self.shed_tool_conf = os.environ.get( 'GALAXY_TEST_SHED_TOOL_CONF' )
# TODO: Figure out a way to alter these attributes during tests.
self.galaxy_tool_dependency_dir = None # os.environ.get(
'GALAXY_TEST_TOOL_DEPENDENCY_DIR' )
self.shed_tools_dict = {}
@@ -431,6 +432,8 @@
checkbox.selected = True
else:
checkbox.selected = False
+ if 'shed_tool_conf' not in kwd:
+ kwd[ 'shed_tool_conf' ] = self.shed_tool_conf
self.submit_form( 1, 'select_tool_panel_section_button', **kwd )
self.initiate_installation_process()
self.wait_for_repository_installation( repository, changeset_revision )
diff -r 8990b28bb0e77dbf06a83e47e0f76045c28968f3 -r
5e60f799a8687d92fb41dd8a764d434623837772 test/tool_shed/functional_tests.py
--- a/test/tool_shed/functional_tests.py
+++ b/test/tool_shed/functional_tests.py
@@ -256,6 +256,7 @@
shed_tool_conf_template_parser = string.Template( shed_tool_conf_xml_template )
shed_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute(
shed_tool_path=galaxy_shed_tool_path )
file( galaxy_shed_tool_conf_file, 'w' ).write( shed_tool_conf_xml )
+ os.environ[ 'GALAXY_TEST_SHED_TOOL_CONF' ] = galaxy_shed_tool_conf_file
# ---- Build Galaxy Application
--------------------------------------------------
galaxy_global_conf = { '__file__' : 'universe_wsgi.ini.sample' }
Repository URL:
https://bitbucket.org/galaxy/galaxy-central/
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