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Add ToolShed metadata comparison method for Data Managers.

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This commit is contained in:
Daniel Blankenberg
2013-05-17 11:26:00 -04:00
parent 535d5e934f
commit a21a87eb4f
1 changed files with 26 additions and 3 deletions
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lib/tool_shed/util/metadata_util.py
+26 -3
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@@ -75,6 +75,7 @@ def compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_
ancestor_repository_dependencies = ancestor_repository_dependencies_dict.get( 'repository_dependencies', [] )
ancestor_tool_dependencies = ancestor_metadata_dict.get( 'tool_dependencies', {} )
ancestor_workflows = ancestor_metadata_dict.get( 'workflows', [] )
ancestor_data_manager = ancestor_metadata_dict.get( 'data_manager', {} )
current_datatypes = current_metadata_dict.get( 'datatypes', [] )
current_tools = current_metadata_dict.get( 'tools', [] )
current_guids = [ tool_dict[ 'guid' ] for tool_dict in current_tools ]
@@ -84,6 +85,7 @@ def compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_
current_repository_dependencies = current_repository_dependencies_dict.get( 'repository_dependencies', [] )
current_tool_dependencies = current_metadata_dict.get( 'tool_dependencies', {} )
current_workflows = current_metadata_dict.get( 'workflows', [] )
current_data_manager = current_metadata_dict.get( 'data_manager', {} )
# Handle case where no metadata exists for either changeset.
no_datatypes = not ancestor_datatypes and not current_datatypes
no_readme_files = not ancestor_readme_files and not current_readme_files
@@ -92,7 +94,8 @@ def compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_
no_tool_dependencies = not ancestor_tool_dependencies and not current_tool_dependencies
no_tools = not ancestor_guids and not current_guids
no_workflows = not ancestor_workflows and not current_workflows
if no_datatypes and no_readme_files and no_repository_dependencies and no_tool_dependencies and no_tools and no_workflows:
no_data_manager = not ancestor_data_manager and not current_data_manager
if no_datatypes and no_readme_files and no_repository_dependencies and no_tool_dependencies and no_tools and no_workflows and no_data_manager:
return 'no metadata'
# Uncomment the following if we decide that README files should affect how installable repository revisions are defined. See the NOTE in the
# compare_readme_files() method.
@@ -101,20 +104,25 @@ def compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_
tool_dependency_comparison = compare_tool_dependencies( ancestor_tool_dependencies, current_tool_dependencies )
workflow_comparison = compare_workflows( ancestor_workflows, current_workflows )
datatype_comparison = compare_datatypes( ancestor_datatypes, current_datatypes )
data_manager_comparison = compare_data_manager( ancestor_data_manager, current_data_manager )
# Handle case where all metadata is the same.
# TODO: these values, ('equal', etc), should be abstracted out to constants
if ancestor_guids == current_guids and \
repository_dependency_comparison == 'equal' and \
tool_dependency_comparison == 'equal' and \
workflow_comparison == 'equal' and \
datatype_comparison == 'equal':
datatype_comparison == 'equal' and \
data_manager_comparison == 'equal':
return 'equal'
# Handle case where ancestor metadata is a subset of current metadata.
# readme_file_is_subset = readme_file_comparision in [ 'equal', 'subset' ]
# TODO: this list [ 'equal', 'subset' ] should be created once
repository_dependency_is_subset = repository_dependency_comparison in [ 'equal', 'subset' ]
tool_dependency_is_subset = tool_dependency_comparison in [ 'equal', 'subset' ]
workflow_dependency_is_subset = workflow_comparison in [ 'equal', 'subset' ]
datatype_is_subset = datatype_comparison in [ 'equal', 'subset' ]
if repository_dependency_is_subset and tool_dependency_is_subset and workflow_dependency_is_subset and datatype_is_subset:
datamanager_is_subset = data_manager_comparison in [ 'equal', 'subset' ]
if repository_dependency_is_subset and tool_dependency_is_subset and workflow_dependency_is_subset and datatype_is_subset and datamanager_is_subset:
is_subset = True
for guid in ancestor_guids:
if guid not in current_guids:
@@ -124,6 +132,21 @@ def compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_
return 'subset'
return 'not equal and not subset'
def compare_data_manager( ancestor_metadata, current_metadata ):
"""Determine if ancestor_metadata is the same as or a subset of current_metadata for data_managers."""
def __data_manager_dict_to_tuple_list( metadata_dict ):
# we do not check tool_guid or tool conf file name
return set( sorted( [ ( name, tuple( sorted( value.get( 'data_tables', [] ) ) ), value.get( 'guid' ), value.get( 'version' ), value.get( 'name' ), value.get( 'id' ) ) for name, value in metadata_dict.iteritems() ] ) )
# only compare valid entries, any invalid entries are ignored
ancestor_metadata = __data_manager_dict_to_tuple_list( ancestor_metadata.get( 'data_managers', {} ) )
current_metadata = __data_manager_dict_to_tuple_list( current_metadata.get( 'data_managers', {} ) )
# use set comparisons
if ancestor_metadata.issubset( current_metadata ):
if ancestor_metadata == current_metadata:
return 'equal'
return 'subset'
return 'not equal and not subset'
def compare_datatypes( ancestor_datatypes, current_datatypes ):
"""Determine if ancestor_datatypes is the same as or a subset of current_datatypes."""
# Each datatype dict looks something like: {"dtype": "galaxy.datatypes.images:Image", "extension": "pdf", "mimetype": "application/pdf"}