1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7cacfb33db90/ Changeset: 7cacfb33db90 Branch: next-stable User: jmchilton Date: 2014-08-04 20:57:31 Summary: Merged in jmchilton/galaxy-central-fork-1/next-stable (pull request #449)
Fix tool shed's logic related to finding tool externally referenced files. Affected #: 4 files
diff -r 7ac5a36c0ce7a6eb280d339de2107740552825ce -r 7cacfb33db90dee8c4e9ce78a3a735cd6cef8490 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -69,7 +69,7 @@ from galaxy.model import Workflow from tool_shed.util import common_util from tool_shed.util import shed_util_common as suc -from .loader import load_tool, template_macro_params +from .loader import load_tool, template_macro_params, raw_tool_xml_tree, imported_macro_paths from .execute import execute as execute_job from .wrappers import ( ToolParameterValueWrapper, @@ -2989,6 +2989,23 @@ def get_default_history_by_trans( self, trans, create=False ): return trans.get_history( create=create )
+ @classmethod + def get_externally_referenced_paths( self, path ): + """ Return relative paths to externally referenced files by the tool + described by file at `path`. External components should not assume things + about the structure of tool xml files (this is the tool's responsibility). + """ + tree = raw_tool_xml_tree(path) + root = tree.getroot() + external_paths = [] + for code_elem in root.findall( 'code' ): + external_path = code_elem.get( 'file' ) + if external_path: + external_paths.append( external_path ) + external_paths.extend( imported_macro_paths( root ) ) + # May also need to load external citation files as well at some point. + return external_paths +
class OutputParameterJSONTool( Tool ): """
diff -r 7ac5a36c0ce7a6eb280d339de2107740552825ce -r 7cacfb33db90dee8c4e9ce78a3a735cd6cef8490 lib/galaxy/tools/loader.py --- a/lib/galaxy/tools/loader.py +++ b/lib/galaxy/tools/loader.py @@ -10,7 +10,7 @@ """ Loads tool from file system and preprocesses tool macros. """ - tree = parse_xml(path) + tree = raw_tool_xml_tree(path) root = tree.getroot()
_import_macros(root, path) @@ -38,14 +38,31 @@ return param_dict
+def raw_tool_xml_tree(path): + """ Load raw (no macro expansion) tree representation of tool represented + at the specified path. + """ + tree = parse_xml(path) + return tree + + +def imported_macro_paths(root): + macros_el = _macros_el(root) + return _imported_macro_paths_from_el(macros_el) + + def _import_macros(root, path): tool_dir = os.path.dirname(path) - macros_el = root.find('macros') + macros_el = _macros_el(root) if macros_el: macro_els = _load_macros(macros_el, tool_dir) _xml_set_children(macros_el, macro_els)
+def _macros_el(root): + return root.find('macros') + + def _macros_of_type(root, type, el_func): macros_el = root.find('macros') macro_dict = {} @@ -159,6 +176,17 @@ def _load_imported_macros(macros_el, tool_dir): macros = []
+ for tool_relative_import_path in _imported_macro_paths_from_el(macros_el): + import_path = \ + os.path.join(tool_dir, tool_relative_import_path) + file_macros = _load_macro_file(import_path, tool_dir) + macros.extend(file_macros) + + return macros + + +def _imported_macro_paths_from_el(macros_el): + imported_macro_paths = [] macro_import_els = [] if macros_el: macro_import_els = macros_el.findall("import") @@ -166,12 +194,8 @@ raw_import_path = macro_import_el.text tool_relative_import_path = \ os.path.basename(raw_import_path) # Sanitize this - import_path = \ - os.path.join(tool_dir, tool_relative_import_path) - file_macros = _load_macro_file(import_path, tool_dir) - macros.extend(file_macros) - - return macros + imported_macro_paths.append( tool_relative_import_path ) + return imported_macro_paths
def _load_macro_file(path, tool_dir):
diff -r 7ac5a36c0ce7a6eb280d339de2107740552825ce -r 7cacfb33db90dee8c4e9ce78a3a735cd6cef8490 lib/tool_shed/tools/tool_validator.py --- a/lib/tool_shed/tools/tool_validator.py +++ b/lib/tool_shed/tools/tool_validator.py @@ -3,6 +3,7 @@ import os import tempfile
+from galaxy.tools import Tool from galaxy.tools import parameters from galaxy.tools.parameters import dynamic_options
@@ -311,15 +312,14 @@ message = '' tmp_tool_config = hg_util.get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) if tmp_tool_config: - element_tree, error_message = xml_util.parse_xml( tmp_tool_config ) - if element_tree is None: + tool_element, error_message = xml_util.parse_xml( tmp_tool_config ) + if tool_element is None: return tool, message - element_tree_root = element_tree.getroot() - # Look for code files required by the tool config. + # Look for external files required by the tool config. tmp_code_files = [] - for code_elem in element_tree_root.findall( 'code' ): - code_file_name = code_elem.get( 'file' ) - tmp_code_file_name = hg_util.copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) + external_paths = Tool.get_externally_referenced_paths( tmp_tool_config ) + for path in external_paths: + tmp_code_file_name = hg_util.copy_file_from_manifest( repo, ctx, path, work_dir ) if tmp_code_file_name: tmp_code_files.append( tmp_code_file_name ) tool, valid, message = self.load_tool_from_config( repository_id, tmp_tool_config )
diff -r 7ac5a36c0ce7a6eb280d339de2107740552825ce -r 7cacfb33db90dee8c4e9ce78a3a735cd6cef8490 test/unit/tools/test_tool_external_files.py --- /dev/null +++ b/test/unit/tools/test_tool_external_files.py @@ -0,0 +1,30 @@ +""" Unit test logic related to finding externally referenced files in tool +descriptions. +""" +import tempfile +import os +import shutil +from galaxy.tools import Tool + + +def test_finds_external_code_file(): + assert __external_files("""<tool><code file="foo.py" /></tool>""") == ["foo.py"] + + +def test_finds_skips_empty_code_file_attribute(): + assert __external_files("""<tool><code /></tool>""") == [] + + +def test_finds_external_macro_file(): + assert __external_files("""<tool><macros><import>cool_macros.xml</import></macros></tool>""") == ["cool_macros.xml"] + + +def __external_files(contents): + base_path = tempfile.mkdtemp() + try: + tool_path = os.path.join(base_path, "tool.xml") + with open(tool_path, "w") as f: + f.write(contents) + return Tool.get_externally_referenced_paths(tool_path) + finally: + shutil.rmtree(base_path)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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