Fix missing index file check

galaxyproject · Dec 1, 2017 · c0887d7 · c0887d7
1 parent b03f16e
commit c0887d7
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/lib/tool_shed/galaxy_install/install_manager.py b/lib/tool_shed/galaxy_install/install_manager.py
@@ -532,7 +532,7 @@ def __handle_repository_contents(self, tool_shed_repository, tool_path, reposito
                 stdtm.install_tool_data_tables(tool_shed_repository, tool_index_sample_files)
             if tool_data_table_elems:
                 self.app.tool_data_tables.add_new_entries_from_config_file(tool_data_table_conf_filename,
-                                                                           self.app.config.shed_tool_data_path,
+                                                                           None,
                                                                            self.app.config.shed_tool_data_table_config,
                                                                            persist=True)
         if 'tools' in irmm_metadata_dict:

diff --git a/lib/tool_shed/tools/data_table_manager.py b/lib/tool_shed/tools/data_table_manager.py
@@ -90,7 +90,7 @@ def handle_missing_data_table_entry(self, relative_install_dir, tool_path, repos
             self.reset_tool_data_tables()
         return repository_tools_tups
 
-    def handle_sample_tool_data_table_conf_file(self, filename, persist=False):
+    def handle_sample_tool_data_table_conf_file(self, filename, persist=False, tool_data_tables=None):
         """
         Parse the incoming filename and add new entries to the in-memory
         self.app.tool_data_tables dictionary.  If persist is True (should
@@ -100,8 +100,9 @@ def handle_sample_tool_data_table_conf_file(self, filename, persist=False):
         """
         error = False
         message = ''
+        tdtm = tool_data_tables or self.tdtm
         try:
-            new_table_elems, message = self.tdtm \
+            new_table_elems, message = tdtm \
                 .add_new_entries_from_config_file(config_filename=filename,
                                                   tool_data_path=self.app.config.shed_tool_data_path,
                                                   shed_tool_data_table_config=self.app.config.shed_tool_data_table_config,

diff --git a/lib/tool_shed/tools/tool_validator.py b/lib/tool_shed/tools/tool_validator.py
@@ -72,7 +72,8 @@ def check_tool_input_params(self, repo_dir, tool_config_name, tool, sample_files
                         if sample_tool_data_table_conf:
                             error, correction_msg = \
                                 self.stdtm.handle_sample_tool_data_table_conf_file(sample_tool_data_table_conf,
-                                                                                  persist=False)
+                                                                                  persist=False,
+                                                                                  tool_data_tables=tool.app.tool_data_tables)
                             if error:
                                 invalid_files_and_errors_tups.append(('tool_data_table_conf.xml.sample', correction_msg))
                         else:
@@ -82,9 +83,9 @@ def check_tool_input_params(self, repo_dir, tool_config_name, tool, sample_files
                             invalid_tup = (tool_config_name, correction_msg)
                             if invalid_tup not in invalid_files_and_errors_tups:
                                 invalid_files_and_errors_tups.append(invalid_tup)
-                    if options.index_file or options.missing_index_file:
+                    if options.index_file or options.tool_data_table and options.tool_data_table.missing_index_file:
                         # Make sure the repository contains the required xxx.loc.sample file.
-                        index_file = options.index_file or options.missing_index_file
+                        index_file = options.index_file or options.tool_data_table.missing_index_file
                         index_file_name = basic_util.strip_path(index_file)
                         sample_found = False
                         for sample_file in sample_files: