Use ValidationContext data tables instead of separately passing in re…

…levant data tables
galaxyproject · Dec 3, 2017 · db88175 · db88175
1 parent 482c9cc
commit db88175
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Showing 2 changed files with 5 additions and 9 deletions.
diff --git a/lib/tool_shed/tools/data_table_manager.py b/lib/tool_shed/tools/data_table_manager.py
@@ -12,7 +12,6 @@
 class ShedToolDataTableManager(object):
 
     def __init__(self, app):
-        self.tdtm = tdtm(app.config.shed_tool_data_path)
         self.app = app
 
     def generate_repository_info_elem(self, tool_shed, repository_name, changeset_revision, owner,
@@ -90,7 +89,7 @@ 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, tool_data_tables=None):
+    def handle_sample_tool_data_table_conf_file(self, filename, persist=False):
         """
         Parse the incoming filename and add new entries to the in-memory
         self.app.tool_data_tables dictionary.  If persist is True (should
@@ -99,10 +98,8 @@ def handle_sample_tool_data_table_conf_file(self, filename, persist=False, tool_
         file on disk.
         """
         error = False
-        message = ''
-        tdtm = tool_data_tables or self.tdtm
         try:
-            new_table_elems, message = tdtm \
+            new_table_elems, message = self.app.tool_data_tables \
                 .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,
@@ -170,9 +167,9 @@ def install_tool_data_tables(self, tool_shed_repository, tool_index_sample_files
             # Remove old data_table
             os.unlink(tool_data_table_conf_filename)
             # Persist new data_table content.
-            self.tdtm.to_xml_file(tool_data_table_conf_filename, elems)
+            self.app.tool_data_tables.to_xml_file(tool_data_table_conf_filename, elems)
         return tool_data_table_conf_filename, elems
 
     def reset_tool_data_tables(self):
         # Reset the tool_data_tables to an empty dictionary.
-        self.tdtm.data_tables = {}
+        self.app.tool_data_tables.data_tables = {}
diff --git a/lib/tool_shed/tools/tool_validator.py b/lib/tool_shed/tools/tool_validator.py
@@ -70,8 +70,7 @@ 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,
-                                                                                  tool_data_tables=tool.app.tool_data_tables)
+                                                                                  persist=False)
                             if error:
                                 invalid_files_and_errors_tups.append(('tool_data_table_conf.xml.sample', correction_msg))
                         else: