Move and rename MiniApp to ValidationContext

This better describes what it used for and since it is tool specific, fits
better here that in utils. Thanks @jmchilton for the suggestion.

lib/galaxy/util/miniapp.py → lib/galaxy/tools/repositories/validationcontext.py

@@ -1,16 +1,16 @@
-"""Create a smaller version of app for verifying tools"""
+"""Provides a subset of app for verifying tools."""
 import os
 import shutil
 import tempfile
 from contextlib import contextmanager
 
 from galaxy.datatypes.registry import Registry
 from galaxy.tools.data import ToolDataTableManager
+from galaxy.util.bunch import Bunch
 from galaxy.util.dbkeys import GenomeBuilds
-from .bunch import Bunch
 
 
-class MiniApp(object):
+class ValidationContext(object):
     """Minimal App object for tool validation."""
 
     def __init__(self, app_name,
@@ -57,14 +57,14 @@ def from_app(app, work_dir=None):
             work_dir = tempfile.mkdtemp()
             cleanup = True
         tool_data_tables = ToolDataTableManager(work_dir)
-        with MiniApp(app_name=app.name,
-                     security=app.security,
-                     model=app.model,
-                     tool_data_path=work_dir,
-                     shed_tool_data_path=work_dir,
-                     tool_data_tables=tool_data_tables,
-                     hgweb_config_manager=getattr(app, 'hgweb_config_manager', None)
-                     ) as app:
+        with ValidationContext(app_name=app.name,
+                               security=app.security,
+                               model=app.model,
+                               tool_data_path=work_dir,
+                               shed_tool_data_path=work_dir,
+                               tool_data_tables=tool_data_tables,
+                               hgweb_config_manager=getattr(app, 'hgweb_config_manager', None)
+                               ) as app:
             yield app
         if cleanup:
             shutil.rmtree(work_dir, ignore_errors=True)

lib/galaxy/webapps/tool_shed/api/tools.py

@@ -12,6 +12,7 @@
     RequestParameterInvalidException
 )
 from galaxy.tools.parameters import params_to_strings
+from galaxy.tools.repositories import ValidationContext
 from galaxy.web import _future_expose_api_raw_anonymous_and_sessionless as expose_api_raw_anonymous_and_sessionless
 from galaxy.web.base.controller import BaseAPIController
 from galaxy.webapps.tool_shed.search.tool_search import ToolSearch
@@ -163,8 +164,8 @@ def json(self, trans, **kwd):
             trans.response.status = 404
             return {'status': 'error', 'message': message}
 
-        with util.miniapp.MiniApp.from_app(trans.app) as miniapp:
-            tv = tool_validator.ToolValidator(miniapp)
+        with ValidationContext.from_app(trans.app) as validation_context:
+            tv = tool_validator.ToolValidator(validation_context)
             repository, tool, message = tv.load_tool_from_changeset_revision(tsr_id,
                                                                              changeset,
                                                                              found_tool.tool_config)

lib/galaxy/webapps/tool_shed/controllers/repository.py

@@ -18,6 +18,7 @@
     util,
     web
 )
+from galaxy.tools.repositories import ValidationContext
 from galaxy.web.base.controller import BaseUIController
 from galaxy.web.form_builder import CheckboxField
 from galaxy.web.framework.helpers import grids
@@ -864,8 +865,8 @@ def display_tool(self, trans, repository_id, tool_config, changeset_revision, **
         message = escape(kwd.get('message', ''))
         status = kwd.get('status', 'done')
         render_repository_actions_for = kwd.get('render_repository_actions_for', 'tool_shed')
-        with util.miniapp.MiniApp.from_app(trans.app) as miniapp:
-            tv = tool_validator.ToolValidator(miniapp)
+        with ValidationContext.from_app(trans.app) as validation_context:
+            tv = tool_validator.ToolValidator(validation_context)
             repository, tool, message = tv.load_tool_from_changeset_revision(repository_id,
                                                                              changeset_revision,
                                                                              tool_config)
@@ -1759,18 +1760,18 @@ def load_invalid_tool(self, trans, repository_id, tool_config, changeset_revisio
         message = escape(kwd.get('message', ''))
         render_repository_actions_for = kwd.get('render_repository_actions_for', 'tool_shed')
 
-        with util.miniapp.MiniApp.from_app(trans.app) as miniapp:
-            tv = tool_validator.ToolValidator(miniapp)
+        with ValidationContext.from_app(trans.app) as validation_context:
+            tv = tool_validator.ToolValidator(validation_context)
             repository, tool, error_message = tv.load_tool_from_changeset_revision(repository_id,
                                                                                    changeset_revision,
                                                                                    tool_config)
-        tool_state = tool_util.new_state(trans, tool, invalid=True)
-        invalid_file_tups = []
-        if tool:
-            invalid_file_tups = tv.check_tool_input_params(repository.repo_path(trans.app),
-                                                           tool_config,
-                                                           tool,
-                                                           [])
+            tool_state = tool_util.new_state(trans, tool, invalid=True)
+            invalid_file_tups = []
+            if tool:
+                invalid_file_tups = tv.check_tool_input_params(repository.repo_path(trans.app),
+                                                               tool_config,
+                                                               tool,
+                                                               [])
         if invalid_file_tups:
             message = tool_util.generate_message_for_invalid_tools(trans.app,
                                                                    invalid_file_tups,
@@ -2894,8 +2895,8 @@ def view_tool_metadata(self, trans, repository_id, changeset_revision, tool_id,
             metadata = repository_metadata.metadata
             if metadata:
                 if 'tools' in metadata:
-                    with util.miniapp.MiniApp.from_app(trans.app) as miniapp:
-                        tv = tool_validator.ToolValidator(miniapp)
+                    with ValidationContext.from_app(trans.app) as validation_context:
+                        tv = tool_validator.ToolValidator(validation_context)
                         for tool_metadata_dict in metadata['tools']:
                             if tool_metadata_dict['id'] == tool_id:
                                 work_dir = tempfile.mkdtemp()

lib/tool_shed/metadata/metadata_generator.py

@@ -9,7 +9,7 @@
 from galaxy.tools.data_manager.manager import DataManager
 from galaxy.tools.loader_directory import looks_like_a_tool
 from galaxy.tools.parser.interface import TestCollectionDef
-from galaxy.util.miniapp import MiniApp
+from galaxy.tools.repositories import ValidationContext
 from galaxy.web import url_for
 from tool_shed.repository_types import util as rt_util
 from tool_shed.tools import tool_validator
@@ -339,9 +339,9 @@ def generate_metadata_for_changeset_revision(self):
             files_dir = self.relative_install_dir
             if self.shed_config_dict.get('tool_path'):
                 files_dir = os.path.join(self.shed_config_dict['tool_path'], files_dir)
-        # Create a MiniApp object to load and validate tools, data tables and datatypes
-        with MiniApp.from_app(app=self.app, work_dir=work_dir) as miniapp:
-            tv = tool_validator.ToolValidator(miniapp)
+        # Create ValidationContext to load and validate tools, data tables and datatypes
+        with ValidationContext.from_app(app=self.app, work_dir=work_dir) as validation_context:
+            tv = tool_validator.ToolValidator(validation_context)
             # Handle proprietary datatypes, if any.
             datatypes_config = hg_util.get_config_from_disk(suc.DATATYPES_CONFIG_FILENAME, files_dir)
             if datatypes_config:
@@ -368,10 +368,10 @@ def generate_metadata_for_changeset_revision(self):
                     # We create a new ToolDataTableManager to avoid adding entries to the app-wide
                     # tool data tables. This is only used for checking that the data table is valid.
                     new_table_elems, error_message = \
-                        miniapp.tool_data_tables.add_new_entries_from_config_file(config_filename=sample_file,
-                                                                              tool_data_path=work_dir,
-                                                                              shed_tool_data_table_config=work_dir,
-                                                                              persist=False)
+                        validation_context.tool_data_tables.add_new_entries_from_config_file(config_filename=sample_file,
+                                                                                             tool_data_path=work_dir,
+                                                                                             shed_tool_data_table_config=work_dir,
+                                                                                             persist=False)
                     if error_message:
                         self.invalid_file_tups.append((filename, error_message))
             for root, dirs, files in os.walk(files_dir):

lib/tool_shed/util/workflow_util.py

@@ -7,7 +7,7 @@
 
 import galaxy.tools
 import galaxy.tools.parameters
-from galaxy.util.miniapp import MiniApp
+from galaxy.tools.repositories import ValidationConext
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.workflow.modules import (
     module_types,
@@ -39,8 +39,8 @@ def __init__(self, trans, repository_id, changeset_revision, tools_metadata, too
         self.tool_version = None
         if trans.webapp.name == 'tool_shed':
             # We're in the tool shed.
-            with MiniApp.from_app(trans.app) as miniapp:
-                tv = tool_validator.ToolValidator(miniapp)
+            with ValidationConext.from_app(trans.app) as validation_context:
+                tv = tool_validator.ToolValidator(validation_context)
                 for tool_dict in tools_metadata:
                     if self.tool_id in [tool_dict['id'], tool_dict['guid']]:
                         repository, self.tool, message = tv.load_tool_from_changeset_revision(repository_id,