Merge pull request #8241 from jmchilton/more_packages_3

Implement galaxy-web-apps package outline.

lib/galaxy/model/store/build_objects.py

@@ -14,17 +14,17 @@ from galaxy.util.bunch import Bunch
 
 DESCRIPTION = """Build import ready model objects from YAML description of files.
 
-The positional argument to this script should be a a YAML file containing a data
-fetch API-like YAML file describing files. This script will then import this data
-into a defined object store and populate metadata corresponding to these files as
-datasets into a "model store".
+The positional argument to this script should be a a YAML file containing a
+data fetch API-like YAML file describing files. This script will then import
+this data into a defined object store and populate metadata corresponding to
+these files as datasets into a "model store".
 
-The YAML file should contain a dictionary of destination+elements objects or a list
-of such dictionaries. Each such destination+elements dictionary should contain at least
-two keys - 'destination' and 'items'.
+The YAML file should contain a dictionary of destination+elements objects or a
+list of such dictionaries. Each such destination+elements dictionary should
+contain at least two keys - 'destination' and 'items'.
 
-Examples of destinations for creating libraries and just populating history datasets
-are as follows:
+Examples of destinations for creating libraries and just populating history
+datasets are as follows:
 
 ```
 destination:
@@ -38,10 +38,10 @@ destination:
   type: hdas
 ````
 
-The 'items' definition should be a list of files or library folders. If library folders
-need to be setup they should each be defined with a name and recursive set of items (
-again files or folders). The following code fragment describes both a library folder
-definition and a file entry:
+The 'items' definition should be a list of files or library folders. If library
+folders need to be setup they should each be defined with a name and recursive
+set of items (again files or folders). The following code fragment describes
+both a library folder definition and a file entry:
 
 ```
 items:
@@ -56,14 +56,15 @@ items:
         md5: e5d21b1ea57fc9a31f8ea0110531bf3d
 ```
 
-Currently for each file a filename must be supplied, url information will be stored if
-provided but not fetched on-demand like the upload 2.0/data fetch endpoint.
+Currently for each file a filename must be supplied, url information will be
+stored if provided but not fetched on-demand like the upload 2.0/data fetch
+endpoint.
 
-Differences with respect to the Upload 2.0 YAML/JSON format: currently various src tags
-such as 'url' are not supported, data cleaning options such as to_posix_lines, and
-space_to_tab are not supported, unpacking zip files and walking directoriesm etc.. are
-not supported either. The format consumed by this script should continue to evolve to
-converge with the upload 2.0 format.
+Differences with respect to the Upload 2.0 YAML/JSON format: currently various
+src tags such as 'url' are not supported, data cleaning options such as
+to_posix_lines, and space_to_tab are not supported, unpacking zip files and
+walking directories etc.. are not supported either. The format consumed by
+this script should continue to evolve to converge with the upload 2.0 format.
 """
 
 logging.basicConfig()
@@ -118,7 +119,7 @@ def main(argv=None):
 
 
 def _arg_parser():
-    parser = argparse.ArgumentParser(description=DESCRIPTION)
+    parser = argparse.ArgumentParser(description=DESCRIPTION, formatter_class=argparse.RawDescriptionHelpFormatter)
     parser.add_argument('objects', metavar='OBJECT_CONFIG', help='config file describing files to build objects for')
     parser.add_argument('--object-store-config', help="object store configuration file")
     parser.add_argument('-e', '--export', default="export", help='export path')

lib/galaxy/web/buildapp.py

@@ -1,5 +1,10 @@
 """For backward compatibility only, pulls app_factor from galaxy.webapps.main"""
 
-from galaxy.webapps.galaxy.buildapp import app_factory
+try:
+    from galaxy.webapps.galaxy.buildapp import app_factory
+except ImportError:
+    # when installed as a library, galaxy-web-apps may not be available - this
+    # is fine - we shouldn't be using this entry point anyway.
+    app_factory = None
 
 __all__ = ('app_factory', )

lib/galaxy/web/framework/webapp.py

@@ -114,8 +114,8 @@ class WebApplication(base.WebApplication):
         Search for UI controllers in `package_name` and add
         them to the webapp.
         """
-        from galaxy.web.base.controller import BaseUIController
-        from galaxy.web.base.controller import ControllerUnavailable
+        from galaxy.webapps.base.controller import BaseUIController
+        from galaxy.webapps.base.controller import ControllerUnavailable
         package = import_module(package_name)
         controller_dir = package.__path__[0]
         for fname in os.listdir(controller_dir):
@@ -139,8 +139,8 @@ class WebApplication(base.WebApplication):
         Search for UI controllers in `package_name` and add
         them to the webapp.
         """
-        from galaxy.web.base.controller import BaseAPIController
-        from galaxy.web.base.controller import ControllerUnavailable
+        from galaxy.webapps.base.controller import BaseAPIController
+        from galaxy.webapps.base.controller import ControllerUnavailable
         package = import_module(package_name)
         controller_dir = package.__path__[0]
         for fname in os.listdir(controller_dir):

lib/galaxy/webapps/galaxy/api/annotations.py

@@ -10,7 +10,7 @@ from galaxy import (
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import expose_api
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     UsesStoredWorkflowMixin
 )

lib/galaxy/webapps/galaxy/api/authenticate.py

@@ -22,7 +22,7 @@ from galaxy.util import (
     unicodify
 )
 from galaxy.web import expose_api_anonymous_and_sessionless
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/cloud.py

@@ -11,7 +11,7 @@ from galaxy.managers import (
     datasets
 )
 from galaxy.web import expose_api
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/cloudauthz.py

@@ -22,7 +22,7 @@ from galaxy.util import unicodify
 from galaxy.web import (
     expose_api
 )
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/configuration.py

@@ -13,7 +13,7 @@ from galaxy.web import (
     expose_api_anonymous_and_sessionless,
     require_admin
 )
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/dataset_collections.py

@@ -3,7 +3,7 @@ from logging import getLogger
 from galaxy import managers
 from galaxy.managers.collections_util import api_payload_to_create_params, dictify_dataset_collection_instance
 from galaxy.web import expose_api
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     UsesLibraryMixinItems
 )

lib/galaxy/webapps/galaxy/api/datasets.py

@@ -22,11 +22,11 @@ from galaxy.visualization.data_providers.genome import (
     FeatureLocationIndexDataProvider,
     SamDataProvider
 )
-from galaxy.web.base.controller import (
+from galaxy.web.framework.helpers import is_true
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     UsesVisualizationMixin
 )
-from galaxy.web.framework.helpers import is_true
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/datatypes.py

@@ -10,7 +10,7 @@ from galaxy.util import (
     unicodify
 )
 from galaxy.web import expose_api_anonymous_and_sessionless
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/display_applications.py

@@ -5,7 +5,7 @@ import logging
 
 from galaxy import queue_worker
 from galaxy.web import legacy_expose_api, require_admin
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/dynamic_tools.py

@@ -4,7 +4,7 @@ from galaxy import util, web
 from galaxy.exceptions import ObjectNotFound
 from galaxy.web import expose_api
 from galaxy.web import expose_api_anonymous_and_sessionless
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/extended_metadata.py

@@ -7,7 +7,7 @@ from galaxy import (
     managers,
     web
 )
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     HTTPNotImplemented,
     UsesExtendedMetadataMixin,

lib/galaxy/webapps/galaxy/api/folder_contents.py

@@ -13,7 +13,7 @@ from galaxy.web import (
     expose_api,
     expose_api_anonymous
 )
-from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems
+from galaxy.webapps.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/folders.py

@@ -9,7 +9,7 @@ from galaxy import (
 )
 from galaxy.managers import folders, roles
 from galaxy.web import expose_api
-from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems
+from galaxy.webapps.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/forms.py

@@ -6,7 +6,7 @@ from xml.etree.ElementTree import XML
 
 from galaxy import web
 from galaxy.forms.forms import form_factory
-from galaxy.web.base.controller import BaseAPIController, url_for
+from galaxy.webapps.base.controller import BaseAPIController, url_for
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/genomes.py

@@ -1,6 +1,6 @@
 from galaxy import web
-from galaxy.web.base.controller import BaseAPIController
 from galaxy.web.framework.helpers import is_true
+from galaxy.webapps.base.controller import BaseAPIController
 
 
 def get_id(base, format):

lib/galaxy/webapps/galaxy/api/group_roles.py

@@ -5,7 +5,7 @@ import logging
 
 from galaxy import web
 from galaxy.util import unicodify
-from galaxy.web.base.controller import BaseAPIController, url_for
+from galaxy.webapps.base.controller import BaseAPIController, url_for
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/group_users.py

@@ -5,7 +5,7 @@ import logging
 
 from galaxy import web
 from galaxy.util import unicodify
-from galaxy.web.base.controller import BaseAPIController, url_for
+from galaxy.webapps.base.controller import BaseAPIController, url_for
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/groups.py

@@ -6,7 +6,7 @@ import logging
 from sqlalchemy import false
 
 from galaxy import web
-from galaxy.web.base.controller import BaseAPIController, url_for
+from galaxy.webapps.base.controller import BaseAPIController, url_for
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/histories.py

@@ -34,7 +34,7 @@ from galaxy.web import (
     expose_api_raw,
     url_for
 )
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     ExportsHistoryMixin,
     ImportsHistoryMixin,

lib/galaxy/webapps/galaxy/api/history_contents.py

@@ -30,7 +30,7 @@ from galaxy.web import (
     expose_api_raw,
     expose_api_raw_anonymous
 )
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     UsesLibraryMixin,
     UsesLibraryMixinItems,

lib/galaxy/webapps/galaxy/api/item_tags.py

@@ -5,7 +5,7 @@ import logging
 
 from galaxy import exceptions
 from galaxy.web import expose_api
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     UsesTagsMixin
 )

lib/galaxy/webapps/galaxy/api/job_files.py

@@ -14,7 +14,7 @@ from galaxy.web import (
     expose_api_anonymous_and_sessionless,
     expose_api_raw_anonymous_and_sessionless,
 )
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/jobs.py

@@ -17,7 +17,7 @@ from galaxy.web import (
     expose_api,
     expose_api_anonymous,
 )
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     UsesVisualizationMixin
 )

lib/galaxy/webapps/galaxy/api/libraries.py

@@ -16,7 +16,7 @@ from galaxy.web import (
     expose_api,
     expose_api_anonymous,
 )
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/library_contents.py

@@ -23,7 +23,7 @@ from galaxy.model import (
     ExtendedMetadataIndex
 )
 from galaxy.web import expose_api
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     HTTPBadRequest,
     url_for,

lib/galaxy/webapps/galaxy/api/library_datasets.py

@@ -32,7 +32,7 @@ from galaxy.web import (
     expose_api,
     expose_api_anonymous,
 )
-from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin
+from galaxy.webapps.base.controller import BaseAPIController, UsesVisualizationMixin
 log = logging.getLogger(__name__)
 
 

lib/galaxy/webapps/galaxy/api/metrics.py

@@ -8,7 +8,7 @@ import datetime
 import logging
 
 from galaxy.web import expose_api_anonymous
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/page_revisions.py

@@ -7,7 +7,7 @@ from galaxy.managers.base import get_object
 from galaxy.managers.pages import PageManager
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.web import expose_api
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     SharableItemSecurityMixin,
     SharableMixin

lib/galaxy/webapps/galaxy/api/pages.py

@@ -10,7 +10,7 @@ from galaxy.managers.pages import (
 )
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.web import expose_api
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     SharableItemSecurityMixin,
     SharableMixin

lib/galaxy/webapps/galaxy/api/plugins.py

@@ -6,7 +6,7 @@ import logging
 from galaxy import exceptions
 from galaxy.managers import hdas, histories
 from galaxy.web import expose_api
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/provenance.py

@@ -12,7 +12,7 @@ from galaxy import (
     managers,
     web
 )
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/quotas.py

@@ -15,12 +15,12 @@ from galaxy import (
 )
 from galaxy.actions.admin import AdminActions
 from galaxy.exceptions import ActionInputError
-from galaxy.web.base.controller import (
+from galaxy.web.params import QuotaParamParser
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     url_for,
     UsesQuotaMixin
 )
-from galaxy.web.params import QuotaParamParser
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/remote_files.py

@@ -18,7 +18,7 @@ from galaxy.util.path import (
     safe_walk
 )
 from galaxy.web import expose_api
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/roles.py

@@ -6,7 +6,7 @@ import logging
 from sqlalchemy import false
 
 from galaxy import web
-from galaxy.web.base.controller import BaseAPIController, url_for
+from galaxy.webapps.base.controller import BaseAPIController, url_for
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/search.py

@@ -7,7 +7,7 @@ from galaxy import web
 from galaxy.exceptions import ItemAccessibilityException
 from galaxy.model.search import GalaxySearchEngine
 from galaxy.util import unicodify
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     SharableItemSecurityMixin
 )

lib/galaxy/webapps/galaxy/api/tool_data.py

@@ -9,7 +9,7 @@ from galaxy.web import (
     expose_api,
     expose_api_raw
 )
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 
 class ToolData(BaseAPIController):

lib/galaxy/webapps/galaxy/api/tool_dependencies.py

@@ -8,7 +8,7 @@ from galaxy.web import (
     expose_api,
     require_admin
 )
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py

@@ -16,7 +16,7 @@ from galaxy import (
     web
 )
 from galaxy.web import expose_api
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 from tool_shed.galaxy_install.install_manager import InstallRepositoryManager
 from tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
 from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager

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

@@ -14,8 +14,8 @@ from galaxy.web import (
     expose_api_anonymous_and_sessionless,
     expose_api_raw_anonymous_and_sessionless,
 )
-from galaxy.web.base.controller import BaseAPIController
-from galaxy.web.base.controller import UsesVisualizationMixin
+from galaxy.webapps.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import UsesVisualizationMixin
 from ._fetch_util import validate_and_normalize_targets
 
 log = logging.getLogger(__name__)

lib/galaxy/webapps/galaxy/api/toolshed.py

@@ -14,7 +14,7 @@ from galaxy import (
 )
 from galaxy.exceptions import MessageException
 from galaxy.web import expose_api
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 from tool_shed.util import (
     common_util,
     repository_util,

lib/galaxy/webapps/galaxy/api/tours.py

@@ -8,7 +8,7 @@ from galaxy.web import (
     legacy_expose_api,
     require_admin
 )
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/uploads.py

@@ -7,7 +7,7 @@ import re
 
 from galaxy import exceptions
 from galaxy.web import legacy_expose_api_anonymous
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/users.py

@@ -35,14 +35,14 @@ from galaxy.web import (
     expose_api,
     expose_api_anonymous
 )
-from galaxy.web.base.controller import (
+from galaxy.web.form_builder import AddressField
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     BaseUIController,
     CreatesApiKeysMixin,
     UsesFormDefinitionsMixin,
     UsesTagsMixin
 )
-from galaxy.web.form_builder import AddressField
 
 
 log = logging.getLogger(__name__)

lib/galaxy/webapps/galaxy/api/visualizations.py

@@ -20,7 +20,7 @@ from galaxy.managers.visualizations import (
 )
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.web import expose_api
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     SharableMixin,
     UsesVisualizationMixin

lib/galaxy/webapps/galaxy/api/webhooks.py

@@ -5,7 +5,7 @@ import imp
 import logging
 
 from galaxy.web import expose_api_anonymous_and_sessionless
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -30,7 +30,7 @@ from galaxy.web import (
     expose_api,
     expose_api_anonymous_and_sessionless,
 )
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     SharableMixin,
     url_for,

lib/galaxy/webapps/galaxy/controllers/admin.py

@@ -25,10 +25,10 @@ from galaxy.util import (
 from galaxy.util.hash_util import new_secure_hash
 from galaxy.util.odict import odict
 from galaxy.web import url_for
-from galaxy.web.base import controller
-from galaxy.web.base.controller import UsesQuotaMixin
 from galaxy.web.framework.helpers import grids, time_ago
 from galaxy.web.params import QuotaParamParser
+from galaxy.webapps.base import controller
+from galaxy.webapps.base.controller import UsesQuotaMixin
 from tool_shed.util import (
     common_util,
     encoding_util,
@@ -889,7 +889,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
         modules.sort()
         modules.reverse()
         for item in modules:
-            if not item.endswith('.py') or item.startswith('0001_tools'):
+            if not item.endswith('_tools.py') or item.startswith('0001_tools'):
                 continue
             module = item.replace('.py', '')
             migration_stage = int(module.replace('_tools', ''))

lib/galaxy/webapps/galaxy/controllers/async.py

@@ -15,7 +15,7 @@ from galaxy.util import (
     unicodify,
 )
 from galaxy.util.hash_util import hmac_new
-from galaxy.web.base.controller import BaseUIController
+from galaxy.webapps.base.controller import BaseUIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/controllers/authnz.py

@@ -9,7 +9,7 @@ import logging
 from galaxy import exceptions
 from galaxy import web
 from galaxy.web import url_for
-from galaxy.web.base.controller import JSAppLauncher
+from galaxy.webapps.base.controller import JSAppLauncher
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/controllers/data_manager.py

@@ -7,7 +7,7 @@ from six import string_types
 import galaxy.queue_worker
 from galaxy import web
 from galaxy.util import nice_size, unicodify
-from galaxy.web.base.controller import BaseUIController
+from galaxy.webapps.base.controller import BaseUIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/controllers/dataset.py

@@ -29,8 +29,8 @@ from galaxy.util import (
 from galaxy.util.checkers import check_binary
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import form_builder
-from galaxy.web.base.controller import BaseUIController, ERROR, SUCCESS, url_for, UsesExtendedMetadataMixin
 from galaxy.web.framework.helpers import grids, iff, time_ago
+from galaxy.webapps.base.controller import BaseUIController, ERROR, SUCCESS, url_for, UsesExtendedMetadataMixin
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/controllers/error.py

@@ -1,4 +1,4 @@
-from galaxy.web.base.controller import BaseUIController, web
+from galaxy.webapps.base.controller import BaseUIController, web
 
 
 class Error(BaseUIController):

lib/galaxy/webapps/galaxy/controllers/forms.py

@@ -6,8 +6,8 @@ import six
 from markupsafe import escape
 
 from galaxy import model, util
-from galaxy.web.base.controller import BaseUIController, web
 from galaxy.web.framework.helpers import grids, iff, time_ago
+from galaxy.webapps.base.controller import BaseUIController, web
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/controllers/history.py

@@ -17,7 +17,8 @@ from galaxy.model.item_attrs import (
 from galaxy.util import listify, Params, parse_int, sanitize_text
 from galaxy.util.odict import odict
 from galaxy.web import url_for
-from galaxy.web.base.controller import (
+from galaxy.web.framework.helpers import grids, iff, time_ago
+from galaxy.webapps.base.controller import (
     BaseUIController,
     ERROR,
     ExportsHistoryMixin,
@@ -27,7 +28,6 @@ from galaxy.web.base.controller import (
     SUCCESS,
     WARNING,
 )
-from galaxy.web.framework.helpers import grids, iff, time_ago
 from ._create_history_template import render_item
 
 

lib/galaxy/webapps/galaxy/controllers/interactive_environments.py

@@ -4,7 +4,7 @@ API check for whether the current session's interactive environment launch is re
 import logging
 
 from galaxy.web import expose, json
-from galaxy.web.base.controller import BaseUIController
+from galaxy.webapps.base.controller import BaseUIController
 
 
 log = logging.getLogger(__name__)

lib/galaxy/webapps/galaxy/controllers/library.py

@@ -1,7 +1,7 @@
 import logging
 
 from galaxy import web
-from galaxy.web.base.controller import BaseUIController
+from galaxy.webapps.base.controller import BaseUIController
 
 
 log = logging.getLogger(__name__)

lib/galaxy/webapps/galaxy/controllers/openid.py

@@ -9,7 +9,7 @@ from galaxy.openid.openid_manager import OpenIDManager
 from galaxy.openid.providers import OpenIDProviders
 from galaxy.util import unicodify
 from galaxy.web import url_for
-from galaxy.web.base.controller import BaseUIController
+from galaxy.webapps.base.controller import BaseUIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/controllers/page.py

@@ -31,16 +31,16 @@ from galaxy.web import (
     error,
     url_for
 )
-from galaxy.web.base.controller import (
+from galaxy.web.framework.helpers import (
+    grids,
+    time_ago
+)
+from galaxy.webapps.base.controller import (
     BaseUIController,
     SharableMixin,
     UsesStoredWorkflowMixin,
     UsesVisualizationMixin
 )
-from galaxy.web.framework.helpers import (
-    grids,
-    time_ago
-)
 
 
 def format_bool(b):

lib/galaxy/webapps/galaxy/controllers/root.py

@@ -24,7 +24,7 @@ from galaxy.util import (
     string_as_bool,
     unicodify,
 )
-from galaxy.web.base import controller
+from galaxy.webapps.base import controller
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py

@@ -4,7 +4,7 @@ import os
 from galaxy import web
 from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.util.path import join, safe_contains
-from galaxy.web.base.controller import BaseUIController
+from galaxy.webapps.base.controller import BaseUIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/controllers/tag.py

@@ -9,7 +9,7 @@ from sqlalchemy.sql import select
 from sqlalchemy.sql.expression import and_, func
 
 from galaxy import web
-from galaxy.web.base.controller import BaseUIController, UsesTagsMixin
+from galaxy.webapps.base.controller import BaseUIController, UsesTagsMixin
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/controllers/tool_runner.py

@@ -9,7 +9,7 @@ import galaxy.util
 from galaxy import web
 from galaxy.tools import DataSourceTool
 from galaxy.web import error, url_for
-from galaxy.web.base.controller import BaseUIController
+from galaxy.webapps.base.controller import BaseUIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/controllers/user.py

@@ -23,7 +23,7 @@ from galaxy.security.validate_user_input import (
 )
 from galaxy.web import expose_api_anonymous_and_sessionless
 from galaxy.web import url_for
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseUIController,
     CreatesApiKeysMixin,
     UsesFormDefinitionsMixin

lib/galaxy/webapps/galaxy/controllers/userskeys.py

@@ -8,7 +8,7 @@ from galaxy import (
     util,
     web
 )
-from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin
+from galaxy.webapps.base.controller import BaseUIController, UsesFormDefinitionsMixin
 
 
 class User(BaseUIController, UsesFormDefinitionsMixin):

lib/galaxy/webapps/galaxy/controllers/visualization.py

@@ -24,12 +24,12 @@ from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider
 from galaxy.visualization.genomes import decode_dbkey
 from galaxy.visualization.genomes import GenomeRegion
 from galaxy.visualization.plugins import registry
-from galaxy.web.base.controller import (
+from galaxy.web.framework.helpers import grids, time_ago
+from galaxy.webapps.base.controller import (
     BaseUIController,
     SharableMixin,
     UsesVisualizationMixin
 )
-from galaxy.web.framework.helpers import grids, time_ago
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -27,15 +27,15 @@ from galaxy.util import (
 )
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import error, url_for
-from galaxy.web.base.controller import (
-    BaseUIController,
-    SharableMixin,
-    UsesStoredWorkflowMixin
-)
 from galaxy.web.framework.helpers import (
     grids,
     time_ago,
 )
+from galaxy.webapps.base.controller import (
+    BaseUIController,
+    SharableMixin,
+    UsesStoredWorkflowMixin
+)
 from galaxy.workflow.extract import (
     extract_workflow,
     summarize

lib/galaxy/webapps/reports/buildapp.py

@@ -35,7 +35,7 @@ def add_ui_controllers(webapp, app):
     Search for controllers in the 'galaxy.webapps.controllers' module and add
     them to the webapp.
     """
-    from galaxy.web.base.controller import BaseUIController
+    from galaxy.webapps.base.controller import BaseUIController
     import galaxy.webapps.reports.controllers
     controller_dir = galaxy.webapps.reports.controllers.__path__[0]
     for fname in os.listdir(controller_dir):

lib/galaxy/webapps/reports/controllers/history.py

@@ -7,7 +7,7 @@ from sqlalchemy import and_
 
 import galaxy.model
 from galaxy import util
-from galaxy.web.base.controller import BaseUIController, web
+from galaxy.webapps.base.controller import BaseUIController, web
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/reports/controllers/home.py

@@ -5,7 +5,7 @@ from datetime import datetime, timedelta
 import sqlalchemy as sa
 
 from galaxy import model
-from galaxy.web.base.controller import BaseUIController, web
+from galaxy.webapps.base.controller import BaseUIController, web
 from galaxy.webapps.reports.controllers.query import ReportQueryBuilder
 
 log = logging.getLogger(__name__)

lib/galaxy/webapps/reports/controllers/jobs.py

@@ -16,7 +16,7 @@ from markupsafe import escape
 from sqlalchemy import and_, not_, or_
 
 from galaxy import model, util
-from galaxy.web.base.controller import BaseUIController, web
+from galaxy.webapps.base.controller import BaseUIController, web
 from galaxy.webapps.reports.controllers.query import ReportQueryBuilder
 from galaxy.webapps.reports.framework import grids
 

lib/galaxy/webapps/reports/controllers/root.py

@@ -1,6 +1,6 @@
 import logging
 
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseUIController,
     web
 )

lib/galaxy/webapps/reports/controllers/system.py

@@ -8,7 +8,7 @@ from sqlalchemy import and_, desc, false, null, true
 from sqlalchemy.orm import eagerload
 
 from galaxy import model, util
-from galaxy.web.base.controller import BaseUIController, web
+from galaxy.webapps.base.controller import BaseUIController, web
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/reports/controllers/tools.py

@@ -11,7 +11,7 @@ from galaxy.util import (
     restore_text,
     unicodify
 )
-from galaxy.web.base.controller import BaseUIController, web
+from galaxy.webapps.base.controller import BaseUIController, web
 
 
 log = logging.getLogger(__name__)

lib/galaxy/webapps/reports/controllers/users.py

@@ -13,7 +13,7 @@ from sqlalchemy import false
 
 import galaxy.model
 from galaxy import util
-from galaxy.web.base.controller import BaseUIController, web
+from galaxy.webapps.base.controller import BaseUIController, web
 from galaxy.webapps.reports.controllers.jobs import sorter
 from galaxy.webapps.reports.controllers.query import ReportQueryBuilder
 

lib/galaxy/webapps/reports/controllers/workflows.py

@@ -17,7 +17,7 @@ from markupsafe import escape
 from sqlalchemy import and_
 
 from galaxy import model, util
-from galaxy.web.base.controller import BaseUIController, web
+from galaxy.webapps.base.controller import BaseUIController, web
 from galaxy.webapps.reports.controllers.jobs import (
     get_spark_time,
     sorter

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

@@ -11,7 +11,7 @@ from galaxy.web import (
     expose_api_anonymous_and_sessionless,
     require_admin as require_admin
 )
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 from tool_shed.util import repository_util
 
 log = logging.getLogger(__name__)

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

@@ -5,7 +5,7 @@ capabilities and configuration settings.
 import logging
 
 from galaxy.web import expose_api_anonymous_and_sessionless
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

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

@@ -15,7 +15,7 @@ from galaxy.web import (
     expose_api_anonymous_and_sessionless,
     require_admin as require_admin
 )
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 from tool_shed.managers import groups
 
 log = logging.getLogger(__name__)

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

@@ -28,7 +28,7 @@ from galaxy.web import (
     expose_api_anonymous_and_sessionless,
     expose_api_raw_anonymous_and_sessionless
 )
-from galaxy.web.base.controller import (
+from galaxy.webapps.base.controller import (
     BaseAPIController,
     HTTPBadRequest
 )

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

@@ -4,7 +4,7 @@ from sqlalchemy import and_
 
 from galaxy import util
 from galaxy import web
-from galaxy.web.base.controller import BaseAPIController, HTTPBadRequest
+from galaxy.webapps.base.controller import BaseAPIController, HTTPBadRequest
 from tool_shed.capsule import capsule_manager
 from tool_shed.util import metadata_util
 from tool_shed.util import repository_util

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

@@ -10,7 +10,7 @@ from galaxy import (
 from galaxy.tools.parameters import params_to_strings
 from galaxy.tools.repositories import ValidationContext
 from galaxy.web import expose_api_raw_anonymous_and_sessionless
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 from galaxy.webapps.tool_shed.search.tool_search import ToolSearch
 from tool_shed.dependencies.repository import relation_builder
 from tool_shed.tools import tool_validator

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

@@ -10,7 +10,7 @@ from galaxy.security.validate_user_input import (
     validate_password,
     validate_publicname
 )
-from galaxy.web.base.controller import BaseAPIController
+from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/tool_shed/buildapp.py

@@ -36,7 +36,7 @@ def add_ui_controllers(webapp, app):
     Search for controllers in the 'galaxy.webapps.controllers' module and add
     them to the webapp.
     """
-    from galaxy.web.base.controller import BaseUIController
+    from galaxy.webapps.base.controller import BaseUIController
     import galaxy.webapps.tool_shed.controllers
     controller_dir = galaxy.webapps.tool_shed.controllers.__path__[0]
     for fname in os.listdir(controller_dir):

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

@@ -6,8 +6,8 @@ from galaxy import (
     web
 )
 from galaxy.util import inflector
-from galaxy.web.base.controller import BaseUIController
 from galaxy.web.framework.helpers import grids
+from galaxy.webapps.base.controller import BaseUIController
 from tool_shed.metadata import repository_metadata_manager
 from tool_shed.util import (
     metadata_util,

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

@@ -1,7 +1,7 @@
 import logging
 
 from galaxy import web
-from galaxy.web.base.controller import BaseUIController
+from galaxy.webapps.base.controller import BaseUIController
 
 log = logging.getLogger(__name__)
 

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

@@ -4,7 +4,7 @@ from mercurial.hgweb.hgwebdir_mod import hgwebdir
 from mercurial.hgweb.request import wsgiapplication
 
 from galaxy import web
-from galaxy.web.base.controller import BaseUIController
+from galaxy.webapps.base.controller import BaseUIController
 from tool_shed.util.repository_util import get_repository_by_name_and_owner
 
 log = logging.getLogger(__name__)

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

@@ -21,8 +21,8 @@ from galaxy import (
     web
 )
 from galaxy.tools.repositories import ValidationContext
-from galaxy.web.base.controller import BaseUIController
 from galaxy.web.form_builder import CheckboxField, SelectField
+from galaxy.webapps.base.controller import BaseUIController
 from galaxy.webapps.reports.framework import grids
 from galaxy.webapps.tool_shed.util import ratings_util
 from tool_shed.capsule import capsule_manager

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

@@ -13,8 +13,8 @@ from galaxy import (
     web
 )
 from galaxy.util.odict import odict
-from galaxy.web.base.controller import BaseUIController
 from galaxy.web.form_builder import CheckboxField
+from galaxy.webapps.base.controller import BaseUIController
 from galaxy.webapps.tool_shed.util import ratings_util
 from tool_shed.util import (
     hg_util,

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

@@ -11,7 +11,7 @@ from galaxy import (
     web
 )
 from galaxy.util import checkers
-from galaxy.web.base.controller import BaseUIController
+from galaxy.webapps.base.controller import BaseUIController
 from tool_shed.dependencies import attribute_handlers
 from tool_shed.galaxy_install import dependency_display
 from tool_shed.metadata import repository_metadata_manager

packages/app/galaxy/jobs

@@ -0,0 +1 @@
+../../../lib/galaxy/jobs

packages/app/galaxy/managers

@@ -0,0 +1 @@
+../../../lib/galaxy/managers

packages/app/galaxy/openid

@@ -0,0 +1 @@
+../../../lib/galaxy/openid

packages/app/galaxy/tools

@@ -0,0 +1 @@
+../../../lib/galaxy/tools