From 0dca559f8ea8bc603cb632cae39bb7ec81b0f1ae Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 26 Jun 2019 19:28:48 -0400 Subject: [PATCH 1/7] Refactor galaxy.web.base -> galaxy.webapps.base. The rest of galaxy.web does not import galaxy.tools, galaxy.workflows, galaxy.managers, etc.. so this makes galaxy.web feel more like a generic galaxy-agnostic framework module - really only the grids helper imports anything from the galaxy-data package at all and it is just some small helpers. --- lib/galaxy/web/framework/webapp.py | 8 ++++---- lib/galaxy/{web => webapps}/base/__init__.py | 0 lib/galaxy/{web => webapps}/base/controller.py | 0 lib/galaxy/webapps/galaxy/api/annotations.py | 2 +- lib/galaxy/webapps/galaxy/api/authenticate.py | 2 +- lib/galaxy/webapps/galaxy/api/cloud.py | 2 +- lib/galaxy/webapps/galaxy/api/cloudauthz.py | 2 +- lib/galaxy/webapps/galaxy/api/configuration.py | 2 +- lib/galaxy/webapps/galaxy/api/dataset_collections.py | 2 +- lib/galaxy/webapps/galaxy/api/datasets.py | 4 ++-- lib/galaxy/webapps/galaxy/api/datatypes.py | 2 +- lib/galaxy/webapps/galaxy/api/display_applications.py | 2 +- lib/galaxy/webapps/galaxy/api/dynamic_tools.py | 2 +- lib/galaxy/webapps/galaxy/api/extended_metadata.py | 2 +- lib/galaxy/webapps/galaxy/api/folder_contents.py | 2 +- lib/galaxy/webapps/galaxy/api/folders.py | 2 +- lib/galaxy/webapps/galaxy/api/forms.py | 2 +- lib/galaxy/webapps/galaxy/api/genomes.py | 2 +- lib/galaxy/webapps/galaxy/api/group_roles.py | 2 +- lib/galaxy/webapps/galaxy/api/group_users.py | 2 +- lib/galaxy/webapps/galaxy/api/groups.py | 2 +- lib/galaxy/webapps/galaxy/api/histories.py | 2 +- lib/galaxy/webapps/galaxy/api/history_contents.py | 2 +- lib/galaxy/webapps/galaxy/api/item_tags.py | 2 +- lib/galaxy/webapps/galaxy/api/job_files.py | 2 +- lib/galaxy/webapps/galaxy/api/jobs.py | 2 +- lib/galaxy/webapps/galaxy/api/libraries.py | 2 +- lib/galaxy/webapps/galaxy/api/library_contents.py | 2 +- lib/galaxy/webapps/galaxy/api/library_datasets.py | 2 +- lib/galaxy/webapps/galaxy/api/metrics.py | 2 +- lib/galaxy/webapps/galaxy/api/page_revisions.py | 2 +- lib/galaxy/webapps/galaxy/api/pages.py | 2 +- lib/galaxy/webapps/galaxy/api/plugins.py | 2 +- lib/galaxy/webapps/galaxy/api/provenance.py | 2 +- lib/galaxy/webapps/galaxy/api/quotas.py | 4 ++-- lib/galaxy/webapps/galaxy/api/remote_files.py | 2 +- lib/galaxy/webapps/galaxy/api/roles.py | 2 +- lib/galaxy/webapps/galaxy/api/search.py | 2 +- lib/galaxy/webapps/galaxy/api/tool_data.py | 2 +- lib/galaxy/webapps/galaxy/api/tool_dependencies.py | 2 +- .../webapps/galaxy/api/tool_shed_repositories.py | 2 +- lib/galaxy/webapps/galaxy/api/tools.py | 4 ++-- lib/galaxy/webapps/galaxy/api/toolshed.py | 2 +- lib/galaxy/webapps/galaxy/api/tours.py | 2 +- lib/galaxy/webapps/galaxy/api/uploads.py | 2 +- lib/galaxy/webapps/galaxy/api/users.py | 4 ++-- lib/galaxy/webapps/galaxy/api/visualizations.py | 2 +- lib/galaxy/webapps/galaxy/api/webhooks.py | 2 +- lib/galaxy/webapps/galaxy/api/workflows.py | 2 +- lib/galaxy/webapps/galaxy/controllers/admin.py | 4 ++-- lib/galaxy/webapps/galaxy/controllers/async.py | 2 +- lib/galaxy/webapps/galaxy/controllers/authnz.py | 2 +- lib/galaxy/webapps/galaxy/controllers/data_manager.py | 2 +- lib/galaxy/webapps/galaxy/controllers/dataset.py | 2 +- lib/galaxy/webapps/galaxy/controllers/error.py | 2 +- lib/galaxy/webapps/galaxy/controllers/forms.py | 2 +- lib/galaxy/webapps/galaxy/controllers/history.py | 4 ++-- .../galaxy/controllers/interactive_environments.py | 2 +- lib/galaxy/webapps/galaxy/controllers/library.py | 2 +- lib/galaxy/webapps/galaxy/controllers/openid.py | 2 +- lib/galaxy/webapps/galaxy/controllers/page.py | 10 +++++----- lib/galaxy/webapps/galaxy/controllers/root.py | 2 +- .../webapps/galaxy/controllers/shed_tool_static.py | 2 +- lib/galaxy/webapps/galaxy/controllers/tag.py | 2 +- lib/galaxy/webapps/galaxy/controllers/tool_runner.py | 2 +- lib/galaxy/webapps/galaxy/controllers/user.py | 2 +- lib/galaxy/webapps/galaxy/controllers/userskeys.py | 2 +- lib/galaxy/webapps/galaxy/controllers/visualization.py | 4 ++-- lib/galaxy/webapps/galaxy/controllers/workflow.py | 10 +++++----- lib/galaxy/webapps/reports/buildapp.py | 2 +- lib/galaxy/webapps/reports/controllers/history.py | 2 +- lib/galaxy/webapps/reports/controllers/home.py | 2 +- lib/galaxy/webapps/reports/controllers/jobs.py | 2 +- lib/galaxy/webapps/reports/controllers/root.py | 2 +- lib/galaxy/webapps/reports/controllers/system.py | 2 +- lib/galaxy/webapps/reports/controllers/tools.py | 2 +- lib/galaxy/webapps/reports/controllers/users.py | 2 +- lib/galaxy/webapps/reports/controllers/workflows.py | 2 +- lib/galaxy/webapps/tool_shed/api/categories.py | 2 +- lib/galaxy/webapps/tool_shed/api/configuration.py | 2 +- lib/galaxy/webapps/tool_shed/api/groups.py | 2 +- lib/galaxy/webapps/tool_shed/api/repositories.py | 2 +- .../webapps/tool_shed/api/repository_revisions.py | 2 +- lib/galaxy/webapps/tool_shed/api/tools.py | 2 +- lib/galaxy/webapps/tool_shed/api/users.py | 2 +- lib/galaxy/webapps/tool_shed/buildapp.py | 2 +- lib/galaxy/webapps/tool_shed/controllers/admin.py | 2 +- lib/galaxy/webapps/tool_shed/controllers/groups.py | 2 +- lib/galaxy/webapps/tool_shed/controllers/hg.py | 2 +- lib/galaxy/webapps/tool_shed/controllers/repository.py | 2 +- .../webapps/tool_shed/controllers/repository_review.py | 2 +- lib/galaxy/webapps/tool_shed/controllers/upload.py | 2 +- 92 files changed, 108 insertions(+), 108 deletions(-) rename lib/galaxy/{web => webapps}/base/__init__.py (100%) rename lib/galaxy/{web => webapps}/base/controller.py (100%) diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py index 284598d0260..f59ac0b8c6b 100644 --- a/lib/galaxy/web/framework/webapp.py +++ b/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): diff --git a/lib/galaxy/web/base/__init__.py b/lib/galaxy/webapps/base/__init__.py similarity index 100% rename from lib/galaxy/web/base/__init__.py rename to lib/galaxy/webapps/base/__init__.py diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/webapps/base/controller.py similarity index 100% rename from lib/galaxy/web/base/controller.py rename to lib/galaxy/webapps/base/controller.py diff --git a/lib/galaxy/webapps/galaxy/api/annotations.py b/lib/galaxy/webapps/galaxy/api/annotations.py index a78c800ebb0..27e7c59619b 100644 --- a/lib/galaxy/webapps/galaxy/api/annotations.py +++ b/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 ) diff --git a/lib/galaxy/webapps/galaxy/api/authenticate.py b/lib/galaxy/webapps/galaxy/api/authenticate.py index 78074926dcf..2f9eb4d442e 100644 --- a/lib/galaxy/webapps/galaxy/api/authenticate.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/cloud.py b/lib/galaxy/webapps/galaxy/api/cloud.py index 697ea736c8e..66f795d5880 100644 --- a/lib/galaxy/webapps/galaxy/api/cloud.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py index 03cc7f17310..a0590eeffb7 100644 --- a/lib/galaxy/webapps/galaxy/api/cloudauthz.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/configuration.py b/lib/galaxy/webapps/galaxy/api/configuration.py index dd57130658f..92e447bc2e0 100644 --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/dataset_collections.py b/lib/galaxy/webapps/galaxy/api/dataset_collections.py index 7048fdd9d19..a66c58839c2 100644 --- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py +++ b/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 ) diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py index b729933f8cf..51bbf0495c7 100644 --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/datatypes.py b/lib/galaxy/webapps/galaxy/api/datatypes.py index 782d6b31ba9..d4891d5e4f8 100644 --- a/lib/galaxy/webapps/galaxy/api/datatypes.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/display_applications.py b/lib/galaxy/webapps/galaxy/api/display_applications.py index bda880e35e0..325c040764a 100644 --- a/lib/galaxy/webapps/galaxy/api/display_applications.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/dynamic_tools.py b/lib/galaxy/webapps/galaxy/api/dynamic_tools.py index 49f1b0942fb..a5c471a7c8f 100644 --- a/lib/galaxy/webapps/galaxy/api/dynamic_tools.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/extended_metadata.py b/lib/galaxy/webapps/galaxy/api/extended_metadata.py index 9d7d5ed2f9f..a4a650774bb 100644 --- a/lib/galaxy/webapps/galaxy/api/extended_metadata.py +++ b/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, diff --git a/lib/galaxy/webapps/galaxy/api/folder_contents.py b/lib/galaxy/webapps/galaxy/api/folder_contents.py index 8ee9745f23c..890b9d2ba74 100644 --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/folders.py b/lib/galaxy/webapps/galaxy/api/folders.py index 4d62f2b9a19..e168f242771 100644 --- a/lib/galaxy/webapps/galaxy/api/folders.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/forms.py b/lib/galaxy/webapps/galaxy/api/forms.py index caa3e518005..5eb17b53a2f 100644 --- a/lib/galaxy/webapps/galaxy/api/forms.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/genomes.py b/lib/galaxy/webapps/galaxy/api/genomes.py index f760d6d11bb..683f9a5707a 100644 --- a/lib/galaxy/webapps/galaxy/api/genomes.py +++ b/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): diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py index f7b68e00dad..dfd5b4972f1 100644 --- a/lib/galaxy/webapps/galaxy/api/group_roles.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/group_users.py b/lib/galaxy/webapps/galaxy/api/group_users.py index 5d5190f83c8..baa48597991 100644 --- a/lib/galaxy/webapps/galaxy/api/group_users.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/groups.py b/lib/galaxy/webapps/galaxy/api/groups.py index 4b4abd4715e..b4ed1d411ef 100644 --- a/lib/galaxy/webapps/galaxy/api/groups.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py index 4ebb6e71b0f..72c17dbcab7 100644 --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/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, diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py index 0d716cf0161..f7b021b5275 100644 --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/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, diff --git a/lib/galaxy/webapps/galaxy/api/item_tags.py b/lib/galaxy/webapps/galaxy/api/item_tags.py index 130f0b33147..c10a5557c4a 100644 --- a/lib/galaxy/webapps/galaxy/api/item_tags.py +++ b/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 ) diff --git a/lib/galaxy/webapps/galaxy/api/job_files.py b/lib/galaxy/webapps/galaxy/api/job_files.py index 5f571b94049..d95a44e1381 100644 --- a/lib/galaxy/webapps/galaxy/api/job_files.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py index 0c4c9985d27..bd6b948f73b 100644 --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/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 ) diff --git a/lib/galaxy/webapps/galaxy/api/libraries.py b/lib/galaxy/webapps/galaxy/api/libraries.py index e6c49026000..e7e6ba0f6d8 100644 --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/library_contents.py b/lib/galaxy/webapps/galaxy/api/library_contents.py index 85d662b55a0..d030f9e92b0 100644 --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/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, diff --git a/lib/galaxy/webapps/galaxy/api/library_datasets.py b/lib/galaxy/webapps/galaxy/api/library_datasets.py index 56d2a8fe61e..7812afb538d 100644 --- a/lib/galaxy/webapps/galaxy/api/library_datasets.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/metrics.py b/lib/galaxy/webapps/galaxy/api/metrics.py index 28ba5bf9c49..9bdea2f7080 100644 --- a/lib/galaxy/webapps/galaxy/api/metrics.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/page_revisions.py b/lib/galaxy/webapps/galaxy/api/page_revisions.py index f240f6e9155..51b26f9bb82 100644 --- a/lib/galaxy/webapps/galaxy/api/page_revisions.py +++ b/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 diff --git a/lib/galaxy/webapps/galaxy/api/pages.py b/lib/galaxy/webapps/galaxy/api/pages.py index c86090a29f0..52fb6e6ffa8 100644 --- a/lib/galaxy/webapps/galaxy/api/pages.py +++ b/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 diff --git a/lib/galaxy/webapps/galaxy/api/plugins.py b/lib/galaxy/webapps/galaxy/api/plugins.py index ba71aa44c54..326fd9bb0e7 100644 --- a/lib/galaxy/webapps/galaxy/api/plugins.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/provenance.py b/lib/galaxy/webapps/galaxy/api/provenance.py index 72361ee2857..2e1f3fab02d 100644 --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/quotas.py b/lib/galaxy/webapps/galaxy/api/quotas.py index 075bc444b42..437b2f9dbaf 100644 --- a/lib/galaxy/webapps/galaxy/api/quotas.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py index 918b830d803..49b914fd821 100644 --- a/lib/galaxy/webapps/galaxy/api/remote_files.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/roles.py b/lib/galaxy/webapps/galaxy/api/roles.py index e849f9ae225..ac2a06a6e66 100644 --- a/lib/galaxy/webapps/galaxy/api/roles.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/search.py b/lib/galaxy/webapps/galaxy/api/search.py index 8f11f776b9a..7c5f4bead44 100644 --- a/lib/galaxy/webapps/galaxy/api/search.py +++ b/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 ) diff --git a/lib/galaxy/webapps/galaxy/api/tool_data.py b/lib/galaxy/webapps/galaxy/api/tool_data.py index b0fede8ba20..a398b7e26ac 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/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): diff --git a/lib/galaxy/webapps/galaxy/api/tool_dependencies.py b/lib/galaxy/webapps/galaxy/api/tool_dependencies.py index 5fea48074d4..ca209a75575 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_dependencies.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py index cf6bfb1da34..0d09fb62f4a 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/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 diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py index cee0fc78524..f920b44b3be 100644 --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/toolshed.py b/lib/galaxy/webapps/galaxy/api/toolshed.py index 1ab675c9175..f16c03862b4 100644 --- a/lib/galaxy/webapps/galaxy/api/toolshed.py +++ b/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, diff --git a/lib/galaxy/webapps/galaxy/api/tours.py b/lib/galaxy/webapps/galaxy/api/tours.py index d0dec04edf2..12cdf3dca6c 100644 --- a/lib/galaxy/webapps/galaxy/api/tours.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/uploads.py b/lib/galaxy/webapps/galaxy/api/uploads.py index 50fa372c478..1519fd8f33f 100644 --- a/lib/galaxy/webapps/galaxy/api/uploads.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/users.py b/lib/galaxy/webapps/galaxy/api/users.py index 8131568d265..8251004130d 100644 --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/visualizations.py b/lib/galaxy/webapps/galaxy/api/visualizations.py index e8fde2ce325..1afdb3164fb 100644 --- a/lib/galaxy/webapps/galaxy/api/visualizations.py +++ b/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 diff --git a/lib/galaxy/webapps/galaxy/api/webhooks.py b/lib/galaxy/webapps/galaxy/api/webhooks.py index 3dc7e6bb4a7..27336080f43 100644 --- a/lib/galaxy/webapps/galaxy/api/webhooks.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py index 51d21275bcc..74271a6f127 100644 --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/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, diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py index c4c24ebed04..484b178c5db 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/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, diff --git a/lib/galaxy/webapps/galaxy/controllers/async.py b/lib/galaxy/webapps/galaxy/controllers/async.py index 68feeb0788b..019b86dd749 100644 --- a/lib/galaxy/webapps/galaxy/controllers/async.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/controllers/authnz.py b/lib/galaxy/webapps/galaxy/controllers/authnz.py index 0a07dbbba3a..28c4ac8a38e 100644 --- a/lib/galaxy/webapps/galaxy/controllers/authnz.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/controllers/data_manager.py b/lib/galaxy/webapps/galaxy/controllers/data_manager.py index fb5c47ce231..e5fa4f69d05 100644 --- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py index 40df1ea0913..c9f7afd31a1 100644 --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/controllers/error.py b/lib/galaxy/webapps/galaxy/controllers/error.py index 25dd69d1896..ea8190898bb 100644 --- a/lib/galaxy/webapps/galaxy/controllers/error.py +++ b/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): diff --git a/lib/galaxy/webapps/galaxy/controllers/forms.py b/lib/galaxy/webapps/galaxy/controllers/forms.py index 57662f69c0b..3fa8a8fb6a7 100644 --- a/lib/galaxy/webapps/galaxy/controllers/forms.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py index e4231ef32df..880354a92c2 100644 --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/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 diff --git a/lib/galaxy/webapps/galaxy/controllers/interactive_environments.py b/lib/galaxy/webapps/galaxy/controllers/interactive_environments.py index 653fb42c640..b0d29c9d50d 100644 --- a/lib/galaxy/webapps/galaxy/controllers/interactive_environments.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/controllers/library.py b/lib/galaxy/webapps/galaxy/controllers/library.py index c12fc458530..73c5106ba49 100644 --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/controllers/openid.py b/lib/galaxy/webapps/galaxy/controllers/openid.py index f892d0d05f7..c50147f7b2f 100644 --- a/lib/galaxy/webapps/galaxy/controllers/openid.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py index 3981b90f860..e7501e4e2c0 100644 --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/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): diff --git a/lib/galaxy/webapps/galaxy/controllers/root.py b/lib/galaxy/webapps/galaxy/controllers/root.py index 00e8e012b57..8a284eedd3a 100644 --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ 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__) diff --git a/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py b/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py index 258eaed3a21..d938f86c958 100644 --- a/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/controllers/tag.py b/lib/galaxy/webapps/galaxy/controllers/tag.py index 0320f2be72e..0085522eb8c 100644 --- a/lib/galaxy/webapps/galaxy/controllers/tag.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py index e3a6b805565..e6778b47b27 100644 --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py index 513475172f1..4baf0e40a19 100644 --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/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 diff --git a/lib/galaxy/webapps/galaxy/controllers/userskeys.py b/lib/galaxy/webapps/galaxy/controllers/userskeys.py index 00fda7343ba..422c6f70734 100644 --- a/lib/galaxy/webapps/galaxy/controllers/userskeys.py +++ b/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): diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py index b56104af9c9..f586aa6b578 100644 --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/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__) diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py index 65f5edb237a..1d84c309f28 100644 --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/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 diff --git a/lib/galaxy/webapps/reports/buildapp.py b/lib/galaxy/webapps/reports/buildapp.py index af42f0d657a..61ce047a643 100644 --- a/lib/galaxy/webapps/reports/buildapp.py +++ b/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): diff --git a/lib/galaxy/webapps/reports/controllers/history.py b/lib/galaxy/webapps/reports/controllers/history.py index f1f61be9f5a..bd3741de938 100644 --- a/lib/galaxy/webapps/reports/controllers/history.py +++ b/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__) diff --git a/lib/galaxy/webapps/reports/controllers/home.py b/lib/galaxy/webapps/reports/controllers/home.py index bdba42cdcb4..6c59fd0294f 100644 --- a/lib/galaxy/webapps/reports/controllers/home.py +++ b/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__) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index 6ec5384568e..2c8c2a5a773 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/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 diff --git a/lib/galaxy/webapps/reports/controllers/root.py b/lib/galaxy/webapps/reports/controllers/root.py index 26f87ddc792..896c61b0a2c 100644 --- a/lib/galaxy/webapps/reports/controllers/root.py +++ b/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 ) diff --git a/lib/galaxy/webapps/reports/controllers/system.py b/lib/galaxy/webapps/reports/controllers/system.py index 246aac7d199..51ec6c9cd56 100644 --- a/lib/galaxy/webapps/reports/controllers/system.py +++ b/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__) diff --git a/lib/galaxy/webapps/reports/controllers/tools.py b/lib/galaxy/webapps/reports/controllers/tools.py index 7ac7e140a25..789685c0cf7 100644 --- a/lib/galaxy/webapps/reports/controllers/tools.py +++ b/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__) diff --git a/lib/galaxy/webapps/reports/controllers/users.py b/lib/galaxy/webapps/reports/controllers/users.py index 58ffd1dcafd..54cf6645b4c 100644 --- a/lib/galaxy/webapps/reports/controllers/users.py +++ b/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 diff --git a/lib/galaxy/webapps/reports/controllers/workflows.py b/lib/galaxy/webapps/reports/controllers/workflows.py index ff17c2b00d4..a61992333f6 100644 --- a/lib/galaxy/webapps/reports/controllers/workflows.py +++ b/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 diff --git a/lib/galaxy/webapps/tool_shed/api/categories.py b/lib/galaxy/webapps/tool_shed/api/categories.py index 550acf2a48d..414a679ed64 100644 --- a/lib/galaxy/webapps/tool_shed/api/categories.py +++ b/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__) diff --git a/lib/galaxy/webapps/tool_shed/api/configuration.py b/lib/galaxy/webapps/tool_shed/api/configuration.py index bca269b94ae..0ea0cc89915 100644 --- a/lib/galaxy/webapps/tool_shed/api/configuration.py +++ b/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__) diff --git a/lib/galaxy/webapps/tool_shed/api/groups.py b/lib/galaxy/webapps/tool_shed/api/groups.py index ffaa025922e..09a261ca647 100644 --- a/lib/galaxy/webapps/tool_shed/api/groups.py +++ b/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__) diff --git a/lib/galaxy/webapps/tool_shed/api/repositories.py b/lib/galaxy/webapps/tool_shed/api/repositories.py index 0d044512a9f..06bc9c1d2b4 100644 --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/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 ) diff --git a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py index 081d14a86c3..af1cc9b186e 100644 --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/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 diff --git a/lib/galaxy/webapps/tool_shed/api/tools.py b/lib/galaxy/webapps/tool_shed/api/tools.py index fd3f08c0373..428d3c37e50 100644 --- a/lib/galaxy/webapps/tool_shed/api/tools.py +++ b/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 diff --git a/lib/galaxy/webapps/tool_shed/api/users.py b/lib/galaxy/webapps/tool_shed/api/users.py index 4bc1acbc960..ba68ab24991 100644 --- a/lib/galaxy/webapps/tool_shed/api/users.py +++ b/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__) diff --git a/lib/galaxy/webapps/tool_shed/buildapp.py b/lib/galaxy/webapps/tool_shed/buildapp.py index 176a0ac750d..bcbcdab7e90 100644 --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/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): diff --git a/lib/galaxy/webapps/tool_shed/controllers/admin.py b/lib/galaxy/webapps/tool_shed/controllers/admin.py index 76ff1b70008..a5e2834d092 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/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, diff --git a/lib/galaxy/webapps/tool_shed/controllers/groups.py b/lib/galaxy/webapps/tool_shed/controllers/groups.py index 78f9572c863..b41ad39e17f 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/groups.py +++ b/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__) diff --git a/lib/galaxy/webapps/tool_shed/controllers/hg.py b/lib/galaxy/webapps/tool_shed/controllers/hg.py index 027de2df7e8..1501550e138 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/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__) diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py index 6f94f913ad2..2a49dbc4778 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/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 diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py index b015a7c6da6..760e065b1ee 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py +++ b/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, diff --git a/lib/galaxy/webapps/tool_shed/controllers/upload.py b/lib/galaxy/webapps/tool_shed/controllers/upload.py index 91bfadc6e68..8043b12a983 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/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 From dee02db3e0a224ff6d9e3c456431589c3a2b269d Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 26 Jun 2019 20:06:26 -0400 Subject: [PATCH 2/7] Move more modules into galaxy-app. --- packages/app/galaxy/jobs | 1 + packages/app/galaxy/managers | 1 + packages/app/galaxy/openid | 1 + packages/app/galaxy/tools | 1 + packages/app/galaxy/visualization | 1 + packages/app/galaxy/work | 1 + packages/app/galaxy/workflow | 1 + packages/app/setup.py | 41 +++++++++++++++++++++++++++++++ 8 files changed, 48 insertions(+) create mode 120000 packages/app/galaxy/jobs create mode 120000 packages/app/galaxy/managers create mode 120000 packages/app/galaxy/openid create mode 120000 packages/app/galaxy/tools create mode 120000 packages/app/galaxy/visualization create mode 120000 packages/app/galaxy/work create mode 120000 packages/app/galaxy/workflow diff --git a/packages/app/galaxy/jobs b/packages/app/galaxy/jobs new file mode 120000 index 00000000000..62e90b08b98 --- /dev/null +++ b/packages/app/galaxy/jobs @@ -0,0 +1 @@ +../../../lib/galaxy/jobs \ No newline at end of file diff --git a/packages/app/galaxy/managers b/packages/app/galaxy/managers new file mode 120000 index 00000000000..14228c5c999 --- /dev/null +++ b/packages/app/galaxy/managers @@ -0,0 +1 @@ +../../../lib/galaxy/managers \ No newline at end of file diff --git a/packages/app/galaxy/openid b/packages/app/galaxy/openid new file mode 120000 index 00000000000..e0bf26b2d37 --- /dev/null +++ b/packages/app/galaxy/openid @@ -0,0 +1 @@ +../../../lib/galaxy/openid \ No newline at end of file diff --git a/packages/app/galaxy/tools b/packages/app/galaxy/tools new file mode 120000 index 00000000000..b77e9bb0152 --- /dev/null +++ b/packages/app/galaxy/tools @@ -0,0 +1 @@ +../../../lib/galaxy/tools \ No newline at end of file diff --git a/packages/app/galaxy/visualization b/packages/app/galaxy/visualization new file mode 120000 index 00000000000..3fe58fc6407 --- /dev/null +++ b/packages/app/galaxy/visualization @@ -0,0 +1 @@ +../../../lib/galaxy/visualization \ No newline at end of file diff --git a/packages/app/galaxy/work b/packages/app/galaxy/work new file mode 120000 index 00000000000..92a02a7cb53 --- /dev/null +++ b/packages/app/galaxy/work @@ -0,0 +1 @@ +../../../lib/galaxy/work \ No newline at end of file diff --git a/packages/app/galaxy/workflow b/packages/app/galaxy/workflow new file mode 120000 index 00000000000..59308093ad1 --- /dev/null +++ b/packages/app/galaxy/workflow @@ -0,0 +1 @@ +../../../lib/galaxy/workflow \ No newline at end of file diff --git a/packages/app/setup.py b/packages/app/setup.py index 73e771657f8..a07a31a86a8 100644 --- a/packages/app/setup.py +++ b/packages/app/setup.py @@ -34,8 +34,49 @@ PACKAGES = [ 'galaxy', 'galaxy.actions', 'galaxy.forms', + 'galaxy.jobs', + 'galaxy.jobs.actions', + 'galaxy.jobs.rules', + 'galaxy.jobs.runners', + 'galaxy.jobs.runners.state_handlers', + 'galaxy.jobs.runners.util', + 'galaxy.jobs.runners.util.cli', + 'galaxy.jobs.runners.util.cli.job', + 'galaxy.jobs.runners.util.cli.shell', + 'galaxy.jobs.runners.util.condor', + 'galaxy.jobs.runners.util.job_script', + 'galaxy.jobs.splitters', + 'galaxy.managers', + 'galaxy.openid', + 'galaxy.tools', + 'galaxy.tools.actions', + 'galaxy.tools.data', + 'galaxy.tools.data_manager', + 'galaxy.tools.error_reports', + 'galaxy.tools.expressions', + 'galaxy.tools.filters', + 'galaxy.tools.imp_exp', + 'galaxy.tools.parameters', + 'galaxy.tools.search', + 'galaxy.tools.toolbox', + 'galaxy.tools.toolbox.filters', + 'galaxy.tools.toolbox.lineages', + 'galaxy.tools.util', + 'galaxy.tools.util.galaxyops', + 'galaxy.tools.verify', + 'galaxy.tools.verify.asserts', 'galaxy.tours', + 'galaxy.visualization', + 'galaxy.visualization.data_providers', + 'galaxy.visualization.data_providers.phyloviz', + 'galaxy.visualization.genome', + 'galaxy.visualization.plugins', + 'galaxy.visualization.tracks', 'galaxy.webhooks', + 'galaxy.work', + 'galaxy.workflow', + 'galaxy.workflow.resources', + 'galaxy.workflow.schedulers', ] ENTRY_POINTS = ''' [console_scripts] From 9b47a2dfe0248fae2d6f5da5d420122575f83152 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 27 Jun 2019 09:05:57 -0400 Subject: [PATCH 3/7] Add galaxy-web-stack and galaxy-web-framework packages. --- lib/galaxy/web/buildapp.py | 7 +- packages/app/requirements.txt | 3 +- packages/test.sh | 4 +- packages/web_framework/HISTORY.rst | 12 ++ packages/web_framework/LICENSE | 1 + packages/web_framework/MANIFEST.in | 1 + packages/web_framework/Makefile | 1 + packages/web_framework/README.rst | 14 +++ packages/web_framework/dev-requirements.txt | 1 + packages/web_framework/galaxy/__init__.py | 1 + .../galaxy/project_galaxy_web_framework.py | 13 +++ packages/web_framework/galaxy/web | 1 + packages/web_framework/requirements.txt | 1 + packages/web_framework/scripts | 1 + packages/web_framework/setup.cfg | 1 + packages/web_framework/setup.py | 104 ++++++++++++++++++ packages/web_stack/HISTORY.rst | 12 ++ packages/web_stack/LICENSE | 1 + packages/web_stack/MANIFEST.in | 1 + packages/web_stack/Makefile | 1 + packages/web_stack/README.rst | 14 +++ packages/web_stack/dev-requirements.txt | 1 + packages/web_stack/galaxy/__init__.py | 1 + .../galaxy/project_galaxy_web_stack.py | 13 +++ packages/web_stack/galaxy/web_stack | 1 + packages/web_stack/requirements.txt | 2 + packages/web_stack/scripts | 1 + packages/web_stack/setup.cfg | 1 + packages/web_stack/setup.py | 100 +++++++++++++++++ 29 files changed, 312 insertions(+), 3 deletions(-) create mode 100644 packages/web_framework/HISTORY.rst create mode 120000 packages/web_framework/LICENSE create mode 100644 packages/web_framework/MANIFEST.in create mode 120000 packages/web_framework/Makefile create mode 100644 packages/web_framework/README.rst create mode 120000 packages/web_framework/dev-requirements.txt create mode 100644 packages/web_framework/galaxy/__init__.py create mode 100644 packages/web_framework/galaxy/project_galaxy_web_framework.py create mode 120000 packages/web_framework/galaxy/web create mode 100644 packages/web_framework/requirements.txt create mode 120000 packages/web_framework/scripts create mode 120000 packages/web_framework/setup.cfg create mode 100644 packages/web_framework/setup.py create mode 100644 packages/web_stack/HISTORY.rst create mode 120000 packages/web_stack/LICENSE create mode 100644 packages/web_stack/MANIFEST.in create mode 120000 packages/web_stack/Makefile create mode 100644 packages/web_stack/README.rst create mode 120000 packages/web_stack/dev-requirements.txt create mode 100644 packages/web_stack/galaxy/__init__.py create mode 100644 packages/web_stack/galaxy/project_galaxy_web_stack.py create mode 120000 packages/web_stack/galaxy/web_stack create mode 100644 packages/web_stack/requirements.txt create mode 120000 packages/web_stack/scripts create mode 120000 packages/web_stack/setup.cfg create mode 100644 packages/web_stack/setup.py diff --git a/lib/galaxy/web/buildapp.py b/lib/galaxy/web/buildapp.py index e6a04c8bfba..7f95507bdae 100644 --- a/lib/galaxy/web/buildapp.py +++ b/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', ) diff --git a/packages/app/requirements.txt b/packages/app/requirements.txt index 9c87be95eff..da8a0e43f0c 100644 --- a/packages/app/requirements.txt +++ b/packages/app/requirements.txt @@ -1,3 +1,4 @@ galaxy-auth galaxy-job-execution - +galaxy-web-framework +galaxy-web-stack diff --git a/packages/test.sh b/packages/test.sh index 5334ace03d7..53ab2a49d0c 100755 --- a/packages/test.sh +++ b/packages/test.sh @@ -24,11 +24,13 @@ PACKAGE_DIRS=( job_execution auth authnz + web_stack + web_framework app ) # containers has no tests, tool_util not yet working 100%, # data has many problems quota, tool shed install database, etc.. -RUN_TESTS=(1 1 1 0 1 0 1 0 1 0) +RUN_TESTS=(1 1 1 0 1 0 1 0 1 0 0 0) for ((i=0; i<${#PACKAGE_DIRS[@]}; i++)); do package_dir=${PACKAGE_DIRS[$i]} diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst new file mode 100644 index 00000000000..ec2f0e746e9 --- /dev/null +++ b/packages/web_framework/HISTORY.rst @@ -0,0 +1,12 @@ +.. :changelog: + +History +------- + +.. to_doc + +--------------------- +19.9.0.dev0 +--------------------- + +* Initial import from dev branch of Galaxy during 19.09 development cycle. diff --git a/packages/web_framework/LICENSE b/packages/web_framework/LICENSE new file mode 120000 index 00000000000..1ef648f64b3 --- /dev/null +++ b/packages/web_framework/LICENSE @@ -0,0 +1 @@ +../../LICENSE.txt \ No newline at end of file diff --git a/packages/web_framework/MANIFEST.in b/packages/web_framework/MANIFEST.in new file mode 100644 index 00000000000..c74cefe0942 --- /dev/null +++ b/packages/web_framework/MANIFEST.in @@ -0,0 +1 @@ +include *.rst LICENSE diff --git a/packages/web_framework/Makefile b/packages/web_framework/Makefile new file mode 120000 index 00000000000..37af8bae5ba --- /dev/null +++ b/packages/web_framework/Makefile @@ -0,0 +1 @@ +../package.Makefile \ No newline at end of file diff --git a/packages/web_framework/README.rst b/packages/web_framework/README.rst new file mode 100644 index 00000000000..2f71d34d375 --- /dev/null +++ b/packages/web_framework/README.rst @@ -0,0 +1,14 @@ + +.. image:: https://badge.fury.io/py/galaxy-web-framework.svg + :target: https://pypi.org/project/galaxy-web-framework/ + + +Overview +-------- + +The Galaxy_ web framework. + +* Free software: Academic Free License version 3.0 +* Code: https://github.com/galaxyproject/galaxy + +.. _Galaxy: http://galaxyproject.org/ diff --git a/packages/web_framework/dev-requirements.txt b/packages/web_framework/dev-requirements.txt new file mode 120000 index 00000000000..467b90d7a23 --- /dev/null +++ b/packages/web_framework/dev-requirements.txt @@ -0,0 +1 @@ +../package-dev-requirements.txt \ No newline at end of file diff --git a/packages/web_framework/galaxy/__init__.py b/packages/web_framework/galaxy/__init__.py new file mode 100644 index 00000000000..69e3be50dac --- /dev/null +++ b/packages/web_framework/galaxy/__init__.py @@ -0,0 +1 @@ +__path__ = __import__('pkgutil').extend_path(__path__, __name__) diff --git a/packages/web_framework/galaxy/project_galaxy_web_framework.py b/packages/web_framework/galaxy/project_galaxy_web_framework.py new file mode 100644 index 00000000000..e6f46b22814 --- /dev/null +++ b/packages/web_framework/galaxy/project_galaxy_web_framework.py @@ -0,0 +1,13 @@ +# -*- coding: utf-8 -*- + +__version__ = '19.9.0.dev0' + +PROJECT_NAME = "galaxy-web-framework" +PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" +PROJECT_URL = "https://github.com/galaxyproject/galaxy" +PROJECT_AUTHOR = 'Galaxy Project and Community' +PROJECT_DESCRIPTION = 'Galaxy Web Framework' +PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org' +RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( + PROJECT_USERAME, PROJECT_NAME +) diff --git a/packages/web_framework/galaxy/web b/packages/web_framework/galaxy/web new file mode 120000 index 00000000000..1f0b59dddb4 --- /dev/null +++ b/packages/web_framework/galaxy/web @@ -0,0 +1 @@ +../../../lib/galaxy/web \ No newline at end of file diff --git a/packages/web_framework/requirements.txt b/packages/web_framework/requirements.txt new file mode 100644 index 00000000000..7dcf8f4def7 --- /dev/null +++ b/packages/web_framework/requirements.txt @@ -0,0 +1 @@ +galaxy-data diff --git a/packages/web_framework/scripts b/packages/web_framework/scripts new file mode 120000 index 00000000000..9aec9dc5a06 --- /dev/null +++ b/packages/web_framework/scripts @@ -0,0 +1 @@ +../build_scripts \ No newline at end of file diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg new file mode 120000 index 00000000000..eb7cf09393f --- /dev/null +++ b/packages/web_framework/setup.cfg @@ -0,0 +1 @@ +../../setup.cfg \ No newline at end of file diff --git a/packages/web_framework/setup.py b/packages/web_framework/setup.py new file mode 100644 index 00000000000..8b894882f6b --- /dev/null +++ b/packages/web_framework/setup.py @@ -0,0 +1,104 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import ast +import os +import re +try: + from setuptools import setup +except ImportError: + from distutils.core import setup + +SOURCE_DIR = "galaxy" + +_version_re = re.compile(r'__version__\s+=\s+(.*)') + +project_short_name = os.path.basename(os.path.dirname(os.path.realpath(__file__))) +with open('%s/project_galaxy_%s.py' % (SOURCE_DIR, project_short_name), 'rb') as f: + init_contents = f.read().decode('utf-8') + + def get_var(var_name): + pattern = re.compile(r'%s\s+=\s+(.*)' % var_name) + match = pattern.search(init_contents).group(1) + return str(ast.literal_eval(match)) + + version = get_var("__version__") + PROJECT_NAME = get_var("PROJECT_NAME") + PROJECT_URL = get_var("PROJECT_URL") + PROJECT_AUTHOR = get_var("PROJECT_AUTHOR") + PROJECT_EMAIL = get_var("PROJECT_EMAIL") + PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION") + +TEST_DIR = 'tests' +PACKAGES = [ + 'galaxy', + 'galaxy.web', + 'galaxy.web.framework', + 'galaxy.web.framework.helpers', + 'galaxy.web.framework.middleware', + 'galaxy.web.proxy', +] +ENTRY_POINTS = ''' + [console_scripts] +''' +PACKAGE_DATA = { + # Be sure to update MANIFEST.in for source dist. + 'galaxy': [ + ], +} +PACKAGE_DIR = { + SOURCE_DIR: SOURCE_DIR, +} + +readme = open('README.rst').read() +history = open('HISTORY.rst').read().replace('.. :changelog:', '') + +if os.path.exists("requirements.txt"): + requirements = open("requirements.txt").read().split("\n") +else: + # In tox, it will cover them anyway. + requirements = [] + + +test_requirements = [ + # TODO: put package test requirements here +] + + +setup( + name=PROJECT_NAME, + version=version, + description=PROJECT_DESCRIPTION, + long_description=readme + '\n\n' + history, + long_description_content_type='text/x-rst', + author=PROJECT_AUTHOR, + author_email=PROJECT_EMAIL, + url=PROJECT_URL, + packages=PACKAGES, + entry_points=ENTRY_POINTS, + package_data=PACKAGE_DATA, + package_dir=PACKAGE_DIR, + include_package_data=True, + install_requires=requirements, + license="AFL", + zip_safe=False, + keywords='galaxy', + classifiers=[ + 'Development Status :: 5 - Production/Stable', + 'Intended Audience :: Developers', + 'Environment :: Console', + 'License :: OSI Approved :: Academic Free License (AFL)', + 'Operating System :: POSIX', + 'Topic :: Software Development', + 'Topic :: Software Development :: Code Generators', + 'Topic :: Software Development :: Testing', + 'Natural Language :: English', + "Programming Language :: Python :: 2", + 'Programming Language :: Python :: 2.7', + 'Programming Language :: Python :: 3.5', + 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', + ], + test_suite=TEST_DIR, + tests_require=test_requirements +) diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst new file mode 100644 index 00000000000..ec2f0e746e9 --- /dev/null +++ b/packages/web_stack/HISTORY.rst @@ -0,0 +1,12 @@ +.. :changelog: + +History +------- + +.. to_doc + +--------------------- +19.9.0.dev0 +--------------------- + +* Initial import from dev branch of Galaxy during 19.09 development cycle. diff --git a/packages/web_stack/LICENSE b/packages/web_stack/LICENSE new file mode 120000 index 00000000000..1ef648f64b3 --- /dev/null +++ b/packages/web_stack/LICENSE @@ -0,0 +1 @@ +../../LICENSE.txt \ No newline at end of file diff --git a/packages/web_stack/MANIFEST.in b/packages/web_stack/MANIFEST.in new file mode 100644 index 00000000000..c74cefe0942 --- /dev/null +++ b/packages/web_stack/MANIFEST.in @@ -0,0 +1 @@ +include *.rst LICENSE diff --git a/packages/web_stack/Makefile b/packages/web_stack/Makefile new file mode 120000 index 00000000000..37af8bae5ba --- /dev/null +++ b/packages/web_stack/Makefile @@ -0,0 +1 @@ +../package.Makefile \ No newline at end of file diff --git a/packages/web_stack/README.rst b/packages/web_stack/README.rst new file mode 100644 index 00000000000..a0a63b19d2d --- /dev/null +++ b/packages/web_stack/README.rst @@ -0,0 +1,14 @@ + +.. image:: https://badge.fury.io/py/galaxy-web-stack.svg + :target: https://pypi.python.org/pypi/galaxy-web-stack/ + + +Overview +-------- + +The Galaxy_ web strack abstraction. + +* Free software: Academic Free License version 3.0 +* Code: https://github.com/galaxyproject/galaxy + +.. _Galaxy: http://galaxyproject.org/ diff --git a/packages/web_stack/dev-requirements.txt b/packages/web_stack/dev-requirements.txt new file mode 120000 index 00000000000..467b90d7a23 --- /dev/null +++ b/packages/web_stack/dev-requirements.txt @@ -0,0 +1 @@ +../package-dev-requirements.txt \ No newline at end of file diff --git a/packages/web_stack/galaxy/__init__.py b/packages/web_stack/galaxy/__init__.py new file mode 100644 index 00000000000..69e3be50dac --- /dev/null +++ b/packages/web_stack/galaxy/__init__.py @@ -0,0 +1 @@ +__path__ = __import__('pkgutil').extend_path(__path__, __name__) diff --git a/packages/web_stack/galaxy/project_galaxy_web_stack.py b/packages/web_stack/galaxy/project_galaxy_web_stack.py new file mode 100644 index 00000000000..987fdbbd1fd --- /dev/null +++ b/packages/web_stack/galaxy/project_galaxy_web_stack.py @@ -0,0 +1,13 @@ +# -*- coding: utf-8 -*- + +__version__ = '19.9.0.dev0' + +PROJECT_NAME = "galaxy-web-stack" +PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" +PROJECT_URL = "https://github.com/galaxyproject/galaxy" +PROJECT_AUTHOR = 'Galaxy Project and Community' +PROJECT_DESCRIPTION = 'Galaxy Web Strack Abstraction' +PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org' +RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( + PROJECT_USERAME, PROJECT_NAME +) diff --git a/packages/web_stack/galaxy/web_stack b/packages/web_stack/galaxy/web_stack new file mode 120000 index 00000000000..e94ddd99c8a --- /dev/null +++ b/packages/web_stack/galaxy/web_stack @@ -0,0 +1 @@ +../../../lib/galaxy/web_stack \ No newline at end of file diff --git a/packages/web_stack/requirements.txt b/packages/web_stack/requirements.txt new file mode 100644 index 00000000000..326493b152d --- /dev/null +++ b/packages/web_stack/requirements.txt @@ -0,0 +1,2 @@ +sqlalchemy +galaxy-util diff --git a/packages/web_stack/scripts b/packages/web_stack/scripts new file mode 120000 index 00000000000..9aec9dc5a06 --- /dev/null +++ b/packages/web_stack/scripts @@ -0,0 +1 @@ +../build_scripts \ No newline at end of file diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg new file mode 120000 index 00000000000..eb7cf09393f --- /dev/null +++ b/packages/web_stack/setup.cfg @@ -0,0 +1 @@ +../../setup.cfg \ No newline at end of file diff --git a/packages/web_stack/setup.py b/packages/web_stack/setup.py new file mode 100644 index 00000000000..e75068a7065 --- /dev/null +++ b/packages/web_stack/setup.py @@ -0,0 +1,100 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import ast +import os +import re +try: + from setuptools import setup +except ImportError: + from distutils.core import setup + +SOURCE_DIR = "galaxy" + +_version_re = re.compile(r'__version__\s+=\s+(.*)') + +project_short_name = os.path.basename(os.path.dirname(os.path.realpath(__file__))) +with open('%s/project_galaxy_%s.py' % (SOURCE_DIR, project_short_name), 'rb') as f: + init_contents = f.read().decode('utf-8') + + def get_var(var_name): + pattern = re.compile(r'%s\s+=\s+(.*)' % var_name) + match = pattern.search(init_contents).group(1) + return str(ast.literal_eval(match)) + + version = get_var("__version__") + PROJECT_NAME = get_var("PROJECT_NAME") + PROJECT_URL = get_var("PROJECT_URL") + PROJECT_AUTHOR = get_var("PROJECT_AUTHOR") + PROJECT_EMAIL = get_var("PROJECT_EMAIL") + PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION") + +TEST_DIR = 'tests' +PACKAGES = [ + 'galaxy', + 'galaxy.web_stack', +] +ENTRY_POINTS = ''' + [console_scripts] +''' +PACKAGE_DATA = { + # Be sure to update MANIFEST.in for source dist. + 'galaxy': [ + ], +} +PACKAGE_DIR = { + SOURCE_DIR: SOURCE_DIR, +} + +readme = open('README.rst').read() +history = open('HISTORY.rst').read().replace('.. :changelog:', '') + +if os.path.exists("requirements.txt"): + requirements = open("requirements.txt").read().split("\n") +else: + # In tox, it will cover them anyway. + requirements = [] + + +test_requirements = [ + # TODO: put package test requirements here +] + + +setup( + name=PROJECT_NAME, + version=version, + description=PROJECT_DESCRIPTION, + long_description=readme + '\n\n' + history, + long_description_content_type='text/x-rst', + author=PROJECT_AUTHOR, + author_email=PROJECT_EMAIL, + url=PROJECT_URL, + packages=PACKAGES, + entry_points=ENTRY_POINTS, + package_data=PACKAGE_DATA, + package_dir=PACKAGE_DIR, + include_package_data=True, + install_requires=requirements, + license="AFL", + zip_safe=False, + keywords='galaxy', + classifiers=[ + 'Development Status :: 5 - Production/Stable', + 'Intended Audience :: Developers', + 'Environment :: Console', + 'License :: OSI Approved :: Academic Free License (AFL)', + 'Operating System :: POSIX', + 'Topic :: Software Development', + 'Topic :: Software Development :: Code Generators', + 'Topic :: Software Development :: Testing', + 'Natural Language :: English', + "Programming Language :: Python :: 2", + 'Programming Language :: Python :: 2.7', + 'Programming Language :: Python :: 3.5', + 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', + ], + test_suite=TEST_DIR, + tests_require=test_requirements +) From 59bc1aff2bdb05c8cdad6d637109107aff959947 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 27 Jun 2019 13:15:44 -0400 Subject: [PATCH 4/7] Implement outline of galaxy-web-apps packages. Bring in more tool shed stuff into app package also. --- .../webapps/galaxy/controllers/admin.py | 2 +- .../model/migrate/versions/__init__.py | 0 .../migrate/versions/__init__.py | 0 packages/app/setup.py | 25 ++++ packages/app/tool_shed | 1 + packages/test.sh | 4 +- packages/web_apps/HISTORY.rst | 12 ++ packages/web_apps/LICENSE | 1 + packages/web_apps/MANIFEST.in | 1 + packages/web_apps/Makefile | 1 + packages/web_apps/README.rst | 14 +++ packages/web_apps/dev-requirements.txt | 1 + packages/web_apps/galaxy/__init__.py | 1 + .../galaxy/project_galaxy_web_apps.py | 13 ++ packages/web_apps/galaxy/webapps | 1 + packages/web_apps/requirements.txt | 2 + packages/web_apps/scripts | 1 + packages/web_apps/setup.cfg | 1 + packages/web_apps/setup.py | 118 ++++++++++++++++++ 19 files changed, 197 insertions(+), 2 deletions(-) create mode 100644 lib/galaxy/webapps/tool_shed/model/migrate/versions/__init__.py create mode 100644 lib/tool_shed/galaxy_install/migrate/versions/__init__.py create mode 120000 packages/app/tool_shed create mode 100644 packages/web_apps/HISTORY.rst create mode 120000 packages/web_apps/LICENSE create mode 100644 packages/web_apps/MANIFEST.in create mode 120000 packages/web_apps/Makefile create mode 100644 packages/web_apps/README.rst create mode 120000 packages/web_apps/dev-requirements.txt create mode 100644 packages/web_apps/galaxy/__init__.py create mode 100644 packages/web_apps/galaxy/project_galaxy_web_apps.py create mode 120000 packages/web_apps/galaxy/webapps create mode 100644 packages/web_apps/requirements.txt create mode 120000 packages/web_apps/scripts create mode 120000 packages/web_apps/setup.cfg create mode 100644 packages/web_apps/setup.py diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py index 484b178c5db..f023ad177bd 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -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', '')) diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/__init__.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/__init__.py new file mode 100644 index 00000000000..e69de29bb2d diff --git a/lib/tool_shed/galaxy_install/migrate/versions/__init__.py b/lib/tool_shed/galaxy_install/migrate/versions/__init__.py new file mode 100644 index 00000000000..e69de29bb2d diff --git a/packages/app/setup.py b/packages/app/setup.py index a07a31a86a8..1f1b2fa3b07 100644 --- a/packages/app/setup.py +++ b/packages/app/setup.py @@ -77,6 +77,28 @@ PACKAGES = [ 'galaxy.workflow', 'galaxy.workflow.resources', 'galaxy.workflow.schedulers', + 'tool_shed', + 'tool_shed.capsule', + 'tool_shed.dependencies', + 'tool_shed.dependencies.repository', + 'tool_shed.dependencies.tool', + 'tool_shed.galaxy_install.datatypes', + 'tool_shed.galaxy_install.grids', + 'tool_shed.galaxy_install.metadata', + 'tool_shed.galaxy_install.migrate', + 'tool_shed.galaxy_install.migrate.versions', + 'tool_shed.galaxy_install.repository_dependencies', + 'tool_shed.galaxy_install.tool_dependencies', + 'tool_shed.galaxy_install.tool_dependencies.recipe', + 'tool_shed.galaxy_install.tools', + 'tool_shed.galaxy_install.utility_containers', + 'tool_shed.grids', + 'tool_shed.managers', + 'tool_shed.metadata', + 'tool_shed.repository_types', + 'tool_shed.tools', + 'tool_shed.util', + 'tool_shed.utility_containers', ] ENTRY_POINTS = ''' [console_scripts] @@ -85,6 +107,9 @@ PACKAGE_DATA = { # Be sure to update MANIFEST.in for source dist. 'galaxy': [ ], + 'tool_shed': [ + 'scripts/bootstrap_tool_shed/user_info.xml', + ], } PACKAGE_DIR = { SOURCE_DIR: SOURCE_DIR, diff --git a/packages/app/tool_shed b/packages/app/tool_shed new file mode 120000 index 00000000000..a24c5c74750 --- /dev/null +++ b/packages/app/tool_shed @@ -0,0 +1 @@ +../../lib/tool_shed \ No newline at end of file diff --git a/packages/test.sh b/packages/test.sh index 53ab2a49d0c..aaf70bd4464 100755 --- a/packages/test.sh +++ b/packages/test.sh @@ -27,10 +27,12 @@ PACKAGE_DIRS=( web_stack web_framework app + web_apps ) # containers has no tests, tool_util not yet working 100%, # data has many problems quota, tool shed install database, etc.. -RUN_TESTS=(1 1 1 0 1 0 1 0 1 0 0 0) +RUN_TESTS=(1 1 1 0 1 0 1 0 1 0 0 0 0) + for ((i=0; i<${#PACKAGE_DIRS[@]}; i++)); do package_dir=${PACKAGE_DIRS[$i]} diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst new file mode 100644 index 00000000000..ec2f0e746e9 --- /dev/null +++ b/packages/web_apps/HISTORY.rst @@ -0,0 +1,12 @@ +.. :changelog: + +History +------- + +.. to_doc + +--------------------- +19.9.0.dev0 +--------------------- + +* Initial import from dev branch of Galaxy during 19.09 development cycle. diff --git a/packages/web_apps/LICENSE b/packages/web_apps/LICENSE new file mode 120000 index 00000000000..1ef648f64b3 --- /dev/null +++ b/packages/web_apps/LICENSE @@ -0,0 +1 @@ +../../LICENSE.txt \ No newline at end of file diff --git a/packages/web_apps/MANIFEST.in b/packages/web_apps/MANIFEST.in new file mode 100644 index 00000000000..c74cefe0942 --- /dev/null +++ b/packages/web_apps/MANIFEST.in @@ -0,0 +1 @@ +include *.rst LICENSE diff --git a/packages/web_apps/Makefile b/packages/web_apps/Makefile new file mode 120000 index 00000000000..37af8bae5ba --- /dev/null +++ b/packages/web_apps/Makefile @@ -0,0 +1 @@ +../package.Makefile \ No newline at end of file diff --git a/packages/web_apps/README.rst b/packages/web_apps/README.rst new file mode 100644 index 00000000000..2f28a9fefb6 --- /dev/null +++ b/packages/web_apps/README.rst @@ -0,0 +1,14 @@ + +.. image:: https://badge.fury.io/py/galaxy-web-apps.svg + :target: https://pypi.python.org/pypi/galaxy-web-apps/ + + +Overview +-------- + +The Galaxy_ web apps (Galaxy, Reports, Tool Shed). + +* Free software: Academic Free License version 3.0 +* Code: https://github.com/galaxyproject/galaxy + +.. _Galaxy: http://galaxyproject.org/ diff --git a/packages/web_apps/dev-requirements.txt b/packages/web_apps/dev-requirements.txt new file mode 120000 index 00000000000..467b90d7a23 --- /dev/null +++ b/packages/web_apps/dev-requirements.txt @@ -0,0 +1 @@ +../package-dev-requirements.txt \ No newline at end of file diff --git a/packages/web_apps/galaxy/__init__.py b/packages/web_apps/galaxy/__init__.py new file mode 100644 index 00000000000..69e3be50dac --- /dev/null +++ b/packages/web_apps/galaxy/__init__.py @@ -0,0 +1 @@ +__path__ = __import__('pkgutil').extend_path(__path__, __name__) diff --git a/packages/web_apps/galaxy/project_galaxy_web_apps.py b/packages/web_apps/galaxy/project_galaxy_web_apps.py new file mode 100644 index 00000000000..3f416bde726 --- /dev/null +++ b/packages/web_apps/galaxy/project_galaxy_web_apps.py @@ -0,0 +1,13 @@ +# -*- coding: utf-8 -*- + +__version__ = '19.9.0.dev0' + +PROJECT_NAME = "galaxy-web-apps" +PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" +PROJECT_URL = "https://github.com/galaxyproject/galaxy" +PROJECT_AUTHOR = 'Galaxy Project and Community' +PROJECT_DESCRIPTION = 'Galaxy Web Apps' +PROJECT_EMAIL = 'jmchilton@gmail.com' +RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( + PROJECT_USERAME, PROJECT_NAME +) diff --git a/packages/web_apps/galaxy/webapps b/packages/web_apps/galaxy/webapps new file mode 120000 index 00000000000..7f4c3888cef --- /dev/null +++ b/packages/web_apps/galaxy/webapps @@ -0,0 +1 @@ +../../../lib/galaxy/webapps \ No newline at end of file diff --git a/packages/web_apps/requirements.txt b/packages/web_apps/requirements.txt new file mode 100644 index 00000000000..eaf79b2a242 --- /dev/null +++ b/packages/web_apps/requirements.txt @@ -0,0 +1,2 @@ +galaxy-app + diff --git a/packages/web_apps/scripts b/packages/web_apps/scripts new file mode 120000 index 00000000000..9aec9dc5a06 --- /dev/null +++ b/packages/web_apps/scripts @@ -0,0 +1 @@ +../build_scripts \ No newline at end of file diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg new file mode 120000 index 00000000000..eb7cf09393f --- /dev/null +++ b/packages/web_apps/setup.cfg @@ -0,0 +1 @@ +../../setup.cfg \ No newline at end of file diff --git a/packages/web_apps/setup.py b/packages/web_apps/setup.py new file mode 100644 index 00000000000..a55e4a3ad29 --- /dev/null +++ b/packages/web_apps/setup.py @@ -0,0 +1,118 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import ast +import os +import re +try: + from setuptools import setup +except ImportError: + from distutils.core import setup + +SOURCE_DIR = "galaxy" + +_version_re = re.compile(r'__version__\s+=\s+(.*)') + +project_short_name = os.path.basename(os.path.dirname(os.path.realpath(__file__))) +with open('%s/project_galaxy_%s.py' % (SOURCE_DIR, project_short_name), 'rb') as f: + init_contents = f.read().decode('utf-8') + + def get_var(var_name): + pattern = re.compile(r'%s\s+=\s+(.*)' % var_name) + match = pattern.search(init_contents).group(1) + return str(ast.literal_eval(match)) + + version = get_var("__version__") + PROJECT_NAME = get_var("PROJECT_NAME") + PROJECT_URL = get_var("PROJECT_URL") + PROJECT_AUTHOR = get_var("PROJECT_AUTHOR") + PROJECT_EMAIL = get_var("PROJECT_EMAIL") + PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION") + +TEST_DIR = 'tests' +PACKAGES = [ + 'galaxy', + 'galaxy.webapps', + 'galaxy.webapps.base', + 'galaxy.webapps.galaxy', + 'galaxy.webapps.galaxy.api', + 'galaxy.webapps.galaxy.controllers', + 'galaxy.webapps.reports', + 'galaxy.webapps.reports.controllers', + 'galaxy.webapps.reports.framework', + 'galaxy.webapps.tool_shed', + 'galaxy.webapps.tool_shed.api', + 'galaxy.webapps.tool_shed.controllers', + 'galaxy.webapps.tool_shed.framework', + 'galaxy.webapps.tool_shed.framework.middleware', + 'galaxy.webapps.tool_shed.model', + 'galaxy.webapps.tool_shed.model.migrate', + 'galaxy.webapps.tool_shed.model.migrate.versions', + 'galaxy.webapps.tool_shed.search', + 'galaxy.webapps.tool_shed.security', + 'galaxy.webapps.tool_shed.util', +] +ENTRY_POINTS = ''' + [console_scripts] +''' +PACKAGE_DATA = { + # Be sure to update MANIFEST.in for source dist. + 'galaxy': [ + ], +} +PACKAGE_DIR = { + SOURCE_DIR: SOURCE_DIR, +} + +readme = open('README.rst').read() +history = open('HISTORY.rst').read().replace('.. :changelog:', '') + +if os.path.exists("requirements.txt"): + requirements = open("requirements.txt").read().split("\n") +else: + # In tox, it will cover them anyway. + requirements = [] + + +test_requirements = [ + # TODO: put package test requirements here +] + + +setup( + name=PROJECT_NAME, + version=version, + description=PROJECT_DESCRIPTION, + long_description=readme + '\n\n' + history, + long_description_content_type='text/x-rst', + author=PROJECT_AUTHOR, + author_email=PROJECT_EMAIL, + url=PROJECT_URL, + packages=PACKAGES, + entry_points=ENTRY_POINTS, + package_data=PACKAGE_DATA, + package_dir=PACKAGE_DIR, + include_package_data=True, + install_requires=requirements, + license="AFL", + zip_safe=False, + keywords='galaxy', + classifiers=[ + 'Development Status :: 5 - Production/Stable', + 'Intended Audience :: Developers', + 'Environment :: Console', + 'License :: OSI Approved :: Academic Free License (AFL)', + 'Operating System :: POSIX', + 'Topic :: Software Development', + 'Topic :: Software Development :: Code Generators', + 'Topic :: Software Development :: Testing', + 'Natural Language :: English', + "Programming Language :: Python :: 2", + 'Programming Language :: Python :: 2.7', + 'Programming Language :: Python :: 3.5', + 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', + ], + test_suite=TEST_DIR, + tests_require=test_requirements +) From ea4f020cdfb38cae3ac99d7d315032551a6bf7f5 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Fri, 5 Jul 2019 09:53:44 +0200 Subject: [PATCH 5/7] Improve help for build objects script. --- lib/galaxy/model/store/build_objects.py | 43 +++++++++++++------------ 1 file changed, 22 insertions(+), 21 deletions(-) diff --git a/lib/galaxy/model/store/build_objects.py b/lib/galaxy/model/store/build_objects.py index bc2c4fea4f6..8cedcaffafe 100644 --- a/lib/galaxy/model/store/build_objects.py +++ b/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') From 49ef4d91c6719e25876e43f58bdd36e454bb8d91 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Fri, 5 Jul 2019 09:53:59 +0200 Subject: [PATCH 6/7] Pin numpy since 1.17 doesn't work on Python 2. --- packages/data/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/data/requirements.txt b/packages/data/requirements.txt index f2b5c80f06e..8cebfd65d71 100644 --- a/packages/data/requirements.txt +++ b/packages/data/requirements.txt @@ -4,7 +4,7 @@ bdbag bx-python h5py isa-rwval -numpy +numpy<=1.16 pycryptodome pysam social_auth_core From bda718b7110e5afed12096638b6944d20ab0b0b4 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Sat, 6 Jul 2019 14:13:06 +0200 Subject: [PATCH 7/7] [packages] Fix pypi links in README badges. --- packages/auth/README.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/packages/auth/README.rst b/packages/auth/README.rst index b493770764f..13915272fcb 100644 --- a/packages/auth/README.rst +++ b/packages/auth/README.rst @@ -3,6 +3,7 @@ :target: https://pypi.org/project/galaxy-auth/ + Overview --------