- %s
-
- ''' % a.get_html()
- else:
- self.select_address.add_option(a.desc, str(a.id))
- if self.value == 'new':
- self.select_address.add_option('Add a new address', 'new', selected=True)
- for field_name, label, help_text in self.fields():
- add_field = TextField(self.name + '_' + field_name,
- 40,
- restore_text(self.params.get(self.name + '_' + field_name, '')))
- address_html += '''
-
-
- %s
- ''' % (label, add_field.get_html(disabled=disabled))
- if help_text:
- address_html += '''
-
- '''
- else:
- self.select_address.add_option('Add a new address', 'new')
- return self.select_address.get_html(disabled=disabled) + address_html
def to_dict(self):
d = super(AddressField, self).to_dict()
@@ -540,29 +146,11 @@ class AddressField(BaseField):
class WorkflowField(BaseField):
- def __init__(self, name, user=None, value=None, params=None, security=None, **kwds):
+ def __init__(self, name, user=None, value=None, security=None, **kwds):
super(WorkflowField, self).__init__(name, value, **kwds)
- self.name = name
self.user = user
self.value = value
self.security = security
- self.select_workflow = None
- self.params = params
-
- def get_html(self, disabled=False):
- self.select_workflow = SelectField(self.name)
- if self.value == 'none':
- self.select_workflow.add_option('Select one', 'none', selected=True)
- else:
- self.select_workflow.add_option('Select one', 'none')
- if self.user:
- for a in self.user.stored_workflows:
- if not a.deleted:
- if str(self.value) == str(a.id):
- self.select_workflow.add_option(a.name, str(a.id), selected=True)
- else:
- self.select_workflow.add_option(a.name, str(a.id))
- return self.select_workflow.get_html(disabled=disabled)
def to_dict(self):
d = super(WorkflowField, self).to_dict()
@@ -576,70 +164,17 @@ class WorkflowField(BaseField):
class WorkflowMappingField(BaseField):
- def __init__(self, name, user=None, value=None, params=None, **kwd):
- # DBTODO integrate this with the new __build_workflow approach in requests_common. As it is, not particularly useful.
- self.name = name
+ def __init__(self, name, user=None, value=None, **kwds):
+ super(WorkflowMappingField, self).__init__(name, value, **kwds)
self.user = user
- self.value = value
- self.select_workflow = None
- self.params = params
- self.workflow_inputs = []
-
- def get_html(self, disabled=False):
- self.select_workflow = SelectField(self.name, refresh_on_change=True)
- workflow_inputs = []
- if self.value == 'none':
- self.select_workflow.add_option('Select one', 'none', selected=True)
- else:
- self.select_workflow.add_option('Select one', 'none')
- if self.user:
- for a in self.user.stored_workflows:
- if not a.deleted:
- if str(self.value) == str(a.id):
- self.select_workflow.add_option(a.name, str(a.id), selected=True)
- else:
- self.select_workflow.add_option(a.name, str(a.id))
- if self.value and self.value != 'none':
- # Workflow selected. Find all inputs.
- for workflow in self.user.stored_workflows:
- if workflow.id == int(self.value):
- for step in workflow.latest_workflow.steps:
- if step.type == 'data_input':
- if step.tool_inputs and "name" in step.tool_inputs:
- workflow_inputs.append((step.tool_inputs['name'], TextField('%s_%s' % (self.name, step.id), 20)))
- # Do something more appropriate here and allow selection of inputs
- return self.select_workflow.get_html(disabled=disabled) + ''.join(['
- %s
-
- ''' % help_text
- address_html += '''
- %s
' % (s[0], s[1].get_html()) for s in workflow_inputs])
class HistoryField(BaseField):
- def __init__(self, name, user=None, value=None, params=None, security=None, **kwds):
+ def __init__(self, name, user=None, value=None, security=None, **kwds):
super(HistoryField, self).__init__(name, value, **kwds)
- self.name = name
self.user = user
self.value = value
self.security = security
- self.select_history = None
- self.params = params
-
- def get_html(self, disabled=False):
- self.select_history = SelectField(self.name)
- if self.value == 'none':
- self.select_history.add_option('No Import', 'none', selected=True)
- self.select_history.add_option('New History', 'new')
- else:
- self.select_history.add_option('No Import', 'none')
- if self.value == 'new':
- self.select_history.add_option('New History', 'new', selected=True)
- else:
- self.select_history.add_option('New History', 'new')
- if self.user:
- for a in self.user.histories:
- if not a.deleted:
- if str(self.value) == str(a.id):
- self.select_history.add_option(a.name, str(a.id), selected=True)
- else:
- self.select_history.add_option(a.name, str(a.id))
- return self.select_history.get_html(disabled=disabled)
def to_dict(self):
d = super(HistoryField, self).to_dict()
@@ -657,55 +192,3 @@ def get_suite():
import doctest
import sys
return doctest.DocTestSuite(sys.modules[__name__])
-
-
-# --------- Utility methods -----------------------------
-def build_select_field(trans, objs, label_attr, select_field_name, initial_value='none',
- selected_value='none', refresh_on_change=False, multiple=False, display=None, size=None):
- """
- Build a SelectField given a set of objects. The received params are:
-
- - objs: the set of objects used to populate the option list
- - label_attr: the attribute of each obj (e.g., name, email, etc ) whose value is used to populate each option label.
-
- - If the string 'self' is passed as label_attr, each obj in objs is assumed to be a string, so the obj itself is used
-
- - select_field_name: the name of the SelectField
- - initial_value: the value of the first option in the SelectField - allows for an option telling the user to select something
- - selected_value: the value of the currently selected option
- - refresh_on_change: True if the SelectField should perform a refresh_on_change
- """
- if initial_value == 'none':
- values = [initial_value]
- else:
- values = []
- for obj in objs:
- if label_attr == 'self':
- # Each obj is a string
- values.append(obj)
- else:
- values.append(trans.security.encode_id(obj.id))
- if refresh_on_change:
- refresh_on_change_values = values
- else:
- refresh_on_change_values = []
- select_field = SelectField(name=select_field_name,
- multiple=multiple,
- display=display,
- refresh_on_change=refresh_on_change,
- refresh_on_change_values=refresh_on_change_values,
- size=size)
- for obj in objs:
- if label_attr == 'self':
- # Each obj is a string
- if str(selected_value) == str(obj):
- select_field.add_option(obj, obj, selected=True)
- else:
- select_field.add_option(obj, obj)
- else:
- label = getattr(obj, label_attr)
- if str(selected_value) == str(obj.id) or str(selected_value) == trans.security.encode_id(obj.id):
- select_field.add_option(label, trans.security.encode_id(obj.id), selected=True)
- else:
- select_field.add_option(label, trans.security.encode_id(obj.id))
- return select_field
diff --git a/lib/galaxy/web/framework/formbuilder.py b/lib/galaxy/web/framework/formbuilder.py
deleted file mode 100644
index 1603e3bf4a8..00000000000
--- a/lib/galaxy/web/framework/formbuilder.py
+++ /dev/null
@@ -1,91 +0,0 @@
-import logging
-
-from galaxy.util import bunch
-
-log = logging.getLogger(__name__)
-
-
-def form(*args, **kwargs):
- return FormBuilder(*args, **kwargs)
-
-
-class FormBuilder(object):
- """
- Simple class describing an HTML form
- """
-
- def __init__(self, action="", title="", name="form", submit_text="submit", use_panels=False):
- self.title = title
- self.name = name
- self.action = action
- self.submit_text = submit_text
- self.inputs = []
- self.use_panels = use_panels
-
- def add_input(self, type, name, label, value=None, error=None, help=None, use_label=True):
- self.inputs.append(FormInput(type, label, name, value, error, help, use_label))
- return self
-
- def add_checkbox(self, name, label, value=None, error=None, help=None):
- return self.add_input('checkbox', label, name, value, error, help)
-
- def add_text(self, name, label, value=None, error=None, help=None):
- return self.add_input('text', label, name, value, error, help)
-
- def add_password(self, name, label, value=None, error=None, help=None):
- return self.add_input('password', label, name, value, error, help)
-
- def add_select(self, name, label, value=None, options=[], error=None, help=None, use_label=True):
- self.inputs.append(SelectInput(name, label, value=value, options=options, error=error, help=help, use_label=use_label))
- return self
-
-
-class FormInput(object):
- """
- Simple class describing a form input element
- """
-
- def __init__(self, type, name, label, value=None, error=None, help=None, use_label=True, extra_attributes={}, **kwargs):
- self.type = type
- self.name = name
- self.label = label
- self.value = value
- self.error = error
- self.help = help
- self.use_label = use_label
- self.extra_attributes = extra_attributes
-
-
-class DatalistInput(FormInput):
- """ Data list input """
-
- def __init__(self, name, *args, **kwargs):
- if 'extra_attributes' not in kwargs:
- kwargs['extra_attributes'] = {}
- kwargs['extra_attributes']['list'] = name
- FormInput.__init__(self, None, name, *args, **kwargs)
- self.options = kwargs.get('options', {})
-
- def body_html(self):
- options = "".join(["" % (key, value) for key, value in self.options.iteritems()])
- return """""" % (self.name, options)
-
-
-class SelectInput(FormInput):
- """ A select form input. """
-
- def __init__(self, name, label, value=None, options=[], error=None, help=None, use_label=True):
- FormInput.__init__(self, "select", name, label, value=value, error=error, help=help, use_label=use_label)
- self.options = options
-
-
-class FormData(object):
- """
- Class for passing data about a form to a template, very rudimentary, could
- be combined with the tool form handling to build something more general.
- """
-
- def __init__(self):
- # TODO: galaxy's two Bunchs are defined differently. Is this right?
- self.values = bunch.Bunch()
- self.errors = bunch.Bunch()
diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py
index 831474246a1..91491195bf4 100644
--- a/lib/galaxy/web/framework/webapp.py
+++ b/lib/galaxy/web/framework/webapp.py
@@ -33,7 +33,6 @@ from galaxy.util import (
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web.framework import (
base,
- formbuilder,
helpers,
url_for
)
@@ -103,8 +102,6 @@ class WebApplication(base.WebApplication):
return trans.show_message(sanitize_html(e.err_msg), e.type)
def make_body_iterable(self, trans, body):
- if isinstance(body, formbuilder.FormBuilder):
- body = trans.show_form(body)
return base.WebApplication.make_body_iterable(self, trans, body)
def transaction_chooser(self, environ, galaxy_app, session_cookie):
@@ -875,15 +872,6 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
"""
return self.show_message(message, 'warning', refresh_frames, use_panels=use_panels, active_view=active_view)
- def show_form(self, form, header=None, template="form.mako", use_panels=False, active_view=""):
- """
- Convenience method for displaying a simple page with a single HTML
- form.
- """
- return self.fill_template(template, form=form, header=header,
- use_panels=(form.use_panels or use_panels),
- active_view=active_view)
-
@property
def session_csrf_token(self):
token = ''
diff --git a/lib/galaxy/webapps/galaxy/api/library_contents.py b/lib/galaxy/webapps/galaxy/api/library_contents.py
index 70f51b5a88d..befe4263a56 100644
--- a/lib/galaxy/webapps/galaxy/api/library_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/library_contents.py
@@ -32,10 +32,6 @@ from galaxy.web.base.controller import (
UsesLibraryMixin,
UsesLibraryMixinItems
)
-from galaxy.web.form_builder import (
- AddressField,
- CheckboxField,
-)
log = logging.getLogger(__name__)
@@ -300,18 +296,12 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
roles = kwd.get('roles', '')
is_admin = trans.user_is_admin()
current_user_roles = trans.get_current_user_roles()
- widgets = []
- info_association, inherited = None, None
- template_id = "None"
if replace_id not in ['', None, 'None']:
replace_dataset = trans.sa_session.query(trans.app.model.LibraryDataset).get(trans.security.decode_id(replace_id))
self._check_access(trans, is_admin, replace_dataset, current_user_roles)
self._check_modify(trans, is_admin, replace_dataset, current_user_roles)
library = replace_dataset.folder.parent_library
folder = replace_dataset.folder
- info_association, inherited = replace_dataset.library_dataset_dataset_association.get_info_association()
- if info_association and (not(inherited) or info_association.inheritable):
- widgets = replace_dataset.library_dataset_dataset_association.get_template_widgets(trans)
# The name is stored - by the time the new ldda is created, replace_dataset.name
# will point to the new ldda, not the one it's replacing.
if not last_used_build:
@@ -342,56 +332,9 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
if error:
return 400, message
else:
- # See if we have any inherited templates.
- if not info_association:
- info_association, inherited = folder.get_info_association(inherited=True)
- if info_association and info_association.inheritable:
- template_id = str(info_association.template.id)
- widgets = folder.get_template_widgets(trans, get_contents=True)
- processed_widgets = []
- # The list of widgets may include an AddressField which we need to save if it is new
- for index, widget_dict in enumerate(widgets):
- widget = widget_dict['widget']
- if isinstance(widget, AddressField):
- value = kwd.get(widget.name, '')
- if value == 'new':
- if self.field_param_values_ok(widget.name, 'AddressField', **kwd):
- # Save the new address
- address = trans.app.model.UserAddress(user=trans.user)
- self.save_widget_field(trans, address, widget.name, **kwd)
- widget.value = str(address.id)
- widget_dict['widget'] = widget
- processed_widgets.append(widget_dict)
- # It is now critical to update the value of 'field_%i', replacing the string
- # 'new' with the new address id. This is necessary because the upload_dataset()
- # method below calls the handle_library_params() method, which does not parse the
- # widget fields, it instead pulls form values from kwd. See the FIXME comments in the
- # handle_library_params() method, and the CheckboxField code in the next conditional.
- kwd[widget.name] = str(address.id)
- else:
- # The invalid address won't be saved, but we cannot display error
- # messages on the upload form due to the ajax upload already occurring.
- # When we re-engineer the upload process ( currently under way ), we
- # will be able to check the form values before the ajax upload occurs
- # in the background. For now, we'll do nothing...
- pass
- elif isinstance(widget, CheckboxField):
- # We need to check the value from kwd since util.Params would have munged the list if
- # the checkbox is checked.
- value = kwd.get(widget.name, '')
- if CheckboxField.is_checked(value):
- widget.value = 'true'
- widget_dict['widget'] = widget
- processed_widgets.append(widget_dict)
- kwd[widget.name] = 'true'
- else:
- processed_widgets.append(widget_dict)
- widgets = processed_widgets
created_outputs_dict = self._upload_dataset(trans,
library_id=trans.security.encode_id(library.id),
folder_id=trans.security.encode_id(folder.id),
- template_id=template_id,
- widgets=widgets,
replace_dataset=replace_dataset,
**kwd)
if created_outputs_dict:
diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
index 5ffbdcfe1b2..60f6e4833af 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -263,8 +263,7 @@ class ToolShedRepositoriesController(BaseAPIController):
else:
repository_data['repository'] = json.loads(util.url_get(tool_shed_url, pathspec=['api', 'repositories', tsr_id]))
repository_data['repository']['metadata'] = json.loads(util.url_get(tool_shed_url, pathspec=['api', 'repositories', tsr_id, 'metadata']))
- repository_data['shed_conf'] = tool_util.build_shed_tool_conf_select_field(trans.app).get_html().replace('\n', '')
- repository_data['panel_section_html'] = tool_panel_section_select_field.get_html(extra_attr={'style': 'width: 30em;'}).replace('\n', '')
+ repository_data['shed_conf'] = tool_util.build_shed_tool_conf_select_field(trans.app).to_dict()
repository_data['panel_section_dict'] = tool_panel_section_dict
for changeset, metadata in repository_data['repository']['metadata'].items():
if changeset not in tool_dependencies:
diff --git a/lib/galaxy/webapps/galaxy/api/toolshed.py b/lib/galaxy/webapps/galaxy/api/toolshed.py
index c06360dbc66..2ecb92a5a99 100644
--- a/lib/galaxy/webapps/galaxy/api/toolshed.py
+++ b/lib/galaxy/webapps/galaxy/api/toolshed.py
@@ -252,8 +252,7 @@ class ToolShedController(BaseAPIController):
else:
repository_data['repository'] = json.loads(util.url_get(tool_shed_url, pathspec=['api', 'repositories', repository_id]))
repository_data['repository']['metadata'] = json.loads(util.url_get(tool_shed_url, pathspec=['api', 'repositories', repository_id, 'metadata']))
- repository_data['shed_conf'] = tool_util.build_shed_tool_conf_select_field(trans.app).get_html().replace('\n', '')
- repository_data['panel_section_html'] = tool_panel_section_select_field.get_html(extra_attr={'style': 'width: 30em;'}).replace('\n', '')
+ repository_data['shed_conf'] = tool_util.build_shed_tool_conf_select_field(trans.app).to_dict()
repository_data['panel_section_dict'] = tool_panel_section_dict
for changeset, metadata in repository_data['repository']['metadata'].items():
if changeset not in tool_dependencies:
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index f9306436e45..c8d2c278d41 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -239,7 +239,7 @@ class AdminToolshed(AdminGalaxy):
message += 'Attempting to uninstall tool dependencies resulted in errors: %s' % errors
status = max(status, statuses.index('error'))
status = statuses[status]
- remove_from_disk_check_box = CheckboxField('remove_from_disk', checked=remove_from_disk_checked)
+ remove_from_disk_check_box = CheckboxField('remove_from_disk', value=remove_from_disk_checked)
return trans.fill_template('/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako',
repository=tool_shed_repositories,
remove_from_disk_check_box=remove_from_disk_check_box,
@@ -535,10 +535,10 @@ class AdminToolshed(AdminGalaxy):
else:
install_tool_dependencies_check_box_checked = True
install_tool_dependencies_check_box = CheckboxField('install_tool_dependencies',
- checked=install_tool_dependencies_check_box_checked)
+ value=install_tool_dependencies_check_box_checked)
view = views.DependencyResolversView(self.app)
if view.installable_resolvers:
- install_resolver_dependencies_check_box = CheckboxField('install_resolver_dependencies', checked=True)
+ install_resolver_dependencies_check_box = CheckboxField('install_resolver_dependencies', value=True)
else:
install_resolver_dependencies_check_box = None
return trans.fill_template('/admin/tool_shed_repository/install_tool_dependencies_with_update.mako',
@@ -1054,12 +1054,12 @@ class AdminToolshed(AdminGalaxy):
else:
install_tool_dependencies_check_box_checked = True
install_tool_dependencies_check_box = CheckboxField('install_tool_dependencies',
- checked=install_tool_dependencies_check_box_checked)
+ value=install_tool_dependencies_check_box_checked)
# Handle repository dependencies check box.
- install_repository_dependencies_check_box = CheckboxField('install_repository_dependencies', checked=True)
+ install_repository_dependencies_check_box = CheckboxField('install_repository_dependencies', value=True)
view = views.DependencyResolversView(self.app)
if view.installable_resolvers:
- install_resolver_dependencies_check_box = CheckboxField('install_resolver_dependencies', checked=True)
+ install_resolver_dependencies_check_box = CheckboxField('install_resolver_dependencies', value=True)
else:
install_resolver_dependencies_check_box = None
encoded_repo_info_dicts = encoding_util.encoding_sep.join(encoded_repo_info_dicts)
@@ -1392,7 +1392,7 @@ class AdminToolshed(AdminGalaxy):
else:
original_section_name = ''
tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field(trans.app)
- no_changes_check_box = CheckboxField('no_changes', checked=True)
+ no_changes_check_box = CheckboxField('no_changes', value=True)
if original_section_name:
message += "The tools contained in your %s repository were last loaded into the tool panel section %s. " \
% (escape(tool_shed_repository.name), original_section_name)
@@ -1423,7 +1423,7 @@ class AdminToolshed(AdminGalaxy):
# whether installed or missing.
containers_dict = dd.merge_missing_repository_dependencies_to_installed_container(containers_dict)
# Handle repository dependencies check box.
- install_repository_dependencies_check_box = CheckboxField('install_repository_dependencies', checked=True)
+ install_repository_dependencies_check_box = CheckboxField('install_repository_dependencies', value=True)
# Handle tool dependencies check box.
if trans.app.config.tool_dependency_dir is None:
if includes_tool_dependencies:
@@ -1433,10 +1433,10 @@ class AdminToolshed(AdminGalaxy):
install_tool_dependencies_check_box_checked = False
else:
install_tool_dependencies_check_box_checked = True
- install_tool_dependencies_check_box = CheckboxField('install_tool_dependencies', checked=install_tool_dependencies_check_box_checked)
+ install_tool_dependencies_check_box = CheckboxField('install_tool_dependencies', value=install_tool_dependencies_check_box_checked)
view = views.DependencyResolversView(self.app)
if view.installable_resolvers:
- install_resolver_dependencies_check_box = CheckboxField('install_resolver_dependencies', checked=True)
+ install_resolver_dependencies_check_box = CheckboxField('install_resolver_dependencies', value=True)
else:
install_resolver_dependencies_check_box = None
return trans.fill_template('/admin/tool_shed_repository/reselect_tool_panel_section.mako',
diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py
index 427856037c7..7b5606b90bb 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -20,7 +20,7 @@ from galaxy import (
)
from galaxy.tools.repositories import ValidationContext
from galaxy.web.base.controller import BaseUIController
-from galaxy.web.form_builder import CheckboxField
+from galaxy.web.form_builder import CheckboxField, SelectField
from galaxy.web.framework.helpers import grids
from galaxy.webapps.tool_shed.util import ratings_util
from tool_shed.capsule import capsule_manager
@@ -974,7 +974,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
repository_dependencies,
repository_metadata,
exclude=exclude)
- export_repository_dependencies_check_box = CheckboxField('export_repository_dependencies', checked=True)
+ export_repository_dependencies_check_box = CheckboxField('export_repository_dependencies', value=True)
else:
containers_dict = None
export_repository_dependencies_check_box = None
@@ -1084,7 +1084,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
else:
message = "No search performed - each field must contain the same number of comma-separated items."
status = "error"
- exact_matches_check_box = CheckboxField('exact_matches', checked=exact_matches_checked)
+ exact_matches_check_box = CheckboxField('exact_matches', value=exact_matches_checked)
return trans.fill_template('/webapps/tool_shed/repository/find_tools.mako',
tool_id=basic_util.stringify(tool_ids),
tool_name=basic_util.stringify(tool_names),
@@ -1176,7 +1176,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
else:
exact_matches_checked = False
workflow_names = []
- exact_matches_check_box = CheckboxField('exact_matches', checked=exact_matches_checked)
+ exact_matches_check_box = CheckboxField('exact_matches', value=exact_matches_checked)
return trans.fill_template('/webapps/tool_shed/repository/find_workflows.mako',
workflow_name=basic_util.stringify(workflow_names),
exact_matches_check_box=exact_matches_check_box,
@@ -1824,7 +1824,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
else:
message = 'You will not receive any email alerts for new valid tool shed repositories.'
checked = new_repo_alert_checked or (user and user.new_repo_alert)
- new_repo_alert_check_box = CheckboxField('new_repo_alert', checked=checked)
+ new_repo_alert_check_box = CheckboxField('new_repo_alert', value=checked)
email_alert_repositories = []
for repository in trans.sa_session.query(trans.model.Repository) \
.filter(and_(trans.model.Repository.table.c.deleted == false(),
@@ -1931,14 +1931,22 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
message = "The repository information has been updated."
if error:
status = 'error'
+ allow_push_select_field = SelectField(name='allow_push',
+ multiple=True)
current_allow_push = repository.allow_push(trans.app)
if current_allow_push:
current_allow_push_list = current_allow_push.split(',')
else:
current_allow_push_list = []
- allow_push_select_field = repository_util.build_allow_push_select_field(trans, current_allow_push_list)
+ options = []
+ for user in trans.sa_session.query(trans.model.User):
+ if user.username not in current_allow_push_list:
+ options.append(user)
+ for obj in options:
+ label = getattr(obj, 'username')
+ allow_push_select_field.add_option(label, trans.security.encode_id(obj.id))
checked = alerts_checked or user.email in email_alerts
- alerts_check_box = CheckboxField('alerts', checked=checked)
+ alerts_check_box = CheckboxField('alerts', value=checked)
changeset_revision_select_field = grids_util.build_changeset_revision_select_field(trans,
repository,
selected_value=changeset_revision,
@@ -2001,7 +2009,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
message += malicious_error
status = 'error'
repository_type_select_field = rt_util.build_repository_type_select_field(trans, repository=repository)
- malicious_check_box = CheckboxField('malicious', checked=is_malicious)
+ malicious_check_box = CheckboxField('malicious', value=is_malicious)
categories = suc.get_categories(trans.app)
selected_categories = [_rca.category_id for _rca in repository.categories]
tsucm = ToolShedUtilityContainerManager(trans.app)
@@ -2821,7 +2829,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
trans.sa_session.add(repository)
trans.sa_session.flush()
checked = alerts_checked or (user and user.email in email_alerts)
- alerts_check_box = CheckboxField('alerts', checked=checked)
+ alerts_check_box = CheckboxField('alerts', value=checked)
changeset_revision_select_field = grids_util.build_changeset_revision_select_field(trans,
repository,
selected_value=changeset_revision,
diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py
index b404f9fdbbe..a5c15816d87 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py
@@ -278,6 +278,7 @@ class RepositoryReviewController(BaseUIController, ratings_util.ItemRatings):
# The star rating form field is a radio button list, so it will not be received if it was not clicked in the form.
# Due to this behavior, default the value to 0.
rating = 0
+ private = False
for k, v in kwd.items():
if k.startswith('%s%s' % (component_name, STRSEP)):
component_review_attr = k.replace('%s%s' % (component_name, STRSEP), '')
diff --git a/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py b/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
index fc2f50dc0a9..20299bc27ea 100644
--- a/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
+++ b/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
@@ -12,7 +12,6 @@ from tool_shed.util import common_util
from tool_shed.util import repository_util
from tool_shed.util import tool_util
from tool_shed.util import xml_util
-
log = logging.getLogger(__name__)
diff --git a/lib/tool_shed/grids/repository_grids.py b/lib/tool_shed/grids/repository_grids.py
index e305bfb8e59..d4228adb59e 100644
--- a/lib/tool_shed/grids/repository_grids.py
+++ b/lib/tool_shed/grids/repository_grids.py
@@ -110,7 +110,11 @@ class RepositoryGrid(grids.Grid):
# A repository's metadata revisions may not all be installable, as some may contain only invalid tools.
select_field = grids_util.build_changeset_revision_select_field(trans, repository, downloadable=False)
if len(select_field.options) > 1:
- return select_field.get_html()
+ tmpl = ""
+ return tmpl
elif len(select_field.options) == 1:
option_items = select_field.options[0][0]
rev_label, rev_date = option_items.split(' ')
@@ -1331,7 +1335,11 @@ class ValidRepositoryGrid(RepositoryGrid):
"""Display a SelectField whose options are the changeset_revision strings of all download-able revisions of this repository."""
select_field = grids_util.build_changeset_revision_select_field(trans, repository, downloadable=True)
if len(select_field.options) > 1:
- return select_field.get_html()
+ tmpl = ""
+ return tmpl
elif len(select_field.options) == 1:
return select_field.options[0][0]
return ''
diff --git a/lib/tool_shed/grids/util.py b/lib/tool_shed/grids/util.py
index 810a0ab42b9..fc2ee84ea48 100644
--- a/lib/tool_shed/grids/util.py
+++ b/lib/tool_shed/grids/util.py
@@ -71,9 +71,7 @@ def build_changeset_revision_select_field(trans, repository, selected_value=None
name = 'changeset_revision_%d' % repository.id
else:
name = 'changeset_revision'
- select_field = SelectField(name=name,
- refresh_on_change=True,
- refresh_on_change_values=refresh_on_change_values)
+ select_field = SelectField(name=name, refresh_on_change=True)
for option_tup in options:
selected = selected_value and option_tup[1] == selected_value
select_field.add_option(option_tup[0], option_tup[1], selected=selected)
diff --git a/lib/tool_shed/util/hg_util.py b/lib/tool_shed/util/hg_util.py
index f979e73c8cc..30b3e5e4d02 100644
--- a/lib/tool_shed/util/hg_util.py
+++ b/lib/tool_shed/util/hg_util.py
@@ -54,6 +54,7 @@ def clone_repository(repository_clone_url, repository_file_dir, ctx_rev):
Clone the repository up to the specified changeset_revision. No subsequent revisions will be
present in the cloned repository.
"""
+ stdouterr = None
try:
stdouterr = subprocess.check_output(['hg', 'clone', '-r', ctx_rev, repository_clone_url, repository_file_dir], stderr=subprocess.STDOUT)
return True, None
diff --git a/lib/tool_shed/util/repository_util.py b/lib/tool_shed/util/repository_util.py
index 9e3c870d3fc..23d39f2f08b 100644
--- a/lib/tool_shed/util/repository_util.py
+++ b/lib/tool_shed/util/repository_util.py
@@ -11,7 +11,6 @@ import tool_shed.dependencies.repository
import tool_shed.util.metadata_util as metadata_util
from galaxy import util
from galaxy import web
-from galaxy.web.form_builder import build_select_field
from tool_shed.util import basic_util, common_util, encoding_util, hg_util
from tool_shed.util.web_util import escape
@@ -20,20 +19,6 @@ log = logging.getLogger(__name__)
VALID_REPOSITORYNAME_RE = re.compile("^[a-z0-9\_]+$")
-def build_allow_push_select_field(trans, current_push_list, selected_value='none'):
- options = []
- for user in trans.sa_session.query(trans.model.User):
- if user.username not in current_push_list:
- options.append(user)
- return build_select_field(trans,
- objs=options,
- label_attr='username',
- select_field_name='allow_push',
- selected_value=selected_value,
- refresh_on_change=False,
- multiple=True)
-
-
def change_repository_name_in_hgrc_file(hgrc_file, new_name):
config = configparser.ConfigParser()
config.read(hgrc_file)
diff --git a/lib/tool_shed/util/tool_dependency_util.py b/lib/tool_shed/util/tool_dependency_util.py
index e470f9fffd8..3b83716a515 100644
--- a/lib/tool_shed/util/tool_dependency_util.py
+++ b/lib/tool_shed/util/tool_dependency_util.py
@@ -6,8 +6,10 @@ from sqlalchemy import and_
from galaxy import util
from galaxy.web.form_builder import SelectField
-from tool_shed.util import hg_util
-from tool_shed.util import xml_util
+from tool_shed.util import (
+ hg_util,
+ xml_util
+)
log = logging.getLogger(__name__)
diff --git a/static/scripts/bundled/adminToolshed.bundled.js b/static/scripts/bundled/adminToolshed.bundled.js
index cd09499b9dd..cb6b84ceaa7 100644
--- a/static/scripts/bundled/adminToolshed.bundled.js
+++ b/static/scripts/bundled/adminToolshed.bundled.js
@@ -47,7 +47,14 @@ r=i,l=e("",{css:{position:"absolute",top:"-200px",left:s?"0px":"-1000px",
if(v === 'i' && !ins.is_loaded(p)) { }
*/
<<<<<<< HEAD
+<<<<<<< HEAD
+p=!0,_=0,f=o.data.nodes.length;_'+e.name+"
"}});t.default={View:h}}).call(t,i(1),i(0))},309:function(e,t,i){"use strict";function s(e){new a.default.GalaxyApp(e)}Object.defineProperty(t,"__esModule",{value:!0}),t.App=s;var n=i(310),a=function(e){return e&&e.__esModule?e:{default:e}}(n);window.adminToolshedApp=s},310:function(e,t,i){"use strict";(function(e){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var n=i(311),a=s(n),o=i(312),r=s(o),l=i(313),d=s(l),c=i(314),h=s(c),u=i(315),p=s(u),_=i(316),f=s(_),g=i(317),m=s(g),v=e.Router.extend({initialize:function(){this.routesHit=0,e.history.on("route",function(){this.routesHit++},this),this.bind("route",this.trackPageview)},routes:{"":"toolsheds",sheds:"toolsheds",queue:"queue",workflows:"workflows","status/r/:repositories":"status",status:"status","categories/s/:tool_shed":"categories","category/s/:tool_shed/c/:cateory_id":"repositories","repository/s/:tool_shed/r/:repository_id":"repository"},back:function(){this.routesHit>1?window.history.back():this.navigate("#",{trigger:!0,replace:!0})}}),b=e.View.extend({app_config:{known_views:["toolsheds","queue","status","categories","repositories","repoository"]},initialize:function(){Galaxy.admintoolshedapp=this,this.admin_toolshed_router=new v,this.admin_toolshed_router.on("route:queue",function(){Galaxy.admintoolshedapp.adminRepoQueueView?Galaxy.admintoolshedapp.adminRepoQueueView.reDraw():Galaxy.admintoolshedapp.adminRepoQueueView=new p.default.RepoQueueView}),this.admin_toolshed_router.on("route:toolsheds",function(){Galaxy.admintoolshedapp.adminShedListView?Galaxy.admintoolshedapp.adminShedListView.reDraw():Galaxy.admintoolshedapp.adminShedListView=new a.default.ShedListView}),this.admin_toolshed_router.on("route:categories",function(e){Galaxy.admintoolshedapp.adminShedCategoriesView?Galaxy.admintoolshedapp.adminShedCategoriesView.reDraw({tool_shed:e.replace(/\//g,"%2f")}):Galaxy.admintoolshedapp.adminShedCategoriesView=new r.default.CategoryView({tool_shed:e.replace(/\//g,"%2f")})}),this.admin_toolshed_router.on("route:repositories",function(e,t){Galaxy.admintoolshedapp.adminShedCategoryView?Galaxy.admintoolshedapp.adminShedCategoryView.reDraw({tool_shed:e.replace(/\//g,"%2f"),category_id:t}):Galaxy.admintoolshedapp.adminShedCategoryView=new d.default.Category({tool_shed:e.replace(/\//g,"%2f"),category_id:t})}),this.admin_toolshed_router.on("route:repository",function(e,t){Galaxy.admintoolshedapp.adminRepositoryView?Galaxy.admintoolshedapp.adminRepositoryView.reDraw({tool_shed:e.replace(/\//g,"%2f"),repository_id:t}):Galaxy.admintoolshedapp.adminRepositoryView=new h.default.RepoDetails({tool_shed:e.replace(/\//g,"%2f"),repository_id:t})}),this.admin_toolshed_router.on("route:status",function(e){Galaxy.admintoolshedapp.adminRepoStatusView?Galaxy.admintoolshedapp.adminRepoStatusView.reDraw({repositories:e.split("|")}):Galaxy.admintoolshedapp.adminRepoStatusView=new f.default.RepoStatus({repositories:e.split("|")})}),this.admin_toolshed_router.on("route:workflows",function(){Galaxy.admintoolshedapp.adminWorkflowsView?Galaxy.admintoolshedapp.adminWorkflowsView.reDraw():Galaxy.admintoolshedapp.adminWorkflowsView=new m.default.Workflows}),e.history.start({pushState:!1})}});t.default={GalaxyApp:b}}).call(t,i(1))},311:function(e,t,i){"use strict";(function(e,s){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(167),o=n(a),r=i(168),l=n(r),d=e.View.extend({defaults:{tool_sheds:[{url:"https://toolshed.g2.bx.psu.edu/",name:"Galaxy Main Tool Shed"}]},initialize:function(e){this.options=s.defaults(this.options||{},this.defaults),this.model=new o.default.ShedsCollection,this.listenTo(this.model,"sync",this.render),this.model.fetch()},el:"#center",render:function(e){this.options=s.defaults(this.options||{},e,this.defaults);var t=this.templateToolshedList;this.$el.html(t({title:"Configured Galaxy Tool Sheds",tool_sheds:this.model.models,queue:l.default.queueLength()}))},reDraw:function(e){this.$el.empty(),this.render(e)},templateToolshedList:s.template(['','
",'<%= title %>
','',"','
"].join(""))});t.default={ShedListView:d}}).call(t,i(1),i(2))},312:function(e,t,i){"use strict";(function(e,s,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(167),r=a(o),l=i(168),d=a(l);i(157);var c=e.View.extend({el:"#center",defaults:{tool_shed:"https://toolshed.g2.bx.psu.edu/"},initialize:function(e){var t=e.tool_shed.replace(/\//g,"%2f");this.options=s.defaults(this.options||e,this.defaults),this.model=new r.default.Categories,this.listenTo(this.model,"sync",this.render),this.model.url=this.model.url+"?tool_shed_url="+this.options.tool_shed,this.model.tool_shed=t,this.model.fetch()},render:function(e){this.options=s.extend(this.options,e),this.options.categories=this.model.models,this.options.queue=d.default.queueLength();var t=this.templateCategoryList;this.$el.html(t(this.options)),n("#center").css("overflow","auto"),this.bindEvents()},bindEvents:function(){var t=this;n("#search_box").autocomplete({source:function(e,i){var s=t.model.tool_shed.replace(/%2f/g,"/"),a=Galaxy.root+"api/tool_shed/search",o={term:e.term,tool_shed_url:s};n.post(a,o,function(e){console.log(e);var t=d.default.shedParser(e);i(t)})},minLength:3,select:function(i,s){var n=s.item.value,a=(Galaxy.root,t.model.tool_shed,"repository/s/"+t.model.tool_shed+"/r/"+n);e.history.navigate(a,{trigger:!0,replace:!0})}})},reDraw:function(e){this.$el.empty(),this.model.url=this.model.url+"?tool_shed_url="+this.options.tool_shed,this.initialize(e)},templateCategoryList:s.template(['",'','',"<% _.each(tool_sheds, function(shed) { %>",'
","
",'',"| ",'"," | ","
','
",'Categories in <%= tool_shed.replace(/%2f/g, "/") %>
','',"','
"].join(""))});t.default={CategoryView:c}}).call(t,i(1),i(2),i(0))},313:function(e,t,i){"use strict";(function(e,s,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(167),r=a(o),l=i(168),d=a(l);i(157);var c=e.View.extend({el:"#center",initialize:function(e){this.model=new r.default.CategoryCollection,this.listenTo(this.model,"sync",this.render);var t=e.tool_shed.replace(/\//g,"%2f");this.model.url+="?tool_shed_url="+t+"&category_id="+e.category_id,this.model.tool_shed=t,this.model.category=e.category_id,this.model.fetch()},render:function(e){this.options=s.extend(this.options,e);var t=this.templateCategoryContents;this.$el.html(t({category:this.model.models[0],tool_shed:this.model.tool_shed,queue:d.default.queueLength()})),n("#center").css("overflow","auto"),this.bindEvents()},bindEvents:function(){var t=this;n("#search_box").autocomplete({source:function(e,i){var s=t.model.tool_shed.replace(/%2f/g,"/"),a=Galaxy.root+"api/tool_shed/search",o={term:e.term,tool_shed_url:s};n.post(a,o,function(e){var t=d.default.shedParser(e);i(t)})},minLength:3,select:function(i,s){var n=s.item.value,a="repository/s/"+t.model.tool_shed+"/r/"+n;e.history.navigate(a,{trigger:!0,replace:!0})}})},reDraw:function(e){this.$el.empty(),this.initialize(e)},templateCategoryContents:s.template(['",'','","
",'','','',"
","
","| Name | ","Description | ","Repositories | ","
|---|---|---|
| ",'"><%= category.get("name") %>'," | ",'<%= category.get("description") %> | ','<%= category.get("repositories") %> | ',"
','
",'Repositories in <%= category.get("name") %>
','',"','
"].join(""))});t.default={Category:c}}).call(t,i(1),i(2),i(0))},314:function(e,t,i){"use strict";(function(e,s,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(167),r=a(o),l=i(198),d=(a(l),i(3)),c=a(d),h=i(9),u=a(h),p=i(20),_=a(p),f=i(168),g=a(f),m=e.View.extend({el:"#center",initialize:function(e){this.options=s.defaults(this.options||{},this.defaults),this.model=new r.default.RepositoryCollection,this.listenTo(this.model,"sync",this.render);var t=e.tool_shed.replace(/\//g,"%2f");this.model.url+="?tool_shed_url="+t+"&repository_id="+e.repository_id,this.model.tool_shed_url=e.tool_shed.replace(/%2f/g,"/"),this.model.tool_shed=t,this.model.category=e.repository_id,this.model.fetch()},render:function(e){var t=this.templateRepoDetails,i=this.model.models[0];this.options={repository:i.get("repository"),tool_shed:this.model.tool_shed,queue:g.default.queueLength()};var a=Object.keys(this.options.repository.metadata);this.options.current_changeset=this.options.current_changeset||a[a.length-1],this.options.current_metadata=this.options.repository.metadata[this.options.current_changeset],this.options.current_metadata.tool_shed_url=this.model.tool_shed_url,this.options.tools=this.options.current_metadata.tools,this.options.repository_dependencies_template=this.templateRepoDependencies,this.options.repository_dependency_template=this.templateRepoDependency,this.options.tps_template_global_select=this.templateGlobalSectionSelect,this.options.tps_template_tool_select=this.templateToolSectionSelect,this.options.tps_select_options=this.templatePanelSelectOptions,this.options.tool_dependencies=i.get("tool_dependencies"),this.options.shed_tool_conf=this.templateShedToolConf({shed_tool_confs:i.get("shed_conf")}),console.log(i.get("shed_conf")),this.options.panel_section_dict=i.get("panel_section_dict"),this.options.api_url=Galaxy.root+"api/tool_shed_repositories/install?async=True",this.options=s.extend(this.options,e),this.$el.html(t(this.options)),this.checkInstalled(this.options.current_metadata),this.bindEvents(),n("#center").css("overflow","auto")},bindEvents:function(){var e=this;n("#changeset").on("change",function(){e.options.current_changeset=n("#changeset").find("option:selected").text(),e.options.current_metadata=e.options.repository.metadata[e.options.current_changeset],e.checkInstalled(e.options.current_metadata),e.reDraw()}),n("#tool_panel_section_select").on("change",function(){e.tpsSelection()}),n("#install_repository").on("click",function(t){n("#repository_installation");t.preventDefault();var i={};i.repositories=JSON.stringify([[n("#install_repository").attr("data-tsrid"),n("#changeset").find("option:selected").val()]]),i.tool_shed_repository_ids=JSON.stringify([n("#install_repository").attr("data-tsrid")]),i.tool_shed_url=e.model.tool_shed_url,i.install_tool_dependencies=n("#install_tool_dependencies").val(),i.install_repository_dependencies=n("#install_repository_dependencies").val(),i.install_resolver_dependencies=n("#install_resolver_dependencies").val();e.panelSelect(i);i.tool_panel_section=JSON.stringify(e.panelSelect(i)),i.shed_tool_conf=n("select[name='shed_tool_conf']").find("option:selected").val(),i.changeset=n("#changeset").find("option:selected").val();var s=n("#repository_installation").attr("action");e.prepareInstall(i,s)}),n("#queue_install").on("click",function(t){e.options.current_changeset=n("#changeset").find("option:selected").text(),e.options.current_metadata=e.options.repository.metadata[e.options.current_changeset];var i=(e.options.current_changeset,{});s.each(Object.keys(e.options.current_metadata),function(t){i[t]||(i[t]=e.options.current_metadata[t])}),i.install_tool_dependencies=n("#install_tool_dependencies").val(),i.install_repository_dependencies=n("#install_repository_dependencies").val(),i.install_resolver_dependencies=n("#install_resolver_dependencies").val(),i.tool_panel_section=JSON.stringify(e.panelSelect({})),i.shed_tool_conf=n("select[name='shed_tool_conf']").find("option:selected").val(),i.tool_shed_url=e.model.tool_shed_url,"/"==i.tool_shed_url.substr(-1)&&(i.tool_shed_url=i.tool_shed_url.substr(0,i.tool_shed_url.length-1)),g.default.addToQueue(i),e.checkInstalled(i)}),n(".tool_panel_section_picker").on("change",function(){n(this).find("option:selected").val()==n("#tool_panel_section_select").find("option:selected").val()?n(this).attr("default","active"):n(this).removeAttr("default")}),n(function(){n("#repository_dependencies").jstree()}),n(".tool_form").on("click",function(){var 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| ",'<%= workflow.get("shed") %> | ','<%= workflow.get("repository") %> | ','<%= workflow.get("owner") %> | ','','
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+>>>>>>> dev
+=======
p=!0,_=0,f=o.data.nodes.length;_
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','
",'",'<%= title %>
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|---|---|---|---|---|
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','',"| Workflows | ','Tool IDs | ','Shed | ','Name | ','Owner | ','Actions | ',"||||||
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| ",'','
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')),this.$el.removeClass().addClass("modal").addClass(this.options.cls),this.$header.find(".title").html(this.options.title),this.$body.html(this.options.body),this.$buttons.empty(),this.buttonList={},this.options.buttons){var t=0;s.each(this.options.buttons,function(i,n){var a=s("").attr("id","button-"+t++).text(i).click(n);e.$buttons.append(a).append(" "),e.buttonList[i]=a})}else this.$footer.hide();this.$backdrop[this.options.backdrop&&"addClass"||"removeClass"]("in"),this.$header[!this.options.title_separator&&"addClass"||"removeClass"]("no-separator"),this.$body.removeAttr("style"),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",s(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width)},getButton:function(e){return this.buttonList[e]},enableButton:function(e){this.getButton(e).prop("disabled",!1)},disableButton:function(e){this.getButton(e).prop("disabled",!0)},showButton:function(e){this.getButton(e).show()},hideButton:function(e){this.getButton(e).hide()},scrollTop:function(){return this.$body.scrollTop()},_template:function(){return'
'}});t.default={View:n}}).call(t,i(1),i(2),i(0))}},[309]);
>>>>>>> 854854cdf6... Rebuild client.
+>>>>>>> dev
diff --git a/static/scripts/bundled/extended.bundled.js b/static/scripts/bundled/extended.bundled.js
index 7798b5f6327..1da46bb4bf3 100644
--- a/static/scripts/bundled/extended.bundled.js
+++ b/static/scripts/bundled/extended.bundled.js
@@ -46,4 +46,4 @@ s=n,l=e("",{css:{position:"absolute",top:"-200px",left:i?"0px":"-1000px",
// the check will work anyway, as when moving the node will be loaded first and checked again
if(v === 'i' && !ins.is_loaded(p)) { }
*/
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- "+a+"
- "+t+"
- ",e.each(r,function(e,t){i+="
- "+t+" "}),i+="
- "+i+"
"+t.substring(2,t.length-1)+"
"}),i.html(a),r.show()):(i.html(a),r.hide())},showAttributes:function(){e(".right-content").hide(),e("#edit-attributes").show()},showForm:function(t,n){var i="right-content",r=i+"-"+n.id,a=e("#"+i);if(t&&0==a.find("#"+r).length){var o=e('');if(t.node=n,t.workflow=this.workflow,t.datatypes=this.datatypes,t.icon=y.default[n.type],t.cls="ui-portlet-narrow",n){var s="tool"==n.type?"Tool":"Default";o.append(new w.default[s](t).form.$el),a.append(o)}else Galaxy.emit.debug("workflow-view::initialize()","Node not found in workflow.")}e("."+i).hide(),a.find("#"+r).show(),a.show(),a.scrollTop()},isSubType:function(e,t){return e=this.ext_to_type[e],t=this.ext_to_type[t],this.type_to_type[e]&&t in this.type_to_type[e]},prebuildNode:function(t,n,i){var r=this,a=e(""),o=e(""+n+"
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loading tool info..."+e+"
";this.config_form=n,t.html(n),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});t.default=d}).call(t,n(2),n(1),n(0))},289:function(e,t,n){"use strict";(function(e,i){function r(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=n(1),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}(a),s=n(290),l=r(s),c=n(292),d=r(c);t.default=e.View.extend({initialize:function(e){this.node=e.node,this.output_width=Math.max(150,this.$el.width()),this.tool_body=this.$el.find(".toolFormBody"),this.tool_body.find("div").remove(),this.newInputsDiv().appendTo(this.tool_body),this.terminalViews={},this.outputViews={}},render:function(){this.renderToolLabel(),this.renderToolErrors(),this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolLabel:function(){this.$(".nodeTitle").text(this.node.label||this.node.name)},renderToolErrors:function(){this.node.errors?this.$el.addClass("tool-node-error"):this.$el.removeClass("tool-node-error")},newInputsDiv:function(){return i("").addClass("inputs")},updateMaxWidth:function(e){this.output_width=Math.max(this.output_width,e)},addRule:function(){this.tool_body.append(i("").addClass("rule"))},addDataInput:function(e,t){var n=!0;t||(t=this.$(".inputs"),n=!1);var i=this.terminalViews[e.name],r="dataset_collection"==e.input_type?l.default.InputCollectionTerminalView:l.default.InputTerminalView;if(!i||i instanceof r||(i.el.terminal.destroy(),i=null),i){var a=i.el.terminal;a.update(e),a.destroyInvalidConnections()}else i=new r({node:this.node,input:e});this.terminalViews[e.name]=i;var o=i.el,s=new d.default.DataInputView({terminalElement:o,input:e,nodeView:this,skipResize:n}),c=s.$el;return t.append(c.prepend(i.terminalElements())),i},addDataOutput:function(e){var t=e.collection?l.default.OutputCollectionTerminalView:l.default.OutputTerminalView,n=new t({node:this.node,output:e}),i=new d.default.DataOutputView({output:e,terminalElement:n.el,nodeView:this});this.outputViews[e.name]=i,this.tool_body.append(i.$el.append(n.terminalElements()))},redrawWorkflowOutputs:function(){o.each(this.outputViews,function(e){e.redrawWorkflowOutput()})},updateDataOutput:function(e){this.node.output_terminals[e.name].update(e)}})}).call(t,n(2),n(0))},290:function(e,t,n){"use strict";(function(e,i,r){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=n(291),s=a(o),l=n(125),c=a(l);window.workflow_globals=window.workflow_globals||{};var d=e.View.extend({tagName:"div",className:"fa-icon-button fa fa-folder-o",initialize:function(e){this.$el.tooltip({delay:500,title:"Run tool in parallel over collection"}),this.model.bind("change",i.bind(this.render,this))},render:function(){this.model.mapOver.isCollection?this.$el.show():this.$el.hide()}}),u=d.extend({events:{click:"onClick",mouseenter:"onMouseEnter",mouseleave:"onMouseLeave"},onMouseEnter:function(e){var t=this.model;!t.terminal.connected()&&t.mapOver.isCollection&&this.$el.css("color","red")},onMouseLeave:function(e){this.$el.css("color","black")},onClick:function(e){var t=this.model;!t.terminal.connected()&&t.mapOver.isCollection&&t.terminal.resetMapping()}}),h=e.View.extend({setupMappingView:function(e){var t=new this.terminalMappingClass({terminal:e}),n=new this.terminalMappingViewClass({model:t});n.render(),e.terminalMappingView=n,this.terminalMappingView=n},terminalElements:function(){return this.terminalMappingView?[this.terminalMappingView.el,this.el]:[this.el]}}),f=h.extend({className:"terminal input-terminal",initialize:function(e){var t=e.node,n=e.input,i=n.name,r=this.terminalForInput(n);r.multiple||this.setupMappingView(r),this.el.terminal=r,r.node=t,r.name=i,t.input_terminals[i]=r},events:{dropinit:"onDropInit",dropstart:"onDropStart",dropend:"onDropEnd",drop:"onDrop",hover:"onHover"},onDropInit:function(e,t){var n=this.el.terminal;return r(t.drag).hasClass("output-terminal")&&n.canAccept(t.drag.terminal)},onDropStart:function(e,t){t.proxy.terminal&&(t.proxy.terminal.connectors[0].inner_color="#BBFFBB")},onDropEnd:function(e,t){t.proxy.terminal&&(t.proxy.terminal.connectors[0].inner_color="#FFFFFF")},onDrop:function(e,t){var n=this.el.terminal;new c.default(t.drag.terminal,n).redraw()},onHover:function(){var e=this.el,t=e.terminal;if(t.connectors.length>0){var n=r("").css({display:"none"}).appendTo("body").append(r("").append(r("").addClass("fa-icon-button fa fa-times").click(function(){r.each(t.connectors,function(e,t){t&&t.destroy()}),n.remove()}))).bind("mouseleave",function(){r(this).remove()});n.css({top:r(e).offset().top-2,left:r(e).offset().left-n.width(),"padding-right":r(e).width()}).show()}}}),p=f.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:u,terminalForInput:function(e){return new s.default.InputTerminal({element:this.el,input:e})}}),_=f.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:u,terminalForInput:function(e){return new s.default.InputCollectionTerminal({element:this.el,input:e})}}),g=h.extend({className:"terminal output-terminal",initialize:function(e){var t=e.node,n=e.output,i=n.name,r=this.terminalForOutput(n);this.setupMappingView(r),this.el.terminal=r,r.node=t,r.name=i,t.output_terminals[i]=r},events:{drag:"onDrag",dragstart:"onDragStart",dragend:"onDragEnd"},onDrag:function(e,t){var n=function(){var e=r(t.proxy).offsetParent().offset(),n=t.offsetX-e.left,i=t.offsetY-e.top;r(t.proxy).css({left:n,top:i}),t.proxy.terminal.redraw(),window.workflow_globals.canvas_manager.update_viewport_overlay()};n(),r("#canvas-container").get(0).scroll_panel.test(e,n)},onDragStart:function(e,t){r(t.available).addClass("input-terminal-active"),window.workflow_globals.workflow.check_changes_in_active_form();var n=r('').appendTo("#canvas-container").get(0);n.terminal=new s.default.OutputTerminal({element:n});var i=new c.default;return i.dragging=!0,i.connect(this.el.terminal,n.terminal),n},onDragEnd:function(e,t){var n=t.proxy.terminal.connectors[0];n&&n.destroy(),r(t.proxy).remove(),r(t.available).removeClass("input-terminal-active"),r("#canvas-container").get(0).scroll_panel.stop()}}),m=g.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:d,terminalForOutput:function(e){var t=e.extensions;return new s.default.OutputTerminal({element:this.el,datatypes:t})}}),v=g.extend({terminalMappingClass:s.default.TerminalMapping,terminalMappingViewClass:d,terminalForOutput:function(e){var t=e.collection_type,n=e.collection_type_source;return new s.default.OutputCollectionTerminal({element:this.el,collection_type:t,collection_type_source:n,datatypes:e.extensions})}});t.default={InputTerminalView:p,OutputTerminalView:m,InputCollectionTerminalView:_,OutputCollectionTerminalView:v}}).call(t,n(2),n(1),n(0))},291:function(e,t,n){"use strict";(function(e,n,i){function r(e){this.collectionType=e,this.isCollection=!0,this.rank=e.split(":").length}Object.defineProperty(t,"__esModule",{value:!0}),window.workflow_globals=window.workflow_globals||{};var a={isCollection:!1,canMatch:function(){return!1},canMapOver:function(){return!1},toString:function(){return"NullCollectionType[]"},append:function(e){return e},equal:function(e){return e===this}},o={isCollection:!0,canMatch:function(e){return a!==e},canMapOver:function(){return!1},toString:function(){return"AnyCollectionType[]"},append:function(){throw"Cannot append to ANY_COLLECTION_TYPE_DESCRIPTION"},equal:function(e){return e===this}};e.extend(r.prototype,{append:function(e){return e===a?this:e===o?e:new r(this.collectionType+":"+e.collectionType)},canMatch:function(e){return e!==a&&(e===o||e.collectionType==this.collectionType)},canMapOver:function(e){if(e===a)return!1;if(e===o)return!1;if(this.rank<=e.rank)return!1;var t=e.collectionType;return this._endsWith(this.collectionType,t)},effectiveMapOver:function(e){var t=e.collectionType;return new r(this.collectionType.substring(0,this.collectionType.length-t.length-1))},equal:function(e){return e.collectionType==this.collectionType},toString:function(){return"CollectionType["+this.collectionType+"]"},_endsWith:function(e,t){return-1!==e.indexOf(t,e.length-t.length)}});var s=n.Model.extend({initialize:function(e){this.mapOver=e.mapOver||a,this.terminal=e.terminal,this.terminal.terminalMapping=this},disableMapOver:function(){this.setMapOver(a)},setMapOver:function(e){this.mapOver=e,this.trigger("change")}}),l=n.Model.extend({initialize:function(e){this.element=e.element,this.connectors=[]},connect:function(e){this.connectors.push(e),this.node&&this.node.markChanged()},disconnect:function(t){this.connectors.splice(e.inArray(t,this.connectors),1),this.node&&(this.node.markChanged(),this.resetMappingIfNeeded())},redraw:function(){e.each(this.connectors,function(e,t){t.redraw()})},destroy:function(){e.each(this.connectors.slice(),function(e,t){t.destroy()})},destroyInvalidConnections:function(){i.each(this.connectors,function(e){e&&e.destroyIfInvalid()})},setMapOver:function(e){this.multiple||this.mapOver().equal(e)||(this.terminalMapping.setMapOver(e),i.each(this.node.output_terminals,function(t){t.setMapOver(e)}))},mapOver:function(){return this.terminalMapping?this.terminalMapping.mapOver:a},isMappedOver:function(){return this.terminalMapping&&this.terminalMapping.mapOver.isCollection},resetMapping:function(){this.terminalMapping.disableMapOver()},resetMappingIfNeeded:function(){}}),c=l.extend({initialize:function(e){l.prototype.initialize.call(this,e),this.datatypes=e.datatypes},resetMappingIfNeeded:function(){this.node.hasConnectedOutputTerminals()||this.node.hasConnectedMappedInputTerminals()||i.each(this.node.mappedInputTerminals(),function(e){e.resetMappingIfNeeded()}),!this.node.hasMappedOverInputTerminals()&&this.resetMapping()},resetMapping:function(){this.terminalMapping.disableMapOver(),i.each(this.connectors,function(e){var t=e.handle2;t&&(t.resetMappingIfNeeded(),e.destroyIfInvalid())})}}),d=l.extend({initialize:function(e){l.prototype.initialize.call(this,e),this.update(e.input)},canAccept:function(e){return!this._inputFilled()&&this.attachable(e)},resetMappingIfNeeded:function(){this.mapOver().isCollection&&((this.node.hasConnectedMappedInputTerminals()||!this.node.hasConnectedOutputTerminals())&&this.resetMapping())},resetMapping:function(){this.terminalMapping.disableMapOver(),this.node.hasMappedOverInputTerminals()||i.each(this.node.output_terminals,function(e){e.resetMapping()})},connected:function(){return 0!==this.connectors.length},_inputFilled:function(){return!!this.connected()&&(!this.multiple||!!this._collectionAttached())},_collectionAttached:function(){if(this.connected()){var e=this.connectors[0].handle1;return!!e&&!!(e.isCollection||e.isMappedOver()||e.datatypes.indexOf("input_collection")>0)}return!1},_mappingConstraints:function(){if(!this.node)return[];var e=this.mapOver();if(e.isCollection)return[e];var t=[];return this.node.hasConnectedOutputTerminals()?t.push(i.first(i.values(this.node.output_terminals)).mapOver()):i.each(this.node.connectedMappedInputTerminals(),function(e){t.push(e.mapOver())}),t},_producesAcceptableDatatype:function(e){for(var t in this.datatypes){var n=this.datatypes[t];if("input"==n)return!0;var i=[];if(i=i.concat(e.datatypes),e.node.post_job_actions)for(var r in e.node.post_job_actions){var a=e.node.post_job_actions[r];"ChangeDatatypeAction"!=a.action_type||""!==a.output_name&&a.output_name!=e.name||!a.action_arguments||i.push(a.action_arguments.newtype)}for(var o in i){var s=i[o];if("input"==s||"_sniff_"==s||"input_collection"==s||window.workflow_globals.app.isSubType(i[o],n))return!0}}return!1},_otherCollectionType:function(e){var t=a;e.isCollection&&(t=e.collectionType);var n=e.mapOver();return n.isCollection&&(t=n.append(t)),t}}),u=d.extend({update:function(e){this.datatypes=e.extensions,this.multiple=e.multiple,this.collection=!1},connect:function(e){d.prototype.connect.call(this,e);var t=e.handle1;if(t){var n=this._otherCollectionType(t);n.isCollection&&this.setMapOver(n)}},attachable:function(e){var t=this._otherCollectionType(e),n=this.mapOver();if(t.isCollection){if(this.multiple)return!(this.connected()&&!this._collectionAttached())&&(1==t.rank&&this._producesAcceptableDatatype(e));if(n.isCollection&&n.canMatch(t))return this._producesAcceptableDatatype(e);return!!this._mappingConstraints().every(i.bind(t.canMatch,t))&&this._producesAcceptableDatatype(e)}return!n.isCollection&&this._producesAcceptableDatatype(e)}}),h=d.extend({update:function(e){this.multiple=!1,this.collection=!0,this.datatypes=e.extensions;var t=[];e.collection_types?i.each(e.collection_types,function(e){t.push(new r(e))}):t.push(o),this.collectionTypes=t},connect:function(e){d.prototype.connect.call(this,e);var t=e.handle1;if(t){var n=this._effectiveMapOver(t);this.setMapOver(n)}},_effectiveMapOver:function(e){var t=this.collectionTypes,n=this._otherCollectionType(e);if(!i.some(t,function(e){return e.canMatch(n)}))for(var r in t){var o=t[r];if(n.canMapOver(o)){var s=n.effectiveMapOver(o);if(s!=a)return s}}return a},_effectiveCollectionTypes:function(){var e=this.mapOver();return i.map(this.collectionTypes,function(t){return e.append(t)})},attachable:function(e){var t=this._otherCollectionType(e);if(t.isCollection){var n=this._effectiveCollectionTypes(),r=this.mapOver();if(i.some(n,function(e){return e.canMatch(t)}))return this._producesAcceptableDatatype(e);if(r.isCollection)return!1;if(i.some(this.collectionTypes,function(e){return t.canMapOver(e)})){var a=this._effectiveMapOver(e);if(!a.isCollection)return!1;if(this._mappingConstraints().every(a.canMatch))return 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| <%= repository.owner %> | ","",'"," | ","<%= repository.description %> | ","<%= repository.type %> | ","
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",'',"
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|---|---|---|---|---|---|
| <%= repository.get("repository").name %> | ','<%= repository.get("repository").owner %> | ','<%= repository.get("changeset_revision") %> | ','<%= repository.get("tool_shed_url") %> | ','','" type="submit" id="install_repository_<%= repository.get("id") %>" name="install_repository" value="Install now" />'," | ",'','" type="submit" id="unqueue_repository_<%= repository.get("id") %>" name="unqueue_repository" value="Remove from queue" />'," | ","
','
",'",'<%= title %>
','',"| Name | ','Description | ','Owner | ','Revision | ','Installation Status | ',"
|---|---|---|---|---|
| ",' ','"," "," | ","",' ','"," "," | ","",' ','"," "," | ","",' ','"," "," | ","",' ','"," "," | ","
','
",'",'<%= title %>
','',"