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Merge pull request #5114 from guerler/remove_formbuilder

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Remove html formbuilder from backend
This commit is contained in:
Dannon Baker
2017-12-11 16:53:46 -05:00
committed by GitHub
parent 1e8c15b3ba 34a71af9e1
commit 7f30028d32
50 changed files with 161 additions and 1276 deletions
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client/galaxy/scripts/mvc/toolshed/repository-view.js
+6 -2
View File
@@ -48,7 +48,7 @@ var ToolShedRepositoryView = Backbone.View.extend({
this.options.tps_select_options = this.templatePanelSelectOptions;
this.options.tool_dependencies = models.get("tool_dependencies");
this.options.shed_tool_conf = this.templateShedToolConf({
stc_html: models.get("shed_conf")
shed_tool_confs: models.get("shed_conf")
});
this.options.panel_section_dict = models.get("panel_section_dict");
this.options.api_url = `${Galaxy.root}api/tool_shed_repositories/install?async=True`;
@@ -474,7 +474,11 @@ var ToolShedRepositoryView = Backbone.View.extend({
'<div class="toolFormTitle">Shed tool configuration file:</div>',
'<div class="toolFormBody">',
'<div class="form-row">',
"<%= stc_html %>",
'<select name="shed_tool_conf">',
"<% _.each(shed_tool_confs.options, function(conf) { %>",
'<option value="<%= conf.value %>"><%= conf.label %></option>',
"<% }); %>",
'</select>',
'<div class="toolParamHelp" style="clear: both;">Select the file whose <b>tool_path</b> setting you want used for installing repositories.</div>',
"</div>",
"</div>"
lib/galaxy/model/__init__.py
+3 -270
View File
@@ -5,7 +5,6 @@ Naming: try to use class names that have a distinct plural form so that
the relationship cardinalities are obvious (e.g. prefer Dataset to Data)
"""
import errno
import json
import logging
import numbers
import operator
@@ -30,8 +29,8 @@ from galaxy.managers import tags
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.model.util import pgcalc
from galaxy.security import get_permitted_actions
from galaxy.util import (directory_hash_id, Params, ready_name_for_url,
restore_text, unicodify, unique_id)
from galaxy.util import (directory_hash_id, ready_name_for_url,
unicodify, unique_id)
from galaxy.util.bunch import Bunch
from galaxy.util.dictifiable import Dictifiable
from galaxy.util.hash_util import new_secure_hash
@@ -2667,32 +2666,6 @@ class Library(object, Dictifiable, HasName):
active_folders.extend(self.get_active_folders(active_folder, folders))
return sort_by_attr(active_folders, 'id')
def get_info_association(self, restrict=False, inherited=False):
if self.info_association:
if not inherited or self.info_association[0].inheritable:
return self.info_association[0], inherited
else:
return None, inherited
return None, inherited
def get_template_widgets(self, trans, get_contents=True):
# See if we have any associated templates - the returned value for
# inherited is not applicable at the library level. The get_contents
# param is passed by callers that are inheriting a template - these
# are usually new library datsets for which we want to include template
# fields on the upload form, but not necessarily the contents of the
# inherited template saved for the parent.
info_association, inherited = self.get_info_association()
if info_association:
template = info_association.template
if get_contents:
# See if we have any field contents
info = info_association.info
if info:
return template.get_widgets(trans.user, contents=info.content)
return template.get_widgets(trans.user)
return []
def get_access_roles(self, trans):
roles = []
for lp in self.actions:
@@ -2723,51 +2696,6 @@ class LibraryFolder(object, Dictifiable, HasName):
folder.order_id = self.item_count
self.item_count += 1
def get_info_association(self, restrict=False, inherited=False):
# If restrict is True, we will return this folder's info_association, not inheriting.
# If restrict is False, we'll return the next available info_association in the
# inheritable hierarchy if it is "inheritable". True is also returned if the
# info_association was inherited and False if not. This enables us to eliminate
# displaying any contents of the inherited template.
if self.info_association:
if not inherited or self.info_association[0].inheritable:
return self.info_association[0], inherited
else:
return None, inherited
if restrict:
return None, inherited
if self.parent:
return self.parent.get_info_association(inherited=True)
if self.library_root:
return self.library_root[0].get_info_association(inherited=True)
return None, inherited
def get_template_widgets(self, trans, get_contents=True):
# See if we have any associated templates. The get_contents
# param is passed by callers that are inheriting a template - these
# are usually new library datsets for which we want to include template
# fields on the upload form.
info_association, inherited = self.get_info_association()
if info_association:
if inherited:
template = info_association.template.current.latest_form
else:
template = info_association.template
# See if we have any field contents, but only if the info_association was
# not inherited ( we do not want to display the inherited contents ).
# (gvk: 8/30/10) Based on conversations with Dan, we agreed to ALWAYS inherit
# contents. We'll use this behavior until we hear from the community that
# contents should not be inherited. If we don't hear anything for a while,
# eliminate the old commented out behavior.
# if not inherited and get_contents:
if get_contents:
info = info_association.info
if info:
return template.get_widgets(trans.user, info.content)
else:
return template.get_widgets(trans.user)
return []
@property
def activatable_library_datasets(self):
# This needs to be a list
@@ -2775,13 +2703,6 @@ class LibraryFolder(object, Dictifiable, HasName):
def to_dict(self, view='collection', value_mapper=None):
rval = super(LibraryFolder, self).to_dict(view=view, value_mapper=value_mapper)
info_association, inherited = self.get_info_association()
if info_association:
if inherited:
template = info_association.template.current.latest_form
else:
template = info_association.template
rval['data_template'] = template.name
rval['library_path'] = self.library_path
rval['parent_library_id'] = self.parent_library.id
return rval
@@ -2855,15 +2776,6 @@ class LibraryDataset(object):
# display in other objects, we can't use the simpler method used by
# other model classes.
ldda = self.library_dataset_dataset_association
template_data = {}
for temp_info in ldda.info_association:
template = temp_info.template
content = temp_info.info.content
tmp_dict = {}
for field in template.fields:
tmp_dict[field['label']] = content[field['name']]
template_data[template.name] = tmp_dict
rval = dict(id=self.id,
ldda_id=ldda.id,
parent_library_id=self.folder.parent_library.id,
@@ -2881,8 +2793,7 @@ class LibraryDataset(object):
genome_build=ldda.dbkey,
misc_info=ldda.info,
misc_blurb=ldda.blurb,
peek=(lambda ldda: ldda.display_peek() if ldda.peek and ldda.peek != 'no peek' else None)(ldda),
template_data=template_data)
peek=(lambda ldda: ldda.display_peek() if ldda.peek and ldda.peek != 'no peek' else None)(ldda))
if ldda.dataset.uuid is None:
rval['uuid'] = None
else:
@@ -2987,19 +2898,6 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName):
def has_manage_permissions_roles(self, trans):
return self.dataset.has_manage_permissions_roles(trans)
def get_info_association(self, restrict=False, inherited=False):
# If restrict is True, we will return this ldda's info_association whether it
# exists or not ( in which case None will be returned ). If restrict is False,
# we'll return the next available info_association in the inheritable hierarchy.
# True is also returned if the info_association was inherited, and False if not.
# This enables us to eliminate displaying any contents of the inherited template.
# SM: Accessing self.info_association can cause a query to be emitted
if self.info_association:
return self.info_association[0], inherited
if restrict:
return None, inherited
return self.library_dataset.folder.get_info_association(inherited=True)
def to_dict(self, view='collection'):
# Since this class is a proxy to rather complex attributes we want to
# display in other objects, we can't use the simpler method used by
@@ -3044,55 +2942,6 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName):
rval['metadata_' + name] = val
return rval
def get_template_widgets(self, trans, get_contents=True):
# See if we have any associated templatesThe get_contents
# param is passed by callers that are inheriting a template - these
# are usually new library datsets for which we want to include template
# fields on the upload form, but not necessarily the contents of the
# inherited template saved for the parent.
info_association, inherited = self.get_info_association()
if info_association:
if inherited:
template = info_association.template.current.latest_form
else:
template = info_association.template
# See if we have any field contents, but only if the info_association was
# not inherited ( we do not want to display the inherited contents ).
# (gvk: 8/30/10) Based on conversations with Dan, we agreed to ALWAYS inherit
# contents. We'll use this behavior until we hear from the community that
# contents should not be inherited. If we don't hear anything for a while,
# eliminate the old commented out behavior.
# if not inherited and get_contents:
if get_contents:
info = info_association.info
if info:
return template.get_widgets(trans.user, info.content)
else:
return template.get_widgets(trans.user)
return []
def templates_dict(self, use_name=False):
"""
Returns a dict of template info
"""
# TODO: Should have a method that allows names and labels to be returned together in a structured way
template_data = {}
for temp_info in self.info_association:
template = temp_info.template
content = temp_info.info.content
tmp_dict = {}
for field in template.fields:
if use_name:
name = field['name']
else:
name = field['label']
tmp_dict[name] = content.get(field['name'])
template_data[template.name] = tmp_dict
return template_data
def templates_json(self, use_name=False):
return json.dumps(self.templates_dict(use_name=use_name))
class ExtendedMetadata(object):
def __init__(self, data):
@@ -4450,98 +4299,6 @@ class FormDefinition(object, Dictifiable):
gridfields[i] = f
return gridfields
def get_widgets(self, user, contents={}, **kwd):
'''
Return the list of widgets that comprise a form definition,
including field contents if any.
'''
params = Params(kwd)
widgets = []
for index, field in enumerate(self.fields):
field_type = field['type']
if 'name' in field:
field_name = field['name']
else:
# Default to names like field_0, field_1, etc for backward compatibility
# (not sure this is necessary)...
field_name = 'field_%i' % index
# Determine the value of the field
if field_name in kwd:
# The form was submitted via refresh_on_change
if field_type == 'CheckboxField':
value = CheckboxField.is_checked(params.get(field_name, False))
else:
value = restore_text(params.get(field_name, ''))
elif contents:
try:
# This field has a saved value.
value = str(contents[field['name']])
except Exception:
# If there was an error getting the saved value, we'll still
# display the widget, but it will be empty.
if field_type == 'AddressField':
value = 'none'
elif field_type == 'CheckboxField':
# Since we do not have contents, set checkbox value to False
value = False
else:
# Set other field types to empty string
value = ''
else:
# If none of the above, then leave the field empty
if field_type == 'AddressField':
value = 'none'
elif field_type == 'CheckboxField':
# Since we do not have contents, set checkbox value to False
value = False
else:
# Set other field types to the default value of the field
value = field.get('default', '')
# Create the field widget
field_widget = eval(field_type)(field_name)
if field_type in ['TextField', 'PasswordField']:
field_widget.set_size(40)
field_widget.value = value
elif field_type == 'TextArea':
field_widget.set_size(3, 40)
field_widget.value = value
elif field_type in ['AddressField', 'WorkflowField', 'WorkflowMappingField', 'HistoryField']:
field_widget.user = user
field_widget.value = value
field_widget.params = params
elif field_type == 'SelectField':
for option in field['selectlist']:
if option == value:
field_widget.add_option(option, option, selected=True)
else:
field_widget.add_option(option, option)
elif field_type == 'CheckboxField':
field_widget.set_checked(value)
if field['required'] == 'required':
req = 'Required'
else:
req = 'Optional'
if field['helptext']:
helptext = '%s (%s)' % (field['helptext'], req)
else:
helptext = '(%s)' % req
widgets.append(dict(label=field['label'], widget=field_widget, helptext=helptext))
return widgets
def field_as_html(self, field):
"""Generates disabled html for a field"""
type = field['type']
form_field = None
for field_type in self.supported_field_types:
if type == field_type.__name__:
# Name it AddressField, CheckboxField, etc.
form_field = field_type(type)
break
if form_field:
return form_field.get_html(disabled=True)
# Return None if unsupported field type
return None
class FormDefinitionCurrent(object):
def __init__(self, form_definition=None):
@@ -4581,30 +4338,6 @@ class UserAddress(object):
'country' : sanitize_html(self.country),
'phone' : sanitize_html(self.phone)}
def get_html(self):
# This should probably be deprecated eventually. It should currently
# sanitize.
# TODO Find out where else uses this and replace with
# templates
html = ''
if self.name:
html = html + sanitize_html(self.name)
if self.institution:
html = html + '<br/>' + sanitize_html(self.institution)
if self.address:
html = html + '<br/>' + sanitize_html(self.address)
if self.city:
html = html + '<br/>' + sanitize_html(self.city)
if self.state:
html = html + ' ' + sanitize_html(self.state)
if self.postal_code:
html = html + ' ' + sanitize_html(self.postal_code)
if self.country:
html = html + '<br/>' + sanitize_html(self.country)
if self.phone:
html = html + '<br/>' + 'phone: ' + sanitize_html(self.phone)
return html
class UserOpenID(object):
def __init__(self, user=None, session=None, openid=None):
lib/galaxy/model/metadata.py
-69
View File
@@ -227,29 +227,6 @@ class MetadataParameter(object):
other_values = other_values or {}
return form_builder.TextField(self.spec.name, value=value)
def get_html(self, value, context=None, other_values=None, **kwd):
"""
The "context" is simply the metadata collection/bunch holding
this piece of metadata. This is passed in to allow for
metadata to validate against each other (note: this could turn
into a huge, recursive mess if not done with care). For
example, a column assignment should validate against the
number of columns in the dataset.
"""
context = context or {}
other_values = other_values or {}
if self.spec.get("readonly"):
return value
if self.spec.get("optional"):
checked = False
if value:
checked = "true"
checkbox = form_builder.CheckboxField("is_" + self.spec.name, checked=checked)
return checkbox.get_html() + self.get_field(value=value, context=context, other_values=other_values, **kwd).get_html()
else:
return self.get_field(value=value, context=context, other_values=other_values, **kwd).get_html()
def to_string(self, value):
return str(value)
@@ -390,16 +367,6 @@ class SelectParameter(MetadataParameter):
field.add_option(val, label, selected=False)
return field
def get_html(self, value, context=None, other_values=None, values=None, **kwd):
context = context or {}
other_values = other_values or {}
if self.spec.get("readonly"):
if value in [None, []]:
return str(self.spec.no_value)
return ", ".join(map(str, value))
return MetadataParameter.get_html(self, value, context=context, other_values=other_values, values=values, **kwd)
def wrap(self, value, session):
# do we really need this (wasteful)? - yes because we are not sure that
# all existing selects have been stored previously as lists. Also this
@@ -433,15 +400,6 @@ class DBKeyParameter(SelectParameter):
pass
return super(DBKeyParameter, self).get_field(value, context, other_values, values, **kwd)
def get_html(self, value=None, context=None, other_values=None, values=None, **kwd):
context = context or {}
other_values = other_values or {}
try:
values = kwd['trans'].app.genome_builds.get_genome_build_names(kwd['trans'])
except KeyError:
pass
return super(DBKeyParameter, self).get_html(value, context, other_values, values, **kwd)
class RangeParameter(SelectParameter):
@@ -460,14 +418,6 @@ class RangeParameter(SelectParameter):
values = list(zip(range(self.min, self.max, self.step), range(self.min, self.max, self.step)))
return SelectParameter.get_field(self, value=value, context=context, other_values=other_values, values=values, **kwd)
def get_html(self, value, context=None, other_values=None, values=None, **kwd):
context = context or {}
other_values = other_values or {}
if values is None:
values = list(zip(range(self.min, self.max, self.step), range(self.min, self.max, self.step)))
return SelectParameter.get_html(self, value, context=context, other_values=other_values, values=values, **kwd)
@classmethod
def marshal(cls, value):
value = SelectParameter.marshal(value)
@@ -486,15 +436,6 @@ class ColumnParameter(RangeParameter):
values = list(zip(column_range, column_range))
return RangeParameter.get_field(self, value=value, context=context, other_values=other_values, values=values, **kwd)
def get_html(self, value, context=None, other_values=None, values=None, **kwd):
context = context or {}
other_values = other_values or {}
if values is None and context:
column_range = range(1, (context.columns or 0) + 1, 1)
values = list(zip(column_range, column_range))
return RangeParameter.get_html(self, value, context=context, other_values=other_values, values=values, **kwd)
class ColumnTypesParameter(MetadataParameter):
@@ -530,11 +471,6 @@ class PythonObjectParameter(MetadataParameter):
other_values = other_values or {}
return form_builder.TextField(self.spec.name, value=self._to_string(value))
def get_html(self, value=None, context=None, other_values=None, **kwd):
context = context or {}
other_values = other_values or {}
return str(self)
@classmethod
def marshal(cls, value):
return value
@@ -556,11 +492,6 @@ class FileParameter(MetadataParameter):
other_values = other_values or {}
return form_builder.TextField(self.spec.name, value=str(value.id))
def get_html(self, value=None, context=None, other_values=None, **kwd):
context = context or {}
other_values = other_values or {}
return "<div>No display available for Metadata Files</div>"
def wrap(self, value, session):
if value is None:
return None
lib/galaxy/tools/__init__.py
+1 -5
View File
@@ -309,11 +309,9 @@ class ToolBox(BaseGalaxyToolBox):
def __build_tool_version_select_field(self, tools, tool_id, set_selected):
"""Build a SelectField whose options are the ids for the received list of tools."""
options = []
refresh_on_change_values = []
for tool in tools:
options.insert(0, (tool.version, tool.id))
refresh_on_change_values.append(tool.id)
select_field = SelectField(name='tool_id', refresh_on_change=True, refresh_on_change_values=refresh_on_change_values)
select_field = SelectField(name='tool_id')
for option_tup in options:
selected = set_selected and option_tup[1] == tool_id
if selected:
@@ -1042,8 +1040,6 @@ class Tool(object, Dictifiable):
group.default_file_type = elem.get('default_file_type', group.default_file_type)
group.metadata_ref = elem.get('metadata_ref', group.metadata_ref)
rval[group.file_type_name].refresh_on_change = True
rval[group.file_type_name].refresh_on_change_values = \
self.app.datatypes_registry.get_composite_extensions()
group_page_source = XmlPageSource(elem)
group.inputs = self.parse_input_elem(group_page_source, enctypes, context)
rval[group.name] = group
lib/galaxy/tools/parameters/basic.py
-1
View File
@@ -75,7 +75,6 @@ class ToolParameter(object, Dictifiable):
def __init__(self, tool, input_source, context=None):
input_source = ensure_input_source(input_source)
self.tool = tool
self.refresh_on_change_values = []
self.argument = input_source.get("argument")
self.name = self.__class__.parse_name(input_source)
self.type = input_source.get("type")
lib/galaxy/web/__init__.py
-4
View File
@@ -23,10 +23,6 @@ from .framework.decorators import (
require_admin,
require_login
)
from .framework.formbuilder import (
form,
FormBuilder
)
__all__ = ('url_for', 'error', 'expose', 'json', 'json_pretty',
'require_admin', 'require_login', 'expose_api', 'expose_api_anonymous',
lib/galaxy/web/form_builder.py
+10 -527
View File
@@ -4,14 +4,9 @@ Classes for generating HTML forms
from __future__ import print_function
import logging
from cgi import escape
from six import string_types
from galaxy.util import (
asbool,
restore_text,
unicodify
asbool
)
log = logging.getLogger(__name__)
@@ -29,16 +24,6 @@ class BaseField(object):
self.optional = kwds.get('required', 'optional') == 'optional'
self.help = kwds.get('helptext')
def get_html(self, prefix=""):
"""Returns the html widget corresponding to the parameter"""
raise TypeError("Abstract Method")
def get_disabled_str(self, disabled=False):
if disabled:
return ' disabled="disabled"'
else:
return ''
def to_dict(self):
return {
'name' : self.name,
@@ -53,25 +38,7 @@ class BaseField(object):
class TextField(BaseField):
"""
A standard text input box.
>>> print(TextField( "foo" ).get_html())
<input type="text" name="foo" size="10" value="">
>>> print(TextField( "bins", size=4, value="default" ).get_html())
<input type="text" name="bins" size="4" value="default">
"""
def __init__(self, name, size=None, value=None, **kwds):
super(TextField, self).__init__(name, value, **kwds)
self.size = int(size or 10)
def get_html(self, prefix="", disabled=False):
value = unicodify(self.value or "")
return unicodify('<input type="text" name="%s%s" size="%d" value="%s"%s>'
% (prefix, self.name, self.size, escape(value, quote=True), self.get_disabled_str(disabled)))
def set_size(self, size):
self.size = int(size)
def to_dict(self):
d = super(TextField, self).to_dict()
d['type'] = 'text'
@@ -81,26 +48,7 @@ class TextField(BaseField):
class PasswordField(BaseField):
"""
A password input box. text appears as "******"
>>> print(PasswordField( "foo" ).get_html())
<input type="password" name="foo" size="10" value="">
>>> print(PasswordField( "bins", size=4, value="default" ).get_html())
<input type="password" name="bins" size="4" value="default">
"""
def __init__(self, name, size=None, value=None, **kwds):
super(PasswordField, self).__init__(name, value, **kwds)
self.name = name
self.size = int(size or 10)
self.value = value or ""
def get_html(self, prefix="", disabled=False):
return unicodify('<input type="password" name="%s%s" size="%d" value="%s"%s>'
% (prefix, self.name, self.size, escape(str(self.value), quote=True), self.get_disabled_str(disabled)))
def set_size(self, size):
self.size = int(size)
def to_dict(self):
d = super(PasswordField, self).to_dict()
d['type'] = 'password'
@@ -110,31 +58,7 @@ class PasswordField(BaseField):
class TextArea(BaseField):
"""
A standard text area box.
>>> print(TextArea( "foo" ).get_html())
<textarea name="foo" rows="5" cols="25"></textarea>
>>> print(TextArea( "bins", size="4x5", value="default" ).get_html())
<textarea name="bins" rows="4" cols="5">default</textarea>
"""
_DEFAULT_SIZE = "5x25"
def __init__(self, name, size=None, value=None, **kwds):
super(TextArea, self).__init__(name, value, **kwds)
self.name = name
size = size or self._DEFAULT_SIZE
self.size = size.split("x")
self.rows = int(self.size[0])
self.cols = int(self.size[-1])
self.value = value or ""
def get_html(self, prefix="", disabled=False):
return unicodify('<textarea name="%s%s" rows="%d" cols="%d"%s>%s</textarea>'
% (prefix, self.name, self.rows, self.cols, self.get_disabled_str(disabled), escape(str(self.value), quote=True)))
def set_size(self, rows, cols):
self.rows = rows
self.cols = cols
def to_dict(self):
d = super(TextArea, self).to_dict()
d['type'] = 'text'
@@ -145,46 +69,12 @@ class TextArea(BaseField):
class CheckboxField(BaseField):
"""
A checkbox (boolean input)
>>> print(CheckboxField( "foo" ).get_html())
<input type="checkbox" id="foo" name="foo" value="__CHECKED__"><input type="hidden" name="foo" value="__NOTHING__">
>>> print(CheckboxField( "bar", checked="yes" ).get_html())
<input type="checkbox" id="bar" name="bar" value="__CHECKED__" checked="checked"><input type="hidden" name="bar" value="__NOTHING__">
"""
def __init__(self, name, checked=None, refresh_on_change=False, refresh_on_change_values=None, value=None, **kwds):
super(CheckboxField, self).__init__(name, value, **kwds)
self.name = name
self.checked = (checked is True) or (isinstance(checked, string_types) and (checked.lower() in ("yes", "true", "on")))
self.refresh_on_change = refresh_on_change
self.refresh_on_change_values = refresh_on_change_values or []
if self.refresh_on_change:
self.refresh_on_change_text = ' refresh_on_change="true" '
if self.refresh_on_change_values:
self.refresh_on_change_text = '%s refresh_on_change_values="%s" ' % (self.refresh_on_change_text, ",".join(self.refresh_on_change_values))
else:
self.refresh_on_change_text = ''
def get_html(self, prefix="", disabled=False):
if self.checked:
checked_text = ' checked="checked"'
else:
checked_text = ''
id_name = prefix + self.name
return unicodify('<input type="checkbox" id="%s" name="%s" value="__CHECKED__"%s%s%s><input type="hidden" name="%s" value="__NOTHING__"%s>'
% (id_name, id_name, checked_text, self.get_disabled_str(disabled), self.refresh_on_change_text, id_name, self.get_disabled_str(disabled)))
@staticmethod
def is_checked(value):
if value in [True, "true"]:
if value in [True, "True", "true"]:
return True
return isinstance(value, list) and ('__CHECKED__' in value or len(value) == 2)
def set_checked(self, value):
if isinstance(value, string_types):
self.checked = value.lower() in ["yes", "true", "on"]
else:
self.checked = value
return False
def to_dict(self):
d = super(CheckboxField, self).to_dict()
@@ -192,122 +82,17 @@ class CheckboxField(BaseField):
return d
class FileField(BaseField):
"""
A file upload input.
>>> print(FileField( "foo" ).get_html())
<input type="file" name="foo">
>>> print(FileField( "foo", ajax = True ).get_html())
<input type="file" name="foo" galaxy-ajax-upload="true">
"""
def __init__(self, name, value=None, ajax=False, **kwds):
super(FileField, self).__init__(name, value, **kwds)
self.name = name
self.ajax = ajax
self.value = value
def get_html(self, prefix=""):
value_text = ""
if self.value:
value_text = ' value="%s"' % escape(str(self.value), quote=True)
ajax_text = ""
if self.ajax:
ajax_text = ' galaxy-ajax-upload="true"'
return unicodify('<input type="file" name="%s%s"%s%s>' % (prefix, self.name, ajax_text, value_text))
class GenomespaceFileField(BaseField):
"""
A genomspace file browser field.
"""
def __init__(self, name, value=None):
self.name = name
self.value = value or ""
def get_html(self, prefix=""):
return unicodify('<script src="https://gsui.genomespace.org/jsui/upload/gsuploadwindow.js"></script>'
'<input type="text" name="{0}{1}" value="{2}">&nbsp;'
'<a href="javascript:gsLocationByGet({{ successCallback: function(config)'
' {{ selector_name = \'{0}{1}\'; selector = \'input[name=\' + selector_name.replace(\'|\', \'\\\\|\') + \']\';'
' $(selector).val(config.destination + \'^\' + config.token); }} }});">'
'Browse</a>'.format(prefix, self.name, escape(str(self.value), quote=True)))
def to_dict(self):
return dict(name=self.name,
token_field=self.token_field)
class HiddenField(BaseField):
"""
A hidden field.
>>> print(HiddenField( "foo", 100 ).get_html())
<input type="hidden" name="foo" value="100">
"""
def __init__(self, name, value=None, **kwds):
super(HiddenField, self).__init__(name, value, **kwds)
self.name = name
self.value = value or ""
def get_html(self, prefix=""):
return unicodify('<input type="hidden" name="%s%s" value="%s">' % (prefix, self.name, escape(str(self.value), quote=True)))
def to_dict(self):
d = super(HiddenField, self).to_dict()
d['type'] = 'hidden'
d['hidden'] = True
return d
class SelectField(BaseField):
"""
A select field.
>>> t = SelectField( "foo", multiple=True )
>>> t.add_option( "tuti", 1 )
>>> t.add_option( "fruity", "x" )
>>> print(t.get_html())
<select name="foo" multiple>
<option value="1">tuti</option>
<option value="x">fruity</option>
</select>
>>> t = SelectField( "bar" )
>>> t.add_option( "automatic", 3 )
>>> t.add_option( "bazooty", 4, selected=True )
>>> print(t.get_html())
<select name="bar" last_selected_value="4">
<option value="3">automatic</option>
<option value="4" selected>bazooty</option>
</select>
>>> t = SelectField( "foo", display="radio" )
>>> t.add_option( "tuti", 1 )
>>> t.add_option( "fruity", "x" )
>>> print(t.get_html())
<div><input type="radio" name="foo" value="1" id="foo|1"><label class="inline" for="foo|1">tuti</label></div>
<div><input type="radio" name="foo" value="x" id="foo|x"><label class="inline" for="foo|x">fruity</label></div>
>>> t = SelectField( "bar", multiple=True, display="checkboxes" )
>>> t.add_option( "automatic", 3 )
>>> t.add_option( "bazooty", 4, selected=True )
>>> print(t.get_html())
<div class="checkUncheckAllPlaceholder" checkbox_name="bar"></div>
<div><input type="checkbox" name="bar" value="3" id="bar|3"><label class="inline" for="bar|3">automatic</label></div>
<div><input type="checkbox" name="bar" value="4" id="bar|4" checked='checked'><label class="inline" for="bar|4">bazooty</label></div>
"""
def __init__(self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=None, size=None, field_id=None, value=None, selectlist=None, **kwds):
def __init__(self, name, multiple=None, display=None, field_id=None, value=None, selectlist=None, refresh_on_change=False, **kwds):
super(SelectField, self).__init__(name, value, **kwds)
self.name = name
self.field_id = field_id
self.multiple = multiple or False
self.refresh_on_change = refresh_on_change
self.selectlist = selectlist or []
self.value = value
self.size = size
self.options = list()
if display == "checkboxes":
assert multiple, "Checkbox display only supported for multiple select"
@@ -316,136 +101,10 @@ class SelectField(BaseField):
elif display is not None:
raise Exception("Unknown display type: %s" % display)
self.display = display
self.refresh_on_change = refresh_on_change
self.refresh_on_change_values = refresh_on_change_values or []
if self.refresh_on_change:
self.refresh_on_change_text = ' refresh_on_change="true"'
if self.refresh_on_change_values:
self.refresh_on_change_text = '%s refresh_on_change_values="%s"' % (self.refresh_on_change_text, escape(",".join(self.refresh_on_change_values), quote=True))
else:
self.refresh_on_change_text = ''
def add_option(self, text, value, selected=False):
self.options.append((text, value, selected))
def get_html(self, prefix="", disabled=False, extra_attr=None):
if extra_attr is not None:
self.extra_attributes = ' %s' % ' '.join(['%s="%s"' % (k, escape(v)) for k, v in extra_attr.items()])
else:
self.extra_attributes = ''
if self.display == "checkboxes":
return self.get_html_checkboxes(prefix, disabled)
elif self.display == "radio":
return self.get_html_radio(prefix, disabled)
else:
return self.get_html_default(prefix, disabled)
def get_html_checkboxes(self, prefix="", disabled=False):
rval = []
ctr = 0
if len(self.options) > 1:
rval.append('<div class="checkUncheckAllPlaceholder" checkbox_name="%s%s"></div>' % (prefix, self.name)) # placeholder for the insertion of the Select All/Unselect All buttons
for text, value, selected in self.options:
style = ""
text = unicodify(text)
escaped_value = escape(unicodify(value), quote=True)
uniq_id = "%s%s|%s" % (prefix, self.name, escaped_value)
if len(self.options) > 2 and ctr % 2 == 1:
style = " class=\"odd_row\""
selected_text = ""
if selected:
selected_text = " checked='checked'"
rval.append('<div%s><input type="checkbox" name="%s%s" value="%s" id="%s"%s%s%s><label class="inline" for="%s">%s</label></div>'
% (style, prefix, self.name, escaped_value, uniq_id, selected_text, self.get_disabled_str(disabled), self.extra_attributes, uniq_id, escape(text, quote=True)))
ctr += 1
return unicodify("\n".join(rval))
def get_html_radio(self, prefix="", disabled=False):
rval = []
ctr = 0
for text, value, selected in self.options:
style = ""
escaped_value = escape(str(value), quote=True)
uniq_id = "%s%s|%s" % (prefix, self.name, escaped_value)
if len(self.options) > 2 and ctr % 2 == 1:
style = " class=\"odd_row\""
selected_text = ""
if selected:
selected_text = " checked='checked'"
rval.append('<div%s><input type="radio" name="%s%s"%s value="%s" id="%s"%s%s%s><label class="inline" for="%s">%s</label></div>'
% (style,
prefix,
self.name,
self.refresh_on_change_text,
escaped_value,
uniq_id,
selected_text,
self.get_disabled_str(disabled),
self.extra_attributes,
uniq_id,
text))
ctr += 1
return unicodify("\n".join(rval))
def get_html_default(self, prefix="", disabled=False):
if self.multiple:
multiple = " multiple"
else:
multiple = ""
if self.size:
size = ' size="%s"' % str(self.size)
else:
size = ''
rval = []
last_selected_value = ""
for text, value, selected in self.options:
if selected:
selected_text = " selected"
last_selected_value = value
if not isinstance(last_selected_value, string_types):
last_selected_value = str(last_selected_value)
else:
selected_text = ""
rval.append('<option value="%s"%s>%s</option>' % (escape(unicodify(value), quote=True), selected_text, escape(unicodify(text), quote=True)))
if last_selected_value:
last_selected_value = ' last_selected_value="%s"' % escape(unicodify(last_selected_value), quote=True)
if self.field_id is not None:
id_string = ' id="%s"' % self.field_id
else:
id_string = ''
rval.insert(0, '<select name="%s%s"%s%s%s%s%s%s%s>'
% (prefix, self.name, multiple, size, self.refresh_on_change_text, last_selected_value, self.get_disabled_str(disabled), id_string, self.extra_attributes))
rval.append('</select>')
return unicodify("\n".join(rval))
def get_selected(self, return_label=False, return_value=False, multi=False):
'''
Return the currently selected option's label, value or both as a tuple. For
multi-select lists, a list is returned.
'''
if multi:
selected_options = []
for label, value, selected in self.options:
if selected:
if return_label and return_value:
if multi:
selected_options.append((label, value))
else:
return (label, value)
elif return_label:
if multi:
selected_options.append(label)
else:
return label
elif return_value:
if multi:
selected_options.append(value)
else:
return value
if multi:
return selected_options
return None
def to_dict(self):
d = super(SelectField, self).to_dict()
d['type'] = 'select'
@@ -470,63 +129,10 @@ class AddressField(BaseField):
("country", "Country", ""),
("phone", "Phone", "")]
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(AddressField, self).__init__(name, value, **kwds)
self.user = user
self.security = security
self.select_address = None
self.params = params
def get_html(self, disabled=False):
address_html = ''
add_ids = ['none']
if self.user:
for a in self.user.addresses:
add_ids.append(str(a.id))
add_ids.append('new')
self.select_address = SelectField(self.name,
refresh_on_change=True,
refresh_on_change_values=add_ids)
if self.value == 'none':
self.select_address.add_option('Select one', 'none', selected=True)
else:
self.select_address.add_option('Select one', 'none')
if self.user:
for a in self.user.addresses:
if not a.deleted:
if self.value == str(a.id):
self.select_address.add_option(a.desc, str(a.id), selected=True)
# Display this address
address_html += '''
<div class="form-row">
%s
</div>
''' % 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 += '''
<div class="form-row">
<label>%s</label>
%s
''' % (label, add_field.get_html(disabled=disabled))
if help_text:
address_html += '''
<div class="toolParamHelp" style="clear: both;">
%s
</div>
''' % help_text
address_html += '''
</div>
'''
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(['<div class="form-row"><label>%s</label>%s</div>' % (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
lib/galaxy/web/framework/formbuilder.py
-91
View File
@@ -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(["<option value='%s'>%s</option>" % (key, value) for key, value in self.options.iteritems()])
return """<datalist id="%s">%s</datalist>""" % (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()
lib/galaxy/web/framework/webapp.py
-12
View File
@@ -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 = ''
lib/galaxy/webapps/galaxy/api/library_contents.py
-57
View File
@@ -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:
lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+1 -2
View File
@@ -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:
lib/galaxy/webapps/galaxy/api/toolshed.py
+1 -2
View File
@@ -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:
lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+10 -10
View File
@@ -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 <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \
% (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',
lib/galaxy/webapps/tool_shed/controllers/repository.py
+17 -9
View File
@@ -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,
lib/galaxy/webapps/tool_shed/controllers/repository_review.py
+1
View File
@@ -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), '')
lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
-1
View File
@@ -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__)
lib/tool_shed/grids/repository_grids.py
+10 -2
View File
@@ -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 = "<select name='%s'>" % select_field.name
for o in select_field.options:
tmpl += "<option value='%s'>%s</option>" % (o[1], o[0])
tmpl += "</select>"
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 = "<select name='%s'>" % select_field.name
for o in select_field.options:
tmpl += "<option value='%s'>%s</option>" % (o[1], o[0])
tmpl += "</select>"
return tmpl
elif len(select_field.options) == 1:
return select_field.options[0][0]
return ''
lib/tool_shed/grids/util.py
+1 -3
View File
@@ -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)
lib/tool_shed/util/hg_util.py
+1
View File
@@ -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
lib/tool_shed/util/repository_util.py
-15
View File
@@ -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)
lib/tool_shed/util/tool_dependency_util.py
+4 -2
View File
@@ -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__)
static/scripts/bundled/adminToolshed.bundled.js
+7
View File
File diff suppressed because one or more lines are too long
static/scripts/bundled/extended.bundled.js
+1 -1
View File
File diff suppressed because one or more lines are too long
static/scripts/libs/bibtex.js
-1
View File
File diff suppressed because one or more lines are too long
static/scripts/mvc/toolshed/repository-view.js
+1 -1
View File
File diff suppressed because one or more lines are too long
templates/admin/tool_shed_repository/common.mako
+4 -3
View File
@@ -1,3 +1,4 @@
<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" />
<%def name="browse_files(title_text, directory_path)">
@@ -148,7 +149,7 @@
%else:
<label>Handle repository dependencies?</label>
%endif
${repository_dependencies_check_box.get_html()}
${render_checkbox(repository_dependencies_check_box)}
<div class="toolParamHelp" style="clear: both;">
%if export:
Select to export the following additional repositories that are required by this repository.
@@ -185,7 +186,7 @@
<div class="form-row">
<label>When available, install Tool Shed managed tool dependencies?</label>
<% disabled = trans.app.config.tool_dependency_dir is None %>
${install_tool_dependencies_check_box.get_html( disabled=disabled )}
${render_checkbox(install_tool_dependencies_check_box, disabled=disabled)}
<div class="toolParamHelp" style="clear: both;">
%if disabled:
Set the tool_dependency_dir configuration value in your Galaxy config to automatically handle tool dependencies.
@@ -221,7 +222,7 @@
%if requirements_status and install_resolver_dependencies_check_box:
<div class="form-row">
<label>When available, install <a href="https://docs.galaxyproject.org/en/master/admin/conda_faq.html" target="_blank">Conda</a> managed tool dependencies?</label>
${install_resolver_dependencies_check_box.get_html()}
${render_checkbox(install_resolver_dependencies_check_box)}
<div class="toolParamHelp" style="clear: both;">
Select to automatically install tool dependencies via Conda.
</div>
templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
+2 -1
View File
@@ -2,6 +2,7 @@
<%namespace file="/message.mako" import="render_msg" />
<%namespace file="/admin/tool_shed_repository/common.mako" import="*" />
<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
<%
repository = context.get( 'repository', None )
@@ -190,7 +191,7 @@ else:
%>
%if can_deactivate_repository and can_uninstall_repository:
<% deactivate_uninstall_button_text = "Deactivate or Uninstall" %>
${remove_from_disk_check_box.get_html()}
${render_checkbox(remove_from_disk_check_box)}
<label for="remove_from_disk" style="display: inline;font-weight:normal;">Check to uninstall or leave blank to deactivate</label>
<br/><br/>
%elif can_deactivate_repository:
templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako
+2 -1
View File
@@ -1,6 +1,7 @@
<%inherit file="/base.mako"/>
<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
<%namespace file="/message.mako" import="render_msg" />
<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
<% import os %>
@@ -31,7 +32,7 @@ ${render_galaxy_repository_actions( repository )}
<div class="form-row">
<label>Handle tool dependencies?</label>
<% disabled = trans.app.config.tool_dependency_dir is None %>
${install_tool_dependencies_check_box.get_html( disabled=disabled )}
${render_checkbox(install_tool_dependencies_check_box, disabled=disabled)}
<div class="toolParamHelp" style="clear: both;">
%if disabled:
Set the tool_dependency_dir configuration value in your Galaxy config to automatically handle tool dependencies.
templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
+3 -3
View File
@@ -1,7 +1,7 @@
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
<%namespace file="/webapps/tool_shed/common/common.mako" import="common_misc_javascripts" />
<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
<%def name="stylesheets()">
${parent.stylesheets()}
@@ -73,7 +73,7 @@ ${render_galaxy_repository_actions( repository )}
</div>
<div style="clear: both"></div>
<div class="form-row">
${uninstalled_tool_dependencies_select_field.get_html()}
${render_select(uninstalled_tool_dependencies_select_field)}
</div>
<div style="clear: both"></div>
<div class="form-row">
@@ -94,7 +94,7 @@ ${render_galaxy_repository_actions( repository )}
</div>
<div style="clear: both"></div>
<div class="form-row">
${installed_tool_dependencies_select_field.get_html()}
${render_select(installed_tool_dependencies_select_field)}
</div>
<div style="clear: both"></div>
<div class="form-row">
templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
+4 -3
View File
@@ -3,6 +3,7 @@
<%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" />
<%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" />
<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" />
<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
<%def name="stylesheets()">
${parent.stylesheets()}
@@ -60,7 +61,7 @@
%>
<div class="form-row">
<label>Shed tool configuration file:</label>
${shed_tool_conf_select_field.get_html()}
${render_select(shed_tool_conf_select_field)}
<div class="toolParamHelp" style="clear: both;">
${select_help|h}
</div>
@@ -72,7 +73,7 @@
%if includes_tools_for_display_in_tool_panel:
<div style="clear: both"></div>
<div class="form-row">
${no_changes_check_box.get_html()}
${render_checkbox(no_changes_check_box)}
<label style="display: inline;">No changes</label>
<div class="toolParamHelp" style="clear: both;">
Uncheck and select a different tool panel section to load the tools into a different section in the tool panel.
@@ -87,7 +88,7 @@
</div>
<div class="form-row">
<label>Select existing tool panel section:</label>
${tool_panel_section_select_field.get_html()}
${render_select(tool_panel_section_select_field)}
<div class="toolParamHelp" style="clear: both;">
Choose an existing section in your tool panel to contain the installed tools (optional).
</div>
templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako
+2 -2
View File
@@ -1,6 +1,6 @@
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
<%namespace file="/webapps/tool_shed/common/common.mako" import="common_misc_javascripts" />
<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
<%def name="javascripts()">
${parent.javascripts()}
@@ -28,7 +28,7 @@
</div>
<div style="clear: both"></div>
<div class="form-row">
${repositories_select_field.get_html()}
${render_select(repositories_select_field)}
</div>
<div style="clear: both"></div>
<div class="form-row">
templates/admin/tool_shed_repository/select_tool_panel_section.mako
+3 -2
View File
@@ -3,6 +3,7 @@
<%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" />
<%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" />
<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" />
<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
<%def name="stylesheets()">
${parent.stylesheets()}
@@ -149,7 +150,7 @@ or manually satisfy the dependencies listed below.</p>
%>
<div class="form-row">
<label>Shed tool configuration file:</label>
${shed_tool_conf_select_field.get_html()}
${render_select(shed_tool_conf_select_field)}
<div class="toolParamHelp" style="clear: both;">
${select_help|h}
</div>
@@ -169,7 +170,7 @@ or manually satisfy the dependencies listed below.</p>
</div>
<div class="form-row">
<label>Select existing tool panel section:</label>
${tool_panel_section_select_field.get_html()}
${render_select(tool_panel_section_select_field)}
<div class="toolParamHelp" style="clear: both;">
Choose an existing section in your tool panel to contain the installed tools (optional).
</div>
templates/form.mako
-112
View File
@@ -1,112 +0,0 @@
<%!
def inherit(context):
if context.get('use_panels'):
if context.get('webapp'):
app_name = context.get('webapp')
elif context.get('app'):
app_name = context.get('app').name
else:
app_name = 'galaxy'
return '/webapps/%s/base_panels.mako' % app_name
else:
return '/base.mako'
%>
<%inherit file="${inherit(context)}"/>
<% _=n_ %>
<%def name="init()">
<%
self.has_left_panel=False
self.has_right_panel=False
self.active_view=active_view
self.message_box_visible=False
%>
</%def>
<%def name="title()">${form.title | h}</%def>
<%def name="javascripts()">
${parent.javascripts()}
${h.js("libs/jquery/jquery.autocomplete")}
<script type="text/javascript">
$(function(){
$("input:text:first").focus();
})
</script>
</%def>
<%def name="stylesheets()">
${parent.stylesheets()}
${h.css("autocomplete_tagging")}
</%def>
<%def name="center_panel()">
${render_form( )}
</%def>
<%def name="body()">
${render_form( )}
</%def>
<%def name="render_form()">
%if header:
${header}
%endif
<div class="form" style="margin: 1em">
<div class="form-title">${util.unicodify( form.title ) | h }</div>
<div class="form-body">
<%
has_file_input = False
for input in form.inputs:
if input.type == 'file':
has_file_input = True
break
%>
<form name="${form.name | h }" action="${form.action}" method="post"
%if has_file_input:
enctype="multipart/form-data"
%endif
>
%for input in form.inputs:
<%
cls = "form-row"
if input.error:
cls += " form-row-error"
%>
<div class="${cls}">
%if input.use_label:
<label>
${_(input.label) | h }:
</label>
%endif
<div class="form-row-input">
%if input.type == 'textarea':
<textarea name="${input.name | h }">${input.value | h }</textarea>
%elif input.type == 'select':
<select name="${input.name | h}">
%for (name, value) in input.options:
<option value="${value | h }">${name | h }</option>
%endfor
</select>
%else:
<input type="${input.type}" name="${input.name | h }" value="${input.value | h }">
%endif
</div>
%if input.error:
<div class="form-row-error-message">${input.error | h }</div>
%endif
%if input.help:
<div class="toolParamHelp" style="clear: both;">
${input.help | h}
</div>
%endif
<div style="clear: both"></div>
</div>
%endfor
<div class="form-row"><input type="submit" value="${form.submit_text}"></div>
</form>
</div>
</div>
</%def>
templates/user/register.mako
+2 -4
View File
@@ -7,6 +7,7 @@ def inherit(context):
return '/base.mako'
%>
<%inherit file="${inherit(context)}"/>
<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
<%def name="init()">
<%
@@ -169,10 +170,7 @@ def inherit(context):
%if trans.app.config.smtp_server and trans.app.config.mailing_join_addr:
<div class="form-row">
<label>Subscribe to mailing list:</label>
%if subscribe_checked:
<% subscribe_check_box.checked = True %>
%endif
${subscribe_check_box.get_html()}
${render_checkbox(subscribe_check_box)}
<p>See <a href="https://galaxyproject.org/mailing-lists/" target="_blank">
all Galaxy project mailing lists</a>.</p>
</div>
templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako
+2 -1
View File
@@ -1,5 +1,6 @@
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
<%def name="javascripts()">
${parent.javascripts()}
@@ -90,7 +91,7 @@ $().ready(function() {
%if create_role_for_group_checked:
<% create_role_for_group_checkbox.checked = True %>
%endif
${create_role_for_group_checkbox.get_html()} Create a new role of the same name for this group
${render_checkbox(create_role_for_group_checkbox)} Create a new role of the same name for this group
</div>
<div class="form-row">
<input type="submit" name="create_group_button" value="Save"/>
templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako
+2 -1
View File
@@ -1,5 +1,6 @@
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
<%def name="javascripts()">
${parent.javascripts()}
@@ -94,7 +95,7 @@
%if create_group_for_role_checked:
<% create_group_for_role_checkbox.checked = True %>
%endif
${create_group_for_role_checkbox.get_html()} Create a new group of the same name for this role
${render_checkbox(create_group_for_role_checkbox)} Create a new group of the same name for this role
</div>
<div class="form-row">
<input type="submit" name="create_role_button" value="Save"/>
templates/webapps/tool_shed/common/common.mako
+34
View File
@@ -1,3 +1,37 @@
<%def name="render_checkbox(checkbox, disabled=False, refresh_on_change=False)">
<% from galaxy.web.form_builder import CheckboxField %>
<input type="checkbox" id="${checkbox.name}" name="${checkbox.name}" value="true"
${"refresh_on_change='true'" if refresh_on_change else ""}
${"checked" if CheckboxField.is_checked(checkbox.value) else ""}
${"disabled" if disabled else ""}
>
</%def>
<%def name="render_select(select)">
<% from markupsafe import escape %>
<% from galaxy.util import listify %>
%if select.display == "checkboxes":
%for o in select.options:
<div>
<% selected = o[1] in listify(select.value) or o[2] %>
<input type="checkbox" name="${select.name}" value="${escape(o[1])}"
${"refresh_on_change='true'" if select.refresh_on_change else ""}"
${"checked" if selected else ""} ${"disabled" if disabled else ""}>
${escape(o[0])}
</div>
%endfor
%else:
<select id="${select.field_id}" name="${select.name}"
${"multiple" if select.multiple else ""}
${"refresh_on_change='true'" if select.refresh_on_change else ""}">
%for o in select.options:
<% selected = o[1] in listify(select.value) or o[2] %>
<option value="${escape(o[1])}" ${"selected" if selected else ""}>${escape(o[0])}</option>
%endfor
</select>
%endif
</%def>
<%def name="common_misc_javascripts()">
<script type="text/javascript">
function checkAllFields( chkAll, name )
templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako
+2 -2
View File
@@ -1,6 +1,6 @@
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
<%namespace file="/webapps/tool_shed/common/common.mako" import="common_misc_javascripts" />
<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
<%def name="javascripts()">
${parent.javascripts()}
@@ -51,7 +51,7 @@
</div>
<div style="clear: both"></div>
<div class="form-row">
${repositories_select_field.get_html()}
${render_select(repositories_select_field)}
</div>
<div style="clear: both"></div>
<div class="form-row">
templates/webapps/tool_shed/repository/common.mako
+2 -1
View File
@@ -1,3 +1,4 @@
<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
<%def name="common_javascripts(repository)">
<script type="text/javascript">
$(function(){
@@ -195,7 +196,7 @@
</div>
%endif
%else:
${repository_type_select_field.get_html()}
${render_select(repository_type_select_field)}
%if render_help:
<div class="toolParamHelp" style="clear: both;">
Select the repository type based on the following criteria.
templates/webapps/tool_shed/repository/find_tools.mako
+2 -1
View File
@@ -1,5 +1,6 @@
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
<%namespace file="/webapps/tool_shed/common/repository_actions_menu.mako" import="render_galaxy_repository_actions" />
<%!
@@ -47,7 +48,7 @@
<div style="clear: both"></div>
<div class="form-row">
<label>Exact matches only:</label>
${exact_matches_check_box.get_html()}
${render_checkbox(exact_matches_check_box)}
<div class="toolParamHelp" style="clear: both;">
Check the box to match text exactly (text case doesn't matter as all strings are forced to lower case).
</div>
templates/webapps/tool_shed/repository/find_workflows.mako
+2 -1
View File
@@ -1,5 +1,6 @@
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
<%namespace file="/webapps/tool_shed/common/repository_actions_menu.mako" import="render_galaxy_repository_actions" />
<%!
@@ -36,7 +37,7 @@
<div style="clear: both"></div>
<div class="form-row">
<label>Exact matches only:</label>
${exact_matches_check_box.get_html()}
${render_checkbox(exact_matches_check_box)}
<div class="toolParamHelp" style="clear: both;">
Check the box to match text exactly (text case doesn't matter as all strings are forced to lower case).
</div>
templates/webapps/tool_shed/repository/manage_repository.mako
+4 -5
View File
@@ -125,14 +125,13 @@ ${render_tool_shed_repository_actions( repository, metadata=metadata, changeset_
%if deprecated_repository_dependency_tups:
${render_deprecated_repository_dependencies_message( deprecated_repository_dependency_tups )}
%endif
%if len( changeset_revision_select_field.options ) > 1:
<div class="toolForm">
<div class="toolFormTitle">Repository revision</div>
<div class="toolFormBody">
<form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
<div class="form-row">
${changeset_revision_select_field.get_html()} <i>${tip_str}</i>
${render_select(changeset_revision_select_field)} <i>${tip_str}</i>
<div class="toolParamHelp" style="clear: both;">
%if can_review_repository:
Select a revision to inspect for adding or managing a review or for download or installation.
@@ -279,7 +278,7 @@ ${render_repository_items( metadata, containers_dict, can_set_metadata=True, ren
<form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
<div class="form-row">
<label>Receive email alerts:</label>
${alerts_check_box.get_html()}
${render_checkbox(alerts_check_box)}
<div class="toolParamHelp" style="clear: both;">
Check the box and click <b>Save</b> to receive email alerts when updates to this repository occur.
</div>
@@ -315,7 +314,7 @@ ${render_repository_items( metadata, containers_dict, can_set_metadata=True, ren
<form name="user_access" id="user_access" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
<div class="form-row">
<label>Username:</label>
${allow_push_select_field.get_html()}
${render_select(allow_push_select_field)}
<div class="toolParamHelp" style="clear: both;">
Multi-select usernames to grant permission to make changes to this repository
</div>
@@ -396,7 +395,7 @@ ${render_repository_items( metadata, containers_dict, can_set_metadata=True, ren
<form name="malicious" id="malicious" action="${h.url_for( controller='repository', action='set_malicious', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post">
<div class="form-row">
<label>Define repository tip as malicious:</label>
${malicious_check_box.get_html()}
${render_checkbox(malicious_check_box)}
<div class="toolParamHelp" style="clear: both;">
Check the box and click <b>Save</b> to define this repository's tip as malicious, restricting it from being download-able.
</div>
templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako
+1 -1
View File
@@ -42,7 +42,7 @@ ${render_galaxy_repository_actions( repository=repository )}
else:
tip_str = ''
%>
${changeset_revision_select_field.get_html()} <i>${tip_str | h}</i>
${render_select(changeset_revision_select_field)} <i>${tip_str | h}</i>
<div class="toolParamHelp" style="clear: both;">
Select a revision to inspect and download versions of Galaxy utilities from this repository.
</div>
templates/webapps/tool_shed/repository/tool_form.mako
+1 -33
View File
@@ -75,40 +75,8 @@
</%def>
<%def name="row_for_param( prefix, param, parent_state, other_values )">
<%
# Disable refresh_on_change for select lists displayed in the tool shed.
param.refresh_on_change = False
label = param.get_label()
if isinstance( param, DataToolParameter ) or isinstance( param, ColumnListParameter ) or isinstance( param, GenomeBuildParameter ):
field = SelectField( param.name )
field.add_option( param.name, param.name )
field_html = field.get_html()
elif isinstance( param, SelectToolParameter ) and hasattr( param, 'data_ref' ):
field = SelectField( param.name, display=param.display, multiple=param.multiple )
field.add_option( param.data_ref, param.data_ref )
field_html = field.get_html( prefix )
elif isinstance( param, SelectToolParameter ) and param.is_dynamic:
field = SelectField( param.name, display=param.display, multiple=param.multiple )
dynamic_options = param.options
if dynamic_options is not None:
if dynamic_options.index_file:
option_label = "Dynamically generated from entries in file %s" % str( dynamic_options.index_file )
field.add_option( option_label, "none" )
elif dynamic_options.missing_index_file:
option_label = "Dynamically generated from entries in missing file %s" % str( dynamic_options.missing_index_file )
field.add_option( option_label, "none" )
else:
field.add_option( "Dynamically generated from old-style Dynamic Options.", "none" )
field_html = field.get_html( prefix )
else:
field = TextField( param.name, value="Parameter type: %s" % param.type )
field_html = field.get_html( prefix, disabled=True )
%>
<div class="form-row">
%if label:
<label for="${param.name}">${label}:</label>
%endif
<div class="form-row-input">${field_html}</div>
<label >${param.label or param.name}:</label>
%if param.help:
<div class="toolParamHelp" style="clear: both;">
${param.help}
templates/webapps/tool_shed/repository/view_repository.mako
+2 -2
View File
@@ -88,7 +88,7 @@
<div class="toolFormBody">
<form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
<div class="form-row">
${changeset_revision_select_field.get_html()} <i>${tip_str}</i>
${render_select(changeset_revision_select_field)} <i>${tip_str}</i>
<div class="toolParamHelp" style="clear: both;">
Select a revision to inspect and download versions of Galaxy utilities from this repository.
</div>
@@ -202,7 +202,7 @@ ${render_repository_items( metadata, containers_dict, can_set_metadata=False, re
<form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
<div class="form-row">
<label>Receive email alerts:</label>
${alerts_check_box.get_html()}
${render_checkbox(alerts_check_box)}
<div class="toolParamHelp" style="clear: both;">
Check the box and click <b>Save</b> to receive email alerts when updates to this repository occur.
</div>
templates/webapps/tool_shed/repository_review/browse_review.mako
+2 -2
View File
@@ -57,7 +57,7 @@ ${render_tool_shed_repository_actions( repository=repository, changeset_revision
if can_browse:
# Initialize Private check box.
private_check_box_name = '%s%sprivate' % ( component.name, STRSEP )
private_check_box = CheckboxField( name=private_check_box_name, checked=component_review.private )
private_check_box = CheckboxField( name=private_check_box_name, value=component_review.private )
# Initialize star rating.
rating_name = '%s%srating' % ( component.name, STRSEP )
@@ -73,7 +73,7 @@ ${render_tool_shed_repository_actions( repository=repository, changeset_revision
<tr>
<td>
<label>Private:</label>
${private_check_box.get_html( disabled=True )}
${render_checkbox(private_check_box, disabled=True)}
<div class="toolParamHelp" style="clear: both;">
A private review can be accessed only by the owner of the repository and authorized repository reviewers.
</div>
templates/webapps/tool_shed/repository_review/edit_review.mako
+4 -4
View File
@@ -45,7 +45,7 @@ ${render_tool_shed_repository_actions( repository=repository, changeset_revision
</div>
<div class="form-row">
<label>Approve this repository revision?</label>
${revision_approved_select_field.get_html()}
${render_select(revision_approved_select_field)}
<div class="toolParamHelp" style="clear: both;">
Individual components below may be approved without approving the repository revision.
</div>
@@ -83,7 +83,7 @@ ${render_tool_shed_repository_actions( repository=repository, changeset_revision
# Initialize Private check box.
private_check_box_name = '%s%sprivate' % ( component_name, STRSEP )
private_check_box = CheckboxField( name=private_check_box_name, checked=private )
private_check_box = CheckboxField( name=private_check_box_name, value=private )
# Initialize star rating.
rating_name = '%s%srating' % ( component_name, STRSEP )
@@ -107,7 +107,7 @@ ${render_tool_shed_repository_actions( repository=repository, changeset_revision
<tr>
<td>
<label>Mark private:</label>
${private_check_box.get_html()}
${render_checkbox(private_check_box)}
<div class="toolParamHelp" style="clear: both;">
A private review can be accessed only by the owner of the repository and authorized repository reviewers.
</div>
@@ -128,7 +128,7 @@ ${render_tool_shed_repository_actions( repository=repository, changeset_revision
<tr>
<td>
<label>Approved:</label>
${approved_select_field.get_html()}
${render_select(approved_select_field)}
<div style="clear: both"></div>
</td>
</tr>
templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako
+1 -1
View File
@@ -90,7 +90,7 @@ ${render_tool_shed_repository_actions( repository=repository, changeset_revision
<td>${render_star_rating( repository_rating_name, review.rating, disabled=True )}</td>
%if review.user == trans.user:
<form name="approve_repository_review" action="${h.url_for( controller='repository_review', action='approve_repository_review', id=encoded_review_id ) }" method="post" >
<td>${approved_select_field.get_html()}</td>
<td>${render_select(approved_select_field)}</td>
<td><input type="submit" name="approve_repository_review_button" value="Save"/></td>
</form>
%else:
templates/webapps/tool_shed/user/manage_email_alerts.mako
+1 -1
View File
@@ -20,7 +20,7 @@
<form name="new_repo_alert" id="new_repo_alert" action="${h.url_for( controller='repository', action='manage_email_alerts' )}" method="post" >
<div class="form-row">
<label>New repository alert:</label>
${new_repo_alert_check_box.get_html()}
${render_checkbox(new_repo_alert_check_box)}
<div class="toolParamHelp" style="clear: both;">
Check the box and click <b>Save</b> to receive email when the first change set is created for a new repository.
</div>
test/shed_functional/base/twilltestcase.py
+2 -2
View File
@@ -1111,12 +1111,12 @@ class ShedTwillTestCase(TwillTestCase):
params = dict(id=encoded_repository_id, no_changes=no_changes, new_tool_panel_section_label=new_tool_panel_section_label)
doseq = False
if install_repository_dependencies:
params['install_repository_dependencies'] = ['True', 'True']
params['install_repository_dependencies'] = True
doseq = True
else:
params['install_repository_dependencies'] = False
if install_tool_dependencies:
params['install_tool_dependencies'] = ['True', 'True']
params['install_tool_dependencies'] = True
doseq = True
else:
params['install_tool_dependencies'] = False