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Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03

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This commit is contained in:
guerler
2015-03-09 13:55:47 -04:00
parent 4d347dcfe1 dd5b7659e8
commit c78b7b67f6
5 changed files with 21 additions and 18 deletions
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client/galaxy/scripts/mvc/tools/tools-form-base.js
+6 -6
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@@ -133,12 +133,12 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
highlight: function (input_id, message, silent) {
// get input field
var input_element = this.element_list[input_id];
// check input element
if (input_element) {
// mark error
input_element.error(message || 'Please verify this parameter.');
// scroll to first input element
if (!silent) {
$('html, body').animate({
@@ -153,7 +153,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
_errors: function(options) {
// hide previous error statements
this.trigger('reset');
// highlight all errors
if (options && options.errors) {
var error_messages = this.tree.matchResponse(options.errors);
@@ -193,7 +193,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
// here we update the tool version (some tools encode the version also in the id)
self.options.id = self.options.id.replace(self.options.version, this.version);
self.options.version = this.version;
// rebuild the model and form
self.deferred.reset();
self.deferred.execute(function(){self._buildModel()});
@@ -223,7 +223,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
window.open(options.biostar_url + '/p/new/post/');
}
});
// create search button
menu_button.addMenu({
icon : 'fa-search',
@@ -305,7 +305,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
ignore : '__ignore__',
value : '__ignore__',
options : [['Yes', this.options.job_id], ['No', '__ignore__']],
help : 'The previous run of this tool failed and other tools were waiting for it to finish successfully, use this option to resume those tools using the outputs of this tool run.'
help : 'The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.'
}
}
lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+4 -3
View File
@@ -331,7 +331,7 @@ class AdminToolshed( AdminGalaxy ):
image can be defined in either a README.rst file contained in the repository or the help section of a Galaxy tool config that
is contained in the repository. The following image definitions are all supported. The former $PATH_TO_IMAGES is no longer
required, and is now ignored.
.. image:: https://raw.github.com/galaxy/some_image.png
.. image:: https://raw.github.com/galaxy/some_image.png
.. image:: $PATH_TO_IMAGES/some_image.png
.. image:: /static/images/some_image.gif
.. image:: some_image.jpg
@@ -343,12 +343,13 @@ class AdminToolshed( AdminGalaxy ):
repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id )
if repository:
repo_files_dir = repository.repo_files_directory( trans.app )
# The following line sometimes returns None. TODO: Figure out why.
path_to_file = suc.get_absolute_path_to_file_in_repository( repo_files_dir, relative_path_to_image_file )
if os.path.exists( path_to_file ):
if path_to_file and os.path.exists( path_to_file ):
file_name = os.path.basename( relative_path_to_image_file )
try:
extension = file_name.split( '.' )[ -1 ]
except Exception, e:
except Exception:
extension = None
if extension:
mimetype = trans.app.datatypes_registry.get_mimetype_by_extension( extension )
lib/galaxy/webapps/tool_shed/model/migrate/check.py
+4 -2
View File
@@ -1,4 +1,6 @@
import sys, os.path, logging
import logging
import os.path
import sys
from galaxy import eggs
@@ -38,7 +40,7 @@ def create_or_verify_database( url, engine_options={} ):
try:
egg = dialect_to_egg[dialect]
try:
pkg_resources.require( egg )
eggs.require( egg )
log.debug( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) )
except:
# If the module is in the path elsewhere (i.e. non-egg), it'll still load.
static/scripts/mvc/tools/tools-form-base.js
+6 -6
View File
@@ -133,12 +133,12 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
highlight: function (input_id, message, silent) {
// get input field
var input_element = this.element_list[input_id];
// check input element
if (input_element) {
// mark error
input_element.error(message || 'Please verify this parameter.');
// scroll to first input element
if (!silent) {
$('html, body').animate({
@@ -153,7 +153,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
_errors: function(options) {
// hide previous error statements
this.trigger('reset');
// highlight all errors
if (options && options.errors) {
var error_messages = this.tree.matchResponse(options.errors);
@@ -193,7 +193,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
// here we update the tool version (some tools encode the version also in the id)
self.options.id = self.options.id.replace(self.options.version, this.version);
self.options.version = this.version;
// rebuild the model and form
self.deferred.reset();
self.deferred.execute(function(){self._buildModel()});
@@ -223,7 +223,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
window.open(options.biostar_url + '/p/new/post/');
}
});
// create search button
menu_button.addMenu({
icon : 'fa-search',
@@ -305,7 +305,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
ignore : '__ignore__',
value : '__ignore__',
options : [['Yes', this.options.job_id], ['No', '__ignore__']],
help : 'The previous run of this tool failed and other tools were waiting for it to finish successfully, use this option to resume those tools using the outputs of this tool run.'
help : 'The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.'
}
}
static/scripts/packed/mvc/tools/tools-form-base.js
+1 -1
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