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Merge remote-tracking branch 'galaxyproject/dev' into Reports_homepage

Browse Source 
Conflicts:
	.ci/pep8_sources.txt
This commit is contained in:
John Chilton
2015-07-17 14:14:12 +01:00
parent 664897e9c6 be3bd7a296
commit 7719ea7ea8
717 changed files with 17398 additions and 12688 deletions
Download Patch File Download Diff File Expand all files Collapse all files
.ci/flake8_wrapper.sh
+1 -5
View File
@@ -2,11 +2,7 @@
set -e
# Run broad range of checks over specific white-listed files, this uses
# the default checks defined in setup.cfg.
while read p; do
flake8 $(eval echo "$p")
done <.ci/pep8_sources.txt
flake8 --exclude database/,.venv/,`paste -sd, .ci/pep8_sources.txt` .
# Look for obviously broken stuff lots more places.
flake8 --select=E901,E902,F821,F822,F823,F831 --exclude lib/galaxy/util/pastescript/serve.py,lib/pkg_resources.py lib/ test/{api,unit}
.ci/pep8_sources.txt
+24 -47
View File
@@ -1,47 +1,24 @@
cron/parse_builds.py
lib/galaxy/auth
lib/galaxy/config.py
lib/galaxy/datatypes/{data,proteomics}.py
lib/galaxy/exceptions/error_codes.py
lib/galaxy/jobs/{__init__,error_level,manager,stock_rules}.py
lib/galaxy/main.py
lib/galaxy/managers/{api_keys,citations,collections,collections_util,datasets,folders,pages,tags,workflows}.py
lib/galaxy/model/orm/{engine_factory,now}.py
lib/galaxy/model/{base,custom_types,search,util}.py
lib/galaxy/model/tool_shed_install/__init__.py
lib/galaxy/objectstore/{__init__,pulsar,rods,s3}.py
lib/galaxy/openid/__init__.py
lib/galaxy/queues.py
lib/galaxy/queue_worker.py
lib/galaxy/tags
lib/galaxy/tools
lib/galaxy/util/{__init__,json,permutations,plugin_config,properties,simplegraph,sockets,sleeper,streamball,submodules,xml_macros}.py
lib/galaxy/web/{proxy,security}
lib/galaxy/web/base/{__init__,interactive_environments}.py
lib/galaxy/web/formatting.py
lib/galaxy/webapps/__init__.py
lib/galaxy/webapps/galaxy/__init__.py
lib/galaxy/webapps/galaxy/api/{__init__,authenticate,dataset_collections,datatypes,folder_contents,folders,lda_datasets,job_files,libraries,library_contents,provenance,remote_files,search,users}.py
lib/galaxy/webapps/galaxy/controllers/{__init__,admin,cloudlaunch,workflow}.py
lib/galaxy/webapps/reports/app.py
lib/galaxy/webapps/reports/controllers/{__init__,jobs,query,workflows,home}.py
lib/galaxy/webapps/tool_shed/app.py
lib/galaxy/webapps/tool_shed/controllers/__init__.py
lib/galaxy/webapps/tool_shed/framework/__init__.py
lib/galaxy/webapps/tool_shed/framework/middleware/__init__.py
lib/galaxy/webapps/tool_shed/util/{__init__,shed_statistics}.py
lib/galaxy/work
lib/galaxy/workflow
lib/galaxy/version.py
lib/pulsar
lib/tool_shed/__init__.py
lib/tool_shed/galaxy_install/{install_manager,repair_repository_manager}.py
lib/tool_shed/galaxy_install/repository_dependencies
lib/tool_shed/galaxy_install/tools/{__init__,tool_panel_manager}.py
lib/tool_shed/repository_types/{__init__,registry,unrestricted}.py
lib/tool_shed/util/{__init__,repository_content_util,tool_util,web_util,workflow_util}.py
test/functional/tools
test/unit/jobs/test_job_configuration.py
test/unit/tools
tools/data_source/upload.py
tools/evolution/codingSnps_filter.py
contrib/
doc/patch.py
doc/source/conf.py
lib/galaxy/model/migrate/versions/
lib/galaxy/model/tool_shed_install/migrate/versions/
lib/galaxy/util/pastescript/serve.py
lib/galaxy/webapps/tool_shed/model/migrate/versions/
lib/galaxy_utils/
lib/pkg_resources.py
lib/tool_shed/
scripts/api/
scripts/data_libraries/
scripts/loc_files/
scripts/microbes/
scripts/others/
scripts/scramble/
scripts/tool_shed/
scripts/tools/
scripts/transfer.py
test/base/
test/casperjs/
test/install_and_test_tool_shed_repositories/
test/tool_shed/
tools/
client/galaxy/scripts/mvc/collection/collection-model.js
+5 -2
View File
@@ -61,15 +61,18 @@ var DatasetCollectionElementMixin = {
/** merge the attributes of the sub-object 'object' into this model */
_mergeObject : function( attributes ){
_.extend( attributes, attributes.object );
// if we don't preserve and correct ids here, the element id becomes the object id
// and collision in backbone's _byId will occur and only
_.extend( attributes, attributes.object, { element_id: attributes.id });
delete attributes.object;
return attributes;
},
/** override to merge this.object into this */
constructor : function( attributes, options ){
this.debug( '\t DatasetCollectionElement.constructor:', attributes, options );
// console.debug( '\t DatasetCollectionElement.constructor:', attributes, options );
attributes = this._mergeObject( attributes );
this.idAttribute = 'element_id';
Backbone.Model.apply( this, arguments );
},
client/galaxy/scripts/mvc/library/library-folderlist-view.js
+7 -4
View File
@@ -28,6 +28,7 @@ var FolderListView = Backbone.View.extend({
events: {
'click #select-all-checkboxes' : 'selectAll',
'click .dataset_row' : 'selectClickedRow',
'click .folder_row' : 'selectClickedRow',
'click .sort-folder-link' : 'sortColumnClicked'
},
@@ -175,7 +176,7 @@ var FolderListView = Backbone.View.extend({
*/
postRender: function(){
var fetched_metadata = this.folderContainer.attributes.metadata;
fetched_metadata.contains_file = typeof this.collection.findWhere({type: 'file'}) !== 'undefined';
fetched_metadata.contains_file_or_folder = typeof this.collection.findWhere({type: 'file'}) !== 'undefined' || typeof this.collection.findWhere({type: 'folder'}) !== 'undefined';
Galaxy.libraries.folderToolbarView.configureElements(fetched_metadata);
$('.library-row').hover(function() {
$(this).find('.show_on_hover').show();
@@ -201,10 +202,10 @@ var FolderListView = Backbone.View.extend({
* @param {Item or FolderAsModel} model of the view that will be rendered
*/
renderOne: function(model){
if (model.get('type') !== 'folder'){
this.options.contains_file = true;
this.options.contains_file_or_folder = true;
//if (model.get('type') !== 'folder'){
// model.set('readable_size', this.size_to_string(model.get('file_size')));
}
//}
model.set('folder_id', this.id);
var rowView = new mod_library_folderrow_view.FolderRowView(model);
@@ -329,12 +330,14 @@ var FolderListView = Backbone.View.extend({
$row.removeClass('light').addClass('dark');
$row.find('a').removeClass('light').addClass('dark');
$row.find('.fa-file-o').removeClass('fa-file-o').addClass('fa-file');
$row.find('.fa-folder-o').removeClass('fa-folder-o').addClass('fa-folder');
},
makeWhiteRow: function($row){
$row.removeClass('dark').addClass('light');
$row.find('a').removeClass('dark').addClass('light');
$row.find('.fa-file').removeClass('fa-file').addClass('fa-file-o');
$row.find('.fa-folder').removeClass('fa-folder').addClass('fa-folder-o');
},
renderSortIcon: function(){
client/galaxy/scripts/mvc/library/library-folderrow-view.js
+1 -1
View File
@@ -85,7 +85,7 @@ var FolderRowView = Backbone.View.extend({
tmpl_array.push(' <td>');
tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');
tmpl_array.push(' </td>');
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');
tmpl_array.push(' <td>');
tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');
tmpl_array.push(' </td>');
client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+25 -7
View File
@@ -26,9 +26,9 @@ var FolderToolbarView = Backbone.View.extend({
},
defaults: {
'can_add_library_item' : false,
'contains_file' : false,
'chain_call_control' : {
'can_add_library_item' : false,
'contains_file_or_folder' : false,
'chain_call_control' : {
'total_number' : 0,
'failed_number' : 0
},
@@ -116,7 +116,7 @@ var FolderToolbarView = Backbone.View.extend({
} else{
$('.add-library-items').hide();
}
if (this.options.contains_file === true){
if (this.options.contains_file_or_folder === true){
if (Galaxy.currUser){
if (!Galaxy.currUser.isAnonymous()){
$('.logged-dataset-manipulation').show();
@@ -250,9 +250,12 @@ var FolderToolbarView = Backbone.View.extend({
// we can save last used history to pre-select it next time
this.options.last_used_history_id = history_id;
var dataset_ids = [];
var folder_ids = [];
$('#folder_table').find(':checked').each(function(){
if (this.parentElement.parentElement.id !== '') {
if (this.parentElement.parentElement.id !== '' && this.parentElement.parentElement.classList.contains('dataset_row') ) {
dataset_ids.push(this.parentElement.parentElement.id);
} else if (this.parentElement.parentElement.id !== '' && this.parentElement.parentElement.classList.contains('folder_row') ) {
folder_ids.push(this.parentElement.parentElement.id);
}
});
// prepare the dataset objects to be imported
@@ -265,6 +268,18 @@ var FolderToolbarView = Backbone.View.extend({
historyItem.source = 'library';
datasets_to_import.push(historyItem);
}
// prepare the folder objects to be imported
var folders_to_import = [];
for (var i = folder_ids.length - 1; i >= 0; i--) {
var library_folder_id = folder_ids[i];
var historyItem = new mod_library_model.HistoryItem();
historyItem.url = historyItem.urlRoot + history_id + '/contents';
historyItem.content = library_folder_id;
historyItem.source = 'library_folder';
datasets_to_import.push(historyItem);
}
this.initChainCallControl( { length: datasets_to_import.length, action: 'to_history', history_name: history_name } );
// set the used history as current so user will see the last one
// that he imported into in the history panel on the 'analysis' page
@@ -289,13 +304,16 @@ var FolderToolbarView = Backbone.View.extend({
*/
download : function( folder_id, format ){
var dataset_ids = [];
var folder_ids = [];
$( '#folder_table' ).find( ':checked' ).each( function(){
if ( this.parentElement.parentElement.id !== '' ) {
if ( this.parentElement.parentElement.id !== '' && this.parentElement.parentElement.classList.contains('dataset_row') ) {
dataset_ids.push( this.parentElement.parentElement.id );
} else if ( this.parentElement.parentElement.id !== '' && this.parentElement.parentElement.classList.contains('folder_row') ) {
folder_ids.push( this.parentElement.parentElement.id );
}
} );
var url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/download/' + format;
var data = { 'ld_ids' : dataset_ids };
var data = { 'ld_ids' : dataset_ids, 'folder_ids' : folder_ids };
this.processDownload( url, data, 'get' );
},
client/galaxy/scripts/templates/compile_templates.py
+34 -33
View File
@@ -1,40 +1,39 @@
#!/usr/bin/env python
# Script requires handlebars compiler be installed; use node package manager
# Script requires handlebars compiler be installed; use node package manager
# to install handlebars.
"""%prog [options] [ specific .handlebars or .html template file to compile ]
Compiles handlebars templates into javascript for better load times and performance.
Handlebars compilation errors will print to stderr.
NOTE!: you will need node.js, npm, and handlebars (installed from npm) in order to compile templates
See http://handlebarsjs.com/precompilation.html for more info.
Should be called from the $GLX_ROOT/static/scripts/templates directory.
Should be called from the $GLX_ROOT/static/scripts/templates directory.
Compiled templates will be written to the compiled/ directory.
If the --multi-ext option is passed a file extension string, the script will:
* search for *.<extension> in the current directory,
* extract each '<script type="text/template"> from the file and write them into a new handlebars file
named using the id of the script tag (eg. id="undeleteMsg" -> undeleteMsg.handlebars)
* these new handlebars scripts will be compiled along with any other handlebars templates in the dir
additionally for each of those files, the script will:
* extract each '<script type="text/javascript"> from the file and write them ALL into a single js file
named using the prefix 'helpers-' and the basename of the enclosing file
(eg. common-templates.html -> helpers-common-templates.js )
* these new handlebars scripts will be compiled along with any other handlebars templates in the dir
These files can be included as if they were templates (eg. h.templates( 'helpers-common-templates' ) )
This hopefully will allow both multiple templates and their associated Handlebars helper functions to be
included in one file.
Currently, this works (best?) if:
* the multiple templates are within one html file
* each template is enclosed in a <script> tag with type="text/template" and some id attribute
* each helper fn is enclosed in a <script> tag with type="text/javascript" and some id attribute
e.g. <script type="text/template" id="history-deletedMsg" class="template">Deleted {{ msg }}</script>
"""
# ------------------------------------------------------------------------------
@@ -52,8 +51,8 @@ import re
import logging as log
log.basicConfig(
#level = log.DEBUG,
name = __name__
# level=log.DEBUG,
name=__name__
)
COMPILED_DIR = 'compiled'
@@ -67,7 +66,8 @@ HELPER_TYPE = 'text/javascript'
# both of these are off by default for backward compat
DEFAULT_MINIMIZATION = False
DEFAULT_MULTI_EXT = None #'.html'
DEFAULT_MULTI_EXT = None # '.html'
# ------------------------------------------------------------------------------
def parse_html_tag_attrs( string ):
@@ -79,15 +79,17 @@ def parse_html_tag_attrs( string ):
attrs[ key ] = val
return attrs
def split_on_html_tag( string, tag ):
tag_pattern = r'<%s\s*(?P<attrs>.*?)>(?P<body>.*?)</%s>' % ( tag, tag )
log.debug( tag_pattern )
tag_pattern = re.compile( tag_pattern, re.MULTILINE | re.DOTALL )
found_list = re.findall( tag_pattern, string )
for attrs, body in found_list:
yield ( parse_html_tag_attrs( attrs ), body )
def filter_on_tag_type( generator, type_attr_to_match ):
for attrs, body in generator:
log.debug( 'attrs: %s', str( attrs ) )
@@ -95,41 +97,41 @@ def filter_on_tag_type( generator, type_attr_to_match ):
and ( attrs[ 'type' ] == type_attr_to_match ) ):
yield attrs, body
# ------------------------------------------------------------------------------
def break_multi_template( multi_template_filename ):
"""parse the multi template, writing each template into a new handlebars tmpl and returning their names"""
template_filenames = []
# parse the multi template
print "\nBreaking multi-template file %s into individual templates and helpers:" % ( multi_template_filename )
with open( multi_template_filename, 'r' ) as multi_template_file:
multi_template_file_text = multi_template_file.read()
# write a template file for each template (name based on id in tag)
tag_generator = split_on_html_tag( multi_template_file_text, TEMPLATE_TAG )
for attrs, template_text in filter_on_tag_type( tag_generator, TEMPLATE_TYPE ):
if( 'id' not in attrs ):
log.warning( 'Template has no "id". attrs: %s' %( str( attrs ) ) )
log.warning( 'Template has no "id". attrs: %s' % ( str( attrs ) ) )
continue
template_id = attrs[ 'id' ]
template_text = template_text.strip()
handlebar_template_filename = template_id + '.handlebars'
with open( handlebar_template_filename, 'w' ) as handlebar_template_file:
handlebar_template_file.write( template_text )
log.debug( "%s\n%s\n", template_id, template_text )
template_filenames.append( handlebar_template_filename )
## write all helpers to a single 'helper-' prefixed js file in the compilation dir
# write all helpers to a single 'helper-' prefixed js file in the compilation dir
helper_fns = []
# same tag, different type
tag_generator = split_on_html_tag( multi_template_file_text, TEMPLATE_TAG )
for attrs, helper_text in filter_on_tag_type( tag_generator, HELPER_TYPE ):
helper_text = helper_text.strip()
print '(helper):', ( attrs[ 'id' ] if 'id' in attrs else '(No id)' )
helper_fns.append( helper_text )
if helper_fns:
@@ -139,7 +141,7 @@ def break_multi_template( multi_template_filename ):
with open( helper_filename, 'w' ) as helper_file:
helper_file.write( '\n'.join( helper_fns ) )
print '(helper functions written to %s)' % helper_filename
print '\n'.join( template_filenames )
return template_filenames
@@ -147,12 +149,12 @@ def break_multi_template( multi_template_filename ):
# ------------------------------------------------------------------------------
def compile_template( template_filename, minimize=False ):
"""compile the given template file (optionally minimizing the js) using subprocess.
Use the basename of the template file for the outputed js.
"""
template_basename = os.path.splitext( os.path.split( template_filename )[1] )[0]
compiled_filename = os.path.join( COMPILED_DIR, template_basename + COMPILED_EXT )
command_string = COMPILE_CMD_STR % ( template_filename, compiled_filename )
if minimize:
command_string += COMPILE_MINIMIZE_SWITCH
@@ -163,16 +165,16 @@ def compile_template( template_filename, minimize=False ):
# ------------------------------------------------------------------------------
def main( options, args ):
"""Break multi template files into single templates, compile all single templates.
If args, compile that as a list of specific handlebars and/or multi template files.
"""
print "(Call this script with the '-h' option for more help)"
handlebars_templates = []
# If specific scripts specified on command line, just compile them,
if len( args ) >= 1:
handlebars_templates = filter( lambda( x ): x.endswith( '.handlebars' ), args )
# otherwise compile all in the current dir
else:
handlebars_templates = glob( '*.handlebars' )
@@ -186,13 +188,13 @@ def main( options, args ):
multi_templates = filter( lambda( x ): x.endswith( options.multi_ext ), args )
else:
multi_templates = glob( '*' + options.multi_ext )
for multi_template_filename in multi_templates:
multi_template_template_filenames.extend( break_multi_template( multi_template_filename ) )
# unique filenames only (Q&D)
handlebars_templates = list( set( handlebars_templates + multi_template_template_filenames ) )
# compile the templates
print "\nCompiling templates:"
filenames_w_possible_errors = []
@@ -200,7 +202,7 @@ def main( options, args ):
shell_ret = compile_template( handlebars_template, options.minimize )
if shell_ret:
filenames_w_possible_errors.append( handlebars_template )
# report any possible errors
if filenames_w_possible_errors:
print "\nThere may have been errors on the following files:"
@@ -234,4 +236,3 @@ if __name__ == '__main__':
( options, args ) = optparser.parse_args()
sys.exit( main( options, args ) )
client/galaxy/scripts/utils/config.js
+24 -24
View File
@@ -4,7 +4,7 @@ define(['libs/underscore', 'viz/trackster/util', 'utils/config'], function(_, ut
* A configuration setting. Currently key is used as id.
*/
var ConfigSetting = Backbone.Model.extend({
initialize: function(options) {
// Use key as id for now.
var key = this.get('key');
@@ -16,8 +16,8 @@ var ConfigSetting = Backbone.Model.extend({
this.set(_.extend({}, defaults, options));
}
if (this.get('value') === undefined) {
// Use default to set value.
if (this.get('value') === undefined && this.get('default_value') !== undefined) {
// Use default to set value (if present).
this.set_value(this.get('default_value'));
// If no default value for color config, set random color.
@@ -134,7 +134,7 @@ var ConfigSettingCollection = Backbone.Collection.extend({
return _.extend({}, m, { value: saved_values[m.key] });
});
}
return new ConfigSettingCollection(models);
}
});
@@ -150,7 +150,7 @@ var ConfigSettingCollectionView = Backbone.View.extend({
*/
render: function() {
var container = this.$el;
this.collection.each(function(param, index) {
// Hidden params have no representation in the form
if (param.get('hidden')) { return; }
@@ -165,7 +165,7 @@ var ConfigSettingCollectionView = Backbone.View.extend({
if ( type === 'bool' ) {
row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', value ) );
}
// Draw parameter as textbox
// Draw parameter as textbox
else if ( type === 'text' ) {
row.append( $('<input type="text"/>').attr("id", id ).val(value).click( function() { $(this).select(); }));
}
@@ -177,39 +177,39 @@ var ConfigSettingCollectionView = Backbone.View.extend({
});
select.val( value );
row.append( select );
}
// Draw parameter as color picker
// Draw parameter as color picker
else if ( type === 'color' ) {
var
var
container_div = $("<div/>").appendTo(row),
input = $('<input />').attr("id", id ).attr("name", id ).val( value ).css("float", "left")
input = $('<input />').attr("id", id ).attr("name", id ).val( value ).css("float", "left")
.appendTo(container_div).click(function(e) {
// Hide other pickers.
$(".tooltip").removeClass( "in" );
// Show input's color picker.
var tip = $(this).siblings(".tooltip").addClass( "in" );
tip.css( {
tip.css( {
// left: $(this).position().left + ( $(input).width() / 2 ) - 60,
// top: $(this).position().top + $(this.height)
// top: $(this).position().top + $(this.height)
left: $(this).position().left + $(this).width() + 5,
top: $(this).position().top - ( $(tip).height() / 2 ) + ( $(this).height() / 2 )
} ).show();
// Click management:
// Click management:
// Keep showing tip if clicking in tip.
tip.click(function(e) {
e.stopPropagation();
});
// Hide tip if clicking outside of tip.
$(document).bind( "click.color-picker", function() {
tip.hide();
$(document).unbind( "click.color-picker" );
});
// No propagation to avoid triggering document click (and tip hiding) above.
e.stopPropagation();
}),
@@ -222,20 +222,20 @@ var ConfigSettingCollectionView = Backbone.View.extend({
tip_inner = $("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(tip),
tip_arrow = $("<div class='tooltip-arrow'></div>").appendTo(tip),
farb_obj = $.farbtastic(tip_inner, { width: 100, height: 100, callback: input, color: value });
// Clear floating.
container_div.append( $("<div/>").css("clear", "both"));
// Use function to fix farb_obj value.
(function(fixed_farb_obj) {
new_color_icon.click(function() {
fixed_farb_obj.setColor(util_mod.get_random_color());
});
});
})(farb_obj);
}
}
else {
row.append( $('<input />').attr("id", id ).attr("name", id ).val( value ) );
row.append( $('<input />').attr("id", id ).attr("name", id ).val( value ) );
}
// Help text
if ( param.help ) {
client/galaxy/scripts/viz/trackster/painters.js
+88 -92
View File
@@ -8,7 +8,7 @@ define( ["libs/underscore"], function( _ ) {
*/
var BEFORE = 1001, CONTAINS = 1002, OVERLAP_START = 1003, OVERLAP_END = 1004, CONTAINED_BY = 1005, AFTER = 1006;
var compute_overlap = function(first_region, second_region) {
var
var
first_start = first_region[0], first_end = first_region[1],
second_start = second_region[0], second_end = second_region[1],
overlap;
@@ -34,7 +34,7 @@ var compute_overlap = function(first_region, second_region) {
overlap = OVERLAP_END;
}
}
return overlap;
};
@@ -60,7 +60,7 @@ var dashedLine = function(ctx, x1, y1, x2, y2, dashLen) {
var dashX = dX / dashes;
var dashY = dY / dashes;
var q;
for (q = 0; q < dashes; q++, x1 += dashX, y1 += dashY) {
if (q % 2 !== 0) {
continue;
@@ -74,11 +74,11 @@ var dashedLine = function(ctx, x1, y1, x2, y2, dashLen) {
*/
var drawDownwardEquilateralTriangle = function(ctx, down_vertex_x, down_vertex_y, side_len) {
// Compute other two points of triangle.
var
var
x1 = down_vertex_x - side_len/2,
x2 = down_vertex_x + side_len/2,
y = down_vertex_y - Math.sqrt( side_len*3/2 );
// Draw and fill.
ctx.beginPath();
ctx.moveTo(x1, y);
@@ -198,16 +198,16 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
ctx.fillStyle = "#aaa";
ctx.fillRect( 0, y_zero, width, 1 );
}
ctx.beginPath();
var x_scaled, y, delta_x_px;
if (data.length > 1) {
delta_x_px = Math.ceil((data[1][0] - data[0][0]) * w_scale);
}
}
else {
delta_x_px = 10;
}
// Painter color can be in either block_color (FeatureTrack) or color pref (LineTrack).
var painter_color = this.prefs.block_color || this.prefs.color,
// Extract RGB from preference color.
@@ -215,10 +215,10 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
pref_r = (pref_color & 0xff0000) >> 16,
pref_g = (pref_color & 0x00ff00) >> 8,
pref_b = pref_color & 0x0000ff,
top_overflow = false,
top_overflow = false,
bot_overflow = false;
// Paint track.
for (var i = 0, len = data.length; i < len; i++) {
// Reset attributes for next point.
@@ -241,20 +241,20 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
if (y < min_value) {
bot_overflow = true;
y = min_value;
}
}
else if (y > max_value) {
top_overflow = true;
y = max_value;
}
// Draw point.
if (mode === "Histogram") {
// y becomes the bar height in pixels, which is the negated for canvas coords
y = Math.round( y / vertical_range * height_px );
ctx.fillRect(x_scaled, y_zero, delta_x_px, - y );
}
}
else if (mode === "Intensity") {
var
var
saturation = (y - min_value) / vertical_range,
// Range is [pref_color, 255] where saturation = 0 --> 255 and saturation = 1 --> pref color
new_r = Math.round( pref_r + (255 - pref_r) * (1 - saturation) ),
@@ -262,23 +262,23 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
new_b = Math.round( pref_b + (255 - pref_b) * (1 - saturation) );
ctx.fillStyle = "rgb(" + new_r + "," + new_g + "," + new_b + ")";
ctx.fillRect(x_scaled, 0, delta_x_px, height_px);
}
}
else { // mode is Coverage/Line or Filled.
// Scale Y value.
y = Math.round( height_px - (y - min_value) / vertical_range * height_px );
if (in_path) {
ctx.lineTo(x_scaled, y);
}
}
else {
in_path = true;
if (mode === "Filled") {
ctx.moveTo(x_scaled, height_px);
ctx.lineTo(x_scaled, y);
}
}
else {
ctx.moveTo(x_scaled, y);
// Use this approach (note: same as for filled) to draw line from 0 to
// Use this approach (note: same as for filled) to draw line from 0 to
// first data point.
//ctx.moveTo(x_scaled, height_px);
//ctx.lineTo(x_scaled, y);
@@ -292,7 +292,7 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
var overflow_x;
if (mode === "Histogram" || mode === "Intensity") {
overflow_x = delta_x_px;
}
}
else { // Line and Filled, which are points
x_scaled -= 2; // Move it over to the left so it's centered on the point
overflow_x = 4;
@@ -312,11 +312,11 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
ctx.lineTo( 0, y_zero );
}
ctx.fill();
}
}
else {
ctx.stroke();
}
ctx.restore();
};
@@ -356,7 +356,7 @@ FeaturePositionMapper.prototype.get_feature_data = function(x, y) {
if (!this.feature_positions[slot]) {
return null;
}
// Find feature using X.
x += this.translation;
for (var i = 0; i < this.feature_positions[slot].length; i++) {
@@ -404,8 +404,8 @@ _.extend(FeaturePainter.prototype, {
* a FeaturePositionMapper object with information about where features were drawn.
*/
draw: function(ctx, width, height, w_scale, slots) {
var data = this.data,
view_start = this.view_start,
var data = this.data,
view_start = this.view_start,
view_end = this.view_end;
ctx.save();
@@ -423,11 +423,11 @@ _.extend(FeaturePainter.prototype, {
feature_uid = feature[0],
feature_start = feature[1],
feature_end = feature[2],
// Slot valid only if features are slotted and this feature is slotted;
// Slot valid only if features are slotted and this feature is slotted;
// feature may not be due to lack of space.
slot = (slots && slots[feature_uid] !== undefined ? slots[feature_uid].slot : null);
// Draw feature if (a) mode is dense or feature is slotted (as it must be for all non-dense modes) and
// Draw feature if (a) mode is dense or feature is slotted (as it must be for all non-dense modes) and
// (b) there's overlap between the feature and drawing region.
if ( (this.mode === "Dense" || slot !== null) && ( feature_start < view_end && feature_end > view_start ) ) {
x_draw_coords = this.draw_element(ctx, this.mode, feature, slot, view_start, view_end, w_scale, y_scale, width);
@@ -449,7 +449,7 @@ _.extend(FeaturePainter.prototype, {
});
},
/**
/**
* Abstract function for drawing an individual feature.
*/
draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) {
@@ -486,7 +486,7 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
get_row_height: function() {
var mode = this.mode, height;
if (mode === "Dense") {
height = DENSE_TRACK_HEIGHT;
height = DENSE_TRACK_HEIGHT;
}
else if (mode === "no_detail") {
height = NO_DETAIL_TRACK_HEIGHT;
@@ -520,20 +520,20 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
// For now, assume '.' === '+'
block_color = (!feature_strand || feature_strand === "+" || feature_strand === "." ? this.prefs.block_color : this.prefs.reverse_strand_color);
label_color = this.prefs.label_color;
// Set global alpha.
ctx.globalAlpha = this.alpha_scaler.gen_val(feature);
// In dense mode, put all data in top slot.
if (mode === "Dense") {
slot = 1;
}
if (mode === "no_detail") {
// No details for feature, so only one way to display.
ctx.fillStyle = block_color;
ctx.fillRect(f_start, y_start + 5, f_end - f_start, NO_DETAIL_FEATURE_HEIGHT);
}
}
else { // Mode is either Squish or Pack:
// Feature details.
var feature_ts = feature[5],
@@ -541,12 +541,12 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
feature_blocks = feature[7],
// Whether we are drawing full height or squished features
full_height = true;
if (feature_ts && feature_te) {
thick_start = Math.floor( Math.max(0, (feature_ts - tile_low) * w_scale) );
thick_end = Math.ceil( Math.min(width, Math.max(0, (feature_te - tile_low) * w_scale)) );
}
// Set vars that depend on mode.
var thin_height, thick_height;
if (mode === "Squish" ) {
@@ -560,7 +560,7 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
thin_height = 5;
thick_height = PACK_FEATURE_HEIGHT;
}
// Draw feature/feature blocks + connectors.
if (!feature_blocks) {
// If there are no blocks, treat the feature as one big exon.
@@ -575,15 +575,15 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
}
ctx.fillRect(f_start, y_start + 1, f_end - f_start, thick_height);
}
} else {
} else {
//
// There are feature blocks and mode is either Squish or Pack.
//
// Approach: (a) draw whole feature as connector/intron and (b) draw blocks as
// Approach: (a) draw whole feature as connector/intron and (b) draw blocks as
// needed. This ensures that whole feature, regardless of whether it starts with
// a block, is visible.
//
// Compute y axis start position and height
var cur_y_start, cur_height;
if (mode === "Squish" || mode === "Dense") {
@@ -620,7 +620,7 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
}
ctx.fillRect(f_start, cur_y_start, f_end - f_start, cur_height);
}
// Draw blocks.
var start_and_height;
for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) {
@@ -630,7 +630,7 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low - 0.5) * w_scale)) ),
last_block_start, last_block_end;
// Skip drawing if block not on tile.
// Skip drawing if block not on tile.
if (block_start > block_end) { continue; }
// Draw thin block.
@@ -666,15 +666,15 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
last_block_start = block_start;
last_block_end = block_end;
}
// FIXME: Height scaling only works in Pack mode right now.
if (mode === "Pack") {
// Reset alpha so height scaling is not impacted by alpha scaling.
ctx.globalAlpha = 1;
// Height scaling: draw white lines to reduce height according to height scale factor.
ctx.fillStyle = "white"; // TODO: set this to background color.
var
var
hscale_factor = this.height_scaler.gen_val(feature),
// Ceil ensures that min height is >= 1.
new_height = Math.ceil(thick_height * hscale_factor),
@@ -682,13 +682,13 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
if (hscale_factor !== 1) {
ctx.fillRect(f_start, cur_y_start + 1, f_end - f_start, ws_height);
ctx.fillRect(f_start, cur_y_start + thick_height - ws_height + 1, f_end - f_start, ws_height);
}
}
}
}
}
// Reset alpha so that label is not transparent.
ctx.globalAlpha = 1;
// Draw label for Pack mode.
if (feature_name && mode === "Pack" && feature_start > tile_low) {
ctx.fillStyle = label_color;
@@ -705,10 +705,10 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
//ctx.fillStyle = block_color;
}
}
// Reset global alpha.
ctx.globalAlpha = 1;
return [draw_start, draw_end];
}
});
@@ -726,7 +726,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
get_row_height: function() {
var height, mode = this.mode;
if (mode === "Dense") {
height = DENSE_TRACK_HEIGHT;
height = DENSE_TRACK_HEIGHT;
}
else if (mode === "Squish") {
height = SQUISH_TRACK_HEIGHT;
@@ -821,7 +821,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
drawing_blocks = [],
s_start,
s_end;
// Keep list of items that need to be drawn on top of initial drawing layer.
var draw_last = [];
@@ -837,7 +837,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
if (is_overlap([feature_start + block[0], feature_start + block[1]], tile_region)) {
s_start = get_draw_coord(feature_start + block[0]);
s_end = get_draw_coord(feature_start + block[1]);
// Make sure that block is drawn even if it too small to be rendered officially; in this case,
// read is drawn at 1px.
// TODO: need to ensure that s_start, s_end are calculated the same for both slotting
@@ -861,7 +861,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
var seq_start = feature_start + base_offset;
s_start = get_draw_coord(seq_start);
s_end = get_draw_coord(seq_start + cig_len);
// Skip feature if it's not in tile.
if (!is_overlap([seq_start, seq_start + cig_len], tile_region)) {
// Update offsets.
@@ -869,7 +869,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
seq_offset = update_seq_offset(seq_offset, cig_op, cig_len);
continue;
}
// Make sure that read is drawn even if it too small to be rendered officially; in this case,
// read is drawn at 1px.
// TODO: need to ensure that s_start, s_end are calculated the same for both slotting
@@ -877,8 +877,8 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
if (s_start === s_end) {
s_end += 1;
}
// Draw read feature.
// Draw read feature.
switch (cig_op) {
case "H": // Hard clipping.
case "S": // Soft clipping.
@@ -932,7 +932,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
// Move forward in sequence only if sequence used to get mismatches.
if (cig_op === 'X') { seq_offset += cig_len; }
base_offset += cig_len;
break;
case "N": // Skipped bases.
ctx.fillStyle = CONNECTOR_COLOR;
@@ -948,7 +948,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
// Check to see if sequence should be drawn at all by looking at the overlap between
// the sequence region and the tile region.
var insert_x_coord = s_start - gap;
if (is_overlap([seq_start, seq_start + cig_len], tile_region)) {
var seq = read_seq.slice(seq_offset, seq_offset + cig_len);
// Insertion point is between the sequence start and the previous base: (-gap) moves
@@ -992,7 +992,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
// Draw block.
ctx.fillStyle = "yellow";
// TODO: This is a pretty hack-ish way to fill rectangle based on mode.
ctx.fillRect(x_center, y_start + (this.mode !== "Dense" ? 2 : 5),
ctx.fillRect(x_center, y_start + (this.mode !== "Dense" ? 2 : 5),
s_end - s_start, (mode !== "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT));
}
}
@@ -1011,7 +1011,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
break;
}
}
//
// Draw last items.
//
@@ -1032,7 +1032,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
}
}
},
/**
* Draw a complete read pair
*/
@@ -1048,7 +1048,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
y_start = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
draw_height = (mode === 'Pack' ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT),
label_color = this.prefs.label_color;
// Draw read.
if (feature[5] instanceof Array) {
// Read is paired.
@@ -1097,7 +1097,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 9, this.max_label_length);
}
}
// FIXME: provide actual coordinates for drawn read.
return [0,0];
}
@@ -1122,7 +1122,7 @@ _.extend(ArcLinkedFeaturePainter.prototype, FeaturePainter.prototype, LinkedFeat
return longest_feature_length;
},
get_top_padding: function( width ) {
get_top_padding: function( width ) {
var view_range = this.view_end - this.view_start,
w_scale = width / view_range;
return Math.min( 128, Math.ceil( ( this.longest_feature_length / 2 ) * w_scale ) );
@@ -1131,7 +1131,7 @@ _.extend(ArcLinkedFeaturePainter.prototype, FeaturePainter.prototype, LinkedFeat
draw_connector: function( ctx, block1_start, block1_end, block2_start, block2_end, y_start ) {
// Arc drawing -- from closest endpoints
var x_center = ( block1_end + block2_start ) / 2,
radius = block2_start - x_center;
radius = block2_start - x_center;
// For full half circles
var angle1 = Math.PI, angle2 = 0;
if ( radius > 0 ) {
@@ -1290,32 +1290,33 @@ SplitRamp.prototype.map_value = function( value ) {
var DiagonalHeatmapPainter = function(data, view_start, view_end, prefs, mode) {
Painter.call( this, data, view_start, view_end, prefs, mode );
var i, len;
if ( this.prefs.min_value === undefined ) {
var min_value = Infinity;
for (i = 0, len = this.data.length; i < len; i++) {
min_value = Math.min( min_value, this.data[i][5] );
min_value = Math.min( min_value, this.data[i][6] );
}
this.prefs.min_value = min_value;
}
if ( this.prefs.max_value === undefined ) {
var max_value = -Infinity;
for (i = 0, len = this.data.length; i < len; i++) {
max_value = Math.max( max_value, this.data[i][5] );
max_value = Math.max( max_value, this.data[i][6] );
}
this.prefs.max_value = max_value;
}
};
DiagonalHeatmapPainter.prototype.default_prefs = {
min_value: undefined,
max_value: undefined,
mode: "Heatmap",
DiagonalHeatmapPainter.prototype.default_prefs = {
min_value: undefined,
max_value: undefined,
mode: "Heatmap",
pos_color: "#FF8C00",
neg_color: "#4169E1"
neg_color: "#4169E1"
};
DiagonalHeatmapPainter.prototype.draw = function(ctx, width, height, w_scale) {
var
var
min_value = this.prefs.min_value,
max_value = this.prefs.max_value,
value_range = max_value - min_value,
@@ -1336,15 +1337,11 @@ DiagonalHeatmapPainter.prototype.draw = function(ctx, width, height, w_scale) {
// Draw into triangle, then rotate and scale
ctx.rotate(-45 * Math.PI / 180);
ctx.scale( invsqrt2, invsqrt2 );
// Paint track.
for (var i = 0, len = data.length; i < len; i++) {
d = data[i];
// Ensure the cell is visible
// if ( )
s1 = scale( d[1] );
e1 = scale( d[2] );
s2 = scale( d[4] );
@@ -1352,10 +1349,9 @@ DiagonalHeatmapPainter.prototype.draw = function(ctx, width, height, w_scale) {
value = d[6];
ctx.fillStyle = ( ramp.map_value( value ) );
ctx.fillRect( s1, s2, ( e1 - s1 ), ( e2 - s2 ) );
}
ctx.restore();
};
@@ -1372,7 +1368,7 @@ var ReadPainterUtils = function(ctx, row_height, px_per_base, mode) {
_.extend(ReadPainterUtils.prototype, {
/**
* Draw deletion of base(s).
* Draw deletion of base(s).
* @param draw_detail if true, drawing in detail and deletion is drawn more subtly
*/
draw_deletion: function(x, y, len) {
@@ -1399,7 +1395,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
get_row_height: function() {
var mode = this.mode, height;
if (mode === "Dense") {
height = DENSE_TRACK_HEIGHT;
height = DENSE_TRACK_HEIGHT;
}
else if (mode === "Squish") {
height = SQUISH_TRACK_HEIGHT;
@@ -1431,8 +1427,8 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
draw: function(ctx, width, height, w_scale) {
ctx.save();
var
/**
var
/**
* Returns dictionary of information about an indel; returns empty if there no indel. Assumes indel is left-aligned.
* Dict attributes:
* -type: 'insertion' or 'deletion'
@@ -1485,7 +1481,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
row_height = (this.mode === 'Squish' ? SQUISH_TRACK_HEIGHT : PACK_TRACK_HEIGHT),
// If zoomed out, fill the whole row with feature to make it easier to read;
// when zoomed in, use feature height so that there are gaps in sample rows.
feature_height = (w_scale < 0.1 ?
feature_height = (w_scale < 0.1 ?
row_height :
(this.mode === 'Squish' ? SQUISH_FEATURE_HEIGHT : PACK_FEATURE_HEIGHT)
),
@@ -1495,7 +1491,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
// If there's a single sample, update drawing variables.
if (num_samples === 1) {
row_height = feature_height =
row_height = feature_height =
(w_scale < ctx.canvas.manager.char_width_px ? this.prefs.summary_height : row_height);
paint_utils.row_height = row_height;
// No summary when there's a single sample.
@@ -1519,7 +1515,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
alt = [ locus_data[4].split(',') ];
sample_gts = locus_data[7].split(',');
allele_counts = locus_data.slice(8);
// Process alterate values to derive information about each alt.
alt = _.map(_.flatten(alt), function(a) {
var alt_info = {
@@ -1528,7 +1524,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
start: 0
},
indel_info = get_indel_info(ref, a);
return _.extend(alt_info, indel_info);
});
@@ -1541,7 +1537,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
if (draw_summary) {
ctx.fillStyle = '#999999';
ctx.globalAlpha = 1;
for (j = 0; j < alt.length; j++) {
for (j = 0; j < alt.length; j++) {
// Draw background for summary.
draw_x_start = this.get_start_draw_pos(pos + alt[j].start, w_scale);
ctx.fillRect(draw_x_start, 0, base_px, this.prefs.summary_height);
@@ -1564,7 +1560,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
draw_y_start = (draw_summary ? this.prefs.summary_height + this.divider_height : 0);
for (j = 0; j < sample_gts.length; j++, draw_y_start += row_height) {
genotype = (sample_gts[j] ? sample_gts[j].split(/\/|\|/) : ['0', '0']);
// Get variant to draw and set drawing properties.
variant = null;
if (genotype[0] === genotype[1]) {
client/galaxy/scripts/viz/trackster/tracks.js
+314 -304
View File
File diff suppressed because it is too large Load Diff
client/galaxy/style/less/trackster.less
+2 -1
View File
@@ -82,6 +82,7 @@
display: inline-block;
width: 15em;
margin: 0 10px;
white-space: nowrap;
}
.intro {
@@ -568,4 +569,4 @@ input {
// elements (e.g. track, group) in order to take precedence.
.dragging {
border: 1px solid blue;
}
}
client/galaxy/style/source_material/circle.py
+5 -5
View File
@@ -12,6 +12,7 @@ from math import pi
assert sys.version_info[:2] >= ( 2, 4 )
def parse_css_color( color ):
if color.startswith( '#' ):
color = color[1:]
@@ -25,11 +26,10 @@ def parse_css_color( color ):
b = int( color[4:6], 16 )
else:
raise Exception( "Color should be 3 hex numbers" )
return r/256, g/256, b/256
return r / 256, g / 256, b / 256
size = int( sys.argv[1] )
surface = cairo.ImageSurface( cairo.FORMAT_ARGB32, size, size )
c = cairo.Context( surface )
@@ -48,8 +48,8 @@ t = size / 4.0
arrow = sys.argv[4]
if arrow == 'right':
c.move_to( t + 1, t )
c.line_to( 3*t - 1, 2*t )
c.line_to( t + 1, 3*t )
c.line_to( 3 * t - 1, 2 * t )
c.line_to( t + 1, 3 * t )
c.stroke()
surface.write_to_png( "/dev/stdout" )
config/datatypes_conf.xml.sample
+6
View File
@@ -59,6 +59,7 @@
<datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/>
<datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" />
<datatype extension="data_manager_json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="True" display_in_upload="False"/>
<datatype extension="dbn" type="galaxy.datatypes.sequence:DotBracket" display_in_upload="true" description="Dot-Bracket format is a text-based format for storing both an RNA sequence and its corresponding 2D structure." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Dbn"/>
<datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true" description="A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than ('>') symbol in the first column. All lines should be shorter than 80 characters." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fasta">
<converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/>
<converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/>
@@ -166,6 +167,7 @@
<datatype extension="mzxml" type="galaxy.datatypes.proteomics:MzXML" mimetype="application/xml" display_in_upload="true" />
<datatype extension="ms2" type="galaxy.datatypes.proteomics:Ms2" display_in_upload="true" />
<datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml" display_in_upload="true" />
<datatype extension="mz.sqlite" type="galaxy.datatypes.proteomics:MzSQlite" mimetype="application/octet-stream" display_in_upload="true" />
<datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml" display_in_upload="true" />
<datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml" display_in_upload="true" />
<datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml" display_in_upload="true" />
@@ -176,6 +178,7 @@
<datatype extension="idpdb" type="galaxy.datatypes.proteomics:IdpDB" display_in_upload="true" />
<datatype extension="sf3" type="galaxy.datatypes.proteomics:Sf3" display_in_upload="true" />
<datatype extension="cps" type="galaxy.datatypes.binary:Binary" subclass="True" display_in_upload="true" />
<datatype extension="ct" type="galaxy.datatypes.tabular:ConnectivityTable" display_in_upload="True"/>
<datatype extension="searchgui_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/>
<datatype extension="peptideshaker_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/>
<!-- End Proteomics Datatypes -->
@@ -421,6 +424,7 @@
<sniffer type="galaxy.datatypes.tabular:Vcf"/>
<sniffer type="galaxy.datatypes.binary:TwoBit"/>
<sniffer type="galaxy.datatypes.binary:GeminiSQLite"/>
<sniffer type="galaxy.datatypes.proteomics:MzSQlite"/>
<sniffer type="galaxy.datatypes.binary:SQlite"/>
<sniffer type="galaxy.datatypes.binary:Bam"/>
<sniffer type="galaxy.datatypes.binary:Sff"/>
@@ -467,6 +471,8 @@
<sniffer type="galaxy.datatypes.text:Ipynb"/>
<sniffer type="galaxy.datatypes.text:Json"/>
<sniffer type="galaxy.datatypes.sequence:RNADotPlotMatrix"/>
<sniffer type="galaxy.datatypes.sequence:DotBracket"/>
<sniffer type="galaxy.datatypes.tabular:ConnectivityTable"/>
<sniffer type="galaxy.datatypes.msa:Hmmer2" />
<sniffer type="galaxy.datatypes.msa:Hmmer3" />
<sniffer type="galaxy.datatypes.msa:Stockholm_1_0" />
config/object_store_conf.xml.sample
+8 -4
View File
@@ -23,9 +23,11 @@
<!-- Sample S3 Object Store
<object_store type="s3">
<auth access_key="...." secret_key="....." />
<bucket name="unique_bucket_name_all_lowercase" use_reduced_redundancy="False" />
<cache path="database/files/" size="1000" />
<auth access_key="...." secret_key="....." />
<bucket name="unique_bucket_name_all_lowercase" use_reduced_redundancy="False" />
<cache path="database/object_store_cache" size="1000" />
<extra_dir type="job_work" path="database/job_working_directory_s3"/>
<extra_dir type="temp" path="database/tmp_s3"/>
</object_store>
-->
@@ -34,7 +36,9 @@
<auth access_key="...." secret_key="....." />
<bucket name="unique_bucket_name" use_reduced_redundancy="False" max_chunk_size="250"/>
<connection host="" port="" is_secure="" conn_path="" multipart="True"/>
<cache path="database/files/" size="1000" />
<cache path="database/object_store_cache" size="1000" />
<extra_dir type="job_work" path="database/job_working_directory_swift"/>
<extra_dir type="temp" path="database/tmp_swift"/>
</object_store>
-->
config/plugins/interactive_environments/ipython/templates/ipython.mako
+3 -2
View File
@@ -1,4 +1,4 @@
<%namespace name="ie" file="ie.mako" />
<%namespace name="ie" file="ie.mako" />
<%
import os
@@ -16,7 +16,7 @@ if ie_request.attr.PASSWORD_AUTH:
m.update( ie_request.notebook_pw + ie_request.notebook_pw_salt )
PASSWORD = 'sha1:%s:%s' % (ie_request.notebook_pw_salt, m.hexdigest())
else:
PASSWORD = "none"
PASSWORD = "none"
## IPython Specific
# Prepare an empty notebook
@@ -26,6 +26,7 @@ with open( os.path.join( ie_request.attr.our_template_dir, 'notebook.ipynb' ), '
empty_nb = empty_nb % notebook_id
# Copy over default notebook, unless the dataset this viz is running on is a notebook
empty_nb_path = os.path.join(temp_dir, 'ipython_galaxy_notebook.ipynb')
if hda.datatype.__class__.__name__ != "Ipynb":
with open( empty_nb_path, 'w+' ) as handle:
handle.write( empty_nb )
config/plugins/visualizations/charts/static/build-app.js
+1 -6
View File
File diff suppressed because one or more lines are too long
config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
+4 -3
View File
@@ -1,6 +1,7 @@
define(['plugin/charts/nvd3/common/config'], function(nvd3_config) {
return $.extend(true, {}, nvd3_config, {
define(['plugin/charts/forms/default'], function(config_default) {
return $.extend(true, {}, config_default, {
library : 'NVD3',
tag : 'svg',
title : 'Histogram',
category : 'Data processing (requires \'charts\' tool from Toolshed)',
execute : 'histogram',
config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
+4 -3
View File
@@ -1,6 +1,7 @@
define(['plugin/charts/nvd3/common/config'], function(nvd3_config) {
return $.extend(true, {}, nvd3_config, {
define(['plugin/charts/forms/default'], function(config_default) {
return $.extend(true, {}, config_default, {
library : 'NVD3',
tag : 'svg',
title : 'Discrete Histogram',
category : 'Data processing (requires \'charts\' tool from Toolshed)',
execute : 'histogramdiscrete',
config/plugins/visualizations/charts/static/views/editor.js
+2 -2
View File
@@ -211,7 +211,7 @@ return Backbone.View.extend({
// add group model
_addGroupModel: function() {
var group = new Group({
id : Utils.uuid()
id : Utils.uid()
});
this.chart.groups.add(group);
return group;
@@ -260,7 +260,7 @@ return Backbone.View.extend({
// reset
_resetChart: function() {
// reset chart details
this.chart.set('id', Utils.uuid());
this.chart.set('id', Utils.uid());
this.chart.set('type', 'nvd3_bar');
this.chart.set('dataset_id', this.app.options.config.dataset_id);
this.chart.set('title', 'New Chart');
config/plugins/visualizations/charts/static/views/viewport.js
+1 -1
View File
@@ -295,7 +295,7 @@ return Backbone.View.extend({
_templateContainer: function(tag, width) {
return '<div class="charts-viewport-container" style="width:' + width + '%;">' +
'<div id="menu"/>' +
'<' + tag + ' id="' + Utils.uuid() + '" class="charts-viewport-canvas">' +
'<' + tag + ' id="' + Utils.uid() + '" class="charts-viewport-canvas">' +
'</div>';
}
contrib/nagios/check_galaxy.py
+1 -1
View File
@@ -217,7 +217,7 @@ class Browser:
for item in self.history_contents:
self.get(item['url'])
hda = json.loads(tc.browser.get_html())
if hda['deleted'] == False:
if hda['deleted'] is False:
rval.append(hda)
return rval
cron/add_manual_builds.py
+17 -13
View File
@@ -7,33 +7,37 @@ Usage:
python add_manual_builds.py input_file builds.txt chrom_length_dir
"""
import sys,os
import os
import sys
def add_manual_builds(input_file, build_file, chr_dir):
#determine existing builds, so as to not overwrite
# determine existing builds, so as to not overwrite
existing_builds = []
for line in open(build_file):
try:
if line.startswith("#"): continue
existing_builds.append(line.replace("\n","").replace("\r","").split("\t")[0])
if line.startswith("#"):
continue
existing_builds.append(line.replace("\n", "").replace("\r", "").split("\t")[0])
except:
continue
build_file_out = open(build_file,'a')
build_file_out = open(build_file, 'a')
for line in open(input_file):
try:
fields = line.replace("\n","").replace("\r","").split("\t")
fields = line.replace("\n", "").replace("\r", "").split("\t")
build = fields.pop(0)
if build in existing_builds: continue # if build exists, leave alone
if build in existing_builds:
continue # if build exists, leave alone
name = fields.pop(0)
try: # get chrom lens if included in file, otherwise still add build
try: # get chrom lens if included in file, otherwise still add build
chrs = fields.pop(0).split(",")
except:
chrs = []
print>>build_file_out, build+"\t"+name+" ("+build+")"
if chrs: # create len file if provided chrom lens
chr_len_out=open( os.path.join(chr_dir,build+".len"),'w')
print>>build_file_out, build + "\t" + name + " (" + build + ")"
if chrs: # create len file if provided chrom lens
chr_len_out = open(os.path.join(chr_dir, build + ".len"), 'w')
for chr in chrs:
print>>chr_len_out, chr.replace("=","\t")
print>>chr_len_out, chr.replace("=", "\t")
chr_len_out.close()
except:
continue
@@ -46,4 +50,4 @@ if __name__ == "__main__":
input_file = sys.argv[1]
build_file = sys.argv[2]
chr_dir = sys.argv[3]
add_manual_builds(input_file,build_file,chr_dir)
add_manual_builds(input_file, build_file, chr_dir)
cron/build_chrom_db.py
+13 -9
View File
@@ -18,6 +18,7 @@ import parse_builds
import urllib
import fileinput
def getchrominfo(url, db):
tableURL = "http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?"
URL = tableURL + urllib.urlencode({
@@ -28,13 +29,14 @@ def getchrominfo(url, db):
"hgta_group" : "allTables",
"hgta_table" : "chromInfo",
"hgta_track" : db,
"hgta_regionType":"",
"position":"",
"hgta_doTopSubmit" : "get info"})
"hgta_regionType": "",
"position": "",
"hgta_doTopSubmit": "get info"})
page = urllib.urlopen(URL)
for line in page:
line = line.rstrip( "\r\n" )
if line.startswith("#"): continue
if line.startswith("#"):
continue
fields = line.split("\t")
if len(fields) > 1:
yield [fields[0], fields[1]]
@@ -49,7 +51,8 @@ if __name__ == "__main__":
try:
buildfile = fileinput.FileInput(sys.argv[2])
for line in buildfile:
if line.startswith("#"): continue
if line.startswith("#"):
continue
builds.append(line.split("\t")[0])
except:
print "Bad input file."
@@ -62,9 +65,10 @@ if __name__ == "__main__":
print "Unable to retrieve builds."
sys.exit(1)
for build in builds:
if build == "?":continue # no lengths for unspecified chrom
if build == "?":
continue # no lengths for unspecified chrom
outfile = open(dbpath + build + ".len", "w")
print "Retrieving "+build
for chrominfo in getchrominfo("http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?",build):
print >> outfile,"\t".join(chrominfo)
print "Retrieving " + build
for chrominfo in getchrominfo("http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?", build):
print >> outfile, "\t".join(chrominfo)
outfile.close()
cron/parse_builds_3_sites.py
+10 -14
View File
@@ -3,23 +3,19 @@
Connects to sites and determines which builds are available at each.
"""
import sys
import urllib
import xml.etree.ElementTree as ElementTree
sites = ['http://genome.ucsc.edu/cgi-bin/',
'http://archaea.ucsc.edu/cgi-bin/',
'http://genome-test.cse.ucsc.edu/cgi-bin/'
]
names = ['main',
'archaea',
'test'
]
'http://archaea.ucsc.edu/cgi-bin/',
'http://genome-test.cse.ucsc.edu/cgi-bin/']
names = ['main', 'archaea', 'test']
def main():
for i in range(len(sites)):
site = sites[i]+"das/dsn"
trackurl = sites[i]+"hgTracks?"
site = sites[i] + "das/dsn"
trackurl = sites[i] + "hgTracks?"
builds = []
try:
page = urllib.urlopen(site)
@@ -32,17 +28,17 @@ def main():
except:
print "#Invalid xml passed back from " + site
continue
print "#Harvested from",site
print "#Harvested from", site
for dsn in tree:
build = dsn.find("SOURCE").attrib['id']
builds.append(build)
build_dict = {}
for build in builds:
build_dict[build]=0
build_dict[build] = 0
builds = build_dict.keys()
yield [names[i],trackurl,builds]
yield [names[i], trackurl, builds]
if __name__ == "__main__":
for site in main():
print site[0]+"\t"+site[1]+"\t"+",".join(site[2])
print site[0] + "\t" + site[1] + "\t" + ",".join(site[2])
doc/patch.py
+1 -1
View File
@@ -118,7 +118,7 @@ def fromfile(filename):
fp = open(filename, "rb")
res = patchset.parse(fp)
fp.close()
if res == True:
if res is True:
return patchset
return False
doc/source/api_doc.rst
+282
View File
@@ -0,0 +1,282 @@
Galaxy API Documentation
************************
Background
==========
In addition to being accessible through a web interface, Galaxy can also be
accessed programmatically, through shell scripts and other programs. The web
interface is appropriate for things like exploratory analysis, visualization,
construction of workflows, and rerunning workflows on new datasets.
The web interface is less suitable for things like
- Connecting a Galaxy instance directly to your sequencer and running
workflows whenever data is ready.
- Running a workflow against multiple datasets (which can be done with the
web interface, but is tedious).
- When the analysis involves complex control, such as looping and
branching.
The Galaxy API addresses these and other situations by exposing Galaxy
internals through an additional interface, known as an Application Programming
Interface, or API.
Quickstart
==========
Log in as your user, navigate to the API Keys page in the User menu, and
generate a new API key. Make a note of the API key, and then pull up a
terminal. Now we'll use the display.py script in your galaxy/scripts/api
directory for a short example::
% ./display.py my_key http://localhost:4096/api/histories
Collection Members
------------------
#1: /api/histories/8c49be448cfe29bc
name: Unnamed history
id: 8c49be448cfe29bc
#2: /api/histories/33b43b4e7093c91f
name: output test
id: 33b43b4e7093c91f
The result is a Collection of the histories of the user specified by the API
key (you). To look at the details of a particular history, say #1 above, do
the following::
% ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc
Member Information
------------------
state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0}
state: ok
contents_url: /api/histories/8c49be448cfe29bc/contents
id: 8c49be448cfe29bc
name: Unnamed history
This gives detailed information about the specific member in question, in this
case the History. To view history contents, do the following::
% ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents
Collection Members
------------------
#1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
name: Pasted Entry
type: file
id: 6f91353f3eb0fa4a
What we have here is another Collection of items containing all of the datasets
in this particular history. Finally, to view details of a particular dataset
in this collection, execute the following::
% ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
Member Information
------------------
misc_blurb: 1 line
name: Pasted Entry
data_type: txt
deleted: False
file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat
state: ok
download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt
visible: True
genome_build: ?
model_class: HistoryDatasetAssociation
file_size: 17
metadata_data_lines: 1
id: 6f91353f3eb0fa4a
misc_info: uploaded txt file
metadata_dbkey: ?
And now you've successfully used the API to request and select a history,
browse the contents of that history, and then look at detailed information
about a particular dataset.
For a more comprehensive Data Library example, set the following option in your
galaxy.ini as well, and restart galaxy again::
admin_users = you@example.org
library_import_dir = /path/to/some/directory
In the directory you specified for 'library_import_dir', create some
subdirectories, and put (or symlink) files to import into Galaxy into those
subdirectories.
In Galaxy, create an account that matches the address you put in 'admin_users',
then browse to that user's preferences and generate a new API Key. Copy the
key to your clipboard and then use these scripts::
% ./display.py my_key http://localhost:4096/api/libraries
Collection Members
------------------
0 elements in collection
% ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library'
Response
--------
/api/libraries/f3f73e481f432006
name: api_test
id: f3f73e481f432006
% ./display.py my_key http://localhost:4096/api/libraries
Collection Members
------------------
/api/libraries/f3f73e481f432006
name: api_test
id: f3f73e481f432006
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006
Member Information
------------------
synopsis: None
contents_url: /api/libraries/f3f73e481f432006/contents
description: API Test Library
name: api_test
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents
Collection Members
------------------
/api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
name: /
type: folder
id: 28202595c0d2591f61ddda595d2c3670
% ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1'
Response
--------
/api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
name: api_test_folder1
id: 28202595c0d2591fa4f9089d2303fd89
% ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19
Response
--------
/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
name: 2.bed
id: e9ef7fdb2db87d7b
/api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
name: 3.bed
id: 3b7f6a31f80a5018
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents
Collection Members
------------------
/api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
name: /
type: folder
id: 28202595c0d2591f61ddda595d2c3670
/api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
name: /api_test_folder1
type: folder
id: 28202595c0d2591fa4f9089d2303fd89
/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
name: /api_test_folder1/2.bed
type: file
id: e9ef7fdb2db87d7b
/api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
name: /api_test_folder1/3.bed
type: file
id: 3b7f6a31f80a5018
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
Member Information
------------------
misc_blurb: 68 regions
metadata_endCol: 3
data_type: bed
metadata_columns: 6
metadata_nameCol: 4
uploaded_by: nate@...
metadata_strandCol: 6
name: 2.bed
genome_build: hg19
metadata_comment_lines: None
metadata_startCol: 2
metadata_chromCol: 1
file_size: 4272
metadata_data_lines: 68
message:
metadata_dbkey: hg19
misc_info: uploaded bed file
date_uploaded: 2010-06-22T17:01:51.266119
metadata_column_types: str, int, int, str, int, str
Other parameters are valid when uploading, they are the same parameters as are
used in the web form, like 'link_data_only' and etc.
The request and response format should be considered alpha and are subject to change.
API Design Guidelines
=====================
The following section outlines guidelines related to extending and/or modifing
the Galaxy API. The Galaxy API has grown in an ad-hoc fashion over time by
many contributors and so clients SHOULD NOT expect the API will conform to
these guidelines - but developers contributing to the Galaxy API SHOULD follow
these guidelines.
- API functionality should include docstring documentation for consumption
by readthedocs.org.
- Developers should familiarize themselves with the HTTP status code definitions
http://www.w3.org/Protocols/rfc2616/rfc2616-sec10.html. The API responses
should properly set the status code according to the result - in particular
2XX responses should be used for successful requests, 4XX for various
kinds of client errors, and 5XX for the errors on the server side.
- If there is an error processing some part of request (one item in a list
for instance), the status code should be set to reflect the error and the
partial result may or may not be returned depending on the controller -
this behavior should be documented.
- API methods should throw a finite number of exceptions
(defined in :doc:`galaxy.exceptions`) and these should subclass
`MessageException` and not paste/wsgi HTTP exceptions. When possible,
the framework itself should be responsible catching these exceptions,
setting the status code, and building an error response.
- Error responses should not consist of plain text strings - they should be
dictionaries describing the error and containing the following::
{
"status_code": 400,
"err_code": 400007,
"err_msg": "Request contained invalid parameter, action could not be completed.",
"type": "error",
"extra_error_info": "Extra information."
}
Various error conditions (once a format has been chosen and framework to
enforce it in place) should be spelled out in this document.
- Backward compatibility is important and should be maintained when possible.
If changing behavior in a non-backward compatibile way please ensure one
of the following holds - there is a strong reason to believe no consumers
depend on a behavior, the behavior is effectively broken, or the API
method being modified has not been part of a tagged dist release.
The following bullet points represent good practices more than guidelines, please
consider them when modifying the API.
- Functionality should not be copied and pasted between controllers -
consider refactoring functionality into associated classes or short of
that into Mixins (http://en.wikipedia.org/wiki/Composition_over_inheritance)
or into Managers (:doc:`galaxy.managers`).
- API additions are more permanent changes to Galaxy than many other potential
changes and so a second opinion on API changes should be sought. (Consider a
pull request!)
- New API functionality should include functional tests. These functional
tests should be implemented in Python and placed in
`test/functional/api`. (Once such a framework is in place - it is not
right now).
- Changes to reflect modifications to the API should be pushed upstream to
the BioBlend project if possible.
Longer term goals/notes.
- It would be advantageous to have a clearer separation of anonymous and
admin handling functionality.
- If at some point in the future, functionality needs to be added that
breaks backward compatibility in a significant way to a component used by
the community - a "dev" variant of the API will be established and
the community should be alerted and given a timeframe for when the old
behavior will be replaced with the new behavior.
- Consistent standards for range-based requests, batch requests, filtered
requests, etc... should be established and documented here.
.. include:: lib/galaxy.webapps.galaxy.api.rst
doc/source/conf.py
+2 -4
View File
@@ -17,8 +17,6 @@ import sys, os, datetime
####### REQUIRED GALAXY INCLUDES
sys.path.append(os.path.join(os.getcwd(), '../../lib'))
import galaxy
from galaxy import eggs
#######
@@ -103,7 +101,7 @@ pygments_style = 'sphinx'
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
html_theme = 'default'
html_theme = 'sphinx_rtd_theme'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
@@ -274,6 +272,6 @@ class Mock(object):
return Mock()
# adding pbs_python, DRMAA_python, markupsafe, and drmaa here had no effect.
MOCK_MODULES = ['tables', 'decorator', 'numpy']
MOCK_MODULES = ['tables', 'decorator']
for mod_name in MOCK_MODULES:
sys.modules[mod_name] = Mock()
doc/source/index.rst
+1 -1
View File
@@ -42,7 +42,7 @@ Contents
.. toctree::
:maxdepth: 5
API Documentation <lib/galaxy.webapps.galaxy.api>
API Documentation <api_doc>
Application Documentation <lib/modules>
doc/source/lib/fpconst.rst
-7
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@@ -1,7 +0,0 @@
fpconst Module
==============
.. automodule:: fpconst
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.actions.rst
+13 -4
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@@ -1,11 +1,20 @@
actions Package
===============
galaxy.actions package
======================
:mod:`admin` Module
-------------------
.. automodule:: galaxy.actions
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.actions.admin module
---------------------------
.. automodule:: galaxy.actions.admin
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.auth.providers.rst
+36
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@@ -0,0 +1,36 @@
galaxy.auth.providers package
=============================
.. automodule:: galaxy.auth.providers
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.auth.providers.alwaysreject module
-----------------------------------------
.. automodule:: galaxy.auth.providers.alwaysreject
:members:
:undoc-members:
:show-inheritance:
galaxy.auth.providers.ldap_ad module
------------------------------------
.. automodule:: galaxy.auth.providers.ldap_ad
:members:
:undoc-members:
:show-inheritance:
galaxy.auth.providers.localdb module
------------------------------------
.. automodule:: galaxy.auth.providers.localdb
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.auth.rst
+15
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@@ -0,0 +1,15 @@
galaxy.auth package
===================
.. automodule:: galaxy.auth
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
galaxy.auth.providers
doc/source/lib/galaxy.dataset_collections.rst
+67
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@@ -0,0 +1,67 @@
galaxy.dataset_collections package
==================================
.. automodule:: galaxy.dataset_collections
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
galaxy.dataset_collections.types
Submodules
----------
galaxy.dataset_collections.builder module
-----------------------------------------
.. automodule:: galaxy.dataset_collections.builder
:members:
:undoc-members:
:show-inheritance:
galaxy.dataset_collections.matching module
------------------------------------------
.. automodule:: galaxy.dataset_collections.matching
:members:
:undoc-members:
:show-inheritance:
galaxy.dataset_collections.registry module
------------------------------------------
.. automodule:: galaxy.dataset_collections.registry
:members:
:undoc-members:
:show-inheritance:
galaxy.dataset_collections.structure module
-------------------------------------------
.. automodule:: galaxy.dataset_collections.structure
:members:
:undoc-members:
:show-inheritance:
galaxy.dataset_collections.subcollections module
------------------------------------------------
.. automodule:: galaxy.dataset_collections.subcollections
:members:
:undoc-members:
:show-inheritance:
galaxy.dataset_collections.type_description module
--------------------------------------------------
.. automodule:: galaxy.dataset_collections.type_description
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.dataset_collections.types.rst
+28
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@@ -0,0 +1,28 @@
galaxy.dataset_collections.types package
========================================
.. automodule:: galaxy.dataset_collections.types
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.dataset_collections.types.list module
--------------------------------------------
.. automodule:: galaxy.dataset_collections.types.list
:members:
:undoc-members:
:show-inheritance:
galaxy.dataset_collections.types.paired module
----------------------------------------------
.. automodule:: galaxy.dataset_collections.types.paired
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.datatypes.converters.rst
+66 -81
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@@ -1,259 +1,244 @@
converters Package
==================
galaxy.datatypes.converters package
===================================
:mod:`bed_to_genetrack_converter` Module
----------------------------------------
.. automodule:: galaxy.datatypes.converters.bed_to_genetrack_converter
.. automodule:: galaxy.datatypes.converters
:members:
:undoc-members:
:show-inheritance:
:mod:`bed_to_gff_converter` Module
----------------------------------
Submodules
----------
galaxy.datatypes.converters.bed_to_gff_converter module
-------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.bed_to_gff_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`bedgraph_to_array_tree_converter` Module
----------------------------------------------
galaxy.datatypes.converters.bedgraph_to_array_tree_converter module
-------------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.bedgraph_to_array_tree_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`bgzip` Module
-------------------
galaxy.datatypes.converters.bgzip module
----------------------------------------
.. automodule:: galaxy.datatypes.converters.bgzip
:members:
:undoc-members:
:show-inheritance:
:mod:`fasta_to_len` Module
--------------------------
galaxy.datatypes.converters.fasta_to_len module
-----------------------------------------------
.. automodule:: galaxy.datatypes.converters.fasta_to_len
:members:
:undoc-members:
:show-inheritance:
:mod:`fasta_to_tabular_converter` Module
----------------------------------------
galaxy.datatypes.converters.fasta_to_tabular_converter module
-------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.fasta_to_tabular_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`fastq_to_fqtoc` Module
----------------------------
galaxy.datatypes.converters.fastq_to_fqtoc module
-------------------------------------------------
.. automodule:: galaxy.datatypes.converters.fastq_to_fqtoc
:members:
:undoc-members:
:show-inheritance:
:mod:`fastqsolexa_to_fasta_converter` Module
--------------------------------------------
galaxy.datatypes.converters.fastqsolexa_to_fasta_converter module
-----------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.fastqsolexa_to_fasta_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`fastqsolexa_to_qual_converter` Module
-------------------------------------------
galaxy.datatypes.converters.fastqsolexa_to_qual_converter module
----------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.fastqsolexa_to_qual_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`gff_to_bed_converter` Module
----------------------------------
galaxy.datatypes.converters.gff_to_bed_converter module
-------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.gff_to_bed_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`gff_to_interval_index_converter` Module
---------------------------------------------
galaxy.datatypes.converters.gff_to_interval_index_converter module
------------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.gff_to_interval_index_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`interval_to_bed_converter` Module
---------------------------------------
galaxy.datatypes.converters.interval_to_bed_converter module
------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.interval_to_bed_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`interval_to_bedstrict_converter` Module
---------------------------------------------
galaxy.datatypes.converters.interval_to_bedstrict_converter module
------------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.interval_to_bedstrict_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`interval_to_coverage` Module
----------------------------------
galaxy.datatypes.converters.interval_to_coverage module
-------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.interval_to_coverage
:members:
:undoc-members:
:show-inheritance:
:mod:`interval_to_fli` Module
-----------------------------
galaxy.datatypes.converters.interval_to_fli module
--------------------------------------------------
.. automodule:: galaxy.datatypes.converters.interval_to_fli
:members:
:undoc-members:
:show-inheritance:
:mod:`interval_to_interval_index_converter` Module
--------------------------------------------------
galaxy.datatypes.converters.interval_to_interval_index_converter module
-----------------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.interval_to_interval_index_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`interval_to_summary_tree_converter` Module
------------------------------------------------
.. automodule:: galaxy.datatypes.converters.interval_to_summary_tree_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`interval_to_tabix_converter` Module
-----------------------------------------
galaxy.datatypes.converters.interval_to_tabix_converter module
--------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.interval_to_tabix_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`lped_to_fped_converter` Module
------------------------------------
galaxy.datatypes.converters.lped_to_fped_converter module
---------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.lped_to_fped_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`lped_to_pbed_converter` Module
------------------------------------
galaxy.datatypes.converters.lped_to_pbed_converter module
---------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.lped_to_pbed_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`maf_to_fasta_converter` Module
------------------------------------
galaxy.datatypes.converters.maf_to_fasta_converter module
---------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.maf_to_fasta_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`maf_to_interval_converter` Module
---------------------------------------
galaxy.datatypes.converters.maf_to_interval_converter module
------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.maf_to_interval_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`pbed_ldreduced_converter` Module
--------------------------------------
galaxy.datatypes.converters.pbed_ldreduced_converter module
-----------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.pbed_ldreduced_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`pbed_to_lped_converter` Module
------------------------------------
galaxy.datatypes.converters.pbed_to_lped_converter module
---------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.pbed_to_lped_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`picard_interval_list_to_bed6_converter` Module
----------------------------------------------------
galaxy.datatypes.converters.picard_interval_list_to_bed6_converter module
-------------------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.picard_interval_list_to_bed6_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`sam_or_bam_to_summary_tree_converter` Module
--------------------------------------------------
galaxy.datatypes.converters.pileup_to_interval_index_converter module
---------------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.sam_or_bam_to_summary_tree_converter
.. automodule:: galaxy.datatypes.converters.pileup_to_interval_index_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`sam_to_bam` Module
------------------------
galaxy.datatypes.converters.sam_to_bam module
---------------------------------------------
.. automodule:: galaxy.datatypes.converters.sam_to_bam
:members:
:undoc-members:
:show-inheritance:
:mod:`vcf_to_interval_index_converter` Module
---------------------------------------------
galaxy.datatypes.converters.vcf_to_interval_index_converter module
------------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.vcf_to_interval_index_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`vcf_to_summary_tree_converter` Module
-------------------------------------------
.. automodule:: galaxy.datatypes.converters.vcf_to_summary_tree_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`vcf_to_vcf_bgzip` Module
------------------------------
galaxy.datatypes.converters.vcf_to_vcf_bgzip module
---------------------------------------------------
.. automodule:: galaxy.datatypes.converters.vcf_to_vcf_bgzip
:members:
:undoc-members:
:show-inheritance:
:mod:`wiggle_to_array_tree_converter` Module
--------------------------------------------
galaxy.datatypes.converters.wiggle_to_array_tree_converter module
-----------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.wiggle_to_array_tree_converter
:members:
:undoc-members:
:show-inheritance:
:mod:`wiggle_to_simple_converter` Module
----------------------------------------
galaxy.datatypes.converters.wiggle_to_simple_converter module
-------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.wiggle_to_simple_converter
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.datatypes.dataproviders.rst
+84
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@@ -0,0 +1,84 @@
galaxy.datatypes.dataproviders package
======================================
.. automodule:: galaxy.datatypes.dataproviders
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.datatypes.dataproviders.base module
------------------------------------------
.. automodule:: galaxy.datatypes.dataproviders.base
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.dataproviders.chunk module
-------------------------------------------
.. automodule:: galaxy.datatypes.dataproviders.chunk
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.dataproviders.column module
--------------------------------------------
.. automodule:: galaxy.datatypes.dataproviders.column
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.dataproviders.dataset module
---------------------------------------------
.. automodule:: galaxy.datatypes.dataproviders.dataset
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.dataproviders.decorators module
------------------------------------------------
.. automodule:: galaxy.datatypes.dataproviders.decorators
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.dataproviders.exceptions module
------------------------------------------------
.. automodule:: galaxy.datatypes.dataproviders.exceptions
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.dataproviders.external module
----------------------------------------------
.. automodule:: galaxy.datatypes.dataproviders.external
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.dataproviders.hierarchy module
-----------------------------------------------
.. automodule:: galaxy.datatypes.dataproviders.hierarchy
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.dataproviders.line module
------------------------------------------
.. automodule:: galaxy.datatypes.dataproviders.line
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.datatypes.display_applications.rst
+17 -8
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@@ -1,27 +1,36 @@
display_applications Package
============================
galaxy.datatypes.display_applications package
=============================================
:mod:`application` Module
-------------------------
.. automodule:: galaxy.datatypes.display_applications
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.datatypes.display_applications.application module
--------------------------------------------------------
.. automodule:: galaxy.datatypes.display_applications.application
:members:
:undoc-members:
:show-inheritance:
:mod:`parameters` Module
------------------------
galaxy.datatypes.display_applications.parameters module
-------------------------------------------------------
.. automodule:: galaxy.datatypes.display_applications.parameters
:members:
:undoc-members:
:show-inheritance:
:mod:`util` Module
------------------
galaxy.datatypes.display_applications.util module
-------------------------------------------------
.. automodule:: galaxy.datatypes.display_applications.util
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.datatypes.rst
+184 -142
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@@ -1,146 +1,7 @@
datatypes Package
=================
galaxy.datatypes package
========================
:mod:`assembly` Module
----------------------
.. automodule:: galaxy.datatypes.assembly
:members:
:undoc-members:
:show-inheritance:
:mod:`binary` Module
--------------------
.. automodule:: galaxy.datatypes.binary
:members:
:undoc-members:
:show-inheritance:
:mod:`checkers` Module
----------------------
.. automodule:: galaxy.datatypes.checkers
:members:
:undoc-members:
:show-inheritance:
:mod:`chrominfo` Module
-----------------------
.. automodule:: galaxy.datatypes.chrominfo
:members:
:undoc-members:
:show-inheritance:
:mod:`coverage` Module
----------------------
.. automodule:: galaxy.datatypes.coverage
:members:
:undoc-members:
:show-inheritance:
:mod:`data` Module
------------------
.. automodule:: galaxy.datatypes.data
:members:
:undoc-members:
:show-inheritance:
:mod:`genetics` Module
----------------------
.. automodule:: galaxy.datatypes.genetics
:members:
:undoc-members:
:show-inheritance:
:mod:`images` Module
--------------------
.. automodule:: galaxy.datatypes.images
:members:
:undoc-members:
:show-inheritance:
:mod:`interval` Module
----------------------
.. automodule:: galaxy.datatypes.interval
:members:
:undoc-members:
:show-inheritance:
:mod:`metadata` Module
----------------------
.. automodule:: galaxy.datatypes.metadata
:members:
:undoc-members:
:show-inheritance:
:mod:`ngsindex` Module
----------------------
.. automodule:: galaxy.datatypes.ngsindex
:members:
:undoc-members:
:show-inheritance:
:mod:`qualityscore` Module
--------------------------
.. automodule:: galaxy.datatypes.qualityscore
:members:
:undoc-members:
:show-inheritance:
:mod:`registry` Module
----------------------
.. automodule:: galaxy.datatypes.registry
:members:
:undoc-members:
:show-inheritance:
:mod:`sequence` Module
----------------------
.. automodule:: galaxy.datatypes.sequence
:members:
:undoc-members:
:show-inheritance:
:mod:`sniff` Module
-------------------
.. automodule:: galaxy.datatypes.sniff
:members:
:undoc-members:
:show-inheritance:
:mod:`tabular` Module
---------------------
.. automodule:: galaxy.datatypes.tabular
:members:
:undoc-members:
:show-inheritance:
:mod:`tracks` Module
--------------------
.. automodule:: galaxy.datatypes.tracks
:members:
:undoc-members:
:show-inheritance:
:mod:`xml` Module
-----------------
.. automodule:: galaxy.datatypes.xml
.. automodule:: galaxy.datatypes
:members:
:undoc-members:
:show-inheritance:
@@ -151,6 +12,187 @@ Subpackages
.. toctree::
galaxy.datatypes.converters
galaxy.datatypes.dataproviders
galaxy.datatypes.display_applications
galaxy.datatypes.util
Submodules
----------
galaxy.datatypes.assembly module
--------------------------------
.. automodule:: galaxy.datatypes.assembly
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.binary module
------------------------------
.. automodule:: galaxy.datatypes.binary
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.checkers module
--------------------------------
.. automodule:: galaxy.datatypes.checkers
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.chrominfo module
---------------------------------
.. automodule:: galaxy.datatypes.chrominfo
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.coverage module
--------------------------------
.. automodule:: galaxy.datatypes.coverage
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.data module
----------------------------
.. automodule:: galaxy.datatypes.data
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.genetics module
--------------------------------
.. automodule:: galaxy.datatypes.genetics
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.graph module
-----------------------------
.. automodule:: galaxy.datatypes.graph
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.images module
------------------------------
.. automodule:: galaxy.datatypes.images
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.interval module
--------------------------------
.. automodule:: galaxy.datatypes.interval
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.metadata module
--------------------------------
.. automodule:: galaxy.datatypes.metadata
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.msa module
---------------------------
.. automodule:: galaxy.datatypes.msa
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.ngsindex module
--------------------------------
.. automodule:: galaxy.datatypes.ngsindex
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.proteomics module
----------------------------------
.. automodule:: galaxy.datatypes.proteomics
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.qualityscore module
------------------------------------
.. automodule:: galaxy.datatypes.qualityscore
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.registry module
--------------------------------
.. automodule:: galaxy.datatypes.registry
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.sequence module
--------------------------------
.. automodule:: galaxy.datatypes.sequence
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.sniff module
-----------------------------
.. automodule:: galaxy.datatypes.sniff
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.tabular module
-------------------------------
.. automodule:: galaxy.datatypes.tabular
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.text module
----------------------------
.. automodule:: galaxy.datatypes.text
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.tracks module
------------------------------
.. automodule:: galaxy.datatypes.tracks
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.xml module
---------------------------
.. automodule:: galaxy.datatypes.xml
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.datatypes.util.rst
+18 -9
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@@ -1,27 +1,36 @@
util Package
============
:mod:`util` Package
-------------------
galaxy.datatypes.util package
=============================
.. automodule:: galaxy.datatypes.util
:members:
:undoc-members:
:show-inheritance:
:mod:`gff_util` Module
----------------------
Submodules
----------
galaxy.datatypes.util.generic_util module
-----------------------------------------
.. automodule:: galaxy.datatypes.util.generic_util
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.util.gff_util module
-------------------------------------
.. automodule:: galaxy.datatypes.util.gff_util
:members:
:undoc-members:
:show-inheritance:
:mod:`image_util` Module
------------------------
galaxy.datatypes.util.image_util module
---------------------------------------
.. automodule:: galaxy.datatypes.util.image_util
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.eggs.rst
+10 -9
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@@ -1,27 +1,28 @@
eggs Package
============
:mod:`eggs` Package
-------------------
galaxy.eggs package
===================
.. automodule:: galaxy.eggs
:members:
:undoc-members:
:show-inheritance:
:mod:`dist` Module
------------------
Submodules
----------
galaxy.eggs.dist module
-----------------------
.. automodule:: galaxy.eggs.dist
:members:
:undoc-members:
:show-inheritance:
:mod:`scramble` Module
----------------------
galaxy.eggs.scramble module
---------------------------
.. automodule:: galaxy.eggs.scramble
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.exceptions.rst
+14 -5
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@@ -1,11 +1,20 @@
exceptions Package
==================
:mod:`exceptions` Package
-------------------------
galaxy.exceptions package
=========================
.. automodule:: galaxy.exceptions
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.exceptions.error_codes module
------------------------------------
.. automodule:: galaxy.exceptions.error_codes
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.external_services.result_handlers.rst
+13 -4
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@@ -1,11 +1,20 @@
result_handlers Package
=======================
galaxy.external_services.result_handlers package
================================================
:mod:`basic` Module
-------------------
.. automodule:: galaxy.external_services.result_handlers
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.external_services.result_handlers.basic module
-----------------------------------------------------
.. automodule:: galaxy.external_services.result_handlers.basic
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.external_services.rst
+31 -22
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@@ -1,26 +1,7 @@
external_services Package
=========================
galaxy.external_services package
================================
:mod:`actions` Module
---------------------
.. automodule:: galaxy.external_services.actions
:members:
:undoc-members:
:show-inheritance:
:mod:`parameters` Module
------------------------
.. automodule:: galaxy.external_services.parameters
:members:
:undoc-members:
:show-inheritance:
:mod:`service` Module
---------------------
.. automodule:: galaxy.external_services.service
.. automodule:: galaxy.external_services
:members:
:undoc-members:
:show-inheritance:
@@ -32,3 +13,31 @@ Subpackages
galaxy.external_services.result_handlers
Submodules
----------
galaxy.external_services.actions module
---------------------------------------
.. automodule:: galaxy.external_services.actions
:members:
:undoc-members:
:show-inheritance:
galaxy.external_services.parameters module
------------------------------------------
.. automodule:: galaxy.external_services.parameters
:members:
:undoc-members:
:show-inheritance:
galaxy.external_services.service module
---------------------------------------
.. automodule:: galaxy.external_services.service
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.forms.rst
+13 -4
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@@ -1,11 +1,20 @@
forms Package
=============
galaxy.forms package
====================
:mod:`forms` Module
-------------------
.. automodule:: galaxy.forms
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.forms.forms module
-------------------------
.. automodule:: galaxy.forms.forms
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.actions.rst
+8 -7
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@@ -1,19 +1,20 @@
actions Package
===============
:mod:`actions` Package
----------------------
galaxy.jobs.actions package
===========================
.. automodule:: galaxy.jobs.actions
:members:
:undoc-members:
:show-inheritance:
:mod:`post` Module
------------------
Submodules
----------
galaxy.jobs.actions.post module
-------------------------------
.. automodule:: galaxy.jobs.actions.post
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.deferred.rst
+12 -35
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@@ -1,59 +1,36 @@
deferred Package
================
:mod:`deferred` Package
-----------------------
galaxy.jobs.deferred package
============================
.. automodule:: galaxy.jobs.deferred
:members:
:undoc-members:
:show-inheritance:
:mod:`data_transfer` Module
---------------------------
Submodules
----------
galaxy.jobs.deferred.data_transfer module
-----------------------------------------
.. automodule:: galaxy.jobs.deferred.data_transfer
:members:
:undoc-members:
:show-inheritance:
:mod:`genome_index` Module
--------------------------
.. automodule:: galaxy.jobs.deferred.genome_index
:members:
:undoc-members:
:show-inheritance:
:mod:`genome_transfer` Module
-----------------------------
.. automodule:: galaxy.jobs.deferred.genome_transfer
:members:
:undoc-members:
:show-inheritance:
:mod:`liftover_transfer` Module
-------------------------------
.. automodule:: galaxy.jobs.deferred.liftover_transfer
:members:
:undoc-members:
:show-inheritance:
:mod:`manual_data_transfer` Module
----------------------------------
galaxy.jobs.deferred.manual_data_transfer module
------------------------------------------------
.. automodule:: galaxy.jobs.deferred.manual_data_transfer
:members:
:undoc-members:
:show-inheritance:
:mod:`pacific_biosciences_smrt_portal` Module
---------------------------------------------
galaxy.jobs.deferred.pacific_biosciences_smrt_portal module
-----------------------------------------------------------
.. automodule:: galaxy.jobs.deferred.pacific_biosciences_smrt_portal
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.metrics.collectl.rst
+44
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@@ -0,0 +1,44 @@
galaxy.jobs.metrics.collectl package
====================================
.. automodule:: galaxy.jobs.metrics.collectl
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.jobs.metrics.collectl.cli module
---------------------------------------
.. automodule:: galaxy.jobs.metrics.collectl.cli
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.metrics.collectl.processes module
---------------------------------------------
.. automodule:: galaxy.jobs.metrics.collectl.processes
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.metrics.collectl.stats module
-----------------------------------------
.. automodule:: galaxy.jobs.metrics.collectl.stats
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.metrics.collectl.subsystems module
----------------------------------------------
.. automodule:: galaxy.jobs.metrics.collectl.subsystems
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.metrics.instrumenters.rst
+60
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@@ -0,0 +1,60 @@
galaxy.jobs.metrics.instrumenters package
=========================================
.. automodule:: galaxy.jobs.metrics.instrumenters
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.jobs.metrics.instrumenters.collectl module
-------------------------------------------------
.. automodule:: galaxy.jobs.metrics.instrumenters.collectl
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.metrics.instrumenters.core module
---------------------------------------------
.. automodule:: galaxy.jobs.metrics.instrumenters.core
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.metrics.instrumenters.cpuinfo module
------------------------------------------------
.. automodule:: galaxy.jobs.metrics.instrumenters.cpuinfo
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.metrics.instrumenters.env module
--------------------------------------------
.. automodule:: galaxy.jobs.metrics.instrumenters.env
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.metrics.instrumenters.meminfo module
------------------------------------------------
.. automodule:: galaxy.jobs.metrics.instrumenters.meminfo
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.metrics.instrumenters.uname module
----------------------------------------------
.. automodule:: galaxy.jobs.metrics.instrumenters.uname
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.metrics.rst
+28
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@@ -0,0 +1,28 @@
galaxy.jobs.metrics package
===========================
.. automodule:: galaxy.jobs.metrics
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
galaxy.jobs.metrics.collectl
galaxy.jobs.metrics.instrumenters
Submodules
----------
galaxy.jobs.metrics.formatting module
-------------------------------------
.. automodule:: galaxy.jobs.metrics.formatting
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.rst
+87 -37
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@@ -1,46 +1,11 @@
jobs Package
============
:mod:`jobs` Package
-------------------
galaxy.jobs package
===================
.. automodule:: galaxy.jobs
:members:
:undoc-members:
:show-inheritance:
:mod:`handler` Module
---------------------
.. automodule:: galaxy.jobs.handler
:members:
:undoc-members:
:show-inheritance:
:mod:`manager` Module
---------------------
.. automodule:: galaxy.jobs.manager
:members:
:undoc-members:
:show-inheritance:
:mod:`mapper` Module
--------------------
.. automodule:: galaxy.jobs.mapper
:members:
:undoc-members:
:show-inheritance:
:mod:`transfer_manager` Module
------------------------------
.. automodule:: galaxy.jobs.transfer_manager
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
@@ -48,7 +13,92 @@ Subpackages
galaxy.jobs.actions
galaxy.jobs.deferred
galaxy.jobs.metrics
galaxy.jobs.rules
galaxy.jobs.runners
galaxy.jobs.splitters
Submodules
----------
galaxy.jobs.command_factory module
----------------------------------
.. automodule:: galaxy.jobs.command_factory
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.datasets module
---------------------------
.. automodule:: galaxy.jobs.datasets
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.error_level module
------------------------------
.. automodule:: galaxy.jobs.error_level
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.handler module
--------------------------
.. automodule:: galaxy.jobs.handler
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.manager module
--------------------------
.. automodule:: galaxy.jobs.manager
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.mapper module
-------------------------
.. automodule:: galaxy.jobs.mapper
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.output_checker module
---------------------------------
.. automodule:: galaxy.jobs.output_checker
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.rule_helper module
------------------------------
.. automodule:: galaxy.jobs.rule_helper
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.stock_rules module
------------------------------
.. automodule:: galaxy.jobs.stock_rules
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.transfer_manager module
-----------------------------------
.. automodule:: galaxy.jobs.transfer_manager
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.runners.cli_job.rst
-19
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@@ -1,19 +0,0 @@
cli_job Package
===============
:mod:`cli_job` Package
----------------------
.. automodule:: galaxy.jobs.runners.cli_job
:members:
:undoc-members:
:show-inheritance:
:mod:`torque` Module
--------------------
.. automodule:: galaxy.jobs.runners.cli_job.torque
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.runners.cli_shell.rst
-19
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@@ -1,19 +0,0 @@
cli_shell Package
=================
:mod:`cli_shell` Package
------------------------
.. automodule:: galaxy.jobs.runners.cli_shell
:members:
:undoc-members:
:show-inheritance:
:mod:`rsh` Module
-----------------
.. automodule:: galaxy.jobs.runners.cli_shell.rsh
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.runners.lwr_client.rst
+132
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@@ -0,0 +1,132 @@
galaxy.jobs.runners.lwr_client package
======================================
.. automodule:: galaxy.jobs.runners.lwr_client
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
galaxy.jobs.runners.lwr_client.staging
galaxy.jobs.runners.lwr_client.transport
Submodules
----------
galaxy.jobs.runners.lwr_client.action_mapper module
---------------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.action_mapper
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr_client.amqp_exchange module
---------------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr_client.amqp_exchange_factory module
-----------------------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange_factory
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr_client.client module
--------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.client
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr_client.config_util module
-------------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.config_util
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr_client.decorators module
------------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.decorators
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr_client.destination module
-------------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.destination
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr_client.interface module
-----------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.interface
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr_client.job_directory module
---------------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.job_directory
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr_client.manager module
---------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.manager
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr_client.object_client module
---------------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.object_client
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr_client.path_mapper module
-------------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.path_mapper
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr_client.setup_handler module
---------------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.setup_handler
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr_client.util module
------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.util
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst
+28
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@@ -0,0 +1,28 @@
galaxy.jobs.runners.lwr_client.staging package
==============================================
.. automodule:: galaxy.jobs.runners.lwr_client.staging
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.jobs.runners.lwr_client.staging.down module
--------------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.staging.down
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr_client.staging.up module
------------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.staging.up
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst
+28
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@@ -0,0 +1,28 @@
galaxy.jobs.runners.lwr_client.transport package
================================================
.. automodule:: galaxy.jobs.runners.lwr_client.transport
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.jobs.runners.lwr_client.transport.curl module
----------------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.transport.curl
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr_client.transport.standard module
--------------------------------------------------------
.. automodule:: galaxy.jobs.runners.lwr_client.transport.standard
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.runners.rst
+88 -63
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@@ -1,76 +1,101 @@
runners Package
===============
:mod:`runners` Package
----------------------
galaxy.jobs.runners package
===========================
.. automodule:: galaxy.jobs.runners
:members:
:undoc-members:
:show-inheritance:
:mod:`cli` Module
-----------------
.. automodule:: galaxy.jobs.runners.cli
:members:
:undoc-members:
:show-inheritance:
:mod:`condor` Module
--------------------
.. automodule:: galaxy.jobs.runners.condor
:members:
:undoc-members:
:show-inheritance:
:mod:`drmaa` Module
-------------------
.. automodule:: galaxy.jobs.runners.drmaa
:members:
:undoc-members:
:show-inheritance:
:mod:`local` Module
-------------------
.. automodule:: galaxy.jobs.runners.local
:members:
:undoc-members:
:show-inheritance:
:mod:`lwr` Module
-----------------
.. automodule:: galaxy.jobs.runners.lwr
:members:
:undoc-members:
:show-inheritance:
:mod:`pbs` Module
-----------------
.. automodule:: galaxy.jobs.runners.pbs
:members:
:undoc-members:
:show-inheritance:
:mod:`tasks` Module
-------------------
.. automodule:: galaxy.jobs.runners.tasks
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
galaxy.jobs.runners.cli_job
galaxy.jobs.runners.cli_shell
galaxy.jobs.runners.lwr_client
galaxy.jobs.runners.state_handlers
galaxy.jobs.runners.util
Submodules
----------
galaxy.jobs.runners.cli module
------------------------------
.. automodule:: galaxy.jobs.runners.cli
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.condor module
---------------------------------
.. automodule:: galaxy.jobs.runners.condor
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.drmaa module
--------------------------------
.. automodule:: galaxy.jobs.runners.drmaa
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.local module
--------------------------------
.. automodule:: galaxy.jobs.runners.local
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.lwr module
------------------------------
.. automodule:: galaxy.jobs.runners.lwr
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.pbs module
------------------------------
.. automodule:: galaxy.jobs.runners.pbs
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.pulsar module
---------------------------------
.. automodule:: galaxy.jobs.runners.pulsar
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.slurm module
--------------------------------
.. automodule:: galaxy.jobs.runners.slurm
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.state_handler_factory module
------------------------------------------------
.. automodule:: galaxy.jobs.runners.state_handler_factory
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.tasks module
--------------------------------
.. automodule:: galaxy.jobs.runners.tasks
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.runners.state_handlers.rst
+20
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@@ -0,0 +1,20 @@
galaxy.jobs.runners.state_handlers package
==========================================
.. automodule:: galaxy.jobs.runners.state_handlers
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.jobs.runners.state_handlers.resubmit module
--------------------------------------------------
.. automodule:: galaxy.jobs.runners.state_handlers.resubmit
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.runners.util.cli.job.rst
+36
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@@ -0,0 +1,36 @@
galaxy.jobs.runners.util.cli.job package
========================================
.. automodule:: galaxy.jobs.runners.util.cli.job
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.jobs.runners.util.cli.job.slurm module
---------------------------------------------
.. automodule:: galaxy.jobs.runners.util.cli.job.slurm
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.util.cli.job.slurm_torque module
----------------------------------------------------
.. automodule:: galaxy.jobs.runners.util.cli.job.slurm_torque
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.util.cli.job.torque module
----------------------------------------------
.. automodule:: galaxy.jobs.runners.util.cli.job.torque
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.runners.util.cli.rst
+28
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@@ -0,0 +1,28 @@
galaxy.jobs.runners.util.cli package
====================================
.. automodule:: galaxy.jobs.runners.util.cli
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
galaxy.jobs.runners.util.cli.job
galaxy.jobs.runners.util.cli.shell
Submodules
----------
galaxy.jobs.runners.util.cli.factory module
-------------------------------------------
.. automodule:: galaxy.jobs.runners.util.cli.factory
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst
+28
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@@ -0,0 +1,28 @@
galaxy.jobs.runners.util.cli.shell package
==========================================
.. automodule:: galaxy.jobs.runners.util.cli.shell
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.jobs.runners.util.cli.shell.local module
-----------------------------------------------
.. automodule:: galaxy.jobs.runners.util.cli.shell.local
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.util.cli.shell.rsh module
---------------------------------------------
.. automodule:: galaxy.jobs.runners.util.cli.shell.rsh
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.runners.util.condor.rst
+8
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@@ -0,0 +1,8 @@
galaxy.jobs.runners.util.condor package
=======================================
.. automodule:: galaxy.jobs.runners.util.condor
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.runners.util.job_script.rst
+8
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@@ -0,0 +1,8 @@
galaxy.jobs.runners.util.job_script package
===========================================
.. automodule:: galaxy.jobs.runners.util.job_script
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.runners.util.rst
+45
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@@ -0,0 +1,45 @@
galaxy.jobs.runners.util package
================================
.. automodule:: galaxy.jobs.runners.util
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
galaxy.jobs.runners.util.cli
galaxy.jobs.runners.util.condor
galaxy.jobs.runners.util.job_script
Submodules
----------
galaxy.jobs.runners.util.env module
-----------------------------------
.. automodule:: galaxy.jobs.runners.util.env
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.util.external module
----------------------------------------
.. automodule:: galaxy.jobs.runners.util.external
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.util.kill module
------------------------------------
.. automodule:: galaxy.jobs.runners.util.kill
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.splitters.rst
+15 -6
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@@ -1,19 +1,28 @@
splitters Package
=================
galaxy.jobs.splitters package
=============================
:mod:`basic` Module
-------------------
.. automodule:: galaxy.jobs.splitters
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.jobs.splitters.basic module
----------------------------------
.. automodule:: galaxy.jobs.splitters.basic
:members:
:undoc-members:
:show-inheritance:
:mod:`multi` Module
-------------------
galaxy.jobs.splitters.multi module
----------------------------------
.. automodule:: galaxy.jobs.splitters.multi
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.managers.rst
+174 -38
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@@ -1,92 +1,228 @@
managers Package
==================
:mod:`managers` Package
-------------------------
galaxy.managers package
=======================
.. automodule:: galaxy.managers
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
:mod:`api_keys` Module
------------------------------
galaxy.managers.annotatable module
----------------------------------
.. automodule:: galaxy.managers.annotatable
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.api_keys module
-------------------------------
.. automodule:: galaxy.managers.api_keys
:members:
:undoc-members:
:show-inheritance:
:mod:`base` Module
------------------------------
galaxy.managers.base module
---------------------------
.. automodule:: galaxy.managers.base
:members:
:undoc-members:
:show-inheritance:
:mod:`citations` Module
------------------------------
galaxy.managers.citations module
--------------------------------
.. automodule:: galaxy.managers.citations
:members:
:undoc-members:
:show-inheritance:
:mod:`collections` Module
------------------------------
galaxy.managers.collections module
----------------------------------
.. automodule:: galaxy.managers.collections
:members:
:undoc-members:
:show-inheritance:
:mod:`collections_util` Module
------------------------------
galaxy.managers.collections_util module
---------------------------------------
.. automodule:: galaxy.managers.collections_util
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.configuration module
------------------------------------
:mod:`context` Module
.. automodule:: galaxy.managers.configuration
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.containers module
---------------------------------
.. automodule:: galaxy.managers.containers
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.context module
------------------------------
.. automodule:: galaxy.managers.context
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.datasets module
-------------------------------
:mod:`folders` Module
.. automodule:: galaxy.managers.datasets
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.deletable module
--------------------------------
.. automodule:: galaxy.managers.deletable
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.folders module
------------------------------
.. automodule:: galaxy.managers.folders
:members:
:undoc-members:
:show-inheritance:
:mod:`hdas` Module
------------------------------
galaxy.managers.hdas module
---------------------------
.. automodule:: galaxy.managers.hdas
:members:
:undoc-members:
:show-inheritance:
:mod:`histories` Module
------------------------------
galaxy.managers.histories module
--------------------------------
.. automodule:: galaxy.managers.histories
:members:
:undoc-members:
:show-inheritance:
:mod:`lddas` Module
------------------------------
galaxy.managers.lddas module
----------------------------
.. automodule:: galaxy.managers.lddas
:members:
:undoc-members:
:show-inheritance:
:mod:`libraries` Module
------------------------------
galaxy.managers.libraries module
--------------------------------
.. automodule:: galaxy.managers.libraries
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.pages module
----------------------------
:mod:`roles` Module
.. automodule:: galaxy.managers.pages
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.ratable module
------------------------------
.. automodule:: galaxy.managers.ratable
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.rbac_secured module
-----------------------------------
.. automodule:: galaxy.managers.rbac_secured
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.roles module
----------------------------
.. automodule:: galaxy.managers.roles
:members:
:undoc-members:
:show-inheritance:
:mod:`tags` Module
galaxy.managers.secured module
------------------------------
.. automodule:: galaxy.managers.secured
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.sharable module
-------------------------------
.. automodule:: galaxy.managers.sharable
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.taggable module
-------------------------------
.. automodule:: galaxy.managers.taggable
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.tags module
---------------------------
.. automodule:: galaxy.managers.tags
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.users module
----------------------------
:mod:`workflows` Module
------------------------------
.. automodule:: galaxy.managers.users
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.visualizations module
-------------------------------------
.. automodule:: galaxy.managers.visualizations
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.workflows module
--------------------------------
.. automodule:: galaxy.managers.workflows
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.model.migrate.rst
+13 -4
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@@ -1,11 +1,20 @@
migrate Package
===============
galaxy.model.migrate package
============================
:mod:`check` Module
-------------------
.. automodule:: galaxy.model.migrate
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.model.migrate.check module
---------------------------------
.. automodule:: galaxy.model.migrate.check
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.model.orm.ext.rst
-19
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@@ -1,19 +0,0 @@
ext Package
===========
:mod:`ext` Package
------------------
.. automodule:: galaxy.model.orm.ext
:members:
:undoc-members:
:show-inheritance:
:mod:`assignmapper` Module
--------------------------
.. automodule:: galaxy.model.orm.ext.assignmapper
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.model.orm.rst
+28 -10
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@@ -1,26 +1,44 @@
orm Package
===========
:mod:`orm` Package
------------------
galaxy.model.orm package
========================
.. automodule:: galaxy.model.orm
:members:
:undoc-members:
:show-inheritance:
:mod:`logging_connection_proxy` Module
Submodules
----------
galaxy.model.orm.engine_factory module
--------------------------------------
.. automodule:: galaxy.model.orm.engine_factory
:members:
:undoc-members:
:show-inheritance:
galaxy.model.orm.logging_connection_proxy module
------------------------------------------------
.. automodule:: galaxy.model.orm.logging_connection_proxy
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
galaxy.model.orm.now module
---------------------------
.. toctree::
.. automodule:: galaxy.model.orm.now
:members:
:undoc-members:
:show-inheritance:
galaxy.model.orm.scripts module
-------------------------------
.. automodule:: galaxy.model.orm.scripts
:members:
:undoc-members:
:show-inheritance:
galaxy.model.orm.ext
doc/source/lib/galaxy.model.rst
+55 -37
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@@ -1,46 +1,11 @@
model Package
=============
:mod:`model` Package
--------------------
galaxy.model package
====================
.. automodule:: galaxy.model
:members:
:undoc-members:
:show-inheritance:
:mod:`custom_types` Module
--------------------------
.. automodule:: galaxy.model.custom_types
:members:
:undoc-members:
:show-inheritance:
:mod:`item_attrs` Module
------------------------
.. automodule:: galaxy.model.item_attrs
:members:
:undoc-members:
:show-inheritance:
:mod:`mapping` Module
---------------------
.. automodule:: galaxy.model.mapping
:members:
:undoc-members:
:show-inheritance:
:mod:`mapping_tests` Module
---------------------------
.. automodule:: galaxy.model.mapping_tests
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
@@ -48,4 +13,57 @@ Subpackages
galaxy.model.migrate
galaxy.model.orm
galaxy.model.tool_shed_install
Submodules
----------
galaxy.model.base module
------------------------
.. automodule:: galaxy.model.base
:members:
:undoc-members:
:show-inheritance:
galaxy.model.custom_types module
--------------------------------
.. automodule:: galaxy.model.custom_types
:members:
:undoc-members:
:show-inheritance:
galaxy.model.item_attrs module
------------------------------
.. automodule:: galaxy.model.item_attrs
:members:
:undoc-members:
:show-inheritance:
galaxy.model.mapping module
---------------------------
.. automodule:: galaxy.model.mapping
:members:
:undoc-members:
:show-inheritance:
galaxy.model.search module
--------------------------
.. automodule:: galaxy.model.search
:members:
:undoc-members:
:show-inheritance:
galaxy.model.util module
------------------------
.. automodule:: galaxy.model.util
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.model.tool_shed_install.migrate.rst
+20
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@@ -0,0 +1,20 @@
galaxy.model.tool_shed_install.migrate package
==============================================
.. automodule:: galaxy.model.tool_shed_install.migrate
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.model.tool_shed_install.migrate.check module
---------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.check
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.model.tool_shed_install.rst
+27
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@@ -0,0 +1,27 @@
galaxy.model.tool_shed_install package
======================================
.. automodule:: galaxy.model.tool_shed_install
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
galaxy.model.tool_shed_install.migrate
Submodules
----------
galaxy.model.tool_shed_install.mapping module
---------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.mapping
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.objectstore.rst
+32 -7
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@@ -1,19 +1,44 @@
objectstore Package
===================
:mod:`objectstore` Package
--------------------------
galaxy.objectstore package
==========================
.. automodule:: galaxy.objectstore
:members:
:undoc-members:
:show-inheritance:
:mod:`s3_multipart_upload` Module
---------------------------------
Submodules
----------
galaxy.objectstore.pulsar module
--------------------------------
.. automodule:: galaxy.objectstore.pulsar
:members:
:undoc-members:
:show-inheritance:
galaxy.objectstore.rods module
------------------------------
.. automodule:: galaxy.objectstore.rods
:members:
:undoc-members:
:show-inheritance:
galaxy.objectstore.s3 module
----------------------------
.. automodule:: galaxy.objectstore.s3
:members:
:undoc-members:
:show-inheritance:
galaxy.objectstore.s3_multipart_upload module
---------------------------------------------
.. automodule:: galaxy.objectstore.s3_multipart_upload
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.openid.rst
+8 -7
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@@ -1,19 +1,20 @@
openid Package
==============
:mod:`openid` Package
---------------------
galaxy.openid package
=====================
.. automodule:: galaxy.openid
:members:
:undoc-members:
:show-inheritance:
:mod:`providers` Module
-----------------------
Submodules
----------
galaxy.openid.providers module
------------------------------
.. automodule:: galaxy.openid.providers
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.quota.rst
+2 -5
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@@ -1,8 +1,5 @@
quota Package
=============
:mod:`quota` Package
--------------------
galaxy.quota package
====================
.. automodule:: galaxy.quota
:members:
doc/source/lib/galaxy.rst
+59 -22
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@@ -1,54 +1,91 @@
galaxy Package
galaxy package
==============
:mod:`galaxy` Package
---------------------
.. automodule:: galaxy
:members:
:undoc-members:
:show-inheritance:
:mod:`app` Module
-----------------
.. automodule:: galaxy.app
:members:
:undoc-members:
:show-inheritance:
:mod:`config` Module
--------------------
.. automodule:: galaxy.config
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
galaxy.actions
galaxy.auth
galaxy.dataset_collections
galaxy.datatypes
galaxy.eggs
galaxy.exceptions
galaxy.external_services
galaxy.forms
galaxy.jobs
galaxy.model
galaxy.managers
galaxy.metadata
galaxy.model
galaxy.objectstore
galaxy.openid
galaxy.quota
galaxy.sample_tracking
galaxy.security
galaxy.tags
galaxy.tool_shed
galaxy.tools
galaxy.util
galaxy.visualization
galaxy.web
galaxy.webapps
galaxy.work
galaxy.workflow
Submodules
----------
galaxy.app module
-----------------
.. automodule:: galaxy.app
:members:
:undoc-members:
:show-inheritance:
galaxy.config module
--------------------
.. automodule:: galaxy.config
:members:
:undoc-members:
:show-inheritance:
galaxy.main module
------------------
.. automodule:: galaxy.main
:members:
:undoc-members:
:show-inheritance:
galaxy.queue_worker module
--------------------------
.. automodule:: galaxy.queue_worker
:members:
:undoc-members:
:show-inheritance:
galaxy.queues module
--------------------
.. automodule:: galaxy.queues
:members:
:undoc-members:
:show-inheritance:
galaxy.version module
---------------------
.. automodule:: galaxy.version
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.sample_tracking.rst
+19 -10
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@@ -1,35 +1,44 @@
sample_tracking Package
=======================
galaxy.sample_tracking package
==============================
:mod:`data_transfer` Module
---------------------------
.. automodule:: galaxy.sample_tracking
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.sample_tracking.data_transfer module
-------------------------------------------
.. automodule:: galaxy.sample_tracking.data_transfer
:members:
:undoc-members:
:show-inheritance:
:mod:`external_service_types` Module
------------------------------------
galaxy.sample_tracking.external_service_types module
----------------------------------------------------
.. automodule:: galaxy.sample_tracking.external_service_types
:members:
:undoc-members:
:show-inheritance:
:mod:`request_types` Module
---------------------------
galaxy.sample_tracking.request_types module
-------------------------------------------
.. automodule:: galaxy.sample_tracking.request_types
:members:
:undoc-members:
:show-inheritance:
:mod:`sample` Module
--------------------
galaxy.sample_tracking.sample module
------------------------------------
.. automodule:: galaxy.sample_tracking.sample
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.security.rst
+16 -7
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@@ -1,19 +1,28 @@
security Package
================
:mod:`security` Package
-----------------------
galaxy.security package
=======================
.. automodule:: galaxy.security
:members:
:undoc-members:
:show-inheritance:
:mod:`validate_user_input` Module
---------------------------------
Submodules
----------
galaxy.security.passwords module
--------------------------------
.. automodule:: galaxy.security.passwords
:members:
:undoc-members:
:show-inheritance:
galaxy.security.validate_user_input module
------------------------------------------
.. automodule:: galaxy.security.validate_user_input
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tags.rst
+2 -13
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@@ -1,19 +1,8 @@
tags Package
============
:mod:`tags` Package
-------------------
galaxy.tags package
===================
.. automodule:: galaxy.tags
:members:
:undoc-members:
:show-inheritance:
:mod:`tag_handler` Module
-------------------------
.. automodule:: galaxy.tags.tag_handler
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tool_shed.migrate.rst
-19
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@@ -1,19 +0,0 @@
migrate Package
===============
:mod:`check` Module
-------------------
.. automodule:: galaxy.tool_shed.migrate.check
:members:
:undoc-members:
:show-inheritance:
:mod:`common` Module
--------------------
.. automodule:: galaxy.tool_shed.migrate.common
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tool_shed.rst
-59
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@@ -1,59 +0,0 @@
tool_shed Package
=================
:mod:`tool_shed` Package
------------------------
.. automodule:: galaxy.tool_shed
:members:
:undoc-members:
:show-inheritance:
:mod:`common_util` Module
-------------------------
.. automodule:: galaxy.tool_shed.common_util
:members:
:undoc-members:
:show-inheritance:
:mod:`encoding_util` Module
---------------------------
.. automodule:: galaxy.tool_shed.encoding_util
:members:
:undoc-members:
:show-inheritance:
:mod:`install_manager` Module
-----------------------------
.. automodule:: galaxy.tool_shed.install_manager
:members:
:undoc-members:
:show-inheritance:
:mod:`tool_shed_registry` Module
--------------------------------
.. automodule:: galaxy.tool_shed.tool_shed_registry
:members:
:undoc-members:
:show-inheritance:
:mod:`update_manager` Module
----------------------------
.. automodule:: galaxy.tool_shed.update_manager
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
galaxy.tool_shed.migrate
galaxy.tool_shed.tool_dependencies
doc/source/lib/galaxy.tool_shed.tool_dependencies.rst
-27
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@@ -1,27 +0,0 @@
tool_dependencies Package
=========================
:mod:`common_util` Module
-------------------------
.. automodule:: galaxy.tool_shed.tool_dependencies.common_util
:members:
:undoc-members:
:show-inheritance:
:mod:`fabric_util` Module
-------------------------
.. automodule:: galaxy.tool_shed.tool_dependencies.fabric_util
:members:
:undoc-members:
:show-inheritance:
:mod:`install_util` Module
--------------------------
.. automodule:: galaxy.tool_shed.tool_dependencies.install_util
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.actions.rst
+30 -21
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@@ -1,51 +1,60 @@
actions Package
===============
:mod:`actions` Package
----------------------
galaxy.tools.actions package
============================
.. automodule:: galaxy.tools.actions
:members:
:undoc-members:
:show-inheritance:
:mod:`history_imp_exp` Module
-----------------------------
Submodules
----------
galaxy.tools.actions.data_manager module
----------------------------------------
.. automodule:: galaxy.tools.actions.data_manager
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.actions.data_source module
---------------------------------------
.. automodule:: galaxy.tools.actions.data_source
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.actions.history_imp_exp module
-------------------------------------------
.. automodule:: galaxy.tools.actions.history_imp_exp
:members:
:undoc-members:
:show-inheritance:
:mod:`index_genome` Module
--------------------------
.. automodule:: galaxy.tools.actions.index_genome
:members:
:undoc-members:
:show-inheritance:
:mod:`metadata` Module
----------------------
galaxy.tools.actions.metadata module
------------------------------------
.. automodule:: galaxy.tools.actions.metadata
:members:
:undoc-members:
:show-inheritance:
:mod:`upload` Module
--------------------
galaxy.tools.actions.upload module
----------------------------------
.. automodule:: galaxy.tools.actions.upload
:members:
:undoc-members:
:show-inheritance:
:mod:`upload_common` Module
---------------------------
galaxy.tools.actions.upload_common module
-----------------------------------------
.. automodule:: galaxy.tools.actions.upload_common
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.data.rst
+2 -5
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@@ -1,8 +1,5 @@
data Package
============
:mod:`data` Package
-------------------
galaxy.tools.data package
=========================
.. automodule:: galaxy.tools.data
:members:
doc/source/lib/galaxy.tools.data_manager.rst
+20
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@@ -0,0 +1,20 @@
galaxy.tools.data_manager package
=================================
.. automodule:: galaxy.tools.data_manager
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.tools.data_manager.manager module
----------------------------------------
.. automodule:: galaxy.tools.data_manager.manager
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.deps.resolvers.rst
+60
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@@ -0,0 +1,60 @@
galaxy.tools.deps.resolvers package
===================================
.. automodule:: galaxy.tools.deps.resolvers
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.tools.deps.resolvers.brewed_tool_shed_packages module
------------------------------------------------------------
.. automodule:: galaxy.tools.deps.resolvers.brewed_tool_shed_packages
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.deps.resolvers.galaxy_packages module
--------------------------------------------------
.. automodule:: galaxy.tools.deps.resolvers.galaxy_packages
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.deps.resolvers.homebrew module
-------------------------------------------
.. automodule:: galaxy.tools.deps.resolvers.homebrew
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.deps.resolvers.modules module
------------------------------------------
.. automodule:: galaxy.tools.deps.resolvers.modules
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.deps.resolvers.resolver_mixins module
--------------------------------------------------
.. automodule:: galaxy.tools.deps.resolvers.resolver_mixins
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.deps.resolvers.tool_shed_packages module
-----------------------------------------------------
.. automodule:: galaxy.tools.deps.resolvers.tool_shed_packages
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.deps.rst
+72 -8
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@@ -1,19 +1,83 @@
deps Package
============
:mod:`deps` Package
-------------------
galaxy.tools.deps package
=========================
.. automodule:: galaxy.tools.deps
:members:
:undoc-members:
:show-inheritance:
:mod:`tests` Module
-------------------
Subpackages
-----------
.. automodule:: galaxy.tools.deps.tests
.. toctree::
galaxy.tools.deps.resolvers
Submodules
----------
galaxy.tools.deps.brew_exts module
----------------------------------
.. automodule:: galaxy.tools.deps.brew_exts
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.deps.brew_util module
----------------------------------
.. automodule:: galaxy.tools.deps.brew_util
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.deps.commands module
---------------------------------
.. automodule:: galaxy.tools.deps.commands
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.deps.containers module
-----------------------------------
.. automodule:: galaxy.tools.deps.containers
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.deps.dependencies module
-------------------------------------
.. automodule:: galaxy.tools.deps.dependencies
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.deps.docker_util module
------------------------------------
.. automodule:: galaxy.tools.deps.docker_util
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.deps.dockerfiles module
------------------------------------
.. automodule:: galaxy.tools.deps.dockerfiles
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.deps.requirements module
-------------------------------------
.. automodule:: galaxy.tools.deps.requirements
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.filters.rst
+8
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@@ -0,0 +1,8 @@
galaxy.tools.filters package
============================
.. automodule:: galaxy.tools.filters
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.genome_index.rst
-19
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@@ -1,19 +0,0 @@
genome_index Package
====================
:mod:`genome_index` Package
---------------------------
.. automodule:: galaxy.tools.genome_index
:members:
:undoc-members:
:show-inheritance:
:mod:`index_genome` Module
--------------------------
.. automodule:: galaxy.tools.genome_index.index_genome
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.imp_exp.rst
+10 -9
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@@ -1,27 +1,28 @@
imp_exp Package
===============
:mod:`imp_exp` Package
----------------------
galaxy.tools.imp_exp package
============================
.. automodule:: galaxy.tools.imp_exp
:members:
:undoc-members:
:show-inheritance:
:mod:`export_history` Module
----------------------------
Submodules
----------
galaxy.tools.imp_exp.export_history module
------------------------------------------
.. automodule:: galaxy.tools.imp_exp.export_history
:members:
:undoc-members:
:show-inheritance:
:mod:`unpack_tar_gz_archive` Module
-----------------------------------
galaxy.tools.imp_exp.unpack_tar_gz_archive module
-------------------------------------------------
.. automodule:: galaxy.tools.imp_exp.unpack_tar_gz_archive
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.linters.rst
+68
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@@ -0,0 +1,68 @@
galaxy.tools.linters package
============================
.. automodule:: galaxy.tools.linters
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.tools.linters.citations module
-------------------------------------
.. automodule:: galaxy.tools.linters.citations
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.linters.command module
-----------------------------------
.. automodule:: galaxy.tools.linters.command
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.linters.help module
--------------------------------
.. automodule:: galaxy.tools.linters.help
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.linters.inputs module
----------------------------------
.. automodule:: galaxy.tools.linters.inputs
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.linters.outputs module
-----------------------------------
.. automodule:: galaxy.tools.linters.outputs
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.linters.tests module
---------------------------------
.. automodule:: galaxy.tools.linters.tests
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.linters.top_level module
-------------------------------------
.. automodule:: galaxy.tools.linters.top_level
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.parameters.rst
+60 -19
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@@ -1,67 +1,108 @@
parameters Package
==================
:mod:`parameters` Package
-------------------------
galaxy.tools.parameters package
===============================
.. automodule:: galaxy.tools.parameters
:members:
:undoc-members:
:show-inheritance:
:mod:`basic` Module
-------------------
Submodules
----------
galaxy.tools.parameters.basic module
------------------------------------
.. automodule:: galaxy.tools.parameters.basic
:members:
:undoc-members:
:show-inheritance:
:mod:`dynamic_options` Module
-----------------------------
galaxy.tools.parameters.dataset_matcher module
----------------------------------------------
.. automodule:: galaxy.tools.parameters.dataset_matcher
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.parameters.dynamic_options module
----------------------------------------------
.. automodule:: galaxy.tools.parameters.dynamic_options
:members:
:undoc-members:
:show-inheritance:
:mod:`grouping` Module
----------------------
galaxy.tools.parameters.grouping module
---------------------------------------
.. automodule:: galaxy.tools.parameters.grouping
:members:
:undoc-members:
:show-inheritance:
:mod:`input_translation` Module
-------------------------------
galaxy.tools.parameters.history_query module
--------------------------------------------
.. automodule:: galaxy.tools.parameters.history_query
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.parameters.input_translation module
------------------------------------------------
.. automodule:: galaxy.tools.parameters.input_translation
:members:
:undoc-members:
:show-inheritance:
:mod:`output` Module
--------------------
galaxy.tools.parameters.meta module
-----------------------------------
.. automodule:: galaxy.tools.parameters.meta
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.parameters.output module
-------------------------------------
.. automodule:: galaxy.tools.parameters.output
:members:
:undoc-members:
:show-inheritance:
:mod:`sanitize` Module
----------------------
galaxy.tools.parameters.output_collect module
---------------------------------------------
.. automodule:: galaxy.tools.parameters.output_collect
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.parameters.sanitize module
---------------------------------------
.. automodule:: galaxy.tools.parameters.sanitize
:members:
:undoc-members:
:show-inheritance:
:mod:`validation` Module
------------------------
galaxy.tools.parameters.validation module
-----------------------------------------
.. automodule:: galaxy.tools.parameters.validation
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.parameters.wrapped module
--------------------------------------
.. automodule:: galaxy.tools.parameters.wrapped
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.parser.rst
+52
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@@ -0,0 +1,52 @@
galaxy.tools.parser package
===========================
.. automodule:: galaxy.tools.parser
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.tools.parser.factory module
----------------------------------
.. automodule:: galaxy.tools.parser.factory
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.parser.interface module
------------------------------------
.. automodule:: galaxy.tools.parser.interface
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.parser.util module
-------------------------------
.. automodule:: galaxy.tools.parser.util
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.parser.xml module
------------------------------
.. automodule:: galaxy.tools.parser.xml
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.parser.yaml module
-------------------------------
.. automodule:: galaxy.tools.parser.yaml
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.rst
+83 -22
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@@ -1,30 +1,11 @@
tools Package
=============
:mod:`tools` Package
--------------------
galaxy.tools package
====================
.. automodule:: galaxy.tools
:members:
:undoc-members:
:show-inheritance:
:mod:`exception_handling` Module
--------------------------------
.. automodule:: galaxy.tools.exception_handling
:members:
:undoc-members:
:show-inheritance:
:mod:`test` Module
------------------
.. automodule:: galaxy.tools.test
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
@@ -32,10 +13,90 @@ Subpackages
galaxy.tools.actions
galaxy.tools.data
galaxy.tools.data_manager
galaxy.tools.deps
galaxy.tools.genome_index
galaxy.tools.filters
galaxy.tools.imp_exp
galaxy.tools.linters
galaxy.tools.parameters
galaxy.tools.parser
galaxy.tools.search
galaxy.tools.toolbox
galaxy.tools.util
Submodules
----------
galaxy.tools.errors module
--------------------------
.. automodule:: galaxy.tools.errors
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.evaluation module
------------------------------
.. automodule:: galaxy.tools.evaluation
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.exception_handling module
--------------------------------------
.. automodule:: galaxy.tools.exception_handling
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.execute module
---------------------------
.. automodule:: galaxy.tools.execute
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.lint module
------------------------
.. automodule:: galaxy.tools.lint
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.loader module
--------------------------
.. automodule:: galaxy.tools.loader
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.loader_directory module
------------------------------------
.. automodule:: galaxy.tools.loader_directory
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.test module
------------------------
.. automodule:: galaxy.tools.test
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.wrappers module
----------------------------
.. automodule:: galaxy.tools.wrappers
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.search.rst
+2 -5
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@@ -1,8 +1,5 @@
search Package
==============
:mod:`search` Package
---------------------
galaxy.tools.search package
===========================
.. automodule:: galaxy.tools.search
:members:
doc/source/lib/galaxy.tools.toolbox.filters.rst
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@@ -0,0 +1,8 @@
galaxy.tools.toolbox.filters package
====================================
.. automodule:: galaxy.tools.toolbox.filters
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.toolbox.lineages.rst
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galaxy.tools.toolbox.lineages package
=====================================
.. automodule:: galaxy.tools.toolbox.lineages
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.tools.toolbox.lineages.factory module
--------------------------------------------
.. automodule:: galaxy.tools.toolbox.lineages.factory
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.toolbox.lineages.interface module
----------------------------------------------
.. automodule:: galaxy.tools.toolbox.lineages.interface
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.toolbox.lineages.stock module
------------------------------------------
.. automodule:: galaxy.tools.toolbox.lineages.stock
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.toolbox.lineages.tool_shed module
----------------------------------------------
.. automodule:: galaxy.tools.toolbox.lineages.tool_shed
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.toolbox.rst
+60
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@@ -0,0 +1,60 @@
galaxy.tools.toolbox package
============================
.. automodule:: galaxy.tools.toolbox
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
galaxy.tools.toolbox.filters
galaxy.tools.toolbox.lineages
Submodules
----------
galaxy.tools.toolbox.base module
--------------------------------
.. automodule:: galaxy.tools.toolbox.base
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.toolbox.integrated_panel module
--------------------------------------------
.. automodule:: galaxy.tools.toolbox.integrated_panel
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.toolbox.panel module
---------------------------------
.. automodule:: galaxy.tools.toolbox.panel
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.toolbox.tags module
--------------------------------
.. automodule:: galaxy.tools.toolbox.tags
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.toolbox.watcher module
-----------------------------------
.. automodule:: galaxy.tools.toolbox.watcher
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.util.galaxyops.rst
+2 -5
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@@ -1,8 +1,5 @@
galaxyops Package
=================
:mod:`galaxyops` Package
------------------------
galaxy.tools.util.galaxyops package
===================================
.. automodule:: galaxy.tools.util.galaxyops
:members:
doc/source/lib/galaxy.tools.util.rst
+14 -13
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util Package
============
:mod:`util` Package
-------------------
galaxy.tools.util package
=========================
.. automodule:: galaxy.tools.util
:members:
:undoc-members:
:show-inheritance:
:mod:`maf_utilities` Module
---------------------------
.. automodule:: galaxy.tools.util.maf_utilities
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
@@ -24,3 +13,15 @@ Subpackages
galaxy.tools.util.galaxyops
Submodules
----------
galaxy.tools.util.maf_utilities module
--------------------------------------
.. automodule:: galaxy.tools.util.maf_utilities
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.util.backports.importlib.rst
+2 -5
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@@ -1,8 +1,5 @@
importlib Package
=================
:mod:`importlib` Package
------------------------
galaxy.util.backports.importlib package
=======================================
.. automodule:: galaxy.util.backports.importlib
:members:

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