").addClass("param-row").appendTo(parent_div);
var run_on_dataset_button = $("").attr("value", "Run on complete dataset").appendTo(run_tool_row);
@@ -1701,7 +1700,7 @@ var TracksterToolView = Backbone.View.extend({
run_on_dataset_button.click( function() {
self.run_on_dataset();
});
-
+
if (tool.is_visible()) {
this.$el.show();
}
@@ -1730,7 +1729,7 @@ var TracksterToolView = Backbone.View.extend({
var tool = this.model;
this.run(
// URL params.
- {
+ {
target_dataset_id: this.model.get('track').dataset.id,
action: 'rerun',
tool_id: tool.id
@@ -1758,8 +1757,8 @@ var TracksterToolView = Backbone.View.extend({
start: track.view.low,
end: track.view.high
}),
- url_params =
- {
+ url_params =
+ {
target_dataset_id: track.dataset.id,
action: 'rerun',
tool_id: tool.id,
@@ -1772,16 +1771,16 @@ var TracksterToolView = Backbone.View.extend({
track_name = tool.get('name') +
current_track.tool_region_and_parameters_str(region),
container;
-
- // If track not in a group, create a group for it and add new track to group. If track
+
+ // If track not in a group, create a group for it and add new track to group. If track
// already in group, add track to group.
if (current_track.container === view) {
// Create new group.
var group = new DrawableGroup(view, view, { name: track.config.get_value('name') });
-
+
// Replace track with group.
var index = current_track.container.replace_drawable(current_track, group, false);
-
+
// Update HTML.
// FIXME: this is ugly way to replace a track with a group -- make this easier via
// a Drawable or DrawableCollection function.
@@ -1794,7 +1793,7 @@ var TracksterToolView = Backbone.View.extend({
// Use current group.
container = current_track.container;
}
-
+
// Create and init new track.
var new_track = new current_track.constructor(view, container, {
name: track_name,
@@ -1806,7 +1805,7 @@ var TracksterToolView = Backbone.View.extend({
new_track.update_icons();
container.add_drawable(new_track);
new_track.tiles_div.text("Starting job.");
-
+
// Run tool.
this.run(url_params, new_track,
// Success callback.
@@ -1837,11 +1836,11 @@ var TracksterToolView = Backbone.View.extend({
return response !== "pending";
}
});
-
+
// Start with this status message.
//new_track.container_div.addClass("pending");
//new_track.content_div.html(DATA_PENDING);
-
+
$.when(ss_deferred.go()).then(function(response) {
if (response === "no converter") {
// No converter available for input datasets, so cannot run tool.
@@ -1856,7 +1855,7 @@ var TracksterToolView = Backbone.View.extend({
else {
// Job submitted and running.
success_callback(response);
- }
+ }
});
}
@@ -1875,7 +1874,7 @@ FilterScaler.prototype.gen_val = function(feature_data) {
if (this.filter.high === Number.MAX_VALUE || this.filter.low === -Number.MAX_VALUE || this.filter.low === this.filter.high) {
return this.default_val;
}
-
+
// Scaling value is ratio of (filter's value compared to low) to (complete filter range).
return ( ( parseFloat(feature_data[this.filter.index]) - this.filter.low ) / ( this.filter.high - this.filter.low ) );
};
@@ -1906,7 +1905,7 @@ var LineTrackTile = function(track, region, w_scale, canvas, data) {
};
LineTrackTile.prototype.predisplay_actions = function() {};
-var FeatureTrackTile = function(track, region, w_scale, canvas, data, mode, message, all_slotted,
+var FeatureTrackTile = function(track, region, w_scale, canvas, data, mode, message, all_slotted,
feature_mapper, incomplete_features, seq_data) {
// Attribute init.
Tile.call(this, track, region, w_scale, canvas, data);
@@ -1918,21 +1917,21 @@ var FeatureTrackTile = function(track, region, w_scale, canvas, data, mode, mess
// Features drawn based on data from other tiles.
this.other_tiles_features_drawn = {};
this.seq_data = seq_data;
-
+
// Add message + action icons to tile's html.
/*
- This does not work right now because a random set of reads is returned by the server.
+ This does not work right now because a random set of reads is returned by the server.
When the server can respond with more data systematically, renable these icons.
if (message) {
this.has_icons = true;
-
- var
+
+ var
tile = this;
canvas = this.html_elt.children()[0],
message_div = $("").addClass("tile-message")
// -1 to account for border.
.css({'height': ERROR_PADDING, 'width': canvas.width}).prependTo(this.html_elt);
-
+
// Handle message; only message currently is that only the first N elements are displayed.
var tile_region = new visualization.GenomeRegion({
chrom: track.view.chrom,
@@ -1985,24 +1984,24 @@ FeatureTrackTile.prototype.predisplay_actions = function() {
//
var tile = this,
popups = {};
-
+
// Only show popups in Pack mode.
if (tile.mode !== "Pack") { return; }
-
+
$(this.html_elt).hover(
function() {
- this.hovered = true;
+ this.hovered = true;
$(this).mousemove();
},
function() {
- this.hovered = false;
- // Clear popup if it is still hanging around (this is probably not needed)
+ this.hovered = false;
+ // Clear popup if it is still hanging around (this is probably not needed)
$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove();
} ).mousemove(function (e) {
// Use the hover plugin to get a delay before showing popup
if ( !this.hovered ) { return; }
// Get feature data for position.
- var
+ var
this_offset = $(this).offset(),
offsetX = e.pageX - this_offset.left,
offsetY = e.pageY - this_offset.top,
@@ -2010,17 +2009,17 @@ FeatureTrackTile.prototype.predisplay_actions = function() {
feature_uid = (feature_data ? feature_data[0] : null);
// Hide visible popup if not over a feature or over a different feature.
$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function() {
- if ( !feature_uid ||
+ if ( !feature_uid ||
$(this).attr("id") !== feature_uid.toString() ) {
$(this).remove();
}
});
-
+
if (feature_data) {
// Get or create popup.
var popup = popups[feature_uid];
if (!popup) {
- // Create feature's popup element.
+ // Create feature's popup element.
var feature_dict = {
name: feature_data[3],
start: feature_data[1],
@@ -2029,13 +2028,13 @@ FeatureTrackTile.prototype.predisplay_actions = function() {
},
filters = tile.track.filters_manager.filters,
filter;
-
- // Add filter values to feature dict.
+
+ // Add filter values to feature dict.
for (var i = 0; i < filters.length; i++) {
filter = filters[i];
feature_dict[filter.name] = feature_data[filter.index];
}
-
+
// Build popup.
popup = $("").attr("id", feature_uid).addClass("feature-popup");
var table = $("
"),
@@ -2047,23 +2046,23 @@ FeatureTrackTile.prototype.predisplay_actions = function() {
$("
").append( table ) );
+ popup.append( $("
").append( table ) );
popups[feature_uid] = popup;
}
-
+
// Attach popup to track's overlay.
popup.appendTo( $(this).parents(".track-content").children(".overlay") );
-
+
// Offsets are within canvas, but popup must be positioned relative to parent element.
// parseInt strips "px" from left, top measurements. +7 so that mouse pointer does not
// overlap popup.
- var
+ var
popupX = offsetX + parseInt( tile.html_elt.css("left"), 10 ) - popup.width() / 2,
popupY = offsetY + parseInt( tile.html_elt.css("top"), 10 ) + 7;
popup.css("left", popupX + "px").css("top", popupY + "px");
}
else if (!e.isPropagationStopped()) {
- // Propogate event to other tiles because overlapping tiles prevent mousemove from being
+ // Propogate event to other tiles because overlapping tiles prevent mousemove from being
// called on tiles under this tile.
e.stopPropagation();
$(this).siblings().each(function() {
@@ -2078,11 +2077,11 @@ FeatureTrackTile.prototype.predisplay_actions = function() {
};
/**
- * Tracks are objects can be added to the View.
- *
+ * Tracks are objects can be added to the View.
+ *
* Track object hierarchy:
* Track
- * -> LabelTrack
+ * -> LabelTrack
* -> TiledTrack
* ----> LineTrack
* ----> ReferenceTrack
@@ -2096,7 +2095,7 @@ var Track = function(view, container, obj_dict) {
drag_handle_class: "draghandle"
});
Drawable.call(this, view, container, obj_dict);
-
+
//
// Attribute init.
//
@@ -2126,12 +2125,12 @@ var Track = function(view, container, obj_dict) {
data_mode_compatible: this.data_and_mode_compatible,
can_subset: this.can_subset
}));
-
+
// Height attributes: min height, max height, and visible height.
this.min_height_px = 16;
this.max_height_px = 800;
this.visible_height_px = this.config.get_value('height');
-
+
//
// Create content div, which is where track is displayed, and add to container if available.
//
@@ -2174,7 +2173,7 @@ extend(Track.prototype, Drawable.prototype, {
on_click_fn: function(drawable) {
// TODO: update Tooltip text.
if (drawable.filters_manager.visible()) {
- drawable.filters_manager.clear_filters();
+ drawable.filters_manager.clear_filters();
}
else {
drawable.filters_manager.init_filters();
@@ -2209,15 +2208,14 @@ extend(Track.prototype, Drawable.prototype, {
title: "Tool parameter space visualization",
css_class: "arrow-split",
on_click_fn: function(track) {
- var template =
- 'Tool: <%= track.tool.get("name") %>
' + - 'Dataset: <%= track.config.get_value("name") %>
' + + var html = + 'Tool:' + track.tool.get("name") + '
' + + 'Dataset:' + track.config.get_value("name") + '
' + 'Region(s): ', - html = _.template(template, { track: track }); + ''; var cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); }, ok_fn = function() { var regions_to_use = $('select[name="regions"] option:selected').val(), @@ -2248,7 +2246,7 @@ extend(Track.prototype, Drawable.prototype, { Galaxy.modal.hide(); // Go to visualization. - window.location.href = + window.location.href = galaxy_config.root + "visualization/sweepster" + "?" + $.param({ dataset_id: track.dataset.id, @@ -2263,7 +2261,7 @@ extend(Track.prototype, Drawable.prototype, { ok_fn(); } }; - + // show dialog Galaxy.modal.show({title: "Visualize tool parameter space and output from different parameter settings?", body: html, buttons : {'No' : cancel_fn, 'Yes' : ok_fn } }); } @@ -2280,7 +2278,7 @@ extend(Track.prototype, Drawable.prototype, { return $("").addClass('track').attr("id", "track_" + this.id); }, - /** + /** * Set track's dataset. */ set_dataset: function(dataset) { @@ -2304,12 +2302,12 @@ extend(Track.prototype, Drawable.prototype, { var in_drag = false; var drag_control = $( "
' + - 'Dataset: <%= track.config.get_value("name") %>
' + + var html = + 'Tool:' + track.tool.get("name") + '
' + + 'Dataset:' + track.config.get_value("name") + '
' + 'Region(s): ', - html = _.template(template, { track: track }); + ''; var cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); }, ok_fn = function() { var regions_to_use = $('select[name="regions"] option:selected').val(), @@ -2248,7 +2246,7 @@ extend(Track.prototype, Drawable.prototype, { Galaxy.modal.hide(); // Go to visualization. - window.location.href = + window.location.href = galaxy_config.root + "visualization/sweepster" + "?" + $.param({ dataset_id: track.dataset.id, @@ -2263,7 +2261,7 @@ extend(Track.prototype, Drawable.prototype, { ok_fn(); } }; - + // show dialog Galaxy.modal.show({title: "Visualize tool parameter space and output from different parameter settings?", body: html, buttons : {'No' : cancel_fn, 'Yes' : ok_fn } }); } @@ -2280,7 +2278,7 @@ extend(Track.prototype, Drawable.prototype, { return $("").addClass('track').attr("id", "track_" + this.id); }, - /** + /** * Set track's dataset. */ set_dataset: function(dataset) { @@ -2304,12 +2302,12 @@ extend(Track.prototype, Drawable.prototype, { var in_drag = false; var drag_control = $( "
" );
// Control shows on hover over track, stays while dragging
- $(track.container_div).hover( function() {
+ $(track.container_div).hover( function() {
if ( track.config.get_value('content_visible') ) {
in_handle = true;
- drag_control.show();
+ drag_control.show();
}
- }, function() {
+ }, function() {
in_handle = false;
if ( ! in_drag ) { drag_control.hide(); }
});
@@ -2351,8 +2349,8 @@ extend(Track.prototype, Drawable.prototype, {
this.request_draw();
},
- /**
- * Returns track type.
+ /**
+ * Returns track type.
*/
get_type: function() {
// Order is important: start with most-specific classes and go up the track hierarchy.
@@ -2397,7 +2395,7 @@ extend(Track.prototype, Drawable.prototype, {
var track = this;
track.enabled = false;
- track.tile_cache.clear();
+ track.tile_cache.clear();
track.data_manager.clear();
/*
if (!track.content_div.text()) {
@@ -2417,12 +2415,12 @@ extend(Track.prototype, Drawable.prototype, {
if (!track.dataset.id) {
return;
}
-
- // Get dataset state; if state is fine, enable and draw track. Otherwise, show message
+
+ // Get dataset state; if state is fine, enable and draw track. Otherwise, show message
// about track status.
var init_deferred = $.Deferred(),
- params = {
- hda_ldda: track.dataset.get('hda_ldda'),
+ params = {
+ hda_ldda: track.dataset.get('hda_ldda'),
data_type: this.dataset_check_type,
chrom: track.view.chrom,
retry: retry
@@ -2446,21 +2444,21 @@ extend(Track.prototype, Drawable.prototype, {
})
);
}
- }
+ }
else if (result === "no converter") {
track.container_div.addClass("error");
track.show_message(DATA_NOCONVERTER);
- }
+ }
else if (result === "no data" || (result.data !== undefined && (result.data === null || result.data.length === 0))) {
track.container_div.addClass("nodata");
track.show_message(DATA_NONE);
- }
+ }
else if (result === "pending") {
track.container_div.addClass("pending");
track.show_message(DATA_PENDING);
//$("![]()
").attr("src", image_path + "/yui/rel_interstitial_loading.gif").appendTo(track.tiles_div);
setTimeout(function() { track.init(); }, track.data_query_wait);
- }
+ }
else if (result === "data" || result.status === "data") {
if (result.valid_chroms) {
track.valid_chroms = result.valid_chroms;
@@ -2483,7 +2481,7 @@ extend(Track.prototype, Drawable.prototype, {
}
}
});
-
+
this.update_icons();
return init_deferred;
},
@@ -2493,11 +2491,11 @@ extend(Track.prototype, Drawable.prototype, {
*/
predraw_init: function() {
var track = this;
- return $.getJSON( track.dataset.url(),
- { data_type: 'data', stats: true, chrom: track.view.chrom, low: 0,
+ return $.getJSON( track.dataset.url(),
+ { data_type: 'data', stats: true, chrom: track.view.chrom, low: 0,
high: track.view.max_high, hda_ldda: track.dataset.get('hda_ldda') }, function(result) {
var data = result.data;
-
+
// Tracks may not have stat data either because there is no data or data is not yet ready.
if (data !== undefined && data.min !== undefined && data.max !== undefined) {
// Compute default minimum and maximum values
@@ -2524,14 +2522,14 @@ extend(Track.prototype, Drawable.prototype, {
}
});
-var TiledTrack = function(view, container, obj_dict) {
+var TiledTrack = function(view, container, obj_dict) {
Track.call(this, view, container, obj_dict);
var track = this;
-
+
// Make track moveable.
moveable(track.container_div, track.drag_handle_class, ".group", track);
-
+
// Attribute init.
this.filters_manager = new filters_mod.FiltersManager(this, ('filters' in obj_dict ? obj_dict.filters : null));
// HACK: set filters manager for data manager.
@@ -2545,13 +2543,13 @@ var TiledTrack = function(view, container, obj_dict) {
: null);
this.tile_cache = new visualization.Cache(TILE_CACHE_SIZE);
this.left_offset = 0;
-
+
if (this.header_div) {
//
// Setup filters.
//
this.set_filters_manager(this.filters_manager);
-
+
//
// Create dynamic tool view.
//
@@ -2562,14 +2560,14 @@ var TiledTrack = function(view, container, obj_dict) {
this.header_div.after(this.dynamic_tool_div);
}
}
-
+
// Add tiles_div, overlay_div to content_div.
this.tiles_div = $("").addClass("tiles").appendTo(this.content_div);
if (!this.config.get_value('content_visible')) {
this.tiles_div.hide();
}
this.overlay_div = $("").addClass("overlay").appendTo(this.content_div);
-
+
if (obj_dict.mode) {
this.change_mode(obj_dict.mode);
}
@@ -2615,8 +2613,8 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
this.header_div.after(this.filters_manager.parent_div);
},
- /**
- * Returns representation of object in a dictionary for easy saving.
+ /**
+ * Returns representation of object in a dictionary for easy saving.
* Use from_dict to recreate object.
*/
to_dict: function() {
@@ -2639,9 +2637,9 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
set_min_max: function() {
var track = this;
- return $.getJSON( track.dataset.url(),
- { data_type: 'data', stats: true, chrom: track.view.chrom, low: 0,
- high: track.view.max_high, hda_ldda: track.dataset.get('hda_ldda') },
+ return $.getJSON( track.dataset.url(),
+ { data_type: 'data', stats: true, chrom: track.view.chrom, low: 0,
+ high: track.view.max_high, hda_ldda: track.dataset.get('hda_ldda') },
function(result) {
var data = result.data;
if ( isNaN(parseFloat(track.config.get_value('min_value'))) ||
@@ -2682,12 +2680,12 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
*/
update_icons: function() {
var track = this;
-
+
//
// Show/hide filter icon.
//
track.action_icons.filters_icon.toggle(track.filters_available);
-
+
//
// Show/hide tool icons.
//
@@ -2748,22 +2746,22 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
w_scale = width / (view.max_high - view.max_low);
resolution = 1 / w_scale;
}
-
+
this.before_draw();
//
// Method for moving and/or removing tiles:
// (a) mark all elements for removal using class 'remove'
- // (b) during tile drawing/placement, remove class for elements that are moved;
+ // (b) during tile drawing/placement, remove class for elements that are moved;
// this occurs in show_tile()
- // (c) after drawing tiles, remove elements still marked for removal
+ // (c) after drawing tiles, remove elements still marked for removal
// (i.e. that still have class 'remove').
//
-
+
// Step (a) for (re)moving tiles.
this.tiles_div.children().addClass("remove");
- var
+ var
// Tile width in bases.
tile_width = Math.floor(TILE_SIZE * resolution),
// Index of first tile that overlaps visible region.
@@ -2790,10 +2788,10 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
// Go to next tile.
tile_index += 1;
}
-
+
// Step (c) for (re)moving tiles when clear_after is false.
if (!clear_after) { this.tiles_div.children(".remove").removeClass("remove").remove(); }
-
+
// When all tiles are drawn, call post-draw actions.
var track = this;
$.when.apply($, tile_promises).then(function() {
@@ -2823,9 +2821,9 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
label = this.container_div.find(".yaxislabel." + css_class);
// Default action for on_change is to redraw track.
- on_change = on_change || function() {
+ on_change = on_change || function() {
track.request_draw({ clear_tile_cache: true });
- };
+ };
if (label.length !== 0) {
// Label already exists, so update value.
@@ -2847,7 +2845,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
},
/**
- * Actions to be taken after draw has been completed. Draw is completed when all tiles have been
+ * Actions to be taken after draw has been completed. Draw is completed when all tiles have been
* drawn/fetched and shown.
*/
postdraw_actions: function(tiles, width, w_scale, clear_after) {
@@ -2883,7 +2881,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
//
// If some tiles have icons, set padding of tiles without icons so features and rows align.
//
- var icons_present = _.find(tiles, function(tile) {
+ var icons_present = _.find(tiles, function(tile) {
return tile.has_icons;
});
@@ -2920,7 +2918,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
},
/**
- * Retrieves from cache, draws, or sets up drawing for a single tile. Returns either a Tile object or a
+ * Retrieves from cache, draws, or sets up drawing for a single tile. Returns either a Tile object or a
* jQuery.Deferred object that is fulfilled when tile can be drawn again. Options include:
* -force: force a redraw rather than use cached tiles (default: false)
* -data_fetch: fetch data if necessary (default: true)
@@ -2938,7 +2936,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
drawables = this._get_drawables(),
key = this._gen_tile_cache_key(w_scale, region),
is_tile = function(o) { return (o && 'track' in o); };
-
+
// Check tile cache, if found show existing tile in correct position
var tile = (force ? undefined : track.tile_cache.get_elt(key));
if (tile) {
@@ -2969,7 +2967,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
return tile_data;
};
-
+
//
// When data is available, draw tile.
//
@@ -2980,9 +2978,9 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
tracks_data = tile_data,
seq_data;
- // Deferreds may show up here if trying to fetch a subset of data from a superset data chunk
- // that cannot be subsetted. This may occur if the superset has a message. If there is a
- // Deferred, try again from the top. NOTE: this condition could (should?) be handled by the
+ // Deferreds may show up here if trying to fetch a subset of data from a superset data chunk
+ // that cannot be subsetted. This may occur if the superset has a message. If there is a
+ // Deferred, try again from the top. NOTE: this condition could (should?) be handled by the
// GenomeDataManager in visualization module.
if (_.find(tile_data, function(d) { return util.is_deferred(d); })) {
track.tile_cache.set_elt(key, undefined);
@@ -2991,12 +2989,12 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
});
return;
}
-
+
// If sequence data is available, subset to get only data in region.
if (view.reference_track) {
seq_data = view.reference_track.data_manager.subset_entry(tile_data.pop(), region);
}
-
+
// Get drawing modes, heights for all tracks.
var drawing_modes = [],
drawing_heights = [];
@@ -3019,7 +3017,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
width = Math.ceil( (tile_high - tile_low) * w_scale ) + track.left_offset,
height = _.max(drawing_heights),
tile;
-
+
//
// Draw all tracks on tile.
//
@@ -3063,7 +3061,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
var canvas = ctx.canvas,
painter = new painters.LinePainter(result.data, region.get('start'), region.get('end'), this.config.to_key_value_dict(), mode);
painter.draw(ctx, canvas.width, canvas.height, w_scale);
-
+
return new LineTrackTile(this, region, w_scale, canvas, result.data);
},
@@ -3085,11 +3083,11 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
show_tile: function(tile, w_scale) {
var track = this,
tile_element = tile.html_elt;
-
+
// -- Show/move tile element. --
-
+
tile.predisplay_actions();
-
+
// Position tile element based on current viewport.
var left = Math.round( ( tile.low - (this.is_overview? this.view.max_low : this.view.low) ) * w_scale );
if (this.left_offset) {
@@ -3110,15 +3108,15 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
// -- Update track, tile heights based on new tile. --
tile_element.css('height', 'auto');
-
+
// Update max height based on current tile's height.
- // BUG/HACK: tile_element.height() returns a height that is always 2 pixels too big, so
+ // BUG/HACK: tile_element.height() returns a height that is always 2 pixels too big, so
// -2 to get the correct height.
this.max_height_px = Math.max(this.max_height_px, tile_element.height() - 2);
// Update height for all tiles based on max height.
tile_element.parent().children().css("height", this.max_height_px + "px");
-
+
// Update track height based on max height and visible height.
var track_height = this.max_height_px;
if (this.visible_height_px !== 0) {
@@ -3150,7 +3148,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
return data.dataset_type === "bigwig";
}
// All other modes--Dense, Squish, Pack--require data + details.
- else if (data.dataset_type === "bigwig" ||
+ else if (data.dataset_type === "bigwig" ||
data.extra_info === "no_detail") {
return false;
}
@@ -3174,7 +3172,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
return true;
},
-
+
/**
* Set up track to receive tool data.
*/
@@ -3183,7 +3181,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
this.data_manager.set('data_type', 'raw_data');
this.data_query_wait = 1000;
this.dataset_check_type = 'state';
-
+
// FIXME: this is optional and is disabled for now because it creates
// additional converter jobs without a clear benefit because indexing
// such a small dataset provides little benefit.
@@ -3194,12 +3192,12 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
this.normal_postdraw_actions = this.postdraw_actions;
this.postdraw_actions = function(tiles, width, w_scale, clear_after) {
var self = this;
-
+
// Do normal postdraw init.
self.normal_postdraw_actions(tiles, width, w_scale, clear_after);
-
+
// Tool-execution specific post-draw init:
-
+
// Reset dataset check, wait time.
self.dataset_check_type = 'converted_datasets_state';
self.data_query_wait = DEFAULT_DATA_QUERY_WAIT;
@@ -3216,7 +3214,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
// Dataset is indexed, so use converted data.
self.data_manager.set('data_type', 'data');
});
-
+
// Reset post-draw actions function.
self.postdraw_actions = self.normal_postdraw_actions;
};
@@ -3234,7 +3232,7 @@ var LabelTrack = function (view, container) {
extend(LabelTrack.prototype, Track.prototype, {
init: function() {
// Enable by default because there should always be data when drawing track.
- this.enabled = true;
+ this.enabled = true;
},
/**
@@ -3266,13 +3264,13 @@ extend(LabelTrack.prototype, Track.prototype, {
// are created for each type of composite track.
/**
- * A tiled track composed of multiple other tracks. Composite tracks only work with
+ * A tiled track composed of multiple other tracks. Composite tracks only work with
* bigwig data for now.
*/
var CompositeTrack = function(view, container, obj_dict) {
TiledTrack.call(this, view, container, obj_dict);
-
- // Init drawables; each drawable is a copy so that config/preferences
+
+ // Init drawables; each drawable is a copy so that config/preferences
// are independent of each other. Also init left offset.
this.drawables = [];
if ('drawables' in obj_dict) {
@@ -3280,7 +3278,7 @@ var CompositeTrack = function(view, container, obj_dict) {
for (var i = 0; i < obj_dict.drawables.length; i++) {
drawable = obj_dict.drawables[i];
this.drawables[i] = object_from_template(drawable, view, null);
-
+
// Track's left offset is the max of all tracks.
if (drawable.left_offset > this.left_offset) {
this.left_offset = drawable.left_offset;
@@ -3295,9 +3293,9 @@ var CompositeTrack = function(view, container, obj_dict) {
d.change_mode("Coverage");
}
});
-
+
this.update_icons();
-
+
// HACK: needed for saving object for now. Need to generalize get_type() to all Drawables and use
// that for object type.
this.obj_type = "CompositeTrack";
@@ -3326,10 +3324,10 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
}
}
].concat(TiledTrack.prototype.action_icons_def),
-
+
// HACK: CompositeTrack should inherit from DrawableCollection as well.
- /**
- * Returns representation of object in a dictionary for easy saving.
+ /**
+ * Returns representation of object in a dictionary for easy saving.
* Use from_dict to recreate object.
*/
to_dict: DrawableCollection.prototype.to_dict,
@@ -3374,7 +3372,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
for (var i = 0; i < this.drawables.length; i++) {
init_deferreds.push(this.drawables[i].init());
}
-
+
// Draw composite when all tracks available.
var track = this;
$.when.apply($, init_deferreds).then(function() {
@@ -3386,7 +3384,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
update_icons: function() {
// For now, hide filters and tool.
this.action_icons.filters_icon.hide();
- this.action_icons.tools_icon.hide();
+ this.action_icons.tools_icon.hide();
this.action_icons.param_space_viz_icon.hide();
},
@@ -3412,7 +3410,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
track.container = group;
group.content_div.append(track.container_div);
}
-
+
// Replace track with group.
var index = this.container.replace_drawable(this, group, true);
group.request_draw({ clear_tile_cache: true });
@@ -3428,14 +3426,14 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
//
// Set min, max for tracks to be largest min, max.
//
-
+
// Get smallest min, biggest max.
var min = _.min(_.map(this.drawables, function(d) { return d.config.get_value('min_value'); })),
max = _.max(_.map(this.drawables, function(d) { return d.config.get_value('max_value'); }));
-
+
this.config.set_value('min_value', min);
this.config.set_value('max_value', max);
-
+
// Set all tracks to smallest min, biggest max.
_.each(this.drawables, function(d) {
d.config.set_value('min_value', min);
@@ -3458,7 +3456,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
},
/**
- * Actions to be taken after draw has been completed. Draw is completed when all tiles have been
+ * Actions to be taken after draw has been completed. Draw is completed when all tiles have been
* drawn/fetched and shown.
*/
postdraw_actions: function(tiles, width, w_scale, clear_after) {
@@ -3470,7 +3468,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
max_height = height;
}
}
-
+
for (i = 0; i < tiles.length; i++) {
var tile = tiles[i];
if (tile.html_elt.find("canvas").height() !== max_height) {
@@ -3480,7 +3478,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
}
// Wrap function so that it can be called without object reference.
- var track = this,
+ var track = this,
t = function() { track.update_all_min_max(); };
// Add min, max labels.
@@ -3490,11 +3488,11 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
});
/**
- * Displays reference genome data.
+ * Displays reference genome data.
*/
var ReferenceTrack = function (view) {
TiledTrack.call(this, view, { content_div: view.top_labeltrack }, { resize: false, header: false });
-
+
// Use offset to ensure that bases at tile edges are drawn.
this.left_offset = view.canvas_manager.char_width_px;
this.container_div.addClass("reference-track");
@@ -3542,7 +3540,7 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
}
// NOTE: viewport resizing conceptually belongs in postdraw_actions(), but currently
- // postdraw_actions is not called when reference track not shown due to no tiles. If
+ // postdraw_actions is not called when reference track not shown due to no tiles. If
// it is moved to postdraw_actions, resize must be called each time because cannot
// easily detect showing/hiding.
@@ -3563,7 +3561,7 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
// Try to subset data.
var subset = this.data_manager.subset_entry(data, region),
seq_data = subset.data;
-
+
// Draw sequence data.
var canvas = ctx.canvas;
ctx.font = ctx.canvas.manager.default_font;
@@ -3593,12 +3591,12 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
{ key: 'mode', type: 'string', default_value: this.mode, hidden: true },
{ key: 'height', type: 'int', default_value: 30, hidden: true }
] ),
-
+
config_onchange: function() {
this.set_name(this.config.get_value('name'));
this.request_draw({ clear_tile_cache: true });
},
-
+
/**
* Actions to be taken before drawing.
*/
@@ -3615,7 +3613,7 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
/**
* Subset data only if data is at single-base pair resolution.
*/
- can_subset: function(entry) {
+ can_subset: function(entry) {
return (entry.data[1][0] - entry.data[0][0] === 1);
},
@@ -3643,8 +3641,8 @@ extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype,
config_params: _.union( Drawable.prototype.config_params, [
{ key: 'pos_color', label: 'Positive Color', type: 'color', default_value: "#FF8C00" },
{ key: 'neg_color', label: 'Negative Color', type: 'color', default_value: "#4169E1" },
- { key: 'min_value', label: 'Min Value', type: 'float', default_value: -1 },
- { key: 'max_value', label: 'Max Value', type: 'float', default_value: 1 },
+ { key: 'min_value', label: 'Min Value', type: 'int', default_value: undefined },
+ { key: 'max_value', label: 'Max Value', type: 'int', default_value: undefined },
{ key: 'mode', type: 'string', default_value: this.mode, hidden: true },
{ key: 'height', type: 'int', default_value: 500, hidden: true }
] ),
@@ -3654,6 +3652,18 @@ extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype,
this.request_draw({ clear_tile_cache: true });
},
+ /**
+ * Additional initialization required before drawing track for the first time.
+ */
+ predraw_init: function() {
+ var track = this;
+ return $.getJSON( track.dataset.url(),
+ { data_type: 'data', stats: true, chrom: track.view.chrom, low: 0,
+ high: track.view.max_high, hda_ldda: track.dataset.get('hda_ldda') }, function(result) {
+ var data = result.data;
+ });
+ },
+
/**
* Draw tile.
*/
@@ -3662,7 +3672,7 @@ extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype,
var canvas = ctx.canvas,
painter = new painters.DiagonalHeatmapPainter(result.data, region.get('start'), region.get('end'), this.config.to_key_value_dict(), mode);
painter.draw(ctx, canvas.width, canvas.height, w_scale);
-
+
return new Tile(this, region, w_scale, canvas, result.data);
}
});
@@ -3688,7 +3698,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
{ key: 'block_color', label: 'Block color', type: 'color' },
{ key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color' },
{ key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
- { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true,
+ { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true,
help: 'Show the number of items in each bin when drawing summary histogram' },
{ key: 'min_value', label: 'Histogram minimum', type: 'float', default_value: null, help: 'clear value to set automatically' },
{ key: 'max_value', label: 'Histogram maximum', type: 'float', default_value: null, help: 'clear value to set automatically' },
@@ -3713,12 +3723,12 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
},
/**
- * Actions to be taken after draw has been completed. Draw is completed when all tiles have been
+ * Actions to be taken after draw has been completed. Draw is completed when all tiles have been
* drawn/fetched and shown.
*/
postdraw_actions: function(tiles, width, w_scale, clear_after) {
TiledTrack.prototype.postdraw_actions.call(this, tiles, width, w_scale, clear_after);
-
+
var track = this,
i,
line_track_tiles = _.filter(tiles, function(t) {
@@ -3742,7 +3752,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
var self = this;
_.each(tiles, function(tile) {
// Remove features already drawn on tile originally.
- var tile_incomplete_features =_.omit(all_incomplete_features,
+ var tile_incomplete_features =_.omit(all_incomplete_features,
_.map(tile.incomplete_features, function(f) { return f[0]; }));
// Remove features already drawn on tile in past postdraw actions.
@@ -3750,17 +3760,17 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
// Draw tile's incomplete features.
if (_.size(tile_incomplete_features) !== 0) {
- // To draw incomplete features, create new canvas, copy original canvas/tile onto new
+ // To draw incomplete features, create new canvas, copy original canvas/tile onto new
// canvas, and then draw incomplete features on the new canvas.
var features = { data: _.values( tile_incomplete_features ) },
new_canvas = self.view.canvas_manager.new_canvas(),
new_canvas_ctx = new_canvas.getContext('2d');
- new_canvas.height = Math.max(tile.canvas.height,
+ new_canvas.height = Math.max(tile.canvas.height,
self.get_canvas_height(features, tile.mode, tile.w_scale, 100));
new_canvas.width = tile.canvas.width;
new_canvas_ctx.drawImage(tile.canvas, 0, 0);
new_canvas_ctx.translate(track.left_offset, 0);
- var new_tile = self.draw_tile(features, new_canvas_ctx, tile.mode,
+ var new_tile = self.draw_tile(features, new_canvas_ctx, tile.mode,
tile.region, tile.w_scale, tile.seq_data);
$(tile.canvas).replaceWith($(new_tile.canvas));
tile.canvas = new_canvas;
@@ -3768,7 +3778,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
}
});
}
-
+
// If mode is Coverage and tiles do not share max, redraw tiles as necessary using new max.
/*
This code isn't used right now because Coverage mode uses predefined max in preferences.
@@ -3781,7 +3791,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
global_max = cur_max;
}
}
-
+
for (i = 0; i < tiles.length; i++) {
var tile = tiles[i];
if (tile.max_val !== global_max) {
@@ -3790,8 +3800,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
}
}
}
- */
-
+ */
+
//
// Update filter attributes, UI.
//
@@ -3814,7 +3824,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
example_feature = tiles[i].data[0];
for (f = 0; f < filters.length; f++) {
filter = filters[f];
- if ( filter.applies_to(example_feature) &&
+ if ( filter.applies_to(example_feature) &&
filter.min !== filter.max ) {
filters_available = true;
break;
@@ -3832,7 +3842,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
track.update_icons();
}
}
-
+
//
// If not all features slotted, show icon for showing more rows (slots).
//
@@ -3869,10 +3879,10 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
* is a Slotter object. Returns the number of slots used to pack features.
*/
incremental_slots: function(level, features, mode) {
-
+
// Get/create incremental slots for level. If display mode changed,
// need to create new slots.
-
+
var dummy_context = this.view.canvas_manager.dummy_context,
slotter = this.slotters[level];
if (!slotter || (slotter.mode !== mode)) {
@@ -3890,11 +3900,11 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
// HACK: use no_detail mode track is in overview to prevent overview from being too large.
if (data.extra_info === "no_detail" || this.is_overview) {
mode = "no_detail";
- }
+ }
else {
// Choose b/t Squish and Pack.
- // Proxy measures for using Squish:
- // (a) error message re: limiting number of features shown;
+ // Proxy measures for using Squish:
+ // (a) error message re: limiting number of features shown;
// (b) X number of features shown;
// (c) size of view shown.
// TODO: cannot use (a) and (b) because it requires coordinating mode across tiles;
@@ -3956,7 +3966,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
// Handle row-by-row tracks
// Preprocessing: filter features and determine whether all unfiltered features have been slotted.
- var
+ var
filtered = [],
slots = this.slotters[w_scale].slots;
all_slotted = true;
@@ -3983,12 +3993,12 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
}
}
}
- }
-
+ }
+
// Create painter.
var filter_alpha_scaler = (this.filters_manager.alpha_filter ? new FilterScaler(this.filters_manager.alpha_filter) : null),
filter_height_scaler = (this.filters_manager.height_filter ? new FilterScaler(this.filters_manager.height_filter) : null),
- painter = new (this.painter)(filtered, tile_low, tile_high, this.config.to_key_value_dict(), mode, filter_alpha_scaler, filter_height_scaler,
+ painter = new (this.painter)(filtered, tile_low, tile_high, this.config.to_key_value_dict(), mode, filter_alpha_scaler, filter_height_scaler,
// HACK: ref_seq only be defined for ReadTracks, and only the ReadPainter accepts that argument
ref_seq,
// Only the ReadPainer will use this function
@@ -3998,7 +4008,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
ctx.fillStyle = this.config.get_value('block_color');
ctx.font = ctx.canvas.manager.default_font;
ctx.textAlign = "right";
-
+
if (result.data) {
// Draw features.
var draw_results = painter.draw(ctx, canvas.width, canvas.height, w_scale, slots);
@@ -4006,11 +4016,11 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
incomplete_features = draw_results.incomplete_features;
feature_mapper.translation = -left_offset;
}
-
+
// If not drawing on current tile, create new tile.
if (!cur_tile) {
- return new FeatureTrackTile(track, region, w_scale, canvas, result.data, mode,
- result.message, all_slotted, feature_mapper,
+ return new FeatureTrackTile(track, region, w_scale, canvas, result.data, mode,
+ result.message, all_slotted, feature_mapper,
incomplete_features, ref_seq);
}
}
@@ -4024,7 +4034,7 @@ var VariantTrack = function(view, container, obj_dict) {
this.painter = painters.VariantPainter;
this.summary_draw_height = 30;
- // Maximum resolution is ~45 pixels/base, so use this size left offset to ensure that full
+ // Maximum resolution is ~45 pixels/base, so use this size left offset to ensure that full
// variant is drawn when variant is at start of tile.
this.left_offset = 30;
};
@@ -4040,7 +4050,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
{ key: 'mode', type: 'string', default_value: this.mode, hidden: true },
{ key: 'height', type: 'int', default_value: 0, hidden: true }
] ),
-
+
config_onchange: function() {
this.set_name(this.config.get_value('name'));
this.request_draw({ clear_tile_cache: true });
@@ -4073,7 +4083,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
}
else {
// HACK: sample_names is not be defined when dataset definition is fetched before
- // dataset is complete (as is done when running tools). In that case, fall back on
+ // dataset is complete (as is done when running tools). In that case, fall back on
// # of samples in data. This can be fixed by re-requesting dataset definition
// in init.
var num_samples = ( this.dataset.get_metadata('sample_names') ? this.dataset.get_metadata('sample_names').length : 0);
@@ -4087,7 +4097,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
num_samples = num_samples.length + 1;
}
}
-
+
var dummy_painter = new (this.painter)(null, null, null, this.config.to_key_value_dict(), mode);
return dummy_painter.get_required_height(num_samples);
}
@@ -4107,7 +4117,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
},
/**
- * Actions to be taken after draw has been completed. Draw is completed when all tiles have been
+ * Actions to be taken after draw has been completed. Draw is completed when all tiles have been
* drawn/fetched and shown.
*/
postdraw_actions: function(tiles, width, w_scale, clear_after) {
@@ -4134,12 +4144,12 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
'top': (this.config.get_value('summary_height') - font_size) / 2 + 'px'
})
);
-
+
// Show sample labels.
if (this.config.get_value('show_sample_data')) {
var samples_div_html = sample_names.join('
'); - this.tiles_div.prepend( + this.tiles_div.prepend( $("").html(samples_div_html).addClass('yaxislabel variant top sample').css({ 'top': this.config.get_value('summary_height') }) @@ -4169,7 +4179,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, { * Track that displays mapped reads. Track expects position data in 1-based, closed format, i.e. SAM/BAM format. */ var ReadTrack = function (view, container, obj_dict) { - FeatureTrack.call(this, view, container, obj_dict); + FeatureTrack.call(this, view, container, obj_dict); this.painter = painters.ReadPainter; this.update_icons(); }; @@ -4211,7 +4221,7 @@ var addable_objects = { }; /** - * Create new object from a template. A template can be either an object dictionary or an + * Create new object from a template. A template can be either an object dictionary or an * object itself. */ var object_from_template = function(template, view, container) { diff --git a/client/galaxy/style/less/trackster.less b/client/galaxy/style/less/trackster.less index 90c6854094c..eabdfcf527a 100644 --- a/client/galaxy/style/less/trackster.less +++ b/client/galaxy/style/less/trackster.less @@ -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; -} \ No newline at end of file +} diff --git a/client/galaxy/style/source_material/circle.py b/client/galaxy/style/source_material/circle.py index 979f42211d9..5331a0e0cc4 100755 --- a/client/galaxy/style/source_material/circle.py +++ b/client/galaxy/style/source_material/circle.py @@ -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" ) diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample index ce2aacac162..efdfc887220 100644 --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -59,6 +59,7 @@
",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. 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r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(e){this.$content.append(e)},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='';return e.icon&&(t+=''),t+=" "+e.title+""+" ",t},_templateMenu:function(){return''},_templateDivider:function(){return''},_template:function(e){var t="",n="";e.title?t="width: 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'},_templateContainer:function(e,t){return'"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i';return e.title&&(t+='
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"+"',e.placement=="top"&&(t+=''),t+='',e.placement=="bottom"&&(t+=''),t+="
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r=[];this.$text.on("keyup",function(e){r[e.which]=!1}),this.$text.on("keydown",function(e){var t=e.which;r[t]=!0,t==8||t==9||t==13||t==37||t==39||t>=48&&t<=57||t==190&&$(this).val().indexOf(".")==-1&&n.options.precise||t==189&&$(this).val().indexOf("-")==-1||r[91]||r[17]||event.preventDefault()})},value:function(e){return e!==undefined&&(isNaN(e)&&(e=0),this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.$slider&&this.$slider.slider("value",e),this.$text.val(e),this.options.onchange&&this.options.onchange(e)),this.$text.val()},_template:function(e){return'"}});return{View:t}}),define("mvc/ui/ui-button-check",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($("")),this.value(this.options.value);var n=this;this.$el.on("click",function(){n.current=!n.current&&2||0,n.value(n.current),n.options.onclick&&n.options.onclick()})},value:function(e){return e!==undefined&&(this.current=e,this.$el.removeClass().addClass("ui-button-check").addClass(this.options.icons[e]),this.options.onchange&&this.options.onchange(e)),this.current}})}),define("mvc/ui/ui-options",["utils/utils","mvc/ui/ui-button-check"],function(e,t){var n=Backbone.View.extend({initialize:function(n){this.optionsDefault={visible:!0,data:[],id:e.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:!1},this.options=e.merge(n,this.optionsDefault),this.setElement(''),this.$message=$(""),this.$options=$(this._template(n)),this.$menu=$(''),this.$el.append(this.$message),this.$el.append(this.$menu),this.$el.append(this.$options),this.options.multiple&&(this.select_button=new t({onclick:function(){r.$("input").prop("checked",r.select_button.value()!==0),r._change()}}),this.$menu.addClass("ui-margin-bottom"),this.$menu.append(this.select_button.$el),this.$menu.append("Select/Unselect all")),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value);var r=this;this.on("change",function(){r._change()})},update:function(e){var t=this._getValue();this.$options.empty();if(this._templateOptions)this.$options.append(this._templateOptions(e));else for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),r.tooltip({title:e[n].tooltip,placement:"bottom"}),this.$options.append(r)}var i=this;this.$("input").on("change",function(){i.value(i._getValue()),i._change()}),this.value(t)},value:function(e){if(e!==undefined){this.$("input").prop("checked",!1);if(e!==null){e instanceof Array||(e=[e]);for(var t in e)this.$('input[value="'+e[t]+'"]').first().prop("checked",!0)}}return this._refresh(),this._getValue()},exists:function(e){if(e!==undefined){e instanceof Array||(e=[e]);for(var t in e)if(this.$('input[value="'+e[t]+'"]').length>0)return!0}return!1},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this._size()==0&&(this._messageShow(this.options.wait_text,"info"),this.$options.hide(),this.$menu.hide())},unwait:function(){this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.error_text,"danger"),this.$options.hide(),this.$menu.hide()):(this._messageHide(),this.$options.css("display","inline-block"),this.$menu.show());if(this.select_button){var e=this._size(),t=this._getValue();t instanceof Array?t.length!==e?this.select_button.value(1):this.select_button.value(2):this.select_button.value(0)}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push($(this).val())}),e.validate(t)?this.options.multiple?t:t[0]:null},_size:function(){return this.$(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()},_template:function(){return''}}),r=n.extend({_templateOption:function(t){var n=e.uuid();return''+'"+"
"}}),i={};i.View=r.extend({initialize:function(e){e.type="radio",r.prototype.initialize.call(this,e)}});var s={};s.View=r.extend({initialize:function(e){e.multiple=!0,e.type="checkbox",r.prototype.initialize.call(this,e)}});var o={};return o.View=n.extend({initialize:function(e){n.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t="fa "+e.icon;e.label||(t+=" no-padding");var n='",n},_template:function(){return''}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e),this.initial=!0},value:function(e){var n=t.BaseIcons.prototype.value.call(this,e);if(this.initial&&n!==null&&this.header_index){this.initial=!1;var r=n;$.isArray(r)||(r=[r]);for(var i in r){var s=this.header_index[r[i]];for(var o in s)this._setState(s[o],!0)}}return n},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("");if(f){var h=e.uuid(),p=$(''),d=$('');l.push(h);var v=$("");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("");return s(o,t),o},_template:function(e){return''}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t=''+'
",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return' '+e.title+"
"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='';return e.title?n+='":n+='',n+="
",n}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(""),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return''}}),v=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'"+"
"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'':''}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='';return e.info&&(t+="
",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f"+e.info+"
"),t+='"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=r.is_text,c=[],h=n[e];o&&c.push({label:"Column: Row Number",value:"auto"}),f&&c.push({label:"Column: None",value:"zero"});var p=t.metadata_column_types;for(var d in p){var v=!1;p[d]=="int"||p[d]=="float"?v=u:v=l||s,v&&c.push({label:"Column: "+(parseInt(d)+1),value:d})}h.update(c),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!h.exists(this.group.get(e))){var m=h.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+m+'".'),this.group.set(e,m)}h.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){h.value(i.group.get(e))}),h.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),h.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("");u.append(s.$el),n.info&&u.append('
'+n.info+"
"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add(''+n.title+"","25%"),this.table.add(u))}else this.table.add(''+n.title+":"),this.table.add($(""));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('');s.append((new t.Label({title:"How many data points would you like to analyze?"})).$el),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(this.library.$el.addClass("ui-margin-bottom")),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o=''+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'
'+"• "+e.title+"
"},_template_item:function(e){return'
'+''+'
'+e.title+"
"+""}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(r,i){var s=this;this.app=r,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){s._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){s.app.go("viewer"),s.app.storage.load()}})}}),this.types=new a(r,{onchange:function(e){var t=s.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),s.chart.definition=t,s.chart.settings.clear(),s.chart.set({type:e}),s.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){s._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=s._addGroupModel();s.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){s.chart.set("title",s.title.value())}});var o=$("");o.append((new t.Label({title:"Provide a chart title:"})).$el),o.append(this.title.$el),o.append($("").addClass("ui-table-form-info").html("This title will appear in the list of 'Saved Visualizations'. Charts are saved upon creation.")),o.append(this.types.$el.addClass("ui-margin-top")),this.tabs.add({id:"main",title:"Start",$el:o}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.tabs.$el.addClass("ui-margin-top")),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var s=this;this.chart.on("change:title",function(e){s._refreshTitle()}),this.chart.on("change:type",function(e){s.types.value(e.get("type"))}),this.chart.on("reset",function(e){s._resetChart()}),this.app.chart.on("redraw",function(e){s.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){s._addGroup(e)}),this.app.chart.groups.on("remove",function(e){s._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){s._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){s._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value()!=e&&this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]==="__null__"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["x_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["x_axis_precision"]}},{label:"Float",value:"f",operations:{show:["x_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["x_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["x_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["x_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["x_axis_precision"]}}]},x_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_y:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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arguments.length?(v=e,E):v},E.yRange=function(e){return arguments.length?(m=e,E):m},E.forceY=function(e){return arguments.length?(f=e,E):f},E.color=function(t){return arguments.length?(l=e.utils.getColor(t),E):l},E.id=function(e){return arguments.length?(i=e,E):i},E.showValues=function(e){return arguments.length?(c=e,E):c},E.valueFormat=function(e){return arguments.length?(h=e,E):h},E.rectClass=function(e){return arguments.length?(y=e,E):y},E},e.models.discreteBarChart=function(){function w(e){return e.each(function(e){var u=d3.select(this),p=this,y=(s||parseInt(u.style("width"))||960)-i.left-i.right,E=(o||parseInt(u.style("height"))||400)-i.top-i.bottom;w.update=function(){g.beforeUpdate(),u.call(w)},w.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var S=u.selectAll(".nv-noData").data([m]);return S.enter().append("text").attr("class","nvd3 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u(s(e,t))}).attr(i+"2",function(e,t){return u(s(e,t))}),f=u.copy()}),l}var t={top:0,right:0,bottom:0,left:0},n=400,r=8,i="x",s=function(e){return e[i]},o=e.utils.defaultColor(),u=d3.scale.linear(),a,f;return l.options=e.utils.optionsFunc.bind(l),l.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,l):t},l.width=function(e){return arguments.length?(n=e,l):n},l.axis=function(e){return arguments.length?(i=e,l):i},l.size=function(e){return arguments.length?(r=e,l):r},l.getData=function(e){return arguments.length?(s=d3.functor(e),l):s},l.scale=function(e){return arguments.length?(u=e,l):u},l.color=function(t){return arguments.length?(o=e.utils.getColor(t),l):o},l},e.models.historicalBarChart=function(){function x(e){return e.each(function(d){var 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var 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K=V.append("g").attr("class","nv-context");K.append("g").attr("class","nv-x nv-axis"),K.append("g").attr("class","nv-y1 nv-axis"),K.append("g").attr("class","nv-y2 nv-axis"),K.append("g").attr("class","nv-barsWrap"),K.append("g").attr("class","nv-linesWrap"),K.append("g").attr("class","nv-brushBackground"),K.append("g").attr("class","nv-x nv-brush"),E&&(c.width(j/2),$.select(".nv-legendWrap").datum(e.map(function(e){return e.originalKey=e.originalKey===undefined?e.key:e.originalKey,e.key=e.originalKey+(e.bar?" 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+p.left,e.pos[1]+p.top],D.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){D.tooltipHide(e)}),r.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+p.left,e.pos[1]+p.top],D.tooltipShow(e)}),r.dispatch.on("elementMouseout.tooltip",function(e){D.tooltipHide(e)}),D.on("tooltipHide",function(){T&&e.tooltip.cleanup()}),B.dispatch=D,B.legend=c,B.lines=t,B.lines2=n,B.bars=r,B.bars2=i,B.xAxis=s,B.x2Axis=o,B.y1Axis=u,B.y2Axis=a,B.y3Axis=f,B.y4Axis=l,d3.rebind(B,t,"defined","size","clipVoronoi","interpolate"),B.options=e.utils.optionsFunc.bind(B),B.x=function(e){return arguments.length?(y=e,t.x(e),r.x(e),B):y},B.y=function(e){return arguments.length?(b=e,t.y(e),r.y(e),B):b},B.margin=function(e){return arguments.length?(p.top=typeof e.top!="undefined"?e.top:p.top,p.right=typeof e.right!="undefined"?e.right:p.right,p.bottom=typeof e.bottom!="undefined"?e.bottom:p.bottom,p.left=typeof 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e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n
'},_templateContainer:function(e,t){return'"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i';return e.title&&(t+='"),t+='
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',"top"==e.placement&&(t+=''),t+='',"bottom"==e.placement&&(t+=''),t+='
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r=[];this.$text.on("keyup",function(e){r[e.which]=!1}),this.$text.on("keydown",function(e){var t=e.which;r[t]=!0,8==t||9==t||13==t||37==t||39==t||t>=48&&57>=t||190==t&&-1==$(this).val().indexOf(".")&&n.options.precise||189==t&&-1==$(this).val().indexOf("-")||r[91]||r[17]||event.preventDefault()})},value:function(e){return void 0!==e&&(null!==e&&""!==e&&(isNaN(e)&&(e=0),null!==this.options.max&&(e=Math.min(e,this.options.max)),null!==this.options.min&&(e=Math.max(e,this.options.min))),this.$slider&&this.$slider.slider("value",e),this.$text.val(e),this.options.onchange&&this.options.onchange(e)),this.$text.val()},_template:function(e){return''}});return{View:t}}),define("mvc/ui/ui-options",["utils/utils","mvc/ui/ui-button-check"],function(e,t){var n=Backbone.View.extend({initialize:function(n){var r=this;this.optionsDefault={visible:!0,data:[],id:e.uid(),error_text:"No data available.",wait_text:"Please wait...",multiple:!1},this.options=e.merge(n,this.optionsDefault),this.setElement(''),this.$message=$(""),this.$options=$(this._template(n)),this.$menu=$(''),this.$el.append(this.$message),this.$el.append(this.$menu),this.$el.append(this.$options),this.options.multiple&&(this.all_button=new t({onclick:function(){r.$("input").prop("checked",0!==r.all_button.value()),r.trigger("change")}}),this.$menu.append(this.all_button.$el)),this.options.visible||this.$el.hide(),this.update(this.options.data),void 0!==this.options.value&&this.value(this.options.value),this.on("change",function(){this.options.onchange&&this.options.onchange(this.value())})},update:function(e){var t=this._getValue();if(this.$options.empty(),this._templateOptions)this.$options.append(this._templateOptions(e));else for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),r.tooltip({title:e[n].tooltip,placement:"bottom"}),this.$options.append(r)}var i=this;this.$("input").on("change",function(){i.value(i._getValue()),i.trigger("change")}),this.value(t),this.unwait()},value:function(e){if(void 0!==e&&(this.$("input").prop("checked",!1),null!==e)){e instanceof Array||(e=[e]);for(var t in e)this.$('input[value="'+e[t]+'"]').first().prop("checked",!0)}var n=this._getValue();if(this.all_button){var r=n;r=r instanceof Array?r.length:0,this.all_button.value(r,this._size())}return n},exists:function(e){if(void 0!==e){e instanceof Array||(e=[e]);for(var t in e)if(this.$('input[value="'+e[t]+'"]').length>0)return!0}return!1},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){0==this._size()&&(this._messageShow(this.options.wait_text,"info"),this.$options.hide(),this.$menu.hide())},unwait:function(){var e=this._size();0==e?(this._messageShow(this.options.error_text,"danger"),this.$options.hide(),this.$menu.hide()):(this._messageHide(),this.$options.css("display","inline-block"),this.$menu.show())},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push($(this).val())}),e.validate(t)?this.options.multiple?t:t[0]:null},_size:function(){return this.$(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()},_template:function(){return''}}),r=n.extend({_templateOption:function(t){var n=e.uid();return'"}}),i={};i.View=r.extend({initialize:function(e){e.type="radio",r.prototype.initialize.call(this,e)}});var s={};s.View=r.extend({initialize:function(e){e.multiple=!0,e.type="checkbox",r.prototype.initialize.call(this,e)}});var o={};return o.View=n.extend({initialize:function(e){n.prototype.initialize.call(this,e)},value:function(e){return void 0!==e&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t="fa "+e.icon;e.label||(t+=" no-padding");var n='"},_template:function(){return''}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple="checkbox"==e.display,t.BaseIcons.prototype.initialize.call(this,e),this.initial=!0},value:function(e){var n=t.BaseIcons.prototype.value.call(this,e);if(this.initial&&null!==n&&this.header_index){this.initial=!1;var r=n;$.isArray(r)||(r=[r]);for(var i in r){var s=this.header_index[r[i]];for(var o in s)this._setState(s[o],!0)}}return n},_setState:function(e,t){var n=this.$(".button-"+e),r=this.$(".subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function n(e,t){var n=e.find(".button-"+t);n.on("click",function(){s._setState(t,!n.data("is_expanded"))})}function r(t,o,u){u=u||[];for(i in o){var f=o[i],l=f.options.length>0,h=u.slice(0);s.header_index[f.value]=h.slice(0);var p=$("");if(l){var v=e.uid(),m=$(''),g=$('');h.push(v);var y=$("");y.append(m),y.append(s._templateOption({label:f.name,value:f.value})),p.append(y),r(g,f.options,h),p.append(g),n(p,v)}else p.append(s._templateOption({label:f.name,value:f.value}));t.append(p)}}var s=this;this.header_index={};var o=$("");return r(o,t),o},_template:function(e){return''}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='
"}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'
'+e.title+"
"}}),c=Backbone.View.extend({optionsDefault:{id:e.uid(),title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},wait:function(){this.$el.removeClass(this.options.cls).addClass("btn btn-info").prop("disabled",!0),this.$(".icon").removeClass(this.options.icon).addClass("fa-spinner fa-spin"),this.$(".title").html("Sending...")},unwait:function(){this.$el.removeClass("btn btn-info").addClass(this.options.cls).prop("disabled",!1),this.$(".icon").removeClass("fa-spinner fa-spin").addClass(this.options.icon),this.$(".title").html(this.options.title)},_template:function(e){var t='"}}),h=Backbone.View.extend({optionsDefault:{id:e.uid(),title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='';return n+=e.title?'":'',n+="
"}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(""),this.options.message&&this.update(this.options)},update:function(t){if(this.options=e.merge(t,this.optionsDefault),""!=t.message){if(this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout),!t.persistent){var n=this;this.timeout=window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return''}}),v=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(){var e=n.$el.find("#search");n.options.onclick(e.val())})},_template:function(e){return''}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),void 0!==this.options.value&&this.value(this.options.value),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return void 0!==e&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'':''}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),void 0!==this.options.value&&this.value(this.options.value)},value:function(e){return void 0!==e&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='';return e.info&&(t+="
'}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f"+e.info+"
"),t+='"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=r.is_text,c=[],h=n[e];o&&c.push({label:"Column: Row Number",value:"auto"}),f&&c.push({label:"Column: None",value:"zero"});var p=t.metadata_column_types;for(var d in p){var v=!1;p[d]=="int"||p[d]=="float"?v=u:v=l||s,v&&c.push({label:"Column: "+(parseInt(d)+1),value:d})}h.update(c),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!h.exists(this.group.get(e))){var m=h.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+m+'".'),this.group.set(e,m)}h.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){h.value(i.group.get(e))}),h.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),h.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("");u.append(s.$el),n.info&&u.append('
'+n.info+"
"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add(''+n.title+"","25%"),this.table.add(u))}else this.table.add(''+n.title+":"),this.table.add($(""));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('');s.append((new t.Label({title:"How many data points would you like to analyze?"})).$el),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(this.library.$el.addClass("ui-margin-bottom")),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o=''+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'
'+"• "+e.title+"
"},_template_item:function(e){return'
'+''+'
'+e.title+"
"+""}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(r,i){var s=this;this.app=r,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){s._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){s.app.go("viewer"),s.app.storage.load()}})}}),this.types=new a(r,{onchange:function(e){var t=s.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),s.chart.definition=t,s.chart.settings.clear(),s.chart.set({type:e}),s.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){s._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=s._addGroupModel();s.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){s.chart.set("title",s.title.value())}});var o=$("");o.append((new t.Label({title:"Provide a chart title:"})).$el),o.append(this.title.$el),o.append($("").addClass("ui-table-form-info").html("This title will appear in the list of 'Saved Visualizations'. Charts are saved upon creation.")),o.append(this.types.$el.addClass("ui-margin-top")),this.tabs.add({id:"main",title:"Start",$el:o}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.tabs.$el.addClass("ui-margin-top")),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var s=this;this.chart.on("change:title",function(e){s._refreshTitle()}),this.chart.on("change:type",function(e){s.types.value(e.get("type"))}),this.chart.on("reset",function(e){s._resetChart()}),this.app.chart.on("redraw",function(e){s.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){s._addGroup(e)}),this.app.chart.groups.on("remove",function(e){s._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){s._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){s._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value()!=e&&this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]==="__null__"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["x_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["x_axis_precision"]}},{label:"Float",value:"f",operations:{show:["x_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["x_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["x_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["x_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["x_axis_precision"]}}]},x_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_y:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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j;L={};for(j in k)k[j]instanceof Array?L[j]=k[j].slice(0):L[j]=k[j]}if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var F=T.selectAll(".nv-noData").data([O]);return F.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),F.attr("x",a.left+C/2).attr("y",a.top+M/2).text(function(e){return e}),B}T.selectAll(".nv-noData").remove(),h=t.xScale(),p=t.yScale(),_=_||h,D=D||p;var I=T.selectAll("g.nv-wrap.nv-scatterChart").data([e]),q=I.enter().append("g").attr("class","nvd3 nv-wrap nv-scatterChart nv-chart-"+t.id()),R=q.append("g"),U=I.select("g");R.append("rect").attr("class","nvd3 nv-background").style("pointer-events","none"),R.append("g").attr("class","nv-x nv-axis"),R.append("g").attr("class","nv-y nv-axis"),R.append("g").attr("class","nv-scatterWrap"),R.append("g").attr("class","nv-regressionLinesWrap"),R.append("g").attr("class","nv-distWrap"),R.append("g").attr("class","nv-legendWrap"),R.append("g").attr("class","nv-controlsWrap"),I.attr("transform","translate("+a.left+","+a.top+")"),b&&U.select(".nv-y.nv-axis").attr("transform","translate("+C+",0)"),m&&(i.width(C/2),I.select(".nv-legendWrap").datum(e).call(i),a.top!=i.height()&&(a.top=i.height(),M=(l||parseInt(T.style("height"))||400)-a.top-a.bottom),I.select(".nv-legendWrap").attr("transform","translate("+C/2+","+ -a.top+")")),w&&(s.width(180).color(["#444"]),U.select(".nv-controlsWrap").datum(H).attr("transform","translate(0,"+ -a.top+")").call(s)),t.width(C).height(M).color(e.map(function(e,t){return e.color||c(e,t)}).filter(function(t,n){return!e[n].disabled})),I.select(".nv-scatterWrap").datum(e.filter(function(e){return!e.disabled})).call(t),I.select(".nv-regressionLinesWrap").attr("clip-path","url(#nv-edge-clip-"+t.id()+")");var z=I.select(".nv-regressionLinesWrap").selectAll(".nv-regLines").data(function(e){return e});z.enter().append("g").attr("class","nv-regLines");var W=z.selectAll(".nv-regLine").data(function(e){return[e]}),X=W.enter().append("line").attr("class","nv-regLine").style("stroke-opacity",0);W.attr("x1",h.range()[0]).attr("x2",h.range()[1]).attr("y1",function(e,t){return p(h.domain()[0]*e.slope+e.intercept)}).attr("y2",function(e,t){return p(h.domain()[1]*e.slope+e.intercept)}).style("stroke",function(e,t,n){return c(e,n)}).style("stroke-opacity",function(e,t){return e.disabled||typeof e.slope=="undefined"||typeof e.intercept=="undefined"?0:1}),g&&(n.scale(h).ticks(n.ticks()?n.ticks():C/100).tickSize(-M,0),U.select(".nv-x.nv-axis").attr("transform","translate(0,"+p.range()[0]+")").call(n)),y&&(r.scale(p).ticks(r.ticks()?r.ticks():M/36).tickSize(-C,0),U.select(".nv-y.nv-axis").call(r)),d&&(o.getData(t.x()).scale(h).width(C).color(e.map(function(e,t){return e.color||c(e,t)}).filter(function(t,n){return!e[n].disabled})),R.select(".nv-distWrap").append("g").attr("class","nv-distributionX"),U.select(".nv-distributionX").attr("transform","translate(0,"+p.range()[0]+")").datum(e.filter(function(e){return!e.disabled})).call(o)),v&&(u.getData(t.y()).scale(p).width(M).color(e.map(function(e,t){return e.color||c(e,t)}).filter(function(t,n){return!e[n].disabled})),R.select(".nv-distWrap").append("g").attr("class","nv-distributionY"),U.select(".nv-distributionY").attr("transform","translate("+(b?C:-u.size())+",0)").datum(e.filter(function(e){return!e.disabled})).call(u)),d3.fisheye&&(U.select(".nv-background").attr("width",C).attr("height",M),U.select(".nv-background").on("mousemove",V),U.select(".nv-background").on("click",function(){S=!S}),t.dispatch.on("elementClick.freezeFisheye",function(){S=!S})),s.dispatch.on("legendClick",function(e,i){e.disabled=!e.disabled,E=e.disabled?0:2.5,U.select(".nv-background").style("pointer-events",e.disabled?"none":"all"),U.select(".nv-point-paths").style("pointer-events",e.disabled?"all":"none"),e.disabled?(h.distortion(E).focus(0),p.distortion(E).focus(0),U.select(".nv-scatterWrap").call(t),U.select(".nv-x.nv-axis").call(n),U.select(".nv-y.nv-axis").call(r)):S=!1,B.update()}),i.dispatch.on("stateChange",function(e){k=e,A.stateChange(k),B.update()}),t.dispatch.on("elementMouseover.tooltip",function(e){d3.select(".nv-chart-"+t.id()+" 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return""+t+""},N=function(e,t,n){return""+n+""},C=function(e,t,n,r){return"2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return r.tickFormat()(e)};o.tooltip.position({left:f+u.left,top:i.mouseY+u.top}).chartContainer(_.parentNode).enabled(g).valueFormatter(m).data({value:v,series:c})(),o.renderGuideLine(f)}),o.dispatch.on("elementMouseout",function(e){N.tooltipHide(),t.clearHighlights()}),N.on("tooltipShow",function(e){g&&O(e,_.parentNode)}),N.on("changeState",function(e){typeof e.disabled!="undefined"&&y.length===e.disabled.length&&(y.forEach(function(t,n){t.disabled=e.disabled[n]}),S.disabled=e.disabled),typeof e.style!="undefined"&&t.style(e.style),M.update()})}),M}var t=e.models.stackedArea(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.interactiveGuideline(),u={top:30,right:25,bottom:50,left:60},a=null,f=null,l=e.utils.defaultColor(),c=!0,h=!0,p=!0,d=!0,v=!1,m=!1,g=!0,y=function(e,t,n,r,i){return"
+ API Documentation
Application Documentation
diff --git a/doc/source/lib/fpconst.rst b/doc/source/lib/fpconst.rst
deleted file mode 100644
index 842351fad4b..00000000000
--- a/doc/source/lib/fpconst.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-fpconst Module
-==============
-
-.. automodule:: fpconst
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/doc/source/lib/galaxy.actions.rst b/doc/source/lib/galaxy.actions.rst
index d022b96ef2b..bd4c48070b6 100644
--- a/doc/source/lib/galaxy.actions.rst
+++ b/doc/source/lib/galaxy.actions.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.auth.providers.rst b/doc/source/lib/galaxy.auth.providers.rst
new file mode 100644
index 00000000000..1c5c1945329
--- /dev/null
+++ b/doc/source/lib/galaxy.auth.providers.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.auth.rst b/doc/source/lib/galaxy.auth.rst
new file mode 100644
index 00000000000..eefcbc6f87d
--- /dev/null
+++ b/doc/source/lib/galaxy.auth.rst
@@ -0,0 +1,15 @@
+galaxy.auth package
+===================
+
+.. automodule:: galaxy.auth
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.auth.providers
+
diff --git a/doc/source/lib/galaxy.dataset_collections.rst b/doc/source/lib/galaxy.dataset_collections.rst
new file mode 100644
index 00000000000..e065d302c50
--- /dev/null
+++ b/doc/source/lib/galaxy.dataset_collections.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.dataset_collections.types.rst b/doc/source/lib/galaxy.dataset_collections.types.rst
new file mode 100644
index 00000000000..639fbf2b5c5
--- /dev/null
+++ b/doc/source/lib/galaxy.dataset_collections.types.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.datatypes.converters.rst b/doc/source/lib/galaxy.datatypes.converters.rst
index 99565bdfd81..7435e980ab5 100644
--- a/doc/source/lib/galaxy.datatypes.converters.rst
+++ b/doc/source/lib/galaxy.datatypes.converters.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.datatypes.dataproviders.rst b/doc/source/lib/galaxy.datatypes.dataproviders.rst
new file mode 100644
index 00000000000..cd85ef190df
--- /dev/null
+++ b/doc/source/lib/galaxy.datatypes.dataproviders.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.datatypes.display_applications.rst b/doc/source/lib/galaxy.datatypes.display_applications.rst
index 371a9eb619d..a6f3e5e53a2 100644
--- a/doc/source/lib/galaxy.datatypes.display_applications.rst
+++ b/doc/source/lib/galaxy.datatypes.display_applications.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.datatypes.rst b/doc/source/lib/galaxy.datatypes.rst
index 6479be38551..e660f27b6e5 100644
--- a/doc/source/lib/galaxy.datatypes.rst
+++ b/doc/source/lib/galaxy.datatypes.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.datatypes.util.rst b/doc/source/lib/galaxy.datatypes.util.rst
index c6eab95c0a9..6b9466b202d 100644
--- a/doc/source/lib/galaxy.datatypes.util.rst
+++ b/doc/source/lib/galaxy.datatypes.util.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.eggs.rst b/doc/source/lib/galaxy.eggs.rst
index 948d631b6d7..52a243b3272 100644
--- a/doc/source/lib/galaxy.eggs.rst
+++ b/doc/source/lib/galaxy.eggs.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.exceptions.rst b/doc/source/lib/galaxy.exceptions.rst
index a164ff81f86..dd83fb808b1 100644
--- a/doc/source/lib/galaxy.exceptions.rst
+++ b/doc/source/lib/galaxy.exceptions.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.external_services.result_handlers.rst b/doc/source/lib/galaxy.external_services.result_handlers.rst
index c8946b14b99..749bfb7c25c 100644
--- a/doc/source/lib/galaxy.external_services.result_handlers.rst
+++ b/doc/source/lib/galaxy.external_services.result_handlers.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.external_services.rst b/doc/source/lib/galaxy.external_services.rst
index 955f82eeb7f..b08913dc425 100644
--- a/doc/source/lib/galaxy.external_services.rst
+++ b/doc/source/lib/galaxy.external_services.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.forms.rst b/doc/source/lib/galaxy.forms.rst
index 004bffe09df..088d52bcb9c 100644
--- a/doc/source/lib/galaxy.forms.rst
+++ b/doc/source/lib/galaxy.forms.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.jobs.actions.rst b/doc/source/lib/galaxy.jobs.actions.rst
index c3f69a190c9..7ec9a937d81 100644
--- a/doc/source/lib/galaxy.jobs.actions.rst
+++ b/doc/source/lib/galaxy.jobs.actions.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.jobs.deferred.rst b/doc/source/lib/galaxy.jobs.deferred.rst
index 19b967685c0..371a1721bb7 100644
--- a/doc/source/lib/galaxy.jobs.deferred.rst
+++ b/doc/source/lib/galaxy.jobs.deferred.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.jobs.metrics.collectl.rst b/doc/source/lib/galaxy.jobs.metrics.collectl.rst
new file mode 100644
index 00000000000..01120a3705a
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.metrics.collectl.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst b/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst
new file mode 100644
index 00000000000..71b1a865ccb
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.jobs.metrics.rst b/doc/source/lib/galaxy.jobs.metrics.rst
new file mode 100644
index 00000000000..b050d0f523f
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.metrics.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.jobs.rst b/doc/source/lib/galaxy.jobs.rst
index 587dff8f124..86c56ad5c51 100644
--- a/doc/source/lib/galaxy.jobs.rst
+++ b/doc/source/lib/galaxy.jobs.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.jobs.runners.cli_job.rst b/doc/source/lib/galaxy.jobs.runners.cli_job.rst
deleted file mode 100644
index b373a06ae3c..00000000000
--- a/doc/source/lib/galaxy.jobs.runners.cli_job.rst
+++ /dev/null
@@ -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:
-
diff --git a/doc/source/lib/galaxy.jobs.runners.cli_shell.rst b/doc/source/lib/galaxy.jobs.runners.cli_shell.rst
deleted file mode 100644
index 9b96bbcfc52..00000000000
--- a/doc/source/lib/galaxy.jobs.runners.cli_shell.rst
+++ /dev/null
@@ -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:
-
diff --git a/doc/source/lib/galaxy.jobs.runners.lwr_client.rst b/doc/source/lib/galaxy.jobs.runners.lwr_client.rst
new file mode 100644
index 00000000000..1c0be4e8fac
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.runners.lwr_client.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst b/doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst
new file mode 100644
index 00000000000..7ae6a269d3a
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst b/doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst
new file mode 100644
index 00000000000..f884599ba2d
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.jobs.runners.rst b/doc/source/lib/galaxy.jobs.runners.rst
index 01c244c7f8a..30c2f598717 100644
--- a/doc/source/lib/galaxy.jobs.runners.rst
+++ b/doc/source/lib/galaxy.jobs.runners.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.jobs.runners.state_handlers.rst b/doc/source/lib/galaxy.jobs.runners.state_handlers.rst
new file mode 100644
index 00000000000..06b15dd3f54
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.runners.state_handlers.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst
new file mode 100644
index 00000000000..ec1149a0d87
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.rst
new file mode 100644
index 00000000000..dadd626718b
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.runners.util.cli.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst
new file mode 100644
index 00000000000..42e5c7ffe73
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.jobs.runners.util.condor.rst b/doc/source/lib/galaxy.jobs.runners.util.condor.rst
new file mode 100644
index 00000000000..823ea51ac3e
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.runners.util.condor.rst
@@ -0,0 +1,8 @@
+galaxy.jobs.runners.util.condor package
+=======================================
+
+.. automodule:: galaxy.jobs.runners.util.condor
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff --git a/doc/source/lib/galaxy.jobs.runners.util.job_script.rst b/doc/source/lib/galaxy.jobs.runners.util.job_script.rst
new file mode 100644
index 00000000000..bcc2b16e9eb
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.runners.util.job_script.rst
@@ -0,0 +1,8 @@
+galaxy.jobs.runners.util.job_script package
+===========================================
+
+.. automodule:: galaxy.jobs.runners.util.job_script
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff --git a/doc/source/lib/galaxy.jobs.runners.util.rst b/doc/source/lib/galaxy.jobs.runners.util.rst
new file mode 100644
index 00000000000..8bdd25fc7b4
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.runners.util.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.jobs.splitters.rst b/doc/source/lib/galaxy.jobs.splitters.rst
index 66545414b2e..d8af934e1be 100644
--- a/doc/source/lib/galaxy.jobs.splitters.rst
+++ b/doc/source/lib/galaxy.jobs.splitters.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.managers.rst b/doc/source/lib/galaxy.managers.rst
index ba29bf24565..5fab9245342 100644
--- a/doc/source/lib/galaxy.managers.rst
+++ b/doc/source/lib/galaxy.managers.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.model.migrate.rst b/doc/source/lib/galaxy.model.migrate.rst
index 7218eff3296..60857c84097 100644
--- a/doc/source/lib/galaxy.model.migrate.rst
+++ b/doc/source/lib/galaxy.model.migrate.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.model.orm.ext.rst b/doc/source/lib/galaxy.model.orm.ext.rst
deleted file mode 100644
index 5794c198b03..00000000000
--- a/doc/source/lib/galaxy.model.orm.ext.rst
+++ /dev/null
@@ -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:
-
diff --git a/doc/source/lib/galaxy.model.orm.rst b/doc/source/lib/galaxy.model.orm.rst
index 827ad79aa31..b6896869c00 100644
--- a/doc/source/lib/galaxy.model.orm.rst
+++ b/doc/source/lib/galaxy.model.orm.rst
@@ -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
diff --git a/doc/source/lib/galaxy.model.rst b/doc/source/lib/galaxy.model.rst
index e9eed834062..748a7ba7710 100644
--- a/doc/source/lib/galaxy.model.rst
+++ b/doc/source/lib/galaxy.model.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst b/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst
new file mode 100644
index 00000000000..56b44de4bc7
--- /dev/null
+++ b/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.model.tool_shed_install.rst b/doc/source/lib/galaxy.model.tool_shed_install.rst
new file mode 100644
index 00000000000..24e6b47e45b
--- /dev/null
+++ b/doc/source/lib/galaxy.model.tool_shed_install.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.objectstore.rst b/doc/source/lib/galaxy.objectstore.rst
index 42999958bd2..71457af109e 100644
--- a/doc/source/lib/galaxy.objectstore.rst
+++ b/doc/source/lib/galaxy.objectstore.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.openid.rst b/doc/source/lib/galaxy.openid.rst
index d5dd49a08d3..ccd8057cfce 100644
--- a/doc/source/lib/galaxy.openid.rst
+++ b/doc/source/lib/galaxy.openid.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.quota.rst b/doc/source/lib/galaxy.quota.rst
index b06c6ba33d3..36802033ce1 100644
--- a/doc/source/lib/galaxy.quota.rst
+++ b/doc/source/lib/galaxy.quota.rst
@@ -1,8 +1,5 @@
-quota Package
-=============
-
-:mod:`quota` Package
---------------------
+galaxy.quota package
+====================
.. automodule:: galaxy.quota
:members:
diff --git a/doc/source/lib/galaxy.rst b/doc/source/lib/galaxy.rst
index b9a9027d131..b811fd86a1a 100644
--- a/doc/source/lib/galaxy.rst
+++ b/doc/source/lib/galaxy.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.sample_tracking.rst b/doc/source/lib/galaxy.sample_tracking.rst
index 52dd1e6c7f6..dbef4b76139 100644
--- a/doc/source/lib/galaxy.sample_tracking.rst
+++ b/doc/source/lib/galaxy.sample_tracking.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.security.rst b/doc/source/lib/galaxy.security.rst
index 9bba56c7e12..5f1ab5fe123 100644
--- a/doc/source/lib/galaxy.security.rst
+++ b/doc/source/lib/galaxy.security.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.tags.rst b/doc/source/lib/galaxy.tags.rst
index eff268d5dc4..d61869f22bd 100644
--- a/doc/source/lib/galaxy.tags.rst
+++ b/doc/source/lib/galaxy.tags.rst
@@ -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:
-
diff --git a/doc/source/lib/galaxy.tool_shed.migrate.rst b/doc/source/lib/galaxy.tool_shed.migrate.rst
deleted file mode 100644
index 095f79a99d7..00000000000
--- a/doc/source/lib/galaxy.tool_shed.migrate.rst
+++ /dev/null
@@ -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:
-
diff --git a/doc/source/lib/galaxy.tool_shed.rst b/doc/source/lib/galaxy.tool_shed.rst
deleted file mode 100644
index d1cb451fd7b..00000000000
--- a/doc/source/lib/galaxy.tool_shed.rst
+++ /dev/null
@@ -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
-
diff --git a/doc/source/lib/galaxy.tool_shed.tool_dependencies.rst b/doc/source/lib/galaxy.tool_shed.tool_dependencies.rst
deleted file mode 100644
index 8115eb4d62a..00000000000
--- a/doc/source/lib/galaxy.tool_shed.tool_dependencies.rst
+++ /dev/null
@@ -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:
-
diff --git a/doc/source/lib/galaxy.tools.actions.rst b/doc/source/lib/galaxy.tools.actions.rst
index 6bc274bd4b0..1cf4863c217 100644
--- a/doc/source/lib/galaxy.tools.actions.rst
+++ b/doc/source/lib/galaxy.tools.actions.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.tools.data.rst b/doc/source/lib/galaxy.tools.data.rst
index 92641efedcb..4435ba549f8 100644
--- a/doc/source/lib/galaxy.tools.data.rst
+++ b/doc/source/lib/galaxy.tools.data.rst
@@ -1,8 +1,5 @@
-data Package
-============
-
-:mod:`data` Package
--------------------
+galaxy.tools.data package
+=========================
.. automodule:: galaxy.tools.data
:members:
diff --git a/doc/source/lib/galaxy.tools.data_manager.rst b/doc/source/lib/galaxy.tools.data_manager.rst
new file mode 100644
index 00000000000..02c75fa28ad
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.data_manager.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.tools.deps.resolvers.rst b/doc/source/lib/galaxy.tools.deps.resolvers.rst
new file mode 100644
index 00000000000..ef2282bb8d3
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.deps.resolvers.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.tools.deps.rst b/doc/source/lib/galaxy.tools.deps.rst
index ef6e24cbf8b..f64c423dc22 100644
--- a/doc/source/lib/galaxy.tools.deps.rst
+++ b/doc/source/lib/galaxy.tools.deps.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.tools.filters.rst b/doc/source/lib/galaxy.tools.filters.rst
new file mode 100644
index 00000000000..bbea7ec45e4
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.filters.rst
@@ -0,0 +1,8 @@
+galaxy.tools.filters package
+============================
+
+.. automodule:: galaxy.tools.filters
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff --git a/doc/source/lib/galaxy.tools.genome_index.rst b/doc/source/lib/galaxy.tools.genome_index.rst
deleted file mode 100644
index 4849080849a..00000000000
--- a/doc/source/lib/galaxy.tools.genome_index.rst
+++ /dev/null
@@ -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:
-
diff --git a/doc/source/lib/galaxy.tools.imp_exp.rst b/doc/source/lib/galaxy.tools.imp_exp.rst
index 2801da055dd..e466f86b0a4 100644
--- a/doc/source/lib/galaxy.tools.imp_exp.rst
+++ b/doc/source/lib/galaxy.tools.imp_exp.rst
@@ -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:
+
diff --git a/doc/source/lib/galaxy.tools.linters.rst b/doc/source/lib/galaxy.tools.linters.rst
new file mode 100644
index 00000000000..a27e6bf42bd
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.linters.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.tools.parameters.rst b/doc/source/lib/galaxy.tools.parameters.rst
index 72cd3447e17..28309e13f58 100644
--- a/doc/source/lib/galaxy.tools.parameters.rst
+++ b/doc/source/lib/galaxy.tools.parameters.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.tools.parser.rst b/doc/source/lib/galaxy.tools.parser.rst
new file mode 100644
index 00000000000..ecdc2b15feb
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.parser.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.tools.rst b/doc/source/lib/galaxy.tools.rst
index 4b57fd3b731..01add8d971c 100644
--- a/doc/source/lib/galaxy.tools.rst
+++ b/doc/source/lib/galaxy.tools.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.tools.search.rst b/doc/source/lib/galaxy.tools.search.rst
index 616079f69b7..edbb5bf3c79 100644
--- a/doc/source/lib/galaxy.tools.search.rst
+++ b/doc/source/lib/galaxy.tools.search.rst
@@ -1,8 +1,5 @@
-search Package
-==============
-
-:mod:`search` Package
----------------------
+galaxy.tools.search package
+===========================
.. automodule:: galaxy.tools.search
:members:
diff --git a/doc/source/lib/galaxy.tools.toolbox.filters.rst b/doc/source/lib/galaxy.tools.toolbox.filters.rst
new file mode 100644
index 00000000000..a5a81d279fb
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.toolbox.filters.rst
@@ -0,0 +1,8 @@
+galaxy.tools.toolbox.filters package
+====================================
+
+.. automodule:: galaxy.tools.toolbox.filters
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff --git a/doc/source/lib/galaxy.tools.toolbox.lineages.rst b/doc/source/lib/galaxy.tools.toolbox.lineages.rst
new file mode 100644
index 00000000000..3159c8d248d
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.toolbox.lineages.rst
@@ -0,0 +1,44 @@
+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:
+
+
diff --git a/doc/source/lib/galaxy.tools.toolbox.rst b/doc/source/lib/galaxy.tools.toolbox.rst
new file mode 100644
index 00000000000..7528cb77e08
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.toolbox.rst
@@ -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:
+
+
diff --git a/doc/source/lib/galaxy.tools.util.galaxyops.rst b/doc/source/lib/galaxy.tools.util.galaxyops.rst
index 2e749eefb13..4ea949a2fac 100644
--- a/doc/source/lib/galaxy.tools.util.galaxyops.rst
+++ b/doc/source/lib/galaxy.tools.util.galaxyops.rst
@@ -1,8 +1,5 @@
-galaxyops Package
-=================
-
-:mod:`galaxyops` Package
-------------------------
+galaxy.tools.util.galaxyops package
+===================================
.. automodule:: galaxy.tools.util.galaxyops
:members:
diff --git a/doc/source/lib/galaxy.tools.util.rst b/doc/source/lib/galaxy.tools.util.rst
index 04efb192a74..f7b6b6f32d0 100644
--- a/doc/source/lib/galaxy.tools.util.rst
+++ b/doc/source/lib/galaxy.tools.util.rst
@@ -1,22 +1,11 @@
-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:
+
+
diff --git a/doc/source/lib/galaxy.util.backports.importlib.rst b/doc/source/lib/galaxy.util.backports.importlib.rst
index 765830ac0bc..974cf47f98d 100644
--- a/doc/source/lib/galaxy.util.backports.importlib.rst
+++ b/doc/source/lib/galaxy.util.backports.importlib.rst
@@ -1,8 +1,5 @@
-importlib Package
-=================
-
-:mod:`importlib` Package
-------------------------
+galaxy.util.backports.importlib package
+=======================================
.. automodule:: galaxy.util.backports.importlib
:members:
diff --git a/doc/source/lib/galaxy.util.backports.rst b/doc/source/lib/galaxy.util.backports.rst
index ead946d6eca..69356d80fcd 100644
--- a/doc/source/lib/galaxy.util.backports.rst
+++ b/doc/source/lib/galaxy.util.backports.rst
@@ -1,8 +1,5 @@
-backports Package
-=================
-
-:mod:`backports` Package
-------------------------
+galaxy.util.backports package
+=============================
.. automodule:: galaxy.util.backports
:members:
diff --git a/doc/source/lib/galaxy.util.log.rst b/doc/source/lib/galaxy.util.log.rst
new file mode 100644
index 00000000000..0f81bc0115c
--- /dev/null
+++ b/doc/source/lib/galaxy.util.log.rst
@@ -0,0 +1,20 @@
+galaxy.util.log package
+=======================
+
+.. automodule:: galaxy.util.log
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+galaxy.util.log.fluent_log module
+---------------------------------
+
+.. automodule:: galaxy.util.log.fluent_log
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.util.pastescript.rst b/doc/source/lib/galaxy.util.pastescript.rst
new file mode 100644
index 00000000000..0a861eb5a4f
--- /dev/null
+++ b/doc/source/lib/galaxy.util.pastescript.rst
@@ -0,0 +1,28 @@
+galaxy.util.pastescript package
+===============================
+
+.. automodule:: galaxy.util.pastescript
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+galaxy.util.pastescript.loadwsgi module
+---------------------------------------
+
+.. automodule:: galaxy.util.pastescript.loadwsgi
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.pastescript.serve module
+------------------------------------
+
+.. automodule:: galaxy.util.pastescript.serve
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.util.rst b/doc/source/lib/galaxy.util.rst
index 6866a5f0fb6..dd2eca1c66b 100644
--- a/doc/source/lib/galaxy.util.rst
+++ b/doc/source/lib/galaxy.util.rst
@@ -1,158 +1,11 @@
-util Package
-============
-
-:mod:`util` Package
--------------------
+galaxy.util package
+===================
.. automodule:: galaxy.util
:members:
:undoc-members:
:show-inheritance:
-:mod:`aliaspickler` Module
---------------------------
-
-.. automodule:: galaxy.util.aliaspickler
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`bunch` Module
--------------------
-
-.. automodule:: galaxy.util.bunch
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`debugging` Module
------------------------
-
-.. automodule:: galaxy.util.debugging
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`expressions` Module
--------------------------
-
-.. automodule:: galaxy.util.expressions
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`hash_util` Module
------------------------
-
-.. automodule:: galaxy.util.hash_util
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`heartbeat` Module
------------------------
-
-.. automodule:: galaxy.util.heartbeat
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`inflection` Module
-------------------------
-
-.. automodule:: galaxy.util.inflection
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`json` Module
-------------------
-
-.. automodule:: galaxy.util.json
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`lrucache` Module
-----------------------
-
-.. automodule:: galaxy.util.lrucache
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`memdump` Module
----------------------
-
-.. automodule:: galaxy.util.memdump
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`none_like` Module
------------------------
-
-.. automodule:: galaxy.util.none_like
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`odict` Module
--------------------
-
-.. automodule:: galaxy.util.odict
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`sanitize_html` Module
----------------------------
-
-.. automodule:: galaxy.util.sanitize_html
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`shed_util` Module
------------------------
-
-.. automodule:: galaxy.util.shed_util
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`shed_util_common` Module
-------------------------------
-
-.. automodule:: galaxy.util.shed_util_common
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`streamball` Module
-------------------------
-
-.. automodule:: galaxy.util.streamball
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`template` Module
-----------------------
-
-.. automodule:: galaxy.util.template
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`topsort` Module
----------------------
-
-.. automodule:: galaxy.util.topsort
- :members:
- :undoc-members:
- :show-inheritance:
-
Subpackages
-----------
@@ -160,4 +13,273 @@ Subpackages
galaxy.util.backports
galaxy.util.log
+ galaxy.util.pastescript
+
+Submodules
+----------
+
+galaxy.util.aliaspickler module
+-------------------------------
+
+.. automodule:: galaxy.util.aliaspickler
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.biostar module
+--------------------------
+
+.. automodule:: galaxy.util.biostar
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.bunch module
+------------------------
+
+.. automodule:: galaxy.util.bunch
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.dbkeys module
+-------------------------
+
+.. automodule:: galaxy.util.dbkeys
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.debugging module
+----------------------------
+
+.. automodule:: galaxy.util.debugging
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.dictobj module
+--------------------------
+
+.. automodule:: galaxy.util.dictobj
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.directory_hash module
+---------------------------------
+
+.. automodule:: galaxy.util.directory_hash
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.expressions module
+------------------------------
+
+.. automodule:: galaxy.util.expressions
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.hash_util module
+----------------------------
+
+.. automodule:: galaxy.util.hash_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.heartbeat module
+----------------------------
+
+.. automodule:: galaxy.util.heartbeat
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.inflection module
+-----------------------------
+
+.. automodule:: galaxy.util.inflection
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.json module
+-----------------------
+
+.. automodule:: galaxy.util.json
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.jstree module
+-------------------------
+
+.. automodule:: galaxy.util.jstree
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.lazy_process module
+-------------------------------
+
+.. automodule:: galaxy.util.lazy_process
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.lrucache module
+---------------------------
+
+.. automodule:: galaxy.util.lrucache
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.none_like module
+----------------------------
+
+.. automodule:: galaxy.util.none_like
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.object_wrapper module
+---------------------------------
+
+.. automodule:: galaxy.util.object_wrapper
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.odict module
+------------------------
+
+.. automodule:: galaxy.util.odict
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.permutations module
+-------------------------------
+
+.. automodule:: galaxy.util.permutations
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.plugin_config module
+--------------------------------
+
+.. automodule:: galaxy.util.plugin_config
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.properties module
+-----------------------------
+
+.. automodule:: galaxy.util.properties
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.sanitize_html module
+--------------------------------
+
+.. automodule:: galaxy.util.sanitize_html
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.simplegraph module
+------------------------------
+
+.. automodule:: galaxy.util.simplegraph
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.sleeper module
+--------------------------
+
+.. automodule:: galaxy.util.sleeper
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.sockets module
+--------------------------
+
+.. automodule:: galaxy.util.sockets
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.specs module
+------------------------
+
+.. automodule:: galaxy.util.specs
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.sqlite module
+-------------------------
+
+.. automodule:: galaxy.util.sqlite
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.streamball module
+-----------------------------
+
+.. automodule:: galaxy.util.streamball
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.submodules module
+-----------------------------
+
+.. automodule:: galaxy.util.submodules
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.template module
+---------------------------
+
+.. automodule:: galaxy.util.template
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.topsort module
+--------------------------
+
+.. automodule:: galaxy.util.topsort
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.validation module
+-----------------------------
+
+.. automodule:: galaxy.util.validation
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.util.xml_macros module
+-----------------------------
+
+.. automodule:: galaxy.util.xml_macros
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff --git a/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst
index 7d51bfb4f84..26b7cb913ca 100644
--- a/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst
+++ b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst
@@ -1,43 +1,44 @@
-phyloviz Package
-================
-
-:mod:`phyloviz` Package
------------------------
+galaxy.visualization.data_providers.phyloviz package
+====================================================
.. automodule:: galaxy.visualization.data_providers.phyloviz
:members:
:undoc-members:
:show-inheritance:
-:mod:`baseparser` Module
-------------------------
+Submodules
+----------
+
+galaxy.visualization.data_providers.phyloviz.baseparser module
+--------------------------------------------------------------
.. automodule:: galaxy.visualization.data_providers.phyloviz.baseparser
:members:
:undoc-members:
:show-inheritance:
-:mod:`newickparser` Module
---------------------------
+galaxy.visualization.data_providers.phyloviz.newickparser module
+----------------------------------------------------------------
.. automodule:: galaxy.visualization.data_providers.phyloviz.newickparser
:members:
:undoc-members:
:show-inheritance:
-:mod:`nexusparser` Module
--------------------------
+galaxy.visualization.data_providers.phyloviz.nexusparser module
+---------------------------------------------------------------
.. automodule:: galaxy.visualization.data_providers.phyloviz.nexusparser
:members:
:undoc-members:
:show-inheritance:
-:mod:`phyloxmlparser` Module
-----------------------------
+galaxy.visualization.data_providers.phyloviz.phyloxmlparser module
+------------------------------------------------------------------
.. automodule:: galaxy.visualization.data_providers.phyloviz.phyloxmlparser
:members:
:undoc-members:
:show-inheritance:
+
diff --git a/doc/source/lib/galaxy.visualization.data_providers.rst b/doc/source/lib/galaxy.visualization.data_providers.rst
index a7561325011..3180ac79181 100644
--- a/doc/source/lib/galaxy.visualization.data_providers.rst
+++ b/doc/source/lib/galaxy.visualization.data_providers.rst
@@ -1,38 +1,11 @@
-data_providers Package
-======================
-
-:mod:`data_providers` Package
------------------------------
+galaxy.visualization.data_providers package
+===========================================
.. automodule:: galaxy.visualization.data_providers
:members:
:undoc-members:
:show-inheritance:
-:mod:`basic` Module
--------------------
-
-.. automodule:: galaxy.visualization.data_providers.basic
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`genome` Module
---------------------
-
-.. automodule:: galaxy.visualization.data_providers.genome
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`registry` Module
-----------------------
-
-.. automodule:: galaxy.visualization.data_providers.registry
- :members:
- :undoc-members:
- :show-inheritance:
-
Subpackages
-----------
@@ -40,3 +13,39 @@ Subpackages
galaxy.visualization.data_providers.phyloviz
+Submodules
+----------
+
+galaxy.visualization.data_providers.basic module
+------------------------------------------------
+
+.. automodule:: galaxy.visualization.data_providers.basic
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.visualization.data_providers.cigar module
+------------------------------------------------
+
+.. automodule:: galaxy.visualization.data_providers.cigar
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.visualization.data_providers.genome module
+-------------------------------------------------
+
+.. automodule:: galaxy.visualization.data_providers.genome
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.visualization.data_providers.registry module
+---------------------------------------------------
+
+.. automodule:: galaxy.visualization.data_providers.registry
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.visualization.genome.rst b/doc/source/lib/galaxy.visualization.genome.rst
index 1605b712107..9097529321c 100644
--- a/doc/source/lib/galaxy.visualization.genome.rst
+++ b/doc/source/lib/galaxy.visualization.genome.rst
@@ -1,19 +1,8 @@
-genome Package
-==============
-
-:mod:`genome` Package
----------------------
+galaxy.visualization.genome package
+===================================
.. automodule:: galaxy.visualization.genome
:members:
:undoc-members:
:show-inheritance:
-:mod:`visual_analytics` Module
-------------------------------
-
-.. automodule:: galaxy.visualization.genome.visual_analytics
- :members:
- :undoc-members:
- :show-inheritance:
-
diff --git a/doc/source/lib/galaxy.visualization.plugins.rst b/doc/source/lib/galaxy.visualization.plugins.rst
new file mode 100644
index 00000000000..b8ded7d9b6d
--- /dev/null
+++ b/doc/source/lib/galaxy.visualization.plugins.rst
@@ -0,0 +1,52 @@
+galaxy.visualization.plugins package
+====================================
+
+.. automodule:: galaxy.visualization.plugins
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+galaxy.visualization.plugins.config_parser module
+-------------------------------------------------
+
+.. automodule:: galaxy.visualization.plugins.config_parser
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.visualization.plugins.plugin module
+------------------------------------------
+
+.. automodule:: galaxy.visualization.plugins.plugin
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.visualization.plugins.registry module
+--------------------------------------------
+
+.. automodule:: galaxy.visualization.plugins.registry
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.visualization.plugins.resource_parser module
+---------------------------------------------------
+
+.. automodule:: galaxy.visualization.plugins.resource_parser
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.visualization.plugins.utils module
+-----------------------------------------
+
+.. automodule:: galaxy.visualization.plugins.utils
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.visualization.rst b/doc/source/lib/galaxy.visualization.rst
index 3d85a78ba4e..1f334499e29 100644
--- a/doc/source/lib/galaxy.visualization.rst
+++ b/doc/source/lib/galaxy.visualization.rst
@@ -1,22 +1,11 @@
-visualization Package
-=====================
-
-:mod:`visualization` Package
-----------------------------
+galaxy.visualization package
+============================
.. automodule:: galaxy.visualization
:members:
:undoc-members:
:show-inheritance:
-:mod:`genomes` Module
----------------------
-
-.. automodule:: galaxy.visualization.genomes
- :members:
- :undoc-members:
- :show-inheritance:
-
Subpackages
-----------
@@ -24,5 +13,18 @@ Subpackages
galaxy.visualization.data_providers
galaxy.visualization.genome
+ galaxy.visualization.plugins
galaxy.visualization.tracks
+Submodules
+----------
+
+galaxy.visualization.genomes module
+-----------------------------------
+
+.. automodule:: galaxy.visualization.genomes
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.visualization.tracks.rst b/doc/source/lib/galaxy.visualization.tracks.rst
index 8242d51dff2..2d279399ef6 100644
--- a/doc/source/lib/galaxy.visualization.tracks.rst
+++ b/doc/source/lib/galaxy.visualization.tracks.rst
@@ -1,19 +1,8 @@
-tracks Package
-==============
-
-:mod:`tracks` Package
----------------------
+galaxy.visualization.tracks package
+===================================
.. automodule:: galaxy.visualization.tracks
:members:
:undoc-members:
:show-inheritance:
-:mod:`summary` Module
----------------------
-
-.. automodule:: galaxy.visualization.tracks.summary
- :members:
- :undoc-members:
- :show-inheritance:
-
diff --git a/doc/source/lib/galaxy.web.base.controllers.rst b/doc/source/lib/galaxy.web.base.controllers.rst
index a37900b0aa5..6c153a18d4d 100644
--- a/doc/source/lib/galaxy.web.base.controllers.rst
+++ b/doc/source/lib/galaxy.web.base.controllers.rst
@@ -1,11 +1,20 @@
-controllers Package
-===================
+galaxy.web.base.controllers package
+===================================
-:mod:`admin` Module
--------------------
+.. automodule:: galaxy.web.base.controllers
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+galaxy.web.base.controllers.admin module
+----------------------------------------
.. automodule:: galaxy.web.base.controllers.admin
:members:
:undoc-members:
:show-inheritance:
+
diff --git a/doc/source/lib/galaxy.web.base.rst b/doc/source/lib/galaxy.web.base.rst
index 3f1078c6b3a..3ac90729275 100644
--- a/doc/source/lib/galaxy.web.base.rst
+++ b/doc/source/lib/galaxy.web.base.rst
@@ -1,10 +1,7 @@
-base Package
-============
+galaxy.web.base package
+=======================
-:mod:`controller` Module
-------------------------
-
-.. automodule:: galaxy.web.base.controller
+.. automodule:: galaxy.web.base
:members:
:undoc-members:
:show-inheritance:
@@ -16,3 +13,31 @@ Subpackages
galaxy.web.base.controllers
+Submodules
+----------
+
+galaxy.web.base.controller module
+---------------------------------
+
+.. automodule:: galaxy.web.base.controller
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.web.base.interactive_environments module
+-----------------------------------------------
+
+.. automodule:: galaxy.web.base.interactive_environments
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.web.base.pluginframework module
+--------------------------------------
+
+.. automodule:: galaxy.web.base.pluginframework
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.web.framework.helpers.rst b/doc/source/lib/galaxy.web.framework.helpers.rst
index 690122ac045..d1916931133 100644
--- a/doc/source/lib/galaxy.web.framework.helpers.rst
+++ b/doc/source/lib/galaxy.web.framework.helpers.rst
@@ -1,19 +1,20 @@
-helpers Package
-===============
-
-:mod:`helpers` Package
-----------------------
+galaxy.web.framework.helpers package
+====================================
.. automodule:: galaxy.web.framework.helpers
:members:
:undoc-members:
:show-inheritance:
-:mod:`grids` Module
--------------------
+Submodules
+----------
+
+galaxy.web.framework.helpers.grids module
+-----------------------------------------
.. automodule:: galaxy.web.framework.helpers.grids
:members:
:undoc-members:
:show-inheritance:
+
diff --git a/doc/source/lib/galaxy.web.framework.middleware.rst b/doc/source/lib/galaxy.web.framework.middleware.rst
index 1ce4b89f9ba..3eb2cbe0ed2 100644
--- a/doc/source/lib/galaxy.web.framework.middleware.rst
+++ b/doc/source/lib/galaxy.web.framework.middleware.rst
@@ -1,51 +1,76 @@
-middleware Package
-==================
-
-:mod:`middleware` Package
--------------------------
+galaxy.web.framework.middleware package
+=======================================
.. automodule:: galaxy.web.framework.middleware
:members:
:undoc-members:
:show-inheritance:
-:mod:`profile` Module
----------------------
+Submodules
+----------
+
+galaxy.web.framework.middleware.error module
+--------------------------------------------
+
+.. automodule:: galaxy.web.framework.middleware.error
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.web.framework.middleware.profile module
+----------------------------------------------
.. automodule:: galaxy.web.framework.middleware.profile
:members:
:undoc-members:
:show-inheritance:
-:mod:`remoteuser` Module
-------------------------
+galaxy.web.framework.middleware.remoteuser module
+-------------------------------------------------
.. automodule:: galaxy.web.framework.middleware.remoteuser
:members:
:undoc-members:
:show-inheritance:
-:mod:`static` Module
---------------------
+galaxy.web.framework.middleware.request_id module
+-------------------------------------------------
+
+.. automodule:: galaxy.web.framework.middleware.request_id
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.web.framework.middleware.sentry module
+---------------------------------------------
+
+.. automodule:: galaxy.web.framework.middleware.sentry
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.web.framework.middleware.static module
+---------------------------------------------
.. automodule:: galaxy.web.framework.middleware.static
:members:
:undoc-members:
:show-inheritance:
-:mod:`translogger` Module
--------------------------
+galaxy.web.framework.middleware.translogger module
+--------------------------------------------------
.. automodule:: galaxy.web.framework.middleware.translogger
:members:
:undoc-members:
:show-inheritance:
-:mod:`xforwardedhost` Module
-----------------------------
+galaxy.web.framework.middleware.xforwardedhost module
+-----------------------------------------------------
.. automodule:: galaxy.web.framework.middleware.xforwardedhost
:members:
:undoc-members:
:show-inheritance:
+
diff --git a/doc/source/lib/galaxy.web.framework.rst b/doc/source/lib/galaxy.web.framework.rst
index 5391c910912..f6357d01eb2 100644
--- a/doc/source/lib/galaxy.web.framework.rst
+++ b/doc/source/lib/galaxy.web.framework.rst
@@ -1,30 +1,11 @@
-framework Package
-=================
-
-:mod:`framework` Package
-------------------------
+galaxy.web.framework package
+============================
.. automodule:: galaxy.web.framework
:members:
:undoc-members:
:show-inheritance:
-:mod:`base` Module
-------------------
-
-.. automodule:: galaxy.web.framework.base
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`openid_manager` Module
-----------------------------
-
-.. automodule:: galaxy.web.framework.openid_manager
- :members:
- :undoc-members:
- :show-inheritance:
-
Subpackages
-----------
@@ -33,3 +14,47 @@ Subpackages
galaxy.web.framework.helpers
galaxy.web.framework.middleware
+Submodules
+----------
+
+galaxy.web.framework.base module
+--------------------------------
+
+.. automodule:: galaxy.web.framework.base
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.web.framework.decorators module
+--------------------------------------
+
+.. automodule:: galaxy.web.framework.decorators
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.web.framework.formbuilder module
+---------------------------------------
+
+.. automodule:: galaxy.web.framework.formbuilder
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.web.framework.openid_manager module
+------------------------------------------
+
+.. automodule:: galaxy.web.framework.openid_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.web.framework.webapp module
+----------------------------------
+
+.. automodule:: galaxy.web.framework.webapp
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.web.proxy.rst b/doc/source/lib/galaxy.web.proxy.rst
new file mode 100644
index 00000000000..53c7c4bbca7
--- /dev/null
+++ b/doc/source/lib/galaxy.web.proxy.rst
@@ -0,0 +1,20 @@
+galaxy.web.proxy package
+========================
+
+.. automodule:: galaxy.web.proxy
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+galaxy.web.proxy.filelock module
+--------------------------------
+
+.. automodule:: galaxy.web.proxy.filelock
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.web.rst b/doc/source/lib/galaxy.web.rst
index c929ad6a40e..762db65e65b 100644
--- a/doc/source/lib/galaxy.web.rst
+++ b/doc/source/lib/galaxy.web.rst
@@ -1,38 +1,11 @@
-web Package
-===========
-
-:mod:`web` Package
-------------------
+galaxy.web package
+==================
.. automodule:: galaxy.web
:members:
:undoc-members:
:show-inheritance:
-:mod:`buildapp` Module
-----------------------
-
-.. automodule:: galaxy.web.buildapp
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`form_builder` Module
---------------------------
-
-.. automodule:: galaxy.web.form_builder
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`params` Module
---------------------
-
-.. automodule:: galaxy.web.params
- :members:
- :undoc-members:
- :show-inheritance:
-
Subpackages
-----------
@@ -40,5 +13,42 @@ Subpackages
galaxy.web.base
galaxy.web.framework
+ galaxy.web.proxy
galaxy.web.security
+Submodules
+----------
+
+galaxy.web.buildapp module
+--------------------------
+
+.. automodule:: galaxy.web.buildapp
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.web.form_builder module
+------------------------------
+
+.. automodule:: galaxy.web.form_builder
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.web.formatting module
+----------------------------
+
+.. automodule:: galaxy.web.formatting
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.web.params module
+------------------------
+
+.. automodule:: galaxy.web.params
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.web.security.rst b/doc/source/lib/galaxy.web.security.rst
index 2904ea1e5cb..276b543abb7 100644
--- a/doc/source/lib/galaxy.web.security.rst
+++ b/doc/source/lib/galaxy.web.security.rst
@@ -1,8 +1,5 @@
-security Package
-================
-
-:mod:`security` Package
------------------------
+galaxy.web.security package
+===========================
.. automodule:: galaxy.web.security
:members:
diff --git a/doc/source/lib/galaxy.webapps.community.controllers.rst b/doc/source/lib/galaxy.webapps.community.controllers.rst
deleted file mode 100644
index d2a1f217603..00000000000
--- a/doc/source/lib/galaxy.webapps.community.controllers.rst
+++ /dev/null
@@ -1,67 +0,0 @@
-controllers Package
-===================
-
-:mod:`controllers` Package
---------------------------
-
-.. automodule:: galaxy.webapps.community.controllers
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`admin` Module
--------------------
-
-.. automodule:: galaxy.webapps.community.controllers.admin
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`common` Module
---------------------
-
-.. automodule:: galaxy.webapps.community.controllers.common
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`hg` Module
-----------------
-
-.. automodule:: galaxy.webapps.community.controllers.hg
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`repository` Module
-------------------------
-
-.. automodule:: galaxy.webapps.community.controllers.repository
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`repository_review` Module
--------------------------------
-
-.. automodule:: galaxy.webapps.community.controllers.repository_review
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`upload` Module
---------------------
-
-.. automodule:: galaxy.webapps.community.controllers.upload
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`user` Module
-------------------
-
-.. automodule:: galaxy.webapps.community.controllers.user
- :members:
- :undoc-members:
- :show-inheritance:
-
diff --git a/doc/source/lib/galaxy.webapps.community.framework.middleware.rst b/doc/source/lib/galaxy.webapps.community.framework.middleware.rst
deleted file mode 100644
index 5bb9965acf6..00000000000
--- a/doc/source/lib/galaxy.webapps.community.framework.middleware.rst
+++ /dev/null
@@ -1,27 +0,0 @@
-middleware Package
-==================
-
-:mod:`middleware` Package
--------------------------
-
-.. automodule:: galaxy.webapps.community.framework.middleware
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`hg` Module
-----------------
-
-.. automodule:: galaxy.webapps.community.framework.middleware.hg
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`remoteuser` Module
-------------------------
-
-.. automodule:: galaxy.webapps.community.framework.middleware.remoteuser
- :members:
- :undoc-members:
- :show-inheritance:
-
diff --git a/doc/source/lib/galaxy.webapps.community.framework.rst b/doc/source/lib/galaxy.webapps.community.framework.rst
deleted file mode 100644
index b428492d31a..00000000000
--- a/doc/source/lib/galaxy.webapps.community.framework.rst
+++ /dev/null
@@ -1,18 +0,0 @@
-framework Package
-=================
-
-:mod:`framework` Package
-------------------------
-
-.. automodule:: galaxy.webapps.community.framework
- :members:
- :undoc-members:
- :show-inheritance:
-
-Subpackages
------------
-
-.. toctree::
-
- galaxy.webapps.community.framework.middleware
-
diff --git a/doc/source/lib/galaxy.webapps.community.model.migrate.rst b/doc/source/lib/galaxy.webapps.community.model.migrate.rst
deleted file mode 100644
index cfd09107747..00000000000
--- a/doc/source/lib/galaxy.webapps.community.model.migrate.rst
+++ /dev/null
@@ -1,11 +0,0 @@
-migrate Package
-===============
-
-:mod:`check` Module
--------------------
-
-.. automodule:: galaxy.webapps.community.model.migrate.check
- :members:
- :undoc-members:
- :show-inheritance:
-
diff --git a/doc/source/lib/galaxy.webapps.community.model.rst b/doc/source/lib/galaxy.webapps.community.model.rst
deleted file mode 100644
index 1c8583259c0..00000000000
--- a/doc/source/lib/galaxy.webapps.community.model.rst
+++ /dev/null
@@ -1,26 +0,0 @@
-model Package
-=============
-
-:mod:`model` Package
---------------------
-
-.. automodule:: galaxy.webapps.community.model
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`mapping` Module
----------------------
-
-.. automodule:: galaxy.webapps.community.model.mapping
- :members:
- :undoc-members:
- :show-inheritance:
-
-Subpackages
------------
-
-.. toctree::
-
- galaxy.webapps.community.model.migrate
-
diff --git a/doc/source/lib/galaxy.webapps.community.rst b/doc/source/lib/galaxy.webapps.community.rst
deleted file mode 100644
index 904044beea8..00000000000
--- a/doc/source/lib/galaxy.webapps.community.rst
+++ /dev/null
@@ -1,46 +0,0 @@
-community Package
-=================
-
-:mod:`community` Package
-------------------------
-
-.. automodule:: galaxy.webapps.community
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`app` Module
------------------
-
-.. automodule:: galaxy.webapps.community.app
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`buildapp` Module
-----------------------
-
-.. automodule:: galaxy.webapps.community.buildapp
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`config` Module
---------------------
-
-.. automodule:: galaxy.webapps.community.config
- :members:
- :undoc-members:
- :show-inheritance:
-
-Subpackages
------------
-
-.. toctree::
-
- galaxy.webapps.community.controllers
- galaxy.webapps.community.framework
- galaxy.webapps.community.model
- galaxy.webapps.community.security
- galaxy.webapps.community.util
-
diff --git a/doc/source/lib/galaxy.webapps.community.security.rst b/doc/source/lib/galaxy.webapps.community.security.rst
deleted file mode 100644
index d4c92a8daf9..00000000000
--- a/doc/source/lib/galaxy.webapps.community.security.rst
+++ /dev/null
@@ -1,11 +0,0 @@
-security Package
-================
-
-:mod:`security` Package
------------------------
-
-.. automodule:: galaxy.webapps.community.security
- :members:
- :undoc-members:
- :show-inheritance:
-
diff --git a/doc/source/lib/galaxy.webapps.community.util.rst b/doc/source/lib/galaxy.webapps.community.util.rst
deleted file mode 100644
index aa8e5fee8dd..00000000000
--- a/doc/source/lib/galaxy.webapps.community.util.rst
+++ /dev/null
@@ -1,35 +0,0 @@
-util Package
-============
-
-:mod:`container_util` Module
-----------------------------
-
-.. automodule:: galaxy.webapps.community.util.container_util
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`hgweb_config` Module
---------------------------
-
-.. automodule:: galaxy.webapps.community.util.hgweb_config
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`shed_statistics` Module
------------------------------
-
-.. automodule:: galaxy.webapps.community.util.shed_statistics
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`workflow_util` Module
----------------------------
-
-.. automodule:: galaxy.webapps.community.util.workflow_util
- :members:
- :undoc-members:
- :show-inheritance:
-
diff --git a/doc/source/lib/galaxy.webapps.galaxy.api.rst b/doc/source/lib/galaxy.webapps.galaxy.api.rst
index 356449d622d..657035ef368 100644
--- a/doc/source/lib/galaxy.webapps.galaxy.api.rst
+++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst
@@ -1,515 +1,324 @@
-Galaxy API Documentation
-************************
+galaxy.webapps.galaxy.api package
+=================================
-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.
+.. automodule:: galaxy.webapps.galaxy.api
+ :members:
+ :undoc-members:
+ :show-inheritance:
-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.
+Submodules
+----------
-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.
-
-API Controllers
-===============
-
-Galaxy offers the following API controllers:
-
-:mod:`annotations` Module
-----------------------
+galaxy.webapps.galaxy.api.annotations module
+--------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.annotations
+ :members:
+ :undoc-members:
+ :show-inheritance:
-:mod:`authenticate` Module
-----------------------
+galaxy.webapps.galaxy.api.authenticate module
+---------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.authenticate
+ :members:
+ :undoc-members:
+ :show-inheritance:
-:mod:`configuration` Module
-----------------------
+galaxy.webapps.galaxy.api.configuration module
+----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.configuration
+ :members:
+ :undoc-members:
+ :show-inheritance:
-:mod:`dataset_collections` Module
-----------------------
+galaxy.webapps.galaxy.api.dataset_collections module
+----------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.dataset_collections
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`datasets` Module
-----------------------
+galaxy.webapps.galaxy.api.datasets module
+-----------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.datasets
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`datatypes` Module
-----------------------
+galaxy.webapps.galaxy.api.datatypes module
+------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.datatypes
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`extended_metadata` Module
-----------------------
+galaxy.webapps.galaxy.api.extended_metadata module
+--------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.extended_metadata
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`folder_contents` Module
------------------------------
+galaxy.webapps.galaxy.api.folder_contents module
+------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.folder_contents
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`folders` Module
----------------------
+galaxy.webapps.galaxy.api.folders module
+----------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.folders
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`forms` Module
--------------------
+galaxy.webapps.galaxy.api.forms module
+--------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.forms
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`genomes` Module
----------------------
+galaxy.webapps.galaxy.api.genomes module
+----------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.genomes
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`group_roles` Module
--------------------------
+galaxy.webapps.galaxy.api.group_roles module
+--------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.group_roles
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`group_users` Module
--------------------------
+galaxy.webapps.galaxy.api.group_users module
+--------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.group_users
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`groups` Module
---------------------
+galaxy.webapps.galaxy.api.groups module
+---------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.groups
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`histories` Module
------------------------
+galaxy.webapps.galaxy.api.histories module
+------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.histories
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`history_contents` Module
-------------------------------
+galaxy.webapps.galaxy.api.history_contents module
+-------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.history_contents
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`item_tags` Module
------------------------
+galaxy.webapps.galaxy.api.item_tags module
+------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.item_tags
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`job_files` Module
-----------------------
+galaxy.webapps.galaxy.api.job_files module
+------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.job_files
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`jobs` Module
-----------------------
+galaxy.webapps.galaxy.api.jobs module
+-------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.jobs
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`lda_datasets` Module
---------------------------
+galaxy.webapps.galaxy.api.lda_datasets module
+---------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.lda_datasets
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`libraries` Module
------------------------
+galaxy.webapps.galaxy.api.libraries module
+------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.libraries
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`library_contents` Module
-------------------------------
+galaxy.webapps.galaxy.api.library_contents module
+-------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.library_contents
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`metrics` Module
-----------------------
+galaxy.webapps.galaxy.api.metrics module
+----------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.metrics
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`page_revisions` Module
-----------------------
+galaxy.webapps.galaxy.api.page_revisions module
+-----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.page_revisions
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`pages` Module
-----------------------
+galaxy.webapps.galaxy.api.pages module
+--------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.pages
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`provenance` Module
-----------------------
+galaxy.webapps.galaxy.api.provenance module
+-------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.provenance
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`quotas` Module
---------------------
+galaxy.webapps.galaxy.api.quotas module
+---------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.quotas
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`remote_files` Module
-----------------------
+galaxy.webapps.galaxy.api.remote_files module
+---------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.remote_files
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`request_types` Module
----------------------------
+galaxy.webapps.galaxy.api.request_types module
+----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.request_types
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`requests` Module
-----------------------
+galaxy.webapps.galaxy.api.requests module
+-----------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.requests
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`roles` Module
--------------------
+galaxy.webapps.galaxy.api.roles module
+--------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.roles
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`samples` Module
----------------------
+galaxy.webapps.galaxy.api.samples module
+----------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.samples
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`search` Module
-----------------------
+galaxy.webapps.galaxy.api.search module
+---------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.search
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`tool_data` Module
-----------------------
+galaxy.webapps.galaxy.api.tool_data module
+------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.tool_data
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`tool_shed_repositories` Module
-----------------------
+galaxy.webapps.galaxy.api.tool_shed_repositories module
+-------------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.tool_shed_repositories
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`tools` Module
--------------------
+galaxy.webapps.galaxy.api.tools module
+--------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.tools
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`users` Module
--------------------
+galaxy.webapps.galaxy.api.users module
+--------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.users
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`visualizations` Module
-----------------------------
+galaxy.webapps.galaxy.api.visualizations module
+-----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.visualizations
+ :members:
+ :undoc-members:
+ :show-inheritance:
-
-:mod:`workflows` Module
------------------------
+galaxy.webapps.galaxy.api.workflows module
+------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.workflows
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff --git a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst
index 4517fc2ba37..5a59cc4af81 100644
--- a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst
+++ b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst
@@ -1,227 +1,252 @@
-controllers Package
-===================
-
-:mod:`controllers` Package
---------------------------
+galaxy.webapps.galaxy.controllers package
+=========================================
.. automodule:: galaxy.webapps.galaxy.controllers
:members:
:undoc-members:
:show-inheritance:
-:mod:`admin` Module
--------------------
+Submodules
+----------
+
+galaxy.webapps.galaxy.controllers.admin module
+----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.admin
:members:
:undoc-members:
:show-inheritance:
-:mod:`admin_toolshed` Module
-----------------------------
+galaxy.webapps.galaxy.controllers.admin_toolshed module
+-------------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.admin_toolshed
:members:
:undoc-members:
:show-inheritance:
-:mod:`async` Module
--------------------
+galaxy.webapps.galaxy.controllers.async module
+----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.async
:members:
:undoc-members:
:show-inheritance:
-:mod:`cloudlaunch` Module
--------------------------
+galaxy.webapps.galaxy.controllers.biostar module
+------------------------------------------------
+
+.. automodule:: galaxy.webapps.galaxy.controllers.biostar
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.webapps.galaxy.controllers.cloudlaunch module
+----------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.cloudlaunch
:members:
:undoc-members:
:show-inheritance:
-:mod:`data_admin` Module
-------------------------
+galaxy.webapps.galaxy.controllers.data_manager module
+-----------------------------------------------------
-.. automodule:: galaxy.webapps.galaxy.controllers.data_admin
+.. automodule:: galaxy.webapps.galaxy.controllers.data_manager
:members:
:undoc-members:
:show-inheritance:
-:mod:`dataset` Module
----------------------
+galaxy.webapps.galaxy.controllers.dataset module
+------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.dataset
:members:
:undoc-members:
:show-inheritance:
-:mod:`error` Module
--------------------
+galaxy.webapps.galaxy.controllers.error module
+----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.error
:members:
:undoc-members:
:show-inheritance:
-:mod:`external_service` Module
-------------------------------
+galaxy.webapps.galaxy.controllers.external_service module
+---------------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.external_service
:members:
:undoc-members:
:show-inheritance:
-:mod:`external_services` Module
--------------------------------
+galaxy.webapps.galaxy.controllers.external_services module
+----------------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.external_services
:members:
:undoc-members:
:show-inheritance:
-:mod:`forms` Module
--------------------
+galaxy.webapps.galaxy.controllers.forms module
+----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.forms
:members:
:undoc-members:
:show-inheritance:
-:mod:`history` Module
----------------------
+galaxy.webapps.galaxy.controllers.history module
+------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.history
:members:
:undoc-members:
:show-inheritance:
-:mod:`library` Module
----------------------
+galaxy.webapps.galaxy.controllers.library module
+------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.library
:members:
:undoc-members:
:show-inheritance:
-:mod:`library_admin` Module
----------------------------
+galaxy.webapps.galaxy.controllers.library_admin module
+------------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.library_admin
:members:
:undoc-members:
:show-inheritance:
-:mod:`library_common` Module
-----------------------------
+galaxy.webapps.galaxy.controllers.library_common module
+-------------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.library_common
:members:
:undoc-members:
:show-inheritance:
-:mod:`mobile` Module
---------------------
+galaxy.webapps.galaxy.controllers.mobile module
+-----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.mobile
:members:
:undoc-members:
:show-inheritance:
-:mod:`page` Module
-------------------
+galaxy.webapps.galaxy.controllers.page module
+---------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.page
:members:
:undoc-members:
:show-inheritance:
-:mod:`request_type` Module
---------------------------
+galaxy.webapps.galaxy.controllers.request_type module
+-----------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.request_type
:members:
:undoc-members:
:show-inheritance:
-:mod:`requests` Module
-----------------------
+galaxy.webapps.galaxy.controllers.requests module
+-------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.requests
:members:
:undoc-members:
:show-inheritance:
-:mod:`requests_admin` Module
-----------------------------
+galaxy.webapps.galaxy.controllers.requests_admin module
+-------------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.requests_admin
:members:
:undoc-members:
:show-inheritance:
-:mod:`requests_common` Module
------------------------------
+galaxy.webapps.galaxy.controllers.requests_common module
+--------------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.requests_common
:members:
:undoc-members:
:show-inheritance:
-:mod:`root` Module
-------------------
+galaxy.webapps.galaxy.controllers.root module
+---------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.root
:members:
:undoc-members:
:show-inheritance:
-:mod:`tag` Module
------------------
+galaxy.webapps.galaxy.controllers.search module
+-----------------------------------------------
+
+.. automodule:: galaxy.webapps.galaxy.controllers.search
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.webapps.galaxy.controllers.tag module
+--------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.tag
:members:
:undoc-members:
:show-inheritance:
-:mod:`tool_runner` Module
--------------------------
+galaxy.webapps.galaxy.controllers.tool_runner module
+----------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.tool_runner
:members:
:undoc-members:
:show-inheritance:
-:mod:`ucsc_proxy` Module
-------------------------
+galaxy.webapps.galaxy.controllers.ucsc_proxy module
+---------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.ucsc_proxy
:members:
:undoc-members:
:show-inheritance:
-:mod:`user` Module
-------------------
+galaxy.webapps.galaxy.controllers.user module
+---------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.user
:members:
:undoc-members:
:show-inheritance:
-:mod:`visualization` Module
----------------------------
+galaxy.webapps.galaxy.controllers.userskeys module
+--------------------------------------------------
+
+.. automodule:: galaxy.webapps.galaxy.controllers.userskeys
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.webapps.galaxy.controllers.visualization module
+------------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.visualization
:members:
:undoc-members:
:show-inheritance:
-:mod:`workflow` Module
-----------------------
+galaxy.webapps.galaxy.controllers.workflow module
+-------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.workflow
:members:
:undoc-members:
:show-inheritance:
+
diff --git a/doc/source/lib/galaxy.webapps.galaxy.rst b/doc/source/lib/galaxy.webapps.galaxy.rst
index 42642bec26c..5256155b1ed 100644
--- a/doc/source/lib/galaxy.webapps.galaxy.rst
+++ b/doc/source/lib/galaxy.webapps.galaxy.rst
@@ -1,10 +1,7 @@
-galaxy Package
-==============
+galaxy.webapps.galaxy package
+=============================
-:mod:`buildapp` Module
-----------------------
-
-.. automodule:: galaxy.webapps.galaxy.buildapp
+.. automodule:: galaxy.webapps.galaxy
:members:
:undoc-members:
:show-inheritance:
@@ -17,3 +14,15 @@ Subpackages
galaxy.webapps.galaxy.api
galaxy.webapps.galaxy.controllers
+Submodules
+----------
+
+galaxy.webapps.galaxy.buildapp module
+-------------------------------------
+
+.. automodule:: galaxy.webapps.galaxy.buildapp
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.webapps.reports.controllers.rst b/doc/source/lib/galaxy.webapps.reports.controllers.rst
index fceead9e86c..122b8e286ba 100644
--- a/doc/source/lib/galaxy.webapps.reports.controllers.rst
+++ b/doc/source/lib/galaxy.webapps.reports.controllers.rst
@@ -1,59 +1,68 @@
-controllers Package
-===================
-
-:mod:`controllers` Package
---------------------------
+galaxy.webapps.reports.controllers package
+==========================================
.. automodule:: galaxy.webapps.reports.controllers
:members:
:undoc-members:
:show-inheritance:
-:mod:`jobs` Module
-------------------
+Submodules
+----------
+
+galaxy.webapps.reports.controllers.jobs module
+----------------------------------------------
.. automodule:: galaxy.webapps.reports.controllers.jobs
:members:
:undoc-members:
:show-inheritance:
-:mod:`root` Module
-------------------
+galaxy.webapps.reports.controllers.query module
+-----------------------------------------------
+
+.. automodule:: galaxy.webapps.reports.controllers.query
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.webapps.reports.controllers.root module
+----------------------------------------------
.. automodule:: galaxy.webapps.reports.controllers.root
:members:
:undoc-members:
:show-inheritance:
-:mod:`sample_tracking` Module
------------------------------
+galaxy.webapps.reports.controllers.sample_tracking module
+---------------------------------------------------------
.. automodule:: galaxy.webapps.reports.controllers.sample_tracking
:members:
:undoc-members:
:show-inheritance:
-:mod:`system` Module
---------------------
+galaxy.webapps.reports.controllers.system module
+------------------------------------------------
.. automodule:: galaxy.webapps.reports.controllers.system
:members:
:undoc-members:
:show-inheritance:
-:mod:`users` Module
--------------------
+galaxy.webapps.reports.controllers.users module
+-----------------------------------------------
.. automodule:: galaxy.webapps.reports.controllers.users
:members:
:undoc-members:
:show-inheritance:
-:mod:`workflows` Module
------------------------
+galaxy.webapps.reports.controllers.workflows module
+---------------------------------------------------
.. automodule:: galaxy.webapps.reports.controllers.workflows
:members:
:undoc-members:
:show-inheritance:
+
diff --git a/doc/source/lib/galaxy.webapps.reports.rst b/doc/source/lib/galaxy.webapps.reports.rst
index 59231f71951..8e9fff62be8 100644
--- a/doc/source/lib/galaxy.webapps.reports.rst
+++ b/doc/source/lib/galaxy.webapps.reports.rst
@@ -1,38 +1,11 @@
-reports Package
-===============
-
-:mod:`reports` Package
-----------------------
+galaxy.webapps.reports package
+==============================
.. automodule:: galaxy.webapps.reports
:members:
:undoc-members:
:show-inheritance:
-:mod:`app` Module
------------------
-
-.. automodule:: galaxy.webapps.reports.app
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`buildapp` Module
-----------------------
-
-.. automodule:: galaxy.webapps.reports.buildapp
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`config` Module
---------------------
-
-.. automodule:: galaxy.webapps.reports.config
- :members:
- :undoc-members:
- :show-inheritance:
-
Subpackages
-----------
@@ -40,3 +13,31 @@ Subpackages
galaxy.webapps.reports.controllers
+Submodules
+----------
+
+galaxy.webapps.reports.app module
+---------------------------------
+
+.. automodule:: galaxy.webapps.reports.app
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.webapps.reports.buildapp module
+--------------------------------------
+
+.. automodule:: galaxy.webapps.reports.buildapp
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.webapps.reports.config module
+------------------------------------
+
+.. automodule:: galaxy.webapps.reports.config
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.webapps.rst b/doc/source/lib/galaxy.webapps.rst
index 4f45cdbc4b6..2e301191c77 100644
--- a/doc/source/lib/galaxy.webapps.rst
+++ b/doc/source/lib/galaxy.webapps.rst
@@ -1,8 +1,5 @@
-webapps Package
-===============
-
-:mod:`webapps` Package
-----------------------
+galaxy.webapps package
+======================
.. automodule:: galaxy.webapps
:members:
@@ -14,7 +11,7 @@ Subpackages
.. toctree::
- galaxy.webapps.community
galaxy.webapps.galaxy
galaxy.webapps.reports
+ galaxy.webapps.tool_shed
diff --git a/doc/source/lib/galaxy.webapps.tool_shed.api.rst b/doc/source/lib/galaxy.webapps.tool_shed.api.rst
index 854f99f3e03..ae4c3b45f24 100644
--- a/doc/source/lib/galaxy.webapps.tool_shed.api.rst
+++ b/doc/source/lib/galaxy.webapps.tool_shed.api.rst
@@ -1,19 +1,68 @@
-api Package
-===========
+galaxy.webapps.tool_shed.api package
+====================================
-:mod:`repositories` Module
---------------------------
+.. automodule:: galaxy.webapps.tool_shed.api
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+galaxy.webapps.tool_shed.api.authenticate module
+------------------------------------------------
+
+.. automodule:: galaxy.webapps.tool_shed.api.authenticate
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.webapps.tool_shed.api.categories module
+----------------------------------------------
+
+.. automodule:: galaxy.webapps.tool_shed.api.categories
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.webapps.tool_shed.api.groups module
+------------------------------------------
+
+.. automodule:: galaxy.webapps.tool_shed.api.groups
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.webapps.tool_shed.api.repositories module
+------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.api.repositories
:members:
:undoc-members:
:show-inheritance:
-:mod:`repository_revisions` Module
-----------------------------------
+galaxy.webapps.tool_shed.api.repository_revisions module
+--------------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.api.repository_revisions
:members:
:undoc-members:
:show-inheritance:
+galaxy.webapps.tool_shed.api.tools module
+-----------------------------------------
+
+.. automodule:: galaxy.webapps.tool_shed.api.tools
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.webapps.tool_shed.api.users module
+-----------------------------------------
+
+.. automodule:: galaxy.webapps.tool_shed.api.users
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst b/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst
index 01163fcd545..6e9e7914c46 100644
--- a/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst
+++ b/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst
@@ -1,59 +1,68 @@
-controllers Package
-===================
-
-:mod:`controllers` Package
---------------------------
+galaxy.webapps.tool_shed.controllers package
+============================================
.. automodule:: galaxy.webapps.tool_shed.controllers
:members:
:undoc-members:
:show-inheritance:
-:mod:`admin` Module
--------------------
+Submodules
+----------
+
+galaxy.webapps.tool_shed.controllers.admin module
+-------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.controllers.admin
:members:
:undoc-members:
:show-inheritance:
-:mod:`hg` Module
-----------------
+galaxy.webapps.tool_shed.controllers.groups module
+--------------------------------------------------
+
+.. automodule:: galaxy.webapps.tool_shed.controllers.groups
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.webapps.tool_shed.controllers.hg module
+----------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.controllers.hg
:members:
:undoc-members:
:show-inheritance:
-:mod:`repository` Module
-------------------------
+galaxy.webapps.tool_shed.controllers.repository module
+------------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.controllers.repository
:members:
:undoc-members:
:show-inheritance:
-:mod:`repository_review` Module
--------------------------------
+galaxy.webapps.tool_shed.controllers.repository_review module
+-------------------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.controllers.repository_review
:members:
:undoc-members:
:show-inheritance:
-:mod:`upload` Module
---------------------
+galaxy.webapps.tool_shed.controllers.upload module
+--------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.controllers.upload
:members:
:undoc-members:
:show-inheritance:
-:mod:`user` Module
-------------------
+galaxy.webapps.tool_shed.controllers.user module
+------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.controllers.user
:members:
:undoc-members:
:show-inheritance:
+
diff --git a/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst b/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst
index 4de7ea427c2..361baef5268 100644
--- a/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst
+++ b/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst
@@ -1,27 +1,28 @@
-middleware Package
-==================
-
-:mod:`middleware` Package
--------------------------
+galaxy.webapps.tool_shed.framework.middleware package
+=====================================================
.. automodule:: galaxy.webapps.tool_shed.framework.middleware
:members:
:undoc-members:
:show-inheritance:
-:mod:`hg` Module
-----------------
+Submodules
+----------
+
+galaxy.webapps.tool_shed.framework.middleware.hg module
+-------------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.framework.middleware.hg
:members:
:undoc-members:
:show-inheritance:
-:mod:`remoteuser` Module
-------------------------
+galaxy.webapps.tool_shed.framework.middleware.remoteuser module
+---------------------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.framework.middleware.remoteuser
:members:
:undoc-members:
:show-inheritance:
+
diff --git a/doc/source/lib/galaxy.webapps.tool_shed.framework.rst b/doc/source/lib/galaxy.webapps.tool_shed.framework.rst
index d0f4b8abdf8..0276dcbd1c4 100644
--- a/doc/source/lib/galaxy.webapps.tool_shed.framework.rst
+++ b/doc/source/lib/galaxy.webapps.tool_shed.framework.rst
@@ -1,8 +1,5 @@
-framework Package
-=================
-
-:mod:`framework` Package
-------------------------
+galaxy.webapps.tool_shed.framework package
+==========================================
.. automodule:: galaxy.webapps.tool_shed.framework
:members:
diff --git a/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst b/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst
index 2d4197c30a3..9fd4bd531e8 100644
--- a/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst
+++ b/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst
@@ -1,11 +1,20 @@
-migrate Package
-===============
+galaxy.webapps.tool_shed.model.migrate package
+==============================================
-:mod:`check` Module
--------------------
+.. automodule:: galaxy.webapps.tool_shed.model.migrate
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+galaxy.webapps.tool_shed.model.migrate.check module
+---------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.model.migrate.check
:members:
:undoc-members:
:show-inheritance:
+
diff --git a/doc/source/lib/galaxy.webapps.tool_shed.model.rst b/doc/source/lib/galaxy.webapps.tool_shed.model.rst
index 429f0d57917..bc60bd734c3 100644
--- a/doc/source/lib/galaxy.webapps.tool_shed.model.rst
+++ b/doc/source/lib/galaxy.webapps.tool_shed.model.rst
@@ -1,22 +1,11 @@
-model Package
-=============
-
-:mod:`model` Package
---------------------
+galaxy.webapps.tool_shed.model package
+======================================
.. automodule:: galaxy.webapps.tool_shed.model
:members:
:undoc-members:
:show-inheritance:
-:mod:`mapping` Module
----------------------
-
-.. automodule:: galaxy.webapps.tool_shed.model.mapping
- :members:
- :undoc-members:
- :show-inheritance:
-
Subpackages
-----------
@@ -24,3 +13,15 @@ Subpackages
galaxy.webapps.tool_shed.model.migrate
+Submodules
+----------
+
+galaxy.webapps.tool_shed.model.mapping module
+---------------------------------------------
+
+.. automodule:: galaxy.webapps.tool_shed.model.mapping
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.webapps.tool_shed.rst b/doc/source/lib/galaxy.webapps.tool_shed.rst
index 1590f2988c1..836aa571014 100644
--- a/doc/source/lib/galaxy.webapps.tool_shed.rst
+++ b/doc/source/lib/galaxy.webapps.tool_shed.rst
@@ -1,38 +1,11 @@
-tool_shed Package
-=================
-
-:mod:`tool_shed` Package
-------------------------
+galaxy.webapps.tool_shed package
+================================
.. automodule:: galaxy.webapps.tool_shed
:members:
:undoc-members:
:show-inheritance:
-:mod:`app` Module
------------------
-
-.. automodule:: galaxy.webapps.tool_shed.app
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`buildapp` Module
-----------------------
-
-.. automodule:: galaxy.webapps.tool_shed.buildapp
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`config` Module
---------------------
-
-.. automodule:: galaxy.webapps.tool_shed.config
- :members:
- :undoc-members:
- :show-inheritance:
-
Subpackages
-----------
@@ -42,6 +15,35 @@ Subpackages
galaxy.webapps.tool_shed.controllers
galaxy.webapps.tool_shed.framework
galaxy.webapps.tool_shed.model
+ galaxy.webapps.tool_shed.search
galaxy.webapps.tool_shed.security
galaxy.webapps.tool_shed.util
+Submodules
+----------
+
+galaxy.webapps.tool_shed.app module
+-----------------------------------
+
+.. automodule:: galaxy.webapps.tool_shed.app
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.webapps.tool_shed.buildapp module
+----------------------------------------
+
+.. automodule:: galaxy.webapps.tool_shed.buildapp
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.webapps.tool_shed.config module
+--------------------------------------
+
+.. automodule:: galaxy.webapps.tool_shed.config
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.webapps.tool_shed.search.rst b/doc/source/lib/galaxy.webapps.tool_shed.search.rst
new file mode 100644
index 00000000000..9daeff111f0
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.tool_shed.search.rst
@@ -0,0 +1,28 @@
+galaxy.webapps.tool_shed.search package
+=======================================
+
+.. automodule:: galaxy.webapps.tool_shed.search
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+galaxy.webapps.tool_shed.search.repo_search module
+--------------------------------------------------
+
+.. automodule:: galaxy.webapps.tool_shed.search.repo_search
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.webapps.tool_shed.search.tool_search module
+--------------------------------------------------
+
+.. automodule:: galaxy.webapps.tool_shed.search.tool_search
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.webapps.tool_shed.security.rst b/doc/source/lib/galaxy.webapps.tool_shed.security.rst
index ac3f17fb38d..4e39d99210a 100644
--- a/doc/source/lib/galaxy.webapps.tool_shed.security.rst
+++ b/doc/source/lib/galaxy.webapps.tool_shed.security.rst
@@ -1,8 +1,5 @@
-security Package
-================
-
-:mod:`security` Package
------------------------
+galaxy.webapps.tool_shed.security package
+=========================================
.. automodule:: galaxy.webapps.tool_shed.security
:members:
diff --git a/doc/source/lib/galaxy.webapps.tool_shed.util.rst b/doc/source/lib/galaxy.webapps.tool_shed.util.rst
index a8623852afa..6ee1d6c7a9f 100644
--- a/doc/source/lib/galaxy.webapps.tool_shed.util.rst
+++ b/doc/source/lib/galaxy.webapps.tool_shed.util.rst
@@ -1,35 +1,36 @@
-util Package
-============
+galaxy.webapps.tool_shed.util package
+=====================================
-:mod:`common_util` Module
--------------------------
-
-.. automodule:: galaxy.webapps.tool_shed.util.common_util
+.. automodule:: galaxy.webapps.tool_shed.util
:members:
:undoc-members:
:show-inheritance:
-:mod:`container_util` Module
-----------------------------
+Submodules
+----------
-.. automodule:: galaxy.webapps.tool_shed.util.container_util
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`hgweb_config` Module
---------------------------
+galaxy.webapps.tool_shed.util.hgweb_config module
+-------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.util.hgweb_config
:members:
:undoc-members:
:show-inheritance:
-:mod:`shed_statistics` Module
------------------------------
+galaxy.webapps.tool_shed.util.ratings_util module
+-------------------------------------------------
+
+.. automodule:: galaxy.webapps.tool_shed.util.ratings_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.webapps.tool_shed.util.shed_statistics module
+----------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.util.shed_statistics
:members:
:undoc-members:
:show-inheritance:
+
diff --git a/doc/source/lib/galaxy.work.rst b/doc/source/lib/galaxy.work.rst
new file mode 100644
index 00000000000..415a5b881c8
--- /dev/null
+++ b/doc/source/lib/galaxy.work.rst
@@ -0,0 +1,20 @@
+galaxy.work package
+===================
+
+.. automodule:: galaxy.work
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+galaxy.work.context module
+--------------------------
+
+.. automodule:: galaxy.work.context
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.workflow.rst b/doc/source/lib/galaxy.workflow.rst
index 52fd8e5fb0a..8d0a2c4dfb6 100644
--- a/doc/source/lib/galaxy.workflow.rst
+++ b/doc/source/lib/galaxy.workflow.rst
@@ -1,11 +1,75 @@
-workflow Package
-================
+galaxy.workflow package
+=======================
-:mod:`modules` Module
----------------------
+.. automodule:: galaxy.workflow
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.workflow.schedulers
+
+Submodules
+----------
+
+galaxy.workflow.extract module
+------------------------------
+
+.. automodule:: galaxy.workflow.extract
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.workflow.modules module
+------------------------------
.. automodule:: galaxy.workflow.modules
:members:
:undoc-members:
:show-inheritance:
+galaxy.workflow.render module
+-----------------------------
+
+.. automodule:: galaxy.workflow.render
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.workflow.run module
+--------------------------
+
+.. automodule:: galaxy.workflow.run
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.workflow.run_request module
+----------------------------------
+
+.. automodule:: galaxy.workflow.run_request
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.workflow.scheduling_manager module
+-----------------------------------------
+
+.. automodule:: galaxy.workflow.scheduling_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+galaxy.workflow.steps module
+----------------------------
+
+.. automodule:: galaxy.workflow.steps
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy.workflow.schedulers.rst b/doc/source/lib/galaxy.workflow.schedulers.rst
new file mode 100644
index 00000000000..43801194aa8
--- /dev/null
+++ b/doc/source/lib/galaxy.workflow.schedulers.rst
@@ -0,0 +1,20 @@
+galaxy.workflow.schedulers package
+==================================
+
+.. automodule:: galaxy.workflow.schedulers
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+galaxy.workflow.schedulers.core module
+--------------------------------------
+
+.. automodule:: galaxy.workflow.schedulers.core
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy_ext.metadata.rst b/doc/source/lib/galaxy_ext.metadata.rst
new file mode 100644
index 00000000000..489f529521f
--- /dev/null
+++ b/doc/source/lib/galaxy_ext.metadata.rst
@@ -0,0 +1,20 @@
+galaxy_ext.metadata package
+===========================
+
+.. automodule:: galaxy_ext.metadata
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+galaxy_ext.metadata.set_metadata module
+---------------------------------------
+
+.. automodule:: galaxy_ext.metadata.set_metadata
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/galaxy_ext.rst b/doc/source/lib/galaxy_ext.rst
new file mode 100644
index 00000000000..040ba0b19c6
--- /dev/null
+++ b/doc/source/lib/galaxy_ext.rst
@@ -0,0 +1,15 @@
+galaxy_ext package
+==================
+
+.. automodule:: galaxy_ext
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy_ext.metadata
+
diff --git a/doc/source/lib/galaxy_utils.rst b/doc/source/lib/galaxy_utils.rst
index 3ed28649f1b..c17a7199d73 100644
--- a/doc/source/lib/galaxy_utils.rst
+++ b/doc/source/lib/galaxy_utils.rst
@@ -1,6 +1,11 @@
-galaxy_utils Package
+galaxy_utils package
====================
+.. automodule:: galaxy_utils
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
Subpackages
-----------
diff --git a/doc/source/lib/galaxy_utils.sequence.rst b/doc/source/lib/galaxy_utils.sequence.rst
index b1900d7421f..f047ab6e219 100644
--- a/doc/source/lib/galaxy_utils.sequence.rst
+++ b/doc/source/lib/galaxy_utils.sequence.rst
@@ -1,43 +1,52 @@
-sequence Package
-================
+galaxy_utils.sequence package
+=============================
-:mod:`fasta` Module
--------------------
+.. automodule:: galaxy_utils.sequence
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+galaxy_utils.sequence.fasta module
+----------------------------------
.. automodule:: galaxy_utils.sequence.fasta
:members:
:undoc-members:
:show-inheritance:
-:mod:`fastq` Module
--------------------
+galaxy_utils.sequence.fastq module
+----------------------------------
.. automodule:: galaxy_utils.sequence.fastq
:members:
:undoc-members:
:show-inheritance:
-:mod:`sequence` Module
-----------------------
+galaxy_utils.sequence.sequence module
+-------------------------------------
.. automodule:: galaxy_utils.sequence.sequence
:members:
:undoc-members:
:show-inheritance:
-:mod:`transform` Module
------------------------
+galaxy_utils.sequence.transform module
+--------------------------------------
.. automodule:: galaxy_utils.sequence.transform
:members:
:undoc-members:
:show-inheritance:
-:mod:`vcf` Module
------------------
+galaxy_utils.sequence.vcf module
+--------------------------------
.. automodule:: galaxy_utils.sequence.vcf
:members:
:undoc-members:
:show-inheritance:
+
diff --git a/doc/source/lib/log_tempfile.rst b/doc/source/lib/log_tempfile.rst
index a5ca8f23b82..51b904985f8 100644
--- a/doc/source/lib/log_tempfile.rst
+++ b/doc/source/lib/log_tempfile.rst
@@ -1,4 +1,4 @@
-log_tempfile Module
+log_tempfile module
===================
.. automodule:: log_tempfile
diff --git a/doc/source/lib/mimeparse.rst b/doc/source/lib/mimeparse.rst
index 0490cfdc8b3..afcdfa0c86b 100644
--- a/doc/source/lib/mimeparse.rst
+++ b/doc/source/lib/mimeparse.rst
@@ -1,4 +1,4 @@
-mimeparse Module
+mimeparse module
================
.. automodule:: mimeparse
diff --git a/doc/source/lib/modules.rst b/doc/source/lib/modules.rst
index c6255ce98fd..bb4749bc352 100644
--- a/doc/source/lib/modules.rst
+++ b/doc/source/lib/modules.rst
@@ -4,10 +4,12 @@ lib
.. toctree::
:maxdepth: 4
- fpconst
galaxy
+ galaxy_ext
galaxy_utils
log_tempfile
mimeparse
pkg_resources
psyco_full
+ pulsar
+ tool_shed
diff --git a/doc/source/lib/pkg_resources.rst b/doc/source/lib/pkg_resources.rst
index ef99aca6efc..e3082f69603 100644
--- a/doc/source/lib/pkg_resources.rst
+++ b/doc/source/lib/pkg_resources.rst
@@ -1,4 +1,4 @@
-pkg_resources Module
+pkg_resources module
====================
.. automodule:: pkg_resources
diff --git a/doc/source/lib/psyco_full.rst b/doc/source/lib/psyco_full.rst
index 9e75f1b0955..370be05776f 100644
--- a/doc/source/lib/psyco_full.rst
+++ b/doc/source/lib/psyco_full.rst
@@ -1,4 +1,4 @@
-psyco_full Module
+psyco_full module
=================
.. automodule:: psyco_full
diff --git a/doc/source/lib/pulsar.client.rst b/doc/source/lib/pulsar.client.rst
new file mode 100644
index 00000000000..3a29f55ffae
--- /dev/null
+++ b/doc/source/lib/pulsar.client.rst
@@ -0,0 +1,132 @@
+pulsar.client package
+=====================
+
+.. automodule:: pulsar.client
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ pulsar.client.staging
+ pulsar.client.transport
+
+Submodules
+----------
+
+pulsar.client.action_mapper module
+----------------------------------
+
+.. automodule:: pulsar.client.action_mapper
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.amqp_exchange module
+----------------------------------
+
+.. automodule:: pulsar.client.amqp_exchange
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.amqp_exchange_factory module
+------------------------------------------
+
+.. automodule:: pulsar.client.amqp_exchange_factory
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.client module
+---------------------------
+
+.. automodule:: pulsar.client.client
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.config_util module
+--------------------------------
+
+.. automodule:: pulsar.client.config_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.decorators module
+-------------------------------
+
+.. automodule:: pulsar.client.decorators
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.destination module
+--------------------------------
+
+.. automodule:: pulsar.client.destination
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.interface module
+------------------------------
+
+.. automodule:: pulsar.client.interface
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.job_directory module
+----------------------------------
+
+.. automodule:: pulsar.client.job_directory
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.manager module
+----------------------------
+
+.. automodule:: pulsar.client.manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.object_client module
+----------------------------------
+
+.. automodule:: pulsar.client.object_client
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.path_mapper module
+--------------------------------
+
+.. automodule:: pulsar.client.path_mapper
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.setup_handler module
+----------------------------------
+
+.. automodule:: pulsar.client.setup_handler
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.util module
+-------------------------
+
+.. automodule:: pulsar.client.util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/pulsar.client.staging.rst b/doc/source/lib/pulsar.client.staging.rst
new file mode 100644
index 00000000000..4d33f6676b8
--- /dev/null
+++ b/doc/source/lib/pulsar.client.staging.rst
@@ -0,0 +1,28 @@
+pulsar.client.staging package
+=============================
+
+.. automodule:: pulsar.client.staging
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+pulsar.client.staging.down module
+---------------------------------
+
+.. automodule:: pulsar.client.staging.down
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.staging.up module
+-------------------------------
+
+.. automodule:: pulsar.client.staging.up
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/pulsar.client.transport.rst b/doc/source/lib/pulsar.client.transport.rst
new file mode 100644
index 00000000000..8b68dbb15a5
--- /dev/null
+++ b/doc/source/lib/pulsar.client.transport.rst
@@ -0,0 +1,52 @@
+pulsar.client.transport package
+===============================
+
+.. automodule:: pulsar.client.transport
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+pulsar.client.transport.curl module
+-----------------------------------
+
+.. automodule:: pulsar.client.transport.curl
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.transport.poster module
+-------------------------------------
+
+.. automodule:: pulsar.client.transport.poster
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.transport.requests module
+---------------------------------------
+
+.. automodule:: pulsar.client.transport.requests
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.transport.ssh module
+----------------------------------
+
+.. automodule:: pulsar.client.transport.ssh
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+pulsar.client.transport.standard module
+---------------------------------------
+
+.. automodule:: pulsar.client.transport.standard
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/pulsar.rst b/doc/source/lib/pulsar.rst
new file mode 100644
index 00000000000..c22c0a95bdb
--- /dev/null
+++ b/doc/source/lib/pulsar.rst
@@ -0,0 +1,15 @@
+pulsar package
+==============
+
+.. automodule:: pulsar
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ pulsar.client
+
diff --git a/doc/source/lib/tool_shed.capsule.rst b/doc/source/lib/tool_shed.capsule.rst
new file mode 100644
index 00000000000..3865f875806
--- /dev/null
+++ b/doc/source/lib/tool_shed.capsule.rst
@@ -0,0 +1,20 @@
+tool_shed.capsule package
+=========================
+
+.. automodule:: tool_shed.capsule
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.capsule.capsule_manager module
+----------------------------------------
+
+.. automodule:: tool_shed.capsule.capsule_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/tool_shed.dependencies.repository.rst b/doc/source/lib/tool_shed.dependencies.repository.rst
new file mode 100644
index 00000000000..bd6356b7531
--- /dev/null
+++ b/doc/source/lib/tool_shed.dependencies.repository.rst
@@ -0,0 +1,20 @@
+tool_shed.dependencies.repository package
+=========================================
+
+.. automodule:: tool_shed.dependencies.repository
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.dependencies.repository.relation_builder module
+---------------------------------------------------------
+
+.. automodule:: tool_shed.dependencies.repository.relation_builder
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/tool_shed.dependencies.rst b/doc/source/lib/tool_shed.dependencies.rst
new file mode 100644
index 00000000000..563583e596f
--- /dev/null
+++ b/doc/source/lib/tool_shed.dependencies.rst
@@ -0,0 +1,28 @@
+tool_shed.dependencies package
+==============================
+
+.. automodule:: tool_shed.dependencies
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ tool_shed.dependencies.repository
+ tool_shed.dependencies.tool
+
+Submodules
+----------
+
+tool_shed.dependencies.attribute_handlers module
+------------------------------------------------
+
+.. automodule:: tool_shed.dependencies.attribute_handlers
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/tool_shed.dependencies.tool.rst b/doc/source/lib/tool_shed.dependencies.tool.rst
new file mode 100644
index 00000000000..3062aa20041
--- /dev/null
+++ b/doc/source/lib/tool_shed.dependencies.tool.rst
@@ -0,0 +1,20 @@
+tool_shed.dependencies.tool package
+===================================
+
+.. automodule:: tool_shed.dependencies.tool
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.dependencies.tool.tag_attribute_handler module
+--------------------------------------------------------
+
+.. automodule:: tool_shed.dependencies.tool.tag_attribute_handler
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/tool_shed.galaxy_install.datatypes.rst b/doc/source/lib/tool_shed.galaxy_install.datatypes.rst
new file mode 100644
index 00000000000..bab6f246f76
--- /dev/null
+++ b/doc/source/lib/tool_shed.galaxy_install.datatypes.rst
@@ -0,0 +1,20 @@
+tool_shed.galaxy_install.datatypes package
+==========================================
+
+.. automodule:: tool_shed.galaxy_install.datatypes
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.galaxy_install.datatypes.custom_datatype_manager module
+-----------------------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.datatypes.custom_datatype_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/tool_shed.galaxy_install.grids.rst b/doc/source/lib/tool_shed.galaxy_install.grids.rst
index c75c5c716ea..b01741c0d70 100644
--- a/doc/source/lib/tool_shed.galaxy_install.grids.rst
+++ b/doc/source/lib/tool_shed.galaxy_install.grids.rst
@@ -1,11 +1,20 @@
-grids Package
-=============
+tool_shed.galaxy_install.grids package
+======================================
-:mod:`admin_toolshed_grids` Module
-----------------------------------
+.. automodule:: tool_shed.galaxy_install.grids
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.galaxy_install.grids.admin_toolshed_grids module
+----------------------------------------------------------
.. automodule:: tool_shed.galaxy_install.grids.admin_toolshed_grids
:members:
:undoc-members:
:show-inheritance:
+
diff --git a/doc/source/lib/tool_shed.galaxy_install.metadata.rst b/doc/source/lib/tool_shed.galaxy_install.metadata.rst
new file mode 100644
index 00000000000..8a63d06e5d0
--- /dev/null
+++ b/doc/source/lib/tool_shed.galaxy_install.metadata.rst
@@ -0,0 +1,20 @@
+tool_shed.galaxy_install.metadata package
+=========================================
+
+.. automodule:: tool_shed.galaxy_install.metadata
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.galaxy_install.metadata.installed_repository_metadata_manager module
+------------------------------------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.metadata.installed_repository_metadata_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/tool_shed.galaxy_install.migrate.rst b/doc/source/lib/tool_shed.galaxy_install.migrate.rst
index 5d553b446d1..4e3291da76b 100644
--- a/doc/source/lib/tool_shed.galaxy_install.migrate.rst
+++ b/doc/source/lib/tool_shed.galaxy_install.migrate.rst
@@ -1,19 +1,28 @@
-migrate Package
-===============
+tool_shed.galaxy_install.migrate package
+========================================
-:mod:`check` Module
--------------------
+.. automodule:: tool_shed.galaxy_install.migrate
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.galaxy_install.migrate.check module
+---------------------------------------------
.. automodule:: tool_shed.galaxy_install.migrate.check
:members:
:undoc-members:
:show-inheritance:
-:mod:`common` Module
---------------------
+tool_shed.galaxy_install.migrate.common module
+----------------------------------------------
.. automodule:: tool_shed.galaxy_install.migrate.common
:members:
:undoc-members:
:show-inheritance:
+
diff --git a/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst b/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst
new file mode 100644
index 00000000000..5110d9fb105
--- /dev/null
+++ b/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst
@@ -0,0 +1,20 @@
+tool_shed.galaxy_install.repository_dependencies package
+========================================================
+
+.. automodule:: tool_shed.galaxy_install.repository_dependencies
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager module
+-------------------------------------------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/tool_shed.galaxy_install.rst b/doc/source/lib/tool_shed.galaxy_install.rst
index 28e61519afe..f4510a24c13 100644
--- a/doc/source/lib/tool_shed.galaxy_install.rst
+++ b/doc/source/lib/tool_shed.galaxy_install.rst
@@ -1,44 +1,74 @@
-galaxy_install Package
-======================
-
-:mod:`galaxy_install` Package
------------------------------
+tool_shed.galaxy_install package
+================================
.. automodule:: tool_shed.galaxy_install
:members:
:undoc-members:
:show-inheritance:
-:mod:`install_manager` Module
------------------------------
-
-.. automodule:: tool_shed.galaxy_install.install_manager
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`repository_util` Module
------------------------------
-
-.. automodule:: tool_shed.galaxy_install.repository_util
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`update_manager` Module
-----------------------------
-
-.. automodule:: tool_shed.galaxy_install.update_manager
- :members:
- :undoc-members:
- :show-inheritance:
-
Subpackages
-----------
.. toctree::
+ tool_shed.galaxy_install.datatypes
tool_shed.galaxy_install.grids
+ tool_shed.galaxy_install.metadata
tool_shed.galaxy_install.migrate
+ tool_shed.galaxy_install.repository_dependencies
tool_shed.galaxy_install.tool_dependencies
+ tool_shed.galaxy_install.tools
+ tool_shed.galaxy_install.utility_containers
+
+Submodules
+----------
+
+tool_shed.galaxy_install.dependency_display module
+--------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.dependency_display
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.galaxy_install.install_manager module
+-----------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.install_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.galaxy_install.installed_repository_manager module
+------------------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.installed_repository_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.galaxy_install.repair_repository_manager module
+---------------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.repair_repository_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.galaxy_install.tool_migration_manager module
+------------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.tool_migration_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.galaxy_install.update_repository_manager module
+---------------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.update_repository_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff --git a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst
new file mode 100644
index 00000000000..29d76529234
--- /dev/null
+++ b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst
@@ -0,0 +1,60 @@
+tool_shed.galaxy_install.tool_dependencies.recipe package
+=========================================================
+
+.. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader module
+----------------------------------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder module
+-------------------------------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.galaxy_install.tool_dependencies.recipe.install_environment module
+----------------------------------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager module
+-----------------------------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.galaxy_install.tool_dependencies.recipe.step_handler module
+---------------------------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.step_handler
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler module
+--------------------------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst
index 4871c0b1f58..5f67bad6c1e 100644
--- a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst
+++ b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst
@@ -1,27 +1,27 @@
-tool_dependencies Package
-=========================
+tool_shed.galaxy_install.tool_dependencies package
+==================================================
-:mod:`common_util` Module
--------------------------
-
-.. automodule:: tool_shed.galaxy_install.tool_dependencies.common_util
+.. automodule:: tool_shed.galaxy_install.tool_dependencies
:members:
:undoc-members:
:show-inheritance:
-:mod:`fabric_util` Module
--------------------------
+Subpackages
+-----------
-.. automodule:: tool_shed.galaxy_install.tool_dependencies.fabric_util
+.. toctree::
+
+ tool_shed.galaxy_install.tool_dependencies.recipe
+
+Submodules
+----------
+
+tool_shed.galaxy_install.tool_dependencies.env_manager module
+-------------------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.tool_dependencies.env_manager
:members:
:undoc-members:
:show-inheritance:
-:mod:`install_util` Module
---------------------------
-
-.. automodule:: tool_shed.galaxy_install.tool_dependencies.install_util
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/doc/source/lib/tool_shed.galaxy_install.tools.rst b/doc/source/lib/tool_shed.galaxy_install.tools.rst
new file mode 100644
index 00000000000..1d1d0f37243
--- /dev/null
+++ b/doc/source/lib/tool_shed.galaxy_install.tools.rst
@@ -0,0 +1,28 @@
+tool_shed.galaxy_install.tools package
+======================================
+
+.. automodule:: tool_shed.galaxy_install.tools
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.galaxy_install.tools.data_manager module
+--------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.tools.data_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.galaxy_install.tools.tool_panel_manager module
+--------------------------------------------------------
+
+.. automodule:: tool_shed.galaxy_install.tools.tool_panel_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst b/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst
new file mode 100644
index 00000000000..347d7317fc2
--- /dev/null
+++ b/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst
@@ -0,0 +1,8 @@
+tool_shed.galaxy_install.utility_containers package
+===================================================
+
+.. automodule:: tool_shed.galaxy_install.utility_containers
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff --git a/doc/source/lib/tool_shed.grids.rst b/doc/source/lib/tool_shed.grids.rst
index 154f92b8369..7ee5fb07ce8 100644
--- a/doc/source/lib/tool_shed.grids.rst
+++ b/doc/source/lib/tool_shed.grids.rst
@@ -1,35 +1,52 @@
-grids Package
-=============
+tool_shed.grids package
+=======================
-:mod:`admin_grids` Module
--------------------------
+.. automodule:: tool_shed.grids
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.grids.admin_grids module
+----------------------------------
.. automodule:: tool_shed.grids.admin_grids
:members:
:undoc-members:
:show-inheritance:
-:mod:`repository_grids` Module
-------------------------------
+tool_shed.grids.repository_grid_filter_manager module
+-----------------------------------------------------
+
+.. automodule:: tool_shed.grids.repository_grid_filter_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.grids.repository_grids module
+---------------------------------------
.. automodule:: tool_shed.grids.repository_grids
:members:
:undoc-members:
:show-inheritance:
-:mod:`repository_review_grids` Module
--------------------------------------
+tool_shed.grids.repository_review_grids module
+----------------------------------------------
.. automodule:: tool_shed.grids.repository_review_grids
:members:
:undoc-members:
:show-inheritance:
-:mod:`util` Module
-------------------
+tool_shed.grids.util module
+---------------------------
.. automodule:: tool_shed.grids.util
:members:
:undoc-members:
:show-inheritance:
+
diff --git a/doc/source/lib/tool_shed.managers.rst b/doc/source/lib/tool_shed.managers.rst
new file mode 100644
index 00000000000..04de3ce0371
--- /dev/null
+++ b/doc/source/lib/tool_shed.managers.rst
@@ -0,0 +1,28 @@
+tool_shed.managers package
+==========================
+
+.. automodule:: tool_shed.managers
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.managers.groups module
+--------------------------------
+
+.. automodule:: tool_shed.managers.groups
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.managers.repositories module
+--------------------------------------
+
+.. automodule:: tool_shed.managers.repositories
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/tool_shed.metadata.rst b/doc/source/lib/tool_shed.metadata.rst
new file mode 100644
index 00000000000..7e2ba80941d
--- /dev/null
+++ b/doc/source/lib/tool_shed.metadata.rst
@@ -0,0 +1,28 @@
+tool_shed.metadata package
+==========================
+
+.. automodule:: tool_shed.metadata
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.metadata.metadata_generator module
+--------------------------------------------
+
+.. automodule:: tool_shed.metadata.metadata_generator
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.metadata.repository_metadata_manager module
+-----------------------------------------------------
+
+.. automodule:: tool_shed.metadata.repository_metadata_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/tool_shed.repository_types.rst b/doc/source/lib/tool_shed.repository_types.rst
new file mode 100644
index 00000000000..5e5cff1b7de
--- /dev/null
+++ b/doc/source/lib/tool_shed.repository_types.rst
@@ -0,0 +1,60 @@
+tool_shed.repository_types package
+==================================
+
+.. automodule:: tool_shed.repository_types
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.repository_types.metadata module
+------------------------------------------
+
+.. automodule:: tool_shed.repository_types.metadata
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.repository_types.registry module
+------------------------------------------
+
+.. automodule:: tool_shed.repository_types.registry
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.repository_types.repository_suite_definition module
+-------------------------------------------------------------
+
+.. automodule:: tool_shed.repository_types.repository_suite_definition
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.repository_types.tool_dependency_definition module
+------------------------------------------------------------
+
+.. automodule:: tool_shed.repository_types.tool_dependency_definition
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.repository_types.unrestricted module
+----------------------------------------------
+
+.. automodule:: tool_shed.repository_types.unrestricted
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.repository_types.util module
+--------------------------------------
+
+.. automodule:: tool_shed.repository_types.util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/tool_shed.rst b/doc/source/lib/tool_shed.rst
index 76794397c1c..9ea2997d843 100644
--- a/doc/source/lib/tool_shed.rst
+++ b/doc/source/lib/tool_shed.rst
@@ -1,10 +1,7 @@
-tool_shed Package
+tool_shed package
=================
-:mod:`tool_shed_registry` Module
---------------------------------
-
-.. automodule:: tool_shed.tool_shed_registry
+.. automodule:: tool_shed
:members:
:undoc-members:
:show-inheritance:
@@ -14,7 +11,34 @@ Subpackages
.. toctree::
+ tool_shed.capsule
+ tool_shed.dependencies
tool_shed.galaxy_install
tool_shed.grids
+ tool_shed.managers
+ tool_shed.metadata
+ tool_shed.repository_types
+ tool_shed.tools
tool_shed.util
+ tool_shed.utility_containers
+
+Submodules
+----------
+
+tool_shed.repository_registry module
+------------------------------------
+
+.. automodule:: tool_shed.repository_registry
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.tool_shed_registry module
+-----------------------------------
+
+.. automodule:: tool_shed.tool_shed_registry
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff --git a/doc/source/lib/tool_shed.tools.rst b/doc/source/lib/tool_shed.tools.rst
new file mode 100644
index 00000000000..bfc71f2f4eb
--- /dev/null
+++ b/doc/source/lib/tool_shed.tools.rst
@@ -0,0 +1,36 @@
+tool_shed.tools package
+=======================
+
+.. automodule:: tool_shed.tools
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.tools.data_table_manager module
+-----------------------------------------
+
+.. automodule:: tool_shed.tools.data_table_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.tools.tool_validator module
+-------------------------------------
+
+.. automodule:: tool_shed.tools.tool_validator
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.tools.tool_version_manager module
+-------------------------------------------
+
+.. automodule:: tool_shed.tools.tool_version_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/tool_shed.util.rst b/doc/source/lib/tool_shed.util.rst
index 17d6e4c490d..47b221ed9b5 100644
--- a/doc/source/lib/tool_shed.util.rst
+++ b/doc/source/lib/tool_shed.util.rst
@@ -1,107 +1,156 @@
-util Package
-============
+tool_shed.util package
+======================
-:mod:`common_install_util` Module
----------------------------------
-
-.. automodule:: tool_shed.util.common_install_util
+.. automodule:: tool_shed.util
:members:
:undoc-members:
:show-inheritance:
-:mod:`common_util` Module
--------------------------
+Submodules
+----------
+
+tool_shed.util.basic_util module
+--------------------------------
+
+.. automodule:: tool_shed.util.basic_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.util.commit_util module
+---------------------------------
+
+.. automodule:: tool_shed.util.commit_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.util.common_util module
+---------------------------------
.. automodule:: tool_shed.util.common_util
:members:
:undoc-members:
:show-inheritance:
-:mod:`data_manager_util` Module
--------------------------------
+tool_shed.util.container_util module
+------------------------------------
-.. automodule:: tool_shed.util.data_manager_util
+.. automodule:: tool_shed.util.container_util
:members:
:undoc-members:
:show-inheritance:
-:mod:`datatype_util` Module
----------------------------
-
-.. automodule:: tool_shed.util.datatype_util
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`encoding_util` Module
----------------------------
+tool_shed.util.encoding_util module
+-----------------------------------
.. automodule:: tool_shed.util.encoding_util
:members:
:undoc-members:
:show-inheritance:
-:mod:`metadata_util` Module
----------------------------
+tool_shed.util.hg_util module
+-----------------------------
+
+.. automodule:: tool_shed.util.hg_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.util.metadata_util module
+-----------------------------------
.. automodule:: tool_shed.util.metadata_util
:members:
:undoc-members:
:show-inheritance:
-:mod:`readme_util` Module
--------------------------
+tool_shed.util.readme_util module
+---------------------------------
.. automodule:: tool_shed.util.readme_util
:members:
:undoc-members:
:show-inheritance:
-:mod:`repository_dependency_util` Module
-----------------------------------------
+tool_shed.util.repository_content_util module
+---------------------------------------------
-.. automodule:: tool_shed.util.repository_dependency_util
+.. automodule:: tool_shed.util.repository_content_util
:members:
:undoc-members:
:show-inheritance:
-:mod:`review_util` Module
--------------------------
+tool_shed.util.repository_util module
+-------------------------------------
+
+.. automodule:: tool_shed.util.repository_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.util.review_util module
+---------------------------------
.. automodule:: tool_shed.util.review_util
:members:
:undoc-members:
:show-inheritance:
-:mod:`shed_util_common` Module
-------------------------------
+tool_shed.util.search_util module
+---------------------------------
+
+.. automodule:: tool_shed.util.search_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.util.shed_util_common module
+--------------------------------------
.. automodule:: tool_shed.util.shed_util_common
:members:
:undoc-members:
:show-inheritance:
-:mod:`tool_dependency_util` Module
-----------------------------------
+tool_shed.util.tool_dependency_util module
+------------------------------------------
.. automodule:: tool_shed.util.tool_dependency_util
:members:
:undoc-members:
:show-inheritance:
-:mod:`tool_util` Module
------------------------
+tool_shed.util.tool_util module
+-------------------------------
.. automodule:: tool_shed.util.tool_util
:members:
:undoc-members:
:show-inheritance:
-:mod:`workflow_util` Module
----------------------------
+tool_shed.util.web_util module
+------------------------------
+
+.. automodule:: tool_shed.util.web_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tool_shed.util.workflow_util module
+-----------------------------------
.. automodule:: tool_shed.util.workflow_util
:members:
:undoc-members:
:show-inheritance:
+tool_shed.util.xml_util module
+------------------------------
+
+.. automodule:: tool_shed.util.xml_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/lib/tool_shed.utility_containers.rst b/doc/source/lib/tool_shed.utility_containers.rst
new file mode 100644
index 00000000000..bfa484d7795
--- /dev/null
+++ b/doc/source/lib/tool_shed.utility_containers.rst
@@ -0,0 +1,20 @@
+tool_shed.utility_containers package
+====================================
+
+.. automodule:: tool_shed.utility_containers
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Submodules
+----------
+
+tool_shed.utility_containers.utility_container_manager module
+-------------------------------------------------------------
+
+.. automodule:: tool_shed.utility_containers.utility_container_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff --git a/doc/source/releases/15.05.rst b/doc/source/releases/15.05.rst
index 7e5aea7fbdb..8e68f3f1989 100644
--- a/doc/source/releases/15.05.rst
+++ b/doc/source/releases/15.05.rst
@@ -9,7 +9,6 @@
Enhancements
-------------------------------
-.. starthighlight
* Pluggable framework to custom authentication (including new LDAP/Active
Directory integration). Thanks to many including Andrew Robinson,
Nicola Soranzo, and David Trudgian. `Pull Request 1`_, `Pull Request 33`_,
@@ -20,7 +19,6 @@ Enhancements
* New UI widgets allowing much more flexibility when creating simple dataset
pair and list collections. `Pull Request 134`_,
`Trello `__
-.. endhighlight
* Improved JavaScript build system for client code and libraries (now
using uglify_ and featuring `Source Maps`_). 72c876c_, 9a7f5fc_, 648a623_,
22f280f_, `Trello `__
diff --git a/lib/galaxy/__init__.py b/lib/galaxy/__init__.py
index 38baf123d8b..61343e2c0ac 100644
--- a/lib/galaxy/__init__.py
+++ b/lib/galaxy/__init__.py
@@ -4,13 +4,12 @@ Galaxy root package -- this is a namespace package.
__import__( "pkg_resources" ).declare_namespace( __name__ )
-import re
-import os
import sys
import platform
import pkg_resources
+
# patch get_platform() for better ABI recognition
def _get_build_platform():
plat = pkg_resources._get_build_platform()
@@ -32,11 +31,11 @@ def _get_build_platform():
if plat_split[-1] == 'universal' and platform.processor() != 'powerpc':
plat_split[-1] = 'intel'
plat = '-'.join( plat_split )
- elif sys.platform == "linux2" and sys.maxint < 2**31 and plat.endswith( '-x86_64' ):
+ elif sys.platform == "linux2" and sys.maxint < 2 ** 31 and plat.endswith( '-x86_64' ):
# 32 bit Python on 64 bit Linux
plat = plat.replace( '-x86_64', '-i686' )
if not (plat.endswith('-ucs2') or plat.endswith('-ucs4')):
- if sys.maxunicode > 2**16:
+ if sys.maxunicode > 2 ** 16:
plat += '-ucs4'
else:
plat += '-ucs2'
@@ -48,8 +47,9 @@ except:
pkg_resources.get_build_platform = _get_build_platform
pkg_resources.get_platform = _get_build_platform
+
# patch to insert eggs at the beginning of sys.path instead of at the end
-def _insert_on(self, path, loc = None):
+def _insert_on(self, path, loc=None):
"""Insert self.location in path before its nearest parent directory"""
loc = loc or self.location
@@ -57,7 +57,7 @@ def _insert_on(self, path, loc = None):
return
nloc = pkg_resources._normalize_cached(loc)
- npath= [(p and pkg_resources._normalize_cached(p) or p) for p in path]
+ npath = [(p and pkg_resources._normalize_cached(p) or p) for p in path]
if path is sys.path:
self.check_version_conflict()
@@ -91,5 +91,3 @@ if not hasattr( logging, 'NullHandler' ):
def emit( self, record ):
pass
logging.NullHandler = NullHandler
-
-import galaxy.eggs
diff --git a/lib/galaxy/actions/admin.py b/lib/galaxy/actions/admin.py
index 9a50f0868d1..458332bc98b 100644
--- a/lib/galaxy/actions/admin.py
+++ b/lib/galaxy/actions/admin.py
@@ -8,6 +8,7 @@ from galaxy.exceptions import ActionInputError
log = logging.getLogger( __name__ )
+
class AdminActions( object ):
"""
Mixin for controllers that provide administrative functionality.
@@ -22,7 +23,7 @@ class AdminActions( object ):
create_amount = False
if not params.name or not params.description:
raise ActionInputError( "Enter a valid name and a description." )
- elif self.sa_session.query( self.app.model.Quota ).filter( self.app.model.Quota.table.c.name==params.name ).first():
+ elif self.sa_session.query( self.app.model.Quota ).filter( self.app.model.Quota.table.c.name == params.name ).first():
raise ActionInputError( "Quota names must be unique and a quota with that name already exists, so choose another name." )
elif not params.get( 'amount', None ):
raise ActionInputError( "Enter a valid quota amount." )
@@ -60,7 +61,7 @@ class AdminActions( object ):
def _rename_quota( self, quota, params ):
if not params.name:
raise ActionInputError( 'Enter a valid name' )
- elif params.name != quota.name and self.sa_session.query( self.app.model.Quota ).filter( self.app.model.Quota.table.c.name==params.name ).first():
+ elif params.name != quota.name and self.sa_session.query( self.app.model.Quota ).filter( self.app.model.Quota.table.c.name == params.name ).first():
raise ActionInputError( 'A quota with that name already exists' )
else:
old_name = quota.name
@@ -150,7 +151,7 @@ class AdminActions( object ):
message += ', '.join( names )
return message
- def _undelete_quota( self, quota, params = None):
+ def _undelete_quota( self, quota, params=None):
quotas = util.listify( quota )
names = []
for q in quotas:
@@ -197,4 +198,3 @@ class AdminActions( object ):
self.sa_session.flush()
message += ', '.join( names )
return message
-
diff --git a/lib/galaxy/auth/providers/pam_auth.py b/lib/galaxy/auth/providers/pam_auth.py
new file mode 100644
index 00000000000..501456de612
--- /dev/null
+++ b/lib/galaxy/auth/providers/pam_auth.py
@@ -0,0 +1,151 @@
+"""
+Created on 13/07/2015
+
+Author Peter van Heusden (pvh@sanbi.ac.za)
+"""
+
+import logging
+from subprocess import Popen, PIPE
+import shlex
+
+from ..providers import AuthProvider
+from galaxy.auth import _get_bool
+
+log = logging.getLogger(__name__)
+
+"""
+This module provides an AuthProvider for PAM (pluggable authentication module) authentication.
+PAM is the Pluggable Authentication Module system (http://www.linux-pam.org/)
+It relies on python-pam (https://pypi.python.org/pypi/python-pam)
+
+Configuration is via config/auth_conf.xml and the following options are supported:
+ - auto-register: True/False: automatically register an account for an unknown user. Default: False
+ - maildomain: string: all valid users fall within the specified mail domain. Default: None
+ - login-use-email: True/False: Parse the email address to get login details. Default: False
+ - login-use-username: True/False: Use the username argument for login details. Default: False
+ Technical note: when a user is not found in the database,
+ their username is the user part of a user@host email
+ address. After user creation, however, the username is
+ the user's public name.
+ - pam-service: string: The service name to use for PAM authentication. Default: galaxy
+ - use-external-helper: True/False: Run an external helper script as root with sudo to do
+ authentication. If False authentication is done
+ by the module directly. Default: False
+ Technical note: some PAM modules (e.g. pam_unix.so)
+ require to be run as root to authenticate users.
+ - authentication-helper-script: string: Absolute path to helper script to run for authentication. Default: None
+ There needs to be a config (in /etc/sudoers or /etc/sudoers.d)
+ that allows the galaxy user to run this as root with no password check
+ For example:
+galaxy ALL=(root) NOPASSWD: /opt/galaxy/scripts/auth/pam_auth_helper.py
+
+
+Configuration example (for internal authentication, use email for user details):
+
+ PAM
+
+ True
+ example.com
+ True
+ ssh
+
+
+"""
+
+
+class PAM(AuthProvider):
+
+ plugin_type = 'PAM'
+
+ def authenticate(self, email, username, password, options):
+ pam_username = None
+ auto_register_username = None
+ auto_register_email = None
+ force_fail = False
+ log.debug("use username: {} use email {} email {} username {}".format(options.get('login-use-username'), options.get('login-use-email', False), email, username))
+ # check email based login first because if email exists in Galaxy DB
+ # we will be given the "public name" as username
+ if _get_bool(options, 'login-use-email', False) and email is not None:
+ if '@' in email:
+ (email_user, email_domain) = email.split('@')
+ pam_username = email_user
+ if email_domain == options.get('maildomain', None):
+ auto_register_email = email
+ if username is not None:
+ auto_register_username = username
+ else:
+ auto_register_username = email_user
+ else:
+ log.debug('PAM authenticate: warning: email does not match configured PAM maildomain')
+ # no need to fail: if auto-register is not enabled, this
+ # might still be a valid user
+ else:
+ log.debug('PAM authenticate: email must be used to login, but no valid email found')
+ force_fail = True
+ elif _get_bool(options, 'login-use-username', False):
+ # if we get here via authenticate_user then
+ # user will be "public name" and
+ # email address will be as per registered user
+ if username is not None:
+ pam_username = username
+ if email is not None:
+ auto_register_email = email
+ elif options.get('maildomain', None) is not None:
+ # we can register a user with this username and mail domain
+ # if auto registration is enabled
+ auto_register_email = '{}@{}'.format(username, options['maildomain'])
+ auto_register_username = username
+ else:
+ log.debug('PAM authenticate: username login selected but no username provided')
+ force_fail = True
+ else:
+ log.debug('PAM authenticate: could not find username for PAM')
+ force_fail = True
+
+ if force_fail:
+ return None, '', ''
+
+ pam_service = options.get('pam-service', 'galaxy')
+ use_helper = _get_bool(options, 'use-external-helper', False)
+ log.debug("PAM auth: will use external helper: {}".format(use_helper))
+ authenticated = False
+ if use_helper:
+ authentication_helper = options.get('authentication-helper-script', '/bin/false').strip()
+ log.debug("PAM auth: external helper script: {}".format(authentication_helper))
+ if not authentication_helper.startswith('/'):
+ # don't accept relative path
+ authenticated = False
+ else:
+ auth_cmd = shlex.split('/usr/bin/sudo -n {}'.format(authentication_helper))
+ log.debug("PAM auth: external helper cmd: {}".format(auth_cmd))
+ proc = Popen(auth_cmd, stdin=PIPE, stdout=PIPE, stderr=PIPE)
+ message = '{}\n{}\n{}\n'.format(pam_service, pam_username, password)
+ (output, error) = proc.communicate(message)
+ status = proc.wait()
+ if status != 0 and error != '':
+ log.debug("PAM auth: external authentication script had errors: status {} error {}".format(status, error))
+ if output.strip() == 'True':
+ authenticated = True
+ else:
+ authenticated = False
+ else:
+ try:
+ import pam
+ except ImportError:
+ log.debug('PAM authenticate: could not load pam module, PAM authentication disabled')
+ return None, '', ''
+
+ p_auth = pam.pam()
+ authenticated = p_auth.authenticate(pam_username, password, service=pam_service)
+
+ if authenticated:
+ log.debug('PAM authentication successful for {}'.format(pam_username))
+ return True, auto_register_email, auto_register_username
+ else:
+ log.debug('PAM authentication failed for {}'.format(pam_username))
+ return False, '', ''
+
+ def authenticate_user(self, user, password, options):
+ return self.authenticate(user.email, user.username, password, options)[0]
+
+__all__ = ['PAM']
diff --git a/lib/galaxy/dataset_collections/subcollections.py b/lib/galaxy/dataset_collections/subcollections.py
index 1d546b47d86..2ee4336c905 100644
--- a/lib/galaxy/dataset_collections/subcollections.py
+++ b/lib/galaxy/dataset_collections/subcollections.py
@@ -11,7 +11,7 @@ def _split_dataset_collection( dataset_collection, collection_type ):
this_collection_type = dataset_collection.collection_type
if not this_collection_type.endswith( collection_type ) or this_collection_type == collection_type:
raise exceptions.MessageException( "Cannot split collection in desired fashion." )
-
+
split_elements = []
for element in dataset_collection.elements:
child_collection = element.child_collection
diff --git a/lib/galaxy/dataset_collections/types/__init__.py b/lib/galaxy/dataset_collections/types/__init__.py
index e0d72e579a9..239b070ae09 100644
--- a/lib/galaxy/dataset_collections/types/__init__.py
+++ b/lib/galaxy/dataset_collections/types/__init__.py
@@ -2,8 +2,6 @@ from galaxy import exceptions
from abc import ABCMeta
from abc import abstractmethod
-from galaxy import model
-
import logging
log = logging.getLogger( __name__ )
diff --git a/lib/galaxy/datatypes/assembly.py b/lib/galaxy/datatypes/assembly.py
index f0232783a9d..4f047e865fa 100644
--- a/lib/galaxy/datatypes/assembly.py
+++ b/lib/galaxy/datatypes/assembly.py
@@ -13,9 +13,9 @@ from galaxy.datatypes import sequence
from galaxy.datatypes.images import Html
from galaxy.datatypes.metadata import MetadataElement
-
log = logging.getLogger(__name__)
+
class Amos( data.Text ):
"""Class describing the AMOS assembly file """
edam_format = "format_2561"
@@ -53,17 +53,18 @@ class Amos( data.Text ):
while not isAmos:
line = fh.readline()
if not line:
- break #EOF
+ break # EOF
line = line.strip()
- if line: #first non-empty line
+ if line: # first non-empty line
if line.startswith( '{' ):
- if re.match(r'{(RED|CTG|TLE)$',line):
+ if re.match(r'{(RED|CTG|TLE)$', line):
isAmos = True
fh.close()
except:
pass
return isAmos
+
class Sequences( sequence.Fasta ):
"""Class describing the Sequences file generated by velveth """
@@ -83,24 +84,25 @@ class Sequences( sequence.Fasta ):
while True:
line = fh.readline()
if not line:
- break #EOF
+ break # EOF
line = line.strip()
- if line: #first non-empty line
+ if line: # first non-empty line
if line.startswith( '>' ):
- if not re.match(r'>[^\t]+\t\d+\t\d+$',line):
+ if not re.match(r'>[^\t]+\t\d+\t\d+$', line):
break
- #The next line.strip() must not be '', nor startwith '>'
+ # The next line.strip() must not be '', nor startwith '>'
line = fh.readline().strip()
if line == '' or line.startswith( '>' ):
break
return True
else:
- break #we found a non-empty line, but it's not a fasta header
+ break # we found a non-empty line, but it's not a fasta header
fh.close()
except:
pass
return False
+
class Roadmaps( data.Text ):
"""Class describing the Sequences file generated by velveth """
edam_format = "format_2561"
@@ -119,23 +121,24 @@ class Roadmaps( data.Text ):
while True:
line = fh.readline()
if not line:
- break #EOF
+ break # EOF
line = line.strip()
- if line: #first non-empty line
- if not re.match(r'\d+\t\d+\t\d+$',line):
+ if line: # first non-empty line
+ if not re.match(r'\d+\t\d+\t\d+$', line):
break
- #The next line.strip() should be 'ROADMAP 1'
+ # The next line.strip() should be 'ROADMAP 1'
line = fh.readline().strip()
- if not re.match(r'ROADMAP \d+$',line):
+ if not re.match(r'ROADMAP \d+$', line):
break
return True
else:
- break #we found a non-empty line, but it's not a fasta header
+ break # we found a non-empty line, but it's not a fasta header
fh.close()
except:
pass
return False
+
class Velvet( Html ):
MetadataElement( name="base_name", desc="base name for velveth dataset", default="velvet", readonly=True, set_in_upload=True)
MetadataElement( name="paired_end_reads", desc="has paired-end reads", default="False", readonly=False, set_in_upload=True)
@@ -147,17 +150,17 @@ class Velvet( Html ):
def __init__( self, **kwd ):
Html.__init__( self, **kwd )
- self.add_composite_file( 'Sequences', mimetype = 'text/html', description = 'Sequences', substitute_name_with_metadata = None, is_binary = False )
- self.add_composite_file( 'Roadmaps', mimetype = 'text/html', description = 'Roadmaps', substitute_name_with_metadata = None, is_binary = False )
- self.add_composite_file( 'Log', mimetype = 'text/html', description = 'Log', optional = 'True', substitute_name_with_metadata = None, is_binary = False )
+ self.add_composite_file( 'Sequences', mimetype='text/html', description='Sequences', substitute_name_with_metadata=None, is_binary=False )
+ self.add_composite_file( 'Roadmaps', mimetype='text/html', description='Roadmaps', substitute_name_with_metadata=None, is_binary=False )
+ self.add_composite_file( 'Log', mimetype='text/html', description='Log', optional='True', substitute_name_with_metadata=None, is_binary=False )
- def generate_primary_file( self, dataset = None ):
- log.debug( "Velvet log info %s %s" % ('JJ generate_primary_file',dataset))
+ def generate_primary_file( self, dataset=None ):
+ log.debug( "Velvet log info %s %s" % ('JJ generate_primary_file', dataset))
rval = ['Velvet Galaxy Composite Dataset ']
rval.append('Velvet Galaxy Composite Dataset ']
# rval.append('
',log_msg))) - rval.append(']
- ## Sort alignments by leftmost coordinates. File .bam will be created.
- ## This command may also create temporary files .%d.bam when the
- ## whole alignment cannot be fitted into memory ( controlled by option -m ).
- #do this in a unique temp directory, because of possible .%d.bam temp files
+ # $ samtools sort
+ # Usage: samtools sort [-on] [-m ]
+ # Sort alignments by leftmost coordinates. File .bam will be created.
+ # This command may also create temporary files .%d.bam when the
+ # whole alignment cannot be fitted into memory ( controlled by option -m ).
+ # do this in a unique temp directory, because of possible .%d.bam temp files
if not self.dataset_content_needs_grooming( file_name ):
# Don't re-sort if already sorted
return
tmp_dir = tempfile.mkdtemp()
tmp_sorted_dataset_file_name_prefix = os.path.join( tmp_dir, 'sorted' )
- stderr_name = tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "bam_sort_stderr" ).name
- samtools_created_sorted_file_name = "%s.bam" % tmp_sorted_dataset_file_name_prefix #samtools accepts a prefix, not a filename, it always adds .bam to the prefix
+ stderr_name = tempfile.NamedTemporaryFile( dir=tmp_dir, prefix="bam_sort_stderr" ).name
+ samtools_created_sorted_file_name = "%s.bam" % tmp_sorted_dataset_file_name_prefix # samtools accepts a prefix, not a filename, it always adds .bam to the prefix
command = "samtools sort %s %s" % ( file_name, tmp_sorted_dataset_file_name_prefix )
proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) )
exit_code = proc.wait()
- #Did sort succeed?
+ # Did sort succeed?
stderr = open( stderr_name ).read().strip()
if stderr:
if exit_code != 0:
- shutil.rmtree( tmp_dir) #clean up
- raise Exception, "Error Grooming BAM file contents: %s" % stderr
+ shutil.rmtree( tmp_dir) # clean up
+ raise Exception( "Error Grooming BAM file contents: %s" % stderr )
else:
print stderr
# Move samtools_created_sorted_file_name to our output dataset location
@@ -309,38 +306,38 @@ class Bam( Binary ):
def init_meta( self, dataset, copy_from=None ):
Binary.init_meta( self, dataset, copy_from=copy_from )
- def set_meta( self, dataset, overwrite = True, **kwd ):
+ def set_meta( self, dataset, overwrite=True, **kwd ):
""" Creates the index for the BAM file. """
# These metadata values are not accessible by users, always overwrite
index_file = dataset.metadata.bam_index
if not index_file:
- index_file = dataset.metadata.spec['bam_index'].param.new_file( dataset = dataset )
+ index_file = dataset.metadata.spec['bam_index'].param.new_file( dataset=dataset )
# Create the Bam index
- ##$ samtools index
- ##Usage: samtools index []
- stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name
+ # $ samtools index
+ # Usage: samtools index []
+ stderr_name = tempfile.NamedTemporaryFile( prefix="bam_index_stderr" ).name
command = [ 'samtools', 'index', dataset.file_name, index_file.file_name ]
proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
exit_code = proc.wait()
- #Did index succeed?
+ # Did index succeed?
if exit_code == -6:
# SIGABRT, most likely samtools 1.0+ which does not accept the index name parameter.
dataset_symlink = os.path.join( os.path.dirname( index_file.file_name ),
- '__dataset_%d_%s' % ( dataset.id, os.path.basename( index_file.file_name ) ) )
+ '__dataset_%d_%s' % ( dataset.id, os.path.basename( index_file.file_name ) ) )
os.symlink( dataset.file_name, dataset_symlink )
try:
command = [ 'samtools', 'index', dataset_symlink ]
exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) )
shutil.move( dataset_symlink + '.bai', index_file.file_name )
- except Exception, e:
+ except Exception as e:
open( stderr_name, 'ab+' ).write( 'Galaxy attempted to build the BAM index with samtools 1.0+ but failed: %s\n' % e)
finally:
os.unlink( dataset_symlink )
stderr = open( stderr_name ).read().strip()
if stderr:
if exit_code != 0:
- os.unlink( stderr_name ) #clean up
- raise Exception, "Error Setting BAM Metadata: %s" % stderr
+ os.unlink( stderr_name ) # clean up
+ raise Exception( "Error Setting BAM Metadata: %s" % stderr )
else:
print stderr
dataset.metadata.bam_index = index_file
@@ -371,7 +368,7 @@ class Bam( Binary ):
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
- dataset.peek = "Binary bam alignments file"
+ dataset.peek = "Binary bam alignments file"
dataset.blurb = data.nice_size( dataset.get_size() )
else:
dataset.peek = 'file does not exist'
@@ -383,14 +380,12 @@ class Bam( Binary ):
except:
return "Binary bam alignments file (%s)" % ( data.nice_size( dataset.get_size() ) )
-
-
# ------------- Dataproviders
# pipe through samtools view
- #ALSO: (as Sam)
+ # ALSO: (as Sam)
# bam does not use '#' to indicate comments/headers - we need to strip out those headers from the std. providers
- #TODO:?? seems like there should be an easier way to do/inherit this - metadata.comment_char?
- #TODO: incorporate samtools options to control output: regions first, then flags, etc.
+ # TODO:?? seems like there should be an easier way to do/inherit this - metadata.comment_char?
+ # TODO: incorporate samtools options to control output: regions first, then flags, etc.
@dataproviders.decorators.dataprovider_factory( 'line', dataproviders.line.FilteredLineDataProvider.settings )
def line_dataprovider( self, dataset, **settings ):
samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset )
@@ -417,13 +412,13 @@ class Bam( Binary ):
# these can't be used directly - may need BamColumn, BamDict (Bam metadata -> column/dict)
# OR - see genomic_region_dataprovider
- #@dataproviders.decorators.dataprovider_factory( 'dataset-column', dataproviders.column.ColumnarDataProvider.settings )
- #def dataset_column_dataprovider( self, dataset, **settings ):
+ # @dataproviders.decorators.dataprovider_factory( 'dataset-column', dataproviders.column.ColumnarDataProvider.settings )
+ # def dataset_column_dataprovider( self, dataset, **settings ):
# settings[ 'comment_char' ] = '@'
# return super( Sam, self ).dataset_column_dataprovider( dataset, **settings )
- #@dataproviders.decorators.dataprovider_factory( 'dataset-dict', dataproviders.column.DictDataProvider.settings )
- #def dataset_dict_dataprovider( self, dataset, **settings ):
+ # @dataproviders.decorators.dataprovider_factory( 'dataset-dict', dataproviders.column.DictDataProvider.settings )
+ # def dataset_dict_dataprovider( self, dataset, **settings ):
# settings[ 'comment_char' ] = '@'
# return super( Sam, self ).dataset_dict_dataprovider( dataset, **settings )
@@ -443,10 +438,10 @@ class Bam( Binary ):
@dataproviders.decorators.dataprovider_factory( 'genomic-region', dataproviders.column.ColumnarDataProvider.settings )
def genomic_region_dataprovider( self, dataset, **settings ):
# GenomicRegionDataProvider currently requires a dataset as source - may not be necc.
- #TODO:?? consider (at least) the possible use of a kwarg: metadata_source (def. to source.dataset),
+ # TODO:?? consider (at least) the possible use of a kwarg: metadata_source (def. to source.dataset),
# or remove altogether...
- #samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset )
- #return dataproviders.dataset.GenomicRegionDataProvider( samtools_source, metadata_source=dataset,
+ # samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset )
+ # return dataproviders.dataset.GenomicRegionDataProvider( samtools_source, metadata_source=dataset,
# 2, 3, 3, **settings )
# instead, set manually and use in-class column gen
@@ -469,6 +464,7 @@ class Bam( Binary ):
Binary.register_sniffable_binary_format("bam", "bam", Bam)
+
class Bcf( Binary):
"""Class describing a BCF file"""
edam_format = "format_3020"
@@ -487,21 +483,21 @@ class Bcf( Binary):
except:
return False
- def set_meta( self, dataset, overwrite = True, **kwd ):
+ def set_meta( self, dataset, overwrite=True, **kwd ):
""" Creates the index for the BCF file. """
# These metadata values are not accessible by users, always overwrite
index_file = dataset.metadata.bcf_index
if not index_file:
- index_file = dataset.metadata.spec['bcf_index'].param.new_file( dataset = dataset )
+ index_file = dataset.metadata.spec['bcf_index'].param.new_file( dataset=dataset )
# Create the bcf index
- ##$ bcftools index
- ##Usage: bcftools index
+ # $ bcftools index
+ # Usage: bcftools index
dataset_symlink = os.path.join( os.path.dirname( index_file.file_name ),
- '__dataset_%d_%s' % ( dataset.id, os.path.basename( index_file.file_name ) ) )
+ '__dataset_%d_%s' % ( dataset.id, os.path.basename( index_file.file_name ) ) )
os.symlink( dataset.file_name, dataset_symlink )
- stderr_name = tempfile.NamedTemporaryFile( prefix = "bcf_index_stderr" ).name
+ stderr_name = tempfile.NamedTemporaryFile( prefix="bcf_index_stderr" ).name
command = [ 'bcftools', 'index', dataset_symlink ]
proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
exit_code = proc.wait()
@@ -510,8 +506,8 @@ class Bcf( Binary):
stderr = open( stderr_name ).read().strip()
if stderr:
if exit_code != 0:
- os.unlink( stderr_name ) #clean up
- raise Exception, "Error Setting BCF Metadata: %s" % stderr
+ os.unlink( stderr_name ) # clean up
+ raise Exception( "Error Setting BCF Metadata: %s" % stderr )
else:
print stderr
dataset.metadata.bcf_index = index_file
@@ -527,7 +523,7 @@ class H5( Binary ):
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
- dataset.peek = "Binary h5 file"
+ dataset.peek = "Binary h5 file"
dataset.blurb = data.nice_size( dataset.get_size() )
else:
dataset.peek = 'file does not exist'
@@ -549,7 +545,7 @@ class Scf( Binary ):
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
- dataset.peek = "Binary scf sequence file"
+ dataset.peek = "Binary scf sequence file"
dataset.blurb = data.nice_size( dataset.get_size() )
else:
dataset.peek = 'file does not exist'
@@ -585,7 +581,7 @@ class Sff( Binary ):
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
- dataset.peek = "Binary sff file"
+ dataset.peek = "Binary sff file"
dataset.blurb = data.nice_size( dataset.get_size() )
else:
dataset.peek = 'file does not exist'
@@ -627,7 +623,7 @@ class BigWig(Binary):
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
- dataset.peek = "Binary UCSC %s file" % self._name
+ dataset.peek = "Binary UCSC %s file" % self._name
dataset.blurb = data.nice_size( dataset.get_size() )
else:
dataset.peek = 'file does not exist'
@@ -699,7 +695,7 @@ class SQlite ( Binary ):
def init_meta( self, dataset, copy_from=None ):
Binary.init_meta( self, dataset, copy_from=copy_from )
- def set_meta( self, dataset, overwrite = True, **kwd ):
+ def set_meta( self, dataset, overwrite=True, **kwd ):
try:
tables = []
columns = dict()
@@ -708,25 +704,25 @@ class SQlite ( Binary ):
c = conn.cursor()
tables_query = "SELECT name,sql FROM sqlite_master WHERE type='table' ORDER BY name"
rslt = c.execute(tables_query).fetchall()
- for table,sql in rslt:
+ for table, sql in rslt:
tables.append(table)
try:
col_query = 'SELECT * FROM %s LIMIT 0' % table
cur = conn.cursor().execute(col_query)
cols = [col[0] for col in cur.description]
columns[table] = cols
- except Exception, exc:
+ except Exception as exc:
log.warn( '%s, set_meta Exception: %s', self, exc )
for table in tables:
try:
row_query = "SELECT count(*) FROM %s" % table
rowcounts[table] = c.execute(row_query).fetchone()[0]
- except Exception, exc:
+ except Exception as exc:
log.warn( '%s, set_meta Exception: %s', self, exc )
dataset.metadata.tables = tables
dataset.metadata.table_columns = columns
dataset.metadata.table_row_count = rowcounts
- except Exception, exc:
+ except Exception as exc:
log.warn( '%s, set_meta Exception: %s', self, exc )
def sniff( self, filename ):
@@ -742,12 +738,12 @@ class SQlite ( Binary ):
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
- dataset.peek = "SQLite Database"
+ dataset.peek = "SQLite Database"
lines = ['SQLite Database']
if dataset.metadata.tables:
for table in dataset.metadata.tables:
try:
- lines.append('%s [%s]' % (table,dataset.metadata.table_row_count[table]))
+ lines.append('%s [%s]' % (table, dataset.metadata.table_row_count[table]))
except:
continue
dataset.peek = '\n'.join(lines)
@@ -762,7 +758,6 @@ class SQlite ( Binary ):
except:
return "SQLite Database (%s)" % ( data.nice_size( dataset.get_size() ) )
-
@dataproviders.decorators.dataprovider_factory( 'sqlite', dataproviders.dataset.SQliteDataProvider.settings )
def sqlite_dataprovider( self, dataset, **settings ):
dataset_source = dataproviders.dataset.DatasetDataProvider( dataset )
@@ -779,7 +774,7 @@ class SQlite ( Binary ):
return dataproviders.dataset.SQliteDataDictProvider( dataset_source, **settings )
-#Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite)
+# Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite)
class GeminiSQLite( SQlite ):
@@ -788,8 +783,8 @@ class GeminiSQLite( SQlite ):
readonly=True, visible=True, no_value='0.10.0' )
file_ext = "gemini.sqlite"
- def set_meta( self, dataset, overwrite = True, **kwd ):
- super( GeminiSQLite, self ).set_meta( dataset, overwrite = overwrite, **kwd )
+ def set_meta( self, dataset, overwrite=True, **kwd ):
+ super( GeminiSQLite, self ).set_meta( dataset, overwrite=overwrite, **kwd )
try:
conn = sqlite.connect( dataset.file_name )
c = conn.cursor()
@@ -798,13 +793,13 @@ class GeminiSQLite( SQlite ):
for version, in result:
dataset.metadata.gemini_version = version
# TODO: Can/should we detect even more attributes, such as use of PED file, what was input annotation type, etc.
- except Exception, e:
+ except Exception as e:
log.warn( '%s, set_meta Exception: %s', self, e )
def sniff( self, filename ):
if super( GeminiSQLite, self ).sniff( filename ):
gemini_table_names = [ "gene_detailed", "gene_summary", "resources", "sample_genotype_counts", "sample_genotypes", "samples",
- "variant_impacts", "variants", "version" ]
+ "variant_impacts", "variants", "version" ]
try:
conn = sqlite.connect( filename )
c = conn.cursor()
@@ -815,13 +810,13 @@ class GeminiSQLite( SQlite ):
if table_name not in result:
return False
return True
- except Exception, e:
+ except Exception as e:
log.warn( '%s, sniff Exception: %s', self, e )
return False
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
- dataset.peek = "Gemini SQLite Database, version %s" % ( dataset.metadata.gemini_version or 'unknown' )
+ dataset.peek = "Gemini SQLite Database, version %s" % ( dataset.metadata.gemini_version or 'unknown' )
dataset.blurb = data.nice_size( dataset.get_size() )
else:
dataset.peek = 'file does not exist'
@@ -841,7 +836,8 @@ Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite)
class Xlsx(Binary):
"""Class for Excel 2007 (xlsx) files"""
- file_ext="xlsx"
+ file_ext = "xlsx"
+
def sniff( self, filename ):
# Xlsx is compressed in zip format and must not be uncompressed in Galaxy.
try:
@@ -878,7 +874,7 @@ class Sra( Binary ):
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
- dataset.peek = 'Binary sra file'
+ dataset.peek = 'Binary sra file'
dataset.blurb = data.nice_size(dataset.get_size())
else:
dataset.peek = 'file does not exist'
diff --git a/lib/galaxy/datatypes/checkers.py b/lib/galaxy/datatypes/checkers.py
index ae5336b376b..94e8a53d447 100644
--- a/lib/galaxy/datatypes/checkers.py
+++ b/lib/galaxy/datatypes/checkers.py
@@ -1,4 +1,3 @@
-import os
import re
import bz2
import gzip
@@ -18,8 +17,9 @@ except ImportError:
except:
PIL = None
+
def check_image( file_path ):
- if PIL != None:
+ if PIL is not None:
try:
im = PIL.open( file_path )
except:
@@ -28,10 +28,11 @@ def check_image( file_path ):
return im
return False
else:
- if imghdr.what( file_path ) != None:
+ if imghdr.what( file_path ) is not None:
return True
return False
+
def check_html( file_path, chunk=None ):
if chunk is None:
temp = open( file_path, "U" )
@@ -58,6 +59,7 @@ def check_html( file_path, chunk=None ):
temp.close()
return False
+
def check_binary( name, file_path=True ):
# Handles files if file_path is True or text if file_path is False
is_binary = False
@@ -65,7 +67,6 @@ def check_binary( name, file_path=True ):
temp = open( name, "U" )
else:
temp = StringIO( name )
- chars_read = 0
try:
for char in temp.read( 100 ):
if util.is_binary( char ):
@@ -75,6 +76,7 @@ def check_binary( name, file_path=True ):
temp.close( )
return is_binary
+
def check_gzip( file_path ):
# This method returns a tuple of booleans representing ( is_gzipped, is_valid )
# Make sure we have a gzipped file
@@ -95,7 +97,7 @@ def check_gzip( file_path ):
return ( True, True )
except:
return( False, False )
- CHUNK_SIZE = 2**15 # 32Kb
+ CHUNK_SIZE = 2 ** 15 # 32Kb
gzipped_file = gzip.GzipFile( file_path, mode='rb' )
chunk = gzipped_file.read( CHUNK_SIZE )
gzipped_file.close()
@@ -104,6 +106,7 @@ def check_gzip( file_path ):
return ( True, False )
return ( True, True )
+
def check_bz2( file_path ):
try:
temp = open( file_path, "U" )
@@ -113,7 +116,7 @@ def check_bz2( file_path ):
return ( False, False )
except:
return( False, False )
- CHUNK_SIZE = 2**15 # reKb
+ CHUNK_SIZE = 2 ** 15 # reKb
bzipped_file = bz2.BZ2File( file_path, mode='rb' )
chunk = bzipped_file.read( CHUNK_SIZE )
bzipped_file.close()
@@ -122,15 +125,18 @@ def check_bz2( file_path ):
return ( True, False )
return ( True, True )
+
def check_zip( file_path ):
if zipfile.is_zipfile( file_path ):
return True
return False
+
def is_bz2( file_path ):
is_bz2, is_valid = check_bz2( file_path )
return is_bz2
+
def is_gzip( file_path ):
is_gzipped, is_valid = check_gzip( file_path )
return is_gzipped
diff --git a/lib/galaxy/datatypes/chrominfo.py b/lib/galaxy/datatypes/chrominfo.py
index 14e73714801..edee9c79f32 100644
--- a/lib/galaxy/datatypes/chrominfo.py
+++ b/lib/galaxy/datatypes/chrominfo.py
@@ -7,4 +7,3 @@ class ChromInfo( Tabular ):
file_ext = "len"
MetadataElement( name="chrom", default=1, desc="Chrom column", param=metadata.ColumnParameter )
MetadataElement( name="length", default=2, desc="Length column", param=metadata.ColumnParameter )
-
diff --git a/lib/galaxy/datatypes/converters/bed_to_gff_converter.py b/lib/galaxy/datatypes/converters/bed_to_gff_converter.py
index 34ba2dcf326..2465a25b4dd 100644
--- a/lib/galaxy/datatypes/converters/bed_to_gff_converter.py
+++ b/lib/galaxy/datatypes/converters/bed_to_gff_converter.py
@@ -4,6 +4,7 @@ import sys
assert sys.version_info[:2] >= ( 2, 4 )
+
def __main__():
input_name = sys.argv[1]
output_name = sys.argv[2]
@@ -67,7 +68,8 @@ def __main__():
out.close()
info_msg = "%i lines converted to GFF version 2. " % ( i + 1 - skipped_lines )
if skipped_lines > 0:
- info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." %( skipped_lines, first_skipped_line )
+ info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line )
print info_msg
-if __name__ == "__main__": __main__()
+if __name__ == "__main__":
+ __main__()
diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
index c2bb35760a5..f66b1d8da27 100644
--- a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
@@ -3,13 +3,16 @@
from __future__ import division
import sys
+
from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
-from bx.arrays.array_tree import *
-# from bx.arrays.wiggle import BedReader
+
+eggs.require('numpy') # noqa
+eggs.require('bx-python') # noqa
+from bx.arrays.array_tree import array_tree_dict_from_reader, FileArrayTreeDict
BLOCK_SIZE = 100
+
class BedGraphReader:
def __init__( self, f ):
self.f = f
@@ -36,6 +39,8 @@ class BedGraphReader:
chrom_end = int(feature[2])
score = float(feature[3])
return chrom, chrom_start, chrom_end, None, score
+
+
def main():
input_fname = sys.argv[1]
@@ -44,7 +49,7 @@ def main():
reader = BedGraphReader( open( input_fname ) )
# Fill array from reader
- d = array_tree_dict_from_reader( reader, {}, block_size = BLOCK_SIZE )
+ d = array_tree_dict_from_reader( reader, {}, block_size=BLOCK_SIZE )
for array_tree in d.itervalues():
array_tree.root.build_summary()
diff --git a/lib/galaxy/datatypes/converters/bgzip.py b/lib/galaxy/datatypes/converters/bgzip.py
index a419257a2b8..5da245265a6 100644
--- a/lib/galaxy/datatypes/converters/bgzip.py
+++ b/lib/galaxy/datatypes/converters/bgzip.py
@@ -6,9 +6,13 @@ Uses pysam to bgzip a file
usage: %prog in_file out_file
"""
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "pysam" )
-import ctabix, subprocess, tempfile, sys, optparse
+import pkg_resources
+pkg_resources.require( "pysam" )
+import ctabix
+import tempfile
+import optparse
+import subprocess
+
def main():
# Read options, args.
@@ -24,17 +28,18 @@ def main():
sort_params = None
if options.chrom_col and options.start_col and options.end_col:
- sort_params = ["sort",
- "-k%(i)s,%(i)s" % { 'i': options.chrom_col },
- "-k%(i)i,%(i)in" % { 'i': options.start_col },
- "-k%(i)i,%(i)in" % { 'i': options.end_col }
- ]
+ sort_params = [
+ "sort",
+ "-k%(i)s,%(i)s" % { 'i': options.chrom_col },
+ "-k%(i)i,%(i)in" % { 'i': options.start_col },
+ "-k%(i)i,%(i)in" % { 'i': options.end_col }
+ ]
elif options.preset == "bed":
sort_params = ["sort", "-k1,1", "-k2,2n", "-k3,3n"]
elif options.preset == "vcf":
sort_params = ["sort", "-k1,1", "-k2,2n"]
elif options.preset == "gff":
- sort_params = ["sort", "-s", "-k1,1", "-k4,4n"] # stable sort on start column
+ sort_params = ["sort", "-s", "-k1,1", "-k4,4n"] # stable sort on start column
# Skip any lines starting with "#" and "track"
grepped = subprocess.Popen(["grep", "-e", "^\"#\"", "-e", "^track", "-v", input_fname], stderr=subprocess.PIPE, stdout=subprocess.PIPE )
after_sort = subprocess.Popen(sort_params, stdin=grepped.stdout, stderr=subprocess.PIPE, stdout=tmpfile )
diff --git a/lib/galaxy/datatypes/converters/fasta_to_len.py b/lib/galaxy/datatypes/converters/fasta_to_len.py
index e4327e03574..bc814d4f91b 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_len.py
+++ b/lib/galaxy/datatypes/converters/fasta_to_len.py
@@ -5,10 +5,10 @@ Output: tabular
Return titles with lengths of corresponding seq
"""
-import sys, os
-
+import sys
assert sys.version_info[:2] >= ( 2, 4 )
+
def compute_fasta_length( fasta_file, out_file, keep_first_char, keep_first_word=False ):
infile = fasta_file
@@ -31,7 +31,7 @@ def compute_fasta_length( fasta_file, out_file, keep_first_char, keep_first_word
if not line or line.startswith( '#' ):
continue
if line[0] == '>':
- if first_entry == False:
+ if first_entry is False:
if keep_first_word:
fasta_title = fasta_title.split()[0]
out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) )
diff --git a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
index 2c7fd815ff4..9914b7d91b6 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
+++ b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
@@ -11,10 +11,12 @@ Input: fasta
Output: tabular
"""
-import sys, os
+import sys
+import os
seq_hash = {}
+
def __main__():
infile = sys.argv[1]
outfile = sys.argv[2]
@@ -46,4 +48,5 @@ def __main__():
out.write("".join(sequence.split()) + '\n')
-if __name__ == "__main__" : __main__()
+if __name__ == "__main__" :
+ __main__()
diff --git a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
index 18c1931e990..ba6ba4079d1 100644
--- a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
+++ b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
@@ -1,6 +1,6 @@
#!/usr/bin/env python
-import sys, os, gzip
+import sys
from galaxy.datatypes.checkers import is_gzip
@@ -24,13 +24,13 @@ def main():
out_file = open(sys.argv[2], 'w')
current_line = 0
- sequences=1000000
- lines_per_chunk = 4*sequences
+ sequences = 1000000
+ lines_per_chunk = 4 * sequences
chunk_begin = 0
in_file = open(input_fname)
- out_file.write('{"sections" : [');
+ out_file.write('{"sections" : [')
for line in in_file:
current_line += 1
diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
index 61269171817..07c9b718d8f 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
@@ -14,15 +14,15 @@ Usage:
%python fastqsolexa_to_fasta_converter.py
"""
-import sys, os
-from math import *
-
+import sys
assert sys.version_info[:2] >= ( 2, 4 )
+
def stop_err( msg ):
sys.stderr.write( "%s" % msg )
sys.exit()
+
def __main__():
infile_name = sys.argv[1]
outfile = open( sys.argv[2], 'w' )
@@ -30,7 +30,7 @@ def __main__():
seq_title_startswith = ''
for i, line in enumerate( file( infile_name ) ):
- line = line.rstrip() # eliminate trailing space and new line characters
+ line = line.rstrip() # eliminate trailing space and new line characters
if not line or line.startswith( '#' ):
continue
fastq_block_lines = ( fastq_block_lines + 1 ) % 4
@@ -40,16 +40,15 @@ def __main__():
if not seq_title_startswith:
seq_title_startswith = line_startswith
if seq_title_startswith != line_startswith:
- stop_err( 'Invalid fastqsolexa format at line %d: %s.' %( i + 1, line ) )
- read_title = line[ 1: ]
+ stop_err( 'Invalid fastqsolexa format at line %d: %s.' % ( i + 1, line ) )
outfile.write( '>%s\n' % line[1:] )
elif fastq_block_lines == 2:
# line 2 is nucleotides
- read_length = len( line )
outfile.write( '%s\n' % line )
else:
pass
outfile.close()
-if __name__ == "__main__": __main__()
+if __name__ == "__main__":
+ __main__()
diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
index c87228f842e..ab24c79a979 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
@@ -13,19 +13,20 @@ the order should be:
Usage:
%python fastqsolexa_to_qual_converter.py
"""
-import sys, os
-from math import *
+import sys
assert sys.version_info[:2] >= ( 2, 4 )
+
def stop_err( msg ):
sys.stderr.write( "%s" % msg )
sys.exit()
+
def __main__():
infile_name = sys.argv[1]
outfile_score = open( sys.argv[2], 'w' )
- datatype = sys.argv[3]
+ # datatype = sys.argv[3]
qual_title_startswith = ''
seq_title_startswith = ''
default_coding_value = 64
@@ -68,12 +69,12 @@ def __main__():
val = line.split()[0]
try:
- check = int( val )
+ int( val )
fastq_integer = True
except:
fastq_integer = False
- if fastq_integer: # digits
+ if fastq_integer: # digits
qual = line
else:
# ascii
@@ -92,4 +93,5 @@ def __main__():
outfile_score.close()
-if __name__ == "__main__": __main__()
+if __name__ == "__main__":
+ __main__()
diff --git a/lib/galaxy/datatypes/converters/gff_to_bed_converter.py b/lib/galaxy/datatypes/converters/gff_to_bed_converter.py
index ac646699afc..94a82e0bac3 100644
--- a/lib/galaxy/datatypes/converters/gff_to_bed_converter.py
+++ b/lib/galaxy/datatypes/converters/gff_to_bed_converter.py
@@ -3,6 +3,7 @@ import sys
assert sys.version_info[:2] >= ( 2, 4 )
+
def __main__():
input_name = sys.argv[1]
output_name = sys.argv[2]
@@ -24,7 +25,7 @@ def __main__():
#
# Replace any spaces in the name with underscores so UCSC will not complain
name = elems[2].replace(" ", "_")
- out.write( "%s\t%s\t%s\t%s\t0\t%s\n" %( elems[0], start, elems[4], name, strand ) )
+ out.write( "%s\t%s\t%s\t%s\t0\t%s\n" % ( elems[0], start, elems[4], name, strand ) )
except:
skipped_lines += 1
if not first_skipped_line:
@@ -36,7 +37,8 @@ def __main__():
out.close()
info_msg = "%i lines converted to BED. " % ( i + 1 - skipped_lines )
if skipped_lines > 0:
- info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." %( skipped_lines, first_skipped_line )
+ info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line )
print info_msg
-if __name__ == "__main__": __main__()
+if __name__ == "__main__":
+ __main__()
diff --git a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
index 07b3631dc71..aeca7a6a4ee 100644
--- a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
+++ b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
@@ -9,12 +9,15 @@ usage:
from __future__ import division
-import sys, fileinput
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
-from galaxy.datatypes.util.gff_util import *
+import sys
+import fileinput
+import pkg_resources
+pkg_resources.require( "bx-python" )
+
+from galaxy.datatypes.util.gff_util import GFFReaderWrapper, GenomicInterval, convert_gff_coords_to_bed
from bx.interval_index_file import Indexes
+
def main():
# Arguments
input_fname, out_fname = sys.argv[1:]
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed_converter.py b/lib/galaxy/datatypes/converters/interval_to_bed_converter.py
index cfa48cedd28..35504e4f210 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.py
@@ -1,17 +1,19 @@
#!/usr/bin/env python
-#Dan Blankenberg
+# Dan Blankenberg
import sys
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
+import pkg_resources
+pkg_resources.require( "bx-python" )
import bx.intervals.io
assert sys.version_info[:2] >= ( 2, 4 )
+
def stop_err( msg ):
sys.stderr.write( msg )
sys.exit()
+
def __main__():
output_name = sys.argv[1]
input_name = sys.argv[2]
@@ -37,7 +39,7 @@ def __main__():
nameCol = -1
skipped_lines = 0
first_skipped_line = 0
- out = open( output_name,'w' )
+ out = open( output_name, 'w' )
count = 0
for count, region in enumerate( bx.intervals.io.NiceReaderWrapper( open( input_name, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False ) ):
try:
@@ -49,7 +51,7 @@ def __main__():
name = "region_%i" % count
try:
- out.write( "%s\t%i\t%i\t%s\t%i\t%s\n" % ( region.chrom, region.start, region.end, name, 0, region.strand ) )
+ out.write( "%s\t%i\t%i\t%s\t%i\t%s\n" % ( region.chrom, region.start, region.end, name, 0, region.strand ) )
except:
skipped_lines += 1
if not first_skipped_line:
@@ -59,4 +61,5 @@ def __main__():
if skipped_lines > 0:
print "Skipped %d blank or invalid lines starting with line # %d." % ( skipped_lines, first_skipped_line )
-if __name__ == "__main__": __main__()
+if __name__ == "__main__":
+ __main__()
diff --git a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
index 2fb612c4d66..dc9869eea5c 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
@@ -1,17 +1,19 @@
#!/usr/bin/env python
-#Dan Blankenberg
+# Dan Blankenberg
import sys
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
+import pkg_resources
+pkg_resources.require( "bx-python" )
import bx.intervals.io
assert sys.version_info[:2] >= ( 2, 4 )
+
def stop_err( msg ):
sys.stderr.write( msg )
sys.exit()
+
def force_bed_field_count( fields, region_count, force_num_columns ):
if force_num_columns >= 4 and len( fields ) < 4:
fields.append( 'region_%i' % ( region_count ) )
@@ -33,6 +35,7 @@ def force_bed_field_count( fields, region_count, force_num_columns ):
fields.append( ',' )
return fields[:force_num_columns]
+
def __main__():
output_name = sys.argv[1]
input_name = sys.argv[2]
@@ -59,7 +62,7 @@ def __main__():
try:
extension = sys.argv[8]
except:
- extension = 'interval' #default extension
+ extension = 'interval' # default extension
try:
force_num_columns = int( sys.argv[9] )
except:
@@ -67,10 +70,10 @@ def __main__():
skipped_lines = 0
first_skipped_line = None
- out = open( output_name,'w' )
+ out = open( output_name, 'w' )
count = 0
- #does file already conform to bed strict?
- #if so, we want to keep extended columns, otherwise we'll create a generic 6 column bed file
+ # does file already conform to bed strict?
+ # if so, we want to keep extended columns, otherwise we'll create a generic 6 column bed file
strict_bed = True
if extension in [ 'bed', 'bedstrict', 'bed6', 'bed12' ] and ( chromCol, startCol, endCol) == ( 0, 1, 2) and ( nameCol < 0 or nameCol == 3 ) and ( strandCol < 0 or strandCol == 5 ):
for count, line in enumerate( open( input_name ) ):
@@ -82,35 +85,35 @@ def __main__():
continue
fields = line.split('\t')
try:
- assert len( fields ) >= 3, 'A BED file requires at least 3 columns' #we can't fix this
+ assert len( fields ) >= 3, 'A BED file requires at least 3 columns' # we can't fix this
if len(fields) > 12:
strict_bed = False
break
- #name (fields[3]) can be anything, no verification needed
+ # name (fields[3]) can be anything, no verification needed
if len( fields ) > 4:
- float( fields[4] ) #score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray).
+ float( fields[4] ) # score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray).
if len( fields ) > 5:
- assert fields[5] in [ '+', '-' ], 'Invalid strand' #strand - Defines the strand - either '+' or '-'.
+ assert fields[5] in [ '+', '-' ], 'Invalid strand' # strand - Defines the strand - either '+' or '-'.
if len( fields ) > 6:
- int( fields[6] ) #thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays).
+ int( fields[6] ) # thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays).
if len( fields ) > 7:
- int( fields[7] ) #thickEnd - The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).
+ int( fields[7] ) # thickEnd - The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).
if len( fields ) > 8:
- if fields[8] != '0': #itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
+ if fields[8] != '0': # itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
fields2 = fields[8].split( ',' )
assert len( fields2 ) == 3, 'RGB value must be 0 or have length of 3'
for field in fields2:
- int( field ) #rgb values are integers
+ int( field ) # rgb values are integers
if len( fields ) > 9:
- int( fields[9] ) #blockCount - The number of blocks (exons) in the BED line.
+ int( fields[9] ) # blockCount - The number of blocks (exons) in the BED line.
if len( fields ) > 10:
- if fields[10] != ',': #blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
- fields2 = fields[10].rstrip( "," ).split( "," ) #remove trailing comma and split on comma
+ if fields[10] != ',': # blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
+ fields2 = fields[10].rstrip( "," ).split( "," ) # remove trailing comma and split on comma
for field in fields2:
int( field )
if len( fields ) > 11:
- if fields[11] != ',': #blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
- fields2 = fields[11].rstrip( "," ).split( "," ) #remove trailing comma and split on comma
+ if fields[11] != ',': # blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
+ fields2 = fields[11].rstrip( "," ).split( "," ) # remove trailing comma and split on comma
for field in fields2:
int( field )
except:
@@ -126,7 +129,7 @@ def __main__():
if not strict_bed:
skipped_lines = 0
first_skipped_line = None
- out = open( output_name,'w' )
+ out = open( output_name, 'w' )
count = 0
for count, region in enumerate( bx.intervals.io.NiceReaderWrapper( open( input_name, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False ) ):
try:
@@ -150,4 +153,5 @@ def __main__():
if skipped_lines > 0:
print "Skipped %d blank or invalid lines starting with line # %d." % ( skipped_lines, first_skipped_line )
-if __name__ == "__main__": __main__()
+if __name__ == "__main__":
+ __main__()
diff --git a/lib/galaxy/datatypes/converters/interval_to_coverage.py b/lib/galaxy/datatypes/converters/interval_to_coverage.py
index 64868ff019a..e55d88214be 100644
--- a/lib/galaxy/datatypes/converters/interval_to_coverage.py
+++ b/lib/galaxy/datatypes/converters/interval_to_coverage.py
@@ -6,14 +6,11 @@ usage: %prog bed_file out_file
-1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in interval file
-2, --cols2=N,N,N,N: Columns for chrom, start, end, strand in coverage file
"""
-import sys
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
+import pkg_resources
+pkg_resources.require( "bx-python" )
from bx.intervals import io
from bx.cookbook import doc_optparse
-import psyco_full
import commands
-import os
from os import environ
import tempfile
from bisect import bisect
@@ -28,6 +25,7 @@ COVERAGE_METADATA = ('chromCol',
'forwardCol',
'reverseCol',)
+
def main( interval, coverage ):
"""
Uses a sliding window of partitions to count coverages.
@@ -40,17 +38,16 @@ def main( interval, coverage ):
partitions = []
forward_covs = []
reverse_covs = []
- offset = 0
chrom = None
lastchrom = None
for record in interval:
chrom = record.chrom
if lastchrom and not lastchrom == chrom and partitions:
- for partition in xrange(0, len(partitions)-1):
+ for partition in xrange(0, len(partitions) - 1):
forward = forward_covs[partition]
reverse = reverse_covs[partition]
- if forward+reverse > 0:
- coverage.write(chrom=chrom, position=xrange(partitions[partition],partitions[partition+1]),
+ if forward + reverse > 0:
+ coverage.write(chrom=chrom, position=xrange(partitions[partition], partitions[partition + 1]),
forward=forward, reverse=reverse)
partitions = []
forward_covs = []
@@ -62,8 +59,8 @@ def main( interval, coverage ):
forward_base = 0
reverse_base = 0
if start_index > 0:
- forward_base = forward_covs[start_index-1]
- reverse_base = reverse_covs[start_index-1]
+ forward_base = forward_covs[start_index - 1]
+ reverse_base = reverse_covs[start_index - 1]
partitions.insert(start_index, record.start)
forward_covs.insert(start_index, forward_base)
reverse_covs.insert(start_index, reverse_base)
@@ -72,15 +69,15 @@ def main( interval, coverage ):
forward_covs[index] += forward
reverse_covs[index] += reverse
partitions.insert(end_index, record.end)
- forward_covs.insert(end_index, forward_covs[end_index-1] - forward )
- reverse_covs.insert(end_index, reverse_covs[end_index-1] - reverse )
+ forward_covs.insert(end_index, forward_covs[end_index - 1] - forward )
+ reverse_covs.insert(end_index, reverse_covs[end_index - 1] - reverse )
if partitions:
for partition in xrange(0, start_index):
forward = forward_covs[partition]
reverse = reverse_covs[partition]
- if forward+reverse > 0:
- coverage.write(chrom=chrom, position=xrange(partitions[partition],partitions[partition+1]),
+ if forward + reverse > 0:
+ coverage.write(chrom=chrom, position=xrange(partitions[partition], partitions[partition + 1]),
forward=forward, reverse=reverse)
partitions = partitions[start_index:]
forward_covs = forward_covs[start_index:]
@@ -90,29 +87,31 @@ def main( interval, coverage ):
# Finish the last chromosome
if partitions:
- for partition in xrange(0, len(partitions)-1):
+ for partition in xrange(0, len(partitions) - 1):
forward = forward_covs[partition]
reverse = reverse_covs[partition]
- if forward+reverse > 0:
- coverage.write(chrom=chrom, position=xrange(partitions[partition],partitions[partition+1]),
+ if forward + reverse > 0:
+ coverage.write(chrom=chrom, position=xrange(partitions[partition], partitions[partition + 1]),
forward=forward, reverse=reverse)
+
class CoverageWriter( object ):
def __init__( self, out_stream=None, chromCol=0, positionCol=1, forwardCol=2, reverseCol=3 ):
self.out_stream = out_stream
self.reverseCol = reverseCol
self.nlines = 0
- positions = {str(chromCol):'%(chrom)s',
- str(positionCol):'%(position)d',
- str(forwardCol):'%(forward)d',
- str(reverseCol):'%(reverse)d'}
+ positions = {str(chromCol): '%(chrom)s',
+ str(positionCol): '%(position)d',
+ str(forwardCol): '%(forward)d',
+ str(reverseCol): '%(reverse)d'}
if reverseCol < 0:
self.template = "%(0)s\t%(1)s\t%(2)s\n" % positions
else:
self.template = "%(0)s\t%(1)s\t%(2)s\t%(3)s\n" % positions
def write(self, **kwargs ):
- if self.reverseCol < 0: kwargs['forward'] += kwargs['reverse']
+ if self.reverseCol < 0:
+ kwargs['forward'] += kwargs['reverse']
posgen = kwargs['position']
for position in posgen:
kwargs['position'] = position
@@ -125,8 +124,8 @@ class CoverageWriter( object ):
if __name__ == "__main__":
options, args = doc_optparse.parse( __doc__ )
try:
- chr_col_1, start_col_1, end_col_1, strand_col_1 = [int(x)-1 for x in options.cols1.split(',')]
- chr_col_2, position_col_2, forward_col_2, reverse_col_2 = [int(x)-1 for x in options.cols2.split(',')]
+ chr_col_1, start_col_1, end_col_1, strand_col_1 = [int(x) - 1 for x in options.cols1.split(',')]
+ chr_col_2, position_col_2, forward_col_2, reverse_col_2 = [int(x) - 1 for x in options.cols2.split(',')]
in_fname, out_fname = args
except:
doc_optparse.exception()
@@ -134,12 +133,12 @@ if __name__ == "__main__":
# Sort through a tempfile first
temp_file = tempfile.NamedTemporaryFile(mode="r")
environ['LC_ALL'] = 'POSIX'
- commandline = "sort -f -n -k %d -k %d -k %d -o %s %s" % (chr_col_1+1,start_col_1+1,end_col_1+1, temp_file.name, in_fname)
+ commandline = "sort -f -n -k %d -k %d -k %d -o %s %s" % (chr_col_1 + 1, start_col_1 + 1, end_col_1 + 1, temp_file.name, in_fname)
errorcode, stdout = commands.getstatusoutput(commandline)
- coverage = CoverageWriter( out_stream = open(out_fname, "a"),
- chromCol = chr_col_2, positionCol = position_col_2,
- forwardCol = forward_col_2, reverseCol = reverse_col_2, )
+ coverage = CoverageWriter( out_stream=open(out_fname, "a"),
+ chromCol=chr_col_2, positionCol=position_col_2,
+ forwardCol=forward_col_2, reverseCol=reverse_col_2, )
temp_file.seek(0)
interval = io.NiceReaderWrapper( temp_file,
chrom_col=chr_col_1,
diff --git a/lib/galaxy/datatypes/converters/interval_to_fli.py b/lib/galaxy/datatypes/converters/interval_to_fli.py
index 22b429d1945..4f58a986c5f 100644
--- a/lib/galaxy/datatypes/converters/interval_to_fli.py
+++ b/lib/galaxy/datatypes/converters/interval_to_fli.py
@@ -13,13 +13,13 @@ where location is formatted as:
and symbols are sorted in lexigraphical order.
'''
-
-import sys, optparse
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
+import optparse
+import pkg_resources
+pkg_resources.require( "bx-python" )
from bx.tabular.io import Comment
from galaxy.datatypes.util.gff_util import GFFReaderWrapper, read_unordered_gtf, convert_gff_coords_to_bed
+
def main():
# Process arguments.
parser = optparse.OptionParser()
@@ -36,7 +36,7 @@ def main():
# Create reader.
if input_format == 'gff':
in_reader = GFFReaderWrapper( open( in_fname, 'r' ) )
- else: #input_format == 'gtf'
+ else: # input_format == 'gtf'
in_reader = read_unordered_gtf( open( in_fname, 'r' ) )
for feature in in_reader:
@@ -82,7 +82,7 @@ def main():
name_loc_dict[ fields[3] ] = {
'contig': fields[0],
'start': int( fields[1] ),
- 'end': int ( fields[2] )
+ 'end': int( fields[2] )
}
# Create sorted list of entries.
diff --git a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
index 8d1b7653cb0..f818060e605 100644
--- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
@@ -16,6 +16,7 @@ from galaxy import eggs
eggs.require( "bx-python" )
from bx.interval_index_file import Indexes
+
def main():
# Read options, args.
@@ -49,4 +50,3 @@ def main():
if __name__ == "__main__":
main()
-
diff --git a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
index 13fb2e53c73..163108459e3 100644
--- a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
@@ -7,9 +7,13 @@ Supported presets: bed, gff, vcf
usage: %prog in_file out_file
"""
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "pysam" )
-import ctabix, subprocess, tempfile, sys, os, optparse
+import pkg_resources
+pkg_resources.require( "pysam" )
+import ctabix
+import sys
+import os
+import optparse
+
def main():
# Read options, args.
diff --git a/lib/galaxy/datatypes/converters/lped_to_fped_converter.py b/lib/galaxy/datatypes/converters/lped_to_fped_converter.py
index dd6daf819d0..c68b03201cc 100644
--- a/lib/galaxy/datatypes/converters/lped_to_fped_converter.py
+++ b/lib/galaxy/datatypes/converters/lped_to_fped_converter.py
@@ -3,7 +3,9 @@
# much slower so best to always
# use numeric alleles internally
-import sys,os,time
+import sys
+import os
+import time
prog = os.path.split(sys.argv[0])[-1]
@@ -22,56 +24,57 @@ galhtmlprefix = """
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arguments.length?(u=e,C):u},C.y=function(e){return arguments.length?(a=e,C):a},C.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,C):t},C.width=function(e){return arguments.length?(n=e,C):n},C.height=function(e){return arguments.length?(r=e,C):r},C.xScale=function(e){return arguments.length?(s=e,C):s},C.yScale=function(e){return arguments.length?(o=e,C):o},C.xDomain=function(e){return arguments.length?(b=e,C):b},C.yDomain=function(e){return arguments.length?(w=e,C):w},C.xRange=function(e){return arguments.length?(E=e,C):E},C.yRange=function(e){return arguments.length?(S=e,C):S},C.forceY=function(e){return arguments.length?(f=e,C):f},C.stacked=function(e){return arguments.length?(p=e,C):p},C.color=function(t){return arguments.length?(l=e.utils.getColor(t),C):l},C.barColor=function(t){return arguments.length?(c=e.utils.getColor(t),C):c},C.disabled=function(e){return arguments.length?(h=e,C):h},C.id=function(e){return arguments.length?(i=e,C):i},C.delay=function(e){return arguments.length?(y=e,C):y},C.showValues=function(e){return arguments.length?(d=e,C):d},C.showBarLabels=function(e){return arguments.length?(v=e,C):v},C.valueFormat=function(e){return arguments.length?(g=e,C):g},C.valuePadding=function(e){return arguments.length?(m=e,C):m},C},e.models.multiBarHorizontalChart=function(){"use strict";function C(e){return e.each(function(e){var d=d3.select(this),m=this,T=(u||parseInt(d.style("width"))||960)-o.left-o.right,k=(a||parseInt(d.style("height"))||400)-o.top-o.bottom;C.update=function(){d.call(C)},C.container=this,b.disabled=e.map(function(e){return!!e.disabled});if(!w){var L;w={};for(L in b)b[L]instanceof Array?w[L]=b[L].slice(0):w[L]=b[L]}if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var A=d.selectAll(".nv-noData").data([E]);return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),C.dispatch=S,C.multibar=t,C.legend=i,C.xAxis=n,C.yAxis=r,d3.rebind(C,t,"x","y","xDomain","yDomain","xRange","yRange","forceX","forceY","clipEdge","id","delay","showValues","showBarLabels","valueFormat","stacked","barColor"),C.options=e.utils.optionsFunc.bind(C),C.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,C):o},C.width=function(e){return arguments.length?(u=e,C):u},C.height=function(e){return arguments.length?(a=e,C):a},C.color=function(t){return arguments.length?(f=e.utils.getColor(t),i.color(f),C):f},C.showControls=function(e){return arguments.length?(l=e,C):l},C.showLegend=function(e){return arguments.length?(c=e,C):c},C.showXAxis=function(e){return arguments.length?(h=e,C):h},C.showYAxis=function(e){return arguments.length?(p=e,C):p},C.tooltip=function(e){return arguments.length?(m=e,C):m},C.tooltips=function(e){return arguments.length?(v=e,C):v},C.tooltipContent=function(e){return arguments.length?(m=e,C):m},C.state=function(e){return arguments.length?(b=e,C):b},C.defaultState=function(e){return arguments.length?(w=e,C):w},C.noData=function(e){return arguments.length?(E=e,C):E},C.transitionDuration=function(e){return arguments.length?(T=e,C):T},C},e.models.multiChart=function(){"use strict";function C(e){return e.each(function(e){var u=d3.select(this),f=this;C.update=function(){u.call(C)},C.container=this;var 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\ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js b/config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js index 121d3451905..7e445747166 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js @@ -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', diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js b/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js index 579cd003c6a..cd01edff775 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js @@ -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', diff --git a/config/plugins/visualizations/charts/static/views/editor.js b/config/plugins/visualizations/charts/static/views/editor.js index 76af75a3da8..e077494e939 100644 --- a/config/plugins/visualizations/charts/static/views/editor.js +++ b/config/plugins/visualizations/charts/static/views/editor.js @@ -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'); diff --git a/config/plugins/visualizations/charts/static/views/viewport.js b/config/plugins/visualizations/charts/static/views/viewport.js index b2b5d8d5651..66595da3b78 100644 --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -295,7 +295,7 @@ return Backbone.View.extend({ _templateContainer: function(tag, width) { return ''; } diff --git a/contrib/nagios/check_galaxy.py b/contrib/nagios/check_galaxy.py index 9da4fbd49b1..fc964785148 100755 --- a/contrib/nagios/check_galaxy.py +++ b/contrib/nagios/check_galaxy.py @@ -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 diff --git a/cron/add_manual_builds.py b/cron/add_manual_builds.py index 6af91cf9ac7..4e62b8df4bc 100644 --- a/cron/add_manual_builds.py +++ b/cron/add_manual_builds.py @@ -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) diff --git a/cron/build_chrom_db.py b/cron/build_chrom_db.py index b064c5fc07e..52ee48c51b6 100644 --- a/cron/build_chrom_db.py +++ b/cron/build_chrom_db.py @@ -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() diff --git a/cron/parse_builds_3_sites.py b/cron/parse_builds_3_sites.py index 90e8f11e508..7a5e5d06fca 100644 --- a/cron/parse_builds_3_sites.py +++ b/cron/parse_builds_3_sites.py @@ -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]) diff --git a/doc/patch.py b/doc/patch.py index 8a89576b180..c6a24111ad9 100755 --- a/doc/patch.py +++ b/doc/patch.py @@ -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 diff --git a/doc/source/api_doc.rst b/doc/source/api_doc.rst new file mode 100644 index 00000000000..119b2216786 --- /dev/null +++ b/doc/source/api_doc.rst @@ -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 diff --git a/doc/source/conf.py b/doc/source/conf.py index 5accee30a00..9444c4cb321 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -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() diff --git a/doc/source/index.rst b/doc/source/index.rst index 02142d04c86..58450c3aaf2 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -42,7 +42,7 @@ Contents .. toctree:: :maxdepth: 5 - API DocumentationThis composite dataset is composed of the following files:
' )
return "\n".join( rval )
- def regenerate_primary_file(self,dataset):
+ def regenerate_primary_file(self, dataset):
"""
cannot do this until we are setting metadata
"""
@@ -176,23 +179,23 @@ class Velvet( Html ):
gen_msg = ''
try:
efp = dataset.extra_files_path
- log_path = os.path.join(efp,'Log')
- f = open(log_path,'r')
+ log_path = os.path.join(efp, 'Log')
+ f = open(log_path, 'r')
log_content = f.read(1000)
f.close()
- log_msg = re.sub('/\S*/','',log_content)
+ log_msg = re.sub('/\S*/', '', log_content)
log.debug( "Velveth log info %s" % log_msg)
- paired_end_reads = re.search('-(short|long)Paired', log_msg) != None
+ paired_end_reads = re.search('-(short|long)Paired', log_msg) is not None
dataset.metadata.paired_end_reads = paired_end_reads
- long_reads = re.search('-long', log_msg) != None
+ long_reads = re.search('-long', log_msg) is not None
dataset.metadata.long_reads = long_reads
- short2_reads = re.search('-short(Paired)?2', log_msg) != None
+ short2_reads = re.search('-short(Paired)?2', log_msg) is not None
dataset.metadata.short2_reads = short2_reads
- dataset.info = re.sub('.*velveth \S+','hash_length',re.sub('\n',' ',log_msg))
+ dataset.info = re.sub('.*velveth \S+', 'hash_length', re.sub('\n', ' ', log_msg))
if paired_end_reads:
- gen_msg = gen_msg + ' Paired-End Reads'
+ gen_msg = gen_msg + ' Paired-End Reads'
if long_reads:
- gen_msg = gen_msg + ' Long Reads'
+ gen_msg = gen_msg + ' Long Reads'
if len(gen_msg) > 0:
gen_msg = 'Uses: ' + gen_msg
except:
@@ -200,12 +203,12 @@ class Velvet( Html ):
log.debug( "Velveth log info %s" % gen_msg)
rval = ['- ')
- for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
+ for composite_name, composite_file in self.get_composite_files( dataset=dataset ).iteritems():
fn = composite_name
- log.debug( "Velvet log info %s %s %s" % ('JJ generate_primary_file',fn,composite_file))
+ log.debug( "Velvet log info %s %s %s" % ('JJ generate_primary_file', fn, composite_file))
opt_text = ''
if composite_file.optional:
opt_text = ' (optional)'
@@ -168,7 +171,7 @@ class Velvet( Html ):
rval.append( '
Generated:
' %(re.sub('\n',' %s ',log_msg))) - rval.append('
Generated: %s
' %(gen_msg))
+ rval.append('Generated: %s
' % (gen_msg))
rval.append('Velveth dataset:
' )
- f = file(dataset.file_name,'w')
+ f = file(dataset.file_name, 'w')
f.write("\n".join( rval ))
f.write('\n')
f.close()
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 4fd0caf968b..3ba39bed2c6 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -1,6 +1,4 @@
-"""
-Binary classes
-"""
+"""Binary classes"""
import binascii
import data
@@ -11,7 +9,6 @@ import shutil
import struct
import subprocess
import tempfile
-import re
import warnings
import zipfile
@@ -35,6 +32,7 @@ log = logging.getLogger(__name__)
# Currently these supported binary data types must be manually set on upload
+
class Binary( data.Data ):
"""Binary data"""
edam_format = "format_2333"
@@ -89,7 +87,7 @@ class Binary( data.Data ):
to_ext = dataset.extension
valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
fname = ''.join(c in valid_chars and c or '_' for c in dataset.name)[0:150]
- trans.response.set_content_type( "application/octet-stream" ) #force octet-stream so Safari doesn't append mime extensions to filename
+ trans.response.set_content_type( "application/octet-stream" ) # force octet-stream so Safari doesn't append mime extensions to filename
trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (dataset.hid, fname, to_ext)
return open( dataset.file_name )
@@ -100,7 +98,7 @@ class Ab1( Binary ):
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
- dataset.peek = "Binary ab1 sequence file"
+ dataset.peek = "Binary ab1 sequence file"
dataset.blurb = data.nice_size( dataset.get_size() )
else:
dataset.peek = 'file does not exist'
@@ -134,7 +132,6 @@ class Idat( Binary ):
Binary.register_sniffable_binary_format("idat", "idat", Idat)
-
class CompressedArchive( Binary ):
"""
Class describing an compressed binary file
@@ -145,7 +142,7 @@ class CompressedArchive( Binary ):
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
- dataset.peek = "Compressed binary file"
+ dataset.peek = "Compressed binary file"
dataset.blurb = data.nice_size( dataset.get_size() )
else:
dataset.peek = 'file does not exist'
@@ -209,7 +206,7 @@ class Bam( Binary ):
if stderr:
if exit_code != 0:
shutil.rmtree(tmp_dir) # clean up
- raise Exception, "Error merging BAM files: %s" % stderr
+ raise Exception( "Error merging BAM files: %s" % stderr )
else:
print stderr
os.unlink(stderr_name)
@@ -243,11 +240,11 @@ class Bam( Binary ):
# seconds to index with samtools, and 45 minutes to sort, so indexing is relatively inexpensive.
if self._is_coordinate_sorted( file_name ):
return False
- index_name = tempfile.NamedTemporaryFile( prefix = "bam_index" ).name
- stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name
+ index_name = tempfile.NamedTemporaryFile( prefix="bam_index" ).name
+ stderr_name = tempfile.NamedTemporaryFile( prefix="bam_index_stderr" ).name
command = 'samtools index %s %s' % ( file_name, index_name )
proc = subprocess.Popen( args=command, shell=True, stderr=open( stderr_name, 'wb' ) )
- exit_code = proc.wait()
+ proc.wait()
stderr = open( stderr_name ).read().strip()
if stderr:
try:
@@ -276,28 +273,28 @@ class Bam( Binary ):
on an output dataset after the content is initially generated.
"""
# Use samtools to sort the Bam file
- ##$ samtools sort
- ##Usage: samtools sort [-on] [-m - ')
- for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
+ for composite_name, composite_file in self.get_composite_files( dataset=dataset ).iteritems():
fn = composite_name
- log.debug( "Velvet log info %s %s %s" % ('JJ regenerate_primary_file',fn,composite_file))
- if re.search('Log',fn) == None:
+ log.debug( "Velvet log info %s %s %s" % ('JJ regenerate_primary_file', fn, composite_file))
+ if re.search('Log', fn) is None:
opt_text = ''
if composite_file.optional:
opt_text = ' (optional)'
@@ -214,7 +217,7 @@ class Velvet( Html ):
else:
rval.append( '
- %s%s ' % ( fn, fn, opt_text ) ) rval.append( '
"""
+
def timenow():
"""return current time as a string
"""
return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
-def rgConv(inpedfilepath,outhtmlname,outfilepath):
- """convert linkage ped/map to fbat"""
- recode={'A':'1','C':'2','G':'3','T':'4','N':'0','0':'0','1':'1','2':'2','3':'3','4':'4'}
- basename = os.path.split(inpedfilepath)[-1] # get basename
- inmap = '%s.map' % inpedfilepath
- inped = '%s.ped' % inpedfilepath
- outf = '%s.ped' % basename # note the fbat exe insists that this is the extension for the ped data
- outfpath = os.path.join(outfilepath,outf) # where to write the fbat format file to
- try:
- mf = file(inmap,'r')
- except:
- sys.stderr.write('%s cannot open inmap file %s - do you have permission?\n' % (prog,inmap))
- sys.exit(1)
- try:
- rsl = [x.split()[1] for x in mf]
- except:
- sys.stderr.write('## cannot parse %s' % inmap)
- sys.exit(1)
- try:
- os.makedirs(outfilepath)
- except:
- pass # already exists
- head = ' '.join(rsl) # list of rs numbers
- # TODO add anno to rs but fbat will prolly barf?
- pedf = file(inped,'r')
- o = file(outfpath,'w',2**20)
- o.write(head)
- o.write('\n')
- for i,row in enumerate(pedf):
- if i == 0:
- lrow = row.split()
- try:
- x = [int(x) for x in lrow[10:50]] # look for non numeric codes
- except:
- dorecode = 1
- if dorecode:
- lrow = row.strip().split()
- p = lrow[:6]
- g = lrow[6:]
- gc = [recode.get(x,'0') for x in g]
- lrow = p+gc
- row = '%s\n' % ' '.join(lrow)
- o.write(row)
- o.close()
+def rgConv(inpedfilepath, outhtmlname, outfilepath):
+ """convert linkage ped/map to fbat"""
+ recode = {'A': '1', 'C': '2', 'G': '3', 'T': '4', 'N': '0', '0': '0', '1': '1', '2': '2', '3': '3', '4': '4'}
+ basename = os.path.split(inpedfilepath)[-1] # get basename
+ inmap = '%s.map' % inpedfilepath
+ inped = '%s.ped' % inpedfilepath
+ outf = '%s.ped' % basename # note the fbat exe insists that this is the extension for the ped data
+ outfpath = os.path.join(outfilepath, outf) # where to write the fbat format file to
+ try:
+ mf = file(inmap, 'r')
+ except:
+ sys.stderr.write('%s cannot open inmap file %s - do you have permission?\n' % (prog, inmap))
+ sys.exit(1)
+ try:
+ rsl = [x.split()[1] for x in mf]
+ except:
+ sys.stderr.write('## cannot parse %s' % inmap)
+ sys.exit(1)
+ try:
+ os.makedirs(outfilepath)
+ except:
+ pass # already exists
+ head = ' '.join(rsl) # list of rs numbers
+ # TODO add anno to rs but fbat will prolly barf?
+ pedf = file(inped, 'r')
+ o = file(outfpath, 'w', 2 ** 20)
+ o.write(head)
+ o.write('\n')
+ for i, row in enumerate(pedf):
+ if i == 0:
+ lrow = row.split()
+ try:
+ x = [int(x) for x in lrow[10:50]] # look for non numeric codes
+ except:
+ dorecode = 1
+ if dorecode:
+ lrow = row.strip().split()
+ p = lrow[:6]
+ g = lrow[6:]
+ gc = [recode.get(z, '0') for z in g]
+ lrow = p + gc
+ row = '%s\n' % ' '.join(lrow)
+ o.write(row)
+ o.close()
def main():
@@ -84,7 +87,7 @@ def main():
"""
nparm = 3
if len(sys.argv) < nparm:
- sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog,sys.argv,nparm))
+ sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog, sys.argv, nparm))
sys.exit(1)
inpedfilepath = sys.argv[1]
outhtmlname = sys.argv[2]
@@ -93,18 +96,17 @@ def main():
os.makedirs(outfilepath)
except:
pass
- rgConv(inpedfilepath,outhtmlname,outfilepath)
- f = file(outhtmlname,'w')
+ rgConv(inpedfilepath, outhtmlname, outfilepath)
+ f = file(outhtmlname, 'w')
f.write(galhtmlprefix % prog)
flist = os.listdir(outfilepath)
- print '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info
- f.write('
## Rgenetics: http://rgenetics.org Galaxy Tools %s %s\n
- ' % (prog,timenow()))
+ print '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog, timenow()) # becomes info
+ f.write('