June 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by Bitbucket 16 Jun '12

16 Jun '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/54898b02d42a/ changeset: 54898b02d42a user: jgoecks date: 2012-06-15 23:43:54 summary: Visualization framework improvements. affected #: 5 files diff -r 0bd0c35351c4eb9c7103b6d737543317abc54ac0 -r 54898b02d42afdacaef261a49bbef18dd563365d static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -68,6 +68,16 @@ }, /** + * Set many input values at once. + */ + set_input_values: function(inputs_dict) { + var self = this; + _.each(_.keys(inputs_dict), function(input_name) { + self.set_input_value(input_name, inputs_dict[input_name]); + }); + }, + + /** * Run tool; returns a Deferred that resolves to the tool's output(s). */ run: function() { diff -r 0bd0c35351c4eb9c7103b6d737543317abc54ac0 -r 54898b02d42afdacaef261a49bbef18dd563365d static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -176,56 +176,6 @@ var extend = require('class').extend, slotting = require('slotting'), painters = require('painters'); - - -// ---- Canvas management and extensions ---- - -/** - * Canvas manager is used to create canvases, for browsers, this deals with - * backward comparibility using excanvas, as well as providing a pattern cache - */ -var CanvasManager = function( document, default_font ) { - this.document = document; - this.default_font = default_font !== undefined ? default_font : "9px Monaco, Lucida Console, monospace"; - - this.dummy_canvas = this.new_canvas(); - this.dummy_context = this.dummy_canvas.getContext('2d'); - this.dummy_context.font = this.default_font; - - this.char_width_px = this.dummy_context.measureText("A").width; - - this.patterns = {}; - - // FIXME: move somewhere to make this more general - this.load_pattern( 'right_strand', "/visualization/strand_right.png" ); - this.load_pattern( 'left_strand', "/visualization/strand_left.png" ); - this.load_pattern( 'right_strand_inv', "/visualization/strand_right_inv.png" ); - this.load_pattern( 'left_strand_inv', "/visualization/strand_left_inv.png" ); -} - -extend( CanvasManager.prototype, { - load_pattern: function( key, path ) { - var patterns = this.patterns, - dummy_context = this.dummy_context, - image = new Image(); - image.src = galaxy_paths.attributes.image_path + path; - image.onload = function() { - patterns[key] = dummy_context.createPattern( image, "repeat" ); - } - }, - get_pattern: function( key ) { - return this.patterns[key]; - }, - new_canvas: function() { - var canvas = this.document.createElement("canvas"); - // If using excanvas in IE, we need to explicately attach the canvas - // methods to the DOM element - if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } - // Keep a reference back to the manager - canvas.manager = this; - return canvas; - } -}); // ---- Web UI specific utilities ---- @@ -2985,18 +2935,20 @@ this.data_url = ('data_url' in obj_dict ? obj_dict.data_url : default_data_url); this.data_url_extra_params = {} this.data_query_wait = ('data_query_wait' in obj_dict ? obj_dict.data_query_wait : DEFAULT_DATA_QUERY_WAIT); - this.dataset_check_url = converted_datasets_state_url; + this.dataset_check_url = ('converted_datasets_state_url' in obj_dict ? obj_dict.converted_datasets_state_url : converted_datasets_state_url); // A little ugly creating data manager right now due to transition to Backbone-based objects. - var dataset = new Dataset({ - id: obj_dict.dataset_id, - hda_ldda: obj_dict.hda_ldda - }); + var track = this, + dataset = new Dataset({ + id: obj_dict.dataset_id, + hda_ldda: obj_dict.hda_ldda + }); this.data_manager = ('data_manager' in obj_dict ? obj_dict.data_manager : new GenomeDataManager({ dataset: dataset, - data_url: default_data_url, + data_url: track.data_url, + dataset_state_url: track.dataset_check_url, data_mode_compatible: this.data_and_mode_compatible, can_subset: this.can_subset, })); diff -r 0bd0c35351c4eb9c7103b6d737543317abc54ac0 -r 54898b02d42afdacaef261a49bbef18dd563365d static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ b/static/scripts/viz/trackster_ui.js @@ -36,7 +36,7 @@ * Create new object from a template. A template can be either an object dictionary or an * object itself. */ -var object_from_template = function(template, container) { +var object_from_template = function(template, view, container) { if ('copy' in template) { // Template is an object. return template.copy(container); @@ -93,7 +93,7 @@ drawable_type, drawable; for (var i = 0; i < drawables_config.length; i++) { - view.add_drawable( object_from_template( drawables_config[i], view ) ); + view.add_drawable( object_from_template( drawables_config[i], view, view ) ); } } diff -r 0bd0c35351c4eb9c7103b6d737543317abc54ac0 -r 54898b02d42afdacaef261a49bbef18dd563365d static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -1,5 +1,7 @@ /** - * Model, view, and controller objects for Galaxy tools and tool panel. + * Model, view, and controller objects for Galaxy visualization framework. + * + * Required libraries: Backbone, jQuery * * Models have no references to views, instead using events to indicate state * changes; this is advantageous because multiple views can use the same object @@ -45,14 +47,66 @@ } }); +// TODO: move to Backbone + +/** + * Canvas manager is used to create canvases, for browsers, this deals with + * backward comparibility using excanvas, as well as providing a pattern cache + */ +var CanvasManager = function(default_font) { + this.default_font = default_font !== undefined ? default_font : "9px Monaco, Lucida Console, monospace"; + + this.dummy_canvas = this.new_canvas(); + this.dummy_context = this.dummy_canvas.getContext('2d'); + this.dummy_context.font = this.default_font; + + this.char_width_px = this.dummy_context.measureText("A").width; + + this.patterns = {}; + + // FIXME: move somewhere to make this more general + this.load_pattern( 'right_strand', "/visualization/strand_right.png" ); + this.load_pattern( 'left_strand', "/visualization/strand_left.png" ); + this.load_pattern( 'right_strand_inv', "/visualization/strand_right_inv.png" ); + this.load_pattern( 'left_strand_inv', "/visualization/strand_left_inv.png" ); +} + +_.extend( CanvasManager.prototype, { + load_pattern: function( key, path ) { + var patterns = this.patterns, + dummy_context = this.dummy_context, + image = new Image(); + image.src = galaxy_paths.attributes.image_path + path; + image.onload = function() { + patterns[key] = dummy_context.createPattern( image, "repeat" ); + } + }, + get_pattern: function( key ) { + return this.patterns[key]; + }, + new_canvas: function() { + var canvas = $("<canvas/>")[0]; + // If using excanvas in IE, we need to explicately attach the canvas + // methods to the DOM element + if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } + // Keep a reference back to the manager + canvas.manager = this; + return canvas; + } +}); + /** * Generic cache that handles key/value pairs. */ var Cache = Backbone.Model.extend({ defaults: { num_elements: 20, - obj_cache: {}, - key_ary: [] + obj_cache: null, + key_ary: null + }, + + initialize: function(options) { + this.clear(); }, get_elt: function(key) { @@ -114,9 +168,36 @@ dataset: null, filters_manager: null, data_url: null, + dataset_state_url: null, data_mode_compatible: function(entry, mode) { return true; }, can_subset: function(entry) { return false; } }), + + /** + * Returns deferred that resolves to true when dataset is ready (or false if dataset + * cannot be used). + */ + data_is_ready: function() { + var dataset = this.get('dataset'), + ready_deferred = $.Deferred(), + ss_deferred = new ServerStateDeferred({ + ajax_settings: { + url: this.get('dataset_state_url'), + data: { + dataset_id: dataset.id, + hda_ldda: dataset.get('hda_ldda') + }, + dataType: "json" + }, + interval: 5000, + success_fn: function(response) { return response !== "pending"; } + }); + + $.when(ss_deferred.go()).then(function(response) { + ready_deferred.resolve(response === "ok" || response === "data" ); + }); + return ready_deferred; + }, /** * Load data from server; returns AJAX object so that use of Deferred is possible. @@ -366,6 +447,10 @@ end: this.get('end') }); }, + + length: function() { + return this.get('end') - this.get('start'); + }, /** Returns region in canonical form chrom:start-end */ toString: function() { @@ -438,6 +523,10 @@ } }); +var GenomeRegionCollection = Backbone.Collection.extend({ + model: GenomeRegion +}); + /** * A genome browser bookmark. */ diff -r 0bd0c35351c4eb9c7103b6d737543317abc54ac0 -r 54898b02d42afdacaef261a49bbef18dd563365d templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -53,7 +53,11 @@ var galaxy_paths = new GalaxyPaths({ root_path: '${h.url_for( "/" )}', image_path: '${h.url_for( "/static/images" )}', - tool_url: '${h.url_for( controller="/api/tools" )}' + tool_url: '${h.url_for( controller="/api/tools" )}', + data_url: '${h.url_for( controller="tracks", action="data" )}', + raw_data_url: '${h.url_for( controller="tracks", action="raw_data" )}', + converted_datasets_state_url: '${h.url_for( controller="tracks", action="converted_datasets_state" )}', + dataset_state_url: '${h.url_for( controller="tracks", action="dataset_state" )}' }); </script></%def> https://bitbucket.org/galaxy/galaxy-central/changeset/aaf5c82a5579/ changeset: aaf5c82a5579 user: jgoecks date: 2012-06-15 23:45:22 summary: Merge affected #: 5 files diff -r ccfcca670dfa5303d09a178473b663c15e5dc80a -r aaf5c82a55794c97125696aecb27056b5087fdb7 static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -68,6 +68,16 @@ }, /** + * Set many input values at once. + */ + set_input_values: function(inputs_dict) { + var self = this; + _.each(_.keys(inputs_dict), function(input_name) { + self.set_input_value(input_name, inputs_dict[input_name]); + }); + }, + + /** * Run tool; returns a Deferred that resolves to the tool's output(s). */ run: function() { diff -r ccfcca670dfa5303d09a178473b663c15e5dc80a -r aaf5c82a55794c97125696aecb27056b5087fdb7 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -176,56 +176,6 @@ var extend = require('class').extend, slotting = require('slotting'), painters = require('painters'); - - -// ---- Canvas management and extensions ---- - -/** - * Canvas manager is used to create canvases, for browsers, this deals with - * backward comparibility using excanvas, as well as providing a pattern cache - */ -var CanvasManager = function( document, default_font ) { - this.document = document; - this.default_font = default_font !== undefined ? default_font : "9px Monaco, Lucida Console, monospace"; - - this.dummy_canvas = this.new_canvas(); - this.dummy_context = this.dummy_canvas.getContext('2d'); - this.dummy_context.font = this.default_font; - - this.char_width_px = this.dummy_context.measureText("A").width; - - this.patterns = {}; - - // FIXME: move somewhere to make this more general - this.load_pattern( 'right_strand', "/visualization/strand_right.png" ); - this.load_pattern( 'left_strand', "/visualization/strand_left.png" ); - this.load_pattern( 'right_strand_inv', "/visualization/strand_right_inv.png" ); - this.load_pattern( 'left_strand_inv', "/visualization/strand_left_inv.png" ); -} - -extend( CanvasManager.prototype, { - load_pattern: function( key, path ) { - var patterns = this.patterns, - dummy_context = this.dummy_context, - image = new Image(); - image.src = galaxy_paths.attributes.image_path + path; - image.onload = function() { - patterns[key] = dummy_context.createPattern( image, "repeat" ); - } - }, - get_pattern: function( key ) { - return this.patterns[key]; - }, - new_canvas: function() { - var canvas = this.document.createElement("canvas"); - // If using excanvas in IE, we need to explicately attach the canvas - // methods to the DOM element - if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } - // Keep a reference back to the manager - canvas.manager = this; - return canvas; - } -}); // ---- Web UI specific utilities ---- @@ -2985,18 +2935,20 @@ this.data_url = ('data_url' in obj_dict ? obj_dict.data_url : default_data_url); this.data_url_extra_params = {} this.data_query_wait = ('data_query_wait' in obj_dict ? obj_dict.data_query_wait : DEFAULT_DATA_QUERY_WAIT); - this.dataset_check_url = converted_datasets_state_url; + this.dataset_check_url = ('converted_datasets_state_url' in obj_dict ? obj_dict.converted_datasets_state_url : converted_datasets_state_url); // A little ugly creating data manager right now due to transition to Backbone-based objects. - var dataset = new Dataset({ - id: obj_dict.dataset_id, - hda_ldda: obj_dict.hda_ldda - }); + var track = this, + dataset = new Dataset({ + id: obj_dict.dataset_id, + hda_ldda: obj_dict.hda_ldda + }); this.data_manager = ('data_manager' in obj_dict ? obj_dict.data_manager : new GenomeDataManager({ dataset: dataset, - data_url: default_data_url, + data_url: track.data_url, + dataset_state_url: track.dataset_check_url, data_mode_compatible: this.data_and_mode_compatible, can_subset: this.can_subset, })); diff -r ccfcca670dfa5303d09a178473b663c15e5dc80a -r aaf5c82a55794c97125696aecb27056b5087fdb7 static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ b/static/scripts/viz/trackster_ui.js @@ -36,7 +36,7 @@ * Create new object from a template. A template can be either an object dictionary or an * object itself. */ -var object_from_template = function(template, container) { +var object_from_template = function(template, view, container) { if ('copy' in template) { // Template is an object. return template.copy(container); @@ -93,7 +93,7 @@ drawable_type, drawable; for (var i = 0; i < drawables_config.length; i++) { - view.add_drawable( object_from_template( drawables_config[i], view ) ); + view.add_drawable( object_from_template( drawables_config[i], view, view ) ); } } diff -r ccfcca670dfa5303d09a178473b663c15e5dc80a -r aaf5c82a55794c97125696aecb27056b5087fdb7 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -1,5 +1,7 @@ /** - * Model, view, and controller objects for Galaxy tools and tool panel. + * Model, view, and controller objects for Galaxy visualization framework. + * + * Required libraries: Backbone, jQuery * * Models have no references to views, instead using events to indicate state * changes; this is advantageous because multiple views can use the same object @@ -45,14 +47,66 @@ } }); +// TODO: move to Backbone + +/** + * Canvas manager is used to create canvases, for browsers, this deals with + * backward comparibility using excanvas, as well as providing a pattern cache + */ +var CanvasManager = function(default_font) { + this.default_font = default_font !== undefined ? default_font : "9px Monaco, Lucida Console, monospace"; + + this.dummy_canvas = this.new_canvas(); + this.dummy_context = this.dummy_canvas.getContext('2d'); + this.dummy_context.font = this.default_font; + + this.char_width_px = this.dummy_context.measureText("A").width; + + this.patterns = {}; + + // FIXME: move somewhere to make this more general + this.load_pattern( 'right_strand', "/visualization/strand_right.png" ); + this.load_pattern( 'left_strand', "/visualization/strand_left.png" ); + this.load_pattern( 'right_strand_inv', "/visualization/strand_right_inv.png" ); + this.load_pattern( 'left_strand_inv', "/visualization/strand_left_inv.png" ); +} + +_.extend( CanvasManager.prototype, { + load_pattern: function( key, path ) { + var patterns = this.patterns, + dummy_context = this.dummy_context, + image = new Image(); + image.src = galaxy_paths.attributes.image_path + path; + image.onload = function() { + patterns[key] = dummy_context.createPattern( image, "repeat" ); + } + }, + get_pattern: function( key ) { + return this.patterns[key]; + }, + new_canvas: function() { + var canvas = $("<canvas/>")[0]; + // If using excanvas in IE, we need to explicately attach the canvas + // methods to the DOM element + if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } + // Keep a reference back to the manager + canvas.manager = this; + return canvas; + } +}); + /** * Generic cache that handles key/value pairs. */ var Cache = Backbone.Model.extend({ defaults: { num_elements: 20, - obj_cache: {}, - key_ary: [] + obj_cache: null, + key_ary: null + }, + + initialize: function(options) { + this.clear(); }, get_elt: function(key) { @@ -114,9 +168,36 @@ dataset: null, filters_manager: null, data_url: null, + dataset_state_url: null, data_mode_compatible: function(entry, mode) { return true; }, can_subset: function(entry) { return false; } }), + + /** + * Returns deferred that resolves to true when dataset is ready (or false if dataset + * cannot be used). + */ + data_is_ready: function() { + var dataset = this.get('dataset'), + ready_deferred = $.Deferred(), + ss_deferred = new ServerStateDeferred({ + ajax_settings: { + url: this.get('dataset_state_url'), + data: { + dataset_id: dataset.id, + hda_ldda: dataset.get('hda_ldda') + }, + dataType: "json" + }, + interval: 5000, + success_fn: function(response) { return response !== "pending"; } + }); + + $.when(ss_deferred.go()).then(function(response) { + ready_deferred.resolve(response === "ok" || response === "data" ); + }); + return ready_deferred; + }, /** * Load data from server; returns AJAX object so that use of Deferred is possible. @@ -366,6 +447,10 @@ end: this.get('end') }); }, + + length: function() { + return this.get('end') - this.get('start'); + }, /** Returns region in canonical form chrom:start-end */ toString: function() { @@ -438,6 +523,10 @@ } }); +var GenomeRegionCollection = Backbone.Collection.extend({ + model: GenomeRegion +}); + /** * A genome browser bookmark. */ diff -r ccfcca670dfa5303d09a178473b663c15e5dc80a -r aaf5c82a55794c97125696aecb27056b5087fdb7 templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -53,7 +53,11 @@ var galaxy_paths = new GalaxyPaths({ root_path: '${h.url_for( "/" )}', image_path: '${h.url_for( "/static/images" )}', - tool_url: '${h.url_for( controller="/api/tools" )}' + tool_url: '${h.url_for( controller="/api/tools" )}', + data_url: '${h.url_for( controller="tracks", action="data" )}', + raw_data_url: '${h.url_for( controller="tracks", action="raw_data" )}', + converted_datasets_state_url: '${h.url_for( controller="tracks", action="converted_datasets_state" )}', + dataset_state_url: '${h.url_for( controller="tracks", action="dataset_state" )}' }); </script></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Updates to tabular dataset display. Ship first data chunk with the page, and use metadata or datatype column_names as a table header row if available.
by Bitbucket 16 Jun '12

16 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ccfcca670dfa/ changeset: ccfcca670dfa user: dannon date: 2012-06-15 23:01:05 summary: Updates to tabular dataset display. Ship first data chunk with the page, and use metadata or datatype column_names as a table header row if available. affected #: 4 files diff -r 0bd0c35351c4eb9c7103b6d737543317abc54ac0 -r ccfcca670dfa5303d09a178473b663c15e5dc80a lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -19,7 +19,7 @@ class Tabular( data.Text ): """Tab delimited data""" - CHUNK_SIZE = 20000 + CHUNK_SIZE = 50000 """Add metadata elements""" MetadataElement( name="comment_lines", default=0, desc="Number of comment lines", readonly=False, optional=True, no_value=0 ) @@ -246,26 +246,40 @@ raise Exception, "Can't create peek rows %s" % str( exc ) return "".join( out ) + def get_chunk(self, trans, dataset, chunk): + ck_index = int(chunk) + f = open(dataset.file_name) + f.seek(ck_index * self.CHUNK_SIZE) + # If we aren't at the start of the file, seek to next newline. Do this better eventually. + if f.tell() != 0: + cursor = f.read(1) + while cursor and cursor != '\n': + cursor = f.read(1) + ck_data = f.read(self.CHUNK_SIZE) + cursor = f.read(1) + while cursor and ck_data[-1] != '\n': + ck_data += cursor + cursor = f.read(1) + return to_json_string({'ck_data': ck_data, 'ck_index': ck_index+1}) + def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None): #TODO Prevent failure when displaying extremely long > 50kb lines. if to_ext: return self._serve_raw(trans, dataset, to_ext) if chunk: - ck_index = int(chunk) - f = open(dataset.file_name) - f.seek(ck_index * self.CHUNK_SIZE) - # If we aren't at the start of the file, seek to next newline. Do this better eventually. - if f.tell() != 0: - cursor = f.read(1) - while cursor and cursor != '\n': - cursor = f.read(1) - ck_data = f.read(self.CHUNK_SIZE) - cursor = f.read(1) - while cursor and ck_data[-1] != '\n': - ck_data += cursor - cursor = f.read(1) - return to_json_string({'ck_data': ck_data, 'ck_index': ck_index+1}) - return trans.fill_template( "/dataset/tabular_chunked.mako",dataset = dataset) + return self.get_chunk(trans, dataset, chunk) + else: + column_names = 'null' + if dataset.metadata.column_names: + column_names = dataset.metadata.column_names + elif hasattr(dataset.datatype, 'column_names'): + column_names = dataset.datatype.column_names + return trans.fill_template( "/dataset/tabular_chunked.mako", + dataset = dataset, + chunk = self.get_chunk(trans, dataset, 0), + column_number = dataset.metadata.columns, + column_names = column_names, + column_types = dataset.metadata.column_types) def set_peek( self, dataset, line_count=None, is_multi_byte=False): super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte) diff -r 0bd0c35351c4eb9c7103b6d737543317abc54ac0 -r ccfcca670dfa5303d09a178473b663c15e5dc80a static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1713,6 +1713,7 @@ top:10px; height:32px; width:32px; + display:none; background:url(largespinner.gif); } diff -r 0bd0c35351c4eb9c7103b6d737543317abc54ac0 -r ccfcca670dfa5303d09a178473b663c15e5dc80a static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -724,7 +724,7 @@ div.toolSectionBody div.toolPanelLabel{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:none outside;} div.toolTitleNoSection{padding-bottom:5px;font-weight:bold;} #tool-search{padding-top:5px;padding-bottom:10px;position:relative;} -#loading_indicator{position:fixed;right:10px;top:10px;height:32px;width:32px;background:url(largespinner.gif);} +#loading_indicator{position:fixed;right:10px;top:10px;height:32px;width:32px;display:none;background:url(largespinner.gif);} #content_table td{text-align:right;white-space:nowrap;padding:2px 10px;} #content_table td.stringalign{text-align:left;} .toolMenuAndView .toolForm{float:left;background-color:white;margin:10px;} diff -r 0bd0c35351c4eb9c7103b6d737543317abc54ac0 -r ccfcca670dfa5303d09a178473b663c15e5dc80a templates/dataset/tabular_chunked.mako --- a/templates/dataset/tabular_chunked.mako +++ b/templates/dataset/tabular_chunked.mako @@ -6,18 +6,19 @@ <%def name="javascripts()"> ${parent.javascripts()} <script type="text/javascript"> + var DATASET_URL = "${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ))}"; + var COLUMN_NUMBER = ${column_number}; + var COLUMN_TYPES = ${column_types}; + var COLUMN_NAMES = ${column_names}; - var DATASET_URL = "${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ))}"; - var DATASET_COLS = ${dataset.metadata.columns}; - var DATASET_TYPES = ${dataset.metadata.column_types}; - + var chunk = ${chunk}; var current_chunk = 0; function renderCell(cell_contents, index, colspan){ if (colspan !== undefined){ return $('<td>').attr('colspan', colspan).addClass('stringalign').text(cell_contents); } - else if (DATASET_TYPES[index] == 'str'){ + else if (COLUMN_TYPES[index] == 'str'){ /* Left align all str columns, right align the rest */ return $('<td>').addClass('stringalign').text(cell_contents);; } @@ -30,19 +31,19 @@ /* Check length of cells to ensure this is a complete row. */ var cells = line.split('\t'); var row = $('<tr>'); - if (cells.length == DATASET_COLS){ + if (cells.length == COLUMN_NUMBER){ $.each(cells, function(index, cell_contents){ row.append(renderCell(cell_contents, index)); }); } - else if(cells.length > DATASET_COLS){ + else if(cells.length > COLUMN_NUMBER){ /* SAM file or like format with optional metadata included */ - $.each(cells.slice(0, DATASET_COLS -1), function(index, cell_contents){ + $.each(cells.slice(0, COLUMN_NUMBER -1), function(index, cell_contents){ row.append(renderCell(cell_contents, index)); }); - row.append(renderCell(cells.slice(DATASET_COLS -1).join('\t'), DATASET_COLS-1)); + row.append(renderCell(cells.slice(COLUMN_NUMBER -1).join('\t'), COLUMN_NUMBER-1)); } - else if(DATASET_COLS > 5 && cells.length == DATASET_COLS - 1 ){ + else if(COLUMN_NUMBER > 5 && cells.length == COLUMN_NUMBER - 1 ){ /* SAM file or like format with optional metadata missing */ $.each(cells, function(index, cell_contents){ row.append(renderCell(cell_contents, index)); @@ -51,41 +52,44 @@ } else{ /* Comment line, just return the one cell*/ - row.append(renderCell(line, 0, DATASET_COLS)); + row.append(renderCell(line, 0, COLUMN_NUMBER)); } return row; } - function fillTable(){ - if (current_chunk !== -1){ - var table = $('#content_table'); - $.getJSON(DATASET_URL, {chunk: current_chunk}, function (result) { - if (result.ck_data !== ""){ - var lines = result.ck_data.split('\n'); - $.each(lines, function(index, line){ - table.append(renderRow(line)); - }); - current_chunk = result.ck_index; - } - else { - current_chunk = -1; - } + function renderChunk(chunk){ + var table = $('#content_table'); + if (chunk.ck_data == ""){ + current_chunk = -1; + } + else if(chunk.ck_index === current_chunk + 1){ + if (current_chunk === 0 && COLUMN_NAMES){ + table.append('<tr><th>' + COLUMN_NAMES.join('</th><th>') + '</th></tr>'); + } + var lines = chunk.ck_data.split('\n'); + $.each(lines, function(index, line){ + table.append(renderRow(line)); }); + current_chunk = chunk.ck_index; } } $(document).ready(function(){ - fillTable(); + renderChunk(chunk); $(window).scroll(function(){ if ($(window).scrollTop() == $(document).height() - $(window).height()){ - fillTable(); + if (current_chunk !== -1){ + $.getJSON(DATASET_URL, + {chunk: current_chunk}, + function(result){renderChunk(result)}); + } } }); - $('#loading_indicator').ajaxStart(function(){ - $(this).show(); - }).ajaxStop(function(){ - $(this).hide(); - }); + $('#loading_indicator').ajaxStart(function(){ + $(this).show(); + }).ajaxStop(function(){ + $(this).hide(); + }); }); </script></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Missing file from previous commit (renaming /cloud to /cloudlaunch)
by Bitbucket 15 Jun '12

15 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0bd0c35351c4/ changeset: 0bd0c35351c4 user: dannon date: 2012-06-15 20:55:18 summary: Missing file from previous commit (renaming /cloud to /cloudlaunch) affected #: 1 file diff -r 38d9e07b58aa99ded2604cdd1aab4ca0f8761aa6 -r 0bd0c35351c4eb9c7103b6d737543317abc54ac0 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -113,9 +113,9 @@ %if app.config.get_bool( 'enable_cloud_launch', False ): <% menu_options = [ - [_('New Cloud Cluster'), h.url_for( controller='/cloud', action='index' ) ], + [_('New Cloud Cluster'), h.url_for( controller='/cloudlaunch', action='index' ) ], ] - tab( "cloud", _("Cloud"), h.url_for( controller='/cloud', action='index'), menu_options=menu_options ) + tab( "cloud", _("Cloud"), h.url_for( controller='/cloudlaunch', action='index'), menu_options=menu_options ) %> %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Rename 'cloud' controller to 'cloudlaunch' to avoid name collisions -- Cloudman interface for cloud instances, and /cloud redirect on main.
by Bitbucket 15 Jun '12

15 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/38d9e07b58aa/ changeset: 38d9e07b58aa user: dannon date: 2012-06-15 20:51:12 summary: Rename 'cloud' controller to 'cloudlaunch' to avoid name collisions -- Cloudman interface for cloud instances, and /cloud redirect on main. affected #: 3 files diff -r 5f3e2ffbae695cd7ae56b2ce4e4c0ed1182e2051 -r 38d9e07b58aa99ded2604cdd1aab4ca0f8761aa6 lib/galaxy/web/controllers/cloud.py --- a/lib/galaxy/web/controllers/cloud.py +++ /dev/null @@ -1,220 +0,0 @@ -""" -Cloud Controller: handles all cloud interactions. - -Adapted from Brad Chapman and Enis Afgan's BioCloudCentral -BioCloudCentral Source: https://github.com/chapmanb/biocloudcentral - -""" - -import datetime -import logging -import time -from galaxy import eggs -import pkg_resources -pkg_resources.require('boto') -import boto -from galaxy import web -from galaxy.web.base.controller import BaseUIController -from boto.ec2.regioninfo import RegionInfo -from boto.exception import EC2ResponseError - -log = logging.getLogger(__name__) - -class CloudController(BaseUIController): - def __init__(self, app): - BaseUIController.__init__(self, app) - - @web.expose - def index(self, trans): - return trans.fill_template("cloud/index.mako") - - @web.expose - def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type): - ec2_error = None - try: - # Create security group & key pair used when starting an instance - ec2_conn = connect_ec2(key_id, secret) - sg_name = create_cm_security_group(ec2_conn) - kp_name, kp_material = create_key_pair(ec2_conn) - except EC2ResponseError, err: - ec2_error = err.error_message - if ec2_error: - return trans.fill_template("cloud/run.mako", error = ec2_error) - else: - user_provided_data={'cluster_name':cluster_name, - 'access_key':key_id, - 'secret_key':secret, - 'instance_type':instance_type} - if password: - user_provided_data['password'] = password - rs = run_instance(ec2_conn=ec2_conn, - user_provided_data=user_provided_data, - key_name=kp_name, - security_groups=[sg_name]) - if rs: - instance = rs.instances[0] - ct = 0 - while not instance.public_dns_name: - # Can take a second to have public dns name registered. - # DBTODO, push this into a page update, this is not ideal. - instance.update() - ct +=1 - time.sleep(1) - return trans.fill_template("cloud/run.mako", - instance = rs.instances[0], - kp_name = kp_name, - kp_material = kp_material) - else: - return trans.fill_template("cloud/run.mako", - error = "Instance failure, but no specific error was detected. Please check your AWS Console.") - -# ## Cloud interaction methods -def connect_ec2(a_key, s_key): - """ Create and return an EC2 connection object. - """ - # Use variables for forward looking flexibility - # AWS connection values - region_name = 'us-east-1' - region_endpoint = 'ec2.amazonaws.com' - is_secure = True - ec2_port = None - ec2_conn_path = '/' - r = RegionInfo(name=region_name, endpoint=region_endpoint) - ec2_conn = boto.connect_ec2(aws_access_key_id=a_key, - aws_secret_access_key=s_key, - api_version='2011-11-01', # needed for availability zone support - is_secure=is_secure, - region=r, - port=ec2_port, - path=ec2_conn_path) - return ec2_conn - -def create_cm_security_group(ec2_conn, sg_name='CloudMan'): - """ Create a security group with all authorizations required to run CloudMan. - If the group already exists, check its rules and add the missing ones. - Return the name of the created security group. - """ - cmsg = None - # Check if this security group already exists - sgs = ec2_conn.get_all_security_groups() - for sg in sgs: - if sg.name == sg_name: - cmsg = sg - log.debug("Security group '%s' already exists; will add authorizations next." % sg_name) - break - # If it does not exist, create security group - if cmsg is None: - log.debug("Creating Security Group %s" % sg_name) - cmsg = ec2_conn.create_security_group(sg_name, 'A security group for CloudMan') - # Add appropriate authorization rules - # If these rules already exist, nothing will be changed in the SG - ports = (('80', '80'), # Web UI - ('20', '21'), # FTP - ('22', '22'), # ssh - ('30000', '30100'), # FTP transfer - ('42284', '42284')) # CloudMan UI - for port in ports: - try: - if not rule_exists(cmsg.rules, from_port=port[0], to_port=port[1]): - cmsg.authorize(ip_protocol='tcp', from_port=port[0], to_port=port[1], cidr_ip='0.0.0.0/0') - else: - log.debug("Rule (%s:%s) already exists in the SG" % (port[0], port[1])) - except EC2ResponseError, e: - log.error("A problem with security group authorizations: %s" % e) - # Add rule that allows communication between instances in the same SG - g_rule_exists = False # Flag to indicate if group rule already exists - for rule in cmsg.rules: - for grant in rule.grants: - if grant.name == cmsg.name: - g_rule_exists = True - log.debug("Group rule already exists in the SG") - if g_rule_exists: - break - if g_rule_exists is False: - try: - cmsg.authorize(src_group=cmsg) - except EC2ResponseError, e: - log.error("A problem w/ security group authorization: %s" % e) - log.info("Done configuring '%s' security group" % cmsg.name) - return cmsg.name - -def rule_exists(rules, from_port, to_port, ip_protocol='tcp', cidr_ip='0.0.0.0/0'): - """ A convenience method to check if an authorization rule in a security - group exists. - """ - for rule in rules: - if rule.ip_protocol == ip_protocol and rule.from_port == from_port and \ - rule.to_port == to_port and cidr_ip in [ip.cidr_ip for ip in rule.grants]: - return True - return False - -def create_key_pair(ec2_conn, key_name='cloudman_key_pair'): - """ Create a key pair with the provided name. - Return the name of the key or None if there was an error creating the key. - """ - kp = None - # Check if a key pair under the given name already exists. If it does not, - # create it, else return. - kps = ec2_conn.get_all_key_pairs() - for akp in kps: - if akp.name == key_name: - log.debug("Key pair '%s' already exists; not creating it again." % key_name) - return akp.name, None - try: - kp = ec2_conn.create_key_pair(key_name) - except EC2ResponseError, e: - log.error("Problem creating key pair '%s': %s" % (key_name, e)) - return None, None - return kp.name, kp.material - -def run_instance(ec2_conn, user_provided_data, image_id='ami-da58aab3', - kernel_id=None, ramdisk_id=None, key_name='cloudman_key_pair', - security_groups=['CloudMan']): - """ Start an instance. If instance start was OK, return the ResultSet object - else return None. - """ - rs = None - instance_type = user_provided_data['instance_type'] - # Remove 'instance_type' key from the dict before creating user data - del user_provided_data['instance_type'] - placement = _find_placement(ec2_conn, instance_type) - ud = "\n".join(['%s: %s' % (key, value) for key, value in user_provided_data.iteritems() if key != 'kp_material']) - try: - rs = ec2_conn.run_instances(image_id=image_id, - instance_type=instance_type, - key_name=key_name, - security_groups=security_groups, - user_data=ud, - kernel_id=kernel_id, - ramdisk_id=ramdisk_id, - placement=placement) - except EC2ResponseError, e: - log.error("Problem starting an instance: %s\n%s" % (e, e.body)) - if rs: - try: - log.info("Started an instance with ID %s" % rs.instances[0].id) - except Exception, e: - log.error("Problem with the started instance object: %s" % e) - else: - log.warning("Problem starting an instance?") - return rs - -def _find_placement(ec2_conn, instance_type): - """Find a region zone that supports our requested instance type. - - We need to check spot prices in the potential availability zones - for support before deciding on a region: - - http://blog.piefox.com/2011/07/ec2-availability-zones-and-instance.html - """ - base = ec2_conn.region.name - yesterday = datetime.datetime.now() - datetime.timedelta(1) - for loc_choice in ["b", "a", "c", "d"]: - cur_loc = "{base}{ext}".format(base=base, ext=loc_choice) - if len(ec2_conn.get_spot_price_history(instance_type=instance_type, - end_time=yesterday.isoformat(), - availability_zone=cur_loc)) > 0: - return cur_loc - log.error("Did not find availabilty zone in {0} for {1}".format(base, instance_type)) - return None - diff -r 5f3e2ffbae695cd7ae56b2ce4e4c0ed1182e2051 -r 38d9e07b58aa99ded2604cdd1aab4ca0f8761aa6 lib/galaxy/web/controllers/cloudlaunch.py --- /dev/null +++ b/lib/galaxy/web/controllers/cloudlaunch.py @@ -0,0 +1,220 @@ +""" +Cloud Controller: handles all cloud interactions. + +Adapted from Brad Chapman and Enis Afgan's BioCloudCentral +BioCloudCentral Source: https://github.com/chapmanb/biocloudcentral + +""" + +import datetime +import logging +import time +from galaxy import eggs +import pkg_resources +pkg_resources.require('boto') +import boto +from galaxy import web +from galaxy.web.base.controller import BaseUIController +from boto.ec2.regioninfo import RegionInfo +from boto.exception import EC2ResponseError + +log = logging.getLogger(__name__) + +class CloudController(BaseUIController): + def __init__(self, app): + BaseUIController.__init__(self, app) + + @web.expose + def index(self, trans): + return trans.fill_template("cloud/index.mako") + + @web.expose + def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type): + ec2_error = None + try: + # Create security group & key pair used when starting an instance + ec2_conn = connect_ec2(key_id, secret) + sg_name = create_cm_security_group(ec2_conn) + kp_name, kp_material = create_key_pair(ec2_conn) + except EC2ResponseError, err: + ec2_error = err.error_message + if ec2_error: + return trans.fill_template("cloud/run.mako", error = ec2_error) + else: + user_provided_data={'cluster_name':cluster_name, + 'access_key':key_id, + 'secret_key':secret, + 'instance_type':instance_type} + if password: + user_provided_data['password'] = password + rs = run_instance(ec2_conn=ec2_conn, + user_provided_data=user_provided_data, + key_name=kp_name, + security_groups=[sg_name]) + if rs: + instance = rs.instances[0] + ct = 0 + while not instance.public_dns_name: + # Can take a second to have public dns name registered. + # DBTODO, push this into a page update, this is not ideal. + instance.update() + ct +=1 + time.sleep(1) + return trans.fill_template("cloud/run.mako", + instance = rs.instances[0], + kp_name = kp_name, + kp_material = kp_material) + else: + return trans.fill_template("cloud/run.mako", + error = "Instance failure, but no specific error was detected. Please check your AWS Console.") + +# ## Cloud interaction methods +def connect_ec2(a_key, s_key): + """ Create and return an EC2 connection object. + """ + # Use variables for forward looking flexibility + # AWS connection values + region_name = 'us-east-1' + region_endpoint = 'ec2.amazonaws.com' + is_secure = True + ec2_port = None + ec2_conn_path = '/' + r = RegionInfo(name=region_name, endpoint=region_endpoint) + ec2_conn = boto.connect_ec2(aws_access_key_id=a_key, + aws_secret_access_key=s_key, + api_version='2011-11-01', # needed for availability zone support + is_secure=is_secure, + region=r, + port=ec2_port, + path=ec2_conn_path) + return ec2_conn + +def create_cm_security_group(ec2_conn, sg_name='CloudMan'): + """ Create a security group with all authorizations required to run CloudMan. + If the group already exists, check its rules and add the missing ones. + Return the name of the created security group. + """ + cmsg = None + # Check if this security group already exists + sgs = ec2_conn.get_all_security_groups() + for sg in sgs: + if sg.name == sg_name: + cmsg = sg + log.debug("Security group '%s' already exists; will add authorizations next." % sg_name) + break + # If it does not exist, create security group + if cmsg is None: + log.debug("Creating Security Group %s" % sg_name) + cmsg = ec2_conn.create_security_group(sg_name, 'A security group for CloudMan') + # Add appropriate authorization rules + # If these rules already exist, nothing will be changed in the SG + ports = (('80', '80'), # Web UI + ('20', '21'), # FTP + ('22', '22'), # ssh + ('30000', '30100'), # FTP transfer + ('42284', '42284')) # CloudMan UI + for port in ports: + try: + if not rule_exists(cmsg.rules, from_port=port[0], to_port=port[1]): + cmsg.authorize(ip_protocol='tcp', from_port=port[0], to_port=port[1], cidr_ip='0.0.0.0/0') + else: + log.debug("Rule (%s:%s) already exists in the SG" % (port[0], port[1])) + except EC2ResponseError, e: + log.error("A problem with security group authorizations: %s" % e) + # Add rule that allows communication between instances in the same SG + g_rule_exists = False # Flag to indicate if group rule already exists + for rule in cmsg.rules: + for grant in rule.grants: + if grant.name == cmsg.name: + g_rule_exists = True + log.debug("Group rule already exists in the SG") + if g_rule_exists: + break + if g_rule_exists is False: + try: + cmsg.authorize(src_group=cmsg) + except EC2ResponseError, e: + log.error("A problem w/ security group authorization: %s" % e) + log.info("Done configuring '%s' security group" % cmsg.name) + return cmsg.name + +def rule_exists(rules, from_port, to_port, ip_protocol='tcp', cidr_ip='0.0.0.0/0'): + """ A convenience method to check if an authorization rule in a security + group exists. + """ + for rule in rules: + if rule.ip_protocol == ip_protocol and rule.from_port == from_port and \ + rule.to_port == to_port and cidr_ip in [ip.cidr_ip for ip in rule.grants]: + return True + return False + +def create_key_pair(ec2_conn, key_name='cloudman_key_pair'): + """ Create a key pair with the provided name. + Return the name of the key or None if there was an error creating the key. + """ + kp = None + # Check if a key pair under the given name already exists. If it does not, + # create it, else return. + kps = ec2_conn.get_all_key_pairs() + for akp in kps: + if akp.name == key_name: + log.debug("Key pair '%s' already exists; not creating it again." % key_name) + return akp.name, None + try: + kp = ec2_conn.create_key_pair(key_name) + except EC2ResponseError, e: + log.error("Problem creating key pair '%s': %s" % (key_name, e)) + return None, None + return kp.name, kp.material + +def run_instance(ec2_conn, user_provided_data, image_id='ami-da58aab3', + kernel_id=None, ramdisk_id=None, key_name='cloudman_key_pair', + security_groups=['CloudMan']): + """ Start an instance. If instance start was OK, return the ResultSet object + else return None. + """ + rs = None + instance_type = user_provided_data['instance_type'] + # Remove 'instance_type' key from the dict before creating user data + del user_provided_data['instance_type'] + placement = _find_placement(ec2_conn, instance_type) + ud = "\n".join(['%s: %s' % (key, value) for key, value in user_provided_data.iteritems() if key != 'kp_material']) + try: + rs = ec2_conn.run_instances(image_id=image_id, + instance_type=instance_type, + key_name=key_name, + security_groups=security_groups, + user_data=ud, + kernel_id=kernel_id, + ramdisk_id=ramdisk_id, + placement=placement) + except EC2ResponseError, e: + log.error("Problem starting an instance: %s\n%s" % (e, e.body)) + if rs: + try: + log.info("Started an instance with ID %s" % rs.instances[0].id) + except Exception, e: + log.error("Problem with the started instance object: %s" % e) + else: + log.warning("Problem starting an instance?") + return rs + +def _find_placement(ec2_conn, instance_type): + """Find a region zone that supports our requested instance type. + + We need to check spot prices in the potential availability zones + for support before deciding on a region: + + http://blog.piefox.com/2011/07/ec2-availability-zones-and-instance.html + """ + base = ec2_conn.region.name + yesterday = datetime.datetime.now() - datetime.timedelta(1) + for loc_choice in ["b", "a", "c", "d"]: + cur_loc = "{base}{ext}".format(base=base, ext=loc_choice) + if len(ec2_conn.get_spot_price_history(instance_type=instance_type, + end_time=yesterday.isoformat(), + availability_zone=cur_loc)) > 0: + return cur_loc + log.error("Did not find availabilty zone in {0} for {1}".format(base, instance_type)) + return None + diff -r 5f3e2ffbae695cd7ae56b2ce4e4c0ed1182e2051 -r 38d9e07b58aa99ded2604cdd1aab4ca0f8761aa6 templates/cloud/index.mako --- a/templates/cloud/index.mako +++ b/templates/cloud/index.mako @@ -56,7 +56,7 @@ <div class="page-container" style="padding: 10px;"><h2>Launch a Galaxy Cloud Instance</h2><div class="toolForm"> - <form action="cloud/launch_instance" method="post"> + <form action="${h.url_for( controller='cloudlaunch', action='launch_instance' )}" method="post"><div class="form-row"><label for="id_cluster_name">Cluster Name</label><input type="text" size="80" name="cluster_name" id="id_cluster_name"/><br/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Allow null password in Cloud Launch form. Include error response in logging.
by Bitbucket 15 Jun '12

15 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5f3e2ffbae69/ changeset: 5f3e2ffbae69 user: dannon date: 2012-06-15 20:41:52 summary: Allow null password in Cloud Launch form. Include error response in logging. affected #: 1 file diff -r 4a1389e037c60d83abdcc38ccb30314c4ef4a530 -r 5f3e2ffbae695cd7ae56b2ce4e4c0ed1182e2051 lib/galaxy/web/controllers/cloud.py --- a/lib/galaxy/web/controllers/cloud.py +++ b/lib/galaxy/web/controllers/cloud.py @@ -41,12 +41,14 @@ if ec2_error: return trans.fill_template("cloud/run.mako", error = ec2_error) else: + user_provided_data={'cluster_name':cluster_name, + 'access_key':key_id, + 'secret_key':secret, + 'instance_type':instance_type} + if password: + user_provided_data['password'] = password rs = run_instance(ec2_conn=ec2_conn, - user_provided_data={'cluster_name':cluster_name, - 'password':password, - 'access_key':key_id, - 'secret_key':secret, - 'instance_type':instance_type}, + user_provided_data=user_provided_data, key_name=kp_name, security_groups=[sg_name]) if rs: @@ -187,7 +189,7 @@ ramdisk_id=ramdisk_id, placement=placement) except EC2ResponseError, e: - log.error("Problem starting an instance: %s" % e) + log.error("Problem starting an instance: %s\n%s" % (e, e.body)) if rs: try: log.info("Started an instance with ID %s" % rs.instances[0].id) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix a typo when creating or updating a tool shed repository db record.
by Bitbucket 15 Jun '12

15 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4a1389e037c6/ changeset: 4a1389e037c6 user: greg date: 2012-06-15 16:21:15 summary: Fix a typo when creating or updating a tool shed repository db record. affected #: 1 file diff -r 622fd4f0a437c897fea83e3e60eba5191f8548f5 -r 4a1389e037c60d83abdcc38ccb30314c4ef4a530 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -340,7 +340,7 @@ name=name, description=description, owner=owner, - installed_changeset_revision=changeset_revision, + installed_changeset_revision=installed_changeset_revision, changeset_revision=current_changeset_revision, ctx_rev=ctx_rev, metadata=metadata_dict, @@ -1492,6 +1492,22 @@ if uninstall: # Write the current in-memory version of the integrated_tool_panel.xml file to disk. trans.app.toolbox.write_integrated_tool_panel_config_file() +def remove_tool_dependency( trans, tool_dependency ): + dependency_install_dir = tool_dependency.installation_directory( trans.app ) + try: + shutil.rmtree( dependency_install_dir ) + removed = True + error_message = '' + log.debug( "Removed tool dependency installation directory: %s" % str( dependency_install_dir ) ) + except Exception, e: + removed = False + error_message = "Error removing tool dependency installation directory %s: %s" % ( str( dependency_install_dir ), str( e ) ) + log.debug( error_message ) + if removed: + tool_dependency.uninstalled = True + trans.sa_session.add( tool_dependency ) + trans.sa_session.flush() + return removed, error_message def reset_tool_data_tables( app ): # Reset the tool_data_tables to an empty dictionary. app.tool_data_tables.data_tables = {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Fix bug in packing track that is a library dataset
by Bitbucket 14 Jun '12

14 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/622fd4f0a437/ changeset: 622fd4f0a437 user: jgoecks date: 2012-06-14 22:57:09 summary: Fix bug in packing track that is a library dataset affected #: 1 file diff -r ea2fbfe6d9db5b9eac1830a7e9de1aea0dcf5806 -r 622fd4f0a437c897fea83e3e60eba5191f8548f5 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -348,7 +348,7 @@ def get_library_dataset( self, trans, id, check_ownership=False, check_accessible=True ): return self.get_object( trans, id, 'LibraryDataset', check_ownership=False, check_accessible=check_accessible ) -class UsesVisualizationMixin( SharableItemSecurityMixin ): +class UsesVisualizationMixin( SharableItemSecurityMixin, UsesLibraryMixinItems ): """ Mixin for controllers that use Visualization objects. """ viz_types = [ "trackster", "circster" ] @@ -468,6 +468,10 @@ def pack_track( track_dict ): dataset_id = track_dict['dataset_id'] hda_ldda = track_dict.get('hda_ldda', 'hda') + if hda_ldda == 'ldda': + # HACK: need to encode library dataset ID because get_hda_or_ldda + # only works for encoded datasets. + dataset_id = trans.security.encode_id( dataset_id ) dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) try: @@ -573,7 +577,7 @@ if hda_ldda == "hda": return self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) else: - return trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + return self.get_library_dataset_dataset_association( trans, dataset_id ) # -- Helper functions -- Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Another fix for the ToolDataTableManager for handling configured directories.
by Bitbucket 14 Jun '12

14 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ea2fbfe6d9db/ changeset: ea2fbfe6d9db user: greg date: 2012-06-14 22:26:13 summary: Another fix for the ToolDataTableManager for handling configured directories. affected #: 1 file diff -r 6498eb3e409adb8ce71241f8e3b94bb23891f30f -r ea2fbfe6d9db5b9eac1830a7e9de1aea0dcf5806 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1151,7 +1151,10 @@ error = False message = '' try: - new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( filename, app.config.tool_data_table_config_path, persist=persist ) + new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( config_filename=filename, + tool_data_path=app.config.tool_data_path, + tool_data_table_config_path=app.config.tool_data_table_config_path, + persist=persist ) except Exception, e: message = str( e ) error = True Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fixes for recent changes to fix ToolDataTableManager to handle defined subdirectory locations in the Galaxy config.
by Bitbucket 14 Jun '12

14 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6498eb3e409a/ changeset: 6498eb3e409a user: greg date: 2012-06-14 21:46:36 summary: Fixes for recent changes to fix ToolDataTableManager to handle defined subdirectory locations in the Galaxy config. affected #: 6 files diff -r 19ed55acf0da8e8ed24f805035defab3009eec4f -r 6498eb3e409adb8ce71241f8e3b94bb23891f30f lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -74,7 +74,7 @@ # Genomes self.genomes = Genomes( self ) # Tool data tables - self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_table_config_path ) + self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path, self.config.tool_data_table_config_path ) # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. tool_configs = self.config.tool_configs if self.config.migrated_tools_config not in tool_configs: diff -r 19ed55acf0da8e8ed24f805035defab3009eec4f -r 6498eb3e409adb8ce71241f8e3b94bb23891f30f lib/galaxy/jobs/deferred/genome_transfer.py --- a/lib/galaxy/jobs/deferred/genome_transfer.py +++ b/lib/galaxy/jobs/deferred/genome_transfer.py @@ -33,7 +33,7 @@ self.app = app self.tool = app.toolbox.tools_by_id['__GENOME_INDEX__'] self.sa_session = app.model.context.current - tdtman = ToolDataTableManager() + tdtman = ToolDataTableManager( app.config.tool_data_path ) xmltree = tdtman.load_from_config_file( app.config.tool_data_table_config_path, app.config.tool_data_path ) for node in xmltree: table = node.get('name') diff -r 19ed55acf0da8e8ed24f805035defab3009eec4f -r 6498eb3e409adb8ce71241f8e3b94bb23891f30f lib/galaxy/jobs/deferred/liftover_transfer.py --- a/lib/galaxy/jobs/deferred/liftover_transfer.py +++ b/lib/galaxy/jobs/deferred/liftover_transfer.py @@ -14,7 +14,6 @@ from galaxy.tools.parameters import visit_input_values from galaxy.tools.parameters.basic import DataToolParameter -from galaxy.tools.data import ToolDataTableManager from galaxy.datatypes.checkers import * diff -r 19ed55acf0da8e8ed24f805035defab3009eec4f -r 6498eb3e409adb8ce71241f8e3b94bb23891f30f lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -13,13 +13,14 @@ class ToolDataTableManager( object ): """Manages a collection of tool data tables""" - def __init__( self, config_filename=None ): + def __init__( self, tool_data_path, config_filename=None ): + self.tool_data_path = tool_data_path self.data_tables = {} # Store config elements for on-the-fly persistence. self.data_table_elems = [] self.data_table_elem_names = [] if config_filename: - self.load_from_config_file( config_filename ) + self.load_from_config_file( config_filename, self.tool_data_path ) def __getitem__( self, key ): return self.data_tables.__getitem__( key ) def __contains__( self, key ): diff -r 19ed55acf0da8e8ed24f805035defab3009eec4f -r 6498eb3e409adb8ce71241f8e3b94bb23891f30f lib/galaxy/tools/genome_index/__init__.py --- a/lib/galaxy/tools/genome_index/__init__.py +++ b/lib/galaxy/tools/genome_index/__init__.py @@ -66,7 +66,7 @@ if gitd: destination = None - tdtman = ToolDataTableManager() + tdtman = ToolDataTableManager( app.config.tool_data_path ) xmltree = tdtman.load_from_config_file( app.config.tool_data_table_config_path, app.config.tool_data_path ) for node in xmltree: table = node.get('name') diff -r 19ed55acf0da8e8ed24f805035defab3009eec4f -r 6498eb3e409adb8ce71241f8e3b94bb23891f30f lib/galaxy/webapps/community/app.py --- a/lib/galaxy/webapps/community/app.py +++ b/lib/galaxy/webapps/community/app.py @@ -37,7 +37,7 @@ # Tag handler self.tag_handler = CommunityTagHandler() # Tool data tables - never pass a config file here because the tool shed should always have an empty dictionary! - self.tool_data_tables = galaxy.tools.data.ToolDataTableManager() + self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path ) # The tool shed has no toolbox, but this attribute is still required. self.toolbox = None # Load security policy Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Refactoring and bug fixes for visualization framework.
by Bitbucket 14 Jun '12

14 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/19ed55acf0da/ changeset: 19ed55acf0da user: jgoecks date: 2012-06-14 21:00:30 summary: Refactoring and bug fixes for visualization framework. affected #: 3 files diff -r b761471d759097f03c0fb904e9543f02ed5096c9 -r 19ed55acf0da8e8ed24f805035defab3009eec4f lib/galaxy/web/api/tools.py --- a/lib/galaxy/web/api/tools.py +++ b/lib/galaxy/web/api/tools.py @@ -1,12 +1,11 @@ -from galaxy import config, tools, web, util -from galaxy.web.base.controller import BaseController, BaseAPIController, UsesHistoryDatasetAssociationMixin, messages, get_highest_priority_msg -from galaxy.util.bunch import Bunch +from galaxy import web, util +from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin, messages, get_highest_priority_msg from galaxy.visualization.tracks.visual_analytics import get_dataset_job from galaxy.visualization.genomes import GenomeRegion from galaxy.util.json import to_json_string, from_json_string from galaxy.visualization.tracks.data_providers import * -class ToolsController( BaseAPIController, UsesHistoryDatasetAssociationMixin ): +class ToolsController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin ): """ RESTful controller for interactions with tools. """ @@ -160,9 +159,12 @@ if not tool: return messages.NO_TOOL tool_params = dict( [ ( p.name, p.value ) for p in original_job.parameters ] ) + + # TODO: rather than set new inputs using dict of json'ed value, unpack parameters and set using set_param_value below. # TODO: need to handle updates to conditional parameters; conditional # params are stored in dicts (and dicts within dicts). - tool_params.update( dict( [ ( key, value ) for key, value in kwargs.items() if key in tool.inputs ] ) ) + new_inputs = payload[ 'inputs' ] + tool_params.update( dict( [ ( key, to_json_string( value ) ) for key, value in new_inputs.items() if key in tool.inputs and new_inputs[ key ] is not None ] ) ) tool_params = tool.params_from_strings( tool_params, self.app ) # @@ -355,5 +357,7 @@ for joda in subset_job.output_datasets: if joda.name == output_name: output_dataset = joda.dataset - - return output_dataset.get_api_value() + + dataset_dict = output_dataset.get_api_value() + dataset_dict[ 'track_config' ] = self.get_new_track_config( trans, output_dataset ); + return dataset_dict diff -r b761471d759097f03c0fb904e9543f02ed5096c9 -r 19ed55acf0da8e8ed24f805035defab3009eec4f lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -542,6 +542,32 @@ return config + def get_new_track_config( self, trans, dataset ): + """ + Returns track configuration dict for a dataset. + """ + # Get data provider. + track_type, _ = dataset.datatype.get_track_type() + track_data_provider_class = get_data_provider( original_dataset=dataset ) + track_data_provider = track_data_provider_class( original_dataset=dataset ) + + if isinstance( dataset, trans.app.model.HistoryDatasetAssociation ): + hda_ldda = "hda" + elif isinstance( dataset, trans.app.model.LibraryDatasetDatasetAssociation ): + hda_ldda = "ldda" + + # Get track definition. + return { + "track_type": track_type, + "name": dataset.name, + "hda_ldda": hda_ldda, + "dataset_id": trans.security.encode_id( dataset.id ), + "prefs": {}, + "filters": { 'filters' : track_data_provider.get_filters() }, + "tool": get_tool_def( trans, dataset ), + "tool_state": {} + } + def get_hda_or_ldda( self, trans, hda_ldda, dataset_id ): """ Returns either HDA or LDDA for hda/ldda and id combination. """ if hda_ldda == "hda": diff -r b761471d759097f03c0fb904e9543f02ed5096c9 -r 19ed55acf0da8e8ed24f805035defab3009eec4f lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -186,22 +186,7 @@ dataset_id = ldda_id dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) - # Get data provider. - track_type, _ = dataset.datatype.get_track_type() - track_data_provider_class = get_data_provider( original_dataset=dataset ) - track_data_provider = track_data_provider_class( original_dataset=dataset ) - - # Get track definition. - return { - "track_type": track_type, - "name": dataset.name, - "hda_ldda": hda_ldda, - "dataset_id": trans.security.encode_id( dataset.id ), - "prefs": {}, - "filters": { 'filters' : track_data_provider.get_filters() }, - "tool": get_tool_def( trans, dataset ), - "tool_state": {} - } + return self.get_new_track_config( trans, dataset ) @web.json def bookmarks_from_dataset( self, trans, hda_id=None, ldda_id=None ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0