October 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: natefoo: Create an HDA delete method for the history contents API.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/750e687b468a/ Changeset: 750e687b468a User: natefoo Date: 2013-10-11 06:21:16 Summary: Create an HDA delete method for the history contents API. Affected #: 1 file diff -r 3e277942307951d816dfc345f619200d186ca954 -r 750e687b468a27978d51dfac9d542a0cc113e64b lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -265,6 +265,75 @@ return changed + @web.expose_api + def delete( self, trans, history_id, id, **kwd ): + """ + delete( self, trans, history_id, id, **kwd ) + * DELETE /api/histories/{history_id}/contents/{id} + delete the HDA with the given ``id`` + .. note:: Currently does not stop any active jobs for which this dataset is an output. + + :type id: str + :param id: the encoded id of the history to delete + :type kwd: dict + :param kwd: (optional) dictionary structure containing: + + * payload: a dictionary itself containing: + * purge: if True, purge the HDA + + :rtype: dict + :returns: an error object if an error occurred or a dictionary containing: + * id: the encoded id of the history, + * deleted: if the history was marked as deleted, + * purged: if the history was purged + """ + # a request body is optional here + purge = False + if kwd.get( 'payload', None ): + purge = string_as_bool( kwd['payload'].get( 'purge', False ) ) + + rval = { 'id' : id } + try: + hda = self.get_dataset( trans, id, + check_ownership=True, check_accessible=True, check_state=True ) + hda.deleted = True + + if purge: + if not trans.app.config.allow_user_dataset_purge: + raise HTTPForbidden( detail='This instance does not allow user dataset purging' ) + + hda.purged = True + trans.sa_session.add( hda ) + trans.sa_session.flush() + + if hda.dataset.user_can_purge: + try: + hda.dataset.full_delete() + trans.sa_session.add( hda.dataset ) + except: + pass + # flush now to preserve deleted state in case of later interruption + trans.sa_session.flush() + + rval[ 'purged' ] = True + + trans.sa_session.flush() + rval[ 'deleted' ] = True + + except HTTPInternalServerError, http_server_err: + log.exception( 'HDA API, delete: uncaught HTTPInternalServerError: %s, %s\n%s', + id, str( kwd ), str( http_server_err ) ) + raise + except HTTPException, http_exc: + raise + except Exception, exc: + log.exception( 'HDA API, delete: uncaught exception: %s, %s\n%s', + id, str( kwd ), str( exc ) ) + trans.response.status = 500 + rval.update({ 'error': str( exc ) }) + + return rval + def _validate_and_parse_update_payload( self, payload ): """ Validate and parse incomming data payload for an HDA. 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.

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commit/galaxy-central: guerler: Add pause option to new upload front end
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3e2779423079/ Changeset: 3e2779423079 User: guerler Date: 2013-10-11 00:23:20 Summary: Add pause option to new upload front end Affected #: 2 files diff -r 657b263294836bbc1847ff66de72ddc7eb94ba11 -r 3e277942307951d816dfc345f619200d186ca954 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -24,9 +24,11 @@ // states state : { - init : 'fa-icon-trash', + init : 'fa-icon-trash', + queued : 'fa-icon-spinner fa-icon-spin', + running : '__running__', success : 'fa-icon-ok', - error : 'fa-icon-warning-sign' + error : 'fa-icon-warning-sign' }, // counter @@ -133,6 +135,10 @@ // get element var it = this.get_upload_item(index); + // update status + var sy = it.find('#symbol'); + sy.addClass(this.state.running); + // get configuration var current_history = Galaxy.currHistoryPanel.model.get('id'); var file_type = it.find('#extension').val(); @@ -208,10 +214,8 @@ // update icon var sy = it.find('#symbol'); - sy.removeClass('fa-icon-spin'); - sy.removeClass('fa-icon-spinner'); - - // set status + sy.removeClass(this.state.running); + sy.removeClass(this.state.queued); sy.addClass(this.state.success); }, @@ -245,10 +249,8 @@ // update icon var sy = it.find('#symbol'); - sy.removeClass('fa-icon-spin'); - sy.removeClass('fa-icon-spinner'); - - // set status + sy.removeClass(this.state.running); + sy.removeClass(this.state.queued); sy.addClass(this.state.error); }, @@ -267,14 +269,14 @@ var symbol = $(this).find('#symbol'); if(symbol.hasClass(self.state.init)) { + // set status symbol.removeClass(self.state.init); - symbol.addClass('fa-icon-spinner'); - symbol.addClass('fa-icon-spin'); + symbol.addClass(self.state.queued); + + // disable options + $(this).find('#extension').attr('disabled', true); + $(this).find('#space_to_tabs').attr('disabled', true); } - - // disable options - $(this).find('#extension').attr('disabled', true); - $(this).find('#space_to_tabs').attr('disabled', true); }); // update running @@ -285,6 +287,35 @@ this.uploadbox.upload(); }, + // pause upload process + event_pause : function() + { + // check + if (this.counter.running == 0) + return; + + // initiate upload procedure in plugin + this.uploadbox.pause(); + + // switch icons for new uploads + var items = $(this.el).find('.upload-item'); + var self = this; + items.each(function() + { + var symbol = $(this).find('#symbol'); + if(symbol.hasClass(self.state.queued) && !symbol.hasClass(self.state.running)) + { + // update status + symbol.removeClass(self.state.queued); + symbol.addClass(self.state.init); + + // disable options + $(this).find('#extension').attr('disabled', false); + $(this).find('#space_to_tabs').attr('disabled', false); + } + }); + }, + // queue is done event_complete: function() { @@ -361,6 +392,7 @@ buttons : { 'Select' : function() {self.uploadbox.select()}, 'Upload' : function() {self.event_upload()}, + 'Pause' : function() {self.event_pause()}, 'Reset' : function() {self.event_reset()}, 'Close' : function() {self.modal.hide()} }, @@ -452,6 +484,12 @@ this.modal.enableButton('Upload'); else this.modal.disableButton('Upload'); + + // pause upload button + if (this.counter.running > 0) + this.modal.enableButton('Pause'); + else + this.modal.disableButton('Pause'); // select upload button if (this.counter.running == 0) diff -r 657b263294836bbc1847ff66de72ddc7eb94ba11 -r 3e277942307951d816dfc345f619200d186ca954 static/scripts/utils/galaxy.uploadbox.js --- a/static/scripts/utils/galaxy.uploadbox.js +++ b/static/scripts/utils/galaxy.uploadbox.js @@ -154,7 +154,7 @@ function process() { // validate - if (queue_length == 0) + if (queue_length == 0 || !queue_status) { queue_status = false; opts.complete(); @@ -229,11 +229,6 @@ // prepare request var xhr = new XMLHttpRequest(); - - // prepare upload progress - xhr.upload.index = index; - xhr.upload.file = file; - xhr.upload.addEventListener('progress', progress, false); // onloadend xhr.onloadend = function() @@ -265,6 +260,11 @@ success(index, file, response); } + // prepare upload progress + xhr.upload.index = index; + xhr.upload.file = file; + xhr.upload.addEventListener('progress', progress, false); + // open request xhr.open('POST', opts.url, true); xhr.setRequestHeader('Accept', 'application/json'); @@ -314,7 +314,17 @@ function upload() { if (!queue_status) + { + queue_status = true; process(); + } + } + + // pause upload process + function pause() + { + // set global status variable to false + queue_status = false; } // set options @@ -338,6 +348,7 @@ 'select' : select, 'remove' : remove, 'upload' : upload, + 'pause' : pause, 'reset' : reset, 'configure' : configure, 'compatible' : compatible 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.

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commit/galaxy-central: jgoecks: Trackster: cleanup for reference track display.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/657b26329483/ Changeset: 657b26329483 User: jgoecks Date: 2013-10-11 00:09:15 Summary: Trackster: cleanup for reference track display. Affected #: 3 files diff -r 4839d50a03a8eb9d302c49eb5151f11c987b6001 -r 657b263294836bbc1847ff66de72ddc7eb94ba11 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3727,13 +3727,9 @@ TiledTrack.call(this, view, { content_div: view.top_labeltrack }, { resize: false }); view.reference_track = this; - this.left_offset = 200; this.visible_height_px = 12; this.container_div.addClass("reference-track"); - this.content_div.css("background", "none"); - this.content_div.css("min-height", "0px"); - this.content_div.css("border", "none"); - this.data_url = galaxy_config.root + "api/genomes/" + "/" + this.view.dbkey; + this.data_url = galaxy_config.root + "api/genomes/" + this.view.dbkey; this.data_url_extra_params = {reference: true}; this.data_manager = new visualization.GenomeReferenceDataManager({ data_url: this.data_url, @@ -3780,6 +3776,7 @@ // Try to subset data. var subset = this.data_manager.subset_entry(data, region), seq_data = subset.data; + console.log(region.toString()); // Draw sequence data. var canvas = ctx.canvas; @@ -4151,6 +4148,7 @@ * @param ref_seq reference sequence data */ draw_tile: function(result, ctx, mode, region, w_scale, ref_seq) { + console.log("FeatureTrack", region.toString()); var track = this, canvas = ctx.canvas, tile_low = region.get('start'), diff -r 4839d50a03a8eb9d302c49eb5151f11c987b6001 -r 657b263294836bbc1847ff66de72ddc7eb94ba11 static/style/blue/trackster.css --- a/static/style/blue/trackster.css +++ b/static/style/blue/trackster.css @@ -27,7 +27,7 @@ .track{background:white} .track-header{text-align:left;padding:4px 0px;color:#666} .track-header .menubutton{margin-left:0px} -.tiles{text-align:center;background:#eee url('../images/tracks/diag_bg.gif');min-height:16px;position:relative;overflow:hidden} +.tiles{text-align:center;background:#eee url('../images/tracks/diag_bg.gif');position:relative;overflow:hidden} .overlay{position:absolute;left:0;top:0} .track-name{float:left;margin-top:2px;height:16px} .label-track .track-content{background:white} diff -r 4839d50a03a8eb9d302c49eb5151f11c987b6001 -r 657b263294836bbc1847ff66de72ddc7eb94ba11 static/style/src/less/trackster.less --- a/static/style/src/less/trackster.less +++ b/static/style/src/less/trackster.less @@ -200,7 +200,6 @@ .tiles { text-align: center; background: #eee url('../images/tracks/diag_bg.gif'); - min-height: 16px; position: relative; overflow: hidden; } 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.

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commit/galaxy-central: martenson: masthead Help menu tweaks
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4839d50a03a8/ Changeset: 4839d50a03a8 User: martenson Date: 2013-10-10 23:09:56 Summary: masthead Help menu tweaks Affected #: 4 files diff -r 13d3054d2f52782fb0a083af9e6e74cbc111e256 -r 4839d50a03a8eb9d302c49eb5151f11c987b6001 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -177,11 +177,12 @@ menu_options = [ [_('Galaxy Q&A Site'), h.url_for( controller='biostar', action='biostar_redirect', biostar_action='show/tag/galaxy' ), "_blank" ], [_('Ask a question'), h.url_for( controller='biostar', action='biostar_question_redirect' ), "_blank" ] ] menu_options.extend( [ - [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], - [_('Tool shed wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/Tool%20Shed" ), "_blank" ], - [_('Galaxy wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], - [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], - [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] + [_('Support'), app.config.get( "support_url", "http://wiki.galaxyproject.org/Support" ), "_blank" ], + [_('Search'), app.config.get( "search_url", "http://galaxyproject.org/search/usegalaxy/" ), "_blank" ], + [_('Mailing Lists'), app.config.get( "mailing_lists", "http://wiki.galaxyproject.org/MailingLists" ), "_blank" ], + [_('Videos'), app.config.get( "videos_url", "http://vimeo.com/galaxyproject" ), "_blank" ], + [_('Wiki'), app.config.get( "wiki_url", "http://galaxyproject.org/" ), "_blank" ], + [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.galaxyproject.org/CitingGalaxy" ), "_blank" ] ] ) if app.config.get( 'terms_url', None ) is not None: menu_options.append( [_('Terms and Conditions'), app.config.get( 'terms_url', None ), '_blank'] ) diff -r 13d3054d2f52782fb0a083af9e6e74cbc111e256 -r 4839d50a03a8eb9d302c49eb5151f11c987b6001 templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -163,11 +163,12 @@ menu_options = [ [_('Galaxy Q&A Site'), h.url_for( controller='biostar', action='biostar_redirect', biostar_action='show/tag/galaxy' ), "_blank" ], [_('Ask a question'), h.url_for( controller='biostar', action='biostar_question_redirect' ), "_blank" ] ] menu_options.extend( [ - [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], - [_('Tool shed wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/Tool%20Shed" ), "_blank" ], - [_('Galaxy wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], - [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], - [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] + [_('Support'), app.config.get( "support_url", "http://wiki.galaxyproject.org/Support" ), "_blank" ], + [_('Search'), app.config.get( "search_url", "http://galaxyproject.org/search/usegalaxy/" ), "_blank" ], + [_('Mailing Lists'), app.config.get( "mailing_lists", "http://wiki.galaxyproject.org/MailingLists" ), "_blank" ], + [_('Videos'), app.config.get( "screencasts_url", "http://vimeo.com/galaxyproject" ), "_blank" ], + [_('Wiki'), app.config.get( "wiki_url", "http://galaxyproject.org/" ), "_blank" ], + [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.galaxyproject.org/CitingGalaxy" ), "_blank" ] ] ) if app.config.get( 'terms_url', None ) is not None: menu_options.append( [_('Terms and Conditions'), app.config.get( 'terms_url', None ), '_blank'] ) diff -r 13d3054d2f52782fb0a083af9e6e74cbc111e256 -r 4839d50a03a8eb9d302c49eb5151f11c987b6001 templates/webapps/tool_shed/base_panels.mako --- a/templates/webapps/tool_shed/base_panels.mako +++ b/templates/webapps/tool_shed/base_panels.mako @@ -79,11 +79,13 @@ if qa_url: menu_options = [ [_('Galaxy Q&A'), qa_url, "_blank" ] ] menu_options.extend( [ - [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], - [_('Tool shed wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/Tool%20Shed" ), "_blank" ], - [_('Galaxy wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], - [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], - [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] + [_('Tool Shed Wiki'), app.config.get( "wiki_url", "http://wiki.galaxyproject.org/Tool%20Shed" ), "_blank" ], + [_('Support'), app.config.get( "support_url", "http://wiki.galaxyproject.org/Support" ), "_blank" ], + [_('Search'), app.config.get( "search_url", "http://galaxyproject.org/search/usegalaxy/" ), "_blank" ], + [_('Mailing Lists'), app.config.get( "mailing_lists_url", "http://wiki.galaxyproject.org/MailingLists" ), "_blank" ], + [_('Videos'), app.config.get( "screencasts_url", "http://vimeo.com/galaxyproject" ), "_blank" ], + [_('Wiki'), app.config.get( "wiki_url", "http://galaxyproject.org/" ), "_blank" ], + [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.galaxyproject.org/CitingGalaxy" ), "_blank" ] ] ) tab( "help", _("Help"), None, menu_options=menu_options ) %> diff -r 13d3054d2f52782fb0a083af9e6e74cbc111e256 -r 4839d50a03a8eb9d302c49eb5151f11c987b6001 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -367,14 +367,23 @@ # The URL linked by the "Galaxy/brand" text. #logo_url = / -# The URL linked by the "Galaxy Wiki" link in the "Help" menu. +# The URL linked by the "Wiki" link in the "Help" menu. #wiki_url = http://wiki.galaxyproject.org/ # The URL linked by the "Support" link in the "Help" menu. -#support_url = http://wiki.g2.bx.psu.edu/Support +#support_url = http://wiki.galaxyproject.org/Support -# The URL linked by the "How to Cite..." link in the "Help" menu. -#citation_url = http://wiki.g2.bx.psu.edu/Citing%20Galaxy +# The URL linked by the "How to Cite Galaxy" link in the "Help" menu. +#citation_url = http://wiki.galaxyproject.org/CitingGalaxy + +#The URL linked by the "Search" link in the "Help" menu. +#search_url = http://galaxyproject.org/search/usegalaxy/ + +#The URL linked by the "Mailing Lists" link in the "Help" menu. +#mailing_lists_url = http://wiki.galaxyproject.org/MailingLists + +#The URL linked by the "Videos" link in the "Help" menu. +#videos_url = http://vimeo.com/galaxyproject # The URL linked by the "Terms and Conditions" link in the "Help" menu, as well # as on the user registration and login forms and in the activation emails. 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.

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commit/galaxy-central: guerler: Improve upload front end
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/13d3054d2f52/ Changeset: 13d3054d2f52 User: guerler Date: 2013-10-10 22:55:22 Summary: Improve upload front end Affected #: 3 files diff -r 085454c899afaaf05a9c17d3818ed2b3029e7210 -r 13d3054d2f52782fb0a083af9e6e74cbc111e256 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -38,12 +38,8 @@ this.$body.css('max-height', maxHeight); // fix height if available - if (this.options.height) { - if (this.options.height < maxHeight) - this.$body.css('height', this.options.height); - else - this.$body.css('height', maxHeight); - } + if (this.options.height) + this.$body.css('height', Math.min(this.options.height, maxHeight)); // remove scroll bar if (this.options.height) diff -r 085454c899afaaf05a9c17d3818ed2b3029e7210 -r 13d3054d2f52782fb0a083af9e6e74cbc111e256 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -133,16 +133,14 @@ // get element var it = this.get_upload_item(index); - // get current history + // get configuration var current_history = Galaxy.currHistoryPanel.model.get('id'); - - // configure tool - this.uploadbox.configure({url : galaxy_config.root + "api/tools/", paramname : "files_0|file_data"}); - - // get var file_type = it.find('#extension').val(); var space_to_tabs = it.find('#space_to_tabs').is(':checked'); + // configure uploadbox + this.uploadbox.configure({url : galaxy_config.root + "api/tools/", paramname : "files_0|file_data"}); + // configure tool tool_input = {}; tool_input['dbkey'] = '?'; @@ -174,7 +172,10 @@ it.find('.progress-bar').css({ width : percentage + '%' }); // update value - it.find('#percentage').html(percentage + '%'); + if (percentage != 100) + it.find('#percentage').html(percentage + '%'); + else + it.find('#percentage').html('Adding to history...'); }, // success @@ -202,6 +203,9 @@ // update progress frame it.addClass('success'); + // update text + it.find('#percentage').html('100%'); + // update icon var sy = it.find('#symbol'); sy.removeClass('fa-icon-spin'); @@ -267,6 +271,10 @@ symbol.addClass('fa-icon-spinner'); symbol.addClass('fa-icon-spin'); } + + // disable options + $(this).find('#extension').attr('disabled', true); + $(this).find('#space_to_tabs').attr('disabled', true); }); // update running diff -r 085454c899afaaf05a9c17d3818ed2b3029e7210 -r 13d3054d2f52782fb0a083af9e6e74cbc111e256 static/scripts/utils/galaxy.uploadbox.js --- a/static/scripts/utils/galaxy.uploadbox.js +++ b/static/scripts/utils/galaxy.uploadbox.js @@ -12,6 +12,7 @@ url : '', paramname : 'content', maxfilesize : 250, + maxfilenumber : 20, dragover : function() {}, dragleave : function() {}, announce : function() {}, @@ -21,7 +22,8 @@ error : function(index, file, message) { alert(message); }, complete : function() {}, error_filesize : "File exceeds 250MB. Please use an FTP client.", - error_default : "Please make sure the file is available." + error_default : "Please make sure the file is available.", + error_toomany : "You can only queue <20 files per upload session." } // options @@ -115,20 +117,23 @@ if (queue_status) return; - // add new files to queue for (var i = 0; i < files.length; i++) { + // check + if(queue_length >= opts.maxfilenumber) + break; + // new identifier var index = String(queue_index++); // add to queue queue[index] = files[i]; + // announce + opts.announce(index, queue[index], ""); + // increase counter queue_length++; - - // announce - opts.announce(index, queue[index], ""); } } @@ -230,13 +235,6 @@ xhr.upload.file = file; xhr.upload.addEventListener('progress', progress, false); - // open request - xhr.open('POST', opts.url, true); - xhr.setRequestHeader('Accept', 'application/json'); - xhr.setRequestHeader('Cache-Control', 'no-cache'); - xhr.setRequestHeader('X-Requested-With', 'XMLHttpRequest'); - xhr.send(formData); - // onloadend xhr.onloadend = function() { @@ -266,6 +264,13 @@ // parse response success(index, file, response); } + + // open request + xhr.open('POST', opts.url, true); + xhr.setRequestHeader('Accept', 'application/json'); + xhr.setRequestHeader('Cache-Control', 'no-cache'); + xhr.setRequestHeader('X-Requested-With', 'XMLHttpRequest'); + xhr.send(formData); } // success 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.

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commit/galaxy-central: dan: One more occurance of fastq_to_fasta that was dropped.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/085454c899af/ Changeset: 085454c899af User: dan Date: 2013-10-10 22:25:43 Summary: One more occurance of fastq_to_fasta that was dropped. Affected #: 1 file diff -r 6621aa022ebad1eee0e808a16137af73aecafd61 -r 085454c899afaaf05a9c17d3818ed2b3029e7210 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -95,6 +95,7 @@ <tool file="maf/maf_to_interval.xml" /><tool file="maf/maf_to_fasta.xml" /><tool file="fasta_tools/tabular_to_fasta.xml" /> + <tool file="fastq/fastq_to_fasta.xml" /><tool file="filters/wiggle_to_simple.xml" /><tool file="filters/sff_extractor.xml" /><tool file="filters/gtf2bedgraph.xml" /> 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.

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commit/galaxy-central: Dave Bouvier: Restore the fastq_to_fasta that was not migrated.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6621aa022eba/ Changeset: 6621aa022eba User: Dave Bouvier Date: 2013-10-10 22:16:19 Summary: Restore the fastq_to_fasta that was not migrated. Affected #: 1 file diff -r e66766f18a58e200391f28157d0993b35014b84d -r 6621aa022ebad1eee0e808a16137af73aecafd61 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -258,6 +258,7 @@ <tool file="fastq/fastq_paired_end_interlacer.xml" /><tool file="fastq/fastq_paired_end_deinterlacer.xml" /><tool file="fastq/fastq_manipulation.xml" /> + <tool file="fastq/fastq_to_fasta.xml" /><tool file="fastq/fastq_to_tabular.xml" /><tool file="fastq/tabular_to_fastq.xml" /> 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.

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commit/galaxy-central: Dave Bouvier: Remove migrated tools that were somehow restored to tool_conf.xml.sample
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e66766f18a58/ Changeset: e66766f18a58 User: Dave Bouvier Date: 2013-10-10 22:12:52 Summary: Remove migrated tools that were somehow restored to tool_conf.xml.sample Affected #: 1 file diff -r ff76fd33b81cdde1fb270de688ec5e86488ba34d -r e66766f18a58e200391f28157d0993b35014b84d tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -1,12 +1,12 @@ -<?xml version="1.0"?> +<?xml version='1.0' encoding='utf-8'?><toolbox> - <section name="Get Data" id="getext"> - <tool file="data_source/upload.xml"/> + <section id="getext" name="Get Data"> + <tool file="data_source/upload.xml" /><tool file="data_source/ucsc_tablebrowser.xml" /><tool file="data_source/ucsc_tablebrowser_test.xml" /><tool file="data_source/ucsc_tablebrowser_archaea.xml" /><tool file="data_source/bx_browser.xml" /> - <tool file="data_source/ebi_sra.xml"/> + <tool file="data_source/ebi_sra.xml" /><tool file="data_source/microbial_import.xml" /><tool file="data_source/biomart.xml" /><tool file="data_source/biomart_test.xml" /> @@ -32,19 +32,19 @@ <tool file="genomespace/genomespace_importer.xml" /><tool file="validation/fix_errors.xml" /></section> - <section name="Send Data" id="send"> + <section id="send" name="Send Data"><tool file="data_destination/epigraph.xml" /><tool file="data_destination/epigraph_test.xml" /><tool file="genomespace/genomespace_exporter.xml" /></section> - <section name="ENCODE Tools" id="EncodeTools"> + <section id="EncodeTools" name="ENCODE Tools"><tool file="encode/gencode_partition.xml" /><tool file="encode/random_intervals.xml" /></section> - <section name="Lift-Over" id="liftOver"> + <section id="liftOver" name="Lift-Over"><tool file="extract/liftOver_wrapper.xml" /></section> - <section name="Text Manipulation" id="textutil"> + <section id="textutil" name="Text Manipulation"><tool file="filters/fixedValueColumn.xml" /><tool file="stats/column_maker.xml" /><tool file="filters/catWrapper.xml" /> @@ -65,25 +65,25 @@ <tool file="stats/dna_filtering.xml" /><tool file="new_operations/tables_arithmetic_operations.xml" /></section> - <section name="Filter and Sort" id="filter"> + <section id="filter" name="Filter and Sort"><tool file="stats/filtering.xml" /><tool file="filters/sorter.xml" /><tool file="filters/grep.xml" /> - <label text="GFF" id="gff" /> + <label id="gff" text="GFF" /><tool file="filters/gff/extract_GFF_Features.xml" /><tool file="filters/gff/gff_filter_by_attribute.xml" /><tool file="filters/gff/gff_filter_by_feature_count.xml" /><tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" /></section> - <section name="Join, Subtract and Group" id="group"> + <section id="group" name="Join, Subtract and Group"><tool file="filters/joiner.xml" /> - <tool file="filters/compare.xml"/> - <tool file="new_operations/subtract_query.xml"/> + <tool file="filters/compare.xml" /> + <tool file="new_operations/subtract_query.xml" /><tool file="stats/grouping.xml" /><tool file="new_operations/column_join.xml" /></section> - <section name="Convert Formats" id="convert"> + <section id="convert" name="Convert Formats"><tool file="filters/axt_to_concat_fasta.xml" /><tool file="filters/axt_to_fasta.xml" /><tool file="filters/axt_to_lav.xml" /> @@ -95,39 +95,38 @@ <tool file="maf/maf_to_interval.xml" /><tool file="maf/maf_to_fasta.xml" /><tool file="fasta_tools/tabular_to_fasta.xml" /> - <tool file="fastq/fastq_to_fasta.xml" /><tool file="filters/wiggle_to_simple.xml" /><tool file="filters/sff_extractor.xml" /><tool file="filters/gtf2bedgraph.xml" /><tool file="filters/wig_to_bigwig.xml" /><tool file="filters/bed_to_bigbed.xml" /></section> - <section name="Extract Features" id="features"> + <section id="features" name="Extract Features"><tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /></section> - <section name="Fetch Sequences" id="fetchSeq"> + <section id="fetchSeq" name="Fetch Sequences"><tool file="extract/extract_genomic_dna.xml" /></section> - <section name="Fetch Alignments" id="fetchAlign"> + <section id="fetchAlign" name="Fetch Alignments"><tool file="maf/interval2maf_pairwise.xml" /><tool file="maf/interval2maf.xml" /> - <tool file="maf/maf_split_by_species.xml"/> + <tool file="maf/maf_split_by_species.xml" /><tool file="maf/interval_maf_to_merged_fasta.xml" /> - <tool file="maf/genebed_maf_to_fasta.xml"/> - <tool file="maf/maf_stats.xml"/> - <tool file="maf/maf_thread_for_species.xml"/> - <tool file="maf/maf_limit_to_species.xml"/> - <tool file="maf/maf_limit_size.xml"/> - <tool file="maf/maf_by_block_number.xml"/> - <tool file="maf/maf_reverse_complement.xml"/> - <tool file="maf/maf_filter.xml"/> + <tool file="maf/genebed_maf_to_fasta.xml" /> + <tool file="maf/maf_stats.xml" /> + <tool file="maf/maf_thread_for_species.xml" /> + <tool file="maf/maf_limit_to_species.xml" /> + <tool file="maf/maf_limit_size.xml" /> + <tool file="maf/maf_by_block_number.xml" /> + <tool file="maf/maf_reverse_complement.xml" /> + <tool file="maf/maf_filter.xml" /></section> - <section name="Get Genomic Scores" id="scores"> + <section id="scores" name="Get Genomic Scores"><tool file="stats/wiggle_to_simple.xml" /><tool file="stats/aggregate_binned_scores_in_intervals.xml" /><tool file="extract/phastOdds/phastOdds_tool.xml" /></section> - <section name="Operate on Genomic Intervals" id="bxops"> + <section id="bxops" name="Operate on Genomic Intervals"><tool file="new_operations/intersect.xml" /><tool file="new_operations/subtract.xml" /><tool file="new_operations/merge.xml" /> @@ -141,21 +140,19 @@ <tool file="new_operations/flanking_features.xml" /><tool file="annotation_profiler/annotation_profiler.xml" /></section> - <section name="Statistics" id="stats"> + <section id="stats" name="Statistics"><tool file="stats/gsummary.xml" /><tool file="filters/uniq.xml" /><tool file="stats/cor.xml" /><tool file="stats/generate_matrix_for_pca_lda.xml" /><tool file="stats/lda_analy.xml" /><tool file="stats/plot_from_lda.xml" /> - <tool file="regVariation/t_test_two_samples.xml" /> - <tool file="regVariation/compute_q_values.xml" /><tool file="stats/MINE.xml" /> - <label text="GFF" id="gff" /> + <label id="gff" text="GFF" /><tool file="stats/count_gff_features.xml" /></section> - <section name="Wavelet Analysis" id="dwt"> + <section id="dwt" name="Wavelet Analysis"><tool file="discreteWavelet/execute_dwt_var_perFeature.xml" /></section> - <section name="Graph/Display Data" id="plots"> + <section id="plots" name="Graph/Display Data"><tool file="plotting/histogram2.xml" /><tool file="plotting/scatterplot.xml" /><tool file="plotting/bar_chart.xml" /> - <tool file="plotting/xy_plot.xml" /><tool file="plotting/boxplot.xml" /><tool file="visualization/GMAJ.xml" /><tool file="visualization/LAJ.xml" /> @@ -177,57 +173,48 @@ <tool file="maf/vcf_to_maf_customtrack.xml" /><tool file="mutation/visualize.xml" /></section> - <section name="Regional Variation" id="regVar"> + <section id="regVar" name="Regional Variation"><tool file="regVariation/windowSplitter.xml" /><tool file="regVariation/featureCounter.xml" /><tool file="regVariation/WeightedAverage.xml" /><tool file="regVariation/quality_filter.xml" /><tool file="regVariation/maf_cpg_filter.xml" /><tool file="regVariation/getIndels_2way.xml" /> - <tool file="regVariation/getIndels_3way.xml" /><tool file="regVariation/getIndelRates_3way.xml" /><tool file="regVariation/substitutions.xml" /><tool file="regVariation/substitution_rates.xml" /><tool file="regVariation/microsats_alignment_level.xml" /><tool file="regVariation/microsats_mutability.xml" /> - <tool file="regVariation/delete_overlapping_indels.xml" /> - <tool file="regVariation/compute_motifs_frequency.xml" /> - <tool file="regVariation/compute_motif_frequencies_for_all_motifs.xml" /> - <tool file="regVariation/categorize_elements_satisfying_criteria.xml" />s - <tool file="regVariation/draw_stacked_barplots.xml" /> - <tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" /> - <tool file="regVariation/microsatellite_birthdeath.xml" /></section> - <section name="Multiple regression" id="multReg"> + <section id="multReg" name="Multiple regression"><tool file="regVariation/linear_regression.xml" /><tool file="regVariation/logistic_regression_vif.xml" /><tool file="regVariation/best_regression_subsets.xml" /><tool file="regVariation/rcve.xml" /><tool file="regVariation/partialR_square.xml" /></section> - <section name="Multivariate Analysis" id="multVar"> + <section id="multVar" name="Multivariate Analysis"><tool file="multivariate_stats/pca.xml" /><tool file="multivariate_stats/cca.xml" /><tool file="multivariate_stats/kpca.xml" /><tool file="multivariate_stats/kcca.xml" /></section> - <section name="Evolution" id="hyphy"> + <section id="hyphy" name="Evolution"><tool file="hyphy/hyphy_branch_lengths_wrapper.xml" /><tool file="hyphy/hyphy_nj_tree_wrapper.xml" /><tool file="hyphy/hyphy_dnds_wrapper.xml" /> - <tool file="evolution/mutate_snp_codon.xml" /><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" /></section> - <section name="Motif Tools" id="motifs"> - <tool file="meme/meme.xml"/> - <tool file="meme/fimo.xml"/> + <section id="motifs" name="Motif Tools"> + <tool file="meme/meme.xml" /> + <tool file="meme/fimo.xml" /><tool file="rgenetics/rgWebLogo3.xml" /></section> - <section name="Multiple Alignments" id="clustal"> + <section id="clustal" name="Multiple Alignments"><tool file="rgenetics/rgClustalw.xml" /></section> - <section name="Metagenomic analyses" id="tax_manipulation"> + <section id="tax_manipulation" name="Metagenomic analyses"><tool file="taxonomy/gi2taxonomy.xml" /><tool file="taxonomy/t2t_report.xml" /><tool file="taxonomy/t2ps_wrapper.xml" /> @@ -235,38 +222,35 @@ <tool file="taxonomy/lca.xml" /><tool file="taxonomy/poisson2test.xml" /></section> - <section name="FASTA manipulation" id="fasta_manipulation"> + <section id="fasta_manipulation" name="FASTA manipulation"><tool file="fasta_tools/fasta_compute_length.xml" /><tool file="fasta_tools/fasta_filter_by_length.xml" /><tool file="fasta_tools/fasta_concatenate_by_species.xml" /><tool file="fasta_tools/fasta_to_tabular.xml" /><tool file="fasta_tools/tabular_to_fasta.xml" /> - <tool file="fastx_toolkit/fasta_formatter.xml" /> - <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" /> - <tool file="fastx_toolkit/fastx_collapser.xml" /></section> - <section name="NGS: QC and manipulation" id="NGS_QC"> + <section id="NGS_QC" name="NGS: QC and manipulation"> - <label text="FastQC: fastq/sam/bam" id="fastqcsambam" /> + <label id="fastqcsambam" text="FastQC: fastq/sam/bam" /><tool file="rgenetics/rgFastQC.xml" /> - <label text="Illumina fastq" id="illumina" /> + <label id="illumina" text="Illumina fastq" /><tool file="fastq/fastq_groomer.xml" /><tool file="fastq/fastq_paired_end_splitter.xml" /><tool file="fastq/fastq_paired_end_joiner.xml" /><tool file="fastq/fastq_stats.xml" /> - <label text="Roche-454 data" id="454" /> + <label id="454" text="Roche-454 data" /><tool file="metag_tools/short_reads_figure_score.xml" /><tool file="metag_tools/short_reads_trim_seq.xml" /><tool file="fastq/fastq_combiner.xml" /> - <label text="AB-SOLiD data" id="solid" /> + <label id="solid" text="AB-SOLiD data" /><tool file="next_gen_conversion/solid2fastq.xml" /><tool file="solid_tools/solid_qual_stats.xml" /><tool file="solid_tools/solid_qual_boxplot.xml" /> - <label text="Generic FASTQ manipulation" id="generic_fastq" /> + <label id="generic_fastq" text="Generic FASTQ manipulation" /><tool file="fastq/fastq_filter.xml" /><tool file="fastq/fastq_trimmer.xml" /><tool file="fastq/fastq_trimmer_by_quality.xml" /> @@ -274,25 +258,10 @@ <tool file="fastq/fastq_paired_end_interlacer.xml" /><tool file="fastq/fastq_paired_end_deinterlacer.xml" /><tool file="fastq/fastq_manipulation.xml" /> - <tool file="fastq/fastq_to_fasta.xml" /><tool file="fastq/fastq_to_tabular.xml" /><tool file="fastq/tabular_to_fastq.xml" /> - <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" /> - <tool file="fastx_toolkit/fastq_quality_converter.xml" /> - <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> - <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> - <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" /> - <tool file="fastx_toolkit/fastq_to_fasta.xml" /> - <tool file="fastx_toolkit/fastq_quality_filter.xml" /> - <tool file="fastx_toolkit/fastq_to_fasta.xml" /> - <tool file="fastx_toolkit/fastx_artifacts_filter.xml" /> - <tool file="fastx_toolkit/fastx_barcode_splitter.xml" /> - <tool file="fastx_toolkit/fastx_clipper.xml" /> - <tool file="fastx_toolkit/fastx_collapser.xml" /> - <tool file="fastx_toolkit/fastx_renamer.xml" /> - <tool file="fastx_toolkit/fastx_reverse_complement.xml" /> - <tool file="fastx_toolkit/fastx_trimmer.xml" /> + <label id="fastx_toolkit" text="FASTX-Toolkit for FASTQ data" /></section> - <section name="NGS: Mapping" id="solexa_tools"> + <section id="solexa_tools" name="NGS: Mapping"><tool file="sr_mapping/bowtie2_wrapper.xml" /><tool file="sr_mapping/bfast_wrapper.xml" /><tool file="metag_tools/megablast_wrapper.xml" /><tool file="metag_tools/megablast_xml_parser.xml" /><tool file="sr_mapping/PerM.xml" /><tool file="sr_mapping/srma_wrapper.xml" /> - <tool file="sr_mapping/mosaik.xml"/> + <tool file="sr_mapping/mosaik.xml" /></section> - <section name="NGS: Indel Analysis" id="indel_analysis"> + <section id="indel_analysis" name="NGS: Indel Analysis"><tool file="indels/sam_indel_filter.xml" /> - <tool file="indels/indel_sam2interval.xml" /><tool file="indels/indel_table.xml" /><tool file="indels/indel_analysis.xml" /></section> - <section name="NGS: RNA Analysis" id="ngs-rna-tools"> + <section id="ngs-rna-tools" name="NGS: RNA Analysis"> - <label text="RNA-seq" id="rna_seq" /> + <label id="rna_seq" text="RNA-seq" /><tool file="ngs_rna/tophat_wrapper.xml" /><tool file="ngs_rna/tophat2_wrapper.xml" /><tool file="ngs_rna/tophat_color_wrapper.xml" /> - <tool file="ngs_rna/cufflinks_wrapper.xml" /> - <tool file="ngs_rna/cuffcompare_wrapper.xml" /> - <tool file="ngs_rna/cuffmerge_wrapper.xml" /> - <tool file="ngs_rna/cuffdiff_wrapper.xml" /><tool file="ngs_rna/express_wrapper.xml" /> - <label text="Filtering" id="filtering" /> + <label id="filtering" text="Filtering" /><tool file="ngs_rna/filter_transcripts_via_tracking.xml" /></section> - <section name="NGS: SAM Tools" id="samtools"> - <tool file="samtools/sam_bitwise_flag_filter.xml" /> - <tool file="samtools/sam2interval.xml" /> - <tool file="samtools/sam_to_bam.xml" /> - <tool file="samtools/bam_to_sam.xml" /> - <tool file="samtools/sam_merge.xml" /> - <tool file="samtools/samtools_mpileup.xml" /> - <tool file="samtools/sam_pileup.xml" /> - <tool file="samtools/pileup_parser.xml" /> - <tool file="samtools/pileup_interval.xml" /> - <tool file="samtools/samtools_flagstat.xml" /> - <tool file="samtools/samtools_rmdup.xml" /> - <tool file="samtools/samtools_slice_bam.xml" /> + <section id="samtools" name="NGS: SAM Tools"></section> - <section name="NGS: GATK Tools (beta)" id="gatk"> - <label text="Alignment Utilities" id="gatk_bam_utilities"/> + <section id="gatk" name="NGS: GATK Tools (beta)"> + <label id="gatk_bam_utilities" text="Alignment Utilities" /><tool file="gatk/depth_of_coverage.xml" /><tool file="gatk/print_reads.xml" /> - <label text="Realignment" id="gatk_realignment" /> + <label id="gatk_realignment" text="Realignment" /><tool file="gatk/realigner_target_creator.xml" /><tool file="gatk/indel_realigner.xml" /> - <label text="Base Recalibration" id="gatk_recalibration" /> + <label id="gatk_recalibration" text="Base Recalibration" /><tool file="gatk/count_covariates.xml" /><tool file="gatk/table_recalibration.xml" /><tool file="gatk/analyze_covariates.xml" /> - <label text="Genotyping" id="gatk_genotyping" /> + <label id="gatk_genotyping" text="Genotyping" /><tool file="gatk/unified_genotyper.xml" /> - <label text="Annotation" id="gatk_annotation" /> + <label id="gatk_annotation" text="Annotation" /><tool file="gatk/variant_annotator.xml" /> - <label text="Filtration" id="gatk_filtration" /> + <label id="gatk_filtration" text="Filtration" /><tool file="gatk/variant_filtration.xml" /><tool file="gatk/variant_select.xml" /> - <label text="Variant Quality Score Recalibration" id="gatk_variant_quality_score_recalibration" /> + <label id="gatk_variant_quality_score_recalibration" text="Variant Quality Score Recalibration" /><tool file="gatk/variant_recalibrator.xml" /><tool file="gatk/variant_apply_recalibration.xml" /> - <label text="Variant Utilities" id="gatk_variant_utilities"/> + <label id="gatk_variant_utilities" text="Variant Utilities" /><tool file="gatk/variants_validate.xml" /><tool file="gatk/variant_eval.xml" /><tool file="gatk/variant_combine.xml" /></section> - <section name="NGS: Peak Calling" id="peak_calling"> + <section id="peak_calling" name="NGS: Peak Calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /><tool file="peak_calling/ccat_wrapper.xml" /><tool file="genetrack/genetrack_indexer.xml" /><tool file="genetrack/genetrack_peak_prediction.xml" /></section> - <section name="NGS: Simulation" id="ngs-simulation"> + <section id="ngs-simulation" name="NGS: Simulation"><tool file="ngs_simulation/ngs_simulation.xml" /></section> - <section name="Phenotype Association" id="hgv"> + <section id="hgv" name="Phenotype Association"><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" /><tool file="phenotype_association/sift.xml" /><tool file="phenotype_association/linkToGProfile.xml" /> - <tool file="phenotype_association/linkToDavid.xml"/> - <tool file="phenotype_association/ctd.xml" /> - <tool file="phenotype_association/funDo.xml" /> + <tool file="phenotype_association/linkToDavid.xml" /><tool file="phenotype_association/snpFreq.xml" /><tool file="phenotype_association/ldtools.xml" /><tool file="phenotype_association/pass.xml" /><tool file="phenotype_association/gpass.xml" /><tool file="phenotype_association/beam.xml" /><tool file="phenotype_association/lps.xml" /> - <tool file="phenotype_association/hilbertvis.xml" /><tool file="phenotype_association/freebayes.xml" /><tool file="phenotype_association/master2pg.xml" /><tool file="phenotype_association/vcf2pgSnp.xml" /> - <tool file="phenotype_association/dividePgSnpAlleles.xml" /></section> - <section name="VCF Tools" id="vcf_tools"> + <section id="vcf_tools" name="VCF Tools"><tool file="vcf_tools/intersect.xml" /><tool file="vcf_tools/annotate.xml" /><tool file="vcf_tools/filter.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Fix exception class name bug I introduced in the last change to the drmaa runner.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ff76fd33b81c/ Changeset: ff76fd33b81c User: natefoo Date: 2013-10-10 21:17:13 Summary: Fix exception class name bug I introduced in the last change to the drmaa runner. Affected #: 1 file diff -r 60a1b0fdccd252c406d8b92ab60005456afe6e7c -r ff76fd33b81cdde1fb270de688ec5e86488ba34d lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -214,7 +214,7 @@ state = self.ds.jobStatus( external_job_id ) # TODO: probably need to keep track of InvalidJobException count and remove after it exceeds some configurable except ( drmaa.DrmCommunicationException, drmaa.InternalException, drmaa.InvalidJobException ), e: - log.warning( "(%s/%s) job check resulted in %s: %s", galaxy_id_tag, external_job_id, e.__class__.name, e ) + log.warning( "(%s/%s) job check resulted in %s: %s", galaxy_id_tag, external_job_id, e.__class__.__name__, e ) new_watched.append( ajs ) continue except Exception, e: 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.

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commit/galaxy-central: guerler: Connect upload front end to upload tool via tools api
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/60a1b0fdccd2/ Changeset: 60a1b0fdccd2 User: guerler Date: 2013-10-10 20:41:47 Summary: Connect upload front end to upload tool via tools api Affected #: 3 files diff -r ab9f5cb3acd8dcfe30fc5b92fc4a792c9815c877 -r 60a1b0fdccd252c406d8b92ab60005456afe6e7c lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -214,69 +214,6 @@ trans.sa_session.flush() return hda.to_dict() - # copy from upload - if source == 'upload': - - # get upload specific features - dbkey = payload.get('dbkey', None) - extension = payload.get('extension', None) - space_to_tabs = payload.get('space_to_tabs', False) - - # check for filename - if content.filename is None: - trans.response.status = 400 - return "history_contents:create() : The contents parameter needs to contain the uploaded file content." - - # create a dataset - dataset = trans.app.model.Dataset() - trans.sa_session.add(dataset) - trans.sa_session.flush() - - # get file destination - file_destination = dataset.get_file_name() - - # check if the directory exists - dn = os.path.dirname(file_destination) - if not os.path.exists(dn): - os.makedirs(dn) - - # get file and directory names - fn = os.path.basename(content.filename) - - # save file locally - open(file_destination, 'wb').write(content.file.read()) - - # log - log.info ('The file "' + fn + '" was uploaded successfully.') - - # replace separation with tabs - if space_to_tabs: - log.info ('Replacing spaces with tabs.') - sniff.convert_newlines_sep2tabs(file_destination) - - # guess extension - if extension is None: - log.info ('Guessing extension.') - extension = sniff.guess_ext(file_destination) - - # create hda - hda = trans.app.model.HistoryDatasetAssociation(dataset = dataset, name = content.filename, - extension = extension, dbkey = dbkey, history = history, sa_session = trans.sa_session) - - # add status ok - hda.state = hda.states.OK - - # add dataset to history - history.add_dataset(hda, genome_build = dbkey) - permissions = trans.app.security_agent.history_get_default_permissions( history ) - trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) - - # add to session - trans.sa_session.add(hda) - trans.sa_session.flush() - - # get name - return hda.to_dict() else: # other options trans.response.status = 501 diff -r ab9f5cb3acd8dcfe30fc5b92fc4a792c9815c877 -r 60a1b0fdccd252c406d8b92ab60005456afe6e7c static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -38,10 +38,12 @@ this.$body.css('max-height', maxHeight); // fix height if available - if (this.options.height < maxHeight) - this.$body.css('height', this.options.height); - else - this.$body.css('height', maxHeight); + if (this.options.height) { + if (this.options.height < maxHeight) + this.$body.css('height', this.options.height); + else + this.$body.css('height', maxHeight); + } // remove scroll bar if (this.options.height) diff -r ab9f5cb3acd8dcfe30fc5b92fc4a792c9815c877 -r 60a1b0fdccd252c406d8b92ab60005456afe6e7c static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -19,9 +19,7 @@ // extension types select_extension : { - 'auto' : 'Auto-detect', - 'bed' : 'bed', - 'ab1' : 'ab1' + 'auto' : 'Auto-detect' }, // states @@ -134,18 +132,31 @@ // get element var it = this.get_upload_item(index); + + // get current history + var current_history = Galaxy.currHistoryPanel.model.get('id'); - // read in configuration - var data = { - source : "upload", - space_to_tabs : it.find('#space_to_tabs').is(':checked'), - extension : it.find('#extension').val() - } + // configure tool + this.uploadbox.configure({url : galaxy_config.root + "api/tools/", paramname : "files_0|file_data"}); - // configure url - var current_history = Galaxy.currHistoryPanel.model.get('id'); - this.uploadbox.configure({url : galaxy_config.root + "api/histories/" + current_history + "/contents"}); + // get + var file_type = it.find('#extension').val(); + var space_to_tabs = it.find('#space_to_tabs').is(':checked'); + // configure tool + tool_input = {}; + tool_input['dbkey'] = '?'; + tool_input['file_type'] = file_type; + tool_input['files_0|NAME'] = file.name; + tool_input['files_0|type'] = 'upload_dataset'; + tool_input['space_to_tabs'] = space_to_tabs; + + // setup data + data = {}; + data['history_id'] = current_history; + data['tool_id'] = 'upload1'; + data['inputs'] = JSON.stringify(tool_input); + // return additional data to be send with file return data; }, 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.

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