- galaxy-commits - lists.galaxyproject.org

galaxy-dist commit 47d6c393f4cf: Add necessary import statement to gff_util module.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1289785639 18000 # Node ID 47d6c393f4cf9562e4e3e10211389f84bf0a2f24 # Parent fd4a22ba5b57a48a2bed45333c2dfddaec61c359 Add necessary import statement to gff_util module. --- a/lib/galaxy/datatypes/util/gff_util.py +++ b/lib/galaxy/datatypes/util/gff_util.py @@ -1,7 +1,7 @@ """ Provides utilities for working with GFF files. """ - +import pkg_resources; pkg_resources.require( "bx-python" ) from bx.intervals.io import * class GFFInterval( GenomicInterval ):

1 0

galaxy-dist commit dbe6ab1eaa7c: merge
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1289568820 18000 # Node ID dbe6ab1eaa7ca7f9754c22bb2f6edd3fc26e3432 # Parent b5b6b92a71e960691bb514af32ba2e21a731bd4e # Parent ba34d996fff5669eca98ff98c6035a68ac93bd34 merge

1 0

galaxy-dist commit b124f54952de: Small fixes and refactor to workflows: remove unused ensure_popup_helper(), and fix extra comma that was returning error in IE.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1289591135 18000 # Node ID b124f54952dee106f4ca87ea89a7f828c41562c3 # Parent b7f712cecaa9f527f1161f923ebe798eba526cb6 Small fixes and refactor to workflows: remove unused ensure_popup_helper(), and fix extra comma that was returning error in IE. --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -13,7 +13,6 @@ ensure_dd_helper(); make_left_panel( $("#left"), $("#center"), $("#left-border" ) ); make_right_panel( $("#right"), $("#center"), $("#right-border" ) ); - ensure_popup_helper(); ## handle_minwidth_hint = rp.handle_minwidth_hint; </script></%def> @@ -82,8 +81,7 @@ "${initial_text}": function() { // Show/hide menu and update vars, user preferences. var menu = $('#tool-search'); - if (menu.is(":visible")) - { + if (menu.is(":visible")) { // Hide menu. pref_value = "False"; menu_option_text = "Search Tools"; @@ -91,9 +89,7 @@ // Reset search. reset_tool_search(true); - } - else - { + } else { // Show menu. pref_value = "True"; menu_option_text = "Hide Search"; @@ -158,18 +154,17 @@ var next = this_label.next(); var no_visible_tools = true; // Look through tools following label and, if none are visible, hide label. - while (next.length != 0 && next.hasClass("toolTitle")) - { - if (next.is(":visible")) - { + while (next.length !== 0 && next.hasClass("toolTitle")) { + if (next.is(":visible")) { no_visible_tools = false; break; + } else { + next = next.next(); } - else - next = next.next(); } - if (no_visible_tools) + if (no_visible_tools) { this_label.hide(); + } }); } else { $("#search-no-results").show(); @@ -211,9 +206,9 @@ scroll_to_nodes(); canvas_manager.draw_overview(); // Determine if any parameters were 'upgraded' and provide message - upgrade_message = "" - $.each( data['upgrade_messages'], function( k, v ) { - upgrade_message += ( "<li>Step " + ( parseInt(k) + 1 ) + ": " + workflow.nodes[k].name + "<ul>"); + upgrade_message = ""; + $.each( data.upgrade_messages, function( k, v ) { + upgrade_message += ( "<li>Step " + ( parseInt(k, 10) + 1 ) + ": " + workflow.nodes[k].name + "<ul>"); $.each( v, function( i, vv ) { upgrade_message += "<li>" + vv +"</li>"; }); @@ -256,7 +251,7 @@ "Layout": layout_editor, "Save" : save_current_workflow, ##"Load a Workflow" : load_workflow, - "Close": close_editor, + "Close": close_editor }); function edit_workflow_outputs(){ @@ -297,21 +292,21 @@ workflow.has_changes = true; }); $('#workflow-output-area').show(); - }; + } function layout_editor() { workflow.layout(); workflow.fit_canvas_to_nodes(); scroll_to_nodes(); canvas_manager.draw_overview(); - }; + } function edit_workflow_attributes() { workflow.clear_active_node(); $('.right-content').hide(); $('#edit-attributes').show(); - }; + } $.jStore.engineReady(function() { // On load, set the size to the pref stored in local storage if it exists @@ -354,7 +349,11 @@ // Lets the overview be toggled visible and invisible, adjusting the arrows accordingly $("#close-viewport").click( function() { - $("#overview-border").css("right") == "0px" ? hide_overview() : show_overview(); + if ( $("#overview-border").css("right") === "0px" ) { + hide_overview(); + } else { + show_overview(); + } }); // Unload handler @@ -405,7 +404,7 @@ function scroll_to_nodes() { var cv = $("#canvas-viewport"); - var cc = $("#canvas-container") + var cc = $("#canvas-container"); var top, left; if ( cc.width() < cv.width() ) { left = ( cv.width() - cc.width() ) / 2; @@ -436,14 +435,14 @@ node.init_field_data( data ); }, error: function( x, e ) { - var m = "error loading field data" - if ( x.status == 0 ) { - m += ", server unavailable" + var m = "error loading field data"; + if ( x.status === 0 ) { + m += ", server unavailable"; } node.error( m ); } }); - }; + } function add_node_for_module( type, title ) { node = prebuild_node( type, title ); @@ -466,7 +465,7 @@ node.error( m ); } }); - }; + } <% from galaxy.jobs.actions.post import ActionBox @@ -500,12 +499,12 @@ } function new_pja(action_type, target, node){ - if (node.post_job_actions == undefined){ + if (node.post_job_actions === undefined){ //New tool node, set up dict. node.post_job_actions = {}; } - if (node.post_job_actions[action_type+target] == undefined){ - var new_pja = new Object(); + if (node.post_job_actions[action_type+target] === undefined){ + var new_pja = {}; new_pja.action_type = action_type; new_pja.output_name = target; node.post_job_actions[action_type+target] = null; @@ -513,7 +512,7 @@ display_pja(new_pja, node); workflow.active_form_has_changes = true; return true; - }else{ + } else { return false; } } @@ -576,7 +575,7 @@ var value = $(this).attr( 'value' ); options[ $(this).text() ] = function() { $(form).append( "<input type='hidden' name='"+name+"' value='"+value+"' />" ).submit(); - } + }; }); b.insertAfter( this ); $(this).remove(); @@ -613,9 +612,9 @@ "Don't Save": do_close } ); } else { - window.document.location = "${next_url}" + window.document.location = "${next_url}"; } - } + }; var save_current_workflow = function ( eventObj, success_callback ) { show_modal( "Saving workflow", "progress" ); @@ -634,14 +633,14 @@ type: "POST", data: { id: "${trans.security.encode_id( stored.id )}", - workflow_data: function() { return JSON.stringify( workflow.to_simple() ) }, + workflow_data: function() { return JSON.stringify( workflow.to_simple() ); }, "_": "true" }, dataType: 'json', success: function( data ) { var body = $("<div></div>").text( data.message ); if ( data.errors ) { - body.addClass( "warningmark" ) + body.addClass( "warningmark" ); var errlist = $( "<ul/>" ); $.each( data.errors, function( i, v ) { $("<li></li>").text( v ).appendTo( errlist ); @@ -663,7 +662,7 @@ } } }); - } + }; // We bind to ajaxStop because of auto-saving, since the form submission ajax // call needs to be completed so that the new data is saved @@ -677,7 +676,7 @@ } else { savefn(success_callback); } - } + }; </script></%def>

1 0

galaxy-dist commit ba34d996fff5: Merge.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1289568520 18000 # Node ID ba34d996fff5669eca98ff98c6035a68ac93bd34 # Parent 2389c323a1e6a50de6d48d5431d16d830ccef021 # Parent a6cd0223a53b4f9498a0dde69dcef53387188e5f Merge. --- a/templates/requests/common/events.mako +++ /dev/null @@ -1,53 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<% - is_admin = cntrller == 'requests_admin' and trans.user_is_admin() - can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted - can_reject_request = is_admin and request.is_submitted - can_add_samples = request.is_unsubmitted -%> - -<br/><br/> -<ul class="manage-table-actions"> - <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request Actions</a></li> - <div popupmenu="request-${request.id}-popup"> - <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> - %if can_edit_request: - <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> - %endif - %if can_add_samples: - <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit this request</a> - %endif - %if can_reject_request: - <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> - %endif - </div> -</ul> - -%if message: - ${render_msg( message, status )} -%endif - -<h2>History of Sequencing Request "${request.name}"</h2> - -<div class="toolForm"> - <table class="grid"> - <thead> - <tr> - <th>State</th> - <th>Last Update</th> - <th>Comments</th> - </tr> - </thead> - <tbody> - %for state, updated, comments in events_list: - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td><b><a>${state}</a></b></td> - <td><a>${updated}</a></td> - <td><a>${comments}</a></td> - </tr> - %endfor - </tbody> - </table> -</div> --- a/tools/ncbi_blast_plus/blast_filter_fasta.py +++ /dev/null @@ -1,38 +0,0 @@ -#!/usr/bin/env python -"""Filter a FASTA file using tabular output, e.g. from BLAST. - -Takes five command line options, tabular BLAST filename, ID column number -(using one based counting), input FASTA filename, and two output FASTA -filenames (for records with and without any BLAST hits). - -In the default NCBI BLAST+ tabular output, the query sequence ID is in column -one, and the ID of the match from the database is in column two. -""" -import sys -from galaxy_utils.sequence.fasta import fastaReader, fastaWriter - -#Parse Command Line -blast_file, blast_col, in_file, out_positive_file, out_negative_file = sys.argv[1:] -blast_col = int(blast_col)-1 -assert blast_col >= 0 - -#Read tabular BLAST file and record all queries with hit(s) -ids = set() -blast_handle = open(blast_file, "rU") -for line in blast_handle: - ids.add(line.split("\t")[blast_col]) -blast_handle.close() - -#Write filtered FASTA file based on IDs from BLAST file -reader = fastaReader(open(in_file, "rU")) -positive_writer = fastaWriter(open(out_positive_file, "w")) -negative_writer = fastaWriter(open(out_negative_file, "w")) -for record in reader: - #The [1:] is because the fastaReader leaves the > on the identifer. - if record.identifier and record.identifier.split()[0][1:] in ids: - positive_writer.write(record) - else: - negative_writer.write(record) -positive_writer.close() -negative_writer.close() -reader.close() --- a/tools/ncbi_blast_plus/blast_filter_fasta.xml +++ /dev/null @@ -1,37 +0,0 @@ -<tool id="blast_filter_fasta" name="Filter FASTA using BLAST output" version="0.0.1"> - <description>Divide a FASTA file based on BLAST hits</description> - <command interpreter="python"> - blast_filter_fasta.py $blast_file $blast_col $in_file $out_positive_file $out_negative_file - </command> - <inputs> - <param name="in_file" type="data" format="fasta" label="FASTA file to filter"/> - <param name="blast_file" type="data" format="tabular" label="Tabular BLAST output"/> - <param name="blast_col" type="select" label="Column containing FASTA identifiers"> - <option value="1">Column 1 - BLAST query ID</option> - <option value="2">Column 2 - BLAST match ID</option> - </param> - </inputs> - <outputs> - <data name="out_positive_file" format="fasta" label="Sequences with BLAST hits" /> - <data name="out_negative_file" format="fasta" label="Sequences without BLAST hits" /> - </outputs> - <requirements> - </requirements> - <tests> - </tests> - <help> - -**What it does** - -Typical use would be to take a multi-sequence FASTA and the tabular output of -running BLAST on it, and divide the FASTA file in two: those sequence with a -BLAST hit, and those without. - -In the default NCBI BLAST+ tabular output, the query sequence ID is in column -one, and the ID of the match from the database is in column two. - -This allows you to filter the FASTA file for the subjects in the BLAST search, -rather than filtering the FASTA file for the queries in the BLAST search. - - </help> -</tool>

1 0

galaxy-dist commit fc1f67023d86: Fixes for building target library and folder SelectFields for transferring sample datasets. All folders are now present in the target folder SelectField. Move security-related methods from the model's User class to the security agent where they belong.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1289574787 18000 # Node ID fc1f67023d86a69ea7229501b093d61748630f4c # Parent dc4af741ffc455c4737aff67c7d7de48c8628392 Fixes for building target library and folder SelectFields for transferring sample datasets. All folders are now present in the target folder SelectField. Move security-related methods from the model's User class to the security agent where they belong. --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -52,40 +52,6 @@ class User( object ): if role not in roles: roles.append( role ) return roles - def accessible_libraries( self, trans, actions ): - # TODO: eliminate this method - instead use - # trans.app.security_agent.get_accessible_libraries(). - # Get all permitted libraries for this user - all_libraries = trans.sa_session.query( trans.app.model.Library ) \ - .filter( trans.app.model.Library.table.c.deleted == False ) \ - .order_by( trans.app.model.Library.name ) - roles = self.all_roles() - actions_to_check = actions - # The libraries dictionary looks like: { library : '1,2' }, library : '3' } - # Its keys are the libraries that should be displayed for the current user and whose values are a - # string of comma-separated folder ids, of the associated folders the should NOT be displayed. - # The folders that should not be displayed may not be a complete list, but it is ultimately passed - # to the calling method to keep from re-checking the same folders when the library / folder - # select lists are rendered. - libraries = {} - for library in all_libraries: - can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( self, roles, library, actions_to_check ) - if can_show: - libraries[ library ] = hidden_folder_ids - return libraries - def accessible_request_types( self, trans ): - active_request_types = trans.sa_session.query( trans.app.model.RequestType ) \ - .filter( trans.app.model.RequestType.table.c.deleted == False ) \ - .order_by( trans.app.model.RequestType.name ) - # Filter active_request_types to those that can be accessed by this user - role_ids = [ r.id for r in self.all_roles() ] - accessible_request_types = set() - for request_type in active_request_types: - for permission in request_type.actions: - if permission.role.id in role_ids: - accessible_request_types.add( request_type ) - accessible_request_types = [ request_type for request_type in accessible_request_types ] - return accessible_request_types class Job( object ): """ --- a/lib/galaxy/web/controllers/requests.py +++ b/lib/galaxy/web/controllers/requests.py @@ -77,7 +77,8 @@ class Requests( BaseController ): kwd[ 'message' ] = message # Allow the user to create a new request only if they have permission to access a # (sequencer configuration) request type. - if len( trans.user.accessible_request_types( trans ) ): + accessible_request_types = trans.app.security_agent.get_accessible_request_types( trans, trans.user ) + if accessible_request_types: self.request_grid.global_actions = [ grids.GridAction( "Create new request", dict( controller='requests_common', action='create_request', cntrller='requests' ) ) ] --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -414,7 +414,7 @@ class RequestsCommon( BaseController, Us cntrller=cntrller, id=request_id, editing_samples=editing_samples ) ) - libraries = self.__get_accessible_libraries( trans, request.user ) + libraries = trans.app.security_agent.get_accessible_libraries( trans, request.user ) # Build a list of sample widgets (based on the attributes of each sample) for display. displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) @@ -815,7 +815,7 @@ class RequestsCommon( BaseController, Us else: sample_index = len( displayable_sample_widgets ) if params.get( 'add_sample_button', False ): - libraries = self.__get_accessible_libraries( trans, request.user ) + libraries = trans.app.security_agent.get_accessible_libraries( trans, request.user ) num_samples_to_add = int( params.get( 'num_sample_to_copy', 1 ) ) # See if the user has selected a sample to copy. copy_sample_index = int( params.get( 'copy_sample_index', -1 ) ) @@ -1214,20 +1214,14 @@ class RequestsCommon( BaseController, Us else: folder = None return library, folder + def __get_active_folders( self, library ): + """Return all of the active folders for the received library""" + root_folder = library.root_folder + active_folders = [ root_folder ] + for folder in root_folder.active_folders: + active_folders.append( folder ) + return active_folders # ===== Methods for handling form definition widgets ===== - def __get_accessible_libraries( self, trans, user ): - # Return a dictionary whose keys are libraries that user can - # access and whose values are empty string ''. This is because - # methods expect the dictionary instead of a simple list because - # this method replaces the deprecated model.User.accessible_libraries() - # method. TODO: fix methods that call this method to expect the list - # returne dby trans.app.securoty_agent.get_accessible_libraries() and - # then eliminate this method. - accessible_libraries = trans.app.security_agent.get_accessible_libraries( trans, user ) - accessible_libraries_dict = odict() - for library in accessible_libraries: - accessible_libraries_dict[ library ] = '' - return accessible_libraries_dict def __get_request_widgets( self, trans, id ): """Get the widgets for the request""" request = trans.sa_session.query( trans.model.Request ).get( id ) @@ -1275,7 +1269,7 @@ class RequestsCommon( BaseController, Us # Build the list of widgets which will be used to render each sample row on the request page if not request: return sample_widgets - libraries = self.__get_accessible_libraries( trans, request.user ) + libraries = trans.app.security_agent.get_accessible_libraries( trans, request.user ) # Build the list if sample widgets, populating the values from kwd. for index, sample in enumerate( samples ): id_index = index + 1 @@ -1361,7 +1355,7 @@ class RequestsCommon( BaseController, Us copy_sample_index_select_field.add_option( sample_dict[ 'name' ], index ) return copy_sample_index_select_field def __build_request_type_id_select_field( self, trans, selected_value='none' ): - accessible_request_types = trans.user.accessible_request_types( trans ) + accessible_request_types = trans.app.security_agent.get_accessible_request_types( trans, trans.user ) return build_select_field( trans, accessible_request_types, 'name', 'request_type_id', selected_value=selected_value, refresh_on_change=True ) def __build_user_id_select_field( self, trans, selected_value='none' ): active_users = trans.sa_session.query( trans.model.User ) \ @@ -1388,11 +1382,9 @@ class RequestsCommon( BaseController, Us def __build_library_and_folder_select_fields( self, trans, user, sample_index, libraries, sample=None, library_id=None, folder_id=None, **kwd ): # Create the library_id SelectField for a specific sample. The received libraries param is a list of all the libraries # accessible to the current user, and we add them as options to the library_select_field. If the user has selected an - # existing library then display all the accessible folders of the selected library in the folder_select_field. - # - # The libraries dictionary looks like: { library : '1,2' }, library : '3' }. Its keys are the libraries that - # should be displayed for the current user and its values are strings of comma-separated folder ids that should - # NOT be displayed. + # existing library then display all the folders of the selected library in the folder_select_field. Library folders do + # not have ACCESS permissions associated with them (only LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE), so all folders will + # be present in the folder_select_field for each library selected. params = util.Params( kwd ) library_select_field_name= "sample_%i_library_id" % sample_index folder_select_field_name = "sample_%i_folder_id" % sample_index @@ -1401,15 +1393,11 @@ class RequestsCommon( BaseController, Us if not folder_id: folder_id = params.get( folder_select_field_name, None ) selected_library = None - selected_hidden_folder_ids = [] - showable_folders = [] if library_id not in [ None, 'none' ]: - # If we have a selected library, get the list of it's folders that are not accessible to the current user - for library, hidden_folder_ids in libraries.items(): + for library in libraries: encoded_id = trans.security.encode_id( library.id ) if encoded_id == str( library_id ): selected_library = library - selected_hidden_folder_ids = hidden_folder_ids.split( ',' ) break elif sample and sample.library and library_id == 'none': # The user previously selected a library but is now resetting the selection to 'none' @@ -1417,21 +1405,17 @@ class RequestsCommon( BaseController, Us elif sample and sample.library: library_id = trans.security.encode_id( sample.library.id ) selected_library = sample.library - # sample_%i_library_id SelectField with refresh on change enabled + # Build the sample_%i_library_id SelectField with refresh on change enabled library_select_field = build_select_field( trans, - libraries.keys(), + libraries, 'name', library_select_field_name, initial_value='none', selected_value=str( library_id ).lower(), refresh_on_change=True ) - # Get all accessible folders for the selected library, if one is indeed selected + # Get all folders for the selected library, if one is indeed selected if selected_library: - showable_folders = trans.app.security_agent.get_showable_folders( user, - user.all_roles(), - selected_library, - [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ], - selected_hidden_folder_ids ) + folders = self.__get_active_folders( selected_library ) if folder_id: selected_folder_id = folder_id elif sample and sample.folder: @@ -1440,11 +1424,12 @@ class RequestsCommon( BaseController, Us selected_folder_id = trans.security.encode_id( selected_library.root_folder.id ) else: selected_folder_id = 'none' + folders = [] # TODO: Change the name of the library root folder to "Library root" to clarify to the # user that it is the root folder. We probably should just change this in the Library code, # and update the data in the db. folder_select_field = build_select_field( trans, - showable_folders, + folders, 'name', folder_select_field_name, initial_value='none', --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -84,7 +84,7 @@ [ 'Find Samples', h.url_for( controller='/requests', action='find_samples_index' ) ], [ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ] ] - tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.user.accessible_request_types( trans ) ) ) ) + tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.app.security_agent.get_accessible_request_types( trans, trans.user ) ) ) ) %> ## Visualization menu. --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -60,6 +60,8 @@ class RBACAgent: raise "Unimplemented Method" def get_private_user_role( self, user ): raise "Unimplemented Method" + def get_accessible_request_types( self, trans, user ): + raise "Unimplemented Method" def user_set_default_permissions( self, user, permissions={}, history=False, dataset=False ): raise "Unimplemented Method" def history_set_default_permissions( self, history, permissions=None, dataset=False, bypass_manage_permission=False ): @@ -76,6 +78,8 @@ class RBACAgent: raise "Unimplemented Method" def get_accessible_libraries( self, trans, user ): raise "Unimplemented Method" + def get_permitted_libraries( self, trans, user, actions ): + raise "Unimplemented Method" def folder_is_public( self, library ): raise "Unimplemented Method" def make_folder_public( self, folder, count=0 ): @@ -247,7 +251,7 @@ class GalaxyRBACAgent( RBACAgent ): def can_access_library( self, roles, library ): return self.library_is_public( library ) or self.allow_action( roles, self.permitted_actions.LIBRARY_ACCESS, library ) def get_accessible_libraries( self, trans, user ): - """Return all data libraries that user can access""" + """Return all data libraries that the received user can access""" accessible_libraries = [] current_user_role_ids = [ role.id for role in user.all_roles() ] library_access_action = self.permitted_actions.LIBRARY_ACCESS.action @@ -499,6 +503,20 @@ class GalaxyRBACAgent( RBACAgent ): else: permissions[ action ] = [ item_permission.role ] return permissions + def get_accessible_request_types( self, trans, user ): + """Return all ReqquestTypes that the received user has permission to access.""" + active_request_types = trans.sa_session.query( trans.app.model.RequestType ) \ + .filter( trans.app.model.RequestType.table.c.deleted == False ) \ + .order_by( trans.app.model.RequestType.name ) + # Filter active_request_types to those that can be accessed by the received user + role_ids = [ r.id for r in user.all_roles() ] + accessible_request_types = set() + for request_type in active_request_types: + for permission in request_type.actions: + if permission.role.id in role_ids: + accessible_request_types.add( request_type ) + accessible_request_types = [ request_type for request_type in accessible_request_types ] + return accessible_request_types def copy_dataset_permissions( self, src, dst ): if not isinstance( src, self.model.Dataset ): src = src.dataset @@ -731,6 +749,34 @@ class GalaxyRBACAgent( RBACAgent ): else: raise 'Invalid class (%s) specified for target_library_item (%s)' % \ ( target_library_item.__class__, target_library_item.__class__.__name__ ) + def get_permitted_libraries( self, trans, user, actions ): + """ + This method is historical (it is not currently used), but may be useful again at some + point. It returns a dictionary whose keys are library objects and whose values are a + comma-separated string of folder ids. This method works with the show_library_item() + method below, and it returns libraries for which the received user has permission to + perform the received actions. Here is an example call to this method to return all + libraries for which the received user has LIBRARY_ADD permission: + libraries = trans.app.security_agent.get_permitted_libraries( trans, user, + [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) + """ + all_libraries = trans.sa_session.query( trans.app.model.Library ) \ + .filter( trans.app.model.Library.table.c.deleted == False ) \ + .order_by( trans.app.model.Library.name ) + roles = user.all_roles() + actions_to_check = actions + # The libraries dictionary looks like: { library : '1,2' }, library : '3' } + # Its keys are the libraries that should be displayed for the current user and whose values are a + # string of comma-separated folder ids, of the associated folders the should NOT be displayed. + # The folders that should not be displayed may not be a complete list, but it is ultimately passed + # to the calling method to keep from re-checking the same folders when the library / folder + # select lists are rendered. + libraries = {} + for library in all_libraries: + can_show, hidden_folder_ids = self.show_library_item( self, roles, library, actions_to_check ) + if can_show: + libraries[ library ] = hidden_folder_ids + return libraries def show_library_item( self, user, roles, library_item, actions_to_check, hidden_folder_ids='' ): """ This method must be sent an instance of Library() or LibraryFolder(). Recursive execution produces a

1 0

galaxy-dist commit ecc1cefbccba: Enhance GFFReader to read and return complete features (genes/transcripts), which are composed of multiple intervals/blocks. This required hacking around a couple limitations of bx-python, but these can be easily fixed when bx-python is updated. Use enhanced functionality to correctly create converted datasets for visualizing GFF files.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1289591537 18000 # Node ID ecc1cefbccba6135f824f9573f06c130fd6d08b4 # Parent b124f54952dee106f4ca87ea89a7f828c41562c3 Enhance GFFReader to read and return complete features (genes/transcripts), which are composed of multiple intervals/blocks. This required hacking around a couple limitations of bx-python, but these can be easily fixed when bx-python is updated. Use enhanced functionality to correctly create converted datasets for visualizing GFF files. Also updated GOPS tools to use a simpler GFF reader wrapper to read in intervals and convert to BED coordinates. --- a/tools/new_operations/gops_subtract.py +++ b/tools/new_operations/gops_subtract.py @@ -44,11 +44,11 @@ def main(): # Set readers to handle either GFF or default format. if in1_gff_format: - in1_reader_wrapper = GFFReaderWrapper + in1_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in1_reader_wrapper = NiceReaderWrapper if in2_gff_format: - in2_reader_wrapper = GFFReaderWrapper + in2_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in2_reader_wrapper = NiceReaderWrapper --- a/tools/new_operations/gops_intersect.py +++ b/tools/new_operations/gops_intersect.py @@ -44,11 +44,11 @@ def main(): # Set readers to handle either GFF or default format. if in1_gff_format: - in1_reader_wrapper = GFFReaderWrapper + in1_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in1_reader_wrapper = NiceReaderWrapper if in2_gff_format: - in2_reader_wrapper = GFFReaderWrapper + in2_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in2_reader_wrapper = NiceReaderWrapper @@ -66,10 +66,10 @@ def main(): fix_strand=True ) out_file = open( out_fname, "w" ) - + try: for line in intersect( [g1,g2], pieces=pieces, mincols=mincols ): - if type( line ) == GenomicInterval: + if isinstance( line, GenomicInterval ): if in1_gff_format: line = convert_bed_coords_to_gff( line ) out_file.write( "%s\n" % "\t".join( line.fields ) ) --- /dev/null +++ b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py @@ -0,0 +1,55 @@ +#!/usr/bin/env python + +""" +Convert from GFF file to interval index file. + +usage: + python gff_to_interval_index_converter.py [input] [output] +""" + +from __future__ import division + +import sys, fileinput +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from galaxy.tools.util.gff_util import * +from bx.interval_index_file import Indexes + +def main(): + # Arguments + input_fname, out_fname = sys.argv[1:] + + # Do conversion. + chr_col, start_col, end_col, strand_col = ( 0, 3, 4, 6 ) + index = Indexes() + offset = 0 + reader_wrapper = GFFReaderWrapper( fileinput.FileInput( input_fname ), + chrom_col=chr_col, + start_col=start_col, + end_col=end_col, + strand_col=strand_col, + fix_strand=True ) + for feature in list( reader_wrapper ): + # TODO: need to address comments: + # if comment: + # increment_offset. + + # Add feature; index expects BED coordinates. + convert_gff_coords_to_bed( feature ) + index.add( feature.chrom, feature.start, feature.end, offset ) + + # Increment offset by feature length; feature length is all + # intervals/lines that comprise feature. + feature_len = 0 + for interval in feature.intervals: + # HACK: +1 for EOL char. Need bx-python to provide raw_line itself + # b/c TableReader strips EOL characters, thus changing the line + # length. + feature_len += len( interval.raw_line ) + 1 + offset += feature_len + + index.write( open(out_fname, "w") ) + +if __name__ == "__main__": + main() + --- a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py @@ -14,7 +14,7 @@ import pkg_resources; pkg_resources.requ from galaxy.visualization.tracks.summary import * from bx.intervals.io import * from bx.cookbook import doc_optparse -from galaxy.tools.util.gff_util import GFFReaderWrapper +from galaxy.tools.util.gff_util import * def main(): # Read options, args. @@ -40,9 +40,12 @@ def main(): strand_col=strand_col, fix_strand=True ) st = SummaryTree(block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30) - for line in list( reader_wrapper ): - if type( line ) is GenomicInterval: - st.insert_range( line.chrom, long( line.start ), long( line.end ) ) + for feature in list( reader_wrapper ): + if isinstance( feature, GenomicInterval ): + # Tree expects BED coordinates. + if type( feature ) is GFFFeature: + convert_gff_coords_to_bed( feature ) + st.insert_range( feature.chrom, long( feature.start ), long( feature.end ) ) st.write(out_fname) --- a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml +++ b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml @@ -1,6 +1,6 @@ -<tool id="CONVERTER_gff_to_interval_index_0" name="Convert BED to Interval Index" version="1.0.0" hidden="true"> +<tool id="CONVERTER_gff_to_interval_index_0" name="Convert GFF to Interval Index" version="1.0.0" hidden="true"> - <command interpreter="python">interval_to_interval_index_converter.py $input1 $output1 --gff</command> + <command interpreter="python">gff_to_interval_index_converter.py $input1 $output1</command><inputs><page><param format="gff" name="input1" type="data" label="Choose GFF file"/> --- a/tools/new_operations/flanking_features.py +++ b/tools/new_operations/flanking_features.py @@ -153,11 +153,11 @@ def main(): # Set readers to handle either GFF or default format. if in1_gff_format: - in1_reader_wrapper = GFFReaderWrapper + in1_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in1_reader_wrapper = NiceReaderWrapper if in2_gff_format: - in2_reader_wrapper = GFFReaderWrapper + in2_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in2_reader_wrapper = NiceReaderWrapper --- a/lib/galaxy/tools/util/gff_util.py +++ b/lib/galaxy/tools/util/gff_util.py @@ -2,25 +2,173 @@ Provides utilities for working with GFF files. """ -from bx.intervals.io import NiceReaderWrapper, GenomicInterval +from bx.intervals.io import * + +class GFFInterval( GenomicInterval ): + """ + A GFF interval, including attributes. If file is strictly a GFF file, + only attribute is 'group.' + """ + def __init__( self, reader, fields, chrom_col, start_col, end_col, strand_col, default_strand, \ + fix_strand=False, raw_line='' ): + GenomicInterval.__init__( self, reader, fields, chrom_col, start_col, end_col, strand_col, \ + default_strand, fix_strand=fix_strand ) + self.raw_line = raw_line + self.attributes = parse_gff_attributes( fields[8] ) + +class GFFFeature( GenomicInterval ): + """ + A GFF feature, which can include multiple intervals. + """ + def __init__( self, reader, chrom_col, start_col, end_col, strand_col, default_strand, \ + fix_strand=False, intervals=[] ): + GenomicInterval.__init__( self, reader, intervals[0].fields, chrom_col, start_col, end_col, \ + strand_col, default_strand, fix_strand=fix_strand ) + self.intervals = intervals + # Use intervals to set feature attributes. + for interval in self.intervals: + # Error checking. + if interval.chrom != self.chrom: + raise ValueError( "interval chrom does not match self chrom: %i != %i" % \ + ( interval.chrom, self.chrom ) ) + if interval.strand != self.strand: + raise ValueError( "interval strand does not match self strand: %s != %s" % \ + ( interval.strand, self.strand ) ) + # Set start, end of interval. + if interval.start < self.start: + self.start = interval.start + if interval.end > self.end: + self.end = interval.end + +class GFFIntervalToBEDReaderWrapper( NiceReaderWrapper ): + """ + Reader wrapper that reads GFF intervals/lines and automatically converts + them to BED format. + """ + + def parse_row( self, line ): + # HACK: this should return a GFF interval, but bx-python operations + # require GenomicInterval objects and subclasses will not work. + interval = GenomicInterval( self, line.split( "\t" ), self.chrom_col, self.start_col, \ + self.end_col, self.strand_col, self.default_strand, \ + fix_strand=self.fix_strand ) + interval = convert_gff_coords_to_bed( interval ) + return interval class GFFReaderWrapper( NiceReaderWrapper ): """ - Reader wrapper converts GFF format--starting and ending coordinates are 1-based, closed--to the - 'traditional'/BED interval format--0 based, half-open. This is useful when using GFF files as inputs - to tools that expect traditional interval format. + Reader wrapper for GFF files. + + Wrapper has two major functions: + (1) group entries for GFF file (via group column), GFF3 (via id attribute ), + or GTF (via gene_id/transcript id); + (2) convert coordinates from GFF format--starting and ending coordinates + are 1-based, closed--to the 'traditional'/BED interval format--0 based, + half-open. This is useful when using GFF files as inputs to tools that + expect traditional interval format. """ + + def __init__( self, reader, **kwargs ): + """ + Create wrapper. Defaults are group_entries=False and + convert_coords_to_bed=True to support backward compatibility. + """ + NiceReaderWrapper.__init__( self, reader, **kwargs ) + self.group_entries = kwargs.get( 'group_entries', False ) + self.convert_coords_to_bed = kwargs.get( 'convert_coords_to_bed', True ) + self.last_line = None + self.cur_offset = 0 + self.seed_interval = None + def parse_row( self, line ): - interval = GenomicInterval( self, line.split( "\t" ), self.chrom_col, self.start_col, self.end_col, \ - self.strand_col, self.default_strand, fix_strand=self.fix_strand ) - interval = convert_gff_coords_to_bed( interval ) + interval = GFFInterval( self, line.split( "\t" ), self.chrom_col, self.start_col, \ + self.end_col, self.strand_col, self.default_strand, \ + fix_strand=self.fix_strand, raw_line=line ) + if self.convert_coords_to_bed: + interval = convert_gff_coords_to_bed( interval ) return interval + def next( self ): + """ Returns next GFFFeature. """ + + # + # Helper function. + # + + def handle_parse_error( parse_error ): + """ Actions to take when ParseError found. """ + if self.outstream: + if self.print_delegate and hasattr(self.print_delegate,"__call__"): + self.print_delegate( self.outstream, e, self ) + self.skipped += 1 + # no reason to stuff an entire bad file into memmory + if self.skipped < 10: + self.skipped_lines.append( ( self.linenum, self.current_line, str( e ) ) ) + + # + # Get next GFFFeature + # + + # If there is no seed interval, set one. Also, if there are no more + # intervals to read, this is where iterator dies. + if not self.seed_interval: + while not self.seed_interval: + try: + self.seed_interval = GenomicIntervalReader.next( self ) + except ParseError, e: + handle_parse_error( e ) + + # Initialize feature name from seed. + feature_group = self.seed_interval.attributes.get( 'group', None ) # For GFF + feature_id = self.seed_interval.attributes.get( 'id', None ) # For GFF3 + feature_gene_id = self.seed_interval.attributes.get( 'gene_id', None ) # For GTF + feature_transcript_id = self.seed_interval.attributes.get( 'transcript_id', None ) # For GTF + + # Read all intervals associated with seed. + feature_intervals = [] + feature_intervals.append( self.seed_interval ) + while True: + try: + interval = GenomicIntervalReader.next( self ) + except StopIteration, e: + # No more intervals to read, but last feature needs to be + # returned. + interval = None + break + except ParseError, e: + handle_parse_error( e ) + + # If interval not associated with feature, break. + group = interval.attributes.get( 'group', None ) + if group and feature_group != group: + break + id = interval.attributes.get( 'id', None ) + if id and feature_id != id: + break + gene_id = interval.attributes.get( 'gene_id', None ) + transcript_id = interval.attributes.get( 'transcript_id', None ) + if transcript_id and transcript_id != feature_transcript_id and gene_id and \ + gene_id != feature_gene_id: + break + + # Interval associated with feature. + feature_intervals.append( interval ) + + # Last interval read is the seed for the next interval. + self.seed_interval = interval + + # Return GFF feature with all intervals. + return GFFFeature( self, self.chrom_col, self.start_col, self.end_col, self.strand_col, \ + self.default_strand, fix_strand=self.fix_strand, \ + intervals=feature_intervals ) + + def convert_bed_coords_to_gff( interval ): """ - Converts an interval object's coordinates from BED format to GFF format. Accepted object types include - GenomicInterval and list (where the first element in the list is the interval's start, and the second - element is the interval's end). + Converts an interval object's coordinates from BED format to GFF format. + Accepted object types include GenomicInterval and list (where the first + element in the list is the interval's start, and the second element is + the interval's end). """ if type( interval ) is GenomicInterval: interval.start += 1 @@ -30,9 +178,10 @@ def convert_bed_coords_to_gff( interval def convert_gff_coords_to_bed( interval ): """ - Converts an interval object's coordinates from GFF format to BED format. Accepted object types include - GenomicInterval and list (where the first element in the list is the interval's start, and the second - element is the interval's end). + Converts an interval object's coordinates from GFF format to BED format. + Accepted object types include GenomicInterval and list (where the first + element in the list is the interval's start, and the second element is + the interval's end). """ if type( interval ) is GenomicInterval: interval.start -= 1 @@ -42,10 +191,15 @@ def convert_gff_coords_to_bed( interval def parse_gff_attributes( attr_str ): """ - Parses a GFF/GTF attribute string and returns a dictionary of name-value pairs. - The general format for a GFF3 attributes string is name1=value1;name2=value2 - The general format for a GTF attribute string is name1 "value1" ; name2 "value2" - """ + Parses a GFF/GTF attribute string and returns a dictionary of name-value + pairs. The general format for a GFF3 attributes string is + name1=value1;name2=value2 + The general format for a GTF attribute string is + name1 "value1" ; name2 "value2" + The general format for a GFF attribute string is a single string that + denotes the interval's group; in this case, method returns a dictionary + with a single key-value pair, and key name is 'group' + """ attributes_list = attr_str.split(";") attributes = {} for name_value_pair in attributes_list: @@ -53,6 +207,9 @@ def parse_gff_attributes( attr_str ): pair = name_value_pair.strip().split(" ") if len( pair ) == 1: pair = name_value_pair.strip().split("=") + if len( pair ) == 1: + # Could not split for some reason -- raise exception? + continue if pair == '': continue name = pair[0].strip() @@ -61,4 +218,9 @@ def parse_gff_attributes( attr_str ): # Need to strip double quote from values value = pair[1].strip(" \"") attributes[ name ] = value + + if len( attributes ) == 0: + # Could not split attributes string, so entire string must be + # 'group' attribute. This is the case for strictly GFF files. + attributes['group'] = attr_str return attributes

1 0

galaxy-dist commit cadf13f67c65: More changes to sample tracking functional tests
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1289597856 18000 # Node ID cadf13f67c6593d99f8134ba10baa211a026439b # Parent ecc1cefbccba6135f824f9573f06c130fd6d08b4 More changes to sample tracking functional tests - assign target data library, editing samples, assign sample barcode --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -4,7 +4,9 @@ from base.twilltestcase import * from base.test_db_util import * sample_states = [ ( 'New', 'Sample entered into the system' ), - ( 'Received', 'Sample tube received' ), + ( 'Received', 'Sample tube received' ), + ( 'Library Started', 'Sample library preparation' ), + ( 'Run Started', 'Sequence run in progress' ), ( 'Done', 'Sequence run complete' ) ] address_dict = dict( short_desc="Office", name="James Bond", @@ -93,6 +95,49 @@ class TestFormsAndRequests( TwillTestCas global role2 role2 = get_role_by_name( name ) assert role2 is not None, 'Problem retrieving role named "Role2" from the database' + def test_006_create_library_and_folder( self ): + """Testing creating the target data library and folder""" + # Logged in as admin_user + for index in range( 0, 2 ): + name = 'library%s' % str( index + 1 ) + description = '%s description' % name + synopsis = '%s synopsis' % name + self.create_library( name=name, description=description, synopsis=synopsis ) + # Get the libraries for later use + global library1 + library1 = get_library( 'library1', 'library1 description', 'library1 synopsis' ) + assert library1 is not None, 'Problem retrieving library (library1) from the database' + global library2 + library2 = get_library( 'library2', 'library2 description', 'library2 synopsis' ) + assert library2 is not None, 'Problem retrieving library (library2) from the database' + # setup add_library_item permission to regular_user1 + # Set permissions on the library, sort for later testing. + permissions_in = [ 'LIBRARY_ACCESS' ] + permissions_out = [] + # Role1 members are: admin_user, regular_user1, regular_user3. + # Each of these users will be permitted for LIBRARY_ACCESS, LIBRARY_ADD on + # library1 and library2. + for library in [ library1, library2 ]: + self.library_permissions( self.security.encode_id( library.id ), + library.name, + str( role1.id ), + permissions_in, + permissions_out ) + # adding a folder + for library in [ library1, library2 ]: + name = "%s_folder1" % library.name + description = "%s description" % name + self.add_folder( 'library_admin', + self.security.encode_id( library.id ), + self.security.encode_id( library.root_folder.id ), + name=name, + description=description ) + global library1_folder1 + library1_folder1 = get_folder( library1.root_folder.id, 'library1_folder1', 'library1_folder1 description' ) + assert library1_folder1 is not None, 'Problem retrieving library folder named "library1_folder1" from the database' + global library2_folder1 + library2_folder1 = get_folder( library2.root_folder.id, 'library2_folder1', 'library2_folder1 description' ) + assert library2_folder1 is not None, 'Problem retrieving library folder named "library2_folder1" from the database' # # ====== Form definition test methods ================================================ # @@ -283,25 +328,25 @@ class TestFormsAndRequests( TwillTestCas self.view_request( cntrller='requests', request_id=self.security.encode_id( request1.id ), strings_displayed=[ 'Sequencing request "%s"' % request1.name, - 'There are no samples.', - sample_form_layout_grid_name ], + 'There are no samples.' ], strings_not_displayed=[ request1.states.SUBMITTED, request1.states.COMPLETE, - request1.states.REJECTED ] ) + request1.states.REJECTED, + 'Submit request' ] ) # this button should NOT show up as there are no samples yet # check if the request is showing in the 'new' filter self.check_request_grid( cntrller='requests', state=request1.states.NEW, strings_displayed=[ request1.name ] ) self.view_request_history( cntrller='requests', request_id=self.security.encode_id( request1.id ), - strings_displayed=[ 'History of Sequencing Request "%s"' % request1.name, + strings_displayed=[ 'History of sequencing request "%s"' % request1.name, request1.states.NEW, 'Request created' ], strings_not_displayed=[ request1.states.SUBMITTED, request1.states.COMPLETE, request1.states.REJECTED ] ) def test_030_edit_basic_request_info( self ): - """Testing editing the basic information of a sequencing request""" + """Testing editing the basic information and email settings of a sequencing request""" # logged in as regular_user1 fields = [ 'option2', str( user_address1.id ), 'field3 value (edited)' ] new_name=request1.name + ' (Renamed)' @@ -315,43 +360,186 @@ class TestFormsAndRequests( TwillTestCas strings_displayed=[ 'Edit sequencing request "%s"' % request1.name ], strings_displayed_after_submit=[ new_name, new_desc ] ) refresh( request1 ) + # now check email notification settings + check_sample_states = [ ( request1.type.states[0].name, request1.type.states[0].id, True ), + ( request1.type.states[2].name, request1.type.states[2].id, True ), + ( request1.type.states[4].name, request1.type.states[4].id, True ) ]#[ ( state.id, True ) for state in request1.type.states ] + strings_displayed = [ 'Edit sequencing request "%s"' % request1.name, + 'Email notification settings' ] + additional_emails = [ 'test@.bx.psu.edu', 'test2@.bx.psu.edu' ] + strings_displayed_after_submit = [ "The changes made to the email notification settings have been saved", + '\r\n'.join( additional_emails ) ] + self.edit_request_email_settings( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + check_request_owner=True, + additional_emails='\r\n'.join( additional_emails ), + check_sample_states=check_sample_states, + strings_displayed=strings_displayed, + strings_displayed_after_submit=strings_displayed_after_submit ) + # lastly check the details in the request page + strings_displayed = [ 'Sequencing request "%s"' % new_name, + new_desc ] + for field in fields: + strings_displayed.append( field ) + for state_name, id, is_checked in check_sample_states: + strings_displayed.append( state_name ) + for email in additional_emails: + strings_displayed.append( email ) + self.view_request( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + strings_displayed=strings_displayed, + strings_not_displayed=[] ) def test_035_add_samples_to_request( self ): """Testing adding samples to request""" # logged in as regular_user1 # Sample fields - the tuple represents a sample name and a list of sample form field values - sample_value_tuples = [ ( 'Sample1', [ 'option1', 'sample1 field2 value', 'sample1 field3 value' ] ), - ( 'Sample2', [ 'option2', 'sample2 field2 value', 'sample2 field3 value' ] ), - ( 'Sample3', [ 'option1', 'sample3 field2 value', 'sample3 field3 value' ] ) ] + target_library_info = dict(library=self.security.encode_id(library2.id), + folder=self.security.encode_id(library2_folder1.id) ) + sample_value_tuples = \ + [ ( 'Sample1', target_library_info, [ 'option1', 'sample1 field2 value', 'sample1 field3 value' ] ), + ( 'Sample2', target_library_info, [ 'option2', 'sample2 field2 value', 'sample2 field3 value' ] ), + ( 'Sample3', target_library_info, [ 'option1', 'sample3 field2 value', 'sample3 field3 value' ] ) ] strings_displayed_after_submit = [ 'Unsubmitted' ] - for sample_name, field_values in sample_value_tuples: + for sample_name, lib_info, field_values in sample_value_tuples: strings_displayed_after_submit.append( sample_name ) + # add the sample values too + for values in field_values: + strings_displayed_after_submit.append( values ) # Add samples to the request self.add_samples( cntrller='requests', request_id=self.security.encode_id( request1.id ), - request_name=request1.name, sample_value_tuples=sample_value_tuples, strings_displayed=[ 'Add Samples to Request "%s"' % request1.name, '<input type="text" name="sample_0_name" value="Sample_1" size="10"/>' ], # sample name input field strings_displayed_after_submit=strings_displayed_after_submit ) -# def test_040_edit_samples_of_new_request( self ): -# """Testing editing the sample information of new request1""" -# # logged in as regular_user1 -# pass -# def test_035_submit_request( self ): -# """Testing editing a sequence run request""" -# # logged in as regular_user1 -# self.submit_request( cntrller='requests', -# request_id=self.security.encode_id( request1.id ), -# request_name=request1.name, -# strings_displayed_after_submit=[ 'The request has been submitted.' ] ) -# refresh( request1 ) -# # Make sure the request is showing in the 'submitted' filter -# self.check_request_grid( cntrller='requests', -# state=request1.states.SUBMITTED, -# strings_displayed=[ request1.name ] ) -# # Make sure the request's state is now set to 'submitted' -# assert request1.state is not request1.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \ -# % ( request1.name, request1.states.SUBMITTED ) + # check the new sample field values on the request page + strings_displayed = [ 'Sequencing request "%s"' % request1.name, + 'Submit request' ] # this button should appear now + strings_displayed.extend( strings_displayed_after_submit ) + strings_displayed_count = [] + strings_displayed_count.append( ( library2.name, len( sample_value_tuples ) ) ) + strings_displayed_count.append( ( library2_folder1.name, len( sample_value_tuples ) ) ) + self.view_request( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + strings_displayed=strings_displayed, + strings_displayed_count=strings_displayed_count ) + def test_040_edit_samples_of_new_request( self ): + """Testing editing the sample information of new request1""" + # logged in as regular_user1 + # target data library - change it to library1 + target_library_info = dict(library=self.security.encode_id(library1.id), + folder=self.security.encode_id(library1_folder1.id) ) + new_sample_value_tuples = \ + [ ( 'Sample1_renamed', target_library_info, [ 'option2', 'sample1 field2 value edited', 'sample1 field3 value edited' ] ), + ( 'Sample2_renamed', target_library_info, [ 'option1', 'sample2 field2 value edited', 'sample2 field3 value edited' ] ), + ( 'Sample3_renamed', target_library_info, [ 'option2', 'sample3 field2 value edited', 'sample3 field3 value edited' ] ) ] + strings_displayed_after_submit = [ 'Unsubmitted' ] + for sample_name, lib_info, field_values in new_sample_value_tuples: + strings_displayed_after_submit.append( sample_name ) + # add the sample values too + for values in field_values: + strings_displayed_after_submit.append( values ) + # Add samples to the request + self.edit_samples( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + sample_value_tuples=new_sample_value_tuples, + strings_displayed=[ 'Edit Current Samples of Request "%s"' % request1.name, + '<input type="text" name="sample_0_name" value="Sample1" size="10"/>' ], # sample name input field + strings_displayed_after_submit=strings_displayed_after_submit ) + # check the changed sample field values on the request page + strings_displayed = [ 'Sequencing request "%s"' % request1.name ] + strings_displayed.extend( strings_displayed_after_submit ) + strings_displayed_count = [] + strings_displayed_count.append( ( library1.name, len( new_sample_value_tuples ) ) ) + strings_displayed_count.append( ( library1_folder1.name, len( new_sample_value_tuples ) ) ) + self.view_request( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + strings_displayed=strings_displayed, + strings_displayed_count=strings_displayed_count ) + def test_045_submit_request( self ): + """Testing submitting a sequencing request""" + # logged in as regular_user1 + self.submit_request( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + request_name=request1.name, + strings_displayed_after_submit=[ 'The request has been submitted.' ] ) + refresh( request1 ) + # Make sure the request is showing in the 'submitted' filter + self.check_request_grid( cntrller='requests', + state=request1.states.SUBMITTED, + strings_displayed=[ request1.name ] ) + # Make sure the request's state is now set to 'submitted' + assert request1.state is not request1.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \ + % ( request1.name, request1.states.SUBMITTED ) + # the sample state should appear once for each sample + strings_displayed_count = [ ( request1.type.states[0].name, len( request1.samples ) ) ] + # after submission, these buttons should not appear + strings_not_displayed = [ 'Add sample', 'Submit request' ] + # check the request page + self.view_request( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + strings_displayed=[ request1.states.SUBMITTED ], + strings_displayed_count=strings_displayed_count, + strings_not_displayed=strings_not_displayed ) + strings_displayed=[ 'History of sequencing request "%s"' % request1.name, + 'Request submitted by %s' % regular_user1.email, + 'Request created' ] + strings_displayed_count = [ ( request1.states.SUBMITTED, 1 ) ] + self.view_request_history( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + strings_displayed=strings_displayed, + strings_displayed_count=strings_displayed_count, + strings_not_displayed=[ request1.states.COMPLETE, + request1.states.REJECTED ] ) + # + # ====== Sequencing request test methods - Admin perspective ================ + # + def test_050_receive_request_as_admin( self ): + """Testing receiving a sequencing request and assigning it barcodes""" + self.logout() + self.login( email=admin_user.email ) + self.check_request_grid( cntrller='requests_admin', + state=request1.states.SUBMITTED, + strings_displayed=[ request1.name ] ) + strings_displayed = [ request1.states.SUBMITTED, + 'Reject this request' ] + strings_not_displayed = [ 'Add sample' ] + self.view_request( cntrller='requests_admin', + request_id=self.security.encode_id( request1.id ), + strings_not_displayed=strings_not_displayed ) + # Set bar codes for the samples + bar_codes = [ '10001', '10002', '10003' ] + strings_displayed_after_submit = [ 'Changes made to the samples have been saved.' ] + strings_displayed_after_submit.extend( bar_codes ) + self.add_bar_codes( cntrller='requests_admin', + request_id=self.security.encode_id( request1.id ), + bar_codes=bar_codes, + strings_displayed=[ 'Edit Current Samples of Request "%s"' % request1.name ], + strings_displayed_after_submit=strings_displayed_after_submit ) + # the second sample state should appear once for each sample + strings_displayed_count = [ ( request1.type.states[1].name, len( request1.samples ) ), + ( request1.type.states[0].name, 0 ) ] + # check the request page + self.view_request( cntrller='requests_admin', + request_id=self.security.encode_id( request1.id ), + strings_displayed=bar_codes, + strings_displayed_count=strings_displayed_count ) + # the sample state descriptions of the future states should not appear + # here the state names are not checked as all of them appear at the top of + # the page like: state1 > state2 > state3 + strings_not_displayed=[ request1.type.states[2].desc, + request1.type.states[3].desc, + request1.type.states[4].desc ] + # check history of each sample + for sample in request1.samples: + strings_displayed = [ 'Events for Sample "%s"' % sample.name, + 'Request submitted and sample state set to %s' % request1.type.states[0].name, + request1.type.states[0].name, + request1.type.states[1].name ] + self.view_sample_history( cntrller='requests_admin', + sample_id=self.security.encode_id( sample.id ), + strings_displayed=strings_displayed, + strings_not_displayed=strings_not_displayed ) # def test_040_request_lifecycle( self ): # """Testing request life-cycle as it goes through all the states""" # # logged in as regular_user1 @@ -478,6 +666,17 @@ class TestFormsAndRequests( TwillTestCas self.logout() self.login( email=admin_user.email ) ################## + # Purge all libraries + ################## + for library in [ library1, library2 ]: + self.delete_library_item( 'library_admin', + self.security.encode_id( library.id ), + self.security.encode_id( library.id ), + library.name, + item_type='library' ) + self.purge_library( self.security.encode_id( library.id ), library.name ) + + ################## # Delete request_type permissions ################## for request_type in [ request_type1 ]: --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -861,16 +861,26 @@ class TwillTestCase( unittest.TestCase ) self.home() # Functions associated with browsers, cookies, HTML forms and page visits - + def check_page_for_string( self, patt ): """Looks for 'patt' in the current browser page""" page = self.last_page() - for subpatt in patt.split(): - if page.find( patt ) == -1: - fname = self.write_temp_file( page ) - errmsg = "no match to '%s'\npage content written to '%s'" % ( patt, fname ) - raise AssertionError( errmsg ) - + if page.find( patt ) == -1: + fname = self.write_temp_file( page ) + errmsg = "no match to '%s'\npage content written to '%s'" % ( patt, fname ) + raise AssertionError( errmsg ) + + def check_string_count_in_page( self, patt, min_count ): + """Checks the number of 'patt' occurrences in the current browser page""" + page = self.last_page() + patt_count = page.count( patt ) + # The number of occurrences of patt in the page should be at least min_count + # so show error if patt_count is less than min_count + if patt_count < min_count: + fname = self.write_temp_file( page ) + errmsg = "%i occurrences of '%s' found instead of %i.\npage content written to '%s' " % ( min_count, patt, patt_count, fname ) + raise AssertionError( errmsg ) + def check_string_not_in_page( self, patt ): """Checks to make sure 'patt' is NOT in the page.""" page = self.last_page() @@ -878,6 +888,16 @@ class TwillTestCase( unittest.TestCase ) fname = self.write_temp_file( page ) errmsg = "string (%s) incorrectly displayed in page.\npage content written to '%s'" % ( patt, fname ) raise AssertionError( errmsg ) + + def check_page(self, strings_displayed, strings_displayed_count, strings_not_displayed): + """Checks a page for strings displayed, not displayed and number of occurrences of a string""" + for check_str in strings_displayed: + self.check_page_for_string(check_str) + for check_str, count in strings_displayed_count: + self.check_string_count_in_page(check_str, count) + for check_str in strings_not_displayed: + self.check_string_not_in_page(check_str) + def write_temp_file( self, content, suffix='.html' ): fd, fname = tempfile.mkstemp( suffix=suffix, prefix='twilltestcase-' ) @@ -1435,7 +1455,7 @@ class TwillTestCase( unittest.TestCase ) self.check_page_for_string( check_str ) self.home() - # Requests stuff + # Sample tracking stuff def check_request_grid( self, cntrller, state, deleted=False, strings_displayed=[] ): self.visit_url( '%s/%s/browse_requests?sort=create_time&f-state=%s&f-deleted=%s' % \ ( self.url, cntrller, state.replace( ' ', '+' ), str( deleted ) ) ) @@ -1510,24 +1530,20 @@ class TwillTestCase( unittest.TestCase ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) self.home() - def view_request( self, cntrller, request_id, strings_displayed=[], strings_not_displayed=[] ): + def view_request( self, cntrller, request_id, strings_displayed=[], strings_displayed_count=[], strings_not_displayed=[] ): self.visit_url( "%s/%s/browse_requests?operation=view_request&id=%s" % ( self.url, cntrller, request_id ) ) - for check_str in strings_displayed: - self.check_page_for_string( check_str ) - for check_str in strings_not_displayed: - self.check_string_not_in_page( check_str ) - def view_request_history( self, cntrller, request_id, strings_displayed=[], strings_not_displayed=[] ): + self.check_page( strings_displayed, strings_displayed_count, strings_not_displayed ) + def view_request_history( self, cntrller, request_id, strings_displayed=[], strings_displayed_count=[], strings_not_displayed=[] ): self.visit_url( "%s/requests_common/view_request_history?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) - for check_str in strings_displayed: - self.check_page_for_string( check_str ) - for check_str in strings_not_displayed: - self.check_string_not_in_page( check_str ) + self.check_page( strings_displayed, strings_displayed_count, strings_not_displayed ) + def view_sample_history( self, cntrller, sample_id, strings_displayed=[], strings_displayed_count=[], strings_not_displayed=[] ): + self.visit_url( "%s/requests_common/sample_events?cntrller=%s&sample_id=%s" % ( self.url, cntrller, sample_id ) ) + self.check_page( strings_displayed, strings_displayed_count, strings_not_displayed ) def edit_basic_request_info( self, cntrller, request_id, name, new_name='', new_desc='', new_fields=[], strings_displayed=[], strings_displayed_after_submit=[] ): self.visit_url( "%s/requests_common/edit_basic_request_info?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.check_page_for_string( 'Edit sequencing request "%s"' % name ) if new_name: tc.fv( "1", "name", new_name ) if new_desc: @@ -1537,15 +1553,29 @@ class TwillTestCase( unittest.TestCase ) tc.submit( "edit_basic_request_info_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - def add_samples( self, cntrller, request_id, request_name, sample_value_tuples, strings_displayed=[], strings_displayed_after_submit=[] ): + def edit_request_email_settings( self, cntrller, request_id, check_request_owner=True, additional_emails='', + check_sample_states=[], strings_displayed=[], strings_displayed_after_submit=[] ): + self.visit_url( "%s/requests_common/edit_basic_request_info?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) + tc.fv( "2", "email_address", check_request_owner ) + tc.fv( "2", "additional_email_addresses", additional_emails ) + for state_name, state_id, is_checked in check_sample_states: + tc.fv( "2", "sample_state_%i" % state_id, is_checked ) + tc.submit( "edit_email_settings_button" ) + for check_str in strings_displayed_after_submit: + self.check_page_for_string( check_str ) + def add_samples( self, cntrller, request_id, sample_value_tuples, strings_displayed=[], strings_displayed_after_submit=[] ): url = "%s/requests_common/add_sample?cntrller=%s&request_id=%s&add_sample_button=Add+sample" % ( self.url, cntrller, request_id ) self.visit_url( url ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - for sample_index, sample_info in enumerate( sample_value_tuples ): - sample_name = sample_info[0] - sample_field_values = sample_info[1] + for sample_index, ( sample_name, target_library_info, sample_field_values ) in enumerate( sample_value_tuples ): tc.fv( "1", "sample_%i_name" % sample_index, sample_name ) + lib_widget_index = sample_index + 1 + tc.fv( "1", "sample_%i_library_id" % lib_widget_index, target_library_info[ 'library' ] ) + self.refresh_form( "sample_%i_library_id" % lib_widget_index, target_library_info[ 'library' ] ) + tc.fv( "1", "sample_%i_folder_id" % lib_widget_index, target_library_info[ 'folder' ] ) for field_index, field_value in enumerate( sample_field_values ): tc.fv( "1", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) # Do not click on Add sample button when all the sample have been added @@ -1556,6 +1586,32 @@ class TwillTestCase( unittest.TestCase ) tc.submit( "save_samples_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) + def edit_samples( self, cntrller, request_id, sample_value_tuples, strings_displayed=[], strings_displayed_after_submit=[] ): + url = "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=True" % ( self.url, cntrller, request_id ) + self.visit_url( url ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) + for sample_index, ( sample_name, target_library_info, sample_field_values ) in enumerate( sample_value_tuples ): + tc.fv( "1", "sample_%i_name" % sample_index, sample_name ) + lib_widget_index = sample_index + 1 + tc.fv( "1", "sample_%i_library_id" % lib_widget_index, target_library_info[ 'library' ] ) + self.refresh_form( "sample_%i_library_id" % lib_widget_index, target_library_info[ 'library' ] ) + tc.fv( "1", "sample_%i_folder_id" % lib_widget_index, target_library_info[ 'folder' ] ) + for field_index, field_value in enumerate( sample_field_values ): + tc.fv( "1", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) + tc.submit( "save_samples_button" ) + for check_str in strings_displayed_after_submit: + self.check_page_for_string( check_str ) + def add_bar_codes( self, cntrller, request_id, bar_codes, strings_displayed=[], strings_displayed_after_submit=[] ): + url = "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=True" % ( self.url, cntrller, request_id ) + self.visit_url( url ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) + for sample_index, bar_code in enumerate( bar_codes ): + tc.fv( "1", "sample_%i_bar_code" % sample_index, bar_code ) + tc.submit( "save_samples_button" ) + for check_str in strings_displayed_after_submit: + self.check_page_for_string( check_str ) def submit_request( self, cntrller, request_id, request_name, strings_displayed_after_submit=[] ): self.visit_url( "%s/requests_common/submit_request?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) for check_str in strings_displayed_after_submit: @@ -1568,20 +1624,6 @@ class TwillTestCase( unittest.TestCase ) tc.submit( "reject_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - def add_bar_codes( self, request_id, request_name, bar_codes, samples, strings_displayed_after_submit=[] ): - # We have to simulate the form submission here since twill barfs on the page - # gvk - 9/22/10 - TODO: make sure the mako template produces valid html - url = "%s/requests_common/edit_samples?cntrller=requests_admin&id=%s&editing_samples=True" % ( self.url, request_id ) - for index, field_value in enumerate( bar_codes ): - sample_field_name = "sample_%i_name" % index - sample_field_value = samples[ index ].name.replace( ' ', '+' ) - field_name = "sample_%i_bar_code" % index - url += "&%s=%s" % ( field_name, field_value ) - url += "&%s=%s" % ( sample_field_name, sample_field_value ) - url += "&save_samples_button=Save" - self.visit_url( url ) - for check_str in strings_displayed_after_submit: - self.check_page_for_string( check_str ) def change_sample_state( self, request_id, request_name, sample_names, sample_ids, new_sample_state_id, new_state_name, comment='', strings_displayed=[], strings_displayed_after_submit=[] ): # We have to simulate the form submission here since twill barfs on the page --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -155,6 +155,8 @@ %elif editing_samples: <p/><div class="form-row"> + ## hidden element to make twill work. + <input type="hidden" name="hidden_input" value=""/><input type="submit" name="save_samples_button" value="Save"/><input type="submit" name="cancel_changes_button" value="Cancel"/><div class="toolParamHelp" style="clear: both;">

1 0

galaxy-dist commit 2389c323a1e6: Fix for compatibility with the refactored base job runner build_command_line.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1289568484 18000 # Node ID 2389c323a1e6a50de6d48d5431d16d830ccef021 # Parent ca23ea683d26df004e666ede82950c712e3ac637 Fix for compatibility with the refactored base job runner build_command_line. DRMAA runner now uses get_id_tag() in *Wrapper instead of job_id directly for creation of .sh .o and .e files, as well as some debugging. This fixes the issue where many tasks for the same job get submitted at the same time and these files overwrite one another or collide in the submission process. --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -295,6 +295,10 @@ class JobWrapper( object ): def get_job( self ): return self.sa_session.query( model.Job ).get( self.job_id ) + def get_id_tag(self): + # For compatability with drmaa, which uses job_id right now, and TaskWrapper + return str(self.job_id) + def get_param_dict( self ): """ Restore the dictionary of parameters from the database. @@ -788,6 +792,10 @@ class TaskWrapper(JobWrapper): def get_task( self ): return self.sa_session.query(model.Task).get(self.task_id) + def get_id_tag(self): + # For compatibility with drmaa job runner and TaskWrapper, instead of using job_id directly + return "%s_%s" % (self.job_id, self.task_id) + def get_param_dict( self ): """ Restore the dictionary of parameters from the database. @@ -964,7 +972,7 @@ class TaskWrapper(JobWrapper): def setup_external_metadata( self, exec_dir = None, tmp_dir = None, dataset_files_path = None, config_root = None, datatypes_config = None, set_extension = True, **kwds ): # There is no metadata setting for tasks. This is handled after the merge, at the job level. - pass + return "" @property def user( self ): --- a/lib/galaxy/jobs/runners/tasks.py +++ b/lib/galaxy/jobs/runners/tasks.py @@ -117,8 +117,12 @@ class TaskedJobRunner( object ): basic.merge(working_directory, output_filename) log.debug('execution finished: %s' % command_line) for tw in task_wrappers: - stdout += tw.get_task().stdout - stderr += tw.get_task().stderr + # Prevent repetitive output, e.g. "Sequence File Aligned"x20 + # Eventually do a reduce for jobs that output "N reads mapped", combining all N for tasks. + if stdout.strip() != tw.get_task().stdout.strip(): + stdout += tw.get_task().stdout + if stderr.strip() != tw.get_task().stderr.strip(): + stderr += tw.get_task().stderr except Exception: job_wrapper.fail( "failure running job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -125,7 +125,7 @@ class DRMAAJobRunner( BaseJobRunner ): command_line = self.build_command_line( job_wrapper, include_metadata=True ) except: job_wrapper.fail( "failure preparing job", exception=True ) - log.exception("failure running job %d" % job_wrapper.job_id) + log.exception("failure running job %d" % job_wrapper.get_id_tag()) return runner_url = job_wrapper.tool.job_runner @@ -137,7 +137,7 @@ class DRMAAJobRunner( BaseJobRunner ): # Check for deletion before we change state if job_wrapper.get_state() == model.Job.states.DELETED: - log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.job_id ) + log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.get_id_tag() ) job_wrapper.cleanup() return @@ -145,10 +145,10 @@ class DRMAAJobRunner( BaseJobRunner ): job_wrapper.change_state( model.Job.states.QUEUED ) # define job attributes - ofile = "%s/database/pbs/%s.o" % (os.getcwd(), job_wrapper.job_id) - efile = "%s/database/pbs/%s.e" % (os.getcwd(), job_wrapper.job_id) + ofile = "%s/database/pbs/%s.o" % (os.getcwd(), job_wrapper.get_id_tag()) + efile = "%s/database/pbs/%s.e" % (os.getcwd(), job_wrapper.get_id_tag()) jt = self.ds.createJobTemplate() - jt.remoteCommand = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job_wrapper.job_id) + jt.remoteCommand = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job_wrapper.get_id_tag()) jt.outputPath = ":%s" % ofile jt.errorPath = ":%s" % efile native_spec = self.get_native_spec( runner_url ) @@ -163,14 +163,16 @@ class DRMAAJobRunner( BaseJobRunner ): # job was deleted while we were preparing it if job_wrapper.get_state() == model.Job.states.DELETED: - log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.job_id ) + log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.get_id_tag() ) self.cleanup( ( ofile, efile, jt.remoteCommand ) ) job_wrapper.cleanup() return - galaxy_job_id = job_wrapper.job_id - log.debug("(%s) submitting file %s" % ( galaxy_job_id, jt.remoteCommand ) ) - log.debug("(%s) command is: %s" % ( galaxy_job_id, command_line ) ) + # wrapper.get_id_tag() instead of job_id for compatibility with TaskWrappers. + galaxy_id_tag = job_wrapper.get_id_tag() + + log.debug("(%s) submitting file %s" % ( galaxy_id_tag, jt.remoteCommand ) ) + log.debug("(%s) command is: %s" % ( galaxy_id_tag, command_line ) ) # runJob will raise if there's a submit problem job_id = self.ds.runJob(jt) log.info("(%s) queued as %s" % ( galaxy_job_id, job_id ) )

1 0

galaxy-dist commit a6cd0223a53b: Add -parse_deflines switch to BLAST+ wrappers
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1287758911 -3600 # Node ID a6cd0223a53b4f9498a0dde69dcef53387188e5f # Parent 082399b4681b878d20a727150832ef30679b7e1c Add -parse_deflines switch to BLAST+ wrappers --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -27,6 +27,7 @@ blastn -word_size $adv_opts.word_size #end if $adv_opts.ungapped +$adv_opts.parse_deflines ## End of advanced options: #end if </command> @@ -99,6 +100,7 @@ blastn <validator type="in_range" min="0" /></param><param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -28,6 +28,7 @@ blastp #end if ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped +$adv_opts.parse_deflines ## End of advanced options: #end if </command> @@ -104,6 +105,7 @@ blastp Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.' <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> --> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -26,6 +26,7 @@ tblastx #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): -word_size $adv_opts.word_size #end if +$adv_opts.parse_deflines ## End of advanced options: #end if </command> @@ -97,6 +98,7 @@ tblastx <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."><validator type="in_range" min="0" /></param> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -27,6 +27,7 @@ blastx -word_size $adv_opts.word_size #end if $adv_opts.ungapped +$adv_opts.parse_deflines ## End of advanced options: #end if </command> @@ -99,6 +100,7 @@ blastx <validator type="in_range" min="0" /></param><param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -27,6 +27,7 @@ tblastn #end if ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped +$adv_opts.parse_deflines ## End of advanced options: #end if </command> @@ -99,6 +100,7 @@ tblastn Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.' <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> --> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/></when></conditional></inputs>

1 0

galaxy-dist commit b7f712cecaa9: Prevent Rename Dataset Action from allowing a blank input.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1289590343 18000 # Node ID b7f712cecaa9f527f1161f923ebe798eba526cb6 # Parent fc1f67023d86a69ea7229501b093d61748630f4c Prevent Rename Dataset Action from allowing a blank input. --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -60,14 +60,12 @@ class DefaultJobAction(object): class EmailAction(DefaultJobAction): name = "EmailAction" verbose_name = "Email Notification" - @classmethod def execute(cls, app, sa_session, action, job): smtp_server = app.config.smtp_server - if action.action_arguments: - if action.action_arguments.has_key('host'): - host = action.action_arguments['host'] + if action.action_arguments and action.action_arguments.has_key('host'): + host = action.action_arguments['host'] else: host = 'usegalaxy.org' if smtp_server is None: @@ -107,9 +105,8 @@ class EmailAction(DefaultJobAction): @classmethod def get_short_str(cls, pja): - if pja.action_arguments: - if pja.action_arguments.has_key('host'): - return "Email the current user from server %s when this job is complete." % pja.action_arguments['host'] + if pja.action_arguments and pja.action_arguments.has_key('host'): + return "Email the current user from server %s when this job is complete." % pja.action_arguments['host'] else: return "Email the current user when this job is complete." @@ -153,9 +150,11 @@ class RenameDatasetAction(DefaultJobActi @classmethod def execute(cls, app, sa_session, action, job): - for dataset_assoc in job.output_datasets: - if action.output_name == '' or dataset_assoc.name == action.output_name: - dataset_assoc.dataset.name = action.action_arguments['newname'] + # Prevent renaming a dataset to the empty string. + if action.action_arguments and action.action_arguments.has_key('newname') and action.action_arguments['newname'] != '': + for dataset_assoc in job.output_datasets: + if action.output_name == '' or dataset_assoc.name == action.output_name: + dataset_assoc.dataset.name = action.action_arguments['newname'] @classmethod def get_config_form(cls, trans): @@ -173,7 +172,11 @@ class RenameDatasetAction(DefaultJobActi @classmethod def get_short_str(cls, pja): - return "Rename output '%s' to '%s'." % (pja.output_name, pja.action_arguments['newname']) + # Prevent renaming a dataset to the empty string. + if pja.action_arguments and pja.action_arguments.has_key('newname') and pja.action_arguments['newname'] != '': + return "Rename output '%s' to '%s'." % (pja.output_name, pja.action_arguments['newname']) + else: + return "Rename action used without a new name specified. Output name will be unchanged." class HideDatasetAction(DefaultJobAction):

1 0