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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>

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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;">

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galaxy-dist commit dfc848840870: Various sample tracking bug fixes: samples no longer require bar codes, change all references to 'barcode' to be 'bar_code' since that is what the model uses, and mixing the 2 is not maintainable, enhance sample popup menu options, fix broken logic that handles bulk sample library and folderr changes.
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 1289503442 18000 # Node ID dfc848840870fa9936a69e62322446fcb940fb40 # Parent ca23ea683d26df004e666ede82950c712e3ac637 Various sample tracking bug fixes: samples no longer require bar codes, change all references to 'barcode' to be 'bar_code' since that is what the model uses, and mixing the 2 is not maintainable, enhance sample popup menu options, fix broken logic that handles bulk sample library and folderr changes. --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -725,7 +725,7 @@ class RequestsCommon( BaseController, Us search_type = params.get( 'search_type', '' ) request_states = util.listify( params.get( 'request_states', '' ) ) samples = [] - if search_type == 'barcode': + if search_type == 'bar_code': samples = trans.sa_session.query( trans.model.Sample ) \ .filter( and_( trans.model.Sample.table.c.deleted==False, func.lower( trans.model.Sample.table.c.bar_code ).like( "%" + search_string.lower() + "%" ) ) ) \ @@ -763,7 +763,7 @@ class RequestsCommon( BaseController, Us display='checkboxes' ) # Build the search_type SelectField selected_value = kwd.get( 'search_type', 'sample name' ) - types = [ 'sample name', 'barcode', 'dataset' ] + types = [ 'sample name', 'bar_code', 'dataset' ] search_type = build_select_field( trans, types, 'self', 'search_type', selected_value=selected_value, refresh_on_change=False ) # Build the search_box TextField search_box = TextField( 'search_box', 50, kwd.get('search_box', '' ) ) @@ -846,7 +846,7 @@ class RequestsCommon( BaseController, Us # Append the new sample to the current list of samples for the request displayable_sample_widgets.append( dict( id=None, name=name, - barcode='', + bar_code='', library=None, library_id=library_id, folder=None, @@ -999,7 +999,7 @@ class RequestsCommon( BaseController, Us **kwd ) displayable_sample_widgets.append( dict( id=None, name=row[0], - barcode='', + bar_code='', library=None, folder=None, library_select_field=library_select_field, @@ -1029,7 +1029,10 @@ class RequestsCommon( BaseController, Us editing_samples=False ) def __save_samples( self, trans, cntrller, request, samples, **kwd ): # Here we handle saving all new samples added by the user as well as saving - # changes to any subset of the request's samples. + # changes to any subset of the request's samples. A sample will not have an + # associated SampleState until the request is submitted, at which time the + # sample is automatically associated with the first SampleState configured by + # the admin for the request's RequestType. params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -1065,7 +1068,7 @@ class RequestsCommon( BaseController, Us # Send the encoded sample_ids to update_sample_state. # TODO: make changes necessary to just send the samples... encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) - # Make sure all samples have a unique barcode if the state is changing + # Make sure all samples have a unique bar_code if the state is changing for sample_index in range( len( samples ) ): current_sample = samples[ sample_index ] if current_sample is None: @@ -1073,13 +1076,15 @@ class RequestsCommon( BaseController, Us # on which to perform the action. continue request_sample = request.samples[ sample_index ] - bc_message = self.__validate_barcode( trans, request_sample, current_sample[ 'barcode' ] ) - if bc_message: - #status = 'error' - message += bc_message - kwd[ 'message' ] = message - del kwd[ 'save_samples_button' ] - handle_error( **kwd ) + bar_code = current_sample[ 'bar_code' ] + if bar_code: + # If the sample has a new bar_code, make sure it is unique. + bc_message = self.__validate_bar_code( trans, request_sample, bar_code ) + if bc_message: + message += bc_message + kwd[ 'message' ] = message + del kwd[ 'save_samples_button' ] + handle_error( **kwd ) self.update_sample_state( trans, cntrller, encoded_selected_sample_ids, new_state, comment=sample_event_comment ) return trans.response.send_redirect( web.url_for( controller='requests_common', cntrller=cntrller, @@ -1088,18 +1093,22 @@ class RequestsCommon( BaseController, Us elif sample_operation == 'Select data library and folder': # TODO: fix the code so that the sample_operation_select_field does not use # sample_0_library_id as it's name. it should use something like sample_operation_library_id - # and sample_operation-folder_id because the name sample_0_library_id should belong to the + # and sample_operation_folder_id because the name sample_0_library_id should belong to the # first sample since all other form field values are named like this. The library and folder # are skewed to be named +1 resulting in the forced use of id_index everywhere... library_id = params.get( 'sample_0_library_id', 'none' ) folder_id = params.get( 'sample_0_folder_id', 'none' ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) + for sample_index in range( len( samples ) ): + current_sample = samples[ sample_index ] + current_sample[ 'library' ] = library + current_sample[ 'folder' ] = folder self.__update_samples( trans, cntrller, request, samples, **kwd ) # Samples will not have an associated SampleState until the request is submitted, at which # time all samples of the request will be set to the first SampleState configured for the # request's RequestType defined by the admin. if request.is_submitted: - # See if all the samples' barcodes are in the same state, and if so send email if configured to. + # See if all the samples' bar_codes are in the same state, and if so send email if configured to. common_state = request.samples_have_common_state if common_state and common_state.id == request.type.states[1].id: comment = "All samples of this request are in the (%s) sample state. " % common_state.name @@ -1136,10 +1145,12 @@ class RequestsCommon( BaseController, Us status=status, message=message ) ) def __update_samples( self, trans, cntrller, request, sample_widgets, **kwd ): - # Determine if the values in kwd require updating the request's samples. The list of - # sample_widgets must have the same number of objects as request.samples, but some of - # the objects can be None. Those that are not None correspond to samples selected by - # the user for performing an action on multiple samples simultaneously. + # The list of sample_widgets must have the same number of objects as request.samples, + # but some of the objects can be None. Those that are not None correspond to samples + # selected by the user for performing an action on multiple samples simultaneously. + # The items in the sample_widgets list have already been populated with any changed + # param values (changed implies the value in kwd is different from the attribute value + # in the database) in kwd before this method is reached. def handle_error( **kwd ): kwd[ 'status' ] = 'error' return trans.response.send_redirect( web.url_for( controller='requests_common', @@ -1147,12 +1158,6 @@ class RequestsCommon( BaseController, Us cntrller=cntrller, **kwd ) ) params = util.Params( kwd ) - sample_operation = params.get( 'sample_operation', 'none' ) - if sample_operation != 'none': - # These values will be in kwd if the user checked 1 or more checkboxes for performing this action - # on a set of samples. - library_id = params.get( 'sample_0_library_id', 'none' ) - folder_id = params.get( 'sample_0_folder_id', 'none' ) for index, sample_widget in enumerate( sample_widgets ): if sample_widget is not None: # sample_widget will be None if the user checked sample check boxes and selected an action @@ -1161,21 +1166,16 @@ class RequestsCommon( BaseController, Us # Get the sample's form values to see if they have changed. form_values = trans.sa_session.query( trans.model.FormValues ).get( sample.values.id ) if sample.name != sample_widget[ 'name' ] or \ - sample.bar_code != sample_widget[ 'barcode' ] or \ + sample.bar_code != sample_widget[ 'bar_code' ] or \ sample.library != sample_widget[ 'library' ] or \ sample.folder != sample_widget[ 'folder' ] or \ form_values.content != sample_widget[ 'field_values' ]: # Information about this sample has been changed. sample.name = sample_widget[ 'name' ] - barcode = sample_widget[ 'barcode' ] - # The bar_code field requires special handling because after a request is submitted, the - # state of a sample cannot be changed without a bar_code associated with the sample. Bar - # codes can only be added to a sample after the request is submitted. Also, a samples will - # not have an associated SampleState until the request is submitted, at which time the sample - # is automatically associated with the first SamplesState configured by the admin for the - # request's RequestType. - if barcode: - bc_message = self.__validate_barcode( trans, sample, bar_code ) + bar_code = sample_widget[ 'bar_code' ] + # If the sample has a new bar_code, make sure it is unique. + if bar_code: + bc_message = self.__validate_bar_code( trans, sample, bar_code ) if bc_message: kwd[ 'message' ] = bc_message del kwd[ 'save_samples_button' ] @@ -1191,7 +1191,7 @@ class RequestsCommon( BaseController, Us 'Bar code associated with the sample' ) trans.sa_session.add( event ) trans.sa_session.flush() - sample.bar_code = barcode + sample.bar_code = bar_code sample.library = sample_widget[ 'library' ] sample.folder = sample_widget[ 'folder' ] form_values.content = sample_widget[ 'field_values' ] @@ -1281,7 +1281,7 @@ class RequestsCommon( BaseController, Us # Update the sample attributes from kwd sample_id = None name = util.restore_text( params.get( 'sample_%i_name' % index, sample.name ) ) - bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, sample.bar_code ) ) + bar_code = util.restore_text( params.get( 'sample_%i_bar_code' % index, sample.bar_code ) ) library_id = util.restore_text( params.get( 'sample_%i_library_id' % id_index, '' ) ) if not library_id and sample.library: library_id = trans.security.encode_id( sample.library.id ) @@ -1303,7 +1303,7 @@ class RequestsCommon( BaseController, Us **kwd ) sample_widgets.append( dict( id=sample_id, name=name, - barcode=bar_code, + bar_code=bar_code, library=library, folder=folder, field_values=field_values, @@ -1317,7 +1317,7 @@ class RequestsCommon( BaseController, Us if not name: break id_index = index + 1 - bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, '' ) ) + bar_code = util.restore_text( params.get( 'sample_%i_bar_code' % index, '' ) ) library_id = util.restore_text( params.get( 'sample_%i_library_id' % id_index, '' ) ) folder_id = util.restore_text( params.get( 'sample_%i_folder_id' % id_index, '' ) ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) @@ -1334,7 +1334,7 @@ class RequestsCommon( BaseController, Us **kwd ) sample_widgets.append( dict( id=None, name=name, - barcode=bar_code, + bar_code=bar_code, library=library, folder=folder, field_values=field_values, @@ -1492,31 +1492,24 @@ class RequestsCommon( BaseController, Us action='edit_samples', cntrller=cntrller, **kwd ) ) - def __validate_barcode( self, trans, sample, barcode ): + def __validate_bar_code( self, trans, sample, bar_code ): """ - Makes sure that the barcode about to be assigned to a sample is globally unique. - That is, barcodes must be unique across requests in Galaxy sample tracking. + Make sure that the bar_code about to be assigned to a sample is globally unique. + That is, bar_codes must be unique across requests in Galaxy sample tracking. + Bar codes are not required, but if used, they can only be added to a sample after + the request is submitted. """ message = '' unique = True for index in range( len( sample.request.samples ) ): - # Check for empty bar code - if not barcode.strip(): - if sample.state.id == sample.request.type.states[0].id: - # The user has not yet filled in the barcode value, but the sample is - # 'new', so all is well. - break - else: - message = "Fill in the barcode for sample (%s) before changing it's state." % sample.name - break # TODO: Add a unique constraint to sample.bar_code table column # Make sure bar code is unique - for sample_with_barcode in trans.sa_session.query( trans.model.Sample ) \ - .filter( trans.model.Sample.table.c.bar_code == barcode ): - if sample_with_barcode and sample_with_barcode.id != sample.id: + for sample_with_bar_code in trans.sa_session.query( trans.model.Sample ) \ + .filter( trans.model.Sample.table.c.bar_code == bar_code ): + if sample_with_bar_code and sample_with_bar_code.id != sample.id: message = '''The bar code (%s) associated with the sample (%s) belongs to another sample. Bar codes must be unique across all samples, so use a different bar code - for this sample.''' % ( barcode, sample.name ) + for this sample.''' % ( bar_code, sample.name ) unique = False break if not unique: --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -122,7 +122,7 @@ is_rejected = request.is_rejected is_submitted = sample.request.is_submitted is_unsubmitted = sample.request.is_unsubmitted - can_delete_samples = not is_complete + can_delete_samples = editing_samples and request.samples and ( ( is_admin and not is_complete ) or is_unsubmitted ) display_checkboxes = editing_samples and ( is_complete or is_rejected or is_submitted ) display_bar_code = request.samples and ( is_complete or is_rejected or is_submitted ) display_datasets = request.samples and ( is_complete or is_submitted ) @@ -153,10 +153,10 @@ %if display_bar_code: <td valign="top"> %if is_admin: - <input type="text" name="sample_${sample_widget_index}_barcode" value="${sample_widget['barcode']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}" size="10"/> %else: - ${sample_widget['barcode']} - <input type="hidden" name="sample_${sample_widget_index}_barcode" value="${sample_widget['barcode']}"/> + ${sample_widget['bar_code']} + <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}"/> %endif </td> %endif @@ -234,7 +234,7 @@ is_submitted = request.is_submitted is_unsubmitted = request.is_unsubmitted can_add_samples = request.is_unsubmitted - can_delete_samples = editing_samples and request.samples and not is_complete + can_delete_samples = editing_samples and request.samples and ( ( is_admin and not is_complete ) or is_unsubmitted ) can_edit_samples = request.samples and ( is_admin or not is_complete ) can_select_datasets = is_admin and displayable_sample_widgets and ( is_submitted or is_complete ) can_transfer_datasets = is_admin and request.samples and not request.is_rejected @@ -280,14 +280,14 @@ <tbody><% trans.sa_session.refresh( request ) %> ## displayable_sample_widgets is a dictionary whose keys are: - ## id, name, barcode, library, folder, field_values, library_select_field, folder_select_field + ## id, name, bar_code, library, folder, field_values, library_select_field, folder_select_field ## A displayable_sample_widget will have an id == None if the widget's associated sample has not ## yet been saved (i.e., the use clicked the "Add sample" button but has not yet clicked the ## "Save" button. %for sample_widget_index, sample_widget in enumerate( displayable_sample_widgets ): <% sample_widget_name = sample_widget[ 'name' ] - sample_widget_barcode = sample_widget[ 'barcode' ] + sample_widget_bar_code = sample_widget[ 'bar_code' ] sample_widget_library = sample_widget[ 'library' ] if sample_widget_library: if cntrller == 'requests': @@ -309,7 +309,12 @@ <td> %if sample.state and ( can_select_datasets or can_transfer_datasets ): ## A sample will have a state only after the request has been submitted. - <% encoded_id = trans.security.encode_id( sample.id ) %> + <% + encoded_id = trans.security.encode_id( sample.id ) + transferred_dataset_files = sample.transferred_dataset_files + if not transferred_dataset_files: + transferred_dataset_files = [] + %><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="sample-${sample.id}-popup"> ${sample.name} </div> @@ -317,8 +322,10 @@ %if can_select_datasets: <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ), sample_id=trans.security.encode_id( sample.id ) )}">Select datasets to transfer</a></li> %endif - %if sample.untransferred_dataset_files: - <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Transfer datasets</a></li> + %if sample.datasets and len( sample.datasets ) > len( transferred_dataset_files ): + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Manage selected datasets</a></li> + %elif sample.datasets and len(sample.datasets ) == len( transferred_dataset_files ): + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=trans.model.SampleDataset.transfer_status.COMPLETE )}">View transferred datasets</a></li> %endif </div> %else: @@ -326,7 +333,7 @@ %endif </td> %if display_bar_code: - <td>${sample_widget_barcode}</td> + <td>${sample_widget_bar_code}</td> %endif %if is_unsubmitted: <td>Unsubmitted</td> @@ -361,9 +368,8 @@ <td> %if is_admin: <% - if sample.transferred_dataset_files: - transferred_dataset_files = sample.transferred_dataset_files - else: + transferred_dataset_files = sample.transferred_dataset_files + if not transferred_dataset_files: transferred_dataset_files = [] %> %if not sample.datasets: --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1575,7 +1575,7 @@ class TwillTestCase( unittest.TestCase ) 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_barcode" % index + 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"

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galaxy-dist commit 10d0ffe5b7e2: Include BLAST-XML to tabular in tool_conf.xml.sample
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 1286962559 -3600 # Node ID 10d0ffe5b7e22b2d122945ab5b7fa951a18c6e4a # Parent caed55b53f5a811226e0bfa1c177e7b3e57a909a Include BLAST-XML to tabular in tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -268,6 +268,7 @@ <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" /><tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /><tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> + <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /><tool file="ncbi_blast_plus/blast_filter_fasta.xml" /></section><section name="NGS: Mapping" id="solexa_tools">

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galaxy-dist commit 122aaabe2c7e: Workaround Issue 397 using 'if' in Cheetah template to avoid hidden parameters
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 1286965628 -3600 # Node ID 122aaabe2c7eb48726f65233370926b838b6b444 # Parent 10d0ffe5b7e22b2d122945ab5b7fa951a18c6e4a Workaround Issue 397 using 'if' in Cheetah template to avoid hidden parameters --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -12,11 +12,12 @@ blastn #end if -task $blast_type -evalue $evalue_cutoff -$adv_opts.filter_query -$adv_opts.strand -out $output1 $out_format -num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": +$adv_opts.filter_query +$adv_opts.strand ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): @@ -26,6 +27,8 @@ blastn -word_size $adv_opts.word_size #end if $adv_opts.ungapped +## End of advanced options: +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -78,13 +81,7 @@ blastn <option value="basic" selected="True">Hide Advanced Options</option><option value="advanced">Show Advanced Options</option></param> - <when value="basic"> - <param name="filter_query" type="hidden" value="" /> - <param name="strand" type="hidden" value="" /> - <param name="max_hits" type="hidden" value="" /> - <param name="word_size" type="hidden" value="" /> - <param name="ungapped" type="hidden" value="" /> - </when> + <when value="basic" /><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -12,11 +12,12 @@ blastp #end if -task $blast_type -evalue $evalue_cutoff -$adv_opts.filter_query -$adv_opts.matrix -out $output1 $out_format -num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": +$adv_opts.filter_query +$adv_opts.matrix ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): @@ -27,6 +28,8 @@ blastp #end if ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped +## End of advanced options: +#end if </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -73,16 +76,7 @@ blastp <option value="basic" selected="True">Hide Advanced Options</option><option value="advanced">Show Advanced Options</option></param> - <when value="basic"> - <param name="filter_query" type="hidden" value="" /> - <param name="matrix" type="hidden" value="" /> - <param name="max_hits" type="hidden" value="" /> - <param name="word_size" type="hidden" value="" /> -  - </when> + <when value="basic" /><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -11,12 +11,13 @@ tblastx -subject "$db_opts.subject" #end if -evalue $evalue_cutoff +-out $output1 +$out_format +-num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": $adv_opts.filter_query $adv_opts.strand $adv_opts.matrix --out $output1 -$out_format --num_threads 8 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): @@ -25,6 +26,8 @@ tblastx #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): -word_size $adv_opts.word_size #end if +## End of advanced options: +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -67,13 +70,7 @@ tblastx <option value="basic" selected="True">Hide Advanced Options</option><option value="advanced">Show Advanced Options</option></param> - <when value="basic"> - <param name="filter_query" type="hidden" value="" /> - <param name="strand" type="hidden" value="" /> - <param name="matrix" type="hidden" value="" /> - <param name="max_hits" type="hidden" value="" /> - <param name="word_size" type="hidden" value="" /> - </when> + <when value="basic" /><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -11,12 +11,13 @@ blastx -subject "$db_opts.subject" #end if -evalue $evalue_cutoff +-out $output1 +$out_format +-num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": $adv_opts.filter_query $adv_opts.strand $adv_opts.matrix --out $output1 -$out_format --num_threads 8 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): @@ -26,6 +27,8 @@ blastx -word_size $adv_opts.word_size #end if $adv_opts.ungapped +## End of advanced options: +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -68,14 +71,7 @@ blastx <option value="basic" selected="True">Hide Advanced Options</option><option value="advanced">Show Advanced Options</option></param> - <when value="basic"> - <param name="filter_query" type="hidden" value="" /> - <param name="strand" type="hidden" value="" /> - <param name="matrix" type="hidden" value="" /> - <param name="max_hits" type="hidden" value="" /> - <param name="word_size" type="hidden" value="" /> - <param name="ungapped" type="hidden" value="" /> - </when> + <when value="basic" /><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -11,11 +11,12 @@ tblastn -subject "$db_opts.subject" #end if -evalue $evalue_cutoff -$adv_opts.filter_query -$adv_opts.matrix -out $output1 $out_format -num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": +$adv_opts.filter_query +$adv_opts.matrix ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): @@ -26,6 +27,8 @@ tblastn #end if ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped +## End of advanced options: +#end if </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -68,16 +71,7 @@ tblastn <option value="basic" selected="True">Hide Advanced Options</option><option value="advanced">Show Advanced Options</option></param> - <when value="basic"> - <param name="filter_query" type="hidden" value="" /> - <param name="matrix" type="hidden" value="" /> - <param name="max_hits" type="hidden" value="" /> - <param name="word_size" type="hidden" value="" /> -  - </when> + <when value="basic" /><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />

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galaxy-dist commit 5c212dfc6189: Fix a caption capitalisation
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 1286980710 -3600 # Node ID 5c212dfc6189bb41d334b0519411ca4f04fde9ec # Parent 122aaabe2c7eb48726f65233370926b838b6b444 Fix a caption capitalisation --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -62,7 +62,7 @@ blastn <option value="vecscreen">vecscreen</option> --></param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="-outfmt 6" selected="True">Tabular</option><option value="-outfmt 5">BLAST XML</option> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -57,7 +57,7 @@ blastp <option value="blastp">blastp</option><option value="blastp-short">blastp-short</option></param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="-outfmt 6" selected="True">Tabular</option><option value="-outfmt 5">BLAST XML</option> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -51,7 +51,7 @@ tblastx <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/></when></conditional> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="-outfmt 6" selected="True">Tabular</option><option value="-outfmt 5">BLAST XML</option> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -52,7 +52,7 @@ blastx <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/></when></conditional> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="-outfmt 6" selected="True">Tabular</option><option value="-outfmt 5">BLAST XML</option> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -52,7 +52,7 @@ tblastn <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/></when></conditional> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="-outfmt 6" selected="True">Tabular</option><option value="-outfmt 5">BLAST XML</option>

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galaxy-dist commit 0f6ace5c397b: Ignore backup files from some editors
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 1286965717 -3600 # Node ID 0f6ace5c397b000993db8e491a33e42423cdc807 # Parent d8184d91928c83f0269bd0267be949bc5d676e8b Ignore backup files from some editors --- a/.hgignore +++ b/.hgignore @@ -43,4 +43,4 @@ run_functional_tests.html *.orig .DS_Store *.rej - +*~

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galaxy-dist commit d8184d91928c: Remove FASTA filter script from BLAST+ tools (I want to generalise it)
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 1287998919 -3600 # Node ID d8184d91928c83f0269bd0267be949bc5d676e8b # Parent 5c212dfc6189bb41d334b0519411ca4f04fde9ec Remove FASTA filter script from BLAST+ tools (I want to generalise it) --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -269,7 +269,6 @@ <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /><tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /><tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /> - <tool file="ncbi_blast_plus/blast_filter_fasta.xml" /></section><section name="NGS: Mapping" id="solexa_tools"><tool file="sr_mapping/lastz_wrapper.xml" /> --- 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>

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galaxy-dist commit f2383b761f4e: Make sure samples have associated target libraries befoe enabling ability to transfer datasets, use better naming convention for request history code and templates, eliminate the ability to submit a request unless it has samples.
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 1289507783 18000 # Node ID f2383b761f4e05442fd5ba6b1cde517732aa2c03 # Parent dfc848840870fa9936a69e62322446fcb940fb40 Make sure samples have associated target libraries befoe enabling ability to transfer datasets, use better naming convention for request history code and templates, eliminate the ability to submit a request unless it has samples. --- a/templates/requests/common/view_sample_datasets.mako +++ b/templates/requests/common/view_sample_datasets.mako @@ -7,14 +7,14 @@ is_complete = sample.request.is_complete is_submitted = sample.request.is_submitted can_select_datasets = is_admin and ( is_complete or is_submitted ) - can_transfer_datasets = is_admin and sample.untransferred_dataset_files + can_transfer_datasets = is_admin and sample.untransferred_dataset_files and sample.library and sample.folder %><br/><br/><ul class="manage-table-actions"> %if can_transfer_datasets: - <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Transfer datasets</a></li> + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Manage selected datasets</a></li> %endif <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=transfer_status )}">Refresh page</a></li><li><a class="action-button" id="sample-${sample.id}-popup" class="menubutton">Dataset Actions</a></li> --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -47,7 +47,7 @@ %if can_edit_request: <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> %endif - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> %if can_reject: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> %endif --- a/lib/galaxy/web/controllers/requests.py +++ b/lib/galaxy/web/controllers/requests.py @@ -57,9 +57,9 @@ class Requests( BaseController ): action='undelete_request', cntrller='requests', **kwd ) ) - if operation == "request_events": + if operation == "view_request_history": return trans.response.send_redirect( web.url_for( controller='requests_common', - action='request_events', + action='view_request_history', cntrller='requests', **kwd ) ) --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -76,7 +76,7 @@ class RequestsGrid( grids.Grid ): StateColumn( "State", key='state', filterable="advanced", - link=( lambda item: iff( item.deleted, None, dict( operation="request_events", id=item.id ) ) ) + link=( lambda item: iff( item.deleted, None, dict( operation="view_request_history", id=item.id ) ) ) ) ] columns.append( grids.MulticolFilterColumn( "Search", @@ -579,8 +579,8 @@ class RequestsCommon( BaseController, Us status=status, message=message ) ) @web.expose - @web.require_login( "sequencing request events" ) - def request_events( self, trans, cntrller, **kwd ): + @web.require_login( "sequencing request history" ) + def view_request_history( self, trans, cntrller, **kwd ): params = util.Params( kwd ) request_id = params.get( 'id', None ) try: @@ -590,7 +590,7 @@ class RequestsCommon( BaseController, Us events_list = [] for event in request.events: events_list.append( ( event.state, time_ago( event.update_time ), event.comment ) ) - return trans.fill_template( '/requests/common/events.mako', + return trans.fill_template( '/requests/common/view_request_history.mako', cntrller=cntrller, events_list=events_list, request=request ) --- a/templates/admin/requests/select_datasets_to_transfer.mako +++ b/templates/admin/requests/select_datasets_to_transfer.mako @@ -72,7 +72,7 @@ <% is_admin = cntrller == 'requests_admin' and trans.user_is_admin() - can_transfer_datasets = is_admin and sample.untransferred_dataset_files + can_transfer_datasets = is_admin and sample.untransferred_dataset_files and sample.library and sample.folder %><br/><br/> @@ -85,8 +85,15 @@ </ul> %if not sample: + <br/><font color="red"><b><i>Select a sample before selecting datasets to transfer</i></b></font> - <br/><br/> + <br/> +%endif + +%if request.samples_without_library_destinations: + <br/> + <font color="red"><b><i>Select a target data library and folder for all samples before starting the sequence run</i></b></font> + <br/> %endif %if message: --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -175,9 +175,9 @@ class RequestsAdmin( BaseController, Use action='view_request', cntrller='requests_admin', **kwd ) ) - if operation == "request_events": + if operation == "view_request_history": return trans.response.send_redirect( web.url_for( controller='requests_common', - action='request_events', + action='view_request_history', cntrller='requests_admin', **kwd ) ) if operation == "reject": --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1517,7 +1517,7 @@ class TwillTestCase( unittest.TestCase ) 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.visit_url( "%s/requests_common/request_events?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) + 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: --- 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>${comments}</a></td> - </tr> - %endfor - </tbody> - </table> -</div> --- a/templates/requests/common/edit_basic_request_info.mako +++ b/templates/requests/common/edit_basic_request_info.mako @@ -3,7 +3,13 @@ <% is_admin = cntrller == 'requests_admin' and trans.user_is_admin() - can_add_samples = request.is_unsubmitted + is_complete = request.is_complete + is_submitted = request.is_submitted + is_unsubmitted = request.is_unsubmitted + can_add_samples = is_unsubmitted + can_reject = is_admin and is_submitted + can_select_datasets = is_admin and ( is_complete or is_submitted ) + can_submit_request = request.samples and is_unsubmitted %><br/><br/> @@ -11,12 +17,14 @@ <li><a class="action-button" id="request-${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_add_samples: + %if can_submit_request: <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit this request</a> %endif - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> - %if is_admin and request.is_submitted: + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> + %if can_reject: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> + %endif + %if can_select_datasets: <a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> %endif </div> --- a/templates/admin/requests/reject.mako +++ b/templates/admin/requests/reject.mako @@ -8,7 +8,7 @@ <h2>Reject Sequencing Request "${request.name}"</h2><ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">View history</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">View history</a></li><li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">Browse this request</a> --- a/templates/requests/common/view_request.mako +++ b/templates/requests/common/view_request.mako @@ -44,7 +44,7 @@ %if can_edit_request: <a class="action-button" href="${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 - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> %if can_reject: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> %endif @@ -52,8 +52,15 @@ </ul> %if request.is_rejected: + <br/><font color="red"><b><i>Reason for rejection: </i></b></font><b>${request.last_comment}</b> - <br/><br/> + <br/> +%endif + +%if request.samples_without_library_destinations: + <br/> + <font color="red"><b><i>Select a target data library and folder for all samples before starting the sequence run</i></b></font> + <br/> %endif %if message: @@ -94,7 +101,7 @@ <div class="form-row"><label>${field_label}:</label> %if field_label == 'State': - <a href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">${field_value}</a> + <a href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">${field_value}</a> %else: ${field_value} %endif @@ -154,6 +161,11 @@ render_buttons = can_edit_samples %> ${render_samples_grid( cntrller, request, displayable_sample_widgets=displayable_sample_widgets, action='view_request', editing_samples=False, encoded_selected_sample_ids=[], render_buttons=render_buttons, grid_header=grid_header )} + ## Render the other grids + <% trans.sa_session.refresh( request.type.sample_form ) %> + %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, editing_samples=False )} + %endfor %else: There are no samples. %if can_add_samples: @@ -162,8 +174,3 @@ </ul> %endif %endif -## Render the other grids -<% trans.sa_session.refresh( request.type.sample_form ) %> -%for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, editing_samples=False )} -%endfor --- /dev/null +++ b/templates/requests/common/view_request_history.mako @@ -0,0 +1,58 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<% + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + is_complete = request.is_complete + is_submitted = request.is_submitted + is_unsubmitted = request.is_unsubmitted + can_add_samples = is_unsubmitted + can_edit_request = ( is_admin and not is_complete ) or is_unsubmitted + can_reject = is_admin and is_submitted + can_select_datasets = is_admin and ( is_complete or is_submitted ) + can_submit_request = request.samples and is_unsubmitted +%> + +<br/><br/> +<ul class="manage-table-actions"> + <li><a class="action-button" id="request-${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="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> + %endif + %if can_submit_request: + <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${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: + <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>${comments}</a></td> + </tr> + %endfor + </tbody> + </table> +</div> --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -322,7 +322,7 @@ %if can_select_datasets: <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ), sample_id=trans.security.encode_id( sample.id ) )}">Select datasets to transfer</a></li> %endif - %if sample.datasets and len( sample.datasets ) > len( transferred_dataset_files ): + %if sample.datasets and len( sample.datasets ) > len( transferred_dataset_files ) and sample.library and sample.folder: <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Manage selected datasets</a></li> %elif sample.datasets and len(sample.datasets ) == len( transferred_dataset_files ): <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=trans.model.SampleDataset.transfer_status.COMPLETE )}">View transferred datasets</a></li>

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galaxy-dist commit caed55b53f5a: Allows the downloading of metadata files associated with datasets (such as bai indices for bam files). This is done by adding a dropdown menu to the Save icon of appropriate datasets. Could potentially be modified to access implicitly converted datatypes as well in the future. Closes #410
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 1289525191 18000 # Node ID caed55b53f5a811226e0bfa1c177e7b3e57a909a # Parent ff7327f2946e9121139cefbf4a45dba2791b7162 Allows the downloading of metadata files associated with datasets (such as bai indices for bam files). This is done by adding a dropdown menu to the Save icon of appropriate datasets. Could potentially be modified to access implicitly converted datatypes as well in the future. Closes #410 --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -1,8 +1,10 @@ <% _=n_ %> ## Render the dataset `data` as history item, using `hid` as the displayed id <%def name="render_dataset( data, hid, show_deleted_on_refresh = False, for_editing = True )"> - <a name="${trans.security.encode_id( data.id )}"></a><% + dataset_id = trans.security.encode_id( data.id ) + from galaxy.datatypes.metadata import FileParameter + if data.state in ['no state','',None]: data_state = "queued" else: @@ -41,7 +43,6 @@ %endif %else: <% - dataset_id = trans.security.encode_id( data.id ) if for_editing: display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' ) else: @@ -117,10 +118,25 @@ %endif </div><div class="info">${_('Info: ')}${data.display_info()}</div> - <div> - <% dataset_id=trans.security.encode_id( data.id ) %> + <div> %if data.has_data(): + + ## Check for downloadable metadata files + <% meta_files = [ k for k in data.metadata.spec.keys() if isinstance( data.metadata.spec[k].param, FileParameter ) ] %> + %if meta_files: + <div popupmenu="dataset-${dataset_id}-popup"> + %for file_type in meta_files: + <a class="action-button" href="${h.url_for( controller='dataset', action='get_metadata_file', hda_id=dataset_id, metadata_type=file_type )}"> + Download ${file_type}</a> + %endfor + </div> + <div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup"> + %endif <a href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title="Save" class="icon-button disk tooltip"></a> + %if meta_files: + </div> + %endif + %if for_editing: <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> %if app.config.get_bool( 'enable_tracks', False ) and data.ext in app.datatypes_registry.get_available_tracks(): --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -277,6 +277,7 @@ var updater_callback = function ( tracke // Keep going (if there are still any items to track) updater( tracked_datasets ); } + make_popup_menus(); }, error: function() { // Just retry, like the old method, should try to be smarter --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -305,7 +305,18 @@ class DatasetInterface( BaseController, return trans.show_error_message( msg ) - + @web.expose + def get_metadata_file(self, trans, hda_id, metadata_type): + """ Allows the downloading of metadata files associated with datasets (eg. bai index for bam files) """ + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( hda_id ) ) + if not data or not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ): + return trans.show_error_message( "You are not allowed to access this dataset" ) + + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150] + trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s].%s" % (data.hid, fname, metadata_type) + return open(data.metadata.get(metadata_type).file_name) + @web.expose def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, **kwd): """Catches the dataset id and displays file contents as directed""" @@ -323,8 +334,7 @@ class DatasetInterface( BaseController, data = None if not data: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) - current_user_roles = trans.get_current_user_roles() - if not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): + if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ): return trans.show_error_message( "You are not allowed to access this dataset" ) if data.state == trans.model.Dataset.states.UPLOAD: @@ -358,8 +368,7 @@ class DatasetInterface( BaseController, if not to_ext: to_ext = data.extension valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = data.name - fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] + fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150] trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s].%s" % (data.hid, fname, to_ext) return open( data.file_name ) if not os.path.exists( data.file_name ):

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