Build #3380 - sanger/limber

Refactor pipeline configuration to include Haplotagging in bespoke PCR #3380

Dasun Pubudumal authored 28ce2aff

complete00:00:25

1	git clone	00:00:01
2	codeclimate validate-config	00:00:01	View output
`codeclimate validate-config No errors or warnings found in .codeclimate.json.`
3	codeclimate prepare	00:00:01	View output
`codeclimate prepare`
4	builder pull-engines	00:00:00	View output
`determining required images`
5	structure	00:00:08	View output
12 Parser process id: 12 codeclimate-parser socket not present waiting 1s... W, [2024-10-24T14:52:44.168898 #1] WARN -- : Skipping app/frontend/javascript/shared/transfersLayouts.js due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:44.168930 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:44.658909 #1] WARN -- : Skipping app/frontend/javascript/multi-stamp/components/MultiStampLibrarySplitter.js due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:44.658949 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:46.189720 #1] WARN -- : Skipping app/models/concerns/presenters/statemachine/state_does_not_allow_child_creation.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:46.189761 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:46.286274 #1] WARN -- : Skipping app/models/concerns/presenters/extended_csv.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:46.286311 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:46.504356 #1] WARN -- : Skipping app/models/utility/pcr_cycles_csv_file_upload_config_base.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:46.504390 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:46.715895 #1] WARN -- : Skipping app/models/presenters/plate_presenter.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:46.715936 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:47.230416 #1] WARN -- : Skipping app/models/labware_metadata.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:47.230458 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:47.417099 #1] WARN -- : Skipping app/models/sequencescape_submission.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:47.417131 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:47.528797 #1] WARN -- : Skipping app/models/labware_creators/final_tube.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:47.528843 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:47.846465 #1] WARN -- : Skipping app/models/labware_creators/tagged_plate.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:47.846501 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:47.899604 #1] WARN -- : Skipping app/models/labware_creators/quadrant_split_plate.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:47.899638 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:48.021128 #1] WARN -- : Skipping app/models/labware_creators/base.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:48.021164 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:48.076961 #1] WARN -- : Skipping app/models/labware_creators/custom_tagged_plate.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:48.076996 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:48.190358 #1] WARN -- : Skipping app/models/labware_creators/plate_split_to_tube_racks.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:48.190396 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:48.308862 #1] WARN -- : Skipping app/models/labware_creators/quadrant_stamp_base.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:48.308893 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:48.322699 #1] WARN -- : Skipping app/models/labware_creators/pooled_tubes_by_sample.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:48.322737 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:48.441662 #1] WARN -- : Skipping app/helpers/page_helper.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:48.441700 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:48.456075 #1] WARN -- : Skipping app/helpers/labware_helper.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:48.456110 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:48.459351 #1] WARN -- : Skipping app/helpers/application_helper.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:48.459383 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:48.493721 #1] WARN -- : Skipping app/helpers/barcode_labels_helper.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:48.493766 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:48.589671 #1] WARN -- : Skipping app/controllers/search_controller.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:48.589717 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:48.683937 #1] WARN -- : Skipping app/controllers/labware_controller.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:48.683981 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:48.769148 #1] WARN -- : Skipping app/sequencescape/sequencescape/api/v2.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:48.769279 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:49.006227 #1] WARN -- : Skipping app/sequencescape/sequencescape/api/v2/shared/has_requests.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:49.006291 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:49.156080 #1] WARN -- : Skipping lib/well_helpers.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:49.156115 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:49.177622 #1] WARN -- : Skipping lib/robot_configuration.rb due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:49.177655 #1] WARN -- : Response status: 422
6	duplication	00:00:06	View output
12 Parser process id: 12 codeclimate-parser socket not present waiting 1s... W, [2024-10-24T14:52:52.845237 #1] WARN -- : Skipping app/frontend/javascript/shared/transfersLayouts.js due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:52.845299 #1] WARN -- : Response status: 422 W, [2024-10-24T14:52:53.473827 #1] WARN -- : Skipping app/frontend/javascript/multi-stamp/components/MultiStampLibrarySplitter.js due to CC::Parser::Client::HTTPError W, [2024-10-24T14:52:53.474123 #1] WARN -- : Response status: 422 I, [2024-10-24T14:52:53.885514 #1] INFO -- : Skipping file ./app/models/concerns/presenters/statemachine/state_does_not_allow_child_creation.rb due to exception (Racc::ParseError): ./app/models/concerns/presenters/statemachine/state_does_not_allow_child_creation.rb:8 :: parse error on value ")" (tRPAREN) I, [2024-10-24T14:52:53.972190 #1] INFO -- : Skipping file ./app/models/concerns/presenters/extended_csv.rb due to exception (RubyParser::SyntaxError): Odd number (2) list for Hash. s(:array, s(:lvar, :index)) I, [2024-10-24T14:52:54.143780 #1] INFO -- : Skipping file ./app/models/utility/pcr_cycles_csv_file_upload_config_base.rb due to exception (RubyParser::SyntaxError): Odd number (2) list for Hash. s(:array, s(:call, nil, :input_amount_desired_min)) I, [2024-10-24T14:52:54.322028 #1] INFO -- : Skipping file ./app/models/presenters/plate_presenter.rb due to exception (Racc::ParseError): ./app/models/presenters/plate_presenter.rb:39 :: parse error on value ":" (tCOLON) I, [2024-10-24T14:52:54.401698 #1] INFO -- : Skipping file ./app/models/labels/tube_label.rb due to exception (RubyParser::SyntaxError): Odd number (2) list for Hash. s(:array, s(:call, nil, :first_line)) I, [2024-10-24T14:52:54.584777 #1] INFO -- : Skipping file ./app/models/labware_metadata.rb due to exception (Racc::ParseError): ./app/models/labware_metadata.rb:8 :: parse error on value ":" (tCOLON) I, [2024-10-24T14:52:54.723644 #1] INFO -- : Skipping file ./app/models/sequencescape_submission.rb due to exception (Racc::ParseError): ./app/models/sequencescape_submission.rb:39 :: parse error on value ":" (tCOLON) I, [2024-10-24T14:52:54.775782 #1] INFO -- : Skipping file ./app/models/labware_creators/final_tube.rb due to exception (RubyParser::SyntaxError): Odd number (2) list for Hash. s(:array, s(:call, nil, :parents)) I, [2024-10-24T14:52:54.826659 #1] INFO -- : Skipping file ./app/models/labware_creators/pcr_cycles_binned_plate/csv_file_base.rb due to exception (Racc::ParseError): ./app/models/labware_creators/pcr_cycles_binned_plate/csv_file_base.rb:18 :: parse error on value ":" (tCOLON) I, [2024-10-24T14:52:54.992633 #1] INFO -- : Skipping file ./app/models/labware_creators/tagged_plate.rb due to exception (RubyParser::SyntaxError): Odd number (2) list for Hash. s(:array, s(:call, nil, :tag_plate)) I, [2024-10-24T14:52:55.057217 #1] INFO -- : Skipping file ./app/models/labware_creators/quadrant_split_plate.rb due to exception (RubyParser::SyntaxError): Odd number (2) list for Hash. s(:array, s(:call, nil, :uuid)) I, [2024-10-24T14:52:55.146641 #1] INFO -- : Skipping file ./app/models/labware_creators/base.rb due to exception (Racc::ParseError): ./app/models/labware_creators/base.rb:21 :: parse error on value "%i[" (error) I, [2024-10-24T14:52:55.223905 #1] INFO -- : Skipping file ./app/models/labware_creators/custom_tagged_plate.rb due to exception (RubyParser::SyntaxError): Odd number (2) list for Hash. s(:array, s(:call, nil, :tag_plate)) I, [2024-10-24T14:52:55.354821 #1] INFO -- : Skipping file ./app/models/labware_creators/plate_split_to_tube_racks.rb due to exception (Racc::ParseError): ./app/models/labware_creators/plate_split_to_tube_racks.rb:48 :: parse error on value "%i[" (error) I, [2024-10-24T14:52:55.404466 #1] INFO -- : Skipping file ./app/models/labware_creators/custom_pooled_tubes/csv_file.rb due to exception (Racc::ParseError): ./app/models/labware_creators/custom_pooled_tubes/csv_file.rb:12 :: parse error on value ":" (tCOLON) I, [2024-10-24T14:52:55.498050 #1] INFO -- : Skipping file ./app/models/labware_creators/quadrant_stamp_base.rb due to exception (RubyParser::SyntaxError): Odd number (2) list for Hash. s(:array, s(:call, nil, :transfers)) I, [2024-10-24T14:52:55.540547 #1] INFO -- : Skipping file ./app/models/labware_creators/pooled_tubes_by_sample.rb due to exception (Racc::ParseError): ./app/models/labware_creators/pooled_tubes_by_sample.rb:20 :: parse error on value ":" (tCOLON) I, [2024-10-24T14:52:55.599604 #1] INFO -- : Skipping file ./app/models/labware_creators/common_file_handling/csv_file_for_tube_rack.rb due to exception (Racc::ParseError): ./app/models/labware_creators/common_file_handling/csv_file_for_tube_rack.rb:54 :: parse error on value "]" (tRBRACK) I, [2024-10-24T14:52:55.621398 #1] INFO -- : Skipping file ./app/models/labware_creators/common_file_handling/csv_file_for_tube_rack_with_rack_barcode.rb due to exception (Racc::ParseError): ./app/models/labware_creators/common_file_handling/csv_file_for_tube_rack_with_rack_barcode.rb:31 :: parse error on value "]" (tRBRACK) I, [2024-10-24T14:52:55.632684 #1] INFO -- : Skipping file ./app/helpers/page_helper.rb due to exception (Racc::ParseError): ./app/helpers/page_helper.rb:5 :: parse error on value ":" (tCOLON) I, [2024-10-24T14:52:55.650272 #1] INFO -- : Skipping file ./app/helpers/labware_helper.rb due to exception (Racc::ParseError): ./app/helpers/labware_helper.rb:5 :: parse error on value ":" (tCOLON) I, [2024-10-24T14:52:55.662053 #1] INFO -- : Skipping file ./app/helpers/application_helper.rb due to exception (Racc::ParseError): ./app/helpers/application_helper.rb:30 :: parse error on value ")" (tRPAREN) I, [2024-10-24T14:52:55.702245 #1] INFO -- : Skipping file ./app/helpers/barcode_labels_helper.rb due to exception (Racc::ParseError): ./app/helpers/barcode_labels_helper.rb:5 :: parse error on value ":" (tSYMBEG) I, [2024-10-24T14:52:55.811741 #1] INFO -- : Skipping file ./app/controllers/search_controller.rb due to exception (Racc::ParseError): ./app/controllers/search_controller.rb:8 :: parse error on value ":" (tCOLON) I, [2024-10-24T14:52:55.923730 #1] INFO -- : Skipping file ./app/controllers/labware_controller.rb due to exception (Racc::ParseError): ./app/controllers/labware_controller.rb:11 :: parse error on value ":" (tCOLON) I, [2024-10-24T14:52:55.947461 #1] INFO -- : Skipping file ./app/controllers/robots_controller.rb due to exception (Racc::ParseError): ./app/controllers/robots_controller.rb:14 :: parse error on value ":" (tCOLON) I, [2024-10-24T14:52:55.987207 #1] INFO -- : Skipping file ./app/sequencescape/sequencescape/api/v2.rb due to exception (RubyParser::SyntaxError): Odd number (2) list for Hash. s(:array, s(:call, nil, :child_plates)) I, [2024-10-24T14:52:56.080656 #1] INFO -- : Skipping file ./app/sequencescape/sequencescape/api/v2/shared/has_requests.rb due to exception (Racc::ParseError): ./app/sequencescape/sequencescape/api/v2/shared/has_requests.rb:44 :: parse error on value "&." (error) I, [2024-10-24T14:52:56.185961 #1] INFO -- : Skipping file ./lib/well_helpers.rb due to exception (Racc::ParseError): ./lib/well_helpers.rb:9 :: parse error on value ":" (tCOLON) I, [2024-10-24T14:52:56.236381 #1] INFO -- : Skipping file ./lib/robot_configuration.rb due to exception (Racc::ParseError): ./lib/robot_configuration.rb:9 :: parse error on value ":" (tCOLON)