sanger/limber

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misc: wip rnaf pipeline #3385
Ben Topping authored fe551b29
complete00:00:22
1
git clone
2
codeclimate validate-config
View output
codeclimate validate-config
No errors or warnings found in .codeclimate.json.
3
codeclimate prepare
View output
codeclimate prepare
4
builder pull-engines
View output
determining required images
5
structure
View output
12
Parser process id: 12
codeclimate-parser socket not present
waiting 1s...
W, [2024-10-28T08:51:09.384326 #1]  WARN -- : Skipping app/frontend/javascript/shared/transfersLayouts.js due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:09.384365 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:09.795541 #1]  WARN -- : Skipping app/frontend/javascript/multi-stamp/components/MultiStampLibrarySplitter.js due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:09.795582 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:10.748764 #1]  WARN -- : Skipping app/models/concerns/presenters/statemachine/state_does_not_allow_child_creation.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:10.748800 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:10.812298 #1]  WARN -- : Skipping app/models/concerns/presenters/extended_csv.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:10.812337 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:11.013102 #1]  WARN -- : Skipping app/models/utility/pcr_cycles_csv_file_upload_config_base.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:11.013135 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:11.194313 #1]  WARN -- : Skipping app/models/presenters/plate_presenter.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:11.194344 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:11.612314 #1]  WARN -- : Skipping app/models/labware_metadata.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:11.612356 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:11.782336 #1]  WARN -- : Skipping app/models/sequencescape_submission.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:11.782366 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:11.849561 #1]  WARN -- : Skipping app/models/labware_creators/final_tube.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:11.849589 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:12.106769 #1]  WARN -- : Skipping app/models/labware_creators/tagged_plate.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:12.106801 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:12.154267 #1]  WARN -- : Skipping app/models/labware_creators/quadrant_split_plate.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:12.154304 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:12.272801 #1]  WARN -- : Skipping app/models/labware_creators/base.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:12.272832 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:12.315890 #1]  WARN -- : Skipping app/models/labware_creators/custom_tagged_plate.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:12.315920 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:12.393657 #1]  WARN -- : Skipping app/models/labware_creators/plate_split_to_tube_racks.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:12.393688 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:12.471762 #1]  WARN -- : Skipping app/models/labware_creators/quadrant_stamp_base.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:12.471792 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:12.482001 #1]  WARN -- : Skipping app/models/labware_creators/pooled_tubes_by_sample.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:12.482037 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:12.586641 #1]  WARN -- : Skipping app/helpers/page_helper.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:12.586674 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:12.596902 #1]  WARN -- : Skipping app/helpers/labware_helper.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:12.596933 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:12.599901 #1]  WARN -- : Skipping app/helpers/application_helper.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:12.599930 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:12.626388 #1]  WARN -- : Skipping app/helpers/barcode_labels_helper.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:12.626423 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:12.698344 #1]  WARN -- : Skipping app/controllers/search_controller.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:12.698376 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:12.761883 #1]  WARN -- : Skipping app/controllers/labware_controller.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:12.761913 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:12.827123 #1]  WARN -- : Skipping app/sequencescape/sequencescape/api/v2.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:12.827154 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:12.980326 #1]  WARN -- : Skipping app/sequencescape/sequencescape/api/v2/shared/has_requests.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:12.980355 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:13.108626 #1]  WARN -- : Skipping lib/well_helpers.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:13.108655 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:13.127599 #1]  WARN -- : Skipping lib/robot_configuration.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:13.127624 #1]  WARN -- : Response status: 422
6
duplication
View output
12
Parser process id: 12
codeclimate-parser socket not present
waiting 1s...
W, [2024-10-28T08:51:16.556014 #1]  WARN -- : Skipping app/frontend/javascript/shared/transfersLayouts.js due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:16.556059 #1]  WARN -- : Response status: 422
W, [2024-10-28T08:51:17.194959 #1]  WARN -- : Skipping app/frontend/javascript/multi-stamp/components/MultiStampLibrarySplitter.js due to CC::Parser::Client::HTTPError
W, [2024-10-28T08:51:17.195137 #1]  WARN -- : Response status: 422
I, [2024-10-28T08:51:17.563697 #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, [2024-10-28T08:51:17.631326 #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, [2024-10-28T08:51:17.749919 #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, [2024-10-28T08:51:17.867885 #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, [2024-10-28T08:51:17.927091 #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, [2024-10-28T08:51:18.094774 #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, [2024-10-28T08:51:18.211991 #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, [2024-10-28T08:51:18.252645 #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, [2024-10-28T08:51:18.312539 #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, [2024-10-28T08:51:18.454396 #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, [2024-10-28T08:51:18.544997 #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, [2024-10-28T08:51:18.610286 #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, [2024-10-28T08:51:18.671457 #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, [2024-10-28T08:51:18.781675 #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, [2024-10-28T08:51:18.816731 #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, [2024-10-28T08:51:18.919292 #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, [2024-10-28T08:51:18.942105 #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, [2024-10-28T08:51:18.998287 #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, [2024-10-28T08:51:19.017543 #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, [2024-10-28T08:51:19.024670 #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, [2024-10-28T08:51:19.041563 #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, [2024-10-28T08:51:19.043725 #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, [2024-10-28T08:51:19.083124 #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, [2024-10-28T08:51:19.202770 #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, [2024-10-28T08:51:19.305062 #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, [2024-10-28T08:51:19.324041 #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, [2024-10-28T08:51:19.352045 #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, [2024-10-28T08:51:19.440125 #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, [2024-10-28T08:51:19.540497 #1]  INFO -- : Skipping file ./lib/well_helpers.rb due to exception (Racc::ParseError): ./lib/well_helpers.rb:9 :: parse error on value ":" (tCOLON)

I, [2024-10-28T08:51:19.589423 #1]  INFO -- : Skipping file ./lib/robot_configuration.rb due to exception (Racc::ParseError): ./lib/robot_configuration.rb:9 :: parse error on value ":" (tCOLON)