sanger/limber

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Update rexml to version 3.3.9 #3394
depfu[bot] authored 26834c77
complete00:00:50
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
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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, [2024-10-28T16:06:50.815566 #1]  WARN -- : Skipping app/frontend/javascript/shared/transfersLayouts.js due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:50.815609 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:51.341641 #1]  WARN -- : Skipping app/frontend/javascript/multi-stamp/components/MultiStampLibrarySplitter.js due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:51.341686 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:52.854279 #1]  WARN -- : Skipping app/models/concerns/presenters/statemachine/state_does_not_allow_child_creation.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:52.854312 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:52.945566 #1]  WARN -- : Skipping app/models/concerns/presenters/extended_csv.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:52.945604 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:53.259408 #1]  WARN -- : Skipping app/models/utility/pcr_cycles_csv_file_upload_config_base.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:53.259462 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:53.533824 #1]  WARN -- : Skipping app/models/presenters/plate_presenter.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:53.533862 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:54.101718 #1]  WARN -- : Skipping app/models/labware_metadata.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:54.101749 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:54.316881 #1]  WARN -- : Skipping app/models/sequencescape_submission.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:54.316925 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:54.420217 #1]  WARN -- : Skipping app/models/labware_creators/final_tube.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:54.420246 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:54.781687 #1]  WARN -- : Skipping app/models/labware_creators/tagged_plate.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:54.781717 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:54.865233 #1]  WARN -- : Skipping app/models/labware_creators/quadrant_split_plate.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:54.865268 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:55.006700 #1]  WARN -- : Skipping app/models/labware_creators/base.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:55.006733 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:55.068931 #1]  WARN -- : Skipping app/models/labware_creators/custom_tagged_plate.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:55.068965 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:55.200617 #1]  WARN -- : Skipping app/models/labware_creators/plate_split_to_tube_racks.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:55.200651 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:55.323203 #1]  WARN -- : Skipping app/models/labware_creators/quadrant_stamp_base.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:55.323242 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:55.338923 #1]  WARN -- : Skipping app/models/labware_creators/pooled_tubes_by_sample.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:55.338953 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:55.489956 #1]  WARN -- : Skipping app/helpers/page_helper.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:55.489984 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:55.503029 #1]  WARN -- : Skipping app/helpers/labware_helper.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:55.503057 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:55.507174 #1]  WARN -- : Skipping app/helpers/application_helper.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:55.507200 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:55.543897 #1]  WARN -- : Skipping app/helpers/barcode_labels_helper.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:55.543930 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:55.655690 #1]  WARN -- : Skipping app/controllers/search_controller.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:55.655724 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:55.753933 #1]  WARN -- : Skipping app/controllers/labware_controller.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:55.753966 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:55.873285 #1]  WARN -- : Skipping app/sequencescape/sequencescape/api/v2.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:55.873316 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:56.098703 #1]  WARN -- : Skipping app/sequencescape/sequencescape/api/v2/shared/has_requests.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:56.098737 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:56.278585 #1]  WARN -- : Skipping lib/well_helpers.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:56.278616 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:06:56.306975 #1]  WARN -- : Skipping lib/robot_configuration.rb due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:06:56.307006 #1]  WARN -- : Response status: 422
6
duplication
View output
12
Parser process id: 12
codeclimate-parser socket not present
waiting 1s...
W, [2024-10-28T16:07:00.134914 #1]  WARN -- : Skipping app/frontend/javascript/shared/transfersLayouts.js due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:07:00.134952 #1]  WARN -- : Response status: 422
W, [2024-10-28T16:07:00.956429 #1]  WARN -- : Skipping app/frontend/javascript/multi-stamp/components/MultiStampLibrarySplitter.js due to CC::Parser::Client::HTTPError
W, [2024-10-28T16:07:00.956745 #1]  WARN -- : Response status: 422
I, [2024-10-28T16:07:01.470659 #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, [2024-10-28T16:07:01.553918 #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, [2024-10-28T16:07:01.707674 #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, [2024-10-28T16:07:01.869317 #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, [2024-10-28T16:07:01.944736 #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, [2024-10-28T16:07:02.145002 #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, [2024-10-28T16:07:02.293359 #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, [2024-10-28T16:07:02.338302 #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, [2024-10-28T16:07:02.399933 #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, [2024-10-28T16:07:02.540009 #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, [2024-10-28T16:07:02.605018 #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, [2024-10-28T16:07:02.687378 #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, [2024-10-28T16:07:02.759413 #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, [2024-10-28T16:07:02.878387 #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, [2024-10-28T16:07:02.914883 #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, [2024-10-28T16:07:03.038888 #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, [2024-10-28T16:07:03.041466 #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, [2024-10-28T16:07:03.105471 #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, [2024-10-28T16:07:03.124700 #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, [2024-10-28T16:07:03.137858 #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, [2024-10-28T16:07:03.152205 #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, [2024-10-28T16:07:03.161558 #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, [2024-10-28T16:07:03.196902 #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, [2024-10-28T16:07:03.308479 #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, [2024-10-28T16:07:03.425575 #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, [2024-10-28T16:07:03.448909 #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, [2024-10-28T16:07:03.482182 #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, [2024-10-28T16:07:03.578408 #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, [2024-10-28T16:07:03.682466 #1]  INFO -- : Skipping file ./lib/well_helpers.rb due to exception (Racc::ParseError): ./lib/well_helpers.rb:9 :: parse error on value ":" (tCOLON)

I, [2024-10-28T16:07:03.730930 #1]  INFO -- : Skipping file ./lib/robot_configuration.rb due to exception (Racc::ParseError): ./lib/robot_configuration.rb:9 :: parse error on value ":" (tCOLON)