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lots of 5xx server errors since March 6th #394

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mr-c opened this issue Mar 27, 2022 · 4 comments
Open

lots of 5xx server errors since March 6th #394

mr-c opened this issue Mar 27, 2022 · 4 comments
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@kinow

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@mr-c
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mr-c commented Mar 27, 2022 •
edited
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Screenshot_20220327-115222

Example URL https://view.commonwl.org/workflows/github.com/heliumdatacommons/cwl_workflows/blob/578066ec5d6847892528f973b22531d4c8487280/workflows/complex-workflow/complex-workflow-1.cwl

See the 2nd sheet at https://docs.google.com/spreadsheets/d/1A3VjklUvJMsIpztpO6InuY63n3Bj2ejlgkdhHb_8eLs/edit?usp=drivesdk for a list of additional URLs
@kinow
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kinow commented Mar 27, 2022 •
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Tried to import this workflow on localhost:8080, with latest version from main (after changing docker-compose.yml to use build: ..)

It failed running cwltool for me. But not sure if that's the cause of the error 500.

Error 
spring_1_c02560f27616 | 2022-03-27 11:15:17,574 ERROR [task-1] org.commonwl.view.cwl.CWLToolRunner: ERROR Tool definition failed validation:
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:38:1: checking field
spring_1_c02560f27616 |                                                                                                    `steps`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:59:3:   checking object
spring_1_c02560f27616 |                                                                                                      `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/echo_step`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:61:5:     checking field
spring_1_c02560f27616 |                                                                                                        `in`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:62:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/echo_step/message`
spring_1_c02560f27616 |                                                                                                            Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_message`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_message,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_message
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:63:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/echo_step/output_location`
spring_1_c02560f27616 |                                                                                                            Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_output_location`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_output_location,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_output_location
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:66:3:   checking object
spring_1_c02560f27616 |                                                                                                      `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/re_tar_step`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:68:5:     checking field
spring_1_c02560f27616 |                                                                                                        `in`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:69:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/re_tar_step/archive_file`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:70:9:         Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:71:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/re_tar_step/file_list`
spring_1_c02560f27616 |                                                                                                            Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_step/file_out`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_step/file_out,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_step/file_out
spring_1_c02560f27616 |                                                                                                            Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:39:3:   checking object
spring_1_c02560f27616 |                                                                                                      `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/tar_step`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:41:5:     checking field
spring_1_c02560f27616 |                                                                                                        `in`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:42:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/tar_step/archive_file`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:43:9:         Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:44:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/tar_step/file_list`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:45:9:         Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:48:3:   checking object
spring_1_c02560f27616 |                                                                                                      `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/touch_step`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:52:5:     checking field
spring_1_c02560f27616 |                                                                                                        `in`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:55:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/touch_step/filename`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:56:9:         Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_files`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_files,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_files
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:53:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/touch_step/waitfor`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:54:9:         Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#tar_step/archive_out`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#tar_step/archive_out,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#tar_step/archive_out
spring_1_c02560f27616 | 
spring_1_c02560f27616 | org.commonwl.view.cwl.CWLValidationException: ERROR Tool definition failed validation:
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:38:1: checking field
spring_1_c02560f27616 |                                                                                                    `steps`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:59:3:   checking object
spring_1_c02560f27616 |                                                                                                      `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/echo_step`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:61:5:     checking field
spring_1_c02560f27616 |                                                                                                        `in`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:62:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/echo_step/message`
spring_1_c02560f27616 |                                                                                                            Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_message`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_message,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_message
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:63:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/echo_step/output_location`
spring_1_c02560f27616 |                                                                                                            Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_output_location`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_output_location,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_output_location
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:66:3:   checking object
spring_1_c02560f27616 |                                                                                                      `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/re_tar_step`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:68:5:     checking field
spring_1_c02560f27616 |                                                                                                        `in`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:69:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/re_tar_step/archive_file`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:70:9:         Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:71:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/re_tar_step/file_list`
spring_1_c02560f27616 |                                                                                                            Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_step/file_out`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_step/file_out,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_step/file_out
spring_1_c02560f27616 |                                                                                                            Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:39:3:   checking object
spring_1_c02560f27616 |                                                                                                      `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/tar_step`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:41:5:     checking field
spring_1_c02560f27616 |                                                                                                        `in`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:42:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/tar_step/archive_file`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:43:9:         Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:44:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/tar_step/file_list`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:45:9:         Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:48:3:   checking object
spring_1_c02560f27616 |                                                                                                      `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/touch_step`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:52:5:     checking field
spring_1_c02560f27616 |                                                                                                        `in`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:55:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/touch_step/filename`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:56:9:         Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_files`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_files,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_files
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:53:7:       checking
spring_1_c02560f27616 |                                                                                                          object
spring_1_c02560f27616 |                                                                                                          `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/touch_step/waitfor`
spring_1_c02560f27616 | ../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:54:9:         Field
spring_1_c02560f27616 |                                                                                                            `source` references
spring_1_c02560f27616 |                                                                                                            unknown identifier
spring_1_c02560f27616 |                                                                                                            `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#tar_step/archive_out`,
spring_1_c02560f27616 |                                                                                                            tried
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#tar_step/archive_out,
spring_1_c02560f27616 |                                                                                                            file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#tar_step/archive_out
spring_1_c02560f27616 | 
spring_1_c02560f27616 | 	at org.commonwl.view.cwl.CWLTool.runCwltoolOnWorkflow(CWLTool.java:121)
spring_1_c02560f27616 | 	at org.commonwl.view.cwl.CWLTool.getRDF(CWLTool.java:50)
spring_1_c02560f27616 | 	at org.commonwl.view.cwl.CWLService.parseWorkflowWithCwltool(CWLService.java:293)
spring_1_c02560f27616 | 	at org.commonwl.view.cwl.CWLToolRunner.createWorkflowFromQueued(CWLToolRunner.java:86)
spring_1_c02560f27616 | 	at org.commonwl.view.cwl.CWLToolRunner$$FastClassBySpringCGLIB$$cd465805.invoke(<generated>)
spring_1_c02560f27616 | 	at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218)
spring_1_c02560f27616 | 	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:783)
spring_1_c02560f27616 | 	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
spring_1_c02560f27616 | 	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:753)
spring_1_c02560f27616 | 	at org.springframework.aop.interceptor.AsyncExecutionInterceptor.lambda$invoke$0(AsyncExecutionInterceptor.java:115)
spring_1_c02560f27616 | 	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
spring_1_c02560f27616 | 	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
spring_1_c02560f27616 | 	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
spring_1_c02560f27616 | 	at java.lang.Thread.run(Thread.java:748)
postgres_1_35f55061ba2a | 2022-03-27 11:15:17.589 UTC [57] LOG:  execute <unnamed>: BEGIN
postgres_1_35f55061ba2a | 2022-03-27 11:15:17.589 UTC [57] LOG:  execute <unnamed>: select queuedwork0_.id as id1_0_0_, queuedwork0_.cwltool_status as cwltool_2_0_0_, queuedwork0_.cwltool_version as cwltool_3_0_0_, queuedwork0_.message as message4_0_0_, queuedwork0_.temp_representation as temp_rep5_0_0_, queuedwork0_.workflow_list as workflow6_0_0_ from queued_workflow queuedwork0_ where queuedwork0_.id=$1
postgres_1_35f55061ba2a | 2022-03-27 11:15:17.589 UTC [57] DETAIL:  parameters: $1 = '9e770cc1-9779-4050-8b08-0ed899b4c22a'
postgres_1_35f55061ba2a | 2022-03-27 11:15:17.604 UTC [57] LOG:  execute <unnamed>: update queued_workflow set cwltool_status=$1, cwltool_version=$2, message=$3, temp_representation=$4, workflow_list=$5 where id=$6
postgres_1_35f55061ba2a | 2022-03-27 11:15:17.604 UTC [57] DETAIL:  parameters: $1 = '"ERROR"', $2 = '', $3 = 'ERROR Tool definition failed validation:
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:38:1: checking field
postgres_1_35f55061ba2a | 	                                                                                                   `steps`
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:59:3:   checking object
postgres_1_35f55061ba2a | 	                                                                                                     `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/echo_step`
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:61:5:     checking field
postgres_1_35f55061ba2a | 	                                                                                                       `in`
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:62:7:       checking
postgres_1_35f55061ba2a | 	                                                                                                         object
postgres_1_35f55061ba2a | 	                                                                                                         `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/echo_step/message`
postgres_1_35f55061ba2a | 	                                                                                                           Field
postgres_1_35f55061ba2a | 	                                                                                                           `source` references
postgres_1_35f55061ba2a | 	                                                                                                           unknown identifier
postgres_1_35f55061ba2a | 	                                                                                                           `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_message`,
postgres_1_35f55061ba2a | 	                                                                                                           tried
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_message,
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_message
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:63:7:       checking
postgres_1_35f55061ba2a | 	                                                                                                         object
postgres_1_35f55061ba2a | 	                                                                                                         `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/echo_step/output_location`
postgres_1_35f55061ba2a | 	                                                                                                           Field
postgres_1_35f55061ba2a | 	                                                                                                           `source` references
postgres_1_35f55061ba2a | 	                                                                                                           unknown identifier
postgres_1_35f55061ba2a | 	                                                                                                           `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_output_location`,
postgres_1_35f55061ba2a | 	                                                                                                           tried
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_output_location,
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#echo_output_location
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:66:3:   checking object
postgres_1_35f55061ba2a | 	                                                                                                     `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/re_tar_step`
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:68:5:     checking field
postgres_1_35f55061ba2a | 	                                                                                                       `in`
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:69:7:       checking
postgres_1_35f55061ba2a | 	                                                                                                         object
postgres_1_35f55061ba2a | 	                                                                                                         `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/re_tar_step/archive_file`
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:70:9:         Field
postgres_1_35f55061ba2a | 	                                                                                                           `source` references
postgres_1_35f55061ba2a | 	                                                                                                           unknown identifier
postgres_1_35f55061ba2a | 	                                                                                                           `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive`,
postgres_1_35f55061ba2a | 	                                                                                                           tried
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive,
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:71:7:       checking
postgres_1_35f55061ba2a | 	                                                                                                         object
postgres_1_35f55061ba2a | 	                                                                                                         `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/re_tar_step/file_list`
postgres_1_35f55061ba2a | 	                                                                                                           Field
postgres_1_35f55061ba2a | 	                                                                                                           `source` references
postgres_1_35f55061ba2a | 	                                                                                                           unknown identifier
postgres_1_35f55061ba2a | 	                                                                                                           `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_step/file_out`,
postgres_1_35f55061ba2a | 	                                                                                                           tried
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_step/file_out,
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_step/file_out
postgres_1_35f55061ba2a | 	                                                                                                           Field
postgres_1_35f55061ba2a | 	                                                                                                           `source` references
postgres_1_35f55061ba2a | 	                                                                                                           unknown identifier
postgres_1_35f55061ba2a | 	                                                                                                           `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files`,
postgres_1_35f55061ba2a | 	                                                                                                           tried
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files,
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:39:3:   checking object
postgres_1_35f55061ba2a | 	                                                                                                     `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/tar_step`
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:41:5:     checking field
postgres_1_35f55061ba2a | 	                                                                                                       `in`
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:42:7:       checking
postgres_1_35f55061ba2a | 	                                                                                                         object
postgres_1_35f55061ba2a | 	                                                                                                         `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/tar_step/archive_file`
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:43:9:         Field
postgres_1_35f55061ba2a | 	                                                                                                           `source` references
postgres_1_35f55061ba2a | 	                                                                                                           unknown identifier
postgres_1_35f55061ba2a | 	                                                                                                           `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive`,
postgres_1_35f55061ba2a | 	                                                                                                           tried
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive,
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#archive
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:44:7:       checking
postgres_1_35f55061ba2a | 	                                                                                                         object
postgres_1_35f55061ba2a | 	                                                                                                         `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/tar_step/file_list`
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:45:9:         Field
postgres_1_35f55061ba2a | 	                                                                                                           `source` references
postgres_1_35f55061ba2a | 	                                                                                                           unknown identifier
postgres_1_35f55061ba2a | 	                                                                                                           `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files`,
postgres_1_35f55061ba2a | 	                                                                                                           tried
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files,
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#files
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:48:3:   checking object
postgres_1_35f55061ba2a | 	                                                                                                     `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/touch_step`
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:52:5:     checking field
postgres_1_35f55061ba2a | 	                                                                                                       `in`
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:55:7:       checking
postgres_1_35f55061ba2a | 	                                                                                                         object
postgres_1_35f55061ba2a | 	                                                                                                         `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/touch_step/filename`
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:56:9:         Field
postgres_1_35f55061ba2a | 	                                                                                                           `source` references
postgres_1_35f55061ba2a | 	                                                                                                           unknown identifier
postgres_1_35f55061ba2a | 	                                                                                                           `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_files`,
postgres_1_35f55061ba2a | 	                                                                                                           tried
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_files,
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#touch_files
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:53:7:       checking
postgres_1_35f55061ba2a | 	                                                                                                         object
postgres_1_35f55061ba2a | 	                                                                                                         `../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/touch_step/waitfor`
postgres_1_35f55061ba2a | 	../data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl:54:9:         Field
postgres_1_35f55061ba2a | 	                                                                                                           `source` references
postgres_1_35f55061ba2a | 	                                                                                                           unknown identifier
postgres_1_35f55061ba2a | 	                                                                                                           `file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#tar_step/archive_out`,
postgres_1_35f55061ba2a | 	                                                                                                           tried
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#complex-workflow/file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#tar_step/archive_out,
postgres_1_35f55061ba2a | 	                                                                                                           file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#file:///data/git/6fb75527b599e32b537698d2a92b871fbc3f6ba2/complex-workflow/complex-workflow-1.cwl#tar_step/archive_out
postgres_1_35f55061ba2a | 	', $4 = '{"@id": "https://w3id.org/cwl/view/git/47618bc8c2ec33780b8ff656e62738ccd0c17481/complex-workflow/complex-workflow-1.cwl", "label": "complex-workflow-1.cwl", "steps": {"tar_step": {"run": "tar.cwl", "sources": {"file_list": {"sourceIDs": ["files"]}, "archive_file": {"sourceIDs": ["archive"]}}}, "echo_step": {"run": "echo.cwl", "sources": {"message": {"sourceIDs": ["echo_message"]}, "output_location": {"sourceIDs": ["echo_output_location"]}}}, "touch_step": {"run": "touch.cwl", "sources": {"waitfor": {"sourceIDs": ["tar_step"]}, "filename": {"sourceIDs": ["touch_files"]}}}, "re_tar_step": {"run": "tar.cwl", "sources": {"file_list": {"sourceIDs": [""]}, "archive_file": {"sourceIDs": ["archive"]}}}}, "inputs": {"files": {"type": "File[]"}, "archive": {"type": "string"}, "new_archive": {"type": "string"}, "touch_files": {"type": "string[]"}, "echo_message": {"type": "string"}, "echo_output_location": {"type": "string"}}, "packed": false, "outputs": {"echo_out": {"type": "File", "sourceIDs": ["echo_step"]}, "touch_out": {"type": "File[]", "sourceIDs": ["touch_step"]}, "re_tar_out": {"type": "File", "sourceIDs": ["re_tar_step"]}, "archive_out": {"type": "File", "sourceIDs": ["tar_step"]}}, "permalink": "https://w3id.org/cwl/view/git/47618bc8c2ec33780b8ff656e62738ccd0c17481/complex-workflow/complex-workflow-1.cwl", "lastCommit": "47618bc8c2ec33780b8ff656e62738ccd0c17481", "retrievedOn": 1648379712127, "retrievedFrom": {"url": "https://github.com/heliumdatacommons/cwl_workflows/blob/master/complex-workflow/complex-workflow-1.cwl", "path": "complex-workflow/complex-workflow-1.cwl", "type": "GITHUB", "branch": "master", "rawUrl": "https://raw.githubusercontent.com/heliumdatacommons/cwl_workflows/master/complex-workflow/complex-workflow-1.cwl", "repoUrl": "https://github.com/heliumdatacommons/cwl_workflows.git", "packedId": null}, "cwltoolVersion": "3.1.20220224085855", "visualisationDot": "digraph workflow {\n  graph [\n    bgcolor = \"#eeeeee\"\n    color = \"black\"\n    fontsize = \"10\"\n    labeljust = \"left\"\n    clusterrank = \"local\"\n    ranksep = \"0.22\"\n    nodesep = \"0.05\"\n  ]\n  node [\n    fontname = \"Helvetica\"\n    fontsize = \"10\"\n    fontcolor = \"black\"\n    shape = \"record\"\n    height = \"0\"\n    width = \"0\"\n    color = \"black\"\n    fillcolor = \"lightgoldenrodyellow\"\n    style = \"filled\"\n  ];\n  edge [\n    fontname=\"Helvetica\"\n    fontsize=\"8\"\n    fontcolor=\"black\"\n    color=\"black\"\n    arrowsize=\"0.7\"\n  ];\n  subgraph cluster_inputs {\n    rank = \"same\";\n    style = \"dashed\";\n    label = \"Workflow Inputs\";\n    \"touch_files\" [fillcolor=\"#94DDF4\"];\n    \"new_archive\" [fillcolor=\"#94DDF4\"];\n    \"files\" [fillcolor=\"#94DDF4\"];\n    \"echo_message\" [fillcolor=\"#94DDF4\"];\n    \"archive\" [fillcolor=\"#94DDF4\"];\n    \"echo_output_location\" [fillcolor=\"#94DDF4\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    label = \"Workflow Outputs\";\n    \"archive_out\" [fillcolor=\"#94DDF4\"];\n    \"echo_out\" [fillcolor=\"#94DDF4\"];\n    \"re_tar_out\" [fillcolor=\"#94DDF4\"];\n    \"touch_out\" [fillcolor=\"#94DDF4\"];\n  }\n  \"echo_step\";\n  \"touch_step\";\n  \"re_tar_step\";\n  \"tar_step\";\n  \"tar_step\" -> \"archive_out\";\n  \"echo_step\" -> \"echo_out\";\n  \"re_tar_step\" -> \"re_tar_out\";\n  \"touch_step\" -> \"touch_out\";\n  \"echo_output_location\" -> \"echo_step\";\n  \"echo_message\" -> \"echo_step\";\n  \"touch_files\" -> \"touch_step\";\n  \"tar_step\" -> \"touch_step\";\n  \"archive\" -> \"re_tar_step\";\n  \"\" -> \"re_tar_step\";\n  \"archive\" -> \"tar_step\";\n  \"files\" -> \"tar_step\";\n\n  // Invisible links to force outputs to be at lowest rank\n  \"echo_step\" -> \"archive_out\" [style=invis];\n  \"touch_step\" -> \"archive_out\" [style=invis];\n  \"re_tar_step\" -> \"archive_out\" [style=invis];\n  \"tar_step\" -> \"archive_out\" [style=invis];\n}\n", "visualisationPng": "/graph/png/github.com/heliumdatacommons/cwl_workflows/blob/master/complex-workflow/complex-workflow-1.cwl", "visualisationSvg": "/graph/svg/github.com/heliumdatacommons/cwl_workflows/blob/master/complex-workflow/complex-workflow-1.cwl", "visualisationXdot": "/graph/xdot/github.com/heliumdatacommons/cwl_workflows/blob/master/complex-workflow/complex-workflow-1.cwl"}', $5 = NULL, $6 = '9e770cc1-9779-4050-8b08-0ed899b4c22a'
Step 10/20 : RUN cwltool --version
 ---> Running in 7d49b6f2aef1
/usr/bin/cwltool 3.1.20220224085855

@kinow
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kinow commented Mar 27, 2022 

(venv) kinow@ranma:~/Development/python/workspace/cwl_workflows/complex-workflow$ cwltool --version
/home/kinow/Development/python/workspace/cwltool/venv/bin/cwltool 3.1.20220204090313
cwltool --validate complex-workflow-1.cwl
# same error as local CWL Viewer

Would have to look at the logs in the server, and whether cwltool is called again when we access an old workflow, but it may be possible that we upgraded the version of cwltool and it's causing HTTP 500 due to these validation errors.

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kinow commented Mar 28, 2022

Confirmed that when the Workflow controller receives a request for a workflow in the format `/workflows/repo-url, it will call a service to parse the workflow file.

image

When loading the workflow file for the first time, it uses CWLTool.java,

image

which executes a cwltool command that fails to parse the workflows that are producing the 5xx errors.

image

(venv) kinow@ranma:~/Development/python/workspace/cwl_workflows$ cwltool --non-strict --quiet --skip-schemas --print-rdf complex-workflow/complex-workflow-1.cwl 
ERROR Tool definition failed validation:
complex-workflow/complex-workflow-1.cwl:38:1: checking field `steps`
complex-workflow/complex-workflow-1.cwl:59:3:   checking object
(...)

So I think there isn't much to look for here in the Java code. Will start digging in the cwltool issues & code.

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kinow commented Mar 28, 2022

Huh, funny. Was trying to get the workflow to pass validation in some old version of cwltool, but even 1.0x failed.

(venv) kinow@ranma:~/Development/python/workspace/cwl_workflows$ cwltool complex-workflow/complex-workflow-1.cwl 
INFO /home/kinow/Development/python/workspace/cwltool/venv/bin/cwltool 1.0.20191225192155
INFO Resolved 'complex-workflow/complex-workflow-1.cwl' to 'file:///home/kinow/Development/python/workspace/cwl_workflows/complex-workflow/complex-workflow-1.cwl'
ERROR Tool definition failed validation:
complex-workflow/complex-workflow-1.cwl:38:1: checking field `steps`
complex-workflow/complex-workflow-1.cwl:59:3:   checking object
(...)

@kinow kinow mentioned this issue Mar 31, 2022
Open
@mr-c mr-c mentioned this issue Sep 30, 2022
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