Code

Introduce workflow run crate#32

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suecharo merged 70 commits intodevelopsapporo-wes/sapporo-service:developfrom introduce-workflow-run-cratesapporo-wes/sapporo-service:introduce-workflow-run-crateCopy head branch name to clipboardNov 7, 2023

+197,157-1,769

Commits

Commits on Feb 8, 2023

• starting to split the functions

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• createAction and more

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• add input/output in the workflow

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• make them arrays

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• add mentions workflow run

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• use subjectOf to link log files from a workflow run

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• copy the original to split

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• leave only run-crate related terms

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Commits on Feb 9, 2023

• add extra terms

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• use encodingFormat for specifying EDAM

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• hide TESTING_EXTRA_TERMS

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  45db975

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• start refactoring

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• define EDAM

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• latest stable

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• comment out unused functions

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• hide unused type defitinition

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• remove pid, uid, gid, mode

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• remove fileStats for main wf file but still remains

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• recovered necessary functions, fix main wf file object

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• fix command not found

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Commits on Jun 8, 2023

• fix ComputatinalWorkflow object initialization

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• refactor

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• refactor

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• refactor wf run

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• add example ro-crate output

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Commits on Jun 9, 2023

• fix conformsTo targets

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• add exampleOfWork to input data entity

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Commits on Jun 13, 2023

• change type of readme as a description

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• remove yevis-id for now

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  2d7d95d

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• easy fix for duplicated v problem

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• remove type WorkflowAttachment

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• use actionStatus

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• remove logs from output of mainEntity

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• remove unused extra terms

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• rollback stats generation functions

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• add status label to actionStatus

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• Improve python package script

  suecharo

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• More generalized uwsgi config

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• Update docker env

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Commits on Jun 14, 2023

• Fix to use Sapporo version as gh_ref of ctx instead of main. Fix overall pylint, mypy error. Add if branch for CWL to wf_params processing

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Commits on Jun 15, 2023

• Fix mypy and pylint errors

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• Remove prev terms csv file

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• Fix for cromwell

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Commits on Jun 16, 2023

• Fix test for cromwell

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• Add test for ro-crate feature

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Commits on Jul 22, 2023

• Support for both path and location of file object in cwl params

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• Add UserAgent header for GitHub

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• Use hasPart instead to attachment

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• Change actionStatus to literal instead of object

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• use schema.org DataType

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• Fix tests

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• Remove prev terms

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• Fix jq error

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Commits on Jul 25, 2023

• Change extra terms to sapporo's ro-terms

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• Remove prev local terms

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• Update ro-crate small example

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• Fix CI/CD scripts ubuntu version

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• Add run-dir from which ro-crate-metadata.json was generated

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Commits on Aug 3, 2023

• Add log files to ro-crate_dir

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• Fix extra context

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• Add entities about run crate profiles

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• Link to from the root data entity to the CreateAction

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• Omit decription props

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Commits on Aug 29, 2023

• Fix context terms

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• Add license props

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Commits on Oct 23, 2023

• remove input/output from json file

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• remove files from index

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Commits on Oct 24, 2023

• revert file remove

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Commits on Oct 25, 2023

• Delete of input, output props and Formal Parameter in mainWorkflow entity

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Commits on Nov 2, 2023

• Fix flake8 error

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