Code

Introduce workflow run crate#32

Code

Merged

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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  7251cfa

• createAction and more

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  59d6c1b

• add input/output in the workflow

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  d806c58

• make them arrays

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  6d50fbe

• add mentions workflow run

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  caada19

• use subjectOf to link log files from a workflow run

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  0c16bda

• 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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  7846d1e

• use encodingFormat for specifying EDAM

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  6c588d2

• hide TESTING_EXTRA_TERMS

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  45db975

• start refactoring

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  68755ee

• define EDAM

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  d100524

• latest stable

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  4e7e2ed

• comment out unused functions

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  aaff313

• hide unused type defitinition

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  0ad018a

• remove pid, uid, gid, mode

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  e880bac

• remove fileStats for main wf file but still remains

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  01ade04

• recovered necessary functions, fix main wf file object

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  2bf3a19

• fix command not found

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  a220a3e

Commits on Jun 8, 2023

• fix ComputatinalWorkflow object initialization

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  2aa534b

• refactor

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  59d21bf

• refactor

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  609ccfb

• refactor wf run

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  1499a4b

• add example ro-crate output

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  733ef3b

Commits on Jun 9, 2023

• fix conformsTo targets

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  36efeda

• 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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  46b212b

• remove yevis-id for now

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  2d7d95d

• easy fix for duplicated v problem

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  5066654

• remove type WorkflowAttachment

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  c345484

• use actionStatus

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  f885dd0

• remove logs from output of mainEntity

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  0529283

• remove unused extra terms

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  055c609

• rollback stats generation functions

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  bbd94f4

• add status label to actionStatus

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  12d3df8

• Improve python package script

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  dc2d867

• More generalized uwsgi config

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  2af11c4

• Update docker env

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  663bbed

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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  4372d04

Commits on Jun 15, 2023

• Fix mypy and pylint errors

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  e8fe62e

• Remove prev terms csv file

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  26f1784

• Fix for cromwell

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  21ce8a5

Commits on Jun 16, 2023

• Fix test for cromwell

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  23a875b

• Add test for ro-crate feature

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  248a8b9

Commits on Jul 22, 2023

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

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  6fd6c77

• Add UserAgent header for GitHub

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• Use hasPart instead to attachment

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  56348b7

• Change actionStatus to literal instead of object

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  76f4b28

• use schema.org DataType

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  7b9332c

• Fix tests

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  f5a86dd

• Remove prev terms

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  a906d09

• Fix jq error

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  327e5a9

Commits on Jul 25, 2023

• Change extra terms to sapporo's ro-terms

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  20f609f

• Remove prev local terms

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  e9a56a5

• Update ro-crate small example

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  362cd7f

• Fix CI/CD scripts ubuntu version

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  9308c16

• 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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  85241ea

• Fix extra context

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  17f2222

• Add entities about run crate profiles

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  31ea971

• Link to from the root data entity to the CreateAction

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  aa123d6

• Omit decription props

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  cbb958e

Commits on Aug 29, 2023

• Fix context terms

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  03681e7

• Add license props

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  c9e8b36

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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  79d2fc0

Commits on Oct 25, 2023

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

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  0b7e990

Commits on Nov 2, 2023

• Fix flake8 error

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  de0f18b