First stage RO-Crate import #90
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Added new `import` command, to import a Workflow-Run profiles compliant RO-Crate into a new staged working directory, in order to run it.
…g args.workflowConfigFilename for imports
Also, detection code has been moved from WfExSBackend to WF class, so it is better reused.
…t is the version of WfExS-backend the one defining the accepted values
…ontainer factories and workflow engines. * Also, added a couple of new command line commands to list them. * Additionally, created wfexs_backend.utils.rocrate.ROCrateToolbox , to move there the methods to generate a WfExS definition from an input RO-Crate metadata. * Other code was also refactored. * Now the list of executions and containers from a WRROC is walked.
…e module to `wfexs_backend.utils.rocrate` one
…here to avoid more complicated dependencies
As this list of containers does not have an explicit representation in the workflow staging definition, explicitly return it.
Next commits should implement rebuilding the input parameters properly.
…py pre-commit hook
…the identification phase.
…ve to be "stringified"
…g a prospective provenance scenario (i.e. all is gathered, but nothing was run)
Also, several type definitions have been moved from common to their most natural place.
Also, a few type definitions have been moved from common to their most natural places.
…wfexs_backend.fetchers`
…actRepoFetcher` Also, refactored previous implementations in wfexs_backend.fetchers.git and wfexs_backend.fetchers.swh under GitFetcher and SoftwareHeritageFetcher. This work is needed to allow future modular repository providers.
…iginal one is used instead of a possibly consolidated one.
It is currently working with WRROCs from CWL workflows. (Nextflow WWROC generation has to be fixed)
Added support for RO-Crate import (only metadata), and input parameters replacement. Still pending to fix RO-Crate generation for Nextflow, so the imported RO-Crates can be consumed without issues.
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Now it is possible to properly import WRROCs produced by WfExS which represent CWL executions.
Technically, properly generated WRROCs from Nextflow executions should also be importable, but RO-Crate generation must be fixed first to properly generate them.