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Version 1.0.0a0 #103

Merged
merged 55 commits into from
Jun 29, 2024
Merged

Version 1.0.0a0 #103

merged 55 commits into from
Jun 29, 2024

Commits on Jun 19, 2024

  1. Initial Dockerfile, with bundled OpenJDK, docker, apptainer and podman. 

    It is still missing gocryptfs.
    @jmfernandez
    jmfernandez committed Jun 19, 2024
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Commits on Jun 20, 2024

  1. Added encfs to Dockerfile recipe

    @jmfernandez
    jmfernandez committed Jun 20, 2024
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  2. Now the Dockerfile also installs gocryptfs and other stuff needed for… 

    … some workflows.
    @jmfernandez
    jmfernandez committed Jun 20, 2024
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Commits on Jun 21, 2024

  1. Renamed bootstrap to bootstrap_config within wfexs_backend.wfexs_… 

    …backend.WfExSBackend .
    @jmfernandez
    jmfernandez committed Jun 21, 2024
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Commits on Jun 25, 2024

  1. Added command populate-side-caches

    @jmfernandez
    jmfernandez committed Jun 25, 2024
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  2. WfExS commands documentation has been moved to f1f7fae

    @jmfernandez
    jmfernandez committed Jun 25, 2024
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  3. Some fixes related to installers relocation. Documentation was also u… 

    …pdated.
    @jmfernandez
    jmfernandez committed Jun 25, 2024
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  4. Trying to fix some race conditions

    @jmfernandez
    jmfernandez committed Jun 25, 2024
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  5. Another attempt to fix corner case installation scenarios

    @jmfernandez
    jmfernandez committed Jun 25, 2024
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  6. Another try fixing the installation issue

    @jmfernandez
    jmfernandez committed Jun 25, 2024
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  7. Finally, fixed corner case in the installer

    @jmfernandez
    jmfernandez committed Jun 25, 2024
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  8. WfExS Dockerfile recipe is ready, and customizable

    @jmfernandez
    jmfernandez committed Jun 25, 2024
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Commits on Jun 26, 2024

  1. Adde additional instructions about building the WfExS docker, podman … 

    …or SIF image.
    @jmfernandez
    jmfernandez committed Jun 26, 2024
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  2. Documented several installation procedures

    @jmfernandez
    jmfernandez committed Jun 26, 2024
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  3. Fixed examples of installation procedures

    @jmfernandez
    jmfernandez committed Jun 26, 2024
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Commits on Jun 27, 2024

  1. Fixed symlink to full installer.

    @jmfernandez
    jmfernandez committed Jun 27, 2024
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  2. Workflow profiles are now represented in the Workflow Run RO-Crate. 

    Added all the needed wiring, backward compatibility and machinery to represent profiles and propagate profiles.
    @jmfernandez
    jmfernandez committed Jun 27, 2024
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  3. Workflow profiles are now properly rescued from imported Workflow Run… 

    … RO-Crate.
    @jmfernandez
    jmfernandez committed Jun 27, 2024
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  4. Switching to WRROC profiles 0.5

    @jmfernandez
    jmfernandez committed Jun 27, 2024
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  5. Fixed hidden issue with command-line provided licences

    @jmfernandez
    jmfernandez committed Jun 27, 2024
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  6. Fixed backward compatible profile mangling

    @jmfernandez
    jmfernandez committed Jun 27, 2024
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  7. Added new method, needed to translate from MaterializedContent to gen… 

    …erated one.
    @jmfernandez
    jmfernandez committed Jun 27, 2024
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  8. Added code to heal what it is represented in an WRROC when an old Nex… 

    …tflow

execution does not properly described the materialized outputs
    @jmfernandez
    jmfernandez committed Jun 27, 2024
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  9. Fixing corner case within corner case

    @jmfernandez
    jmfernandez committed Jun 27, 2024
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  10. Added forgotten variable assignment

    @jmfernandez
    jmfernandez committed Jun 27, 2024
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  11. Added all the needed changes to allow having directories in the relPa… 

    …thFiles element from LocalWorkflow
    @jmfernandez
    jmfernandez committed Jun 27, 2024
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  12. Local names of directories should end with a slash (recommended)

    @jmfernandez
    jmfernandez committed Jun 27, 2024
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Commits on Jun 28, 2024

  1. Reimplemented write methods for File and Dataset, so path in zip file… 

    … is properly set
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  2. destpath is now always provided for local contents, even if they ar… 

    …e not going to be included.
    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  3. Avoid creating empty directories in the exported zip file

    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  4. Fixed an assertion which arises in a corner case of Datasets (its fil… 

    …es did not have name)
    @jmfernandez
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  5. Also propagate alternate_name when a Dataset is included

    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  6. Additional minor details in RO-Crate generation improved

    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  7. Fixed issue for foreign development versions of cwltool

    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  8. Minor changes to avoid using inherited __new__ method from pathlib.Path

    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  9. Removed internal debug trace which was added in a previous commit

    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  10. Reworked logic to accept an injected container

    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  11. Cosmetic adjustment, so nonsensical warning does not appear

    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  12. Finally, injected singularity containers are now properly transferred

    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  13. Sevearl additional adjustments to allow having an agnostic canonical … 

    …tag, used wherever it is needed
    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  14. Nextflow workflows following nf-core also depend on nextflow_schema.j… 

    …son for runtime parameter parsing.
    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  15. Fixed corner case issue in unmarshalling code of dictionaries whose k… 

    …eys are not strings
    @jmfernandez
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  16. Fixed misidentification of types when it is translated to RO-Crate ad… 

    …ditionalType
    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  17. Fixed SPARQL query fragments for collections of PropertyValues

    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  18. Second fix in SPARQL query fragments for collections of PropertyValues

    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  19. Fixed capturing of collections of property values

    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  20. Hopefully, nailed down last corner case of collections of atomic values

    @jmfernandez
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  21. Surrendered to the fact that Nextflow workflows can use custom relati… 

    …ve resources
    @jmfernandez
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  22. Added code to preserve both modification time and permissions when co… 

    …ntents come from a zip archive
    @jmfernandez
    jmfernandez committed Jun 28, 2024
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  23. Added quoting and unquoting of paths when they are used as relative i… 

    …dentifiers for JSON-LD entities.
    @jmfernandez
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Commits on Jun 29, 2024

  1. Added degraded mode for container resolutions. 

    This is needed when specific layers (referenced by sha256)
do not exist any more in the remote container registry.
So, the strategy is degrading to the tag in order to retry the
image materialization.
    @jmfernandez
    jmfernandez committed Jun 29, 2024
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  2. Fixed canonicalization of cases like docker.io/node into docker.io/li… 

    …brary/node
    @jmfernandez
    jmfernandez committed Jun 29, 2024
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  3. Fixed canonicalization of cases like docker.io/node into docker.io/li… 

    …brary/node
    @jmfernandez
    jmfernandez committed Jun 29, 2024
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  4. Version bump to 1.0.0a

    @jmfernandez
    jmfernandez committed Jun 29, 2024
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  5. Fixed issue which appeared with Python 3.7 and mypy (the code cannot … 

    …import modules twice).
    @jmfernandez
    jmfernandez committed Jun 29, 2024
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