diff --git a/Workflow-RO-Crate/1.1-DRAFT/changelog.md b/Workflow-RO-Crate/1.1-DRAFT/changelog.md index 67c86e9..a5cf0ef 100644 --- a/Workflow-RO-Crate/1.1-DRAFT/changelog.md +++ b/Workflow-RO-Crate/1.1-DRAFT/changelog.md @@ -2,4 +2,8 @@ ## 1.1.0 -* Profile conformance should now be declared on the root data entity (inherited from [RO-Crate 1.2](https://www.researchobject.org/ro-crate/specification/1.2/root-data-entity.html#ro-crate-metadata-descriptor)) +* Updated examples and Profile Crate to align with RO-Crate 1.2 ([#83](https://github.com/workflowhub-eu/about/pull/83/files)) ([#86](https://github.com/workflowhub-eu/about/pull/86)) +* Profile conformance should now be declared on the root data entity (inherited from [RO-Crate 1.2](https://www.researchobject.org/ro-crate/specification/1.2/root-data-entity.html#ro-crate-metadata-descriptor)) ([#83](https://github.com/workflowhub-eu/about/pull/83/files)) +* Clarified that additional types may be included for the main workflow ([#87](https://github.com/workflowhub-eu/about/pull/87)) +* Added guidance for describing workflow parameters & steps (aligned with the [Workflow Run Crate profile](https://www.researchobject.org/workflow-run-crate/profiles/workflow_run_crate/)) ([#87](https://github.com/workflowhub-eu/about/pull/87)) + * This addition means that the profile is no longer backward compatible with RO-Crate 1.1, because the IRI mappings for the properties `input` and `output` were updated in the [RO-Crate 1.2 JSON-LD context](https://www.researchobject.org/ro-crate/specification/1.2/context.jsonld). diff --git a/Workflow-RO-Crate/1.1-DRAFT/index.md b/Workflow-RO-Crate/1.1-DRAFT/index.md index 7a1dd77..b3a169d 100644 --- a/Workflow-RO-Crate/1.1-DRAFT/index.md +++ b/Workflow-RO-Crate/1.1-DRAFT/index.md @@ -35,6 +35,7 @@ title: Workflow RO-Crate profile 1.1-DRAFT + ![Workflow RO-Crate]({{ '/assets/img/ro-crate-workflow.svg' | relative_url }}){: height="300px" width="300px"} @@ -74,13 +75,12 @@ This section uses terminology from the [RO-Crate 1.2 specification](https://w3id ### Context -The _Crate_ JSON-LD MUST be valid according to [RO-Crate 1.1](https://w3id.org/ro/crate/1.1) or later minor version, and SHOULD use the corresponding version of the RO-Crate `@context` - such as for RO-Crate 1.1. +The _Crate_ JSON-LD MUST be valid according to [RO-Crate 1.2](https://w3id.org/ro/crate/1.2) or later minor version, and SHOULD use the corresponding version of the RO-Crate `@context` - such as for RO-Crate 1.2. ### Declaring Profile Conformance The [Root Data Entity](https://www.researchobject.org/ro-crate/specification/1.2/root-data-entity.html#direct-properties-of-the-root-data-entity) `conformsTo` SHOULD be an array that contains at least . -For historical reasons, in Workflow RO-Crates conforming to RO-Crate version 1.1, MAY instead be included in `conformsTo` on the [Metadata File Descriptor](https://www.researchobject.org/ro-crate/specification/1.2/root-data-entity.html#ro-crate-metadata-file-descriptor). ### Main Workflow @@ -408,3 +408,13 @@ A minimal example of _Workflow RO-Crate_ metadata, containing a CWL workflow, an ] } ``` + +## Backward compatibility + +This section is aimed at implementers of Workflow RO-Crate who wish to support both current and previous versions of the profile. + +In RO-Crates conforming to Workflow RO-Crate 1.0 and RO-Crate 1.1, MAY be included in `conformsTo` on the [Metadata File Descriptor](https://www.researchobject.org/ro-crate/specification/1.2/root-data-entity.html#ro-crate-metadata-file-descriptor) rather than the Root Data Entity. + +Note that the IRI mappings for the `input` and `output` properties were updated in the [RO-Crate 1.2 JSON-LD context](https://www.researchobject.org/ro-crate/specification/1.2/context.jsonld). These properties were not mentioned in version 1.0 of this profile, but some conforming crates and implementations may use them, as they are referenced in both the [RO-Crate specification](https://www.researchobject.org/ro-crate/specification/1.2/workflows.html#describing-inputs-and-outputs) and the [Workflow Run Crate profile](https://www.researchobject.org/workflow-run-crate/profiles/workflow_run_crate/). Implementers should therefore be aware of the previous IRIs when reading older crates. + * `input` changed from `https://bioschemas.org/ComputationalWorkflow#input` to `https://bioschemas.org/properties/input` . + * `output` changed from `https://bioschemas.org/ComputationalWorkflow#output` to `https://bioschemas.org/properties/output`. diff --git a/Workflow-RO-Crate/1.1-DRAFT/ro-crate-metadata.json b/Workflow-RO-Crate/1.1-DRAFT/ro-crate-metadata.json index e8ab7ab..715f8b0 100644 --- a/Workflow-RO-Crate/1.1-DRAFT/ro-crate-metadata.json +++ b/Workflow-RO-Crate/1.1-DRAFT/ro-crate-metadata.json @@ -39,6 +39,9 @@ ], "datePublished": "2023-03-13T10:43:00Z", "description": "This is the Profile Crate for Workflow RO-Crate. Workflow RO-Crates are a specialization of RO-Crate for packaging an executable workflow with all necessary documentation. It is aligned with, and intends to strictly extend, the more general Bioschemas ComputationalWorkflow profile.\n\nWorkflowHub uses Workflow RO-Crates as an exchange format for users to upload a packaged workflow.", + "keywords": [ + "workflow" + ], "hasPart": [ { "@id": "index.html" @@ -66,6 +69,12 @@ }, { "@id": "example/" + }, + { + "@id": "https://github.com/KockataEPich/CheckMyCrate/blob/master/CheckMyCrate/profile_library/ro_crate_1.1_basic.json" + }, + { + "@id": "https://github.com/crs4/rocrate-validator/tree/develop/rocrate_validator/profiles/workflow-ro-crate/" } ], "mentions": [ diff --git a/Workflow-RO-Crate/1.1-DRAFT/ro-crate-preview.html b/Workflow-RO-Crate/1.1-DRAFT/ro-crate-preview.html index a7b8c15..dd49e94 100644 --- a/Workflow-RO-Crate/1.1-DRAFT/ro-crate-preview.html +++ b/Workflow-RO-Crate/1.1-DRAFT/ro-crate-preview.html @@ -54,6 +54,7 @@ ], "datePublished": "2023-03-13T10:43:00Z", "description": "This is the Profile Crate for Workflow RO-Crate. Workflow RO-Crates are a specialization of RO-Crate for packaging an executable workflow with all necessary documentation. It is aligned with, and intends to strictly extend, the more general Bioschemas ComputationalWorkflow profile.\n\nWorkflowHub uses Workflow RO-Crates as an exchange format for users to upload a packaged workflow.", + "keywords": "workflow", "hasPart": [ { "@id": "index.html" @@ -81,6 +82,12 @@ }, { "@id": "example/" + }, + { + "@id": "https://github.com/KockataEPich/CheckMyCrate/blob/master/CheckMyCrate/profile_library/ro_crate_1.1_basic.json" + }, + { + "@id": "https://github.com/crs4/rocrate-validator/tree/develop/rocrate_validator/profiles/workflow-ro-crate/" } ], "mentions": [ @@ -517,6 +524,22 @@ } ] }, + { + "@id": "https://github.com/KockataEPich/CheckMyCrate/blob/master/CheckMyCrate/profile_library/ro_crate_1.1_basic.json", + "@type": "File", + "encodingFormat": [ + "application/json", + { + "@id": "https://github.com/KockataEPich/CheckMyCrate#profiles" + } + ], + "name": "CheckMyCrate profile for Workflow RO-Crate" + }, + { + "@id": "https://github.com/crs4/rocrate-validator/tree/develop/rocrate_validator/profiles/workflow-ro-crate/", + "@type": "Dataset", + "name": "rocrate-validator profile for Workflow RO-Crate 1.0" + }, { "@id": "https://workflowhub.eu/", "@type": "RepositoryCollection", @@ -544,22 +567,6 @@ "url": "https://github.com/inab/WfExS-backend/", "version": "0.4.2" }, - { - "@id": "https://github.com/KockataEPich/CheckMyCrate/blob/master/CheckMyCrate/profile_library/ro_crate_1.1_basic.json", - "@type": "File", - "encodingFormat": [ - "application/json", - { - "@id": "https://github.com/KockataEPich/CheckMyCrate#profiles" - } - ], - "name": "CheckMyCrate profile for Workflow RO-Crate" - }, - { - "@id": "https://github.com/crs4/rocrate-validator/tree/develop/rocrate_validator/profiles/workflow-ro-crate/", - "@type": "Dataset", - "name": "rocrate-validator profile for Workflow RO-Crate 1.0" - }, { "@id": "https://spdx.org/licenses/BSD-3-Clause", "@type": "CreativeWork", @@ -1521,6 +1528,9 @@

Workflow RO-Crate profile

  • Stian Soiland-Reyes
    • + keywords [?] + workflow + hasPart [?] mentions [?] @@ -2239,33 +2253,34 @@

    Example RO-Crate following this profile



    -

    Go to: WorkflowHub

    +

    Go to: CheckMyCrate profile for Workflow RO-Crate

    -
    +
    - + - + - - - - - - - + - - + + + + + @@ -2274,36 +2289,27 @@

    Go to: WorkflowHub



    -

    Go to: ro-crate-py

    +

    Go to: rocrate-validator profile for Workflow RO-Crate 1.0

    -
    +
    @idhttps://workflowhub.eu/https://github.com/KockataEPich/CheckMyCrate/blob/master/CheckMyCrate/profile_library/ro_crate_1.1_basic.json
    name [?]WorkflowHubCheckMyCrate profile for Workflow RO-Crate
    @typeRepositoryCollection
    description [?]WorkflowHub is a registry for describing, sharing and publishing scientific computational workflows.
    publisher [?]WorkflowHub projectFile
    title [?]WorkflowHubencodingFormat [?]
    Items that reference this one
    hasPart [?]Workflow RO-Crate profile
    mentions [?] Workflow RO-Crate profile
    - + - + - - - - - - - - - - - - - + + + + @@ -2312,32 +2318,32 @@

    Go to: ro-crate-py



    -

    Go to: WfExS-backend

    +

    Go to: WorkflowHub

    -
    +
    @idhttps://pypi.org/project/rocrate/https://github.com/crs4/rocrate-validator/tree/develop/rocrate_validator/profiles/workflow-ro-crate/
    name [?]ro-crate-pyrocrate-validator profile for Workflow RO-Crate 1.0
    @typeSoftwareApplication
    description [?]Python library to create/parse RO-Crate (Research Object Crate) metadata.
    identifier [?]https://doi.org/10.5281/zenodo.5653266
    url [?]https://pypi.org/project/rocrate/
    version [?]0.5.0Dataset
    Items that reference this one
    hasPart [?]Workflow RO-Crate profile
    mentions [?] Workflow RO-Crate profile
    - + - + - + - + - - + + - - + + @@ -2347,30 +2353,35 @@

    Go to: WfExS-backend


    -

    Go to: CheckMyCrate profile for Workflow RO-Crate

    +

    Go to: ro-crate-py

    -
    +

    @idhttps://github.com/inab/WfExS-backend/https://workflowhub.eu/
    name [?]WfExS-backendWorkflowHub
    @typeSoftwareApplicationRepositoryCollection
    description [?]Workflow Execution Service backendWorkflowHub is a registry for describing, sharing and publishing scientific computational workflows.
    url [?]https://github.com/inab/WfExS-backend/publisher [?]WorkflowHub project
    version [?]0.4.2title [?]WorkflowHub
    Items that reference this one
    mentions [?] Workflow RO-Crate profile
    - + - + - + - - + + + + + + + + + + + @@ -2380,23 +2391,32 @@

    Go to: rocrate-validator profile for Workflow RO-Crate 1.0

    +

    Go to: WfExS-backend

    -
    +
    @idhttps://github.com/KockataEPich/CheckMyCrate/blob/master/CheckMyCrate/profile_library/ro_crate_1.1_basic.jsonhttps://pypi.org/project/rocrate/
    name [?]CheckMyCrate profile for Workflow RO-Cratero-crate-py
    @typeFileSoftwareApplication
    encodingFormat [?]description [?]Python library to create/parse RO-Crate (Research Object Crate) metadata.
    identifier [?]https://doi.org/10.5281/zenodo.5653266
    url [?]https://pypi.org/project/rocrate/
    version [?]0.5.0
    Items that reference this one
    mentions [?] Workflow RO-Crate profile
    - + - + - + + + + + + + + + +
    @idhttps://github.com/crs4/rocrate-validator/tree/develop/rocrate_validator/profiles/workflow-ro-crate/https://github.com/inab/WfExS-backend/
    name [?]rocrate-validator profile for Workflow RO-Crate 1.0WfExS-backend
    @typeDatasetSoftwareApplication
    description [?]Workflow Execution Service backend
    url [?]https://github.com/inab/WfExS-backend/
    version [?]0.4.2
    Items that reference this one
    mentions [?] Workflow RO-Crate profile