From f64377357f275c8dfcf2732289a4c6c7ce27b516 Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Tue, 6 Jan 2026 09:10:41 +0000 Subject: [PATCH 01/22] remove unpaired bracket --- docs/index.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/index.md b/docs/index.md index 145d980..d2190d3 100644 --- a/docs/index.md +++ b/docs/index.md @@ -92,7 +92,7 @@ Several workflow engines have implemented the [WRROC profiles](https://www.resea [WfExS](https://wfexs-backend.readthedocs.io/) | Workflow | [WfExS 0.10.1](https://github.com/inab/WfExS-backend/releases/tag/0.10.1) or later | [10.5281/zenodo.10091550](https://doi.org/10.5281/zenodo.10091550) | [Sapporo](https://github.com/sapporo-wes/sapporo) | Workflow | [sapporo-service 1.5.1](https://github.com/sapporo-wes/sapporo-service/releases/tag/1.5.1) or later | [10.5281/zenodo.10134581](https://doi.org/10.5281/zenodo.10134581) | [Autosubmit](https://autosubmit.readthedocs.io/) | Workflow | [Autosubmit v4.0.100](https://pypi.org/project/autosubmit/4.0.100/) or later | [10.5281/zenodo.8144612](https://doi.org/10.5281/zenodo.8144612) | -[Nextflow](https://nextflow.io/) | Provenance | ([nf-prov](https://github.com/nextflow-io/nf-prov/blob/main/docs/WRROC.md) 1.4.0 or later | [example](https://github.com/nextflow-io/nf-prov/files/13070992/ro-crate-metadata.json) | +[Nextflow](https://nextflow.io/) | Provenance | [nf-prov](https://github.com/nextflow-io/nf-prov/blob/main/docs/WRROC.md) 1.4.0 or later | [example](https://github.com/nextflow-io/nf-prov/files/13070992/ro-crate-metadata.json) | The Process Crate profile can also be implemented outside workflow systems, see for example [BY-COVID WP5 T5.2 Baseline Use Case](https://w3id.org/ro/doi/10.5281/zenodo.6913045) and [combination with Common Provenance Model](https://doi.org/10.5281/zenodo.7676923). Editors like [Crate-O](https://language-research-technology.github.io/crate-o/) can be used for making such crates by hand. @@ -158,4 +158,3 @@ Unless required by applicable law or agreed to in writing, software distributed Profile Crates and JSON-LD examples within this specification are distributed under [CC0 1.0 Universal (CC0 1.0) Public Domain Dedication](https://creativecommons.org/publicdomain/zero/1.0/). - From 3d9c32fa16124e8b72e669b1c1857d2bb1956784 Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Tue, 6 Jan 2026 09:12:48 +0000 Subject: [PATCH 02/22] add datePublished to profile crates --- docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json | 1 + .../0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json | 1 + .../profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json | 1 + 3 files changed, 3 insertions(+) diff --git a/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json index 4941de2..e261073 100644 --- a/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json @@ -28,6 +28,7 @@ "identifier": "https://w3id.org/ro/wfrun/process/0.6-DRAFT", "name": "Process Run Crate profile", "version": "0.6-DRAFT", + "datePublished": "2024-06-19", "license": { "@id": "https://www.apache.org/licenses/LICENSE-2.0" }, diff --git a/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json index 2b147a3..c03ad22 100644 --- a/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json @@ -28,6 +28,7 @@ "identifier": "https://w3id.org/ro/wfrun/provenance/0.6-DRAFT", "name": "Provenance Run Crate profile", "version": "0.6-DRAFT", + "datePublished": "2024-06-19", "license": { "@id": "https://www.apache.org/licenses/LICENSE-2.0" }, diff --git a/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json index 3d4b148..91b95bf 100644 --- a/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json @@ -28,6 +28,7 @@ "identifier": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT", "name": "Workflow Run Crate profile", "version": "0.6-DRAFT", + "datePublished": "2024-06-19", "license": { "@id": "https://www.apache.org/licenses/LICENSE-2.0" }, From 456f09c0717dc22c56aecbe2b594b72a3ba270a8 Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Tue, 6 Jan 2026 09:18:18 +0000 Subject: [PATCH 03/22] add keywords to profile crates --- .../0.6-DRAFT/process_run_crate/ro-crate-metadata.json | 5 +++++ .../0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json | 7 +++++++ .../0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json | 7 +++++++ 3 files changed, 19 insertions(+) diff --git a/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json index e261073..47743fb 100644 --- a/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json @@ -35,6 +35,11 @@ "author": [ {"@id": "https://www.researchobject.org/workflow-run-crate/"} ], + "keywords": [ + "informatics", + "process", + "provenance" + ], "hasPart": [ { "@id": "index.html" }, { "@id": "example1/" }, diff --git a/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json index c03ad22..c2b2706 100644 --- a/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json @@ -35,6 +35,13 @@ "author": [ {"@id": "https://www.researchobject.org/workflow-run-crate/"} ], + "keywords": [ + "informatics", + "process", + "provenance", + "workflow", + "workflow execution" + ], "hasPart": [ { "@id": "index.html" }, { "@id": "example3/" }, diff --git a/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json index 91b95bf..f97dce4 100644 --- a/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json @@ -35,6 +35,13 @@ "author": [ {"@id": "https://www.researchobject.org/workflow-run-crate/"} ], + "keywords": [ + "informatics", + "process", + "provenance", + "workflow", + "workflow execution" + ], "hasPart": [ { "@id": "index.html" }, { "@id": "example2/" }, From c6b27dd9233ef44b9e7ecbcc1993c9a0ad3c9f04 Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Tue, 6 Jan 2026 09:31:01 +0000 Subject: [PATCH 04/22] 1.2-DRAFT -> 1.2 --- docs/index.md | 4 ++-- .../0.6-DRAFT/process_run_crate/ro-crate-metadata.json | 6 +++--- .../0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json | 6 +++--- .../0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json | 6 +++--- 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/docs/index.md b/docs/index.md index d2190d3..4f05fd2 100644 --- a/docs/index.md +++ b/docs/index.md @@ -121,8 +121,8 @@ In addition, some computational workflow approaches have RO-Crate support which ### RO-Crate links - [RO-Crate homepage](https://w3id.org/ro/crate) -- [RO-Crate specification 1.1](https://www.researchobject.org/ro-crate/1.1/) -- [RO-Crate profiles](https://www.researchobject.org/ro-crate/1.2-DRAFT/profiles) (from 1.2-DRAFT -- feedback welcome) +- [RO-Crate specification 1.2](https://www.researchobject.org/ro-crate/1.2/) +- [RO-Crate profiles](https://www.researchobject.org/ro-crate/1.2/profiles) (within the specification above) - [Workflow Crate](https://w3id.org/workflowhub/workflow-ro-crate/) (profile for a workflow _definition_) - [Workflow Testing Crate](https://lifemonitor.eu/workflow_testing_ro_crate) (profile for defining workflow tests) - [Adding a ComputationalWorkflow in RO-Crate](https://www.researchobject.org/ro-crate/1.1/workflows.html) diff --git a/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json index 47743fb..8fd7c09 100644 --- a/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json @@ -1,5 +1,5 @@ { "@context": [ - "https://w3id.org/ro/crate/1.2-DRAFT/context", + "https://w3id.org/ro/crate/1.2/context", { "@base": "https://www.researchobject.org/workflow-run-crate/profiles/0.6-DRAFT/process_run_crate/"} ], "@graph": [ @@ -7,7 +7,7 @@ "@id": "ro-crate-metadata.json", "@type": "CreativeWork", "license": { "@id": "http://spdx.org/licenses/CC0-1.0" }, - "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"}, + "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2"}, "about": {"@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT"} }, { @@ -23,7 +23,7 @@ "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT", "@type": ["Dataset","Profile"], "isProfileOf": [ - {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"} + {"@id": "https://w3id.org/ro/crate/1.2"} ], "identifier": "https://w3id.org/ro/wfrun/process/0.6-DRAFT", "name": "Process Run Crate profile", diff --git a/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json index c2b2706..5d3757b 100644 --- a/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json @@ -1,5 +1,5 @@ { "@context": [ - "https://w3id.org/ro/crate/1.2-DRAFT/context", + "https://w3id.org/ro/crate/1.2/context", { "@base": "https://www.researchobject.org/workflow-run-crate/profiles/0.6-DRAFT/provenance_run_crate/"} ], "@graph": [ @@ -7,7 +7,7 @@ "@id": "ro-crate-metadata.json", "@type": "CreativeWork", "license": { "@id": "http://spdx.org/licenses/CC0-1.0" }, - "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"}, + "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2"}, "about": {"@id": "https://w3id.org/ro/wfrun/provenance/0.6-DRAFT"} }, { @@ -23,7 +23,7 @@ "@id": "https://w3id.org/ro/wfrun/provenance/0.6-DRAFT", "@type": ["Dataset","Profile"], "isProfileOf": [ - {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"} + {"@id": "https://w3id.org/ro/crate/1.2"} ], "identifier": "https://w3id.org/ro/wfrun/provenance/0.6-DRAFT", "name": "Provenance Run Crate profile", diff --git a/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json index f97dce4..b64c4e5 100644 --- a/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json @@ -1,5 +1,5 @@ { "@context": [ - "https://w3id.org/ro/crate/1.2-DRAFT/context", + "https://w3id.org/ro/crate/1.2/context", { "@base": "https://www.researchobject.org/workflow-run-crate/profiles/0.6-DRAFT/workflow_run_crate/"} ], "@graph": [ @@ -7,7 +7,7 @@ "@id": "ro-crate-metadata.json", "@type": "CreativeWork", "license": { "@id": "http://spdx.org/licenses/CC0-1.0" }, - "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"}, + "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2"}, "about": {"@id": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT"} }, { @@ -23,7 +23,7 @@ "@id": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT", "@type": ["Dataset","Profile"], "isProfileOf": [ - {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"} + {"@id": "https://w3id.org/ro/crate/1.2"} ], "identifier": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT", "name": "Workflow Run Crate profile", From 653b9086a8326c04d154a7de48d0c67d623a399c Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Tue, 6 Jan 2026 09:37:11 +0000 Subject: [PATCH 05/22] add description to profile crates --- docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json | 1 + .../0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json | 1 + .../profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json | 1 + 3 files changed, 3 insertions(+) diff --git a/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json index 8fd7c09..8bda60c 100644 --- a/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json @@ -27,6 +27,7 @@ ], "identifier": "https://w3id.org/ro/wfrun/process/0.6-DRAFT", "name": "Process Run Crate profile", + "description": "This profile is used to describe the execution of an implicit workflow, indicating that one or more computational tools have been executed, typically generating some result files that are represented as data entities in the RO-Crate.", "version": "0.6-DRAFT", "datePublished": "2024-06-19", "license": { diff --git a/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json index 5d3757b..4e169d5 100644 --- a/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json @@ -27,6 +27,7 @@ ], "identifier": "https://w3id.org/ro/wfrun/provenance/0.6-DRAFT", "name": "Provenance Run Crate profile", + "description": "This profile extends Workflow Run Crate with specifications to describe internal details of the workflow run, such as step executions and intermediate outputs.", "version": "0.6-DRAFT", "datePublished": "2024-06-19", "license": { diff --git a/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json index b64c4e5..f3af027 100644 --- a/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json @@ -27,6 +27,7 @@ ], "identifier": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT", "name": "Workflow Run Crate profile", + "description": "This profile is used to describe the execution of a computational tool that has orchestrated the execution of other tools. Such a tool is represented as a workflow that can be executed using a Workflow Management System (WMS), or workflow engine (e.g. cwltool).", "version": "0.6-DRAFT", "datePublished": "2024-06-19", "license": { From 181bc6322923719a39d9f3d5c873a1de2a113282 Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Tue, 6 Jan 2026 10:00:23 +0000 Subject: [PATCH 06/22] 1.1 -> 1.2 --- .../example1/ro-crate-metadata.json | 4 ++-- .../0.6-DRAFT/process_run_crate/index.md | 24 +++++++++---------- .../example3/ro-crate-metadata.json | 4 ++-- .../0.6-DRAFT/provenance_run_crate/index.md | 18 +++++++------- .../example2/ro-crate-metadata.json | 4 ++-- .../0.6-DRAFT/workflow_run_crate/index.md | 12 +++++----- 6 files changed, 33 insertions(+), 33 deletions(-) diff --git a/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-metadata.json index 05cd8d6..70f38ea 100644 --- a/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-metadata.json @@ -1,9 +1,9 @@ -{ "@context": "https://w3id.org/ro/crate/1.1/context", +{ "@context": "https://w3id.org/ro/crate/1.2/context", "@graph": [ { "@id": "ro-crate-metadata.json", "@type": "CreativeWork", - "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"}, + "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2"}, "about": {"@id": "./"} }, { diff --git a/docs/profiles/0.6-DRAFT/process_run_crate/index.md b/docs/profiles/0.6-DRAFT/process_run_crate/index.md index aa48bea..24b842d 100644 --- a/docs/profiles/0.6-DRAFT/process_run_crate/index.md +++ b/docs/profiles/0.6-DRAFT/process_run_crate/index.md @@ -12,20 +12,20 @@ title: Process Run Crate * Example conforming crate: [ro-crate-metadata.json](example1/ro-crate-metadata.json) [ro-crate-preview.html](example1/ro-crate-preview.html) * Profile Crate: [ro-crate-metadata.json](ro-crate-metadata.json) [ro-crate-preview.html](ro-crate-preview.html) * Extends: - - [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1) + - [RO-Crate 1.2 specification](https://w3id.org/ro/crate/1.2) * JSON-LD context: * Vocabulary terms: -This profile uses terminology from the [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1), and [extends it](https://www.researchobject.org/ro-crate/specification/1.1/appendix/jsonld.html#extending-ro-crate) with additional terms from the [workflow-run](https://github.com/ResearchObject/ro-terms/tree/master/workflow-run) ro-terms namespace. +This profile uses terminology from the [RO-Crate 1.2 specification](https://w3id.org/ro/crate/1.2), and [extends it](https://www.researchobject.org/ro-crate/specification/1.2/appendix/jsonld.html#extending-ro-crate) with additional terms from the [workflow-run](https://github.com/ResearchObject/ro-terms/tree/master/workflow-run) ro-terms namespace. ## Overview -This profile is used to describe the execution of an _implicit_ workflow, indicating that one or more computational tools have been executed, typically generating some result files that are represented as [data entities](https://www.researchobject.org/ro-crate/specification/1.1/data-entities.html) in the RO-Crate. +This profile is used to describe the execution of an _implicit_ workflow, indicating that one or more computational tools have been executed, typically generating some result files that are represented as [data entities](https://www.researchobject.org/ro-crate/specification/1.2/data-entities.html) in the RO-Crate. By "implicit workflow" we mean that the composition of these tools may have been done by hand (a user executes one tool following another) or by some script that has not yet been included as part of the crate (for instance because it is an embedded part of a larger application). -This profile requires the indication of [Software used to create files](https://www.researchobject.org/ro-crate/specification/1.1/provenance.html#software-used-to-create-files), namely a [SoftwareApplication](http://schema.org/SoftwareApplication) (the tool) and a [CreateAction](http://schema.org/CreateAction) (the execution of said tool). +This profile requires the indication of [Software used to create files](https://www.researchobject.org/ro-crate/specification/1.2/provenance.html#software-used-to-create-files), namely a [SoftwareApplication](http://schema.org/SoftwareApplication) (the tool) and a [CreateAction](http://schema.org/CreateAction) (the execution of said tool). The following diagram shows the relationships between provenance-related entities. Note the distinction between *prospective* provenance (plans for activities, e.g., an application) and *retrospective* provenance (what actually happened, e.g. the execution of an application). @@ -41,14 +41,14 @@ The following diagram shows the relationships between provenance-related entitie ```json { "@context": [ - "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/crate/1.2/context", "https://w3id.org/ro/terms/workflow-run/context" ], "@graph": [ { "@id": "ro-crate-metadata.json", "@type": "CreativeWork", - "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"}, + "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2"}, "about": {"@id": "./"} }, { @@ -122,7 +122,7 @@ Note that the command line shown in the action's `description` is not directly r - Dataset (the root data entity, e.g. "@id": "./") + Dataset (the root data entity, e.g. "@id": "./") conformsTo @@ -177,7 +177,7 @@ Note that the command line shown in the action's `description` is not directly r @id MUST - A unique identifier for the execution, e.g. "urn:uuid:50ec5c76-1f7a-4130-8ef6-846756b228c1", "#f99a8e6c". MAY be an absolute URI, e.g. http://example.com/runs/846756b228c1. The use of randomly generated UUIDs (type 4) is RECOMMENDED. SHOULD be listed under mentions of the root data entity. + A unique identifier for the execution, e.g. "urn:uuid:50ec5c76-1f7a-4130-8ef6-846756b228c1", "#f99a8e6c". MAY be an absolute URI, e.g. http://example.com/runs/846756b228c1. The use of randomly generated UUIDs (type 4) is RECOMMENDED. SHOULD be listed under mentions of the root data entity. @@ -213,7 +213,7 @@ Note that the command line shown in the action's `description` is not directly r agent SHOULD - Identifier of a Person or Organization contextual entity that started/executed this tool. + Identifier of a Person or Organization contextual entity that started/executed this tool. @@ -242,7 +242,7 @@ Note that the command line shown in the action's `description` is not directly r -For each entity described in the table, the most important properties are highlighted. Other properties supported by the entity (e.g. [minValue](http://schema.org/minValue) for a [PropertyValue](http://schema.org/PropertyValue)) can also be used (they are an implicit MAY requirement). See also [Extending RO-Crate](https://www.researchobject.org/ro-crate/specification/1.1/appendix/jsonld.html#extending-ro-crate) for guidance on defining and using terms not included in the RO-Crate context. +For each entity described in the table, the most important properties are highlighted. Other properties supported by the entity (e.g. [minValue](http://schema.org/minValue) for a [PropertyValue](http://schema.org/PropertyValue)) can also be used (they are an implicit MAY requirement). See also [Extending RO-Crate](https://www.researchobject.org/ro-crate/specification/1.2/appendix/jsonld.html#extending-ro-crate) for guidance on defining and using terms not included in the RO-Crate context. Entities referenced by an action's [object](http://schema.org/object) or [result](http://schema.org/result) SHOULD be of type `File` (an RO-Crate alias for [MediaObject](http://schema.org/MediaObject)) for files, [Dataset](http://schema.org/Dataset) for directories and [Collection](http://schema.org/Collection) for [multi-file datasets](#representing-multi-file-objects), but MAY be a [CreativeWork](http://schema.org/CreativeWork) for other types of data (e.g. an online database); they MAY be of type [PropertyValue](http://schema.org/PropertyValue) to capture numbers/strings that are not stored as files. @@ -299,7 +299,7 @@ Mirax2-Fluorescence-2/Data0001.dat Mirax2-Fluorescence-2/Data0023.dat ``` -An application that reads [this format](https://openslide.org/formats/mirax/) needs to be pointed to the `.mrxs` file, and expects to find a directory containing the other files in the same location as the `.mrxs` file, with the same name minus the extension. Thus, even though an application that processes MIRAX files would probably take only the `.mrxs` file as argument, the other ones must be present in the expected location and with the expected names (in CWL, this kind of relationship is expressed via `secondaryFiles`). In this case, the object SHOULD be represented by a [contextual entity](https://www.researchobject.org/ro-crate/1.1/contextual-entities.html) of type [Collection](http://schema.org/Collection) listing all files under `hasPart`, with a `mainEntity` referencing the main file. The collection SHOULD be referenced from the root data entity via `mentions`. +An application that reads [this format](https://openslide.org/formats/mirax/) needs to be pointed to the `.mrxs` file, and expects to find a directory containing the other files in the same location as the `.mrxs` file, with the same name minus the extension. Thus, even though an application that processes MIRAX files would probably take only the `.mrxs` file as argument, the other ones must be present in the expected location and with the expected names (in CWL, this kind of relationship is expressed via `secondaryFiles`). In this case, the object SHOULD be represented by a [contextual entity](https://www.researchobject.org/ro-crate/1.2/contextual-entities.html) of type [Collection](http://schema.org/Collection) listing all files under `hasPart`, with a `mainEntity` referencing the main file. The collection SHOULD be referenced from the root data entity via `mentions`. ```json { @@ -410,7 +410,7 @@ The behavior of some applications may be modified by setting appropriate environ ```json { "@context": [ - "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/crate/1.2/context", "https://w3id.org/ro/terms/workflow-run/context" ], "@graph": [ diff --git a/docs/profiles/0.6-DRAFT/provenance_run_crate/example3/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/provenance_run_crate/example3/ro-crate-metadata.json index 9fb0384..de27c87 100644 --- a/docs/profiles/0.6-DRAFT/provenance_run_crate/example3/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/provenance_run_crate/example3/ro-crate-metadata.json @@ -1,11 +1,11 @@ -{ "@context": "https://w3id.org/ro/crate/1.1/context", +{ "@context": "https://w3id.org/ro/crate/1.2/context", "@graph": [ { "@id": "ro-crate-metadata.json", "@type": "CreativeWork", "about": {"@id": "./"}, "conformsTo": [ - {"@id": "https://w3id.org/ro/crate/1.1"}, + {"@id": "https://w3id.org/ro/crate/1.2"}, {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"} ] }, diff --git a/docs/profiles/0.6-DRAFT/provenance_run_crate/index.md b/docs/profiles/0.6-DRAFT/provenance_run_crate/index.md index 98e748b..ea7550e 100644 --- a/docs/profiles/0.6-DRAFT/provenance_run_crate/index.md +++ b/docs/profiles/0.6-DRAFT/provenance_run_crate/index.md @@ -16,7 +16,7 @@ title: Provenance Run Crate * JSON-LD context: * Vocabulary terms: -This profile uses terminology from the [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1), and [extends it](https://www.researchobject.org/ro-crate/specification/1.1/appendix/jsonld.html#extending-ro-crate) with additional terms from the [workflow-run](https://github.com/ResearchObject/ro-terms/tree/master/workflow-run) ro-terms namespace. +This profile uses terminology from the [RO-Crate 1.2 specification](https://w3id.org/ro/crate/1.2), and [extends it](https://www.researchobject.org/ro-crate/specification/1.2/appendix/jsonld.html#extending-ro-crate) with additional terms from the [workflow-run](https://github.com/ResearchObject/ro-terms/tree/master/workflow-run) ro-terms namespace. ## Overview @@ -29,7 +29,7 @@ The crate SHOULD also record *step* executions via [ControlAction](http://schema The crate MAY also include an [OrganizeAction](http://schema.org/OrganizeAction) representing the execution of the workflow *engine* (e.g. cwltool), which MUST point to: an entity representing the workflow engine (e.g. a [SoftwareApplication](http://schema.org/SoftwareApplication)) via `instrument`; the `CreateAction` that represents the workflow run via `result`; the `ControlAction` instances representing the step executions via `object`. -The tool that implements a step can in turn be a workflow (*nested workflow* or *subworkflow*): in this case, it MUST be represented as a `ComputationalWorkflow`, and all of the above directions apply to it recursively. If the subworkflow is described in a section of the main workflow (e.g. as in [packed CWL workflows](https://www.commonwl.org/v1.2/CommandLineTool.html#Packed_documents)), rather than in a file of its own, it SHOULD be added to the crate as a [contextual entity](https://www.researchobject.org/ro-crate/specification/1.1/contextual-entities.html): in this case, its type list MUST NOT include `File`. +The tool that implements a step can in turn be a workflow (*nested workflow* or *subworkflow*): in this case, it MUST be represented as a `ComputationalWorkflow`, and all of the above directions apply to it recursively. If the subworkflow is described in a section of the main workflow (e.g. as in [packed CWL workflows](https://www.commonwl.org/v1.2/CommandLineTool.html#Packed_documents)), rather than in a file of its own, it SHOULD be added to the crate as a [contextual entity](https://www.researchobject.org/ro-crate/specification/1.2/contextual-entities.html): in this case, its type list MUST NOT include `File`. The following diagram shows the relationships between all provenance-related entities. Note the distinction between *prospective* provenance (plans for activities, e.g. a workflow) and *retrospective* provenance (what actually happened, e.g. the execution of a workflow). @@ -46,7 +46,7 @@ The following diagram shows the relationships between all provenance-related ent ```json { "@context": [ - "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/crate/1.2/context", "https://w3id.org/ro/terms/workflow-run/context" ], "@graph": [ @@ -55,7 +55,7 @@ The following diagram shows the relationships between all provenance-related ent "@type": "CreativeWork", "about": {"@id": "./"}, "conformsTo": [ - {"@id": "https://w3id.org/ro/crate/1.1"}, + {"@id": "https://w3id.org/ro/crate/1.2"}, {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"} ] }, @@ -394,7 +394,7 @@ Note that the `workflow-run` terms are not part of the standard RO-Crate context ```json { "@context": [ - "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/crate/1.2/context", "https://w3id.org/ro/terms/workflow-run/context" ], "@graph": [...] @@ -508,12 +508,12 @@ For instance, to indicate a [Conda environment](https://conda.io/projects/conda/ The `encodingFormat` and/or contextual identifier for `conformsTo` SHOULD be provided for machine-readable build/dependency environment files, but it is currently out of scope for this profile to list all possible package environment systems. -The term `buildInstructions` is taken from [CodeMeta terms](https://codemeta.github.io/terms/), which are [scheduled to be included](https://github.com/ResearchObject/ro-crate/pull/276) in the RO-Crate 1.2 JSON-LD context. For RO-Crate 1.1, the term must be added to the `@context` as: +The term `buildInstructions` is taken from [CodeMeta terms](https://codemeta.github.io/terms/), which are [scheduled to be included](https://github.com/ResearchObject/ro-crate/pull/276) in the RO-Crate 1.2 JSON-LD context. For RO-Crate 1.2, the term must be added to the `@context` as: ```json { "@context": [ - "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/crate/1.2/context", "https://w3id.org/ro/terms/workflow-run", { "buildInstructions": "https://codemeta.github.io/terms/buildInstructions" } ], @@ -579,7 +579,7 @@ The requirements of this profile are those of [Workflow Run Crate](../workflow_r - Dataset (the root data entity, e.g. "@id": "./") + Dataset (the root data entity, e.g. "@id": "./") conformsTo @@ -689,4 +689,4 @@ The requirements of this profile are those of [Workflow Run Crate](../workflow_r -For each entity described in the table, the most important properties are highlighted. Other properties supported by the entity (e.g. [minValue](http://schema.org/minValue) for a [PropertyValue](http://schema.org/PropertyValue)) can also be used (they are an implicit MAY requirement). See also [Extending RO-Crate](https://www.researchobject.org/ro-crate/specification/1.1/appendix/jsonld.html#extending-ro-crate) for guidance on defining and using terms not included in the RO-Crate context. +For each entity described in the table, the most important properties are highlighted. Other properties supported by the entity (e.g. [minValue](http://schema.org/minValue) for a [PropertyValue](http://schema.org/PropertyValue)) can also be used (they are an implicit MAY requirement). See also [Extending RO-Crate](https://www.researchobject.org/ro-crate/specification/1.2/appendix/jsonld.html#extending-ro-crate) for guidance on defining and using terms not included in the RO-Crate context. diff --git a/docs/profiles/0.6-DRAFT/workflow_run_crate/example2/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/workflow_run_crate/example2/ro-crate-metadata.json index 0e4d295..f03dfa9 100644 --- a/docs/profiles/0.6-DRAFT/workflow_run_crate/example2/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/workflow_run_crate/example2/ro-crate-metadata.json @@ -1,11 +1,11 @@ -{ "@context": "https://w3id.org/ro/crate/1.1/context", +{ "@context": "https://w3id.org/ro/crate/1.2/context", "@graph": [ { "@id": "ro-crate-metadata.json", "@type": "CreativeWork", "about": {"@id": "./"}, "conformsTo": [ - {"@id": "https://w3id.org/ro/crate/1.1"}, + {"@id": "https://w3id.org/ro/crate/1.2"}, {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"} ] }, diff --git a/docs/profiles/0.6-DRAFT/workflow_run_crate/index.md b/docs/profiles/0.6-DRAFT/workflow_run_crate/index.md index dd4aaa2..e873171 100644 --- a/docs/profiles/0.6-DRAFT/workflow_run_crate/index.md +++ b/docs/profiles/0.6-DRAFT/workflow_run_crate/index.md @@ -17,12 +17,12 @@ title: Workflow Run Crate * JSON-LD context: * Vocabulary terms: -This profile uses terminology from the [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1). +This profile uses terminology from the [RO-Crate 1.2 specification](https://w3id.org/ro/crate/1.2). ## Overview -This profile is used to describe the execution of a computational tool that has orchestrated the execution of other tools. Such a tool is represented as a [workflow](https://www.researchobject.org/ro-crate/specification/1.1/workflows.html) that can be executed using a *Workflow Management System (WMS)*, or *workflow engine* (e.g. [cwltool](https://github.com/common-workflow-language/cwltool)). +This profile is used to describe the execution of a computational tool that has orchestrated the execution of other tools. Such a tool is represented as a [workflow](https://www.researchobject.org/ro-crate/specification/1.2/workflows.html) that can be executed using a *Workflow Management System (WMS)*, or *workflow engine* (e.g. [cwltool](https://github.com/common-workflow-language/cwltool)). Workflow Run Crate is a combination of [Process Run Crate](../process_run_crate) and [Workflow RO-Crate](https://w3id.org/workflowhub/workflow-ro-crate/). In particular, the RO-Crate MUST have a `ComputationalWorkflow` [mainEntity](http://schema.org/mainEntity) described according to the Workflow RO-Crate specification (*main workflow*), and `CreateAction` instances corresponding to its execution (thus having the main workflow as `instrument`) MUST be described as specified in Process Run Crate and this profile. Details regarding the execution of individual workflow steps can be described with the [Provenance Run Crate](../provenance_run_crate) profile. @@ -46,7 +46,7 @@ The following diagram shows the relationships between provenance-related entitie ```json { "@context": [ - "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/crate/1.2/context", "https://w3id.org/ro/terms/workflow-run/context" ], "@graph": [ @@ -55,7 +55,7 @@ The following diagram shows the relationships between provenance-related entitie "@type": "CreativeWork", "about": {"@id": "./"}, "conformsTo": [ - {"@id": "https://w3id.org/ro/crate/1.1"}, + {"@id": "https://w3id.org/ro/crate/1.2"}, {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"} ] }, @@ -305,7 +305,7 @@ This profile inherits the requirements of [Process Run Crate](../process_run_cra - Dataset (the root data entity, e.g. "@id": "./") + Dataset (the root data entity, e.g. "@id": "./") conformsTo @@ -353,4 +353,4 @@ This profile inherits the requirements of [Process Run Crate](../process_run_cra -For each entity described in the table, the most important properties are highlighted. Other properties supported by the entity (e.g. [minValue](http://schema.org/minValue) for a [PropertyValue](http://schema.org/PropertyValue)) can also be used (they are an implicit MAY requirement). See also [Extending RO-Crate](https://www.researchobject.org/ro-crate/specification/1.1/appendix/jsonld.html#extending-ro-crate) for guidance on defining and using terms not included in the RO-Crate context. +For each entity described in the table, the most important properties are highlighted. Other properties supported by the entity (e.g. [minValue](http://schema.org/minValue) for a [PropertyValue](http://schema.org/PropertyValue)) can also be used (they are an implicit MAY requirement). See also [Extending RO-Crate](https://www.researchobject.org/ro-crate/specification/1.2/appendix/jsonld.html#extending-ro-crate) for guidance on defining and using terms not included in the RO-Crate context. From b16f36106dbdb7790bdc2214d559938a4e6026ac Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Tue, 6 Jan 2026 10:04:50 +0000 Subject: [PATCH 07/22] update context isBasedOn --- .../profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json | 2 +- .../0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json index 8bda60c..674d4c5 100644 --- a/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-metadata.json @@ -185,7 +185,7 @@ "encodingFormat": "application/ld+json", "isBasedOn": [ { - "@id": "https://w3id.org/ro/crate/1.1/context" + "@id": "https://w3id.org/ro/crate/1.2/context" }, { "@id": "https://w3id.org/ro/terms/workflow-run#" diff --git a/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json index 4e169d5..aebbb10 100644 --- a/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-metadata.json @@ -194,7 +194,7 @@ "encodingFormat": "application/ld+json", "isBasedOn": [ { - "@id": "https://w3id.org/ro/crate/1.1/context" + "@id": "https://w3id.org/ro/crate/1.2/context" }, { "@id": "https://w3id.org/ro/terms/workflow-run#" From 116726c0b98c0439ddbcfc772319371cdd7dcd1e Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Tue, 6 Jan 2026 10:08:41 +0000 Subject: [PATCH 08/22] regenerate html previews --- .../example1/ro-crate-preview.html | 85 ++- .../process_run_crate/ro-crate-preview.html | 668 +++++++++--------- .../example3/ro-crate-preview.html | 164 ++--- .../ro-crate-preview.html | 464 ++++++------ .../example2/ro-crate-preview.html | 149 ++-- .../workflow_run_crate/ro-crate-preview.html | 625 ++++++++-------- 6 files changed, 1053 insertions(+), 1102 deletions(-) diff --git a/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-preview.html b/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-preview.html index 7877d6b..466404e 100644 --- a/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-preview.html +++ b/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-preview.html @@ -6,13 +6,15 @@