diff --git a/docs/profiles/0.1-DRAFT/process_run_crate.md b/docs/profiles/0.1-DRAFT/process_run_crate.md index 66dfeea..50df0df 100644 --- a/docs/profiles/0.1-DRAFT/process_run_crate.md +++ b/docs/profiles/0.1-DRAFT/process_run_crate.md @@ -21,13 +21,21 @@ By "implicit workflow" we mean that the composition of these tools may have been This profile requires the indication of [Software used to create files](https://www.researchobject.org/ro-crate/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). -## Example +## Example Metadata File (`ro-crate-metadata.json`) ```json -[ +{ "@context": "https://w3id.org/ro/crate/1.1/context", + "@graph": [ + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"}, + "about": {"@id": "./"} + }, { "@id": "./", "@type": "Dataset", + "conformsTo": { "@id": "https://w3id.org/ro/wfrun/process/0.1" }, "hasPart": [ {"@id": "pics/2017-06-11%2012.56.14.jpg"}, {"@id": "pics/sepia_fence.jpg"} @@ -35,6 +43,11 @@ This profile requires the indication of [Software used to create files](https:// "mentions": {"@id": "#SepiaConversion_1"}, "name": "My Pictures" }, + { "@id": "https://w3id.org/ro/wfrun/process/0.1", + "@type": "CreativeWork", + "name": "Process Run Crate", + "version": "0.1" + }, { "@id": "https://www.imagemagick.org/", "@type": "SoftwareApplication", @@ -73,11 +86,14 @@ This profile requires the indication of [Software used to create files](https:// "name": "Stian Soiland-Reyes" } ] +} ``` Note that the command line shown in the action's `description` is not directly re-executable, as file paths are not required to match the RO-Crate locations. For a more structural and reproducible description of tool executions, see [Workflow Run Crate](workflow_run_crate). + + ## Requirements @@ -88,6 +104,15 @@ Note that the command line shown in the action's `description` is not directly r + + + + + + + + diff --git a/docs/profiles/0.1-DRAFT/provenance_run_crate.md b/docs/profiles/0.1-DRAFT/provenance_run_crate.md index acebf5e..a15d31a 100644 --- a/docs/profiles/0.1-DRAFT/provenance_run_crate.md +++ b/docs/profiles/0.1-DRAFT/provenance_run_crate.md @@ -29,13 +29,29 @@ The following diagram shows the relationships between all provenance-related ent Entity-relationship diagram -## Example +## Example Metadata File (`ro-crate-metadata.json`) ```json -[ +{ "@context": "https://w3id.org/ro/crate/1.1/context", + "@graph": [ + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "about": {"@id": "./"}, + "conformsTo": [ + {"@id": "https://w3id.org/ro/crate/1.1"}, + {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"} + ] + }, { "@id": "./", "@type": "Dataset", + "conformsTo": [ + { "@id": "https://w3id.org/ro/wfrun/process/0.1" }, + { "@id": "https://w3id.org/ro/wfrun/workflow/0.1" }, + { "@id": "https://w3id.org/ro/wfrun/provenance/0.1" }, + { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"} + ], "hasPart": [ {"@id": "packed.cwl"}, {"@id": "327fc7aedf4f6b69a42a7c8b808dc5a7aff61376"}, @@ -47,14 +63,25 @@ The following diagram shows the relationships between all provenance-related ent {"@id": "#4154dad3-00cc-4e35-bb8f-a2de5cd7dc49"} ] }, - { - "@id": "ro-crate-metadata.json", + { "@id": "https://w3id.org/ro/wfrun/process/0.1", "@type": "CreativeWork", - "about": {"@id": "./"}, - "conformsTo": [ - {"@id": "https://w3id.org/ro/crate/1.1"}, - {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"} - ] + "name": "Process Run Crate", + "version": "0.1" + }, + { "@id": "https://w3id.org/ro/wfrun/workflow/0.1", + "@type": "CreativeWork", + "name": "Workflow Run Crate", + "version": "0.1" + }, + { "@id": "https://w3id.org/ro/wfrun/provenance/0.1", + "@type": "CreativeWork", + "name": "Provenance Run Crate", + "version": "0.1" + }, + { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0", + "@type": "CreativeWork", + "name": "Workflow RO-Crate", + "version": "1.0" }, { "@id": "packed.cwl", @@ -415,6 +442,15 @@ The requirements of this profile are those of [Workflow Run Crate](workflow_run_ + + + + + + + + diff --git a/docs/profiles/0.1-DRAFT/workflow_run_crate.md b/docs/profiles/0.1-DRAFT/workflow_run_crate.md index 206f605..4538427 100644 --- a/docs/profiles/0.1-DRAFT/workflow_run_crate.md +++ b/docs/profiles/0.1-DRAFT/workflow_run_crate.md @@ -24,10 +24,25 @@ Some workflows have multiple inputs/outputs that, in conformance with the [Biosc ## Example ```json -[ +{ "@context": "https://w3id.org/ro/crate/1.1/context", + "@graph": [ + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "about": {"@id": "./"}, + "conformsTo": [ + {"@id": "https://w3id.org/ro/crate/1.1"}, + {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"} + ] + }, { "@id": "./", "@type": "Dataset", + "conformsTo": [ + { "@id": "https://w3id.org/ro/wfrun/process/0.1" }, + { "@id": "https://w3id.org/ro/wfrun/workflow/0.1" }, + { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"} + ], "hasPart": [ {"@id": "Galaxy-Workflow-Hello_World.ga"}, {"@id": "inputs/abcdef.txt"}, @@ -38,6 +53,21 @@ Some workflows have multiple inputs/outputs that, in conformance with the [Biosc "mainEntity": {"@id": "Galaxy-Workflow-Hello_World.ga"}, "mentions": {"@id": "#wfrun-5a5970ab-4375-444d-9a87-a764a66e3a47"} }, + { "@id": "https://w3id.org/ro/wfrun/process/0.1", + "@type": "CreativeWork", + "name": "Process Run Crate", + "version": "0.1" + }, + { "@id": "https://w3id.org/ro/wfrun/workflow/0.1", + "@type": "CreativeWork", + "name": "Workflow Run Crate", + "version": "0.1" + }, + { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0", + "@type": "CreativeWork", + "name": "Workflow RO-Crate", + "version": "1.0" + }, { "@id": "Galaxy-Workflow-Hello_World.ga", "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], @@ -186,6 +216,15 @@ This profile inherits the requirements of [Process Run Crate](process_run_crate) + + + + + + + +
Description
Dataset (the root data entity, e.g. "@id": "./")
conformsToMUSTMUST reference a CreativeWork entity with an @id URI that is consistent with the versioned Permalink of this document, e.g. {"@id": "https://w3id.org/ro/wfrun/process/0.1"} +
SoftwareApplication
Description
Dataset (the root data entity, e.g. "@id": "./")
conformsToMUSTArray MUST reference a CreativeWork entity with an @id URI that is consistent with the versioned Permalink of this document, and SHOULD also reference versioned permalinks for Process Run Crate, Workflow Run Crate and Workflow RO-Crate. +
ComputationalWorkflow
Description
Dataset (the root data entity, e.g. "@id": "./")
conformsToMUSTArray MUST reference a CreativeWork entity with an @id URI that is consistent with the versioned Permalink of this document, and SHOULD also reference versioned permalinks for Process Run Crate and Workflow RO-Crate. +
CreateAction