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docs/profiles/0.6-DRAFT/workflow_run_crate/example2/ro-crate-preview.html diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/index.md b/docs/profiles/0.6-DRAFT/workflow_run_crate/index.md similarity index 100% rename from docs/profiles/0.5-DRAFT/workflow_run_crate/index.md rename to docs/profiles/0.6-DRAFT/workflow_run_crate/index.md diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json similarity index 100% rename from docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json rename to docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.jsonld b/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.jsonld similarity index 100% rename from docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.jsonld rename to docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.jsonld diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html b/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-preview.html similarity index 100% rename from docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html rename to docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-preview.html From 61a0c1ae5243ba7d4639d2fe49fdcffe1482f39e Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Tue, 18 Jun 2024 10:46:34 +0100 Subject: [PATCH 2/8] next: 0.6-DRAFT --- .../0.6-DRAFT/process_run_crate/index.md | 4 +- .../process_run_crate/ro-crate-metadata.json | 10 +- .../process_run_crate/ro-crate-preview.html | 102 +++++++-------- .../0.6-DRAFT/provenance_run_crate/index.md | 8 +- .../ro-crate-metadata.json | 26 ++-- .../ro-crate-preview.html | 114 ++++++++--------- .../0.6-DRAFT/workflow_run_crate/index.md | 8 +- .../workflow_run_crate/ro-crate-metadata.json | 18 +-- .../workflow_run_crate/ro-crate-preview.html | 116 +++++++++--------- 9 files changed, 203 insertions(+), 203 deletions(-) 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 6fd31ac..33e0af2 100644 --- a/docs/profiles/0.6-DRAFT/process_run_crate/index.md +++ b/docs/profiles/0.6-DRAFT/process_run_crate/index.md @@ -5,8 +5,8 @@ title: Process Run Crate # Process Run Crate -* Version: 0.5-DRAFT -* Permalink: +* Version: 0.6-DRAFT +* Permalink: * Authors: [Workflow Run RO-Crate working group](https://www.researchobject.org/workflow-run-crate/#community) * License: [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0) (SPDX: [`Apache-2.0`](http://spdx.org/licenses/Apache-2.0)) * Example conforming crate: [ro-crate-metadata.json](example1/ro-crate-metadata.json) [ro-crate-preview.html](example1/ro-crate-preview.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 ceb765c..bbf68e1 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 @@ -6,7 +6,7 @@ "@type": "CreativeWork", "license": { "@id": "http://spdx.org/licenses/CC0-1.0" }, "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"}, - "about": {"@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT"} + "about": {"@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT"} }, { "@id": "ro-crate-preview.html", @@ -15,17 +15,17 @@ "isBasedOn": {"@id": "ro-crate-metadata.json" }, "name": "RO-Crate preview of the Process Run Crate profile", "encodingFormat": "text/html", - "about": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" + "about": "https://w3id.org/ro/wfrun/process/0.6-DRAFT" }, { - "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT", + "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT", "@type": ["Dataset","Profile"], "isProfileOf": [ {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"} ], - "identifier": "https://w3id.org/ro/wfrun/process/0.5-DRAFT", + "identifier": "https://w3id.org/ro/wfrun/process/0.6-DRAFT", "name": "Process Run Crate profile", - "version": "0.5-DRAFT", + "version": "0.6-DRAFT", "license": { "@id": "https://www.apache.org/licenses/LICENSE-2.0" }, diff --git a/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-preview.html b/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-preview.html index e65aeba..d0a5143 100644 --- a/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.6-DRAFT/process_run_crate/ro-crate-preview.html @@ -20,7 +20,7 @@ "@id": "https://w3id.org/ro/crate/1.2-DRAFT" }, "about": { - "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" + "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT" } }, { @@ -31,7 +31,7 @@ "value": "CC0-1.0" }, { - "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT", + "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT", "@type": [ "Dataset", "Profile" @@ -39,9 +39,9 @@ "isProfileOf": { "@id": "https://w3id.org/ro/crate/1.2-DRAFT" }, - "identifier": "https://w3id.org/ro/wfrun/process/0.5-DRAFT", + "identifier": "https://w3id.org/ro/wfrun/process/0.6-DRAFT", "name": "Process Run Crate profile", - "version": "0.5-DRAFT", + "version": "0.6-DRAFT", "license": { "@id": "https://www.apache.org/licenses/LICENSE-2.0" }, @@ -181,7 +181,7 @@ }, "name": "RO-Crate preview of the Process Run Crate profile", "encodingFormat": "text/html", - "about": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" + "about": "https://w3id.org/ro/wfrun/process/0.6-DRAFT" }, { "@id": "https://www.apache.org/licenses/LICENSE-2.0", @@ -1308,17 +1308,17 @@

Process Run Crate profile

-

Go to: Process Run Crate profile

+

Go to: Process Run Crate profile

-
+ @@ -1571,7 +1571,7 @@

Go to: Apache Lic spdx: Apache-2.0 Items that reference this one license [?] - Process Run Crate profile + Process Run Crate profile

@@ -1604,7 +1604,7 @@

⬇️ Download: Process Run Crate (HTML)

Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile hasArtifact [?] #hasSpecification @@ -1647,7 +1647,7 @@

Example Process Run Crate

Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile hasArtifact [?] #hasExample @@ -1679,7 +1679,7 @@

G Recording provenance of workflow runs with RO-Crate (RO-Crate and mapping) Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile hasArtifact [?] #hasMappingToProv @@ -1743,7 +1743,7 @@

Go to: Namespace for Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile isBasedOn [?] JSON-LD context for workflow-run terms @@ -1794,7 +1794,7 @@

Go to: JSON-LD context Creative Commons Zero v1.0 Universal Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile

@@ -1823,7 +1823,7 @@

Go to: Workflow Run RO-Crate Introd Simone Leo Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile hasArtifact [?] #hasGuidance @@ -1858,7 +1858,7 @@

Go to: runcrate

https://pypi.org/project/runcrate/ Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile
@@ -1884,7 +1884,7 @@

Go to: SoftwareApplicat DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile domainIncludes [?] environment @@ -1913,7 +1913,7 @@

Go to: SoftwareSourceCod DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile domainIncludes [?] environment @@ -1942,7 +1942,7 @@

Go to: Computati DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile domainIncludes [?] connection @@ -1971,7 +1971,7 @@

Go to: CreateAction

DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile domainIncludes [?]
@@ -2032,7 +2032,7 @@

Go to: description

DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2058,7 +2058,7 @@

Go to: endTime

DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2084,7 +2084,7 @@

Go to: startTime

DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2110,7 +2110,7 @@

Go to: instrument

DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2136,7 +2136,7 @@

Go to: agent

DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2162,7 +2162,7 @@

Go to: Person

DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2188,7 +2188,7 @@

Go to: Organization

DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2214,7 +2214,7 @@

Go to: object

DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2240,7 +2240,7 @@

Go to: result

DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2266,7 +2266,7 @@

Go to: actionStatus

DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2292,7 +2292,7 @@

Go to: error

DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2318,7 +2318,7 @@

Go to: CompletedActio DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2344,7 +2344,7 @@

Go to: FailedActionStatu DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2373,7 +2373,7 @@

Go to: MediaObject

File Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile domainIncludes [?]
    @@ -2410,7 +2410,7 @@

    Go to: Dataset

    DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2436,7 +2436,7 @@

    Go to: Collection

    DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2462,7 +2462,7 @@

    Go to: CreativeWork

    DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2488,7 +2488,7 @@

    Go to: PropertyValue

    DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile rangeIncludes [?]
      @@ -2521,7 +2521,7 @@

      Go to: alternateName

      DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2547,7 +2547,7 @@

      Go to: mainEntity

      DefinedTerm Items that reference this one hasPart [?] - Process Run Crate profile + Process Run Crate profile @@ -2576,7 +2576,7 @@

      #hasSpecification

      Process Run Crate (HTML) Items that reference this one hasResource [?] - Process Run Crate profile + Process Run Crate profile @@ -2605,7 +2605,7 @@

      #hasConstraints

      Process Run Crate requirements Items that reference this one hasResource [?] - Process Run Crate profile + Process Run Crate profile @@ -2634,7 +2634,7 @@

      #hasVocabulary

      Namespace for Workflow Run RO-Crate model Items that reference this one hasResource [?] - Process Run Crate profile + Process Run Crate profile @@ -2663,7 +2663,7 @@

      #hasGuidance

      Workflow Run RO-Crate Introduction Items that reference this one hasResource [?] - Process Run Crate profile + Process Run Crate profile @@ -2692,7 +2692,7 @@

      #hasExample

      Example Process Run Crate Items that reference this one hasResource [?] - Process Run Crate profile + Process Run Crate profile @@ -2721,7 +2721,7 @@

      #hasMappingToProv

      SSSOM mapping from PROV to Workflow Run Crate Items that reference this one hasResource [?] - Process Run Crate profile + Process Run Crate profile @@ -2789,7 +2789,7 @@

      Go to: Recording pr Simone Leo, et al. (2024): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852 Items that reference this one citation [?] - Process Run Crate profile + Process Run Crate profile 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 0b1d22e..5200869 100644 --- a/docs/profiles/0.6-DRAFT/provenance_run_crate/index.md +++ b/docs/profiles/0.6-DRAFT/provenance_run_crate/index.md @@ -5,14 +5,14 @@ title: Provenance Run Crate # Provenance Run Crate -* Version: 0.5-DRAFT -* Permalink: +* Version: 0.6-DRAFT +* Permalink: * Authors: [Workflow Run RO-Crate working group](https://www.researchobject.org/workflow-run-crate/#community) * License: [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0) (SPDX: [`Apache-2.0`](http://spdx.org/licenses/Apache-2.0)) * Example conforming crate: [ro-crate-metadata.json](example3/ro-crate-metadata.json) [ro-crate-preview.html](example3/ro-crate-preview.html) * Profile Crate: [ro-crate-metadata.json](ro-crate-metadata.json) [ro-crate-preview.html](ro-crate-preview.html) * Extends: - - [Workflow Run Crate](https://w3id.org/ro/wfrun/workflow/0.5-DRAFT) + - [Workflow Run Crate](https://w3id.org/ro/wfrun/workflow/0.6-DRAFT) * JSON-LD context: * Vocabulary terms: @@ -584,7 +584,7 @@ The requirements of this profile are those of [Workflow Run Crate](../workflow_r conformsTo MUST - Array 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. + Array 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. 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 072845b..f7feaaf 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 @@ -6,7 +6,7 @@ "@type": "CreativeWork", "license": { "@id": "http://spdx.org/licenses/CC0-1.0" }, "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"}, - "about": {"@id": "https://w3id.org/ro/wfrun/provenance/0.5-DRAFT"} + "about": {"@id": "https://w3id.org/ro/wfrun/provenance/0.6-DRAFT"} }, { "@id": "ro-crate-preview.html", @@ -15,17 +15,17 @@ "isBasedOn": {"@id": "ro-crate-metadata.json" }, "name": "RO-Crate preview of the Provenance Run Crate profile", "encodingFormat": "text/html", - "about": "https://w3id.org/ro/wfrun/provenance/0.5-DRAFT" + "about": "https://w3id.org/ro/wfrun/provenance/0.6-DRAFT" }, { - "@id": "https://w3id.org/ro/wfrun/provenance/0.5-DRAFT", + "@id": "https://w3id.org/ro/wfrun/provenance/0.6-DRAFT", "@type": ["Dataset","Profile"], "isProfileOf": [ {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"} ], - "identifier": "https://w3id.org/ro/wfrun/provenance/0.5-DRAFT", + "identifier": "https://w3id.org/ro/wfrun/provenance/0.6-DRAFT", "name": "Provenance Run Crate profile", - "version": "0.5-DRAFT", + "version": "0.6-DRAFT", "license": { "@id": "https://www.apache.org/licenses/LICENSE-2.0" }, @@ -40,8 +40,8 @@ { "@id": "https://w3id.org/ro/terms/workflow-run" }, { "@id": "https://gxy.io/GTN:T00343" }, { "@id": "https://pypi.org/project/runcrate/" }, - { "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" }, - { "@id": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT" }, + { "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT" }, + { "@id": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT" }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" }, { "@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection" }, { "@id": "https://w3id.org/ro/terms/workflow-run#connection" }, @@ -115,10 +115,10 @@ "name": "RO-Crate Community" }, { - "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT", + "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT", "@type": ["CreativeWork", "Profile"], "name": "Process Run Crate profile", - "version": "0.5-DRAFT" + "version": "0.6-DRAFT" }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0", @@ -127,10 +127,10 @@ "version": "1.0" }, { - "@id": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT", + "@id": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT", "@type": ["CreativeWork", "Profile"], "name": "Workflow Run Crate profile", - "version": "0.5-DRAFT" + "version": "0.6-DRAFT" }, { "@id": "index.html", @@ -269,14 +269,14 @@ "@type": "ResourceDescriptor", "name": "SHOULD conform to Process Crate profile", "hasRole": { "@id": "http://purl.org/dc/terms/conformsTo" }, - "hasArtifact": {"@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT"} + "hasArtifact": {"@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT"} }, { "@id": "#shouldConformToWorkflowCrateProfile", "@type": "ResourceDescriptor", "name": "SHOULD conform to Workflow Crate profile", "hasRole": { "@id": "http://purl.org/dc/terms/conformsTo" }, - "hasArtifact": {"@id": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT"} + "hasArtifact": {"@id": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT"} }, { "@id": "https://gxy.io/GTN:T00343", diff --git a/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-preview.html b/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-preview.html index b110671..a0702d2 100644 --- a/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.6-DRAFT/provenance_run_crate/ro-crate-preview.html @@ -18,7 +18,7 @@ "@id": "https://w3id.org/ro/crate/1.2-DRAFT" }, "about": { - "@id": "https://w3id.org/ro/wfrun/provenance/0.5-DRAFT" + "@id": "https://w3id.org/ro/wfrun/provenance/0.6-DRAFT" } }, { @@ -29,7 +29,7 @@ "value": "CC0-1.0" }, { - "@id": "https://w3id.org/ro/wfrun/provenance/0.5-DRAFT", + "@id": "https://w3id.org/ro/wfrun/provenance/0.6-DRAFT", "@type": [ "Dataset", "Profile" @@ -37,9 +37,9 @@ "isProfileOf": { "@id": "https://w3id.org/ro/crate/1.2-DRAFT" }, - "identifier": "https://w3id.org/ro/wfrun/provenance/0.5-DRAFT", + "identifier": "https://w3id.org/ro/wfrun/provenance/0.6-DRAFT", "name": "Provenance Run Crate profile", - "version": "0.5-DRAFT", + "version": "0.6-DRAFT", "license": { "@id": "https://www.apache.org/licenses/LICENSE-2.0" }, @@ -69,10 +69,10 @@ "@id": "https://pypi.org/project/runcrate/" }, { - "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" + "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT" }, { - "@id": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT" + "@id": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT" }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" @@ -137,7 +137,7 @@ }, "name": "RO-Crate preview of the Provenance Run Crate profile", "encodingFormat": "text/html", - "about": "https://w3id.org/ro/wfrun/provenance/0.5-DRAFT" + "about": "https://w3id.org/ro/wfrun/provenance/0.6-DRAFT" }, { "@id": "https://www.apache.org/licenses/LICENSE-2.0", @@ -363,22 +363,22 @@ "url": "https://pypi.org/project/runcrate/" }, { - "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT", + "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT", "@type": [ "CreativeWork", "Profile" ], "name": "Process Run Crate profile", - "version": "0.5-DRAFT" + "version": "0.6-DRAFT" }, { - "@id": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT", + "@id": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT", "@type": [ "CreativeWork", "Profile" ], "name": "Workflow Run Crate profile", - "version": "0.5-DRAFT" + "version": "0.6-DRAFT" }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0", @@ -518,7 +518,7 @@ "@id": "http://purl.org/dc/terms/conformsTo" }, "hasArtifact": { - "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" + "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT" } }, { @@ -529,7 +529,7 @@ "@id": "http://purl.org/dc/terms/conformsTo" }, "hasArtifact": { - "@id": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT" + "@id": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT" } }, { @@ -924,17 +924,17 @@

      Provenance Run Crate profile

      -

      Go to: Provenance Run Crate profile

      +

      Go to: Provenance Run Crate profile

      - @@ -1195,7 +1195,7 @@

      ⬇️ Download: Provenance Run Crate (HTML)

    Items that reference this one hasPart [?] - Provenance Run Crate profile + Provenance Run Crate profile hasArtifact [?] #hasSpecification @@ -1245,7 +1245,7 @@

    Example Process Run Crate

Items that reference this one hasPart [?] - Provenance Run Crate profile + Provenance Run Crate profile hasArtifact [?] #hasExample @@ -1278,7 +1278,7 @@

G Recording provenance of workflow runs with RO-Crate (RO-Crate and mapping) Items that reference this one hasPart [?] - Provenance Run Crate profile + Provenance Run Crate profile hasArtifact [?] #hasMappingToProv @@ -1308,7 +1308,7 @@

Go to: Namespace for DefinedTermSet Items that reference this one hasPart [?] - Provenance Run Crate profile + Provenance Run Crate profile isBasedOn [?] JSON-LD context for workflow-run terms @@ -1371,7 +1371,7 @@

Go to: JSON-LD context Creative Commons Zero v1.0 Universal Items that reference this one hasPart [?] - Provenance Run Crate profile + Provenance Run Crate profile @@ -1401,7 +1401,7 @@

Go to: Workflow Run RO-Crate Introd Simone Leo Items that reference this one hasPart [?] - Provenance Run Crate profile + Provenance Run Crate profile hasArtifact [?] #hasGuidance @@ -1437,7 +1437,7 @@

Go to: runcrate

https://pypi.org/project/runcrate/ Items that reference this one hasPart [?] - Provenance Run Crate profile + Provenance Run Crate profile @@ -1445,17 +1445,17 @@

Go to: runcrate



-

Go to: Process Run Crate profile

+

Go to: Process Run Crate profile

-
+
- + @@ -1468,10 +1468,10 @@

Go to: Process Ru

- + - + @@ -1482,17 +1482,17 @@

Go to: Process Ru


-

Go to: Workflow Run Crate profile

+

Go to: Workflow Run Crate profile

-
+

@idhttps://w3id.org/ro/wfrun/process/0.5-DRAFThttps://w3id.org/ro/wfrun/process/0.6-DRAFT
name [?] Process Run Crate profile
version [?]0.5-DRAFT0.6-DRAFT
Items that reference this one
hasPart [?]Provenance Run Crate profileProvenance Run Crate profile
hasArtifact [?] SHOULD conform to Process Crate profile
- + @@ -1505,10 +1505,10 @@

Go to: Workflow

- + - + @@ -1545,7 +1545,7 @@

Go to: Wor

- + @@ -1587,7 +1587,7 @@

Go to:

- +
@idhttps://w3id.org/ro/wfrun/workflow/0.5-DRAFThttps://w3id.org/ro/wfrun/workflow/0.6-DRAFT
name [?] Workflow Run Crate profile
version [?]0.5-DRAFT0.6-DRAFT
Items that reference this one
hasPart [?]Provenance Run Crate profileProvenance Run Crate profile
hasArtifact [?] SHOULD conform to Workflow Crate profile1.0
Items that reference this one
hasPart [?]Provenance Run Crate profileProvenance Run Crate profile
conformsTo [?] Example Process Run CrateNamespace for Workflow Run RO-Crate model
Items that reference this one
hasPart [?]Provenance Run Crate profileProvenance Run Crate profile
@@ -1623,7 +1623,7 @@

Go to: conn Namespace for Workflow Run RO-Crate model Items that reference this one hasPart [?] - Provenance Run Crate profile + Provenance Run Crate profile

@@ -1659,7 +1659,7 @@

Go to: Namespace for Workflow Run RO-Crate model Items that reference this one hasPart [?] - Provenance Run Crate profile + Provenance Run Crate profile

@@ -1695,7 +1695,7 @@

Go to: Namespace for Workflow Run RO-Crate model Items that reference this one hasPart [?] - Provenance Run Crate profile + Provenance Run Crate profile @@ -1731,7 +1731,7 @@

Go to: bui Codemeta Terms Items that reference this one hasPart [?] - Provenance Run Crate profile + Provenance Run Crate profile @@ -1761,7 +1761,7 @@

#hasSpecification

Provenance Run Crate (HTML) Items that reference this one hasResource [?] - Provenance Run Crate profile + Provenance Run Crate profile @@ -1791,7 +1791,7 @@

#hasConstraints

Provenance Run Crate requirements Items that reference this one hasResource [?] - Provenance Run Crate profile + Provenance Run Crate profile @@ -1821,7 +1821,7 @@

#hasVocabulary

Namespace for Workflow Run RO-Crate model Items that reference this one hasResource [?] - Provenance Run Crate profile + Provenance Run Crate profile @@ -1851,7 +1851,7 @@

#hasGuidance

Workflow Run RO-Crate Introduction Items that reference this one hasResource [?] - Provenance Run Crate profile + Provenance Run Crate profile @@ -1881,7 +1881,7 @@

#hasExample

Example Process Run Crate Items that reference this one hasResource [?] - Provenance Run Crate profile + Provenance Run Crate profile @@ -1911,7 +1911,7 @@

#hasMappingToProv

SSSOM mapping from PROV to Workflow Run Crate Items that reference this one hasResource [?] - Provenance Run Crate profile + Provenance Run Crate profile @@ -1944,7 +1944,7 @@

SHOULD conform to Workflow RO-Crate profile

Workflow RO-Crate profile Items that reference this one hasResource [?] - Provenance Run Crate profile + Provenance Run Crate profile @@ -1974,10 +1974,10 @@

SHOULD conform to Process Crate profile

http://purl.org/dc/terms/conformsTo hasArtifact [?] - Process Run Crate profile + Process Run Crate profile Items that reference this one hasResource [?] - Provenance Run Crate profile + Provenance Run Crate profile @@ -2007,10 +2007,10 @@

SHOULD conform to Workflow Crate profile

http://purl.org/dc/terms/conformsTo hasArtifact [?] - Workflow Run Crate profile + Workflow Run Crate profile Items that reference this one hasResource [?] - Provenance Run Crate profile + Provenance Run Crate profile @@ -2079,7 +2079,7 @@

Go to: Recording pr Simone Leo, et al. (2024): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852 Items that reference this one citation [?] - Provenance Run Crate profile + Provenance Run Crate profile 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 2df1b9b..f351339 100644 --- a/docs/profiles/0.6-DRAFT/workflow_run_crate/index.md +++ b/docs/profiles/0.6-DRAFT/workflow_run_crate/index.md @@ -5,14 +5,14 @@ title: Workflow Run Crate # Workflow Run Crate -* Version: 0.5-DRAFT -* Permalink: +* Version: 0.6-DRAFT +* Permalink: * Authors: [Workflow Run RO-Crate working group](https://www.researchobject.org/workflow-run-crate/#community) * License: [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0) (SPDX: [`Apache-2.0`](http://spdx.org/licenses/Apache-2.0)) * Example conforming crate: [ro-crate-metadata.json](example2/ro-crate-metadata.json) [ro-crate-preview.html](example2/ro-crate-preview.html) * Profile Crate: [ro-crate-metadata.json](ro-crate-metadata.json) [ro-crate-preview.html](ro-crate-preview.html) * Extends: - - [Process Run Crate](https://w3id.org/ro/wfrun/process/0.5-DRAFT) + - [Process Run Crate](https://w3id.org/ro/wfrun/process/0.6-DRAFT) - [Workflow RO-Crate](https://w3id.org/workflowhub/workflow-ro-crate/) * JSON-LD context: * Vocabulary terms: @@ -310,7 +310,7 @@ This profile inherits the requirements of [Process Run Crate](../process_run_cra conformsTo MUST - Array 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. + Array 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. 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 7a35f77..6365434 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 @@ -6,7 +6,7 @@ "@type": "CreativeWork", "license": { "@id": "http://spdx.org/licenses/CC0-1.0" }, "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"}, - "about": {"@id": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT"} + "about": {"@id": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT"} }, { "@id": "ro-crate-preview.html", @@ -15,17 +15,17 @@ "isBasedOn": {"@id": "ro-crate-metadata.json" }, "name": "RO-Crate preview of the Workflow Run Crate profile", "encodingFormat": "text/html", - "about": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT" + "about": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT" }, { - "@id": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT", + "@id": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT", "@type": ["Dataset","Profile"], "isProfileOf": [ {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"} ], - "identifier": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT", + "identifier": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT", "name": "Workflow Run Crate profile", - "version": "0.5-DRAFT", + "version": "0.6-DRAFT", "license": { "@id": "https://www.apache.org/licenses/LICENSE-2.0" }, @@ -39,7 +39,7 @@ { "@id": "https://w3id.org/ro/terms/workflow-run" }, { "@id": "https://gxy.io/GTN:T00343" }, { "@id": "https://pypi.org/project/runcrate/" }, - { "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" }, + { "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT" }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" }, { "@id": "http://schema.org/MediaObject" }, { "@id": "http://schema.org/additionalType" }, @@ -143,10 +143,10 @@ "name": "RO-Crate Community" }, { - "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT", + "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT", "@type": ["CreativeWork", "Profile"], "name": "Process Run Crate profile", - "version": "0.5-DRAFT" + "version": "0.6-DRAFT" }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0", @@ -276,7 +276,7 @@ "@type": "ResourceDescriptor", "name": "SHOULD conform to Process Crate profile", "hasRole": { "@id": "http://purl.org/dc/terms/conformsTo" }, - "hasArtifact": {"@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT"} + "hasArtifact": {"@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT"} }, { "@id": "https://gxy.io/GTN:T00343", diff --git a/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-preview.html b/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-preview.html index a6531d3..ce7b0ee 100644 --- a/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-preview.html @@ -18,7 +18,7 @@ "@id": "https://w3id.org/ro/crate/1.2-DRAFT" }, "about": { - "@id": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT" + "@id": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT" } }, { @@ -29,7 +29,7 @@ "value": "CC0-1.0" }, { - "@id": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT", + "@id": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT", "@type": [ "Dataset", "Profile" @@ -37,9 +37,9 @@ "isProfileOf": { "@id": "https://w3id.org/ro/crate/1.2-DRAFT" }, - "identifier": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT", + "identifier": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT", "name": "Workflow Run Crate profile", - "version": "0.5-DRAFT", + "version": "0.6-DRAFT", "license": { "@id": "https://www.apache.org/licenses/LICENSE-2.0" }, @@ -66,7 +66,7 @@ "@id": "https://pypi.org/project/runcrate/" }, { - "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" + "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT" }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" @@ -170,7 +170,7 @@ }, "name": "RO-Crate preview of the Workflow Run Crate profile", "encodingFormat": "text/html", - "about": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT" + "about": "https://w3id.org/ro/wfrun/workflow/0.6-DRAFT" }, { "@id": "https://www.apache.org/licenses/LICENSE-2.0", @@ -380,13 +380,13 @@ "url": "https://pypi.org/project/runcrate/" }, { - "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT", + "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT", "@type": [ "CreativeWork", "Profile" ], "name": "Process Run Crate profile", - "version": "0.5-DRAFT" + "version": "0.6-DRAFT" }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0", @@ -571,7 +571,7 @@ "@id": "http://purl.org/dc/terms/conformsTo" }, "hasArtifact": { - "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" + "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT" } }, { @@ -958,17 +958,17 @@

Workflow Run Crate profile

-

Go to: Workflow Run Crate profile

+

Go to: Workflow Run Crate profile

-
+ @@ -1217,7 +1217,7 @@

Go to: Apache Lic spdx: Apache-2.0 Items that reference this one license [?] - Workflow Run Crate profile + Workflow Run Crate profile

@@ -1251,7 +1251,7 @@

⬇️ Download: Workflow Run Crate (HTML)

Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile hasArtifact [?] #hasSpecification @@ -1299,7 +1299,7 @@

Example Workflow Run Crate

Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile hasArtifact [?] #hasExample @@ -1332,7 +1332,7 @@

G Recording provenance of workflow runs with RO-Crate (RO-Crate and mapping) Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile hasArtifact [?] #hasMappingToProv @@ -1374,7 +1374,7 @@

Go to: JSON-LD context Creative Commons Zero v1.0 Universal Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile

@@ -1404,7 +1404,7 @@

Go to: Workflow Run RO-Crate Introd Simone Leo Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile hasArtifact [?] #hasGuidance @@ -1440,7 +1440,7 @@

Go to: runcrate

https://pypi.org/project/runcrate/ Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile
@@ -1448,17 +1448,17 @@

Go to: runcrate



-

Go to: Process Run Crate profile

+

Go to: Process Run Crate profile

-
+
- + @@ -1471,10 +1471,10 @@

Go to: Process Ru

- + - + @@ -1511,7 +1511,7 @@

Go to: Wor

- + @@ -1547,7 +1547,7 @@

Go to: MediaObject

- +
@idhttps://w3id.org/ro/wfrun/process/0.5-DRAFThttps://w3id.org/ro/wfrun/process/0.6-DRAFT
name [?] Process Run Crate profile
version [?]0.5-DRAFT0.6-DRAFT
Items that reference this one
hasPart [?]Workflow Run Crate profileWorkflow Run Crate profile
hasArtifact [?] SHOULD conform to Process Crate profile1.0
Items that reference this one
hasPart [?]Workflow Run Crate profileWorkflow Run Crate profile
conformsTo [?] Example Workflow Run Crate File
Items that reference this one
hasPart [?]Workflow Run Crate profileWorkflow Run Crate profile
@@ -1574,7 +1574,7 @@

Go to: additionalType

DefinedTerm Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile
@@ -1601,7 +1601,7 @@

Go to: CreateAction

DefinedTerm Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile
@@ -1628,7 +1628,7 @@

Go to: exampleOfWork

DefinedTerm Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -1655,7 +1655,7 @@

Go to: instrument

DefinedTerm Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -1682,7 +1682,7 @@

Go to: name

DefinedTerm Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -1709,7 +1709,7 @@

Go to: object

DefinedTerm Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -1736,7 +1736,7 @@

Go to: PropertyValue

DefinedTerm Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -1763,7 +1763,7 @@

Go to: result

DefinedTerm Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -1790,7 +1790,7 @@

Go to: DataType

DefinedTerm Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -1817,7 +1817,7 @@

Go to: Integer

DefinedTerm Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -1844,7 +1844,7 @@

Go to: about

DefinedTerm Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -1871,7 +1871,7 @@

Go to: defaultValue

DefinedTerm Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -1898,7 +1898,7 @@

Go to: valueRequired

DefinedTerm Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -1925,7 +1925,7 @@

Go to: FormalParameter DefinedTerm Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -1952,7 +1952,7 @@

Go to: Computati DefinedTerm Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -1982,7 +1982,7 @@

Go to: inp input Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -2012,7 +2012,7 @@

Go to: ou output Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -2042,7 +2042,7 @@

Go to: conformsTo

conformsTo Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile hasRole [?]
    @@ -2079,7 +2079,7 @@

    Go to: env environment Items that reference this one hasPart [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -2109,7 +2109,7 @@

    #hasSpecification

    Workflow Run Crate (HTML) Items that reference this one hasResource [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -2139,7 +2139,7 @@

    #hasConstraints

    Workflow Run Crate requirements Items that reference this one hasResource [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -2169,7 +2169,7 @@

    #hasGuidance

    Workflow Run RO-Crate Introduction Items that reference this one hasResource [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -2199,7 +2199,7 @@

    #hasExample

    Example Workflow Run Crate Items that reference this one hasResource [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -2229,7 +2229,7 @@

    #hasMappingToProv

    SSSOM mapping from PROV to Workflow Run Crate Items that reference this one hasResource [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -2262,7 +2262,7 @@

    SHOULD conform to Workflow RO-Crate profile

    Workflow RO-Crate profile Items that reference this one hasResource [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -2292,10 +2292,10 @@

    SHOULD conform to Process Crate profile

    conformsTo hasArtifact [?] - Process Run Crate profile + Process Run Crate profile Items that reference this one hasResource [?] - Workflow Run Crate profile + Workflow Run Crate profile @@ -2364,7 +2364,7 @@

    Go to: Recording pr Simone Leo, et al. (2024): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852 Items that reference this one citation [?] - Workflow Run Crate profile + Workflow Run Crate profile From 69bef681d810f87df6c5cdd28d3f3f5ce468d0ba Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Tue, 18 Jun 2024 10:48:25 +0100 Subject: [PATCH 3/8] 0.5 release --- docs/profiles/0.5/img/er_diagram_process.svg | 1 + .../0.5/img/er_diagram_provenance.svg | 1 + docs/profiles/0.5/img/er_diagram_workflow.svg | 1 + docs/profiles/0.5/img/multiple_processes.svg | 471 +++ docs/profiles/0.5/img/revsort.svg | 79 + .../0.5/img/wrroc-figure-example.drawio.svg | 4 + .../profiles/0.5/img/wrroc-figure1.drawio.svg | 4 + .../profiles/0.5/img/wrroc-figure2.drawio.svg | 4 + .../profiles/0.5/img/wrroc-figure3.drawio.svg | 4 + docs/profiles/0.5/img/wrroc-venn.drawio.svg | 4 + docs/profiles/0.5/index.md | 12 + .../0.5/process_run_crate/example1/index.html | 1 + .../example1/pics/2017-06-11 12.56.14.jpg | Bin 0 -> 4867 bytes 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.../example2/inputs/abcdef.txt | 6 + .../outputs/Select_first_on_data_1_2.txt | 6 + .../example2/outputs/tac_on_data_360_1.txt | 6 + .../example2/ro-crate-metadata.json | 177 ++ .../example2/ro-crate-preview.html | 711 +++++ docs/profiles/0.5/workflow_run_crate/index.md | 354 +++ .../workflow_run_crate/ro-crate-metadata.json | 705 +++++ .../ro-crate-metadata.jsonld | 1 + .../workflow_run_crate/ro-crate-preview.html | 2381 ++++++++++++++ 42 files changed, 14544 insertions(+) create mode 100644 docs/profiles/0.5/img/er_diagram_process.svg create mode 100644 docs/profiles/0.5/img/er_diagram_provenance.svg create mode 100644 docs/profiles/0.5/img/er_diagram_workflow.svg create mode 100644 docs/profiles/0.5/img/multiple_processes.svg create mode 100644 docs/profiles/0.5/img/revsort.svg create mode 100644 docs/profiles/0.5/img/wrroc-figure-example.drawio.svg create mode 100644 docs/profiles/0.5/img/wrroc-figure1.drawio.svg create mode 100644 docs/profiles/0.5/img/wrroc-figure2.drawio.svg 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docs/profiles/0.5/provenance_run_crate/example3/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 create mode 100644 docs/profiles/0.5/provenance_run_crate/example3/97fe1b50b4582cebc7d853796ebd62e3e163aa3f create mode 100644 docs/profiles/0.5/provenance_run_crate/example3/b9214658cc453331b62c2282b772a5c063dbd284 create mode 120000 docs/profiles/0.5/provenance_run_crate/example3/index.hml create mode 100644 docs/profiles/0.5/provenance_run_crate/example3/packed.cwl create mode 100644 docs/profiles/0.5/provenance_run_crate/example3/ro-crate-metadata.json create mode 100644 docs/profiles/0.5/provenance_run_crate/example3/ro-crate-preview.html create mode 100644 docs/profiles/0.5/provenance_run_crate/index.md create mode 100644 docs/profiles/0.5/provenance_run_crate/ro-crate-metadata.json create mode 120000 docs/profiles/0.5/provenance_run_crate/ro-crate-metadata.jsonld create mode 100644 docs/profiles/0.5/provenance_run_crate/ro-crate-preview.html create mode 100644 docs/profiles/0.5/workflow_run_crate/example2/Galaxy-Workflow-Hello_World.ga create mode 120000 docs/profiles/0.5/workflow_run_crate/example2/index.hml create mode 100644 docs/profiles/0.5/workflow_run_crate/example2/inputs/abcdef.txt create mode 100644 docs/profiles/0.5/workflow_run_crate/example2/outputs/Select_first_on_data_1_2.txt create mode 100644 docs/profiles/0.5/workflow_run_crate/example2/outputs/tac_on_data_360_1.txt create mode 100644 docs/profiles/0.5/workflow_run_crate/example2/ro-crate-metadata.json create mode 100644 docs/profiles/0.5/workflow_run_crate/example2/ro-crate-preview.html create mode 100644 docs/profiles/0.5/workflow_run_crate/index.md create mode 100644 docs/profiles/0.5/workflow_run_crate/ro-crate-metadata.json create mode 120000 docs/profiles/0.5/workflow_run_crate/ro-crate-metadata.jsonld create mode 100644 docs/profiles/0.5/workflow_run_crate/ro-crate-preview.html diff --git a/docs/profiles/0.5/img/er_diagram_process.svg 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Text is not SVG - cannot display     \ No newline at end of file diff --git a/docs/profiles/0.5/index.md b/docs/profiles/0.5/index.md new file mode 100644 index 0000000..6316a5a --- /dev/null +++ b/docs/profiles/0.5/index.md @@ -0,0 +1,12 @@ +--- +title: The Workflow Run RO-Crate Profile Collection +--- + + +# The Workflow Run RO-Crate Profile Collection + +This section defines three [RO-Crate profiles](https://www.researchobject.org/ro-crate/profiles.html) for capturing the provenance of an execution of a computational workflow with increasing granularity: + +* [Process Run Crate](process_run_crate) can be used to describe the execution of one or more tools that contribute to the same computation; +* [Workflow Run Crate](workflow_run_crate) is similar to Process Run Crate, but assumes that the coordinated execution of the tools is driven by a [computational workflow](https://bioschemas.org/types/ComputationalWorkflow/1.0-RELEASE) +* [Provenance Run Crate](provenance_run_crate) extends 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    +

    +

    My Pictures

    + + +⬇️🏷️ Download all the metadata for My Pictures in JSON-LD format + + +
    + + +
    + + + +
    +
    +
    +

    My Pictures

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    Items that reference this one
    about [?]ro-crate-metadata.json
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    + +
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    +
    +

    Go to: Process Run Crate

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    + +
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    +
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    ⬇️ Download: 2017-06-11 12.56.14.jpg (input)

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    + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Items that reference this one
    hasPart [?]My Pictures
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    +
    + +
    +


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    ⬇️ Download: sepia_fence (output)

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    @idpics/sepia_fence.jpg
    name [?]sepia_fence (output)
    @typeFile
    description [?]The converted picture, now sepia-colored
    encodingFormat [?]image/jpeg
    Items that reference this one
    hasPart [?]My Pictures
    result [?]Convert dog image to sepia
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    Convert dog image to sepia

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    @id#SepiaConversion_1
    name [?]Convert dog image to sepia
    @typeCreateAction
    description [?]convert -sepia-tone 80% pics/2017-06-11\ 12.56.14.jpg pics/sepia_fence.jpg
    endTime [?]2024-05-17T01:04:52+01:00
    instrument [?]ImageMagick
    object [?]2017-06-11 12.56.14.jpg (input)
    result [?]sepia_fence (output)
    agent [?]Stian Soiland-Reyes
    Items that reference this one
    mentions [?]My Pictures
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    + + + + + + + diff --git a/docs/profiles/0.5/process_run_crate/index.md b/docs/profiles/0.5/process_run_crate/index.md new file mode 100644 index 0000000..0b1fa20 --- /dev/null +++ b/docs/profiles/0.5/process_run_crate/index.md @@ -0,0 +1,504 @@ +--- +title: Process Run Crate +--- + + +# Process Run Crate + +* Version: 0.5 +* Permalink: +* Authors: [Workflow Run RO-Crate working group](https://www.researchobject.org/workflow-run-crate/#community) +* License: [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0) (SPDX: [`Apache-2.0`](http://spdx.org/licenses/Apache-2.0)) +* 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) +* 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. + + +## 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. + +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). + +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). + +Entity-relationship diagram + + +## Example Metadata File (`ro-crate-metadata.json`) + +* [ro-crate-metadata.json](example1/ro-crate-metadata.json) +* [ro-crate-preview.html](example1/ro-crate-preview.html) + + + +```json +{ "@context": [ + "https://w3id.org/ro/crate/1.1/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"}, + "about": {"@id": "./"} + }, + { + "@id": "./", + "@type": "Dataset", + "conformsTo": {"@id": "https://w3id.org/ro/wfrun/process/0.4"}, + "hasPart": [ + {"@id": "pics/2017-06-11%2012.56.14.jpg"}, + {"@id": "pics/sepia_fence.jpg"} + ], + "mentions": {"@id": "#SepiaConversion_1"}, + "name": "My Pictures" + }, + { "@id": "https://w3id.org/ro/wfrun/process/0.4", + "@type": "CreativeWork", + "name": "Process Run Crate", + "version": "0.1" + }, + { + "@id": "https://www.imagemagick.org/", + "@type": "SoftwareApplication", + "url": "https://www.imagemagick.org/", + "name": "ImageMagick", + "softwareVersion": "6.9.7-4" + }, + { + "@id": "#SepiaConversion_1", + "@type": "CreateAction", + "name": "Convert dog image to sepia", + "description": "convert -sepia-tone 80% test_data/sample/pics/2017-06-11\\ 12.56.14.jpg test_data/sample/pics/sepia_fence.jpg", + "endTime": "2018-09-19T17:01:07+10:00", + "instrument": {"@id": "https://www.imagemagick.org/"}, + "object": {"@id": "pics/2017-06-11%2012.56.14.jpg"}, + "result": {"@id": "pics/sepia_fence.jpg"}, + "agent": {"@id": "https://orcid.org/0000-0001-9842-9718"} + }, + { + "@id": "pics/2017-06-11%2012.56.14.jpg", + "@type": "File", + "description": "Original image", + "encodingFormat": "image/jpeg", + "name": "2017-06-11 12.56.14.jpg (input)" + }, + { + "@id": "pics/sepia_fence.jpg", + "@type": "File", + "description": "The converted picture, now sepia-colored", + "encodingFormat": "image/jpeg", + "name": "sepia_fence (output)" + }, + { + "@id": "https://orcid.org/0000-0001-9842-9718", + "@type": "Person", + "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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    PropertyRequired?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/0.4"}
    SoftwareApplication
    @typeMUSTSHOULD include SoftwareApplication, SoftwareSourceCode or ComputationalWorkflow
    @idMUSTSHOULD be an absolute URI, but MAY be a relative URI to a data entity in the crate (e.g. "bin/simulation4") or a local identifier for tools that are not otherwise described on the web (e.g. "#statistical-analysis")
    nameSHOULDA human readable name for the tool in general (not just how it was used here)
    urlSHOULDHomepage, documentation or source for the tool
    versionSHOULDThe version string for the software application. In the case of a SoftwareApplication, this MAY be provided via the more specific softwareVersion. SoftwareApplication entities SHOULD NOT specify both version and softwareVersion: in this case, consumers SHOULD prioritize softwareVersion. In order to facilitate comparison attempts by consumers, it is RECOMMENDED to specify a machine-readable version string if available (see for instance Python's PEP 440).
    CreateAction
    @typeMUSTSHOULD be CreateAction to indicate that this tool created the result data entities. MAY be ActivateAction if the provenance does not include any result. MAY be UpdateAction if the tool modified an existing data entity or database in-place.
    @idMUSTA 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.
    nameSHOULDShort human-readable description of the execution.
    descriptionSHOULDDetails of the execution, for instance command line arguments or settings. This field is for information only, no particular structure is to be assumed.
    endTimeSHOULDThe time the process ended, i.e. when the last of the entities in result has been created. SHOULD be a DateTime in ISO 8601 format.
    startTimeMAYThe time the process started, i.e. the earliest time the process may have accessed an entity in object. SHOULD be a DateTime in ISO 8601 format.
    instrumentMUSTIdentifier of the executed tool.
    agentSHOULDIdentifier of a Person or Organization contextual entity that started/executed this tool.
    objectMAYThe identifier of one or more entities of the RO-Crate that were consumed by this action, e.g. input files or reference datasets.
    resultSHOULDThe identifier of one or more entities that were created or modified by this action, e.g. output files.
    actionStatusMAYSHOULD be CompletedActionStatus if the process completed successfully or FailedActionStatus if it failed to complete. In the latter case, consumers should be prepared for the absence of any dependent actions in the metadata. If this attribute is not specified, consumers should assume that the process completed successfully.
    errorMAYAdditional information on the cause of the failure, such as an error message from the application, if available. SHOULD NOT be specified unless actionStatus is set to FailedActionStatus.
    + +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. + +Data entities involved in an application's input and output SHOULD have an `@id` that reflects the original file or directory name as processed by the application, but MAY be renamed to avoid clashes with other entities in the crate. In this case, they SHOULD refer to the original name via [alternateName](http://schema.org/alternateName). This is particularly important to support reproducibility in cases where an application expects to find input in specific locations and with specific names (see the MIRAX example in [Representing multi-file objects](#representing-multi-file-objects)). + + +## Multiple processes + +A process crate can be used to indicate one single execution as a single `CreateAction`, or a series of processes that generate different data entities. These actions MAY form an *implicit workflow* by following the links between entities that appear as `result` in an action and as `object` in the following one, but a process crate is not required to ensure such consistency (e.g. there may be an intermediate action that has not been recorded). + +Multiple processes diagram + + +## Referencing configuration files + +Some applications support the modification of their behavior via configuration files. Typically, these are not part of the input interface, but are searched for by the application among a set of possible predefined file system paths. In the case of applications that support a configuration file, the specific configuration file used during a run SHOULD be added to the `object` attribute of the corresponding `CreateAction`, especially if its settings are different from the default ones. + +```json + { + "@id": "#SepiaConversion_1", + "@type": "CreateAction", + "name": "Convert dog image to sepia", + "description": "convert -sepia-tone 80% test_data/sample/pics/2017-06-11\\ 12.56.14.jpg test_data/sample/pics/sepia_fence.jpg", + "endTime": "2018-09-19T17:01:07+10:00", + "instrument": {"@id": "https://www.imagemagick.org/"}, + "object": [ + {"@id": "pics/2017-06-11%2012.56.14.jpg"}, + {"@id": "SepiaConversion_1/colors.xml"} + ], + "result": {"@id": "pics/sepia_fence.jpg"}, + "agent": {"@id": "https://orcid.org/0000-0001-9842-9718"} + }, + { + "@id": "SepiaConversion_1/colors.xml", + "@type": "File", + "description": "Imagemagick color names configuration", + "encodingFormat": "text/xml", + "name": "colors" + } +``` + + +## Representing multi-file objects + +In some formats, the data belonging to a digital entity is stored in more than one file. For instance, the [Mirax2-Fluorescence-2](https://openslide.cs.cmu.edu/download/openslide-testdata/Mirax/Mirax2-Fluorescence-2.zip) image is stored as the following set of files: + +``` +Mirax2-Fluorescence-2.mrxs +Mirax2-Fluorescence-2/Index.dat +Mirax2-Fluorescence-2/Slidedat.ini +Mirax2-Fluorescence-2/Data0000.dat +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`. + +```json +{ + "@id": "./", + "@type": "Dataset", + "hasPart": [ + {"@id": "Mirax2-Fluorescence-2.mrxs"}, + {"@id": "Mirax2-Fluorescence-2/"}, + {"@id": "Mirax2-Fluorescence-2.png"} + ], + "mentions": [ + {"@id": "https://openslide.cs.cmu.edu/download/openslide-testdata/Mirax/Mirax2-Fluorescence-2.zip"}, + {"@id": "#conversion_1"} + ] +}, +{ + "@id": "https://openslide.org/", + "@type": "SoftwareApplication", + "url": "https://openslide.org/", + "name": "OpenSlide", + "version": "3.4.1" +}, +{ + "@id": "#conversion_1", + "@type": "CreateAction", + "name": "Convert image to PNG", + "endTime": "2018-09-19T17:01:07+10:00", + "instrument": {"@id": "https://openslide.org/"}, + "object": {"@id": "https://openslide.cs.cmu.edu/download/openslide-testdata/Mirax/Mirax2-Fluorescence-2.zip"}, + "result": {"@id": "Mirax2-Fluorescence-2.png"} +}, +{ + "@id": "https://openslide.cs.cmu.edu/download/openslide-testdata/Mirax/Mirax2-Fluorescence-2.zip", + "@type": "Collection", + "mainEntity": {"@id": "Mirax2-Fluorescence-2.mrxs"}, + "hasPart": [ + {"@id": "Mirax2-Fluorescence-2.mrxs"}, + {"@id": "Mirax2-Fluorescence-2/"} + ] +}, +{ + "@id": "Mirax2-Fluorescence-2.mrxs", + "@type": "File" +}, +{ + "@id": "Mirax2-Fluorescence-2/", + "@type": "Dataset" +}, +{ + "@id": "Mirax2-Fluorescence-2.png", + "@type": "File" +} +``` + +If the collection does not have a web presence, its `@id` can be an arbitrary internal one, possibly randomly generated (as for any other contextual entity): + +```json +{ + "@id": "#af0253d688f3409a2c6d24bf6b35df7c4e271292", + "@type": "Collection", + "mainEntity": {"@id": "Mirax2-Fluorescence-2.mrxs"}, + "hasPart": [ + {"@id": "Mirax2-Fluorescence-2.mrxs"}, + {"@id": "Mirax2-Fluorescence-2/"} + ] +} +``` + +The use case shown here is an example of a situation where it's important to refer to the original names in case any renamings took place, as described in [Requirements](#requirements): + +```json +{ + "@id": "#af0253d688f3409a2c6d24bf6b35df7c4e271292", + "@type": "Collection", + "mainEntity": {"@id": "f62aa607a75508ac5fc6a22e9c0e39ef58a2c852"}, + "hasPart": [ + {"@id": "f62aa607a75508ac5fc6a22e9c0e39ef58a2c852"}, + {"@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/"} + ] +}, +{ + "@id": "f62aa607a75508ac5fc6a22e9c0e39ef58a2c852", + "@type": "File", + "alternateName": "Mirax2-Fluorescence-2.mrxs" +}, +{ + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/", + "@type": "Dataset", + "alternateName": "Mirax2-Fluorescence-2/", + "hasPart": [ + {"@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/46c443af080a36000c9298b49b675eb240eeb41c"}, + ... + ] +}, +{ + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/46c443af080a36000c9298b49b675eb240eeb41c", + "@type": "File", + "alternateName": "Mirax2-Fluorescence-2/Index.dat" +}, +... +``` + + +## Representing environment variable settings + +The behavior of some applications may be modified by setting appropriate environment variables. These are different from ordinary application inputs in that they are part of the environment in which the process runs, rather than parameters supplied through a command line or a graphical interface. To represent the fact that an environment variable was set to a certain value during the execution of an action, use the `environment` property from the [workflow-run](https://w3id.org/ro/terms/workflow-run#) ro-terms namespace, making it point to a `PropertyValue` that describes the setting: + +```json +{ + "@context": [ + "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/terms/workflow-run/context" + ], + "@graph": [ + ... + { + "@id": "#SepiaConversion_1", + "@type": "CreateAction", + "instrument": {"@id": "https://www.imagemagick.org/"}, + "object": {"@id": "pics/2017-06-11%2012.56.14.jpg"}, + "result": {"@id": "pics/sepia_fence.jpg"}, + "environment": [ + {"@id": "#height-limit-pv"}, + {"@id": "#width-limit-pv"} + ] + }, + { + "@id": "#width-limit-pv", + "@type": "PropertyValue", + "name": "MAGICK_WIDTH_LIMIT", + "value": "4096" + }, + { + "@id": "#height-limit-pv", + "@type": "PropertyValue", + "name": "MAGICK_HEIGHT_LIMIT", + "value": "3072" + } + ] +} +``` + +Note that we added the `workflow-run` context to the `@context` entry in order to bring in the definition of `environment`. + +Environment variable settings SHOULD be listed if they are different from the default ones (usually unset) and affected the results of the action. + + +## Representing container images + +An application may use one or more container images (e.g. [Docker](https://www.docker.com) container images) to perform its duty. An action MAY indicate that a container image was used during the execution via the `containerImage` property, defined in the [workflow-run](https://github.com/ResearchObject/ro-terms/tree/master/workflow-run) ro-terms namespace. + +```json +{ + "@id": "#cb04c897-eb92-4c53-8a38-bcc1a16fd650", + "@type": "CreateAction", + "instrument": {"@id": "bam2fastq.cwl"}, + ... + "containerImage": {"@id": "#samtools-image"} +}, +{ + "@id": "#samtools-image", + "@type": "ContainerImage", + "additionalType": {"@id": "https://w3id.org/ro/terms/workflow-run#DockerImage"}, + "registry": "docker.io", + "name": "biocontainers/samtools", + "tag": "v1.9-4-deb_cv1", + "sha256": "da61624fda230e94867c9429ca1112e1e77c24e500b52dfc84eaf2f5820b4a2a" +} +``` + +The `ContainerImage` type (note the leading lowercase "C") and most of the properties shown above are also defined in the workflow-run namespace. The `additionalType` describes the specific image type (e.g., `DockerImage`, `SIFImage`); the registry is the service that hosts the image (e.g., "docker.io", "quay.io"); the `name` is the identifier of the image within the registry; `tag` describes the image tag and `sha256` its sha256 checksum. A `ContainerImage` entity SHOULD list at least the `additionalType`, `registry` and `name` properties. + +Alternatively, the `containerImage` could point to a `URL`. For instance: + +```json +{ + "@id": "#cb04c897-eb92-4c53-8a38-bcc1a16fd650", + "@type": "CreateAction", + "instrument": {"@id": "bam2fastq.cwl"}, + ... + "containerImage": "https://example.com/samtools.sif" +} +``` + + +## Specifying software dependencies + +Software dependencies MAY be specified using `softwareRequirements` to a `SoftwareApplication`: + +```json +{ + "@id": "script.py", + "@type": "SoftwareApplication", + "name": "Analysis Script", + "version": "0.1", + "softwareRequirements": {"@id": "https://pypi.org/project/numpy/1.26.2/"} +}, +{ + "@id": "https://pypi.org/project/numpy/1.26.2/", + "@type": "SoftwareApplication", + "name": "NumPy", + "version": "1.26.2" +} +``` diff --git a/docs/profiles/0.5/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.5/process_run_crate/ro-crate-metadata.json new file mode 100644 index 0000000..7f13945 --- /dev/null +++ b/docs/profiles/0.5/process_run_crate/ro-crate-metadata.json @@ -0,0 +1,930 @@ +{ "@context": + "https://w3id.org/ro/crate/1.2-DRAFT/context", + "@graph": [ + { + "@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"}, + "about": {"@id": "https://w3id.org/ro/wfrun/process/0.5"} + }, + { + "@id": "ro-crate-preview.html", + "@type": "CreativeWork", + "license": { "@id": "http://spdx.org/licenses/CC0-1.0" }, + "isBasedOn": {"@id": "ro-crate-metadata.json" }, + "name": "RO-Crate preview of the Process Run Crate profile", + "encodingFormat": "text/html", + "about": "https://w3id.org/ro/wfrun/process/0.5" + }, + { + "@id": "https://w3id.org/ro/wfrun/process/0.5", + "@type": ["Dataset","Profile"], + "isProfileOf": [ + {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"} + ], + "identifier": "https://w3id.org/ro/wfrun/process/0.5", + "name": "Process Run Crate profile", + "version": "0.5", + "license": { + "@id": "https://www.apache.org/licenses/LICENSE-2.0" + }, + 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"https://orcid.org/0000-0002-0003-2024", + "@type": "Person", + "name": "Rudolf Wittner" +}, +{ + "@id": "https://orcid.org/0000-0002-9464-6640", + "@type": "Person", + "name": "Wolfgang Maier" +}, +{ + "@id": "https://orcid.org/0000-0001-5845-8880", + "@type": "Person", + "name": "Sebastiaan Huber" +}, +{ + "@id": "https://orcid.org/0000-0003-4894-4660", + "@type": "Person", + "name": "Kevin Jablonka" +}, +{ + "@id": "https://orcid.org/0000-0002-4405-6802", + "@type": "Person", + "name": "Haris Zafeiropoulos" +}, +{ + "@id": "https://orcid.org/0000-0001-9290-2017", + "@type": "Person", + "name": "Iacopo Colonnelli" +}, +{ + "@id": "https://orcid.org/0000-0003-0617-9219", + "@type": "Person", + "name": "Jake Emerson" +}, +{ + "@id": "https://orcid.org/0000-0001-9228-2882", + "@type": "Person", + "name": "Abigail Miller" +}, +{ + "@id": "https://orcid.org/0000-0003-3898-9451", + "@type": "Person", + "name": "Stelios Ninidakis" +}, +{ + "@id": "https://orcid.org/0000-0003-3777-5945", + "@type": "Person", + "name": "Tazro Ohta" +}, +{ + "@id": "https://orcid.org/0000-0003-2765-0049", + "@type": "Person", + "name": "Hirotaka Suetake" +}, +{ + "@id": "https://orcid.org/0000-0001-9818-9320", + "@type": "Person", + "name": "Johannes Köster" +}, +{ + "@id": "https://orcid.org/0000-0002-8122-9522", + "@type": "Person", + "name": "Luiz Gadelha" +}, +{ + "@id": "https://orcid.org/0000-0002-8330-4071", + "@type": "Person", + "name": "Mahnoor Zulfiqar" +}, +{ + "@id": "https://orcid.org/0000-0003-4073-7456", + "@type": "Person", + "name": "Romain David" +}, +{ + "@id": "https://orcid.org/0000-0003-1361-7301", + "@type": "Person", + "name": "Maciek Bąk" +}, +{ + "@id": "https://orcid.org/0000-0002-5358-616X", + "@type": "Person", + "name": "Petr Holub" +}, +{ + "@id": "https://orcid.org/0000-0002-5477-287X", + "@type": "Person", + "name": "Milan Markovic" +}, +{ + "@id": "https://orcid.org/0000-0001-8250-4074", + "@type": "Person", + "name": "Bruno P. Kinoshita" +}, +{ + "@id": "https://orcid.org/0000-0003-0902-0086", + "@type": "Person", + "name": "Renske de Wit" +}, +{ + "@id": "https://orcid.org/0000-0001-8172-8981", + "@type": "Person", + "name": "Jasper Koehorst" +}, +{ + "@id": "https://orcid.org/0000-0001-6740-9212", + "@type": "Person", + "name": "Samuel Lampa" +}, +{ + "@id": "https://orcid.org/0000-0001-5411-356X", + "@type": "Person", + "name": "Samuel Grayson" +}, +{ + "@id": "https://orcid.org/0000-0003-0035-0951", + "@type": "Person", + "name": "Jörg F. Unger" +}, +{ + "@id": "https://orcid.org/0000-0003-0711-5196", + "@type": "Person", + "name": "Felix Bartusch" +}, +{ + "@id": "https://orcid.org/0000-0002-4663-5613", + "@type": "Person", + "name": "Luca Pireddu" +}, +{ + "@id": "https://orcid.org/0000-0002-1119-1792", + "@type": "Person", + "name": "Matej Gallo" +}, +{ + "@id": "https://orcid.org/0000-0002-0309-604X", + "@type": "Person", + "name": "Salvador Capella-Gutierrez" +}, +{ + "@id": "https://www.apache.org/licenses/LICENSE-2.0", + "@type": "CreativeWork", + "name": "Apache License 2.0", + "version": "2.0", + "identifier": { "@id": "http://spdx.org/licenses/Apache-2.0"} +}, +{ + "@id": "https://creativecommons.org/publicdomain/zero/1.0/", + "@type": "CreativeWork", + "identifier": { "@id": "http://spdx.org/licenses/CC0-1.0"}, + "name": "Creative Commons Zero v1.0 Universal", + "version": "1.0" +}, +{ + "@id": "http://spdx.org/licenses/Apache-2.0", + "@type": "PropertyValue", + "propertyID": "http://spdx.org/rdf/terms#licenseId", + "name": "spdx", + "value": "Apache-2.0" +}, +{ + "@id": "http://spdx.org/licenses/CC0-1.0", + "@type": "PropertyValue", + "propertyID": "http://spdx.org/rdf/terms#licenseId", + "name": "spdx", + "value": "CC0-1.0" +} + + +] +} diff --git a/docs/profiles/0.5/process_run_crate/ro-crate-metadata.jsonld b/docs/profiles/0.5/process_run_crate/ro-crate-metadata.jsonld new file mode 120000 index 0000000..8024224 --- /dev/null +++ b/docs/profiles/0.5/process_run_crate/ro-crate-metadata.jsonld @@ -0,0 +1 @@ +ro-crate-metadata.json \ No newline at end of file diff --git a/docs/profiles/0.5/process_run_crate/ro-crate-preview.html b/docs/profiles/0.5/process_run_crate/ro-crate-preview.html new file mode 100644 index 0000000..e270d95 --- /dev/null +++ b/docs/profiles/0.5/process_run_crate/ro-crate-preview.html @@ -0,0 +1,2805 @@ + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    +

    +

    Process Run Crate profile

    + + +⬇️🏷️ Download all the metadata for Process Run Crate profile in JSON-LD format + + +
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    Go to: Process Run Crate profile

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    Go to: Workflow Run Crate task force

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    Go to: Apache License 2.0

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    @idhttps://www.apache.org/licenses/LICENSE-2.0
    name [?]Apache License 2.0
    @typeCreativeWork
    version [?]2.0
    identifier [?]spdx: Apache-2.0
    Items that reference this one
    license [?]Process Run Crate profile
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    ⬇️ Download: Process Run Crate (HTML)

    + + + + +
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    @idindex.html
    name [?]Process Run Crate (HTML)
    @typeFile
    encodingFormat [?]
    Items that reference this one
    hasPart [?]Process Run Crate profile
    hasArtifact [?]#hasSpecification
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    Example Process Run Crate

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    @idexample1/
    name [?]Example Process Run Crate
    @typeDataset
    conformsTo [?]
    subjectOf [?]
    Items that reference this one
    hasPart [?]Process Run Crate profile
    hasArtifact [?]#hasExample
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    Go to: SSSOM mapping from PROV to Workflow Run Crate

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    @idhttps://www.researchobject.org/workflow-run-crate-paper/mapping/
    name [?]SSSOM mapping from PROV to Workflow Run Crate
    @typeDataset
    isPartOf [?]Recording provenance of workflow runs with RO-Crate (RO-Crate and mapping)
    Items that reference this one
    hasPart [?]Process Run Crate profile
    hasArtifact [?]#hasMappingToProv
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    Go to: Namespace for Workflow Run RO-Crate model

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    @idhttps://w3id.org/ro/terms/workflow-run#
    name [?]Namespace for Workflow Run RO-Crate model
    @typeDefinedTermSet
    hasDefinedTerm [?]
    Items that reference this one
    hasPart [?]Process Run Crate profile
    isBasedOn [?]JSON-LD context for workflow-run terms
    hasArtifact [?]#hasVocabulary
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    Go to: JSON-LD context for workflow-run terms

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    @idhttps://w3id.org/ro/terms/workflow-run
    name [?]JSON-LD context for workflow-run terms
    @typeFile
    encodingFormat [?]application/ld+json
    contentUrl [?]https://www.researchobject.org/ro-terms/workflow-run/context.json
    conformsTo [?]http://www.w3.org/ns/json-ld#Context
    isBasedOn [?]
    license [?]Creative Commons Zero v1.0 Universal
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: Workflow Run RO-Crate Introduction

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    @idhttps://gxy.io/GTN:T00343
    name [?]Workflow Run RO-Crate Introduction
    @typeLearningResource
    author [?]Simone Leo
    Items that reference this one
    hasPart [?]Process Run Crate profile
    hasArtifact [?]#hasGuidance
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    Go to: runcrate

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    @idhttps://pypi.org/project/runcrate/
    name [?]runcrate
    @typeSoftwareApplication
    version [?]0.5.0
    url [?]https://pypi.org/project/runcrate/
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: SoftwareApplication

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    @idhttp://schema.org/SoftwareApplication
    name [?]SoftwareApplication
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
    domainIncludes [?]environment
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    Go to: SoftwareSourceCode

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    @idhttp://schema.org/SoftwareSourceCode
    name [?]SoftwareSourceCode
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
    domainIncludes [?]environment
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    Go to: ComputationalWorkflow

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    @idhttps://bioschemas.org/ComputationalWorkflow
    name [?]ComputationalWorkflow
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
    domainIncludes [?]connection
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    Go to: CreateAction

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    @idhttp://schema.org/CreateAction
    name [?]CreateAction
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
    domainIncludes [?]
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    Go to: name

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    @idhttp://schema.org/name
    name [?]name
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: description

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    @idhttp://schema.org/description
    name [?]description
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: endTime

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    @idhttp://schema.org/endTime
    name [?]endTime
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: startTime

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    @idhttp://schema.org/startTime
    name [?]startTime
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: instrument

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    @idhttp://schema.org/instrument
    name [?]instrument
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: agent

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    @idhttp://schema.org/agent
    name [?]agent
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: Person

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    @idhttp://schema.org/Person
    name [?]Person
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: Organization

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    @idhttp://schema.org/Organization
    name [?]Organization
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: object

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    @idhttp://schema.org/object
    name [?]object
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: result

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    @idhttp://schema.org/result
    name [?]result
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: actionStatus

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    @idhttp://schema.org/actionStatus
    name [?]actionStatus
    @typeDefinedTerm
    Items that reference this one
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    Go to: error

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    @idhttp://schema.org/error
    name [?]error
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: CompletedActionStatus

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    @idhttp://schema.org/CompletedActionStatus
    name [?]CompletedActionStatus
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: FailedActionStatus

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    @idhttp://schema.org/FailedActionStatus
    name [?]FailedActionStatus
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: MediaObject

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    @idhttp://schema.org/MediaObject
    name [?]MediaObject
    @typeDefinedTerm
    termCode [?]File
    Items that reference this one
    hasPart [?]Process Run Crate profile
    domainIncludes [?]
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    Go to: Dataset

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    @idhttp://schema.org/Dataset
    name [?]Dataset
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: Collection

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    @idhttp://schema.org/Collection
    name [?]Collection
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: CreativeWork

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    @idhttp://schema.org/CreativeWork
    name [?]CreativeWork
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
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    Go to: PropertyValue

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    @idhttp://schema.org/PropertyValue
    name [?]PropertyValue
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Process Run Crate profile
    rangeIncludes [?]
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    Go to: alternateName

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    @idhttp://schema.org/alternateName
    name [?]alternateName
    @typeDefinedTerm
    Items that reference this one
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    Go to: mainEntity

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    @idhttp://schema.org/mainEntity
    name [?]mainEntity
    @typeDefinedTerm
    Items that reference this one
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    #hasSpecification

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    @id#hasSpecification
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/specification
    hasArtifact [?]Process Run Crate (HTML)
    Items that reference this one
    hasResource [?]Process Run Crate profile
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    #hasConstraints

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    @id#hasConstraints
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/constraints
    hasArtifact [?]Process Run Crate requirements
    Items that reference this one
    hasResource [?]Process Run Crate profile
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    #hasVocabulary

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    @id#hasVocabulary
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/vocabulary
    hasArtifact [?]Namespace for Workflow Run RO-Crate model
    Items that reference this one
    hasResource [?]Process Run Crate profile
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    #hasGuidance

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    @id#hasGuidance
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/guidance
    hasArtifact [?]Workflow Run RO-Crate Introduction
    Items that reference this one
    hasResource [?]Process Run Crate profile
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    #hasExample

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    @id#hasExample
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/example
    hasArtifact [?]Example Process Run Crate
    Items that reference this one
    hasResource [?]Process Run Crate profile
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    #hasMappingToProv

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    @id#hasMappingToProv
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/mapping
    hasArtifact [?]SSSOM mapping from PROV to Workflow Run Crate
    Items that reference this one
    hasResource [?]Process Run Crate profile
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    Go to: Recording provenance of workflow runs with RO-Crate

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    @idhttps://doi.org/10.48550/arXiv.2312.07852
    name [?]Recording provenance of workflow runs with RO-Crate
    @typeScholarlyArticle
    author [?]
    creditText [?]Simone Leo, et al. (2024): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852
    Items that reference this one
    citation [?]Process Run Crate profile
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    +


    +
    + + + + + + + diff --git a/docs/profiles/0.5/provenance_run_crate/example3/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 b/docs/profiles/0.5/provenance_run_crate/example3/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 new file mode 100644 index 0000000..425d1ed --- /dev/null +++ b/docs/profiles/0.5/provenance_run_crate/example3/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 @@ -0,0 +1,16 @@ +Call me Ishmael. Some years ago--never mind how long precisely--having +little or no money in my purse, and nothing particular to interest me on +shore, I thought I would sail about a little and see the watery part of +the world. It is a way I have of driving off the spleen and regulating +the circulation. Whenever I find myself growing grim about the mouth; +whenever it is a damp, drizzly November in my soul; whenever I find +myself involuntarily pausing before coffin warehouses, and bringing up +the rear of every funeral I meet; and especially whenever my hypos get +such an upper hand of me, that it requires a strong moral principle to +prevent me from deliberately stepping into the street, and methodically +knocking people's hats off--then, I account it high time to get to sea +as soon as I can. This is my substitute for pistol and ball. With a +philosophical flourish Cato throws himself upon his sword; I quietly +take to the ship. There is nothing surprising in this. If they but knew +it, almost all men in their degree, some time or other, cherish very +nearly the same feelings towards the ocean with me. diff --git a/docs/profiles/0.5/provenance_run_crate/example3/97fe1b50b4582cebc7d853796ebd62e3e163aa3f b/docs/profiles/0.5/provenance_run_crate/example3/97fe1b50b4582cebc7d853796ebd62e3e163aa3f new file mode 100644 index 0000000..1001666 --- /dev/null +++ b/docs/profiles/0.5/provenance_run_crate/example3/97fe1b50b4582cebc7d853796ebd62e3e163aa3f @@ -0,0 +1,16 @@ +gnivah--ylesicerp gnol woh dnim reven--oga sraey emoS .leamhsI em llaC +no em tseretni ot ralucitrap gnihton dna ,esrup ym ni yenom on ro elttil +fo trap yretaw eht ees dna elttil a tuoba lias dluow I thguoht I ,erohs +gnitaluger dna neelps eht ffo gnivird fo evah I yaw a si tI .dlrow eht +;htuom eht tuoba mirg gniworg flesym dnif I revenehW .noitalucric eht +dnif I revenehw ;luos ym ni rebmevoN ylzzird ,pmad a si ti revenehw +pu gnignirb dna ,sesuoheraw niffoc erofeb gnisuap yliratnulovni flesym +teg sopyh ym revenehw yllaicepse dna ;teem I larenuf yreve fo raer eht +ot elpicnirp larom gnorts a seriuqer ti taht ,em fo dnah reppu na hcus +yllacidohtem dna ,teerts eht otni gnippets yletarebiled morf em tneverp +aes ot teg ot emit hgih ti tnuocca I ,neht--ffo stah s'elpoep gnikconk +a htiW .llab dna lotsip rof etutitsbus ym si sihT .nac I sa noos sa +ylteiuq I ;drows sih nopu flesmih sworht otaC hsiruolf lacihposolihp +wenk tub yeht fI .siht ni gnisirprus gnihton si erehT .pihs eht ot ekat +yrev hsirehc ,rehto ro emit emos ,eerged rieht ni nem lla tsomla ,ti +.em htiw naeco eht sdrawot sgnileef emas eht ylraen diff --git a/docs/profiles/0.5/provenance_run_crate/example3/b9214658cc453331b62c2282b772a5c063dbd284 b/docs/profiles/0.5/provenance_run_crate/example3/b9214658cc453331b62c2282b772a5c063dbd284 new file mode 100644 index 0000000..97b096c --- /dev/null +++ b/docs/profiles/0.5/provenance_run_crate/example3/b9214658cc453331b62c2282b772a5c063dbd284 @@ -0,0 +1,16 @@ +yrev hsirehc ,rehto ro emit emos ,eerged rieht ni nem lla tsomla ,ti +ylteiuq I ;drows sih nopu flesmih sworht otaC hsiruolf lacihposolihp +yllacidohtem dna ,teerts eht otni gnippets yletarebiled morf em tneverp +wenk tub yeht fI .siht ni gnisirprus gnihton si erehT .pihs eht ot ekat +teg sopyh ym revenehw yllaicepse dna ;teem I larenuf yreve fo raer eht +pu gnignirb dna ,sesuoheraw niffoc erofeb gnisuap yliratnulovni flesym +ot elpicnirp larom gnorts a seriuqer ti taht ,em fo dnah reppu na hcus +no em tseretni ot ralucitrap gnihton dna ,esrup ym ni yenom on ro elttil +gnivah--ylesicerp gnol woh dnim reven--oga sraey emoS .leamhsI em llaC +gnitaluger dna neelps eht ffo gnivird fo evah I yaw a si tI .dlrow eht +fo trap yretaw eht ees dna elttil a tuoba lias dluow I thguoht I ,erohs +dnif I revenehw ;luos ym ni rebmevoN ylzzird ,pmad a si ti revenehw +aes ot teg ot emit hgih ti tnuocca I ,neht--ffo stah s'elpoep gnikconk +a htiW .llab dna lotsip rof etutitsbus ym si sihT .nac I sa noos sa +;htuom eht tuoba mirg gniworg flesym dnif I revenehW .noitalucric eht +.em htiw naeco eht sdrawot sgnileef emas eht ylraen diff --git a/docs/profiles/0.5/provenance_run_crate/example3/index.hml b/docs/profiles/0.5/provenance_run_crate/example3/index.hml new file mode 120000 index 0000000..a33a179 --- /dev/null +++ b/docs/profiles/0.5/provenance_run_crate/example3/index.hml @@ -0,0 +1 @@ +ro-crate-preview.html \ No newline at end of file diff --git a/docs/profiles/0.5/provenance_run_crate/example3/packed.cwl b/docs/profiles/0.5/provenance_run_crate/example3/packed.cwl new file mode 100644 index 0000000..251587d --- /dev/null +++ b/docs/profiles/0.5/provenance_run_crate/example3/packed.cwl @@ -0,0 +1,137 @@ +{ + "$graph": [ + { + "class": "Workflow", + "doc": "Reverse the lines in a document, then sort those lines.", + "hints": [ + { + "class": "DockerRequirement", + "dockerPull": "debian:8" + } + ], + "inputs": [ + { + "type": "File", + "doc": "The input file to be processed.", + "format": "https://www.iana.org/assignments/media-types/text/plain", + "default": { + "class": "File", + "location": "file:///home/stain/src/cwltool/tests/wf/hello.txt" + }, + "id": "#main/input" + }, + { + "type": "boolean", + "default": true, + "doc": "If true, reverse (decending) sort", + "id": "#main/reverse_sort" + } + ], + "outputs": [ + { + "type": "File", + "outputSource": "#main/sorted/output", + "doc": "The output with the lines reversed and sorted.", + "id": "#main/output" + } + ], + "steps": [ + { + "in": [ + { + "source": "#main/input", + "id": "#main/rev/input" + } + ], + "out": [ + "#main/rev/output" + ], + "run": "#revtool.cwl", + "id": "#main/rev" + }, + { + "in": [ + { + "source": "#main/rev/output", + "id": "#main/sorted/input" + }, + { + "source": "#main/reverse_sort", + "id": "#main/sorted/reverse" + } + ], + "out": [ + "#main/sorted/output" + ], + "run": "#sorttool.cwl", + "id": "#main/sorted" + } + ], + "id": "#main", + "$namespaces": { + "iana": "https://www.iana.org/assignments/media-types/" + } + }, + { + "class": "CommandLineTool", + "doc": "Reverse each line using the `rev` command", + "inputs": [ + { + "type": "File", + "inputBinding": {}, + "id": "#revtool.cwl/input" + } + ], + "outputs": [ + { + "type": "File", + "outputBinding": { + "glob": "output.txt" + }, + "id": "#revtool.cwl/output" + } + ], + "baseCommand": "rev", + "stdout": "output.txt", + "id": "#revtool.cwl" + }, + { + "class": "CommandLineTool", + "doc": "Sort lines using the `sort` command", + "inputs": [ + { + "id": "#sorttool.cwl/reverse", + "type": "boolean", + "inputBinding": { + "position": 1, + "prefix": "--reverse" + } + }, + { + "id": "#sorttool.cwl/input", + "type": "File", + "inputBinding": { + "position": 2 + } + } + ], + "outputs": [ + { + "id": "#sorttool.cwl/output", + "type": "File", + "outputBinding": { + "glob": "output.txt" + } + } + ], + "baseCommand": "sort", + "stdout": "output.txt", + "id": "#sorttool.cwl" + } + ], + "cwlVersion": "v1.0", + "$schemas": [ + "file:///home/stain/src/cwltool/tests/wf/empty.ttl", + "file:///home/stain/src/cwltool/tests/wf/empty2.ttl" + ] +} \ No newline at end of file diff --git a/docs/profiles/0.5/provenance_run_crate/example3/ro-crate-metadata.json b/docs/profiles/0.5/provenance_run_crate/example3/ro-crate-metadata.json new file mode 100644 index 0000000..9fb0384 --- /dev/null +++ b/docs/profiles/0.5/provenance_run_crate/example3/ro-crate-metadata.json @@ -0,0 +1,290 @@ +{ "@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/0.4"}, + {"@id": "https://w3id.org/ro/wfrun/workflow/0.4"}, + {"@id": "https://w3id.org/ro/wfrun/provenance/0.4"}, + {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"} + ], + "hasPart": [ + {"@id": "packed.cwl"}, + {"@id": "327fc7aedf4f6b69a42a7c8b808dc5a7aff61376"}, + {"@id": "b9214658cc453331b62c2282b772a5c063dbd284"}, + {"@id": "97fe1b50b4582cebc7d853796ebd62e3e163aa3f"} + ], + "mainEntity": {"@id": "packed.cwl"}, + "mentions": [ + {"@id": "#4154dad3-00cc-4e35-bb8f-a2de5cd7dc49"} + ] + }, + { "@id": "https://w3id.org/ro/wfrun/process/0.4", + "@type": "CreativeWork", + "name": "Process Run Crate", + "version": "0.4" + }, + { "@id": "https://w3id.org/ro/wfrun/workflow/0.4", + "@type": "CreativeWork", + "name": "Workflow Run Crate", + "version": "0.4" + }, + { "@id": "https://w3id.org/ro/wfrun/provenance/0.4", + "@type": "CreativeWork", + "name": "Provenance Run Crate", + "version": "0.4" + }, + { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0", + "@type": "CreativeWork", + "name": "Workflow RO-Crate", + "version": "1.0" + }, + { + "@id": "packed.cwl", + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow", "HowTo"], + "hasPart": [ + {"@id": "packed.cwl#revtool.cwl"}, + {"@id": "packed.cwl#sorttool.cwl"} + ], + "input": [ + {"@id": "packed.cwl#main/input"}, + {"@id": "packed.cwl#main/reverse_sort"} + ], + "name": "packed.cwl", + "output": [ + {"@id": "packed.cwl#main/output"} + ], + "programmingLanguage": {"@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl"}, + "step": [ + {"@id": "packed.cwl#main/rev"}, + {"@id": "packed.cwl#main/sorted"} + ] + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl", + "@type": "ComputerLanguage", + "alternateName": "CWL", + "identifier": {"@id": "https://w3id.org/cwl/v1.0/"}, + "name": "Common Workflow Language", + "url": {"@id": "https://www.commonwl.org/"}, + "version": "v1.0" + }, + { + "@id": "packed.cwl#main/input", + "@type": "FormalParameter", + "additionalType": "File", + "defaultValue": "file:///home/stain/src/cwltool/tests/wf/hello.txt", + "encodingFormat": "https://www.iana.org/assignments/media-types/text/plain", + "name": "main/input" + }, + { + "@id": "packed.cwl#main/reverse_sort", + "@type": "FormalParameter", + "additionalType": "Boolean", + "defaultValue": "True", + "name": "main/reverse_sort" + }, + { + "@id": "packed.cwl#main/output", + "@type": "FormalParameter", + "additionalType": "File", + "name": "main/output" + }, + { + "@id": "packed.cwl#main/rev", + "@type": "HowToStep", + "position": "0", + "workExample": {"@id": "packed.cwl#revtool.cwl"} + }, + { + "@id": "packed.cwl#revtool.cwl", + "@type": "SoftwareApplication", + "description": "Reverse each line using the `rev` command", + "input": [ + {"@id": "packed.cwl#revtool.cwl/input"} + ], + "name": "revtool.cwl", + "output": [ + {"@id": "packed.cwl#revtool.cwl/output"} + ] + }, + { + "@id": "packed.cwl#revtool.cwl/input", + "@type": "FormalParameter", + "additionalType": "File", + "name": "revtool.cwl/input" + }, + { + "@id": "packed.cwl#revtool.cwl/output", + "@type": "FormalParameter", + "additionalType": "File", + "name": "revtool.cwl/output" + }, + { + "@id": "packed.cwl#main/sorted", + "@type": "HowToStep", + "position": "1", + "workExample": {"@id": "packed.cwl#sorttool.cwl"} + }, + { + "@id": "packed.cwl#sorttool.cwl", + "@type": "SoftwareApplication", + "description": "Sort lines using the `sort` command", + "input": [ + {"@id": "packed.cwl#sorttool.cwl/reverse"}, + {"@id": "packed.cwl#sorttool.cwl/input"} + ], + "name": "sorttool.cwl", + "output": [ + {"@id": "packed.cwl#sorttool.cwl/output"} + ] + }, + { + "@id": "packed.cwl#sorttool.cwl/reverse", + "@type": "FormalParameter", + "additionalType": "Boolean", + "name": "sorttool.cwl/reverse" + }, + { + "@id": "packed.cwl#sorttool.cwl/input", + "@type": "FormalParameter", + "additionalType": "File", + "name": "sorttool.cwl/input" + }, + { + "@id": "packed.cwl#sorttool.cwl/output", + "@type": "FormalParameter", + "additionalType": "File", + "name": "sorttool.cwl/output" + }, + { + "@id": "#a73fd902-8d14-48c9-835b-a5ba2f9149fd", + "@type": "SoftwareApplication", + "name": "cwltool 1.0.20181012180214" + }, + { + "@id": "#d6ab3175-88f5-4b6a-b028-1b13e6d1a158", + "@type": "OrganizeAction", + "agent": {"@id": "https://orcid.org/0000-0001-9842-9718"}, + "instrument": {"@id": "#a73fd902-8d14-48c9-835b-a5ba2f9149fd"}, + "name": "Run of cwltool 1.0.20181012180214", + "object": [ + {"@id": "#4f7f887f-1b9b-4417-9beb-58618a125cc5"}, + {"@id": "#793b3df4-cbb7-4d17-94d4-0edb18566ed3"} + ], + "result": {"@id": "#4154dad3-00cc-4e35-bb8f-a2de5cd7dc49"}, + "startTime": "2018-10-25T15:46:35.210973" + }, + { + "@id": "https://orcid.org/0000-0001-9842-9718", + "@type": "Person", + "name": "Stian Soiland-Reyes" + }, + { + "@id": "#4154dad3-00cc-4e35-bb8f-a2de5cd7dc49", + "@type": "CreateAction", + "endTime": "2018-10-25T15:46:43.020168", + "instrument": {"@id": "packed.cwl"}, + "name": "Run of workflow/packed.cwl#main", + "object": [ + {"@id": "327fc7aedf4f6b69a42a7c8b808dc5a7aff61376"}, + {"@id": "#pv-main/reverse_sort"} + ], + "result": [ + {"@id": "b9214658cc453331b62c2282b772a5c063dbd284"} + ], + "startTime": "2018-10-25T15:46:35.211153" + }, + { + "@id": "327fc7aedf4f6b69a42a7c8b808dc5a7aff61376", + "@type": "File", + "exampleOfWork": [ + {"@id": "packed.cwl#main/input"}, + {"@id": "packed.cwl#revtool.cwl/input"} + ] + }, + { + "@id": "#pv-main/reverse_sort", + "@type": "PropertyValue", + "exampleOfWork": {"@id": "packed.cwl#main/reverse_sort"}, + "name": "main/reverse_sort", + "value": "True" + }, + { + "@id": "b9214658cc453331b62c2282b772a5c063dbd284", + "@type": "File", + "exampleOfWork": [ + {"@id": "packed.cwl#main/output"}, + {"@id": "packed.cwl#sorttool.cwl/output"} + ] + }, + { + "@id": "#6933cce1-f8f0-4032-8848-e0fc9166e92f", + "@type": "CreateAction", + "endTime": "2018-10-25T15:46:36.967359", + "instrument": {"@id": "packed.cwl#revtool.cwl"}, + "name": "Run of workflow/packed.cwl#main/rev", + "object": [ + {"@id": "327fc7aedf4f6b69a42a7c8b808dc5a7aff61376"} + ], + "result": [ + {"@id": "97fe1b50b4582cebc7d853796ebd62e3e163aa3f"} + ], + "startTime": "2018-10-25T15:46:35.314101" + }, + { + "@id": "#4f7f887f-1b9b-4417-9beb-58618a125cc5", + "@type": "ControlAction", + "instrument": {"@id": "packed.cwl#main/rev"}, + "name": "orchestrate revtool.cwl", + "object": {"@id": "#6933cce1-f8f0-4032-8848-e0fc9166e92f"} + }, + { + "@id": "97fe1b50b4582cebc7d853796ebd62e3e163aa3f", + "@type": "File", + "exampleOfWork": [ + {"@id": "packed.cwl#revtool.cwl/output"}, + {"@id": "packed.cwl#sorttool.cwl/input"} + ] + }, + { + "@id": "#9eac64b2-c2c8-401f-9af8-7cfb0e998107", + "@type": "CreateAction", + "endTime": "2018-10-25T15:46:38.069110", + "instrument": {"@id": "packed.cwl#sorttool.cwl"}, + "name": "Run of workflow/packed.cwl#main/sorted", + "object": [ + {"@id": "97fe1b50b4582cebc7d853796ebd62e3e163aa3f"}, + {"@id": "#pv-main/sorted/reverse"} + ], + "result": [ + {"@id": "b9214658cc453331b62c2282b772a5c063dbd284"} + ], + "startTime": "2018-10-25T15:46:36.975235" + }, + { + "@id": "#793b3df4-cbb7-4d17-94d4-0edb18566ed3", + "@type": "ControlAction", + "instrument": {"@id": "packed.cwl#main/sorted"}, + "name": "orchestrate sorttool.cwl", + "object": {"@id": "#9eac64b2-c2c8-401f-9af8-7cfb0e998107"} + }, + { + "@id": "#pv-main/sorted/reverse", + "@type": "PropertyValue", + "exampleOfWork": {"@id": "packed.cwl#sorttool.cwl/reverse"}, + "name": "main/sorted/reverse", + "value": "True" + } +] +} \ No newline at end of file diff --git a/docs/profiles/0.5/provenance_run_crate/example3/ro-crate-preview.html b/docs/profiles/0.5/provenance_run_crate/example3/ro-crate-preview.html new file mode 100644 index 0000000..acd4784 --- /dev/null +++ b/docs/profiles/0.5/provenance_run_crate/example3/ro-crate-preview.html @@ -0,0 +1,866 @@ + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    +

    +

    + + +⬇️🏷️ Download all the metadata for in JSON-LD format + + +
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    mainEntity [?]packed.cwl
    mentions [?]Run of workflow/packed.cwl#main
    Items that reference this one
    about [?]ro-crate-metadata.json
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    Items that reference this one
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    name [?]Workflow Run Crate
    @typeCreativeWork
    version [?]0.4
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    name [?]Provenance Run Crate
    @typeCreativeWork
    version [?]0.4
    Items that reference this one
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    name [?]packed.cwl
    @type
      +
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    • ComputationalWorkflow
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    • HowTo
      • +
    hasPart [?]
    input [?]
    output [?]main/output
    programmingLanguage [?]Common Workflow Language
    step [?]
    Items that reference this one
    hasPart [?]./
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    hasPart [?]./
    result [?]Run of workflow/packed.cwl#main/rev
    object [?]Run of workflow/packed.cwl#main/sorted
    +
    + +
    +


    +
    +

    Run of workflow/packed.cwl#main

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    @id#4154dad3-00cc-4e35-bb8f-a2de5cd7dc49
    name [?]Run of workflow/packed.cwl#main
    @typeCreateAction
    endTime [?]2018-10-25T15:46:43.020168
    instrument [?]packed.cwl
    object [?]
    result [?]b9214658cc453331b62c2282b772a5c063dbd284
    startTime [?]2018-10-25T15:46:35.211153
    Items that reference this one
    mentions [?]./
    result [?]Run of cwltool 1.0.20181012180214
    +
    + +
    +


    +
    + + + + + + + diff --git a/docs/profiles/0.5/provenance_run_crate/index.md b/docs/profiles/0.5/provenance_run_crate/index.md new file mode 100644 index 0000000..3f5e69e --- /dev/null +++ b/docs/profiles/0.5/provenance_run_crate/index.md @@ -0,0 +1,690 @@ +--- +title: Provenance Run Crate +--- + + +# Provenance Run Crate + +* Version: 0.5 +* Permalink: +* Authors: [Workflow Run RO-Crate working group](https://www.researchobject.org/workflow-run-crate/#community) +* License: [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0) (SPDX: [`Apache-2.0`](http://spdx.org/licenses/Apache-2.0)) +* Example conforming crate: [ro-crate-metadata.json](example3/ro-crate-metadata.json) [ro-crate-preview.html](example3/ro-crate-preview.html) +* Profile Crate: [ro-crate-metadata.json](ro-crate-metadata.json) [ro-crate-preview.html](ro-crate-preview.html) +* Extends: + - [Workflow Run Crate](https://w3id.org/ro/wfrun/workflow/0.5) +* 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. + + +## Overview + +This profile extends [Workflow Run Crate](../workflow_run_crate) with specifications to describe internal details of the workflow run, such as step executions and intermediate outputs. + +A Provenance Run Crate MUST record the details of *tool* executions orchestrated by the workflow through additional [CreateAction](http://schema.org/CreateAction) entities, each of which MUST refer to an entity representing the tool itself via [instrument](http://schema.org/instrument) as specified in [Process Run Crate](../process_run_crate). Entities representing the tools MAY reference formal parameter definitions via `input` and `output` (and `environment`, in the case of [environment variables](../workflow_run_crate#environment-variables-as-formal-parameters)) as specified in [Workflow Run Crate](../workflow_run_crate). The workflow MUST refer to the orchestrated tools via [hasPart](http://schema.org/hasPart) (the usage of `hasPart` for this purpose follows the Bioschemas [ComputationalWorkflow profile](http://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE)). + +The crate SHOULD also record *step* executions via [ControlAction](http://schema.org/ControlAction) instances, each of which MUST reference: a [HowToStep](http://schema.org/HowToStep) instance representing the step via `instrument`; the `CreateAction` representing the corresponding tool run via `object`. The workflow MUST reference any `HowToStep` instances that represent its steps via [step](http://schema.org/step). Each `HowToStep` instance MUST reference the entity that represents its corresponding tool via [workExample](http://schema.org/workExample), and MAY indicate its position in the execution order via [position](http://schema.org/position). In addition to `File`, `SoftwareSourceCode` and `ComputationalWorkflow`, a workflow that points to step metadata via `step` MUST have a type of [HowTo](http://schema.org/HowTo). + +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 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). + +Entity-relationship diagram + + +## Example Metadata File (`ro-crate-metadata.json`) + +* [ro-crate-metadata.json](example3/ro-crate-metadata.json) +* [ro-crate-preview.html](example3/ro-crate-preview.html) + + + + +```json +{ "@context": [ + "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/terms/workflow-run/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"}, + {"@id": "b9214658cc453331b62c2282b772a5c063dbd284"}, + {"@id": "97fe1b50b4582cebc7d853796ebd62e3e163aa3f"} + ], + "mainEntity": {"@id": "packed.cwl"}, + "mentions": [ + {"@id": "#4154dad3-00cc-4e35-bb8f-a2de5cd7dc49"} + ] + }, + { "@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/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", + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow", "HowTo"], + "hasPart": [ + {"@id": "packed.cwl#revtool.cwl"}, + {"@id": "packed.cwl#sorttool.cwl"} + ], + "input": [ + {"@id": "packed.cwl#main/input"}, + {"@id": "packed.cwl#main/reverse_sort"} + ], + "name": "packed.cwl", + "output": [ + {"@id": "packed.cwl#main/output"} + ], + "programmingLanguage": {"@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl"}, + "step": [ + {"@id": "packed.cwl#main/rev"}, + {"@id": "packed.cwl#main/sorted"} + ] + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl", + "@type": "ComputerLanguage", + "alternateName": "CWL", + "identifier": {"@id": "https://w3id.org/cwl/v1.0/"}, + "name": "Common Workflow Language", + "url": {"@id": "https://www.commonwl.org/"}, + "version": "v1.0" + }, + { + "@id": "packed.cwl#main/input", + "@type": "FormalParameter", + "additionalType": "File", + "defaultValue": "file:///home/stain/src/cwltool/tests/wf/hello.txt", + "encodingFormat": "https://www.iana.org/assignments/media-types/text/plain", + "name": "main/input" + }, + { + "@id": "packed.cwl#main/reverse_sort", + "@type": "FormalParameter", + "additionalType": "Boolean", + "defaultValue": "True", + "name": "main/reverse_sort" + }, + { + "@id": "packed.cwl#main/output", + "@type": "FormalParameter", + "additionalType": "File", + "name": "main/output" + }, + { + "@id": "packed.cwl#main/rev", + "@type": "HowToStep", + "position": "0", + "workExample": {"@id": "packed.cwl#revtool.cwl"} + }, + { + "@id": "packed.cwl#revtool.cwl", + "@type": "SoftwareApplication", + "description": "Reverse each line using the `rev` command", + "input": [ + {"@id": "packed.cwl#revtool.cwl/input"} + ], + "name": "revtool.cwl", + "output": [ + {"@id": "packed.cwl#revtool.cwl/output"} + ] + }, + { + "@id": "packed.cwl#revtool.cwl/input", + "@type": "FormalParameter", + "additionalType": "File", + "name": "revtool.cwl/input" + }, + { + "@id": "packed.cwl#revtool.cwl/output", + "@type": "FormalParameter", + "additionalType": "File", + "name": "revtool.cwl/output" + }, + { + "@id": "packed.cwl#main/sorted", + "@type": "HowToStep", + "position": "1", + "workExample": {"@id": "packed.cwl#sorttool.cwl"} + }, + { + "@id": "packed.cwl#sorttool.cwl", + "@type": "SoftwareApplication", + "description": "Sort lines using the `sort` command", + "input": [ + {"@id": "packed.cwl#sorttool.cwl/reverse"}, + {"@id": "packed.cwl#sorttool.cwl/input"} + ], + "name": "sorttool.cwl", + "output": [ + {"@id": "packed.cwl#sorttool.cwl/output"} + ] + }, + { + "@id": "packed.cwl#sorttool.cwl/reverse", + "@type": "FormalParameter", + "additionalType": "Boolean", + "name": "sorttool.cwl/reverse" + }, + { + "@id": "packed.cwl#sorttool.cwl/input", + "@type": "FormalParameter", + "additionalType": "File", + "name": "sorttool.cwl/input" + }, + { + "@id": "packed.cwl#sorttool.cwl/output", + "@type": "FormalParameter", + "additionalType": "File", + "name": "sorttool.cwl/output" + }, + { + "@id": "#a73fd902-8d14-48c9-835b-a5ba2f9149fd", + "@type": "SoftwareApplication", + "name": "cwltool 1.0.20181012180214" + }, + { + "@id": "#d6ab3175-88f5-4b6a-b028-1b13e6d1a158", + "@type": "OrganizeAction", + "agent": {"@id": "https://orcid.org/0000-0001-9842-9718"}, + "instrument": {"@id": "#a73fd902-8d14-48c9-835b-a5ba2f9149fd"}, + "name": "Run of cwltool 1.0.20181012180214", + "object": [ + {"@id": "#4f7f887f-1b9b-4417-9beb-58618a125cc5"}, + {"@id": "#793b3df4-cbb7-4d17-94d4-0edb18566ed3"} + ], + "result": {"@id": "#4154dad3-00cc-4e35-bb8f-a2de5cd7dc49"}, + "startTime": "2018-10-25T15:46:35.210973" + }, + { + "@id": "https://orcid.org/0000-0001-9842-9718", + "@type": "Person", + "name": "Stian Soiland-Reyes" + }, + { + "@id": "#4154dad3-00cc-4e35-bb8f-a2de5cd7dc49", + "@type": "CreateAction", + "endTime": "2018-10-25T15:46:43.020168", + "instrument": {"@id": "packed.cwl"}, + "name": "Run of workflow/packed.cwl#main", + "object": [ + {"@id": "327fc7aedf4f6b69a42a7c8b808dc5a7aff61376"}, + {"@id": "#pv-main/reverse_sort"} + ], + "result": [ + {"@id": "b9214658cc453331b62c2282b772a5c063dbd284"} + ], + "startTime": "2018-10-25T15:46:35.211153" + }, + { + "@id": "327fc7aedf4f6b69a42a7c8b808dc5a7aff61376", + "@type": "File", + "exampleOfWork": [ + {"@id": "packed.cwl#main/input"}, + {"@id": "packed.cwl#revtool.cwl/input"} + ] + }, + { + "@id": "#pv-main/reverse_sort", + "@type": "PropertyValue", + "exampleOfWork": {"@id": "packed.cwl#main/reverse_sort"}, + "name": "main/reverse_sort", + "value": "True" + }, + { + "@id": "b9214658cc453331b62c2282b772a5c063dbd284", + "@type": "File", + "exampleOfWork": [ + {"@id": "packed.cwl#main/output"}, + {"@id": "packed.cwl#sorttool.cwl/output"} + ] + }, + { + "@id": "#6933cce1-f8f0-4032-8848-e0fc9166e92f", + "@type": "CreateAction", + "endTime": "2018-10-25T15:46:36.967359", + "instrument": {"@id": "packed.cwl#revtool.cwl"}, + "name": "Run of workflow/packed.cwl#main/rev", + "object": [ + {"@id": "327fc7aedf4f6b69a42a7c8b808dc5a7aff61376"} + ], + "result": [ + {"@id": "97fe1b50b4582cebc7d853796ebd62e3e163aa3f"} + ], + "startTime": "2018-10-25T15:46:35.314101" + }, + { + "@id": "#4f7f887f-1b9b-4417-9beb-58618a125cc5", + "@type": "ControlAction", + "instrument": {"@id": "packed.cwl#main/rev"}, + "name": "orchestrate revtool.cwl", + "object": {"@id": "#6933cce1-f8f0-4032-8848-e0fc9166e92f"} + }, + { + "@id": "97fe1b50b4582cebc7d853796ebd62e3e163aa3f", + "@type": "File", + "exampleOfWork": [ + {"@id": "packed.cwl#revtool.cwl/output"}, + {"@id": "packed.cwl#sorttool.cwl/input"} + ] + }, + { + "@id": "#9eac64b2-c2c8-401f-9af8-7cfb0e998107", + "@type": "CreateAction", + "endTime": "2018-10-25T15:46:38.069110", + "instrument": {"@id": "packed.cwl#sorttool.cwl"}, + "name": "Run of workflow/packed.cwl#main/sorted", + "object": [ + {"@id": "97fe1b50b4582cebc7d853796ebd62e3e163aa3f"}, + {"@id": "#pv-main/sorted/reverse"} + ], + "result": [ + {"@id": "b9214658cc453331b62c2282b772a5c063dbd284"} + ], + "startTime": "2018-10-25T15:46:36.975235" + }, + { + "@id": "#793b3df4-cbb7-4d17-94d4-0edb18566ed3", + "@type": "ControlAction", + "instrument": {"@id": "packed.cwl#main/sorted"}, + "name": "orchestrate sorttool.cwl", + "object": {"@id": "#9eac64b2-c2c8-401f-9af8-7cfb0e998107"} + }, + { + "@id": "#pv-main/sorted/reverse", + "@type": "PropertyValue", + "exampleOfWork": {"@id": "packed.cwl#sorttool.cwl/reverse"}, + "name": "main/sorted/reverse", + "value": "True" + } +] +} +``` + + +## Representing parameter connections + +In most workflows, the outputs of one or more steps are needed as input for subsequent steps: this creates a *connection* between the corresponding parameters of the tools that implement those steps. For instance, consider the "revsort" workflow represented in the above example: + +

    revsort workflow diagram

    + +In this workflow, the output of the `rev` step is used as input by the `sorted` step, creating a connection between the `output` parameter of `revtool.cwl` and the `input` parameter of `sorttool.cwl`. A connection can also occur between tool parameters and workflow parameters: looking again at the above example, the `reverse_sort` workflow parameter is connected to the `reverse` parameter of `sorttool.cwl`. + +A provenance run crate MAY describe parameter connections using the `ParameterConnection` type from the [workflow-run](https://github.com/ResearchObject/ro-terms/tree/master/workflow-run) ro-terms namespace. References to the `ParameterConnection` instances SHOULD follow the CWL convention, where connections to workflow output parameters are referenced by the workflow while other connections are referenced by the receiving step: + +```json +{ + "@id": "packed.cwl", + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow", "HowTo"], + "connection": [ + {"@id": "#150ffba3-9dc2-4b14-8a6b-3f826f70e41b"} + ], + ... +}, +{ + "@id": "#150ffba3-9dc2-4b14-8a6b-3f826f70e41b", + "@type": "ParameterConnection", + "sourceParameter": {"@id": "packed.cwl#sorttool.cwl/output"}, + "targetParameter": {"@id": "packed.cwl#main/output"} +}, +{ + "@id": "packed.cwl#main/sorted", + "@type": "HowToStep", + "connection": [ + {"@id": "#548ab27a-3abf-4035-b3dd-f2989762d5c0"}, + {"@id": "#ed883346-fb32-43dd-b965-18aa5cac9350"} + ], + "workExample": {"@id": "packed.cwl#sorttool.cwl"} +}, +{ + "@id": "#548ab27a-3abf-4035-b3dd-f2989762d5c0", + "@type": "ParameterConnection", + "sourceParameter": {"@id": "packed.cwl#revtool.cwl/output"}, + "targetParameter": {"@id": "packed.cwl#sorttool.cwl/input"} +}, +{ + "@id": "#ed883346-fb32-43dd-b965-18aa5cac9350", + "@type": "ParameterConnection", + "sourceParameter": {"@id": "packed.cwl#main/reverse_sort"}, + "targetParameter": {"@id": "packed.cwl#sorttool.cwl/reverse"} +} +``` + +Note that the `workflow-run` terms are not part of the standard RO-Crate context, so they have to be added to the crate's `@context` to be used: + +```json +{ + "@context": [ + "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/terms/workflow-run/context" + ], + "@graph": [...] +} +``` + + +## Engine configuration files + +A workflow engine may support configuration through a configuration file. In this case, the specific configuration file used in the engine run SHOULD be added to the `object` attribute of the corresponding `OrganizeAction`. + +```json +{ + "@id": "#e55c4723-7814-4cef-b3b6-96c1dbf1ae9b", + "@type": "SoftwareApplication", + "name": "StreamFlow 0.2.0.dev2" +}, +{ + "@id": "#7ff2f0b6-0294-4da5-9ecc-5846b8aa4e66", + "@type": "OrganizeAction", + "instrument": {"@id": "#e55c4723-7814-4cef-b3b6-96c1dbf1ae9b"}, + "name": "Run of StreamFlow 0.2.0.dev2", + "object": [ + {"@id": "7ff2f0b6-0294-4da5-9ecc-5846b8aa4e66/streamflow.yml"}, + {"@id": "#a203c665-668d-4488-bf57-5b2eedf77905"}, + ... + ], + "result": {"@id": "#9984d778-7cd8-49ea-984d-7c58a0404f85"} +}, +{ + "@id": "7ff2f0b6-0294-4da5-9ecc-5846b8aa4e66/streamflow.yml", + "@type": "File", + "name": "StreamFlow configuration file", + "encodingFormat": "application/yaml" +}, +{ + "@id": "#a203c665-668d-4488-bf57-5b2eedf77905", + "@type": "ControlAction", + "instrument": {"@id": "predictions.cwl#extract-tissue-low"}, + "object": {"@id": "#465dafb2-66cf-4af9-a6cf-b8fea0e8acc9"} +}, +... +``` + +See also the [section on referencing configuration files of executed tools](../process_run_crate#referencing-configuration-files). + + +## Tool wrapper dependencies + +In some workflow systems (e.g., CWL, Galaxy), tools are typically wrappers for an executable written in a scripting programming language. This MAY be represented by listing the wrapped tool and its dependencies as described in [Specifying software dependencies](../process_run_crate#specifying-software-dependencies). The wrapped tool can be highlighted by using `mainEntity`: + +```json +{ + "@id": "data_analysis_tool.cwl", + "@type": "SoftwareApplication", + "softwareRequirements": [ + {"@id": "scripts/data_analysis_script.py"}, + {"@id": "https://pypi.org/project/numpy/1.26.2/"} + ], + "mainEntity": {"@id": "scripts/data_analysis_script.py"} +}, +{ + "@id": "scripts/data_analysis_script.py", + "@type": "SoftwareApplication", + "version": "0.1" +}, +{ + "@id": "https://pypi.org/project/numpy/1.26.2/", + "@type": "SoftwareApplication", + "name": "NumPy", + "version": "1.26.2" +} +``` + +## Tool runtime environment + +While the `softwareRequirements` of a tool can [specify software dependencies](../process_run_crate#specifying-software-dependencies) (as above) in terms of naming software, a more reproducible definition of a tool's runtime environment may need to include a particular set of binaries that are compiled and/or distributed to work together. (Note that _runtime environment_ here refers to a set of software, configuration and other dependency files, not [environment variables](../workflow_run_crate#environment-variables-as-formal-parameters)). + +Some workflow engines support such package systems as a way to distribute tool dependencies, typically by referring to an _environment file_ which can be programmatically instantiated to retrieve and install a given set of binaries. In a Provenance Crate, environment files are indicated as `buildInstructions` for either the `HowToStep` (for a given step) or the `HowTo` (for the whole workflow). + +For instance, to indicate a [Conda environment](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) for a Nextflow workflow: + +```json +{ + "@id": "main.nf", + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow", "HowTo"], + "name": "Hello world in Nextflow", + "programmingLanguage": { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" + }, + "buildInstructions": { + "@id": "environment.yml" + } +}, +{ + "@id": "environment.yml", + "@type": "File", + "name": "Conda environment", + "encodingFormat": "application/yaml", + "conformsTo": { + "@id": "https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#create-env-file-manually", + } +}, +{ + "@id": "https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#create-env-file-manually", + "@type": "WebPageElement", + "name": "Conda environment file" +} +``` + + +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: + +```json +{ + "@context": [ + "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/terms/workflow-run", + { "buildInstructions": "https://codemeta.github.io/terms/buildInstructions" } + ], + "@graph": [...] +} +``` + + + +## Conditional step execution + +Some workflow languages provide a mechanism to execute a step only when some condition is verified. An example of this is the [when](https://www.commonwl.org/v1.2/Workflow.html#Conditional_execution_(Optional)) clause in CWL. If an execution of a step is skipped in this way, the corresponding action SHOULD NOT be included in the RO-Crate metadata, while the step itself and the tool it executes MAY be represented. + + +## Representing resource usage + +It can often be desirable to have information on the resources used in the course of the execution: how much memory, CPU, etc. One obvious use for such information is as estimate of the amount of resources that will be needed for future runs. Representing resource usage for a tool run is OPTIONAL; if represented, it MUST link the corresponding [CreateAction](http://schema.org/CreateAction) to one or more [PropertyValue](http://schema.org/PropertyValue) instances via the `resourceUsage` property, defined in the namespace. A `PropertyValue` instance used to represent an element of resource usage MUST have a unique identifier representing the quantity being measured as its [propertyID](http://schema.org/propertyID), and SHOULD refer to a unit of measurement via [unitCode](http://schema.org/unitCode), except for dimensionless numbers. Example: + +```json +{ + "@id": "#a1be3cab", + "@type": "CreateAction", + "instrument": {"@id": "foobar.nf#foo"}, + "resourceUsage": [ + { + "@id": "#a1be3cab-realTime" + }, + { + "@id": "#a1be3cab-percentCPU" + } + ] +}, +{ + "@id": "#a1be3cab-realTime", + "@type": "PropertyValue", + "name": "realTime", + "propertyID": "https://w3id.org/ro/terms/nf-trace#realTime", + "unitCode": "https://qudt.org/vocab/unit/MilliSEC", + "value": "12" +}, +{ + "@id": "#a1be3cab-percentCPU", + "@type": "PropertyValue", + "name": "percentCPU", + "propertyID": "https://w3id.org/ro/terms/nf-trace#percentCPU", + "value": "80.0" +} +``` + +The values of `propertyID` SHOULD be URLs that univocally identify the quantity. The set of possible `propertyID` values can be defined by the workflow engine that implements the profile; ideally, each URL would point to a detailed description of the quantity. In the above example, ro-terms is used to create a namespace for the `propertyID`s. In this case, [QUDT](https://qudt.org/) is used to specify the `unitCode`. + + +## Requirements + +The requirements of this profile are those of [Workflow Run Crate](../workflow_run_crate) plus the ones listed below. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    PropertyRequired?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
    @typeMUSTMUST include File, SoftwareSourceCode and ComputationalWorkflow. If the step property is used, MUST also include HowTo. In the case of a subworkflow added to the crate as a contextual entity, MUST NOT include File.
    hasPartMUSTIdentifiers of the tools (including subworkflows) orchestrated by this workflow, represented as specified in the Process Run Crate requirements under "SoftwareApplication". The referenced tools MAY also incude formal parameter definitions via input and output as specified in Workflow Run Crate. In the case of subworkflows, the type MUST include ComputationalWorkflow
    stepSHOULDIdentifiers of the HowToStep instances representing this workflow's steps. If this property is used, the workflow MUST include HowTo among its types.
    HowToStep
    workExampleMUSTIdentifier of the tool (or subworkflow) that implements this step.
    positionMAYAn integer indicating the step's position in the execution order. In general, there may be more than one valid execution order for a workflow. For instance, if step C needs outputs from steps A and B, but A and B don't need each other's output, both A-B-C and B-A-C are valid execution orders (A and B might even be executed in parallel). For this reason, the only requirement is that for each step pair (S1, S2), if S2 needs outputs from S1, S2's position MUST be greater than S1's.
    ControlAction
    instrumentMUSTIdentifier of the HowToStep whose execution is represented by this action.
    objectMUSTIdentifier(s) of the CreateAction describing the tool execution(s) corresponding to this step execution.
    actionStatusMAYSHOULD be CompletedActionStatus if the step completed successfully or FailedActionStatus if it failed to complete. In the latter case, consumers should be prepared for the absence of any dependent actions (i.e., CreateAction instances corresponding to tool executions; the opposite is not necessarily true: a step can be successful even if some of its associated tool executions failed, e.g. in fault tolerant engines). If this attribute is not specified, consumers should assume that the step completed successfully.
    errorMAYAdditional information on the cause of the failure, if available. SHOULD NOT be specified unless actionStatus is set to FailedActionStatus.
    OrganizeAction
    instrumentMUSTIdentifier of the entity (e.g. a SoftwareApplication) that represents the workflow engine (e.g. cwltool).
    objectMUSTIdentifiers of the ControlAction instances representing the step executions.
    resultMUSTIdentifier of the CreateAction representing the workflow execution.
    actionStatusMAYSHOULD be CompletedActionStatus if the engine execution was successful or FailedActionStatus if it failed. In the latter case, consumers should be prepared for the absence of any dependent actions (i.e., CreateAction instances corresponding to workflow and tool executions, ControlAction instances corresponding to step executions). If this attribute is not specified, consumers should assume that the execution was successful.
    errorMAYAdditional information on the cause of the failure, if available. SHOULD NOT be specified unless actionStatus is set to FailedActionStatus.
    diff --git a/docs/profiles/0.5/provenance_run_crate/ro-crate-metadata.json b/docs/profiles/0.5/provenance_run_crate/ro-crate-metadata.json new file mode 100644 index 0000000..239f4cd --- /dev/null +++ b/docs/profiles/0.5/provenance_run_crate/ro-crate-metadata.json @@ -0,0 +1,652 @@ +{ "@context": + "https://w3id.org/ro/crate/1.2-DRAFT/context", + "@graph": [ + { + "@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"}, + "about": {"@id": "https://w3id.org/ro/wfrun/provenance/0.5"} + }, + { + "@id": "ro-crate-preview.html", + "@type": "CreativeWork", + "license": { "@id": "http://spdx.org/licenses/CC0-1.0" }, + "isBasedOn": {"@id": "ro-crate-metadata.json" }, + "name": "RO-Crate preview of the Provenance Run Crate profile", + "encodingFormat": "text/html", + "about": "https://w3id.org/ro/wfrun/provenance/0.5" + }, + { + "@id": "https://w3id.org/ro/wfrun/provenance/0.5", + "@type": ["Dataset","Profile"], + "isProfileOf": [ + {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"} + ], + "identifier": "https://w3id.org/ro/wfrun/provenance/0.5", + "name": "Provenance Run Crate profile", + "version": "0.5", + "license": { + "@id": "https://www.apache.org/licenses/LICENSE-2.0" + }, + "author": [ + {"@id": "https://www.researchobject.org/workflow-run-crate/"} + ], + "hasPart": [ + { "@id": "index.html" }, + { "@id": "example3/" }, + { "@id": "https://www.researchobject.org/workflow-run-crate-paper/mapping/"}, + { "@id": "https://w3id.org/ro/terms/workflow-run#" }, + { "@id": "https://w3id.org/ro/terms/workflow-run" }, + { "@id": "https://gxy.io/GTN:T00343" }, + { "@id": "https://pypi.org/project/runcrate/" }, + { "@id": "https://w3id.org/ro/wfrun/process/0.5" }, + { "@id": "https://w3id.org/ro/wfrun/workflow/0.5" }, + { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" }, + { "@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection" }, + { "@id": "https://w3id.org/ro/terms/workflow-run#connection" }, + { "@id": "https://w3id.org/ro/terms/workflow-run#sourceParameter" }, + { "@id": "https://w3id.org/ro/terms/workflow-run#targetParameter" }, + { "@id": "https://codemeta.github.io/terms/buildInstructions" } + ], + "hasResource": [ + { "@id": "#hasSpecification" }, + { "@id": "#hasConstraints" }, + { "@id": "#hasVocabulary" }, + { "@id": "#hasGuidance" }, + { "@id": "#hasExample" }, + { "@id": "#hasMappingToProv" }, + { "@id": "#shouldConformToWorkflowROCrate" }, + { "@id": "#shouldConformToProcessCrateProfile" }, + { "@id": "#shouldConformToWorkflowCrateProfile" } + ], + "citation": { "@id": "https://doi.org/10.48550/arXiv.2312.07852" } + }, + { + "@id": "https://www.researchobject.org/workflow-run-crate/", + "@type": "Project", + "name": "Provenance Run Crate task force", + "member": [ + + { "@id": "https://orcid.org/0000-0001-8271-5429"}, + { "@id": "https://orcid.org/0000-0003-4929-1219"}, + { "@id": "https://orcid.org/0000-0001-9842-9718"}, + { "@id": "https://orcid.org/0000-0002-5432-2748"}, + { "@id": "https://orcid.org/0000-0002-4806-5140"}, + { "@id": "https://orcid.org/0000-0003-3156-2105"}, + { "@id": "https://orcid.org/0000-0002-6190-122X"}, + { "@id": "https://orcid.org/0000-0003-0454-7145"}, + { "@id": "https://orcid.org/0000-0002-8940-4946"}, + { "@id": "https://orcid.org/0000-0003-0606-2512"}, + { "@id": "https://orcid.org/0000-0002-3468-0652"}, + { "@id": "https://orcid.org/0000-0002-2961-9670"}, + { "@id": "https://orcid.org/0000-0003-3986-0510"}, + { "@id": "https://orcid.org/0000-0002-0003-2024"}, + { "@id": "https://orcid.org/0000-0002-9464-6640"}, + { "@id": "https://orcid.org/0000-0001-5845-8880"}, + { "@id": "https://orcid.org/0000-0003-4894-4660"}, + { "@id": "https://orcid.org/0000-0002-4405-6802"}, + { "@id": "https://orcid.org/0000-0001-9290-2017"}, + { "@id": "https://orcid.org/0000-0003-0617-9219"}, + { "@id": "https://orcid.org/0000-0001-9228-2882"}, + { "@id": "https://orcid.org/0000-0003-3898-9451"}, + { "@id": "https://orcid.org/0000-0003-3777-5945"}, + { "@id": "https://orcid.org/0000-0003-2765-0049"}, + { "@id": "https://orcid.org/0000-0001-9818-9320"}, + { "@id": "https://orcid.org/0000-0002-8122-9522"}, + { "@id": "https://orcid.org/0000-0002-8330-4071"}, + { "@id": "https://orcid.org/0000-0003-4073-7456"}, + { "@id": "https://orcid.org/0000-0003-1361-7301"}, + { "@id": "https://orcid.org/0000-0002-5358-616X"}, + { "@id": "https://orcid.org/0000-0002-5477-287X"}, + { "@id": "https://orcid.org/0000-0001-8250-4074"}, + { "@id": "https://orcid.org/0000-0003-0902-0086"}, + { "@id": "https://orcid.org/0000-0001-8172-8981"}, + { "@id": "https://orcid.org/0000-0001-6740-9212"}, + { "@id": "https://orcid.org/0000-0001-5411-356X"}, + { "@id": "https://orcid.org/0000-0003-0035-0951"}, + { "@id": "https://orcid.org/0000-0003-0711-5196"} + ], + "parentOrganization": { "@id": "https://www.researchobject.org/ro-crate/community" } + }, + { + "@id": "https://www.researchobject.org/ro-crate/community", + "@type": "Project", + "name": "RO-Crate Community" + }, + { + "@id": "https://w3id.org/ro/wfrun/process/0.5", + "@type": ["CreativeWork", "Profile"], + "name": "Process Run Crate profile", + "version": "0.5" +}, +{ + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0", + "@type": ["CreativeWork", "Profile"], + "name": "Workflow RO-Crate profile", + "version": "1.0" +}, + { + "@id": "https://w3id.org/ro/wfrun/workflow/0.5", + "@type": ["CreativeWork", "Profile"], + "name": "Workflow Run Crate profile", + "version": "0.5" + }, + { + "@id": "index.html", + "@type": "File", + "name": "Provenance Run Crate (HTML)", + "encodingFormat": [ + "text/html", + {"@id": "https://www.nationalarchives.gov.uk/PRONOM/fmt/471"} + ] + }, + { + "@id": "index.html#requirements", + "@type": "WebPageElement", + "name": "Provenance Run Crate requirements" + }, + { + "@id": "example3/", + "@type": "Dataset", + "name": "Example Process Run Crate", + "conformsTo": [ + { "@id": "https://w3id.org/ro/crate" }, + { "@id": "https://w3id.org/ro/wfrun/process/0.4" }, + { "@id": "https://w3id.org/ro/wfrun/workflow/0.4" }, + { "@id": "https://w3id.org/ro/wfrun/provenance/0.4" }, + { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" } + ], + "subjectOf": [ + { "@id": "example3/ro-crate-metadata.json" }, + { "@id": "example3/ro-crate-preview.html" } + ] + }, + { + "@id": "example3/ro-crate-metadata.json", + "@type": "CreativeWork", + "encodingFormat": "application/ld+json" + }, + { + "@id": "example3/ro-crate-preview.html", + "@type": "CreativeWork", + "encodingFormat": "text/html" + }, + { + "@id": "https://w3id.org/ro/terms/workflow-run", + "@type": "File", + "name": "JSON-LD context for workflow-run terms", + "contentUrl": "https://www.researchobject.org/ro-terms/workflow-run/context.json", + "conformsTo": { + "@id": "http://www.w3.org/ns/json-ld#Context" + }, + "encodingFormat": "application/ld+json", + "isBasedOn": [ + { + "@id": "https://w3id.org/ro/crate/1.1/context" + }, + { + "@id": "https://w3id.org/ro/terms/workflow-run#" + } + ], + "license": { + "@id": "https://creativecommons.org/publicdomain/zero/1.0/" + } + }, + { + "@id": "#hasSpecification", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/specification" }, + "hasArtifact": {"@id": "index.html"} + }, + { + "@id": "#hasConstraints", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/constraints" }, + "hasArtifact": {"@id": "index.html#requirements"} + }, + { + "@id": "#hasVocabulary", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/vocabulary" }, + "hasArtifact": {"@id": "https://w3id.org/ro/terms/workflow-run#"} + }, + { + "@id": "#hasGuidance", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/guidance" }, + "hasArtifact": {"@id": "https://gxy.io/GTN:T00343"} + }, + { + "@id": "#hasExample", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/example" }, + "hasArtifact": { "@id": "example3/" } + }, + { + "@id": "#hasMappingToProv", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/mapping" }, + "hasArtifact": { "@id": "https://www.researchobject.org/workflow-run-crate-paper/mapping/" } + }, + { + "@id": "https://www.researchobject.org/workflow-run-crate-paper/mapping/", + "@type": "Dataset", + "name": "SSSOM mapping from PROV to Workflow Run Crate", + "isPartOf": { + "@id": "https://w3id.org/ro/doi/10.5281/zenodo.10368989" + } + }, + { + "@id": "https://w3id.org/ro/doi/10.5281/zenodo.10368989", + "@type": "Dataset", + "name": "Recording provenance of workflow runs with RO-Crate (RO-Crate and mapping)", + "conformsTo": { "@id": "https://w3id.org/ro/crate" }, + "subjectOf": [ + { "@id": "https://www.researchobject.org/workflow-run-crate-paper/ro-crate-metadata.jsonld" }, + { "@id": "https://www.researchobject.org/workflow-run-crate-paper/ro-crate-preview.html" } + ] + }, + { + "@id": "https://www.researchobject.org/workflow-run-crate-paper/ro-crate-metadata.jsonld", + "@type": "CreativeWork", + "encodingFormat": "application/ld+json" + }, + { + "@id": "https://www.researchobject.org/workflow-run-crate-paper/ro-crate-preview.html", + "@type": "CreativeWork", + "encodingFormat": "text/html" + }, + { + "@id": "#shouldConformToWorkflowROCrate", + "@type": "ResourceDescriptor", + "name": "SHOULD conform to Workflow RO-Crate profile", + "hasRole": { "@id": "http://purl.org/dc/terms/conformsTo" }, + "hasArtifact": {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"} +}, +{ + "@id": "#shouldConformToProcessCrateProfile", + "@type": "ResourceDescriptor", + "name": "SHOULD conform to Process Crate profile", + "hasRole": { "@id": "http://purl.org/dc/terms/conformsTo" }, + "hasArtifact": {"@id": "https://w3id.org/ro/wfrun/process/0.5"} +}, +{ + "@id": "#shouldConformToWorkflowCrateProfile", + "@type": "ResourceDescriptor", + "name": "SHOULD conform to Workflow Crate profile", + "hasRole": { "@id": "http://purl.org/dc/terms/conformsTo" }, + "hasArtifact": {"@id": "https://w3id.org/ro/wfrun/workflow/0.5"} +}, + { + "@id": "https://gxy.io/GTN:T00343", + "@type": "LearningResource", + "name": "Workflow Run RO-Crate Introduction", + "author": { + "@id": "https://orcid.org/0000-0001-8271-5429" + } + }, + { "@id": "https://doi.org/10.48550/arXiv.2312.07852", + "@type": "ScholarlyArticle", + "name": "Recording provenance of workflow runs with RO-Crate", + "author": [ + { + "@id": "https://orcid.org/0000-0001-8271-5429" + }, + { + "@id": "https://orcid.org/0000-0002-2961-9670" + }, + { + "@id": "https://orcid.org/0000-0003-4929-1219" + }, + { + "@id": "https://orcid.org/0000-0003-0606-2512" + }, + { + "@id": "https://orcid.org/0000-0002-3468-0652" + }, + { + "@id": "https://orcid.org/0000-0002-8940-4946" + }, + { + "@id": "https://orcid.org/0000-0002-0003-2024" + }, + { + "@id": "https://orcid.org/0000-0002-4663-5613" + }, + { + "@id": "https://orcid.org/0000-0003-0454-7145" + }, + { + "@id": "https://orcid.org/0000-0002-4806-5140" + }, + { + "@id": "https://orcid.org/0000-0001-9290-2017" + }, + { + "@id": "https://orcid.org/0000-0002-1119-1792" + }, + { + "@id": "https://orcid.org/0000-0003-3777-5945" + }, + { + "@id": "https://orcid.org/0000-0003-2765-0049" + }, + { + "@id": "https://orcid.org/0000-0002-0309-604X" + }, + { + "@id": "https://orcid.org/0000-0003-0902-0086" + }, + { + "@id": "https://orcid.org/0000-0001-8250-4074" + }, + { + "@id": "https://orcid.org/0000-0001-9842-9718" + } + ], + + "creditText": "Simone Leo, et al. (2024): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852" + }, + { + "@id": "https://w3id.org/ro/terms/workflow-run#", + "@type": "DefinedTermSet", + "name": "Namespace for Workflow Run RO-Crate model" + }, + + { + "@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection", + "@type": "DefinedTerm", + "termCode": "ParameterConnection", + "name": "Parameter Connection", + "inDefinedTermSet": { "@id": "https://w3id.org/ro/terms/workflow-run#" }, + "description": "A connection between parameters of different applications" + }, + { + "@id": "https://w3id.org/ro/terms/workflow-run#connection", + "@type": "DefinedTerm", + "termCode": "connection", + "name": "connection", + "inDefinedTermSet": { "@id": "https://w3id.org/ro/terms/workflow-run#" }, + "description": "A parameter connection created by this workflow" + }, + { + "@id": "https://w3id.org/ro/terms/workflow-run#sourceParameter", + "@type": "DefinedTerm", + "termCode": "sourceParameter", + "name": "source parameter", + "inDefinedTermSet": { "@id": "https://w3id.org/ro/terms/workflow-run#" }, + "description": "The source (upstream) parameter" + }, + { + "@id": "https://w3id.org/ro/terms/workflow-run#targetParameter", + "@type": "DefinedTerm", + "termCode": "targetParameter", + "name": "target parameter", + "inDefinedTermSet": { "@id": "https://w3id.org/ro/terms/workflow-run#" }, + "description": "The target (upstream) parameter" + }, + { + "@id": "https://codemeta.github.io/terms/buildInstructions", + "@type": "DefinedTerm", + "name": "buildInstructions", + "termCode": "buildInstructions", + "description": "Build environment file (e.g. for Conda)", + "inDefinedTermSet": { "@id": "https://codemeta.github.io/terms/" } + }, + { + "@id": "https://codemeta.github.io/terms/", + "@type": "DefinedTermSet", + "name": "Codemeta Terms", + "url": "https://codemeta.github.io/terms/", + "version": "3.0" + }, + { + "@id": "https://pypi.org/project/runcrate/", + "@type": "SoftwareApplication", + "name": "runcrate", + "version": "0.5.0", + "url": "https://pypi.org/project/runcrate/" + }, + { + "@id": "http://schema.org/MediaObject", + "@type": "DefinedTerm", + "name": "MediaObject", + "termCode": "file" + }, +{ + "@id": "https://orcid.org/0000-0001-8271-5429", + "@type": "Person", + "name": "Simone Leo" +}, +{ + "@id": "https://orcid.org/0000-0003-4929-1219", + "@type": "Person", + "name": "Laura Rodríguez-Navas" +}, +{ + "@id": "https://orcid.org/0000-0001-9842-9718", + "@type": "Person", + "name": "Stian Soiland-Reyes" +}, +{ + "@id": "https://orcid.org/0000-0002-5432-2748", + "@type": "Person", + "name": "Paul Brack" +}, +{ + "@id": "https://orcid.org/0000-0002-4806-5140", + "@type": "Person", + "name": "José María Fernández" +}, +{ + "@id": "https://orcid.org/0000-0003-3156-2105", + "@type": "Person", + "name": "Alan R Williams" +}, +{ + "@id": "https://orcid.org/0000-0002-6190-122X", + "@type": "Person", + "name": "Ignacio Eguinoa" +}, +{ + "@id": "https://orcid.org/0000-0003-0454-7145", + "@type": "Person", + "name": "Daniel Garijo" +}, +{ + "@id": "https://orcid.org/0000-0002-8940-4946", + "@type": "Person", + "name": "Paul De Geest" +}, +{ + "@id": "https://orcid.org/0000-0003-0606-2512", + "@type": "Person", + "name": "Raül Sirvent" +}, +{ + "@id": "https://orcid.org/0000-0002-3468-0652", + "@type": "Person", + "name": "Alexander Kanitz" +}, +{ + "@id": "https://orcid.org/0000-0002-2961-9670", + "@type": "Person", + "name": "Michael R Crusoe" +}, +{ + "@id": "https://orcid.org/0000-0003-3986-0510", + "@type": "Person", + "name": "LJ Garcia Castro" +}, +{ + "@id": "https://orcid.org/0000-0002-0003-2024", + "@type": "Person", + "name": "Rudolf Wittner" +}, +{ + "@id": "https://orcid.org/0000-0002-9464-6640", + "@type": "Person", + "name": "Wolfgang Maier" +}, +{ + "@id": "https://orcid.org/0000-0001-5845-8880", + "@type": "Person", + "name": "Sebastiaan Huber" +}, +{ + "@id": "https://orcid.org/0000-0003-4894-4660", + "@type": "Person", + "name": "Kevin Jablonka" +}, +{ + "@id": "https://orcid.org/0000-0002-4405-6802", + "@type": "Person", + "name": "Haris Zafeiropoulos" +}, +{ + "@id": "https://orcid.org/0000-0001-9290-2017", + "@type": "Person", + "name": "Iacopo Colonnelli" +}, +{ + "@id": "https://orcid.org/0000-0003-0617-9219", + "@type": "Person", + "name": "Jake Emerson" +}, +{ + "@id": "https://orcid.org/0000-0001-9228-2882", + "@type": "Person", + "name": "Abigail Miller" +}, +{ + "@id": "https://orcid.org/0000-0003-3898-9451", + "@type": "Person", + "name": "Stelios Ninidakis" +}, +{ + "@id": "https://orcid.org/0000-0003-3777-5945", + "@type": "Person", + "name": "Tazro Ohta" +}, +{ + "@id": "https://orcid.org/0000-0003-2765-0049", + "@type": "Person", + "name": "Hirotaka Suetake" +}, +{ + "@id": "https://orcid.org/0000-0001-9818-9320", + "@type": "Person", + "name": "Johannes Köster" +}, +{ + "@id": "https://orcid.org/0000-0002-8122-9522", + "@type": "Person", + "name": "Luiz Gadelha" +}, +{ + "@id": "https://orcid.org/0000-0002-8330-4071", + "@type": "Person", + "name": "Mahnoor Zulfiqar" +}, +{ + "@id": "https://orcid.org/0000-0003-4073-7456", + "@type": "Person", + "name": "Romain David" +}, +{ + "@id": "https://orcid.org/0000-0003-1361-7301", + "@type": "Person", + "name": "Maciek Bąk" +}, +{ + "@id": "https://orcid.org/0000-0002-5358-616X", + "@type": "Person", + "name": "Petr Holub" +}, +{ + "@id": "https://orcid.org/0000-0002-5477-287X", + "@type": "Person", + "name": "Milan Markovic" +}, +{ + "@id": "https://orcid.org/0000-0001-8250-4074", + "@type": "Person", + "name": "Bruno P. Kinoshita" +}, +{ + "@id": "https://orcid.org/0000-0003-0902-0086", + "@type": "Person", + "name": "Renske de Wit" +}, +{ + "@id": "https://orcid.org/0000-0001-8172-8981", + "@type": "Person", + "name": "Jasper Koehorst" +}, +{ + "@id": "https://orcid.org/0000-0001-6740-9212", + "@type": "Person", + "name": "Samuel Lampa" +}, +{ + "@id": "https://orcid.org/0000-0001-5411-356X", + "@type": "Person", + "name": "Samuel Grayson" +}, +{ + "@id": "https://orcid.org/0000-0003-0035-0951", + "@type": "Person", + "name": "Jörg F. 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    +
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    Provenance Run Crate profile

    + + +⬇️🏷️ Download all the metadata for Provenance Run Crate profile in JSON-LD format + + +
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    Go to: Provenance Run Crate profile

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    Go to: Provenance Run Crate task force

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    Go to: Apache License 2.0

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    @idhttps://www.apache.org/licenses/LICENSE-2.0
    name [?]Apache License 2.0
    @typeCreativeWork
    version [?]2.0
    identifier [?]spdx: Apache-2.0
    Items that reference this one
    license [?]Provenance Run Crate profile
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    ⬇️ Download: Provenance Run Crate (HTML)

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    @idindex.html
    name [?]Provenance Run Crate (HTML)
    @typeFile
    encodingFormat [?]
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
    hasArtifact [?]#hasSpecification
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    Example Process Run Crate

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    @idexample3/
    name [?]Example Process Run Crate
    @typeDataset
    conformsTo [?]
    subjectOf [?]
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
    hasArtifact [?]#hasExample
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    Go to: SSSOM mapping from PROV to Workflow Run Crate

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    @idhttps://www.researchobject.org/workflow-run-crate-paper/mapping/
    name [?]SSSOM mapping from PROV to Workflow Run Crate
    @typeDataset
    isPartOf [?]Recording provenance of workflow runs with RO-Crate (RO-Crate and mapping)
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
    hasArtifact [?]#hasMappingToProv
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    Go to: Namespace for Workflow Run RO-Crate model

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    @idhttps://w3id.org/ro/terms/workflow-run#
    name [?]Namespace for Workflow Run RO-Crate model
    @typeDefinedTermSet
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
    isBasedOn [?]JSON-LD context for workflow-run terms
    hasArtifact [?]#hasVocabulary
    inDefinedTermSet [?]
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    Go to: JSON-LD context for workflow-run terms

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    @idhttps://w3id.org/ro/terms/workflow-run
    name [?]JSON-LD context for workflow-run terms
    @typeFile
    encodingFormat [?]application/ld+json
    contentUrl [?]https://www.researchobject.org/ro-terms/workflow-run/context.json
    conformsTo [?]http://www.w3.org/ns/json-ld#Context
    isBasedOn [?]
    license [?]Creative Commons Zero v1.0 Universal
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
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    Go to: Workflow Run RO-Crate Introduction

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    @idhttps://gxy.io/GTN:T00343
    name [?]Workflow Run RO-Crate Introduction
    @typeLearningResource
    author [?]Simone Leo
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
    hasArtifact [?]#hasGuidance
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    Go to: runcrate

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    @idhttps://pypi.org/project/runcrate/
    name [?]runcrate
    @typeSoftwareApplication
    version [?]0.5.0
    url [?]https://pypi.org/project/runcrate/
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
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    Go to: Process Run Crate profile

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    @idhttps://w3id.org/ro/wfrun/process/0.5
    name [?]Process Run Crate profile
    @type
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    • CreativeWork
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    • Profile
      • +
    version [?]0.5
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
    hasArtifact [?]SHOULD conform to Process Crate profile
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    Go to: Workflow Run Crate profile

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    @idhttps://w3id.org/ro/wfrun/workflow/0.5
    name [?]Workflow Run Crate profile
    @type
      +
    • CreativeWork
      • + +
    • Profile
      • +
    version [?]0.5
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
    hasArtifact [?]SHOULD conform to Workflow Crate profile
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    Go to: Workflow RO-Crate profile

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    @idhttps://w3id.org/workflowhub/workflow-ro-crate/1.0
    name [?]Workflow RO-Crate profile
    @type
      +
    • CreativeWork
      • + +
    • Profile
      • +
    version [?]1.0
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
    conformsTo [?]Example Process Run Crate
    hasArtifact [?]SHOULD conform to Workflow RO-Crate profile
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    Go to: Parameter Connection

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    @idhttps://w3id.org/ro/terms/workflow-run#ParameterConnection
    name [?]Parameter Connection
    @typeDefinedTerm
    description [?]A connection between parameters of different applications
    termCode [?]ParameterConnection
    inDefinedTermSet [?]Namespace for Workflow Run RO-Crate model
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
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    Go to: connection

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    @idhttps://w3id.org/ro/terms/workflow-run#connection
    name [?]connection
    @typeDefinedTerm
    description [?]A parameter connection created by this workflow
    termCode [?]connection
    inDefinedTermSet [?]Namespace for Workflow Run RO-Crate model
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
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    Go to: source parameter

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    @idhttps://w3id.org/ro/terms/workflow-run#sourceParameter
    name [?]source parameter
    @typeDefinedTerm
    description [?]The source (upstream) parameter
    termCode [?]sourceParameter
    inDefinedTermSet [?]Namespace for Workflow Run RO-Crate model
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
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    Go to: target parameter

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    @idhttps://w3id.org/ro/terms/workflow-run#targetParameter
    name [?]target parameter
    @typeDefinedTerm
    description [?]The target (upstream) parameter
    termCode [?]targetParameter
    inDefinedTermSet [?]Namespace for Workflow Run RO-Crate model
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
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    Go to: buildInstructions

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    @idhttps://codemeta.github.io/terms/buildInstructions
    name [?]buildInstructions
    @typeDefinedTerm
    description [?]Build environment file (e.g. for Conda)
    termCode [?]buildInstructions
    inDefinedTermSet [?]Codemeta Terms
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
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    #hasSpecification

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    @id#hasSpecification
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/specification
    hasArtifact [?]Provenance Run Crate (HTML)
    Items that reference this one
    hasResource [?]Provenance Run Crate profile
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    #hasConstraints

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    @id#hasConstraints
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/constraints
    hasArtifact [?]Provenance Run Crate requirements
    Items that reference this one
    hasResource [?]Provenance Run Crate profile
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    #hasVocabulary

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    @id#hasVocabulary
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/vocabulary
    hasArtifact [?]Namespace for Workflow Run RO-Crate model
    Items that reference this one
    hasResource [?]Provenance Run Crate profile
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    #hasGuidance

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    @id#hasGuidance
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/guidance
    hasArtifact [?]Workflow Run RO-Crate Introduction
    Items that reference this one
    hasResource [?]Provenance Run Crate profile
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    #hasExample

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    @id#hasExample
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/example
    hasArtifact [?]Example Process Run Crate
    Items that reference this one
    hasResource [?]Provenance Run Crate profile
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    #hasMappingToProv

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    @id#hasMappingToProv
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/mapping
    hasArtifact [?]SSSOM mapping from PROV to Workflow Run Crate
    Items that reference this one
    hasResource [?]Provenance Run Crate profile
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    SHOULD conform to Workflow RO-Crate profile

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    @id#shouldConformToWorkflowROCrate
    name [?]SHOULD conform to Workflow RO-Crate profile
    @typeResourceDescriptor
    hasRole [?]http://purl.org/dc/terms/conformsTo
    hasArtifact [?]Workflow RO-Crate profile
    Items that reference this one
    hasResource [?]Provenance Run Crate profile
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    SHOULD conform to Process Crate profile

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    @id#shouldConformToProcessCrateProfile
    name [?]SHOULD conform to Process Crate profile
    @typeResourceDescriptor
    hasRole [?]http://purl.org/dc/terms/conformsTo
    hasArtifact [?]Process Run Crate profile
    Items that reference this one
    hasResource [?]Provenance Run Crate profile
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    SHOULD conform to Workflow Crate profile

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    @id#shouldConformToWorkflowCrateProfile
    name [?]SHOULD conform to Workflow Crate profile
    @typeResourceDescriptor
    hasRole [?]http://purl.org/dc/terms/conformsTo
    hasArtifact [?]Workflow Run Crate profile
    Items that reference this one
    hasResource [?]Provenance Run Crate profile
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    Go to: Recording provenance of workflow runs with RO-Crate

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    @idhttps://doi.org/10.48550/arXiv.2312.07852
    name [?]Recording provenance of workflow runs with RO-Crate
    @typeScholarlyArticle
    author [?]
    creditText [?]Simone Leo, et al. (2024): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852
    Items that reference this one
    citation [?]Provenance Run Crate profile
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    + + + + + + + diff --git a/docs/profiles/0.5/workflow_run_crate/example2/Galaxy-Workflow-Hello_World.ga b/docs/profiles/0.5/workflow_run_crate/example2/Galaxy-Workflow-Hello_World.ga new file mode 100644 index 0000000..8bd9b1b --- /dev/null +++ b/docs/profiles/0.5/workflow_run_crate/example2/Galaxy-Workflow-Hello_World.ga @@ -0,0 +1,157 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "From https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-editor/tutorial.html#creating-a-new-workflow", + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0001-9842-9718", + "name": "Stian Soiland-Reyes" + } + ], + "format-version": "0.1", + "license": "CC0-1.0", + "name": "Hello World", + "steps": { + "0": { + "annotation": "A simple set of lines in a text file", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "A simple set of lines in a text file", + "name": "simple_input" + } + ], + "label": "simple_input", + "name": "Input dataset", + "outputs": [], + "position": { + "bottom": 519.227779812283, + "height": 55.616668701171875, + "left": 626.0000271267361, + "right": 806.0000271267361, + "top": 463.6111111111111, + "width": 180, + "x": 626.0000271267361, + "y": 463.6111111111111 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "75e4b93c-1b01-4332-8e2d-974bc03870b2", + "workflow_outputs": [] + }, + "1": { + "annotation": "Return all the lines of a text file reversed, last to first", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0", + "errors": null, + "id": 1, + "input_connections": { + "infile": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool tac", + "name": "infile" + } + ], + "label": "Reverse dataset", + "name": "tac", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "bottom": 669.8444400363499, + "height": 102.23332214355469, + "left": 883.9999728732639, + "right": 1063.999972873264, + "top": 567.6111178927952, + "width": 180, + "x": 883.9999728732639, + "y": 567.6111178927952 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0", + "tool_shed_repository": { + "changeset_revision": "ddf54b12c295", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"infile\": {\"__class__\": \"RuntimeValue\"}, \"separator\": {\"separator_select\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.0", + "type": "tool", + "uuid": "1e2bcc37-edad-4d9d-9ae8-a27e183ee55a", + "workflow_outputs": [ + { + "label": "reversed", + "output_name": "outfile", + "uuid": "bb56259b-0460-4187-a4a1-2b7b3a868d6d" + } + ] + }, + "2": { + "annotation": "The last lines of workflow input are the first lines of the reversed input.", + "content_id": "Show beginning1", + "errors": null, + "id": 2, + "input_connections": { + "input": { + "id": 1, + "output_name": "outfile" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Select first", + "name": "input" + } + ], + "label": "Select last lines", + "name": "Select first", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "bottom": 819.8444061279297, + "height": 102.23332214355469, + "left": 1168.999972873264, + "right": 1348.999972873264, + "top": 717.611083984375, + "width": 180, + "x": 1168.999972873264, + "y": 717.611083984375 + }, + "post_job_actions": {}, + "tool_id": "Show beginning1", + "tool_state": "{\"header\": \"false\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineNum\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.1", + "type": "tool", + "uuid": "b378a19a-2126-4302-aace-c3311b7ef64e", + "workflow_outputs": [ + { + "label": "last_lines", + "output_name": "out_file1", + "uuid": "8fe82179-555b-4ace-ad8b-ab3a6587aea8" + } + ] + } + }, + "tags": [ + "example" + ], + "uuid": "576ba0e9-b112-47f0-845e-32d8af3a1f35", + "version": 3 +} \ No newline at end of file diff --git a/docs/profiles/0.5/workflow_run_crate/example2/index.hml b/docs/profiles/0.5/workflow_run_crate/example2/index.hml new file mode 120000 index 0000000..a33a179 --- /dev/null +++ b/docs/profiles/0.5/workflow_run_crate/example2/index.hml @@ -0,0 +1 @@ +ro-crate-preview.html \ No newline at end of file diff --git a/docs/profiles/0.5/workflow_run_crate/example2/inputs/abcdef.txt b/docs/profiles/0.5/workflow_run_crate/example2/inputs/abcdef.txt new file mode 100644 index 0000000..cead32e --- /dev/null +++ b/docs/profiles/0.5/workflow_run_crate/example2/inputs/abcdef.txt @@ -0,0 +1,6 @@ +A +B +C +D +E +F diff --git a/docs/profiles/0.5/workflow_run_crate/example2/outputs/Select_first_on_data_1_2.txt b/docs/profiles/0.5/workflow_run_crate/example2/outputs/Select_first_on_data_1_2.txt new file mode 100644 index 0000000..f296888 --- /dev/null +++ b/docs/profiles/0.5/workflow_run_crate/example2/outputs/Select_first_on_data_1_2.txt @@ -0,0 +1,6 @@ +F +E +D +C +B +A diff --git a/docs/profiles/0.5/workflow_run_crate/example2/outputs/tac_on_data_360_1.txt b/docs/profiles/0.5/workflow_run_crate/example2/outputs/tac_on_data_360_1.txt new file mode 100644 index 0000000..f296888 --- /dev/null +++ b/docs/profiles/0.5/workflow_run_crate/example2/outputs/tac_on_data_360_1.txt @@ -0,0 +1,6 @@ +F +E +D +C +B +A diff --git a/docs/profiles/0.5/workflow_run_crate/example2/ro-crate-metadata.json b/docs/profiles/0.5/workflow_run_crate/example2/ro-crate-metadata.json new file mode 100644 index 0000000..0e4d295 --- /dev/null +++ b/docs/profiles/0.5/workflow_run_crate/example2/ro-crate-metadata.json @@ -0,0 +1,177 @@ +{ "@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/0.4"}, + {"@id": "https://w3id.org/ro/wfrun/workflow/0.4"}, + {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"} + ], + "hasPart": [ + {"@id": "Galaxy-Workflow-Hello_World.ga"}, + {"@id": "inputs/abcdef.txt"}, + {"@id": "outputs/Select_first_on_data_1_2.txt"}, + {"@id": "outputs/tac_on_data_360_1.txt"} + ], + "license": {"@id": "http://spdx.org/licenses/CC0-1.0"}, + "mainEntity": {"@id": "Galaxy-Workflow-Hello_World.ga"}, + "mentions": {"@id": "#wfrun-5a5970ab-4375-444d-9a87-a764a66e3a47"} + }, + { "@id": "https://w3id.org/ro/wfrun/process/0.4", + "@type": "CreativeWork", + "name": "Process Run Crate", + "version": "0.4" + }, + { "@id": "https://w3id.org/ro/wfrun/workflow/0.4", + "@type": "CreativeWork", + "name": "Workflow Run Crate", + "version": "0.4" + }, + { "@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"], + "name": "Hello World (Galaxy Workflow)", + "author": {"@id": "https://orcid.org/0000-0001-9842-9718"}, + "creator": {"@id": "https://orcid.org/0000-0001-9842-9718"}, + "programmingLanguage": {"@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy"}, + "input": [ + {"@id": "#simple_input"}, + {"@id": "#verbose-param"} + ], + "output": [ + {"@id": "#reversed"}, + {"@id": "#last_lines"} + ] + }, + { + "@id": "#simple_input", + "@type": "FormalParameter", + "additionalType": "File", + "conformsTo": {"@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"}, + "description": "A simple set of lines in a text file", + "encodingFormat": [ + "text/plain", + {"@id": "http://edamontology.org/format_2330"} + ], + "workExample": {"@id": "inputs/abcdef.txt"}, + "name": "simple_input", + "valueRequired": "True" + }, + { + "@id": "#verbose-param", + "@type": "FormalParameter", + "additionalType": "Boolean", + "conformsTo": {"@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"}, + "description": "Increase logging output", + "workExample": {"@id": "#verbose-pv"}, + "name": "verbose", + "valueRequired": "False" + }, + { + "@id": "#reversed", + "@type": "FormalParameter", + "additionalType": "File", + "conformsTo": {"@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"}, + "description": "All the lines, reversed", + "encodingFormat": [ + "text/plain", + {"@id": "http://edamontology.org/format_2330"} + ], + "name": "reversed", + "workExample": {"@id": "outputs/tac_on_data_360_1.txt"} + }, + { + "@id": "#last_lines", + "@type": "FormalParameter", + "additionalType": "File", + "conformsTo": {"@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"}, + "description": "The last lines of workflow input are the first lines of the reversed input", + "encodingFormat": [ + "text/plain", + {"@id": "http://edamontology.org/format_2330"} + ], + "name": "last_lines", + "workExample": {"@id": "outputs/Select_first_on_data_1_2.txt"} + }, + { + "@id": "https://orcid.org/0000-0001-9842-9718", + "@type": "Person", + "name": "Stian Soiland-Reyes" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy", + "@type": "ComputerLanguage", + "identifier": "https://galaxyproject.org/", + "name": "Galaxy", + "url": "https://galaxyproject.org/" + }, + { + "@id": "#wfrun-5a5970ab-4375-444d-9a87-a764a66e3a47", + "@type": "CreateAction", + "name": "Galaxy workflow run 5a5970ab-4375-444d-9a87-a764a66e3a47", + "endTime": "2018-09-19T17:01:07+10:00", + "instrument": {"@id": "Galaxy-Workflow-Hello_World.ga"}, + "subjectOf": {"@id": "https://usegalaxy.eu/u/5dbf7f05329e49c98b31243b5f35045c/p/invocation-report-a3a1d27edb703e5c"}, + "object": [ + {"@id": "inputs/abcdef.txt"}, + {"@id": "#verbose-pv"} + ], + "result": [ + {"@id": "outputs/Select_first_on_data_1_2.txt"}, + {"@id": "outputs/tac_on_data_360_1.txt"} + ] + }, + { + "@id": "inputs/abcdef.txt", + "@type": "File", + "description": "Example input, a simple text file", + "encodingFormat": "text/plain", + "exampleOfWork": {"@id": "#simple_input"} + }, + { + "@id": "#verbose-pv", + "@type": "PropertyValue", + "exampleOfWork": {"@id": "#verbose-param"}, + "name": "verbose", + "value": "True" + }, + { + "@id": "outputs/Select_first_on_data_1_2.txt", + "@type": "File", + "name": "Select_first_on_data_1_2 (output)", + "description": "Example output of the last (aka first of reversed) lines", + "encodingFormat": "text/plain", + "exampleOfWork": {"@id": "#last_lines"} + }, + { + "@id": "outputs/tac_on_data_360_1.txt", + "@type": "File", + "name": "tac_on_data_360_1 (output)", + "description": "Example output of the reversed lines", + "encodingFormat": "text/plain", + "exampleOfWork": {"@id": "#reversed"} + }, + { + "@id": "https://usegalaxy.eu/u/5dbf7f05329e49c98b31243b5f35045c/p/invocation-report-a3a1d27edb703e5c", + "@type": "CreativeWork", + "encodingFormat": "text/html", + "datePublished": "2021-11-18T02:02:00Z", + "name": "Workflow Execution Summary of Hello World" + } +] +} \ No newline at end of file diff --git a/docs/profiles/0.5/workflow_run_crate/example2/ro-crate-preview.html b/docs/profiles/0.5/workflow_run_crate/example2/ro-crate-preview.html new file mode 100644 index 0000000..b66ff47 --- /dev/null +++ b/docs/profiles/0.5/workflow_run_crate/example2/ro-crate-preview.html @@ -0,0 +1,711 @@ + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    +

    +

    + + +⬇️🏷️ Download all the metadata for in JSON-LD format + + +
    + + +
    + + + +
    +
    +
    +

    ./

    + + + + + + +
    +


    +
    +

    Go to: Process Run Crate

    + + + + +
    + + + + + + + + + + + + + + + + + + +
    @idhttps://w3id.org/ro/wfrun/process/0.4
    name [?]Process Run Crate
    @typeCreativeWork
    version [?]0.4
    Items that reference this one
    conformsTo [?]./
    +
    + +
    +


    +
    +

    Go to: Workflow Run Crate

    + + + + +
    + + + + + + + + + + + + + + + + + + +
    @idhttps://w3id.org/ro/wfrun/workflow/0.4
    name [?]Workflow Run Crate
    @typeCreativeWork
    version [?]0.4
    Items that reference this one
    conformsTo [?]./
    +
    + +
    +


    +
    +

    Go to: Workflow RO-Crate

    + + + + +
    + + + + + + + + + + + + + + + + + + +
    @idhttps://w3id.org/workflowhub/workflow-ro-crate/1.0
    name [?]Workflow RO-Crate
    @typeCreativeWork
    version [?]1.0
    Items that reference this one
    conformsTo [?]
    +
    + +
    +


    +
    +

    ⬇️ Download: Hello World (Galaxy Workflow)

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    @idGalaxy-Workflow-Hello_World.ga
    name [?]Hello World (Galaxy Workflow)
    @type
      +
    • File
      • + +
    • SoftwareSourceCode
      • + +
    • ComputationalWorkflow
      • +
    author [?]Stian Soiland-Reyes
    creator [?]Stian Soiland-Reyes
    programmingLanguage [?]Galaxy
    input [?]
    output [?]
    Items that reference this one
    hasPart [?]./
    mainEntity [?]./
    instrument [?]Galaxy workflow run 5a5970ab-4375-444d-9a87-a764a66e3a47
    +
    + +
    +


    +
    +

    ⬇️ Download: inputs/abcdef.txt

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    @idinputs/abcdef.txt
    @typeFile
    description [?]Example input, a simple text file
    encodingFormat [?]text/plain
    exampleOfWork [?]simple_input
    Items that reference this one
    hasPart [?]./
    workExample [?]simple_input
    object [?]Galaxy workflow run 5a5970ab-4375-444d-9a87-a764a66e3a47
    +
    + +
    +


    +
    +

    ⬇️ Download: Select_first_on_data_1_2 (output)

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    @idoutputs/Select_first_on_data_1_2.txt
    name [?]Select_first_on_data_1_2 (output)
    @typeFile
    description [?]Example output of the last (aka first of reversed) lines
    encodingFormat [?]text/plain
    exampleOfWork [?]last_lines
    Items that reference this one
    hasPart [?]./
    workExample [?]last_lines
    result [?]Galaxy workflow run 5a5970ab-4375-444d-9a87-a764a66e3a47
    +
    + +
    +


    +
    +

    ⬇️ Download: tac_on_data_360_1 (output)

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    @idoutputs/tac_on_data_360_1.txt
    name [?]tac_on_data_360_1 (output)
    @typeFile
    description [?]Example output of the reversed lines
    encodingFormat [?]text/plain
    exampleOfWork [?]reversed
    Items that reference this one
    hasPart [?]./
    workExample [?]reversed
    result [?]Galaxy workflow run 5a5970ab-4375-444d-9a87-a764a66e3a47
    +
    + +
    +




    +
    +

    Galaxy workflow run 5a5970ab-4375-444d-9a87-a764a66e3a47

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    @id#wfrun-5a5970ab-4375-444d-9a87-a764a66e3a47
    name [?]Galaxy workflow run 5a5970ab-4375-444d-9a87-a764a66e3a47
    @typeCreateAction
    endTime [?]2018-09-19T17:01:07+10:00
    instrument [?]Hello World (Galaxy Workflow)
    subjectOf [?]Workflow Execution Summary of Hello World
    object [?]
    result [?]
    Items that reference this one
    mentions [?]./
    +
    + +
    +


    +
    + + + + + + + diff --git a/docs/profiles/0.5/workflow_run_crate/index.md b/docs/profiles/0.5/workflow_run_crate/index.md new file mode 100644 index 0000000..baa1306 --- /dev/null +++ b/docs/profiles/0.5/workflow_run_crate/index.md @@ -0,0 +1,354 @@ +--- +title: Workflow Run Crate +--- + + +# Workflow Run Crate + +* Version: 0.5 +* Permalink: +* Authors: [Workflow Run RO-Crate working group](https://www.researchobject.org/workflow-run-crate/#community) +* License: [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0) (SPDX: [`Apache-2.0`](http://spdx.org/licenses/Apache-2.0)) +* Example conforming crate: [ro-crate-metadata.json](example2/ro-crate-metadata.json) [ro-crate-preview.html](example2/ro-crate-preview.html) +* Profile Crate: [ro-crate-metadata.json](ro-crate-metadata.json) [ro-crate-preview.html](ro-crate-preview.html) +* Extends: + - [Process Run Crate](https://w3id.org/ro/wfrun/process/0.5) + - [Workflow RO-Crate](https://w3id.org/workflowhub/workflow-ro-crate/) +* JSON-LD context: +* Vocabulary terms: + +This profile uses terminology from the [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1). + + +## 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)). + +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. + +Workflows can have multiple input and output parameter slots that have to be mapped to actual files, directories or other values (e.g., a string or a number) before they can be executed. It is OPTIONAL to define such entities for a `ComputationalWorkflow`. If included, parameter definitions MUST be provided as [FormalParameter](https://bioschemas.org/types/FormalParameter/1.0-RELEASE) entities and referenced from the `ComputationalWorkflow` via `input` and `output` (see the [Bioschemas ComputationalWorkflow profile](https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE)). + +A data entity or `PropertyValue` that realizes a `FormalParameter` definition SHOULD refer to it via [exampleOfWork](https://schema.org/exampleOfWork); additionally, if the data entity or `PropertyValue` is an illustrative example of the parameter, the latter MAY refer back to the former using the reverse property [workExample](https://schema.org/workExample). This links the `input` of a `ComputationalWorkflow` to the `object` of a `CreateAction`, and the `output` of a `ComputationalWorkflow` to the `result` of a `CreateAction`. An `object` item that does not match a slot in the workflow's input interface (e.g., a [configuration file](../process_run_crate#referencing-configuration-files) read from a predefined path) MUST NOT refer to a `FormalParameter` of the `ComputationalWorkflow` via `exampleOfWork`. A `FormalParameter` that maps to a `PropertyValue` SHOULD have a subclass of [DataType](https://schema.org/DataType) (e.g., [Integer](https://schema.org/Integer)) — or [PropertyValue](https://schema.org/PropertyValue), in the case of dictionary-like structured types — as its `additionalType`. See [CWL parameter mapping](/workflow-run-crate/cwl_param_mapping) for an example. To support reproducibility, the `name` field of a `FormalParameter` instance SHOULD match the name of the corresponding workflow parameter slot. + +Additional properties described in the [Bioschemas FormalParameter profile](https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE) (e.g., `defaultValue`) MAY be used to provide additional information, but strict conformance is not required. A `FormalParameter` definition that strictly conforms to the Bioschemas profile SHOULD reference the relevant versioned URL via `conformsTo`. + +The following diagram shows the relationships between 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). + +Entity-relationship diagram + + +## Example Metadata File (`ro-crate-metadata.json`) + +* [ro-crate-metadata.json](example2/ro-crate-metadata.json) +* [ro-crate-preview.html](example2/ro-crate-preview.html) + + + +```json +{ "@context": [ + "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/terms/workflow-run/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"}, + {"@id": "outputs/Select_first_on_data_1_2.txt"}, + {"@id": "outputs/tac_on_data_360_1.txt"} + ], + "license": {"@id": "http://spdx.org/licenses/CC0-1.0"}, + "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"], + "name": "Hello World (Galaxy Workflow)", + "author": {"@id": "https://orcid.org/0000-0001-9842-9718"}, + "creator": {"@id": "https://orcid.org/0000-0001-9842-9718"}, + "programmingLanguage": {"@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy"}, + "input": [ + {"@id": "#simple_input"}, + {"@id": "#verbose-param"} + ], + "output": [ + {"@id": "#reversed"}, + {"@id": "#last_lines"} + ] + }, + { + "@id": "#simple_input", + "@type": "FormalParameter", + "additionalType": "File", + "conformsTo": {"@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"}, + "description": "A simple set of lines in a text file", + "encodingFormat": [ + "text/plain", + {"@id": "http://edamontology.org/format_2330"} + ], + "workExample": {"@id": "inputs/abcdef.txt"}, + "name": "simple_input", + "valueRequired": "True" + }, + { + "@id": "#verbose-param", + "@type": "FormalParameter", + "additionalType": "Boolean", + "conformsTo": {"@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"}, + "description": "Increase logging output", + "workExample": {"@id": "#verbose-pv"}, + "name": "verbose", + "valueRequired": "False" + }, + { + "@id": "#reversed", + "@type": "FormalParameter", + "additionalType": "File", + "conformsTo": {"@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"}, + "description": "All the lines, reversed", + "encodingFormat": [ + "text/plain", + {"@id": "http://edamontology.org/format_2330"} + ], + "name": "reversed", + "workExample": {"@id": "outputs/tac_on_data_360_1.txt"} + }, + { + "@id": "#last_lines", + "@type": "FormalParameter", + "additionalType": "File", + "conformsTo": {"@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"}, + "description": "The last lines of workflow input are the first lines of the reversed input", + "encodingFormat": [ + "text/plain", + {"@id": "http://edamontology.org/format_2330"} + ], + "name": "last_lines", + "workExample": {"@id": "outputs/Select_first_on_data_1_2.txt"} + }, + { + "@id": "https://orcid.org/0000-0001-9842-9718", + "@type": "Person", + "name": "Stian Soiland-Reyes" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy", + "@type": "ComputerLanguage", + "identifier": "https://galaxyproject.org/", + "name": "Galaxy", + "url": "https://galaxyproject.org/" + }, + { + "@id": "#wfrun-5a5970ab-4375-444d-9a87-a764a66e3a47", + "@type": "CreateAction", + "name": "Galaxy workflow run 5a5970ab-4375-444d-9a87-a764a66e3a47", + "endTime": "2018-09-19T17:01:07+10:00", + "instrument": {"@id": "Galaxy-Workflow-Hello_World.ga"}, + "subjectOf": {"@id": "https://usegalaxy.eu/u/5dbf7f05329e49c98b31243b5f35045c/p/invocation-report-a3a1d27edb703e5c"}, + "object": [ + {"@id": "inputs/abcdef.txt"}, + {"@id": "#verbose-pv"} + ], + "result": [ + {"@id": "outputs/Select_first_on_data_1_2.txt"}, + {"@id": "outputs/tac_on_data_360_1.txt"} + ] + }, + { + "@id": "inputs/abcdef.txt", + "@type": "File", + "description": "Example input, a simple text file", + "encodingFormat": "text/plain", + "exampleOfWork": {"@id": "#simple_input"} + }, + { + "@id": "#verbose-pv", + "@type": "PropertyValue", + "exampleOfWork": {"@id": "#verbose-param"}, + "name": "verbose", + "value": "True" + }, + { + "@id": "outputs/Select_first_on_data_1_2.txt", + "@type": "File", + "name": "Select_first_on_data_1_2 (output)", + "description": "Example output of the last (aka first of reversed) lines", + "encodingFormat": "text/plain", + "exampleOfWork": {"@id": "#last_lines"} + }, + { + "@id": "outputs/tac_on_data_360_1.txt", + "@type": "File", + "name": "tac_on_data_360_1 (output)", + "description": "Example output of the reversed lines", + "encodingFormat": "text/plain", + "exampleOfWork": {"@id": "#reversed"} + }, + { + "@id": "https://usegalaxy.eu/u/5dbf7f05329e49c98b31243b5f35045c/p/invocation-report-a3a1d27edb703e5c", + "@type": "CreativeWork", + "encodingFormat": "text/html", + "datePublished": "2021-11-18T02:02:00Z", + "name": "Workflow Execution Summary of Hello World" + } +] +} +``` + + +## Adding engine-specific traces + +Some engines are able to generate contextual information about workflow runs in the form of logs, reports, etc. These are not workflow outputs, but rather additional files automatically generated by the engine, either by default or when activated via a configuration parameter or command line flag. It is RECOMMENDED to add any such files to the RO-Crate; the corresponding entities SHOULD refer to the relevant `Action` instance via [about](http://schema.org/about): + +```json +{ + "@id": "#action-1", + "@type": "CreateAction", + ... +}, +{ + "@id": "trace-20230120-40360336.txt", + "@type": "File", + "name": "Nextflow trace for action-1", + "conformsTo": "https://www.nextflow.io/docs/latest/tracing.html#trace-report", + "encodingFormat": "text/tab-separated-values", + "about": "#action-1" +}, +{ + "@id": "https://www.nextflow.io/docs/latest/tracing.html#trace-report", + "@type": "CreativeWork", + "name": "Nextflow trace report CSV profile" +} +``` + + +## Environment variables as formal parameters + +The Process Run Crate profile specifies how to [represent environment variable settings](../process_run_crate#representing-environment-variable-settings) that affected the execution of a particular action via `environment`. A workflow, in turn, MAY indicate that it is affected by a certain environment variable by using the same `environment` property and having it point to a `FormalParameter` whose `name` is equal to the variable's name. If an action corresponding to an execution of the workflow sets that variable, the `PropertyValue` SHOULD point to the `FormalParameter` via `exampleOfWork`: + +```json +{ + "@id": "run_blast.cwl", + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], + ... + "environment": [ + {"@id": "run_blast.cwl#batch_size"} + ] +}, +{ + "@id": "run_blast.cwl#batch_size", + "@type": "FormalParameter", + "additionalType": "Integer", + "name": "BATCH_SIZE", +}, +{ + "@id": "#cb04c897-eb92-4c53-8a38-bcc1a16fd650", + "@type": "CreateAction", + "instrument": {"@id": "run_blast.cwl"}, + ... + "environment": [ + {"@id": "#batch_size-pv"} + ] +}, +{ + "@id": "#batch_size-pv", + "@type": "PropertyValue", + "exampleOfWork": {"@id": "run_blast.cwl#batch_size"}, + "name": "BATCH_SIZE", + "value": "100" +} +``` + + +## Requirements + +This profile inherits the requirements of [Process Run Crate](../process_run_crate) and [Workflow RO-Crate](https://w3id.org/workflowhub/workflow-ro-crate/). Additional specifications are listed below. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    PropertyRequired?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.
    PropertyValue or data entity that realizes a FormalParameter
    exampleOfWorkSHOULDIdentifier of the FormalParameter instance realized by this entity.
    FormalParameter
    nameSHOULDSHOULD match the name of the corresponding workflow parameter slot, e.g. n_lines
    descriptionMAYA description of the parameter's purpose, e.g. Number of lines
    workExampleMAYIdentifier of the data entity or PropertyValue instance that realizes this parameter. The data entity or PropertyValue instance SHOULD refer to this parameter via exampleOfWork.
    additionalTypeMUSTSHOULD include: File, Dataset or Collection if it maps to a file, directory or multi-file dataset, respectively; PropertyValue if it maps to a dictionary-like structured value (e.g. a CWL record); DataType or one of its subtypes (e.g. Integer) if it maps to a non-structured value.
    diff --git a/docs/profiles/0.5/workflow_run_crate/ro-crate-metadata.json b/docs/profiles/0.5/workflow_run_crate/ro-crate-metadata.json new file mode 100644 index 0000000..db5ee6d --- /dev/null +++ b/docs/profiles/0.5/workflow_run_crate/ro-crate-metadata.json @@ -0,0 +1,705 @@ +{ "@context": + "https://w3id.org/ro/crate/1.2-DRAFT/context", + "@graph": [ + { + "@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"}, + "about": {"@id": "https://w3id.org/ro/wfrun/workflow/0.5"} + }, + { + "@id": "ro-crate-preview.html", + "@type": "CreativeWork", + "license": { "@id": "http://spdx.org/licenses/CC0-1.0" }, + "isBasedOn": {"@id": "ro-crate-metadata.json" }, + "name": "RO-Crate preview of the Workflow Run Crate profile", + "encodingFormat": "text/html", + "about": "https://w3id.org/ro/wfrun/workflow/0.5" + }, + { + "@id": "https://w3id.org/ro/wfrun/workflow/0.5", + "@type": ["Dataset","Profile"], + "isProfileOf": [ + {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"} + ], + "identifier": "https://w3id.org/ro/wfrun/workflow/0.5", + "name": "Workflow Run Crate profile", + "version": "0.5", + "license": { + "@id": "https://www.apache.org/licenses/LICENSE-2.0" + }, + "author": [ + {"@id": "https://www.researchobject.org/workflow-run-crate/"} + ], + "hasPart": [ + { "@id": "index.html" }, + { "@id": "example2/" }, + { "@id": "https://www.researchobject.org/workflow-run-crate-paper/mapping/" }, + { "@id": "https://w3id.org/ro/terms/workflow-run" }, + { "@id": "https://gxy.io/GTN:T00343" }, + { "@id": "https://pypi.org/project/runcrate/" }, + { "@id": "https://w3id.org/ro/wfrun/process/0.5" }, + { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" }, + { "@id": "http://schema.org/MediaObject" }, + { "@id": "http://schema.org/additionalType" }, + { "@id": "http://schema.org/CreateAction" }, + { "@id": "http://schema.org/exampleOfWork" }, + { "@id": "http://schema.org/instrument" }, + { "@id": "http://schema.org/name" }, + { "@id": "http://schema.org/object" }, + { "@id": "http://schema.org/PropertyValue" }, + { "@id": "http://schema.org/result" }, + { "@id": "http://schema.org/DataType" }, + { "@id": "http://schema.org/Integer" }, + { "@id": "http://schema.org/about" }, + { "@id": "http://schema.org/defaultValue" }, + { "@id": "http://schema.org/valueRequired" }, + { "@id": "https://bioschemas.org/FormalParameter" }, + { + "@id": "https://bioschemas.org/ComputationalWorkflow" + }, + { + "@id": "http://schema.org/defaultValue" + }, + { + "@id": "http://schema.org/valueRequired" + }, + { + "@id": "https://bioschemas.org/ComputationalWorkflow#input" + }, + { + "@id": "https://bioschemas.org/ComputationalWorkflow#output" + }, + { + "@id": "http://purl.org/dc/terms/conformsTo" + }, + { + "@id": "https://w3id.org/ro/terms/workflow-run#environment" + } + + ], + "hasResource": [ + { "@id": "#hasSpecification" }, + { "@id": "#hasConstraints" }, + { "@id": "#hasGuidance" }, + { "@id": "#hasExample" }, + { "@id": "#hasMappingToProv" }, + { "@id": "#shouldConformToWorkflowROCrate" }, + { "@id": "#shouldConformToProcessCrateProfile" } + ], + "citation": { "@id": "https://doi.org/10.48550/arXiv.2312.07852" } + }, + { + "@id": "https://www.researchobject.org/workflow-run-crate/", + "@type": "Project", + "name": "Workflow Run Crate task force", + "member": [ + + { "@id": "https://orcid.org/0000-0001-8271-5429"}, + { "@id": "https://orcid.org/0000-0003-4929-1219"}, + { "@id": "https://orcid.org/0000-0001-9842-9718"}, + { "@id": "https://orcid.org/0000-0002-5432-2748"}, + { "@id": "https://orcid.org/0000-0002-4806-5140"}, + { "@id": "https://orcid.org/0000-0003-3156-2105"}, + { "@id": "https://orcid.org/0000-0002-6190-122X"}, + { "@id": "https://orcid.org/0000-0003-0454-7145"}, + { "@id": "https://orcid.org/0000-0002-8940-4946"}, + { "@id": "https://orcid.org/0000-0003-0606-2512"}, + { "@id": "https://orcid.org/0000-0002-3468-0652"}, + { "@id": "https://orcid.org/0000-0002-2961-9670"}, + { "@id": "https://orcid.org/0000-0003-3986-0510"}, + { "@id": "https://orcid.org/0000-0002-0003-2024"}, + { "@id": "https://orcid.org/0000-0002-9464-6640"}, + { "@id": "https://orcid.org/0000-0001-5845-8880"}, + { "@id": "https://orcid.org/0000-0003-4894-4660"}, + { "@id": "https://orcid.org/0000-0002-4405-6802"}, + { "@id": "https://orcid.org/0000-0001-9290-2017"}, + { "@id": "https://orcid.org/0000-0003-0617-9219"}, + { "@id": "https://orcid.org/0000-0001-9228-2882"}, + { "@id": "https://orcid.org/0000-0003-3898-9451"}, + { "@id": "https://orcid.org/0000-0003-3777-5945"}, + { "@id": "https://orcid.org/0000-0003-2765-0049"}, + { "@id": "https://orcid.org/0000-0001-9818-9320"}, + { "@id": "https://orcid.org/0000-0002-8122-9522"}, + { "@id": "https://orcid.org/0000-0002-8330-4071"}, + { "@id": "https://orcid.org/0000-0003-4073-7456"}, + { "@id": "https://orcid.org/0000-0003-1361-7301"}, + { "@id": "https://orcid.org/0000-0002-5358-616X"}, + { "@id": "https://orcid.org/0000-0002-5477-287X"}, + { "@id": "https://orcid.org/0000-0001-8250-4074"}, + { "@id": "https://orcid.org/0000-0003-0902-0086"}, + { "@id": "https://orcid.org/0000-0001-8172-8981"}, + { "@id": "https://orcid.org/0000-0001-6740-9212"}, + { "@id": "https://orcid.org/0000-0001-5411-356X"}, + { "@id": "https://orcid.org/0000-0003-0035-0951"}, + { "@id": "https://orcid.org/0000-0003-0711-5196"} + ], + "parentOrganization": { "@id": "https://www.researchobject.org/ro-crate/community" } + }, + { + "@id": "https://www.researchobject.org/ro-crate/community", + "@type": "Project", + "name": "RO-Crate Community" + }, + { + "@id": "https://w3id.org/ro/wfrun/process/0.5", + "@type": ["CreativeWork", "Profile"], + "name": "Process Run Crate profile", + "version": "0.5" +}, +{ + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0", + "@type": ["CreativeWork", "Profile"], + "name": "Workflow RO-Crate profile", + "version": "1.0" +}, + { + "@id": "index.html", + "@type": "File", + "name": "Workflow Run Crate (HTML)", + "encodingFormat": [ + "text/html", + {"@id": "https://www.nationalarchives.gov.uk/PRONOM/fmt/471"} + ] + }, + { + "@id": "index.html#requirements", + "@type": "WebPageElement", + "name": "Workflow Run Crate requirements" + }, + { + "@id": "example2/", + "@type": "Dataset", + "name": "Example Workflow Run Crate", + "conformsTo": [ + { "@id": "https://w3id.org/ro/crate"}, + { "@id": "https://w3id.org/ro/wfrun/process/0.4" }, + { "@id": "https://w3id.org/ro/wfrun/workflow/0.4" }, + { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" } + ], + "subjectOf": [ + { "@id": "example2/ro-crate-metadata.json" }, + { "@id": "example2/ro-crate-preview.html" } + ] + }, + { + "@id": "example2/ro-crate-metadata.json", + "@type": "CreativeWork", + "encodingFormat": "application/ld+json" + }, + { + "@id": "example2/ro-crate-preview.html", + "@type": "CreativeWork", + "encodingFormat": "text/html" + }, + { + "@id": "https://w3id.org/ro/terms/workflow-run", + "@type": "File", + "name": "JSON-LD context for workflow-run terms", + "contentUrl": "https://www.researchobject.org/ro-terms/workflow-run/context.json", + "conformsTo": { + "@id": "http://www.w3.org/ns/json-ld#Context" + }, + "encodingFormat": "application/ld+json", + "license": { + "@id": "https://creativecommons.org/publicdomain/zero/1.0/" + } + }, + { + "@id": "#hasSpecification", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/specification" }, + "hasArtifact": {"@id": "index.html"} + }, + { + "@id": "#hasConstraints", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/constraints" }, + "hasArtifact": {"@id": "index.html#requirements"} + }, + { + "@id": "#hasGuidance", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/guidance" }, + "hasArtifact": {"@id": "https://gxy.io/GTN:T00343"} + }, + { + "@id": "#hasExample", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/example" }, + "hasArtifact": { "@id": "example2/" } + }, + { + "@id": "#hasMappingToProv", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/mapping" }, + "hasArtifact": { "@id": "https://www.researchobject.org/workflow-run-crate-paper/mapping/" } + }, + { + "@id": "https://www.researchobject.org/workflow-run-crate-paper/mapping/", + "@type": "Dataset", + "name": "SSSOM mapping from PROV to Workflow Run Crate", + "isPartOf": { + "@id": "https://w3id.org/ro/doi/10.5281/zenodo.10368989" + } + }, + { + "@id": "https://w3id.org/ro/doi/10.5281/zenodo.10368989", + "@type": "Dataset", + "name": "Recording provenance of workflow runs with RO-Crate (RO-Crate and mapping)", + "conformsTo": { "@id": "https://w3id.org/ro/crate" }, + "subjectOf": [ + { "@id": "https://www.researchobject.org/workflow-run-crate-paper/ro-crate-metadata.jsonld" }, + { "@id": "https://www.researchobject.org/workflow-run-crate-paper/ro-crate-preview.html" } + ] + }, + { + "@id": "https://www.researchobject.org/workflow-run-crate-paper/ro-crate-metadata.jsonld", + "@type": "CreativeWork", + "encodingFormat": "application/ld+json" + }, + { + "@id": "https://www.researchobject.org/workflow-run-crate-paper/ro-crate-preview.html", + "@type": "CreativeWork", + "encodingFormat": "text/html" + }, + { + "@id": "#shouldConformToWorkflowROCrate", + "@type": "ResourceDescriptor", + "name": "SHOULD conform to Workflow RO-Crate profile", + "hasRole": { "@id": "http://purl.org/dc/terms/conformsTo" }, + "hasArtifact": {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"} +}, +{ + "@id": "#shouldConformToProcessCrateProfile", + "@type": "ResourceDescriptor", + "name": "SHOULD conform to Process Crate profile", + "hasRole": { "@id": "http://purl.org/dc/terms/conformsTo" }, + "hasArtifact": {"@id": "https://w3id.org/ro/wfrun/process/0.5"} +}, + { + "@id": "https://gxy.io/GTN:T00343", + "@type": "LearningResource", + "name": "Workflow Run RO-Crate Introduction", + "author": { + "@id": "https://orcid.org/0000-0001-8271-5429" + } + }, + { "@id": "https://doi.org/10.48550/arXiv.2312.07852", + "@type": "ScholarlyArticle", + "name": "Recording provenance of workflow runs with RO-Crate", + "author": [ + { + "@id": "https://orcid.org/0000-0001-8271-5429" + }, + { + "@id": "https://orcid.org/0000-0002-2961-9670" + }, + { + "@id": "https://orcid.org/0000-0003-4929-1219" + }, + { + "@id": "https://orcid.org/0000-0003-0606-2512" + }, + { + "@id": "https://orcid.org/0000-0002-3468-0652" + }, + { + "@id": "https://orcid.org/0000-0002-8940-4946" + }, + { + "@id": "https://orcid.org/0000-0002-0003-2024" + }, + { + "@id": "https://orcid.org/0000-0002-4663-5613" + }, + { + "@id": "https://orcid.org/0000-0003-0454-7145" + }, + { + "@id": "https://orcid.org/0000-0002-4806-5140" + }, + { + "@id": "https://orcid.org/0000-0001-9290-2017" + }, + { + "@id": "https://orcid.org/0000-0002-1119-1792" + }, + { + "@id": "https://orcid.org/0000-0003-3777-5945" + }, + { + "@id": "https://orcid.org/0000-0003-2765-0049" + }, + { + "@id": "https://orcid.org/0000-0002-0309-604X" + }, + { + "@id": "https://orcid.org/0000-0003-0902-0086" + }, + { + "@id": "https://orcid.org/0000-0001-8250-4074" + }, + { + "@id": "https://orcid.org/0000-0001-9842-9718" + } + ], + + "creditText": "Simone Leo, et al. (2024): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852" + }, + { + "@id": "https://w3id.org/ro/terms/workflow-run#", + "@type": "DefinedTermSet", + "name": "Namespace for Workflow Run RO-Crate model" + }, + { + "@id": "https://pypi.org/project/runcrate/", + "@type": "SoftwareApplication", + "name": "runcrate", + "version": "0.5.0", + "url": "https://pypi.org/project/runcrate/" + }, + { + "@id": "http://schema.org/MediaObject", + "@type": "DefinedTerm", + "name": "MediaObject", + "termCode": "File" + }, + +{ + "@id": "http://schema.org/additionalType", + "@type": "DefinedTerm", + "name": "additionalType" +}, +{ + "@id": "http://schema.org/CreateAction", + "@type": "DefinedTerm", + "name": "CreateAction" +}, +{ + "@id": "http://schema.org/exampleOfWork", + "@type": "DefinedTerm", + "name": "exampleOfWork" +}, +{ + "@id": "http://schema.org/instrument", + "@type": "DefinedTerm", + "name": "instrument" +}, +{ + "@id": "http://schema.org/name", + "@type": "DefinedTerm", + "name": "name" +}, +{ + "@id": "http://schema.org/object", + "@type": "DefinedTerm", + "name": "object" +}, +{ + "@id": "http://schema.org/PropertyValue", + "@type": "DefinedTerm", + "name": "PropertyValue" +}, +{ + "@id": "http://schema.org/result", + "@type": "DefinedTerm", + "name": "result" +}, +{ + "@id": "http://schema.org/DataType", + "@type": "DefinedTerm", + "name": "DataType" +}, +{ + "@id": "http://schema.org/Integer", + "@type": "DefinedTerm", + "name": "Integer" +}, +{ + "@id": "http://schema.org/about", + "@type": "DefinedTerm", + "name": "about" +}, + { + "@id": "https://bioschemas.org/FormalParameter", + "@type": "DefinedTerm", + "name": "FormalParameter" + }, + { + "@id": "https://bioschemas.org/ComputationalWorkflow", + "@type": "DefinedTerm", + "name": "ComputationalWorkflow" + }, + { + "@id": "http://schema.org/defaultValue", + "@type": "DefinedTerm", + "name": "defaultValue" + }, + { + "@id": "http://schema.org/valueRequired", + "@type": "DefinedTerm", + "name": "valueRequired" + }, + { + "@id": "https://bioschemas.org/ComputationalWorkflow#input", + "@type": "DefinedTerm", + "termCode": "input", + "name": "input" + }, + { + "@id": "https://bioschemas.org/ComputationalWorkflow#output", + "@type": "DefinedTerm", + "name": "output", + "termCode": "output" + }, +{ + "@id": "http://purl.org/dc/terms/conformsTo", + "@type": "DefinedTerm", + "name": "conformsTo", + "termCode": "conformsTo" +}, +{ + "@id": "https://w3id.org/ro/terms/workflow-run#environment", + "@type": "DefinedTerm", + "termCode": "environment", + "name": "environment" +}, + +{ + "@id": "https://orcid.org/0000-0001-8271-5429", + "@type": "Person", + "name": "Simone Leo" +}, +{ + "@id": "https://orcid.org/0000-0003-4929-1219", + "@type": "Person", + "name": "Laura Rodríguez-Navas" +}, +{ + "@id": "https://orcid.org/0000-0001-9842-9718", + "@type": "Person", + "name": "Stian Soiland-Reyes" +}, +{ + "@id": "https://orcid.org/0000-0002-5432-2748", + "@type": "Person", + "name": "Paul Brack" +}, +{ + "@id": "https://orcid.org/0000-0002-4806-5140", + "@type": "Person", + "name": "José María Fernández" +}, +{ + "@id": "https://orcid.org/0000-0003-3156-2105", + "@type": "Person", + "name": "Alan R Williams" +}, +{ + "@id": "https://orcid.org/0000-0002-6190-122X", + "@type": "Person", + "name": "Ignacio Eguinoa" +}, +{ + "@id": "https://orcid.org/0000-0003-0454-7145", + "@type": "Person", + "name": "Daniel Garijo" +}, +{ + "@id": "https://orcid.org/0000-0002-8940-4946", + "@type": "Person", + "name": "Paul De Geest" +}, +{ + "@id": "https://orcid.org/0000-0003-0606-2512", + "@type": "Person", + "name": "Raül Sirvent" +}, +{ + "@id": "https://orcid.org/0000-0002-3468-0652", + "@type": "Person", + "name": "Alexander Kanitz" +}, +{ + "@id": "https://orcid.org/0000-0002-2961-9670", + "@type": "Person", + "name": "Michael R Crusoe" +}, +{ + "@id": "https://orcid.org/0000-0003-3986-0510", + "@type": "Person", + "name": "LJ Garcia Castro" +}, +{ + "@id": "https://orcid.org/0000-0002-0003-2024", + "@type": "Person", + "name": "Rudolf Wittner" +}, +{ + "@id": "https://orcid.org/0000-0002-9464-6640", + "@type": "Person", + "name": "Wolfgang Maier" +}, +{ + "@id": "https://orcid.org/0000-0001-5845-8880", + "@type": "Person", + "name": "Sebastiaan Huber" +}, +{ + "@id": "https://orcid.org/0000-0003-4894-4660", + "@type": "Person", + "name": "Kevin Jablonka" +}, +{ + "@id": "https://orcid.org/0000-0002-4405-6802", + "@type": "Person", + "name": "Haris Zafeiropoulos" +}, +{ + "@id": "https://orcid.org/0000-0001-9290-2017", + "@type": "Person", + "name": "Iacopo Colonnelli" +}, +{ + "@id": "https://orcid.org/0000-0003-0617-9219", + "@type": "Person", + "name": "Jake Emerson" +}, +{ + "@id": "https://orcid.org/0000-0001-9228-2882", + "@type": "Person", + "name": "Abigail Miller" +}, +{ + "@id": "https://orcid.org/0000-0003-3898-9451", + "@type": "Person", + "name": "Stelios Ninidakis" +}, +{ + "@id": "https://orcid.org/0000-0003-3777-5945", + "@type": "Person", + "name": "Tazro Ohta" +}, +{ + "@id": "https://orcid.org/0000-0003-2765-0049", + "@type": "Person", + "name": "Hirotaka Suetake" +}, +{ + "@id": "https://orcid.org/0000-0001-9818-9320", + "@type": "Person", + "name": "Johannes Köster" +}, +{ + "@id": "https://orcid.org/0000-0002-8122-9522", + "@type": "Person", + "name": "Luiz Gadelha" +}, +{ + "@id": "https://orcid.org/0000-0002-8330-4071", + "@type": "Person", + "name": "Mahnoor Zulfiqar" +}, +{ + "@id": "https://orcid.org/0000-0003-4073-7456", + "@type": "Person", + "name": "Romain David" +}, +{ + "@id": "https://orcid.org/0000-0003-1361-7301", + "@type": "Person", + "name": "Maciek Bąk" +}, +{ + "@id": "https://orcid.org/0000-0002-5358-616X", + "@type": "Person", + "name": "Petr Holub" +}, +{ + "@id": "https://orcid.org/0000-0002-5477-287X", + "@type": "Person", + "name": "Milan Markovic" +}, +{ + "@id": "https://orcid.org/0000-0001-8250-4074", + "@type": "Person", + "name": "Bruno P. Kinoshita" +}, +{ + "@id": "https://orcid.org/0000-0003-0902-0086", + "@type": "Person", + "name": "Renske de Wit" +}, +{ + "@id": "https://orcid.org/0000-0001-8172-8981", + "@type": "Person", + "name": "Jasper Koehorst" +}, +{ + "@id": "https://orcid.org/0000-0001-6740-9212", + "@type": "Person", + "name": "Samuel Lampa" +}, +{ + "@id": "https://orcid.org/0000-0001-5411-356X", + "@type": "Person", + "name": "Samuel Grayson" +}, +{ + "@id": "https://orcid.org/0000-0003-0035-0951", + "@type": "Person", + "name": "Jörg F. Unger" +}, +{ + "@id": "https://orcid.org/0000-0003-0711-5196", + "@type": "Person", + "name": "Felix Bartusch" +}, +{ + "@id": "https://orcid.org/0000-0002-4663-5613", + "@type": "Person", + "name": "Luca Pireddu" +}, +{ + "@id": "https://orcid.org/0000-0002-1119-1792", + "@type": "Person", + "name": "Matej Gallo" +}, +{ + "@id": "https://orcid.org/0000-0002-0309-604X", + "@type": "Person", + "name": "Salvador Capella-Gutierrez" +}, +{ + "@id": "https://www.apache.org/licenses/LICENSE-2.0", + "@type": "CreativeWork", + "name": "Apache License 2.0", + "version": "2.0", + "identifier": { "@id": "http://spdx.org/licenses/Apache-2.0"} +}, +{ + "@id": "https://creativecommons.org/publicdomain/zero/1.0/", + "@type": "CreativeWork", + "identifier": { "@id": "http://spdx.org/licenses/CC0-1.0"}, + "name": "Creative Commons Zero v1.0 Universal", + "version": "1.0" +}, +{ + "@id": "http://spdx.org/licenses/Apache-2.0", + "@type": "PropertyValue", + "propertyID": "http://spdx.org/rdf/terms#licenseId", + "name": "spdx", + "value": "Apache-2.0" +}, +{ + "@id": "http://spdx.org/licenses/CC0-1.0", + "@type": "PropertyValue", + "propertyID": "http://spdx.org/rdf/terms#licenseId", + "name": "spdx", + "value": "CC0-1.0" +} + +] +} diff --git a/docs/profiles/0.5/workflow_run_crate/ro-crate-metadata.jsonld b/docs/profiles/0.5/workflow_run_crate/ro-crate-metadata.jsonld new file mode 120000 index 0000000..8024224 --- /dev/null +++ b/docs/profiles/0.5/workflow_run_crate/ro-crate-metadata.jsonld @@ -0,0 +1 @@ +ro-crate-metadata.json \ No newline at end of file diff --git a/docs/profiles/0.5/workflow_run_crate/ro-crate-preview.html b/docs/profiles/0.5/workflow_run_crate/ro-crate-preview.html new file mode 100644 index 0000000..2bce499 --- /dev/null +++ b/docs/profiles/0.5/workflow_run_crate/ro-crate-preview.html @@ -0,0 +1,2381 @@ + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    +

    +

    Workflow Run Crate profile

    + + +⬇️🏷️ Download all the metadata for Workflow Run Crate profile in JSON-LD format + + +
    + + +
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    +
    +

    Go to: Workflow Run Crate profile

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    +


    +
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    Go to: Workflow Run Crate task force

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    +




    +
    +

    Go to: Apache License 2.0

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + +
    @idhttps://www.apache.org/licenses/LICENSE-2.0
    name [?]Apache License 2.0
    @typeCreativeWork
    version [?]2.0
    identifier [?]spdx: Apache-2.0
    Items that reference this one
    license [?]Workflow Run Crate profile
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    + +
    +


    +
    +

    ⬇️ Download: Workflow Run Crate (HTML)

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + +
    @idindex.html
    name [?]Workflow Run Crate (HTML)
    @typeFile
    encodingFormat [?]
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
    hasArtifact [?]#hasSpecification
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    + +
    +


    +
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    Example Workflow Run Crate

    + + + + +
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    @idexample2/
    name [?]Example Workflow Run Crate
    @typeDataset
    conformsTo [?]
    subjectOf [?]
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
    hasArtifact [?]#hasExample
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    +
    +

    Go to: SSSOM mapping from PROV to Workflow Run Crate

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + +
    @idhttps://www.researchobject.org/workflow-run-crate-paper/mapping/
    name [?]SSSOM mapping from PROV to Workflow Run Crate
    @typeDataset
    isPartOf [?]Recording provenance of workflow runs with RO-Crate (RO-Crate and mapping)
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
    hasArtifact [?]#hasMappingToProv
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    + +
    +


    +
    +

    Go to: JSON-LD context for workflow-run terms

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    @idhttps://w3id.org/ro/terms/workflow-run
    name [?]JSON-LD context for workflow-run terms
    @typeFile
    encodingFormat [?]application/ld+json
    contentUrl [?]https://www.researchobject.org/ro-terms/workflow-run/context.json
    conformsTo [?]http://www.w3.org/ns/json-ld#Context
    license [?]Creative Commons Zero v1.0 Universal
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    + +
    +


    +
    +

    Go to: Workflow Run RO-Crate Introduction

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + +
    @idhttps://gxy.io/GTN:T00343
    name [?]Workflow Run RO-Crate Introduction
    @typeLearningResource
    author [?]Simone Leo
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
    hasArtifact [?]#hasGuidance
    +
    + +
    +


    +
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    Go to: runcrate

    + + + + +
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    @idhttps://pypi.org/project/runcrate/
    name [?]runcrate
    @typeSoftwareApplication
    version [?]0.5.0
    url [?]https://pypi.org/project/runcrate/
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    +
    +

    Go to: Process Run Crate profile

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    @idhttps://w3id.org/ro/wfrun/process/0.5
    name [?]Process Run Crate profile
    @type
      +
    • CreativeWork
      • + +
    • Profile
      • +
    version [?]0.5
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
    hasArtifact [?]SHOULD conform to Process Crate profile
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    Go to: Workflow RO-Crate profile

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    @idhttps://w3id.org/workflowhub/workflow-ro-crate/1.0
    name [?]Workflow RO-Crate profile
    @type
      +
    • CreativeWork
      • + +
    • Profile
      • +
    version [?]1.0
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
    conformsTo [?]Example Workflow Run Crate
    hasArtifact [?]SHOULD conform to Workflow RO-Crate profile
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    Go to: MediaObject

    + + + + +
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    @idhttp://schema.org/MediaObject
    name [?]MediaObject
    @typeDefinedTerm
    termCode [?]File
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
    +
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    Go to: additionalType

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    @idhttp://schema.org/additionalType
    name [?]additionalType
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: CreateAction

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    @idhttp://schema.org/CreateAction
    name [?]CreateAction
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: exampleOfWork

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    @idhttp://schema.org/exampleOfWork
    name [?]exampleOfWork
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    + +
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    Go to: instrument

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    @idhttp://schema.org/instrument
    name [?]instrument
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: name

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    @idhttp://schema.org/name
    name [?]name
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: object

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    @idhttp://schema.org/object
    name [?]object
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: PropertyValue

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    @idhttp://schema.org/PropertyValue
    name [?]PropertyValue
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: result

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    @idhttp://schema.org/result
    name [?]result
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: DataType

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    @idhttp://schema.org/DataType
    name [?]DataType
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: Integer

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    @idhttp://schema.org/Integer
    name [?]Integer
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: about

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    @idhttp://schema.org/about
    name [?]about
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: defaultValue

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    @idhttp://schema.org/defaultValue
    name [?]defaultValue
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: valueRequired

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    @idhttp://schema.org/valueRequired
    name [?]valueRequired
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: FormalParameter

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    @idhttps://bioschemas.org/FormalParameter
    name [?]FormalParameter
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: ComputationalWorkflow

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    @idhttps://bioschemas.org/ComputationalWorkflow
    name [?]ComputationalWorkflow
    @typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: input

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    @idhttps://bioschemas.org/ComputationalWorkflow#input
    name [?]input
    @typeDefinedTerm
    termCode [?]input
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: output

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    @idhttps://bioschemas.org/ComputationalWorkflow#output
    name [?]output
    @typeDefinedTerm
    termCode [?]output
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    Go to: conformsTo

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    @idhttp://purl.org/dc/terms/conformsTo
    name [?]conformsTo
    @typeDefinedTerm
    termCode [?]conformsTo
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
    hasRole [?]
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    Go to: environment

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    @idhttps://w3id.org/ro/terms/workflow-run#environment
    name [?]environment
    @typeDefinedTerm
    termCode [?]environment
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
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    #hasSpecification

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    @id#hasSpecification
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/specification
    hasArtifact [?]Workflow Run Crate (HTML)
    Items that reference this one
    hasResource [?]Workflow Run Crate profile
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    #hasConstraints

    + + + + +
    + + + + + + + + + + + + + + + + + + +
    @id#hasConstraints
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/constraints
    hasArtifact [?]Workflow Run Crate requirements
    Items that reference this one
    hasResource [?]Workflow Run Crate profile
    +
    + +
    +


    +
    +

    #hasGuidance

    + + + + +
    + + + + + + + + + + + + + + + + + + +
    @id#hasGuidance
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/guidance
    hasArtifact [?]Workflow Run RO-Crate Introduction
    Items that reference this one
    hasResource [?]Workflow Run Crate profile
    +
    + +
    +


    +
    +

    #hasExample

    + + + + +
    + + + + + + + + + + + + + + + + + + +
    @id#hasExample
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/example
    hasArtifact [?]Example Workflow Run Crate
    Items that reference this one
    hasResource [?]Workflow Run Crate profile
    +
    + +
    +


    +
    +

    #hasMappingToProv

    + + + + +
    + + + + + + + + + + + + + + + + + + +
    @id#hasMappingToProv
    @typeResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/mapping
    hasArtifact [?]SSSOM mapping from PROV to Workflow Run Crate
    Items that reference this one
    hasResource [?]Workflow Run Crate profile
    +
    + +
    +


    +
    +

    SHOULD conform to Workflow RO-Crate profile

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + +
    @id#shouldConformToWorkflowROCrate
    name [?]SHOULD conform to Workflow RO-Crate profile
    @typeResourceDescriptor
    hasRole [?]conformsTo
    hasArtifact [?]Workflow RO-Crate profile
    Items that reference this one
    hasResource [?]Workflow Run Crate profile
    +
    + +
    +


    +
    +

    SHOULD conform to Process Crate profile

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + +
    @id#shouldConformToProcessCrateProfile
    name [?]SHOULD conform to Process Crate profile
    @typeResourceDescriptor
    hasRole [?]conformsTo
    hasArtifact [?]Process Run Crate profile
    Items that reference this one
    hasResource [?]Workflow Run Crate profile
    +
    + +
    +


    +
    +

    Go to: Recording provenance of workflow runs with RO-Crate

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + +
    @idhttps://doi.org/10.48550/arXiv.2312.07852
    name [?]Recording provenance of workflow runs with RO-Crate
    @typeScholarlyArticle
    author [?]
    creditText [?]Simone Leo, et al. (2024): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852
    Items that reference this one
    citation [?]Workflow Run Crate profile
    +
    + +
    +


    +
    + + + + + + + From 4406772f7a8faa0379a5f212edc311ebaf7030c6 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Tue, 18 Jun 2024 10:53:54 +0100 Subject: [PATCH 4/8] set @base for next draft --- .../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 ++++-- 3 files changed, 12 insertions(+), 6 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 bbf68e1..563a81c 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 +1,7 @@ -{ "@context": - "https://w3id.org/ro/crate/1.2-DRAFT/context", +{ "@context": [ + "https://w3id.org/ro/crate/1.2-DRAFT/context", + { "@base": "https://www.researchobject.org/workflow-run-crate/profiles/0.6-DRAFT/process_run_crate/"} + ], "@graph": [ { "@id": "ro-crate-metadata.json", 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 f7feaaf..60cf82e 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 +1,7 @@ -{ "@context": - "https://w3id.org/ro/crate/1.2-DRAFT/context", +{ "@context": [ + "https://w3id.org/ro/crate/1.2-DRAFT/context", + { "@base": "https://www.researchobject.org/workflow-run-crate/profiles/0.6-DRAFT/provenance_run_crate/"} + ], "@graph": [ { "@id": "ro-crate-metadata.json", 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 6365434..330b0a2 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 +1,7 @@ -{ "@context": - "https://w3id.org/ro/crate/1.2-DRAFT/context", +{ "@context": [ + "https://w3id.org/ro/crate/1.2-DRAFT/context", + { "@base": "https://www.researchobject.org/workflow-run-crate/profiles/0.6-DRAFT/workflow_run_crate/"} + ], "@graph": [ { "@id": "ro-crate-metadata.json", From 3ec946734f25438f4002f94e16ae11148ce9a16d Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Tue, 18 Jun 2024 10:54:06 +0100 Subject: [PATCH 5/8] set @base so this works versionless --- docs/profiles/0.5/process_run_crate/ro-crate-metadata.json | 4 +++- .../0.5/provenance_run_crate/ro-crate-metadata.json | 6 ++++-- docs/profiles/0.5/workflow_run_crate/ro-crate-metadata.json | 6 ++++-- 3 files changed, 11 insertions(+), 5 deletions(-) diff --git a/docs/profiles/0.5/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.5/process_run_crate/ro-crate-metadata.json index 7f13945..8348a4f 100644 --- a/docs/profiles/0.5/process_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5/process_run_crate/ro-crate-metadata.json @@ -1,5 +1,7 @@ -{ "@context": +{ "@context": [ "https://w3id.org/ro/crate/1.2-DRAFT/context", + { "@base": "https://www.researchobject.org/workflow-run-crate/profiles/0.5/process_run_crate/"} + ], "@graph": [ { "@id": "ro-crate-metadata.json", diff --git a/docs/profiles/0.5/provenance_run_crate/ro-crate-metadata.json b/docs/profiles/0.5/provenance_run_crate/ro-crate-metadata.json index 239f4cd..4190a71 100644 --- a/docs/profiles/0.5/provenance_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5/provenance_run_crate/ro-crate-metadata.json @@ -1,5 +1,7 @@ -{ "@context": - "https://w3id.org/ro/crate/1.2-DRAFT/context", +{ "@context": [ + "https://w3id.org/ro/crate/1.2-DRAFT/context", + { "@base": "https://www.researchobject.org/workflow-run-crate/profiles/0.5/provenance_run_crate/"} + ], "@graph": [ { "@id": "ro-crate-metadata.json", diff --git a/docs/profiles/0.5/workflow_run_crate/ro-crate-metadata.json b/docs/profiles/0.5/workflow_run_crate/ro-crate-metadata.json index db5ee6d..6ef1598 100644 --- a/docs/profiles/0.5/workflow_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5/workflow_run_crate/ro-crate-metadata.json @@ -1,5 +1,7 @@ -{ "@context": - "https://w3id.org/ro/crate/1.2-DRAFT/context", +{ "@context": [ + "https://w3id.org/ro/crate/1.2-DRAFT/context", + { "@base": "https://www.researchobject.org/workflow-run-crate/profiles/0.5/workflow_run_crate/"} + ], "@graph": [ { "@id": "ro-crate-metadata.json", From 150be0e9edd61786ff4f4b1ad08d97e78f0f99df Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Tue, 18 Jun 2024 10:55:10 +0100 Subject: [PATCH 6/8] regenerate rocrate previews --- .../process_run_crate/ro-crate-preview.html | 639 ++++++++++-------- .../ro-crate-preview.html | 7 +- .../workflow_run_crate/ro-crate-preview.html | 7 +- .../process_run_crate/ro-crate-preview.html | 639 ++++++++++-------- .../ro-crate-preview.html | 7 +- .../workflow_run_crate/ro-crate-preview.html | 7 +- 6 files changed, 708 insertions(+), 598 deletions(-) diff --git a/docs/profiles/0.5/process_run_crate/ro-crate-preview.html b/docs/profiles/0.5/process_run_crate/ro-crate-preview.html index e270d95..657cfec 100644 --- a/docs/profiles/0.5/process_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5/process_run_crate/ro-crate-preview.html @@ -7,7 +7,10 @@