From c20190407abdccbd50919b7b3bb2efcf7155b3e2 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Thu, 16 May 2024 21:16:18 +0100 Subject: [PATCH 01/27] draft of ro-crate profile crate --- .../index.md} | 7 +- .../process_run_crate/ro-crate-metadata.json | 535 ++++++++ .../process_run_crate/ro-crate-preview.html | 1171 +++++++++++++++++ 3 files changed, 1710 insertions(+), 3 deletions(-) rename docs/profiles/0.5-DRAFT/{process_run_crate.md => process_run_crate/index.md} (98%) create mode 100644 docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json create mode 100644 docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html diff --git a/docs/profiles/0.5-DRAFT/process_run_crate.md b/docs/profiles/0.5-DRAFT/process_run_crate/index.md similarity index 98% rename from docs/profiles/0.5-DRAFT/process_run_crate.md rename to docs/profiles/0.5-DRAFT/process_run_crate/index.md index 9c53b29..e252ac7 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate.md +++ b/docs/profiles/0.5-DRAFT/process_run_crate/index.md @@ -8,6 +8,7 @@ title: Process Run Crate * Version: 0.5-DRAFT * Permalink: * Authors: Workflow Run RO-Crate working group +* Profile Crate: [ro-crate-metadata.json](ro-crate-metadata.json) [ro-crate-preview.html](ro-crate-preview.html) 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/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. @@ -22,7 +23,7 @@ This profile requires the indication of [Software used to create files](https:// 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 +Entity-relationship diagram ## Example Metadata File (`ro-crate-metadata.json`) @@ -236,7 +237,7 @@ Data entities involved in an application's input and output SHOULD have an `@id` 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 +Multiple processes diagram ## Referencing configuration files @@ -254,7 +255,7 @@ Some applications support the modification of their behavior via configuration f "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"} }, diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json new file mode 100644 index 0000000..dfcbbe3 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json @@ -0,0 +1,535 @@ +{ "@context": + "https://w3id.org/ro/crate/1.2-DRAFT/context", + "@graph": [ + + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "conformsTo": {"@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/0.5-DRAFT", + "@type": ["Dataset","Profile"], + "isProfileOf": [ + {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"} + ], + "identifier": "https://w3id.org/ro/wfrun/process/0.5-DRAFT", + "name": "Process Run Crate profile", + "version": "0.5-DRAFT", + "includedInDataCatalog": { "@id": "https://w3id.org/ro/wfrun" }, + "author": [ + {"@id": "https://researchobject.org/workflow-run-crate/"} + ], + "hasPart": [ + { "@id": "index.html" }, + { "@id": "https://w3id.org/ro/terms/workflow-run#" } + ], + "hasResource": [ + { "@id": "#hasSpecification" }, + { "@id": "#hasVocabulary" } + ], + "citation": { "@id": "https://doi.org/10.48550/arXiv.2312.07852" } + }, + { + "@id": 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"name": "Recording provenance of workflow runs with RO-Crate", + "creditText": "Simone Leo, Michael R. 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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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@idhttps://w3id.org/ro/wfrun/process/0.5-DRAFT
name [?]Process Run Crate profile
@type
    +
  • Dataset
    • + +
  • Profile
    • +
author [?]Workflow Run Crate task force
isProfileOf [?]https://w3id.org/ro/crate/1.2-DRAFT
identifier [?]https://w3id.org/ro/wfrun/process/0.5-DRAFT
version [?]0.5-DRAFT
includedInDataCatalog [?]https://w3id.org/ro/wfrun
hasPart [?]
hasResource [?]
citation [?]Recording provenance of workflow runs with RO-Crate
Items that reference this one
about [?]ro-crate-metadata.json
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+ +
+


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Go to: Workflow Run Crate task force

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+






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+

⬇️ Download: Process Run Crate (HTML)

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@idindex.html
name [?]Process Run Crate (HTML)
@typeFile
encodingFormat [?]text/html
Items that reference this one
hasPart [?]Process Run Crate profile
hasArtifact [?]#hasSpecification
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Go to: Namespace for Common Provenance Model RO-Crate model

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@idhttps://w3id.org/ro/terms/workflow-run#
name [?]Namespace for Common Provenance Model RO-Crate model
@typeDefinedTermSet
hasDefinedTerm [?]
Items that reference this one
hasPart [?]Process Run Crate profile
hasArtifact [?]#hasVocabulary
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#hasSpecification

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@id#hasSpecification
name [?]
@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
+
+ +
+


+
+

#hasVocabulary

+ + + + +
+ + + + + + + + + + + + + + + + + + +
@id#hasVocabulary
@typeResourceDescriptor
hasRole [?]http://www.w3.org/ns/dx/prof/role/vocabulary
hasArtifact [?]Namespace for Common Provenance Model RO-Crate model
Items that reference this one
hasResource [?]Process 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
creditText [?]Simone Leo, Michael R. Crusoe, Laura Rodríguez-Navas, Raül Sirvent, Alexander Kanitz, Paul De Geest, Rudolf Wittner, Luca Pireddu, Daniel Garijo, José M. Fernández, Iacopo Colonnelli, Matej Gallo, Tazro Ohta, Hirotaka Suetake, Salvador Capella-Gutierrez, Renske de Wit, Bruno de Paula Kinoshita, Stian Soiland-Reyes (2024): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852
Items that reference this one
citation [?]Process Run Crate profile
+
+ +
+


+
+ + + + + + + From 1dd4760b5e89ccc8425f9c1bceaf7a186a20f3bb Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Thu, 16 May 2024 22:42:47 +0100 Subject: [PATCH 02/27] pretty much matches ro-crate profile crate specs --- .../process_run_crate/ro-crate-metadata.json | 191 +++++++- .../process_run_crate/ro-crate-preview.html | 450 +++++++++++++++++- 2 files changed, 613 insertions(+), 28 deletions(-) diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json index dfcbbe3..0e4638c 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json @@ -5,9 +5,19 @@ { "@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-DRAFT"} }, + { + "@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-DRAFT" + }, { "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT", "@type": ["Dataset","Profile"], @@ -17,22 +27,29 @@ "identifier": "https://w3id.org/ro/wfrun/process/0.5-DRAFT", "name": "Process Run Crate profile", "version": "0.5-DRAFT", - "includedInDataCatalog": { "@id": "https://w3id.org/ro/wfrun" }, + "license": { + "@id": "https://www.apache.org/licenses/LICENSE-2.0" + }, "author": [ - {"@id": "https://researchobject.org/workflow-run-crate/"} + {"@id": "https://www.researchobject.org/workflow-run-crate/"} ], "hasPart": [ { "@id": "index.html" }, - { "@id": "https://w3id.org/ro/terms/workflow-run#" } + { "@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/" } ], "hasResource": [ { "@id": "#hasSpecification" }, - { "@id": "#hasVocabulary" } + { "@id": "#hasConstraints" }, + { "@id": "#hasVocabulary" }, + { "@id": "#hasGuidance" } ], "citation": { "@id": "https://doi.org/10.48550/arXiv.2312.07852" } }, { - "@id": "https://researchobject.org/workflow-run-crate/", + "@id": "https://www.researchobject.org/workflow-run-crate/", "@type": "Project", "name": "Workflow Run Crate task force", "member": [ @@ -87,25 +104,130 @@ "@id": "index.html", "@type": "File", "name": "Process Run Crate (HTML)", - "encodingFormat": "text/html" + "encodingFormat": [ + "text/html", + {"@id": "https://www.nationalarchives.gov.uk/PRONOM/fmt/471"} + ] + }, + { + "@id": "index.html#requirements", + "@type": "WebPageElement", + "name": "Process Run Crate requirements" }, + { + "@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", - "name": "", "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": "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", - "creditText": "Simone Leo, Michael R. Crusoe, Laura Rodríguez-Navas, Raül Sirvent, Alexander Kanitz, Paul De Geest, Rudolf Wittner, Luca Pireddu, Daniel Garijo, José M. Fernández, Iacopo Colonnelli, Matej Gallo, Tazro Ohta, Hirotaka Suetake, Salvador Capella-Gutierrez, Renske de Wit, Bruno de Paula Kinoshita, Stian Soiland-Reyes (2024): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852" + "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#", @@ -313,7 +435,14 @@ "rangeIncludes": [ {"@id": "http://schema.org/Text"} ] - }, + }, + { + "@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", @@ -529,7 +658,51 @@ "@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-DRAFT/process_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html index 2e0018c..136fb45 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html @@ -11,6 +11,9 @@ { "@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" }, @@ -18,6 +21,13 @@ "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" } }, + { + "@id": "http://spdx.org/licenses/CC0-1.0", + "@type": "PropertyValue", + "propertyID": "http://spdx.org/rdf/terms#licenseId", + "name": "spdx", + "value": "CC0-1.0" + }, { "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT", "@type": [ @@ -30,11 +40,11 @@ "identifier": "https://w3id.org/ro/wfrun/process/0.5-DRAFT", "name": "Process Run Crate profile", "version": "0.5-DRAFT", - "includedInDataCatalog": { - "@id": "https://w3id.org/ro/wfrun" + "license": { + "@id": "https://www.apache.org/licenses/LICENSE-2.0" }, "author": { - "@id": "https://researchobject.org/workflow-run-crate/" + "@id": "https://www.researchobject.org/workflow-run-crate/" }, "hasPart": [ { @@ -42,14 +52,26 @@ }, { "@id": "https://w3id.org/ro/terms/workflow-run#" + }, + { + "@id": "https://w3id.org/ro/terms/workflow-run" + }, + { + "@id": "https://gxy.io/GTN:T00343" } ], "hasResource": [ { "@id": "#hasSpecification" }, + { + "@id": "#hasConstraints" + }, { "@id": "#hasVocabulary" + }, + { + "@id": "#hasGuidance" } ], "citation": { @@ -57,7 +79,29 @@ } }, { - "@id": "https://researchobject.org/workflow-run-crate/", + "@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-DRAFT" + }, + { + "@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://www.researchobject.org/workflow-run-crate/", "@type": "Project", "name": "Workflow Run Crate task force", "member": [ @@ -184,7 +228,12 @@ "@id": "index.html", "@type": "File", "name": "Process Run Crate (HTML)", - "encodingFormat": "text/html" + "encodingFormat": [ + "text/html", + { + "@id": "https://www.nationalarchives.gov.uk/PRONOM/fmt/471" + } + ] }, { "@id": "https://w3id.org/ro/terms/workflow-run#", @@ -238,10 +287,38 @@ } ] }, + { + "@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": "https://gxy.io/GTN:T00343", + "@type": "LearningResource", + "name": "Workflow Run RO-Crate Introduction", + "author": { + "@id": "https://orcid.org/0000-0001-8271-5429" + } + }, { "@id": "#hasSpecification", "@type": "ResourceDescriptor", - "name": "", "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/specification" }, @@ -249,6 +326,16 @@ "@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", @@ -259,11 +346,77 @@ "@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": "https://doi.org/10.48550/arXiv.2312.07852", "@type": "ScholarlyArticle", "name": "Recording provenance of workflow runs with RO-Crate", - "creditText": "Simone Leo, Michael R. Crusoe, Laura Rodríguez-Navas, Raül Sirvent, Alexander Kanitz, Paul De Geest, Rudolf Wittner, Luca Pireddu, Daniel Garijo, José M. Fernández, Iacopo Colonnelli, Matej Gallo, Tazro Ohta, Hirotaka Suetake, Salvador Capella-Gutierrez, Renske de Wit, Bruno de Paula Kinoshita, Stian Soiland-Reyes (2024): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852" + "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://orcid.org/0000-0001-8271-5429", @@ -460,6 +613,35 @@ "@type": "Project", "name": "RO-Crate Community" }, + { + "@id": "index.html#requirements", + "@type": "WebPageElement", + "name": "Process Run Crate requirements" + }, + { + "@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": "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://w3id.org/ro/terms/workflow-run#ParameterConnection", "@type": [ @@ -750,6 +932,13 @@ "@type": "DefinedTerm", "name": "MediaObject", "termCode": "file" + }, + { + "@id": "http://spdx.org/licenses/Apache-2.0", + "@type": "PropertyValue", + "propertyID": "http://spdx.org/rdf/terms#licenseId", + "name": "spdx", + "value": "Apache-2.0" } ] } @@ -824,7 +1013,7 @@

Go to: Process Ru author [?] - Workflow Run Crate task force + Workflow Run Crate task force isProfileOf [?] https://w3id.org/ro/crate/1.2-DRAFT @@ -835,21 +1024,29 @@

Go to: Process Ru version [?] 0.5-DRAFT - includedInDataCatalog [?] - https://w3id.org/ro/wfrun + license [?] + Apache License 2.0 hasPart [?] hasResource [?] citation [?] @@ -864,17 +1061,17 @@

Go to: Process Ru



-

Go to: Workflow Run Crate task force

+

Go to: Workflow Run Crate task force

-
+
- + @@ -971,7 +1168,40 @@

Go to: Workflo -






+




+
+

Go to: Apache License 2.0

+ + + + +
+ +

@idhttps://researchobject.org/workflow-run-crate/https://www.researchobject.org/workflow-run-crate/
name [?] Workflow Run Crate task force
+ + + + + + + + + + + + + + + + + + + +
@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
+
+ +
+


⬇️ Download: Process Run Crate (HTML)

@@ -992,7 +1222,11 @@

⬇️ Download: Process Run Crate (HTML)

File encodingFormat [?] - text/html + Items that reference this one hasPart [?] Process Run Crate profile @@ -1060,12 +1294,94 @@

Go to: Namespace for hasPart [?] Process Run Crate profile + isBasedOn [?] + JSON-LD context for workflow-run terms + hasArtifact [?] #hasVocabulary

+
+


+
+

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

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
@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
+
+ +
+


+
+

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 [?]Process Run Crate profile
hasArtifact [?]#hasGuidance
+
+


@@ -1081,9 +1397,6 @@

#hasSpecification

@id #hasSpecification - name [?] - - @type ResourceDescriptor @@ -1099,6 +1412,36 @@

#hasSpecification

+ +


+
+

#hasConstraints

+ + + + +
+ + + + + + + + + + + + + + + + + + +
@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
+
+


@@ -1129,6 +1472,36 @@

#hasVocabulary

+ +


+
+

#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 [?]Process Run Crate profile
+
+


@@ -1150,8 +1523,47 @@

Go to: Recording pr @type ScholarlyArticle + author [?] + + creditText [?] - Simone Leo, Michael R. Crusoe, Laura Rodríguez-Navas, Raül Sirvent, Alexander Kanitz, Paul De Geest, Rudolf Wittner, Luca Pireddu, Daniel Garijo, José M. Fernández, Iacopo Colonnelli, Matej Gallo, Tazro Ohta, Hirotaka Suetake, Salvador Capella-Gutierrez, Renske de Wit, Bruno de Paula Kinoshita, Stian Soiland-Reyes (2024): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852 + 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 From a2f523834be4b87085ac7a6156954705351882b8 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Thu, 16 May 2024 23:00:22 +0100 Subject: [PATCH 03/27] workflow run crate profile crate --- .../index.md} | 11 +- .../workflow_run_crate/ro-crate-metadata.json | 734 +++++++ .../workflow_run_crate/ro-crate-preview.html | 1820 +++++++++++++++++ 3 files changed, 2563 insertions(+), 2 deletions(-) rename docs/profiles/0.5-DRAFT/{workflow_run_crate.md => workflow_run_crate/index.md} (95%) create mode 100644 docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json create mode 100644 docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate.md b/docs/profiles/0.5-DRAFT/workflow_run_crate/index.md similarity index 95% rename from docs/profiles/0.5-DRAFT/workflow_run_crate.md rename to docs/profiles/0.5-DRAFT/workflow_run_crate/index.md index 7af62c7..fca784c 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate.md +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/index.md @@ -7,7 +7,14 @@ title: Workflow Run Crate * Version: 0.5-DRAFT * Permalink: -* Authors: Workflow Run RO-Crate working group +* 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)) +* 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) + - [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). @@ -26,7 +33,7 @@ Additional properties described in the [Bioschemas FormalParameter profile](http 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 +Entity-relationship diagram ## Example Metadata File (`ro-crate-metadata.json`) diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json new file mode 100644 index 0000000..4b5aaee --- /dev/null +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json @@ -0,0 +1,734 @@ +{ "@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-DRAFT"} + }, + { + "@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-DRAFT" + }, + { + "@id": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT", + "@type": ["Dataset","Profile"], + "isProfileOf": [ + {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"} + ], + "identifier": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT", + "name": "Workflow Run Crate profile", + "version": "0.5-DRAFT", + "license": { + "@id": "https://www.apache.org/licenses/LICENSE-2.0" + }, + "author": [ + {"@id": "https://www.researchobject.org/workflow-run-crate/"} + ], + "hasPart": [ + { "@id": "index.html" }, + { "@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-DRAFT" }, + { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" } + ], + "hasResource": [ + { "@id": "#hasSpecification" }, + { "@id": "#hasConstraints" }, + { "@id": "#hasVocabulary" }, + { "@id": "#hasGuidance" }, + { "@id": "#shouldConformToWorkflowROCrate" }, + { "@id": "#shouldConformToProcess" } + ], + "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": 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"version": "0.5-DRAFT" +}, +{ + "@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": "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": 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"@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-DRAFT/workflow_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html new file mode 100644 index 0000000..0ef75a8 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html @@ -0,0 +1,1820 @@ + + + + + + + + + + + + + + + + + + + + + + + + +
+
+

+

Workflow Run Crate profile

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

Go to: Workflow Run Crate profile

+ + + + + + +
+


+
+

Go to: Workflow Run Crate task force

+ + + + + + +
+




+
+

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
+
+ +
+


+
+

⬇️ 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
+
+ +
+


+
+

Go to: Namespace for Common Provenance Model RO-Crate model

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


+
+

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

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
@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 [?]Workflow Run Crate profile
+
+ +
+


+
+

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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+ +
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Go to: Process Run Crate profile

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


+
+

Go to: Workflow RO-Crate profile

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + +
@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
hasArtifact [?]#shouldConformToWorkflowROCrate
+
+ +
+


+
+

#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

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@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
+
+ +
+


+
+

#hasVocabulary

+ + + + +
+ + + + + + + + + + + + + + + + + + +
@id#hasVocabulary
@typeResourceDescriptor
hasRole [?]http://www.w3.org/ns/dx/prof/role/vocabulary
hasArtifact [?]Namespace for Common Provenance Model RO-Crate model
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
+
+ +
+


+
+

#shouldConformToWorkflowROCrate

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


+
+

#shouldConformToProcess

+ + + + +
+ + + + + + + + + + + + + + + + + + +
@id#shouldConformToProcess
@typeResourceDescriptor
hasRole [?]http://purl.org/dc/terms/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 092a552576fb96e3cd47c040c63e7336764f50e8 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Thu, 16 May 2024 23:00:36 +0100 Subject: [PATCH 04/27] explicit license --- docs/profiles/0.5-DRAFT/process_run_crate/index.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/index.md b/docs/profiles/0.5-DRAFT/process_run_crate/index.md index e252ac7..a1a4082 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/index.md +++ b/docs/profiles/0.5-DRAFT/process_run_crate/index.md @@ -7,8 +7,13 @@ title: Process Run Crate * Version: 0.5-DRAFT * Permalink: -* Authors: Workflow Run RO-Crate working group +* 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)) * 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/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. From 0eb50aa6168aa616c36b8b5122eeb01257d22869 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Thu, 16 May 2024 23:05:44 +0100 Subject: [PATCH 05/27] copyright and license --- docs/index.md | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/docs/index.md b/docs/index.md index 2d8ba84..6137b69 100644 --- a/docs/index.md +++ b/docs/index.md @@ -135,3 +135,22 @@ In addition, some computational workflow approaches have RO-Crate support which - [EOSC-Life Common Provenance Model](https://doi.org/10.5281/zenodo.4705074) (deliverable showing ISO 23494 model) - [P-Plan ontology](https://www.opmw.org/model/p-plan/), [OPMW ontology](https://www.opmw.org/model/OPMW/) and [OPMW-PROV](https://www.opmw.org/interoperability.html) - [ProvONE+: A Provenance Model for Scientific Workflows](https://doi.org/10.1007/978-3-030-62008-0_30) (not Open Access) [[PROV-One ontology](https://purl.dataone.org/provone-v1-dev)] + + +## License for specifications + +© 2021--2024 The University of Manchester, UK +© 2022--2024 Centro di Ricerca, Sviluppo e Studi Superiori in Sardegna (CRS4), IT +© 2022--2024 Workflow Run Crate task force contributors + +Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at + + + +Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. + +### License for examples + +Profile Crates and JSON-LD examples within this specification are distributed +under [CC0 1.0 Universal (CC0 1.0) Public Domain Dedication](https://creativecommons.org/publicdomain/zero/1.0/). + From ab041b036a62991752da3f6e52f771aa29dc56d6 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Thu, 16 May 2024 23:06:03 +0100 Subject: [PATCH 06/27] whitespace --- docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json index 0e4638c..c20f95c 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json @@ -1,7 +1,6 @@ { "@context": "https://w3id.org/ro/crate/1.2-DRAFT/context", "@graph": [ - { "@id": "ro-crate-metadata.json", "@type": "CreativeWork", From a6c7232809e62b2b63a797332f6bee646b27e47c Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Thu, 16 May 2024 23:42:37 +0100 Subject: [PATCH 07/27] provenance run crate --- .../index.md} | 12 +- .../ro-crate-metadata.json | 535 ++++++++++++++++++ 2 files changed, 544 insertions(+), 3 deletions(-) rename docs/profiles/0.5-DRAFT/{provenance_run_crate.md => provenance_run_crate/index.md} (97%) create mode 100644 docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json diff --git a/docs/profiles/0.5-DRAFT/provenance_run_crate.md b/docs/profiles/0.5-DRAFT/provenance_run_crate/index.md similarity index 97% rename from docs/profiles/0.5-DRAFT/provenance_run_crate.md rename to docs/profiles/0.5-DRAFT/provenance_run_crate/index.md index f1c7b86..85c282f 100644 --- a/docs/profiles/0.5-DRAFT/provenance_run_crate.md +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/index.md @@ -7,7 +7,13 @@ title: Provenance Run Crate * Version: 0.5-DRAFT * Permalink: -* Authors: Workflow Run RO-Crate working group +* 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)) +* 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) +* 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/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. @@ -26,7 +32,7 @@ The tool that implements a step can in turn be a workflow (*nested workflow* or 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 +Entity-relationship diagram ## Example Metadata File (`ro-crate-metadata.json`) @@ -329,7 +335,7 @@ The following diagram shows the relationships between all provenance-related ent 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

+

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`. diff --git a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json new file mode 100644 index 0000000..1f1ac0a --- /dev/null +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json @@ -0,0 +1,535 @@ +{ "@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-DRAFT"} + }, + { + "@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-DRAFT" + }, + { + "@id": "https://w3id.org/ro/wfrun/provenance/0.5-DRAFT", + "@type": ["Dataset","Profile"], + "isProfileOf": [ + {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"} + ], + "identifier": "https://w3id.org/ro/wfrun/provenance/0.5-DRAFT", + "name": "Provenance Run Crate profile", + "version": "0.5-DRAFT", + "license": { + "@id": "https://www.apache.org/licenses/LICENSE-2.0" + }, + "author": [ + {"@id": "https://www.researchobject.org/workflow-run-crate/"} + ], + "hasPart": [ + { "@id": "index.html" }, + { "@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/workflow/0.5-DRAFT" }, + { "@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" } + ], + "hasResource": [ + { "@id": "#hasSpecification" }, + { "@id": "#hasConstraints" }, + { "@id": "#hasVocabulary" }, + { "@id": "#hasGuidance" }, + { "@id": "#shouldConformToWorkflow" } + ], + "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/workflow/0.5-DRAFT", + "@type": ["CreativeWork", "Profile"], + "name": "Workflow Run Crate profile", + "version": "0.5-DRAFT" + }, + { + "@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": "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": "#shouldConformToWorkflow", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://purl.org/dc/terms/conformsTo" }, + "hasArtifact": {"@id": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT"} +}, + { + "@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 Common Provenance Model 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://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 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"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" +} + +] +} From d8c268984e71fe21bb79f77aa05a6e53fc3cf946 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Thu, 16 May 2024 23:47:21 +0100 Subject: [PATCH 08/27] http on schema.org --- docs/profiles/0.5-DRAFT/process_run_crate/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/index.md b/docs/profiles/0.5-DRAFT/process_run_crate/index.md index a1a4082..6b0410c 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/index.md +++ b/docs/profiles/0.5-DRAFT/process_run_crate/index.md @@ -222,7 +222,7 @@ Note that the command line shown in the action's `description` is not directly r actionStatus MAY - SHOULD 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. + SHOULD 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. From 234820410d9343210a322242dd2b40bb419cc146 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Thu, 16 May 2024 23:50:19 +0100 Subject: [PATCH 09/27] avoid https://schema.org --- docs/profiles/0.5-DRAFT/provenance_run_crate/index.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/profiles/0.5-DRAFT/provenance_run_crate/index.md b/docs/profiles/0.5-DRAFT/provenance_run_crate/index.md index 85c282f..da80875 100644 --- a/docs/profiles/0.5-DRAFT/provenance_run_crate/index.md +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/index.md @@ -581,7 +581,7 @@ The requirements of this profile are those of [Workflow Run Crate](workflow_run_ actionStatus MAY - SHOULD 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. + SHOULD 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. error @@ -616,7 +616,7 @@ The requirements of this profile are those of [Workflow Run Crate](workflow_run_ actionStatus MAY - SHOULD 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. + SHOULD 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. error From 3f611db4f949eee9cb4d23978cebb61fb2314bbb Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Thu, 16 May 2024 23:50:30 +0100 Subject: [PATCH 10/27] explicit reference schema.org term we use in profile --- .../process_run_crate/ro-crate-metadata.json | 146 ++- .../process_run_crate/ro-crate-preview.html | 1015 ++++++++++++++++- 2 files changed, 1148 insertions(+), 13 deletions(-) diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json index c20f95c..0442b9c 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json @@ -37,7 +37,32 @@ { "@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://pypi.org/project/runcrate/" }, + { "@id": "http://schema.org/SoftwareApplication" }, + { "@id": "http://schema.org/SoftwareSourceCode" }, + { "@id": "https://bioschemas.org/ComputationalWorkflow" }, + { "@id": "http://schema.org/CreateAction" }, + { "@id": "http://schema.org/name" }, + { "@id": "http://schema.org/description" }, + { "@id": "http://schema.org/endTime" }, + { "@id": "http://schema.org/startTime" }, + { "@id": "http://schema.org/instrument" }, + { "@id": "http://schema.org/agent" }, + { "@id": "http://schema.org/Person" }, + { "@id": "http://schema.org/Organization" }, + { "@id": "http://schema.org/object" }, + { "@id": "http://schema.org/result" }, + { "@id": "http://schema.org/actionStatus" }, + { "@id": "http://schema.org/error" }, + { "@id": "http://schema.org/CompletedActionStatus" }, + { "@id": "http://schema.org/FailedActionStatus" }, + { "@id": "http://schema.org/MediaObject" }, + { "@id": "http://schema.org/Dataset" }, + { "@id": "http://schema.org/Collection" }, + { "@id": "http://schema.org/CreativeWork" }, + { "@id": "http://schema.org/PropertyValue" }, + { "@id": "http://schema.org/alternateName" }, + { "@id": "http://schema.org/mainEntity" } ], "hasResource": [ { "@id": "#hasSpecification" }, @@ -468,7 +493,124 @@ "@type": "DefinedTerm", "name": "HowToStep" }, -{ + { + "@id": "http://schema.org/CreateAction", + "@type": "DefinedTerm", + "name": "CreateAction" + }, + { + "@id": "http://schema.org/name", + "@type": "DefinedTerm", + "name": "name" + }, + { + "@id": "http://schema.org/description", + "@type": "DefinedTerm", + "name": "description" + }, + { + "@id": "http://schema.org/endTime", + "@type": "DefinedTerm", + "name": "endTime" + }, + { + "@id": "http://schema.org/startTime", + "@type": "DefinedTerm", + "name": "startTime" + }, + { + "@id": "http://schema.org/instrument", + "@type": "DefinedTerm", + "name": "instrument" + }, + { + "@id": "http://schema.org/agent", + "@type": "DefinedTerm", + "name": "agent" + }, + { + "@id": "http://schema.org/Person", + "@type": "DefinedTerm", + "name": "Person" + }, + { + "@id": "http://schema.org/Organization", + "@type": "DefinedTerm", + "name": "Organization" + }, + { + "@id": "http://schema.org/object", + "@type": "DefinedTerm", + "name": "object" + }, + { + "@id": "http://schema.org/result", + "@type": "DefinedTerm", + "name": "result" + }, + { + "@id": "http://schema.org/actionStatus", + "@type": "DefinedTerm", + "name": "actionStatus" + }, + { + "@id": "http://schema.org/CompletedActionStatus", + "@type": "DefinedTerm", + "name": "CompletedActionStatus" + }, + { + "@id": "http://schema.org/FailedActionStatus", + "@type": "DefinedTerm", + "name": "FailedActionStatus" + }, + { + "@id": "http://schema.org/error", + "@type": "DefinedTerm", + "name": "error" + }, + { + "@id": "http://schema.org/Dataset", + "@type": "DefinedTerm", + "name": "Dataset" + }, + { + "@id": "http://schema.org/Collection", + "@type": "DefinedTerm", + "name": "Collection" + }, + { + "@id": "http://schema.org/CreativeWork", + "@type": "DefinedTerm", + "name": "CreativeWork" + }, + { + "@id": "http://schema.org/PropertyValue", + "@type": "DefinedTerm", + "name": "PropertyValue" + }, + { + "@id": "http://schema.org/alternateName", + "@type": "DefinedTerm", + "name": "alternateName" + }, + { + "@id": "http://schema.org/mainEntity", + "@type": "DefinedTerm", + "name": "mainEntity" + }, + { + "@id": "http://schema.org/SoftwareApplication", + "@type": "DefinedTerm", + "name": "SoftwareApplication" + }, + { + "@id": "http://schema.org/SoftwareSourceCode", + "@type": "DefinedTerm", + "name": "SoftwareSourceCode" + }, + + + { "@id": "https://orcid.org/0000-0001-8271-5429", "@type": "Person", "name": "Simone Leo" diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html index 136fb45..d818c3f 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html @@ -58,6 +58,84 @@ }, { "@id": "https://gxy.io/GTN:T00343" + }, + { + "@id": "https://pypi.org/project/runcrate/" + }, + { + "@id": "http://schema.org/SoftwareApplication" + }, + { + "@id": "http://schema.org/SoftwareSourceCode" + }, + { + "@id": "https://bioschemas.org/ComputationalWorkflow" + }, + { + "@id": "http://schema.org/CreateAction" + }, + { + "@id": "http://schema.org/name" + }, + { + "@id": "http://schema.org/description" + }, + { + "@id": "http://schema.org/endTime" + }, + { + "@id": "http://schema.org/startTime" + }, + { + "@id": "http://schema.org/instrument" + }, + { + "@id": "http://schema.org/agent" + }, + { + "@id": "http://schema.org/Person" + }, + { + "@id": "http://schema.org/Organization" + }, + { + "@id": "http://schema.org/object" + }, + { + "@id": "http://schema.org/result" + }, + { + "@id": "http://schema.org/actionStatus" + }, + { + "@id": "http://schema.org/error" + }, + { + "@id": "http://schema.org/CompletedActionStatus" + }, + { + "@id": "http://schema.org/FailedActionStatus" + }, + { + "@id": "http://schema.org/MediaObject" + }, + { + "@id": "http://schema.org/Dataset" + }, + { + "@id": "http://schema.org/Collection" + }, + { + "@id": "http://schema.org/CreativeWork" + }, + { + "@id": "http://schema.org/PropertyValue" + }, + { + "@id": "http://schema.org/alternateName" + }, + { + "@id": "http://schema.org/mainEntity" } ], "hasResource": [ @@ -316,6 +394,139 @@ "@id": "https://orcid.org/0000-0001-8271-5429" } }, + { + "@id": "https://pypi.org/project/runcrate/", + "@type": "SoftwareApplication", + "name": "runcrate", + "version": "0.5.0", + "url": "https://pypi.org/project/runcrate/" + }, + { + "@id": "http://schema.org/SoftwareApplication", + "@type": "DefinedTerm", + "name": "SoftwareApplication" + }, + { + "@id": "http://schema.org/SoftwareSourceCode", + "@type": "DefinedTerm", + "name": "SoftwareSourceCode" + }, + { + "@id": "https://bioschemas.org/ComputationalWorkflow", + "@type": "DefinedTerm", + "name": "ComputationalWorkflow" + }, + { + "@id": "http://schema.org/CreateAction", + "@type": "DefinedTerm", + "name": "CreateAction" + }, + { + "@id": "http://schema.org/name", + "@type": "DefinedTerm", + "name": "name" + }, + { + "@id": "http://schema.org/description", + "@type": "DefinedTerm", + "name": "description" + }, + { + "@id": "http://schema.org/endTime", + "@type": "DefinedTerm", + "name": "endTime" + }, + { + "@id": "http://schema.org/startTime", + "@type": "DefinedTerm", + "name": "startTime" + }, + { + "@id": "http://schema.org/instrument", + "@type": "DefinedTerm", + "name": "instrument" + }, + { + "@id": "http://schema.org/agent", + "@type": "DefinedTerm", + "name": "agent" + }, + { + "@id": "http://schema.org/Person", + "@type": "DefinedTerm", + "name": "Person" + }, + { + "@id": "http://schema.org/Organization", + "@type": "DefinedTerm", + "name": "Organization" + }, + { + "@id": "http://schema.org/object", + "@type": "DefinedTerm", + "name": "object" + }, + { + "@id": "http://schema.org/result", + "@type": "DefinedTerm", + "name": "result" + }, + { + "@id": "http://schema.org/actionStatus", + "@type": "DefinedTerm", + "name": "actionStatus" + }, + { + "@id": "http://schema.org/error", + "@type": "DefinedTerm", + "name": "error" + }, + { + "@id": "http://schema.org/CompletedActionStatus", + "@type": "DefinedTerm", + "name": "CompletedActionStatus" + }, + { + "@id": "http://schema.org/FailedActionStatus", + "@type": "DefinedTerm", + "name": "FailedActionStatus" + }, + { + "@id": "http://schema.org/MediaObject", + "@type": "DefinedTerm", + "name": "MediaObject", + "termCode": "file" + }, + { + "@id": "http://schema.org/Dataset", + "@type": "DefinedTerm", + "name": "Dataset" + }, + { + "@id": "http://schema.org/Collection", + "@type": "DefinedTerm", + "name": "Collection" + }, + { + "@id": "http://schema.org/CreativeWork", + "@type": "DefinedTerm", + "name": "CreativeWork" + }, + { + "@id": "http://schema.org/PropertyValue", + "@type": "DefinedTerm", + "name": "PropertyValue" + }, + { + "@id": "http://schema.org/alternateName", + "@type": "DefinedTerm", + "name": "alternateName" + }, + { + "@id": "http://schema.org/mainEntity", + "@type": "DefinedTerm", + "name": "mainEntity" + }, { "@id": "#hasSpecification", "@type": "ResourceDescriptor", @@ -907,11 +1118,6 @@ "@id": "http://schema.org/Text" } }, - { - "@id": "https://bioschemas.org/ComputationalWorkflow", - "@type": "DefinedTerm", - "name": "ComputationalWorkflow" - }, { "@id": "http://schema.org/HowToStep", "@type": "DefinedTerm", @@ -927,12 +1133,6 @@ "@type": "DefinedTerm", "name": "Text" }, - { - "@id": "http://schema.org/MediaObject", - "@type": "DefinedTerm", - "name": "MediaObject", - "termCode": "file" - }, { "@id": "http://spdx.org/licenses/Apache-2.0", "@type": "PropertyValue", @@ -1036,6 +1236,58 @@

Go to: Process Ru
  • JSON-LD context for workflow-run terms
  • Workflow Run RO-Crate Introduction
    • + +
  • runcrate
    • + +
  • SoftwareApplication
    • + +
  • SoftwareSourceCode
    • + +
  • ComputationalWorkflow
    • + +
  • CreateAction
    • + +
  • name
    • + +
  • description
    • + +
  • endTime
    • + +
  • startTime
    • + +
  • instrument
    • + +
  • agent
    • + +
  • Person
    • + +
  • Organization
    • + +
  • object
    • + +
  • result
    • + +
  • actionStatus
    • + +
  • error
    • + +
  • CompletedActionStatus
    • + +
  • FailedActionStatus
    • + +
  • MediaObject
    • + +
  • Dataset
    • + +
  • Collection
    • + +
  • CreativeWork
    • + +
  • PropertyValue
    • + +
  • alternateName
    • + +
  • mainEntity
    • hasResource [?] @@ -1382,6 +1634,747 @@

    Go to: Workflow Run RO-Crate Introd

    +

    +


    +
    +

    Go to: runcrate

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + +
    @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
    +
    + +
    +


    +
    +

    Go to: SoftwareApplication

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


    +
    +

    Go to: SoftwareSourceCode

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


    +
    +

    Go to: ComputationalWorkflow

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


    +
    +

    Go to: CreateAction

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


    +
    +

    Go to: name

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


    +
    +

    Go to: description

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


    +
    +

    Go to: endTime

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


    +
    +

    Go to: startTime

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


    +
    +

    Go to: instrument

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


    +
    +

    Go to: agent

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


    +
    +

    Go to: Person

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


    +
    +

    Go to: Organization

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


    +
    +

    Go to: object

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


    +
    +

    Go to: result

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


    +
    +

    Go to: actionStatus

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


    +
    +

    Go to: error

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


    +
    +

    Go to: CompletedActionStatus

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


    +
    +

    Go to: FailedActionStatus

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


    +
    +

    Go to: MediaObject

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


    +
    +

    Go to: Dataset

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


    +
    +

    Go to: Collection

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


    +
    +

    Go to: CreativeWork

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


    +
    +

    Go to: PropertyValue

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


    +
    +

    Go to: alternateName

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


    +
    +

    Go to: mainEntity

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


    From 458923af274f70f116a5984754cb5cf8053e0a88 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Fri, 17 May 2024 00:35:48 +0100 Subject: [PATCH 11/27] file -> File --- .../profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json index 0442b9c..1f29b7a 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json @@ -471,7 +471,7 @@ "@id": "http://schema.org/MediaObject", "@type": "DefinedTerm", "name": "MediaObject", - "termCode": "file" + "termCode": "File" }, { "@id": "http://schema.org/Text", From 6174c8eeecdb9d3d93aea52722f0b10c20bbd345 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Fri, 17 May 2024 00:39:08 +0100 Subject: [PATCH 12/27] reference new terms in this profile --- .../workflow_run_crate/ro-crate-metadata.json | 359 +++++++----------- 1 file changed, 130 insertions(+), 229 deletions(-) diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json index 4b5aaee..4f40fb7 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json @@ -34,17 +34,53 @@ ], "hasPart": [ { "@id": "index.html" }, - { "@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-DRAFT" }, - { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" } - ], + { "@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": "#hasVocabulary" }, { "@id": "#hasGuidance" }, { "@id": "#shouldConformToWorkflowROCrate" }, { "@id": "#shouldConformToProcess" } @@ -138,14 +174,6 @@ "@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/" } @@ -162,12 +190,6 @@ "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", @@ -259,209 +281,7 @@ { "@id": "https://w3id.org/ro/terms/workflow-run#", "@type": "DefinedTermSet", - "name": "Namespace for Common Provenance Model RO-Crate model", - "hasDefinedTerm": [ - { "@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection" }, - { "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" }, - { "@id": "https://w3id.org/ro/terms/workflow-run#DockerImage" }, - { "@id": "https://w3id.org/ro/terms/workflow-run#SIFImage" }, - { "@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://w3id.org/ro/terms/workflow-run#environment" }, - { "@id": "https://w3id.org/ro/terms/workflow-run#registry" }, - { "@id": "https://w3id.org/ro/terms/workflow-run#tag" }, - { "@id": "https://w3id.org/ro/terms/workflow-run#containerImage" }, - { "@id": "https://w3id.org/ro/terms/workflow-run#md5" }, - { "@id": "https://w3id.org/ro/terms/workflow-run#sha1" }, - { "@id": "https://w3id.org/ro/terms/workflow-run#sha256" }, - { "@id": "https://w3id.org/ro/terms/workflow-run#sha512" } - ] - }, - - { - "@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection", - "@type": ["DefinedTerm", "rdfs:Class"], - "termCode": "ParameterConnection", - "name": "Parameter Connection", - "description": "A connection between parameters of different applications" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage", - "@type": ["DefinedTerm", "rdfs:Class"], - "termCode": "ContainerImage", - "name": "Container Image", - "description": "A containerization software container image" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#DockerImage", - "@type": ["DefinedTerm", "rdfs:Class"], - "termCode": "DockerImage", - "name": "Docker Image", - "description": "A docker container image" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#SIFImage", - "@type": ["DefinedTerm", "rdfs:Class"], - "termCode": "SIFImage", - "name": "SIF Image", - "description": "A Singularity Image Format container image" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#connection", - "@type": ["DefinedTerm", "rdf:Property"], - "termCode": "connection", - "name": "connection", - "description": "A parameter connection created by this workflow", - "domainIncludes": [ - {"@id": "https://bioschemas.org/ComputationalWorkflow"}, - {"@id": "http://schema.org/HowToStep"} - ], - "rangeIncludes": [ - {"@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection"} - ] - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#sourceParameter", - "@type": ["DefinedTerm", "rdf:Property"], - "termCode": "sourceParameter", - "name": "source parameter", - "description": "The source (upstream) parameter", - "domainIncludes": [ - {"@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection"} - ], - "rangeIncludes": [ - {"@id": "https://bioschemas.org/FormalParameter"} - ] - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#targetParameter", - "@type": ["DefinedTerm", "rdf:Property"], - "termCode": "targetParameter", - "name": "target parameter", - "description": "The target (upstream) parameter", - "domainIncludes": [ - {"@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection"} - ], - "rangeIncludes": [ - {"@id": "https://bioschemas.org/FormalParameter"} - ] - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#environment", - "@type": ["DefinedTerm", "rdf:Property"], - "termCode": "environment", - "name": "environment", - "description": "environment variables used by the application", - "domainIncludes": [ - {"@id": "http://schema.org/SoftwareApplication"}, - {"@id": "http://schema.org/SoftwareSourceCode"}, - {"@id": "http://schema.org/CreateAction"}, - {"@id": "https://bioschema.org/ComputationalWorkflow"} - ], - "rangeIncludes": [ - {"@id": "https://bioschemas.org/FormalParameter"}, - {"@id": "http://schema.org/PropertyValue"} - ] - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#registry", - "@type": ["DefinedTerm", "rdf:Property"], - "termCode": "registry", - "name": "registry", - "description": "A service to register software products, such as container images", - "domainIncludes": [ - { "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" } - ], - "rangeIncludes": [ - {"@id": "http://schema.org/Text"} - ] - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#tag", - "@type": ["DefinedTerm", "rdf:Property"], - "termCode": "tag", - "name": "tag", - "description": "A tag assigned to a software product, such as a container image", - "domainIncludes": [ - { "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" } - ], - "rangeIncludes": [ - {"@id": "http://schema.org/Text"} - ] - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#containerImage", - "@type": ["DefinedTerm", "rdf:Property"], - "termCode": "containerImage", - "name": "container image", - "description": "A container image associated with this entity", - "domainIncludes": [ - {"@id": "http://schema.org/CreateAction"} - ], - "rangeIncludes": [ - { "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" }, - { "@id": "http://schema.org/URL" } - ] - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#md5", - "@type": ["DefinedTerm", "rdf:Property"], - "termCode": "md5", - "name": "md5 checksum", - "description": "md5 checksum as a hexadecimal string", - "domainIncludes": [ - {"@id": "http://schema.org/MediaObject"}, - { "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" } - ], - "rangeIncludes": [ - {"@id": "http://schema.org/Text"} - ] - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#sha1", - "@type": ["DefinedTerm", "rdf:Property"], - "termCode": "sha1", - "name": "sha1 checksum", - "description": "sha1 checksum as a hexadecimal string", - "domainIncludes": [ - {"@id": "http://schema.org/MediaObject"}, - { "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" } - ], - "rangeIncludes": [ - {"@id": "http://schema.org/Text"} - ] - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#sha256", - "@type": ["DefinedTerm", "rdf:Property"], - "termCode": "sha256", - "name": "sha256 checksum", - "description": "sha256 checksum as a hexadecimal string", - "domainIncludes": [ - {"@id": "http://schema.org/MediaObject"}, - { "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" } - ], - "rangeIncludes": [ - {"@id": "http://schema.org/Text"} - ], - "sameAs": { - "@id": "http://schema.org/sha256" - } - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#sha512", - "@type": ["DefinedTerm", "rdf:Property"], - "termCode": "sha512", - "name": "sha512 checksum", - "description": "sha512 checksum as a hexadecimal string", - "domainIncludes": [ - {"@id": "http://schema.org/MediaObject"}, - { "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" } - ], - "rangeIncludes": [ - {"@id": "http://schema.org/Text"} - ] + "name": "Namespace for Common Provenance Model RO-Crate model" }, { "@id": "https://pypi.org/project/runcrate/", @@ -474,13 +294,64 @@ "@id": "http://schema.org/MediaObject", "@type": "DefinedTerm", "name": "MediaObject", - "termCode": "file" + "termCode": "File" }, - { - "@id": "http://schema.org/Text", + +{ + "@id": "http://schema.org/additionalType", "@type": "DefinedTerm", - "name": "Text" - }, + "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", @@ -492,10 +363,40 @@ "name": "ComputationalWorkflow" }, { - "@id": "http://schema.org/HowToStep", - "@type": "DefinedTerm", - "name": "HowToStep" + "@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", From ef5b10d9c8d15dfc349bc187fb29190ca5c45d25 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Fri, 17 May 2024 00:39:47 +0100 Subject: [PATCH 13/27] ro-crate preview --- .../process_run_crate/ro-crate-preview.html | 4 +- .../ro-crate-preview.html | 1574 +++++++++++++++++ .../workflow_run_crate/ro-crate-preview.html | 1290 ++++++++------ 3 files changed, 2370 insertions(+), 498 deletions(-) create mode 100644 docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html index d818c3f..321915c 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html @@ -495,7 +495,7 @@ "@id": "http://schema.org/MediaObject", "@type": "DefinedTerm", "name": "MediaObject", - "termCode": "file" + "termCode": "File" }, { "@id": "http://schema.org/Dataset", @@ -2191,7 +2191,7 @@

    Go to: MediaObject

    DefinedTerm termCode [?] - file + File Items that reference this one hasPart [?] Process Run Crate profile diff --git a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html new file mode 100644 index 0000000..3cb51fa --- /dev/null +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html @@ -0,0 +1,1574 @@ + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    +

    +

    Provenance Run Crate profile

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

    Go to: Provenance Run Crate profile

    + + + + + + +
    +


    +
    +

    Go to: Provenance Run Crate task force

    + + + + + + +
    +




    +
    +

    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 [?]Provenance Run Crate profile
    +
    + +
    +


    +
    +

    ⬇️ Download: Provenance Run Crate (HTML)

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + +
    @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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    + +
    +


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    Go to: Namespace for Common Provenance Model RO-Crate model

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    @idhttps://w3id.org/ro/terms/workflow-run#
    name [?]Namespace for Common Provenance Model 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 [?]
    +
    + +
    +


    +
    +

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

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    @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
    +
    + +
    +


    +
    +

    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 [?]Provenance Run Crate profile
    hasArtifact [?]#hasGuidance
    +
    + +
    +


    +
    +

    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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    + +
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    Go to: Workflow Run Crate profile

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + +
    @idhttps://w3id.org/ro/wfrun/workflow/0.5-DRAFT
    name [?]Workflow Run Crate profile
    @type
      +
    • CreativeWork
      • + +
    • Profile
      • +
    version [?]0.5-DRAFT
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
    hasArtifact [?]#shouldConformToWorkflow
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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 Common Provenance Model RO-Crate model
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
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    + +
    +


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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 Common Provenance Model 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 Common Provenance Model 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 Common Provenance Model RO-Crate model
    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 Common Provenance Model RO-Crate model
    Items that reference this one
    hasResource [?]Provenance Run Crate profile
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    +
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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
    +
    + +
    +


    +
    +

    #shouldConformToWorkflow

    + + + + +
    + + + + + + + + + + + + + + + + + + +
    @id#shouldConformToWorkflow
    @typeResourceDescriptor
    hasRole [?]http://purl.org/dc/terms/conformsTo
    hasArtifact [?]Workflow Run Crate profile
    Items that reference this one
    hasResource [?]Provenance 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 [?]Provenance Run Crate profile
    +
    + +
    +


    +
    + + + + + + + diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html index 0ef75a8..e855291 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html @@ -50,9 +50,6 @@ { "@id": "index.html" }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#" - }, { "@id": "https://w3id.org/ro/terms/workflow-run" }, @@ -67,6 +64,66 @@ }, { "@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": "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": [ @@ -76,9 +133,6 @@ { "@id": "#hasConstraints" }, - { - "@id": "#hasVocabulary" - }, { "@id": "#hasGuidance" }, @@ -250,58 +304,6 @@ } ] }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#", - "@type": "DefinedTermSet", - "name": "Namespace for Common Provenance Model RO-Crate model", - "hasDefinedTerm": [ - { - "@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#DockerImage" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#SIFImage" - }, - { - "@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://w3id.org/ro/terms/workflow-run#environment" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#registry" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#tag" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#containerImage" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#md5" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#sha1" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#sha256" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#sha512" - } - ] - }, { "@id": "https://w3id.org/ro/terms/workflow-run", "@type": "File", @@ -311,14 +313,6 @@ "@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/" } @@ -356,6 +350,111 @@ "name": "Workflow RO-Crate profile", "version": "1.0" }, + { + "@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": "http://schema.org/defaultValue", + "@type": "DefinedTerm", + "name": "defaultValue" + }, + { + "@id": "http://schema.org/valueRequired", + "@type": "DefinedTerm", + "name": "valueRequired" + }, + { + "@id": "https://bioschemas.org/FormalParameter", + "@type": "DefinedTerm", + "name": "FormalParameter" + }, + { + "@id": "https://bioschemas.org/ComputationalWorkflow", + "@type": "DefinedTerm", + "name": "ComputationalWorkflow" + }, + { + "@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": "#hasSpecification", "@type": "ResourceDescriptor", @@ -376,16 +475,6 @@ "@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", @@ -703,295 +792,9 @@ "name": "Salvador Capella-Gutierrez" }, { - "@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection", - "@type": [ - "DefinedTerm", - "rdfs:Class" - ], - "termCode": "ParameterConnection", - "name": "Parameter Connection", - "description": "A connection between parameters of different applications" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage", - "@type": [ - "DefinedTerm", - "rdfs:Class" - ], - "termCode": "ContainerImage", - "name": "Container Image", - "description": "A containerization software container image" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#DockerImage", - "@type": [ - "DefinedTerm", - "rdfs:Class" - ], - "termCode": "DockerImage", - "name": "Docker Image", - "description": "A docker container image" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#SIFImage", - "@type": [ - "DefinedTerm", - "rdfs:Class" - ], - "termCode": "SIFImage", - "name": "SIF Image", - "description": "A Singularity Image Format container image" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#connection", - "@type": [ - "DefinedTerm", - "rdf:Property" - ], - "termCode": "connection", - "name": "connection", - "description": "A parameter connection created by this workflow", - "domainIncludes": [ - { - "@id": "https://bioschemas.org/ComputationalWorkflow" - }, - { - "@id": "http://schema.org/HowToStep" - } - ], - "rangeIncludes": { - "@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection" - } - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#sourceParameter", - "@type": [ - "DefinedTerm", - "rdf:Property" - ], - "termCode": "sourceParameter", - "name": "source parameter", - "description": "The source (upstream) parameter", - "domainIncludes": { - "@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection" - }, - "rangeIncludes": { - "@id": "https://bioschemas.org/FormalParameter" - } - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#targetParameter", - "@type": [ - "DefinedTerm", - "rdf:Property" - ], - "termCode": "targetParameter", - "name": "target parameter", - "description": "The target (upstream) parameter", - "domainIncludes": { - "@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection" - }, - "rangeIncludes": { - "@id": "https://bioschemas.org/FormalParameter" - } - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#environment", - "@type": [ - "DefinedTerm", - "rdf:Property" - ], - "termCode": "environment", - "name": "environment", - "description": "environment variables used by the application", - "domainIncludes": [ - { - "@id": "http://schema.org/SoftwareApplication" - }, - { - "@id": "http://schema.org/SoftwareSourceCode" - }, - { - "@id": "http://schema.org/CreateAction" - }, - { - "@id": "https://bioschema.org/ComputationalWorkflow" - } - ], - "rangeIncludes": [ - { - "@id": "https://bioschemas.org/FormalParameter" - }, - { - "@id": "http://schema.org/PropertyValue" - } - ] - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#registry", - "@type": [ - "DefinedTerm", - "rdf:Property" - ], - "termCode": "registry", - "name": "registry", - "description": "A service to register software products, such as container images", - "domainIncludes": { - "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" - }, - "rangeIncludes": { - "@id": "http://schema.org/Text" - } - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#tag", - "@type": [ - "DefinedTerm", - "rdf:Property" - ], - "termCode": "tag", - "name": "tag", - "description": "A tag assigned to a software product, such as a container image", - "domainIncludes": { - "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" - }, - "rangeIncludes": { - "@id": "http://schema.org/Text" - } - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#containerImage", - "@type": [ - "DefinedTerm", - "rdf:Property" - ], - "termCode": "containerImage", - "name": "container image", - "description": "A container image associated with this entity", - "domainIncludes": { - "@id": "http://schema.org/CreateAction" - }, - "rangeIncludes": [ - { - "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" - }, - { - "@id": "http://schema.org/URL" - } - ] - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#md5", - "@type": [ - "DefinedTerm", - "rdf:Property" - ], - "termCode": "md5", - "name": "md5 checksum", - "description": "md5 checksum as a hexadecimal string", - "domainIncludes": [ - { - "@id": "http://schema.org/MediaObject" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" - } - ], - "rangeIncludes": { - "@id": "http://schema.org/Text" - } - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#sha1", - "@type": [ - "DefinedTerm", - "rdf:Property" - ], - "termCode": "sha1", - "name": "sha1 checksum", - "description": "sha1 checksum as a hexadecimal string", - "domainIncludes": [ - { - "@id": "http://schema.org/MediaObject" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" - } - ], - "rangeIncludes": { - "@id": "http://schema.org/Text" - } - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#sha256", - "@type": [ - "DefinedTerm", - "rdf:Property" - ], - "termCode": "sha256", - "name": "sha256 checksum", - "description": "sha256 checksum as a hexadecimal string", - "domainIncludes": [ - { - "@id": "http://schema.org/MediaObject" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" - } - ], - "rangeIncludes": { - "@id": "http://schema.org/Text" - }, - "sameAs": { - "@id": "http://schema.org/sha256" - } - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#sha512", - "@type": [ - "DefinedTerm", - "rdf:Property" - ], - "termCode": "sha512", - "name": "sha512 checksum", - "description": "sha512 checksum as a hexadecimal string", - "domainIncludes": [ - { - "@id": "http://schema.org/MediaObject" - }, - { - "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" - } - ], - "rangeIncludes": { - "@id": "http://schema.org/Text" - } - }, - { - "@id": "https://bioschemas.org/ComputationalWorkflow", - "@type": "DefinedTerm", - "name": "ComputationalWorkflow" - }, - { - "@id": "http://schema.org/HowToStep", - "@type": "DefinedTerm", - "name": "HowToStep" - }, - { - "@id": "https://bioschemas.org/FormalParameter", - "@type": "DefinedTerm", - "name": "FormalParameter" - }, - { - "@id": "http://schema.org/Text", - "@type": "DefinedTerm", - "name": "Text" - }, - { - "@id": "http://schema.org/MediaObject", - "@type": "DefinedTerm", - "name": "MediaObject", - "termCode": "file" + "@id": "https://w3id.org/ro/terms/workflow-run#", + "@type": "DefinedTermSet", + "name": "Namespace for Common Provenance Model RO-Crate model" }, { "@id": "http://spdx.org/licenses/Apache-2.0", @@ -1091,8 +894,6 @@

    Go to: Workflow hasResource [?] @@ -1110,8 +951,6 @@

    Go to: Workflow
  • #hasConstraints
    • -
  • #hasVocabulary
    • -
  • #hasGuidance
  • #shouldConformToWorkflowROCrate
    • @@ -1307,72 +1146,6 @@

    ⬇️ Download: Workflow Run Crate (HTML)

    -
    -


    -
    -

    Go to: Namespace for Common Provenance Model RO-Crate model

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


    @@ -1403,13 +1176,6 @@

    Go to: JSON-LD context conformsTo [?] http://www.w3.org/ns/json-ld#Context - isBasedOn [?] - - license [?] Creative Commons Zero v1.0 Universal Items that reference this one @@ -1562,28 +1328,28 @@

    Go to: Wor



    -

    #hasSpecification

    +

    Go to: MediaObject

    -
    +
    - + - - + + - - + + - - + + - +
    @id#hasSpecificationhttp://schema.org/MediaObject
    @typeResourceDescriptorname [?]MediaObject
    hasRole [?]http://www.w3.org/ns/dx/prof/role/specification@typeDefinedTerm
    hasArtifact [?]Workflow Run Crate (HTML)termCode [?]File
    Items that reference this one
    hasResource [?]hasPart [?] Workflow Run Crate profile
    @@ -1592,28 +1358,25 @@

    #hasSpecification



    -

    #hasConstraints

    +

    Go to: additionalType

    -
    +
    - - - - + - - + + - - + + - +
    @id#hasConstraints
    @typeResourceDescriptorhttp://schema.org/additionalType
    hasRole [?]http://www.w3.org/ns/dx/prof/role/constraintsname [?]additionalType
    hasArtifact [?]Workflow Run Crate requirements@typeDefinedTerm
    Items that reference this one
    hasResource [?]hasPart [?] Workflow Run Crate profile
    @@ -1622,28 +1385,52 @@

    #hasConstraints



    -

    #hasVocabulary

    +

    Go to: CreateAction

    -
    +
    - + + + + - + + + + + +
    @id#hasVocabularyhttp://schema.org/CreateAction
    name [?]CreateAction
    @typeResourceDescriptorDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
    +
    + +
    +


    +
    +

    Go to: exampleOfWork

    + + + + +
    + + + + + - - + + - - + + - +
    @idhttp://schema.org/exampleOfWork
    hasRole [?]http://www.w3.org/ns/dx/prof/role/vocabularyname [?]exampleOfWork
    hasArtifact [?]Namespace for Common Provenance Model RO-Crate model@typeDefinedTerm
    Items that reference this one
    hasResource [?]hasPart [?] Workflow Run Crate profile
    @@ -1652,28 +1439,52 @@

    #hasVocabulary



    -

    #hasGuidance

    +

    Go to: instrument

    -
    +
    - + + + + - + + + + + +
    @id#hasGuidancehttp://schema.org/instrument
    name [?]instrument
    @typeResourceDescriptorDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
    +
    + +
    +


    +
    +

    Go to: name

    + + + + +
    + + + + + - - + + - - + + - +
    @idhttp://schema.org/name
    hasRole [?]http://www.w3.org/ns/dx/prof/role/guidancename [?]name
    hasArtifact [?]Workflow Run RO-Crate Introduction@typeDefinedTerm
    Items that reference this one
    hasResource [?]hasPart [?] Workflow Run Crate profile
    @@ -1682,28 +1493,52 @@

    #hasGuidance



    -

    #shouldConformToWorkflowROCrate

    +

    Go to: object

    -
    +
    - + + + + - + + + + + +
    @id#shouldConformToWorkflowROCratehttp://schema.org/object
    name [?]object
    @typeResourceDescriptorDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
    +
    + +
    +


    +
    +

    Go to: PropertyValue

    + + + + +
    + + + + + - - + + - - + + - +
    @idhttp://schema.org/PropertyValue
    hasRole [?]http://purl.org/dc/terms/conformsToname [?]PropertyValue
    hasArtifact [?]Workflow RO-Crate profile@typeDefinedTerm
    Items that reference this one
    hasResource [?]hasPart [?] Workflow Run Crate profile
    @@ -1712,24 +1547,487 @@

    #shouldConformToWorkflowROCrate



    -

    #shouldConformToProcess

    +

    Go to: result

    -
    +
    - + - - + + - + + + + + + +
    @id#shouldConformToProcesshttp://schema.org/result
    @typeResourceDescriptorname [?]result
    hasRole [?]@typeDefinedTerm
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
    +
    + +
    +


    +
    +

    Go to: DataType

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


    +
    +

    Go to: Integer

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


    +
    +

    Go to: about

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


    +
    +

    Go to: defaultValue

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


    +
    +

    Go to: valueRequired

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


    +
    +

    Go to: FormalParameter

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


    +
    +

    Go to: ComputationalWorkflow

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


    +
    +

    Go to: input

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


    +
    +

    Go to: output

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


    +
    +

    Go to: conformsTo

    + + + + +
    + + + + + + + + + + + + + + + + + + + +
    @id http://purl.org/dc/terms/conformsTo
    name [?]conformsTo
    @typeDefinedTerm
    termCode [?]conformsTo
    Items that reference this one
    hasPart [?]Workflow Run Crate profile
    hasRole [?]
    +
    + +
    +


    +
    +

    Go to: environment

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


    +
    +

    #hasSpecification

    + + + + +
    + + + + + + + + + + + + + + + + + + +
    @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
    +
    + +
    +


    +
    +

    #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
    +
    + +
    +


    +
    +

    #shouldConformToWorkflowROCrate

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


    +
    +

    #shouldConformToProcess

    + + + + +
    + + + + + + + + + + + + From 2ad27586bf913dc834c6102e49f2f1fdf2ec6ce2 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Fri, 17 May 2024 00:46:49 +0100 Subject: [PATCH 14/27] profiles explicit --- .../0.5-DRAFT/provenance_run_crate/index.md | 2 +- .../ro-crate-metadata.json | 35 ++- .../ro-crate-preview.html | 218 +++++++++++++++++- .../0.5-DRAFT/workflow_run_crate/index.md | 2 +- .../workflow_run_crate/ro-crate-metadata.json | 6 +- .../workflow_run_crate/ro-crate-preview.html | 32 ++- 6 files changed, 270 insertions(+), 25 deletions(-) diff --git a/docs/profiles/0.5-DRAFT/provenance_run_crate/index.md b/docs/profiles/0.5-DRAFT/provenance_run_crate/index.md index da80875..f53dd6f 100644 --- a/docs/profiles/0.5-DRAFT/provenance_run_crate/index.md +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/index.md @@ -521,7 +521,7 @@ The requirements of this profile are those of [Workflow Run Crate](workflow_run_ - + diff --git a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json index 1f1ac0a..96b263f 100644 --- a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json @@ -38,7 +38,9 @@ { "@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/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" }, @@ -49,7 +51,9 @@ { "@id": "#hasConstraints" }, { "@id": "#hasVocabulary" }, { "@id": "#hasGuidance" }, - { "@id": "#shouldConformToWorkflow" } + { "@id": "#shouldConformToWorkflowROCrate" }, + { "@id": "#shouldConformToProcessCrateProfile" }, + { "@id": "#shouldConformToWorkflowCrateProfile" } ], "citation": { "@id": "https://doi.org/10.48550/arXiv.2312.07852" } }, @@ -105,6 +109,18 @@ "@type": "Project", "name": "RO-Crate Community" }, + { + "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT", + "@type": ["CreativeWork", "Profile"], + "name": "Process Run Crate profile", + "version": "0.5-DRAFT" +}, +{ + "@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-DRAFT", "@type": ["CreativeWork", "Profile"], @@ -170,9 +186,24 @@ "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/guidance" }, "hasArtifact": {"@id": "https://gxy.io/GTN:T00343"} }, + { + "@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-DRAFT"} +}, { - "@id": "#shouldConformToWorkflow", + "@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"} }, diff --git a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html index 3cb51fa..9ddb7ba 100644 --- a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html @@ -62,9 +62,15 @@ { "@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/workflowhub/workflow-ro-crate/1.0" + }, { "@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection" }, @@ -92,7 +98,13 @@ "@id": "#hasGuidance" }, { - "@id": "#shouldConformToWorkflow" + "@id": "#shouldConformToWorkflowROCrate" + }, + { + "@id": "#shouldConformToProcessCrateProfile" + }, + { + "@id": "#shouldConformToWorkflowCrateProfile" } ], "citation": { @@ -297,6 +309,15 @@ "version": "0.5.0", "url": "https://pypi.org/project/runcrate/" }, + { + "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT", + "@type": [ + "CreativeWork", + "Profile" + ], + "name": "Process Run Crate profile", + "version": "0.5-DRAFT" + }, { "@id": "https://w3id.org/ro/wfrun/workflow/0.5-DRAFT", "@type": [ @@ -306,6 +327,15 @@ "name": "Workflow Run Crate profile", "version": "0.5-DRAFT" }, + { + "@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/terms/workflow-run#ParameterConnection", "@type": "DefinedTerm", @@ -387,8 +417,31 @@ } }, { - "@id": "#shouldConformToWorkflow", + "@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-DRAFT" + } + }, + { + "@id": "#shouldConformToWorkflowCrateProfile", "@type": "ResourceDescriptor", + "name": "SHOULD conform to Workflow Crate profile", "hasRole": { "@id": "http://purl.org/dc/terms/conformsTo" }, @@ -794,8 +847,12 @@

    Go to: Provena
  • runcrate
    • +
  • Process Run Crate profile
    • +
  • Workflow Run Crate profile
    • +
  • Workflow RO-Crate profile
    • +
  • Parameter Connection
  • connection
    • @@ -815,7 +872,11 @@

    Go to: Provena
  • #hasGuidance
    • -
  • #shouldConformToWorkflow
    • +
  • SHOULD conform to Workflow RO-Crate profile
    • + +
  • SHOULD conform to Process Crate profile
    • + +
  • SHOULD conform to Workflow Crate profile

    • @@ -1162,6 +1223,43 @@

    Go to: runcrate

    @id#shouldConformToProcess
    @typeResourceDescriptor
    hasRole [?]conformsTo
    hasArtifact [?] Process Run Crate profile
    Items that reference this one
    conformsTo MUSTArray 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.
    citation [?]
    +
    +


    +
    +

    Go to: Process Run Crate profile

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


    + +
    +


    +
    +

    Go to: Workflow RO-Crate profile

    + + + + +
    + + + + + + + + + + + + + + + + + + + +
    @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
    hasArtifact [?]SHOULD conform to Workflow RO-Crate profile
    @@ -1466,17 +1601,86 @@

    #hasGuidance



    -

    #shouldConformToWorkflow

    +

    SHOULD conform to Workflow RO-Crate profile

    -
    +
    - + + + + + + + + + + + + + + + + + +
    @id#shouldConformToWorkflow#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
    +
    + +
    +


    +
    +

    SHOULD conform to Process Crate profile

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + +
    @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
    +
    + +
    +


    +
    +

    SHOULD conform to Workflow Crate profile

    + + + + +
    + + + + + + + + diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/index.md b/docs/profiles/0.5-DRAFT/workflow_run_crate/index.md index fca784c..2b552b2 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/index.md +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/index.md @@ -301,7 +301,7 @@ This profile inherits the requirements of [Process Run Crate](process_run_crate) - + diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json index 4f40fb7..89adc3e 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json @@ -83,7 +83,7 @@ { "@id": "#hasConstraints" }, { "@id": "#hasGuidance" }, { "@id": "#shouldConformToWorkflowROCrate" }, - { "@id": "#shouldConformToProcess" } + { "@id": "#shouldConformToProcessCrateProfile" } ], "citation": { "@id": "https://doi.org/10.48550/arXiv.2312.07852" } }, @@ -199,12 +199,14 @@ { "@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": "#shouldConformToProcess", + "@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-DRAFT"} }, diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html index e855291..4607fa5 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html @@ -140,7 +140,7 @@ "@id": "#shouldConformToWorkflowROCrate" }, { - "@id": "#shouldConformToProcess" + "@id": "#shouldConformToProcessCrateProfile" } ], "citation": { @@ -488,6 +488,7 @@ { "@id": "#shouldConformToWorkflowROCrate", "@type": "ResourceDescriptor", + "name": "SHOULD conform to Workflow RO-Crate profile", "hasRole": { "@id": "http://purl.org/dc/terms/conformsTo" }, @@ -496,8 +497,9 @@ } }, { - "@id": "#shouldConformToProcess", + "@id": "#shouldConformToProcessCrateProfile", "@type": "ResourceDescriptor", + "name": "SHOULD conform to Process Crate profile", "hasRole": { "@id": "http://purl.org/dc/terms/conformsTo" }, @@ -953,9 +955,9 @@

    Go to: Workflow
  • #hasGuidance
    • -
  • #shouldConformToWorkflowROCrate
    • +
  • SHOULD conform to Workflow RO-Crate profile
    • -
  • #shouldConformToProcess
    • +
  • SHOULD conform to Process Crate profile

    • @@ -1283,7 +1285,7 @@

    Go to: Process Ru

    - +
    @id#shouldConformToWorkflowCrateProfile
    name [?]SHOULD conform to Workflow Crate profile
    @type ResourceDescriptor
    conformsTo MUSTArray 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.
    citation [?]Workflow Run Crate profile
    hasArtifact [?]#shouldConformToProcessSHOULD conform to Process Crate profile
    @@ -1320,7 +1322,7 @@

    Go to: Wor Workflow Run Crate profile hasArtifact [?] - #shouldConformToWorkflowROCrate + SHOULD conform to Workflow RO-Crate profile

    @@ -1849,9 +1851,9 @@

    Go to: conformsTo

    hasRole [?] @@ -1980,7 +1982,7 @@

    #hasGuidance



    -

    #shouldConformToWorkflowROCrate

    +

    SHOULD conform to Workflow RO-Crate profile

    @@ -1992,6 +1994,9 @@

    #shouldConformToWorkflowROCrate

    @id #shouldConformToWorkflowROCrate + name [?] + SHOULD conform to Workflow RO-Crate profile + @type ResourceDescriptor @@ -2010,17 +2015,20 @@

    #shouldConformToWorkflowROCrate



    -

    #shouldConformToProcess

    +

    SHOULD conform to Process Crate profile

    -
    +
    - + + + + From 5ba85e9243eccf31a3c0ec9c7a48515f0fc2e230 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Fri, 17 May 2024 01:09:41 +0100 Subject: [PATCH 15/27] Peter's pictures are back! --- .../example1/pics/2017-06-11 12.56.14.jpg | Bin 0 -> 4867 bytes .../example1/pics/sepia_fence.jpg | Bin 0 -> 4759 bytes .../example1/ro-crate-metadata.json | 74 ++++ .../example1/ro-crate-preview.html | 351 ++++++++++++++++++ .../process_run_crate/ro-crate-metadata.json | 25 +- .../process_run_crate/ro-crate-preview.html | 114 ++++++ 6 files changed, 563 insertions(+), 1 deletion(-) create mode 100644 docs/profiles/0.5-DRAFT/process_run_crate/example1/pics/2017-06-11 12.56.14.jpg create mode 100644 docs/profiles/0.5-DRAFT/process_run_crate/example1/pics/sepia_fence.jpg create mode 100644 docs/profiles/0.5-DRAFT/process_run_crate/example1/ro-crate-metadata.json create mode 100644 docs/profiles/0.5-DRAFT/process_run_crate/example1/ro-crate-preview.html diff --git 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"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% pics/2017-06-11\\ 12.56.14.jpg pics/sepia_fence.jpg", + "endTime": "2024-05-17T01:04:52+01:00", + "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)", + "author": { + "@id": "https://orcid.org/0000-0002-3545-944X" + } + }, + { + "@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" + }, + { + "@id": "https://orcid.org/0000-0002-3545-944X", + "@type": "Person", + "name": "Peter Sefton" + } +] +} \ No newline at end of file diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/example1/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/process_run_crate/example1/ro-crate-preview.html new file mode 100644 index 0000000..300076c --- /dev/null +++ b/docs/profiles/0.5-DRAFT/process_run_crate/example1/ro-crate-preview.html @@ -0,0 +1,351 @@ + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    +

    +

    My Pictures

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

    My Pictures

    + + + + +
    + +
    @id#shouldConformToProcess#shouldConformToProcessCrateProfile
    name [?]SHOULD conform to Process Crate profile
    @type ResourceDescriptor
    + + + + + + + + + + + + + + + + + + + + + + + + + +
    @id./
    name [?]My Pictures
    @typeDataset
    conformsTo [?]Process Run Crate
    hasPart [?]
    isBasedOn [?]https://doi.org/10.5281/zenodo.1009240
    mentions [?]Convert dog image to sepia
    Items that reference this one
    about [?]ro-crate-metadata.json
    +
    + +
    +


    +
    +

    Go to: Process Run Crate

    + + + + +
    + + + + + + + + + + + + + + + + + + +
    @idhttps://w3id.org/ro/wfrun/process/0.1
    name [?]Process Run Crate
    @typeCreativeWork
    version [?]0.1
    Items that reference this one
    conformsTo [?]My Pictures
    +
    + +
    +


    +
    +

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

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    @idpics/2017-06-11%2012.56.14.jpg
    name [?]2017-06-11 12.56.14.jpg (input)
    @typeFile
    description [?]Original image
    author [?]Peter Sefton
    encodingFormat [?]image/jpeg
    Items that reference this one
    hasPart [?]My Pictures
    object [?]Convert dog image to sepia
    +
    + +
    +


    +
    +

    ⬇️ Download: sepia_fence (output)

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + +
    @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
    +
    + +
    +




    +
    +

    Convert dog image to sepia

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    @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
    +
    + +
    +


    +
    + + + + + + + diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json index 1f29b7a..de5c5ae 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json @@ -34,6 +34,7 @@ ], "hasPart": [ { "@id": "index.html" }, + { "@id": "example1/" }, { "@id": "https://w3id.org/ro/terms/workflow-run#" }, { "@id": "https://w3id.org/ro/terms/workflow-run" }, { "@id": "https://gxy.io/GTN:T00343" }, @@ -68,7 +69,8 @@ { "@id": "#hasSpecification" }, { "@id": "#hasConstraints" }, { "@id": "#hasVocabulary" }, - { "@id": "#hasGuidance" } + { "@id": "#hasGuidance" }, + { "@id": "#hasExample" } ], "citation": { "@id": "https://doi.org/10.48550/arXiv.2312.07852" } }, @@ -138,6 +140,21 @@ "@type": "WebPageElement", "name": "Process Run Crate requirements" }, + { + "@id": "example1/", + "@type": "Dataset", + "name": "Example Process Run Crate", + "conformsTo": [ + { "@id": "https://w3id.org/ro/crate"}, + { "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" } + ], + "subjectOf": { "@id": "example1/ro-crate-metadata.json" } + }, + { + "@id": "example1/ro-crate-metadata.json", + "@type": "CreativeWork", + "encodingFormat": "application/ld+json" + }, { "@id": "https://w3id.org/ro/terms/workflow-run", "@type": "File", @@ -183,6 +200,12 @@ "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": "example1/" } + }, { "@id": "https://gxy.io/GTN:T00343", "@type": "LearningResource", diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html index 321915c..eb3e341 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html @@ -50,6 +50,9 @@ { "@id": "index.html" }, + { + "@id": "example1/" + }, { "@id": "https://w3id.org/ro/terms/workflow-run#" }, @@ -150,6 +153,9 @@ }, { "@id": "#hasGuidance" + }, + { + "@id": "#hasExample" } ], "citation": { @@ -313,6 +319,22 @@ } ] }, + { + "@id": "example1/", + "@type": "Dataset", + "name": "Example Process Run Crate", + "conformsTo": [ + { + "@id": "https://w3id.org/ro/crate" + }, + { + "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" + } + ], + "subjectOf": { + "@id": "example1/ro-crate-metadata.json" + } + }, { "@id": "https://w3id.org/ro/terms/workflow-run#", "@type": "DefinedTermSet", @@ -567,6 +589,16 @@ "@id": "https://gxy.io/GTN:T00343" } }, + { + "@id": "#hasExample", + "@type": "ResourceDescriptor", + "hasRole": { + "@id": "http://www.w3.org/ns/dx/prof/role/example" + }, + "hasArtifact": { + "@id": "example1/" + } + }, { "@id": "https://doi.org/10.48550/arXiv.2312.07852", "@type": "ScholarlyArticle", @@ -829,6 +861,11 @@ "@type": "WebPageElement", "name": "Process Run Crate requirements" }, + { + "@id": "example1/ro-crate-metadata.json", + "@type": "CreativeWork", + "encodingFormat": "application/ld+json" + }, { "@id": "https://creativecommons.org/publicdomain/zero/1.0/", "@type": "CreativeWork", @@ -1231,6 +1268,8 @@

    Go to: Process Ru citation [?] @@ -1306,6 +1347,9 @@

    Go to: Process Ru Items that reference this one about [?] ro-crate-metadata.json + + conformsTo [?] + Example Process Run Crate

    @@ -1489,6 +1533,46 @@

    ⬇️ Download: Process Run Crate (HTML)

    +
    +


    +
    +

    Example Process Run Crate

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + +
    @idexample1/
    name [?]Example Process Run Crate
    @typeDataset
    conformsTo [?]
    subjectOf [?]example1/ro-crate-metadata.json
    Items that reference this one
    hasPart [?]Process Run Crate profile
    hasArtifact [?]#hasExample
    +
    +


    @@ -2495,6 +2579,36 @@

    #hasGuidance

    +
    +


    +
    +

    #hasExample

    + + + + +
    + + + + + + + + + + + + + + + + + + +
    @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
    +
    +


    From 0042d9067f886c4607bde4195a687336beb31690 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Fri, 17 May 2024 01:11:33 +0100 Subject: [PATCH 16/27] link to example --- docs/profiles/0.5-DRAFT/process_run_crate/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/index.md b/docs/profiles/0.5-DRAFT/process_run_crate/index.md index 6b0410c..107f796 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/index.md +++ b/docs/profiles/0.5-DRAFT/process_run_crate/index.md @@ -9,6 +9,7 @@ title: Process Run Crate * 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) From 15cf60d0530c5c71e51493d181d10418765f82f9 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Fri, 17 May 2024 01:23:37 +0100 Subject: [PATCH 17/27] add example --- .../example2/Galaxy-Workflow-Hello_World.ga | 157 ++++ .../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 ++++++++++++++++++ .../0.5-DRAFT/workflow_run_crate/index.md | 6 + .../workflow_run_crate/ro-crate-metadata.json | 34 +- .../workflow_run_crate/ro-crate-preview.html | 85 +++ 9 files changed, 1187 insertions(+), 1 deletion(-) create mode 100644 docs/profiles/0.5-DRAFT/workflow_run_crate/example2/Galaxy-Workflow-Hello_World.ga create mode 100644 docs/profiles/0.5-DRAFT/workflow_run_crate/example2/inputs/abcdef.txt create mode 100644 docs/profiles/0.5-DRAFT/workflow_run_crate/example2/outputs/Select_first_on_data_1_2.txt create mode 100644 docs/profiles/0.5-DRAFT/workflow_run_crate/example2/outputs/tac_on_data_360_1.txt create mode 100644 docs/profiles/0.5-DRAFT/workflow_run_crate/example2/ro-crate-metadata.json create mode 100644 docs/profiles/0.5-DRAFT/workflow_run_crate/example2/ro-crate-preview.html diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/example2/Galaxy-Workflow-Hello_World.ga b/docs/profiles/0.5-DRAFT/workflow_run_crate/example2/Galaxy-Workflow-Hello_World.ga new file mode 100644 index 0000000..8bd9b1b --- /dev/null +++ b/docs/profiles/0.5-DRAFT/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-DRAFT/workflow_run_crate/example2/inputs/abcdef.txt b/docs/profiles/0.5-DRAFT/workflow_run_crate/example2/inputs/abcdef.txt new file mode 100644 index 0000000..cead32e --- /dev/null +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/example2/inputs/abcdef.txt @@ -0,0 +1,6 @@ +A +B +C +D +E +F diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/example2/outputs/Select_first_on_data_1_2.txt b/docs/profiles/0.5-DRAFT/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-DRAFT/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-DRAFT/workflow_run_crate/example2/outputs/tac_on_data_360_1.txt b/docs/profiles/0.5-DRAFT/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-DRAFT/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-DRAFT/workflow_run_crate/example2/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/workflow_run_crate/example2/ro-crate-metadata.json new file mode 100644 index 0000000..0e4d295 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/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-DRAFT/workflow_run_crate/example2/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/workflow_run_crate/example2/ro-crate-preview.html new file mode 100644 index 0000000..b66ff47 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/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-DRAFT/workflow_run_crate/index.md b/docs/profiles/0.5-DRAFT/workflow_run_crate/index.md index 2b552b2..b73176d 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/index.md +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/index.md @@ -9,6 +9,7 @@ title: Workflow Run Crate * 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) @@ -38,6 +39,11 @@ The following diagram shows the relationships between provenance-related entitie ## 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", "@graph": [ diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json index 89adc3e..f399563 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json @@ -83,7 +83,8 @@ { "@id": "#hasConstraints" }, { "@id": "#hasGuidance" }, { "@id": "#shouldConformToWorkflowROCrate" }, - { "@id": "#shouldConformToProcessCrateProfile" } + { "@id": "#shouldConformToProcessCrateProfile" }, + { "@id": "#hasExample" } ], "citation": { "@id": "https://doi.org/10.48550/arXiv.2312.07852" } }, @@ -165,6 +166,31 @@ "@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": "example1/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", @@ -196,6 +222,12 @@ "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": "#shouldConformToWorkflowROCrate", "@type": "ResourceDescriptor", diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html index 4607fa5..74e74bc 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html @@ -141,6 +141,9 @@ }, { "@id": "#shouldConformToProcessCrateProfile" + }, + { + "@id": "#hasExample" } ], "citation": { @@ -507,6 +510,16 @@ "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" } }, + { + "@id": "#hasExample", + "@type": "ResourceDescriptor", + "hasRole": { + "@id": "http://www.w3.org/ns/dx/prof/role/example" + }, + "hasArtifact": { + "@id": "example2/" + } + }, { "@id": "https://doi.org/10.48550/arXiv.2312.07852", "@type": "ScholarlyArticle", @@ -769,6 +782,43 @@ "@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": "example1/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://creativecommons.org/publicdomain/zero/1.0/", "@type": "CreativeWork", @@ -958,6 +1008,8 @@

    Go to: Workflow
  • SHOULD conform to Workflow RO-Crate profile
  • SHOULD conform to Process Crate profile
    • + +
  • #hasExample
    • citation [?] @@ -1321,6 +1373,9 @@

    Go to: Wor hasPart [?] Workflow Run Crate profile + conformsTo [?] + Example Workflow Run Crate + hasArtifact [?] SHOULD conform to Workflow RO-Crate profile @@ -2045,6 +2100,36 @@

    SHOULD conform to Process 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
    +
    +


    From 11ddc6db3b19a21f09765af87d6b0469cd52bf3c Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Fri, 17 May 2024 01:32:54 +0100 Subject: [PATCH 18/27] example for provenance run crate Taken from workflow-run-crate/docs/examples/draft/revsort-run-1-crate --- .../327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 | 16 + .../97fe1b50b4582cebc7d853796ebd62e3e163aa3f | 16 + .../b9214658cc453331b62c2282b772a5c063dbd284 | 16 + .../provenance_run_crate/example3/packed.cwl | 137 +++ .../example3/ro-crate-metadata.json | 290 ++++++ .../example3/ro-crate-preview.html | 866 ++++++++++++++++++ .../0.5-DRAFT/provenance_run_crate/index.md | 7 + .../ro-crate-metadata.json | 35 + .../ro-crate-preview.html | 143 +++ 9 files changed, 1526 insertions(+) create mode 100644 docs/profiles/0.5-DRAFT/provenance_run_crate/example3/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 create mode 100644 docs/profiles/0.5-DRAFT/provenance_run_crate/example3/97fe1b50b4582cebc7d853796ebd62e3e163aa3f create mode 100644 docs/profiles/0.5-DRAFT/provenance_run_crate/example3/b9214658cc453331b62c2282b772a5c063dbd284 create mode 100644 docs/profiles/0.5-DRAFT/provenance_run_crate/example3/packed.cwl create mode 100644 docs/profiles/0.5-DRAFT/provenance_run_crate/example3/ro-crate-metadata.json create mode 100644 docs/profiles/0.5-DRAFT/provenance_run_crate/example3/ro-crate-preview.html diff --git a/docs/profiles/0.5-DRAFT/provenance_run_crate/example3/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 b/docs/profiles/0.5-DRAFT/provenance_run_crate/example3/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 new file mode 100644 index 0000000..425d1ed --- /dev/null +++ b/docs/profiles/0.5-DRAFT/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-DRAFT/provenance_run_crate/example3/97fe1b50b4582cebc7d853796ebd62e3e163aa3f b/docs/profiles/0.5-DRAFT/provenance_run_crate/example3/97fe1b50b4582cebc7d853796ebd62e3e163aa3f new file mode 100644 index 0000000..1001666 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/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-DRAFT/provenance_run_crate/example3/b9214658cc453331b62c2282b772a5c063dbd284 b/docs/profiles/0.5-DRAFT/provenance_run_crate/example3/b9214658cc453331b62c2282b772a5c063dbd284 new file mode 100644 index 0000000..97b096c --- /dev/null +++ b/docs/profiles/0.5-DRAFT/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-DRAFT/provenance_run_crate/example3/packed.cwl b/docs/profiles/0.5-DRAFT/provenance_run_crate/example3/packed.cwl new file mode 100644 index 0000000..251587d --- /dev/null +++ b/docs/profiles/0.5-DRAFT/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-DRAFT/provenance_run_crate/example3/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/provenance_run_crate/example3/ro-crate-metadata.json new file mode 100644 index 0000000..9fb0384 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/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-DRAFT/provenance_run_crate/example3/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/provenance_run_crate/example3/ro-crate-preview.html new file mode 100644 index 0000000..acd4784 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/example3/ro-crate-preview.html @@ -0,0 +1,866 @@ + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    +

    +

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

    ./

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + +
    @id./
    @typeDataset
    conformsTo [?]
    hasPart [?]
    mainEntity [?]packed.cwl
    mentions [?]Run of workflow/packed.cwl#main
    Items that reference this one
    about [?]ro-crate-metadata.json
    +
    + +
    +


    +
    +

    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: Provenance Run Crate

    + + + + +
    + + + + + + + + + + + + + + + + + + +
    @idhttps://w3id.org/ro/wfrun/provenance/0.4
    name [?]Provenance 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: packed.cwl

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    @idpacked.cwl
    name [?]packed.cwl
    @type
      +
    • File
      • + +
    • SoftwareSourceCode
      • + +
    • ComputationalWorkflow
      • + +
    • HowTo
      • +
    hasPart [?]
    input [?]
    output [?]main/output
    programmingLanguage [?]Common Workflow Language
    step [?]
    Items that reference this one
    hasPart [?]./
    mainEntity [?]./
    instrument [?]Run of workflow/packed.cwl#main
    +
    + +
    +


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    ⬇️ Download: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376

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    @id327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
    @typeFile
    exampleOfWork [?]
    Items that reference this one
    hasPart [?]./
    object [?]
    +
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    ⬇️ Download: b9214658cc453331b62c2282b772a5c063dbd284

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    @idb9214658cc453331b62c2282b772a5c063dbd284
    @typeFile
    exampleOfWork [?]
    Items that reference this one
    hasPart [?]./
    result [?]
    +
    + +
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    +
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    ⬇️ Download: 97fe1b50b4582cebc7d853796ebd62e3e163aa3f

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    @id97fe1b50b4582cebc7d853796ebd62e3e163aa3f
    @typeFile
    exampleOfWork [?]
    Items that reference this one
    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-DRAFT/provenance_run_crate/index.md b/docs/profiles/0.5-DRAFT/provenance_run_crate/index.md index f53dd6f..5baaabf 100644 --- a/docs/profiles/0.5-DRAFT/provenance_run_crate/index.md +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/index.md @@ -9,6 +9,7 @@ title: Provenance Run Crate * 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) @@ -37,6 +38,12 @@ The following diagram shows the relationships between all provenance-related ent ## 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", "@graph": [ diff --git a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json index 96b263f..9ab1789 100644 --- a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json @@ -34,6 +34,7 @@ ], "hasPart": [ { "@id": "index.html" }, + { "@id": "example3/" }, { "@id": "https://w3id.org/ro/terms/workflow-run#" }, { "@id": "https://w3id.org/ro/terms/workflow-run" }, { "@id": "https://gxy.io/GTN:T00343" }, @@ -51,6 +52,7 @@ { "@id": "#hasConstraints" }, { "@id": "#hasVocabulary" }, { "@id": "#hasGuidance" }, + { "@id": "#hasExample" }, { "@id": "#shouldConformToWorkflowROCrate" }, { "@id": "#shouldConformToProcessCrateProfile" }, { "@id": "#shouldConformToWorkflowCrateProfile" } @@ -141,6 +143,32 @@ "@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", @@ -186,6 +214,13 @@ "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": "#shouldConformToWorkflowROCrate", "@type": "ResourceDescriptor", diff --git a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html index 9ddb7ba..ded53ba 100644 --- a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html @@ -50,6 +50,9 @@ { "@id": "index.html" }, + { + "@id": "example3/" + }, { "@id": "https://w3id.org/ro/terms/workflow-run#" }, @@ -97,6 +100,9 @@ { "@id": "#hasGuidance" }, + { + "@id": "#hasExample" + }, { "@id": "#shouldConformToWorkflowROCrate" }, @@ -268,6 +274,36 @@ } ] }, + { + "@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": "https://w3id.org/ro/terms/workflow-run#", "@type": "DefinedTermSet", @@ -416,6 +452,16 @@ "@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": "#shouldConformToWorkflowROCrate", "@type": "ResourceDescriptor", @@ -711,6 +757,16 @@ "@type": "WebPageElement", "name": "Provenance Run Crate requirements" }, + { + "@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://creativecommons.org/publicdomain/zero/1.0/", "@type": "CreativeWork", @@ -839,6 +895,8 @@

    Go to: Provena

    +
    +


    +
    +

    Example Process Run Crate

    + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + +
    @idexample3/
    name [?]Example Process Run Crate
    @typeDataset
    conformsTo [?]
    subjectOf [?]
    Items that reference this one
    hasPart [?]Provenance Run Crate profile
    hasArtifact [?]#hasExample
    +
    +


    @@ -1328,6 +1438,9 @@

    Go to: Wor hasPart [?] Provenance Run Crate profile + conformsTo [?] + Example Process Run Crate + hasArtifact [?] SHOULD conform to Workflow RO-Crate profile @@ -1598,6 +1711,36 @@

    #hasGuidance

    +
    +


    +
    +

    #hasExample

    + + + + +
    + + + + + + + + + + + + + + + + + + +
    @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
    +
    +


    From be6ded717ae0221d06963bc704e887c0ddba0d8e Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Fri, 17 May 2024 01:33:52 +0100 Subject: [PATCH 19/27] regenerate previews --- .../example1/ro-crate-metadata.json | 7 +- .../example1/ro-crate-preview.html | 24 ++- .../0.5-DRAFT/process_run_crate/index.md | 11 +- .../process_run_crate/ro-crate-metadata.json | 12 +- .../process_run_crate/ro-crate-preview.html | 29 ++- .../workflow_run_crate/ro-crate-metadata.json | 8 +- .../workflow_run_crate/ro-crate-preview.html | 173 ++++++++++++------ 7 files changed, 174 insertions(+), 90 deletions(-) diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/example1/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/process_run_crate/example1/ro-crate-metadata.json index 552e0d4..05cd8d6 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/example1/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/process_run_crate/example1/ro-crate-metadata.json @@ -9,7 +9,7 @@ { "@id": "./", "@type": "Dataset", - "conformsTo": {"@id": "https://w3id.org/ro/wfrun/process/0.1"}, + "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"} @@ -17,13 +17,14 @@ "isBasedOn": { "@id": "https://doi.org/10.5281/zenodo.1009240" }, + "license": {"@id": "http://spdx.org/licenses/CC0-1.0"}, "mentions": {"@id": "#SepiaConversion_1"}, "name": "My Pictures" }, - { "@id": "https://w3id.org/ro/wfrun/process/0.1", + { "@id": "https://w3id.org/ro/wfrun/process/0.4", "@type": "CreativeWork", "name": "Process Run Crate", - "version": "0.1" + "version": "0.5" }, { "@id": "https://www.imagemagick.org/", diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/example1/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/process_run_crate/example1/ro-crate-preview.html index 300076c..7877d6b 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/example1/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/process_run_crate/example1/ro-crate-preview.html @@ -22,7 +22,7 @@ "@id": "./", "@type": "Dataset", "conformsTo": { - "@id": "https://w3id.org/ro/wfrun/process/0.1" + "@id": "https://w3id.org/ro/wfrun/process/0.4" }, "hasPart": [ { @@ -35,16 +35,19 @@ "isBasedOn": { "@id": "https://doi.org/10.5281/zenodo.1009240" }, + "license": { + "@id": "http://spdx.org/licenses/CC0-1.0" + }, "mentions": { "@id": "#SepiaConversion_1" }, "name": "My Pictures" }, { - "@id": "https://w3id.org/ro/wfrun/process/0.1", + "@id": "https://w3id.org/ro/wfrun/process/0.4", "@type": "CreativeWork", "name": "Process Run Crate", - "version": "0.1" + "version": "0.5" }, { "@id": "pics/2017-06-11%2012.56.14.jpg", @@ -168,7 +171,7 @@

    My Pictures

    Dataset conformsTo [?] - Process Run Crate + Process Run Crate hasPart [?]


    -

    Go to: Process Run Crate

    +

    Go to: Process Run Crate

    -
    +
    - + @@ -211,7 +217,7 @@

    Go to: Process Run Crat

    - + @@ -295,7 +301,7 @@

    ⬇️ Download: sepia_fence (output) -




    +






    Convert dog image to sepia

    diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/index.md b/docs/profiles/0.5-DRAFT/process_run_crate/index.md index 107f796..f156c42 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/index.md +++ b/docs/profiles/0.5-DRAFT/process_run_crate/index.md @@ -34,6 +34,11 @@ The following diagram shows the relationships between provenance-related entitie ## 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", "@graph": [ @@ -46,7 +51,7 @@ The following diagram shows the relationships between provenance-related entitie { "@id": "./", "@type": "Dataset", - "conformsTo": {"@id": "https://w3id.org/ro/wfrun/process/0.1"}, + "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"} @@ -54,7 +59,7 @@ The following diagram shows the relationships between provenance-related entitie "mentions": {"@id": "#SepiaConversion_1"}, "name": "My Pictures" }, - { "@id": "https://w3id.org/ro/wfrun/process/0.1", + { "@id": "https://w3id.org/ro/wfrun/process/0.4", "@type": "CreativeWork", "name": "Process Run Crate", "version": "0.1" @@ -119,7 +124,7 @@ Note that the command line shown in the action's `description` is not directly r

    - + diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json index de5c5ae..97d1d24 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json @@ -146,15 +146,23 @@ "name": "Example Process Run Crate", "conformsTo": [ { "@id": "https://w3id.org/ro/crate"}, - { "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" } + { "@id": "https://w3id.org/ro/wfrun/process/0.4" } ], - "subjectOf": { "@id": "example1/ro-crate-metadata.json" } + "subjectOf": [ + { "@id": "example1/ro-crate-metadata.json" }, + { "@id": "example1/ro-crate-preview.html" } + ] }, { "@id": "example1/ro-crate-metadata.json", "@type": "CreativeWork", "encodingFormat": "application/ld+json" }, + { + "@id": "example1/ro-crate-preview.html", + "@type": "CreativeWork", + "encodingFormat": "text/html" + }, { "@id": "https://w3id.org/ro/terms/workflow-run", "@type": "File", diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html index eb3e341..5445f9d 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html @@ -328,12 +328,17 @@ "@id": "https://w3id.org/ro/crate" }, { - "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" + "@id": "https://w3id.org/ro/wfrun/process/0.4" } ], - "subjectOf": { - "@id": "example1/ro-crate-metadata.json" - } + "subjectOf": [ + { + "@id": "example1/ro-crate-metadata.json" + }, + { + "@id": "example1/ro-crate-preview.html" + } + ] }, { "@id": "https://w3id.org/ro/terms/workflow-run#", @@ -866,6 +871,11 @@ "@type": "CreativeWork", "encodingFormat": "application/ld+json" }, + { + "@id": "example1/ro-crate-preview.html", + "@type": "CreativeWork", + "encodingFormat": "text/html" + }, { "@id": "https://creativecommons.org/publicdomain/zero/1.0/", "@type": "CreativeWork", @@ -1347,9 +1357,6 @@

    Go to: Process Ru

    - - -
    @idhttps://w3id.org/ro/wfrun/process/0.1https://w3id.org/ro/wfrun/process/0.4
    name [?] Process Run CrateCreativeWork
    version [?]0.10.5
    Items that reference this one
    conformsTo [?] My Pictures
    conformsTo MUSTMUST reference a CreativeWork entity with an @id URI that is consistent with the versioned Permalink of this document, e.g. {"@id": "https://w3id.org/ro/wfrun/process/0.1"}MUST 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"}
    Items that reference this one
    about [?] ro-crate-metadata.json
    conformsTo [?]Example Process Run Crate
    @@ -1558,11 +1565,15 @@

    Example Process Run Crate

    subjectOf [?] - example1/ro-crate-metadata.json + Items that reference this one hasPart [?] Process Run Crate profile diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json index f399563..1f259cb 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json @@ -34,6 +34,7 @@ ], "hasPart": [ { "@id": "index.html" }, + { "@id": "example2/" }, { "@id": "https://w3id.org/ro/terms/workflow-run" }, { "@id": "https://gxy.io/GTN:T00343" }, { "@id": "https://pypi.org/project/runcrate/" }, @@ -75,16 +76,15 @@ { "@id": "https://w3id.org/ro/terms/workflow-run#environment" } - - + ], "hasResource": [ { "@id": "#hasSpecification" }, { "@id": "#hasConstraints" }, { "@id": "#hasGuidance" }, + { "@id": "#hasExample" }, { "@id": "#shouldConformToWorkflowROCrate" }, - { "@id": "#shouldConformToProcessCrateProfile" }, - { "@id": "#hasExample" } + { "@id": "#shouldConformToProcessCrateProfile" } ], "citation": { "@id": "https://doi.org/10.48550/arXiv.2312.07852" } }, diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html index 74e74bc..cda7077 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html @@ -50,6 +50,9 @@ { "@id": "index.html" }, + { + "@id": "example2/" + }, { "@id": "https://w3id.org/ro/terms/workflow-run" }, @@ -137,13 +140,13 @@ "@id": "#hasGuidance" }, { - "@id": "#shouldConformToWorkflowROCrate" + "@id": "#hasExample" }, { - "@id": "#shouldConformToProcessCrateProfile" + "@id": "#shouldConformToWorkflowROCrate" }, { - "@id": "#hasExample" + "@id": "#shouldConformToProcessCrateProfile" } ], "citation": { @@ -307,6 +310,33 @@ } ] }, + { + "@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": "example1/ro-crate-preview.html" + } + ] + }, { "@id": "https://w3id.org/ro/terms/workflow-run", "@type": "File", @@ -489,35 +519,35 @@ } }, { - "@id": "#shouldConformToWorkflowROCrate", + "@id": "#hasExample", "@type": "ResourceDescriptor", - "name": "SHOULD conform to Workflow RO-Crate profile", "hasRole": { - "@id": "http://purl.org/dc/terms/conformsTo" + "@id": "http://www.w3.org/ns/dx/prof/role/example" }, "hasArtifact": { - "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" + "@id": "example2/" } }, { - "@id": "#shouldConformToProcessCrateProfile", + "@id": "#shouldConformToWorkflowROCrate", "@type": "ResourceDescriptor", - "name": "SHOULD conform to Process Crate profile", + "name": "SHOULD conform to Workflow RO-Crate profile", "hasRole": { "@id": "http://purl.org/dc/terms/conformsTo" }, "hasArtifact": { - "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" } }, { - "@id": "#hasExample", + "@id": "#shouldConformToProcessCrateProfile", "@type": "ResourceDescriptor", + "name": "SHOULD conform to Process Crate profile", "hasRole": { - "@id": "http://www.w3.org/ns/dx/prof/role/example" + "@id": "http://purl.org/dc/terms/conformsTo" }, "hasArtifact": { - "@id": "example2/" + "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" } }, { @@ -782,33 +812,6 @@ "@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": "example1/ro-crate-preview.html" - } - ] - }, { "@id": "example2/ro-crate-metadata.json", "@type": "CreativeWork", @@ -946,6 +949,8 @@

    Go to: Workflow citation [?] @@ -1200,6 +1205,54 @@

    ⬇️ Download: Workflow Run Crate (HTML)

    +
    +


    +
    +

    Example Workflow Run Crate

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


    @@ -2037,29 +2090,26 @@

    #hasGuidance



    -

    SHOULD conform to Workflow RO-Crate profile

    +

    #hasExample

    -
    +
    - - - - + - + - + @@ -2070,20 +2120,20 @@

    SHOULD conform to Workflow RO-Crate profile



    -

    SHOULD conform to Process Crate profile

    +

    SHOULD conform to Workflow RO-Crate profile

    -
    +
    @id#shouldConformToWorkflowROCrate
    name [?]SHOULD conform to Workflow RO-Crate profile#hasExample
    @type ResourceDescriptor
    hasRole [?]conformsTohttp://www.w3.org/ns/dx/prof/role/example
    hasArtifact [?]Workflow RO-Crate profileExample Workflow Run Crate
    Items that reference this one
    hasResource [?] Workflow Run Crate profile
    - + - + @@ -2092,7 +2142,7 @@

    SHOULD conform to Process Crate profile

    - + @@ -2103,26 +2153,29 @@

    SHOULD conform to Process Crate profile



    -

    #hasExample

    +

    SHOULD conform to Process Crate profile

    -
    +
    @id#shouldConformToProcessCrateProfile#shouldConformToWorkflowROCrate
    name [?]SHOULD conform to Process Crate profileSHOULD conform to Workflow RO-Crate profile
    @type ResourceDescriptor conformsTo
    hasArtifact [?]Process Run Crate profileWorkflow RO-Crate profile
    Items that reference this one
    hasResource [?] Workflow Run Crate profile
    - + + + + - + - + From ac569ffd95b34245efda15184ed0de504822623a Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Fri, 17 May 2024 01:37:43 +0100 Subject: [PATCH 20/27] index.html symlinks but only in examples --- docs/profiles/0.5-DRAFT/process_run_crate/example1/index.html | 1 + .../0.5-DRAFT/provenance_run_crate/example3/index.hml | 1 + docs/profiles/0.5-DRAFT/workflow_run_crate/example2/index.hml | 1 + .../0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json | 2 +- .../0.5-DRAFT/workflow_run_crate/ro-crate-preview.html | 4 ++-- 5 files changed, 6 insertions(+), 3 deletions(-) create mode 120000 docs/profiles/0.5-DRAFT/process_run_crate/example1/index.html create mode 120000 docs/profiles/0.5-DRAFT/provenance_run_crate/example3/index.hml create mode 120000 docs/profiles/0.5-DRAFT/workflow_run_crate/example2/index.hml diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/example1/index.html b/docs/profiles/0.5-DRAFT/process_run_crate/example1/index.html new file mode 120000 index 0000000..a33a179 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/process_run_crate/example1/index.html @@ -0,0 +1 @@ +ro-crate-preview.html \ No newline at end of file diff --git a/docs/profiles/0.5-DRAFT/provenance_run_crate/example3/index.hml b/docs/profiles/0.5-DRAFT/provenance_run_crate/example3/index.hml new file mode 120000 index 0000000..a33a179 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/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-DRAFT/workflow_run_crate/example2/index.hml b/docs/profiles/0.5-DRAFT/workflow_run_crate/example2/index.hml new file mode 120000 index 0000000..a33a179 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/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-DRAFT/workflow_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json index 1f259cb..adeb62e 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json @@ -178,7 +178,7 @@ ], "subjectOf": [ { "@id": "example2/ro-crate-metadata.json" }, - { "@id": "example1/ro-crate-preview.html" } + { "@id": "example2/ro-crate-preview.html" } ] }, { diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html index cda7077..d097c4e 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html @@ -333,7 +333,7 @@ "@id": "example2/ro-crate-metadata.json" }, { - "@id": "example1/ro-crate-preview.html" + "@id": "example2/ro-crate-preview.html" } ] }, @@ -1241,7 +1241,7 @@

    Example Workflow Run Crate

     From 129e053def10e4edfd38b4ecb203554da36ca87b Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Fri, 17 May 2024 01:52:55 +0100 Subject: [PATCH 21/27] symlinks --- .../0.5-DRAFT/process_run_crate/ro-crate-metadata.jsonld | 1 + .../0.5-DRAFT/provenance_run_crate/ro-crate-metadata.jsonld | 1 + .../0.5-DRAFT/workflow_run_crate/ro-crate-metadata.jsonld | 1 + 3 files changed, 3 insertions(+) create mode 120000 docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.jsonld create mode 120000 docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.jsonld create mode 120000 docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.jsonld diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.jsonld b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.jsonld new file mode 120000 index 0000000..8024224 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/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-DRAFT/provenance_run_crate/ro-crate-metadata.jsonld b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.jsonld new file mode 120000 index 0000000..8024224 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/provenance_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-DRAFT/workflow_run_crate/ro-crate-metadata.jsonld b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.jsonld new file mode 120000 index 0000000..8024224 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.jsonld @@ -0,0 +1 @@ +ro-crate-metadata.json \ No newline at end of file From 310c4f599965df228fe21dcde8557384e1c6c8fb Mon Sep 17 00:00:00 2001 From: simleo Date: Fri, 17 May 2024 11:09:24 +0200 Subject: [PATCH 22/27] fix defined term set name --- .../profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json | 2 +- .../0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json | 2 +- .../0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json index 97d1d24..6edb421 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json @@ -287,7 +287,7 @@ { "@id": "https://w3id.org/ro/terms/workflow-run#", "@type": "DefinedTermSet", - "name": "Namespace for Common Provenance Model RO-Crate model", + "name": "Namespace for Workflow Run RO-Crate model", "hasDefinedTerm": [ { "@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection" }, { "@id": "https://w3id.org/ro/terms/workflow-run#ContainerImage" }, diff --git a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json index 9ab1789..a165305 100644 --- a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json @@ -315,7 +315,7 @@ { "@id": "https://w3id.org/ro/terms/workflow-run#", "@type": "DefinedTermSet", - "name": "Namespace for Common Provenance Model RO-Crate model" + "name": "Namespace for Workflow Run RO-Crate model" }, { diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json index adeb62e..edf277b 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json @@ -315,7 +315,7 @@ { "@id": "https://w3id.org/ro/terms/workflow-run#", "@type": "DefinedTermSet", - "name": "Namespace for Common Provenance Model RO-Crate model" + "name": "Namespace for Workflow Run RO-Crate model" }, { "@id": "https://pypi.org/project/runcrate/", From 9f0c0d5cdd12abcb244fa3dde8601fe898d1bd49 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Mon, 20 May 2024 19:52:12 +0100 Subject: [PATCH 23/27] link to prov mapping --- .../process_run_crate/ro-crate-metadata.json | 38 +++++- .../process_run_crate/ro-crate-preview.html | 117 ++++++++++++++++++ .../ro-crate-metadata.json | 37 +++++- .../ro-crate-preview.html | 117 ++++++++++++++++++ .../workflow_run_crate/ro-crate-metadata.json | 36 ++++++ .../workflow_run_crate/ro-crate-preview.html | 117 ++++++++++++++++++ 6 files changed, 460 insertions(+), 2 deletions(-) diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json index 97d1d24..8669428 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json @@ -35,6 +35,7 @@ "hasPart": [ { "@id": "index.html" }, { "@id": "example1/" }, + { "@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" }, @@ -70,7 +71,8 @@ { "@id": "#hasConstraints" }, { "@id": "#hasVocabulary" }, { "@id": "#hasGuidance" }, - { "@id": "#hasExample" } + { "@id": "#hasExample" }, + { "@id": "#hasMappingToProv"} ], "citation": { "@id": "https://doi.org/10.48550/arXiv.2312.07852" } }, @@ -214,6 +216,40 @@ "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/example" }, "hasArtifact": { "@id": "example1/" } }, + { + "@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": "https://gxy.io/GTN:T00343", "@type": "LearningResource", diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html index 5445f9d..26d0c97 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html @@ -53,6 +53,9 @@ { "@id": "example1/" }, + { + "@id": "https://www.researchobject.org/workflow-run-crate-paper/mapping/" + }, { "@id": "https://w3id.org/ro/terms/workflow-run#" }, @@ -156,6 +159,9 @@ }, { "@id": "#hasExample" + }, + { + "@id": "#hasMappingToProv" } ], "citation": { @@ -340,6 +346,14 @@ } ] }, + { + "@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/terms/workflow-run#", "@type": "DefinedTermSet", @@ -604,6 +618,16 @@ "@id": "example1/" } }, + { + "@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://doi.org/10.48550/arXiv.2312.07852", "@type": "ScholarlyArticle", @@ -885,6 +909,32 @@ "name": "Creative Commons Zero v1.0 Universal", "version": "1.0" }, + { + "@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": "https://orcid.org/0000-0002-4663-5613", "@type": "Person", @@ -1280,6 +1330,8 @@

    Go to: Process Ru
  • Example Process Run Crate
    • +
  • SSSOM mapping from PROV to Workflow Run Crate
    • +
  • Namespace for Common Provenance Model RO-Crate model
  • JSON-LD context for workflow-run terms
    • @@ -1350,6 +1402,8 @@

    Go to: Process Ru
  • #hasGuidance
  • #hasExample
    • + +
  • #hasMappingToProv

    •  @@ -1584,6 +1638,39 @@

    Example Process Run Crate

    @id#hasExample#shouldConformToProcessCrateProfile
    name [?]SHOULD conform to Process Crate profile
    @type ResourceDescriptor
    hasRole [?]http://www.w3.org/ns/dx/prof/role/exampleconformsTo
    hasArtifact [?]Example Workflow Run CrateProcess Run Crate profile
    Items that reference this one
    hasResource [?] Workflow Run Crate profile
    Items that reference this one
    hasPart [?]
    citation [?]
    +
    +


    +
    +

    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 [?]Process Run Crate profile
    hasArtifact [?]#hasMappingToProv
    +
    +


    @@ -2620,6 +2707,36 @@

    #hasExample

    +
    +


    +
    +

    #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 [?]Process Run Crate profile
    +
    +


    diff --git a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json index 9ab1789..e4379ce 100644 --- a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json @@ -35,6 +35,7 @@ "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" }, @@ -53,6 +54,7 @@ { "@id": "#hasVocabulary" }, { "@id": "#hasGuidance" }, { "@id": "#hasExample" }, + { "@id": "#hasMappingToProv" }, { "@id": "#shouldConformToWorkflowROCrate" }, { "@id": "#shouldConformToProcessCrateProfile" }, { "@id": "#shouldConformToWorkflowCrateProfile" } @@ -220,7 +222,40 @@ "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", diff --git a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html index ded53ba..4dcba4a 100644 --- a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html @@ -53,6 +53,9 @@ { "@id": "example3/" }, + { + "@id": "https://www.researchobject.org/workflow-run-crate-paper/mapping/" + }, { "@id": "https://w3id.org/ro/terms/workflow-run#" }, @@ -103,6 +106,9 @@ { "@id": "#hasExample" }, + { + "@id": "#hasMappingToProv" + }, { "@id": "#shouldConformToWorkflowROCrate" }, @@ -304,6 +310,14 @@ } ] }, + { + "@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/terms/workflow-run#", "@type": "DefinedTermSet", @@ -462,6 +476,16 @@ "@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": "#shouldConformToWorkflowROCrate", "@type": "ResourceDescriptor", @@ -776,6 +800,32 @@ "name": "Creative Commons Zero v1.0 Universal", "version": "1.0" }, + { + "@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": "https://orcid.org/0000-0002-4663-5613", "@type": "Person", @@ -897,6 +947,8 @@

    Go to: Provena
  • Example Process Run Crate
    • +
  • SSSOM mapping from PROV to Workflow Run Crate
    • +
  • Namespace for Common Provenance Model RO-Crate model
  • JSON-LD context for workflow-run terms
    • @@ -932,6 +984,8 @@

    Go to: Provena
  • #hasExample
    • +
  • #hasMappingToProv
    • +
  • SHOULD conform to Workflow RO-Crate profile
  • SHOULD conform to Process Crate profile
    • @@ -1177,6 +1231,39 @@

    Example Process Run Crate

    +
    +


    +
    +

    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 [?]Provenance Run Crate profile
    hasArtifact [?]#hasMappingToProv
    +
    +


    @@ -1741,6 +1828,36 @@

    #hasExample

    +
    +


    +
    +

    #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 [?]Provenance Run Crate profile
    +
    +


    diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json index adeb62e..3f0c488 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json @@ -35,6 +35,7 @@ "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/" }, @@ -83,6 +84,7 @@ { "@id": "#hasConstraints" }, { "@id": "#hasGuidance" }, { "@id": "#hasExample" }, + { "@id": "#hasMappingToProv" }, { "@id": "#shouldConformToWorkflowROCrate" }, { "@id": "#shouldConformToProcessCrateProfile" } ], @@ -228,6 +230,40 @@ "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", diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html index d097c4e..9e34f50 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html @@ -53,6 +53,9 @@ { "@id": "example2/" }, + { + "@id": "https://www.researchobject.org/workflow-run-crate-paper/mapping/" + }, { "@id": "https://w3id.org/ro/terms/workflow-run" }, @@ -142,6 +145,9 @@ { "@id": "#hasExample" }, + { + "@id": "#hasMappingToProv" + }, { "@id": "#shouldConformToWorkflowROCrate" }, @@ -337,6 +343,14 @@ } ] }, + { + "@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/terms/workflow-run", "@type": "File", @@ -528,6 +542,16 @@ "@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": "#shouldConformToWorkflowROCrate", "@type": "ResourceDescriptor", @@ -831,6 +855,32 @@ "name": "Creative Commons Zero v1.0 Universal", "version": "1.0" }, + { + "@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": "https://orcid.org/0000-0002-4663-5613", "@type": "Person", @@ -951,6 +1001,8 @@

    Go to: Workflow
  • Example Workflow Run Crate
    • +
  • SSSOM mapping from PROV to Workflow Run Crate
    • +
  • JSON-LD context for workflow-run terms
  • Workflow Run RO-Crate Introduction
    • @@ -1012,6 +1064,8 @@

    Go to: Workflow
  • #hasExample
    • +
  • #hasMappingToProv
    • +
  • SHOULD conform to Workflow RO-Crate profile
  • SHOULD conform to Process Crate profile
    • @@ -1253,6 +1307,39 @@

    Example Workflow Run Crate

    +
    +


    +
    +

    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
    +
    +


    @@ -2117,6 +2204,36 @@

    #hasExample

    +
    +


    +
    +

    #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
    +
    +


    From 3a6d16fbea5250795d716c61d20fe2c3b65a5b4e Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Mon, 20 May 2024 19:53:18 +0100 Subject: [PATCH 24/27] rochtml --- .../process_run_crate/ro-crate-preview.html | 12 +++++------ .../ro-crate-preview.html | 20 +++++++++---------- .../workflow_run_crate/ro-crate-preview.html | 2 +- 3 files changed, 17 insertions(+), 17 deletions(-) diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html index 26d0c97..f143730 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-preview.html @@ -357,7 +357,7 @@ { "@id": "https://w3id.org/ro/terms/workflow-run#", "@type": "DefinedTermSet", - "name": "Namespace for Common Provenance Model RO-Crate model", + "name": "Namespace for Workflow Run RO-Crate model", "hasDefinedTerm": [ { "@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection" @@ -1332,7 +1332,7 @@

    Go to: Process Ru
  • SSSOM mapping from PROV to Workflow Run Crate
    • -
  • Namespace for Common Provenance Model RO-Crate model
    • +
  • Namespace for Workflow Run RO-Crate model
  • JSON-LD context for workflow-run terms
    • @@ -1674,7 +1674,7 @@

    G



    -

    Go to: Namespace for Common Provenance Model RO-Crate model

    +

    Go to: Namespace for Workflow Run RO-Crate model

    @@ -1687,7 +1687,7 @@

    Go to: Namespace for https://w3id.org/ro/terms/workflow-run# name [?] - Namespace for Common Provenance Model RO-Crate model + Namespace for Workflow Run RO-Crate model @type DefinedTermSet @@ -1771,7 +1771,7 @@

    Go to: JSON-LD context license [?] @@ -2639,7 +2639,7 @@

    #hasVocabulary

    http://www.w3.org/ns/dx/prof/role/vocabulary hasArtifact [?] - Namespace for Common Provenance Model RO-Crate model + Namespace for Workflow Run RO-Crate model Items that reference this one hasResource [?] Process Run Crate profile diff --git a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html index 4dcba4a..f461de9 100644 --- a/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html @@ -321,7 +321,7 @@ { "@id": "https://w3id.org/ro/terms/workflow-run#", "@type": "DefinedTermSet", - "name": "Namespace for Common Provenance Model RO-Crate model" + "name": "Namespace for Workflow Run RO-Crate model" }, { "@id": "https://w3id.org/ro/terms/workflow-run", @@ -949,7 +949,7 @@

    Go to: Provena
  • SSSOM mapping from PROV to Workflow Run Crate
    • -
  • Namespace for Common Provenance Model RO-Crate model
    • +
  • Namespace for Workflow Run RO-Crate model
  • JSON-LD context for workflow-run terms
    • @@ -1267,7 +1267,7 @@

    G



    -

    Go to: Namespace for Common Provenance Model RO-Crate model

    +

    Go to: Namespace for Workflow Run RO-Crate model

    @@ -1280,7 +1280,7 @@

    Go to: Namespace for https://w3id.org/ro/terms/workflow-run# name [?] - Namespace for Common Provenance Model RO-Crate model + Namespace for Workflow Run RO-Crate model @type DefinedTermSet @@ -1342,7 +1342,7 @@

    Go to: JSON-LD context license [?] @@ -1562,7 +1562,7 @@

    Go to: ParameterConnection inDefinedTermSet [?] - Namespace for Common Provenance Model RO-Crate model + Namespace for Workflow Run RO-Crate model Items that reference this one hasPart [?] Provenance Run Crate profile @@ -1598,7 +1598,7 @@

    Go to: conn connection inDefinedTermSet [?] - Namespace for Common Provenance Model RO-Crate model + Namespace for Workflow Run RO-Crate model Items that reference this one hasPart [?] Provenance Run Crate profile @@ -1634,7 +1634,7 @@

    Go to: sourceParameter inDefinedTermSet [?] - Namespace for Common Provenance Model RO-Crate model + Namespace for Workflow Run RO-Crate model Items that reference this one hasPart [?] Provenance Run Crate profile @@ -1670,7 +1670,7 @@

    Go to: targetParameter inDefinedTermSet [?] - Namespace for Common Provenance Model RO-Crate model + Namespace for Workflow Run RO-Crate model Items that reference this one hasPart [?] Provenance Run Crate profile @@ -1760,7 +1760,7 @@

    #hasVocabulary

    http://www.w3.org/ns/dx/prof/role/vocabulary hasArtifact [?] - Namespace for Common Provenance Model RO-Crate model + Namespace for Workflow Run RO-Crate model Items that reference this one hasResource [?] Provenance Run Crate profile diff --git a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html index 9e34f50..a6531d3 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html @@ -899,7 +899,7 @@ { "@id": "https://w3id.org/ro/terms/workflow-run#", "@type": "DefinedTermSet", - "name": "Namespace for Common Provenance Model RO-Crate model" + "name": "Namespace for Workflow Run RO-Crate model" }, { "@id": "http://spdx.org/licenses/Apache-2.0", From 61994907406377dadd597118b48ea67cbb5ed504 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Tue, 21 May 2024 16:18:19 +0100 Subject: [PATCH 25/27] rdfs vocabulary --- docs/wfrun.ttl | 128 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 128 insertions(+) create mode 100644 docs/wfrun.ttl diff --git a/docs/wfrun.ttl b/docs/wfrun.ttl new file mode 100644 index 0000000..ee9d6f4 --- /dev/null +++ b/docs/wfrun.ttl @@ -0,0 +1,128 @@ +@prefix s: . +@prefix rdf: . +@prefix rdfs: . +@prefix wrroc: . +@prefix bioschemas: . + +wrroc: a s:DefinedTermSet ; + s:name "Workflow Run Crate namespace" ; + s:description "A Schema.org style Schema definitin of WRROC terms" ; + s:url "https://www.researchobject.org/ro-terms/workflow-run/" ; + s:creator ; + s:license ; + s:version "0.5.0" ; + s:hasDefinedTerm + wrroc:connection, + wrroc:containerImage, + wrroc:environment, + wrroc:md5, + wrroc:registry, + wrroc:sha1, + wrroc:sha256, + wrroc:sha512, + wrroc:sourceParameter, + wrroc:tag, + wrroc:targetParameter, + wrroc:ContainerImage, + wrroc:DockerImage, + wrroc:ParameterConnection, + wrroc:SIFImage . + + a s:Project ; + s:name "Workflow Run Crate task force"@en-gb . + +wrroc:connection rdf:type rdf:Property ; + s:domainIncludes s:HowToStep, bioschemas:ComputationalWorkflow; + s:rangeIncludes wrroc:ParameterConnection ; + rdfs:label "connection"@en-gb ; + rdfs:comment "A parameter connection created by this workflow"@en-gb . + +wrroc:containerImage rdf:type rdf:Property ; + s:domainIncludes s:CreateAction ; + s:rangeIncludes :ContainerImage ; + rdfs:label "containerImage"@en-gb ; + rdfs:comment "A container image associated with this entity"@en-gb . + +wrroc:environment rdf:type rdf:Property ; + s:domainIncludes s:CreateAction, + s:SoftwareApplication, + s:SoftwareSourceCode, + bioschemas:ComputationalWorkflow ; + s:rangeIncludes s:PropertyValue, bioschemas:FormalParameter ; + rdfs:label "environment"@en-gb ; + rdfs:comment "Environment variables used by the application"@en-gb . + +wrroc:md5 rdf:type rdf:Property ; + s:domainIncludes s:MediaObject, wrroc:ContainerImage ; + s:rangeIncludes s:Text ; + rdfs:label "md5"@en-gb ; + rdfs:comment "md5 checksum as a hexadecimal string"@en-gb . + + + + +wrroc:registry rdf:type rdf:Property ; + s:domainIncludes wrroc:ContainerImage ; + rdfs:label "registry"@en-gb ; + rdfs:comment "A service to register software products, such as container images"@en-gb . + +wrroc:sha1 rdf:type rdf:Property ; + s:domainIncludes s:MediaObject, wrroc:ContainerImage ; + s:rangeIncludes s:Text ; + rdfs:label "sha1"@en-gb ; + rdfs:comment "sha1 checksum as a hexadecimal string"@en-gb . + +wrroc:sha256 rdf:type rdf:Property ; + s:domainIncludes s:MediaObject, wrroc:ContainerImage ; + s:rangeIncludes s:Text ; + rdfs:label "sha256"@en-gb ; + rdfs:comment "sha256 checksum as a hexadecimal string"@en-gb . + +wrroc:sha512 rdf:type rdf:Property ; + s:domainIncludes s:MediaObject, wrroc:ContainerImage ; + s:rangeIncludes s:Text ; + rdfs:label "sha512"@en-gb ; + rdfs:comment "sha512 checksum as a hexadecimal string"@en-gb . + +wrroc:sourceParameter rdf:type rdf:Property ; + s:domainIncludes wrroc:ParameterConnection ; + s:rangeIncludes bioschemas:FormalParameter ; + rdfs:label "sourceParameter"@en-gb ; + rdfs:comment "The source (upstream) parameter"@en-gb . + +wrroc:targetParameter rdf:type rdf:Property ; + s:domainIncludes wrroc:ParameterConnection ; + s:rangeIncludes bioschemas:FormalParameter ; + rdfs:label "targetParameter"@en-gb ; + rdfs:comment "The target (downstream) parameter"@en-gb . + +wrroc:tag rdf:type rdf:Property ; + s:domainIncludes wrroc:ContainerImage ; + s:rangeIncludes s:Text ; + rdfs:label "tag"@en-gb ; + rdfs:comment "A tag assigned to a software product, such as a container image"@en-gb . + +wrroc:ContainerImage rdf:type rdfs:Class ; + rdfs:subClassOf s:CreativeWork ; + rdfs:label "ContainerImage"@en-gb ; + rdfs:comment "A containerisation software container image"@en-gb . + +wrroc:DockerImage rdf:type rdfs:Class ; + rdfs:subClassOf wrroc:ContainerImage ; + rdfs:label "DockerImage"@en-gb ; + rdfs:comment "A Docker container image"@en-gb . + +wrroc:ParameterConnection rdf:type rdfs:Class ; + rdfs:subClassOf s:Intangible ; + rdfs:label "ParameterConnection"@en-gb ; + rdfs:comment "A connection between parameters of different applications"@en-gb . + +wrroc:SIFImage rdf:type rdfs:Class ; + rdfs:subClassOf wrroc:ContainerImage ; + rdfs:label "SIFImage"@en-gb ; + rdfs:comment "A Singularity Image Format container image"@en-gb . + + + + + From 98889cbaa216704b1b972bbc217ae923a64ceddf Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Tue, 21 May 2024 16:29:57 +0100 Subject: [PATCH 26/27] old skool with vann/dct/owl --- docs/wfrun.ttl | 115 ++++++++++++++++++++++++++++++------------------- 1 file changed, 70 insertions(+), 45 deletions(-) diff --git a/docs/wfrun.ttl b/docs/wfrun.ttl index ee9d6f4..2fba1a7 100644 --- a/docs/wfrun.ttl +++ b/docs/wfrun.ttl @@ -1,124 +1,149 @@ @prefix s: . @prefix rdf: . @prefix rdfs: . -@prefix wrroc: . +@prefix wfrun: . @prefix bioschemas: . +@prefix vann: . +@prefix dct: +@prefix owl: . -wrroc: a s:DefinedTermSet ; +wfrun: a s:DefinedTermSet, owl:Ontology ; s:name "Workflow Run Crate namespace" ; + dct:title"Workflow Run Crate namespace" ; + vann:preferredNamespacePrefix "wfrun" ; + vann:preferredNamespaceUri "https://w3id.org/ro/terms/workflow-run#"; s:description "A Schema.org style Schema definitin of WRROC terms" ; + dct:description "A Schema.org style Schema definitin of WRROC terms" ; s:url "https://www.researchobject.org/ro-terms/workflow-run/" ; s:creator ; + dct:creator ; s:license ; + dct:license ; + s:version "0.5.0" ; s:hasDefinedTerm - wrroc:connection, - wrroc:containerImage, - wrroc:environment, - wrroc:md5, - wrroc:registry, - wrroc:sha1, - wrroc:sha256, - wrroc:sha512, - wrroc:sourceParameter, - wrroc:tag, - wrroc:targetParameter, - wrroc:ContainerImage, - wrroc:DockerImage, - wrroc:ParameterConnection, - wrroc:SIFImage . - - a s:Project ; + wfrun:connection, + wfrun:containerImage, + wfrun:environment, + wfrun:md5, + wfrun:registry, + wfrun:sha1, + wfrun:sha256, + wfrun:sha512, + wfrun:sourceParameter, + wfrun:tag, + wfrun:targetParameter, + wfrun:ContainerImage, + wfrun:DockerImage, + wfrun:ParameterConnection, + wfrun:SIFImage . + + a s:Project, dct:Agent ; s:name "Workflow Run Crate task force"@en-gb . -wrroc:connection rdf:type rdf:Property ; +wfrun:connection rdf:type rdf:Property ; s:domainIncludes s:HowToStep, bioschemas:ComputationalWorkflow; - s:rangeIncludes wrroc:ParameterConnection ; + s:rangeIncludes wfrun:ParameterConnection ; + rdfs:isDefinedBy wfrun: ; rdfs:label "connection"@en-gb ; rdfs:comment "A parameter connection created by this workflow"@en-gb . -wrroc:containerImage rdf:type rdf:Property ; +wfrun:containerImage rdf:type rdf:Property ; s:domainIncludes s:CreateAction ; s:rangeIncludes :ContainerImage ; + rdfs:isDefinedBy wfrun: ; rdfs:label "containerImage"@en-gb ; rdfs:comment "A container image associated with this entity"@en-gb . -wrroc:environment rdf:type rdf:Property ; +wfrun:environment rdf:type rdf:Property ; s:domainIncludes s:CreateAction, s:SoftwareApplication, s:SoftwareSourceCode, bioschemas:ComputationalWorkflow ; s:rangeIncludes s:PropertyValue, bioschemas:FormalParameter ; + rdfs:isDefinedBy wfrun: ; rdfs:label "environment"@en-gb ; rdfs:comment "Environment variables used by the application"@en-gb . -wrroc:md5 rdf:type rdf:Property ; - s:domainIncludes s:MediaObject, wrroc:ContainerImage ; +wfrun:md5 rdf:type rdf:Property ; + s:domainIncludes s:MediaObject, wfrun:ContainerImage ; s:rangeIncludes s:Text ; + rdfs:isDefinedBy wfrun: ; rdfs:label "md5"@en-gb ; rdfs:comment "md5 checksum as a hexadecimal string"@en-gb . -wrroc:registry rdf:type rdf:Property ; - s:domainIncludes wrroc:ContainerImage ; +wfrun:registry rdf:type rdf:Property ; + s:domainIncludes wfrun:ContainerImage ; + rdfs:isDefinedBy wfrun: ; rdfs:label "registry"@en-gb ; rdfs:comment "A service to register software products, such as container images"@en-gb . -wrroc:sha1 rdf:type rdf:Property ; - s:domainIncludes s:MediaObject, wrroc:ContainerImage ; +wfrun:sha1 rdf:type rdf:Property ; + s:domainIncludes s:MediaObject, wfrun:ContainerImage ; s:rangeIncludes s:Text ; + rdfs:isDefinedBy wfrun: ; rdfs:label "sha1"@en-gb ; rdfs:comment "sha1 checksum as a hexadecimal string"@en-gb . -wrroc:sha256 rdf:type rdf:Property ; - s:domainIncludes s:MediaObject, wrroc:ContainerImage ; +wfrun:sha256 rdf:type rdf:Property ; + s:domainIncludes s:MediaObject, wfrun:ContainerImage ; s:rangeIncludes s:Text ; + rdfs:isDefinedBy wfrun: ; rdfs:label "sha256"@en-gb ; rdfs:comment "sha256 checksum as a hexadecimal string"@en-gb . -wrroc:sha512 rdf:type rdf:Property ; - s:domainIncludes s:MediaObject, wrroc:ContainerImage ; +wfrun:sha512 rdf:type rdf:Property ; + s:domainIncludes s:MediaObject, wfrun:ContainerImage ; s:rangeIncludes s:Text ; + rdfs:isDefinedBy wfrun: ; rdfs:label "sha512"@en-gb ; rdfs:comment "sha512 checksum as a hexadecimal string"@en-gb . -wrroc:sourceParameter rdf:type rdf:Property ; - s:domainIncludes wrroc:ParameterConnection ; +wfrun:sourceParameter rdf:type rdf:Property ; + s:domainIncludes wfrun:ParameterConnection ; s:rangeIncludes bioschemas:FormalParameter ; + rdfs:isDefinedBy wfrun: ; rdfs:label "sourceParameter"@en-gb ; rdfs:comment "The source (upstream) parameter"@en-gb . -wrroc:targetParameter rdf:type rdf:Property ; - s:domainIncludes wrroc:ParameterConnection ; +wfrun:targetParameter rdf:type rdf:Property ; + s:domainIncludes wfrun:ParameterConnection ; s:rangeIncludes bioschemas:FormalParameter ; + rdfs:isDefinedBy wfrun: ; rdfs:label "targetParameter"@en-gb ; rdfs:comment "The target (downstream) parameter"@en-gb . -wrroc:tag rdf:type rdf:Property ; - s:domainIncludes wrroc:ContainerImage ; +wfrun:tag rdf:type rdf:Property ; + s:domainIncludes wfrun:ContainerImage ; s:rangeIncludes s:Text ; + rdfs:isDefinedBy wfrun: ; rdfs:label "tag"@en-gb ; rdfs:comment "A tag assigned to a software product, such as a container image"@en-gb . -wrroc:ContainerImage rdf:type rdfs:Class ; +wfrun:ContainerImage rdf:type rdfs:Class ; rdfs:subClassOf s:CreativeWork ; + rdfs:isDefinedBy wfrun: ; rdfs:label "ContainerImage"@en-gb ; rdfs:comment "A containerisation software container image"@en-gb . -wrroc:DockerImage rdf:type rdfs:Class ; - rdfs:subClassOf wrroc:ContainerImage ; +wfrun:DockerImage rdf:type rdfs:Class ; + rdfs:subClassOf wfrun:ContainerImage ; + rdfs:isDefinedBy wfrun: ; rdfs:label "DockerImage"@en-gb ; rdfs:comment "A Docker container image"@en-gb . -wrroc:ParameterConnection rdf:type rdfs:Class ; +wfrun:ParameterConnection rdf:type rdfs:Class ; rdfs:subClassOf s:Intangible ; + rdfs:isDefinedBy wfrun: ; rdfs:label "ParameterConnection"@en-gb ; rdfs:comment "A connection between parameters of different applications"@en-gb . -wrroc:SIFImage rdf:type rdfs:Class ; - rdfs:subClassOf wrroc:ContainerImage ; +wfrun:SIFImage rdf:type rdfs:Class ; + rdfs:subClassOf wfrun:ContainerImage ; + rdfs:isDefinedBy wfrun: ; rdfs:label "SIFImage"@en-gb ; rdfs:comment "A Singularity Image Format container image"@en-gb . From 285470c77b3fc64c61a3da82ed51d68902ca4c81 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Tue, 21 May 2024 16:56:26 +0100 Subject: [PATCH 27/27] rdfs vocabulary and rdf syntaxes --- docs/wfrun.csv | 16 ++ docs/wfrun.jsonld | 456 ++++++++++++++++++++++++++++++++++++++++++++++ docs/wfrun.nt | 126 +++++++++++++ docs/wfrun.rdf | 170 +++++++++++++++++ docs/wfrun.ttl | 4 +- 5 files changed, 770 insertions(+), 2 deletions(-) create mode 100644 docs/wfrun.csv create mode 100644 docs/wfrun.jsonld create mode 100644 docs/wfrun.nt create mode 100644 docs/wfrun.rdf diff --git a/docs/wfrun.csv b/docs/wfrun.csv new file mode 100644 index 0000000..ccae83c --- /dev/null +++ b/docs/wfrun.csv @@ -0,0 +1,16 @@ +"term","type","label","description","domain","range" +"ParameterConnection","Class","ParameterConnection","A connection between parameters of different applications",, +"ContainerImage","Class","ContainerImage","A containerization software container image",, +"DockerImage","Class","DockerImage","A Docker container image",, +"SIFImage","Class","SIFImage","A Singularity Image Format container image",, +"connection","Property","connection","A parameter connection created by this workflow","ComputationalWorkflow HowToStep","ParameterConnection" +"sourceParameter","Property","sourceParameter","The source (upstream) parameter","ParameterConnection","FormalParameter" +"targetParameter","Property","targetParameter","The target (downstream) parameter","ParameterConnection","FormalParameter" +"md5","Property","md5","md5 checksum as a hexadecimal string","File ContainerImage","Text" +"sha1","Property","sha1","sha1 checksum as a hexadecimal string","File ContainerImage","Text" +"sha256","Property","sha256","sha256 checksum as a hexadecimal string","File ContainerImage","Text" +"sha512","Property","sha512","sha512 checksum as a hexadecimal string","File ContainerImage","Text" +"environment","Property","environment","environment variables used by the application","SoftwareApplication SoftwareSourceCode ComputationalWorkflow CreateAction","FormalParameter PropertyValue" +"registry","Property","registry","A service to register software products, such as container images","ContainerImage","Text" +"tag","Property","tag","A tag assigned to a software product, such as a container image","ContainerImage","Text" +"containerImage","Property","containerImage","A container image associated with this entity","CreateAction","ContainerImage URL" diff --git a/docs/wfrun.jsonld b/docs/wfrun.jsonld new file mode 100644 index 0000000..c28005d --- /dev/null +++ b/docs/wfrun.jsonld @@ -0,0 +1,456 @@ +{ + "@context": [ + "https://w3id.org/ro/crate/1.1/context", + { + "ParameterConnection": "https://w3id.org/ro/terms/workflow-run#ParameterConnection", + "ContainerImage": "https://w3id.org/ro/terms/workflow-run#ContainerImage", + "DockerImage": "https://w3id.org/ro/terms/workflow-run#DockerImage", + "SIFImage": "https://w3id.org/ro/terms/workflow-run#SIFImage", + "connection": "https://w3id.org/ro/terms/workflow-run#connection", + "sourceParameter": "https://w3id.org/ro/terms/workflow-run#sourceParameter", + "targetParameter": "https://w3id.org/ro/terms/workflow-run#targetParameter", + "md5": "https://w3id.org/ro/terms/workflow-run#md5", + "sha1": "https://w3id.org/ro/terms/workflow-run#sha1", + "sha256": "https://w3id.org/ro/terms/workflow-run#sha256", + "sha512": "https://w3id.org/ro/terms/workflow-run#sha512", + "environment": "https://w3id.org/ro/terms/workflow-run#environment", + "registry": "https://w3id.org/ro/terms/workflow-run#registry", + "tag": "https://w3id.org/ro/terms/workflow-run#tag", + "containerImage": "https://w3id.org/ro/terms/workflow-run#containerImage", + + "input": "https://bioschemas.org/properties/input", + "output": "https://bioschemas.org/properties/output", + "wfrun": "https://w3id.org/ro/terms/workflow-run#", + "owl": "http://www.w3.org/2002/07/owl#", + "vann": "http://purl.org/vocab/vann/" + } + ], + "@graph": [ + { + "@id": "wfrun:registry", + "rdfs:comment": { + "@language": "en-gb", + "@value": "A service to register software products, such as container images" + }, + "rdfs:label": { + "@language": "en-gb", + "@value": "registry" + }, + "rdfs:isDefinedBy": { + "@id": "https://w3id.org/ro/terms/workflow-run#" + }, + "domainIncludes": { + "@id": "wfrun:ContainerImage" + }, + "@type": "rdf:Property" + }, + { + "@id": "https://w3id.org/ro/terms/workflow-run#", + "hasDefinedTerm": [ + { + "@id": "wfrun:sha256" + }, + { + "@id": "wfrun:SIFImage" + }, + { + "@id": "wfrun:tag" + }, + { + "@id": "wfrun:sourceParameter" + }, + { + "@id": "wfrun:environment" + }, + { + "@id": "wfrun:containerImage" + }, + { + "@id": "wfrun:md5" + }, + { + "@id": "wfrun:DockerImage" + }, + { + "@id": "wfrun:connection" + }, + { + "@id": "wfrun:ContainerImage" + }, + { + "@id": "wfrun:ParameterConnection" + }, + { + "@id": "wfrun:sha512" + }, + { + "@id": "wfrun:sha1" + }, + { + "@id": "wfrun:targetParameter" + }, + { + "@id": "wfrun:registry" + } + ], + "@type": [ + "owl:Ontology", + "DefinedTermSet" + ], + "dct:title": "Workflow Run Crate namespace", + "license": { + "@id": "http://spdx.org/licenses/Apache-2.0" + }, + "vann:preferredNamespaceUri": "https://w3id.org/ro/terms/workflow-run#", + "dct:license": { + "@id": "http://spdx.org/licenses/Apache-2.0" + }, + "description": "A Schema.org style Schema definitin of WRROC terms", + "vann:preferredNamespacePrefix": "wfrun", + "version": "0.5.0", + "dct:description": "A Schema.org style Schema definitin of WRROC terms", + "dct:creator": { + "@id": "https://researchobject.org/workflow-run-crate/" + }, + "url": "https://www.researchobject.org/ro-terms/workflow-run/", + "name": "Workflow Run Crate namespace", + "creator": { + "@id": "https://researchobject.org/workflow-run-crate/" + } + }, + { + "@id": "wfrun:ContainerImage", + "rdfs:comment": { + "@language": "en-gb", + "@value": "A containerisation software container image" + }, + "rdfs:label": { + "@language": "en-gb", + "@value": "ContainerImage" + }, + "rdfs:isDefinedBy": { + "@id": "https://w3id.org/ro/terms/workflow-run#" + }, + "rdfs:subClassOf": { + "@id": "CreativeWork" + }, + "@type": "rdfs:Class" + }, + { + "@id": "https://researchobject.org/workflow-run-crate/", + "name": { + "@language": "en-gb", + "@value": "Workflow Run Crate task force" + }, + "@type": [ + "dct:Agent", + "Project" + ] + }, + { + "@id": "wfrun:sha512", + "rdfs:comment": { + "@language": "en-gb", + "@value": "sha512 checksum as a hexadecimal string" + }, + "rdfs:label": { + "@language": "en-gb", + "@value": "sha512" + }, + "rdfs:isDefinedBy": { + "@id": "https://w3id.org/ro/terms/workflow-run#" + }, + "rangeIncludes": { + "@id": "Text" + }, + "domainIncludes": [ + { + "@id": "wfrun:ContainerImage" + }, + { + "@id": "MediaObject" + } + ], + "@type": "rdf:Property" + }, + { + "@id": "wfrun:sha256", + "rdfs:comment": { + "@language": "en-gb", + "@value": "sha256 checksum as a hexadecimal string" + }, + "rdfs:label": { + "@language": "en-gb", + "@value": "sha256" + }, + "rdfs:isDefinedBy": { + "@id": "https://w3id.org/ro/terms/workflow-run#" + }, + "rangeIncludes": { + "@id": "Text" + }, + "domainIncludes": [ + { + "@id": "wfrun:ContainerImage" + }, + { + "@id": "MediaObject" + } + ], + "@type": "rdf:Property" + }, + { + "@id": "wfrun:connection", + "rdfs:comment": { + "@language": "en-gb", + "@value": "A parameter connection created by this workflow" + }, + "rdfs:label": { + "@language": "en-gb", + "@value": "connection" + }, + "rdfs:isDefinedBy": { + "@id": "https://w3id.org/ro/terms/workflow-run#" + }, + "rangeIncludes": { + "@id": "wfrun:ParameterConnection" + }, + "domainIncludes": [ + { + "@id": "ComputationalWorkflow" + }, + { + "@id": "HowToStep" + } + ], + "@type": "rdf:Property" + }, + { + "@id": "wfrun:ParameterConnection", + "rdfs:comment": { + "@language": "en-gb", + "@value": "A connection between parameters of different applications" + }, + "rdfs:label": { + "@language": "en-gb", + "@value": "ParameterConnection" + }, + "rdfs:isDefinedBy": { + "@id": "https://w3id.org/ro/terms/workflow-run#" + }, + "rdfs:subClassOf": { + "@id": "Intangible" + }, + "@type": "rdfs:Class" + }, + { + "@id": "wfrun:SIFImage", + "rdfs:comment": { + "@language": "en-gb", + "@value": "A Singularity Image Format container image" + }, + "rdfs:label": { + "@language": "en-gb", + "@value": "SIFImage" + }, + "rdfs:isDefinedBy": { + "@id": "https://w3id.org/ro/terms/workflow-run#" + }, + "rdfs:subClassOf": { + "@id": "wfrun:ContainerImage" + }, + "@type": "rdfs:Class" + }, + { + "@id": "wfrun:targetParameter", + "rdfs:comment": { + "@language": "en-gb", + "@value": "The target (downstream) parameter" + }, + "rdfs:label": { + "@language": "en-gb", + "@value": "targetParameter" + }, + "rdfs:isDefinedBy": { + "@id": "https://w3id.org/ro/terms/workflow-run#" + }, + "rangeIncludes": { + "@id": "FormalParameter" + }, + "domainIncludes": { + "@id": "wfrun:ParameterConnection" + }, + "@type": "rdf:Property" + }, + { + "@id": "wfrun:DockerImage", + "rdfs:comment": { + "@language": "en-gb", + "@value": "A Docker container image" + }, + "rdfs:label": { + "@language": "en-gb", + "@value": "DockerImage" + }, + "rdfs:isDefinedBy": { + "@id": "https://w3id.org/ro/terms/workflow-run#" + }, + "rdfs:subClassOf": { + "@id": "wfrun:ContainerImage" + }, + "@type": "rdfs:Class" + }, + { + "@id": "wfrun:tag", + "rdfs:comment": { + "@language": "en-gb", + "@value": "A tag assigned to a software product, such as a container image" + }, + "rdfs:label": { + "@language": "en-gb", + "@value": "tag" + }, + "rdfs:isDefinedBy": { + "@id": "https://w3id.org/ro/terms/workflow-run#" + }, + "rangeIncludes": { + "@id": "Text" + }, + "domainIncludes": { + "@id": "wfrun:ContainerImage" + }, + "@type": "rdf:Property" + }, + { + "@id": "wfrun:sourceParameter", + "rdfs:comment": { + "@language": "en-gb", + "@value": "The source (upstream) parameter" + }, + "rdfs:label": { + "@language": "en-gb", + "@value": "sourceParameter" + }, + "rdfs:isDefinedBy": { + "@id": "https://w3id.org/ro/terms/workflow-run#" + }, + "rangeIncludes": { + "@id": "FormalParameter" + }, + "domainIncludes": { + "@id": "wfrun:ParameterConnection" + }, + "@type": "rdf:Property" + }, + { + "@id": "wfrun:environment", + "@type": "rdf:Property", + "domainIncludes": [ + { + "@id": "CreateAction" + }, + { + "@id": "SoftwareApplication" + }, + { + "@id": "ComputationalWorkflow" + }, + { + "@id": "SoftwareSourceCode" + } + ], + "rangeIncludes": [ + { + "@id": "FormalParameter" + }, + { + "@id": "PropertyValue" + } + ], + "rdfs:comment": { + "@language": "en-gb", + "@value": "Environment variables used by the application" + }, + "rdfs:label": { + "@language": "en-gb", + "@value": "environment" + }, + "rdfs:isDefinedBy": { + "@id": "https://w3id.org/ro/terms/workflow-run#" + } + }, + { + "@id": "wfrun:containerImage", + "rdfs:comment": { + "@language": "en-gb", + "@value": "A container image associated with this entity" + }, + "rdfs:label": { + "@language": "en-gb", + "@value": "containerImage" + }, + "rdfs:isDefinedBy": { + "@id": "https://w3id.org/ro/terms/workflow-run#" + }, + "rangeIncludes": { + "@id": "wfrun:ContainerImage" + }, + "domainIncludes": { + "@id": "CreateAction" + }, + "@type": "rdf:Property" + }, + { + "@id": "wfrun:md5", + "rdfs:comment": { + "@language": "en-gb", + "@value": "md5 checksum as a hexadecimal string" + }, + "rdfs:label": { + "@language": "en-gb", + "@value": "md5" + }, + "rdfs:isDefinedBy": { + "@id": "https://w3id.org/ro/terms/workflow-run#" + }, + "rangeIncludes": { + "@id": "Text" + }, + "domainIncludes": [ + { + "@id": "wfrun:ContainerImage" + }, + { + "@id": "MediaObject" + } + ], + "@type": "rdf:Property" + }, + { + "@id": "wfrun:sha1", + "rdfs:comment": { + "@language": "en-gb", + "@value": "sha1 checksum as a hexadecimal string" + }, + "rdfs:label": { + "@language": "en-gb", + "@value": "sha1" + }, + "rdfs:isDefinedBy": { + "@id": "https://w3id.org/ro/terms/workflow-run#" + }, + "rangeIncludes": { + "@id": "Text" + }, + "domainIncludes": [ + { + "@id": "wfrun:ContainerImage" + }, + { + "@id": "MediaObject" + } + ], + "@type": "rdf:Property" + } + ] +} diff --git a/docs/wfrun.nt b/docs/wfrun.nt new file mode 100644 index 0000000..f11c8fa --- /dev/null +++ b/docs/wfrun.nt @@ -0,0 +1,126 @@ + . + . + "Workflow Run Crate namespace" . + "Workflow Run Crate namespace" . + "wfrun" . + "https://w3id.org/ro/terms/workflow-run#" . + "A Schema.org style Schema definitin of WRROC terms" . + "A Schema.org style Schema definitin of WRROC terms" . + "https://www.researchobject.org/ro-terms/workflow-run/" . + . + . + . + . + "0.5.0" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Workflow Run Crate task force"@en-gb . + . + . + . + . + . + "connection"@en-gb . + "A parameter connection created by this workflow"@en-gb . + . + . + . + . + "containerImage"@en-gb . + "A container image associated with this entity"@en-gb . + . + . + . + . + . + . + . + . + "environment"@en-gb . + "Environment variables used by the application"@en-gb . + . + . + . + . + . + "md5"@en-gb . + "md5 checksum as a hexadecimal string"@en-gb . + . + . + . + "registry"@en-gb . + "A service to register software products, such as container images"@en-gb . + . + . + . + . + . + "sha1"@en-gb . + "sha1 checksum as a hexadecimal string"@en-gb . + . + . + . + . + . + "sha256"@en-gb . + "sha256 checksum as a hexadecimal string"@en-gb . + . + . + . + . + . + "sha512"@en-gb . + "sha512 checksum as a hexadecimal string"@en-gb . + . + . + . + . + "sourceParameter"@en-gb . + "The source (upstream) parameter"@en-gb . + . + . + . + . + "targetParameter"@en-gb . + "The target (downstream) parameter"@en-gb . + . + . + . + . + "tag"@en-gb . + "A tag assigned to a software product, such as a container image"@en-gb . + . + . + . + "ContainerImage"@en-gb . + "A containerisation software container image"@en-gb . + . + . + . + "DockerImage"@en-gb . + "A Docker container image"@en-gb . + . + . + . + "ParameterConnection"@en-gb . + "A connection between parameters of different applications"@en-gb . + . + . + . + "SIFImage"@en-gb . + "A Singularity Image Format container image"@en-gb . diff --git a/docs/wfrun.rdf b/docs/wfrun.rdf new file mode 100644 index 0000000..5a150a0 --- /dev/null +++ b/docs/wfrun.rdf @@ -0,0 +1,170 @@ + + + The source (upstream) parameter + sourceParameter + + + + + + + A Docker container image + DockerImage + + + + + + sha1 checksum as a hexadecimal string + sha1 + + + + + + + + sha512 checksum as a hexadecimal string + sha512 + + + + + + + + A tag assigned to a software product, such as a container image + tag + + + + + + + + + + Workflow Run Crate namespace + + + + https://w3id.org/ro/terms/workflow-run# + + + + + A Schema.org style Schema definitin of WRROC terms + + + + + wfrun + 0.5.0 + A Schema.org style Schema definitin of WRROC terms + + + + + https://www.researchobject.org/ro-terms/workflow-run/ + + Workflow Run Crate namespace + + + + + A container image associated with this entity + containerImage + + + + + + + A connection between parameters of different applications + ParameterConnection + + + + + + A Singularity Image Format container image + SIFImage + + + + + + Workflow Run Crate task force + + + + + sha256 checksum as a hexadecimal string + sha256 + + + + + + + + A parameter connection created by this workflow + connection + + + + + + + + The target (downstream) parameter + targetParameter + + + + + + + + + + + Environment variables used by the application + environment + + + + + + + A containerisation software container image + ContainerImage + + + + + + A service to register software products, such as container images + registry + + + + + + md5 checksum as a hexadecimal string + md5 + + + + + + + diff --git a/docs/wfrun.ttl b/docs/wfrun.ttl index 2fba1a7..38a3826 100644 --- a/docs/wfrun.ttl +++ b/docs/wfrun.ttl @@ -4,7 +4,7 @@ @prefix wfrun: . @prefix bioschemas: . @prefix vann: . -@prefix dct: +@prefix dct: . @prefix owl: . wfrun: a s:DefinedTermSet, owl:Ontology ; @@ -50,7 +50,7 @@ wfrun:connection rdf:type rdf:Property ; wfrun:containerImage rdf:type rdf:Property ; s:domainIncludes s:CreateAction ; - s:rangeIncludes :ContainerImage ; + s:rangeIncludes wfrun:ContainerImage ; rdfs:isDefinedBy wfrun: ; rdfs:label "containerImage"@en-gb ; rdfs:comment "A container image associated with this entity"@en-gb .