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/). + 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/process_run_crate/example1/pics/2017-06-11 12.56.14.jpg b/docs/profiles/0.5-DRAFT/process_run_crate/example1/pics/2017-06-11 12.56.14.jpg new file mode 100644 index 0000000..0c3f703 Binary files /dev/null and b/docs/profiles/0.5-DRAFT/process_run_crate/example1/pics/2017-06-11 12.56.14.jpg differ diff --git a/docs/profiles/0.5-DRAFT/process_run_crate/example1/pics/sepia_fence.jpg b/docs/profiles/0.5-DRAFT/process_run_crate/example1/pics/sepia_fence.jpg new file mode 100644 index 0000000..9da77b8 Binary files /dev/null and b/docs/profiles/0.5-DRAFT/process_run_crate/example1/pics/sepia_fence.jpg differ 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 new file mode 100644 index 0000000..05cd8d6 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/process_run_crate/example1/ro-crate-metadata.json @@ -0,0 +1,75 @@ +{ "@context": "https://w3id.org/ro/crate/1.1/context", + "@graph": [ + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"}, + "about": {"@id": "./"} + }, + { + "@id": "./", + "@type": "Dataset", + "conformsTo": {"@id": "https://w3id.org/ro/wfrun/process/0.4"}, + "hasPart": [ + {"@id": "pics/2017-06-11%2012.56.14.jpg"}, + {"@id": "pics/sepia_fence.jpg"} + ], + "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/0.4", + "@type": "CreativeWork", + "name": "Process Run Crate", + "version": "0.5" + }, + { + "@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..7877d6b --- /dev/null +++ b/docs/profiles/0.5-DRAFT/process_run_crate/example1/ro-crate-preview.html @@ -0,0 +1,357 @@ + + + + + + + + + + + + + + + + + + + + + + + + +
+
+

+

My Pictures

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

My Pictures

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
@id./
name [?]My Pictures
@typeDataset
conformsTo [?]Process Run Crate
hasPart [?]
isBasedOn [?]https://doi.org/10.5281/zenodo.1009240
license [?]http://spdx.org/licenses/CC0-1.0
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/0.4
name [?]Process Run Crate
@typeCreativeWork
version [?]0.5
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.md b/docs/profiles/0.5-DRAFT/process_run_crate/index.md similarity index 92% 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..f156c42 100644 --- a/docs/profiles/0.5-DRAFT/process_run_crate.md +++ b/docs/profiles/0.5-DRAFT/process_run_crate/index.md @@ -7,7 +7,14 @@ 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)) +* Example conforming crate: [ro-crate-metadata.json](example1/ro-crate-metadata.json) [ro-crate-preview.html](example1/ro-crate-preview.html) +* Profile Crate: [ro-crate-metadata.json](ro-crate-metadata.json) [ro-crate-preview.html](ro-crate-preview.html) +* Extends: + - [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1) +* JSON-LD context: +* Vocabulary terms: This profile uses terminology from the [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1), and [extends it](https://www.researchobject.org/ro-crate/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. @@ -22,11 +29,16 @@ 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`) +* [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": [ @@ -39,7 +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"} @@ -47,7 +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" @@ -112,7 +124,7 @@ Note that the command line shown in the action's `description` is not directly r conformsTo MUST - 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/0.1"} + 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"} @@ -216,7 +228,7 @@ 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. @@ -236,7 +248,7 @@ 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 +266,7 @@ 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..e781247 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/process_run_crate/ro-crate-metadata.json @@ -0,0 +1,916 @@ +{ "@context": + "https://w3id.org/ro/crate/1.2-DRAFT/context", + "@graph": [ + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "license": { "@id": "http://spdx.org/licenses/CC0-1.0" }, + "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"}, + "about": {"@id": "https://w3id.org/ro/wfrun/process/0.5-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"], + "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", + "license": { + "@id": "https://www.apache.org/licenses/LICENSE-2.0" + }, + "author": [ + {"@id": "https://www.researchobject.org/workflow-run-crate/"} + ], + "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" }, + { "@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" }, + { "@id": "#hasConstraints" }, + { "@id": "#hasVocabulary" }, + { "@id": "#hasGuidance" }, + { "@id": "#hasExample" }, + { "@id": "#hasMappingToProv"} + ], + "citation": { "@id": "https://doi.org/10.48550/arXiv.2312.07852" } + }, + { + "@id": "https://www.researchobject.org/workflow-run-crate/", + "@type": "Project", + "name": "Workflow Run Crate task force", + "member": [ + + { "@id": "https://orcid.org/0000-0001-8271-5429"}, + { "@id": "https://orcid.org/0000-0003-4929-1219"}, + { "@id": "https://orcid.org/0000-0001-9842-9718"}, + { "@id": "https://orcid.org/0000-0002-5432-2748"}, + { "@id": "https://orcid.org/0000-0002-4806-5140"}, + { "@id": "https://orcid.org/0000-0003-3156-2105"}, + { "@id": "https://orcid.org/0000-0002-6190-122X"}, + { "@id": "https://orcid.org/0000-0003-0454-7145"}, + { "@id": "https://orcid.org/0000-0002-8940-4946"}, + { "@id": "https://orcid.org/0000-0003-0606-2512"}, + { "@id": "https://orcid.org/0000-0002-3468-0652"}, + { "@id": "https://orcid.org/0000-0002-2961-9670"}, + { "@id": "https://orcid.org/0000-0003-3986-0510"}, + { "@id": "https://orcid.org/0000-0002-0003-2024"}, + { "@id": "https://orcid.org/0000-0002-9464-6640"}, + { "@id": "https://orcid.org/0000-0001-5845-8880"}, + { "@id": "https://orcid.org/0000-0003-4894-4660"}, + { "@id": "https://orcid.org/0000-0002-4405-6802"}, + { "@id": "https://orcid.org/0000-0001-9290-2017"}, + { "@id": "https://orcid.org/0000-0003-0617-9219"}, + { "@id": "https://orcid.org/0000-0001-9228-2882"}, + { "@id": "https://orcid.org/0000-0003-3898-9451"}, + { "@id": "https://orcid.org/0000-0003-3777-5945"}, + { "@id": "https://orcid.org/0000-0003-2765-0049"}, + { "@id": "https://orcid.org/0000-0001-9818-9320"}, + { "@id": "https://orcid.org/0000-0002-8122-9522"}, + { "@id": "https://orcid.org/0000-0002-8330-4071"}, + { "@id": "https://orcid.org/0000-0003-4073-7456"}, + { "@id": "https://orcid.org/0000-0003-1361-7301"}, + { "@id": "https://orcid.org/0000-0002-5358-616X"}, + { "@id": "https://orcid.org/0000-0002-5477-287X"}, + { "@id": "https://orcid.org/0000-0001-8250-4074"}, + { "@id": "https://orcid.org/0000-0003-0902-0086"}, + { "@id": "https://orcid.org/0000-0001-8172-8981"}, + { "@id": "https://orcid.org/0000-0001-6740-9212"}, + { "@id": "https://orcid.org/0000-0001-5411-356X"}, + { "@id": "https://orcid.org/0000-0003-0035-0951"}, + { "@id": "https://orcid.org/0000-0003-0711-5196"} + ], + "parentOrganization": { "@id": "https://www.researchobject.org/ro-crate/community" } + }, + { + "@id": "https://www.researchobject.org/ro-crate/community", + "@type": "Project", + "name": "RO-Crate Community" + }, + { + "@id": "index.html", + "@type": "File", + "name": "Process Run Crate (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": "example1/", + "@type": "Dataset", + "name": "Example Process Run Crate", + "conformsTo": [ + { "@id": "https://w3id.org/ro/crate"}, + { "@id": "https://w3id.org/ro/wfrun/process/0.4" } + ], + "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", + "name": "JSON-LD context for workflow-run terms", + "contentUrl": "https://www.researchobject.org/ro-terms/workflow-run/context.json", + "conformsTo": { + "@id": "http://www.w3.org/ns/json-ld#Context" + }, + "encodingFormat": "application/ld+json", + "isBasedOn": [ + { + "@id": "https://w3id.org/ro/crate/1.1/context" + }, + { + "@id": "https://w3id.org/ro/terms/workflow-run#" + } + ], + "license": { + "@id": "https://creativecommons.org/publicdomain/zero/1.0/" + } + }, + { + "@id": "#hasSpecification", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/specification" }, + "hasArtifact": {"@id": "index.html"} + }, + { + "@id": "#hasConstraints", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/constraints" }, + "hasArtifact": {"@id": "index.html#requirements"} + }, + { + "@id": "#hasVocabulary", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/vocabulary" }, + "hasArtifact": {"@id": "https://w3id.org/ro/terms/workflow-run#"} + }, + { + "@id": "#hasGuidance", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/guidance" }, + "hasArtifact": {"@id": "https://gxy.io/GTN:T00343"} + }, + { + "@id": "#hasExample", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/example" }, + "hasArtifact": { "@id": "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": 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+
+

+

Process Run Crate profile

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

Go to: Process 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 [?]Process Run Crate profile
+
+ +
+


+
+

⬇️ Download: Process Run Crate (HTML)

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


+
+

Example Process Run Crate

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + +
@idexample1/
name [?]Example Process Run Crate
@typeDataset
conformsTo [?]
subjectOf [?]
Items that reference this one
hasPart [?]Process Run Crate profile
hasArtifact [?]#hasExample
+
+ +
+


+
+

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
+
+ +
+


+
+

Go to: Namespace for Workflow Run RO-Crate model

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

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@idhttps://w3id.org/ro/terms/workflow-run
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@typeFile
encodingFormat [?]application/ld+json
contentUrl [?]https://www.researchobject.org/ro-terms/workflow-run/context.json
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license [?]Creative Commons Zero v1.0 Universal
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Go to: Workflow Run RO-Crate Introduction

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@idhttps://gxy.io/GTN:T00343
name [?]Workflow Run RO-Crate Introduction
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author [?]Simone Leo
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@idhttps://pypi.org/project/runcrate/
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Go to: Recording provenance of workflow runs with RO-Crate

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@idhttps://doi.org/10.48550/arXiv.2312.07852
name [?]Recording provenance of workflow runs with RO-Crate
@typeScholarlyArticle
author [?]
creditText [?]Simone Leo, et al. (2024): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852
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+ + + + + + + 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/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/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
+
+ +
+


+
+

⬇️ Download: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376

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


+
+

⬇️ Download: b9214658cc453331b62c2282b772a5c063dbd284

+ + + + +
+ + + + + + + + + + + + + + + + + + +
@idb9214658cc453331b62c2282b772a5c063dbd284
@typeFile
exampleOfWork [?]
Items that reference this one
hasPart [?]./
result [?]
+
+ +
+


+
+

⬇️ Download: 97fe1b50b4582cebc7d853796ebd62e3e163aa3f

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + +
@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.md b/docs/profiles/0.5-DRAFT/provenance_run_crate/index.md similarity index 91% 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..5baaabf 100644 --- a/docs/profiles/0.5-DRAFT/provenance_run_crate.md +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/index.md @@ -7,7 +7,14 @@ 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)) +* 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) +* 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. @@ -26,11 +33,17 @@ 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`) +* [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": [ @@ -329,7 +342,7 @@ 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`. @@ -515,7 +528,7 @@ The requirements of this profile are those of [Workflow Run Crate](workflow_run_ conformsTo MUST - Array MUST reference a CreativeWork entity with an @id URI that is consistent with the versioned Permalink of this document, and SHOULD also reference versioned permalinks for Process Run Crate, Workflow Run Crate and Workflow RO-Crate. + Array MUST reference a CreativeWork entity with an @id URI that is consistent with the versioned Permalink of this document, and SHOULD also reference versioned permalinks for Process Run Crate, Workflow Run Crate and Workflow RO-Crate. @@ -575,7 +588,7 @@ 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 @@ -610,7 +623,7 @@ 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 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..98df992 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json @@ -0,0 +1,636 @@ +{ "@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", + 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+
+

+

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
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+ +
+


+
+

⬇️ Download: Provenance Run Crate (HTML)

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


+
+

Example Process Run Crate

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


+
+

Go to: SSSOM mapping from PROV to Workflow Run Crate

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

Go to: Namespace for Workflow Run RO-Crate model

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

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

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

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@idhttps://pypi.org/project/runcrate/
name [?]runcrate
@typeSoftwareApplication
version [?]0.5.0
url [?]https://pypi.org/project/runcrate/
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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
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version [?]0.5-DRAFT
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hasPart [?]Provenance Run Crate profile
hasArtifact [?]SHOULD conform to Process Crate profile
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Go to: Workflow Run Crate profile

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@idhttps://w3id.org/ro/wfrun/workflow/0.5-DRAFT
name [?]Workflow Run Crate profile
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version [?]0.5-DRAFT
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hasPart [?]Provenance Run Crate profile
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Go to: Workflow RO-Crate profile

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@idhttps://w3id.org/workflowhub/workflow-ro-crate/1.0
name [?]Workflow RO-Crate profile
@type
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version [?]1.0
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hasPart [?]Provenance Run Crate profile
conformsTo [?]Example Process Run Crate
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Go to: Parameter Connection

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

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

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

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@idhttps://w3id.org/ro/terms/workflow-run#targetParameter
name [?]target parameter
@typeDefinedTerm
description [?]The target (upstream) parameter
termCode [?]targetParameter
inDefinedTermSet [?]Namespace for Workflow Run RO-Crate model
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#hasSpecification

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@id#hasSpecification
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hasRole [?]http://www.w3.org/ns/dx/prof/role/specification
hasArtifact [?]Provenance Run Crate (HTML)
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#hasConstraints

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@id#hasConstraints
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hasArtifact [?]Provenance Run Crate requirements
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#hasVocabulary

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@id#hasVocabulary
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#hasGuidance

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@id#hasGuidance
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hasArtifact [?]Workflow Run RO-Crate Introduction
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#hasExample

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@id#hasExample
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#hasMappingToProv

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

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@id#shouldConformToWorkflowROCrate
name [?]SHOULD conform to Workflow RO-Crate profile
@typeResourceDescriptor
hasRole [?]http://purl.org/dc/terms/conformsTo
hasArtifact [?]Workflow RO-Crate profile
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SHOULD conform to Process Crate profile

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@id#shouldConformToProcessCrateProfile
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SHOULD conform to Workflow Crate profile

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@id#shouldConformToWorkflowCrateProfile
name [?]SHOULD conform to Workflow Crate profile
@typeResourceDescriptor
hasRole [?]http://purl.org/dc/terms/conformsTo
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Go to: Recording provenance of workflow runs with RO-Crate

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@idhttps://doi.org/10.48550/arXiv.2312.07852
name [?]Recording provenance of workflow runs with RO-Crate
@typeScholarlyArticle
author [?]
creditText [?]Simone Leo, et al. (2024): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852
Items that reference this one
citation [?]Provenance Run Crate profile
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+ + + + + + + diff --git a/docs/profiles/0.5-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/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/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 + + +
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+

./

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Go to: Process Run Crate

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@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

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

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


+
+

⬇️ Download: Hello World (Galaxy Workflow)

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@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
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+
+

⬇️ Download: inputs/abcdef.txt

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@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
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⬇️ Download: Select_first_on_data_1_2 (output)

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@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
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⬇️ Download: tac_on_data_360_1 (output)

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@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
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+

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

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@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 [?]./
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+
+ + + + + + + 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 92% 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..b73176d 100644 --- a/docs/profiles/0.5-DRAFT/workflow_run_crate.md +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/index.md @@ -7,7 +7,15 @@ 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)) +* 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) + - [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). @@ -26,11 +34,16 @@ 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`) +* [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": [ @@ -294,7 +307,7 @@ This profile inherits the requirements of [Process Run Crate](process_run_crate) conformsTo MUST - Array MUST reference a CreativeWork entity with an @id URI that is consistent with the versioned Permalink of this document, and SHOULD also reference versioned permalinks for Process Run Crate and Workflow RO-Crate. + Array MUST reference a CreativeWork entity with an @id URI that is consistent with the versioned Permalink of this document, and SHOULD also reference versioned permalinks for Process Run Crate and Workflow RO-Crate. diff --git a/docs/profiles/0.5-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..7a35f77 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-metadata.json @@ -0,0 +1,705 @@ +{ "@context": + "https://w3id.org/ro/crate/1.2-DRAFT/context", + "@graph": [ + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "license": { "@id": "http://spdx.org/licenses/CC0-1.0" }, + "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"}, + "about": {"@id": "https://w3id.org/ro/wfrun/workflow/0.5-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": "example2/" }, + { "@id": "https://www.researchobject.org/workflow-run-crate-paper/mapping/" }, + { "@id": "https://w3id.org/ro/terms/workflow-run" }, + { "@id": "https://gxy.io/GTN:T00343" }, + { "@id": "https://pypi.org/project/runcrate/" }, + { "@id": "https://w3id.org/ro/wfrun/process/0.5-DRAFT" }, + { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" }, + { "@id": "http://schema.org/MediaObject" }, + { "@id": "http://schema.org/additionalType" }, + { "@id": "http://schema.org/CreateAction" }, + { "@id": "http://schema.org/exampleOfWork" }, + { "@id": "http://schema.org/instrument" }, + { "@id": "http://schema.org/name" }, + { "@id": "http://schema.org/object" }, + { "@id": "http://schema.org/PropertyValue" }, + { "@id": "http://schema.org/result" }, + { "@id": "http://schema.org/DataType" }, + { "@id": "http://schema.org/Integer" }, + { "@id": "http://schema.org/about" }, + { "@id": "http://schema.org/defaultValue" }, + { "@id": "http://schema.org/valueRequired" }, + { "@id": "https://bioschemas.org/FormalParameter" }, + { + "@id": "https://bioschemas.org/ComputationalWorkflow" + }, + { + "@id": "http://schema.org/defaultValue" + }, + { + "@id": "http://schema.org/valueRequired" + }, + { + "@id": "https://bioschemas.org/ComputationalWorkflow#input" + }, + { + "@id": "https://bioschemas.org/ComputationalWorkflow#output" + }, + { + "@id": "http://purl.org/dc/terms/conformsTo" + }, + { + "@id": "https://w3id.org/ro/terms/workflow-run#environment" + } + + ], + "hasResource": [ + { "@id": "#hasSpecification" }, + { "@id": "#hasConstraints" }, + { "@id": "#hasGuidance" }, + { "@id": "#hasExample" }, + { "@id": "#hasMappingToProv" }, + { "@id": "#shouldConformToWorkflowROCrate" }, + { "@id": "#shouldConformToProcessCrateProfile" } + ], + "citation": { "@id": "https://doi.org/10.48550/arXiv.2312.07852" } + }, + { + "@id": "https://www.researchobject.org/workflow-run-crate/", + "@type": "Project", + "name": "Workflow Run Crate task force", + "member": [ + + { "@id": "https://orcid.org/0000-0001-8271-5429"}, + { "@id": "https://orcid.org/0000-0003-4929-1219"}, + { "@id": "https://orcid.org/0000-0001-9842-9718"}, + { "@id": "https://orcid.org/0000-0002-5432-2748"}, + { "@id": "https://orcid.org/0000-0002-4806-5140"}, + { "@id": "https://orcid.org/0000-0003-3156-2105"}, + { "@id": "https://orcid.org/0000-0002-6190-122X"}, + { "@id": "https://orcid.org/0000-0003-0454-7145"}, + { "@id": "https://orcid.org/0000-0002-8940-4946"}, + { "@id": "https://orcid.org/0000-0003-0606-2512"}, + { "@id": "https://orcid.org/0000-0002-3468-0652"}, + { "@id": "https://orcid.org/0000-0002-2961-9670"}, + { "@id": "https://orcid.org/0000-0003-3986-0510"}, + { "@id": "https://orcid.org/0000-0002-0003-2024"}, + { "@id": "https://orcid.org/0000-0002-9464-6640"}, + { "@id": "https://orcid.org/0000-0001-5845-8880"}, + { "@id": "https://orcid.org/0000-0003-4894-4660"}, + { "@id": "https://orcid.org/0000-0002-4405-6802"}, + { "@id": "https://orcid.org/0000-0001-9290-2017"}, + { "@id": "https://orcid.org/0000-0003-0617-9219"}, + { "@id": "https://orcid.org/0000-0001-9228-2882"}, + { "@id": "https://orcid.org/0000-0003-3898-9451"}, + { "@id": "https://orcid.org/0000-0003-3777-5945"}, + { "@id": "https://orcid.org/0000-0003-2765-0049"}, + { "@id": "https://orcid.org/0000-0001-9818-9320"}, + { "@id": "https://orcid.org/0000-0002-8122-9522"}, + { "@id": "https://orcid.org/0000-0002-8330-4071"}, + { "@id": "https://orcid.org/0000-0003-4073-7456"}, + { "@id": "https://orcid.org/0000-0003-1361-7301"}, + { "@id": "https://orcid.org/0000-0002-5358-616X"}, + { "@id": "https://orcid.org/0000-0002-5477-287X"}, + { "@id": "https://orcid.org/0000-0001-8250-4074"}, + { "@id": "https://orcid.org/0000-0003-0902-0086"}, + { "@id": "https://orcid.org/0000-0001-8172-8981"}, + { "@id": "https://orcid.org/0000-0001-6740-9212"}, + { "@id": "https://orcid.org/0000-0001-5411-356X"}, + { "@id": "https://orcid.org/0000-0003-0035-0951"}, + { "@id": "https://orcid.org/0000-0003-0711-5196"} + ], + "parentOrganization": { "@id": "https://www.researchobject.org/ro-crate/community" } + }, + { + "@id": "https://www.researchobject.org/ro-crate/community", + "@type": "Project", + "name": "RO-Crate Community" + }, + { + "@id": "https://w3id.org/ro/wfrun/process/0.5-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": "index.html", + "@type": "File", + "name": "Workflow Run Crate (HTML)", + "encodingFormat": [ + "text/html", + {"@id": "https://www.nationalarchives.gov.uk/PRONOM/fmt/471"} + ] + }, + { + "@id": "index.html#requirements", + "@type": "WebPageElement", + "name": "Workflow Run Crate requirements" + }, + { + "@id": "example2/", + "@type": "Dataset", + "name": "Example Workflow Run Crate", + "conformsTo": [ + { "@id": "https://w3id.org/ro/crate"}, + { "@id": "https://w3id.org/ro/wfrun/process/0.4" }, + { "@id": "https://w3id.org/ro/wfrun/workflow/0.4" }, + { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" } + ], + "subjectOf": [ + { "@id": "example2/ro-crate-metadata.json" }, + { "@id": "example2/ro-crate-preview.html" } + ] + }, + { + "@id": "example2/ro-crate-metadata.json", + "@type": "CreativeWork", + "encodingFormat": "application/ld+json" + }, + { + "@id": "example2/ro-crate-preview.html", + "@type": "CreativeWork", + "encodingFormat": "text/html" + }, + { + "@id": "https://w3id.org/ro/terms/workflow-run", + "@type": "File", + "name": "JSON-LD context for workflow-run terms", + "contentUrl": "https://www.researchobject.org/ro-terms/workflow-run/context.json", + "conformsTo": { + "@id": "http://www.w3.org/ns/json-ld#Context" + }, + "encodingFormat": "application/ld+json", + "license": { + "@id": "https://creativecommons.org/publicdomain/zero/1.0/" + } + }, + { + "@id": "#hasSpecification", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/specification" }, + "hasArtifact": {"@id": "index.html"} + }, + { + "@id": "#hasConstraints", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/constraints" }, + "hasArtifact": {"@id": "index.html#requirements"} + }, + { + "@id": "#hasGuidance", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/guidance" }, + "hasArtifact": {"@id": "https://gxy.io/GTN:T00343"} + }, + { + "@id": "#hasExample", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/example" }, + "hasArtifact": { "@id": "example2/" } + }, + { + "@id": "#hasMappingToProv", + "@type": "ResourceDescriptor", + "hasRole": { "@id": "http://www.w3.org/ns/dx/prof/role/mapping" }, + "hasArtifact": { "@id": "https://www.researchobject.org/workflow-run-crate-paper/mapping/" } + }, + { + "@id": "https://www.researchobject.org/workflow-run-crate-paper/mapping/", + "@type": "Dataset", + "name": "SSSOM mapping from PROV to Workflow Run Crate", + "isPartOf": { + "@id": "https://w3id.org/ro/doi/10.5281/zenodo.10368989" + } + }, + { + "@id": "https://w3id.org/ro/doi/10.5281/zenodo.10368989", + "@type": "Dataset", + "name": "Recording provenance of workflow runs with RO-Crate (RO-Crate and mapping)", + "conformsTo": { "@id": "https://w3id.org/ro/crate" }, + "subjectOf": [ + { "@id": "https://www.researchobject.org/workflow-run-crate-paper/ro-crate-metadata.jsonld" }, + { "@id": "https://www.researchobject.org/workflow-run-crate-paper/ro-crate-preview.html" } + ] + }, + { + "@id": "https://www.researchobject.org/workflow-run-crate-paper/ro-crate-metadata.jsonld", + "@type": "CreativeWork", + "encodingFormat": "application/ld+json" + }, + { + "@id": "https://www.researchobject.org/workflow-run-crate-paper/ro-crate-preview.html", + "@type": "CreativeWork", + "encodingFormat": "text/html" + }, + { + "@id": "#shouldConformToWorkflowROCrate", + "@type": "ResourceDescriptor", + "name": "SHOULD conform to Workflow RO-Crate profile", + "hasRole": { "@id": "http://purl.org/dc/terms/conformsTo" }, + "hasArtifact": {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"} +}, +{ + "@id": "#shouldConformToProcessCrateProfile", + "@type": "ResourceDescriptor", + "name": "SHOULD conform to Process Crate profile", + "hasRole": { "@id": "http://purl.org/dc/terms/conformsTo" }, + "hasArtifact": {"@id": "https://w3id.org/ro/wfrun/process/0.5-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 Workflow Run RO-Crate model" + }, + { + "@id": "https://pypi.org/project/runcrate/", + "@type": "SoftwareApplication", + "name": "runcrate", + "version": "0.5.0", + "url": "https://pypi.org/project/runcrate/" + }, + { + "@id": "http://schema.org/MediaObject", + "@type": "DefinedTerm", + "name": "MediaObject", + "termCode": "File" + }, + +{ + "@id": "http://schema.org/additionalType", + "@type": "DefinedTerm", + "name": "additionalType" +}, +{ + "@id": "http://schema.org/CreateAction", + "@type": "DefinedTerm", + "name": "CreateAction" +}, +{ + "@id": "http://schema.org/exampleOfWork", + "@type": "DefinedTerm", + "name": "exampleOfWork" +}, +{ + "@id": "http://schema.org/instrument", + "@type": "DefinedTerm", + "name": "instrument" +}, +{ + "@id": "http://schema.org/name", + "@type": "DefinedTerm", + "name": "name" +}, +{ + "@id": "http://schema.org/object", + "@type": "DefinedTerm", + "name": "object" +}, +{ + "@id": "http://schema.org/PropertyValue", + "@type": "DefinedTerm", + "name": "PropertyValue" +}, +{ + "@id": "http://schema.org/result", + "@type": "DefinedTerm", + "name": "result" +}, +{ + "@id": "http://schema.org/DataType", + "@type": "DefinedTerm", + "name": "DataType" +}, +{ + "@id": "http://schema.org/Integer", + "@type": "DefinedTerm", + "name": "Integer" +}, +{ + "@id": "http://schema.org/about", + "@type": "DefinedTerm", + "name": "about" +}, + { + "@id": "https://bioschemas.org/FormalParameter", + "@type": "DefinedTerm", + "name": "FormalParameter" + }, + { + "@id": "https://bioschemas.org/ComputationalWorkflow", + "@type": "DefinedTerm", + "name": "ComputationalWorkflow" + }, + { + "@id": "http://schema.org/defaultValue", + "@type": "DefinedTerm", + "name": "defaultValue" + }, + { + "@id": "http://schema.org/valueRequired", + "@type": "DefinedTerm", + "name": "valueRequired" + }, + { + "@id": "https://bioschemas.org/ComputationalWorkflow#input", + "@type": "DefinedTerm", + "termCode": "input", + "name": "input" + }, + { + "@id": "https://bioschemas.org/ComputationalWorkflow#output", + "@type": "DefinedTerm", + "name": "output", + "termCode": "output" + }, +{ + "@id": "http://purl.org/dc/terms/conformsTo", + "@type": "DefinedTerm", + "name": "conformsTo", + "termCode": "conformsTo" +}, +{ + "@id": "https://w3id.org/ro/terms/workflow-run#environment", + "@type": "DefinedTerm", + "termCode": "environment", + "name": "environment" +}, + +{ + "@id": "https://orcid.org/0000-0001-8271-5429", + "@type": "Person", + "name": "Simone Leo" +}, +{ + "@id": "https://orcid.org/0000-0003-4929-1219", + "@type": "Person", + "name": "Laura Rodríguez-Navas" +}, +{ + "@id": "https://orcid.org/0000-0001-9842-9718", + "@type": "Person", + "name": "Stian Soiland-Reyes" +}, +{ + "@id": "https://orcid.org/0000-0002-5432-2748", + "@type": "Person", + "name": "Paul Brack" +}, +{ + "@id": "https://orcid.org/0000-0002-4806-5140", + "@type": "Person", + "name": "José María Fernández" +}, +{ + "@id": "https://orcid.org/0000-0003-3156-2105", + "@type": "Person", + "name": "Alan R Williams" +}, +{ + "@id": "https://orcid.org/0000-0002-6190-122X", + "@type": "Person", + "name": "Ignacio Eguinoa" +}, +{ + "@id": "https://orcid.org/0000-0003-0454-7145", + "@type": "Person", + "name": "Daniel Garijo" +}, +{ + "@id": "https://orcid.org/0000-0002-8940-4946", + "@type": "Person", + "name": "Paul De Geest" +}, +{ + "@id": "https://orcid.org/0000-0003-0606-2512", + "@type": "Person", + "name": "Raül Sirvent" +}, +{ + "@id": "https://orcid.org/0000-0002-3468-0652", + "@type": "Person", + "name": "Alexander Kanitz" +}, +{ + "@id": "https://orcid.org/0000-0002-2961-9670", + "@type": "Person", + "name": "Michael R Crusoe" +}, +{ + "@id": "https://orcid.org/0000-0003-3986-0510", + "@type": "Person", + "name": "LJ Garcia Castro" +}, +{ + "@id": "https://orcid.org/0000-0002-0003-2024", + "@type": "Person", + "name": "Rudolf Wittner" +}, +{ + "@id": "https://orcid.org/0000-0002-9464-6640", + "@type": "Person", + "name": "Wolfgang Maier" +}, +{ + "@id": "https://orcid.org/0000-0001-5845-8880", + "@type": "Person", + "name": "Sebastiaan Huber" +}, +{ + "@id": "https://orcid.org/0000-0003-4894-4660", + "@type": "Person", + "name": "Kevin Jablonka" +}, +{ + "@id": "https://orcid.org/0000-0002-4405-6802", + "@type": "Person", + "name": "Haris Zafeiropoulos" +}, +{ + "@id": "https://orcid.org/0000-0001-9290-2017", + "@type": "Person", + "name": "Iacopo Colonnelli" +}, +{ + "@id": "https://orcid.org/0000-0003-0617-9219", + "@type": "Person", + "name": "Jake Emerson" +}, +{ + "@id": "https://orcid.org/0000-0001-9228-2882", + "@type": "Person", + "name": "Abigail Miller" +}, +{ + "@id": "https://orcid.org/0000-0003-3898-9451", + "@type": "Person", + "name": "Stelios Ninidakis" +}, +{ + "@id": "https://orcid.org/0000-0003-3777-5945", + "@type": "Person", + "name": "Tazro Ohta" +}, +{ + "@id": "https://orcid.org/0000-0003-2765-0049", + "@type": "Person", + "name": "Hirotaka Suetake" +}, +{ + "@id": "https://orcid.org/0000-0001-9818-9320", + "@type": "Person", + "name": "Johannes Köster" +}, +{ + "@id": "https://orcid.org/0000-0002-8122-9522", + "@type": "Person", + "name": "Luiz Gadelha" +}, +{ + "@id": "https://orcid.org/0000-0002-8330-4071", + "@type": "Person", + "name": "Mahnoor Zulfiqar" +}, +{ + "@id": "https://orcid.org/0000-0003-4073-7456", + "@type": "Person", + "name": "Romain David" +}, +{ + "@id": "https://orcid.org/0000-0003-1361-7301", + "@type": "Person", + "name": "Maciek Bąk" +}, +{ + "@id": "https://orcid.org/0000-0002-5358-616X", + "@type": "Person", + "name": "Petr Holub" +}, +{ + "@id": "https://orcid.org/0000-0002-5477-287X", + "@type": "Person", + "name": "Milan Markovic" +}, +{ + "@id": "https://orcid.org/0000-0001-8250-4074", + "@type": "Person", + "name": "Bruno P. Kinoshita" +}, +{ + "@id": "https://orcid.org/0000-0003-0902-0086", + "@type": "Person", + "name": "Renske de Wit" +}, +{ + "@id": "https://orcid.org/0000-0001-8172-8981", + "@type": "Person", + "name": "Jasper Koehorst" +}, +{ + "@id": "https://orcid.org/0000-0001-6740-9212", + "@type": "Person", + "name": "Samuel Lampa" +}, +{ + "@id": "https://orcid.org/0000-0001-5411-356X", + "@type": "Person", + "name": "Samuel Grayson" +}, +{ + "@id": "https://orcid.org/0000-0003-0035-0951", + "@type": "Person", + "name": "Jörg F. Unger" +}, +{ + "@id": "https://orcid.org/0000-0003-0711-5196", + "@type": "Person", + "name": "Felix Bartusch" +}, +{ + "@id": "https://orcid.org/0000-0002-4663-5613", + "@type": "Person", + "name": "Luca Pireddu" +}, +{ + "@id": "https://orcid.org/0000-0002-1119-1792", + "@type": "Person", + "name": "Matej Gallo" +}, +{ + "@id": "https://orcid.org/0000-0002-0309-604X", + "@type": "Person", + "name": "Salvador Capella-Gutierrez" +}, +{ + "@id": "https://www.apache.org/licenses/LICENSE-2.0", + "@type": "CreativeWork", + "name": "Apache License 2.0", + "version": "2.0", + "identifier": { "@id": "http://spdx.org/licenses/Apache-2.0"} +}, +{ + "@id": "https://creativecommons.org/publicdomain/zero/1.0/", + "@type": "CreativeWork", + "identifier": { "@id": "http://spdx.org/licenses/CC0-1.0"}, + "name": "Creative Commons Zero v1.0 Universal", + "version": "1.0" +}, +{ + "@id": "http://spdx.org/licenses/Apache-2.0", + "@type": "PropertyValue", + "propertyID": "http://spdx.org/rdf/terms#licenseId", + "name": "spdx", + "value": "Apache-2.0" +}, +{ + "@id": "http://spdx.org/licenses/CC0-1.0", + "@type": "PropertyValue", + "propertyID": "http://spdx.org/rdf/terms#licenseId", + "name": "spdx", + "value": "CC0-1.0" +} + +] +} diff --git a/docs/profiles/0.5-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 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..a6531d3 --- /dev/null +++ b/docs/profiles/0.5-DRAFT/workflow_run_crate/ro-crate-preview.html @@ -0,0 +1,2381 @@ + + + + + + + + + + + + + + + + + + + + + + + + +
+
+

+

Workflow Run Crate profile

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

Go to: Workflow Run Crate profile

+ + + + + + +
+


+
+

Go to: Workflow Run Crate task force

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+




+
+

Go to: Apache License 2.0

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


+
+

⬇️ Download: Workflow Run Crate (HTML)

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


+
+

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
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+ +
+


+
+

Go to: SSSOM mapping from PROV to Workflow Run Crate

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


+
+

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

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


+
+

Go to: Workflow Run RO-Crate Introduction

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


+
+

Go to: runcrate

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + +
@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 [?]SHOULD conform to Process Crate profile
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+ +
+


+
+

Go to: Workflow RO-Crate profile

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

Go to: MediaObject

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

Go to: additionalType

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

Go to: CreateAction

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

Go to: exampleOfWork

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


+
+

Go to: instrument

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

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

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

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

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

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

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

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

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

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

Go to: FormalParameter

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

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

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

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

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

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

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

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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
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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 [?]Workflow Run Crate profile
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#hasExample

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

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

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

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@id#shouldConformToProcessCrateProfile
name [?]SHOULD conform to Process Crate profile
@typeResourceDescriptor
hasRole [?]conformsTo
hasArtifact [?]Process Run Crate profile
Items that reference this one
hasResource [?]Workflow Run Crate profile
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Go to: Recording provenance of workflow runs with RO-Crate

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@idhttps://doi.org/10.48550/arXiv.2312.07852
name [?]Recording provenance of workflow runs with RO-Crate
@typeScholarlyArticle
author [?]
creditText [?]Simone Leo, et al. (2024): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852
Items that reference this one
citation [?]Workflow Run Crate profile
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+
+ + + + + + + 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 new file mode 100644 index 0000000..38a3826 --- /dev/null +++ b/docs/wfrun.ttl @@ -0,0 +1,153 @@ +@prefix s: . +@prefix rdf: . +@prefix rdfs: . +@prefix wfrun: . +@prefix bioschemas: . +@prefix vann: . +@prefix dct: . +@prefix owl: . + +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 + 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 . + +wfrun:connection rdf:type rdf:Property ; + s:domainIncludes s:HowToStep, bioschemas:ComputationalWorkflow; + s:rangeIncludes wfrun:ParameterConnection ; + rdfs:isDefinedBy wfrun: ; + rdfs:label "connection"@en-gb ; + rdfs:comment "A parameter connection created by this workflow"@en-gb . + +wfrun:containerImage rdf:type rdf:Property ; + s:domainIncludes s:CreateAction ; + s:rangeIncludes wfrun:ContainerImage ; + rdfs:isDefinedBy wfrun: ; + rdfs:label "containerImage"@en-gb ; + rdfs:comment "A container image associated with this entity"@en-gb . + +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 . + +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 . + + + + +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 . + +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 . + +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 . + +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 . + +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 . + +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 . + +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 . + +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 . + +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 . + +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 . + +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 . + + + + +