From 545803a248a41fefe6ce62952457252118a084a9 Mon Sep 17 00:00:00 2001 From: simleo Date: Fri, 31 May 2024 12:04:10 +0200 Subject: [PATCH] add sparql query for cq3 --- docs/sparql/cq3.py | 34 + docs/sparql/crate/ro-crate-metadata.json | 1599 +++++++++++----------- 2 files changed, 855 insertions(+), 778 deletions(-) create mode 100644 docs/sparql/cq3.py diff --git a/docs/sparql/cq3.py b/docs/sparql/cq3.py new file mode 100644 index 0000000..f9513e1 --- /dev/null +++ b/docs/sparql/cq3.py @@ -0,0 +1,34 @@ +"""\ +This script contains the SPARQL query for Competency Question 3 "What are the +configuration files used in a workflow execution step?". The discussion on +https://github.com/ResearchObject/workflow-run-crate/issues/11 resulted in +realizing that the use case needed in practice was representing a +configuration file for the workflow engine, especially from the example given +by StreamFlow. The configuration file is added to the "object" attribute of +the "OrganizeAction" corresponding to the workflow execution. Since the other +objects of the OrganizeAction are of "ControlAction" type, in the query we +filter them out to get the configuration file. +""" + +import rdflib +from pathlib import Path + +CRATE = Path("crate") + +g = rdflib.Graph() +g.parse(CRATE/"ro-crate-metadata.json") + +QUERY = """\ +PREFIX s: + +SELECT ?conf +WHERE { +?action a s:OrganizeAction . +?action s:object ?conf . +FILTER NOT EXISTS { ?conf a s:ControlAction } +} +""" + +qres = g.query(QUERY) +for row in qres: + print(row.conf) diff --git a/docs/sparql/crate/ro-crate-metadata.json b/docs/sparql/crate/ro-crate-metadata.json index a10ec47..1a5f5f4 100644 --- a/docs/sparql/crate/ro-crate-metadata.json +++ b/docs/sparql/crate/ro-crate-metadata.json @@ -27,52 +27,53 @@ "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" } ], - "datePublished": "2023-03-24T15:24:13+00:00", + "datePublished": "2023-05-09T05:28:14+00:00", + "description": "Run of digital pathology tissue/tumor prediction workflow", "hasPart": [ { - "@id": "README.md" + "@id": "extract_tissue.cwl" }, { - "@id": "packed.cwl" + "@id": "classify_tumor.cwl" }, { - "@id": "f62aa607a75508ac5fc6a22e9c0e39ef58a2c852" + "@id": "predictions.cwl" }, { - "@id": "254eb2d60fd6705c88a6b7746336ba86e09e23c7" + "@id": "68fee2b5ca70773e7e4bc74b85853d8d4271c28b" }, { - "@id": "a1e03e58562319274d4ff792d2090763b7926d72" + "@id": "06133ec5f8973ec3cc5281e5df56421c3228c221" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/" + "@id": "4fd6110ee3c544182027f82ffe84b5ae7db5fb81" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/862eeec8b906cff93bcd1c5ab5e5ec8fc93a2ef1" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/4a1a998cf56818c183b02f93011a6c1c9ec47468" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/862eeec8b906cff93bcd1c5ab5e5ec8fc93a2ef1" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/8e9d580e86f48791871b086f3c27269a03f57897" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/9e748097f79d8317b30fcc11833553434e19b02c" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/590783315f628a3acd02b9341572138b3a3224db" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/b43c1cd0875d23bd20dc794fa20255cf272108ec" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/854db6bca6b11fb9f6198dce67b3dcbb371f7ebb" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/ae7c542bebbacf8d167fae831b69480e19e9c3b0" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/acc92df58c498b2567f6975c3e128aebc0c524c5" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/d55cbe9ea0ac43eaa69bb8c21eac07539249734f" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/bc709e1a4da6e506f81150ee39907d0224e066fb" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/8e9d580e86f48791871b086f3c27269a03f57897" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/ae7c542bebbacf8d167fae831b69480e19e9c3b0" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/cf03a8a5713c038c566734cf11f81cc03a41efa6" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/b43c1cd0875d23bd20dc794fa20255cf272108ec" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/a1ad0dfd5f6e24aa90bdf9da0a688e6a0c268905" }, { "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/46c443af080a36000c9298b49b675eb240eeb41c" @@ -81,66 +82,76 @@ "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/ce3d0d6addaced3e58578e42c341f44737b5aa84" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/9575fdaa42c448ea550d982cf8e27d0b46320874" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/52e0419ea116b78bc330d36f93bc2b4ec2bf8210" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/6c1bc911505dc65551c4f0576e1c684723e57897" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/bc709e1a4da6e506f81150ee39907d0224e066fb" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/9e748097f79d8317b30fcc11833553434e19b02c" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/a16fec38b4b7adf7dc1f8e9e58f6956a249a0a08" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/f642fc608c0edc49db59dfc1d38be7abeda0263a" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/590783315f628a3acd02b9341572138b3a3224db" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/3099f7344d2004c58bfb3282dae47a0d204e12da" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/6c1bc911505dc65551c4f0576e1c684723e57897" + }, + { + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/d4061bed85711676d337bd8835e32413957485e3" }, { "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/7f0a219f3c842e0c3eaae848caea165940b1ec48" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/1d3d88c43eb7f44a667170a0e6cb8cd950a4ea16" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/3099f7344d2004c58bfb3282dae47a0d204e12da" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/cf03a8a5713c038c566734cf11f81cc03a41efa6" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/e238dcdb6aa71dac71335591439442c7cfef60e6" }, { "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/06d5def8140f8e14b729a584f78289bc25e7f5ec" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/52e0419ea116b78bc330d36f93bc2b4ec2bf8210" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/acc92df58c498b2567f6975c3e128aebc0c524c5" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/e238dcdb6aa71dac71335591439442c7cfef60e6" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/854db6bca6b11fb9f6198dce67b3dcbb371f7ebb" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/d55cbe9ea0ac43eaa69bb8c21eac07539249734f" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/9575fdaa42c448ea550d982cf8e27d0b46320874" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/a16fec38b4b7adf7dc1f8e9e58f6956a249a0a08" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/f642fc608c0edc49db59dfc1d38be7abeda0263a" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/d4061bed85711676d337bd8835e32413957485e3" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/1d3d88c43eb7f44a667170a0e6cb8cd950a4ea16" }, { - "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/a1ad0dfd5f6e24aa90bdf9da0a688e6a0c268905" + "@id": "c7398fbf741b851e80ae731d60cbee9258ff81f3/4a1a998cf56818c183b02f93011a6c1c9ec47468" }, { - "@id": "8cdd835383bcc344a0dbc6892ac6949765400b5c" + "@id": "f62aa607a75508ac5fc6a22e9c0e39ef58a2c852" + }, + { + "@id": "6b15de40dd0ee3234062d0f261c77575a60de0f2" + }, + { + "@id": "README.md" } ], - "license": "MIT", + "license": "https://spdx.org/licenses/MIT", "mainEntity": { - "@id": "packed.cwl" + "@id": "predictions.cwl" }, "mentions": [ { - "@id": "#5d08a759-9b0e-434f-a5f0-ac95dc0ad619" + "@id": "#30a65cba-1b75-47dc-ad47-1d33819cf156" }, { - "@id": "#b6b5f30b-d459-4b37-ad6c-3cab115d138d" + "@id": "#af0253d688f3409a2c6d24bf6b35df7c4e271292" } - ] + ], + "name": "DeepHealth Pipeline" }, { "@id": "ro-crate-metadata.json", @@ -157,14 +168,6 @@ } ] }, - { - "@id": "README.md", - "@type": "File", - "about": { - "@id": "./" - }, - "encodingFormat": "text/markdown" - }, { "@id": "https://w3id.org/ro/wfrun/process/0.1", "@type": "CreativeWork", @@ -189,104 +192,6 @@ "name": "Workflow RO-Crate", "version": "1.0" }, - { - "@id": "packed.cwl", - "@type": [ - "File", - "SoftwareSourceCode", - "ComputationalWorkflow", - "HowTo" - ], - "connection": [ - { - "@id": "#2defc4a1-642d-4e75-a6f7-907ad273b109" - }, - { - "@id": "#a3100d97-d225-4460-be39-89940e9cd1b8" - } - ], - "hasPart": [ - { - "@id": "packed.cwl#classify_tumor.cwl" - }, - { - "@id": "packed.cwl#extract_tissue.cwl" - } - ], - "input": [ - { - "@id": "packed.cwl#main/gpu" - }, - { - "@id": "packed.cwl#main/slide" - }, - { - "@id": "packed.cwl#main/tissue-high-batch-size" - }, - { - "@id": "packed.cwl#main/tissue-high-chunk-size" - }, - { - "@id": "packed.cwl#main/tissue-high-filter" - }, - { - "@id": "packed.cwl#main/tissue-high-label" - }, - { - "@id": "packed.cwl#main/tissue-high-level" - }, - { - "@id": "packed.cwl#main/tissue-low-batch-size" - }, - { - "@id": "packed.cwl#main/tissue-low-chunk-size" - }, - { - "@id": "packed.cwl#main/tissue-low-label" - }, - { - "@id": "packed.cwl#main/tissue-low-level" - }, - { - "@id": "packed.cwl#main/tumor-batch-size" - }, - { - "@id": "packed.cwl#main/tumor-chunk-size" - }, - { - "@id": "packed.cwl#main/tumor-filter" - }, - { - "@id": "packed.cwl#main/tumor-label" - }, - { - "@id": "packed.cwl#main/tumor-level" - } - ], - "name": "tissue / tumor prediction", - "output": [ - { - "@id": "packed.cwl#main/tissue" - }, - { - "@id": "packed.cwl#main/tumor" - } - ], - "programmingLanguage": { - "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl" - }, - "step": [ - { - "@id": "packed.cwl#main/classify-tumor" - }, - { - "@id": "packed.cwl#main/extract-tissue-high" - }, - { - "@id": "packed.cwl#main/extract-tissue-low" - } - ] - }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl", "@type": "ComputerLanguage", @@ -301,1046 +206,1086 @@ "version": "v1.1" }, { - "@id": "packed.cwl#main/gpu", + "@id": "predictions.cwl#gpu", "@type": "FormalParameter", "additionalType": "Integer", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "gpu", "valueRequired": "False" }, { - "@id": "packed.cwl#main/slide", + "@id": "predictions.cwl#slide", "@type": "FormalParameter", "additionalType": "Collection", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "slide" }, { - "@id": "packed.cwl#main/tissue-high-batch-size", + "@id": "predictions.cwl#tissue-high-batch-size", "@type": "FormalParameter", "additionalType": "Integer", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tissue-high-batch-size", "valueRequired": "False" }, { - "@id": "packed.cwl#main/tissue-high-chunk-size", + "@id": "predictions.cwl#tissue-high-chunk-size", "@type": "FormalParameter", "additionalType": "Integer", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tissue-high-chunk-size", "valueRequired": "False" }, { - "@id": "packed.cwl#main/tissue-high-filter", + "@id": "predictions.cwl#tissue-high-filter", "@type": "FormalParameter", "additionalType": "Text", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tissue-high-filter" }, { - "@id": "packed.cwl#main/tissue-high-label", + "@id": "predictions.cwl#tissue-high-label", "@type": "FormalParameter", "additionalType": "Text", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tissue-high-label" }, { - "@id": "packed.cwl#main/tissue-high-level", + "@id": "predictions.cwl#tissue-high-level", "@type": "FormalParameter", "additionalType": "Integer", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tissue-high-level" }, { - "@id": "packed.cwl#main/tissue-low-batch-size", + "@id": "predictions.cwl#tissue-low-batch-size", "@type": "FormalParameter", "additionalType": "Integer", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tissue-low-batch-size", "valueRequired": "False" }, { - "@id": "packed.cwl#main/tissue-low-chunk-size", + "@id": "predictions.cwl#tissue-low-chunk-size", "@type": "FormalParameter", "additionalType": "Integer", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tissue-low-chunk-size", "valueRequired": "False" }, { - "@id": "packed.cwl#main/tissue-low-label", + "@id": "predictions.cwl#tissue-low-label", "@type": "FormalParameter", "additionalType": "Text", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tissue-low-label" }, { - "@id": "packed.cwl#main/tissue-low-level", + "@id": "predictions.cwl#tissue-low-level", "@type": "FormalParameter", "additionalType": "Integer", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tissue-low-level" }, { - "@id": "packed.cwl#main/tumor-batch-size", + "@id": "predictions.cwl#tumor-batch-size", "@type": "FormalParameter", "additionalType": "Integer", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tumor-batch-size", "valueRequired": "False" }, { - "@id": "packed.cwl#main/tumor-chunk-size", + "@id": "predictions.cwl#tumor-chunk-size", "@type": "FormalParameter", "additionalType": "Integer", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tumor-chunk-size", "valueRequired": "False" }, { - "@id": "packed.cwl#main/tumor-filter", + "@id": "predictions.cwl#tumor-filter", "@type": "FormalParameter", "additionalType": "Text", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tumor-filter" }, { - "@id": "packed.cwl#main/tumor-label", + "@id": "predictions.cwl#tumor-label", "@type": "FormalParameter", "additionalType": "Text", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tumor-label" }, { - "@id": "packed.cwl#main/tumor-level", + "@id": "predictions.cwl#tumor-level", "@type": "FormalParameter", "additionalType": "Integer", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tumor-level" }, { - "@id": "packed.cwl#main/tissue", + "@id": "predictions.cwl#tissue", "@type": "FormalParameter", "additionalType": "File", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tissue" }, { - "@id": "packed.cwl#main/tumor", + "@id": "predictions.cwl#tumor", "@type": "FormalParameter", "additionalType": "File", + "conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/", "name": "tumor" }, { - "@id": "packed.cwl#main/classify-tumor", - "@type": "HowToStep", - "connection": [ - { - "@id": "#a90b3772-fc6d-40e2-91b5-3d9637e01c8d" - }, - { - "@id": "#5af2fbf5-28f4-49d0-bca5-796d062cc58f" - }, - { - "@id": "#df46fccf-2d34-41af-a242-292f439a8896" - }, - { - "@id": "#6b7fce0f-2b05-4c6f-af69-61ddc3d50e1b" - }, - { - "@id": "#597eed34-0780-49e9-bc6a-429b0331f937" - }, - { - "@id": "#f00c83cd-a910-4d49-8f09-3bafe5ea5515" - }, - { - "@id": "#8c801cd8-838e-40e4-88b6-4bab188a919c" - }, - { - "@id": "#8c383714-73c8-47f8-a47c-a8b022bab62b" - } - ], - "position": "1", - "workExample": { - "@id": "packed.cwl#classify_tumor.cwl" - } - }, - { - "@id": "packed.cwl#classify_tumor.cwl", - "@type": "SoftwareApplication", - "input": [ - { - "@id": "packed.cwl#classify_tumor.cwl/batch-size" - }, - { - "@id": "packed.cwl#classify_tumor.cwl/chunk-size" - }, - { - "@id": "packed.cwl#classify_tumor.cwl/filter" - }, - { - "@id": "packed.cwl#classify_tumor.cwl/filter_slide" - }, - { - "@id": "packed.cwl#classify_tumor.cwl/gpu" - }, - { - "@id": "packed.cwl#classify_tumor.cwl/label" - }, - { - "@id": "packed.cwl#classify_tumor.cwl/level" - }, - { - "@id": "packed.cwl#classify_tumor.cwl/src" - } - ], - "name": "classify_tumor.cwl", - "output": [ - { - "@id": "packed.cwl#classify_tumor.cwl/tumor" - } - ] - }, - { - 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