From 23f5a696e6f96efeef0aa7667fb0e26e917be486 Mon Sep 17 00:00:00 2001 From: learner97 Date: Wed, 4 Sep 2024 09:20:27 -0600 Subject: [PATCH 1/2] added sbol3 pages to master json, updated component3 (still not done yet) --- .../components/Viewing/PageJSON/MasterJSON.js | 31 +++++- .../Viewing/PageJSON/Types/Component3.json | 97 +++++++++++++++++-- .../Viewing/PageJSON/Types/Model3.json | 2 +- frontend/components/Viewing/Shell.js | 2 + frontend/public/commitHash.txt | 2 +- 5 files changed, 122 insertions(+), 12 deletions(-) diff --git a/frontend/components/Viewing/PageJSON/MasterJSON.js b/frontend/components/Viewing/PageJSON/MasterJSON.js index e07757c1..39945eb1 100644 --- a/frontend/components/Viewing/PageJSON/MasterJSON.js +++ b/frontend/components/Viewing/PageJSON/MasterJSON.js @@ -34,7 +34,19 @@ import SubComponent3 from './Types/SubComponent3.json'; import LocalSubComponent3 from './Types/LocalSubComponent3.json'; import ExternallyDefined3 from './Types/ExternallyDefined3.json'; import SequenceFeature3 from './Types/SequenceFeature3.json'; - +import Attachment3 from './Types/Attachment3.json'; +import Collection3 from './Types/Collection3.json'; +import Cut3 from './Types/Cut3.json'; +import CombinatorialDerivation3 from './Types/CombinatorialDerivation3.json'; +import EntireSequence3 from './Types/EntireSequence3.json'; +import Experiment3 from './Types/Experiment3.json'; +import ExperimentalData3 from './Types/ExperimentalData3.json'; +import Implementation3 from './Types/Implementation3.json'; +import Location3 from './Types/Location3.json'; +import Model3 from './Types/Model3.json'; +import Participation3 from './Types/Participation3.json'; +import Range3 from './Types/Range3.json'; +import VariableFeature3 from './Types/VariableFeature3.json'; const TypeToJson = { 'http://sbols.org/v2#ComponentDefinition': ComponentDefinition, @@ -72,8 +84,21 @@ const TypeToJson = { 'http://sbols.org/v3#SubComponent': SubComponent3, 'http://sbols.org/v3#LocalSubComponent': LocalSubComponent3, 'http://sbols.org/v3#ExternallyDefined': ExternallyDefined3, - 'http://sbols.org/v3#SequenceFeature': SequenceFeature3 - + 'http://sbols.org/v3#SequenceFeature': SequenceFeature3, + 'http://sbols.org/v3#Attachment': Attachment3, + 'http://sbols.org/v3#Collection': Collection3, + 'http://sbols.org/v3#Cut': Cut3, + 'http://sbols.org/v3#CombinatorialDerivation': CombinatorialDerivation3, + 'http://sbols.org/v3#EntireSequence': EntireSequence3, + 'http://sbols.org/v3#Experiment': Experiment3, + 'http://sbols.org/v3#ExperimentalData': ExperimentalData3, + 'http://sbols.org/v3#Implementation': Implementation3, + 'http://sbols.org/v3#Interaction': Interaction3, + 'http://sbols.org/v3#Location': Location3, + 'http://sbols.org/v3#Model': Model3, + 'http://sbols.org/v3#Participation': Participation3, + 'http://sbols.org/v3#Range': Range3, + 'http://sbols.org/v3#VariableFeature': VariableFeature3 }; export default TypeToJson; diff --git a/frontend/components/Viewing/PageJSON/Types/Component3.json b/frontend/components/Viewing/PageJSON/Types/Component3.json index 3b5751ba..c5dc28e9 100644 --- a/frontend/components/Viewing/PageJSON/Types/Component3.json +++ b/frontend/components/Viewing/PageJSON/Types/Component3.json @@ -79,7 +79,6 @@ "title": "SubComponents", "infoLink": "https://sbols.org/v3#SubComponent", "predicates": [ - "rdf:type" ], "stripAfter": "#", "link": "$" @@ -112,22 +111,36 @@ ] }, { - "title": "Sequence Constraints", + "title": "Constraints", "rootPredicate": "sbol:hasConstraint", "icon": "faVirusSlash", "sections": [ { - "title": "Sequence Constraint", + "title": "Constraint", "infoLink": "https://sbols.org/v3#Constraint", "predicates": [ - "sbol:Constraint" ], + "stripAfter": "#", "link": "$" }, { "title": "constraintLink", "hide": true, "predicates": [] + }, + { + "title": "Subject", + "infoLink": "https://sbols.org/v3#Subject", + "predicates": [ + "sbol:subject" + ], + "stripAfter": "#", + "link": "$" + }, + { + "title": "subjectLink", + "hide": true, + "predicates": [] } ] }, @@ -140,7 +153,6 @@ "title": "Interface", "infoLink": "https://sbols.org/v3#Interface", "predicates": [ - ], "link": "$" }, @@ -148,6 +160,32 @@ "title": "interfaceLink", "hide": true, "predicates": [] + }, + { + "title": "Output", + "infoLink": "https://sbols.org/v3#Output", + "predicates": [ + "sbol:output" + ], + "link": "$" + }, + { + "title": "outputLink", + "hide": true, + "predicates": [] + }, + { + "title": "Input", + "infoLink": "https://sbols.org/v3#Input", + "predicates": [ + "sbol:input" + ], + "link": "$" + }, + { + "title": "inputLink", + "hide": true, + "predicates": [] } ] }, @@ -160,7 +198,7 @@ "title": "Model", "infoLink": "https://sbols.org/v3#Model", "predicates": [ - + "sbol:displayId" ], "link": "$" }, @@ -168,6 +206,51 @@ "title": "modelLink", "hide": true, "predicates": [] + }, + { + "title": "Framework", + "infoLink": "https://sbols.org/v3#Framework", + "predicates": [ + "sbol:framework" + ], + "link": "$" + }, + { + "title": "frameworkLink", + "hide": true, + "predicates": [ + "sbol:framework" + ] + }, + { + "title": "Source", + "infoLink": "https://sbols.org/v3#Source", + "predicates": [ + "sbol:source" + ], + "link": "$" + }, + { + "title": "sourceLink", + "hide": true, + "predicates": [ + "sbol:source" + ] + }, + { + "title": "Language", + "infoLink": "https://sbols.org/v3#Language", + "predicates": [ + "sbol:language" + ], + "link": "$" + }, + { + "title": "languageLink", + "hide": true, + "predicates": [ + "sbol:language" + ] } ] } @@ -177,7 +260,7 @@ "$TABLES[Sequences]", "$TABLES[Features]", "$TABLES[Interactions]", - "$TABLES[Sequence Constraints]", + "$TABLES[Constraints]", "$TABLES[Interfaces]", "$TABLES[Models]", "Other Properties", diff --git a/frontend/components/Viewing/PageJSON/Types/Model3.json b/frontend/components/Viewing/PageJSON/Types/Model3.json index 0a0326ba..2b56d562 100644 --- a/frontend/components/Viewing/PageJSON/Types/Model3.json +++ b/frontend/components/Viewing/PageJSON/Types/Model3.json @@ -8,7 +8,7 @@ "PREFIX dc: ", "PREFIX sbh: ", "PREFIX prov: ", - "PREFIX sbol: ", + "PREFIX sbol: ", "PREFIX xsd: ", "PREFIX rdfs: ", "PREFIX purl: " diff --git a/frontend/components/Viewing/Shell.js b/frontend/components/Viewing/Shell.js index 9f91afae..eaffe57d 100644 --- a/frontend/components/Viewing/Shell.js +++ b/frontend/components/Viewing/Shell.js @@ -10,6 +10,7 @@ import systemsBiologyOntology from '../../namespace/systems-biology-ontology'; import edamOntology from '../../namespace/edam-ontology'; export default function Shell(properties) { + console.log(properties); const plugins = properties.plugins; const metadata = properties.metadata; @@ -22,6 +23,7 @@ export default function Shell(properties) { metadata.search = getSearchData; if (!json) { + console.log("NO JSON"); return (
Date: Wed, 4 Sep 2024 09:22:34 -0600 Subject: [PATCH 2/2] missed one json page --- .../components/Viewing/PageJSON/MasterJSON.js | 1 + tests/SBOL3 data/New_combine2020.rdf | 168 +++++++++--------- 2 files changed, 85 insertions(+), 84 deletions(-) diff --git a/frontend/components/Viewing/PageJSON/MasterJSON.js b/frontend/components/Viewing/PageJSON/MasterJSON.js index 39945eb1..22b813b0 100644 --- a/frontend/components/Viewing/PageJSON/MasterJSON.js +++ b/frontend/components/Viewing/PageJSON/MasterJSON.js @@ -47,6 +47,7 @@ import Model3 from './Types/Model3.json'; import Participation3 from './Types/Participation3.json'; import Range3 from './Types/Range3.json'; import VariableFeature3 from './Types/VariableFeature3.json'; +import Interaction3 from './Types/Interaction3.json'; const TypeToJson = { 'http://sbols.org/v2#ComponentDefinition': ComponentDefinition, diff --git a/tests/SBOL3 data/New_combine2020.rdf b/tests/SBOL3 data/New_combine2020.rdf index d482bb8e..a5086310 100644 --- a/tests/SBOL3 data/New_combine2020.rdf +++ b/tests/SBOL3 data/New_combine2020.rdf @@ -7,53 +7,53 @@ xmlns:prov="http://www.w3.org/ns/prov#" xmlns:SBO="https://identifiers.org/SBO:" xmlns:GO="https://identifiers.org/GO:" - xmlns="https://synbiohub.org/public/igem/" + xmlns="http://dummy.org/" xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/" - xml:base="https://synbiohub.org/public/igem/"> - - + xml:base="http://dummy.org/"> + + gfp coding sequence gfp - + E0040 - - + + j23106 - - + + - - + + SubComponent2 - + - - + + SubComponent1 - + - + 738 19 - + Range1 - + SubComponent2 @@ -61,17 +61,17 @@ - + - - + + Participation2 - - + + Participation1 @@ -81,36 +81,36 @@ i13504 system - + i13504_system - + - + - + 826 747 - + Range1 - + SubComponent3 - + i13504 - + - + 746 739 - + Range1 @@ -118,35 +118,35 @@ - + - + - + 18 13 - + Range1 SequenceFeature1 - + - + - + 11 1 - + Range1 - + SubComponent1 @@ -154,33 +154,33 @@ Screening plasmid intermediate - - + + B0015 double terminator terminator - + B0015 - + - + - + - - + + SubComponent2 - + ComponentReference1 - - + + SubComponent1 @@ -188,40 +188,40 @@ Constraint1 - - - - + + + + interlab16device1 - - + + RBS (Elowitz 1999) B0034 - + B0034 - + - + - + - - + + SubComponent2 - + ComponentReference1 - - + + SubComponent1 @@ -229,53 +229,53 @@ Constraint1 - - - - + + + + interlab16device2 - - + + j23101 - + GFP GFP - + GFP_protein - + aaagaggagaaa - + B0034_Sequence - + aaagaggagaaatactagatgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataatactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctc i13504 sequence Sequence1 - + i13504_Sequence1 - + ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctc terminator sequence Sequence1 - + B0015_Sequence1 - + atgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataa gfp sequence Sequence1 - + E0040_Sequence1 \ No newline at end of file