From 75d2c56f48d54af353493bf7f226bc7dba576481 Mon Sep 17 00:00:00 2001 From: hadleyking Date: Thu, 18 Feb 2021 14:57:07 -0500 Subject: [PATCH] Update example BCO files - check extension formats - update etags Changes to be committed: modified: HCV1a.json modified: HIVE_metagenomics.json modified: UVP.json modified: glycosylation-sites-UniCarbKB.json --- examples/HCV1a.json | 8 ++++---- examples/HIVE_metagenomics.json | 6 +++--- examples/UVP.json | 19 +++++++++++-------- examples/glycosylation-sites-UniCarbKB.json | 8 ++++---- 4 files changed, 22 insertions(+), 19 deletions(-) diff --git a/examples/HCV1a.json b/examples/HCV1a.json index 69536f8..885d20e 100644 --- a/examples/HCV1a.json +++ b/examples/HCV1a.json @@ -1,6 +1,6 @@ { - "object_id": "https://w3id.org/biocompute/1.3.0/examples/HCV1a.json", - "etag": "8e03f6f65e2caae86770a64a9ebef3e0651d4675a96687e5b148fda181c9cdc0", + "object_id": "https://raw.githubusercontent.com/biocompute-objects/BCO_Specification/1.4.2/examples/HCV1a.json", + "etag": "11ee4c3b8a04ad16dcca19a6f478c0870d3fe668ed6454096ab7165deb1ab8ea", "spec_version": "https://w3id.org/ieee/ieee-2791-schema/", "provenance_domain": { "name": "HCV1a ledipasvir resistance SNP detection", @@ -71,7 +71,7 @@ ], "extension_domain": [ { - "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/master/FHIR/fhir_extension.json", + "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/fhir/fhir_extension.json", "fhir_extension": [ { "fhir_endpoint": "http://fhirtest.uhn.ca/baseDstu3", @@ -102,7 +102,7 @@ ] }, { - "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/master/SCM/scm_extension.json", + "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/scm/scm_extension.json", "scm_extension": { "scm_repository": "https://github.com/example/repo1", "scm_type": "git", diff --git a/examples/HIVE_metagenomics.json b/examples/HIVE_metagenomics.json index 7c2f07b..ef13b4e 100644 --- a/examples/HIVE_metagenomics.json +++ b/examples/HIVE_metagenomics.json @@ -1,6 +1,6 @@ { - "object_id": "https://w3id.org/biocompute/1.3.0/examples/HIVE_metagenomics.json", - "etag": "09d55a44601184330b05dae6c3d49e9c3821f528a93f958edec92504fef41970", + "object_id": "https://raw.githubusercontent.com/biocompute-objects/BCO_Specification/1.4.2/examples/HIVE_metagenomics.json", + "etag": "caed07395b6afb58c8810d174a315260124f687740bc3bb14387de5e84c7e3d4", "spec_version" : "https://w3id.org/ieee/ieee-2791-schema/", "provenance_domain": { "name": "Healthy human fecal metagenomic diversity", @@ -50,7 +50,7 @@ ], "extension_domain":[ { - "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/master/SCM/scm_extension.json", + "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/scm/scm_extension.json", "scm_extension": { "scm_repository": "https://github.com/biocompute-objects/HIVE_metagenomics", "scm_type": "git", diff --git a/examples/UVP.json b/examples/UVP.json index 04bb20d..be6983a 100644 --- a/examples/UVP.json +++ b/examples/UVP.json @@ -1,6 +1,6 @@ { "object_id": "https://w3id.org/biocompute/1.3.0/examples/UVP_BCO.json", - "checksum": "e07ad61a2e13272437dc052de7502d8af8a122dc2865ff0f382f459983c0bccc", + "etag": "39fb1c62f43ff72ac95f91a433d5e425fb08bc07ec0f719ecfd27fb3cd3a3635", "spec_version": "https://w3id.org/biocompute/1.3.0/", "provenance_domain": { "name": "Lineage assignment for an isolate of M. tuberculosis based on its single nucleotide polymorphism (SNP) profile based on UVC v1.0.", @@ -110,14 +110,17 @@ "usability_domain": [ "Lineage assignment for an isolate of M. tuberculosis[taxonomy:1773] based on its single nucleotide polymorphism [so:0000694] (SNP) profile." ], - "extension_domain": { - "scm_extension": { - "scm_repository": "https://github.com/CPTR-ReSeqTB/UVP", - "scm_type": "git", - "scm_commit": "9e8f588b3cd3f5eebde29f7d2879e1a1e1c1aed3", - "scm_path": "UVP/scripts/UVP.py" + "extension_domain": [ + { + "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/scm/scm_extension.json", + "scm_extension": { + "scm_repository": "https://github.com/CPTR-ReSeqTB/UVP", + "scm_type": "git", + "scm_commit": "9e8f588b3cd3f5eebde29f7d2879e1a1e1c1aed3", + "scm_path": "UVP/scripts/UVP.py" + } } - }, + ], "description_domain": { "keywords": [ "Mycobacterium tuberculosis", diff --git a/examples/glycosylation-sites-UniCarbKB.json b/examples/glycosylation-sites-UniCarbKB.json index 4b4ffc5..be49e02 100644 --- a/examples/glycosylation-sites-UniCarbKB.json +++ b/examples/glycosylation-sites-UniCarbKB.json @@ -1,6 +1,6 @@ { - "object_id": "https://w3id.org/biocompute/1.3.0/examples/glycosylation-sites-UniCarbKB", - "etag": "c0b41938a47f7b7689a34f5d89707f039e210f3cc22857b80070f73cbcd2e669", + "object_id": "https://raw.githubusercontent.com/biocompute-objects/BCO_Specification/1.4.2glycosylation-sites-UniCarbKB", + "etag": "5741d66ddf7881db33f7075ce8b64b941bd7cc001965f31682e5da9966c7f3ba", "spec_version" : "https://w3id.org/ieee/ieee-2791-schema/", "provenance_domain":{ "name": "glycosylation-sites-UniCarbKB", @@ -46,7 +46,7 @@ ], "extension_domain":[ { - "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/master/License/license_extension.json", + "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/license/license_extension.json", "license_extension":{ "data_license": "https://creativecommons.org/licenses/by/4.0/", "scripts_license": "https://www.gnu.org/licenses/gpl-3.0.en.html" @@ -54,7 +54,7 @@ }, { - "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/master/SCM/scm_extension.json", + "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/scm/scm_extension.json", "scm_extension":{ "scm_repository": "https://github.com/GW-HIVE/glygen-backend-integration/", "scm_type": "git",