diff --git a/Best_Practices b/Best_Practices new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/Best_Practices @@ -0,0 +1 @@ + diff --git a/VERSION.py b/VERSION.py new file mode 100644 index 0000000..8aae92b --- /dev/null +++ b/VERSION.py @@ -0,0 +1,3 @@ +VERSION_MAJOR = "1.4" +VERSION_MINOR = ".0" +VERSION = VERSION_MAJOR + ('.' + VERSION_MINOR if VERSION_MINOR else '') \ No newline at end of file diff --git a/docs/io-domain.md b/docs/io-domain.md index 33bc357..22c4d87 100644 --- a/docs/io-domain.md +++ b/docs/io-domain.md @@ -12,8 +12,8 @@ Condensed exampled: ```json "io_domain": { - "input_subdomain": { - }, + "input_subdomain": [ + ], "output_subdomain": [ ] }, diff --git a/docs/provenance-domain.md b/docs/provenance-domain.md index 1a6ac99..9f475a5 100644 --- a/docs/provenance-domain.md +++ b/docs/provenance-domain.md @@ -93,6 +93,7 @@ The fields from the `contributor` object (described in [section 2.1.9](/provenan ### 2.1.4 Inheritance/derivation "derived_from" If the object is derived from another, this field will specify the parent object, in the form of the ‘object_id’. If the object is novel than the field is not included. +======= ```json "derived_from" : "https://github.com/biocompute-objects/BCO_Specification/blob/1.2.1-beta/HCV1a.json" @@ -159,7 +160,7 @@ This is a list to hold contributor identifiers and a description of their type o ### 2.1.10 License "license" -A space for Creative Commons licence or other licence information (text). The default or recommended licence can be _Creative Commons Attribution 4.0 International_ identified as https://spdx.org/licenses/CC-BY-4.0.html +A space for Creative Commons licence or other license information (text). The default or recommended licence can be _Creative Commons Attribution 4.0 International_ identified as https://spdx.org/licenses/CC-BY-4.0.html ```json "license": "https://spdx.org/licenses/CC-BY-4.0.html" diff --git a/examples/HCV1a.json b/examples/HCV1a.json index abb6f0a..69536f8 100644 --- a/examples/HCV1a.json +++ b/examples/HCV1a.json @@ -1,7 +1,7 @@ { "object_id": "https://w3id.org/biocompute/1.3.0/examples/HCV1a.json", "etag": "8e03f6f65e2caae86770a64a9ebef3e0651d4675a96687e5b148fda181c9cdc0", - "spec_version": "https://w3id.org/biocompute/1.3.0/", + "spec_version": "https://w3id.org/ieee/ieee-2791-schema/", "provenance_domain": { "name": "HCV1a ledipasvir resistance SNP detection", "version": "2.9", @@ -71,7 +71,7 @@ ], "extension_domain": [ { - "extension_schema": "https://github.com/biocompute-objects/BCO_Specification/blob/1.4.0/schemas/extension_domain/fhir_extension.json", + "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/master/FHIR/fhir_extension.json", "fhir_extension": [ { "fhir_endpoint": "http://fhirtest.uhn.ca/baseDstu3", @@ -102,7 +102,7 @@ ] }, { - "extension_schema": "https://github.com/biocompute-objects/BCO_Specification/blob/1.4.0/schemas/extension_domain/fhir_extension.json", + "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/master/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 2761290..7c2f07b 100644 --- a/examples/HIVE_metagenomics.json +++ b/examples/HIVE_metagenomics.json @@ -1,7 +1,7 @@ { "object_id": "https://w3id.org/biocompute/1.3.0/examples/HIVE_metagenomics.json", - "checksum": "09d55a44601184330b05dae6c3d49e9c3821f528a93f958edec92504fef41970", - "spec_version" : "https://w3id.org/biocompute/1.3.0/", + "etag": "09d55a44601184330b05dae6c3d49e9c3821f528a93f958edec92504fef41970", + "spec_version" : "https://w3id.org/ieee/ieee-2791-schema/", "provenance_domain": { "name": "Healthy human fecal metagenomic diversity", "version": "1.0.0", @@ -48,15 +48,18 @@ "Identify the general community composition of organisms in a human [taxID:9606] fecal [UBERON:0001988] sample, ", "CensuScope is used to do a census of the composition of the read files. Based on a user-defined threshold, organisms identified are used for alignment in the Hexagon alignment." ], - "extension_domain":{ - "scm_extension": { - "scm_repository": "https://github.com/biocompute-objects/HIVE_metagenomics", - "scm_type": "git", - "scm_commit": "e4620f642fb20557f6c679397696614305ed07b1", - "scm_path": "biocompute-objects/HIVE_metagenomics", - "scm_preview": "https://github.com/example/repo1/blob/c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21/workflow/hive-viral-mutation-detection.cwl" - } - }, + "extension_domain":[ + { + "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/master/SCM/scm_extension.json", + "scm_extension": { + "scm_repository": "https://github.com/biocompute-objects/HIVE_metagenomics", + "scm_type": "git", + "scm_commit": "e4620f642fb20557f6c679397696614305ed07b1", + "scm_path": "biocompute-objects/HIVE_metagenomics", + "scm_preview": "https://github.com/example/repo1/blob/c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21/workflow/hive-viral-mutation-detection.cwl" + } + } + ], "description_domain": { "keywords": [ "metagenome", diff --git a/examples/glycosylation-sites-UniCarbKB.json b/examples/glycosylation-sites-UniCarbKB.json index fb482f0..4b4ffc5 100644 --- a/examples/glycosylation-sites-UniCarbKB.json +++ b/examples/glycosylation-sites-UniCarbKB.json @@ -1,7 +1,7 @@ { "object_id": "https://w3id.org/biocompute/1.3.0/examples/glycosylation-sites-UniCarbKB", - "checksum": "c0b41938a47f7b7689a34f5d89707f039e210f3cc22857b80070f73cbcd2e669", - "spec_version" : "https://w3id.org/biocompute/1.3.0/", + "etag": "c0b41938a47f7b7689a34f5d89707f039e210f3cc22857b80070f73cbcd2e669", + "spec_version" : "https://w3id.org/ieee/ieee-2791-schema/", "provenance_domain":{ "name": "glycosylation-sites-UniCarbKB", "version": "1.0", @@ -44,18 +44,26 @@ "usability_domain":[ "List of human [taxid:9606] proteins with information on glycosylation sites from UniCarbKB database [https://academic.oup.com/nar/article/42/D1/D215/1052197, https://doi.org/10.1093/nar/gkt1128]" ], - "extension_domain":{ - "license":{ - "data_license": "https://creativecommons.org/licenses/by/4.0/", - "scripts_license": "https://www.gnu.org/licenses/gpl-3.0.en.html" + "extension_domain":[ + { + "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/master/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" + } }, - "scm_extension":{ - "scm_repository": "https://github.com/GW-HIVE/glygen-backend-integration/", - "scm_type": "git", - "scm_commit": "d34b85553e775dd5452005d786fe6e47d6048ee0", - "scm_path": "/data/projects/glygen/generated/datasets/reviewed/human_proteoform_glycosylation_sites_unicarbkb_glytoucan.readme.txt" + { + + "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/master/SCM/scm_extension.json", + "scm_extension":{ + "scm_repository": "https://github.com/GW-HIVE/glygen-backend-integration/", + "scm_type": "git", + "scm_commit": "d34b85553e775dd5452005d786fe6e47d6048ee0", + "scm_path": "/data/projects/glygen/generated/datasets/reviewed/human_proteoform_glycosylation_sites_unicarbkb_glytoucan.readme.txt" + } } - }, + + ], "description_domain":{ "keywords":[ "protein", @@ -214,10 +222,8 @@ }, "error_domain":{ "empirical_error":{ + "comment": "Unique value statistics for the dataset", "statistics":[ - { - "comment": "Unique value statistics for the dataset" - }, { "key": "uniprotkb_canonical_ac", "value":92, @@ -251,7 +257,7 @@ { "key": "glycosylation_type", "value":3, - "description": "Type of glycosylation [linkage type]" + "description": "Type of glycosylation linkage type" } ] }, diff --git a/scripts/validate.py b/scripts/validate.py index 0619423..76e6d60 100755 --- a/scripts/validate.py +++ b/scripts/validate.py @@ -6,7 +6,6 @@ """Used to test a BCO against the schema. The following commands were used to run the script: cd BCO_specification/ - python -m venv env source env/bin/activate pip install jsonschema jsonref python validate.py HCV1a.json $PWD/schemas/biocomputeobject.json