From 6621fa820166aec009e4ca79e5ed8ed7bc722d02 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Fri, 12 Jan 2024 12:01:41 +0000 Subject: [PATCH 1/4] Add gene_annotation_version field in analysis_protocol.json. Fixes #1543 --- docs/jsonBrowser/type.md | 1 + json_schema/type/protocol/analysis/analysis_protocol.json | 7 +++++++ json_schema/update_log.csv | 1 + 3 files changed, 9 insertions(+) diff --git a/docs/jsonBrowser/type.md b/docs/jsonBrowser/type.md index a4ef467f3..c6b8b98d8 100644 --- a/docs/jsonBrowser/type.md +++ b/docs/jsonBrowser/type.md @@ -147,6 +147,7 @@ computational_method | A URI to a versioned workflow and versioned execution env matrix | Information related to protocols that output a matrix. | object | no | [See module matrix](module.md#matrix) | Matrix | | alignment_software | Name of alignment software used to map FASTQ files to reference genome. | string | no | | Alignment software | | Cellranger; kallisto bustools; GSNAP; STAR alignment_software_version | Version of alignment software used to map FASTQ files to reference genome. | string | no | | Alignment software version | | v2.0.1; 2.4.2a; v0.45.2 +gene_annotation_version | The Ensembl release version accession number or NCBI RefSeq assembly version used for gene annotation. | string | no | | Gene annotation version | | v110; GCF_000001405.40; GCF_000001635.27 ## Aggregate generation protocol _Information about how cultured cells are developed into cell aggregates._ diff --git a/json_schema/type/protocol/analysis/analysis_protocol.json b/json_schema/type/protocol/analysis/analysis_protocol.json index 4b54ce341..30a33b667 100644 --- a/json_schema/type/protocol/analysis/analysis_protocol.json +++ b/json_schema/type/protocol/analysis/analysis_protocol.json @@ -73,6 +73,13 @@ "type": "string", "user_friendly": "Alignment software version", "example": "v2.0.1; 2.4.2a; v0.45.2" + }, + "gene_annotation_version": { + "description": "The Ensembl release version accession number or NCBI RefSeq assembly version used for gene annotation.", + "type": "string", + "pattern": "^v[0-9]{2,}$|^GCF_[0-9]{9}\\.[0-9]{1,}$", + "user_friendly": "Gene annotation version", + "example": "v110; GCF_000001405.40; GCF_000001635.27" } } } diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 3231ff199..310b5f7ee 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1 +1,2 @@ Schema,Change type,Change message,Version,Date +type/protocol/analysis/analysis_protocol,minor,"Added gene_annotation_version field in analysis_protocol Fixes#1543",, \ No newline at end of file From 7741c3829cc525d2952e30f88fd178f37cdb628a Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 22 Jan 2024 14:51:56 +0000 Subject: [PATCH 2/4] Use compact forms in regex Co-authored-by: Amnon Khen --- json_schema/type/protocol/analysis/analysis_protocol.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/type/protocol/analysis/analysis_protocol.json b/json_schema/type/protocol/analysis/analysis_protocol.json index 30a33b667..72b0a6bec 100644 --- a/json_schema/type/protocol/analysis/analysis_protocol.json +++ b/json_schema/type/protocol/analysis/analysis_protocol.json @@ -77,7 +77,7 @@ "gene_annotation_version": { "description": "The Ensembl release version accession number or NCBI RefSeq assembly version used for gene annotation.", "type": "string", - "pattern": "^v[0-9]{2,}$|^GCF_[0-9]{9}\\.[0-9]{1,}$", + "pattern": "^v\\d{2,}$|^GCF_\\d{9}\\.\\d+$", "user_friendly": "Gene annotation version", "example": "v110; GCF_000001405.40; GCF_000001635.27" } From a95dc8caf2dc9f73d63317fe91f1d6c38bbccb4b Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 5 Feb 2024 16:11:57 +0000 Subject: [PATCH 3/4] Ran release_prepare.py script. --- changelog.md | 4 ++++ json_schema/update_log.csv | 1 - json_schema/versions.json | 4 ++-- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/changelog.md b/changelog.md index 96ded8f04..553d0965b 100644 --- a/changelog.md +++ b/changelog.md @@ -7,6 +7,10 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http:// ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging) +### [type/protocol/analysis/analysis_protocol.json - v10.2.0] - 2024-02-05 +### Added +Added gene_annotation_version field in analysis_protocol Fixes#1543 + ## [Released](https://github.com/HumanCellAtlas/metadata-schema/) ### [type/protocol/analysis/analysis_protocol.json - v10.1.0] - 2023-11-07 diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 310b5f7ee..3231ff199 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,2 +1 @@ Schema,Change type,Change message,Version,Date -type/protocol/analysis/analysis_protocol,minor,"Added gene_annotation_version field in analysis_protocol Fixes#1543",, \ No newline at end of file diff --git a/json_schema/versions.json b/json_schema/versions.json index 6f9079ecf..8f47b78e5 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -1,5 +1,5 @@ { - "last_update_date": "2023-11-07T15:13:34Z", + "last_update_date": "2024-02-05T16:10:39Z", "version_numbers": { "core": { "biomaterial": { @@ -114,7 +114,7 @@ }, "protocol": { "analysis": { - "analysis_protocol": "10.1.0" + "analysis_protocol": "10.2.0" }, "biomaterial_collection": { "aggregate_generation_protocol": "2.1.0", From e9e7c74ab2f110b0b8a9dccef9169c1e6991bfcb Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 5 Feb 2024 16:18:33 +0000 Subject: [PATCH 4/4] Release from staging to master 2024-02-05 --- changelog.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/changelog.md b/changelog.md index 553d0965b..28b2299d3 100644 --- a/changelog.md +++ b/changelog.md @@ -7,12 +7,12 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http:// ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging) +## [Released](https://github.com/HumanCellAtlas/metadata-schema/) + ### [type/protocol/analysis/analysis_protocol.json - v10.2.0] - 2024-02-05 ### Added Added gene_annotation_version field in analysis_protocol Fixes#1543 -## [Released](https://github.com/HumanCellAtlas/metadata-schema/) - ### [type/protocol/analysis/analysis_protocol.json - v10.1.0] - 2023-11-07 ### Added Added alignment_software & alignment_software_version field in analysis_protocol Fixes#1533