From 1b4c34cf98febb41948aface6360280e59564ede Mon Sep 17 00:00:00 2001 From: willrockout Date: Wed, 26 Jul 2023 10:26:03 -0700 Subject: [PATCH 1/4] Removed timecourse from types and added to biomaterial core. --- docs/jsonBrowser/core.md | 1 + docs/jsonBrowser/type.md | 3 --- .../core/biomaterial/biomaterial_core.json | 6 +++++ json_schema/property_migrations.json | 27 +++++++++++++++++++ json_schema/type/biomaterial/cell_line.json | 6 ----- .../type/biomaterial/cell_suspension.json | 6 ----- .../type/biomaterial/donor_organism.json | 6 ----- json_schema/update_log.csv | 4 +++ 8 files changed, 38 insertions(+), 21 deletions(-) diff --git a/docs/jsonBrowser/core.md b/docs/jsonBrowser/core.md index 707f2a4ec..b0b253019 100644 --- a/docs/jsonBrowser/core.md +++ b/docs/jsonBrowser/core.md @@ -61,6 +61,7 @@ supplementary_files | A list of filenames of biomaterial-level supplementary fil biosamples_accession | A BioSamples accession. | string | no | | BioSamples accession | | SAMN00000000 insdc_sample_accession | An International Nucleotide Sequence Database Collaboration (INSDC) sample accession. | string | no | | INSDC sample accession | | SRS0000000 HDBR_accession | A Human Developmental Biology Resource (HDBR) sample accession. | string | no | | HDBR accession | | 34526; 14758, 2, liver +timecourse | Information relating to a timecourse associated with this cell line. | object | no | [See module timecourse](module.md#timecourse) | Timecourse | | ## Process core _Information relevant to how a biomaterial or file was converted into another biomaterial or file._ diff --git a/docs/jsonBrowser/type.md b/docs/jsonBrowser/type.md index 77cca6ddc..374e72da2 100644 --- a/docs/jsonBrowser/type.md +++ b/docs/jsonBrowser/type.md @@ -361,7 +361,6 @@ genus_species | The scientific binomial name for the species of the suspension. selected_cell_types | The cell type(s) selected to be present in the suspension. | array | no | [See module cell_type_ontology](module.md#cell-type-ontology) | Selected cell type(s) | | estimated_cell_count | Estimated number of cells in the suspension. | integer | no | | Estimated cell count | | 1; 2100 plate_based_sequencing | Fields specific for plate-based sequencing experiments. | object | no | [See module plate_based_sequencing](module.md#plate-based-sequencing) | Plate-based sequencing | | -timecourse | Information relating to a timecourse associated with this cell suspension. | object | no | [See module timecourse](module.md#timecourse) | Timecourse | | ## Cell line _Information about the cell line or cell culture biomaterial._ @@ -390,7 +389,6 @@ date_established | Date when the cell line was established. | string | no | | D disease | Short description of any disease association to the cell type. | object | no | [See module disease_ontology](module.md#disease-ontology) | Disease | | genus_species | The scientific binomial name for the species of the cell line. | array | no | [See module species_ontology](module.md#species-ontology) | Genus species | | publication | A publication that cites the cell line creation. | object | no | [See module publication](module.md#publication) | Publication | | -timecourse | Information relating to a timecourse associated with this cell line. | object | no | [See module timecourse](module.md#timecourse) | Timecourse | | ## Imaged specimen _Information about a tissue specimen after it has been sectioned and prepared for imaging._ @@ -434,7 +432,6 @@ height | Height of organism in Height unit. | string | no | | Height | | 160; height_unit | The unit in which Height is expressed. | object | no | [See module length_unit_ontology](module.md#length-unit-ontology) | Height unit | | weight | Weight of organism in Weight unit. | string | no | | Weight | | 60; 40-60 weight_unit | The unit in which Weight is expressed. | object | no | [See module mass_unit_ontology](module.md#mass-unit-ontology) | Weight unit | | -timecourse | Information relating to a timecourse associated with this biomaterial. | object | no | [See module timecourse](module.md#timecourse) | Timecourse | | ## Organoid _Information about an organoid biomaterial._ diff --git a/json_schema/core/biomaterial/biomaterial_core.json b/json_schema/core/biomaterial/biomaterial_core.json index 75fd66fe8..bfa582117 100644 --- a/json_schema/core/biomaterial/biomaterial_core.json +++ b/json_schema/core/biomaterial/biomaterial_core.json @@ -83,6 +83,12 @@ "user_friendly": "HDBR accession", "example": "34526; 14758, 2, liver", "guidelines": "Enter accession if sample has been obtained from the Human Developmental Biology Resource (HDBR)." + }, + "timecourse": { + "description": "Information relating to a timecourse associated with this cell line.", + "type": "object", + "$ref": "module/biomaterial/timecourse.json", + "user_friendly": "Timecourse" } } } diff --git a/json_schema/property_migrations.json b/json_schema/property_migrations.json index 8ea311a3c..9e94837b8 100644 --- a/json_schema/property_migrations.json +++ b/json_schema/property_migrations.json @@ -1,5 +1,32 @@ { "migrations": [ + { + "source_schema": "cell_line", + "property": "timecourse", + "target_schema": "cell_line", + "replaced_by": "biomaterial_core.timecourse", + "effective_from": "16.0.0", + "reason": "Timecourse module has been moved to biomaterial core", + "type": "moved property" + }, + { + "source_schema": "donor_organism", + "property": "timecourse", + "target_schema": "donor_organism", + "replaced_by": "biomaterial_core.timecourse", + "effective_from": "16.0.0", + "reason": "Timecourse module has been moved to biomaterial core", + "type": "moved property" + }, + { + "source_schema": "cell_suspension", + "property": "timecourse", + "target_schema": "cell_suspension", + "replaced_by": "biomaterial_core.timecourse", + "effective_from": "14.0.0", + "reason": "Timecourse module has been moved to biomaterial core", + "type": "moved property" + }, { "source_schema": "analysis_file", "property": "genome_assembly_version", diff --git a/json_schema/type/biomaterial/cell_line.json b/json_schema/type/biomaterial/cell_line.json index ddc08a599..2446640d0 100644 --- a/json_schema/type/biomaterial/cell_line.json +++ b/json_schema/type/biomaterial/cell_line.json @@ -155,12 +155,6 @@ "type": "object", "$ref": "module/project/publication.json", "user_friendly": "Publication" - }, - "timecourse": { - "description": "Information relating to a timecourse associated with this cell line.", - "type": "object", - "$ref": "module/biomaterial/timecourse.json", - "user_friendly": "Timecourse" } } } diff --git a/json_schema/type/biomaterial/cell_suspension.json b/json_schema/type/biomaterial/cell_suspension.json index 1c4a8e092..99c5ec00e 100644 --- a/json_schema/type/biomaterial/cell_suspension.json +++ b/json_schema/type/biomaterial/cell_suspension.json @@ -83,12 +83,6 @@ "type": "object", "$ref": "module/process/sequencing/plate_based_sequencing.json", "user_friendly": "Plate-based sequencing" - }, - "timecourse": { - "description": "Information relating to a timecourse associated with this cell suspension.", - "type": "object", - "$ref": "module/biomaterial/timecourse.json", - "user_friendly": "Timecourse" } } } diff --git a/json_schema/type/biomaterial/donor_organism.json b/json_schema/type/biomaterial/donor_organism.json index ade07376f..6bab6b746 100644 --- a/json_schema/type/biomaterial/donor_organism.json +++ b/json_schema/type/biomaterial/donor_organism.json @@ -178,12 +178,6 @@ "type": "object", "$ref": "module/ontology/mass_unit_ontology.json", "user_friendly": "Weight unit" - }, - "timecourse": { - "description": "Information relating to a timecourse associated with this biomaterial.", - "type": "object", - "$ref": "module/biomaterial/timecourse.json", - "user_friendly": "Timecourse" } } } diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 3231ff199..98de26f27 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1 +1,5 @@ Schema,Change type,Change message,Version,Date +core/biomaterial/biomaterial_core,minor,Added timecourse module. Fixes #1511,, +type/biomaterial.donor_organism,major,Removed timecourse module.,, +type/biomaterial.cell_suspension,major,Removed timecourse module.,, +type/biomaterial.cell_line,major,Removed timecourse module.,, \ No newline at end of file From 504234bcb166f6d00254f604c6517b54a23622b1 Mon Sep 17 00:00:00 2001 From: William Sullivan Date: Fri, 28 Jul 2023 07:57:12 -0700 Subject: [PATCH 2/4] Update json_schema/core/biomaterial/biomaterial_core.json Fixed description to be more general. Co-authored-by: Hannes Schmidt --- json_schema/core/biomaterial/biomaterial_core.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/core/biomaterial/biomaterial_core.json b/json_schema/core/biomaterial/biomaterial_core.json index bfa582117..5ba53012e 100644 --- a/json_schema/core/biomaterial/biomaterial_core.json +++ b/json_schema/core/biomaterial/biomaterial_core.json @@ -85,7 +85,7 @@ "guidelines": "Enter accession if sample has been obtained from the Human Developmental Biology Resource (HDBR)." }, "timecourse": { - "description": "Information relating to a timecourse associated with this cell line.", + "description": "Information relating to a timecourse associated with this biomaterial.", "type": "object", "$ref": "module/biomaterial/timecourse.json", "user_friendly": "Timecourse" From f76fbface3faf30e2889635ca38fd2b3e9039b1e Mon Sep 17 00:00:00 2001 From: willrockout Date: Fri, 28 Jul 2023 11:10:06 -0700 Subject: [PATCH 3/4] Fixed issue in core.md --- docs/jsonBrowser/core.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/jsonBrowser/core.md b/docs/jsonBrowser/core.md index b0b253019..32e90bd70 100644 --- a/docs/jsonBrowser/core.md +++ b/docs/jsonBrowser/core.md @@ -61,7 +61,7 @@ supplementary_files | A list of filenames of biomaterial-level supplementary fil biosamples_accession | A BioSamples accession. | string | no | | BioSamples accession | | SAMN00000000 insdc_sample_accession | An International Nucleotide Sequence Database Collaboration (INSDC) sample accession. | string | no | | INSDC sample accession | | SRS0000000 HDBR_accession | A Human Developmental Biology Resource (HDBR) sample accession. | string | no | | HDBR accession | | 34526; 14758, 2, liver -timecourse | Information relating to a timecourse associated with this cell line. | object | no | [See module timecourse](module.md#timecourse) | Timecourse | | +timecourse | Information relating to a timecourse associated with this biomaterial. | object | no | [See module timecourse](module.md#timecourse) | Timecourse | | ## Process core _Information relevant to how a biomaterial or file was converted into another biomaterial or file._ From bb1d78f85f564abd7948e29fa8d71ac5cee252e3 Mon Sep 17 00:00:00 2001 From: willrockout Date: Tue, 22 Aug 2023 11:37:15 -0700 Subject: [PATCH 4/4] Ran release_prepare.py script. --- changelog.md | 28 ++++++++++++++++++++++++++++ json_schema/update_log.csv | 4 ---- json_schema/versions.json | 16 ++++++++-------- 3 files changed, 36 insertions(+), 12 deletions(-) diff --git a/changelog.md b/changelog.md index 7e64c31a3..fee646f73 100644 --- a/changelog.md +++ b/changelog.md @@ -7,6 +7,34 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http:// ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging) +### [core/biomaterial/biomaterial_core.json - v8.4.0] - 2023-08-22 +### Added +Added timecourse module. Fixes #1511 + +### [type/biomaterial/donor_organism.json - v16.0.0] - 2023-08-22 +### Removed +Removed timecourse module. + +### [type/biomaterial/cell_suspension.json - v14.0.0] - 2023-08-22 +### Removed +Removed timecourse module. + +### [type/biomaterial/cell_line.json - v16.0.0] - 2023-08-22 +### Removed +Removed timecourse module. + +### [type/biomaterial/imaged_specimen.json - v3.5.0] - 2023-08-22 +### Added +Added timecourse module. Fixes #1511 + +### [type/biomaterial/specimen_from_organism.json - v10.8.0] - 2023-08-22 +### Added +Added timecourse module. Fixes #1511 + +### [type/biomaterial/organoid.json - v11.5.0] - 2023-08-22 +### Added +Added timecourse module. Fixes #1511 + ## [Released](https://github.com/HumanCellAtlas/metadata-schema/) ### [module/project/hca_bionetwork.json - v1.0.1] - 2023-05-22 diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 98de26f27..3231ff199 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,5 +1 @@ Schema,Change type,Change message,Version,Date -core/biomaterial/biomaterial_core,minor,Added timecourse module. Fixes #1511,, -type/biomaterial.donor_organism,major,Removed timecourse module.,, -type/biomaterial.cell_suspension,major,Removed timecourse module.,, -type/biomaterial.cell_line,major,Removed timecourse module.,, \ No newline at end of file diff --git a/json_schema/versions.json b/json_schema/versions.json index 94820c2ee..70132bcc1 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -1,9 +1,9 @@ { - "last_update_date": "2023-05-22T11:01:09Z", + "last_update_date": "2023-08-22T11:35:16Z", "version_numbers": { "core": { "biomaterial": { - "biomaterial_core": "8.2.0" + "biomaterial_core": "8.4.0" }, "file": { "file_core": "6.4.0" @@ -89,12 +89,12 @@ }, "type": { "biomaterial": { - "cell_line": "15.1.0", - "cell_suspension": "13.3.0", - "donor_organism": "15.6.1", - "imaged_specimen": "3.3.0", - "organoid": "11.3.0", - "specimen_from_organism": "10.6.0" + "cell_line": "16.0.0", + "cell_suspension": "14.0.0", + "donor_organism": "16.0.0", + "imaged_specimen": "3.5.0", + "organoid": "11.5.0", + "specimen_from_organism": "10.8.0" }, "file": { "analysis_file": "7.0.0",