From 6b4a86cfc3a5dedd2bc0bb0b05bf411d35d4eb4e Mon Sep 17 00:00:00 2001 From: Branwen Snelling Date: Mon, 7 Oct 2024 09:34:36 +0100 Subject: [PATCH] update demographics ages, omics formatting and required fields --- docs/GWDM/2.0.form.json | 36 +++++++++--------- docs/GWDM/2.0.md | 4 +- docs/GWDM/2.0.structure.json | 4 +- docs/HDRUK/3.0.0.form.json | 40 ++++++++++---------- docs/HDRUK/3.0.0.md | 8 ++-- docs/HDRUK/3.0.0.structure.json | 8 ++-- hdr_schemata/definitions/HDRUK/AgeEnum.py | 4 +- hdr_schemata/definitions/HDRUK/Assay.py | 32 ++++++++-------- hdr_schemata/models/GWDM/2.0/schema.json | 36 +++++++++--------- hdr_schemata/models/HDRUK/3.0.0/schema.json | 36 +++++++++--------- hdr_schemata/models/HDRUK/v3_0_0/Coverage.py | 2 +- hdr_schemata/models/HDRUK/v3_0_0/Temporal.py | 2 +- 12 files changed, 106 insertions(+), 106 deletions(-) diff --git a/docs/GWDM/2.0.form.json b/docs/GWDM/2.0.form.json index 403d29a..94c5e9b 100644 --- a/docs/GWDM/2.0.form.json +++ b/docs/GWDM/2.0.form.json @@ -1419,7 +1419,7 @@ "5-9 years", "10-14 years", "15-19 years", - "20-14 years", + "20-24 years", "25-29 years", "30-34 years", "35-39 years", @@ -1434,7 +1434,7 @@ "80-84 years", "85-89 years", "90-94 years", - "65-99 years", + "95-99 years", "100+ years" ] }, @@ -1547,22 +1547,22 @@ "type": "string", "options": [ "NMR spectroscopy", - "mass-spectrometry", - "whole genome sequencing", - "exome sequencing", - "genotyping by array", - "transcriptome profiling by high-throughput sequencing", - "transcriptome profiling by array", - "amplicon sequencing", - "methylation binding domain sequencing", - "methylation profiling by high-throughput sequencing", - "genomic variant calling", - "chromatin accessibility profiling by high-throughput sequencing", - "histone modification profiling by high-throughput sequencing", - "chromatin immunoprecipitation sequencing", - "whole genome shotgun sequencing", - "whole transcriptome sequencing", - "targeted mutation analysis" + "Mass-spectrometry", + "Whole genome sequencing", + "Exome sequencing", + "Genotyping by array", + "Transcriptome profiling by high-throughput sequencing", + "Transcriptome profiling by array", + "Amplicon sequencing", + "Methylation binding domain sequencing", + "Methylation profiling by high-throughput sequencing", + "Genomic variant calling", + "Chromatin accessibility profiling by high-throughput sequencing", + "Histone modification profiling by high-throughput sequencing", + "Chromatin immunoprecipitation sequencing", + "Whole genome shotgun sequencing", + "Whole transcriptome sequencing", + "Targeted mutation analysis" ] }, "location": "omics.assay" diff --git a/docs/GWDM/2.0.md b/docs/GWDM/2.0.md index e4d3a59..7cf72e3 100644 --- a/docs/GWDM/2.0.md +++ b/docs/GWDM/2.0.md @@ -1391,7 +1391,7 @@ None | title | guidance | is_list | required | type | |:--------|:-----------|:----------|:-----------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| Age bin | | False | True | ["AgeEnum['0-6 days','7-27 days','1-11 months','1-4 years','5-9 years','10-14 years','15-19 years','20-14 years','25-29 years','30-34 years','35-39 years','40-44 years','45-49 years','50-54 years','55-59 years','60-64 years','65-69 years','70-74 years','75-79 years','80-84 years','85-89 years','90-94 years','65-99 years','100+ years']"] | +| Age bin | | False | True | ["AgeEnum['0-6 days','7-27 days','1-11 months','1-4 years','5-9 years','10-14 years','15-19 years','20-24 years','25-29 years','30-34 years','35-39 years','40-44 years','45-49 years','50-54 years','55-59 years','60-64 years','65-69 years','70-74 years','75-79 years','80-84 years','85-89 years','90-94 years','95-99 years','100+ years']"] | @@ -1495,7 +1495,7 @@ The specific 'omics assay that generated the dataset. | title | guidance | is_list | required | type | |:------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------|:-----------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| Omics assay | The specific 'omics assay that generated the dataset. If the assay used to generate your dataset is not listed, please contract the gateway team by submitting an enquiry. | False | False | ["Assay['NMR spectroscopy','mass-spectrometry','whole genome sequencing','exome sequencing','genotyping by array','transcriptome profiling by high-throughput sequencing','transcriptome profiling by array','amplicon sequencing','methylation binding domain sequencing','methylation profiling by high-throughput sequencing','genomic variant calling','chromatin accessibility profiling by high-throughput sequencing','histone modification profiling by high-throughput sequencing','chromatin immunoprecipitation sequencing','whole genome shotgun sequencing','whole transcriptome sequencing','targeted mutation analysis']", 'null'] | +| Omics assay | The specific 'omics assay that generated the dataset. If the assay used to generate your dataset is not listed, please contract the gateway team by submitting an enquiry. | False | False | ["Assay['NMR spectroscopy','Mass-spectrometry','Whole genome sequencing','Exome sequencing','Genotyping by array','Transcriptome profiling by high-throughput sequencing','Transcriptome profiling by array','Amplicon sequencing','Methylation binding domain sequencing','Methylation profiling by high-throughput sequencing','Genomic variant calling','Chromatin accessibility profiling by high-throughput sequencing','Histone modification profiling by high-throughput sequencing','Chromatin immunoprecipitation sequencing','Whole genome shotgun sequencing','Whole transcriptome sequencing','Targeted mutation analysis']", 'null'] | diff --git a/docs/GWDM/2.0.structure.json b/docs/GWDM/2.0.structure.json index 8bd3945..b88942e 100644 --- a/docs/GWDM/2.0.structure.json +++ b/docs/GWDM/2.0.structure.json @@ -1898,7 +1898,7 @@ "guidance": "", "examples": null, "type": [ - "AgeEnum['0-6 days','7-27 days','1-11 months','1-4 years','5-9 years','10-14 years','15-19 years','20-14 years','25-29 years','30-34 years','35-39 years','40-44 years','45-49 years','50-54 years','55-59 years','60-64 years','65-69 years','70-74 years','75-79 years','80-84 years','85-89 years','90-94 years','65-99 years','100+ years']" + "AgeEnum['0-6 days','7-27 days','1-11 months','1-4 years','5-9 years','10-14 years','15-19 years','20-24 years','25-29 years','30-34 years','35-39 years','40-44 years','45-49 years','50-54 years','55-59 years','60-64 years','65-69 years','70-74 years','75-79 years','80-84 years','85-89 years','90-94 years','95-99 years','100+ years']" ], "is_list": false, "is_optional": false @@ -2038,7 +2038,7 @@ "guidance": "The specific 'omics assay that generated the dataset. If the assay used to generate your dataset is not listed, please contract the gateway team by submitting an enquiry.", "examples": null, "type": [ - "Assay['NMR spectroscopy','mass-spectrometry','whole genome sequencing','exome sequencing','genotyping by array','transcriptome profiling by high-throughput sequencing','transcriptome profiling by array','amplicon sequencing','methylation binding domain sequencing','methylation profiling by high-throughput sequencing','genomic variant calling','chromatin accessibility profiling by high-throughput sequencing','histone modification profiling by high-throughput sequencing','chromatin immunoprecipitation sequencing','whole genome shotgun sequencing','whole transcriptome sequencing','targeted mutation analysis']", + "Assay['NMR spectroscopy','Mass-spectrometry','Whole genome sequencing','Exome sequencing','Genotyping by array','Transcriptome profiling by high-throughput sequencing','Transcriptome profiling by array','Amplicon sequencing','Methylation binding domain sequencing','Methylation profiling by high-throughput sequencing','Genomic variant calling','Chromatin accessibility profiling by high-throughput sequencing','Histone modification profiling by high-throughput sequencing','Chromatin immunoprecipitation sequencing','Whole genome shotgun sequencing','Whole transcriptome sequencing','Targeted mutation analysis']", "null" ], "is_list": false, diff --git a/docs/HDRUK/3.0.0.form.json b/docs/HDRUK/3.0.0.form.json index b8fe386..5d12bc1 100644 --- a/docs/HDRUK/3.0.0.form.json +++ b/docs/HDRUK/3.0.0.form.json @@ -357,7 +357,7 @@ "location": "documentation.inPipeline" }, { - "required": false, + "required": true, "title": "Geographic coverage", "description": "The geographical area covered by the dataset. It is recommended that links are to entries in one of the recommended standards:\\n- For locations in the UK: [ONS standards](https://geoportal.statistics.gov.uk/datasets/ons::index-of-place-names-in-great-britain-november-2021/about)\\n- For locations in other countries: [ISO 3166-1 & ISO 3166-2](https://github.com/HDRUK/reference-codes)", "guidance": "- The geographical area covered by the dataset.\\n- Please provide a valid location.\\n- For locations in the UK, this location should conform to [ONS standards](https://geoportal.statistics.gov.uk/datasets/ons::index-of-place-names-in-great-britain-november-2021/about).\\n- For locations in other countries we use [ISO 3166-1 & ISO 3166-2](https://github.com/HDRUK/reference-codes).", @@ -747,7 +747,7 @@ "location": "provenance.temporal.distributionReleaseDate" }, { - "required": false, + "required": true, "title": "Start date", "description": "The start of the time period that the dataset provides coverage for. If there are multiple cohorts in the dataset with varying start dates, please provide the earliest date and use the description or the media attribute to provide more information.", "guidance": "- The start of the time period that the dataset provides coverage for.\\n- If there are multiple cohorts in the dataset with varying start dates, please provide the earliest date and use the description or the media attribute to provide more information.", @@ -1668,7 +1668,7 @@ "5-9 years", "10-14 years", "15-19 years", - "20-14 years", + "20-24 years", "25-29 years", "30-34 years", "35-39 years", @@ -1683,7 +1683,7 @@ "80-84 years", "85-89 years", "90-94 years", - "65-99 years", + "95-99 years", "100+ years" ] }, @@ -1796,22 +1796,22 @@ "type": "string", "options": [ "NMR spectroscopy", - "mass-spectrometry", - "whole genome sequencing", - "exome sequencing", - "genotyping by array", - "transcriptome profiling by high-throughput sequencing", - "transcriptome profiling by array", - "amplicon sequencing", - "methylation binding domain sequencing", - "methylation profiling by high-throughput sequencing", - "genomic variant calling", - "chromatin accessibility profiling by high-throughput sequencing", - "histone modification profiling by high-throughput sequencing", - "chromatin immunoprecipitation sequencing", - "whole genome shotgun sequencing", - "whole transcriptome sequencing", - "targeted mutation analysis" + "Mass-spectrometry", + "Whole genome sequencing", + "Exome sequencing", + "Genotyping by array", + "Transcriptome profiling by high-throughput sequencing", + "Transcriptome profiling by array", + "Amplicon sequencing", + "Methylation binding domain sequencing", + "Methylation profiling by high-throughput sequencing", + "Genomic variant calling", + "Chromatin accessibility profiling by high-throughput sequencing", + "Histone modification profiling by high-throughput sequencing", + "Chromatin immunoprecipitation sequencing", + "Whole genome shotgun sequencing", + "Whole transcriptome sequencing", + "Targeted mutation analysis" ] }, "location": "omics.assay" diff --git a/docs/HDRUK/3.0.0.md b/docs/HDRUK/3.0.0.md index facc8d0..6dba5e4 100644 --- a/docs/HDRUK/3.0.0.md +++ b/docs/HDRUK/3.0.0.md @@ -319,7 +319,7 @@ The geographical area covered by the dataset. It is recommended that links are t | title | guidance | is_list | required | type | |:--------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------|:-----------|:----------------------------------------------------------------------------------------------------------| -| Geographic coverage | - The geographical area covered by the dataset.
- Please provide a valid location.
- For locations in the UK, this location should conform to [ONS standards](https://geoportal.statistics.gov.uk/datasets/ons::index-of-place-names-in-great-britain-november-2021/about).
- For locations in other countries we use [ISO 3166-1 & ISO 3166-2](https://github.com/HDRUK/reference-codes). | False | False | ["CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]", 'List'] | +| Geographic coverage | - The geographical area covered by the dataset.
- Please provide a valid location.
- For locations in the UK, this location should conform to [ONS standards](https://geoportal.statistics.gov.uk/datasets/ons::index-of-place-names-in-great-britain-november-2021/about).
- For locations in other countries we use [ISO 3166-1 & ISO 3166-2](https://github.com/HDRUK/reference-codes). | False | True | ["CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]", 'List'] | Examples: @@ -519,7 +519,7 @@ The start of the time period that the dataset provides coverage for. If there ar | title | guidance | is_list | required | type | |:-----------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------|:-----------|:---------------------| -| Start date | - The start of the time period that the dataset provides coverage for.
- If there are multiple cohorts in the dataset with varying start dates, please provide the earliest date and use the description or the media attribute to provide more information. | False | False | ['date', 'datetime'] | +| Start date | - The start of the time period that the dataset provides coverage for.
- If there are multiple cohorts in the dataset with varying start dates, please provide the earliest date and use the description or the media attribute to provide more information. | False | True | ['date', 'datetime'] | @@ -1229,7 +1229,7 @@ None | title | guidance | is_list | required | type | |:-------------|:-----------|:----------|:-----------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| Age grouping | | False | True | ["AgeEnum['0-6 days','7-27 days','1-11 months','1-4 years','5-9 years','10-14 years','15-19 years','20-14 years','25-29 years','30-34 years','35-39 years','40-44 years','45-49 years','50-54 years','55-59 years','60-64 years','65-69 years','70-74 years','75-79 years','80-84 years','85-89 years','90-94 years','65-99 years','100+ years']"] | +| Age grouping | | False | True | ["AgeEnum['0-6 days','7-27 days','1-11 months','1-4 years','5-9 years','10-14 years','15-19 years','20-24 years','25-29 years','30-34 years','35-39 years','40-44 years','45-49 years','50-54 years','55-59 years','60-64 years','65-69 years','70-74 years','75-79 years','80-84 years','85-89 years','90-94 years','95-99 years','100+ years']"] | @@ -1333,7 +1333,7 @@ The specific 'omics assay that generated the dataset. | title | guidance | is_list | required | type | |:------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------|:-----------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| Omics assay | The specific 'omics assay that generated the dataset. If the assay used to generate your dataset is not listed, please contract the gateway team by submitting an enquiry. | False | False | ["Assay['NMR spectroscopy','mass-spectrometry','whole genome sequencing','exome sequencing','genotyping by array','transcriptome profiling by high-throughput sequencing','transcriptome profiling by array','amplicon sequencing','methylation binding domain sequencing','methylation profiling by high-throughput sequencing','genomic variant calling','chromatin accessibility profiling by high-throughput sequencing','histone modification profiling by high-throughput sequencing','chromatin immunoprecipitation sequencing','whole genome shotgun sequencing','whole transcriptome sequencing','targeted mutation analysis']", 'null'] | +| Omics assay | The specific 'omics assay that generated the dataset. If the assay used to generate your dataset is not listed, please contract the gateway team by submitting an enquiry. | False | False | ["Assay['NMR spectroscopy','Mass-spectrometry','Whole genome sequencing','Exome sequencing','Genotyping by array','Transcriptome profiling by high-throughput sequencing','Transcriptome profiling by array','Amplicon sequencing','Methylation binding domain sequencing','Methylation profiling by high-throughput sequencing','Genomic variant calling','Chromatin accessibility profiling by high-throughput sequencing','Histone modification profiling by high-throughput sequencing','Chromatin immunoprecipitation sequencing','Whole genome shotgun sequencing','Whole transcriptome sequencing','Targeted mutation analysis']", 'null'] | diff --git a/docs/HDRUK/3.0.0.structure.json b/docs/HDRUK/3.0.0.structure.json index 36ac2b2..29e50a9 100644 --- a/docs/HDRUK/3.0.0.structure.json +++ b/docs/HDRUK/3.0.0.structure.json @@ -419,7 +419,7 @@ "subItems": [ { "name": "spatial", - "required": false, + "required": true, "title": "Geographic coverage", "description": "The geographical area covered by the dataset. It is recommended that links are to entries in one of the recommended standards:- For locations in the UK: ONS standards- For locations in other countries: ISO 3166-1 & ISO 3166-2", "guidance": "The geographical area covered by the dataset.- Please provide a valid location.- For locations in the UK, this location should conform to ONS standards.- For locations in other countries we use ISO 3166-1 & ISO 3166-2.", @@ -679,7 +679,7 @@ }, { "name": "startDate", - "required": false, + "required": true, "title": "Start date", "description": "The start of the time period that the dataset provides coverage for. If there are multiple cohorts in the dataset with varying start dates, please provide the earliest date and use the description or the media attribute to provide more information.", "guidance": "The start of the time period that the dataset provides coverage for.- If there are multiple cohorts in the dataset with varying start dates, please provide the earliest date and use the description or the media attribute to provide more information.", @@ -1654,7 +1654,7 @@ "guidance": "", "examples": null, "type": [ - "AgeEnum['0-6 days','7-27 days','1-11 months','1-4 years','5-9 years','10-14 years','15-19 years','20-14 years','25-29 years','30-34 years','35-39 years','40-44 years','45-49 years','50-54 years','55-59 years','60-64 years','65-69 years','70-74 years','75-79 years','80-84 years','85-89 years','90-94 years','65-99 years','100+ years']" + "AgeEnum['0-6 days','7-27 days','1-11 months','1-4 years','5-9 years','10-14 years','15-19 years','20-24 years','25-29 years','30-34 years','35-39 years','40-44 years','45-49 years','50-54 years','55-59 years','60-64 years','65-69 years','70-74 years','75-79 years','80-84 years','85-89 years','90-94 years','95-99 years','100+ years']" ], "is_list": false, "is_optional": false @@ -1794,7 +1794,7 @@ "guidance": "The specific 'omics assay that generated the dataset. If the assay used to generate your dataset is not listed, please contract the gateway team by submitting an enquiry.", "examples": null, "type": [ - "Assay['NMR spectroscopy','mass-spectrometry','whole genome sequencing','exome sequencing','genotyping by array','transcriptome profiling by high-throughput sequencing','transcriptome profiling by array','amplicon sequencing','methylation binding domain sequencing','methylation profiling by high-throughput sequencing','genomic variant calling','chromatin accessibility profiling by high-throughput sequencing','histone modification profiling by high-throughput sequencing','chromatin immunoprecipitation sequencing','whole genome shotgun sequencing','whole transcriptome sequencing','targeted mutation analysis']", + "Assay['NMR spectroscopy','Mass-spectrometry','Whole genome sequencing','Exome sequencing','Genotyping by array','Transcriptome profiling by high-throughput sequencing','Transcriptome profiling by array','Amplicon sequencing','Methylation binding domain sequencing','Methylation profiling by high-throughput sequencing','Genomic variant calling','Chromatin accessibility profiling by high-throughput sequencing','Histone modification profiling by high-throughput sequencing','Chromatin immunoprecipitation sequencing','Whole genome shotgun sequencing','Whole transcriptome sequencing','Targeted mutation analysis']", "null" ], "is_list": false, diff --git a/hdr_schemata/definitions/HDRUK/AgeEnum.py b/hdr_schemata/definitions/HDRUK/AgeEnum.py index 39ab081..8dcd996 100644 --- a/hdr_schemata/definitions/HDRUK/AgeEnum.py +++ b/hdr_schemata/definitions/HDRUK/AgeEnum.py @@ -9,7 +9,7 @@ class AgeEnum(Enum): YEARS_5_9 = '5-9 years' YEARS_10_14 = '10-14 years' YEARS_15_19 = '15-19 years' - YEARS_20_14 = '20-14 years' + YEARS_20_14 = '20-24 years' YEARS_25_29 = '25-29 years' YEARS_30_34 = '30-34 years' YEARS_35_39 = '35-39 years' @@ -24,5 +24,5 @@ class AgeEnum(Enum): YEARS_80_84 = '80-84 years' YEARS_85_89 = '85-89 years' YEARS_90_94 = '90-94 years' - YEARS_65_99 = '65-99 years' + YEARS_65_99 = '95-99 years' YEARS_100_PLUS = '100+ years' diff --git a/hdr_schemata/definitions/HDRUK/Assay.py b/hdr_schemata/definitions/HDRUK/Assay.py index d6bf24b..79583e9 100644 --- a/hdr_schemata/definitions/HDRUK/Assay.py +++ b/hdr_schemata/definitions/HDRUK/Assay.py @@ -2,20 +2,20 @@ class Assay(Enum): NMR_SPECTROSCOPY = 'NMR spectroscopy' - MASS_SPECTROMETRY = 'mass-spectrometry' - WHOLE_GENOME_SEQUENCING = 'whole genome sequencing' - EXOME_SEQUENCING = 'exome sequencing' - GENOTYPING_BY_ARRAY = 'genotyping by array' - TRANSCRIPTOME_PROFILING_BY_HIGH_THROUGHPUT_SEQUENCING = 'transcriptome profiling by high-throughput sequencing' - TRANSCRIPTOME_PROFILING_BY_ARRAY = 'transcriptome profiling by array' - AMPLICON_SEQUENCING = 'amplicon sequencing' - METHYLATION_BINDING_DOMAIN_SEQUENCING = 'methylation binding domain sequencing' - METHYLATION_PROFILING_BY_HIGH_THROUGHPUT_SEQUENCING = 'methylation profiling by high-throughput sequencing' - GENOMIC_VARIANT_CALLING = 'genomic variant calling' - CHROMATIN_ACCESSIBILITY_PROFILING_BY_HIGH_THROUGHPUT_SEQUENCING = 'chromatin accessibility profiling by high-throughput sequencing' - HISTONE_MODIFICATION_PROFILING_BY_HIGH_THROUGHPUT_SEQUENCING = 'histone modification profiling by high-throughput sequencing' - CHROMATIN_IMMUNOPRECIPITATION_SEQUENCING = 'chromatin immunoprecipitation sequencing' - WHOLE_GENOME_SHOTGUN_SEQUENCING = 'whole genome shotgun sequencing' - WHOLE_TRANSCRIPTOME_SEQUENCING = 'whole transcriptome sequencing' - TARGETED_MUTATION_ANALYSIS = 'targeted mutation analysis' + MASS_SPECTROMETRY = 'Mass-spectrometry' + WHOLE_GENOME_SEQUENCING = 'Whole genome sequencing' + EXOME_SEQUENCING = 'Exome sequencing' + GENOTYPING_BY_ARRAY = 'Genotyping by array' + TRANSCRIPTOME_PROFILING_BY_HIGH_THROUGHPUT_SEQUENCING = 'Transcriptome profiling by high-throughput sequencing' + TRANSCRIPTOME_PROFILING_BY_ARRAY = 'Transcriptome profiling by array' + AMPLICON_SEQUENCING = 'Amplicon sequencing' + METHYLATION_BINDING_DOMAIN_SEQUENCING = 'Methylation binding domain sequencing' + METHYLATION_PROFILING_BY_HIGH_THROUGHPUT_SEQUENCING = 'Methylation profiling by high-throughput sequencing' + GENOMIC_VARIANT_CALLING = 'Genomic variant calling' + CHROMATIN_ACCESSIBILITY_PROFILING_BY_HIGH_THROUGHPUT_SEQUENCING = 'Chromatin accessibility profiling by high-throughput sequencing' + HISTONE_MODIFICATION_PROFILING_BY_HIGH_THROUGHPUT_SEQUENCING = 'Histone modification profiling by high-throughput sequencing' + CHROMATIN_IMMUNOPRECIPITATION_SEQUENCING = 'Chromatin immunoprecipitation sequencing' + WHOLE_GENOME_SHOTGUN_SEQUENCING = 'Whole genome shotgun sequencing' + WHOLE_TRANSCRIPTOME_SEQUENCING = 'Whole transcriptome sequencing' + TARGETED_MUTATION_ANALYSIS = 'Targeted mutation analysis' diff --git a/hdr_schemata/models/GWDM/2.0/schema.json b/hdr_schemata/models/GWDM/2.0/schema.json index c7d624a..b9ae36a 100644 --- a/hdr_schemata/models/GWDM/2.0/schema.json +++ b/hdr_schemata/models/GWDM/2.0/schema.json @@ -205,7 +205,7 @@ "5-9 years", "10-14 years", "15-19 years", - "20-14 years", + "20-24 years", "25-29 years", "30-34 years", "35-39 years", @@ -220,7 +220,7 @@ "80-84 years", "85-89 years", "90-94 years", - "65-99 years", + "95-99 years", "100+ years" ], "title": "AgeEnum", @@ -241,22 +241,22 @@ "Assay": { "enum": [ "NMR spectroscopy", - "mass-spectrometry", - "whole genome sequencing", - "exome sequencing", - "genotyping by array", - "transcriptome profiling by high-throughput sequencing", - "transcriptome profiling by array", - "amplicon sequencing", - "methylation binding domain sequencing", - "methylation profiling by high-throughput sequencing", - "genomic variant calling", - "chromatin accessibility profiling by high-throughput sequencing", - "histone modification profiling by high-throughput sequencing", - "chromatin immunoprecipitation sequencing", - "whole genome shotgun sequencing", - "whole transcriptome sequencing", - "targeted mutation analysis" + "Mass-spectrometry", + "Whole genome sequencing", + "Exome sequencing", + "Genotyping by array", + "Transcriptome profiling by high-throughput sequencing", + "Transcriptome profiling by array", + "Amplicon sequencing", + "Methylation binding domain sequencing", + "Methylation profiling by high-throughput sequencing", + "Genomic variant calling", + "Chromatin accessibility profiling by high-throughput sequencing", + "Histone modification profiling by high-throughput sequencing", + "Chromatin immunoprecipitation sequencing", + "Whole genome shotgun sequencing", + "Whole transcriptome sequencing", + "Targeted mutation analysis" ], "title": "Assay", "type": "string" diff --git a/hdr_schemata/models/HDRUK/3.0.0/schema.json b/hdr_schemata/models/HDRUK/3.0.0/schema.json index 566b543..25190eb 100644 --- a/hdr_schemata/models/HDRUK/3.0.0/schema.json +++ b/hdr_schemata/models/HDRUK/3.0.0/schema.json @@ -234,7 +234,7 @@ "5-9 years", "10-14 years", "15-19 years", - "20-14 years", + "20-24 years", "25-29 years", "30-34 years", "35-39 years", @@ -249,7 +249,7 @@ "80-84 years", "85-89 years", "90-94 years", - "65-99 years", + "95-99 years", "100+ years" ], "title": "AgeEnum", @@ -258,22 +258,22 @@ "Assay": { "enum": [ "NMR spectroscopy", - "mass-spectrometry", - "whole genome sequencing", - "exome sequencing", - "genotyping by array", - "transcriptome profiling by high-throughput sequencing", - "transcriptome profiling by array", - "amplicon sequencing", - "methylation binding domain sequencing", - "methylation profiling by high-throughput sequencing", - "genomic variant calling", - "chromatin accessibility profiling by high-throughput sequencing", - "histone modification profiling by high-throughput sequencing", - "chromatin immunoprecipitation sequencing", - "whole genome shotgun sequencing", - "whole transcriptome sequencing", - "targeted mutation analysis" + "Mass-spectrometry", + "Whole genome sequencing", + "Exome sequencing", + "Genotyping by array", + "Transcriptome profiling by high-throughput sequencing", + "Transcriptome profiling by array", + "Amplicon sequencing", + "Methylation binding domain sequencing", + "Methylation profiling by high-throughput sequencing", + "Genomic variant calling", + "Chromatin accessibility profiling by high-throughput sequencing", + "Histone modification profiling by high-throughput sequencing", + "Chromatin immunoprecipitation sequencing", + "Whole genome shotgun sequencing", + "Whole transcriptome sequencing", + "Targeted mutation analysis" ], "title": "Assay", "type": "string" diff --git a/hdr_schemata/models/HDRUK/v3_0_0/Coverage.py b/hdr_schemata/models/HDRUK/v3_0_0/Coverage.py index 482669a..030862d 100644 --- a/hdr_schemata/models/HDRUK/v3_0_0/Coverage.py +++ b/hdr_schemata/models/HDRUK/v3_0_0/Coverage.py @@ -14,7 +14,7 @@ class Config: extra = "forbid" spatial: Union[CommaSeparatedValues, List[Url]] = Field( - None, **an.spatial.__dict__, json_schema_extra={"guidance": an.spatial.guidance} + ..., **an.spatial.__dict__, json_schema_extra={"guidance": an.spatial.guidance} ) typicalAgeRangeMin: Optional[int] = Field( diff --git a/hdr_schemata/models/HDRUK/v3_0_0/Temporal.py b/hdr_schemata/models/HDRUK/v3_0_0/Temporal.py index 0504b7a..b96312f 100644 --- a/hdr_schemata/models/HDRUK/v3_0_0/Temporal.py +++ b/hdr_schemata/models/HDRUK/v3_0_0/Temporal.py @@ -26,7 +26,7 @@ class Config: ) startDate: Union[date, datetime] = Field( - None, + ..., **an.startDate.__dict__, json_schema_extra={"guidance": an.startDate.guidance} )