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Merged
merged 4 commits into from
May 27, 2025
Merged

feat: improve schema descriptions (#375) #541

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81ad451
feat: more detailed schema descriptions
d-callan May 21, 2025
a8fff56
fix: schema formatting
d-callan May 21, 2025
7812e6a
Merge branch 'main' into schema-descriptions
d-callan May 27, 2025
e466845
fix: correct taxonomy id schema description for organisms
d-callan May 27, 2025
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104 changes: 52 additions & 52 deletions catalog/build/py/generated_schema/schema.py
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10 changes: 5 additions & 5 deletions catalog/schema/assemblies.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/assemblies.yaml#
name: assemblies
description: Schema for source assembly list.
description: Schema for defining genomic assemblies available in the BRC Analytics platform.

prefixes:
linkml: https://w3id.org/linkml/
Expand All @@ -10,19 +10,19 @@ imports:

classes:
Assemblies:
description: Object containing list of assemblies.
description: Root object containing a collection of genomic assembly definitions for the BRC Analytics platform.
tree_root: true
attributes:
assemblies:
description: List of assemblies.
description: Collection of genomic assembly entries that will be available for analysis in the BRC Analytics platform.
required: true
multivalued: true
range: Assembly

Assembly:
description: An assembly.
description: Definition of a genomic assembly with its unique identifier.
attributes:
accession:
description: The assembly's accession.
description: The unique accession identifier for the assembly (e.g., GCA_000001405.28 for GRCh38), used to retrieve the assembly data from public repositories.
required: true
range: string
12 changes: 6 additions & 6 deletions catalog/schema/generated/assemblies.json
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Expand Up @@ -2,10 +2,10 @@
"$defs": {
"Assemblies": {
"additionalProperties": false,
"description": "Object containing list of assemblies.",
"description": "Root object containing a collection of genomic assembly definitions for the BRC Analytics platform.",
"properties": {
"assemblies": {
"description": "List of assemblies.",
"description": "Collection of genomic assembly entries that will be available for analysis in the BRC Analytics platform.",
"items": {
"$ref": "#/$defs/Assembly"
},
Expand All @@ -20,10 +20,10 @@
},
"Assembly": {
"additionalProperties": false,
"description": "An assembly.",
"description": "Definition of a genomic assembly with its unique identifier.",
"properties": {
"accession": {
"description": "The assembly's accession.",
"description": "The unique accession identifier for the assembly (e.g., GCA_000001405.28 for GRCh38), used to retrieve the assembly data from public repositories.",
"type": "string"
}
},
Expand All @@ -37,11 +37,11 @@
"$id": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/assemblies.yaml#",
"$schema": "https://json-schema.org/draft/2019-09/schema",
"additionalProperties": true,
"description": "Object containing list of assemblies.",
"description": "Root object containing a collection of genomic assembly definitions for the BRC Analytics platform.",
"metamodel_version": "1.7.0",
"properties": {
"assemblies": {
"description": "List of assemblies.",
"description": "Collection of genomic assembly entries that will be available for analysis in the BRC Analytics platform.",
"items": {
"$ref": "#/$defs/Assembly"
},
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14 changes: 7 additions & 7 deletions catalog/schema/generated/organisms.json
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Expand Up @@ -2,17 +2,17 @@
"$defs": {
"Organism": {
"additionalProperties": false,
"description": "Info for an organism.",
"description": "Definition of an organism with its taxonomic and genetic characteristics.",
"properties": {
"ploidy": {
"description": "The ploidies that the organism may have.",
"description": "The possible ploidy states (number of chromosome sets) that the organism may have, which determines compatible workflows.",
"items": {
"$ref": "#/$defs/OrganismPloidy"
},
"type": "array"
},
"taxonomy_id": {
"description": "The organism's NCBI taxonomy ID.",
"description": "An NCBI Taxonomy ID at rank 'species'.",
"type": "integer"
}
},
Expand All @@ -35,10 +35,10 @@
},
"Organisms": {
"additionalProperties": false,
"description": "Object containing list of organisms.",
"description": "Root object containing a collection of organism definitions for the BRC Analytics platform.",
"properties": {
"organisms": {
"description": "List of organisms.",
"description": "Collection of organism entries that will be available in the BRC Analytics platform.",
"items": {
"$ref": "#/$defs/Organism"
},
Expand All @@ -55,11 +55,11 @@
"$id": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/organisms.yaml#",
"$schema": "https://json-schema.org/draft/2019-09/schema",
"additionalProperties": true,
"description": "Object containing list of organisms.",
"description": "Root object containing a collection of organism definitions for the BRC Analytics platform.",
"metamodel_version": "1.7.0",
"properties": {
"organisms": {
"description": "List of organisms.",
"description": "Collection of organism entries that will be available in the BRC Analytics platform.",
"items": {
"$ref": "#/$defs/Organism"
},
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36 changes: 18 additions & 18 deletions catalog/schema/generated/outbreaks.json
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Expand Up @@ -2,10 +2,10 @@
"$defs": {
"MarkdownFileReference": {
"additionalProperties": false,
"description": "A reference to a markdown file",
"description": "A reference to a markdown file containing detailed content about a priority pathogen.",
"properties": {
"path": {
"description": "Path to the markdown file",
"description": "Relative path to the markdown file from the project root. Must end with .md extension.",
"pattern": ".*\\.md$",
"type": "string"
}
Expand All @@ -18,18 +18,18 @@
},
"Outbreak": {
"additionalProperties": false,
"description": "Info for an outbreak.",
"description": "Definition of a priority pathogen with its taxonomic classification, priority level, and associated resources.",
"properties": {
"active": {
"description": "Determines if outbreak should be included, as they presumably change over time.",
"description": "Boolean flag that determines if the pathogen should be included in the BRC Analytics interface. Used to manage visibility as pathogen relevance changes over time.",
"type": "boolean"
},
"description": {
"$ref": "#/$defs/MarkdownFileReference",
"description": "The description of the outbreak."
"description": "Reference to a markdown file containing detailed information about the pathogen."
},
"highlight_descendant_taxonomy_ids": {
"description": "Taxonomy IDs of child taxa that should be highlighted.",
"description": "List of NCBI Taxonomy IDs for descendant taxa (e.g., specific strains or serotypes) that should be highlighted within the outbreak category.",
"items": {
"type": "integer"
},
Expand All @@ -39,22 +39,22 @@
]
},
"name": {
"description": "The name of the outbreak/ pathogen.",
"description": "The display name of the pathogen as it will appear in the BRC Analytics interface.",
"type": "string"
},
"priority": {
"$ref": "#/$defs/OutbreakPriority",
"description": "The priority of the outbreak."
"description": "The priority level of the pathogen, which determines its visibility and prominence in the BRC Analytics interface."
},
"resources": {
"description": "The resources associated with the outbreak.",
"description": "Collection of external resources (references, tools, databases) related to the pathogen.",
"items": {
"$ref": "#/$defs/OutbreakResource"
},
"type": "array"
},
"taxonomy_id": {
"description": "The outbreak's NCBI taxonomy ID.",
"description": "The NCBI Taxonomy ID for the pathogen. Used to link to relevant genomic data and workflows.",
"type": "integer"
}
},
Expand Down Expand Up @@ -83,18 +83,18 @@
},
"OutbreakResource": {
"additionalProperties": false,
"description": "A resource associated with an outbreak.",
"description": "Definition of an external resource (reference, tool, database) associated with a priority pathogen.",
"properties": {
"title": {
"description": "The title of the resource.",
"description": "The display title for the resource link as it will appear in the BRC Analytics interface.",
"type": "string"
},
"type": {
"$ref": "#/$defs/OutbreakResourceType",
"description": "The type of the resource."
"description": "The category or type of the resource (e.g., REFERENCE, TOOL, DATABASE), which determines how it is displayed and organized."
},
"url": {
"description": "The URL of the resource.",
"description": "The complete URL (including http/https protocol) to the external resource.",
"type": "string"
}
},
Expand Down Expand Up @@ -122,10 +122,10 @@
},
"Outbreaks": {
"additionalProperties": false,
"description": "Object containing list of outbreaks.",
"description": "Root object containing a collection of pathogen definitions for the BRC Analytics platform to highlight as outbreaks/priority pathogens.",
"properties": {
"outbreaks": {
"description": "List of outbreaks.",
"description": "Collection of pathogen entries that will be displayed in the BRC Analytics platform as outbreaks/priority pathogens.",
"items": {
"$ref": "#/$defs/Outbreak"
},
Expand All @@ -142,11 +142,11 @@
"$id": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/outbreaks.yaml#",
"$schema": "https://json-schema.org/draft/2019-09/schema",
"additionalProperties": true,
"description": "Object containing list of outbreaks.",
"description": "Root object containing a collection of pathogen definitions for the BRC Analytics platform to highlight as outbreaks/priority pathogens.",
"metamodel_version": "1.7.0",
"properties": {
"outbreaks": {
"description": "List of outbreaks.",
"description": "Collection of pathogen entries that will be displayed in the BRC Analytics platform as outbreaks/priority pathogens.",
"items": {
"$ref": "#/$defs/Outbreak"
},
Expand Down
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