Add JSON schema for top-level config file + use for validation #489
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| { | ||
| "$schema": "https://json-schema.org/draft/2020-12/schema", | ||
| "$id": "https://raw.githubusercontent.com/imperialCHEPI/healthgps/main/schemas/v1/age_range.json", | ||
| "type": "array", | ||
| "prefixItems": [ | ||
| { | ||
| "type": "integer", | ||
| "minimum": 0 | ||
| }, | ||
| { | ||
| "type": "integer", | ||
| "minimum": 0 | ||
| } | ||
| ], | ||
| "minItems": 2, | ||
| "items": false | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| { | ||
| "$schema": "https://json-schema.org/draft/2020-12/schema", | ||
| "$id": "https://raw.githubusercontent.com/imperialCHEPI/healthgps/main/schemas/v1/config.json", | ||
| "type": "object", | ||
| "properties": { | ||
| "$schema": { | ||
| "type": "string" | ||
| }, | ||
| "data": { | ||
| "$ref": "/imperialCHEPI/healthgps/main/schemas/v1/config/data.json" | ||
| }, | ||
| "inputs": { | ||
| "$ref": "/imperialCHEPI/healthgps/main/schemas/v1/config/inputs.json" | ||
| }, | ||
| "modelling": { | ||
| "$ref": "/imperialCHEPI/healthgps/main/schemas/v1/config/modelling.json" | ||
| }, | ||
| "running": { | ||
| "$ref": "/imperialCHEPI/healthgps/main/schemas/v1/config/running.json" | ||
| }, | ||
| "output": { | ||
| "$ref": "/imperialCHEPI/healthgps/main/schemas/v1/config/output.json" | ||
| } | ||
| }, | ||
| "required": [ | ||
| "$schema", | ||
| "inputs", | ||
| "modelling", | ||
| "running", | ||
| "output" | ||
| ], | ||
| "additionalProperties": false | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| { | ||
| "$schema": "https://json-schema.org/draft/2020-12/schema", | ||
| "$id": "https://raw.githubusercontent.com/imperialCHEPI/healthgps/main/schemas/v1/config/data.json", | ||
| "type": "object", | ||
| "properties": { | ||
| "source": { | ||
| "type": "string" | ||
| }, | ||
| "checksum": { | ||
| "type": "string" | ||
| } | ||
| }, | ||
| "required": [ | ||
| "source" | ||
| ], | ||
| "additionalProperties": false | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| { | ||
| "$schema": "https://json-schema.org/draft/2020-12/schema", | ||
| "$id": "https://raw.githubusercontent.com/imperialCHEPI/healthgps/main/schemas/v1/config/inputs.json", | ||
| "type": "object", | ||
| "properties": { | ||
| "dataset": { | ||
| "type": "object", | ||
| "properties": { | ||
| "name": { | ||
| "type": "string" | ||
| }, | ||
| "format": { | ||
| "const": "csv" | ||
| }, | ||
| "delimiter": { | ||
| "type": "string" | ||
| }, | ||
| "encoding": { | ||
| "type": "string" | ||
| }, | ||
| "columns": { | ||
| "type": "object", | ||
| "additionalProperties": { | ||
| "anyOf": [ | ||
| { | ||
| "const": "integer" | ||
| }, | ||
| { | ||
| "const": "double" | ||
| } | ||
| ] | ||
| } | ||
| } | ||
| }, | ||
| "required": [ | ||
| "name", | ||
| "format", | ||
| "delimiter", | ||
| "encoding", | ||
| "columns" | ||
| ], | ||
| "additionalProperties": false | ||
| }, | ||
| "settings": { | ||
| "type": "object", | ||
| "properties": { | ||
| "country_code": { | ||
| "type": "string" | ||
| }, | ||
| "size_fraction": { | ||
| "type": "number" | ||
| }, | ||
| "age_range": { | ||
| "$ref": "/imperialCHEPI/healthgps/main/schemas/v1/age_range.json" | ||
| } | ||
| }, | ||
| "required": [ | ||
| "country_code", | ||
| "size_fraction", | ||
| "age_range" | ||
| ], | ||
| "additionalProperties": false | ||
| } | ||
| }, | ||
| "required": [ | ||
| "dataset", | ||
| "settings" | ||
| ], | ||
| "additionalProperties": false | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| { | ||
| "$schema": "https://json-schema.org/draft/2020-12/schema", | ||
| "$id": "https://raw.githubusercontent.com/imperialCHEPI/healthgps/main/schemas/v1/config/interventions.json", | ||
| "type": "object", | ||
| "properties": { | ||
| "active_type_id": { | ||
| "anyOf": [ | ||
| { | ||
| "type": "string" | ||
| }, | ||
| { | ||
| "type": "null" | ||
| } | ||
| ] | ||
| }, | ||
| "types": { | ||
| "type": "object", | ||
| "additionalProperties": { | ||
| "type": "object", | ||
| "properties": { | ||
| "active_period": { | ||
| "type": "object", | ||
| "properties": { | ||
| "start_time": { | ||
| "type": "integer" | ||
| }, | ||
| "finish_time": { | ||
| "anyOf": [ | ||
| { | ||
| "type": "integer" | ||
| }, | ||
| { | ||
| "type": "null" | ||
| } | ||
| ] | ||
| } | ||
| }, | ||
| "required": [ | ||
| "start_time", | ||
| "finish_time" | ||
| ], | ||
| "additionalProperties": false | ||
| }, | ||
| "impacts": { | ||
| "type": "array" | ||
| }, | ||
| "impact_type": { | ||
| "type": "string" | ||
| }, | ||
| "dynamics": { | ||
| "type": "array", | ||
| "items": { | ||
| "type": "number" | ||
| } | ||
| }, | ||
| "coefficients": { | ||
| "type": "array", | ||
| "items": { | ||
| "type": "number" | ||
| } | ||
| }, | ||
| "coverage_rates": { | ||
| "type": "array", | ||
| "items": { | ||
| "type": "number" | ||
| } | ||
| }, | ||
| "coverage_cutoff_time": { | ||
| "type": "integer", | ||
| "minValue": 0 | ||
| }, | ||
| "child_cutoff_age": { | ||
| "type": "integer", | ||
| "minValue": 0 | ||
|
|
||
| }, | ||
| "adjustments": { | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "properties": { | ||
| "risk_factor": { | ||
| "type": "string" | ||
| }, | ||
| "value": { | ||
| "type": "number" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "required": [ | ||
| "active_period", | ||
| "impacts" | ||
| ], | ||
| "additionalProperties": false | ||
| } | ||
| } | ||
| }, | ||
| "required": [ | ||
| "active_type_id", | ||
| "types" | ||
| ], | ||
| "additionalProperties": false | ||
| } | ||
|
There was a problem hiding this comment. Do any of the string types here require a There was a problem hiding this comment. That's a good idea. I don't know whether I can be bothered to put What do you think @jamesturner246? How pedantic do we want to be? There was a problem hiding this comment. I won't push you -- one would hope users know not to put empty string fields... Certainly won't hurt though. |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,112 @@ | ||
| { | ||
| "$schema": "https://json-schema.org/draft/2020-12/schema", | ||
| "$id": "https://raw.githubusercontent.com/imperialCHEPI/healthgps/main/schemas/v1/config/modelling.json", | ||
| "type": "object", | ||
| "properties": { | ||
| "ses_model": { | ||
| "type": "object", | ||
| "properties": { | ||
| "function_name": { | ||
| "type": "string" | ||
| }, | ||
| "function_parameters": { | ||
| "type": "array", | ||
| "items": { | ||
| "type": "number" | ||
| } | ||
|
Comment on lines
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There was a problem hiding this comment. Just checking this array doesn't require a minimum number of values? Same applies for other arrays in this schema I guess. There was a problem hiding this comment. I'm not sure... @jamesturner246? There was a problem hiding this comment. I think these depend on the SES model -- e.g. normal has mean, std. Maybe there are other models that have none? Never uses the SES module. There was a problem hiding this comment. Hmm... ok. I'll leave as is for now. We can always add extra constraints in future if needed. |
||
| } | ||
| }, | ||
| "required": [ | ||
| "function_name", | ||
| "function_parameters" | ||
| ], | ||
| "additionalProperties": false | ||
| }, | ||
| "risk_factors": { | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "properties": { | ||
| "name": { | ||
| "type": "string" | ||
| }, | ||
| "level": { | ||
| "type": "integer" | ||
| }, | ||
| "range": { | ||
| "type": "array", | ||
| "items": { | ||
| "type": "number" | ||
| } | ||
| } | ||
| }, | ||
| "required": [ | ||
| "name", | ||
| "level", | ||
| "range" | ||
| ], | ||
| "additionalProperties": false | ||
| } | ||
| }, | ||
| "risk_factor_models": { | ||
| "type": "object", | ||
| "properties": { | ||
| "static": { | ||
| "type": "string" | ||
| }, | ||
| "dynamic": { | ||
| "type": "string" | ||
| } | ||
| }, | ||
| "required": [ | ||
| "static", | ||
| "dynamic" | ||
| ], | ||
| "additionalProperties": false | ||
| }, | ||
| "baseline_adjustments": { | ||
| "type": "object", | ||
| "properties": { | ||
| "format": { | ||
| "const": "csv" | ||
| }, | ||
| "delimiter": { | ||
| "type": "string" | ||
| }, | ||
| "encoding": { | ||
| "type": "string" | ||
| }, | ||
| "file_names": { | ||
| "type": "object", | ||
| "properties": { | ||
| "factorsmean_male": { | ||
| "type": "string" | ||
| }, | ||
| "factorsmean_female": { | ||
| "type": "string" | ||
| } | ||
| }, | ||
| "required": [ | ||
| "factorsmean_male", | ||
| "factorsmean_female" | ||
| ], | ||
| "additionalProperties": false | ||
| } | ||
| }, | ||
| "required": [ | ||
| "format", | ||
| "delimiter", | ||
| "encoding", | ||
| "file_names" | ||
| ], | ||
| "additionalProperties": false | ||
| } | ||
| }, | ||
| "required": [ | ||
| "ses_model", | ||
| "risk_factors", | ||
| "risk_factor_models", | ||
| "baseline_adjustments" | ||
| ], | ||
| "additionalProperties": false | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| { | ||
| "$schema": "https://json-schema.org/draft/2020-12/schema", | ||
| "$id": "https://raw.githubusercontent.com/imperialCHEPI/healthgps/main/schemas/v1/config.json", | ||
| "type": "object", | ||
| "properties": { | ||
| "comorbidities": { | ||
| "type": "integer" | ||
| }, | ||
| "folder": { | ||
| "type": "string" | ||
| }, | ||
| "file_name": { | ||
| "type": "string" | ||
| } | ||
| }, | ||
| "required": [ | ||
| "comorbidities", | ||
| "folder", | ||
| "file_name" | ||
| ], | ||
| "additionalProperties": false | ||
| } |
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I don't really know, but it seems the keyword for setting a minimum value is
minimum, rather thanminValue. See here:https://json-schema.org/understanding-json-schema/reference/numeric#range
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Good spot! I'm not sure how I managed that 🤦. We also have a
pre-commithook to check the schemas are valid, but it seems you can add extra properties and it won't complain 🤷