Validate MAE object against a schema. Currently only SEs are validated TODO: add mae.json schema and validate full MAE object
Usage
validate_mae_with_schema(
mae,
schema_package = Sys.getenv("SCHEMA_PACKAGE", "gDRutils"),
schema_dir_path = Sys.getenv("SCHEMA_DIR_PATH", "schemas"),
schema = c(se = "se.json", mae = "mae.json")
)Arguments
- mae
MultiAssayExperiment object
- schema_package
string name of the package with JSON schema files
- schema_dir_path
path to the dir with JSON schema files
- schema
named charvec with filenames of schemas to validate against.
Examples
mae <- get_synthetic_data("finalMAE_small")
validate_mae_with_schema(mae)
#> $mae
#> [1] TRUE
#> attr(,"exit_code")
#> [1] 0
#>
#> $`experiment:single-agent`
#> [1] FALSE
#> attr(,"error")
#> [1] "JSON validation of data model failed"
#> attr(,"exit_code")
#> [1] 2
#> attr(,"derror")
#> instancePath schemaPath keyword missingProperty
#> 1 #/required required title
#> 2 #/required required description
#> 3 #/required required experimentalist
#> 4 #/required required sources
#> message schema
#> 1 must have required property 'title' title, d....
#> 2 must have required property 'description' title, d....
#> 3 must have required property 'experimentalist' title, d....
#> 4 must have required property 'sources' title, d....
#> parentSchema.$schema parentSchema.title
#> 1 http://json-schema.org/draft-07/schema SummarizedExperiment
#> 2 http://json-schema.org/draft-07/schema SummarizedExperiment
#> 3 http://json-schema.org/draft-07/schema SummarizedExperiment
#> 4 http://json-schema.org/draft-07/schema SummarizedExperiment
#> parentSchema.description parentSchema.type parentSchema.properties.type
#> 1 object string
#> 2 object string
#> 3 object string
#> 4 object string
#> parentSchema.properties.description.type
#> 1 string
#> 2 string
#> 3 string
#> 4 string
#> parentSchema.properties.description.description
#> 1 A free text description of the experiment performed.
#> 2 A free text description of the experiment performed.
#> 3 A free text description of the experiment performed.
#> 4 A free text description of the experiment performed.
#> parentSchema.properties.experimentalist.type
#> 1 string
#> 2 string
#> 3 string
#> 4 string
#> parentSchema.properties.experimentalist.description
#> 1 Unix id or name of experimentalist.
#> 2 Unix id or name of experimentalist.
#> 3 Unix id or name of experimentalist.
#> 4 Unix id or name of experimentalist.
#> parentSchema.properties.experimentalist.examples
#> 1 eqlin
#> 2 eqlin
#> 3 eqlin
#> 4 eqlin
#> parentSchema.properties.duration.description
#> 1 Number of days cells were treated with perturbation in days.
#> 2 Number of days cells were treated with perturbation in days.
#> 3 Number of days cells were treated with perturbation in days.
#> 4 Number of days cells were treated with perturbation in days.
#> parentSchema.properties.duration.type parentSchema.properties.duration.type
#> 1 array integer
#> 2 array integer
#> 3 array integer
#> 4 array integer
#> parentSchema.properties.cellline.description
#> 1 Identifier of the given cell line
#> 2 Identifier of the given cell line
#> 3 Identifier of the given cell line
#> 4 Identifier of the given cell line
#> parentSchema.properties.cellline.type parentSchema.properties.cellline.type
#> 1 array string
#> 2 array string
#> 3 array string
#> 4 array string
#> parentSchema.properties.cellline_name.description
#> 1 Name of the given cell line
#> 2 Name of the given cell line
#> 3 Name of the given cell line
#> 4 Name of the given cell line
#> parentSchema.properties.cellline_name.type
#> 1 array
#> 2 array
#> 3 array
#> 4 array
#> parentSchema.properties.cellline_name.type
#> 1 string
#> 2 string
#> 3 string
#> 4 string
#> parentSchema.properties.cellline_tissue.description
#> 1 Tissue origin of the given cell line
#> 2 Tissue origin of the given cell line
#> 3 Tissue origin of the given cell line
#> 4 Tissue origin of the given cell line
#> parentSchema.properties.cellline_tissue.type
#> 1 array
#> 2 array
#> 3 array
#> 4 array
#> parentSchema.properties.cellline_tissue.type
#> 1 string
#> 2 string
#> 3 string
#> 4 string
#> parentSchema.properties.cellline_ref_div_time.description
#> 1 Reference division time of the given cell line
#> 2 Reference division time of the given cell line
#> 3 Reference division time of the given cell line
#> 4 Reference division time of the given cell line
#> parentSchema.properties.cellline_ref_div_time.type
#> 1 array
#> 2 array
#> 3 array
#> 4 array
#> parentSchema.properties.cellline_ref_div_time.items.type
#> 1 integer,....
#> 2 integer,....
#> 3 integer,....
#> 4 integer,....
#> parentSchema.properties.cellline_ref_div_time.items.pattern
#> 1 [0-9]+|NA
#> 2 [0-9]+|NA
#> 3 [0-9]+|NA
#> 4 [0-9]+|NA
#> parentSchema.properties.drug.description parentSchema.properties.drug.type
#> 1 Identifier of the given drug array
#> 2 Identifier of the given drug array
#> 3 Identifier of the given drug array
#> 4 Identifier of the given drug array
#> parentSchema.properties.drug.type
#> 1 string
#> 2 string
#> 3 string
#> 4 string
#> parentSchema.properties.drug_name.description
#> 1 Name of the given drug
#> 2 Name of the given drug
#> 3 Name of the given drug
#> 4 Name of the given drug
#> parentSchema.properties.drug_name.type parentSchema.properties.drug_name.type
#> 1 array string
#> 2 array string
#> 3 array string
#> 4 array string
#> parentSchema.properties.drug_moa.description
#> 1 Mechanism of action of the given drug
#> 2 Mechanism of action of the given drug
#> 3 Mechanism of action of the given drug
#> 4 Mechanism of action of the given drug
#> parentSchema.properties.drug_moa.type parentSchema.properties.drug_moa.type
#> 1 array string
#> 2 array string
#> 3 array string
#> 4 array string
#> parentSchema.properties.sources.type
#> 1 array
#> 2 array
#> 3 array
#> 4 array
#> parentSchema.properties.sources.description
#> 1 Data source
#> 2 Data source
#> 3 Data source
#> 4 Data source
#> parentSchema.properties.sources.items.type
#> 1 object
#> 2 object
#> 3 object
#> 4 object
#> parentSchema.properties.sources.items.required
#> 1 name, id
#> 2 name, id
#> 3 name, id
#> 4 name, id
#> parentSchema.properties.sources.items.additionalProperties
#> 1 FALSE
#> 2 FALSE
#> 3 FALSE
#> 4 FALSE
#> parentSchema.properties.sources.items.properties.name.type
#> 1 string
#> 2 string
#> 3 string
#> 4 string
#> parentSchema.properties.sources.items.properties.name.examples
#> 1 GeneData....
#> 2 GeneData....
#> 3 GeneData....
#> 4 GeneData....
#> parentSchema.properties.sources.items.properties.id.type
#> 1 string
#> 2 string
#> 3 string
#> 4 string
#> parentSchema.properties.sources.items.properties.id.description
#> 1 An identifier for the source.
#> 2 An identifier for the source.
#> 3 An identifier for the source.
#> 4 An identifier for the source.
#> parentSchema.properties.sources.items.properties.id.examples
#> 1 IDS-12345
#> 2 IDS-12345
#> 3 IDS-12345
#> 4 IDS-12345
#> parentSchema.required data.drug data.drug_name data.drug_moa data.duration
#> 1 title, d.... G00002, .... drug_002.... moa_A, m.... 72, 72, ....
#> 2 title, d.... G00002, .... drug_002.... moa_A, m.... 72, 72, ....
#> 3 title, d.... G00002, .... drug_002.... moa_A, m.... 72, 72, ....
#> 4 title, d.... G00002, .... drug_002.... moa_A, m.... 72, 72, ....
#> data.cellline data.cellline_name data.cellline_tissue
#> 1 CL00011,.... cellline.... tissue_x....
#> 2 CL00011,.... cellline.... tissue_x....
#> 3 CL00011,.... cellline.... tissue_x....
#> 4 CL00011,.... cellline.... tissue_x....
#> data.cellline_ref_div_time dataPath
#> 1 26, 30, ....
#> 2 26, 30, ....
#> 3 26, 30, ....
#> 4 26, 30, ....
#>