Instruction File

Owned by Luke Cook
Dec 11, 2019
3 min read

Specification



{ "$schema": "http://json-schema.org/draft-04/schema#", "title": "Digester Instruction File", "description": "The Instruction File describing the file to be digested", "type": "object", "properties": { "metadata": {"$redf": "#/definitions/GobiiLoaderMetadata"}, "instructions": { "$type": "array", "items": {"$ref": "#/definitions/GobiiLoaderInstruction"} } }, "definitions": { "GobiiLoaderMetadata": { "type": "object", "properties": { "project": {"$ref": "#/definitions/PropNameId"}, "platform": {"$ref": "#/definitions/PropNameId"}, "dataset": {"$ref": "#/definitions/PropNameId"}, "datasetType": {"$ref": "#/definitions/PropNameId"}, "experiment": {"$ref": "#/definitions/PropNameId"}, "mapset": {"$ref": "#/definitions/PropNameId"}, "gobiiCropType": { "type": "string" }, "jobPayloadType": {"$ref": "#/definitions/JobPayloadType"}, "qcCheck": { "type": "boolean" }, "contactEmail": { "type": "string" }, "contactId": { "type": "integer" }, "datasetOrientationType": {"$ref": "#/definitions/DatasetOrientationType"}, "gobiiJobStatus": {"$ref": "#/definitions/JobProgressStatusType"} } }, "GobiiLoaderInstruction": { "type": "object", "properties": { "table": { "type": "string" }, "gobiiFileColumns": { "type": "array", "items": {"$ref": "#/definitions/GobiiFileColumn"} } } }, "PropNameId": { "type": "object", "properties": { "id": { "type": "integer", "minimum": 0 }, "name": { "type": "string" } } }, "GobiiFileColumn": { "type": "object", "properties": { "gobiiColumnType": {"$ref": "#/definitions/GobiiColumnType"}, "rCoord": { "type": "integer" }, "cCoord": { "type": "integer" }, "name": { "type": "string" }, "filterFrom": { "type": "string" }, "filterTo": { "type": "string" }, "constantValue": { "type": "string" }, "index": { "type": "string" }, "subcolumn": { "type": "boolean" }, "subcolumnDelimiter": { "type": "string" }, "metaDataId": { "type": "string" } } }, "GobiiColumnType": { "type": "string", "enum": ["CSV_COLUMN", "CSV_ROW", "CSV_BOTH", "CONSTANT", "AUTOINCREMENT"] }, "JobPayloadType": { "type": "string", "enum": ["samples", "markers", "matrix", "marker_samples", "all_meta"] }, "DatasetOrientationType": { "type": "string", "enum": ["SAMPLE_FAST", "MARKER_FAST"] }, "JobProgressStatusType": { "type": "string", "enum": ["pending", "in_progress", "completed", "failed", "validation", "digest", "transformation", "metadata_load", "matrix_load", "aborted", "metadata_extract", "final_assembly", "qc_processing", "no_status"] }, } }
GobiiLoaderProcedure:: { metadata :: GobiiLoaderMetadata, instructions: :: List[GobiiLoaderInstruction] } GobiiLoaderMetadata :: { project :: PropNameId, platform :: PropNameId, dataset :: PropNameId, datasetType :: PropNameId, experiment :: PropNameId, mapset :: PropNameId, gobiiCropType :: String, jobPayloadType :: JobPayloadType, qcCheck :: Boolean, contactEmail :: String, contactId :: Integer, datasetOrientationType :: DatasetOrientationType, gobiiJobStatus :: JobProgressStatusType } GobiiLoaderInstruction :: { table :: String, gobiiFileColumns :: List[GobiiFileColumn] } PropNameId :: { id :: Integer, name :: String } GobiiFileColumn :: { gobiiColumnType :: GobiiColumnType, rCoord :: Integer, cCoord :: Integer, name :: String, filterFrom :: String, filterTo :: String, constantValue :: String, index :: String, subcolumn :: boolean, subcolumnDelimiter :: String, metaDataId :: String } GobiiColumnType :: String["CSV_COLUMN", "CSV_ROW", "CSV_BOTH", "CONSTANT", "AUTOINCREMENT"] JobPayloadType :: String["samples", "markers", "matrix", "marker_samples", "all_meta"] DatasetOrientationType :: String["SAMPLE_FAST", "MARKER_FAST"] JobProgressStatusType :: String["pending", "in_progress", "completed", "failed", "validation", "digest", "transformation", "metadata_load", "matrix_load", "aborted", "metadata_extract", "final_assembly", "qc_processing", "no_status"] GobiiLoaderInstruction project :: Moved to GobiiLoaderMetadata dataset :: Moved to GobiiLoaderMetadata datasetType :: Moved to GobiiLoaderMetadata, ~~Renamed from dataSetType experiment :: Moved to GobiiLoaderMetadata mapset :: moved to GobiiLoaderMetadata gobiiCropType :: Moved to GobiiLoaderMetadata gobiiFile :: Moved to GobiiLoaderMetadata jobPayloadType :: Moved to GobiiLoaderMetadata qcCheck :: Moved to GobiiLoaderMetadata contactEmail :: Moved to GobiiLoaderMetadata contactId :: Moved to GobiiLoaderMetadata datasetOrientationType :: Moved to GobiiLoaderMetadata, ~~Renamed from dataSetOrientationType gobiiJobStatus :: Moved to GobiiLoaderMetadata vcfParameters :: !!Removed columnsByTableName :: !!Removed GobiiLoaderMetadata project :: Moved from GobiiLoaderInstruction, first element in list platform :: Moved from GobiiLoaderInstruction, first element in list dataset :: Moved from GobiiLoaderInstruction, first element in list datasetType :: Moved from GobiiLoaderInstruction, first element in list experiment :: Moved from GobiiLoaderInstruction, first element in list, ~~Renamed from Experiment mapset :: Moved from GobiiLoaderInstruction, first element in list gobiiCropType :: Moved from GobiiLoaderInstruction, first element in list gobiiFile :: Moved from GobiiLoaderInstruction, first element in list jobPayloadType :: Moved from GobiiLoaderInstruction, first element in list qcCheck :: Moved from GobiiLoaderInstruction, first element in list contactEmail :: Moved from GobiiLoaderInstruction, first element in list contactId :: Moved from GobiiLoaderInstruction, first element in list datasetOrientationType :: Moved from GobiiLoaderInstruction, first element in list gobiiJobStatus :: Moved from GobiiLoaderInstruction, first element in list GobiiLoaderProcedure metadata :: **Added instructions :: **Added GobiiFileColumn findText :: !!Removed replaceText :: !!Removed

Changes from Original

  • The overall structure has been changed from a list to an object

  • All information that was encoded in only the first entry to the list has been moved to a metadata object

Deprecated Parameters

  • GobiiLoaderInstruction → vcfParameters

  • GobiiLoaderInstruction → columnsByTableName

  • GobiiFileColumn → findtext

  • GobiiFilecolumn → replaceText

Renames

  • dataSetOrientationType has been renamed to datasetOrientationType

  • dataSetType has been renamed to datasetType

  • Experiment has been renamed to experiment

GobiiColumnType

Removed Options: "VCF_SAMPLE", "VCF_MARKER", "VCF_VARIANT", "VCF_METADATA", "VCF_INFO", "VCF_MARKER_POS"