cdd-vault-update-december-2021-3

Written by Abe Wang | Dec 27, 2021 8:00:00 AM

Happy Holidays, Everyone!

Get Mapping Templates via the API

The API can now be used to retrieve all mapping templates in CDD Vault. The new API endpoint returns summary information for all available templates in the specified Vault.

GET /api/v1/vaults//mapping_templates

[ 
   {
        "id": 22704,
        "name": "Protac Registration",
        "created_at": "2021-12-23T17:59:22.000-06:00",
        "modified_at": "2021-12-23T17:59:22.000-06:00",
        "owner": "Charlie Weatherall"
    }
]

To retrieve specific header mapping details for a specific mapping template, use the same API endpoint and include a mapping template ID.

GET /api/v1/vaults/<vault_id>/mapping_templates/22704

The JSON returned contains:

A "header_mappings" section that identifies the field/readout each header is mapped to
A “file” section that provides details on the original file used to create the template

{
    "id": 22704,
    "name": "Protac Registration",
    "created_at": "2021-12-23T17:59:22.000-06:00",
    "modified_at": "2021-12-23T17:59:22.000-06:00",
    "owner": "Charlie Weatherall",  
    "header_mappings" : [
        {
            "header": {
                "id": 13606653,"name": "SMILES"},
            "definition": {
                "id": 2,
                "type": "InternalFieldDefinition::MoleculeStructure",
                "name": "Structure"
            }
        },
        {
            "header": {
                "id": 13606654,"name": "Synonym"},
            "definition": {
                "id": 3,
                "type": "InternalFieldDefinition::MoleculeSynonym",
                "name": "Molecule Name or Synonym"
            }
        },
        {
            "header": {
                "id": 13606655,"name": "Common Name"},
            "definition": {
                "id": 75648,
                "type": "MoleculeFieldDefinition",
                "name": "Name",
                "data_type_name": "Text"
            }
        },
        {
            "header": {
                "id": 13606656,"name": "External ID"},
            "definition": {
                "id": 75657,
                "type": "BatchFieldDefinition",
                "name": "E3 Ligand",
                "data_type_name": "BatchLink"
            }
        },
        {
            "header": {
                "id": 13606657,"name": "Linker"},
            "definition": {
                "id": 75656,
                "type": "BatchFieldDefinition",
                "name": "Linker",
                "data_type_name": "BatchLink"
            }
        },
        {
            "header": {
                "id": 13606658,"name": "Initial Amount"},
            "definition": {
                "id": 75644,
                "type": "BatchFieldDefinition",
                "name": "Initial Amount",
                "data_type_name": "Number"
            }
        },
        {
            "header": {
                "id": 13606659,"name": "Plate Name"},
            "definition": {
                "id": 148,
                "type": "InternalFieldDefinition::PlateName",
                "name": "Plate Name"
            }
        },
        {
            "header": {
                "id": 13606660,"name": "Well Location"},
            "definition": {
                "id": 147,
                "type": "InternalFieldDefinition::WellLocation",
                "name": "Well Location"
            }
        },
        {
            "header": {
                "id": 13606661,"name": "Concentration"},
            "definition": {
                "id": 731567,
                "name": "Conc",
                "data_type_name": "Number",
                "protocol_name": "Degradation Assay",
                "type": "ReadoutDefinition"
            },
            "run_grouping": 641224
        },
        {
            "header": {
                "id": 13606662,"name": "Degradation"},
            "definition": {
                "id": 731568,
                "name": "Degradation",
                "data_type_name": "Number",
                "protocol_name": "Degradation Assay",
                "type": "ReadoutDefinition"
            },
            "run_grouping": 641224
        },
        {
            "header": {
                "id": 13606663,"name": "Time"},
            "definition": {
                "id": 749638,
                "name": "Time Point",
                "data_type_name": "PickList",
                "protocol_name": "Degradation Assay",
                "pick_list_values": [
                    "12hr",
                    "24hr"
                ],
                "type": "ReadoutDefinition"
            },
            "run_grouping": 641224
        },
        {
            "header": {
                "id": 13606664,"name": "Target"},
            "definition": {
                "id": 749962,
                "name": "Target",
                "data_type_name": "PickList",
                "protocol_name": "Degradation Assay",
                "pick_list_values": [
                    "AR",
                    "BCL6",
                    "BCR-ABL",
                    "BRD4"
                ],
                "type": "ReadoutDefinition"
            },
            "run_grouping": 641224
        },
        {
            "header": {
                "id": 13606665,"name": "Cell"},
            "definition": {
                "id": 749601,
                "name": "Cell Type",
                "data_type_name": "BatchLink",
                "protocol_name": "Degradation Assay",
                "type": "ReadoutDefinition"
            },
            "run_grouping": 641224
        }
    ],
    "file": {
        "file_name": "MappingTemplate_Protac.csv",
        "value"  : 11010509
    }
}

New Parameter for Automatically Rejecting Imports/Slurps via the API

When using the POST Slurps API call to import data files into a CDD Vault, you can now control whether slurps with Suspicious Events or Errors will be automatically rejected. This new autoreject parameter is set to true by default so that imports initiated via the API will be rejected when Suspicious Events or Errors occur. This allows other file imports in the queue to continue processing.

POST /api/v1/vaults//slurps

{
"project":"MyProject",
"mapping_template":"SomeMappingTemplate",
"autoreject":"true",
"runs":[
            {"run_date":"2021-12-25","place":"SCRNLab", "person":"DrGina"}
           ]
}

Noteworthy tips:

Change the autoreject parameter to false to maintain the old behavior where an import with Suspicious Events or Errors must be handled via the CDD Vault Import Data interface:

POST /api/v1/vaults//slurps

{
"project":"MyProject",
"mapping_template":"SomeMappingTemplate",
"autoreject":"false",
"runs":[
            {"run_date":"2021-12-25","place":"SCRNLab", "person":"DrGina"}
           ]
}

Email notifications are still sent when imports are rejected or left in the queue.

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