{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://raw.githubusercontent.com/api-evangelist/benchling/main/json-schema/benchling-entities-bulk-upsert-request-schema.json",
  "title": "EntitiesBulkUpsertRequest",
  "x-generated": "2026-10-12",
  "x-method": "derived",
  "x-generator": "derive-json-schema.py",
  "x-source": "openapi/benchling-entities-api-openapi.yml#/components/schemas/EntitiesBulkUpsertRequest",
  "additionalProperties": false,
  "properties": {
    "aaSequences": {
      "items": {
        "$ref": "#/$defs/AaSequenceBulkUpsertRequest"
      },
      "type": "array"
    },
    "customEntities": {
      "items": {
        "$ref": "#/$defs/CustomEntityBulkUpsertRequest"
      },
      "type": "array"
    },
    "dnaOligos": {
      "items": {
        "$ref": "#/$defs/OligoBulkUpsertRequest"
      },
      "type": "array"
    },
    "dnaSequences": {
      "items": {
        "$ref": "#/$defs/DnaSequenceBulkUpsertRequest"
      },
      "type": "array"
    },
    "molecules": {
      "items": {
        "$ref": "#/$defs/MoleculeBulkUpsertRequest"
      },
      "type": "array"
    },
    "rnaOligos": {
      "items": {
        "$ref": "#/$defs/OligoBulkUpsertRequest"
      },
      "type": "array"
    }
  },
  "type": "object",
  "$defs": {
    "AaAnnotation": {
      "properties": {
        "color": {
          "type": "string"
        },
        "end": {
          "description": "0-based exclusive end index. The end of the AA sequence is always represented as 0.",
          "type": "integer"
        },
        "id": {
          "type": "string"
        },
        "name": {
          "maxLength": 255,
          "type": "string"
        },
        "notes": {
          "maxLength": 10000,
          "type": "string"
        },
        "start": {
          "description": "0-based inclusive start index.",
          "type": "integer"
        },
        "type": {
          "maxLength": 255,
          "type": "string"
        }
      },
      "type": "object"
    },
    "AaSequenceBaseRequest": {
      "properties": {
        "aliases": {
          "description": "Aliases to add to the AA sequence",
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        "aminoAcids": {
          "description": "Amino acids for the AA sequence.\n",
          "type": "string"
        },
        "annotations": {
          "description": "Annotations to create on the AA sequence.\n",
          "items": {
            "$ref": "#/$defs/AaAnnotation"
          },
          "type": "array"
        },
        "authorIds": {
          "description": "IDs of users to set as the AA sequence's authors.",
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        "customFields": {
          "allOf": [
            {
              "$ref": "#/$defs/CustomFields"
            }
          ],
          "description": "Custom fields to add to the AA sequence. Every field should have its name as a key, mapping to an object with information about the value of the field.\n"
        },
        "fields": {
          "allOf": [
            {
              "$ref": "#/$defs/Fields"
            }
          ],
          "description": "Fields to set on the AA sequence. Must correspond with the schema's field definitions. Every field should have its name as a key, mapping to an object with information about the value of the field.\n"
        },
        "folderId": {
          "description": "ID of the folder containing the AA sequence.\n",
          "type": "string"
        },
        "name": {
          "description": "Name of the AA sequence.\n",
          "type": "string"
        },
        "schemaId": {
          "description": "ID of the AA sequence's schema.\n",
          "type": "string"
        }
      },
      "type": "object"
    },
    "AaSequenceBaseRequestForCreate": {
      "allOf": [
        {
          "$ref": "#/$defs/AaSequenceBaseRequest"
        },
        {
          "required": [
            "aminoAcids",
            "name"
          ]
        }
      ]
    },
    "AaSequenceBulkUpsertRequest": {
      "allOf": [
        {
          "$ref": "#/$defs/EntityBulkUpsertBaseRequest"
        },
        {
          "$ref": "#/$defs/AaSequenceBaseRequestForCreate"
        },
        {
          "required": [
            "annotations"
          ]
        }
      ]
    },
    "ArchiveRecordSet": {
      "additionalProperties": false,
      "description": "Currently, we only support setting a null value for archiveRecord, which unarchives the item",
      "type": [
        "object",
        "null"
      ]
    },
    "CustomEntityBaseRequest": {
      "properties": {
        "aliases": {
          "description": "Aliases to add to the custom entity",
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        "authorIds": {
          "description": "IDs of users to set as the custom entity's authors.",
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        "customFields": {
          "allOf": [
            {
              "$ref": "#/$defs/CustomFields"
            }
          ],
          "description": "Custom fields to add to the custom entity. Every field should have its name as a key, mapping to an object with information about the value of the field.\n"
        },
        "fields": {
          "allOf": [
            {
              "$ref": "#/$defs/Fields"
            }
          ],
          "description": "Schema fields to set on the custom entity. Must correspond with the schema's field definitions. Every field should have its name as a key, mapping to an object with information about the value of the field.\n"
        },
        "folderId": {
          "description": "ID of the folder that the entity is moved into",
          "type": "string"
        },
        "name": {
          "type": "string"
        },
        "schemaId": {
          "type": "string"
        }
      },
      "type": "object"
    },
    "CustomEntityBaseRequestForCreate": {
      "allOf": [
        {
          "$ref": "#/$defs/CustomEntityBaseRequest"
        },
        {
          "required": [
            "name",
            "schemaId"
          ]
        }
      ]
    },
    "CustomEntityBulkUpsertRequest": {
      "allOf": [
        {
          "$ref": "#/$defs/EntityBulkUpsertBaseRequest"
        },
        {
          "$ref": "#/$defs/CustomEntityBaseRequestForCreate"
        }
      ]
    },
    "CustomField": {
      "properties": {
        "value": {
          "type": "string"
        }
      },
      "type": "object"
    },
    "CustomFields": {
      "additionalProperties": {
        "$ref": "#/$defs/CustomField"
      },
      "type": "object"
    },
    "DnaAnnotation": {
      "allOf": [
        {
          "$ref": "#/$defs/SequenceFeatureBase"
        },
        {
          "properties": {
            "end": {
              "description": "0-based exclusive end index. The end of the sequence is always represented as 0.",
              "type": "integer"
            },
            "start": {
              "description": "0-based inclusive start index.",
              "type": "integer"
            },
            "strand": {
              "maximum": 1,
              "minimum": -1,
              "type": "integer"
            },
            "type": {
              "type": "string"
            }
          },
          "type": "object"
        }
      ]
    },
    "DnaSequenceBaseRequest": {
      "properties": {
        "aliases": {
          "description": "Aliases to add to the DNA sequence",
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        "annotations": {
          "description": "Annotations to create on the DNA sequence.\n",
          "items": {
            "$ref": "#/$defs/DnaAnnotation"
          },
          "type": "array"
        },
        "authorIds": {
          "description": "IDs of users to set as the DNA sequence's authors.",
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        "bases": {
          "description": "Base pairs for the DNA sequence.\n",
          "type": "string"
        },
        "customFields": {
          "allOf": [
            {
              "$ref": "#/$defs/CustomFields"
            }
          ],
          "description": "Custom fields to add to the DNA sequence. Every field should have its name as a key, mapping to an object with information about the value of the field.\n"
        },
        "fields": {
          "allOf": [
            {
              "$ref": "#/$defs/Fields"
            }
          ],
          "description": "Fields to set on the DNA sequence. Must correspond with the schema's field definitions. Every field should have its name as a key, mapping to an object with information about the value of the field.\n"
        },
        "folderId": {
          "description": "ID of the folder containing the DNA sequence.\n",
          "type": "string"
        },
        "isCircular": {
          "description": "Whether the DNA sequence is circular or linear.\n",
          "type": "boolean"
        },
        "name": {
          "description": "Name of the DNA sequence.\n",
          "type": "string"
        },
        "parts": {
          "items": {
            "$ref": "#/$defs/DnaSequencePart"
          },
          "type": "array"
        },
        "primers": {
          "items": {
            "$ref": "#/$defs/Primer"
          },
          "type": "array"
        },
        "schemaId": {
          "description": "ID of the DNA sequence's schema.\n",
          "type": "string"
        },
        "translations": {
          "description": "Translations to create on the DNA sequence. Translations are specified by either a combination of 'start' and 'end' fields, or a list of regions. Both cannot be provided.\n",
          "items": {
            "$ref": "#/$defs/Translation"
          },
          "type": "array"
        }
      },
      "type": "object"
    },
    "DnaSequenceBaseRequestForCreate": {
      "additionalProperties": false,
      "allOf": [
        {
          "$ref": "#/$defs/DnaSequenceBaseRequest"
        },
        {
          "required": [
            "bases",
            "isCircular",
            "name"
          ]
        }
      ]
    },
    "DnaSequenceBulkUpsertRequest": {
      "allOf": [
        {
          "$ref": "#/$defs/EntityBulkUpsertBaseRequest"
        },
        {
          "$ref": "#/$defs/DnaSequenceBaseRequestForCreate"
        },
        {
          "required": [
            "annotations",
            "primers"
          ]
        }
      ]
    },
    "DnaSequencePart": {
      "allOf": [
        {
          "$ref": "#/$defs/NucleotideSequencePart"
        },
        {
          "properties": {
            "strand": {
              "maximum": 1,
              "minimum": -1,
              "type": "integer"
            }
          },
          "type": "object"
        }
      ]
    },
    "EntityBulkUpsertBaseRequest": {
      "allOf": [
        {
          "$ref": "#/$defs/EntityUpsertBaseRequest"
        },
        {
          "properties": {
            "entityRegistryId": {
              "description": "Registry ID of the entity in Benchling.",
              "type": "string"
            }
          }
        },
        {
          "required": [
            "entityRegistryId"
          ]
        }
      ]
    },
    "EntityUpsertBaseRequest": {
      "properties": {
        "archiveRecord": {
          "$ref": "#/$defs/ArchiveRecordSet"
        },
        "fields": {
          "$ref": "#/$defs/FieldsWithResolution"
        },
        "name": {
          "type": "string"
        },
        "registryId": {
          "type": "string"
        },
        "schemaId": {
          "type": "string"
        }
      },
      "required": [
        "registryId",
        "name",
        "schemaId"
      ],
      "type": "object"
    },
    "Field": {
      "properties": {
        "displayValue": {
          "readOnly": true,
          "type": [
            "string",
            "null"
          ]
        },
        "isMulti": {
          "readOnly": true,
          "type": "boolean"
        },
        "textValue": {
          "readOnly": true,
          "type": [
            "string",
            "null"
          ]
        },
        "type": {
          "allOf": [
            {
              "$ref": "#/$defs/FieldType"
            }
          ],
          "readOnly": true
        },
        "value": {
          "description": "For single link fields, use the id of the item you want to link (eg. \"seq_jdf8BV24\").\nFor multi-link fields, use an array of ids of the items you want to link (eg. [\"seq_jdf8BV24\"])\n",
          "oneOf": [
            {
              "type": "string"
            },
            {
              "type": "boolean"
            },
            {
              "type": "number"
            },
            {
              "type": "object"
            },
            {
              "items": {
                "type": "string"
              },
              "type": "array"
            }
          ]
        }
      },
      "required": [
        "value"
      ],
      "type": "object"
    },
    "FieldType": {
      "enum": [
        "dna_sequence_link",
        "aa_sequence_link",
        "custom_entity_link",
        "entity_link",
        "mixture_link",
        "molecule_link",
        "dropdown",
        "part_link",
        "translation_link",
        "aa_part_link",
        "base_molecule_link",
        "blob_link",
        "text",
        "long_text",
        "batch_link",
        "storage_link",
        "entry_link",
        "assay_request_link",
        "assay_result_link",
        "assay_run_link",
        "boolean",
        "float",
        "integer",
        "datetime",
        "date",
        "json"
      ],
      "type": "string"
    },
    "FieldValueWithResolution": {
      "oneOf": [
        {
          "type": "string"
        },
        {
          "type": "boolean"
        },
        {
          "type": "number"
        },
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "additionalProperties": false,
          "description": "Look up an entity by its entity registry ID",
          "properties": {
            "entityRegistryId": {
              "type": "string"
            }
          },
          "required": [
            "entityRegistryId"
          ],
          "type": "object"
        }
      ]
    },
    "FieldWithResolution": {
      "allOf": [
        {
          "$ref": "#/$defs/Field"
        },
        {
          "properties": {
            "value": {
              "allOf": [
                {
                  "$ref": "#/$defs/FieldValueWithResolution"
                }
              ]
            }
          },
          "type": "object"
        }
      ]
    },
    "Fields": {
      "additionalProperties": {
        "$ref": "#/$defs/Field"
      },
      "type": "object"
    },
    "FieldsWithResolution": {
      "additionalProperties": {
        "$ref": "#/$defs/FieldWithResolution"
      },
      "type": "object"
    },
    "MoleculeBaseRequest": {
      "additionalProperties": false,
      "properties": {
        "aliases": {
          "description": "Aliases to add to the Molecule.",
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        "authorIds": {
          "description": "IDs of users to set as the Molecule's authors.",
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        "chemicalStructure": {
          "allOf": [
            {
              "$ref": "#/$defs/MoleculeStructure"
            }
          ],
          "description": "Chemical structure of the Molecule.\n"
        },
        "customFields": {
          "allOf": [
            {
              "$ref": "#/$defs/CustomFields"
            }
          ],
          "description": "Custom fields to add to the Molecule. Every field should have its name as a key, mapping to an object with information about the value of the field.\n"
        },
        "fields": {
          "allOf": [
            {
              "$ref": "#/$defs/Fields"
            }
          ],
          "description": "Fields to set on the Molecule. Must correspond with the schema's field definitions. Every field should have its name as a key, mapping to an object with information about the value of the field.\n"
        },
        "folderId": {
          "description": "ID of the folder containing the Molecule.\n",
          "type": "string"
        },
        "name": {
          "description": "Name of the Molecule.\n",
          "type": "string"
        },
        "schemaId": {
          "description": "ID of the Molecule's schema.\n",
          "type": "string"
        }
      },
      "type": "object"
    },
    "MoleculeBaseRequestForCreate": {
      "allOf": [
        {
          "$ref": "#/$defs/MoleculeBaseRequest"
        },
        {
          "required": [
            "name",
            "chemicalStructure"
          ]
        }
      ]
    },
    "MoleculeBulkUpsertRequest": {
      "allOf": [
        {
          "$ref": "#/$defs/EntityBulkUpsertBaseRequest"
        },
        {
          "$ref": "#/$defs/MoleculeBaseRequestForCreate"
        }
      ]
    },
    "MoleculeStructure": {
      "additionalProperties": false,
      "properties": {
        "structureFormat": {
          "description": "Format of the chemical structure.\n- smiles\n- molfile\n",
          "enum": [
            "smiles",
            "molfile"
          ],
          "type": "string"
        },
        "value": {
          "description": "Chemical structure in SMILES or molfile format.",
          "type": "string"
        }
      },
      "type": "object"
    },
    "NucleotideSequencePart": {
      "properties": {
        "end": {
          "description": "0-based exclusive end index. The end of the sequence is always represented as 0.",
          "type": "integer"
        },
        "sequenceId": {
          "type": "string"
        },
        "start": {
          "description": "0-based inclusive start index.",
          "type": "integer"
        }
      },
      "type": "object"
    },
    "OligoBaseRequest": {
      "properties": {
        "aliases": {
          "description": "Aliases to add to the Oligo",
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        "authorIds": {
          "description": "IDs of users to set as the Oligo's authors.",
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        "bases": {
          "description": "Base pairs of the oligo.\n",
          "type": "string"
        },
        "customFields": {
          "allOf": [
            {
              "$ref": "#/$defs/CustomFields"
            }
          ],
          "description": "Custom fields to add to the Oligo. Every field should have its name as a key, mapping to an object with information about the value of the field.\n"
        },
        "fields": {
          "allOf": [
            {
              "$ref": "#/$defs/Fields"
            }
          ],
          "description": "Fields to set on the Oligo. Must correspond with the schema's field definitions. Every field should have its name as a key, mapping to an object with information about the value of the field.\n"
        },
        "folderId": {
          "description": "ID of the folder containing the Oligo.\n",
          "type": "string"
        },
        "name": {
          "description": "Name of the Oligo.\n",
          "type": "string"
        },
        "schemaId": {
          "description": "ID of the oligo's schema.\n",
          "type": "string"
        }
      },
      "type": "object"
    },
    "OligoBaseRequestForCreate": {
      "allOf": [
        {
          "$ref": "#/$defs/OligoBaseRequest"
        },
        {
          "required": [
            "name"
          ]
        }
      ]
    },
    "OligoBulkUpsertRequest": {
      "allOf": [
        {
          "$ref": "#/$defs/EntityBulkUpsertBaseRequest"
        },
        {
          "$ref": "#/$defs/OligoBaseRequestForCreate"
        }
      ]
    },
    "Primer": {
      "properties": {
        "bases": {
          "readOnly": true,
          "type": "string"
        },
        "bindPosition": {
          "readOnly": true,
          "type": "integer"
        },
        "color": {
          "readOnly": true,
          "type": "string"
        },
        "end": {
          "description": "0-based exclusive end index. The end of the sequence is always represented as 0.",
          "type": "integer"
        },
        "name": {
          "readOnly": true,
          "type": "string"
        },
        "oligoId": {
          "type": "string"
        },
        "overhangLength": {
          "readOnly": true,
          "type": "integer"
        },
        "start": {
          "description": "0-based inclusive start index.",
          "type": "integer"
        },
        "strand": {
          "type": "integer"
        }
      },
      "type": "object"
    },
    "SequenceFeatureBase": {
      "properties": {
        "color": {
          "description": "Hex color code used when displaying this feature in the UI.",
          "type": "string"
        },
        "customFields": {
          "items": {
            "$ref": "#/$defs/SequenceFeatureCustomField"
          },
          "maxItems": 100,
          "type": "array"
        },
        "name": {
          "maxLength": 2048,
          "type": "string"
        },
        "notes": {
          "maxLength": 10000,
          "type": "string"
        }
      },
      "type": "object"
    },
    "SequenceFeatureCustomField": {
      "description": "A name and value pair associated with a sequence feature (annotation or translation). For genbank imports, these are the qualifiers associated with each feature.",
      "properties": {
        "name": {
          "description": "Name of the custom field",
          "type": "string"
        },
        "value": {
          "description": "Value of the custom field",
          "type": "string"
        }
      },
      "type": "object"
    },
    "Translation": {
      "allOf": [
        {
          "$ref": "#/$defs/SequenceFeatureBase"
        },
        {
          "properties": {
            "aminoAcids": {
              "readOnly": true,
              "type": "string"
            },
            "coerceStartCodonToMethionine": {
              "default": false,
              "description": "Whether to override the translation of the start codon to Methionine. Has no effect when the start codon already translates to Methionine.",
              "type": "boolean"
            },
            "end": {
              "description": "0-based exclusive end index. The end of the sequence is always represented as 0.",
              "type": "integer"
            },
            "geneticCode": {
              "default": "STANDARD",
              "description": "The genetic code to use when translating the nucleotide sequence into amino acids.",
              "enum": [
                "STANDARD",
                "VERTEBRATE_MITOCHONDRIAL",
                "YEAST_MITOCHONDRIAL",
                "MOLD_PROTOZOAN_COELENTERATE_MITOCHONDRIAL_MYCOPLASMA_SPIROPLASMA",
                "INVERTEBRATE_MITOCHONDRIAL",
                "CILIATE_DASYCLADACEAN_HEXAMITA_NUCLEAR",
                "ECHINODERM_FLATWORM_MITOCHONDRIAL",
                "EUPLOTID_NUCLEAR",
                "BACTERIAL_ARCHAEAL_PLANT_PLASTID",
                "ALTERNATIVE_YEAST_NUCLEAR",
                "ASCIDIAN_MITOCHONDRIAL",
                "ALTERNATIVE_FLATWORM_MITOCHONDRIAL",
                "CHLOROPHYCEAN_MITOCHONDRIAL",
                "TREMATODE_MITOCHONDRIAL",
                "SCENEDESMUS_OBLIQUUS_MITOCHONDRIAL",
                "THRAUSTOCHYTRIUM_MITOCHONDRIAL",
                "RHABDOPLEURIDAE_MITOCHONDRIAL",
                "CANDIDATE_DIVISION_SR1_GRACILIBACTERIA",
                "PACHYSOLEN_TANNOPHILUS_NUCLEAR",
                "MESODINIUM_NUCLEAR",
                "PERITRICH_NUCLEAR",
                "CEPHALODISCIDAE_MITOCHONDRIAL_UAA_TYR"
              ],
              "type": "string"
            },
            "regions": {
              "items": {
                "properties": {
                  "end": {
                    "description": "0-based exclusive end index. The end of the sequence is always represented as 0.",
                    "type": "integer"
                  },
                  "start": {
                    "description": "0-based inclusive start index.",
                    "type": "integer"
                  }
                },
                "type": "object"
              },
              "type": "array"
            },
            "start": {
              "description": "0-based inclusive start index.",
              "type": "integer"
            },
            "strand": {
              "type": "integer"
            }
          },
          "type": "object"
        }
      ]
    }
  }
}