{
    "swagger": "2.0",
    "info": {
        "description": "Rest API for communication between SciCat frontend and depositor backend. Backend service enables deposition of datasets to OneDep API.",
        "title": "OpenEm Depositor API",
        "contact": {},
        "version": "api/v1"
    },
    "paths": {
        "/empiar/metadata": {
            "post": {
                "description": "NA",
                "consumes": [
                    "application/json"
                ],
                "produces": [
                    "application/json"
                ],
                "tags": [
                    "empiar"
                ],
                "summary": "creates a json file with metadata for deposition to EMPIAR",
                "parameters": [
                    {
                        "description": "Scientific metadata as a JSON string; expects elements from OSCEM on the top level",
                        "name": "scientificMetadata",
                        "in": "body",
                        "required": true,
                        "schema": {
                            "type": "object"
                        }
                    }
                ],
                "responses": {
                    "200": {
                        "description": "json file with metadata",
                        "schema": {
                            "$ref": "#/definitions/empiar.Imageset"
                        }
                    },
                    "400": {
                        "description": "Error response",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    },
                    "500": {
                        "description": "Internal server error",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    }
                }
            }
        },
        "/empiar/schema": {
            "get": {
                "description": "NA",
                "consumes": [
                    "application/json"
                ],
                "produces": [
                    "application/json"
                ],
                "tags": [
                    "empiar"
                ],
                "summary": "creates a json file with metadata for deposition to EMPIAR",
                "responses": {
                    "200": {
                        "description": "base64 encoded schema",
                        "schema": {
                            "type": "string"
                        }
                    },
                    "400": {
                        "description": "Error response",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    },
                    "500": {
                        "description": "Internal server error",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    }
                }
            }
        },
        "/onedep": {
            "post": {
                "description": "Create a new deposition by uploading experiment and user details to OneDep API.",
                "consumes": [
                    "application/json"
                ],
                "produces": [
                    "application/json"
                ],
                "tags": [
                    "onedep"
                ],
                "summary": "Create a new deposition to OneDep",
                "parameters": [
                    {
                        "description": "User information",
                        "name": "request",
                        "in": "body",
                        "required": true,
                        "schema": {
                            "$ref": "#/definitions/onedep.RequestCreate"
                        }
                    }
                ],
                "responses": {
                    "201": {
                        "description": "Success response with Deposition ID",
                        "schema": {
                            "$ref": "#/definitions/onedep.DepositionResponse"
                        }
                    },
                    "400": {
                        "description": "Error response",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    },
                    "500": {
                        "description": "Internal server error",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    }
                }
            }
        },
        "/onedep/metadata": {
            "post": {
                "description": "Downloading a metadata file. Invokes converter and starts download.",
                "consumes": [
                    "application/json"
                ],
                "produces": [
                    "application/octet-stream"
                ],
                "tags": [
                    "onedep"
                ],
                "summary": "Get a cif file with metadata for manual deposition in OneDep",
                "parameters": [
                    {
                        "description": "Scientific metadata as a JSON string; expects elements from OSCEM on the top level",
                        "name": "scientificMetadata",
                        "in": "body",
                        "required": true,
                        "schema": {
                            "type": "object"
                        }
                    }
                ],
                "responses": {
                    "200": {
                        "description": "OK",
                        "schema": {
                            "type": "file"
                        }
                    },
                    "400": {
                        "description": "Error response",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    },
                    "500": {
                        "description": "Internal server error",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    }
                }
            }
        },
        "/onedep/pdb": {
            "post": {
                "description": "Downloading a metadata file. Invokes converter and starts download.",
                "consumes": [
                    "multipart/form-data"
                ],
                "produces": [
                    "application/octet-stream"
                ],
                "tags": [
                    "onedep"
                ],
                "summary": "Get a cif file with metadata and coordinates for manual deposition in OneDep",
                "parameters": [
                    {
                        "type": "string",
                        "description": "Scientific metadata as a JSON string; expects elements from OSCEM on the top level",
                        "name": "scientificMetadata",
                        "in": "formData",
                        "required": true
                    },
                    {
                        "type": "file",
                        "description": "File to upload",
                        "name": "file",
                        "in": "formData",
                        "required": true
                    }
                ],
                "responses": {
                    "200": {
                        "description": "OK",
                        "schema": {
                            "type": "file"
                        }
                    },
                    "400": {
                        "description": "Error response",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    },
                    "500": {
                        "description": "Internal server error",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    }
                }
            }
        },
        "/onedep/{depID}/file": {
            "post": {
                "description": "Uploading file, and metadata to OneDep API.",
                "consumes": [
                    "multipart/form-data"
                ],
                "produces": [
                    "application/json"
                ],
                "tags": [
                    "onedep"
                ],
                "summary": "Add file, pixel spacing, contour level and description to deposition in OneDep",
                "parameters": [
                    {
                        "type": "string",
                        "description": "Deposition ID to which a file should be uploaded",
                        "name": "depID",
                        "in": "path",
                        "required": true
                    },
                    {
                        "type": "array",
                        "items": {
                            "type": "file"
                        },
                        "collectionFormat": "multi",
                        "description": "File to upload",
                        "name": "file",
                        "in": "formData",
                        "required": true
                    },
                    {
                        "type": "string",
                        "description": "File metadata as a JSON string",
                        "name": "fileMetadata",
                        "in": "formData",
                        "required": true
                    },
                    {
                        "type": "string",
                        "description": "JWT token for OneDep API",
                        "name": "jwtToken",
                        "in": "formData",
                        "required": true
                    }
                ],
                "responses": {
                    "200": {
                        "description": "File ID",
                        "schema": {
                            "$ref": "#/definitions/onedep.FileResponse"
                        }
                    },
                    "400": {
                        "description": "Error response",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    },
                    "500": {
                        "description": "Internal server error",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    }
                }
            }
        },
        "/onedep/{depID}/metadata": {
            "post": {
                "description": "Uploading metadata file to OneDep API. This is created by parsing the JSON metadata into the converter.",
                "consumes": [
                    "multipart/form-data"
                ],
                "produces": [
                    "application/json"
                ],
                "tags": [
                    "onedep"
                ],
                "summary": "Add a cif file with metadata to deposition in OneDep",
                "parameters": [
                    {
                        "type": "string",
                        "description": "Deposition ID to which a file should be uploaded",
                        "name": "depID",
                        "in": "path",
                        "required": true
                    },
                    {
                        "type": "string",
                        "description": "JWT token for OneDep API",
                        "name": "jwtToken",
                        "in": "formData",
                        "required": true
                    },
                    {
                        "type": "string",
                        "description": "Scientific metadata as a JSON string; expects elements from OSCEM on the top level",
                        "name": "scientificMetadata",
                        "in": "formData",
                        "required": true
                    }
                ],
                "responses": {
                    "200": {
                        "description": "File ID",
                        "schema": {
                            "$ref": "#/definitions/onedep.FileResponse"
                        }
                    },
                    "400": {
                        "description": "Error response",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    },
                    "500": {
                        "description": "Internal server error",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    }
                }
            }
        },
        "/onedep/{depID}/pdb": {
            "post": {
                "description": "Uploading file to OneDep API.",
                "consumes": [
                    "multipart/form-data"
                ],
                "produces": [
                    "application/json"
                ],
                "tags": [
                    "onedep"
                ],
                "summary": "Add coordinates and description to deposition in OneDep",
                "parameters": [
                    {
                        "type": "string",
                        "description": "Deposition ID to which a file should be uploaded",
                        "name": "depID",
                        "in": "path",
                        "required": true
                    },
                    {
                        "type": "string",
                        "description": "JWT token for OneDep API",
                        "name": "jwtToken",
                        "in": "formData",
                        "required": true
                    },
                    {
                        "type": "file",
                        "description": "File to upload",
                        "name": "file",
                        "in": "formData",
                        "required": true
                    },
                    {
                        "type": "string",
                        "description": "Scientific metadata as a JSON string; expects elements from OSCEM on the top level",
                        "name": "scientificMetadata",
                        "in": "formData",
                        "required": true
                    }
                ],
                "responses": {
                    "200": {
                        "description": "File ID",
                        "schema": {
                            "$ref": "#/definitions/onedep.FileResponse"
                        }
                    },
                    "400": {
                        "description": "Error response",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    },
                    "500": {
                        "description": "Internal server error",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    }
                }
            }
        },
        "/onedep/{depID}/process": {
            "post": {
                "description": "Process a deposition in OneDep API.",
                "consumes": [
                    "application/json"
                ],
                "produces": [
                    "application/json"
                ],
                "tags": [
                    "onedep"
                ],
                "summary": "Process deposition to OneDep",
                "parameters": [
                    {
                        "type": "string",
                        "description": "Deposition ID to which a file should be uploaded",
                        "name": "depID",
                        "in": "path",
                        "required": true
                    },
                    {
                        "type": "string",
                        "description": "JWT token for OneDep API",
                        "name": "jwtToken",
                        "in": "formData",
                        "required": true
                    }
                ],
                "responses": {
                    "200": {
                        "description": "Deposition ID",
                        "schema": {
                            "$ref": "#/definitions/onedep.CreatedDeposition"
                        }
                    },
                    "400": {
                        "description": "Error response",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    },
                    "500": {
                        "description": "Internal server error",
                        "schema": {
                            "$ref": "#/definitions/onedep.ResponseType"
                        }
                    }
                }
            }
        },
        "/version": {
            "get": {
                "description": "Create a new deposition by uploading experiments, files, and metadata to OneDep API.",
                "produces": [
                    "application/json"
                ],
                "tags": [
                    "version"
                ],
                "summary": "Return current version",
                "responses": {
                    "200": {
                        "description": "Depositior version",
                        "schema": {
                            "type": "string"
                        }
                    },
                    "400": {
                        "description": "Error response",
                        "schema": {
                            "type": "string"
                        }
                    }
                }
            }
        }
    },
    "definitions": {
        "empiar.Imageset": {
            "type": "object",
            "properties": {
                "category": {
                    "type": "string"
                },
                "data_format": {
                    "type": "string"
                },
                "details": {
                    "type": "string"
                },
                "directory": {
                    "type": "string"
                },
                "frames_per_image": {
                    "type": "integer"
                },
                "header_format": {
                    "type": "string"
                },
                "image_height": {
                    "type": "integer"
                },
                "image_width": {
                    "type": "integer"
                },
                "micrographs_file_pattern": {
                    "type": "string"
                },
                "name": {
                    "type": "string"
                },
                "num_images_or_tilt_series": {
                    "type": "integer"
                },
                "picked_particles_directory": {
                    "type": "string"
                },
                "picked_particles_file_pattern": {
                    "type": "string"
                },
                "pixel_height": {
                    "type": "number"
                },
                "pixel_width": {
                    "type": "number"
                },
                "voxel_type": {
                    "type": "string"
                }
            }
        },
        "onedep.CreatedDeposition": {
            "type": "object",
            "properties": {
                "depID": {
                    "type": "string"
                }
            }
        },
        "onedep.DepositionResponse": {
            "type": "object",
            "properties": {
                "bmrb_id": {
                    "type": "string"
                },
                "code": {
                    "type": "string"
                },
                "created": {
                    "type": "string"
                },
                "email": {
                    "type": "string"
                },
                "emdb_id": {
                    "type": "string"
                },
                "errors": {
                    "$ref": "#/definitions/onedep.OneDepError"
                },
                "experiments": {
                    "description": "FIX ME actual response type does not correspond to the documented."
                },
                "hold_exp_date": {
                    "type": "string"
                },
                "id": {
                    "type": "string"
                },
                "last_login": {
                    "type": "string"
                },
                "message": {
                    "type": "string"
                },
                "pdb_id": {
                    "type": "string"
                },
                "site": {
                    "type": "string"
                },
                "site_url": {
                    "type": "string"
                },
                "status": {
                    "$ref": "#/definitions/onedep.Status"
                },
                "title": {
                    "type": "string"
                }
            }
        },
        "onedep.FileResponse": {
            "type": "object",
            "properties": {
                "created": {
                    "type": "string"
                },
                "errors": {
                    "description": "FIX ME actual response type does not correspond to the documented."
                },
                "id": {
                    "type": "integer"
                },
                "metadata": {
                    "description": "not there",
                    "type": "object",
                    "additionalProperties": {}
                },
                "name": {
                    "description": "not there",
                    "type": "string"
                },
                "type": {
                    "$ref": "#/definitions/onedep.OneDepType"
                },
                "warnings": {
                    "description": "FIX ME actual response type does not correspond to the documented."
                }
            }
        },
        "onedep.OneDepError": {
            "type": "object",
            "properties": {
                "code": {
                    "type": "string"
                },
                "extras": {
                    "type": "object",
                    "additionalProperties": {
                        "type": "array",
                        "items": {}
                    }
                },
                "message": {
                    "type": "string"
                }
            }
        },
        "onedep.OneDepType": {
            "type": "string",
            "enum": [
                "add-map",
                "co-cif",
                "md-cif",
                "co-pdb",
                "fsc-xml",
                "half-map",
                "img-emdb",
                "layer-lines",
                "mask-map",
                "nm-aux-amb",
                "nm-aux-gro",
                "nm-pea-any",
                "nm-res-amb",
                "nm-res-bio",
                "nm-res-cha",
                "nm-res-cns",
                "nm-res-cya",
                "nm-res-dyn",
                "nm-res-gro",
                "nm-res-isd",
                "nm-res-oth",
                "nm-res-ros",
                "nm-res-syb",
                "nm-res-xpl",
                "nm-shi",
                "nm-uni-nef",
                "nm-uni-str",
                "vo-map",
                "xa-mat",
                "xa-par",
                "xa-top",
                "xs-cif",
                "xs-mtz"
            ],
            "x-enum-varnames": [
                "ADD_MAP",
                "CO_CIF",
                "MD_CIF",
                "CO_PDB",
                "FSC_XML",
                "HALF_MAP",
                "IMG_EMDB",
                "LAYER_LINES",
                "MASK_MAP",
                "NM_AUX_AMB",
                "NM_AUX_GRO",
                "NM_PEA_ANY",
                "NM_RES_AMB",
                "NM_RES_BIO",
                "NM_RES_CHA",
                "NM_RES_CNS",
                "NM_RES_CYA",
                "NM_RES_DYN",
                "NM_RES_GRO",
                "NM_RES_ISD",
                "NM_RES_OTH",
                "NM_RES_ROS",
                "NM_RES_SYB",
                "NM_RES_XPL",
                "NM_SHI",
                "NM_UNI_NEF",
                "NM_UNI_STR",
                "VO_MAP",
                "XA_MAT",
                "XA_PAR",
                "XA_TOP",
                "XS_CIF",
                "XS_MTZ"
            ]
        },
        "onedep.RequestCreate": {
            "type": "object",
            "required": [
                "country",
                "email",
                "jwtToken",
                "method",
                "orcidIds"
            ],
            "properties": {
                "coordinates": {
                    "type": "boolean"
                },
                "country": {
                    "type": "string"
                },
                "email": {
                    "type": "string"
                },
                "jwtToken": {
                    "type": "string"
                },
                "method": {
                    "type": "string"
                },
                "orcidIds": {
                    "type": "array",
                    "items": {
                        "type": "string"
                    }
                },
                "password": {
                    "type": "string"
                }
            }
        },
        "onedep.ResponseType": {
            "type": "object",
            "properties": {
                "message": {
                    "type": "string"
                },
                "status": {
                    "type": "string"
                }
            }
        },
        "onedep.Status": {
            "type": "string",
            "enum": [
                "auco",
                "auth",
                "auxs",
                "auxu",
                "dep",
                "hold",
                "hpub",
                "obs",
                "polc",
                "proc",
                "rel",
                "repl",
                "reup",
                "wait",
                "wdrn"
            ],
            "x-enum-varnames": [
                "AUCO",
                "AUTH",
                "AUXS",
                "AUXU",
                "DEP",
                "HOLD",
                "HPUB",
                "OBS",
                "POLC",
                "PROC",
                "REL",
                "REPL",
                "REUP",
                "WAIT",
                "WDRN"
            ]
        }
    }
}