@cirrobio/api-client 0.2.19 → 0.2.21

package/.openapi-generator/FILES

@@ -55,6 +55,7 @@ src/models/CustomPipelineSettings.ts
 src/models/CustomerType.ts
 src/models/Dashboard.ts
 src/models/DashboardRequest.ts
+src/models/DataFile.ts
 src/models/Dataset.ts
 src/models/DatasetAssetsManifest.ts
 src/models/DatasetCondition.ts
@@ -150,6 +151,7 @@ src/models/UploadDatasetRequest.ts
 src/models/User.ts
 src/models/UserDetail.ts
 src/models/UserProjectAssignment.ts
+src/models/UserSettings.ts
 src/models/ValidateFileRequirementsRequest.ts
 src/models/index.ts
 src/runtime.ts

package/README.md

@@ -36,7 +36,7 @@ navigate to the folder of your consuming project and run one of the following co
 _published:_
 
 ```
-npm install @cirrobio/api-client@0.2.19 --save
+npm install @cirrobio/api-client@0.2.21 --save
 ```
 
 _unPublished (not recommended):_

package/dist/apis/MetadataApi.d.ts

@@ -11,6 +11,10 @@
  */
 import * as runtime from '../runtime';
 import type { FormSchema, PaginatedResponseSampleDto, Sample, SampleRequest } from '../models/index';
+export interface GetDatasetSamplesRequest {
+    projectId: string;
+    datasetId: string;
+}
 export interface GetProjectSamplesRequest {
     projectId: string;
     limit?: number;
@@ -32,6 +36,16 @@ export interface UpdateSampleRequest {
  *
  */
 export declare class MetadataApi extends runtime.BaseAPI {
+    /**
+     * Retrieves a list of samples associated with a dataset along with their metadata
+     * Get dataset samples
+     */
+    getDatasetSamplesRaw(requestParameters: GetDatasetSamplesRequest, initOverrides?: RequestInit | runtime.InitOverrideFunction): Promise<runtime.ApiResponse<Array<Sample>>>;
+    /**
+     * Retrieves a list of samples associated with a dataset along with their metadata
+     * Get dataset samples
+     */
+    getDatasetSamples(requestParameters: GetDatasetSamplesRequest, initOverrides?: RequestInit | runtime.InitOverrideFunction): Promise<Array<Sample>>;
     /**
      * Retrieves a list of samples associated with a project along with their metadata
      * Get project samples

package/dist/apis/MetadataApi.js

@@ -75,6 +75,64 @@ var MetadataApi = /** @class */ (function (_super) {
     function MetadataApi() {
         return _super !== null && _super.apply(this, arguments) || this;
     }
+    /**
+     * Retrieves a list of samples associated with a dataset along with their metadata
+     * Get dataset samples
+     */
+    MetadataApi.prototype.getDatasetSamplesRaw = function (requestParameters, initOverrides) {
+        return __awaiter(this, void 0, void 0, function () {
+            var queryParameters, headerParameters, token, tokenString, response;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        if (requestParameters.projectId === null || requestParameters.projectId === undefined) {
+                            throw new runtime.RequiredError('projectId', 'Required parameter requestParameters.projectId was null or undefined when calling getDatasetSamples.');
+                        }
+                        if (requestParameters.datasetId === null || requestParameters.datasetId === undefined) {
+                            throw new runtime.RequiredError('datasetId', 'Required parameter requestParameters.datasetId was null or undefined when calling getDatasetSamples.');
+                        }
+                        queryParameters = {};
+                        headerParameters = {};
+                        if (!(this.configuration && this.configuration.accessToken)) return [3 /*break*/, 2];
+                        token = this.configuration.accessToken;
+                        return [4 /*yield*/, token("accessToken", [])];
+                    case 1:
+                        tokenString = _a.sent();
+                        if (tokenString) {
+                            headerParameters["Authorization"] = "Bearer ".concat(tokenString);
+                        }
+                        _a.label = 2;
+                    case 2: return [4 /*yield*/, this.request({
+                            path: "/projects/{projectId}/datasets/{datasetId}/samples".replace("{".concat("projectId", "}"), encodeURIComponent(String(requestParameters.projectId))).replace("{".concat("datasetId", "}"), encodeURIComponent(String(requestParameters.datasetId))),
+                            method: 'GET',
+                            headers: headerParameters,
+                            query: queryParameters,
+                        }, initOverrides)];
+                    case 3:
+                        response = _a.sent();
+                        return [2 /*return*/, new runtime.JSONApiResponse(response, function (jsonValue) { return jsonValue.map(index_1.SampleFromJSON); })];
+                }
+            });
+        });
+    };
+    /**
+     * Retrieves a list of samples associated with a dataset along with their metadata
+     * Get dataset samples
+     */
+    MetadataApi.prototype.getDatasetSamples = function (requestParameters, initOverrides) {
+        return __awaiter(this, void 0, void 0, function () {
+            var response;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getDatasetSamplesRaw(requestParameters, initOverrides)];
+                    case 1:
+                        response = _a.sent();
+                        return [4 /*yield*/, response.value()];
+                    case 2: return [2 /*return*/, _a.sent()];
+                }
+            });
+        });
+    };
     /**
      * Retrieves a list of samples associated with a project along with their metadata
      * Get project samples

package/dist/models/DataFile.d.ts

@@ -0,0 +1,39 @@
+/**
+ * Cirro Data
+ * Cirro Data Platform service API
+ *
+ * The version of the OpenAPI document: latest
+ * Contact: support@cirro.bio
+ *
+ * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+ * https://openapi-generator.tech
+ * Do not edit the class manually.
+ */
+/**
+ *
+ * @export
+ * @interface DataFile
+ */
+export interface DataFile {
+    /**
+     *
+     * @type {string}
+     * @memberof DataFile
+     */
+    path: string;
+    /**
+     *
+     * @type {{ [key: string]: any; }}
+     * @memberof DataFile
+     */
+    metadata: {
+        [key: string]: any;
+    };
+}
+/**
+ * Check if a given object implements the DataFile interface.
+ */
+export declare function instanceOfDataFile(value: object): boolean;
+export declare function DataFileFromJSON(json: any): DataFile;
+export declare function DataFileFromJSONTyped(json: any, ignoreDiscriminator: boolean): DataFile;
+export declare function DataFileToJSON(value?: DataFile | null): any;

package/dist/models/DataFile.js

@@ -0,0 +1,53 @@
+"use strict";
+/* tslint:disable */
+/* eslint-disable */
+/**
+ * Cirro Data
+ * Cirro Data Platform service API
+ *
+ * The version of the OpenAPI document: latest
+ * Contact: support@cirro.bio
+ *
+ * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+ * https://openapi-generator.tech
+ * Do not edit the class manually.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.DataFileToJSON = exports.DataFileFromJSONTyped = exports.DataFileFromJSON = exports.instanceOfDataFile = void 0;
+/**
+ * Check if a given object implements the DataFile interface.
+ */
+function instanceOfDataFile(value) {
+    var isInstance = true;
+    isInstance = isInstance && "path" in value;
+    isInstance = isInstance && "metadata" in value;
+    return isInstance;
+}
+exports.instanceOfDataFile = instanceOfDataFile;
+function DataFileFromJSON(json) {
+    return DataFileFromJSONTyped(json, false);
+}
+exports.DataFileFromJSON = DataFileFromJSON;
+function DataFileFromJSONTyped(json, ignoreDiscriminator) {
+    if ((json === undefined) || (json === null)) {
+        return json;
+    }
+    return {
+        'path': json['path'],
+        'metadata': json['metadata'],
+    };
+}
+exports.DataFileFromJSONTyped = DataFileFromJSONTyped;
+function DataFileToJSON(value) {
+    if (value === undefined) {
+        return undefined;
+    }
+    if (value === null) {
+        return null;
+    }
+    return {
+        'path': value.path,
+        'metadata': value.metadata,
+    };
+}
+exports.DataFileToJSON = DataFileToJSON;

package/dist/models/Process.d.ts

@@ -100,6 +100,12 @@ export interface Process {
      * @memberof Process
      */
     allowMultipleSources?: boolean;
+    /**
+     * Whether the pipeline uses the Cirro-provided sample sheet
+     * @type {boolean}
+     * @memberof Process
+     */
+    usesSampleSheet?: boolean;
     /**
      * Whether the pipeline is marked as archived
      * @type {boolean}

package/dist/models/Process.js

@@ -52,6 +52,7 @@ function ProcessFromJSONTyped(json, ignoreDiscriminator) {
         'owner': !(0, runtime_1.exists)(json, 'owner') ? undefined : json['owner'],
         'linkedProjectIds': !(0, runtime_1.exists)(json, 'linkedProjectIds') ? undefined : json['linkedProjectIds'],
         'allowMultipleSources': !(0, runtime_1.exists)(json, 'allowMultipleSources') ? undefined : json['allowMultipleSources'],
+        'usesSampleSheet': !(0, runtime_1.exists)(json, 'usesSampleSheet') ? undefined : json['usesSampleSheet'],
         'isArchived': !(0, runtime_1.exists)(json, 'isArchived') ? undefined : json['isArchived'],
     };
 }
@@ -78,6 +79,7 @@ function ProcessToJSON(value) {
         'owner': value.owner,
         'linkedProjectIds': value.linkedProjectIds,
         'allowMultipleSources': value.allowMultipleSources,
+        'usesSampleSheet': value.usesSampleSheet,
         'isArchived': value.isArchived,
     };
 }

package/dist/models/ProcessDetail.d.ts

@@ -115,6 +115,12 @@ export interface ProcessDetail {
      * @memberof ProcessDetail
      */
     allowMultipleSources?: boolean;
+    /**
+     * Whether the pipeline uses the Cirro-provided sample sheet
+     * @type {boolean}
+     * @memberof ProcessDetail
+     */
+    usesSampleSheet?: boolean;
     /**
      *
      * @type {CustomPipelineSettings}

package/dist/models/ProcessDetail.js

@@ -59,6 +59,7 @@ function ProcessDetailFromJSONTyped(json, ignoreDiscriminator) {
         'linkedProjectIds': json['linkedProjectIds'],
         'isTenantWide': !(0, runtime_1.exists)(json, 'isTenantWide') ? undefined : json['isTenantWide'],
         'allowMultipleSources': !(0, runtime_1.exists)(json, 'allowMultipleSources') ? undefined : json['allowMultipleSources'],
+        'usesSampleSheet': !(0, runtime_1.exists)(json, 'usesSampleSheet') ? undefined : json['usesSampleSheet'],
         'customSettings': !(0, runtime_1.exists)(json, 'customSettings') ? undefined : (0, CustomPipelineSettings_1.CustomPipelineSettingsFromJSON)(json['customSettings']),
         'isArchived': !(0, runtime_1.exists)(json, 'isArchived') ? undefined : json['isArchived'],
         'fileMappingRules': !(0, runtime_1.exists)(json, 'fileMappingRules') ? undefined : (json['fileMappingRules'] === null ? null : json['fileMappingRules'].map(FileMappingRule_1.FileMappingRuleFromJSON)),
@@ -89,6 +90,7 @@ function ProcessDetailToJSON(value) {
         'linkedProjectIds': value.linkedProjectIds,
         'isTenantWide': value.isTenantWide,
         'allowMultipleSources': value.allowMultipleSources,
+        'usesSampleSheet': value.usesSampleSheet,
         'customSettings': (0, CustomPipelineSettings_1.CustomPipelineSettingsToJSON)(value.customSettings),
         'isArchived': value.isArchived,
         'fileMappingRules': value.fileMappingRules === undefined ? undefined : (value.fileMappingRules === null ? null : value.fileMappingRules.map(FileMappingRule_1.FileMappingRuleToJSON)),

package/dist/models/RunAnalysisRequest.d.ts

@@ -39,6 +39,12 @@ export interface RunAnalysisRequest {
      * @memberof RunAnalysisRequest
      */
     sourceDatasetIds: Array<string>;
+    /**
+     * Samples within the source datasets that will be used as inputs to this workflow. If not specified, all samples will be used.
+     * @type {Array<string>}
+     * @memberof RunAnalysisRequest
+     */
+    sourceSampleIds?: Array<string> | null;
     /**
      * Used for caching task execution. If the parameters are the same as the dataset specified here, it will re-use the output to minimize duplicate work
      * @type {string}

package/dist/models/RunAnalysisRequest.js

@@ -41,6 +41,7 @@ function RunAnalysisRequestFromJSONTyped(json, ignoreDiscriminator) {
         'description': !(0, runtime_1.exists)(json, 'description') ? undefined : json['description'],
         'processId': json['processId'],
         'sourceDatasetIds': json['sourceDatasetIds'],
+        'sourceSampleIds': !(0, runtime_1.exists)(json, 'sourceSampleIds') ? undefined : json['sourceSampleIds'],
         'resumeDatasetId': !(0, runtime_1.exists)(json, 'resumeDatasetId') ? undefined : json['resumeDatasetId'],
         'params': json['params'],
         'notificationEmails': json['notificationEmails'],
@@ -60,6 +61,7 @@ function RunAnalysisRequestToJSON(value) {
         'description': value.description,
         'processId': value.processId,
         'sourceDatasetIds': value.sourceDatasetIds,
+        'sourceSampleIds': value.sourceSampleIds,
         'resumeDatasetId': value.resumeDatasetId,
         'params': value.params,
         'notificationEmails': value.notificationEmails,

package/dist/models/Sample.d.ts

@@ -9,6 +9,7 @@
  * https://openapi-generator.tech
  * Do not edit the class manually.
  */
+import type { DataFile } from './DataFile';
 /**
  *
  * @export
@@ -35,6 +36,12 @@ export interface Sample {
     metadata?: {
         [key: string]: any;
     } | null;
+    /**
+     * Files associated with this sample
+     * @type {Array<DataFile>}
+     * @memberof Sample
+     */
+    files?: Array<DataFile> | null;
     /**
      *
      * @type {Array<string>}

package/dist/models/Sample.js

@@ -15,6 +15,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SampleToJSON = exports.SampleFromJSONTyped = exports.SampleFromJSON = exports.instanceOfSample = void 0;
 var runtime_1 = require("../runtime");
+var DataFile_1 = require("./DataFile");
 /**
  * Check if a given object implements the Sample interface.
  */
@@ -37,6 +38,7 @@ function SampleFromJSONTyped(json, ignoreDiscriminator) {
         'id': json['id'],
         'name': json['name'],
         'metadata': !(0, runtime_1.exists)(json, 'metadata') ? undefined : json['metadata'],
+        'files': !(0, runtime_1.exists)(json, 'files') ? undefined : (json['files'] === null ? null : json['files'].map(DataFile_1.DataFileFromJSON)),
         'datasetIds': !(0, runtime_1.exists)(json, 'datasetIds') ? undefined : json['datasetIds'],
         'createdAt': !(0, runtime_1.exists)(json, 'createdAt') ? undefined : (json['createdAt'] === null ? null : new Date(json['createdAt'])),
         'updatedAt': !(0, runtime_1.exists)(json, 'updatedAt') ? undefined : (json['updatedAt'] === null ? null : new Date(json['updatedAt'])),
@@ -54,6 +56,7 @@ function SampleToJSON(value) {
         'id': value.id,
         'name': value.name,
         'metadata': value.metadata,
+        'files': value.files === undefined ? undefined : (value.files === null ? null : value.files.map(DataFile_1.DataFileToJSON)),
         'datasetIds': value.datasetIds,
         'createdAt': value.createdAt === undefined ? undefined : (value.createdAt === null ? null : value.createdAt.toISOString()),
         'updatedAt': value.updatedAt === undefined ? undefined : (value.updatedAt === null ? null : value.updatedAt.toISOString()),

package/dist/models/UpdateUserRequest.d.ts

@@ -9,6 +9,7 @@
  * https://openapi-generator.tech
  * Do not edit the class manually.
  */
+import type { UserSettings } from './UserSettings';
 /**
  *
  * @export
@@ -39,6 +40,12 @@ export interface UpdateUserRequest {
      * @memberof UpdateUserRequest
      */
     department?: string;
+    /**
+     * Job title or role of the user
+     * @type {string}
+     * @memberof UpdateUserRequest
+     */
+    jobTitle?: string;
     /**
      * The organization the user belongs to, only editable by administrators
      * @type {string}
@@ -46,13 +53,11 @@ export interface UpdateUserRequest {
      */
     organization?: string;
     /**
-     * Additional settings for the user
-     * @type {{ [key: string]: any; }}
+     *
+     * @type {UserSettings}
      * @memberof UpdateUserRequest
      */
-    settings?: {
-        [key: string]: any;
-    };
+    settings?: UserSettings | null;
     /**
      * Groups the user belongs to, only editable by administrators
      * @type {Array<string>}

package/dist/models/UpdateUserRequest.js

@@ -15,6 +15,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.UpdateUserRequestToJSON = exports.UpdateUserRequestFromJSONTyped = exports.UpdateUserRequestFromJSON = exports.instanceOfUpdateUserRequest = void 0;
 var runtime_1 = require("../runtime");
+var UserSettings_1 = require("./UserSettings");
 /**
  * Check if a given object implements the UpdateUserRequest interface.
  */
@@ -38,8 +39,9 @@ function UpdateUserRequestFromJSONTyped(json, ignoreDiscriminator) {
         'email': json['email'],
         'phone': !(0, runtime_1.exists)(json, 'phone') ? undefined : json['phone'],
         'department': !(0, runtime_1.exists)(json, 'department') ? undefined : json['department'],
+        'jobTitle': !(0, runtime_1.exists)(json, 'jobTitle') ? undefined : json['jobTitle'],
         'organization': !(0, runtime_1.exists)(json, 'organization') ? undefined : json['organization'],
-        'settings': !(0, runtime_1.exists)(json, 'settings') ? undefined : json['settings'],
+        'settings': !(0, runtime_1.exists)(json, 'settings') ? undefined : (0, UserSettings_1.UserSettingsFromJSON)(json['settings']),
         'groups': !(0, runtime_1.exists)(json, 'groups') ? undefined : json['groups'],
     };
 }
@@ -56,8 +58,9 @@ function UpdateUserRequestToJSON(value) {
         'email': value.email,
         'phone': value.phone,
         'department': value.department,
+        'jobTitle': value.jobTitle,
         'organization': value.organization,
-        'settings': value.settings,
+        'settings': (0, UserSettings_1.UserSettingsToJSON)(value.settings),
         'groups': value.groups,
     };
 }

package/dist/models/UserDetail.d.ts

@@ -10,6 +10,7 @@
  * Do not edit the class manually.
  */
 import type { UserProjectAssignment } from './UserProjectAssignment';
+import type { UserSettings } from './UserSettings';
 /**
  *
  * @export
@@ -46,6 +47,12 @@ export interface UserDetail {
      * @memberof UserDetail
      */
     organization: string;
+    /**
+     *
+     * @type {string}
+     * @memberof UserDetail
+     */
+    jobTitle: string;
     /**
      *
      * @type {string}
@@ -76,6 +83,12 @@ export interface UserDetail {
      * @memberof UserDetail
      */
     groups: Array<string>;
+    /**
+     *
+     * @type {UserSettings}
+     * @memberof UserDetail
+     */
+    settings: UserSettings;
 }
 /**
  * Check if a given object implements the UserDetail interface.

package/dist/models/UserDetail.js

@@ -16,6 +16,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.UserDetailToJSON = exports.UserDetailFromJSONTyped = exports.UserDetailFromJSON = exports.instanceOfUserDetail = void 0;
 var runtime_1 = require("../runtime");
 var UserProjectAssignment_1 = require("./UserProjectAssignment");
+var UserSettings_1 = require("./UserSettings");
 /**
  * Check if a given object implements the UserDetail interface.
  */
@@ -26,10 +27,12 @@ function instanceOfUserDetail(value) {
     isInstance = isInstance && "phone" in value;
     isInstance = isInstance && "email" in value;
     isInstance = isInstance && "organization" in value;
+    isInstance = isInstance && "jobTitle" in value;
     isInstance = isInstance && "department" in value;
     isInstance = isInstance && "invitedBy" in value;
     isInstance = isInstance && "projectAssignments" in value;
     isInstance = isInstance && "groups" in value;
+    isInstance = isInstance && "settings" in value;
     return isInstance;
 }
 exports.instanceOfUserDetail = instanceOfUserDetail;
@@ -47,11 +50,13 @@ function UserDetailFromJSONTyped(json, ignoreDiscriminator) {
         'phone': json['phone'],
         'email': json['email'],
         'organization': json['organization'],
+        'jobTitle': json['jobTitle'],
         'department': json['department'],
         'invitedBy': json['invitedBy'],
         'signUpTime': !(0, runtime_1.exists)(json, 'signUpTime') ? undefined : (json['signUpTime'] === null ? null : new Date(json['signUpTime'])),
         'projectAssignments': (json['projectAssignments'].map(UserProjectAssignment_1.UserProjectAssignmentFromJSON)),
         'groups': json['groups'],
+        'settings': (0, UserSettings_1.UserSettingsFromJSON)(json['settings']),
     };
 }
 exports.UserDetailFromJSONTyped = UserDetailFromJSONTyped;
@@ -68,11 +73,13 @@ function UserDetailToJSON(value) {
         'phone': value.phone,
         'email': value.email,
         'organization': value.organization,
+        'jobTitle': value.jobTitle,
         'department': value.department,
         'invitedBy': value.invitedBy,
         'signUpTime': value.signUpTime === undefined ? undefined : (value.signUpTime === null ? null : value.signUpTime.toISOString()),
         'projectAssignments': (value.projectAssignments.map(UserProjectAssignment_1.UserProjectAssignmentToJSON)),
         'groups': value.groups,
+        'settings': (0, UserSettings_1.UserSettingsToJSON)(value.settings),
     };
 }
 exports.UserDetailToJSON = UserDetailToJSON;

package/dist/models/UserSettings.d.ts

@@ -0,0 +1,32 @@
+/**
+ * Cirro Data
+ * Cirro Data Platform service API
+ *
+ * The version of the OpenAPI document: latest
+ * Contact: support@cirro.bio
+ *
+ * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+ * https://openapi-generator.tech
+ * Do not edit the class manually.
+ */
+/**
+ * Additional settings for the user
+ * @export
+ * @interface UserSettings
+ */
+export interface UserSettings {
+    [key: string]: any | any;
+    /**
+     *
+     * @type {boolean}
+     * @memberof UserSettings
+     */
+    analysisUpdateNotificationsEnabled: boolean;
+}
+/**
+ * Check if a given object implements the UserSettings interface.
+ */
+export declare function instanceOfUserSettings(value: object): boolean;
+export declare function UserSettingsFromJSON(json: any): UserSettings;
+export declare function UserSettingsFromJSONTyped(json: any, ignoreDiscriminator: boolean): UserSettings;
+export declare function UserSettingsToJSON(value?: UserSettings | null): any;

package/dist/models/UserSettings.js

@@ -0,0 +1,57 @@
+"use strict";
+/* tslint:disable */
+/* eslint-disable */
+/**
+ * Cirro Data
+ * Cirro Data Platform service API
+ *
+ * The version of the OpenAPI document: latest
+ * Contact: support@cirro.bio
+ *
+ * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+ * https://openapi-generator.tech
+ * Do not edit the class manually.
+ */
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.UserSettingsToJSON = exports.UserSettingsFromJSONTyped = exports.UserSettingsFromJSON = exports.instanceOfUserSettings = void 0;
+/**
+ * Check if a given object implements the UserSettings interface.
+ */
+function instanceOfUserSettings(value) {
+    var isInstance = true;
+    isInstance = isInstance && "analysisUpdateNotificationsEnabled" in value;
+    return isInstance;
+}
+exports.instanceOfUserSettings = instanceOfUserSettings;
+function UserSettingsFromJSON(json) {
+    return UserSettingsFromJSONTyped(json, false);
+}
+exports.UserSettingsFromJSON = UserSettingsFromJSON;
+function UserSettingsFromJSONTyped(json, ignoreDiscriminator) {
+    if ((json === undefined) || (json === null)) {
+        return json;
+    }
+    return __assign(__assign({}, json), { 'analysisUpdateNotificationsEnabled': json['analysisUpdateNotificationsEnabled'] });
+}
+exports.UserSettingsFromJSONTyped = UserSettingsFromJSONTyped;
+function UserSettingsToJSON(value) {
+    if (value === undefined) {
+        return undefined;
+    }
+    if (value === null) {
+        return null;
+    }
+    return __assign(__assign({}, value), { 'analysisUpdateNotificationsEnabled': value.analysisUpdateNotificationsEnabled });
+}
+exports.UserSettingsToJSON = UserSettingsToJSON;

package/dist/models/index.d.ts

@@ -30,6 +30,7 @@ export * from './CustomPipelineSettings';
 export * from './CustomerType';
 export * from './Dashboard';
 export * from './DashboardRequest';
+export * from './DataFile';
 export * from './Dataset';
 export * from './DatasetAssetsManifest';
 export * from './DatasetCondition';
@@ -125,4 +126,5 @@ export * from './UploadDatasetRequest';
 export * from './User';
 export * from './UserDetail';
 export * from './UserProjectAssignment';
+export * from './UserSettings';
 export * from './ValidateFileRequirementsRequest';

package/dist/models/index.js

@@ -48,6 +48,7 @@ __exportStar(require("./CustomPipelineSettings"), exports);
 __exportStar(require("./CustomerType"), exports);
 __exportStar(require("./Dashboard"), exports);
 __exportStar(require("./DashboardRequest"), exports);
+__exportStar(require("./DataFile"), exports);
 __exportStar(require("./Dataset"), exports);
 __exportStar(require("./DatasetAssetsManifest"), exports);
 __exportStar(require("./DatasetCondition"), exports);
@@ -143,4 +144,5 @@ __exportStar(require("./UploadDatasetRequest"), exports);
 __exportStar(require("./User"), exports);
 __exportStar(require("./UserDetail"), exports);
 __exportStar(require("./UserProjectAssignment"), exports);
+__exportStar(require("./UserSettings"), exports);
 __exportStar(require("./ValidateFileRequirementsRequest"), exports);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cirrobio/api-client",
-  "version": "0.2.19",
+  "version": "0.2.21",
   "description": "API client for Cirro",
   "author": "CirroBio",
   "repository": {

package/src/apis/MetadataApi.ts

@@ -31,6 +31,11 @@ import {
     SampleRequestToJSON,
 } from '../models/index';
 
+export interface GetDatasetSamplesRequest {
+    projectId: string;
+    datasetId: string;
+}
+
 export interface GetProjectSamplesRequest {
     projectId: string;
     limit?: number;
@@ -57,6 +62,50 @@ export interface UpdateSampleRequest {
  */
 export class MetadataApi extends runtime.BaseAPI {
 
+    /**
+     * Retrieves a list of samples associated with a dataset along with their metadata
+     * Get dataset samples
+     */
+    async getDatasetSamplesRaw(requestParameters: GetDatasetSamplesRequest, initOverrides?: RequestInit | runtime.InitOverrideFunction): Promise<runtime.ApiResponse<Array<Sample>>> {
+        if (requestParameters.projectId === null || requestParameters.projectId === undefined) {
+            throw new runtime.RequiredError('projectId','Required parameter requestParameters.projectId was null or undefined when calling getDatasetSamples.');
+        }
+
+        if (requestParameters.datasetId === null || requestParameters.datasetId === undefined) {
+            throw new runtime.RequiredError('datasetId','Required parameter requestParameters.datasetId was null or undefined when calling getDatasetSamples.');
+        }
+
+        const queryParameters: any = {};
+
+        const headerParameters: runtime.HTTPHeaders = {};
+
+        if (this.configuration && this.configuration.accessToken) {
+            const token = this.configuration.accessToken;
+            const tokenString = await token("accessToken", []);
+
+            if (tokenString) {
+                headerParameters["Authorization"] = `Bearer ${tokenString}`;
+            }
+        }
+        const response = await this.request({
+            path: `/projects/{projectId}/datasets/{datasetId}/samples`.replace(`{${"projectId"}}`, encodeURIComponent(String(requestParameters.projectId))).replace(`{${"datasetId"}}`, encodeURIComponent(String(requestParameters.datasetId))),
+            method: 'GET',
+            headers: headerParameters,
+            query: queryParameters,
+        }, initOverrides);
+
+        return new runtime.JSONApiResponse(response, (jsonValue) => jsonValue.map(SampleFromJSON));
+    }
+
+    /**
+     * Retrieves a list of samples associated with a dataset along with their metadata
+     * Get dataset samples
+     */
+    async getDatasetSamples(requestParameters: GetDatasetSamplesRequest, initOverrides?: RequestInit | runtime.InitOverrideFunction): Promise<Array<Sample>> {
+        const response = await this.getDatasetSamplesRaw(requestParameters, initOverrides);
+        return await response.value();
+    }
+
     /**
      * Retrieves a list of samples associated with a project along with their metadata
      * Get project samples

package/src/models/DataFile.ts

@@ -0,0 +1,75 @@
+/* tslint:disable */
+/* eslint-disable */
+/**
+ * Cirro Data
+ * Cirro Data Platform service API
+ *
+ * The version of the OpenAPI document: latest
+ * Contact: support@cirro.bio
+ *
+ * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+ * https://openapi-generator.tech
+ * Do not edit the class manually.
+ */
+
+import { exists, mapValues } from '../runtime';
+/**
+ * 
+ * @export
+ * @interface DataFile
+ */
+export interface DataFile {
+    /**
+     * 
+     * @type {string}
+     * @memberof DataFile
+     */
+    path: string;
+    /**
+     * 
+     * @type {{ [key: string]: any; }}
+     * @memberof DataFile
+     */
+    metadata: { [key: string]: any; };
+}
+
+/**
+ * Check if a given object implements the DataFile interface.
+ */
+export function instanceOfDataFile(value: object): boolean {
+    let isInstance = true;
+    isInstance = isInstance && "path" in value;
+    isInstance = isInstance && "metadata" in value;
+
+    return isInstance;
+}
+
+export function DataFileFromJSON(json: any): DataFile {
+    return DataFileFromJSONTyped(json, false);
+}
+
+export function DataFileFromJSONTyped(json: any, ignoreDiscriminator: boolean): DataFile {
+    if ((json === undefined) || (json === null)) {
+        return json;
+    }
+    return {
+        
+        'path': json['path'],
+        'metadata': json['metadata'],
+    };
+}
+
+export function DataFileToJSON(value?: DataFile | null): any {
+    if (value === undefined) {
+        return undefined;
+    }
+    if (value === null) {
+        return null;
+    }
+    return {
+        
+        'path': value.path,
+        'metadata': value.metadata,
+    };
+}
+

package/src/models/Process.ts

@@ -110,6 +110,12 @@ export interface Process {
      * @memberof Process
      */
     allowMultipleSources?: boolean;
+    /**
+     * Whether the pipeline uses the Cirro-provided sample sheet
+     * @type {boolean}
+     * @memberof Process
+     */
+    usesSampleSheet?: boolean;
     /**
      * Whether the pipeline is marked as archived
      * @type {boolean}
@@ -156,6 +162,7 @@ export function ProcessFromJSONTyped(json: any, ignoreDiscriminator: boolean): P
         'owner': !exists(json, 'owner') ? undefined : json['owner'],
         'linkedProjectIds': !exists(json, 'linkedProjectIds') ? undefined : json['linkedProjectIds'],
         'allowMultipleSources': !exists(json, 'allowMultipleSources') ? undefined : json['allowMultipleSources'],
+        'usesSampleSheet': !exists(json, 'usesSampleSheet') ? undefined : json['usesSampleSheet'],
         'isArchived': !exists(json, 'isArchived') ? undefined : json['isArchived'],
     };
 }
@@ -183,6 +190,7 @@ export function ProcessToJSON(value?: Process | null): any {
         'owner': value.owner,
         'linkedProjectIds': value.linkedProjectIds,
         'allowMultipleSources': value.allowMultipleSources,
+        'usesSampleSheet': value.usesSampleSheet,
         'isArchived': value.isArchived,
     };
 }

package/src/models/ProcessDetail.ts

@@ -140,6 +140,12 @@ export interface ProcessDetail {
      * @memberof ProcessDetail
      */
     allowMultipleSources?: boolean;
+    /**
+     * Whether the pipeline uses the Cirro-provided sample sheet
+     * @type {boolean}
+     * @memberof ProcessDetail
+     */
+    usesSampleSheet?: boolean;
     /**
      * 
      * @type {CustomPipelineSettings}
@@ -202,6 +208,7 @@ export function ProcessDetailFromJSONTyped(json: any, ignoreDiscriminator: boole
         'linkedProjectIds': json['linkedProjectIds'],
         'isTenantWide': !exists(json, 'isTenantWide') ? undefined : json['isTenantWide'],
         'allowMultipleSources': !exists(json, 'allowMultipleSources') ? undefined : json['allowMultipleSources'],
+        'usesSampleSheet': !exists(json, 'usesSampleSheet') ? undefined : json['usesSampleSheet'],
         'customSettings': !exists(json, 'customSettings') ? undefined : CustomPipelineSettingsFromJSON(json['customSettings']),
         'isArchived': !exists(json, 'isArchived') ? undefined : json['isArchived'],
         'fileMappingRules': !exists(json, 'fileMappingRules') ? undefined : (json['fileMappingRules'] === null ? null : (json['fileMappingRules'] as Array<any>).map(FileMappingRuleFromJSON)),
@@ -233,6 +240,7 @@ export function ProcessDetailToJSON(value?: ProcessDetail | null): any {
         'linkedProjectIds': value.linkedProjectIds,
         'isTenantWide': value.isTenantWide,
         'allowMultipleSources': value.allowMultipleSources,
+        'usesSampleSheet': value.usesSampleSheet,
         'customSettings': CustomPipelineSettingsToJSON(value.customSettings),
         'isArchived': value.isArchived,
         'fileMappingRules': value.fileMappingRules === undefined ? undefined : (value.fileMappingRules === null ? null : (value.fileMappingRules as Array<any>).map(FileMappingRuleToJSON)),

package/src/models/RunAnalysisRequest.ts

@@ -43,6 +43,12 @@ export interface RunAnalysisRequest {
      * @memberof RunAnalysisRequest
      */
     sourceDatasetIds: Array<string>;
+    /**
+     * Samples within the source datasets that will be used as inputs to this workflow. If not specified, all samples will be used.
+     * @type {Array<string>}
+     * @memberof RunAnalysisRequest
+     */
+    sourceSampleIds?: Array<string> | null;
     /**
      * Used for caching task execution. If the parameters are the same as the dataset specified here, it will re-use the output to minimize duplicate work
      * @type {string}
@@ -97,6 +103,7 @@ export function RunAnalysisRequestFromJSONTyped(json: any, ignoreDiscriminator:
         'description': !exists(json, 'description') ? undefined : json['description'],
         'processId': json['processId'],
         'sourceDatasetIds': json['sourceDatasetIds'],
+        'sourceSampleIds': !exists(json, 'sourceSampleIds') ? undefined : json['sourceSampleIds'],
         'resumeDatasetId': !exists(json, 'resumeDatasetId') ? undefined : json['resumeDatasetId'],
         'params': json['params'],
         'notificationEmails': json['notificationEmails'],
@@ -117,6 +124,7 @@ export function RunAnalysisRequestToJSON(value?: RunAnalysisRequest | null): any
         'description': value.description,
         'processId': value.processId,
         'sourceDatasetIds': value.sourceDatasetIds,
+        'sourceSampleIds': value.sourceSampleIds,
         'resumeDatasetId': value.resumeDatasetId,
         'params': value.params,
         'notificationEmails': value.notificationEmails,

package/src/models/Sample.ts

@@ -13,6 +13,13 @@
  */
 
 import { exists, mapValues } from '../runtime';
+import type { DataFile } from './DataFile';
+import {
+    DataFileFromJSON,
+    DataFileFromJSONTyped,
+    DataFileToJSON,
+} from './DataFile';
+
 /**
  * 
  * @export
@@ -37,6 +44,12 @@ export interface Sample {
      * @memberof Sample
      */
     metadata?: { [key: string]: any; } | null;
+    /**
+     * Files associated with this sample
+     * @type {Array<DataFile>}
+     * @memberof Sample
+     */
+    files?: Array<DataFile> | null;
     /**
      * 
      * @type {Array<string>}
@@ -81,6 +94,7 @@ export function SampleFromJSONTyped(json: any, ignoreDiscriminator: boolean): Sa
         'id': json['id'],
         'name': json['name'],
         'metadata': !exists(json, 'metadata') ? undefined : json['metadata'],
+        'files': !exists(json, 'files') ? undefined : (json['files'] === null ? null : (json['files'] as Array<any>).map(DataFileFromJSON)),
         'datasetIds': !exists(json, 'datasetIds') ? undefined : json['datasetIds'],
         'createdAt': !exists(json, 'createdAt') ? undefined : (json['createdAt'] === null ? null : new Date(json['createdAt'])),
         'updatedAt': !exists(json, 'updatedAt') ? undefined : (json['updatedAt'] === null ? null : new Date(json['updatedAt'])),
@@ -99,6 +113,7 @@ export function SampleToJSON(value?: Sample | null): any {
         'id': value.id,
         'name': value.name,
         'metadata': value.metadata,
+        'files': value.files === undefined ? undefined : (value.files === null ? null : (value.files as Array<any>).map(DataFileToJSON)),
         'datasetIds': value.datasetIds,
         'createdAt': value.createdAt === undefined ? undefined : (value.createdAt === null ? null : value.createdAt.toISOString()),
         'updatedAt': value.updatedAt === undefined ? undefined : (value.updatedAt === null ? null : value.updatedAt.toISOString()),

package/src/models/UpdateUserRequest.ts

@@ -13,6 +13,13 @@
  */
 
 import { exists, mapValues } from '../runtime';
+import type { UserSettings } from './UserSettings';
+import {
+    UserSettingsFromJSON,
+    UserSettingsFromJSONTyped,
+    UserSettingsToJSON,
+} from './UserSettings';
+
 /**
  * 
  * @export
@@ -43,6 +50,12 @@ export interface UpdateUserRequest {
      * @memberof UpdateUserRequest
      */
     department?: string;
+    /**
+     * Job title or role of the user
+     * @type {string}
+     * @memberof UpdateUserRequest
+     */
+    jobTitle?: string;
     /**
      * The organization the user belongs to, only editable by administrators
      * @type {string}
@@ -50,11 +63,11 @@ export interface UpdateUserRequest {
      */
     organization?: string;
     /**
-     * Additional settings for the user
-     * @type {{ [key: string]: any; }}
+     * 
+     * @type {UserSettings}
      * @memberof UpdateUserRequest
      */
-    settings?: { [key: string]: any; };
+    settings?: UserSettings | null;
     /**
      * Groups the user belongs to, only editable by administrators
      * @type {Array<string>}
@@ -88,8 +101,9 @@ export function UpdateUserRequestFromJSONTyped(json: any, ignoreDiscriminator: b
         'email': json['email'],
         'phone': !exists(json, 'phone') ? undefined : json['phone'],
         'department': !exists(json, 'department') ? undefined : json['department'],
+        'jobTitle': !exists(json, 'jobTitle') ? undefined : json['jobTitle'],
         'organization': !exists(json, 'organization') ? undefined : json['organization'],
-        'settings': !exists(json, 'settings') ? undefined : json['settings'],
+        'settings': !exists(json, 'settings') ? undefined : UserSettingsFromJSON(json['settings']),
         'groups': !exists(json, 'groups') ? undefined : json['groups'],
     };
 }
@@ -107,8 +121,9 @@ export function UpdateUserRequestToJSON(value?: UpdateUserRequest | null): any {
         'email': value.email,
         'phone': value.phone,
         'department': value.department,
+        'jobTitle': value.jobTitle,
         'organization': value.organization,
-        'settings': value.settings,
+        'settings': UserSettingsToJSON(value.settings),
         'groups': value.groups,
     };
 }

package/src/models/UserDetail.ts

@@ -19,6 +19,12 @@ import {
     UserProjectAssignmentFromJSONTyped,
     UserProjectAssignmentToJSON,
 } from './UserProjectAssignment';
+import type { UserSettings } from './UserSettings';
+import {
+    UserSettingsFromJSON,
+    UserSettingsFromJSONTyped,
+    UserSettingsToJSON,
+} from './UserSettings';
 
 /**
  * 
@@ -56,6 +62,12 @@ export interface UserDetail {
      * @memberof UserDetail
      */
     organization: string;
+    /**
+     * 
+     * @type {string}
+     * @memberof UserDetail
+     */
+    jobTitle: string;
     /**
      * 
      * @type {string}
@@ -86,6 +98,12 @@ export interface UserDetail {
      * @memberof UserDetail
      */
     groups: Array<string>;
+    /**
+     * 
+     * @type {UserSettings}
+     * @memberof UserDetail
+     */
+    settings: UserSettings;
 }
 
 /**
@@ -98,10 +116,12 @@ export function instanceOfUserDetail(value: object): boolean {
     isInstance = isInstance && "phone" in value;
     isInstance = isInstance && "email" in value;
     isInstance = isInstance && "organization" in value;
+    isInstance = isInstance && "jobTitle" in value;
     isInstance = isInstance && "department" in value;
     isInstance = isInstance && "invitedBy" in value;
     isInstance = isInstance && "projectAssignments" in value;
     isInstance = isInstance && "groups" in value;
+    isInstance = isInstance && "settings" in value;
 
     return isInstance;
 }
@@ -121,11 +141,13 @@ export function UserDetailFromJSONTyped(json: any, ignoreDiscriminator: boolean)
         'phone': json['phone'],
         'email': json['email'],
         'organization': json['organization'],
+        'jobTitle': json['jobTitle'],
         'department': json['department'],
         'invitedBy': json['invitedBy'],
         'signUpTime': !exists(json, 'signUpTime') ? undefined : (json['signUpTime'] === null ? null : new Date(json['signUpTime'])),
         'projectAssignments': ((json['projectAssignments'] as Array<any>).map(UserProjectAssignmentFromJSON)),
         'groups': json['groups'],
+        'settings': UserSettingsFromJSON(json['settings']),
     };
 }
 
@@ -143,11 +165,13 @@ export function UserDetailToJSON(value?: UserDetail | null): any {
         'phone': value.phone,
         'email': value.email,
         'organization': value.organization,
+        'jobTitle': value.jobTitle,
         'department': value.department,
         'invitedBy': value.invitedBy,
         'signUpTime': value.signUpTime === undefined ? undefined : (value.signUpTime === null ? null : value.signUpTime.toISOString()),
         'projectAssignments': ((value.projectAssignments as Array<any>).map(UserProjectAssignmentToJSON)),
         'groups': value.groups,
+        'settings': UserSettingsToJSON(value.settings),
     };
 }
 

package/src/models/UserSettings.ts

@@ -0,0 +1,69 @@
+/* tslint:disable */
+/* eslint-disable */
+/**
+ * Cirro Data
+ * Cirro Data Platform service API
+ *
+ * The version of the OpenAPI document: latest
+ * Contact: support@cirro.bio
+ *
+ * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+ * https://openapi-generator.tech
+ * Do not edit the class manually.
+ */
+
+import { exists, mapValues } from '../runtime';
+/**
+ * Additional settings for the user
+ * @export
+ * @interface UserSettings
+ */
+export interface UserSettings {
+    [key: string]: any | any;
+    /**
+     * 
+     * @type {boolean}
+     * @memberof UserSettings
+     */
+    analysisUpdateNotificationsEnabled: boolean;
+}
+
+/**
+ * Check if a given object implements the UserSettings interface.
+ */
+export function instanceOfUserSettings(value: object): boolean {
+    let isInstance = true;
+    isInstance = isInstance && "analysisUpdateNotificationsEnabled" in value;
+
+    return isInstance;
+}
+
+export function UserSettingsFromJSON(json: any): UserSettings {
+    return UserSettingsFromJSONTyped(json, false);
+}
+
+export function UserSettingsFromJSONTyped(json: any, ignoreDiscriminator: boolean): UserSettings {
+    if ((json === undefined) || (json === null)) {
+        return json;
+    }
+    return {
+        
+            ...json,
+        'analysisUpdateNotificationsEnabled': json['analysisUpdateNotificationsEnabled'],
+    };
+}
+
+export function UserSettingsToJSON(value?: UserSettings | null): any {
+    if (value === undefined) {
+        return undefined;
+    }
+    if (value === null) {
+        return null;
+    }
+    return {
+        
+            ...value,
+        'analysisUpdateNotificationsEnabled': value.analysisUpdateNotificationsEnabled,
+    };
+}
+

package/src/models/index.ts

@@ -32,6 +32,7 @@ export * from './CustomPipelineSettings';
 export * from './CustomerType';
 export * from './Dashboard';
 export * from './DashboardRequest';
+export * from './DataFile';
 export * from './Dataset';
 export * from './DatasetAssetsManifest';
 export * from './DatasetCondition';
@@ -127,4 +128,5 @@ export * from './UploadDatasetRequest';
 export * from './User';
 export * from './UserDetail';
 export * from './UserProjectAssignment';
+export * from './UserSettings';
 export * from './ValidateFileRequirementsRequest';