@cirrobio/api-client 0.0.27-alpha → 0.0.29-alpha

package/dist/models/RepositoryType.js

@@ -0,0 +1,40 @@
+"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.RepositoryTypeToJSON = exports.RepositoryTypeFromJSONTyped = exports.RepositoryTypeFromJSON = exports.RepositoryType = void 0;
+/**
+ * Type of repository
+ * @export
+ * @enum {string}
+ */
+var RepositoryType;
+(function (RepositoryType) {
+    RepositoryType["None"] = "NONE";
+    RepositoryType["Aws"] = "AWS";
+    RepositoryType["GithubPublic"] = "GITHUB_PUBLIC";
+    RepositoryType["GithubPrivate"] = "GITHUB_PRIVATE";
+})(RepositoryType = exports.RepositoryType || (exports.RepositoryType = {}));
+function RepositoryTypeFromJSON(json) {
+    return RepositoryTypeFromJSONTyped(json, false);
+}
+exports.RepositoryTypeFromJSON = RepositoryTypeFromJSON;
+function RepositoryTypeFromJSONTyped(json, ignoreDiscriminator) {
+    return json;
+}
+exports.RepositoryTypeFromJSONTyped = RepositoryTypeFromJSONTyped;
+function RepositoryTypeToJSON(value) {
+    return value;
+}
+exports.RepositoryTypeToJSON = RepositoryTypeToJSON;

package/dist/models/index.d.ts

@@ -32,8 +32,10 @@ export * from './NotebookInstanceStatusResponse';
 export * from './OpenNotebookInstanceResponse';
 export * from './PaginatedResponseDatasetListDto';
 export * from './PaginatedResponseSampleDto';
+export * from './PipelineCode';
 export * from './Process';
 export * from './ProcessDetail';
+export * from './ProcessDetailAllOfPipelineCode';
 export * from './Project';
 export * from './ProjectDetail';
 export * from './ProjectMetrics';
@@ -43,6 +45,7 @@ export * from './ProjectSettings';
 export * from './ProjectUser';
 export * from './Reference';
 export * from './ReferenceType';
+export * from './RepositoryType';
 export * from './RunAnalysisRequest';
 export * from './S3Credentials';
 export * from './Sample';

package/dist/models/index.js

@@ -50,8 +50,10 @@ __exportStar(require("./NotebookInstanceStatusResponse"), exports);
 __exportStar(require("./OpenNotebookInstanceResponse"), exports);
 __exportStar(require("./PaginatedResponseDatasetListDto"), exports);
 __exportStar(require("./PaginatedResponseSampleDto"), exports);
+__exportStar(require("./PipelineCode"), exports);
 __exportStar(require("./Process"), exports);
 __exportStar(require("./ProcessDetail"), exports);
+__exportStar(require("./ProcessDetailAllOfPipelineCode"), exports);
 __exportStar(require("./Project"), exports);
 __exportStar(require("./ProjectDetail"), exports);
 __exportStar(require("./ProjectMetrics"), exports);
@@ -61,6 +63,7 @@ __exportStar(require("./ProjectSettings"), exports);
 __exportStar(require("./ProjectUser"), exports);
 __exportStar(require("./Reference"), exports);
 __exportStar(require("./ReferenceType"), exports);
+__exportStar(require("./RepositoryType"), exports);
 __exportStar(require("./RunAnalysisRequest"), exports);
 __exportStar(require("./S3Credentials"), exports);
 __exportStar(require("./Sample"), exports);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cirrobio/api-client",
-  "version": "0.0.27-alpha",
+  "version": "0.0.29-alpha",
   "description": "API client for Cirro",
   "author": "CirroBio",
   "repository": {

package/src/apis/ProcessesApi.ts

@@ -15,6 +15,8 @@
 
 import * as runtime from '../runtime';
 import type {
+  CreateResponse,
+  CustomPipelineSettings,
   FileRequirements,
   FormSchema,
   Process,
@@ -22,6 +24,10 @@ import type {
   ValidateFileRequirementsRequest,
 } from '../models/index';
 import {
+    CreateResponseFromJSON,
+    CreateResponseToJSON,
+    CustomPipelineSettingsFromJSON,
+    CustomPipelineSettingsToJSON,
     FileRequirementsFromJSON,
     FileRequirementsToJSON,
     FormSchemaFromJSON,
@@ -34,6 +40,14 @@ import {
     ValidateFileRequirementsRequestToJSON,
 } from '../models/index';
 
+export interface ArchiveCustomProcessRequest {
+    processId: string;
+}
+
+export interface CreateCustomProcessRequest {
+    processDetail: ProcessDetail;
+}
+
 export interface GetProcessRequest {
     processId: string;
 }
@@ -46,6 +60,15 @@ export interface GetProcessesRequest {
     includeArchived?: boolean;
 }
 
+export interface SyncCustomProcessRequest {
+    processId: string;
+}
+
+export interface UpdateCustomProcessRequest {
+    processId: string;
+    processDetail: ProcessDetail;
+}
+
 export interface ValidateFileRequirementsOperationRequest {
     processId: string;
     validateFileRequirementsRequest: ValidateFileRequirementsRequest;
@@ -56,6 +79,88 @@ export interface ValidateFileRequirementsOperationRequest {
  */
 export class ProcessesApi extends runtime.BaseAPI {
 
+    /**
+     * Removes the process from the list of available options
+     * Archive custom process
+     */
+    async archiveCustomProcessRaw(requestParameters: ArchiveCustomProcessRequest, initOverrides?: RequestInit | runtime.InitOverrideFunction): Promise<runtime.ApiResponse<void>> {
+        if (requestParameters.processId === null || requestParameters.processId === undefined) {
+            throw new runtime.RequiredError('processId','Required parameter requestParameters.processId was null or undefined when calling archiveCustomProcess.');
+        }
+
+        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 ${tokenString}`;
+            }
+        }
+        const response = await this.request({
+            path: `/processes/{processId}`.replace(`{${"processId"}}`, encodeURIComponent(String(requestParameters.processId))),
+            method: 'DELETE',
+            headers: headerParameters,
+            query: queryParameters,
+        }, initOverrides);
+
+        return new runtime.VoidApiResponse(response);
+    }
+
+    /**
+     * Removes the process from the list of available options
+     * Archive custom process
+     */
+    async archiveCustomProcess(requestParameters: ArchiveCustomProcessRequest, initOverrides?: RequestInit | runtime.InitOverrideFunction): Promise<void> {
+        await this.archiveCustomProcessRaw(requestParameters, initOverrides);
+    }
+
+    /**
+     * Creates a custom data type or pipeline which you can use in the listed projects.
+     * Create custom process
+     */
+    async createCustomProcessRaw(requestParameters: CreateCustomProcessRequest, initOverrides?: RequestInit | runtime.InitOverrideFunction): Promise<runtime.ApiResponse<CreateResponse>> {
+        if (requestParameters.processDetail === null || requestParameters.processDetail === undefined) {
+            throw new runtime.RequiredError('processDetail','Required parameter requestParameters.processDetail was null or undefined when calling createCustomProcess.');
+        }
+
+        const queryParameters: any = {};
+
+        const headerParameters: runtime.HTTPHeaders = {};
+
+        headerParameters['Content-Type'] = 'application/json';
+
+        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: `/processes`,
+            method: 'POST',
+            headers: headerParameters,
+            query: queryParameters,
+            body: ProcessDetailToJSON(requestParameters.processDetail),
+        }, initOverrides);
+
+        return new runtime.JSONApiResponse(response, (jsonValue) => CreateResponseFromJSON(jsonValue));
+    }
+
+    /**
+     * Creates a custom data type or pipeline which you can use in the listed projects.
+     * Create custom process
+     */
+    async createCustomProcess(requestParameters: CreateCustomProcessRequest, initOverrides?: RequestInit | runtime.InitOverrideFunction): Promise<CreateResponse> {
+        const response = await this.createCustomProcessRaw(requestParameters, initOverrides);
+        return await response.value();
+    }
+
     /**
      * Retrieves detailed information on a process
      * Get process
@@ -176,6 +281,92 @@ export class ProcessesApi extends runtime.BaseAPI {
         return await response.value();
     }
 
+    /**
+     * Updates the process definition from the repository
+     * Sync custom process
+     */
+    async syncCustomProcessRaw(requestParameters: SyncCustomProcessRequest, initOverrides?: RequestInit | runtime.InitOverrideFunction): Promise<runtime.ApiResponse<CustomPipelineSettings>> {
+        if (requestParameters.processId === null || requestParameters.processId === undefined) {
+            throw new runtime.RequiredError('processId','Required parameter requestParameters.processId was null or undefined when calling syncCustomProcess.');
+        }
+
+        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 ${tokenString}`;
+            }
+        }
+        const response = await this.request({
+            path: `/processes/{processId}:sync`.replace(`{${"processId"}}`, encodeURIComponent(String(requestParameters.processId))),
+            method: 'PUT',
+            headers: headerParameters,
+            query: queryParameters,
+        }, initOverrides);
+
+        return new runtime.JSONApiResponse(response, (jsonValue) => CustomPipelineSettingsFromJSON(jsonValue));
+    }
+
+    /**
+     * Updates the process definition from the repository
+     * Sync custom process
+     */
+    async syncCustomProcess(requestParameters: SyncCustomProcessRequest, initOverrides?: RequestInit | runtime.InitOverrideFunction): Promise<CustomPipelineSettings> {
+        const response = await this.syncCustomProcessRaw(requestParameters, initOverrides);
+        return await response.value();
+    }
+
+    /**
+     * Updates the custom process
+     * Update custom process
+     */
+    async updateCustomProcessRaw(requestParameters: UpdateCustomProcessRequest, initOverrides?: RequestInit | runtime.InitOverrideFunction): Promise<runtime.ApiResponse<void>> {
+        if (requestParameters.processId === null || requestParameters.processId === undefined) {
+            throw new runtime.RequiredError('processId','Required parameter requestParameters.processId was null or undefined when calling updateCustomProcess.');
+        }
+
+        if (requestParameters.processDetail === null || requestParameters.processDetail === undefined) {
+            throw new runtime.RequiredError('processDetail','Required parameter requestParameters.processDetail was null or undefined when calling updateCustomProcess.');
+        }
+
+        const queryParameters: any = {};
+
+        const headerParameters: runtime.HTTPHeaders = {};
+
+        headerParameters['Content-Type'] = 'application/json';
+
+        if (this.configuration && this.configuration.accessToken) {
+            const token = this.configuration.accessToken;
+            const tokenString = await token("accessToken", []);
+
+            if (tokenString) {
+                headerParameters["Authorization"] = `Bearer ${tokenString}`;
+            }
+        }
+        const response = await this.request({
+            path: `/processes/{processId}`.replace(`{${"processId"}}`, encodeURIComponent(String(requestParameters.processId))),
+            method: 'PUT',
+            headers: headerParameters,
+            query: queryParameters,
+            body: ProcessDetailToJSON(requestParameters.processDetail),
+        }, initOverrides);
+
+        return new runtime.VoidApiResponse(response);
+    }
+
+    /**
+     * Updates the custom process
+     * Update custom process
+     */
+    async updateCustomProcess(requestParameters: UpdateCustomProcessRequest, initOverrides?: RequestInit | runtime.InitOverrideFunction): Promise<void> {
+        await this.updateCustomProcessRaw(requestParameters, initOverrides);
+    }
+
     /**
      * Checks the input file names with the expected files for a data type (ingest processes only)
      * Validate file requirements

package/src/models/CustomPipelineSettings.ts

@@ -20,41 +20,41 @@ import { exists, mapValues } from '../runtime';
  */
 export interface CustomPipelineSettings {
     /**
-     * 
+     * GitHub repository that contains the process definition
      * @type {string}
      * @memberof CustomPipelineSettings
      */
     repository: string;
     /**
-     * 
+     * Branch, tag, or commit hash of the repo that contains the process definition
      * @type {string}
      * @memberof CustomPipelineSettings
      */
-    branch: string;
+    branch?: string;
     /**
-     * 
+     * Folder within the repo that contains the process definition
      * @type {string}
      * @memberof CustomPipelineSettings
      */
-    folder: string;
+    folder?: string;
     /**
      * 
      * @type {Date}
      * @memberof CustomPipelineSettings
      */
-    lastSync: Date;
+    lastSync?: Date | null;
     /**
      * 
      * @type {string}
      * @memberof CustomPipelineSettings
      */
-    syncStatus: string;
+    syncStatus?: string | null;
     /**
      * 
      * @type {string}
      * @memberof CustomPipelineSettings
      */
-    commitHash: string;
+    commitHash?: string | null;
 }
 
 /**
@@ -63,11 +63,6 @@ export interface CustomPipelineSettings {
 export function instanceOfCustomPipelineSettings(value: object): boolean {
     let isInstance = true;
     isInstance = isInstance && "repository" in value;
-    isInstance = isInstance && "branch" in value;
-    isInstance = isInstance && "folder" in value;
-    isInstance = isInstance && "lastSync" in value;
-    isInstance = isInstance && "syncStatus" in value;
-    isInstance = isInstance && "commitHash" in value;
 
     return isInstance;
 }
@@ -83,11 +78,11 @@ export function CustomPipelineSettingsFromJSONTyped(json: any, ignoreDiscriminat
     return {
         
         'repository': json['repository'],
-        'branch': json['branch'],
-        'folder': json['folder'],
-        'lastSync': (new Date(json['lastSync'])),
-        'syncStatus': json['syncStatus'],
-        'commitHash': json['commitHash'],
+        'branch': !exists(json, 'branch') ? undefined : json['branch'],
+        'folder': !exists(json, 'folder') ? undefined : json['folder'],
+        'lastSync': !exists(json, 'lastSync') ? undefined : (json['lastSync'] === null ? null : new Date(json['lastSync'])),
+        'syncStatus': !exists(json, 'syncStatus') ? undefined : json['syncStatus'],
+        'commitHash': !exists(json, 'commitHash') ? undefined : json['commitHash'],
     };
 }
 
@@ -103,7 +98,7 @@ export function CustomPipelineSettingsToJSON(value?: CustomPipelineSettings | nu
         'repository': value.repository,
         'branch': value.branch,
         'folder': value.folder,
-        'lastSync': (value.lastSync.toISOString()),
+        'lastSync': value.lastSync === undefined ? undefined : (value.lastSync === null ? null : value.lastSync.toISOString()),
         'syncStatus': value.syncStatus,
         'commitHash': value.commitHash,
     };

package/src/models/Executor.ts

@@ -13,7 +13,7 @@
  */
 
 /**
- * Process executor
+ * How the workflow is executed
  * @export
  * @enum {string}
  */

package/src/models/FileNamePattern.ts

@@ -31,12 +31,6 @@ export interface FileNamePattern {
      * @memberof FileNamePattern
      */
     description: string;
-    /**
-     * 
-     * @type {string}
-     * @memberof FileNamePattern
-     */
-    sampleMatchingPattern: string;
 }
 
 /**
@@ -46,7 +40,6 @@ export function instanceOfFileNamePattern(value: object): boolean {
     let isInstance = true;
     isInstance = isInstance && "exampleName" in value;
     isInstance = isInstance && "description" in value;
-    isInstance = isInstance && "sampleMatchingPattern" in value;
 
     return isInstance;
 }
@@ -63,7 +56,6 @@ export function FileNamePatternFromJSONTyped(json: any, ignoreDiscriminator: boo
         
         'exampleName': json['exampleName'],
         'description': json['description'],
-        'sampleMatchingPattern': json['sampleMatchingPattern'],
     };
 }
 
@@ -78,7 +70,6 @@ export function FileNamePatternToJSON(value?: FileNamePattern | null): any {
         
         'exampleName': value.exampleName,
         'description': value.description,
-        'sampleMatchingPattern': value.sampleMatchingPattern,
     };
 }
 

package/src/models/GenerateSftpCredentialsRequest.ts

@@ -20,11 +20,11 @@ import { exists, mapValues } from '../runtime';
  */
 export interface GenerateSftpCredentialsRequest {
     /**
-     * 
+     * Number of days the credentials are valid for
      * @type {number}
      * @memberof GenerateSftpCredentialsRequest
      */
-    lifetimeDays: number;
+    lifetimeDays?: number;
 }
 
 /**
@@ -32,7 +32,6 @@ export interface GenerateSftpCredentialsRequest {
  */
 export function instanceOfGenerateSftpCredentialsRequest(value: object): boolean {
     let isInstance = true;
-    isInstance = isInstance && "lifetimeDays" in value;
 
     return isInstance;
 }
@@ -47,7 +46,7 @@ export function GenerateSftpCredentialsRequestFromJSONTyped(json: any, ignoreDis
     }
     return {
         
-        'lifetimeDays': json['lifetimeDays'],
+        'lifetimeDays': !exists(json, 'lifetimeDays') ? undefined : json['lifetimeDays'],
     };
 }
 

package/src/models/PipelineCode.ts

@@ -0,0 +1,97 @@
+/* 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';
+import type { RepositoryType } from './RepositoryType';
+import {
+    RepositoryTypeFromJSON,
+    RepositoryTypeFromJSONTyped,
+    RepositoryTypeToJSON,
+} from './RepositoryType';
+
+/**
+ * Used to describe the pipeline analysis code
+ * @export
+ * @interface PipelineCode
+ */
+export interface PipelineCode {
+    /**
+     * GitHub repository which contains the workflow code
+     * @type {string}
+     * @memberof PipelineCode
+     */
+    repositoryPath: string;
+    /**
+     * Branch, tag, or commit hash of the pipeline code
+     * @type {string}
+     * @memberof PipelineCode
+     */
+    version?: string;
+    /**
+     * 
+     * @type {RepositoryType}
+     * @memberof PipelineCode
+     */
+    repositoryType?: RepositoryType;
+    /**
+     * Main script for running the pipeline
+     * @type {string}
+     * @memberof PipelineCode
+     */
+    entryPoint?: string;
+}
+
+/**
+ * Check if a given object implements the PipelineCode interface.
+ */
+export function instanceOfPipelineCode(value: object): boolean {
+    let isInstance = true;
+    isInstance = isInstance && "repositoryPath" in value;
+
+    return isInstance;
+}
+
+export function PipelineCodeFromJSON(json: any): PipelineCode {
+    return PipelineCodeFromJSONTyped(json, false);
+}
+
+export function PipelineCodeFromJSONTyped(json: any, ignoreDiscriminator: boolean): PipelineCode {
+    if ((json === undefined) || (json === null)) {
+        return json;
+    }
+    return {
+        
+        'repositoryPath': json['repositoryPath'],
+        'version': !exists(json, 'version') ? undefined : json['version'],
+        'repositoryType': !exists(json, 'repositoryType') ? undefined : RepositoryTypeFromJSON(json['repositoryType']),
+        'entryPoint': !exists(json, 'entryPoint') ? undefined : json['entryPoint'],
+    };
+}
+
+export function PipelineCodeToJSON(value?: PipelineCode | null): any {
+    if (value === undefined) {
+        return undefined;
+    }
+    if (value === null) {
+        return null;
+    }
+    return {
+        
+        'repositoryPath': value.repositoryPath,
+        'version': value.version,
+        'repositoryType': RepositoryTypeToJSON(value.repositoryType),
+        'entryPoint': value.entryPoint,
+    };
+}
+

package/src/models/Process.ts

@@ -33,7 +33,7 @@ export interface Process {
      */
     id: string;
     /**
-     * 
+     * Friendly name for the process
      * @type {string}
      * @memberof Process
      */
@@ -43,7 +43,7 @@ export interface Process {
      * @type {string}
      * @memberof Process
      */
-    description?: string;
+    description: string;
     /**
      * 
      * @type {Executor}
@@ -61,7 +61,7 @@ export interface Process {
      * @type {string}
      * @memberof Process
      */
-    fileRequirementsMessage?: string;
+    fileRequirementsMessage?: string | null;
     /**
      * IDs of pipelines that can be ran downstream
      * @type {Array<string>}
@@ -94,6 +94,7 @@ export interface Process {
 export function instanceOfProcess(value: object): boolean {
     let isInstance = true;
     isInstance = isInstance && "id" in value;
+    isInstance = isInstance && "description" in value;
 
     return isInstance;
 }
@@ -110,7 +111,7 @@ export function ProcessFromJSONTyped(json: any, ignoreDiscriminator: boolean): P
         
         'id': json['id'],
         'name': !exists(json, 'name') ? undefined : json['name'],
-        'description': !exists(json, 'description') ? undefined : json['description'],
+        'description': json['description'],
         'executor': !exists(json, 'executor') ? undefined : ExecutorFromJSON(json['executor']),
         'documentationUrl': !exists(json, 'documentationUrl') ? undefined : json['documentationUrl'],
         'fileRequirementsMessage': !exists(json, 'fileRequirementsMessage') ? undefined : json['fileRequirementsMessage'],