@cirrobio/api-client 0.1.8 → 0.1.10

package/.openapi-generator/FILES

@@ -46,6 +46,7 @@ src/models/ErrorMessage.ts
 src/models/Executor.ts
 src/models/FileAccessRequest.ts
 src/models/FileEntry.ts
+src/models/FileMappingRule.ts
 src/models/FileNamePattern.ts
 src/models/FileRequirements.ts
 src/models/FormSchema.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@0.1.8 --save
+npm install @cirrobio/api-client@0.1.10 --save
 ```
 
 _unPublished (not recommended):_

package/dist/models/Executor.d.ts

@@ -17,7 +17,8 @@
 export declare enum Executor {
     Ingest = "INGEST",
     Nextflow = "NEXTFLOW",
-    Cromwell = "CROMWELL"
+    Cromwell = "CROMWELL",
+    OmicsReady2Run = "OMICS_READY2RUN"
 }
 export declare function ExecutorFromJSON(json: any): Executor;
 export declare function ExecutorFromJSONTyped(json: any, ignoreDiscriminator: boolean): Executor;

package/dist/models/Executor.js

@@ -24,6 +24,7 @@ var Executor;
     Executor["Ingest"] = "INGEST";
     Executor["Nextflow"] = "NEXTFLOW";
     Executor["Cromwell"] = "CROMWELL";
+    Executor["OmicsReady2Run"] = "OMICS_READY2RUN";
 })(Executor = exports.Executor || (exports.Executor = {}));
 function ExecutorFromJSON(json) {
     return ExecutorFromJSONTyped(json, false);

package/dist/models/FileMappingRule.d.ts

@@ -0,0 +1,56 @@
+/**
+ * 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 type { FileNamePattern } from './FileNamePattern';
+/**
+ *
+ * @export
+ * @interface FileMappingRule
+ */
+export interface FileMappingRule {
+    /**
+     * Describes the group of possible files that meet a single file type criteria.
+     * @type {string}
+     * @memberof FileMappingRule
+     */
+    description: string;
+    /**
+     * Minimum number of files to expect for the file type group.
+     * @type {number}
+     * @memberof FileMappingRule
+     */
+    min?: number;
+    /**
+     * Maximum number of files to expect for the file type group.
+     * @type {number}
+     * @memberof FileMappingRule
+     */
+    max?: number;
+    /**
+     * Specifies if the file type will be associated with a sample.
+     * @type {boolean}
+     * @memberof FileMappingRule
+     */
+    isSample?: boolean;
+    /**
+     * Describes the possible file patterns to expect for the file type group.
+     * @type {Array<FileNamePattern>}
+     * @memberof FileMappingRule
+     */
+    fileNamePatterns: Array<FileNamePattern>;
+}
+/**
+ * Check if a given object implements the FileMappingRule interface.
+ */
+export declare function instanceOfFileMappingRule(value: object): boolean;
+export declare function FileMappingRuleFromJSON(json: any): FileMappingRule;
+export declare function FileMappingRuleFromJSONTyped(json: any, ignoreDiscriminator: boolean): FileMappingRule;
+export declare function FileMappingRuleToJSON(value?: FileMappingRule | null): any;

package/dist/models/FileMappingRule.js

@@ -0,0 +1,61 @@
+"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.FileMappingRuleToJSON = exports.FileMappingRuleFromJSONTyped = exports.FileMappingRuleFromJSON = exports.instanceOfFileMappingRule = void 0;
+var runtime_1 = require("../runtime");
+var FileNamePattern_1 = require("./FileNamePattern");
+/**
+ * Check if a given object implements the FileMappingRule interface.
+ */
+function instanceOfFileMappingRule(value) {
+    var isInstance = true;
+    isInstance = isInstance && "description" in value;
+    isInstance = isInstance && "fileNamePatterns" in value;
+    return isInstance;
+}
+exports.instanceOfFileMappingRule = instanceOfFileMappingRule;
+function FileMappingRuleFromJSON(json) {
+    return FileMappingRuleFromJSONTyped(json, false);
+}
+exports.FileMappingRuleFromJSON = FileMappingRuleFromJSON;
+function FileMappingRuleFromJSONTyped(json, ignoreDiscriminator) {
+    if ((json === undefined) || (json === null)) {
+        return json;
+    }
+    return {
+        'description': json['description'],
+        'min': !(0, runtime_1.exists)(json, 'min') ? undefined : json['min'],
+        'max': !(0, runtime_1.exists)(json, 'max') ? undefined : json['max'],
+        'isSample': !(0, runtime_1.exists)(json, 'isSample') ? undefined : json['isSample'],
+        'fileNamePatterns': (json['fileNamePatterns'].map(FileNamePattern_1.FileNamePatternFromJSON)),
+    };
+}
+exports.FileMappingRuleFromJSONTyped = FileMappingRuleFromJSONTyped;
+function FileMappingRuleToJSON(value) {
+    if (value === undefined) {
+        return undefined;
+    }
+    if (value === null) {
+        return null;
+    }
+    return {
+        'description': value.description,
+        'min': value.min,
+        'max': value.max,
+        'isSample': value.isSample,
+        'fileNamePatterns': (value.fileNamePatterns.map(FileNamePattern_1.FileNamePatternToJSON)),
+    };
+}
+exports.FileMappingRuleToJSON = FileMappingRuleToJSON;

package/dist/models/FileNamePattern.d.ts

@@ -16,17 +16,23 @@
  */
 export interface FileNamePattern {
     /**
-     *
+     * User-readable name for the file type used for display.
      * @type {string}
      * @memberof FileNamePattern
      */
     exampleName: string;
     /**
-     *
+     * File description.
      * @type {string}
      * @memberof FileNamePattern
      */
     description: string;
+    /**
+     * File name pattern, formatted as a valid regex, to extract sample name and other metadata.
+     * @type {string}
+     * @memberof FileNamePattern
+     */
+    sampleMatchingPattern: string;
 }
 /**
  * Check if a given object implements the FileNamePattern interface.

package/dist/models/FileNamePattern.js

@@ -21,6 +21,7 @@ function instanceOfFileNamePattern(value) {
     var isInstance = true;
     isInstance = isInstance && "exampleName" in value;
     isInstance = isInstance && "description" in value;
+    isInstance = isInstance && "sampleMatchingPattern" in value;
     return isInstance;
 }
 exports.instanceOfFileNamePattern = instanceOfFileNamePattern;
@@ -35,6 +36,7 @@ function FileNamePatternFromJSONTyped(json, ignoreDiscriminator) {
     return {
         'exampleName': json['exampleName'],
         'description': json['description'],
+        'sampleMatchingPattern': json['sampleMatchingPattern'],
     };
 }
 exports.FileNamePatternFromJSONTyped = FileNamePatternFromJSONTyped;
@@ -48,6 +50,7 @@ function FileNamePatternToJSON(value) {
     return {
         'exampleName': value.exampleName,
         'description': value.description,
+        'sampleMatchingPattern': value.sampleMatchingPattern,
     };
 }
 exports.FileNamePatternToJSON = FileNamePatternToJSON;

package/dist/models/ProcessDetail.d.ts

@@ -11,6 +11,7 @@
  */
 import type { CustomPipelineSettings } from './CustomPipelineSettings';
 import type { Executor } from './Executor';
+import type { FileMappingRule } from './FileMappingRule';
 import type { PipelineCode } from './PipelineCode';
 /**
  *
@@ -108,6 +109,12 @@ export interface ProcessDetail {
      * @memberof ProcessDetail
      */
     isArchived?: boolean;
+    /**
+     * Describes the files that this dataset type expects.
+     * @type {Array<FileMappingRule>}
+     * @memberof ProcessDetail
+     */
+    fileMappingRules?: Array<FileMappingRule> | null;
 }
 /**
  * Check if a given object implements the ProcessDetail interface.

package/dist/models/ProcessDetail.js

@@ -17,6 +17,7 @@ exports.ProcessDetailToJSON = exports.ProcessDetailFromJSONTyped = exports.Proce
 var runtime_1 = require("../runtime");
 var CustomPipelineSettings_1 = require("./CustomPipelineSettings");
 var Executor_1 = require("./Executor");
+var FileMappingRule_1 = require("./FileMappingRule");
 var PipelineCode_1 = require("./PipelineCode");
 /**
  * Check if a given object implements the ProcessDetail interface.
@@ -57,6 +58,7 @@ function ProcessDetailFromJSONTyped(json, ignoreDiscriminator) {
         'allowMultipleSources': !(0, runtime_1.exists)(json, 'allowMultipleSources') ? undefined : json['allowMultipleSources'],
         '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)),
     };
 }
 exports.ProcessDetailFromJSONTyped = ProcessDetailFromJSONTyped;
@@ -83,6 +85,7 @@ function ProcessDetailToJSON(value) {
         'allowMultipleSources': value.allowMultipleSources,
         '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)),
     };
 }
 exports.ProcessDetailToJSON = ProcessDetailToJSON;

package/dist/models/index.d.ts

@@ -26,6 +26,7 @@ export * from './ErrorMessage';
 export * from './Executor';
 export * from './FileAccessRequest';
 export * from './FileEntry';
+export * from './FileMappingRule';
 export * from './FileNamePattern';
 export * from './FileRequirements';
 export * from './FormSchema';

package/dist/models/index.js

@@ -44,6 +44,7 @@ __exportStar(require("./ErrorMessage"), exports);
 __exportStar(require("./Executor"), exports);
 __exportStar(require("./FileAccessRequest"), exports);
 __exportStar(require("./FileEntry"), exports);
+__exportStar(require("./FileMappingRule"), exports);
 __exportStar(require("./FileNamePattern"), exports);
 __exportStar(require("./FileRequirements"), exports);
 __exportStar(require("./FormSchema"), exports);

package/dist/runtime.js

@@ -76,7 +76,7 @@ var __generator = (this && this.__generator) || function (thisArg, body) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.TextApiResponse = exports.BlobApiResponse = exports.VoidApiResponse = exports.JSONApiResponse = exports.canConsumeForm = exports.mapValues = exports.querystring = exports.exists = exports.COLLECTION_FORMATS = exports.RequiredError = exports.FetchError = exports.ResponseError = exports.BaseAPI = exports.DefaultConfig = exports.Configuration = exports.BASE_PATH = void 0;
-exports.BASE_PATH = "http://localhost:8080/api".replace(/\/+$/, "");
+exports.BASE_PATH = "https://dev.cirro.bio/api".replace(/\/+$/, "");
 var Configuration = /** @class */ (function () {
     function Configuration(configuration) {
         if (configuration === void 0) { configuration = {}; }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cirrobio/api-client",
-  "version": "0.1.8",
+  "version": "0.1.10",
   "description": "API client for Cirro",
   "author": "CirroBio",
   "repository": {

package/src/models/Executor.ts

@@ -20,7 +20,8 @@
 export enum Executor {
     Ingest = 'INGEST',
     Nextflow = 'NEXTFLOW',
-    Cromwell = 'CROMWELL'
+    Cromwell = 'CROMWELL',
+    OmicsReady2Run = 'OMICS_READY2RUN'
 }
 
 

package/src/models/FileMappingRule.ts

@@ -0,0 +1,106 @@
+/* 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 { FileNamePattern } from './FileNamePattern';
+import {
+    FileNamePatternFromJSON,
+    FileNamePatternFromJSONTyped,
+    FileNamePatternToJSON,
+} from './FileNamePattern';
+
+/**
+ * 
+ * @export
+ * @interface FileMappingRule
+ */
+export interface FileMappingRule {
+    /**
+     * Describes the group of possible files that meet a single file type criteria.
+     * @type {string}
+     * @memberof FileMappingRule
+     */
+    description: string;
+    /**
+     * Minimum number of files to expect for the file type group.
+     * @type {number}
+     * @memberof FileMappingRule
+     */
+    min?: number;
+    /**
+     * Maximum number of files to expect for the file type group.
+     * @type {number}
+     * @memberof FileMappingRule
+     */
+    max?: number;
+    /**
+     * Specifies if the file type will be associated with a sample.
+     * @type {boolean}
+     * @memberof FileMappingRule
+     */
+    isSample?: boolean;
+    /**
+     * Describes the possible file patterns to expect for the file type group.
+     * @type {Array<FileNamePattern>}
+     * @memberof FileMappingRule
+     */
+    fileNamePatterns: Array<FileNamePattern>;
+}
+
+/**
+ * Check if a given object implements the FileMappingRule interface.
+ */
+export function instanceOfFileMappingRule(value: object): boolean {
+    let isInstance = true;
+    isInstance = isInstance && "description" in value;
+    isInstance = isInstance && "fileNamePatterns" in value;
+
+    return isInstance;
+}
+
+export function FileMappingRuleFromJSON(json: any): FileMappingRule {
+    return FileMappingRuleFromJSONTyped(json, false);
+}
+
+export function FileMappingRuleFromJSONTyped(json: any, ignoreDiscriminator: boolean): FileMappingRule {
+    if ((json === undefined) || (json === null)) {
+        return json;
+    }
+    return {
+        
+        'description': json['description'],
+        'min': !exists(json, 'min') ? undefined : json['min'],
+        'max': !exists(json, 'max') ? undefined : json['max'],
+        'isSample': !exists(json, 'isSample') ? undefined : json['isSample'],
+        'fileNamePatterns': ((json['fileNamePatterns'] as Array<any>).map(FileNamePatternFromJSON)),
+    };
+}
+
+export function FileMappingRuleToJSON(value?: FileMappingRule | null): any {
+    if (value === undefined) {
+        return undefined;
+    }
+    if (value === null) {
+        return null;
+    }
+    return {
+        
+        'description': value.description,
+        'min': value.min,
+        'max': value.max,
+        'isSample': value.isSample,
+        'fileNamePatterns': ((value.fileNamePatterns as Array<any>).map(FileNamePatternToJSON)),
+    };
+}
+

package/src/models/FileNamePattern.ts

@@ -20,17 +20,23 @@ import { exists, mapValues } from '../runtime';
  */
 export interface FileNamePattern {
     /**
-     * 
+     * User-readable name for the file type used for display.
      * @type {string}
      * @memberof FileNamePattern
      */
     exampleName: string;
     /**
-     * 
+     * File description.
      * @type {string}
      * @memberof FileNamePattern
      */
     description: string;
+    /**
+     * File name pattern, formatted as a valid regex, to extract sample name and other metadata.
+     * @type {string}
+     * @memberof FileNamePattern
+     */
+    sampleMatchingPattern: string;
 }
 
 /**
@@ -40,6 +46,7 @@ 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;
 }
@@ -56,6 +63,7 @@ export function FileNamePatternFromJSONTyped(json: any, ignoreDiscriminator: boo
         
         'exampleName': json['exampleName'],
         'description': json['description'],
+        'sampleMatchingPattern': json['sampleMatchingPattern'],
     };
 }
 
@@ -70,6 +78,7 @@ export function FileNamePatternToJSON(value?: FileNamePattern | null): any {
         
         'exampleName': value.exampleName,
         'description': value.description,
+        'sampleMatchingPattern': value.sampleMatchingPattern,
     };
 }
 

package/src/models/ProcessDetail.ts

@@ -25,6 +25,12 @@ import {
     ExecutorFromJSONTyped,
     ExecutorToJSON,
 } from './Executor';
+import type { FileMappingRule } from './FileMappingRule';
+import {
+    FileMappingRuleFromJSON,
+    FileMappingRuleFromJSONTyped,
+    FileMappingRuleToJSON,
+} from './FileMappingRule';
 import type { PipelineCode } from './PipelineCode';
 import {
     PipelineCodeFromJSON,
@@ -128,6 +134,12 @@ export interface ProcessDetail {
      * @memberof ProcessDetail
      */
     isArchived?: boolean;
+    /**
+     * Describes the files that this dataset type expects.
+     * @type {Array<FileMappingRule>}
+     * @memberof ProcessDetail
+     */
+    fileMappingRules?: Array<FileMappingRule> | null;
 }
 
 /**
@@ -171,6 +183,7 @@ export function ProcessDetailFromJSONTyped(json: any, ignoreDiscriminator: boole
         'allowMultipleSources': !exists(json, 'allowMultipleSources') ? undefined : json['allowMultipleSources'],
         '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)),
     };
 }
 
@@ -198,6 +211,7 @@ export function ProcessDetailToJSON(value?: ProcessDetail | null): any {
         'allowMultipleSources': value.allowMultipleSources,
         '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/index.ts

@@ -28,6 +28,7 @@ export * from './ErrorMessage';
 export * from './Executor';
 export * from './FileAccessRequest';
 export * from './FileEntry';
+export * from './FileMappingRule';
 export * from './FileNamePattern';
 export * from './FileRequirements';
 export * from './FormSchema';

package/src/runtime.ts

@@ -13,7 +13,7 @@
  */
 
 
-export const BASE_PATH = "http://localhost:8080/api".replace(/\/+$/, "");
+export const BASE_PATH = "https://dev.cirro.bio/api".replace(/\/+$/, "");
 
 export interface ConfigurationParameters {
     basePath?: string; // override base path