regenerate

Author: sruthymathew123

.gitignore

@@ -0,0 +1,15 @@
+# ref: https://github.com/github/gitignore/blob/master/Composer.gitignore
+
+composer.phar
+/vendor/
+
+# Commit your application's lock file https://getcomposer.org/doc/01-basic-usage.md#commit-your-composer-lock-file-to-version-control
+# You may choose to ignore a library lock file http://getcomposer.org/doc/02-libraries.md#lock-file
+# composer.lock
+
+# php-cs-fixer cache
+.php_cs.cache
+.php-cs-fixer.cache
+
+# PHPUnit cache
+.phpunit.result.cache

README.md

@@ -1,33 +1,31 @@
-# LORIS PHP API Client
-API for interacting with the LORIS Platform
+# OpenAPIClient-php
 
-This PHP package is automatically generated by the [OpenAPI Generator](https://github.com/OpenAPITools/openapi-generator) project:
+LORIS REST API for clinical data ingestion pipelines.
+Authentication via JWT - POST /login to get token, use as \"Bearer <token>\".
 
-- API version: 0.0.4
-- Build package: openapi-generator (php)
-- OpenAPI specification: [schema.yml](schema.yml)
 
-For more information, please visit [https://github.com/aces/Loris](https://github.com/aces/Loris)
+For more information, please visit [https://github.com/aces/loris](https://github.com/aces/loris).
 
-## Requirements
+## Installation & Usage
 
-PHP 8.1 and later
+### Requirements
+
+PHP 8.1 and later.
 
-## Installation & Usage
 ### Composer
 
-To install the bindings via [Composer](http://getcomposer.org/), add the following to `composer.json`:
+To install the bindings via [Composer](https://getcomposer.org/), add the following to `composer.json`:
 
 ```json
 {
   "repositories": [
     {
-      "type": "git",
-      "url": "https://github.com/aces/loris-php-client.git"
+      "type": "vcs",
+      "url": "https://github.com/aces/loris-php-api-client.git"
     }
   ],
   "require": {
-    "loris/php-client": "dev-main"
+    "aces/loris-php-api-client": "*@dev"
   }
 }
 ```
@@ -39,16 +37,8 @@ Then run `composer install`
 Download the files and include `autoload.php`:
 
 ```php
-require_once('/path/to/loris-php-client/vendor/autoload.php');
-```
-
-## Tests
-
-To run the unit tests:
-
-```bash
-composer install
-./vendor/bin/phpunit
+<?php
+require_once('/path/to/OpenAPIClient-php/vendor/autoload.php');
 ```
 
 ## Getting Started
@@ -59,137 +49,106 @@ Please follow the [installation procedure](#installation--usage) and then run th
 <?php
 require_once(__DIR__ . '/vendor/autoload.php');
 
-use LORISClient\Configuration;
-use LORISClient\Api\AuthenticationApi;
-use LORISClient\Api\ClinicalApi;
-use GuzzleHttp\Client;
 
-// Configure API client
-$config = Configuration::getDefaultConfiguration()
-    ->setHost('https://loris.example.com/api/v0.0.3');
 
-$httpClient = new Client(['verify' => true]);
 
-// Authenticate and get token
-$authApi = new AuthenticationApi($httpClient, $config);
+$apiInstance = new LORISClient\Api\AuthenticationApi(
+    // If you want use custom http client, pass your client which implements `GuzzleHttp\ClientInterface`.
+    // This is optional, `GuzzleHttp\Client` will be used as default.
+    new GuzzleHttp\Client()
+);
+$loginRequest = new \LORISClient\LORISClient\Model\LoginRequest(); // \LORISClient\LORISClient\Model\LoginRequest
 
 try {
-    $result = $authApi->authenticate([
-        'username' => 'your_username',
-        'password' => 'your_password'
-    ]);
-    
-    $token = $result['token'];
-    
-    // Configure API with token
-    $config->setAccessToken($token);
-    
-    // Use the Clinical API
-    $clinicalApi = new ClinicalApi($httpClient, $config);
-    
-    
+    $result = $apiInstance->login($loginRequest);
+    print_r($result);
 } catch (Exception $e) {
-    echo 'Exception: ', $e->getMessage(), PHP_EOL;
+    echo 'Exception when calling AuthenticationApi->login: ', $e->getMessage(), PHP_EOL;
 }
 
-?>
 ```
 
-## Documentation for API Endpoints
+## API Endpoints
 
-All URIs are relative to your LORIS instance API endpoint (e.g., *https://loris.example.com/api/v0.0.3*)
+All URIs are relative to *https://demo.loris.ca/api/v0.0.4-dev*
 
 Class | Method | HTTP request | Description
 ------------ | ------------- | ------------- | -------------
-*AuthenticationApi* | [**authenticate**](docs/Api/AuthenticationApi.md#authenticate) | **POST** /login | Authenticate and obtain JWT token
-*ClinicalApi* | [**getInstruments**](docs/Api/ClinicalApi.md#getinstruments) | **GET** /instruments | Get list of instruments
-*ClinicalApi* | [**getCandidates**](docs/Api/ClinicalApi.md#getcandidates) | **GET** /candidates | Get list of candidates
-*ClinicalApi* | [**createCandidate**](docs/Api/ClinicalApi.md#createcandidate) | **POST** /candidates | Create a new candidate
-*ClinicalApi* | [**getCandidate**](docs/Api/ClinicalApi.md#getcandidate) | **GET** /candidates/{candID} | Get candidate details
-*ClinicalApi* | [**getVisit**](docs/Api/ClinicalApi.md#getvisit) | **GET** /candidates/{candID}/{visitLabel} | Get visit information
-*ClinicalApi* | [**createTimepoint**](docs/Api/ClinicalApi.md#createtimepoint) | **PUT** /candidates/{candID}/{visitLabel} | Create timepoint/visit
-*ClinicalApi* | [**getInstrumentData**](docs/Api/ClinicalApi.md#getinstrumentdata) | **GET** /candidates/{candID}/{visitLabel}/instruments/{instrument} | Get instrument data
-*ClinicalApi* | [**uploadInstrumentData**](docs/Api/ClinicalApi.md#uploadinstrumentdata) | **PUT** /candidates/{candID}/{visitLabel}/instruments/{instrument} | Upload instrument data
-*ClinicalApi* | [**uploadInstrumentCSV**](docs/Api/ClinicalApi.md#uploadinstrumentcsv) | **POST** /instrument_manager/instrument_data | Bulk upload instrument data via CSV
-
-
-## Documentation For Models
-
-- [Authenticate200Response](docs/Model/Authenticate200Response.md)
-- [AuthenticateRequest](docs/Model/AuthenticateRequest.md)
-- [Candidate](docs/Model/Candidate.md)
-- [CandidateCreate](docs/Model/CandidateCreate.md)
-- [CandidateCreateCandidate](docs/Model/CandidateCreateCandidate.md)
-- [CandidateDetail](docs/Model/CandidateDetail.md)
-- [CreateCandidate201Response](docs/Model/CreateCandidate201Response.md)
-- [CreateCandidate201ResponseMeta](docs/Model/CreateCandidate201ResponseMeta.md)
-- [GetCandidates200Response](docs/Model/GetCandidates200Response.md)
-- [GetInstruments200Response](docs/Model/GetInstruments200Response.md)
-- [GetInstruments401Response](docs/Model/GetInstruments401Response.md)
-- [UploadInstrumentCSV200Response](docs/Model/UploadInstrumentCSV200Response.md)
-- [Visit](docs/Model/Visit.md)
-- [VisitCreate](docs/Model/VisitCreate.md)
-
-
-## Documentation For Authorization
-
-
-## BearerAuth
-
-- **Type**: HTTP Bearer Token authentication
-- **Bearer format**: JWT
-- **Description**: JWT token obtained from /login endpoint
-
-Example:
-```php
-$config = Configuration::getDefaultConfiguration()
-    ->setAccessToken('YOUR_JWT_TOKEN');
-```
-
-
-## Development
+*AuthenticationApi* | [**login**](docs/Api/AuthenticationApi.md#login) | **POST** /login | Authenticate and obtain JWT token
+*CandidatesApi* | [**createCandidate**](docs/Api/CandidatesApi.md#createcandidate) | **POST** /candidates | Create a new candidate
+*CandidatesApi* | [**getCandidate**](docs/Api/CandidatesApi.md#getcandidate) | **GET** /candidates/{candid} | Get candidate details
+*CandidatesApi* | [**getCandidates**](docs/Api/CandidatesApi.md#getcandidates) | **GET** /candidates | Get list of candidates
+*InstrumentManagerApi* | [**createInstrument**](docs/Api/InstrumentManagerApi.md#createinstrument) | **POST** /instrument_manager | Create instrument from LINST or REDCap data dictionary
+*InstrumentManagerApi* | [**getInstrumentDataHeaders**](docs/Api/InstrumentManagerApi.md#getinstrumentdataheaders) | **GET** /instrument_manager/instrument_data | Get expected CSV headers for instrument data
+*InstrumentManagerApi* | [**uploadInstrumentData**](docs/Api/InstrumentManagerApi.md#uploadinstrumentdata) | **POST** /instrument_manager/instrument_data | Bulk insert instrument data from CSV
+*InstrumentsApi* | [**getInstrumentData**](docs/Api/InstrumentsApi.md#getinstrumentdata) | **GET** /candidates/{candid}/{visit}/instruments/{instrument} | Get instrument data for a candidate/visit
+*InstrumentsApi* | [**getVisitInstruments**](docs/Api/InstrumentsApi.md#getvisitinstruments) | **GET** /candidates/{candid}/{visit}/instruments | Get instruments for a visit
+*InstrumentsApi* | [**patchInstrumentData**](docs/Api/InstrumentsApi.md#patchinstrumentdata) | **PATCH** /candidates/{candid}/{visit}/instruments/{instrument} | Update instrument data
+*InstrumentsApi* | [**putInstrumentData**](docs/Api/InstrumentsApi.md#putinstrumentdata) | **PUT** /candidates/{candid}/{visit}/instruments/{instrument} | Replace instrument data
+*ProjectsApi* | [**getProject**](docs/Api/ProjectsApi.md#getproject) | **GET** /projects/{project} | Get project details including instruments
+*ProjectsApi* | [**getProjectInstruments**](docs/Api/ProjectsApi.md#getprojectinstruments) | **GET** /projects/{project}/instruments | Get instruments for a project
+*ProjectsApi* | [**getProjects**](docs/Api/ProjectsApi.md#getprojects) | **GET** /projects | Get list of projects
+*SitesApi* | [**getSites**](docs/Api/SitesApi.md#getsites) | **GET** /sites | Get list of sites
+*VisitsApi* | [**createVisit**](docs/Api/VisitsApi.md#createvisit) | **PUT** /candidates/{candid}/{visit} | Create a new visit
+*VisitsApi* | [**getVisit**](docs/Api/VisitsApi.md#getvisit) | **GET** /candidates/{candid}/{visit} | Get visit details
+
+## Models
+
+- [CandidateCreateRequest](docs/Model/CandidateCreateRequest.md)
+- [CandidateCreateRequestCandidate](docs/Model/CandidateCreateRequestCandidate.md)
+- [CandidateObject](docs/Model/CandidateObject.md)
+- [CandidatesResponse](docs/Model/CandidatesResponse.md)
+- [ErrorResponse](docs/Model/ErrorResponse.md)
+- [IdMapping](docs/Model/IdMapping.md)
+- [InstrumentData](docs/Model/InstrumentData.md)
+- [InstrumentDataMeta](docs/Model/InstrumentDataMeta.md)
+- [InstrumentDataRequest](docs/Model/InstrumentDataRequest.md)
+- [InstrumentDataRequestMeta](docs/Model/InstrumentDataRequestMeta.md)
+- [InstrumentDataResponse](docs/Model/InstrumentDataResponse.md)
+- [InstrumentDataResponseMessage](docs/Model/InstrumentDataResponseMessage.md)
+- [InstrumentMeta](docs/Model/InstrumentMeta.md)
+- [InstrumentsResponse](docs/Model/InstrumentsResponse.md)
+- [LoginRequest](docs/Model/LoginRequest.md)
+- [LoginResponse](docs/Model/LoginResponse.md)
+- [ProjectResponse](docs/Model/ProjectResponse.md)
+- [ProjectResponseMeta](docs/Model/ProjectResponseMeta.md)
+- [ProjectsResponse](docs/Model/ProjectsResponse.md)
+- [Site](docs/Model/Site.md)
+- [SitesResponse](docs/Model/SitesResponse.md)
+- [StageObject](docs/Model/StageObject.md)
+- [SuccessResponse](docs/Model/SuccessResponse.md)
+- [VisitCreateRequest](docs/Model/VisitCreateRequest.md)
+- [VisitInstrumentsResponse](docs/Model/VisitInstrumentsResponse.md)
+- [VisitInstrumentsResponseMeta](docs/Model/VisitInstrumentsResponseMeta.md)
+- [VisitObject](docs/Model/VisitObject.md)
+- [VisitObjectMeta](docs/Model/VisitObjectMeta.md)
+- [VisitObjectStages](docs/Model/VisitObjectStages.md)
+
+## Authorization
+
+Authentication schemes defined for the API:
+### BearerAuth
+
+- **Type**: Bearer authentication (JWT)
 
-This client is generated from the OpenAPI specification using OpenAPI Generator.
-
-To regenerate the client:
-
-```bash
-./generate.sh
-```
+## Tests
 
-Or manually:
+To run the tests, use:
 
 ```bash
-openapi-generator-cli generate \
-  -i schema.yml \
-  -g php \
-  -o . \
-  -c openapi-config.json \
-  --additional-properties=composerPackageName=loris/php-client
-```
-
-## API Version Compatibility
-
-This client supports LORIS API versions:
-- v0.0.3
-- v0.0.4
-
-Configure the version in the base URL:
-```php
-$config->setHost('https://loris.example.com/api/v0.0.3');
+composer install
+vendor/bin/phpunit
 ```
 
-## Contributing
-
-Issues and pull requests are welcome on [GitHub](https://github.com/aces/loris-php-client).
+## Author
 
-## License
 
-[GPL-3.0](LICENSE)
 
-## Related Projects
+## About this package
 
-- [LORIS](https://github.com/aces/Loris) - Longitudinal Online Research and Imaging System
-## Author
+This PHP package is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
 
-The LORIS Team
+- API version: `0.0.4-dev`
+    - Package version: `0.0.4-dev`
+    - Generator version: `7.17.0`
+- Build package: `org.openapitools.codegen.languages.PhpClientCodegen`

composer.json

@@ -1,6 +1,7 @@
 {
-    "name": "loris/php-client",
-    "description": "LORIS (Longitudinal Online Research and Imaging System) REST API for managing clinical neuroimaging and behavioral research data.",
+    "name": "aces/loris-php-api-client",
+    "version": "0.0.4-dev",
+    "description": "LORIS REST API for clinical data ingestion pipelines. Authentication via JWT - POST /login to get token, use as \"Bearer <token>\".",
     "keywords": [
         "openapitools",
         "openapi-generator",

docs/Api/AuthenticationApi.md

@@ -1,24 +1,22 @@
 # LORISClient\AuthenticationApi
 
-Authentication and token management
+Login and JWT token
 
-All URIs are relative to https://localhost/api/v0.0.4, except if the operation defines another base path.
+All URIs are relative to https://demo.loris.ca/api/v0.0.4-dev, except if the operation defines another base path.
 
 | Method | HTTP request | Description |
 | ------------- | ------------- | ------------- |
-| [**authenticate()**](AuthenticationApi.md#authenticate) | **POST** /login | Authenticate and obtain JWT token |
+| [**login()**](AuthenticationApi.md#login) | **POST** /login | Authenticate and obtain JWT token |
 
 
-## `authenticate()`
+## `login()`
 
 ```php
-authenticate($authenticateRequest): \LORISClient\LORISClient\Model\Authenticate200Response
+login($loginRequest): \LORISClient\LORISClient\Model\LoginResponse
 ```
 
 Authenticate and obtain JWT token
 
-Login to LORIS API with username and password credentials
-
 ### Example
 
 ```php
@@ -32,25 +30,25 @@ $apiInstance = new LORISClient\Api\AuthenticationApi(
     // This is optional, `GuzzleHttp\Client` will be used as default.
     new GuzzleHttp\Client()
 );
-$authenticateRequest = new \LORISClient\LORISClient\Model\AuthenticateRequest(); // \LORISClient\LORISClient\Model\AuthenticateRequest
+$loginRequest = new \LORISClient\LORISClient\Model\LoginRequest(); // \LORISClient\LORISClient\Model\LoginRequest
 
 try {
-    $result = $apiInstance->authenticate($authenticateRequest);
+    $result = $apiInstance->login($loginRequest);
     print_r($result);
 } catch (Exception $e) {
-    echo 'Exception when calling AuthenticationApi->authenticate: ', $e->getMessage(), PHP_EOL;
+    echo 'Exception when calling AuthenticationApi->login: ', $e->getMessage(), PHP_EOL;
 }
 ```
 
 ### Parameters
 
 | Name | Type | Description  | Notes |
 | ------------- | ------------- | ------------- | ------------- |
-| **authenticateRequest** | [**\LORISClient\LORISClient\Model\AuthenticateRequest**](../Model/AuthenticateRequest.md)|  | |
+| **loginRequest** | [**\LORISClient\LORISClient\Model\LoginRequest**](../Model/LoginRequest.md)|  | |
 
 ### Return type
 
-[**\LORISClient\LORISClient\Model\Authenticate200Response**](../Model/Authenticate200Response.md)
+[**\LORISClient\LORISClient\Model\LoginResponse**](../Model/LoginResponse.md)
 
 ### Authorization