UploadController.php

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<?php
/*
 SPDX-FileCopyrightText: © 2018, 2020 Siemens AG
 SPDX-FileContributor: Gaurav Mishra <mishra.gaurav@siemens.com>
 SPDX-FileCopyrightText: © 2022 Soham Banerjee <sohambanerjee4abc@hotmail.com>
 SPDX-FileCopyrightText: © 2022, 2023 Samuel Dushimimana <dushsam100@gmail.com>
 SPDX-FileContributor: Kaushlendra Pratap <kaushlendra-pratap.singh@siemens.com>
 
 SPDX-License-Identifier: GPL-2.0-only
*/
 
namespace Fossology\UI\Api\Controllers;
 
use Fossology\DelAgent\UI\DeleteMessages;
use Fossology\Lib\Auth\Auth;
use Fossology\Lib\BusinessRules\ReuseReportProcessor;
use Fossology\Lib\Dao\AgentDao;
use Fossology\Lib\Dao\ClearingDao;
use Fossology\Lib\Dao\LicenseDao;
use Fossology\Lib\Data\AgentRef;
use Fossology\Lib\Data\UploadStatus;
use Fossology\Lib\Exception;
use Fossology\Lib\Proxy\ScanJobProxy;
use Fossology\Lib\Proxy\UploadBrowseProxy;
use Fossology\Lib\Proxy\UploadTreeProxy;
use Fossology\UI\Api\Exceptions\HttpBadRequestException;
use Fossology\UI\Api\Exceptions\HttpErrorException;
use Fossology\UI\Api\Exceptions\HttpForbiddenException;
use Fossology\UI\Api\Exceptions\HttpInternalServerErrorException;
use Fossology\UI\Api\Exceptions\HttpNotFoundException;
use Fossology\UI\Api\Exceptions\HttpPreconditionFailException;
use Fossology\UI\Api\Exceptions\HttpServiceUnavailableException;
use Fossology\UI\Api\Helper\ResponseHelper;
use Fossology\UI\Api\Helper\UploadHelper;
use Fossology\UI\Api\Models\Agent;
use Fossology\UI\Api\Models\ApiVersion;
use Fossology\UI\Api\Models\EditedLicense;
use Fossology\UI\Api\Models\GroupPermission;
use Fossology\UI\Api\Models\Info;
use Fossology\UI\Api\Models\InfoType;
use Fossology\UI\Api\Models\License;
use Fossology\UI\Api\Models\Obligation;
use Fossology\UI\Api\Models\Permissions;
use Fossology\UI\Api\Models\ScannedLicense;
use Fossology\UI\Api\Models\SuccessfulAgent;
use Psr\Http\Message\ServerRequestInterface;
use Slim\Psr7\Factory\StreamFactory;
 
class UploadController extends RestController
{
 
  const AGENT_PARAM = "agent";
 
  const FOLDER_PARAM = "folderId";
 
  const RECURSIVE_PARAM = "recursive";
 
  const FILTER_NAME = "name";
 
  const FILTER_STATUS = "status";
 
  const FILTER_ASSIGNEE = "assignee";
 
  const FILTER_DATE = "since";
 
  const PAGE_PARAM = "page";
 
  const LIMIT_PARAM = "limit";
 
  const UPLOAD_FETCH_LIMIT = 100;
 
  const CONTAINER_PARAM = "containers";
 
  const VALID_STATUS = ["open", "inprogress", "closed", "rejected"];
 
  private $agentNames = AgentRef::AGENT_LIST;
 
  private $agentDao;
 
  public function __construct($container)
  {
    parent::__construct($container);
    $groupId = $this->restHelper->getGroupId();
    $dbManager = $this->dbHelper->getDbManager();
    $this->agentDao = $this->container->get('dao.agent');
    $uploadBrowseProxy = new UploadBrowseProxy($groupId, 0, $dbManager, false);
    $uploadBrowseProxy->sanity();
  }
 
  public function getUploads($request, $response, $args)
  {
    $id = null;
    $folderId = null;
    $recursive = true;
    $query = $request->getQueryParams();
    $name = null;
    $status = null;
    $assignee = null;
    $since = null;
    $apiVersion = ApiVersion::getVersion($request);
 
    if (array_key_exists(self::FOLDER_PARAM, $query)) {
      $folderId = filter_var($query[self::FOLDER_PARAM], FILTER_VALIDATE_INT);
      if (! $this->restHelper->getFolderDao()->isFolderAccessible($folderId,
        $this->restHelper->getUserId())) {
        throw new HttpNotFoundException("Folder does not exist");
      }
    }
 
    if (array_key_exists(self::RECURSIVE_PARAM, $query)) {
      $recursive = filter_var($query[self::RECURSIVE_PARAM],
        FILTER_VALIDATE_BOOLEAN);
    }
    if (array_key_exists(self::FILTER_NAME, $query)) {
      $name = $query[self::FILTER_NAME];
    }
    if (array_key_exists(self::FILTER_STATUS, $query)) {
      switch (strtolower($query[self::FILTER_STATUS])) {
        case "open":
          $status = UploadStatus::OPEN;
          break;
        case "inprogress":
          $status = UploadStatus::IN_PROGRESS;
          break;
        case "closed":
          $status = UploadStatus::CLOSED;
          break;
        case "rejected":
          $status = UploadStatus::REJECTED;
          break;
        default:
          $status = null;
      }
    }
    if (array_key_exists(self::FILTER_ASSIGNEE, $query)) {
      $username = $query[self::FILTER_ASSIGNEE];
      if (strcasecmp($username, "-me-") === 0) {
        $assignee = $this->restHelper->getUserId();
      } elseif (strcasecmp($username, "-unassigned-") === 0) {
        $assignee = 1;
      } else {
        $assignee = $this->restHelper->getUserDao()->getUserByName($username);
        if (empty($assignee)) {
          throw new HttpNotFoundException("No user with user name '$username'");
        }
        $assignee = $assignee['user_pk'];
      }
    }
    if (array_key_exists(self::FILTER_DATE, $query)) {
      $date = filter_var($query[self::FILTER_DATE], FILTER_VALIDATE_REGEXP,
        ["options" => [
          "regexp" => "/^\d{4}\-\d{2}\-\d{2}$/",
          "flags" => FILTER_NULL_ON_FAILURE
        ]]);
      $since = strtotime($date);
    }
    if ($apiVersion == ApiVersion::V2) {
      $page = $query[self::PAGE_PARAM] ?? "";
      $limit = $query[self::LIMIT_PARAM] ?? "";
    } else {
      $page = $request->getHeaderLine(self::PAGE_PARAM);
      $limit = $request->getHeaderLine(self::LIMIT_PARAM);
    }
    if (! empty($page) || $page == "0") {
      $page = filter_var($page, FILTER_VALIDATE_INT);
      if ($page <= 0) {
        throw new HttpBadRequestException(
          "page should be positive integer > 0");
      }
    } else {
      $page = 1;
    }
    if (! empty($limit)) {
      $limit = filter_var($limit, FILTER_VALIDATE_INT);
      if ($limit < 1) {
        throw new HttpBadRequestException(
          "limit should be positive integer > 1");
      }
    } else {
      $limit = self::UPLOAD_FETCH_LIMIT;
    }
 
    if (isset($args['id'])) {
      $id = intval($args['id']);
      $this->uploadAccessible($id);
      $this->isAdj2nestDone($id);
    }
    $options = [
      "folderId" => $folderId,
      "name"     => $name,
      "status"   => $status,
      "assignee" => $assignee,
      "since"    => $since
    ];
    list($pages, $uploads) = $this->dbHelper->getUploads(
      $this->restHelper->getUserId(), $this->restHelper->getGroupId(), $limit,
      $page, $id, $options, $recursive, $apiVersion);
    if ($id !== null && ! empty($uploads)) {
      $uploads = $uploads[0];
      $pages = 1;
    }
    return $response->withHeader("X-Total-Pages", $pages)->withJson($uploads,
      200);
  }
 
  public function uploadDownload($request, $response, $args)
  {
    $ui_download = $this->restHelper->getPlugin('download');
    $id = null;
 
    if (isset($args['id'])) {
      $id = intval($args['id']);
      $this->uploadAccessible($id);
    }
    $dbManager = $this->restHelper->getDbHelper()->getDbManager();
    $uploadDao = $this->restHelper->getUploadDao();
    $uploadTreeTableName = $uploadDao->getUploadtreeTableName($id);
    $itemTreeBounds = $uploadDao->getParentItemBounds($id,$uploadTreeTableName);
    $sql =  "SELECT pfile_fk , ufile_name FROM uploadtree_a WHERE uploadtree_pk=$1";
    $params = array($itemTreeBounds->getItemId());
    $descendants = $dbManager->getSingleRow($sql,$params);
    $path= RepPath(($descendants['pfile_fk']));
    $responseFile = $ui_download->getDownload($path, $descendants['ufile_name']);
    $responseContent = $responseFile->getFile();
    $newResponse = $response->withHeader('Content-Description',
        'File Transfer')
        ->withHeader('Content-Type',
        $responseContent->getMimeType())
        ->withHeader('Content-Disposition',
        $responseFile->headers->get('Content-Disposition'))
        ->withHeader('Cache-Control', 'must-revalidate')
        ->withHeader('Pragma', 'private')
        ->withHeader('Content-Length', filesize($responseContent->getPathname()));
    $sf = new StreamFactory();
    return $newResponse->withBody(
      $sf->createStreamFromFile($responseContent->getPathname())
    );
  }
 
  public function getUploadSummary($request, $response, $args)
  {
    $id = intval($args['id']);
    $query = $request->getQueryParams();
    $selectedAgentId = $query['agentId'] ?? null;
    $agentDao = $this->container->get('dao.agent');
    $this->uploadAccessible($id);
    if ($selectedAgentId !== null && !$this->dbHelper->doesIdExist("agent", "agent_pk", $selectedAgentId)) {
      throw new HttpNotFoundException("Agent does not exist");
    }
    $this->isAdj2nestDone($id);
    $uploadHelper = new UploadHelper();
    $uploadSummary = $uploadHelper->generateUploadSummary($id, $this->restHelper->getGroupId());
    $browseLicense = $this->restHelper->getPlugin('license');
    $uploadDao = $this->restHelper->getUploadDao();
    $uploadTreeTableName = $uploadDao->getUploadtreeTableName($id);
    $itemTreeBounds = $uploadDao->getParentItemBounds($id, $uploadTreeTableName);
    $scanJobProxy = new ScanJobProxy($agentDao, $id);
    $scannerAgents = array_keys(AgentRef::AGENT_LIST);
    $scanJobProxy->createAgentStatus($scannerAgents);
    $selectedAgentIds = empty($selectedAgentId) ? $scanJobProxy->getLatestSuccessfulAgentIds() : $selectedAgentId;
    $res = $browseLicense->createLicenseHistogram("", "", $itemTreeBounds, $selectedAgentIds, $this->restHelper->getGroupId());
    $uploadSummary->setUniqueConcludedLicenses($res['editedUniqueLicenseCount']);
    $uploadSummary->setTotalConcludedLicenses($res['editedLicenseCount']);
    $uploadSummary->setTotalLicenses($res['scannerLicenseCount']);
    $uploadSummary->setUniqueLicenses($res['uniqueLicenseCount']);
    $uploadSummary->setConcludedNoLicenseFoundCount($res['editedNoLicenseFoundCount']);
    $uploadSummary->setFileCount($res['fileCount']);
    $uploadSummary->setNoScannerLicenseFoundCount($res['noScannerLicenseFoundCount']);
    $uploadSummary->setScannerUniqueLicenseCount($res['scannerUniqueLicenseCount']);
 
    return $response->withJson($uploadSummary->getArray(), 200);
  }
 
  public function deleteUpload($request, $response, $args)
  {
    require_once dirname(__DIR__, 4) . "/delagent/ui/delete-helper.php";
    $id = intval($args['id']);
 
    $this->uploadAccessible($id);
    $result = TryToDelete($id, $this->restHelper->getUserId(),
      $this->restHelper->getGroupId(), $this->restHelper->getUploadDao());
    if ($result->getDeleteMessageCode() !== DeleteMessages::SUCCESS) {
      throw new HttpInternalServerErrorException(
        $result->getDeleteMessageString());
    }
    $returnVal = new Info(202, "Delete Job for file with id " . $id,
      InfoType::INFO);
    return $response->withJson($returnVal->getArray(), $returnVal->getCode());
  }
 
  public function moveUpload($request, $response, $args)
  {
    if (ApiVersion::getVersion($request) == ApiVersion::V2) {
      $queryParams = $request->getQueryParams();
      $action = $queryParams['action'] ?? "";
    } else {
      $action = $request->getHeaderLine('action');
    }
    if (strtolower($action) == "move") {
      $copy = false;
    } else {
      $copy = true;
    }
    return $this->changeUpload($request, $response, $args, $copy);
  }
 
  private function changeUpload($request, $response, $args, $isCopy)
  {
    $queryParams = $request->getQueryParams();
    $isApiVersionV2 = (ApiVersion::getVersion($request) == ApiVersion::V2);
    $paramType = ($isApiVersionV2) ? 'parameter' : 'header';
 
    if ((!$isApiVersionV2 && !$request->hasHeader('folderId') || $isApiVersionV2 && !isset($queryParams['folderId']))
    || !is_numeric($newFolderID = ($isApiVersionV2 ? $queryParams['folderId'] : $request->getHeaderLine('folderId')))) {
      throw new HttpBadRequestException("For API version " . ($isApiVersionV2 ? 'V2' : 'V1') . ", 'folderId' $paramType should be present and an integer.");
    }
 
    $id = intval($args['id']);
    $returnVal = $this->restHelper->copyUpload($id, $newFolderID, $isCopy);
    return $response->withJson($returnVal->getArray(), $returnVal->getCode());
  }
 
  public function postUpload($request, $response, $args)
  {
    $reqBody = $this->getParsedBody($request);
    if (ApiVersion::getVersion($request) == ApiVersion::V2) {
      $uploadType = $reqBody['uploadType'] ?? null;
      $folderId = $reqBody['folderId'] ?? null;
      $description = $reqBody['uploadDescription'] ?? "";
      $public = $reqBody['public'] ?? null;
      $applyGlobal = filter_var($reqBody['applyGlobal'] ?? null,
        FILTER_VALIDATE_BOOLEAN);
      $ignoreScm = $reqBody['ignoreScm'] ?? null;
      $excludefolder = $reqBody['excludefolder'] ?? false;
    } else {
      $uploadType = $request->getHeaderLine('uploadType');
      $folderId = $request->getHeaderLine('folderId');
      $description = $request->getHeaderLine('uploadDescription');
      $public = $request->getHeaderLine('public');
      $applyGlobal = filter_var($request->getHeaderLine('applyGlobal'),
        FILTER_VALIDATE_BOOLEAN);
      $ignoreScm = $request->getHeaderLine('ignoreScm');
    }
 
    $public = empty($public) ? 'protected' : $public;
 
    if (empty($uploadType)) {
      throw new HttpBadRequestException("Require uploadType");
    }
    $scanOptions = [];
    if (array_key_exists('scanOptions', $reqBody)) {
      if ($uploadType == 'file') {
        $scanOptions = json_decode($reqBody['scanOptions'], true);
      } else {
        $scanOptions = $reqBody['scanOptions'];
      }
    }
 
    if (! is_array($scanOptions)) {
      $scanOptions = [];
    }
 
    $uploadHelper = new UploadHelper();
 
    if ($uploadType != "file" && (empty($reqBody) ||
        ! array_key_exists("location", $reqBody))) {
      throw new HttpBadRequestException(
        "Require location object if uploadType != file");
    }
    if (empty($folderId) ||
        !is_numeric($folderId) && $folderId > 0) {
      throw new HttpBadRequestException("folderId must be a positive integer!");
    }
 
    $allFolderIds = $this->restHelper->getFolderDao()->getAllFolderIds();
    if (!in_array($folderId, $allFolderIds)) {
      throw new HttpNotFoundException("folderId $folderId does not exists!");
    }
    if (!$this->restHelper->getFolderDao()->isFolderAccessible($folderId)) {
      throw new HttpForbiddenException("folderId $folderId is not accessible!");
    }
 
    $locationObject = [];
    if (array_key_exists("location", $reqBody)) {
      $locationObject = $reqBody["location"];
    } elseif ($uploadType != 'file') {
      throw new HttpBadRequestException(
        "Require location object if uploadType != file");
    }
 
    if (ApiVersion::getVersion($request) == ApiVersion::V2) {
      $uploadResponse = $uploadHelper->createNewUpload($locationObject,
        $folderId, $description, $public, $ignoreScm, $uploadType,
        $applyGlobal, $excludefolder);
    } else {
      $uploadResponse = $uploadHelper->createNewUpload($locationObject,
        $folderId, $description, $public, $ignoreScm, $uploadType,
        $applyGlobal);
    }
    $status = $uploadResponse[0];
    $message = $uploadResponse[1];
    $statusDescription = $uploadResponse[2];
    if (! $status) {
      throw new HttpInternalServerErrorException($message . "\n" .
        $statusDescription);
    }
 
    $uploadId = $uploadResponse[3];
    if (! empty($scanOptions)) {
      $info =  $uploadHelper->handleScheduleAnalysis(intval($uploadId),
        intval($folderId), $scanOptions, true);
      if ($info->getCode() == 201) {
        $info = new Info($info->getCode(), intval($uploadId), $info->getType());
      }
    } else {
      $info = new Info(201, intval($uploadId), InfoType::INFO);
    }
    if (array_key_exists("mainLicense", $reqBody) &&
        ! empty($reqBody["mainLicense"])) {
      global $container;
      $licenseDao = $container->get('dao.license');
      $mainLicense = $licenseDao
        ->getLicenseByShortName($reqBody["mainLicense"]);
      if ($mainLicense !== null) {
        $clearingDao = $container->get('dao.clearing');
        $clearingDao->makeMainLicense($uploadId,
          $this->restHelper->getGroupId(), $mainLicense->getId());
      }
    }
    return $response->withJson($info->getArray(), $info->getCode());
  }
 
  public function getUploadLicenses($request, $response, $args)
  {
    $id = intval($args['id']);
    $query = $request->getQueryParams();
    $apiVersion = ApiVersion::getVersion($request);
    if ($apiVersion == ApiVersion::V2) {
      $page = $query['page'] ?? "";
      $limit = $query['limit'] ?? "";
    } else {
      $page = $request->getHeaderLine("page");
      $limit = $request->getHeaderLine("limit");
    }
    if (! array_key_exists(self::AGENT_PARAM, $query)) {
      throw new HttpBadRequestException("agent parameter missing from query.");
    }
    $agents = explode(",", $query[self::AGENT_PARAM]);
    $containers = true;
    if (array_key_exists(self::CONTAINER_PARAM, $query)) {
      $containers = (strcasecmp($query[self::CONTAINER_PARAM], "true") === 0);
    }
 
    $license = true;
    if (array_key_exists('license', $query)) {
      $license = (strcasecmp($query['license'], "true") === 0);
    }
 
    $copyright = false;
    if (array_key_exists('copyright', $query)) {
      $copyright = (strcasecmp($query['copyright'], "true") === 0);
    }
 
    if (!$license && !$copyright) {
      throw new HttpBadRequestException(
        "'license' and 'copyright' atleast one should be true.");
    }
 
    $this->uploadAccessible($id);
    $this->isAdj2nestDone($id);
 
    $this->areAgentsScheduled($id, $agents, $response);
 
    /*
     * check if page && limit are numeric, if existing
     */
    if ((! ($page==='') && (! is_numeric($page) || $page < 1)) ||
      (! ($limit==='') && (! is_numeric($limit) || $limit < 1))) {
      throw new HttpBadRequestException(
        "page and limit need to be positive integers!");
    }
 
    // set page to 1 by default
    if (empty($page)) {
      $page = 1;
    }
 
    // set limit to 50 by default and max as 1000
    if (empty($limit)) {
      $limit = 50;
    } else if ($limit > 1000) {
      $limit = 1000;
    }
 
    $uploadHelper = new UploadHelper();
    list($licenseList, $count) = $uploadHelper->getUploadLicenseList($id, $agents, $containers, $license, $copyright, $page-1, $limit, $apiVersion);
    $totalPages = intval(ceil($count / $limit));
    return $response->withHeader("X-Total-Pages", $totalPages)->withJson($licenseList, 200);
  }
 
  public function getUploadCopyrights($request, $response, $args)
  {
    $id = intval($args['id']);
    $this->uploadAccessible($id);
    $this->isAdj2nestDone($id);
    $uploadHelper = new UploadHelper();
    $licenseList = $uploadHelper->getUploadCopyrightList($id);
    return $response->withJson($licenseList, 200);
  }
 
  public function updateUpload($request, $response, $args)
  {
    $id = intval($args['id']);
    $query = $request->getQueryParams();
    $userDao = $this->restHelper->getUserDao();
    $userId = $this->restHelper->getUserId();
    $groupId = $this->restHelper->getGroupId();
    $isJsonRequest = $this->isJsonRequest($request);
 
    $perm = $userDao->isAdvisorOrAdmin($userId, $groupId);
    if (!$perm) {
      throw new HttpForbiddenException("Not advisor or admin of current group. " .
        "Can not update upload.");
    }
    $uploadBrowseProxy = new UploadBrowseProxy(
      $groupId,
      $perm,
      $this->dbHelper->getDbManager()
    );
 
    $assignee = null;
    $status = null;
    $comment = null;
    $newName = null;
    $newDescription = null;
 
    if ($isJsonRequest) {
      $bodyContent = $this->getParsedBody($request);
    } else {
      $body = $request->getBody();
      $bodyContent = $body->getContents();
      $body->close();
    }
 
    // Handle assignee info
    if (array_key_exists(self::FILTER_ASSIGNEE, $query)) {
      $assignee = filter_var($query[self::FILTER_ASSIGNEE], FILTER_VALIDATE_INT);
      $userList = $userDao->getUserChoices($groupId);
      if (!array_key_exists($assignee, $userList)) {
        throw new HttpNotFoundException(
          "New assignee does not have permission on upload.");
      }
      $uploadBrowseProxy->updateTable("assignee", $id, $assignee);
    }
    // Handle new status
    if (
      array_key_exists(self::FILTER_STATUS, $query) &&
      in_array(strtolower($query[self::FILTER_STATUS]), self::VALID_STATUS)
    ) {
      $newStatus = strtolower($query[self::FILTER_STATUS]);
      $comment = '';
      if (in_array($newStatus, ["closed", "rejected"])) {
        if ($isJsonRequest && array_key_exists("comment", $bodyContent)) {
          $comment = $bodyContent["comment"];
        } else {
          $comment = $bodyContent;
        }
      }
      $status = 0;
      if ($newStatus == self::VALID_STATUS[1]) {
        $status = UploadStatus::IN_PROGRESS;
      } elseif ($newStatus == self::VALID_STATUS[2]) {
        $status = UploadStatus::CLOSED;
      } elseif ($newStatus == self::VALID_STATUS[3]) {
        $status = UploadStatus::REJECTED;
      } else {
        $status = UploadStatus::OPEN;
      }
      $uploadBrowseProxy->setStatusAndComment($id, $status, $comment);
    }
    // Handle update of name
    if (
      $isJsonRequest &&
      array_key_exists(self::FILTER_NAME, $bodyContent) &&
      strlen(trim($bodyContent[self::FILTER_NAME])) > 0
    ) {
      $newName = trim($bodyContent[self::FILTER_NAME]);
    }
    // Handle update of description
    if (
      $isJsonRequest &&
      array_key_exists("uploadDescription", $bodyContent) &&
      strlen(trim($bodyContent["uploadDescription"])) > 0
    ) {
      $newDescription = trim($bodyContent["uploadDescription"]);
    }
    if ($newName != null || $newDescription != null) {
      $uploadProperties = $this->restHelper->getPlugin('upload_properties');
      $updated = $uploadProperties->UpdateUploadProperties($id, $newName, $newDescription);
      if ($updated == 2) {
        throw new HttpBadRequestException("Invalid request to update upload name and description.");
      }
    }
 
    $returnVal = new Info(202, "Upload updated successfully.", InfoType::INFO);
    return $response->withJson($returnVal->getArray(), $returnVal->getCode());
  }
 
  private function isAdj2nestDone($id): void
  {
    $itemTreeBounds = $this->restHelper->getUploadDao()->getParentItemBounds(
      $id);
    if ($itemTreeBounds === false || empty($itemTreeBounds->getLeft())) {
      throw (new HttpServiceUnavailableException(
        "Ununpack job not started. Please check job status at " .
        "/api/v1/jobs?upload=" . $id))
        ->setHeaders(['Retry-After' => '60',
          'Look-at' => "/api/v1/jobs?upload=" . $id]);
    }
  }
 
  private function areAgentsScheduled($uploadId, $agents, $response): void
  {
    global $container;
    $agentDao = $container->get('dao.agent');
 
    $agentList = array_keys(AgentRef::AGENT_LIST);
    $intersectArray = array_intersect($agents, $agentList);
 
    if (count($agents) != count($intersectArray)) {
      throw new HttpBadRequestException("Agent should be any of " .
        implode(", ", $agentList) . ". " . implode(",", $agents) . " passed.");
    } else {
      // Agent is valid, check if they have ars tables.
      foreach ($agents as $agent) {
        if (! $agentDao->arsTableExists($agent)) {
          throw new HttpPreconditionFailException(
            "Agent $agent not scheduled for the upload. " .
            "Please POST to /jobs");
        }
      }
    }
 
    $scanProxy = new ScanJobProxy($agentDao, $uploadId);
    $agentList = $scanProxy->createAgentStatus($agents);
 
    foreach ($agentList as $agent) {
      if (! array_key_exists('currentAgentId', $agent)) {
        throw new HttpPreconditionFailException(
          "Agent " . $agent["agentName"] .
          " not scheduled for the upload. Please POST to /jobs");
      }
      if (array_key_exists('isAgentRunning', $agent) &&
          $agent['isAgentRunning']) {
        throw (new HttpServiceUnavailableException(
          "Agent " . $agent["agentName"] . " is running. " .
          "Please check job status at /api/v1/jobs?upload=" . $uploadId))
        ->setHeaders(['Retry-After' => '60',
          'Look-at' => "/api/v1/jobs?upload=" . $uploadId]);
      }
    }
  }
 
  public function setUploadPermissions($request, $response, $args)
  {
    $returnVal = null;
    // checking if the scheduler is running or not
    $commu_status = fo_communicate_with_scheduler('status', $response_from_scheduler, $error_info);
    if (!$commu_status) {
      throw new HttpServiceUnavailableException("Scheduler is not running!");
    }
    // Initialising upload-permissions plugin
    global $container;
    $restHelper = $container->get('helper.restHelper');
    $uploadPermissionObj = $restHelper->getPlugin('upload_permissions');
 
    $dbManager = $this->dbHelper->getDbManager();
    // parsing the request body
    $reqBody = $this->getParsedBody($request);
 
    $folder_pk = intval($reqBody['folderId']);
    $upload_pk = intval($args['id']);
    $this->uploadAccessible($upload_pk);
    $allUploadsPerm = $reqBody['allUploadsPermission'] ? 1 : 0;
    $newgroup = intval($reqBody['groupId']);
    $newperm = $this->getEquivalentValueForPermission($reqBody['newPermission']);
    $public_perm = isset($reqBody['publicPermission']) ? $this->getEquivalentValueForPermission($reqBody['publicPermission']) : -1;
 
    $query = "SELECT perm, perm_upload_pk FROM perm_upload WHERE upload_fk=$1 and group_fk=$2;";
    $result = $dbManager->getSingleRow($query, [$upload_pk, $newgroup], __METHOD__.".getOldPerm");
    $perm_upload_pk = 0;
    $perm = 0;
    if (!empty($result)) {
      $perm_upload_pk = intVal($result['perm_upload_pk']);
      $perm = $newperm;
    }
 
    $uploadPermissionObj->editPermissionsForUpload($commu_status, $folder_pk, $upload_pk, $allUploadsPerm, $perm_upload_pk, $perm, $newgroup, $newperm, $public_perm);
 
    $returnVal = new Info(202, "Permissions updated successfully!", InfoType::INFO);
    return $response->withJson($returnVal->getArray(), $returnVal->getCode());
  }
 
  public function getEquivalentValueForPermission($perm)
  {
    switch ($perm) {
      case 'read_only':
        return Auth::PERM_READ;
      case 'read_write':
        return Auth::PERM_WRITE;
      case 'clearing_admin':
        return Auth::PERM_CADMIN;
      case 'admin':
        return Auth::PERM_ADMIN;
      default:
        return Auth::PERM_NONE;
    }
  }
 
  public function getGroupsWithPermissions($request, $response, $args)
  {
    $apiVersion = ApiVersion::getVersion($request);
    $upload_pk = intval($args['id']);
    $this->uploadAccessible($upload_pk);
    $publicPerm = $this->restHelper->getUploadPermissionDao()->getPublicPermission($upload_pk);
    $permGroups = $this->restHelper->getUploadPermissionDao()->getPermissionGroups($upload_pk);
 
    // Removing the perm_upload_pk parameter in response
    $finalPermGroups = [];
    foreach ($permGroups as $value) {
      $groupPerm = new GroupPermission($value['perm'], $value['group_pk'], $value['group_name']);
      $finalPermGroups[] = $groupPerm->getArray($apiVersion);
    }
    $res = new Permissions($publicPerm, $finalPermGroups);
    return $response->withJson($res->getArray($apiVersion), 200);
  }
 
  public function getMainLicenses($request, $response, $args)
  {
    $uploadId = intval($args['id']);
    $this->uploadAccessible($uploadId);
 
    $clearingDao = $this->container->get('dao.clearing');
    $licenseIds = $clearingDao->getMainLicenseIds($uploadId, $this->restHelper->getGroupId());
    $licenseDao = $this->container->get('dao.license');
    $licenses = array();
 
    foreach ($licenseIds as $value) {
      $licenseId = intval($value);
      $obligations = $licenseDao->getLicenseObligations([$licenseId],
        false);
      $obligations = array_merge($obligations,
        $licenseDao->getLicenseObligations([$licenseId], true));
      $obligationList = [];
      foreach ($obligations as $obligation) {
        $obligationList[] = new Obligation(
          $obligation['ob_pk'],
          $obligation['ob_topic'],
          $obligation['ob_type'],
          $obligation['ob_text'],
          $obligation['ob_classification'],
          $obligation['ob_comment']
        );
      }
      $license = $licenseDao->getLicenseById($licenseId);
      $licenseObj = new License(
        $license->getId(),
        $license->getShortName(),
        $license->getFullName(),
        $license->getText(),
        $license->getUrl(),
        $obligationList,
        $license->getRisk()
      );
      $licenses[] = $licenseObj->getArray();
    }
    return $response->withJson($licenses, 200);
  }
 
  public function setMainLicense($request, $response, $args)
  {
    $uploadId = intval($args['id']);
    $body = $this->getParsedBody($request);
    $shortName = $body['shortName'];
    $licenseDao = $this->container->get('dao.license');
    $clearingDao = $this->container->get('dao.clearing');
 
    $this->uploadAccessible($uploadId);
 
    if (empty($shortName)) {
      throw new HttpBadRequestException("Short name missing from request.");
    }
    $license = $licenseDao->getLicenseByShortName($shortName,
      $this->restHelper->getGroupId());
 
    if ($license === null) {
      throw new HttpNotFoundException(
        "No license with shortname '$shortName' found.");
    }
 
    $licenseIds = $clearingDao->getMainLicenseIds($uploadId, $this->restHelper->getGroupId());
    if (in_array($license->getId(), $licenseIds)) {
      throw new HttpBadRequestException(
        "License already exists for this upload.");
    }
 
    $clearingDao = $this->container->get('dao.clearing');
    $clearingDao->makeMainLicense($uploadId, $this->restHelper->getGroupId(), $license->getId());
    $returnVal = new Info(200, "Successfully added new main license", InfoType::INFO);
    return $response->withJson($returnVal->getArray(), $returnVal->getCode());
  }
 
  /***
   * Remove the main license from the upload
   *
   * @param ServerRequestInterface $request
   * @param ResponseHelper $response
   * @param array $args
   * @return ResponseHelper
   * @throws HttpErrorException
   */
  public function removeMainLicense($request, $response, $args)
  {
    $uploadId = intval($args['id']);
    $shortName = $args['shortName'];
    $licenseDao = $this->container->get('dao.license');
    $clearingDao = $this->container->get('dao.clearing');
    $license = $licenseDao->getLicenseByShortName($shortName, $this->restHelper->getGroupId());
 
    $this->uploadAccessible($uploadId);
 
    if ($license === null) {
      throw new HttpNotFoundException(
        "No license with shortname '$shortName' found.");
    }
    $licenseIds = $clearingDao->getMainLicenseIds($uploadId, $this->restHelper->getGroupId());
    if (!in_array($license->getId(), $licenseIds)) {
      throw new HttpBadRequestException(
        "License '$shortName' is not a main license for this upload.");
    }
 
    $clearingDao = $this->container->get('dao.clearing');
    $clearingDao->removeMainLicense($uploadId, $this->restHelper->getGroupId(), $license->getId());
    $returnVal = new Info(200, "Main license removed successfully.", InfoType::INFO);
 
    return $response->withJson($returnVal->getArray(), $returnVal->getCode());
  }
 
  public function getClearingProgressInfo($request, $response, $args)
  {
    $uploadId = intval($args['id']);
    $uploadDao = $this->restHelper->getUploadDao();
 
    $this->uploadAccessible($uploadId);
 
    $uploadTreeTableName = $uploadDao->getUploadtreeTableName($uploadId);
 
    $noLicenseUploadTreeView = new UploadTreeProxy($uploadId,
      array(UploadTreeProxy::OPT_SKIP_THESE => "noLicense",
        UploadTreeProxy::OPT_GROUP_ID => $this->restHelper->getGroupId()),
      $uploadTreeTableName,
      'no_license_uploadtree' . $uploadId);
 
    $filesOfInterest = $noLicenseUploadTreeView->count();
 
    $nonClearedUploadTreeView = new UploadTreeProxy($uploadId,
      array(UploadTreeProxy::OPT_SKIP_THESE => "alreadyCleared",
        UploadTreeProxy::OPT_GROUP_ID =>  $this->restHelper->getGroupId()),
      $uploadTreeTableName,
      'already_cleared_uploadtree' . $uploadId);
    $filesToBeCleared = $nonClearedUploadTreeView->count();
 
    $filesAlreadyCleared = $filesOfInterest - $filesToBeCleared;
 
    $res = [
      "totalFilesOfInterest" => intval($filesOfInterest),
      "totalFilesCleared" => intval($filesAlreadyCleared),
    ];
    return $response->withJson($res, 200);
  }
 
  public function getLicensesHistogram($request, $response, $args)
  {
    $agentDao = $this->container->get('dao.agent');
    $clearingDao = $this->container->get('dao.clearing');
    $licenseDao = $this->container->get('dao.license');
 
    $uploadId = intval($args['id']);
    $uploadDao = $this->restHelper->getUploadDao();
    $query = $request->getQueryParams();
    $selectedAgentId = $query['agentId'] ?? null;
 
    $this->uploadAccessible($uploadId);
 
    if ($selectedAgentId !== null && !$this->dbHelper->doesIdExist("agent", "agent_pk", $selectedAgentId)) {
      throw new HttpNotFoundException("Agent does not exist.");
    }
 
    $scannerAgents = array_keys($this->agentNames);
    $scanJobProxy = new ScanJobProxy($agentDao, $uploadId);
    $scanJobProxy->createAgentStatus($scannerAgents);
    $uploadTreeTableName = $uploadDao->getUploadtreeTableName($uploadId);
    $itemTreeBounds = $uploadDao->getParentItemBounds($uploadId, $uploadTreeTableName);
    $editedLicenses = $clearingDao->getClearedLicenseIdAndMultiplicities($itemTreeBounds, $this->restHelper->getGroupId());
    $selectedAgentIds = empty($selectedAgentId) ? $scanJobProxy->getLatestSuccessfulAgentIds() : $selectedAgentId;
    $scannedLicenses = $licenseDao->getLicenseHistogram($itemTreeBounds, $selectedAgentIds);
    $allScannerLicenseNames = array_keys($scannedLicenses);
    $allEditedLicenseNames = array_keys($editedLicenses);
    $allLicNames = array_unique(array_merge($allScannerLicenseNames, $allEditedLicenseNames));
    $realLicNames = array_diff($allLicNames, array(LicenseDao::NO_LICENSE_FOUND));
    $totalScannerLicenseCount = 0;
    $editedTotalLicenseCount = 0;
 
    $res = array();
    foreach ($realLicNames as $licenseShortName) {
      $count = 0;
      if (array_key_exists($licenseShortName, $scannedLicenses)) {
        $count = $scannedLicenses[$licenseShortName]['unique'];
        $rfId = $scannedLicenses[$licenseShortName]['rf_pk'];
      } else {
        $rfId = $editedLicenses[$licenseShortName]['rf_pk'];
      }
      $editedCount = array_key_exists($licenseShortName, $editedLicenses) ? $editedLicenses[$licenseShortName]['count'] : 0;
      $totalScannerLicenseCount += $count;
      $editedTotalLicenseCount += $editedCount;
      $scannerCountLink = $count;
      $editedLink = $editedCount;
 
      $res[] = array($scannerCountLink, $editedLink, array($licenseShortName, $rfId));
    }
 
    $outputArray = [];
 
    foreach ($res as $item) {
      $outputArray[] = [
        "id" => intval($item[2][1]),
        "name" => $item[2][0],
        "scannerCount" => intval($item[0]),
        "concludedCount" => intval($item[1]),
      ];
    }
    return $response->withJson($outputArray, 200);
  }
 
  public function getAllAgents($request, $response, $args)
  {
    $uploadId = intval($args['id']);
 
    $this->uploadAccessible($uploadId);
 
    $scannerAgents = array_keys($this->agentNames);
    $agentDao = $this->container->get('dao.agent');
    $scanJobProxy = new ScanJobProxy($agentDao, $uploadId);
    $res = $scanJobProxy->createAgentStatus($scannerAgents);
 
    $outputArray = [];
    foreach ($res as &$item) {
      $successfulAgents = [];
      if (count($item['successfulAgents']) > 0) {
        $item['isAgentRunning'] = false;
      } else {
        $item['currentAgentId'] = $agentDao->getCurrentAgentRef($item["agentName"])->getAgentId();
        $item['currentAgentRev'] = "";
      }
      foreach ($item['successfulAgents'] as &$agent) {
        $successfulAgent = new SuccessfulAgent(intval($agent['agent_id']), $agent['agent_rev'], $agent['agent_name']);
        $successfulAgents[] = $successfulAgent->getArray(ApiVersion::getVersion($request));
      }
      $agent = new Agent($successfulAgents, $item['uploadId'], $item['agentName'], $item['currentAgentId'], $item['currentAgentRev'], $item['isAgentRunning']);
      $outputArray[] = $agent->getArray(ApiVersion::getVersion($request));
    }
    return $response->withJson($outputArray, 200);
  }
 
  public function getEditedLicenses($request, $response, $args)
  {
    $uploadId = intval($args['id']);
 
    $this->uploadAccessible($uploadId);
 
    $clearingDao = $this->container->get('dao.clearing');
    $uploadDao = $this->restHelper->getUploadDao();
    $uploadTreeTableName = $uploadDao->getUploadtreeTableName($uploadId);
    $itemTreeBounds = $uploadDao->getParentItemBounds($uploadId, $uploadTreeTableName);
    $res = $clearingDao->getClearedLicenseIdAndMultiplicities($itemTreeBounds, $this->restHelper->getGroupId());
    $outputArray = [];
 
    foreach ($res as $key => $value) {
      $editedLicense = new EditedLicense(intval($value["rf_pk"]), $key, intval($value["count"]), $value["spdx_id"]);
      $outputArray[] = $editedLicense->getArray(ApiVersion::getVersion($request));
    }
    return $response->withJson($outputArray, 200);
  }
 
  public function getReuseReportSummary($request, $response, $args)
  {
    $uploadId = intval($args['id']);
    $this->uploadAccessible($uploadId);
 
    $reuseReportProcess = $this->container->get('businessrules.reusereportprocessor');
    $res = $reuseReportProcess->getReuseSummary($uploadId);
    return $response->withJson($res, 200);
  }
 
  public function getScannedLicenses($request, $response, $args)
  {
    $uploadId = intval($args['id']);
    $query = $request->getQueryParams();
    $selectedAgentId = $query['agentId'] ?? null;
    $licenseDao = $this->container->get('dao.license');
 
    $this->uploadAccessible($uploadId);
    if ($selectedAgentId !== null && !$this->dbHelper->doesIdExist("agent", "agent_pk", $selectedAgentId)) {
      throw new HttpNotFoundException("Agent does not exist.");
    }
    $scannerAgents = array_keys(AgentRef::AGENT_LIST);
    $scanJobProxy = new ScanJobProxy($this->agentDao, $uploadId);
    $scanJobProxy->createAgentStatus($scannerAgents);
    $uploadDao = $this->restHelper->getUploadDao();
    $uploadTreeTableName = $uploadDao->getUploadtreeTableName($uploadId);
    $itemTreeBounds = $uploadDao->getParentItemBounds($uploadId, $uploadTreeTableName);
    $selectedAgentIds = empty($selectedAgentId) ? $scanJobProxy->getLatestSuccessfulAgentIds() : $selectedAgentId;
    $res = $licenseDao->getLicenseHistogram($itemTreeBounds, $selectedAgentIds);
    $outputArray = [];
 
    foreach ($res as $key => $value) {
      $scannedLicense = new ScannedLicense($licenseDao->getLicenseByShortName($key)->getId(), $key, $value['count'], $value['unique'], $value['spdx_id']);
      $outputArray[] = $scannedLicense->getArray(ApiVersion::getVersion($request));
    }
    return $response->withJson($outputArray, 200);
  }
  public function getAgentsRevision($request, $response, $args)
  {
    $agentDao = $this->container->get('dao.agent');
    $uploadId = intval($args['id']);
 
    $this->uploadAccessible($uploadId);
 
    $scannerAgents = array_keys($this->agentNames);
    $scanJobProxy = new ScanJobProxy($agentDao, $uploadId);
    $scanJobProxy->createAgentStatus($scannerAgents);
 
    $res = array();
    foreach ($scanJobProxy->getSuccessfulAgents() as $agent) {
      $res[] = array(
        "id" => $agent->getAgentId(),
        "name" => $agent->getAgentName(),
        "revision" => $agent->getAgentRevision(),
      );
    }
    return $response->withJson($res, 200);
  }
 
  public function getTopItem($request, $response, $args)
  {
    $uploadId = intval($args['id']);
    if (!$this->dbHelper->doesIdExist("upload", "upload_pk", $uploadId)) {
      $returnVal = new Info(404, "Upload does not exist", InfoType::ERROR);
      return $response->withJson($returnVal->getArray(), $returnVal->getCode());
    }
    $uploadDao = $this->restHelper->getUploadDao();
    $itemTreeBounds = $uploadDao->getParentItemBounds($uploadId,
      $uploadDao->getUploadtreeTableName($uploadId));
    if ($itemTreeBounds === false) {
      $error = new Info(500, "Unable to get top item.", InfoType::ERROR);
      return $response->withJson($error->getArray(), $error->getCode());
    }
    $info = new Info(200, $itemTreeBounds->getItemId(), InfoType::INFO);
    return $response->withJson($info->getArray(), $info->getCode());
  }
}