update develop

.gitignore

@@ -42,10 +42,15 @@ test-config.ini
 /tests/web/coverage-data/*
 !/tests/web/coverage-data/README.md
 
+<<<<<<< HEAD
 
 # Ignore dependencies directory
 /dependencies
 
 # Composer lock file
 composer.lock
 composer.*
+=======
+# Dependencies directory
+/dependencies
+>>>>>>> develop

classes/ServerConfig.php

@@ -6,10 +6,9 @@
 
 namespace IU\RedCapEtlModule;
 
-use phpseclib\Crypt\RSA;
-use phpseclib\Net\SCP;
-use phpseclib\Net\SFTP;
-use phpseclib\Net\SSH2;
+use phpseclib3\Net\SFTP;
+use phpseclib3\Crypt\PublicKeyLoader;
+
 
 class ServerConfig implements \JsonSerializable
 {
@@ -227,6 +226,9 @@ public function run($etlConfig, $isCronJob = false, $moduleLog = null, $runWorkf
  $properties[Configuration::PRINT_LOGGING] = false;
  } 
 
+ $properties = $etlConfig->getPropertiesArray();
+ $properties[Configuration::PRINT_LOGGING] = false;
+
  $logger = new \IU\REDCapETL\Logger('REDCap-ETL');
  $logId = $logger->getLogId();
 
@@ -250,48 +252,13 @@ public function run($etlConfig, $isCronJob = false, $moduleLog = null, $runWorkf
  # Remote server
  #-------------------------------------------------
 
- if (empty($this->serverAddress)) {
- $message = $this->createServerErrorMessageForUser('no server address specified');
- throw new \Exception($message);
- }
-
- if ($this->authMethod == self::AUTH_METHOD_PASSWORD) {
- $ssh = new SSH2($this->serverAddress);
- $ssh->login($username, $this->password);
-
- } elseif ($this->authMethod == self::AUTH_METHOD_SSH_KEY) {
- $keyFile = $this->getSshKeyFile();
-
- if (empty($keyFile)) {
- $message = $this->createServerErrorMessageForUser('no SSH key file was specified');
- throw new \Exception($message);
- }
-
- #\REDCap::logEvent('REDCap-ETL run current user: '.get_current_user());
-
- $key = new RSA();
- $key->setPassword($this->sshKeyPassword);
-
- $keyFileContents = file_get_contents($keyFile);
-
- if ($keyFileContents === false) {
- $message = $this->createServerErrorMessageForUser('SSH key file could not be accessed');
- throw new \Exception($message);
- }
- $key->loadKey($keyFileContents);
- $ssh = new SSH2($this->serverAddress);
- $ssh->login($this->username, $key);
- } else {
- $message = $this->createServerErrorMessageForUser('unrecognized authentication menthod');
- throw new \Exception($message);
- }
+ $ssh = $this->getRemoteConnection();
 
  #------------------------------------------------
  # Copy configuration file and transformation
  # rules file (if any) to the server.
  #------------------------------------------------
  $fileNameSuffix = uniqid('', true);
- $scp = new SCP($ssh);
 
  if ($runWorkflow) {
  $propertiesJson = Configuration::getRedCapEtlJsonProperties($runWorkflow, $etlConfig);
@@ -300,10 +267,17 @@ public function run($etlConfig, $isCronJob = false, $moduleLog = null, $runWorkf
  }
  $configFileName = 'etl_config_' . $fileNameSuffix . '.json';
  $configFilePath = $this->configDir . '/' . $configFileName;
- $scpResult = $scp->put($configFilePath, $propertiesJson);
- if (!$scpResult) {
+
+ $sftpResult = $ssh->put($configFilePath, $propertiesJson);
+ if (!$sftpResult) {
  $message = 'Copy of ETL configuration to server failed.'
  . ' Please contact your system administrator for assistance.';
+
+ $error = error_get_last();
+ if (isset($error) && is_array($error) && array_key_exists('message', $error)) {
+ $message .= " Error: " . $error['message'];
+ }
+
  throw new \Exception($message);
  }
 
@@ -325,51 +299,70 @@ public function run($etlConfig, $isCronJob = false, $moduleLog = null, $runWorkf
  return $output;
  }
 
+ /**
+ * Returns an ssh/ftp connection for the server represented by this class.
+ *
+ * @return SFTP ssh/sftp connection.
+ */
+ public function getRemoteConnection()
+ {
+ $ssh = null;
+
+ if (empty($this->serverAddress)) {
+ $message = $this->createServerErrorMessageForUser('no server address specified');
+ throw new \Exception($message);
+ }
+
+ if ($this->authMethod == self::AUTH_METHOD_PASSWORD) {
+ $ssh = new SFTP($this->serverAddress); # SFTP class provides SSH functionality also
+ $ssh->login($this->username, $this->password);
+ } elseif ($this->authMethod == self::AUTH_METHOD_SSH_KEY) {
+ $keyFile = $this->getSshKeyFile();
+
+ if (empty($keyFile)) {
+ $message = $this->createServerErrorMessageForUser('no SSH key file was specified');
+ throw new \Exception($message);
+ }
+
+ $keyFileContents = file_get_contents($keyFile);
+
+ if ($keyFileContents === false) {
+ $message = $this->createServerErrorMessageForUser('SSH key file could not be accessed');
+ throw new \Exception($message);
+ }
+
+ $key = PublicKeyLoader::load($keyFileContents, $this->sshKeyPassword);
+ $ssh = new SFTP($this->serverAddress);
+ $ssh->login($this->username, $key);
+ } else {
+ $message = $this->createServerErrorMessageForUser('unrecognized authentication menthod');
+ throw new \Exception($message);
+ }
+ return $ssh;
+ }
+
  public function test()
  {
  $testOutput = '';
  try {
  if ($this->isEmbeddedServer()) {
  $testOutput = 'REDCap-ETL ' . \IU\REDCapETL\Version::RELEASE_NUMBER . ' found.';
  } else {
- $serverAddress = $this->getServerAddress();
- if (empty($serverAddress)) {
- throw new \Exception('No server address found.');
- }
-
- $username = $this->getUsername();
- if ($this->getAuthMethod() == ServerConfig::AUTH_METHOD_SSH_KEY) {
- $keyFile = $this->getSshKeyFile();
- if (empty($keyFile)) {
- throw new \Exception('SSH key file cound not be found.');
- }
-
- $keyPassword = $this->getSshKeyPassword();
-
- $key = new RSA();
-
- #if (!empty($keyPassword)) {
- $key->setPassword($keyPassword);
- #}
-
- $keyFileContents = file_get_contents($keyFile);
- if ($keyFileContents === false) {
- throw new \Exception('SSH key file could not be accessed.');
- }
- $key->loadKey($keyFileContents);
+ $ssh = $this->getRemoteConnection();
 
-  $ssh = new SSH2($serverAddress);
- $ssh->login($username, $key);
+ if ($this->getAuthMethod() == ServerConfig::AUTH_METHOD_SSH_KEY) {
+  $authMethod = "SSH key";
  } else {
- $password = $this->getPassword();
-
- $ssh = new SSH2($serverAddress);
- $ssh->login($username, $password);
+ $authMethod = "password";
  }
 
  $output = $ssh->exec('hostname');
+
  if (!$output) {
- $testOutput = "ERROR: ssh command failed.";
+ $err = $ssh->getLastError();
+ $testOutput = "ERROR: ssh command failed. Server: '{$this->serverAddress}'."
+ . " Username: '{$this->username}' . Authentication method: {$authMethod}."
+ ;
  } else {
  $testOutput = "SUCCESS:\noutput of hostname command:\n"
  . $output . "\n";

composer.json

@@ -0,0 +1,32 @@
+{
+ "name" : "iu-redcap/redcap-etl-module",
+ "license" : "BSD 3-Clause",
+ "description" : "REDCap-ETL Module",
+ "keywords" : [
+ "REDCap", "ETL", "REDCap-ETL"
+ ],
+ "require" : {
+ "phpseclib/phpseclib" : "3.0.8",
+ "iu-redcap/redcap-etl" : "1.5.9"
+ },
+ "require-dev": {
+ "phpunit/phpunit": "9.5.2",
+ "squizlabs/php_codesniffer": "3.4.2",
+ "erusev/parsedown": "^1.7"
+ },
+ "autoload" : {
+ "psr-4" : {
+ "IU\\RedCapEtlModule\\" : ["./", "./classes/"]
+ }
+ },
+ "autoload-dev": {
+ "psr-4" : {
+ "IU\\RedCapEtlModule\\": [
+ "tests/unit"
+ ],
+ "ExternalModules\\": [
+ "tests/external"
+ ]
+ }
+ }
+}