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[instrument_manager] Use JSON data for uploaded linst instruments #9324

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merged 1 commit into from
Sep 6, 2024
Merged

[instrument_manager] Use JSON data for uploaded linst instruments #9324

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120 changes: 23 additions & 97 deletions modules/instrument_manager/php/instrument_manager.class.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,6 @@ class Instrument_Manager extends \DataFrameworkMenu
*/
protected function handlePOST(ServerRequestInterface $request): ResponseInterface
{
$loris = $request->getAttribute('loris');
// Ensure the user is allowed to upload.
if (! $request->getAttribute('user')->hasPermission(
'instrument_manager_write'
Expand All @@ -94,7 +93,6 @@ class Instrument_Manager extends \DataFrameworkMenu
$filename = $uploaded_file->getClientFilename();
$instrument = pathinfo($filename)['filename'];
$targetdir = new \SplFileInfo($this->_path . 'project/instruments/');
$fullpath = $targetdir->getPathname() . '/' . $filename;

if ($this->instrumentExists($instrument)) {
// An instrument with this name already exists in the test_names
Expand Down Expand Up @@ -128,37 +126,33 @@ class Instrument_Manager extends \DataFrameworkMenu
return $response;
}

// Scripts in tools/ often make relative imports, so we must change
// our effective directory in order to use them.
chdir($this->_path . "/tools");
// Use tools/ script to generate an SQL patch file based on the
// structure of the uploaded .linst file.
exec(
'php generate_tables_sql_and_testNames.php < '
. escapeshellarg($fullpath)
);

if (!$this->isAdminUserConfigured()) {
// If no adminUser is configured, automatic installation is not
// possible, so this is the last step.
return new \LORIS\Http\Response\JSON\OK(
['success' => self::UPLOAD_NO_INSTALL]
);
}

// Install the instrument by directly sourcing the SQL file
// generated by `generate_tables_sql_and_testNames.php` using bash.
// If installation is successful, `exec` will complete
// silently. Otherwise, it will return the exit code and error
// messsage from MySQL. This will be stored in $result and
// logged via LorisException.
try {
$table_name = \NDB_BVL_Instrument::factory(

$inst = \NDB_BVL_Instrument::factory(
$this->loris,
$instrument,
'',
'',
)->table;
);

$DB = $this->loris->getDatabaseConnection();
$DB->insert(
"test_names",
[
'test_name' => $instrument,
'Full_name' => $inst->getFullName(),
'Sub_group' => 1,
]
);
file_put_contents(
\Utility::pathJoin(
$targetdir->getPath(),
$targetdir->getFilename(),
$instrument . ".meta"
),
"jsondata{@}true\n"
);

} catch (\NotFound $e) {
return (new \LORIS\Http\Response\JSON\NotFound(
$e->getMessage()
Expand All @@ -168,34 +162,6 @@ class Instrument_Manager extends \DataFrameworkMenu
$e->getMessage()
);
}

$db_config = $loris->getConfiguration()->getSetting('database');
exec(
"mysql".
" -h" . escapeshellarg($db_config['host']).
" -u" . escapeshellarg($db_config['adminUser']).
" -p" . escapeshellarg($db_config['adminPassword']).
" " . escapeshellarg($db_config['database']).
" < " . $this->_path . "project/tables_sql/".
escapeshellarg($table_name . '.sql'),
$output, // $output and $status are created automatically
$status // by `exec` and so need not be declared above.
);
// An exit code of 0 is a success and 1 means failure
if ($status) {
$this->logger->error(
"The installation of $instrument.sql failed. "
. "Either: the instrument table exists (but is not in the "
. "test_names table), or "
. "LORIS could not connect to the database using the "
. "credentials supplied in the config file. "
. "Exec output: `" . implode("\n", $output) . "`"
);
return new \LORIS\Http\Response\JSON\InternalServerError(
self::UPLOAD_INSTALL_FAILED
);
}

return new \LORIS\Http\Response\JSON\Created(["ok"=>"ok"]);
}
/**
Expand Down Expand Up @@ -232,7 +198,6 @@ class Instrument_Manager extends \DataFrameworkMenu
return [
'allPermissionCodes' => $perms,
'writable' => $this->canWriteFiles(),
'caninstall' => $this->isAdminUserConfigured()
];

}
Expand All @@ -255,49 +220,10 @@ class Instrument_Manager extends \DataFrameworkMenu
{
$this->_path = $this->loris->getConfiguration()->getSetting('base');
$instrument_dir = $this->_path . 'project/instruments';
$table_dir = $this->_path . 'project/tables_sql';

return is_writable($instrument_dir) && is_writable($table_dir);
return is_writable($instrument_dir);
}
/**
* Return whether the adminUser is properly configured, ie. credentials are
* set and are valid.
* The adminUser is a MySQL user with CREATE table permissions.
* `empty` is used instead of `isset` as blank values in the config file
* are still considered set.
*
* @return bool True if a adminUser is configured properly. False if not.
*/
protected function isAdminUserConfigured() : bool
{
$db = $this->loris->getDatabaseConnection();
$db_config = $this->loris->getConfiguration()->getSetting('database');

$credentials_set = !empty($db_config['adminUser'])
&& !empty($db_config['adminPassword']);
if (!$credentials_set) {
return false;
}
// Check if supplied credentials are valid by making a DB connection.
// If the credentials are invalid, an error message will be logged to
// the backend.
try {
$dbname = $db_config['database'];
putenv("LORIS_{$dbname}_USERNAME=" . $db_config['adminUser']);
putenv("LORIS_{$dbname}_PASSWORD=" . $db_config['adminPassword']);
putenv("LORIS_{$dbname}_HOST=" . $db_config['host']);
$connected = $db->connect(
$dbname,
false
);
putenv("LORIS_{$dbname}_USERNAME=");
putenv("LORIS_{$dbname}_PASSWORD=");
putenv("LORIS_{$dbname}_HOST=");
} catch (\DatabaseException $e) {
$connected = false;
}
return $connected;
}
/**
* Checks the test_names table for the existence of the instrument
*
Expand Down
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