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Merge pull request #113 from TripalCultivate/g5.112-updateValidDataFi…
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…leTests

Updates file validator test
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@reynoldtan
reynoldtan authored Oct 29, 2024
2 parents 79bb75f + a3e6e2d commit 7551244
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81 changes: 27 additions & 54 deletions trpcultivate_phenotypes/tests/src/Kernel/Validators/ValidatorValidDataFileTest.php
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@

use Drupal\Tests\tripal_chado\Kernel\ChadoTestKernelBase;
use Drupal\Tests\trpcultivate_phenotypes\Traits\PhenotypeImporterTestTrait;
use Drupal\file\Entity\File;

/**
* Tests Tripal Cultivate Phenotypes Data File Validator Plugins.
Expand Down Expand Up @@ -83,50 +82,58 @@ protected function setUp(): void {
'file-valid' => [
'ext' => 'tsv',
'mime' => 'text/tab-separated-values',
'content' => implode("\t", ['Header 1', 'Header 2', 'Header 3']),
'filesize' => 1024
'content' => [
'string' => implode("\t", ['Header 1', 'Header 2', 'Header 3'])
],
],

// A valid file type, an empty file.
'file-empty' => [
'ext' => 'tsv',
'mime' => 'text/tab-separated-values',
'content' => '',
'content' => [
'string' => ''
],
'filesize' => 0
],

// An alternative file type.
'file-alternative' => [
'ext' => 'txt',
'mime' => 'text/plain',
'content' => implode("\t", ['Header 1', 'Header 2', 'Header 3']),
'filesize' => 1024,
'content' => [
'string' => implode("\t", ['Header 1', 'Header 2', 'Header 3'])
],
],

// Not valid file.
'file-image' => [
'ext' => 'png',
'mime' => 'image/png',
'content' => '',
'filesize' => 1024,
'file' => 'png.png' // Can be found in the test Fixtures folder.
'content' => [
'string' => '',
'file' => 'png.png' // Can be found in the test Fixtures folder.
]
],

// Pretend tsv file.
'file-pretend' => [
'ext' => 'tsv',
'mime' => 'application/pdf',
'filesize' => 1024,
'file' => 'pdf.txt' // Can be found in the test Fixtures folder.
'content' => [
'string' => '',
'file' => 'pdf.txt' // Can be found in the test Fixtures folder.
]
],

// Could not open the file - not permitted to read.
'file-locked' => [
'ext' => 'tsv',
'mime' => 'text/tab-separated-values',
'content' => implode("\t", ['Header 1', 'Header 2', 'Header 3']),
'filesize' => 1024,
'lock' => TRUE
'content' => [
'string' => implode("\t", ['Header 1', 'Header 2', 'Header 3'])
],
'permissions' => 'none'
]
];

Expand All @@ -137,22 +144,9 @@ protected function setUp(): void {
// Create the file for each test file scenario.
foreach($test_file_scenario as $test_scenario => $file_properties) {
$filename = 'test_data_file_' . $test_scenario . '.' . $file_properties['ext'];
$file_properties['filename'] = $filename;

$file = File::create([
'filename' => $filename,
'filemime' => $file_properties['mime'],
'uri' => 'public://' . $filename,
'status' => 0
]);

// Update test scenario file properties.

// Set the file size.
if (isset($file_properties['filesize'])) {
$file->setSize($file_properties['filesize']);
}

$file->save();
$file = $this->createTestFile($file_properties);

// Reference relevant file properties that will be used
// to indicate attributes of the file that failed the validation.
Expand All @@ -162,27 +156,6 @@ protected function setUp(): void {
$file_filename = $file->getFileName();
$file_extension = pathinfo($file_filename, PATHINFO_EXTENSION);

// Write contents into the file.
if (!empty($file_properties['content'])) {
file_put_contents($file_uri, $file_properties['content']);
}

// If an existing file was specified, move the file fixture into the uri
// to override the created file and use it in lieu of the created file.
if (!empty($file_properties['file'])) {
$path_to_fixtures = __DIR__ . '/../../Fixtures/';
$full_path = $path_to_fixtures . $file_properties['file'];
$this->assertFileIsReadable($full_path,
"Unable to setup FILE ". $test_scenario . " because cannot access Fixture file at $full_path.");

copy($full_path, $file_uri);
}

// If file should be locked.
if (isset($file_properties['lock']) && $file_properties['lock']) {
chmod($file_uri, 0000);
}

// Create a test scenario file input parameter and attach the file properties.
$test_file_param[ $test_scenario ] = [
'test_param' =>[
Expand Down Expand Up @@ -510,15 +483,15 @@ public function provideFileForDataFileValidator() {
*/
public function testDataFileExceptionCase() {
// The filename is set to a different name than the set filename of valid-file test file input scenario.
$filename = 'not-the-filename.tsv';
$filename = 'not-the-filename.tsv';
$fid = $this->test_files['file-valid']['test_file']['fid'];

$exception_caught = FALSE;
$exception_message = '';

try {
$this->validator_instance->validateFile($filename, $fid);
}
}
catch (\Exception $e) {
$exception_caught = TRUE;
$exception_message = $e->getMessage();
Expand All @@ -529,7 +502,7 @@ public function testDataFileExceptionCase() {
$exception_message,
'The filename provided does not match the filename set in the file object.',
'The exception message thrown by data file validator filename mismatch case does not match excepted message'
);
);
}

/**
Expand Down
76 changes: 42 additions & 34 deletions trpcultivate_phenotypes/tests/src/Traits/PhenotypeImporterTestTrait.php
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Original file line number Diff line number Diff line change
Expand Up @@ -183,69 +183,77 @@ protected function createTestFile($details) {

// Set Defaults.
$details['extension'] = @$details['extension'] ?: 'txt';
$details['mime'] = @$details['mime'] ?: 'text/tab-separated-values';
$details['filename'] = @$details['filename'] ?: 'testFile.' . uniqid() . '.' . $details['extension'];
$details['mime'] = @$details['mime'] ?: 'text/tab-separated-values';
$details['is_temporary'] = @$details['is_temporary'] ?: FALSE;
$details['content'] = @$details['content'] ?: ['string' => uniqid()];

// Determine the fullpath to test files for use later
if (array_key_exists('file', $details['content'])) {
$path_to_fixtures = __DIR__ . '/../Fixtures/';
$full_path = $path_to_fixtures . $details['content']['file'];
}

// Set directory.
$directory = ($details['is_temporary']) ? 'temporary://' : 'public://';
$uri = $directory . $details['filename'];
$file_uri = $directory . $details['filename'];

// Create file object.
$file = File::create([
'filename' => $details['filename'],
'filemime' => $details['mime'],
'uri' => $uri,
'uri' => $file_uri,
'status' => 0,
]);

// Set the size of the file.
// This is usually used if the file is empty in which case this is 0
if (isset($details['filesize'])) {
$file->setSize($details['filesize']);
}
else if (array_key_exists('file', $details['content'])) {
$size = @filesize($full_path);
// Set size unless there was an error.
$this->assertNotFalse($size, 'Unable to determine size of test file: ' . $full_path);
$file->setSize($size);
}
// Reference file attributes:
$file_id = $file->id();
$file_uri = $file->getFileUri();

// Save the file to Drupal.
$file->save();
$id = $file->id();
// If a test file fixture was provided, create a copy and set this file copy as
// the file uri value in the file object for this test file.
if (array_key_exists('file', $details['content']) && !empty($details['content']['file'])) {
$path_to_file_fixture = __DIR__ . '/../Fixtures/' . $details['content']['file'];

$this->assertFileIsReadable(
$path_to_file_fixture,
'Unable to setup FILE ' . $file_id . ' because cannot access Fixture file at ' . $path_to_file_fixture
);

copy($path_to_file_fixture, $file_uri);
}

// Write something on file with content key set to a string.
if (!empty($details['content']['string'])) {
$fileuri = $file->getFileUri();
file_put_contents($fileuri, $details['content']['string']);
file_put_contents($file_uri, $details['content']['string']);
}

// If an existing file was specified then we can add that in here.
if (!empty($details['content']['file'])) {
$fileuri = $file->getFileUri();
// Set other file attributes:

// Set the size of the file.
// This is usually used if the file is empty in which case this is 0.
if (isset($details['filesize'])) {
// File size was provided.
$file->setSize($details['filesize']);
}
else {
// File size is to be determined.
// Get the file size.
$file_size = @filesize($file_uri);

$this->assertFileIsReadable($full_path,
"Unable to setup FILE ". $id . " because cannot access Fixture file at $full_path.");
// Assert that a file size was established.
$this->assertNotFalse($file_size, 'Unable to determine size of test file: ' . $file_uri);

copy($full_path, $fileuri);
// Set the file size.
$file->setSize($file_size);
}

// Save all set attributes.
$file->save();

// Set file permissions if needed.
if (!empty($details['permissions'])) {
$fileuri = $file->getFileUri();
if ($details['permissions'] == 'none') {
chmod($fileuri, octdec(0000));
chmod($file_uri, octdec(0000));
}
elseif (is_numeric($details['permissions'])) {
$decoded = decoct(octdec($details['permissions']));
if ($details['permissions'] == $decoded) {
chmod($fileuri, $details['permissions']);
chmod($file_uri, $details['permissions']);
}
}
}
Expand Down

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