tripal/tripal_galaxy

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            '%state' => $submission->status,

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          'width' => '25%',

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          'header' => TRUE,

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       $dataset_id = $history_content['id'];

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        '#type' => 'markup',

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Array indentation error, expected 10 spaces but found 12

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            'width' => '25%',

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Array indentation error, expected 8 spaces but found 10

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          'header' => TRUE,

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Inline comments must end in full-stops, exclamation marks, colons, question marks, or closing parentheses

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    // Dig down through dataset_collections to find the real dataset

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Array indentation error, expected 4 spaces but found 6

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      '#collapsed' => TRUE,

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Expected 1 blank line before function; 2 found

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function tripal_galaxy_workflow_report(int $sid) {

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        'status' => 'deleted',

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            'data' => 'Submission ID',

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            'header' => TRUE,

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      tripal_galaxy_get_history_name($submission),

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       // same.

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    // retrieve the pertinents needed to download the file.

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  ->fetchObject();

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  // Get the list of input files so we can exclude them from the results

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Array indentation error, expected 6 spaces but found 8

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        '#type' => 'item',

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Array indentation error, expected 8 spaces but found 10

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          'data' => 'Status',

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Array indentation error, expected 4 spaces but found 6

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      format_date($submission->submit_date),

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Array indentation error, expected 4 spaces but found 6

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      '#type' => 'fieldset',

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}

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Line exceeds 80 characters; contains 103 characters

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       '#markup' => l($history_content['name'], $proxy_url, ['attributes' => ['target' => '_blank']] ),

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Line indented incorrectly; expected 6 spaces, found 7

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       ];

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Missing file doc comment

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<?php

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The PHP open tag must be followed by exactly one blank line

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<?php

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Line indented incorrectly; expected 4 spaces, found 2

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  ->fields('tg')

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Array indentation error, expected 6 spaces but found 8

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        '#title' => t('Results deleted from Galaxy Server'),

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Object operator not indented correctly; expected 6 spaces but found 4

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    ->condition('sid', $submission->sid)

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Array indentation error, expected 10 spaces but found 12

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            'header' => TRUE,

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Array indentation error, expected 8 spaces but found 10

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          'header' => TRUE,

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Array indentation error, expected 8 spaces but found 10

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          'data' => 'Start Time',

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Line indented incorrectly; expected 6 spaces, found 7

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       if ($history_content['file_size'] < pow(10, 6)) {

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Object operator not indented correctly; expected 4 spaces but found 2

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  ->fields('tg')

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  ->execute()

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Array indentation error, expected 4 spaces but found 6

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      '#type' => 'item',

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Array indentation error, expected 6 spaces but found 8

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        '#markup' => t('Currently, no results exist for this job. The current state of the job is:  %state.', [

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A comma should follow the last multiline array item. Found: ''

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              '<pre>' . $history_content['creating_job']['stderr'] . '</pre>'

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Array indentation error, expected 8 spaces but found 10

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          'header' => TRUE,

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Inline comments must end in full-stops, exclamation marks, colons, question marks, or closing parentheses

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        // $submission and matching dataset ids and where visible == FALSE

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Array indentation error, expected 10 spaces but found 12

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            'data' => 'Workflow ID',

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Line exceeds 80 characters; contains 98 characters

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       $proxy_url = tripal_galaxy_get_proxy_url($submission, $dataset, $node->uid, 'viewer-full');

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Array indentation error, expected 6 spaces but found 8

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        $submission->workflow_id,

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Line indented incorrectly; expected 6 spaces, found 7

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       $proxy_url = tripal_galaxy_get_proxy_url($submission, $dataset, $node->uid, 'viewer-full');

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Array indentation error, expected 4 spaces but found 6

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      $submission->start_time ? format_date($submission->start_time) : '',

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Array indentation error, expected 8 spaces but found 10

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          'header' => TRUE,

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A comma should follow the last multiline array item. Found: 'tripal-galaxy-submission-table'

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        'class' => 'tripal-galaxy-submission-table'

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Expected 1 space after closing parenthesis; found 9

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        foreach ($submission->errors['history_contents'] as $dc_history_content)

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Expected 1 space after closing parenthesis; found 11

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          if ($dc_history_content['id'] == $inner_elements['object']['id'])

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Line indented incorrectly; expected 6 spaces, found 7

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       $dataset = tripal_galaxy_get_dataset($submission, $dataset_id);

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       } */

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Array indentation error, expected 6 spaces but found 8

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        '#type' => 'item',

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Array indentation error, expected 6 spaces but found 8

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        $submission->sid,

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Array indentation error, expected 10 spaces but found 12

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            'header' => TRUE,

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Array indentation error, expected 10 spaces but found 12

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            'data' => 'Invocation ID',

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Array indentation error, expected 4 spaces but found 6

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      array_key_exists('error', $submission->errors) ? $submission->errors['error'] : '',

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Functions must not contain multiple empty lines in a row; found 2 empty lines

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Line indented incorrectly; expected 6 spaces, found 4

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    ->execute();

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Functions must not contain multiple empty lines in a row; found 2 empty lines

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Line indented incorrectly; expected 6 spaces, found 7

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       // SPF: originally this was $history_content['dataset_id'] but for

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Array indentation error, expected 6 spaces but found 8

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        '#description' => t('It appears this analysis result has been deleted from the galaxy server on which it was run. Please return to the previous page and delete this from your workflow listing.'),

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A comma should follow the last multiline array item. Found: 'tripal-galaxy-error-table'

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          'class' => 'tripal-galaxy-error-table'

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Array indentation error, expected 4 spaces but found 6

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      $title,

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Array indentation error, expected 8 spaces but found 10

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          'data' => 'Submission Error',

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Array indentation error, expected 4 spaces but found 6

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      '#attributes' => [

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Array indentation error, expected 4 spaces but found 6

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      '#attached' => [

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Array indentation error, expected 8 spaces but found 10

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          'misc/collapse.js',

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Line indented incorrectly; expected 6 spaces, found 7

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       // in v18.01 it seems fixed and both 'id' and 'dataset_id' are the

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Line indented incorrectly; expected 4 spaces, found 2

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  ->condition('galaxy_id', $submission->galaxy_id)

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Expected 1 space before "=="; 2 found

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        if ($history_content['history_content_type']  == 'dataset_collection') {

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Array indentation error, expected 6 spaces but found 8

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        '#markup' => t('The result files are listed below. Click the filename to view or download results. Expand the field for the result below to

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Array indentation error, expected 4 spaces but found 6

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      $submission->status,

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Array indentation error, expected 8 spaces but found 10

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          'data' => 'Galaxy Server',

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Array indentation error, expected 4 spaces but found 6

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      '#title' => t('Submission Details'),

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  // If this is a file add viewing and download links

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Line indented incorrectly; expected 6 spaces, found 4

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    ->condition('sid', $submission->sid)

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Array indentation error, expected 6 spaces but found 8

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        '#title' => t('Results'),

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Array indentation error, expected 8 spaces but found 10

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          'header' => TRUE,

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Array indentation error, expected 8 spaces but found 10

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          'data' => 'History Name',

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Line exceeds 80 characters; contains 111 characters

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        // Get the $history_content for each of the dataset ids we just dug up. These can be found by examining

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Expected 1 blank line after function; 2 found

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}

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Functions must not contain multiple empty lines in a row; found 2 empty lines

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Functions must not contain multiple empty lines in a row; found 2 empty lines

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Array indentation error, expected 8 spaces but found 10

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          'data' => 'Workflow Name',

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Array indentation error, expected 10 spaces but found 12

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            'width' => '25%',

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Array indentation error, expected 8 spaces but found 10

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          'header' => TRUE,

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Array indentation error, expected 8 spaces but found 10

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          'data' => 'End Time',

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Array indentation error, expected 4 spaces but found 6

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      '#collapsible' => TRUE,

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Expected 1 blank line after function; 0 found

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}

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Expected 1 space after closing parenthesis; found 5

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    if ($element['element_type'] == 'dataset_collection')

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Line exceeds 80 characters; contains 86 characters

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      /*             // Any files that are smaller than 1MB can be shown in a browser.

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Array indentation error, expected 6 spaces but found 8

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        '#type' => 'item',

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Array indentation error, expected 6 spaces but found 8

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        '#title' => t('Result Files'),

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Array indentation error, expected 10 spaces but found 12

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            'width' => '25%',

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Array indentation error, expected 6 spaces but found 8

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        $submission->invocation_id,

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Array indentation error, expected 4 spaces but found 6

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      $submission->end_time ? format_date($submission->end_time) : '',

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Array indentation error, expected 8 spaces but found 10

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          'misc/form.js',

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Line indented incorrectly; expected 6 spaces, found 7

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       // some reason that value seems off for v17.09 as it does not

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Line indented incorrectly; expected 6 spaces, found 7

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       '#type' => 'item',

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Line indented incorrectly; expected 6 spaces, found 7

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       '#title' => t('View File'),

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Array indentation error, expected 8 spaces but found 10

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          'header' => TRUE,

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Array indentation error, expected 8 spaces but found 10

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          'data' => 'Submission Date',

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Array indentation error, expected 4 spaces but found 6

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      $galaxy->servername . '<br>' . $galaxy_logo,

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Line indented incorrectly; expected 6 spaces, found 7

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       // point to the correct dataset. Rather the 'id' does.  However,

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Line indented incorrectly; expected 6 spaces, found 7

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       $step_content['html_view'] = [

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Line indented incorrectly; expected 6 spaces, found 7

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       '#markup' => l($history_content['name'], $proxy_url, ['attributes' => ['target' => '_blank']] ),

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Array indentation error, expected 6 spaces but found 8

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        '#markup' => t('This link has expired. Please reload the job results page for uploaded links.'),

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Array indentation error, expected 6 spaces but found 8

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        '#type' => 'item',

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Expected 1 blank line after function; 2 found

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}

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Return type missing for @return tag in function comment

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 * @return

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Array indentation error, expected 6 spaces but found 8

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        '#type' => 'markup',

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Array indentation error, expected 6 spaces but found 8

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        '#markup' => t('This link has expired. Please reload the job results page for uploaded links.'),

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Inline comments must start with a capital letter

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    // retrieve the pertinents needed to download the file.

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Array indentation error, expected 6 spaces but found 8

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        '#markup' => t('This page has expired. Please reload the job results page for uploaded links.'),

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Concat operator must be surrounded by a single space

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    $breadcrumb[] = l(t('Analysis Results'), 'user/' . $uid . '/galaxy-jobs/'  . $sid);

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Array indentation error, expected 6 spaces but found 8

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        '#type' => 'markup',

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Array indentation error, expected 6 spaces but found 8

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        '#markup' => '<iframe src="' . url('galaxy/viewer-full/' . $proxy_id) . '" id="tripal-galaxy-results-viewer-iframe"></iframe>',

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Expected 1 blank line after function; 2 found

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}

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Array indentation error, expected 6 spaces but found 8

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        '#markup' => '<h2>Viewing results for ' . $name . '</h2>',

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Expected "object" but found "stdClass" for parameter type

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 * @param stdClass $submission

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Array indentation error, expected 6 spaces but found 8

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        '#type' => 'markup',

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Inline comments must start with a capital letter

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  // retrieve the pertinents needed to download the file.

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Array indentation error, expected 6 spaces but found 8

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        '#type' => 'markup',

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Inline comments must start with a capital letter

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  // retrieve the pertinents needed to download the file.

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Array indentation error, expected 6 spaces but found 8

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        '#markup' => l(t('View full screen'), 'galaxy/viewer-full/' . $proxy_id),

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