zenodo.inc File Reference

Go to the source code of this file.

Functions
	tpps_doi_create ()
	tpps_doi_format_name ($name)
	tpps_doi_load ($id)
	tpps_doi_metadata ($id, $metadata)
	tpps_doi_publish ($id)
	tpps_doi_upload_files ($id, array &$state)
	tpps_generate_doi ($accession)

Detailed Description

Defines functions to create and populate Zenodo DOIs.

Definition in file zenodo.inc.

Function Documentation

tpps_doi_create()

tpps_doi_create

(

)

Creates a blank Zenodo DOI Deposition. Returns the Zenodo id number.

Returns

int The Zenodo Deposition id number.

Definition at line 81 of file zenodo.inc.

                           {
  $token = variable_get('tpps_zenodo_api_key', NULL);
  $prefix = variable_get('tpps_zenodo_prefix', '');
  $ch = curl_init("https://{$prefix}zenodo.org/api/deposit/depositions?" . http_build_query(array('access_token' => $token)));
  curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
  curl_setopt($ch, CURLOPT_HTTPHEADER, array('Content-Type: application/json'));
  curl_setopt($ch, CURLOPT_POST, 1);
  curl_setopt($ch, CURLOPT_POSTFIELDS, '{}');

  $out = json_decode(curl_exec($ch));
  curl_close($ch);
  return $out->id;
}

tpps_doi_format_name()

tpps_doi_format_name

(

$name

)

Formats an author name for Zenodo metadata fields.

Parameters

string

$name

The name to format.

Returns

string The formatted name.

Definition at line 267 of file zenodo.inc.

                                     {
  $parts = explode(' ', $name);
  $first = $parts[0];
  $last = implode(' ', array_slice($parts, 1));
  return "$last, $first";
}

tpps_doi_load()

tpps_doi_load

(

$id

)

Loads and returns the Deposition object for an existing Zenodo Deposition.

Parameters

int

$id

The identifier for the Deposition.

Returns

object The loaded Deposition object.

Definition at line 247 of file zenodo.inc.

                            {
  $token = variable_get('tpps_zenodo_api_key', NULL);
  $prefix = variable_get('tpps_zenodo_prefix', '');
  $ch = curl_init("https://{$prefix}zenodo.org/api/deposit/depositions/$id?" . http_build_query(array('access_token' => $token)));
  curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);

  $out = json_decode(curl_exec($ch));
  curl_close($ch);
  return $out;
}

tpps_doi_metadata()

tpps_doi_metadata	(		$id,
			$metadata
	)

Adds metadata to a Zenodo DOI Deposition. Returns the Deposition object.

Parameters

int	$id	The Deposition identifier.
object	$metadata	The metadata object describing the deposition.

Returns

object The updated Deposition object.

Definition at line 106 of file zenodo.inc.

                                           {

  $data = new stdClass();
  $data->metadata = $metadata;
  $data_json = json_encode($data);

  $token = variable_get('tpps_zenodo_api_key', NULL);
  $prefix = variable_get('tpps_zenodo_prefix', '');
  $ch = curl_init("https://{$prefix}zenodo.org/api/deposit/depositions/$id?" . http_build_query(array('access_token' => $token)));
  curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
  curl_setopt($ch, CURLOPT_HTTPHEADER, array(
    'Content-Type: application/json',
    'Content-Length: ' . strlen($data_json),
  ));
  curl_setopt($ch, CURLOPT_CUSTOMREQUEST, 'PUT');
  curl_setopt($ch, CURLOPT_POSTFIELDS, $data_json);

  $out = json_decode(curl_exec($ch));
  curl_close($ch);
  return $out;
}

tpps_doi_publish()

tpps_doi_publish

(

$id

)

Publishes a completed Zenodo Deposition. Returns the Deposition object.

Parameters

int

$id

The identifier for the Deposition.

Returns

object The updated Deposition object.

Definition at line 225 of file zenodo.inc.

                               {
  $token = variable_get('tpps_zenodo_api_key', NULL);
  $prefix = variable_get('tpps_zenodo_prefix', '');
  $ch = curl_init("https://{$prefix}zenodo.org/api/deposit/depositions/$id/actions/publish?" . http_build_query(array('access_token' => $token)));
  curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
  curl_setopt($ch, CURLOPT_POST, 1);
  curl_setopt($ch, CURLOPT_POSTFIELDS, '');

  $out = json_decode(curl_exec($ch));
  curl_close($ch);
  return $out;
}

tpps_doi_upload_files()

tpps_doi_upload_files	(		$id,
		array &	$state
	)

Adds files to a Zenodo Deposition from the state of a TPPS Submission form.

Parameters

int	$id	The identifier for the Deposition.
array	$state	The form_state of the TPPS Submission form.

Definition at line 136 of file zenodo.inc.

                                                   {
  $token = variable_get('tpps_zenodo_api_key', NULL);
  $prefix = variable_get('tpps_zenodo_prefix', '');
  $files = array();

  for ($i = 1; $i <= $state['stats']['species_count']; $i++) {
    $files[] = $state['saved_values'][TPPS_PAGE_3]['tree-accession']["species-$i"]['file'];
    if (empty($state['saved_values'][TPPS_PAGE_3]['tree-accession']['check'])) {
      break;
    }
  }

  for ($i = 1; $i <= $state['saved_values'][TPPS_PAGE_1]['organism']['number']; $i++) {
    if (isset($state['saved_values'][TPPS_PAGE_4]["organism-$i"]['phenotype'])) {
      $phenotype = &$state['saved_values'][TPPS_PAGE_4]["organism-$i"]['phenotype'];
      if (!empty($phenotype['normal-check'])) {
        $files[] = $phenotype['file'];
        if ($phenotype['check']) {
          $files[] = $phenotype['metadata'];
        }
      }

      if (!empty($phenotype['iso-check'])) {
        $files[] = $phenotype['iso'];
      }
    }

    if (isset($state['saved_values'][TPPS_PAGE_4]["organism-$i"]['genotype'])) {
      $genotype = &$state['saved_values'][TPPS_PAGE_4]["organism-$i"]['genotype'];
      if ($genotype['ref-genome'] == 'manual' or $genotype['ref-genome'] == 'manual2' or $genotype['ref-genome'] == 'url') {
        if ($genotype['tripal_fasta']['file_upload']) {
          $files[] = $genotype['tripal_fasta']['file_upload'];
        }

        if ($genotype['tripal_fasta']['file_upload_existing']) {
          $files[] = $genotype['tripal_fasta']['file_upload_existing'];
        }
      }

      if (!empty($genotype['files']['file-type']['SNPs Genotype Assay'])) {
        $files[] = $genotype['files']['snps-assay'];
      }

      if (!empty($genotype['files']['file-type']['Assay Design']) and $genotype['marker-type']['SNPs']) {
        $files[] = $genotype['files']['assay-design'];
      }

      if (!empty($genotype['files']['file-type']['SSRs/cpSSRs Genotype Spreadsheet'])) {
        $files[] = $genotype['files']['ssrs'];
      }

      if (!empty($genotype['files']['file-type']['Other Marker Genotype Spreadsheet'])) {
        $files[] = $genotype['files']['other'];
      }

      if (!empty($genotype['files']['file-type']['VCF'])) {
        $files[] = $genotype['files']['vcf'];
      }
    }
  }

  foreach ($files as $file) {
    $file = file_load($file);
    if ($file->filesize < 20000000000) {
      $path = drupal_realpath($file->uri);
      $data = array(
        'file' => curl_file_create($path, $file->filemime, $file->filename),
      );

      $ch = curl_init("https://{$prefix}zenodo.org/api/deposit/depositions/$id/files?" . http_build_query(array('access_token' => $token)));
      curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
      curl_setopt($ch, CURLOPT_HTTPHEADER, array('Content-Type: multipart/form-data'));
      curl_setopt($ch, CURLOPT_POST, 1);
      curl_setopt($ch, CURLOPT_POSTFIELDS, $data);
      curl_exec($ch);
      curl_close($ch);
    }
  }
}

tpps_generate_doi()

tpps_generate_doi

(

$accession

)

Creates a Zenodo DOI and loads metadata from a TPPS Submission accession.

Parameters

string

$accession

The accession number of the TPPS Submission.

string $base_url The base URL of the site.

Returns

object The Zenodo DOI Deposition object.

Definition at line 20 of file zenodo.inc.

                                       {
  global $base_url;
  $state = tpps_load_submission($accession);

  $id = tpps_doi_create();
  $creators = array(
    (object) array(
      'name' => tpps_doi_format_name($state['saved_values'][TPPS_PAGE_1]['primaryAuthor']),
      'affiliation' => $state['saved_values'][TPPS_PAGE_1]['organization'],
    ),
  );
  for ($i = 1; $i <= $state['saved_values'][TPPS_PAGE_1]['publication']['secondaryAuthors']['number']; $i++) {
    $creators[] = (object) array(
      'name' => tpps_doi_format_name($state['saved_values'][TPPS_PAGE_1]['publication']['secondaryAuthors'][$i]),
    );
  }

  $keywords = array();
  for ($i = 1; $i <= $state['saved_values'][TPPS_PAGE_1]['organism']['number']; $i++) {
    $keywords[] = $state['saved_values'][TPPS_PAGE_1]['organism'][$i]['name'];
  }

  $study_type_options = array(
    1 => 'Natural Population (Landscape)',
    2 => 'Growth Chamber',
    3 => 'Greenhouse',
    4 => 'Experimental/Common Garden',
    5 => 'Plantation',
  );

  $keywords[] = $study_type_options[$state['saved_values'][TPPS_PAGE_2]['study_type']];

  $metadata = (object) array(
    'title' => $state['saved_values'][TPPS_PAGE_1]['publication']['title'],
    'upload_type' => 'dataset',
    'description' => $state['saved_values'][TPPS_PAGE_1]['publication']['abstract'],
    'creators' => $creators,
    // 'access_right' => 'embargoed', //TODO: collect embargo date from user.
    'keywords' => $keywords,
    'notes' => $state['saved_values']['summarypage']['comments'],
    'related_identifiers' => array(
      (object) array(
        'relation' => 'isAlternateIdentifier',
        'identifier' => "$base_url/tpps/details/$accession",
      ),
    ),
  );

  tpps_doi_upload_files($id, $state);

  $upload = tpps_doi_metadata($id, $metadata);

  return $upload;
}