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cgrb_data_import.module
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<?php
$log_file = "/data/www/planteome_dev/curate/logs/php.log";
/**
* @file
* A module to pull in initial data for the OSU CGRB site
*/
/**
* Implements hook_help().
*
* Displays help and module information.
*
* @param path
* Which path of the site we're using to display help
* @param arg
* Array that holds the current path as returned from arg() function
*/
function cgrb_data_import_help($path, $arg) {
switch ($path) {
case "admin/help#cgrb_data_import":
return t("Initial data population for CGRB site.");
break;
}
}
/**
* Implements hook_menu().
*
*/
function cgrb_data_import_menu() {
$items['importowl'] = array(
'title' => 'Import OWL data from URL',
'page callback' => 'drupal_get_form',
'page arguments' => array('owl_import_form'),
'access callback' => 'access_function',);
$items['importgene'] = array(
'title' => 'Import gene data from TSV files',
'page callback' => 'drupal_get_form',
'page arguments' => array('gene_import_form'),
'access callback' => 'access_function',);
$items['autocomplete/species'] = array(
'page callback' => 'autocomplete_species',
'type' => MENU_CALLBACK,
'access callback' => 'access_function',);
$items['autocomplete/sources'] = array(
'page callback' => 'autocomplete_sources',
'type' => MENU_CALLBACK,
'access callback' => 'access_function',);
$items['autocomplete/genes'] = array(
'page callback' => 'autocomplete_genes',
'type' => MENU_CALLBACK,
'access callback' => 'access_function',);
$items['autocomplete/aspect'] = array(
'page callback' => 'autocomplete_aspect',
'type' => MENU_CALLBACK,
'access callback' => 'access_function',);
$items['autocomplete/ontology_term'] = array(
'page callback' => 'autocomplete_ontology_term',
'type' => MENU_CALLBACK,
'access callback' => 'access_function',);
$items['autocomplete/ontology_term_extended'] = array(
'page callback' => 'autocomplete_ontology_term_extended',
'type' => MENU_CALLBACK,
'access callback' => 'access_function',);
$items['autocomplete/evidence_code'] = array(
'page callback' => 'autocomplete_evidence_code',
'type' => MENU_CALLBACK,
'access callback' => 'access_function',);
$items['importgaf'] = array(
'title' => 'Import GAF data',
'page callback' => 'drupal_get_form',
'page arguments' => array('gaf_import_form'),
'access callback' => 'access_function',);
$items['updatesources'] = array(
'title' => 'Update source data',
'page callback' => 'drupal_get_form',
'page arguments' => array('update_sources_form'),
'access callback' => 'access_function',);
$items['exportgaf'] = array(
'title' => 'Export selected annotations to a gaf file',
'page callback' => 'drupal_get_form',
'page arguments' => array('gaf_export_form'),
'access callback' => 'access_function',);
$items['browse_annotations'] = array(
'title' => 'Annotations',
'page callback' => 'browse_annotation_page',
'type' => MENU_NORMAL_ITEM,
'access callback' => 'access_function',);
$items['clear_malformed_genes'] = array(
'title' => 'Clear Malformed Genes',
'page callback' => 'drupal_get_form',
'page arguments' => array('clear_malformed_genes_form'),
'access callback' => 'access_function',);
$items['translate_gaf_id'] = array(
'title' => 'Translate GAF file ID',
'page callback' => 'drupal_get_form',
'page arguments' => array('translate_gaf_id_form'),
'access callback' => 'access_function',);
$items['add_gene_synonyms'] = array(
'title' => 'Add Gene Synonyms',
'page callback' => 'drupal_get_form',
'page arguments' => array('add_gene_synonyms_form'),
'access callback' => 'access_function',);
$items['update_gene_counts'] = [
'title' => 'Update Taxon Gene Counts',
'page callback' => 'drupal_get_form',
'page arguments' => ['update_gene_counts_form'],
'access callback' => 'access_function',];
$items['update_gene_ontology_terms'] = [
'title' => 'Update Gene Ontology term lists',
'page callback' => 'drupal_get_form',
'page arguments' => ['update_gene_ontology_terms_form'],
'access callback' => 'access_function',];
return $items;
}
/*************ANNOTATION VIEWER*************/
function browse_annotation_page(){
$filter_form = drupal_get_form('filter_annotation_form');
$browse_form = drupal_get_form('browse_annotation_form');
// $ecodes = taxonomy_vocabulary_machine_name_load('evidence_code');
// $ecodes_array = taxonomy_get_tree($ecodes->vid);
// $ecodes_legend = '<div style="display: inline-block;float:left;"><h3>Evidence Code Key</h3><ul>';
// foreach($ecodes_array as $ecode){
// $ecodes_legend.= '<li>'.$ecode->name.'</li>';
// }
// $ecodes_legend.= '</ul></div>';
$output = '';
// $output.= $ecodes_legend;
$output.= drupal_render($filter_form);
$output.= drupal_render($browse_form);
return $output;
}
function filter_annotation_form($form, &$form_state){
$form['#method'] = 'get';
$form['filters'] = array(
'#type' => 'fieldset',
'#title' => t('Show annotations matching the following criteria:'),
'#attributes'=> array(
'style' => 'display: inline-block;'
),
);
$form['filters']['aspect'] = array(
'#type' => 'select',
'#title' => 'Aspect is:',
'#options' => taxonomy_to_select_array('aspect'),
'#default_value' => (isset($_GET['aspect']) ? urldecode($_GET['aspect']) : ''),
);
$form['filters']['species'] = array(
'#type' => 'textfield',
'#title' => 'Species is:',
'#autocomplete_path'=> 'autocomplete/species',
'#default_value' => (isset($_GET['species']) ? urldecode($_GET['species']) : ''),
);
$form['filters']['gene'] = array(
'#type' => 'textfield',
'#title' => 'Gene is:',
'#autocomplete_path'=> 'autocomplete/genes',
'#default_value' => (isset($_GET['gene']) ? urldecode($_GET['gene']) : ''),
);
$form['filters']['ontology_term'] = array(
'#type' => 'textfield',
'#title' => 'Ontology term is:',
'#autocomplete_path'=> 'autocomplete/ontology_term',
'#default_value' => (isset($_GET['ontology_term']) ? urldecode($_GET['ontology_term']) : ''),
);
// $form['filters']['data_source'] = array(
// '#type' => 'textfield',
// '#title' => 'Data Source is:',
// '#autocomplete_path'=> 'autocomplete/sources',
// '#default_value' => (isset($_GET['data_source']) ? urldecode($_GET['data_source']) : ''),
// );
$form['filters']['evidence_code'] = array(
'#type' => 'select',
// '#multiple' => TRUE,
'#title' => 'Evidence code is one of:',
'#options' => array_merge(array(''=>''),(taxonomy_to_select_array('evidence_code'))),
'#default' => (isset($_GET['evidence_code']) ? urldecode($_GET['evidence_code']) : ''),
);
$form['filters']['submit'] = array(
'#type' => 'submit',
'#value' => t('Filter'),
'#prefix' => '<span style="display:block;">',
'#suffix' => '</span>',
);
return $form;
}
function browse_annotation_form($form, &$form_state){
global $pager_total_items;
$num_items = (int)$pager_total_items[0];
drupal_set_message('Currently applied filters give '.$num_items.' results. Please filter until there are '.variable_get('export_gaf_annotation_limit').' items or less. If you need to export more than '.variable_get('export_gaf_annotation_limit').' items, please contact a system administrator.');
$header = array(
t('Annotation Accession'),
[
'data' => t('Aspect'),
'type' => 'field',
'specifier' => array('field' => 'field_aspect', 'column' => 'tid'),
],
// t('Aspect'),
[
'data' => t('Ontology ID Term'),
'type' => 'field',
'specifier' => array('field' => 'field_ontology_id', 'column' => 'value'),
],
// t('Ontology ID Term'),
[
'data' => t('Species'),
'type' => 'field',
'specifier' => array('field' => 'field_ontology_id', 'column' => 'value'),
],
// t('Species'),
[
'data' => t('Gene'),
'type' => 'field',
'specifier' => array('field' => 'field_gene', 'column' => 'target_id'),
],
// t('Gene'),
// t('Data Source Name'),
[
'data' => t('Evidence Code'),
'type' => 'field',
'specifier' => array('field' => 'field_evidence_code', 'column' => 'tid'),
],
// t('Evidence Code')
);
$query = new EntityFieldQuery();
$query->entityCondition('entity_type','node')
->entityCondition('bundle', 'annotation');
if(isset($_GET['gene']) && !empty($_GET['gene'])){
$q = new EntityFieldQuery();
$q->entityCondition('entity_type','node')
->entityCondition('bundle', 'gene')
->propertyCondition('title',$_GET['gene']);
$r = $q->execute();
if (!empty($r['node'])) {
$arrkeys = array_keys($r['node']);
$key = array_shift($arrkeys);
$gene = node_load($key);
$query->fieldCondition('field_gene','target_id',$gene->nid,'=');
}
}
if(isset($_GET['species']) && !empty($_GET['species'])){
$q = new EntityFieldQuery();
$q->entityCondition('entity_type','node')
->entityCondition('bundle', 'taxon')
->propertyCondition('title',$_GET['species']);
$r = $q->execute();
if (!empty($r['node'])) {
$arrkeys = array_keys($r['node']);
$key = array_shift($arrkeys);
$species = node_load($key);
$query->fieldCondition('field_ref_species','target_id',$species->nid,'=');
}
}
if(isset($_GET['aspect']) && !empty($_GET['aspect'])){
$term = taxonomy_term_load($_GET['aspect']);
$query->fieldCondition('field_aspect','tid',$term->tid,'=');
}
if(isset($_GET['evidence_code']) && !empty($_GET['evidence_code'])){
$term = taxonomy_term_load($_GET['evidence_code']);
$query->fieldCondition('field_evidence_code','tid',$term->tid,'=');
}
if(isset($_GET['ontology_term']) && !empty($_GET['ontology_term'])){
$query->fieldCondition('field_ontology_id','value', get_ontology_id_from_term($_GET['ontology_term']),'=');
}
/*if(isset($_GET['data_source']) && !empty($_GET['data_source'])){
$ttl = taxonomy_get_term_by_name($_GET['data_source']);
$ttl2 = array_shift($ttl);
$q = new EntityFieldQuery();
$r = $q->entityCondition('entity_type', 'field_collection_item')
->propertyCondition('field_name','field_data_source')
->fieldCondition('field_source_name', 'tid', $ttl2->tid, '=')
->execute();
if(empty($r)){
$query->fieldCondition('field_data_source','value', $_GET['data_source']);
} else {
$keys = array_keys($r['field_collection_item']);
$query->fieldCondition('field_data_source','value', $keys);
}
}*/
$query = $query->tableSort($header);
$query->pager(50)->propertyOrderBy('title', 'DESC');
$results = $query->execute();
$num_items = count($results['node']);
$rows = array();
global $user;
if(!empty($results['node'])){
foreach($results['node'] as $result){
$annotation = node_load($result->nid);
$species = node_load($annotation->field_ref_species[$annotation->language][0]['target_id']);
$gene = node_load($annotation->field_gene[$annotation->language][0]['target_id']);
$aspect = taxonomy_term_load($annotation->field_aspect[$annotation->language][0]['tid']);
$evidence = taxonomy_term_load($annotation->field_evidence_code[$annotation->language][0]['tid']);
$data_source_fc_id = $annotation->field_data_source[$annotation->language][0]['value'];
$data_source = entity_load('field_collection_item', array($data_source_fc_id));
$source_term = taxonomy_term_load($data_source[$data_source_fc_id]->field_source_name[$annotation->language][0]['tid']);
$db = $source_term->field_machine_name['und'][0]['value'];
$rows[$annotation->title] = array(
'<a href="/osu-cgrb/website/content/'.$annotation->title.'">'.$annotation->title.'</a>',
$aspect->name,
'<a href="http://browser.planteome.org/amigo/term/'.$annotation->field_ontology_id[$annotation->language][0]['value'].'">'.$annotation->field_ontology_id[$annotation->language][0]['value'].' - '.get_ontology_term_from_id($annotation->field_ontology_id[$annotation->language][0]['value']).'</a>',
'<a href="/osu-cgrb/website/node/'.$species->nid.'">'.$species->title.'</a>',
'<a href="/osu-cgrb/website/node/'.$gene->nid.'">'.$gene->field_gene_id[$gene->language][0]['value'].'</a>',
$db,
$evidence->field_machine_name[$annotation->language][0]['value'],
);
}
}
$form['tableselect'] = array(
'#type' => 'tableselect',
'#header' => $header,
'#options' => $rows,
'#empty' => t('No Records found'),
);
$form['num_items'] = [
'#type' => 'textfield',
'#access' => FALSE,
'#default_value' => $num_items,
];
$form['pager'] = array('#markup' => theme('pager'));
$form['gaf_notes'] = [
'#title' => t('Add a note to the exported GAF file. (GAF version & current date added automatically)'),
'#type' => 'textarea',
];
$form['submit_selected'] = array(
'#type' => 'submit',
'#value' => t('Export Selected'),
'#submit' => array('browse_annotation_form_submit_selected'),
'#disabled' => true,
);
$form['submit_all'] = array(
'#type' => 'submit',
'#value' => t('Export All (matching criteria)'),
'#submit' => array('browse_annotation_form_submit_all')
);
$form['#attached']['js'] = array(
drupal_get_path('module', 'cgrb_data_import') . '/cgrb_data_import.js',
);
// drupal_add_js(drupal_get_path('module', 'cgrb_data_import') . '/cgrb_data_import.js');
return $form;
}
function browse_annotation_form_validate($form, &$form_state){
$results = array_filter($form_state['values']['tableselect']);
global $pager_total_items;
$num_items = (int)$pager_total_items[0];
if($num_items > variable_get('export_gaf_annotation_limit')){
form_set_error('tableselect', "Currently there are ".$num_items." annotations that match the filter criteria.\nUnable to export more than ".variable_get('export_gaf_annotation_limit')." annotations at a time with this method.\nPlease filter your query further.");
}
// echo'<pre>';var_dump($num_items);exit;
}
function browse_annotation_form_submit_selected($form, &$form_state){
$results = array_filter($form_state['values']['tableselect']);
// echo(count($results));exit;
$gaf_data = "!gaf-version: 2.0\n!date: ".date("Y/m/d")."\n";
// $gaf_data.= variable_get('export_gaf_header_value')
$gaf_data.= format_gaf_text(variable_get('export_gaf_header_value'));
$gaf_data.= format_gaf_text($form_state['values']['gaf_notes']);
$gaf_data.= "!DB\tDB Object ID\tDB Object Symbol\tQualifier\tGO ID\tDB:Reference\tEvidence Code\tWith (or) From\tAspect\tDB Object Name\tDB Object Synonym\tDB Object Type\tTaxon\tDate\tAssigned By\tAnnotation Extension\tGene Product Form ID\n";
// echo '<pre>'.$gaf_data;exit;
// echo'<pre>';var_dump('ye');exit;
foreach($results as $ann_acc){
$query = new EntityFieldQuery();
$query->entityCondition('entity_type','node')
->entityCondition('bundle', 'annotation')
->propertyCondition('title',$ann_acc);
$results = $query->execute();
if(count($results['node'])){
$annotation = array_pop(array_reverse($results['node']));
$gaf_data .= annotation_to_gaf_line($annotation->nid);
}
}
$filename = 'planteome_gaf_'.format_date(time(), 'custom', 'YMdHi').'.assoc';
$file = file_save_data($gaf_data, 'public://'.$filename);
// echo'<pre>';
// echo(file_get_contents($file->uri));
// echo'<pre>';var_dump($file);exit;
header('Content-Description: File Transfer');
header('Content-Type: '.$file->filemime);
header('Content-Disposition: attachment; filename="'.$file->filename.'"');
header('Expires: 0');
header('Cache-Control: must-revalidate');
header('Pragma: public');
header('Content-Length: '.$file->filesize);
readfile($file->uri);
// exit;
file_delete($file);
exit;
// $file = file_save_data($gaf_data, 'public://'.$filename);
// echo'<pre>';
// echo(file_get_contents($file->uri));
// file_delete($file);
// exit;
// echo'<pre>';var_dump($results);exit;
}
function format_gaf_text($text){
$lines_array = explode("\n", $text);
$out = '';
// echo'<pre>';var_dump($lines_array);exit;
foreach($lines_array as $line){
$out.= "!".$line."\n";
}
return $out;
}
//TODO 2 - Lakshit
//will need a batch process
function browse_annotation_form_submit_all($form, &$form_state){
$query = new EntityFieldQuery();
$query->entityCondition('entity_type','node')
->entityCondition('bundle', 'annotation');
if(isset($_GET['gene']) && !empty($_GET['gene'])){
$q = new EntityFieldQuery();
$q->entityCondition('entity_type','node')
->entityCondition('bundle', 'gene')
->propertyCondition('title',$_GET['gene']);
$r = $q->execute();
if (!empty($r['node'])) {
$arrkeys = array_keys($r['node']);
$key = array_shift($arrkeys);
$gene = node_load($key);
$query->fieldCondition('field_gene','target_id',$gene->nid,'=');
}
}
if(isset($_GET['species']) && !empty($_GET['species'])){
$q = new EntityFieldQuery();
$q->entityCondition('entity_type','node')
->entityCondition('bundle', 'taxon')
->propertyCondition('title',$_GET['species']);
$r = $q->execute();
if (!empty($r['node'])) {
$arrkeys = array_keys($r['node']);
$key = array_shift($arrkeys);
$species = node_load($key);
$query->fieldCondition('field_ref_species','target_id',$species->nid,'=');
}
}
if(isset($_GET['aspect']) && !empty($_GET['aspect'])){
$term = taxonomy_term_load($_GET['aspect']);
$query->fieldCondition('field_aspect','tid',$term->tid,'=');
}
if(isset($_GET['evidence_code']) && !empty($_GET['evidence_code'])){
$term = taxonomy_term_load($_GET['evidence_code']);
$query->fieldCondition('field_evidence_code','tid',$term->tid,'=');
}
$results = $query->execute();
$gaf_data = "!gaf-version: 2.0\n!date: ".date("Y/m/d")."\n";
// $gaf_data.= variable_get('export_gaf_header_value')
$gaf_data.= format_gaf_text(variable_get('export_gaf_header_value'));
$gaf_data.= format_gaf_text($form_state['values']['gaf_notes']);
$gaf_data.= "!DB\tDB Object ID\tDB Object Symbol\tQualifier\tGO ID\tDB:Reference\tEvidence Code\tWith (or) From\tAspect\tDB Object Name\tDB Object Synonym\tDB Object Type\tTaxon\tDate\tAssigned By\tAnnotation Extension\tGene Product Form ID\n";
if(array_key_exists('node',$results)){
foreach($results['node'] as $annotation){
$gaf_data .= annotation_to_gaf_line($annotation->nid);
}
$filename = 'planteome_gaf_'.format_date(time(), 'custom', 'YMdHi').'.assoc';
$file = file_save_data($gaf_data, 'public://'.$filename);
// echo'<pre>';
// echo(file_get_contents($file->uri));
// echo'<pre>';var_dump($file);exit;
header('Content-Description: File Transfer');
header('Content-Type: '.$file->filemime);
header('Content-Disposition: attachment; filename="'.$file->filename.'"');
header('Expires: 0');
header('Cache-Control: must-revalidate');
header('Pragma: public');
header('Content-Length: '.$file->filesize);
readfile($file->uri);
// exit;
file_delete($file);
exit;
}
// echo'<pre>';var_dump($results);exit;
}
/*************OWL FORM*************/
/**
* Implements hook_form().
*
* Creates a form .
*
* @param form
* The form we're working with
* @param &form_state
* Reference to the state of the form
*/
function owl_import_form($form, &$form_state){
$form['input'] = array(
'#type' => 'textfield',
'#title' => 'Enter OWL url',
'#required' => TRUE,
);
$form['submit'] = array(
'#type' => 'submit',
'#value' => t('Submit'),
);
return $form;
}
function owl_import_form_validate($form, &$form_state){}
function owl_import_form_submit($form, &$form_state){
$url = $form_state['values']['input'];
$bio_tree = get_children(1,(parse_owl($url)));
iterate($bio_tree);
}
/*************GENE IMPORT FORM*************/
/**
* Implements hook_form().
*
* Creates a form .
*
* @param form
* The form we're working with
* @param &form_state
* Reference to the state of the form
*/
function gene_import_form($form, &$form_state){
//phpinfo();
$form['gene_file'] = array(
'#type' => 'file',
'#title' => t('Upload gene file'),
);
$form['gene_file_alt'] = array(
'#type' => 'checkbox',
'#title' => t('Use alternative file parser? (for files from UNIX/Mac OS X+)'),
);
$form['alias_file'] = array(
'#type' => 'file',
'#title' => t('Upload alias file'),
);
$form['alias_file_alt'] = array(
'#type' => 'checkbox',
'#title' => t('Use alternative file parser? (for files from UNIX/Mac OS X+)'),
);
$form['data'] = array(
'#type' => 'textfield',
'#title' => 'Enter species.',
'#required' => TRUE,
'#autocomplete_path'=> 'autocomplete/species',
);
$form['source'] = array(
'#type' => 'textfield',
'#title' => 'Enter source.',
'#required' => TRUE,
'#autocomplete_path'=> 'autocomplete/sources',
);
$form['submit'] = array(
'#type' => 'submit',
'#value' => t('Submit'),
);
return $form;
}
function gene_import_form_validate($form, &$form_state){}
function gene_import_form_submit($form, &$form_state){
$query = new EntityFieldQuery();
$query->entityCondition('entity_type','node')
->entityCondition('bundle','taxon')
->propertyCondition('type',array('taxon'))
->propertyCondition('title', $form_state['values']['data']);
//this will be updated when we change the context, and can likely be moved outside the batch process altogether
$results = $query->execute();
$species_nid = array_keys($results['node'])[0];
$source_name = $form_state['values']['source'];
if(db_table_exists('tmptable')){
db_drop_table('tmptable');
}
//TODO 3- Lakshit
// - add a new form to reset the accession table
// - this should require a password
/*if(db_table_exists('accession')){
db_drop_table('accession');
exit('accession dropped');
}*/
if(db_table_exists('accession') == FALSE){
$schema = array(
'description' => 'Table to track accession incrementation',
'fields' => array(
'accession' => array(
'type' => 'int',
'not null' => TRUE,
'description' => 'Primary Key: Unique aggregator static media asset ID.'),),
'primary key' => array('accession'),
);
db_create_table('accession',$schema);
db_insert('accession')
->fields(array(
'accession' => 1,
))
->execute();
}
$file1 = file_save_upload('gene_file', array(
'file_validate_extensions' => array('txt'),
));
$file2 = file_save_upload('alias_file', array(
'file_validate_extensions' => array('txt'),
));
//get the content in the file
$content1 = file_get_contents($file1->uri);
$content2 = file_get_contents($file2->uri);
//remove the file in temp and the pointer in the database
file_delete($file1);
file_delete($file2);
if($form_state['values']['gene_file_alt']){
//use UNIX/MACOSX \n
$arr1 = tabbed_file_to_array_alt($content1);
} else {
//use windows \r\n
$arr1 = tabbed_file_to_array($content1);
}
if($form_state['values']['alias_file_alt']){
//use UNIX/MACOSX \n
$arr2 = tabbed_file_to_array_alt($content2);
} else {
//use windows \r\n
$arr2 = tabbed_file_to_array($content2);
}
$chunks1 = array_chunk($arr1, 100);
$chunks2 = array_chunk($arr2, 100);
if(db_table_exists('tmptable') == FALSE){
$schema = array(
'description' => 'tmp table',
'fields' => array(
'pid' => array(
'type' => 'serial',
'not null' => TRUE,
'description' => 'Primary Key: Unique aggregator static media asset ID.'),
'gene_stable_id' => array(
'type' => 'varchar',
'length' => 255,
'not null' => TRUE,
'default' => '',),
'gene_symbol' => array(
'type' => 'varchar',
'length' => 255,
'not null' => FALSE,
'default' => '',),
'gene_name' => array(
'type' => 'varchar',
'length' => 255,
'not null' => FALSE,),),
'primary key' => array('pid'),
);
db_create_table('tmptable',$schema);
}
$operations = array();
foreach($chunks2 as $chunk2){
$operations[] = array('insert_gene_aliases', array($chunk2));
}
foreach($chunks1 as $chunk1){
$operations[] = array('import_gene_data_to_node', array($chunk1, $species_nid, $source_name));
}
$batch = array(
'operations' => $operations,
'finished' => 'biomart_process_finished',
'title' => t('processing biomart gene batch'),
'init_message' => t('starting biomart batch process'),
'progress_message' => t('processed @current out of @total')
);
batch_set($batch);
}
/*************GAF FORM*************/
/**
* Implements hook_form().
*
* Creates a form .
*
* @param form
* The form we're working with
* @param &form_state
* Reference to the state of the form
*/
function gaf_import_form($form, &$form_state){
$form['gaf_file'] = array(
'#type' => 'file',
'#title' => t('Upload gaf file'),
);
$form['id_syntax'] = array(
'#type' => 'textfield',
'#title' => 'Enter the syntax for gene ID present in the uploaded annotation file, using # to represent a number. Example: AT#G#####',
'#required' => TRUE,
);
$form['gaf_url'] = array(
'#type' => 'textfield',
'#title' => 'Enter URL.',
);
$form['submit'] = array(
'#type' => 'submit',
'#value' => t('Submit'),
);
return $form;
}
function gaf_import_form_validate($form, &$form_state){}
function gaf_import_form_submit($form, &$form_state){
//TODO 4 - Lakshit
// - see TODO 3
// if(db_table_exists('annotation_accession')){
// db_drop_table('annotation_accession');
// exit('annotation_accession dropped');
// }
if(db_table_exists('annotation_accession') == FALSE){
$schema = array(
'description' => 'Table to track annotation accession incrementation',
'fields' => array(
'accession' => array(
'type' => 'int',
'not null' => TRUE,
'description' => 'Primary Key'),),
'primary key' => array('accession'),
);
db_create_table('annotation_accession',$schema);
db_insert('annotation_accession')
->fields(array(
'accession' => 1,
))
->execute();
}
$file = file_save_upload('gaf_file', array(
'file_validate_extensions' => array('assoc'),
));
$content = file_get_contents($file->uri);
file_delete($file);
$chunk_amount = 50;
$gaf_rows = explode("\n", $content);
$chunks = array_chunk($gaf_rows, $chunk_amount);
$id_syntax = $form_state['values']['id_syntax'];
$operations = array();
foreach($chunks as $chunk){
$operations[] = array('import_annotation_to_node', array($chunk,$id_syntax));
}
$batch = array(
'operations' => $operations,
'finished' => 'gaf_process_finished',
'title' => t('processing gene annotation batch'),
'init_message' => t('starting gaf batch process'),
'progress_message' => t('processed @current out of @total')
);
batch_set($batch);
}
/*************GAF EXPORT FORM*************/
/**
* Implements hook_form().
*
* Creates a form .
*
* @param form
* The form we're working with
* @param &form_state
* Reference to the state of the form
*/
function gaf_export_form($form, &$form_state){
$form['text'] = array(
'#type' => 'textfield',
'#title'=> t('title'),
);
$form['submit'] = array(
'#type' => 'submit',
'#value' => t('submit'),
);
return $form;
}
function gaf_export_form_validate($form, &$form_state){
}
//TODO 5 - Lakshit
// - Please verify that this is working correctly with a batch process
function gaf_export_form_submit($form, &$form_state){
$annotation_ids = explode("|",$form_state['values']['text']);
$gaf_data = "!gaf-version: 2.0\n!This data in GAF 2.0 format is provided by the NSF-funded Planteome project (www.planteome.org).\n!Date: ".date("Y/m/d");
//foreach version
foreach($annotation_ids as $annotation_id){
$gaf_data .= annotation_to_gaf_line($annotation_id);
}
$filename = 'planteome_gaf_'.format_date(time(), 'custom', 'YMdHi').'.assoc';
//exit($filename);
//file_put_contents($filename, $gaf_data);exit;
$file = file_save_data($gaf_data, 'public://'.$filename);
echo'<pre>';/*var_dump($file);echo'<br><br>';*/echo(file_get_contents($file->uri));file_delete($file);exit;
//might need to uncomment the pre to print nicely
// echo'<pre>';echo $gaf_data;var_dump($gaf_data);exit;
//batch version
// $chunks = array_chunk($annotation_ids, 40);
// //echo '<pre>';var_dump($chunks);exit;
// //$id_syntax = $form_state['values']['id_syntax'];
// $operations = array();
// foreach($chunks as $chunk){
// $operations[] = array('export', array($chunk));
// }
// $batch = array(
// 'operations' => $operations,
// 'finished' => 'gaf_process_finished',
// 'title' => t('processing gene annotation batch'),
// 'init_message' => t('starting gaf batch process'),
// 'progress_message' => t('processed @current out of @total')
// );
// //echo '<pre>';var_dump($batch);exit;
// batch_set($batch);
}
/*************SOURCES FORM*************/
/**
* Implements hook_form().
*
* Creates a form .
*
* @param form
* The form we're working with
* @param &form_state
* Reference to the state of the form
*/
function update_sources_form($form, &$form_state){
$form['submit'] = array(
'#type' => 'submit',
'#value' => t('Click to run the source update script.'),
);
return $form;
}
function update_sources_form_validate($form, &$form_state){
}
function update_sources_form_submit($form, &$form_state){
update_sources();
drupal_set_message(t('Sources have been updated.'));
}
/*************GENE COUNT FORM*************/
function update_gene_counts_form($form, &$form_state){
$form['submit'] = [
'#type' => 'submit',
'#value' => t('Click to run the gene count update script'),
];
return $form;
}
function update_gene_counts_form_validate($form, &$form_state){
}
function update_gene_counts_form_submit($form, &$form_state){
$query = new EntityFieldQuery();
$query->entityCondition('entity_type', 'node')
->entityCondition('bundle', 'taxon')
->propertyCondition('type', ['taxon']);
$results = $query->execute();
// echo'<pre>';var_dump($results);exit;
$chunks = array_chunk($results['node'], 50);
$operations = [];
foreach($chunks as $chunk){
$operations[] = ['update_taxon_gene_count', [$chunk]];
}
$batch = [
'operations' => $operations,
'finished' => 'batch_update_finished',
'title' => t('processing gene count update'),
'title' => t('starting taxon gene count update process'),
'title' => t('processed @current out of @total')
];
batch_set($batch);
// echo'<pre>';var_dump($results);exit;
}
function update_taxon_gene_count($chunk, &$context){
foreach($chunk as $taxon){
$taxon = node_load($taxon->nid);
$query = new EntityFieldQuery();
$query->entityCondition('entity_type', 'node')
->entityCondition('bundle', 'gene')
->fieldCondition('field_ref_species', 'target_id', $taxon->nid, '=');
// ->propertyCondition('type', 'gene');
$results = $query->execute();
$taxon->field_gene_count[$taxon->language][0]['value'] = count($results['node']);
node_save($taxon);
// echo'<pre>';var_dump($taxon);exit;
/*if(isset($results['node']) && count($results['node']) > 3){
echo'<pre>';var_dump($taxon->title);var_dump($results['node']);exit;
}*/
}
}
function batch_update_finished($success, $results, $operations) {
//Let the user know we have finished!
print t('Finished updating!');
}
/*************GENE COUNT FORM*************/
function update_gene_ontology_terms_form($form, &$form_state){
$form['submit'] = [
'#type' => 'submit',
'#value' => t('Click to run the gene ontology term update script'),
];
return $form;
}
function update_gene_ontology_terms_form_validate($form, &$form_state){
}
function update_gene_ontology_terms_form_submit($form, &$form_state){
$query = new EntityFieldQuery();
$query->entityCondition('entity_type', 'node')
->entityCondition('bundle', 'gene')
->propertyCondition('type', ['gene']);
$results = $query->execute();
// echo'<pre>';var_dump($results);exit;
$chunks = array_chunk($results['node'], 50);
$operations = [];
foreach($chunks as $chunk){
$operations[] = ['update_gene_ontology_terms', [$chunk]];
}
$batch = [
'operations' => $operations,
'finished' => 'batch_update_finished',
'title' => t('processing gene ontology terms update'),
'title' => t('starting gene ontology terms update process'),
'title' => t('processed @current out of @total')
];
batch_set($batch);
// echo'<pre>';var_dump($results);exit;
}
function update_gene_ontology_terms($chunk, &$context){
foreach($chunk as $gene){
$gene = node_load($gene->nid);
$query = new EntityFieldQuery();
$query->entityCondition('entity_type', 'node')
->entityCondition('bundle', 'annotation')
->fieldCondition('field_gene', 'target_id', $gene->nid, '=');
$results = $query->execute();
if(isset($results['node'])){
// echo'<pre>';var_dump($results['node']);exit;
$ontology_terms = '';
foreach($results['node'] as $result){