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Tripal v1.0 (6.x-1.0)
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Tripal v1.0 (6.x-1.0)
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Go to the source code of this file.
Functions | |
| tripal_feature_delete_form () | |
| tripal_feature_delete_form_validate ($form, &$form_state) | |
| tripal_feature_delete_form_submit ($form, &$form_state) | |
| tripal_feature_delete_features ($organism_id, $analysis_id, $seq_type, $is_unique, $feature_names, $job=NULL) | |
| tripal_feature_delete_by_analysis ($organism_id, $analysis_id, $seq_type, $is_unique, $feature_names, $job=NULL) | |
Definition in file tripal_feature-delete.inc.
| tripal_feature_delete_by_analysis | ( | $ | organism_id, |
| $ | analysis_id, | ||
| $ | seq_type, | ||
| $ | is_unique, | ||
| $ | feature_names, | ||
| $ | job = NULL |
||
| ) |
Definition at line 162 of file tripal_feature-delete.inc.
{
}
| tripal_feature_delete_features | ( | $ | organism_id, |
| $ | analysis_id, | ||
| $ | seq_type, | ||
| $ | is_unique, | ||
| $ | feature_names, | ||
| $ | job = NULL |
||
| ) |
Definition at line 113 of file tripal_feature-delete.inc.
{
global $user;
$match = array();
// if feature names have been provided then handle that separately
if ($feature_names) {
$names = preg_split('/\s+/', $feature_names);
if (sizeof($names) == 1) {
$names = $names[0];
}
if ($is_unique) {
$match['uniquename'] = $names;
}
else {
$match['name'] = $names;
}
$num_deletes = tripal_core_chado_select('feature', array('count(*) as cnt'), $match);
print "Deleting " . $num_deletes[0]->cnt . " features\n";
tripal_core_chado_delete('feature', $match);
}
// if the user has provided an analysis_id then handle that separately
elseif ($analysis_id) {
tripal_feature_delete_by_analysis();
}
else {
if ($organism_id) {
$match['organism_id'] = $organism_id;
}
if ($seq_type) {
$match['type_id'] = array(
'name' => $seq_type,
'cv_id' => array(
'name' => 'sequence'
),
);
}
$num_deletes = tripal_core_chado_select('feature', array('count(*) as cnt'), $match);
print "Deleting " . $num_deletes[0]->cnt . " features\n";
tripal_core_chado_delete('feature', $match);
}
print "Removing orphaned feature pages\n";
tripal_features_cleanup(array(), $user->uid);
}
| tripal_feature_delete_form | ( | ) |
Definition at line 7 of file tripal_feature-delete.inc.
{
// get the list of organisms
$sql = "SELECT * FROM {organism} ORDER BY genus, species";
$org_rset = chado_query($sql);
$organisms = array();
$organisms[''] = '';
while ($organism = db_fetch_object($org_rset)) {
$organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
}
$form['desc'] = array(
'#type' => 'markup',
'#value' => t("Use one or more of the following fields to identify sets of features to be deleted."),
);
$form['feature_names']= array(
'#type' => 'textarea',
'#title' => t('Feature Names'),
'#description' => t('Please provide a list of feature names or unique names,
separated by spaces or by new lines to be delete. If you specify feature names then
all other options below will be ignored (except the unique checkbox).'),
);
$form['is_unique'] = array(
'#title' => t('Names are Unique Names'),
'#type' => 'checkbox',
'#description' => t('Select this checbox if the names listed in the feature
names box above are the unique name of the feature rather than the human readable names.'),
);
$form['seq_type']= array(
'#type' => 'textfield',
'#title' => t('Sequence Type'),
'#description' => t('Please enter the Sequence Ontology term that describes the features to be deleted. Use in conjunction with an organism or anaylysis.'),
);
$form['organism_id'] = array(
'#title' => t('Organism'),
'#type' => t('select'),
'#description' => t("Choose the organism for which features will be deleted."),
'#options' => $organisms,
);
// get the list of analyses
$sql = "SELECT * FROM {analysis} ORDER BY name";
$org_rset = chado_query($sql);
$analyses = array();
$analyses[''] = '';
while ($analysis = db_fetch_object($org_rset)) {
$analyses[$analysis->analysis_id] = "$analysis->name ($analysis->program $analysis->programversion, $analysis->sourcename)";
}
// TODO: ADD THIS BACK IN LATER
//
// $form['analysis']['analysis_id'] = array (
// '#title' => t('Analysis'),
// '#type' => t('select'),
// '#description' => t("Choose the analysis for which associated features will be deleted."),
// '#options' => $analyses,
// );
$form['button'] = array(
'#type' => 'submit',
'#value' => t('Delete Features'),
);
return $form;
}
| tripal_feature_delete_form_submit | ( | $ | form, |
| &$ | form_state | ||
| ) |
Definition at line 97 of file tripal_feature-delete.inc.
{
global $user;
$organism_id = $form_state['values']['organism_id'];
$seq_type = trim($form_state['values']['seq_type']);
$analysis_id = $form_state['values']['analysis_id'];
$is_unique = $form_state['values']['is_unique'];
$feature_names = $form_state['values']['feature_names'];
$args = array($organism_id, $analysis_id, $seq_type, $is_unique, $feature_names);
tripal_add_job("Delete features", 'tripal_feature',
'tripal_feature_delete_features', $args, $user->uid);
}
| tripal_feature_delete_form_validate | ( | $ | form, |
| &$ | form_state | ||
| ) |
Definition at line 72 of file tripal_feature-delete.inc.
{
$organism_id = $form_state['values']['organism_id'];
$seq_type = trim($form_state['values']['seq_type']);
$analysis_id = $form_state['values']['analysis_id'];
$is_unique = $form_state['values']['is_unique'];
$feature_names = $form_state['values']['feature_names'];
if (!$organism_id and !$anaysis_id and !$seq_type and !$feature_names) {
form_set_error('feature_names', t("Please select at least one option"));
}
// check to make sure the types exists
if ($seq_type) {
$cvtermsql = "SELECT CVT.cvterm_id
FROM {cvterm} CVT
INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
WHERE cv.name = '%s' and (CVT.name = '%s' or CVTS.synonym = '%s')";
$cvterm = db_fetch_object(db_query($cvtermsql, 'sequence', $seq_type, $seq_type));
if (!$cvterm) {
form_set_error('seq_type', t("The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."));
}
}
}
1.7.4