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Merge pull request #1161 from tripal/tv3.5-pre-release-fixes
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@laceysanderson
laceysanderson committed Jan 30, 2021
2 parents 1c504ae + ed753c5 commit 286d823
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Showing 5 changed files with 96 additions and 126 deletions.
6 changes: 6 additions & 0 deletions tripal_chado/includes/TripalFields/data__sequence_record/data__sequence_record.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -98,6 +98,12 @@ class data__sequence_record extends ChadoField {
else {
$this->addGenericReference($entity, $feature, $field_name);
}

// The field should always return a 'value' key so even if we don't
// have a sequence we still need to add it
if (count(array_keys($entity->{$field_name}['und'])) == 0) {
$entity->{$field_name}['und'][0]['value'] = '';
}
}

/**
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15 changes: 4 additions & 11 deletions tripal_chado/includes/TripalFields/data__sequence_record/data__sequence_record_formatter.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -28,10 +28,8 @@ class data__sequence_record_formatter extends ChadoFieldFormatter {
$phase_term = chado_get_semweb_term('featureloc', 'phase');
$fasta_defline = 'local:fasta_definition';

$content = [];

foreach ($items as $delta => $item) {
if (empty($item['value'])) {
if (!$item['value']) {
continue;
}

Expand All @@ -41,24 +39,19 @@ class data__sequence_record_formatter extends ChadoFieldFormatter {
$residues .= wordwrap($item['value'][$sequence_term], $num_bases, "<br>", TRUE);
$residues .= '</pre>';

$content[] = [
$element[$delta] = [
'#type' => 'item',
'#title' => $item['value'][$label_term],
'#description' => $item['value'][$description_term],
'#markup' => $residues,
];


}

if (empty($content)) {
if (count($element) == 0) {
$element[0] = [
'#type' => 'markup',
'#markup' => '',
'#markup' => 'There are no sequences for this feature.',
];
return;
}

$element[0] = $content;
}
}
2 changes: 1 addition & 1 deletion tripal_ds/api/tripal_ds.pane.api.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ function tripal_ds_create_field($field_label, $field_name, $bundle_name) {
//Build the rest of the passes parameters.
$group_field_name = 'gp_' . $field_name;
//Create the field groups.
tripal_ds_additional_fields_field_group_info($bundle_name, $field_label, $group_field_name, $field_name);
tripal_ds_add_generic_field_group($bundle_name, $field_label, $group_field_name, $field_name);
//Place the field groups in the layout.
tripal_ds_update_ds_layout($bundle_name, $field_name, $group_field_name);
}
189 changes: 80 additions & 109 deletions tripal_ds/includes/tripal_ds.ds.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -41,117 +41,113 @@ function _ds_layout_settings_info($bundle_name, $instances) {
$region_left = [];
$prop_fields = [];
$summary_fields = [];
$data_sequence_fields = [];
$all_other_fields = [];
$unhandled_fields = [];
$fields_with_regions = [];
$i = 0;
$all_fields = [];


try {

// Get the bundle and term objects.
$bundle = tripal_load_bundle_entity(['name' => $bundle_name]);
$term = tripal_load_term_entity(['term_id' => $bundle->term_id]);

// Build one large multidimensional array of all instances to sort in alpha
// order to display fields in label alpha order.
// Get the list of fields and sort them by label.
$sorted_instances = [];
foreach ($instances as $key => $instance) {
$all_fields[$i] = $instance;
$sorted_instances[$i] = $instance;
$i++;
}
usort($all_fields, tripal_ds_sort_array('label'));
usort($sorted_instances, tripal_ds_sort_array('label'));

// Iterate through the fields of this bundle.
foreach ($all_fields as $key => $instance) {
// Iterate through the fields of this bundle and put them into appropriate
// field groups.
foreach ($sorted_instances as $key => $instance) {
$base_table = array_key_exists('base_table', $instance['settings']) ? $instance['settings']['base_table'] : '';
$chado_table = array_key_exists('chado_table', $instance['settings']) ? $instance['settings']['chado_table'] : '';
$instance_name = $instance['field_name'];

// Add the bundle type to the summary fields.
if ($instance_name == "rdfs__type") {
array_push($summary_fields, $instance_name);
continue;
}
else {
//TODO: How do we handle non-chado dbs, placement of fields within
// tripal panes might need to be done in a hook.
$instance_base_table = array_key_exists('base_table', $instance['settings']) ? $instance['settings']['base_table'] : '';
$instance_base_chado = array_key_exists('chado_table', $instance['settings']) ? $instance['settings']['chado_table'] : '';
$prop_table = strpos($instance_base_chado, 'prop');
$data_sequence_record = strpos($instance_name, 'data__sequence_record');
$data_sequence = strpos($instance_name, 'data__sequence');
if ($instance_base_chado && $instance_base_table) {

if ($instance_base_chado == $instance_base_table) {
if ($data_sequence_record !== FALSE) {
array_push($data_sequence_fields, $instance_name);
}
elseif ($data_sequence !== FALSE or $instance_name == 'so__cds' or $instance_name == 'data__protein_sequence') {
// Do nothing as these chado column sequence fields
// should be hidden by default.
}
elseif ($prop_table !== FALSE) {
array_push($prop_fields, $instance_name);
}
else {
array_push($summary_fields, $instance_name);
}

}
elseif ($instance_base_chado != $instance_base_table) {
if ($data_sequence_record !== FALSE) {
array_push($data_sequence_fields, $instance_name);
}
elseif ($data_sequence !== FALSE or $instance_name == 'so__cds' or $instance_name == 'data__protein_sequence') {
// Do nothing as these chado column sequence fields
// should be hidden by default.
}
elseif ($prop_table !== FALSE) {
array_push($prop_fields, $instance_name);
}
else {
array_push($all_other_fields, $instance);
// The tripal_chado module adds an image to the organism content
// type so we want to make sure that image goes in the summary.
// It is not a TripalField so it won't have a chado table.
if ($instance_name == 'data__image' and $term->name == 'organism') {
array_push($summary_fields, $instance_name);
continue;
}

// Update the display settings so that the title is hidden.
$instance['display']['default']['label'] = 'hidden';
field_update_instance($instance);
}
}
}
else {
// The tripal_chado module adds an image to the organism content
// type so we want to make sure that image goes in the summary.
// It is not a TripalField so it won't have a chado table.
if ($instance_name == 'data__image' and $term->name == 'organism') {
array_push($summary_fields, $instance_name);
}
// For fields that have a data__sequence prefix we want to hide these
// unless it's the data__sequence_record field which displays all of the
// sequence data and should be in it's own fieldset.
if (preg_match('/data__sequence/', $instance_name)) {
if ($instance_name == 'data__sequence_record') {
$instance['display']['default']['label'] = 'hidden';
field_update_instance($instance);
array_push($unhandled_fields, $instance);
}
continue;
}

// For the same reason, hide the CDS and protein fields
if ($instance_name == 'so__cds' or $instance_name == 'data__protein_sequence'){
continue;
}

// If this field holds a value from the prop table then add it to the
// properties field group.
if (preg_match('/_prop$/', $chado_table)) {
array_push($prop_fields, $instance_name);
continue;
}
}

// Consolidate the field sets.
// Put all fields from the base table in the summary and all other
// fields that were not handled above into a different array for
// handling later.
if ($base_table == $chado_table) {
array_push($summary_fields, $instance_name);
continue;
}
else {
// Update the display settings so that the title is hidden.
$instance['display']['default']['label'] = 'hidden';
field_update_instance($instance);
array_push($unhandled_fields, $instance);
}
} // end looping over fields.

// Create the summary and properties field groups.
if (!empty($summary_fields)) {
_summary_field_group_info($bundle_name, $summary_fields);
tripal_ds_add_summary_field_group($bundle_name, $summary_fields);
}
if (!empty($prop_fields)) {
_prop_field_group_info($bundle_name, $prop_fields);
}
if (!empty($data_sequence_fields)) {
_data_sequence_field_group_info($bundle_name, $data_sequence_fields);
tripal_ds_add_prop_field_group($bundle_name, $prop_fields);
}
if (!empty($all_other_fields)) {
foreach ($all_other_fields as $key => $other_field) {
$group_field_name = 'gp_' . $other_field['field_name'];

// Need to truncate the names because of database field size restrictions,
// updating fields here to ensure name consistency.
$group_field_name = substr($group_field_name, 0, 27);

// Add random numbers to ensure the field name is unique within the 32
// character limit of the field.
$group_field_name = $group_field_name . rand(0, 99999);
tripal_ds_additional_fields_field_group_info($bundle_name, $other_field['label'], $group_field_name, $other_field['field_name']);
}

// All other fields get their own field group (i.e. Tripal Pane).
foreach ($unhandled_fields as $key => $other_field) {
$group_field_name = 'gp_' . $other_field['field_name'];

// Need to truncate the names because of database field size restrictions,
// updating fields here to ensure name consistency.
$group_field_name = substr($group_field_name, 0, 27);

// Add random numbers to ensure the field name is unique within the 32
// character limit of the field.
$group_field_name = $group_field_name . rand(0, 99999);

// Now add a generic field group for this field.
tripal_ds_add_generic_field_group($bundle_name, $other_field['label'], $group_field_name, $other_field['field_name']);
}

// Build one large multidimensional array of all instances to sort in alpha
// order to display fields in label alpha order.
// Build one large multidimensional array of all field groups to sort
// in alpha order to display fields in label alpha order.
$right_fields = [];
$all_field_groups = field_group_info_groups('TripalEntity', $bundle_name);
$all_field_groups = field_group_info_groups('TripalEntity', $bundle_name, NULL, TRUE);

if (!empty($all_field_groups)) {
if (is_array($all_field_groups)) {
Expand All @@ -164,31 +160,6 @@ function _ds_layout_settings_info($bundle_name, $instances) {
usort($right_fields, tripal_ds_sort_object('label'));
}
}
elseif (empty($all_field_groups)) {
//Add the original instances that were passed and the field_groups that
//were created.
$field_group_fields = db_select('field_group', 'fg')
->fields('fg', ['group_name', 'data'])
->condition('bundle', $bundle_name, '=')
->execute()
->fetchAll();

$instance_names = [];
$field_group_names = [];
foreach ($all_fields as $key => $instance) {
$instance_names[$key]['field_name'] = $instance['field_name'];
$instance_names[$key]['label'] = $instance['label'];

}
foreach ($field_group_fields as $key => $field_group_name) {
$data = unserialize($field_group_name->data);
$field_group_names[$key]['field_name'] = $field_group_name->group_name;
$field_group_names[$key]['label'] = $data['format_settings']['label'];

}
$all_field_groups = array_merge($instance_names, $field_group_names);
usort($all_field_groups, tripal_ds_sort_array('label'));
}

// Now build the $region_right array and the fields array.
$i = 0;
Expand Down Expand Up @@ -337,7 +308,7 @@ function _ds_layout_pub_settings_info($bundle_name, $instances) {
$group_field_name = $group_field_name . rand(0, 99999);

// Build the field group.
tripal_ds_additional_fields_field_group_info($bundle_name, $other_field['label'], $group_field_name, $other_field['field_name']);
tripal_ds_add_generic_field_group($bundle_name, $other_field['label'], $group_field_name, $other_field['field_name']);

// Update arrays.
array_push($temporary_field, $group_field_name, $other_field['field_name']);
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10 changes: 5 additions & 5 deletions tripal_ds/includes/tripal_ds.field_group.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
* @param $fields
* Array of the machine names of the children of the field group being created.
*/
function _summary_field_group_info($bundle_name, $fields) {
function tripal_ds_add_summary_field_group($bundle_name, $fields) {
//Tripal pane to nest the summary fieldset within.
$field_group_tripalpane = new stdClass();
$field_group_tripalpane->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
Expand Down Expand Up @@ -80,7 +80,7 @@ function _summary_field_group_info($bundle_name, $fields) {
* @param $fields
* Array of the machine names of the children of the field group being created.
*/
function _prop_field_group_info($bundle_name, $fields) {
function tripal_ds_add_prop_field_group($bundle_name, $fields) {
//Tripal pane to nest the fieldset within.
$field_group_tripalpane = new stdClass();
$field_group_tripalpane->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
Expand Down Expand Up @@ -152,7 +152,7 @@ function _prop_field_group_info($bundle_name, $fields) {
* @param $fields
* Array of the machine names of the children of the field group being created.
*/
function _data_sequence_field_group_info($bundle_name, $fields) {
function tripal_ds_add_sequences_field_group($bundle_name, $fields) {
//Tripal pane to nest the fieldset within.
$field_group_tripalpane = new stdClass();
$field_group_tripalpane->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
Expand Down Expand Up @@ -182,7 +182,7 @@ function _data_sequence_field_group_info($bundle_name, $fields) {
];
drupal_write_record('field_group', $field_group_tripalpane);
//Write to the tripal_ds table to record the new tripal pane.
tripal_ds_bundle_menu_item($bundle_name, 'Sequence', 'group_sequence_tripalpane', 'TripalEntity');
tripal_ds_bundle_menu_item($bundle_name, 'Sequences', 'group_sequence_tripalpane', 'TripalEntity');

//Table of fields.
$field_group = new stdClass();
Expand Down Expand Up @@ -230,7 +230,7 @@ function _data_sequence_field_group_info($bundle_name, $fields) {
* @param $field_name
* Machine name of the child element.
*/
function tripal_ds_additional_fields_field_group_info($bundle_name, $field_label, $group_field_name, $field_name) {
function tripal_ds_add_generic_field_group($bundle_name, $field_label, $group_field_name, $field_name) {
//Write to the tripal_ds table to record the new tripal pane.
tripal_ds_bundle_menu_item($bundle_name, $field_label, $group_field_name, 'TripalEntity');

Expand Down

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