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Tripal 4 Upgrade Progress #16

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Tripal 4 Upgrade Progress #16

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cad7a92
First commit, Configure Field identifier, install, libraries, route
Jul 5, 2021
b1ebb6a
Implements hook_bundle_create_user
Jul 5, 2021
6d21da3
Field single series chart
Jul 6, 2021
169c6f3
Load tripal d3 libraries
Jul 6, 2021
699a42f
Load tripal d3 default settings
Jul 6, 2021
80addf3
co 010 parentage of pedigree field
Jul 6, 2021
12965f7
data identifier field
Jul 6, 2021
9d05791
local quick browse field
Jul 6, 2021
36a3c2f
local quick search field
Jul 7, 2021
3fa0254
local single series bar chart
Jul 7, 2021
7391cf8
local single series donut
Jul 7, 2021
be4ee2c
local single series pie field
Jul 7, 2021
57ee653
Update readme
Jul 7, 2021
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6 changes: 3 additions & 3 deletions README.md
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@@ -1,11 +1,11 @@
# Tripal Fancy Fields

This module provides additional fields for use with Tripal 3. The current version provides a single-series chart field that can be displayed as a pie, donut, or bar chart, as well as, a simple table. Future versions will provide support for multi-series datasets, pedigree's, hierarchy/relationship diagrams, and quick searches. These fields are highly configurable and use your existing materialized views as the datasource which allows them to be fast and flexible.
This module provides additional fields for use with Tripal 4. The current version provides a single-series chart field that can be displayed as a pie, donut, or bar chart, as well as, a simple table. Future versions will provide support for multi-series datasets, pedigree's, hierarchy/relationship diagrams, and quick searches. These fields are highly configurable and use your existing materialized views as the datasource which allows them to be fast and flexible.

## Installation
This module is installed the same as any Drupal module.
### Dependencies
1. [Tripal 3.x](https://github.com/tripal/tripal)
1. [Tripal 4.x](https://github.com/tripal/tripal)
2. [Tripal D3](https://github.com/tripal/tripald3)

## How To Use this Module
Expand All @@ -18,7 +18,7 @@ If you simply want to use the existing charts, you can add these fields through

### Extend the Base Classes
If you would like even more control over the field then is provided through the UI, you can extend the ChadoChart base classes in your own custom module.
1. Create a custom module. See the [Drupal Documentation](https://www.drupal.org/docs/7/creating-custom-modules) for how to do this.
1. Create a custom module. See the [Drupal Documentation](https://www.drupal.org/docs/creating-custom-modules) for how to do this.
2. Create your child class extending the base class of your choice in `[your module]/includes/TripalFields/[field name]/[field name].inc`
3. Set the various settings under `EDITABLE STATIC CONSTANTS`.
4. Implement hook_bundle_fields_info() and hook_bundle_instances_info() to attach your field to a Tripal Content Type or add it through the UI just like you would a regular Tripal Fancy Field.
Expand Down
7 changes: 7 additions & 0 deletions config/install/trpfancy_fields.settings.yml
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# @file
# Tripal Fancy Fields module variables/configuration.

# FIELD IDENTIFIER CONFIGURATIONS:
tripal_fancyfields_identifier_config:
prefix: 'KP:GERM'

17 changes: 17 additions & 0 deletions css/tripal-fancyfields-config.css
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/*
* @file
* Style Tripal Fancy Fields Configuration.
*/

#tripal-fancyfields-box-id {
border: 1px solid #CCCCCC;
display: inline-block;
font-family: courier, serif;
font-size: 2em;
margin: 5px 0 20px 0;
padding: 10px;
}

#tripal-fancyfields-box-id span {
color: #666666;
}
111 changes: 55 additions & 56 deletions includes/TripalFields/ChadoChartField.inc
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Expand Up @@ -44,16 +44,16 @@ class ChadoChartField extends TripalField {
// Drupal will automatically change these settings for all fields.
// Once instances exist for a field type then these settings cannot be
// changed.
public static $default_settings = array(
public static $default_settings = [
'storage' => 'tripal_no_storage',
// It is expected that all fields set a 'value' in the load() function.
// In many cases, the value may be an associative array of key/value pairs.
// In order for Tripal to provide context for all data, the keys should
// be a controlled vocabulary term (e.g. rdfs:type). Keys in the load()
// function that are supported by the query() function should be
// listed here.
'searchable_keys' => array(),
);
'searchable_keys' => [],
];

// Provide a list of instance specific settings. These can be access within
// the instanceSettingsForm. When the instanceSettingsForm is submitted
Expand All @@ -62,7 +62,7 @@ class ChadoChartField extends TripalField {
// If you override this variable in a child class be sure to replicate the
// term_name, term_vocab, term_accession and term_fixed keys as these are
// required for all TripalFields.
public static $default_instance_settings = array(
public static $default_instance_settings = [
// The short name for the vocabulary (e.g. shcema, SO, GO, PATO, etc.).
'term_vocabulary' => NULL,
// The name of the term.
Expand All @@ -86,7 +86,7 @@ class ChadoChartField extends TripalField {
// features. This is done using a combination of the filter_field (Drupal)
// and filter_column (Materialized View).
//-----------------------------------------------------
'data_options' => array(
'data_options' => [

// The following relate to the materialized view:
//-----------------------------------------------------
Expand All @@ -99,8 +99,8 @@ class ChadoChartField extends TripalField {

// To Filter the materialized view for a specific page:
//-----------------------------------------------------
'filters' => array(
array(
'filters' => [
[
// Use this setting to specify the Drupal/Tripal/Chado field containing the
// value to filter the materialized view on. For example, if you want
// `organism_feature_count.species = taxrank__species` then you set the
Expand All @@ -114,10 +114,10 @@ class ChadoChartField extends TripalField {
// The column to filter the materialized view based on. This is usually
// a foreign key but doesn't have to be.
'filter_column' => NULL,
)
),
),
);
]
],
],
];

// A boolean specifying that users should not be allowed to create
// fields and instances of this field type through the UI. Such
Expand Down Expand Up @@ -155,11 +155,8 @@ class ChadoChartField extends TripalField {
* The array may contain as many other keys at the same level as 'value'
* but those keys are for internal field use and are not considered the
* value of the field.
*
*
*/
public function load($entity) {

// We need the field name to ensure we save the data in the correct field!
$field_name = $this->instance['field_name'];

Expand All @@ -171,11 +168,11 @@ class ChadoChartField extends TripalField {
// Backwards compatible filters.
// Originally, we only supported a single filter.
if (isset($this->instance['settings']['data_options']['filter_column'])) {
$this->instance['settings']['data_options']['filters'] = array( array(
$this->instance['settings']['data_options']['filters'] = [[
'filter_column' => $this->instance['settings']['data_options']['filter_column'],
'filter_field' => $this->instance['settings']['data_options']['filter_field'],
'use_record_id' => $this->instance['settings']['data_options']['use_record_id'],
));
]];

unset(
$this->instance['settings']['data_options']['filter_column'],
Expand All @@ -185,8 +182,8 @@ class ChadoChartField extends TripalField {
}

// Fill in the filters.
$where_clause = array();
$where_args = array();
$where_clause = [];
$where_args = [];
foreach ($this->instance['settings']['data_options']['filters'] as $k => $filter_info) {

$where_clause[$k] = $filter_info['filter_column'] . '=:filter_value' . $k;
Expand All @@ -205,8 +202,9 @@ class ChadoChartField extends TripalField {
'trpfancy_fields',
TRIPAL_ERROR,
'Attempted to display %field but there was no value to filter on. Specifically, either field %filter_field had no value or a filter field was not specified.',
array('%field' => $field_name, '%filter_field' => $filter_info['filter_field'])
['%field' => $field_name, '%filter_field' => $filter_info['filter_field']]
);

return FALSE;
}
}
Expand All @@ -228,13 +226,13 @@ class ChadoChartField extends TripalField {
}

// Interate through results, adding them to the value.
$entity->{$field_name}['und'][0]['value'] = array();
$entity->{$field_name}['und'][0]['value']['hydra:member'] = array();
$entity->{$field_name}['und'][0]['value'] = [];
$entity->{$field_name}['und'][0]['value']['hydra:member'] = [];
foreach ($results as $r) {
$entity->{$field_name}['und'][0]['value']['hydra:member'][] = array(
$entity->{$field_name}['und'][0]['value']['hydra:member'][] = [
'rdfs:label' => $r->{$label_column},
'local:count' => $r->{$count_column},
);
];
}

// Ensure we don't return markup if there is no data.
Expand Down Expand Up @@ -273,42 +271,43 @@ class ChadoChartField extends TripalField {
// Allow the parent Tripal Field to set up the form element for us.
$element = parent::instanceSettingsForm();

$element['data_options'] = array(
$element['data_options'] = [
'#type' => 'fieldset',
'#title' => 'Chart Data Source',
'#description' => 'The data for this chart will be pulled from the materialized view specified below. Additonally you must configure which columns in the materialized view should be the source of the data and which should be used to filter the results.',
);
];

// The following relate to the materialized view:
//-----------------------------------------------------
// The table name of the materialized view to pull data from.
$options = array();
$options = [];
foreach (tripal_get_mviews() as $mview) {
$options[ $mview->name ] = $mview->name;
}
$element['data_options']['materialized_view'] = array(

$element['data_options']['materialized_view'] = [
'#type' => 'select',
'#required' => TRUE,
'#options' => $options,
'#title' => 'Materialized View',
'#description' => 'The materialized view you would like to pull the data for the chart from.',
'#default_value' => $settings['data_options']['materialized_view'],
'#weight' => -10,
);
];

// Supports unlimited filters, although the form needs to be saved to make
// another filter available.
// @todo support AJAX.
$element['data_options']['filters'] = array(
$element['data_options']['filters'] = [
'#type' => 'fieldset',
'#title' => 'Filters',
'#description' => 'The materialized view indicated likely has data for multiple Tripal Content Pages. Thus, to ensure the chart is specific to the current page, we must filter the materialized view. This is done by indicated a column in the materialized view (the filter column) that should equal the value of a Drupal/Tripal/Chado field (the filter field) for the current page.',
'#weight' => 100,
);
];

// Drupal/Tripal/Chado field to filter the materialized view on.
$fields = field_info_instances($this->instance['entity_type'], $this->instance['bundle']);
$options = array();
$options = [];
foreach ($fields as $f) {
$options[ $f['field_name'] ] = $f['field_name'];
}
Expand All @@ -320,12 +319,12 @@ class ChadoChartField extends TripalField {
}
$filter_queue = $settings['data_options']['filters'];

$element['data_options']['filters']['m1'] = array(
$element['data_options']['filters']['m1'] = [
'#type' => 'markup',
'#markup' => '
<table>
<tr><th>Filter Column</th><th>Filter Field</th><th>OR use Record ID</th></tr>'
);
];

// Now, we want elements for all the current filters +1 :-).
for ($i=0; $i< ($num_filters+1); $i++) {
Expand All @@ -335,30 +334,30 @@ class ChadoChartField extends TripalField {
$current_element = array_shift($filter_queue);
}
else {
$current_element = array(
$current_element = [
'filter_column' => NULL,
'filter_field' => ' ',
'use_record_id' => FALSE,
);
];
}

$element['data_options']['filters'][$i]['m1'] = array(
$element['data_options']['filters'][$i]['m1'] = [
'#type' => 'markup',
'#markup' => '<tr>'
);
];

// The column to filter the materialized view based on. This is usually
// a foreign key but doesn't have to be.
$element['data_options']['filters'][$i]['filter_column'] = array(
$element['data_options']['filters'][$i]['filter_column'] = [
'#type' => 'textfield',
'#title' => 'Filter Column',
'#title_display' => 'invisible',
'#default_value' => $current_element['filter_column'],
'#prefix' => '<td>',
'#suffix' => '</td>',
);
];

$element['data_options']['filters'][$i]['filter_field'] = array(
$element['data_options']['filters'][$i]['filter_field'] = [
'#type' => 'select',
'#title' => 'Filter Field',
'#title_display' => 'invisible',
Expand All @@ -367,26 +366,26 @@ class ChadoChartField extends TripalField {
'#options' => $options,
'#prefix' => '<td>',
'#suffix' => '</td>',
);
];

// Use the chado primary key instead of the filter field above.
$element['data_options']['filters'][$i]['use_record_id'] = array(
$element['data_options']['filters'][$i]['use_record_id'] = [
'#type' => 'checkbox',
'#title' => 'Use Chado Record ID',
'#title_display' => 'invisible',
'#default_value' => $current_element['use_record_id'],
'#prefix' => '<td>',
'#suffix' => '</td>',
);
];

$element['data_options']['filters'][$i]['m2'] = array(
$element['data_options']['filters'][$i]['m2'] = [
'#type' => 'markup',
'#markup' => '</tr>'
);
];
}

// Add in help text
$element['data_options']['filters']['m2'] = array(
$element['data_options']['filters']['m2'] = [
'#type' => 'markup',
'#markup' => '<tr class="help-text">'
// Filter Column
Expand All @@ -396,12 +395,12 @@ class ChadoChartField extends TripalField {
// Use Record ID
. '<td>Filter on the primary key of the chado record being displayed on the page (e.g. organism_id).</td>'
. '</tr>'
);
];

$element['data_options']['filters']['m3'] = array(
$element['data_options']['filters']['m3'] = [
'#type' => 'markup',
'#markup' => '</table>'
);
];

return $element;
}
Expand Down Expand Up @@ -439,19 +438,19 @@ class ChadoChartField extends TripalField {
if ($has_filter_column && !$has_drupal_field_or_pkey) {
form_set_error('instance][settings][data_options][filters]['.$k.'][filter_field',
t('Filter #:k: You must indicate the <em>Filter Field</em> to filter the materialized view based on.',
array(':k' => $readable_k)));
[':k' => $readable_k]));
}
if (!$has_filter_column && $has_drupal_field_or_pkey) {
form_set_error('instance][settings][data_options][filters]['.$k.'][filter_column',
t('Filter #:k: You must indicate the <em>Filter Column</em> to filter the materialized view based on.',
array(':k' => $readable_k)));
[':k' => $readable_k]));
}

// Check the filter column exists.
if (!chado_column_exists($values['materialized_view'], $current_filter['filter_column'])) {
form_set_error('instance][settings][data_options][filters]['.$k.'][filter_column',
t('Filter #:k: The <em>Filter Column</em> must exist in the %mview materialized view.',
array('%mview' => $values['materialized_view'], ':k' => $readable_k)));
['%mview' => $values['materialized_view'], ':k' => $readable_k]));
}

// Retrieve the field info for the filter field chosen.
Expand All @@ -460,23 +459,23 @@ class ChadoChartField extends TripalField {
// Check that the field exists.
if (!$field) {
form_set_error('instance][settings][data_options][filters]['.$k.'][filter_field',
t('Filter #:k: The <em>Filter Field</em> must exist.', array(':k' => $readable_k)));
t('Filter #:k: The <em>Filter Field</em> must exist.', [':k' => $readable_k]));
}
elseif (!isset($field['bundles']['TripalEntity'])) {
form_set_error('instance][settings][data_options][filters]['.$k.'][filter_field',
t('Filter #:k: The <em>Filter Field</em> must be attached to the current Tripal Content Type.',
array(':k' => $readable_k)));
[':k' => $readable_k]));
}
else {
// Check that this field is attached to the current Tripal Entity type.
$bundle = $form_state['values']['instance']['bundle'];
if (array_search($bundle, $field['bundles']['TripalEntity']) === FALSE) {
form_set_error('instance][settings][data_options][filters]['.$k.'][filter_field',
t('Filter #:k: The <em>Filter Field</em> must be attached to the current Tripal Content Type.',
array(':k' => $readable_k)));
[':k' => $readable_k]));
}
}
}
}
}
}
}