<?php
/**
* Purpose: this function returns the portion of the data array
* which describes the analysis table, it's fields and any joins between it and other tables
* @see tripal_analysis_views_data() --in tripal_analysis.views.inc
*
* @todo Add support for analysisprop table
* @todo Add support for multiple analysis' listed per feature
* @todo Add join to node table within if <chado/drupal same db>; also addd if not around nid field
*
* BASE TABLE: analysis
* @code
* create table analysis (
* analysis_id serial not null,
* primary key (analysis_id),
* name varchar(255),
* description text,
* program varchar(255) not null,
* programversion varchar(255) not null,
* algorithm varchar(255),
* sourcename varchar(255),
* sourceversion varchar(255),
* sourceuri text,
* timeexecuted timestamp not null default current_timestamp,
* constraint analysis_c1 unique (program,programversion,sourcename)
* );
* @endcode
*
* @ingroup tripal_analysis
*/
function retrieve_analysis_views_data() {
global $db_url;
$data = array();
// if the chado database is not local to the drupal database
// then we need to set the database name. This should always
// be 'chado'.
if(is_array($db_url) and array_key_exists('chado',$db_url)){
$database = 'chado';
}
// Basic table definition
$data['analysis']['table']['group'] = 'Chado Analysis';
$data['analysis']['table']['base'] = array(
'field' => 'analysis_id',
'title' => t('Chado Analysis'),
'help' => t("An analysis is a particular type of a computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit of computation."),
);
if($database){
$data['analysis']['table']['database'] = $database;
}
// Define relationships between this table and others
$data['analysis']['table']['join'] = array(
'analysisfeature' => array(
'left_field' => 'analysis_id',
'field' => 'analysis_id',
),
'feature' => array(
'left_table' => 'analysisfeature',
'left_field' => 'analysis_id',
'field' => 'analysis_id',
),
);
// Describe the joins with the analysis_feature table
$data['analysisfeature']['table']['join'] = array(
'feature' => array(
'left_field' => 'feature_id',
'field' => 'feature_id',
),
);
// Table Field Definitions----------------------
// Field: analysis_id (primary key)
$data['analysis']['analysis_id'] = array(
'title' => 'analysis ID',
'help' => 'The primary key of the analysis table.',
'field' => array(
'handler' => 'views_handler_field_numeric',
'click sortable' => TRUE,
),
'filter' => array(
'handler' => 'views_handler_filter_numeric',
),
'sort' => array(
'handler' => 'views_handler_sort',
),
);
// Calculated Field: Node ID
// use custom field handler to query drupal for the node ID
// this is only needed if chado is in a separate database from drupal
if($database){
$data['analysis']['analysis_nid'] = array(
'title' => 'Node ID',
'help' => 'The node ID for the current analysis',
'field' => array(
'handler' => 'views_handler_field_computed_analysis_nid',
),
);
}
// Field: name (varchar 255)
$data['analysis']['name'] = array(
'title' => t('Name'),
'help' => t(''),
'field' => array(
'handler' => 'views_handler_field',
'click sortable' => TRUE,
),
'sort' => array(
'handler' => 'views_handler_sort',
),
'filter' => array(
'handler' => 'views_handler_filter_string',
),
'argument' => array(
'handler' => 'views_handler_argument_string',
),
);
// if joined to the node table add a "Link to Node" option for the field
if (!$database) {
$data['analysis']['name']['field']['handler'] = 'views_handler_field_node_optional';
}
// Field: description (text)
$data['analysis']['description'] = array(
'title' => t('Description'),
'help' => t(''),
'field' => array(
'handler' => 'views_handler_field',
'click sortable' => TRUE,
),
'sort' => array(
'handler' => 'views_handler_sort',
),
'filter' => array(
'handler' => 'views_handler_filter_string',
),
'argument' => array(
'handler' => 'views_handler_argument_string',
),
);
// Field: program (varchar 255)
$data['analysis']['program'] = array(
'title' => t('Program'),
'help' => t('Program name, e.g. blastx, blastp, sim4, genscan.'),
'field' => array(
'handler' => 'views_handler_field',
'click sortable' => TRUE,
),
'sort' => array(
'handler' => 'views_handler_sort',
),
'filter' => array(
'handler' => 'views_handler_filter_chado_select_string',
),
'argument' => array(
'handler' => 'views_handler_argument_string',
),
);
// Field: program version (varchar 255)
$data['analysis']['programversion'] = array(
'title' => t('Program Version'),
'help' => t('Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000].'),
'field' => array(
'handler' => 'views_handler_field',
'click sortable' => TRUE,
),
'sort' => array(
'handler' => 'views_handler_sort',
),
'filter' => array(
'handler' => 'views_handler_filter_chado_select_string',
),
'argument' => array(
'handler' => 'views_handler_argument_string',
),
);
// Field: algorithm (varchar 255)
$data['analysis']['algorithm'] = array(
'title' => t('Algorithm'),
'help' => t('Algorithm name, e.g. blast.'),
'field' => array(
'handler' => 'views_handler_field',
'click sortable' => TRUE,
),
'sort' => array(
'handler' => 'views_handler_sort',
),
'filter' => array(
'handler' => 'views_handler_filter_chado_select_string',
),
'argument' => array(
'handler' => 'views_handler_argument_string',
),
);
$data['analysis']['sourcename'] = array(
'title' => t('Source Name'),
'help' => t('Source name, e.g. cDNA, SwissProt.'),
'field' => array(
'handler' => 'views_handler_field',
'click sortable' => TRUE,
),
'sort' => array(
'handler' => 'views_handler_sort',
),
'filter' => array(
'handler' => 'views_handler_filter_string',
),
'argument' => array(
'handler' => 'views_handler_argument_string',
),
);
// Field: source version (varchar 255)
$data['analysis']['sourceversion'] = array(
'title' => t('Source Version'),
'help' => t('The version of the source.'),
'field' => array(
'handler' => 'views_handler_field',
'click sortable' => TRUE,
),
'sort' => array(
'handler' => 'views_handler_sort',
),
'filter' => array(
'handler' => 'views_handler_filter_string',
),
'argument' => array(
'handler' => 'views_handler_argument_string',
),
);
// Field: source URI/URL (text)
$data['analysis']['sourceuri'] = array(
'title' => t('Source URL'),
'help' => t('This is an optional, permanent URL or URI for the source of the analysis.'),
'field' => array(
'handler' => 'views_handler_field',
'click sortable' => TRUE,
),
'sort' => array(
'handler' => 'views_handler_sort',
),
'filter' => array(
'handler' => 'views_handler_filter_string',
),
'argument' => array(
'handler' => 'views_handler_argument_string',
),
);
// Field: time executed (datetime)
$data['analysis']['timeexecuted'] = array(
'title' => 'Time Executed',
'help' => 'The date & time when this analysis was executed.',
'field' => array(
'handler' => 'views_handler_field_readable_date',
'click sortable' => TRUE,
),
'sort' => array(
'handler' => 'views_handler_sort_date',
),
);
return $data;
}