simple-oai-pmh/ands_tpa.php

<?php
/**
 * \file
 * \brief classes related to generating RIF-CS XML response file for ANDS from repository.
 * It also serves as an exmaple how class ANDS_RIFCS can be used in a particular case.
 *
 */

require_once('ands_rifcs.php');

/**
 * \brief For creating RIF-CS metadata to meet the requirement of ANDS.
 *
 * Class ANDS_RIFCS provides all essential functionalities for creating ANDS RIF-CS records.
 * The protected member functions are the backbone functions which can be used for creating any ANDS RIF-CS records.
 * At the time of design only data source is database and there is only one set of outputs. Therefore there is only one class has been designed. 
 * Ideally, there should be a separated class for creating actual records which reflect data source and data models.
 *
 * Example usage: publish records meet ANDS RIF-CS requirements
 *
 * \code
 * $metadata_node = $outputObj->create_metadata($cur_record);
 * $obj_node = new ANDS_TPA($outputObj, $metadata_node, $db);
 * try {
 * 	$obj_node->create_obj_node($record[$SQL['set']], $identifier);
 * } catch (Exception $e) {
 * 		echo 'Caught exception: ',  $e->getMessage(), " when adding $identifier\n";
 * } 
 * \endcode
 * \see Code in action can be seen in record_rif.php
 */

class ANDS_TPA extends ANDS_RIFCS {
    //! Type: PDO. The database connection of the data source. 
    //! \see __construct. 
    private $db;

    /**
     * Constructor
     * The first two parameters are used by its parent class ANDS_RIFCS. The third is its own private property.
     *
     * \param $ands_response_doc ANDS_Response_XML. A XML Doc acts as the parent node.
     * \param $metadata_node DOMElement. The meta node which all subsequent nodes will be added to.
     * \param $db Type: PDO. The database connection of the data source.
     */
    function __construct($ands_response_doc, $metadata_node, $db) {
        parent::__construct($ands_response_doc, $metadata_node);
        $this->db = $db;
    }


    /**
     * This is the general entrence of creating actual content. It calls different functions for different type of RIF-CS model.
     * When anything goes wrong, e.g. found no record, or $set_name is not recognised, an exception will be thrown.
     * And for this implementation, data are stored in a database therefore a PDO is needed. But the source can be any.
     *
     * \param $set_name Type: string. The name of set is going to be created. Can be one of activity, collection or party.
     * \param $key Type: string. The main identifier used in ANDS system. There can be other identifier.
     *
     * \see create_activity, create_collection, create_party
     */
    function create_obj_node($set_name, $key) {
        $db = $this->db;
        $set_name = strtolower($set_name);
        if (in_array($set_name,prepare_set_names())) {
            try {
                // Get ori_id and which the original table is:
                $query = "select ori_table_name, ori_id from oai_headers where oai_identifier = '".$key."'";
                $res = exec_pdo_query($db, $query);
                $record = $res->fetch(PDO::FETCH_ASSOC);
            } catch (PDOException $e) {
                echo "$key returned no record.\n";
                echo $e->getMessage();
            }

            $processor = 'create_'.substr($set_name,6);
            $this->create_regObject(REG_OBJ_GROUP, $key, MY_URI);
            $this->$processor($record['ori_table_name'],$record['ori_id']);	
            $this->create_identifier_node($key);
            $this->create_identifier_node('table='.$record['ori_table_name'].'+id='.$record['ori_id']);
        } else {
            throw new Exception('Wrong set name was used: '.$set_name);
        }
    }

    /** The processor for creating metadata node of Activity. Called from create_obj_node.
     * \param $table_name Type: string. The table name will be used to retrieve data from.
     * \param $id_project Type: integer. Internal project id associated to this activity-project.
     * \see Function create_obj_node.
     */
    private function create_activity($table_name, $id_project) {
        $db = $this->db;
#		// Get ori_id and which the original table is:
#		$query = "select ori_table_name, ori_id from oai_headers where oai_identifier = '".$key."'";
#		$res = exec_pdo_query($db, $query);
#		$record = $res->fetch(PDO::FETCH_ASSOC);
#		// $id_project will e used later, so save it:
#		$id_project = $record['ori_id'];
        // Get the content using the previously obtained infor:
        $query = sprintf("select inter_no,start_date, end_date,pub_descrip from %s where id_project = %s",$table_name,$id_project);

        try {
            $res = exec_pdo_query($db,$query);
            $record = $res->fetch(PDO::FETCH_ASSOC);
        } catch (Exception $e) {
            echo $e->getMessage();
        }

        $this->create_rifcs_node('activity','project');
        $c = $this->create_name_node();
        $this->create_namePart($c,'The Plant Accelerator Project '.$record['inter_no']);
        // Test codes for rich format.		
#		// \n works
#		$this->create_description_node(sprintf("Line one:%s,\nLine two:%s.\nThird",'a','b'));
        $this->create_description_node(str_replace("\r\n","\n",$record['pub_descrip']));

        $this->create_description_node('The experiment was carried out between '.$record['start_date'].' and '.$record['end_date'],'note');
        $query = sprintf("select idr,stype from list_prj_ids_v2 where stype in ('dataset','person')",$id_project);
        // echo $query;	
        try {
            $res = $db->query($query,PDO::FETCH_ASSOC);
            if ($res==false) {
                throw new Exception($query."\nIt found nothing.\n");
            }
            foreach ($res as $record) {
                switch ($record['stype']) {
                    case 'dataset':
                        $this->create_relatedObject($record['idr'],'hasOutput');
                        break;
                    case 'person':
                        $this->create_relatedObject($record['idr'],'isManagedBy');
                        break;
                } 
            }
            // The Plant Accelerator always participates in Activity
            $this->create_relatedObject('0874ad60-ab4d-11df-aebd-0002a5d5c51b','hasParticipant');
        } catch (PDOException $e) {
            process_pdo_error($query, $e);
        }// end of try-catch block
    } // end of function create_activity($key, $id_project) 

    /** The processor for creating metadata node of Collection. Called from create_obj_node.
     * \param $table_name Type: string. The table name will be used to retrieve data from.
     * \param $id_collect Type: integer. Internal collection id associated to this collection-dataset.
     * \see Function create_obj_node.
     */
    private function create_collection($table_name, $id_collect) {
        $db = $this->db;
        try {
            $query = sprintf("select plant,variety,start_date,end_date,img_freq,anzsrc from %s where id_collect =  %s",$table_name,$id_collect);
            $res = exec_pdo_query($db, $query);
            $dataset = $res->fetch(PDO::FETCH_ASSOC);

            $res = exec_pdo_query($db, $query);
            $record = $res->fetch(PDO::FETCH_ASSOC);

            $query = 'select id_rep, inter_no, id_project from tpa_project_ids where id_collect = '.$id_collect;
            $res = exec_pdo_query($db, $query);
            $prj_info = $res->fetch(PDO::FETCH_ASSOC);

            $query = 'select email from tpa_person where id_rep = '.$prj_info['id_rep'];
            $res = exec_pdo_query($db, $query);
            $email = $res->fetch(PDO::FETCH_ASSOC);
        } catch (PDOException $e) {
            echo $query.' was failed\n';
            echo $e->getMessage();
        }

        $this->create_rifcs_node('collection','dataset');
        // Get the project inter_no as the name of this dataset
        $c = $this->create_name_node();
        $this->create_namePart($c,'Data set of Plant Accelerator Project '.$prj_info['inter_no']);

        // locatin node: contact person
        $l_node = $this->create_location_node();
        $a_node = $this->create_address_node($l_node);
        $this->create_e_node($a_node, $email['email']);
        // location node: TPA's physical address
        $l_node = $this->create_location_node();
        $a_node = $this->create_address_node($l_node);
        $this->create_physcial_addr_txt($a_node, 'The Plant Accelerator, Hartley Grove, Urrbrae, SA 5064') ;
        // Temporal coverage of colletion
        $dates = array(array('date'=>$dataset['start_date'],'type'=>'dateFrom'),array('date'=>$dataset['end_date'],'type'=>'dateTo'));
        $this->create_coverage_tempo($dates);
        // subject
        $this->create_subject_node($dataset['aznsrc']);
        // relatedOjbects
        $query = sprintf("select idr,stype from list_prj_ids_v2(%d) where stype in ('project','person')",$prj_info['id_project']);	
        try {
            $res = $db->query($query,PDO::FETCH_ASSOC);
            if ($res==false) {
                throw new Exception($query."\nIt found nothing.\n");
            }
            foreach ($res as $record) {
                switch ($record['stype']) {
                    case 'project':
                        $this->create_relatedObject($record['idr'],'isOutputOf');
                        break;
                    case 'person':
                        $this->create_relatedObject($record['idr'],'isOwnedBy');
                        break;
                } 
            }
        } catch (PDOException $e) {
            process_pdo_error($query, $e);
        }// end of try-catch block

        // right of accessing
        $this->create_description_node('For information on rights and access to this dataset, please contact the owner.','accessRights');

        // image data:
        $imgs = ''; $ex_conf = '';
        $dic = array('im_type_rgb'=>'RGB','im_type_nir'=>'NIR','im_type_fir'=>'FIR','im_type_nir_roots'=>'NIR Roots','im_type_fluo'=>'Fluorescence');
        $query = 'select im_type_rgb,im_type_nir,im_type_fir,im_type_nir_roots,im_type_fluo, lines, treatments, replicates, total from ands_collection where id_collect = '. $id_collect;
        $res = $db->query($query,PDO::FETCH_ASSOC);
        if ($res==false) {
            throw new Exception($query."\nIt found nothing.\n");
        }
        $info = $res->fetch();
        foreach ($info as $item => $v) {
            switch ($item) {
                case 'im_type_rgb':
                case 'im_type_nir':
                case 'im_type_fir':
                case 'im_type_nir_roots':
                case 'im_type_fluo':
                    if (!empty($v)) { $imgs .= $dic[$item].', '; }
                    break;
                default:
                    if (!empty($v)) { $ex_conf .= ' '.$item.' = '.$v.', '; }
                    break;
            }
        }
        if (empty($imgs)) 		$imgs = "Images data of RGB, FIR, NIR, NIR Roots and Fluorescence cameras., ";
        $imgs = substr($imgs,0,-2);
        if (!empty($ex_conf)) $imgs = $imgs."\n".substr($ex_conf,0,-2);
        $this->create_description_node($imgs);
        // imaging frequency
        $this->create_description_node('Imaging frequency: '.$dataset['img_freq'],'note');
    } // end of function create_collection($key,$id_collect)

    /** The processor for creating metadata node of Party. Called from create_obj_node. As party-person is different to party-group, there are two sub-functions are called accordingly.
     * \param $table_name Type: string. The table name will be used to retrieve data from.
     * \param $id_party Type: integer. Internal party id associated to this party.
     * \see Function create_obj_node.
     */
    private function create_party($table_name, $id_party) {
        $db = $this->db;
        $query = sprintf("SELECT set_type FROM oai_headers WHERE ori_table_name = '%s' AND ori_id = %s",$table_name,$id_party);
        $res = exec_pdo_query($db, $query);
        $party_type = $res->fetch(PDO::FETCH_ASSOC);

        if (in_array($party_type['set_type'],array('person','group'))) {
            $this->create_rifcs_node('party',$party_type['set_type']);

            if ($party_type['set_type']=='person') {
                $this->create_person($table_name, $id_party);
            } elseif ($party_type['set_type']=='group') { 
                $this->create_group($table_name, $id_party); }
        } else {
            throw new Exception('Unsupported set_type: '.$party_type['set_type']);		
        }
    } // end of function create_part($key,$id_party)

    /** The processor for creating metadata node of Party. Called from create_obj_node. As party-person is different to party-group, there are two sub-functions are called accordingly.
     * \param $table_name Type: string. The table name will be used to retrieve data from.
     * \param $id_party Type: integer. Internal party id associated to this party-person.
     * \see Function create_party.
     */
    private 	function create_person($table_name, $id_party) {
        $db = $this->db;
        $query = sprintf("SELECT id_org, title, first_name, family_name, tel, fax, email, www, address, post_code, city,state,country,duty FROM %s WHERE id_rep = %s",$table_name, $id_party);
        $res = exec_pdo_query($db, $query);	
        $info = $res->fetch(PDO::FETCH_ASSOC);
        $c = $this->create_name_node();
        if (!empty($info['title'])) $this->create_namePart($c,$info['title'],'title');
        $this->create_namePart($c,$info['family_name'],'family');
        $this->create_namePart($c,$info['first_name'],'given');

        // locatin node: contact person
        $l_node = $this->create_location_node();
        $a_node = $this->create_address_node($l_node);
        $this->create_e_node($a_node, $info['email']);
        if (!empty($info['www'])) $this->create_e_node($a_node, $info['www'],'url');
        $this->create_physcial_fone_fax($a_node, $info['tel'],'telephoneNumber');
        if (!empty($info['fax'])) $this->create_physcial_fone_fax($a_node, $info['fax'],'faxNumber');
        $add_txt = trim($info['address']).', '.$info['city'].' '.$info['state'].' '.$info['post_code'].', '.$info['country'];
        // the strlength of ',   , ' is 6
        if (strlen($add_txt)>6) $this->create_physcial_addr_txt($a_node,$add_txt);

        // related objects:
        // their group: id_customer is a foreign key of tpa_organisation
        $query = sprintf("SELECT get_identifier('tpa_organisation',%s)",$info['id_org']);
        $res = exec_pdo_query($db, $query);
        $info = $res->fetch(PDO::FETCH_NUM);
        $this->create_relatedObject($info[0],'isMemberOf');

        // their activities
        $query = "SELECT list_persons_objs($id_party,'project')";
        $res = exec_pdo_query($db, $query);
        $info = $res->fetch(PDO::FETCH_NUM);
        foreach ($info as $item) {
            $this->create_relatedObject($item,'isManagerOf');
        }
        // their collections
        $query = "SELECT list_persons_objs($id_party,'dataset')";
        $res = exec_pdo_query($db, $query);
        $info = $res->fetch(PDO::FETCH_NUM);
        foreach ($info as $item) {
            $this->create_relatedObject($item,'isOwnerOf');
        }
    }

    /** The processor for creating metadata node of Party. Called from create_obj_node. As party-person is different to party-group, there are two sub-functions are called accordingly.
     * \param $table_name Type: string. The table name will be used to retrieve data from.
     * \param $id_party Type: integer. Internal party id associated to this party-group.
     * \see Function create_party.
     */
    private function create_group($table_name, $id_party) {
        $db = $this->db;
        // echo 'table: ',$table_name,' party: ',$id_party,"\n";
        $query = sprintf("SELECT customer_name, abn, post_code, address, city, state, country, tel, fax, email, www, description FROM %s WHERE id_org = %s",$table_name, $id_party);
        //echo $query;
        $res = exec_pdo_query($db, $query);
        $info = $res->fetch(PDO::FETCH_ASSOC);
        $c = $this->create_name_node();
        $this->create_namePart($c,$info['customer_name']);
        if (!empty($info['abn'])) $this->create_identifier_node($info['abn'],'abn');

        if (!empty($info['description'])) $this->create_description_node($info['description']);

        $l_node = $this->create_location_node();
        $a_node = $this->create_address_node($l_node);
        $this->create_physcial_fone_fax($a_node, $info['tel'],'telephoneNumber');
        $this->create_physcial_fone_fax($a_node, $info['fax'],'faxNumber');
        $add_txt = trim($info['address']).', '.$info['city'].' '.$info['state'].' '.$info['post_code'].', '.$info['country'];
        $this->create_physcial_addr_txt($a_node,$add_txt);

        // related objects:
        // their members:
        $query = "SELECT list_pub_members($id_party)";
        $res = exec_pdo_query($db, $query);
        $info = $res->fetch(PDO::FETCH_NUM);
        foreach ($info as $item) {
            $this->create_relatedObject($item,'hasMember');
        }
    }
} // end of class ANDS_TPA