string values with generic names.
svn path=/; revision=321
--- /dev/null
+<?php
+// JSON web service for PO terms: autocomplete and search methods
+
+/* require the user as the parameter */
+if(isset($_GET['user']) && ($_GET['user']) == 'paw') {
+
+ $arr_field_names = array('name','acc');
+ $arr_ontologies = array('go','po');
+
+ /* read the params and/or set our own */
+ $type = isset($_GET['type']) ? $_GET['type'] : autocomplete; // autocomplete is the default
+
+ // security measures; helps to avoid SQL injection attacks
+ $field = isset($_GET['field']) && in_array($_GET['field'],$arr_field_names)
+ ? $_GET['field']
+ : die('"field" is a required parameter and must match an available data field.');
+
+ $number_of_terms = isset($_GET['max']) ? intval($_GET['max']) : 10; //10 is the default
+ if ($number_of_terms > 50) { $number_of_terms = 50; }
+
+ $ont = isset($_GET['ontology']) && in_array(strtolower($_GET['ontology']),$arr_ontologies)
+ ? strtolower($_GET['ontology'])
+ : die('"ontology" is a required parameter and must match an available data field.');
+
+ $qval = $_GET['qval'];
+
+ $qval = isset($_GET['qval']) && strlen($_GET['qval']) > 0
+ ? strtolower($_GET['qval'])
+ : die('Please provide a searchable value');
+
+ $format = strtolower($_GET['format']) != 'json'
+ ? strtolower($_GET['format'])
+ : 'json'; //json is the default
+
+ /* connect to the appropriate db */
+ switch ($ont) {
+ case 'po':
+ $link = mysql_connect($_SERVER['po_host'], $_SERVER['po_user'], $_SERVER['po_pw']) or die('Cannot connect to the DB');
+ mysql_select_db($_SERVER['po_db'],$link) or die('Cannot select the DB');
+
+ $term_types = "'plant_anatomy','plant_growth_and_development_stage'";
+ break;
+
+ case 'go':
+ $link = mysql_connect($_SERVER['go_host'], $_SERVER['go_user'], $_SERVER['go_pw']) or die('Cannot connect to the DB');
+ mysql_select_db($_SERVER['go_db'],$link) or die('Cannot select the DB');
+
+ $term_types = "'biological_process','cellular_component','molecular_function'";
+ break;
+
+ default:
+ die('Sorry, this ontology type is not available.');
+ }
+
+ switch ($type) {
+ case 'autocomplete':
+ /* grab the terms from the db */
+ $query = "SELECT t.$field FROM term t"
+ . " LEFT JOIN term_definition d ON d.term_id = t.id"
+ . " WHERE t.$field LIKE '%$qval%'"
+ . " AND t.term_type in ($term_types)"
+ . " AND t.is_obsolete = 0"
+ . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'"
+ . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'"
+ . " ORDER BY name LIMIT $number_of_terms";
+ $result = mysql_query($query,$link) or die('Errant query: '.$query);
+
+ /* create one master array of the records */
+ $terms = array();
+ if(mysql_num_rows($result)) {
+ while($term = mysql_fetch_assoc($result)) {
+ $terms[] = array('title'=>$term[$field]);
+ }
+ }
+
+ /* output in necessary format */
+ if($format == 'json') {
+ header('Content-type: application/json');
+ echo json_encode(array('sfautocomplete'=>$terms));
+ }
+ else {
+ die('Sorry, this request cannot be fulfilled in '.$format.' format.');
+ }
+ break;
+
+ case 'term_detail':
+ /* grab the ontology data from the db */
+ $query = "SELECT DISTINCT t.name as 'name', t.acc as 'acc', t.term_type as 'type', d.term_definition as 'definition', d.term_comment as 'comment'"
+ . " FROM term t"
+ . " LEFT JOIN term_definition d ON d.term_id = t.id"
+ . " WHERE t.$field = '$qval'"
+ . " AND t.term_type in ($term_types)"
+ . " AND t.is_obsolete = 0"
+ . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'"
+ . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'"
+ . " ORDER BY t.name LIMIT 1";
+ $result = mysql_query($query,$link) or die('Errant query: '.$query);
+
+ /* create one master array of the records */
+ $terms = array();
+ if(mysql_num_rows($result)) {
+ while($term = mysql_fetch_assoc($result)) {
+ switch($term['type']) {
+ case 'plant_anatomy':
+ $term_type_formal = "Plant Anatomy"; break;
+ case 'plant_growth_and_development_stage':
+ $term_type_formal = "Plant Growth and Development Stage"; break;
+ case 'biological_process':
+ $term_type_formal = "Biological Process"; break;
+ case 'cellular_component':
+ $term_type_formal = "Cellular Component"; break;
+ case 'molecular_function':
+ $term_type_formal = "Molecular Function"; break;
+ }
+ $terms[] = array(
+ 'name'=>$term['name'],
+ 'id'=>$term['acc'],
+ 'aspect'=>$term_type_formal,
+ 'definition'=>$term['definition'],
+ 'comment'=>$term['comment']);
+ }
+ }
+ /* output in necessary format */
+ if($format == 'json') {
+ header('Content-type: application/json');
+ echo json_encode(array('term_detail_result'=>$terms));
+ }
+ else {
+ die('Sorry, this request cannot be fulfilled in '.$format.' format.');
+ }
+ break;
+ default:
+ die('Sorry, this web service method is not available.');
+ }
+ /* disconnect from the db */
+ @mysql_close($link);
+}
+else { die('Not authorized.'); }
+?>
+
+++ /dev/null
-<?php
-// JSON web service for PO terms: autocomplete and search methods
-
-/* require the user as the parameter */
-if(isset($_GET['user']) && ($_GET['user']) == 'paw') {
-
- $arr_field_names = array('name','acc');
- $arr_ontologies = array('go','po');
-
- /* read the params and/or set our own */
- $type = isset($_GET['type']) ? $_GET['type'] : autocomplete; // autocomplete is the default
-
- // security measures; helps to avoid SQL injection attacks
- $field = isset($_GET['field']) && in_array($_GET['field'],$arr_field_names)
- ? $_GET['field']
- : die('"field" is a required parameter and must match an available data field.');
-
- $number_of_terms = isset($_GET['max']) ? intval($_GET['max']) : 10; //10 is the default
- if ($number_of_terms > 50) { $number_of_terms = 50; }
-
- $ont = isset($_GET['ontology']) && in_array(strtolower($_GET['ontology']),$arr_ontologies)
- ? strtolower($_GET['ontology'])
- : die('"ontology" is a required parameter and must match an available data field.');
-
- $qval = $_GET['qval'];
-
- $qval = isset($_GET['qval']) && strlen($_GET['qval']) > 0
- ? strtolower($_GET['qval'])
- : die('Please provide a searchable value');
-
- $format = strtolower($_GET['format']) != 'json'
- ? strtolower($_GET['format'])
- : 'json'; //json is the default
-
- /* connect to the appropriate db */
- switch ($ont) {
- case 'po':
- $link = mysql_connect($_SERVER['dev_po_host'], $_SERVER['dev_po_user'], $_SERVER['dev_po_pw']) or die('Cannot connect to the DB');
- mysql_select_db($_SERVER['dev_po_db'],$link) or die('Cannot select the DB');
-
- $term_types = "'plant_anatomy','plant_growth_and_development_stage'";
- break;
-
- case 'go':
- $link = mysql_connect($_SERVER['dev_go_host'], $_SERVER['dev_go_user'], $_SERVER['dev_go_pw']) or die('Cannot connect to the DB');
- mysql_select_db($_SERVER['dev_go_db'],$link) or die('Cannot select the DB');
-
- $term_types = "'biological_process','cellular_component','molecular_function'";
- break;
-
- default:
- die('Sorry, this ontology type is not available.');
- }
-
- switch ($type) {
- case 'autocomplete':
- /* grab the terms from the db */
- $query = "SELECT t.$field FROM term t"
- . " LEFT JOIN term_definition d ON d.term_id = t.id"
- . " WHERE t.$field LIKE '%$qval%'"
- . " AND t.term_type in ($term_types)"
- . " AND t.is_obsolete = 0"
- . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'"
- . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'"
- . " ORDER BY name LIMIT $number_of_terms";
- $result = mysql_query($query,$link) or die('Errant query: '.$query);
-
- /* create one master array of the records */
- $terms = array();
- if(mysql_num_rows($result)) {
- while($term = mysql_fetch_assoc($result)) {
- $terms[] = array('title'=>$term[$field]);
- }
- }
-
- /* output in necessary format */
- if($format == 'json') {
- header('Content-type: application/json');
- echo json_encode(array('sfautocomplete'=>$terms));
- }
- else {
- die('Sorry, this request cannot be fulfilled in '.$format.' format.');
- }
- break;
-
- case 'term_detail':
- /* grab the ontology data from the db */
- $query = "SELECT DISTINCT t.name as 'name', t.acc as 'acc', t.term_type as 'type', d.term_definition as 'definition', d.term_comment as 'comment'"
- . " FROM term t"
- . " LEFT JOIN term_definition d ON d.term_id = t.id"
- . " WHERE t.$field = '$qval'"
- . " AND t.term_type in ($term_types)"
- . " AND t.is_obsolete = 0"
- . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'"
- . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'"
- . " ORDER BY t.name LIMIT 1";
- $result = mysql_query($query,$link) or die('Errant query: '.$query);
-
- /* create one master array of the records */
- $terms = array();
- if(mysql_num_rows($result)) {
- while($term = mysql_fetch_assoc($result)) {
- switch($term['type']) {
- case 'plant_anatomy':
- $term_type_formal = "Plant Anatomy"; break;
- case 'plant_growth_and_development_stage':
- $term_type_formal = "Plant Growth and Development Stage"; break;
- case 'biological_process':
- $term_type_formal = "Biological Process"; break;
- case 'cellular_component':
- $term_type_formal = "Cellular Component"; break;
- case 'molecular_function':
- $term_type_formal = "Molecular Function"; break;
- }
- $terms[] = array(
- 'name'=>$term['name'],
- 'id'=>$term['acc'],
- 'aspect'=>$term_type_formal,
- 'definition'=>$term['definition'],
- 'comment'=>$term['comment']);
- }
- }
- /* output in necessary format */
- if($format == 'json') {
- header('Content-type: application/json');
- echo json_encode(array('term_detail_result'=>$terms));
- }
- else {
- die('Sorry, this request cannot be fulfilled in '.$format.' format.');
- }
- break;
- default:
- die('Sorry, this web service method is not available.');
- }
- /* disconnect from the db */
- @mysql_close($link);
-}
-else { die('Not authorized.'); }
-?>
-
+++ /dev/null
-<?php
-// JSON web service for PO terms: autocomplete and search methods
-
-/* require the user as the parameter */
-if(isset($_GET['user']) && ($_GET['user']) == 'paw') {
-
- $arr_field_names = array('name','acc');
- $arr_ontologies = array('go','po');
-
- /* read the params and/or set our own */
- $type = isset($_GET['type']) ? $_GET['type'] : autocomplete; // autocomplete is the default
-
- // security measures; helps to avoid SQL injection attacks
- $field = isset($_GET['field']) && in_array($_GET['field'],$arr_field_names)
- ? $_GET['field']
- : die('"field" is a required parameter and must match an available data field.');
-
- $number_of_terms = isset($_GET['max']) ? intval($_GET['max']) : 10; //10 is the default
- if ($number_of_terms > 50) { $number_of_terms = 50; }
-
- $ont = isset($_GET['ontology']) && in_array(strtolower($_GET['ontology']),$arr_ontologies)
- ? strtolower($_GET['ontology'])
- : die('"ontology" is a required parameter and must match an available data field.');
-
- $qval = $_GET['qval'];
-
- $qval = isset($_GET['qval']) && strlen($_GET['qval']) > 0
- ? strtolower($_GET['qval'])
- : die('Please provide a searchable value');
-
- $format = strtolower($_GET['format']) != 'json'
- ? strtolower($_GET['format'])
- : 'json'; //json is the default
-
- /* connect to the appropriate db */
- switch ($ont) {
- case 'po':
- $link = mysql_connect($_SERVER['test_po_host'], $_SERVER['test_po_user'], $_SERVER['test_po_pw']) or die('Cannot connect to the DB');
- mysql_select_db($_SERVER['test_po_db'],$link) or die('Cannot select the DB');
-
- $term_types = "'plant_anatomy','plant_growth_and_development_stage'";
- break;
-
- case 'go':
- $link = mysql_connect($_SERVER['test_go_host'], $_SERVER['test_go_user'], $_SERVER['test_go_pw']) or die('Cannot connect to the DB');
- mysql_select_db($_SERVER['test_go_db'],$link) or die('Cannot select the DB');
-
- $term_types = "'biological_process','cellular_component','molecular_function'";
- break;
-
- default:
- die('Sorry, this ontology type is not available.');
- }
-
- switch ($type) {
- case 'autocomplete':
- /* grab the terms from the db */
- $query = "SELECT t.$field FROM term t"
- . " LEFT JOIN term_definition d ON d.term_id = t.id"
- . " WHERE t.$field LIKE '%$qval%'"
- . " AND t.term_type in ($term_types)"
- . " AND t.is_obsolete = 0"
- . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'"
- . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'"
- . " ORDER BY name LIMIT $number_of_terms";
- $result = mysql_query($query,$link) or die('Errant query: '.$query);
-
- /* create one master array of the records */
- $terms = array();
- if(mysql_num_rows($result)) {
- while($term = mysql_fetch_assoc($result)) {
- $terms[] = array('title'=>$term[$field]);
- }
- }
-
- /* output in necessary format */
- if($format == 'json') {
- header('Content-type: application/json');
- echo json_encode(array('sfautocomplete'=>$terms));
- }
- else {
- die('Sorry, this request cannot be fulfilled in '.$format.' format.');
- }
- break;
-
- case 'term_detail':
- /* grab the ontology data from the db */
- $query = "SELECT DISTINCT t.name as 'name', t.acc as 'acc', t.term_type as 'type', d.term_definition as 'definition', d.term_comment as 'comment'"
- . " FROM term t"
- . " LEFT JOIN term_definition d ON d.term_id = t.id"
- . " WHERE t.$field = '$qval'"
- . " AND t.term_type in ($term_types)"
- . " AND t.is_obsolete = 0"
- . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'"
- . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'"
- . " ORDER BY t.name LIMIT 1";
- $result = mysql_query($query,$link) or die('Errant query: '.$query);
-
- /* create one master array of the records */
- $terms = array();
- if(mysql_num_rows($result)) {
- while($term = mysql_fetch_assoc($result)) {
- switch($term['type']) {
- case 'plant_anatomy':
- $term_type_formal = "Plant Anatomy"; break;
- case 'plant_growth_and_development_stage':
- $term_type_formal = "Plant Growth and Development Stage"; break;
- case 'biological_process':
- $term_type_formal = "Biological Process"; break;
- case 'cellular_component':
- $term_type_formal = "Cellular Component"; break;
- case 'molecular_function':
- $term_type_formal = "Molecular Function"; break;
- }
- $terms[] = array(
- 'name'=>$term['name'],
- 'id'=>$term['acc'],
- 'aspect'=>$term_type_formal,
- 'definition'=>$term['definition'],
- 'comment'=>$term['comment']);
- }
- }
- /* output in necessary format */
- if($format == 'json') {
- header('Content-type: application/json');
- echo json_encode(array('term_detail_result'=>$terms));
- }
- else {
- die('Sorry, this request cannot be fulfilled in '.$format.' format.');
- }
- break;
- default:
- die('Sorry, this web service method is not available.');
- }
- /* disconnect from the db */
- @mysql_close($link);
-}
-else { die('Not authorized.'); }
-?>
-
projects / old-jaiswallab-svn / .git / commitdiff