Bugfix: Rewrote as parser function instead of tag function. Now works…

… with SMW facts

GeneIdConvert.i18n.php

@@ -0,0 +1,7 @@
+<?php 
+
+$magicWords = array();
+
+$magicWords['en'] = array(
+    'geneidconv' => array( 0, 'geneidconv' ),
+);

GeneIdConvert.php

@@ -1,4 +1,4 @@
-<?php
+<?php 
 /**
  * Simple MediaWiki extension that converts from Ensembl Gene ID to 
  * desired target gene ID type, by using the CrossRef endpoint of the
@@ -21,7 +21,7 @@
  *
  * Example usage of the extension within a MediaWiki article:
  *
- *      <geneidconv to="EntrezGene">ENSG00000157764</gene>
+ *      {{ #geneidconv: ENSG00000157764 | EntrezGene }}
  *
  * A few of the avaible options for the "to" parameter, is (as of 
  * writing this):
@@ -37,30 +37,65 @@
  *
  */
 
-$wgHooks['ParserFirstCallInit'][] = 'wfGeneIdConvertParserInit';
+// Take credit for your work.
+$wgExtensionCredits['parserhook'][] = array(
 
+   // The full path and filename of the file. This allows MediaWiki
+   // to display the Subversion revision number on Special:Version.
+   'path' => __FILE__,
+
+   // The name of the extension, which will appear on Special:Version.
+   'name' => 'Gene ID Convert',
+
+   // A description of the extension, which will appear on Special:Version.
+   'description' => 'Simple MediaWiki extension that converts from Ensembl Gene ID to desired target gene ID type',
+
+   // Alternatively, you can specify a message key for the description.
+   // 'descriptionmsg' => 'exampleextension-desc',
+
+   // The version of the extension, which will appear on Special:Version.
+   // This can be a number or a string.
+   'version' => 1, 
+
+   // Your name, which will appear on Special:Version.
+   'author' => 'Samuel Lampa',
+
+   // The URL to a wiki page/web page with information about the extension,
+   // which will appear on Special:Version.
+   'url' => 'https://www.mediawiki.org/wiki/Manual:Parser_functions',
+
+);
+
+// Specify the function that will initialize the parser function.
+$wgHooks['ParserFirstCallInit'][] = 'GeneIdConvertSetupParserFunction';
+
+// Allow translation of the parser function name
+$wgExtensionMessagesFiles['GeneIdConvert'] = __DIR__ . '/GeneIdConvert.i18n.php';
+
 // Hook our callback function into the parser
-function wfGeneIdConvertParserInit( Parser $parser ) {
+function GeneIdConvertSetupParserFunction( &$parser ) {
     // When the parser sees the <geneidconv> tag, it executes 
-    $parser->setHook( 'geneidconv', 'wfGeneIdConvRender' );
+    $parser->setFunctionHook( 'geneidconv', 'GeneIdConvertRenderParserFunction' );
     // Always return true from this function. The return value does not denote
     // success or otherwise have meaning - it just must always be true.
     return true;
 }
 
-// Execute 
-function wfGeneIdConvRender( $srcGeneId, array $args, Parser $parser, PPFrame $frame ) {
+// function geneIDConvert( $srcGeneId, array $args, Parser $parser, PPFrame $frame ) {
+function GeneIdConvertRenderParserFunction( $parser, $srcGeneId = '', $toFormat = '' ) {
 
+    if ( $srcGeneId === '' ) {
+        return 'ERROR:Field_1_gene_id_missing';
+    }
+    if ( $toFormat === '' ) {
+        return 'ERROR:Field_2_target_format_missing';
+    }
     // Disable cache, at least for debugging purposes
     $parser->disableCache();
 
-    // Parse any wiki text in the content of the tag:
-    $srcGeneId = $parser->recursiveTagParse( $srcGeneId, $frame );
-
     // Set some variables
     $ensemblRestBaseUrl = "http://beta.rest.ensembl.org/xrefs/id"; // Without trailing slash
-    $targetId = "";
-    $toFormat = $args['to'];
+    $targetId = '';
 
     // Construct the Query URL
     $queryUrl = $ensemblRestBaseUrl . '/' . $srcGeneId . '?content-type=application/json';
@@ -87,8 +122,7 @@ function wfGeneIdConvRender( $srcGeneId, array $args, Parser $parser, PPFrame $f
     } else {
         $targetId = 'N/A';
     }
-    // echo "TargetId: [$targetId]";
-    return (string)$targetId;
+    return $targetId;
 }
 
 function wfGetRemoteData( $url ) {

README.md

@@ -3,7 +3,7 @@ desired target gene ID type, by using the CrossRef endpoint of the
 new Ensembl REST API.
 
 Author:  Samuel Lampa - samuel.lampa@gmail.com
-Date:    2013-05-31
+Created Date:    2013-05-31
 
 More info on the REST API Here:
 
@@ -24,11 +24,14 @@ require_once("$IP/extensions/GeneIdConvert/GeneIdConvert.php");
 - Example usage of the extension within a MediaWiki article:
 
 ````
-<geneidconv to="EntrezGene">ENSG00000157764</gene>
+{{ #geneidconv: ENSG00000157764 | EntrezGene }}
 ````
 
- A few of the avaible options for the "to" parameter, is (as of 
- writing this):
+... where the first field is the source ID (in Ensembl ID format) 
+and the second field is the target id type.
+
+A few of the avaible options for the "to" parameter, is (as of 
+writing this) are the following:
 
 - OTTG
 - ArrayExpress