Lemat export unification

.gitignore

@@ -1,5 +1,5 @@
 engine/templates_c/*
-engine/include/vendor
+vendor
 config/config.local.php
 docker/www/config/config.local.php
 secured_data/ccls

composer.json

@@ -1,7 +1,6 @@
 {
     "config": {
-	"platform": {"php":"5.6"},
-        "vendor-dir": "engine/include/vendor"
+	"platform": {"php":"5.6"}
     },
 
     "autoload": {

docker-compose.yml

@@ -13,6 +13,7 @@ services:
         - ./docker/www/config:/home/inforex/config
         - ./secured_data:/home/inforex/secured_data
         - ./phpunit:/home/inforex/phpunit
+        - ./vendor:/home/inforex/vendor
       depends_on:
       - db
       restart: always     

docker-dev-up.sh

@@ -2,12 +2,12 @@
 
 composer update
 
-AUTOLOAD=engine/include/vendor/autoload.php
+AUTOLOAD=vendor/autoload.php
 
 if [ -f $AUTOLOAD ]; then
     docker-compose build
     docker-compose up -d
 else
     echo -e "[\e[31mERROR\e[0m] $AUTOLOAD not found"
     echo -e "Make sure that '\e[32mcomposer\e[0m' is installed in order to run '\e[32mcomposer update\e[0m' and generate $AUTOLOAD"
-fi
+fi

engine/external/pear/HTML/Select.php

@@ -13,7 +13,7 @@
  * @link     http://pear.php.net/package/HTML_Select
  */
 
-require_once __DIR__ . '/../../../include/vendor/autoload.php';
+require_once __DIR__ . '/../../../../vendor/autoload.php';
 
 /**
  * Class to dynamically create an HTML SELECT

engine/include.php

@@ -5,4 +5,4 @@
 $include_paths[] = get_include_path();
 set_include_path( implode(PATH_SEPARATOR, $include_paths) );
 
-require_once __DIR__ . '/include/vendor/autoload.php';
+require_once __DIR__ . '/../vendor/autoload.php';

engine/include/database/CDbAnnotation.php

@@ -166,7 +166,7 @@ static function getAnnotationTypesBySets($report_ids, $relation_ids){
 
 	static function getAnnotationsBySets($report_ids=null, $annotation_layers=null, $annotation_names=null, $stage = null){
 		global $db;
-		$sql = "SELECT *, raa.`value` AS `prop` " .
+		$sql = "SELECT ra.*, at.*, raa.annotation_id, raa.annotation_attribute_id, raa.`user_id` AS `attr_user_id`, raa.`value` AS `prop` " .
 				" FROM reports_annotations ra" .
 				" LEFT JOIN annotation_types at ON (ra.type=at.name) " .
 				" LEFT JOIN reports_annotations_attributes raa ON (ra.id=raa.annotation_id) ";
@@ -203,7 +203,7 @@ static function getAnnotationsBySets($report_ids=null, $annotation_layers=null,
 	 */
 	static function getAnnotationsBySubsets($report_ids=null, $annotation_subset_ids=null){
 		global $db;
-		$sql = "SELECT *, ra.type, raa.`value` AS `prop` " .
+		$sql = "SELECT ra.*, at.*, raa.annotation_id, raa.annotation_attribute_id, raa.`user_id` AS `attr_user_id`, raa.`value` AS `prop` " .
 				" FROM reports_annotations ra" .
 				" LEFT JOIN annotation_types at ON (ra.type=at.name) " .
 				" LEFT JOIN reports_annotations_attributes raa ON (ra.id=raa.annotation_id) ";

engine/include/database/CDbCorpusRelation.php

@@ -163,28 +163,20 @@ static function getRelationsByRelationSetIds($relation_set_ids){
 		return $db->fetch_rows($sql);		
 	}
 
-	//TODO to delete
-	static function getRelationsBySets($report_ids, $relation_type_ids){
-		global $db;
-	    $sql = "SELECT reports_annotations.report_id as report_id, rel.id, rel.relation_type_id, rel.source_id, rel.target_id, relation_types.name " .
-	            "FROM " .
-	                "(SELECT * " .
-	                "FROM relations " .
-	                "WHERE source_id IN " .
-	                    "(SELECT id " .
-	                    "FROM reports_annotations " .
-	                    "WHERE report_id IN('" . implode("','",$report_ids) . "')) " .
-	                "AND relation_type_id " .
-	                "IN (".implode(",",$relation_type_ids).")) rel " .
-	            "LEFT JOIN relation_types " .
-	            "ON rel.relation_type_id=relation_types.id " .
-	            "LEFT JOIN reports_annotations " .
-	            "ON rel.source_id=reports_annotations.id ";
-		return $db->fetch_rows($sql);		            				
-	}
-
-	static function getRelationsBySets2($report_ids=null, $relation_set_ids=null, $relation_type_ids=null, $stage_ids=null, $user_ids=null){
+	static function getRelationsBySets($report_ids=null, $relation_set_ids=null, $relation_type_ids=null, $stage_ids=null, $user_ids=null, $relation_stages=array()){
 		global $db;
+
+        // if $relation_stages not set is equal $stage_ids - stages of
+        // relation are identical as stages of annotations
+        if( is_array($relation_stages) && (count($relation_stages)==0)) {
+            $relation_stages = $stage_ids;
+        } // if not set
+
+        if (is_array($relation_stages) && (count($relation_stages)>0)) {
+            $relationStages = "stage IN('".implode("','",$relation_stages)."') AND";
+        } else { // if $relation_stages==null default is 'final'
+            $relationStages = "stage = 'final' AND"; 
+        }
 	    $sql = "SELECT reports_annotations.report_id as report_id, " .
 	    		"      rel.id, " .
 	    		"      rel.relation_type_id, " .
@@ -196,7 +188,7 @@ static function getRelationsBySets2($report_ids=null, $relation_set_ids=null, $r
 	            "FROM " .
 	                "(SELECT * " .
 	                "FROM relations " .
-	                "WHERE stage = 'final' AND source_id IN " .
+	                "WHERE ".$relationStages." source_id IN " .
 	                    "(SELECT id " .
 	                    "FROM reports_annotations " .
 	                    "WHERE report_id IN('0','" . implode("','",$report_ids) . "')) " .

engine/include/export/CCclFactory.php → engine/include/export/CclExportDocument.php

@@ -6,22 +6,26 @@
  * See LICENCE 
  */
 
-class CclFactory{
+class CclExportDocument extends CclDocument {
 
 	/**
 	 * $report --- tablica asocjacyjna z atrybutami dokumentu (jak z tabeli reports)
 	 * $tokens --- tablica asocjacyjna z wartościami 'from', 'to' i 'eos'
 	 * $tags --- 
 	 * function creates ccl document using 'eos' token attributes to match end of sentence
-	 * see: createFromReportAndTokensSentence 
+	 * see: createFromReportAndTokensSentence, was createFromReportAndTokens()
 	 */	 
-	function createFromReportAndTokens(&$report, &$tokens, &$tags){
+	public function __construct(&$report, &$tokens, &$tags){
 		$fileName = str_pad($report['id'],8,'0',STR_PAD_LEFT);
 
-		$ccl = new CclDocument();
-		$ccl->setFileName($fileName);
-		$ccl->setSubcorpus(preg_replace("/[^\p{L}|\p{N}]+/u","_",$report['name']));
-		$ccl->setReport($report);
+		$this->setFileName($fileName);
+		$this->setSubcorpus(
+            // SW ?? there are not 'name' column  in DB table reports 
+            isset($report['name'])
+            ? preg_replace("/[^\p{L}|\p{N}]+/u","_",$report['name'])
+            : ""
+        );
+		$this->setReport($report);
 
 		$chunkList = explode('<\\chunk>', $report['content']);
 
@@ -34,7 +38,10 @@ function createFromReportAndTokens(&$report, &$tokens, &$tags){
 			$chunk = str_replace(">","> ",$chunk);
 			preg_match_all($pattern, $chunk, $matches);
 			$type = "p";
-			if (is_array($matches) && array_key_exists(1, $matches))
+			if (is_array($matches) 
+                && array_key_exists(1, $matches)
+                && array_key_exists(0,$matches[1])
+            )
 				$type = $matches[1][0];					
 			$tmpStr = trim(preg_replace("/\s\s+/"," ",custom_html_entity_decode(strip_tags($chunk))));
 			$tmpStr2 = preg_replace("/\n+|\r+|\s+/","",$tmpStr);
@@ -93,7 +100,7 @@ function createFromReportAndTokens(&$report, &$tokens, &$tags){
 				}
 
 				$s->addToken($t);
-				$ccl->addToken($t);
+				$this->addToken($t);
 				if ( $token['eos'] ){
 					$c->addSentence($s);
 					$s = new CclSentence();
@@ -108,37 +115,36 @@ function createFromReportAndTokens(&$report, &$tokens, &$tags){
 				else 
 					$sentenceIndex--;
 			}
-			$ccl->addChunk($c);
+			$this->addChunk($c);
 		}			
 
-		return $ccl;
-	}
+	} // __construct()
 
 
-	function setAnnotationLemmas(&$ccl, &$annotation_lemmas){
+	protected function setAnnotationLemmas($annotation_lemmas){
 		if (empty($annotation_lemmas)){
 			return false;
 		}
 
 		foreach($annotation_lemmas as $lemma){
-			$ccl->setAnnotationLemma($lemma);
+			$this->setAnnotationLemma($lemma);
 		}
 	}
 
-    function setAnnotationProperties(&$ccl, &$annotation_properties){
+    protected function setAnnotationProperties($annotation_properties){
         if (empty($annotation_properties)){
         	return false;
 		}
 
         foreach($annotation_properties as $property){
-            $ccl->setAnnotationProperty($property);
+            $this->setAnnotationProperty($property);
         }
     }
 
 	/**
 	 * 
 	 */	
-	function setAnnotationsAndRelations(&$ccl, &$annotations, &$relations){
+	protected function setAnnotationsAndRelations(&$annotations, &$relations){
 		if (empty($annotations)) return false;
 		$annotationsById = array();
 		$continuousAnnotationIds = array();
@@ -157,7 +163,7 @@ function setAnnotationsAndRelations(&$ccl, &$annotations, &$relations){
 
 		foreach ($annotations as &$annotation){
 			if ( !in_array($annotation['id'], $continuousAnnotationIds)){
-				$ccl->setAnnotation($annotation);
+				$this->setAnnotation($annotation);
 			} else {
 				$continuousAnnotations[$annotation['id']] =& $annotation;
 			}
@@ -169,7 +175,7 @@ function setAnnotationsAndRelations(&$ccl, &$annotations, &$relations){
 			$target_id = $cRelation['target_id'];
 			if (array_key_exists($source_id, $annotationsById) && 
 				array_key_exists($target_id, $annotationsById)){
-				$ccl->setContinuousAnnotation2(
+				$this->setContinuousAnnotation2(
 					$continuousAnnotations[$source_id],
 					$continuousAnnotations[$target_id]);
 			} else if (array_key_exists($source_id, $annotationsById) ||
@@ -179,7 +185,7 @@ function setAnnotationsAndRelations(&$ccl, &$annotations, &$relations){
 				$e->setFunctionName("setAnnotationsAndRelations");
 				$e->addObject("relation", $cRelation);
 				$e->addComment("008 no source or target annotation in a continuous relation");
-				$ccl->addError($e);					
+				$this->addError($e);					
 			}
 		}
 
@@ -188,7 +194,7 @@ function setAnnotationsAndRelations(&$ccl, &$annotations, &$relations){
 			$target_id = $nRelation['target_id'];
 			if (array_key_exists($source_id, $annotationsById) && 
 				array_key_exists($target_id, $annotationsById)){			
-				$ccl->setRelation(
+				$this->setRelation(
 					$annotationsById[$nRelation['source_id']],
 					$annotationsById[$nRelation['target_id']],
 					$nRelation);
@@ -198,10 +204,21 @@ function setAnnotationsAndRelations(&$ccl, &$annotations, &$relations){
 				$e->setFunctionName("setAnnotationsAndRelations");
 				$e->addObject("relation", $nRelation);
 				$e->addComment("009 no source or target annotation in a normal relation");
-				$ccl->addError($e);						
+				$this->addError($e);						
 			}
 		}
 		return true;
 	}
 
-}
+    public function setCclProperties(&$annotations, &$relations, $lemmas, $attributes ) {
+
+        $this->setAnnotationsAndRelations($annotations, $relations);
+        // Lemmas will be added only if annotations are too
+        if(is_array($annotations) && (count($annotations)>0)) {
+            $this->setAnnotationLemmas($lemmas);
+        }
+        $this->setAnnotationProperties($attributes);
+
+    } // setCclProperties()
+
+} // CclExportDocument class