Merge pull request #14 from BioKIC/master

Pull from bioKIC/Symbiota

classes/DwcArchiverCore.php

@@ -942,6 +942,7 @@ private function writeMetaFile(){
 		$occCnt = 1;
 		$termArr = $this->occurrenceFieldArr['terms'];
 		if ($this->schemaType == 'dwc' || $this->schemaType == 'pensoft') {
+			unset($termArr['eventDate2']);
 			unset($termArr['localitySecurity']);
 		}
 		if ($this->schemaType == 'dwc' || $this->schemaType == 'pensoft' || $this->schemaType == 'backup') {

classes/ImageLibrarySearch.php

@@ -34,21 +34,23 @@ public function getImageArr($pageRequest,$cntPerPage){
 		$retArr = Array();
 		$this->setSqlWhere();
 		$this->setRecordCnt();
-		$sql = 'SELECT DISTINCT i.imgid, i.tid, IFNULL(t.sciname,o.sciname) as sciname, i.url, i.thumbnailurl, i.originalurl, i.photographeruid, i.caption, i.occid ';
+		$sql = 'SELECT i.imgid, i.tid, IFNULL(t.sciname,o.sciname) as sciname, i.url, i.thumbnailurl, i.originalurl, i.photographeruid, i.caption, i.occid ';
 		/*
 		$sql = 'SELECT DISTINCT i.imgid, o.tidinterpreted, t.tid, t.sciname, i.url, i.thumbnailurl, i.originalurl, i.photographeruid, i.caption, '.
 			'o.occid, o.stateprovince, o.catalognumber, CONCAT_WS("-",c.institutioncode, c.collectioncode) as instcode ';
 		*/
 		$sqlWhere = $this->sqlWhere;
 		if($this->imageCount == 'taxon') $sqlWhere .= 'GROUP BY sciname ';
 		elseif($this->imageCount == 'specimen') $sqlWhere .= 'GROUP BY i.occid ';
-		if($this->sqlWhere) $sqlWhere .= 'ORDER BY sciname ';
+		if($this->sqlWhere) $sqlWhere .= 'ORDER BY o.sciname ';
 		$bottomLimit = ($pageRequest - 1)*$cntPerPage;
 		$sql .= $this->getSqlBase().$sqlWhere.'LIMIT '.$bottomLimit.','.$cntPerPage;
 		//echo '<div>Spec sql: '.$sql.'</div>';
 		$occArr = array();
 		$result = $this->conn->query($sql);
+		$imgId = 0;
 		while($r = $result->fetch_object()){
+			if($imgId == $r->imgid) continue;
 			$imgId = $r->imgid;
 			$retArr[$imgId]['imgid'] = $r->imgid;
 			//$retArr[$imgId]['tidaccepted'] = $r->tidinterpreted;

classes/OccurrenceCollectionProfile.php

@@ -215,7 +215,7 @@ public function batchTriggerGBIFCrawl($collIdArr){
 	}
 
 	public function triggerGBIFCrawl($dwcUri, $collid, $collectionName){
-		if(isset($GLOBALS['GBIF_USERNAME'])){
+		if(isset($GLOBALS['GBIF_USERNAME']) && $GLOBALS['GBIF_USERNAME']){
 			if($this->organizationKey){
 				if(!$this->logFH){
 					$this->setVerboseMode(3);

classes/OccurrenceIndividual.php

@@ -117,6 +117,7 @@ public function getOccData($fieldKey = ""){
 	}
 
 	public function setOccurData(){
+		/*
 		$sql = 'SELECT o.occid, o.collid, o.institutioncode, o.collectioncode, '.
 			'o.occurrenceid, o.catalognumber, o.occurrenceremarks, o.tidinterpreted, o.family, o.sciname, '.
 			'o.scientificnameauthorship, o.identificationqualifier, o.identificationremarks, o.identificationreferences, o.taxonremarks, '.
@@ -128,6 +129,8 @@ public function setOccurData(){
 			'o.typestatus, o.dbpk, o.habitat, o.substrate, o.associatedtaxa, o.dynamicProperties, o.reproductivecondition, o.cultivationstatus, o.establishmentmeans, '.
 			'o.ownerinstitutioncode, o.othercatalognumbers, o.disposition, o.informationwithheld, o.modified, o.observeruid, o.recordenteredby, o.dateentered, o.datelastmodified '.
 			'FROM omoccurrences o ';
+		*/
+		$sql = 'SELECT o.*, MAKEDATE(YEAR(o.eventDate),o.enddayofyear) AS eventdateend FROM omoccurrences o ';
 		if($this->occid) $sql .= 'WHERE (o.occid = '.$this->occid.')';
 		elseif($this->collid && $this->dbpk) $sql .= 'WHERE (o.collid = '.$this->collid.') AND (o.dbpk = "'.$this->dbpk.'")';
 		else{

config/schema-1.0/dev/db_schema_patch-dev.sql

@@ -410,6 +410,7 @@ ALTER TABLE `omoccurdatasets`
   CHANGE COLUMN `sortsequence` `sortSequence` INT(11) NULL DEFAULT NULL ,
   CHANGE COLUMN `initialtimestamp` `initialTimestamp` TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP() ;
 
+
 ALTER TABLE `omoccurdeterminations` 
   DROP FOREIGN KEY `FK_omoccurdets_idby`;
 
@@ -430,14 +431,25 @@ ALTER TABLE `omoccurdeterminations`
   ADD COLUMN `taxonRank` VARCHAR(45) NULL AFTER `verbatimTaxonRank`,
   ADD COLUMN `infraSpecificEpithet` VARCHAR(45) NULL AFTER `taxonRank`,
   ADD COLUMN `securityStatus` INT NOT NULL DEFAULT 0 AFTER `appliedStatus`,
+  ADD COLUMN `securityStatusReason` VARCHAR(100) NULL AFTER `securityStatus`,
   ADD COLUMN `identificationVerificationStatus` VARCHAR(45) NULL AFTER `taxonRemarks`,
-  ADD COLUMN `taxonConceptID` VARCHAR(45) NULL AFTER `scientificNameID`,
+  ADD COLUMN `taxonConceptID` VARCHAR(45) NULL AFTER `identificationVerificationStatus`,
   ADD COLUMN `recordID` VARCHAR(45) NULL AFTER `sortSequence`,
   CHANGE COLUMN `identifiedBy` `identifiedBy` VARCHAR(60) NOT NULL DEFAULT 'unknown' ,
   CHANGE COLUMN `dateIdentified` `dateIdentified` VARCHAR(45) NOT NULL DEFAULT 's.d.' ,
   CHANGE COLUMN `sourceIdentifier` `identificationID` VARCHAR(45) NULL DEFAULT NULL ,
   ADD INDEX `FK_omoccurdets_agentID_idx` (`identifiedByAgentID` ASC);
 
+ALTER TABLE `omoccurdeterminations` 
+  CHANGE COLUMN `identifiedBy` `identifiedBy` VARCHAR(255) NOT NULL ,
+  CHANGE COLUMN `family` `family` VARCHAR(255) NULL DEFAULT NULL ,
+  CHANGE COLUMN `sciname` `sciname` VARCHAR(255) NOT NULL ,
+  CHANGE COLUMN `scientificNameAuthorship` `scientificNameAuthorship` VARCHAR(255) NULL DEFAULT NULL ,
+  CHANGE COLUMN `identificationQualifier` `identificationQualifier` VARCHAR(255) NULL DEFAULT NULL ,
+  CHANGE COLUMN `identificationReferences` `identificationReferences` VARCHAR(2000) NULL DEFAULT NULL ,
+  CHANGE COLUMN `identificationRemarks` `identificationRemarks` VARCHAR(2000) NULL DEFAULT NULL ,
+  CHANGE COLUMN `taxonRemarks` `taxonRemarks` VARCHAR(2000) NULL DEFAULT NULL;
+
 ALTER TABLE `omoccurdeterminations` 
   ADD CONSTRAINT `FK_omoccurdets_agentID`  FOREIGN KEY (`identifiedByAgentID`)  REFERENCES `agents` (`agentID`)  ON DELETE SET NULL  ON UPDATE CASCADE;
 
@@ -463,7 +475,7 @@ FROM omoccurrences;
 INSERT IGNORE INTO omoccurdeterminations(occid, identifiedBy, dateIdentified, family, sciname, verbatimIdentification, scientificNameAuthorship, tidInterpreted, 
 identificationQualifier, genus, specificEpithet, verbatimTaxonRank, infraSpecificEpithet, isCurrent, identificationReferences, identificationRemarks, 
 taxonRemarks)
-SELECT o.occid, IFNULL(identifiedBy, "unknown"), IFNULL(dateIdentified, "s.d."), o.family, IFNULL(o.sciname, "undefined"), o.scientificName, o.scientificNameAuthorship, o.tidInterpreted, 
+SELECT o.occid, IFNULL(o.identifiedBy, "unknown"), IFNULL(o.dateIdentified, "s.d."), o.family, IFNULL(o.sciname, "undefined"), o.scientificName, o.scientificNameAuthorship, o.tidInterpreted, 
 o.identificationQualifier, o.genus, o.specificEpithet, o.taxonRank, o.infraSpecificEpithet, 1 as isCurrent, o.identificationReferences, o.identificationRemarks, 
 o.taxonRemarks
 FROM omoccurrences o LEFT JOIN omoccurdeterminations d ON o.occid = d.occid
@@ -736,10 +748,6 @@ ALTER TABLE `taxalinks`
 ALTER TABLE `taxalinks` 
   DROP INDEX `Index_unique` ;
 
-ALTER TABLE `uploadspectemp` 
-  ADD COLUMN `eventTime` VARCHAR(45) NULL AFTER `verbatimEventDate`,
-  CHANGE COLUMN `LatestDateCollected` `eventDate2` DATE NULL DEFAULT NULL AFTER `eventDate`;
-
 ALTER TABLE `uploadspecparameters` 
   DROP FOREIGN KEY `FK_uploadspecparameters_coll`;
 
@@ -764,18 +772,22 @@ ALTER TABLE `uploadspecparameters`
   ADD CONSTRAINT `FK_uploadspecparameters_coll`  FOREIGN KEY (`collid`)  REFERENCES `omcollections` (`collID`)  ON DELETE CASCADE  ON UPDATE CASCADE;
 
 ALTER TABLE `uploadspectemp` 
+  ADD COLUMN `eventTime` VARCHAR(45) NULL AFTER `verbatimEventDate`,
+  ADD COLUMN `observeruid` INT NULL AFTER `language`,
+  ADD COLUMN `dateEntered` DATETIME NULL AFTER `recordEnteredBy`,
+  ADD COLUMN `eventID` VARCHAR(45) NULL AFTER `fieldnumber`,
+  CHANGE COLUMN `taxonRemarks` `taxonRemarks` VARCHAR(2000) NULL DEFAULT NULL ,
+  CHANGE COLUMN `identificationReferences` `identificationReferences` VARCHAR(2000) NULL DEFAULT NULL ,
+  CHANGE COLUMN `identificationRemarks` `identificationRemarks` VARCHAR(2000) NULL DEFAULT NULL ,
   CHANGE COLUMN `establishmentMeans` `establishmentMeans` VARCHAR(150) NULL DEFAULT NULL,
   CHANGE COLUMN `disposition` `disposition` varchar(250) NULL DEFAULT NULL,
-  ADD COLUMN `observeruid` INT NULL AFTER `language`,
-  ADD COLUMN `dateEntered` DATETIME NULL AFTER `recordEnteredBy`;
-
-ALTER TABLE `uploadspectemp` 
-  ADD COLUMN `eventID` VARCHAR(45) NULL AFTER `fieldnumber`;
+  CHANGE COLUMN `LatestDateCollected` `eventDate2` DATE NULL DEFAULT NULL AFTER `eventDate`;
 
 ALTER TABLE `uploadspectemp` 
   DROP COLUMN `materialSampleID`,
   ADD COLUMN `materialSampleJSON` TEXT NULL AFTER `paleoJSON`;
 
+
 UPDATE userroles SET tablename = "fmprojects" WHERE tablename = "fmproject";