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Merge pull request #4 from BioKIC/master
Merge BioKIC/Symbiota developments
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,148 @@ | ||
| <?php | ||
| require_once('../config/symbini.php'); | ||
| require_once($SERVER_ROOT.'/classes/PortalIndex.php'); | ||
| //include_once($SERVER_ROOT.'/content/lang/admin/portalindex.'.$LANG_TAG.'.php'); | ||
| header("Content-Type: text/html; charset=".$CHARSET); | ||
|
|
||
| if(!$SYMB_UID) header('Location: '.$CLIENT_ROOT.'/profile/index.php?refurl=../admin/portalindex.php?'.htmlspecialchars($_SERVER['QUERY_STRING'], ENT_QUOTES)); | ||
|
|
||
| $portalID = array_key_exists('portalid',$_REQUEST)?$_REQUEST['portalid']:0; | ||
| $remoteID = array_key_exists('remoteid',$_REQUEST)?$_REQUEST['remoteid']:0; | ||
| $formSubmit = array_key_exists('formsubmit',$_POST)?$_POST['formsubmit']:''; | ||
|
|
||
| //Sanitation | ||
| if(!is_numeric($portalID)) $portalID = 0; | ||
| if(!is_numeric($remoteID)) $remoteID = 0; | ||
|
|
||
| $portalManager = new PortalIndex(); | ||
|
|
||
| $isEditor = 0; | ||
| if($IS_ADMIN) $isEditor = 1; | ||
| ?> | ||
| <html> | ||
| <head> | ||
| <title><?php echo $DEFAULT_TITLE; ?> Portal Index Control Panel</title> | ||
| <?php | ||
| $activateJQuery = true; | ||
| include_once($SERVER_ROOT.'/includes/head.php'); | ||
| ?> | ||
| <script src="<?php echo $CLIENT_ROOT; ?>/js/jquery.js" type="text/javascript"></script> | ||
| <script src="<?php echo $CLIENT_ROOT; ?>/js/jquery-ui.js" type="text/javascript"></script> | ||
| <script type="text/javascript"> | ||
| </script> | ||
| <style type="text/css"> | ||
| fieldset{ margin:20px; padding:15px; } | ||
| legend{ font-weight: bold; } | ||
| label{ font-weight: bold; } | ||
| hr{ margin-top: 15px; margin-bottom: 15px; } | ||
| </style> | ||
| </head> | ||
| <body> | ||
| <?php | ||
| $displayLeftMenu = true; | ||
| include($SERVER_ROOT.'/includes/header.php'); | ||
| ?> | ||
| <div class="navpath"> | ||
| <a href="../../index.php">Home</a> >> | ||
| <b>Portal Index Control Panel</b> | ||
| </div> | ||
| <div id="innertext"> | ||
| <?php | ||
| if($isEditor){ | ||
| if($formSubmit == 'importProfile'){ | ||
| if($collid = $portalManager->importProfile($portalID, $remoteID)) | ||
| echo '<div><a href="../collections/misc/collprofiles.php?collid='.$collid.'" target="_blank">New snapshot collection created</a></div>'; | ||
| else echo '<div>failed to insert new collections: '.$portalManager->getErrorMessage().'</div>'; | ||
| } | ||
| $indexArr = $portalManager->getPortalIndexArr($portalID); | ||
| ?> | ||
| <fieldset> | ||
| <legend>Portal Index</legend> | ||
| <?php | ||
| foreach($indexArr as $portalID => $portalArr){ | ||
| foreach($portalArr as $fieldName => $fieldValue){ | ||
| if($fieldValue){ | ||
| echo '<div><label>'.$fieldName.'</label>: '; | ||
| $href = ''; | ||
| if($fieldName=='urlRoot') $href = $fieldValue; | ||
| elseif($fieldName=='guid') $href = $portalArr['urlRoot'].'/api/v2/installation/ping'; | ||
| if($href) echo '<a href="'.$href.'" target="_blank">'; | ||
| echo $fieldValue; | ||
| if($href) echo '</a>'; | ||
| echo '</div>'; | ||
| } | ||
| } | ||
| echo '<hr/>'; | ||
| if($remoteID){ | ||
| $collectArr = $portalManager->getCollectionList($portalArr['urlRoot'], $remoteID); | ||
| $collTitle = $collectArr['collectionName'].' ('.$collectArr['institutionCode'].($collectArr['collectionCode']?':'.$collectArr['collectionCode']:'').')'; | ||
| echo '<div style="font-weight:bold">#'.$remoteID.': '.$collTitle.'</div>'; | ||
| $collectArr['remoteID'] = $collectArr['collID']; | ||
| unset($collectArr['collID']); | ||
| echo '<div style="margin:15px 30px;">'; | ||
| foreach($collectArr as $fName => $fValue){ | ||
| if($fValue){ | ||
| if($fName == 'fullDescription') $fValue = htmlentities($fValue); | ||
| elseif($fName == 'internalCollid') $fValue = '<a href="'.$CLIENT_ROOT.'/collections/misc/collprofiles.php?collid='.$fValue.'" target="_blank">Mapped Internally</a>'; | ||
| echo '<div><label>'.$fName.'</label>: '.$fValue.'</div>'; | ||
| } | ||
| } | ||
| echo '</div>'; | ||
| if(!$collectArr['internalCollid']){ | ||
| ?> | ||
| <div style="margin: 0px 30px"> | ||
| <form name="collPubForm" method="post" action="portalindex.php"> | ||
| <input name="portalid" type="hidden" value="<?php echo $portalID; ?>" /> | ||
| <input name="remoteid" type="hidden" value="<?php echo $remoteID; ?>" /> | ||
| <input name="collid" type="hidden" value="<?php echo $collectArr['internalCollid']; ?>" /> | ||
| <button name="formsubmit" type="submit" value="importProfile">Import Profile</button> | ||
| </form> | ||
| </div> | ||
| <?php | ||
| } | ||
| } | ||
| elseif($formSubmit == 'listCollections'){ | ||
| if($collList = $portalManager->getCollectionList($portalArr['urlRoot'])){ | ||
| echo '<div><label>Collection Count</label>: '.count($collList).'</div>'; | ||
| echo '<table class="styledtable">'; | ||
| echo '<tr><th>ID</th><th>Institution Code</th><th>Collection Code</th><th>Collection Name</th><th>Dataset Type</th><th>Management</th><th>Mapped Internally</th></tr>'; | ||
| foreach($collList as $collArr){ | ||
| echo '<tr>'; | ||
| echo '<td><a href="portalindex.php?portalid='.$portalID.'&remoteid='.$collArr['collID'].'">'.$collArr['collID'].'</a></td>'; | ||
| echo '<td>'.$collArr['institutionCode'].'</td>'; | ||
| echo '<td>'.$collArr['collectionCode'].'</td>'; | ||
| echo '<td>'.$collArr['collectionName'].'</td>'; | ||
| echo '<td>'.$collArr['collType'].'</td>'; | ||
| echo '<td>'.$collArr['managementType'].'</td>'; | ||
| if($collArr['internalCollid']) $internal = '<a href="'.$CLIENT_ROOT.'/collections/misc/collprofiles.php?collid='.$collArr['internalCollid'].'" target="_blank">Yes</a>'; | ||
| else $internal = 'No'; | ||
| echo '<td>'.$internal.'</td>'; | ||
| echo '</tr>'; | ||
| } | ||
| echo '</table>'; | ||
| } | ||
| } | ||
| else{ | ||
| ?> | ||
| <div> | ||
| <form name="portalActionForm" method="post" action="portalindex.php"> | ||
| <input name="portalid" type="hidden" value="<?php echo $portalID; ?>" /> | ||
| <button name="formsubmit" type="submit" value="listCollections">List Collections</button> | ||
| </form> | ||
| </div> | ||
| <?php | ||
| } | ||
| echo '<hr/>'; | ||
| } | ||
| ?> | ||
| </fieldset> | ||
| <?php | ||
| } | ||
| else echo '<h2>ERROR: access denied</h2>'; | ||
| ?> | ||
| </div> | ||
| <?php | ||
| include($SERVER_ROOT.'/includes/footer.php'); | ||
| ?> | ||
| </body> | ||
| </html> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| APP_NAME=Lumen | ||
| APP_ENV=local | ||
| APP_KEY= | ||
| APP_DEBUG=true | ||
| APP_DEBUG=false | ||
| APP_URL= | ||
| APP_TIMEZONE=UTC | ||
|
|
||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| <?php | ||
| namespace App; | ||
|
|
||
| use Illuminate\Database\Eloquent\Model; | ||
|
|
||
| class Collection extends Model{ | ||
|
|
||
| protected $table = 'omcollections'; | ||
| protected $primaryKey = 'collid'; | ||
| public $timestamps = false; | ||
|
|
||
| protected $fillable = [ | ||
| 'institutionCode', 'collectionCode', 'collectionName', 'collectionID', 'datasetID', 'datasetName', 'fullDescription', 'resourceJson', 'IndividualUrl', 'contactJson', | ||
| 'latitudeDecimal', 'longitudeDecimal', 'icon', 'collType', 'managementType', 'publicEdits', 'collectionGuid', 'rightsHolder', 'rights', 'usageTerm', 'dwcaUrl', | ||
| 'bibliographicCitation', 'accessRights', 'sortSeq' | ||
| ]; | ||
|
|
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| protected $hidden = ['securityKey', 'guidTarget', 'aggKeysStr', 'dwcTermJson', 'publishToGbif', 'publishToIdigbio', 'dynamicProperties']; | ||
|
|
||
| public function occurrence(){ | ||
| return $this->hasMany(Occurrence::class, 'collid', 'collid'); | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| <?php | ||
|
|
||
| namespace App\Http\Controllers; | ||
|
|
||
| use App\Collection; | ||
| use Illuminate\Http\Request; | ||
| use Illuminate\Support\Facades\DB; | ||
|
|
||
| class CollectionController extends Controller{ | ||
| /** | ||
| * Collection controller instance. | ||
| * | ||
| * @return void | ||
| */ | ||
| public function __construct(){ | ||
| } | ||
|
|
||
| /** | ||
| * @OA\Get( | ||
| * path="/api/v2/collection", | ||
| * operationId="/api/v2/collection", | ||
| * tags={""}, | ||
| * @OA\Parameter( | ||
| * name="managementType", | ||
| * in="query", | ||
| * description="live, snapshot, aggregate", | ||
| * required=false, | ||
| * @OA\Schema(type="string") | ||
| * ), | ||
| * @OA\Parameter( | ||
| * name="collectionType", | ||
| * in="query", | ||
| * description="preservedSpecimens, observations, researchObservation", | ||
| * required=false, | ||
| * @OA\Schema(type="string") | ||
| * ), | ||
| * @OA\Parameter( | ||
| * name="limit", | ||
| * in="query", | ||
| * description="Pagination parameter: maximum number of records per page", | ||
| * required=false, | ||
| * @OA\Schema(type="integer", default=1000) | ||
| * ), | ||
| * @OA\Parameter( | ||
| * name="offset", | ||
| * in="query", | ||
| * description="Pagination parameter: page number", | ||
| * required=false, | ||
| * @OA\Schema(type="integer", default=0) | ||
| * ), | ||
| * @OA\Response( | ||
| * response="200", | ||
| * description="Returns list of collections", | ||
| * @OA\JsonContent() | ||
| * ), | ||
| * @OA\Response( | ||
| * response="400", | ||
| * description="Error: Bad request. ", | ||
| * ), | ||
| * ) | ||
| */ | ||
| public function showAllCollections(Request $request){ | ||
| $this->validate($request, [ | ||
| 'limit' => ['integer', 'max:1000'], | ||
| 'offset' => 'integer' | ||
| ]); | ||
| $limit = $request->input('limit',1000); | ||
| $offset = $request->input('offset',0); | ||
|
|
||
| $conditions = []; | ||
| if($request->has('managementType')){ | ||
| if($request->managementType == 'live') $conditions[] = ['managementType','Live Data']; | ||
| elseif($request->managementType == 'snapshot') $conditions[] = ['managementType','Snapshot']; | ||
| elseif($request->managementType == 'aggregate') $conditions[] = ['managementType','Aggregate']; | ||
| } | ||
| if($request->has('collectionType')){ | ||
| if($request->collectionType == 'specimens') $conditions[] = ['collType','Preserved Specimens']; | ||
| elseif($request->collectionType == 'observations') $conditions[] = ['collType','Observations']; | ||
| elseif($request->collectionType == 'researchObservations') $conditions[] = ['collType','General Observations']; | ||
| } | ||
|
|
||
| $fullCnt = Collection::where($conditions)->count(); | ||
| $result = Collection::where($conditions)->skip($offset)->take($limit)->get(); | ||
|
|
||
| $eor = false; | ||
| $retObj = [ | ||
| "offset" => (int)$offset, | ||
| "limit" => (int)$limit, | ||
| "endOfRecords" => $eor, | ||
| "count" => $fullCnt, | ||
| "results" => $result | ||
| ]; | ||
| return response()->json($retObj); | ||
| } | ||
|
|
||
| /** | ||
| * @OA\Get( | ||
| * path="/api/v2/collection/{identifier}", | ||
| * operationId="/api/v2/collection/identifier", | ||
| * tags={""}, | ||
| * @OA\Parameter( | ||
| * name="identifier", | ||
| * in="path", | ||
| * description="Installation ID or GUID associated with target collection", | ||
| * required=true, | ||
| * @OA\Schema(type="string") | ||
| * ), | ||
| * @OA\Response( | ||
| * response="200", | ||
| * description="Returns collection data", | ||
| * @OA\JsonContent() | ||
| * ), | ||
| * @OA\Response( | ||
| * response="400", | ||
| * description="Error: Bad request. Collection identifier is required.", | ||
| * ), | ||
| * ) | ||
| */ | ||
| public function showOneCollection($id, Request $request){ | ||
| $collectionObj = null; | ||
| if(is_numeric($id)) $collectionObj = Collection::find($id); | ||
| else $collectionObj = Collection::where('collectionGuid',$id)->first(); | ||
| if(!$collectionObj->count()) $collectionObj = ["status"=>false,"error"=>"Unable to locate collection based on identifier"]; | ||
| return response()->json($collectionObj); | ||
| } | ||
|
|
||
| public function create(Request $request){ | ||
| //$collection = Collection::create($request->all()); | ||
| //return response()->json($collection, 201); | ||
| } | ||
|
|
||
| public function update($id, Request $request){ | ||
| //$collection = Collection::findOrFail($id); | ||
| //$collection->update($request->all()); | ||
| //return response()->json($collection, 200); | ||
| } | ||
|
|
||
| public function delete($id){ | ||
| //Collection::findOrFail($id)->delete(); | ||
| //return response('Collection Deleted Successfully', 200); | ||
| } | ||
| } |
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