Renaming.

Proximify · Oct 28, 2020 · e5de480 · e5de480
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Showing 18 changed files with 62 additions and 68 deletions.
diff --git a/README.md b/README.md
@@ -26,9 +26,9 @@ or create a project:
 The publication-fetcher imports from bibtex, Google Scholar (bibtex) and endnode files. Sample bibtex and endnodes files are available docs folder.
 
 <pre>
-    use Proximify\PublicationImporter\PublicationImporter;
+    use Proximify\PublicationFetcher\PublicationFetcher;
 
-    $importer = new PublicationImporter();
+    $importer = new PublicationFetcher();
     $type = 'bibtex';
     $source = 'PATH_TO_FILE;
     $res = $importer->importPublications($type, $source);
@@ -83,6 +83,13 @@ You can also use the web interface for testing under the dev folder:
 **Note:** Please set the correct path for the autoloader.php under the dev/www/api/index.php and dev/tests/Test.php. Otherwise, the test script will fail.
 
 
+## Known Issues
+Publication fetcher component was created by using UNIWeb's publication importing system which includes features like reference deduplication. Deduplication process involves ignoring references already in user's CV. Features like this requires direct access to the database which is not supported by this component yet.
+
+## Future Work
+A possible future work would be creating another component (i.e. publication importer) which both employs publication fetcher and deduplicater components to prevent importing references that currently exists in database.
+
+
 ## Contributing
 This project welcomes contributions and suggestions. Most contributions require you to agree to a Contributor License Agreement (CLA) declaring that you have the right to and actually do, grant us the rights to use your contribution. For details, visit our Contributor License Agreement.
 

diff --git a/composer.json b/composer.json
@@ -4,8 +4,7 @@
     "minimum-stability": "dev",
     "require": {
         "php": ">=7.1.0",
-        "proximify/foreign-packages": "^1.0",
-        "symfony/yaml": "5.x-dev"
+        "proximify/foreign-packages": "^1.0"
     },
     "authors": [
         {
@@ -15,11 +14,11 @@
     ],
     "autoload": {
         "psr-4": {
-            "Proximify\\PublicationImporter\\": "src/"
+            "Proximify\\PublicationFetcher\\": "src/"
         }
     },
     "scripts": {
-        "post-install-cmd": "Proximify\\PublicationImporter\\PublicationImporterCLI::auto",        
-        "import-pubs": "Proximify\\PublicationImporter\\PublicationImporterCLI::auto"
+        "post-install-cmd": "Proximify\\PublicationFetcher\\PublicationFetcherCLI::auto",        
+        "import-pubs": "Proximify\\PublicationFetcher\\PublicationFetcherCLI::auto"
     }
 }
diff --git a/composer.lock b/composer.lock
diff --git a/dev/tests/Test.php b/dev/tests/Test.php
@@ -2,9 +2,9 @@
 
 require_once('../../vendor/autoload.php');
 
-use Proximify\PublicationImporter\PublicationImporter;
+use Proximify\PublicationFetcher\PublicationFetcher;
 
-$importer = new PublicationImporter();
+$importer = new PublicationFetcher();
 
 print('Running tests...');
 

diff --git a/dev/www/api/index.php b/dev/www/api/index.php
@@ -10,7 +10,7 @@
  */
 require_once __DIR__ . '/../../../vendor/autoload.php';
 
-use Proximify\PublicationImporter;
+use Proximify\PublicationFetcher;
 
 $action = $_POST['action'];
 
@@ -30,17 +30,17 @@
 function importFromURL() {
     $type = $_POST['type'];
     $source = $_POST['source'];
-    $importer = new PublicationImporter\PublicationImporter();
-    $res =  $importer->importFromFile($type, $source);
+    $importer = new PublicationFetcher\PublicationFetcher();
+    $res =  $importer->importPublications($type, $source);
 
     return $res;
 }
 
 function importFromFile() {
     $type = $_POST['type'];
     $source = $_FILES['source']['tmp_name'];
-    $importer = new PublicationImporter\PublicationImporter();
-    $res =  $importer->importFromFile($type, $source);
+    $importer = new PublicationFetcher\PublicationFetcher();
+    $res =  $importer->importPublications($type, $source);
 
     return $res;
 }
diff --git a/dev/www/index.html b/dev/www/index.html
@@ -1,6 +1,6 @@
 <html>
     <head>
-        <title>Publications Importer - Test</title>
+        <title>Publication Fetcher - Test</title>
         <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.5.3/css/bootstrap.min.css">
         <style>
             #field-file-uploader, #field-text-area, #btn-pub-import {
@@ -41,7 +41,7 @@
     </head>
     <body>
 
-        <h3 class="text-center mb-3 mt-3">Publications Importer</h3>
+        <h3 class="text-center mb-3 mt-3">Publication Fetcher</h3>
 
         <div class="container">
             <h4>Select data source</h4>

diff --git a/settings/PublicationImporter.json → settings/PublicationFetcher.json b/settings/PublicationImporter.json → settings/PublicationFetcher.json
diff --git a/settings/cli-actions/import-pubs.yaml b/settings/cli-actions/import-pubs.yaml
@@ -1,4 +1,4 @@
-class: Proximify\PublicationImporter\PublicationImporterCLI
+class: Proximify\PublicationFetcher\PublicationFetcherCLI
 method: outputPublicationImport
 isStatic: false
 askConfirm: false

diff --git a/settings/cli-actions/post-install-cmd.yaml b/settings/cli-actions/post-install-cmd.yaml
@@ -1,2 +1,2 @@
-class: Proximify\PublicationImporter\DependencyInstaller
+class: Proximify\PublicationFetcher\PublicationFetcherCLI
 method: checkDependencies
diff --git a/src/DependencyInstaller.php b/src/DependencyInstaller.php
@@ -1,6 +1,6 @@
 <?php
 
-namespace Proximify\PublicationImporter;
+namespace Proximify\PublicationFetcher;
 
 /**
  * File for class DependencyInstaller.

diff --git a/src/DomWalker.php b/src/DomWalker.php
@@ -6,7 +6,7 @@
 // ==========================================================================
 // require_once('debug_utils.php');
 
-namespace Proximify\PublicationImporter;
+namespace Proximify\PublicationFetcher;
 
 use \DOMDocument;
 use \DOMXpath;

diff --git a/src/EndNoteImport.php b/src/EndNoteImport.php
@@ -5,9 +5,9 @@
 // UniWeb by Proximify is proprietary software.
 // ==========================================================================
 
-namespace Proximify\PublicationImporter;
+namespace Proximify\PublicationFetcher;
 
-use Proximify\PublicationImporter\PublicationSource;
+use Proximify\PublicationFetcher\PublicationSource;
 use \Exception;
 
 /**

diff --git a/src/ModsImporter.php b/src/ModsImporter.php
@@ -4,10 +4,11 @@
 // All Rights Reserved
 // UniWeb by Proximify is proprietary software.
 // ==========================================================================
-namespace Proximify\PublicationImporter;
+namespace Proximify\PublicationFetcher;
 
-use Proximify\PublicationImporter\DOMWalker;
-use Proximify\PublicationImporter\PublicationSource;
+use Proximify\PublicationFetcher\DOMWalker;
+use Proximify\PublicationFetcher\PublicationSource;
+use \Exception;
 
 /**
  * See http://www.loc.gov/standards/mods/mods-outline-3-7.htm

diff --git a/src/PublicationImporter.php → src/PublicationFetcher.php b/src/PublicationImporter.php → src/PublicationFetcher.php
@@ -1,11 +1,10 @@
 <?php
 
-namespace Proximify\PublicationImporter;
+namespace Proximify\PublicationFetcher;
 
-use Proximify\PublicationImporter\EndNoteImport;
-use Proximify\PublicationImporter\PubMedImport;
-use Proximify\PublicationImporter\ModsImporter;
-use Symfony\Component\Yaml\Yaml;
+use Proximify\PublicationFetcher\EndNoteImport;
+use Proximify\PublicationFetcher\PubMedImport;
+use Proximify\PublicationFetcher\ModsImporter;
 use \Exception;
 
 /** 
@@ -16,12 +15,12 @@
  * @version   1.0 UNIWeb Module
  */
 
-class PublicationImporter { 
+class PublicationFetcher { 
     const DEFAULT_LIBRARY = 'bibutils';
     const AVAILABLE_LIBRARIES = ['BibUtils'];
     const HASH_KEYS_PATH = __DIR__ . '/../settings/publicationHashKeys.yaml'; // was .ini before
 	const FIELD_MAP_PATH = __DIR__ . '/../settings/publicationFieldMap.yaml'; // was .ini before
-    const SETTINGS_FILE = '../settings/PublicationImporter.json';
+    const SETTINGS_FILE = '../settings/PublicationFetcher.json';
     const TITLE_KEY = 'TITLE_KEY';
 	const PUB_DATE_KEY = 'PUBDATE_KEY';
 	const UNDEFINED_SECTION = 'undefined';
@@ -180,6 +179,9 @@ function importPublications($type, $source, $checkAuthor = false, $deleteAfterIm
 			$doiList = [];
         }
 
+        if ($type == 'gscholar')
+            $type = 'bibtex';
+
         // $this->loadPublicationAndIntelectualPropertyProfileData();
 
 
@@ -196,7 +198,7 @@ function importPublications($type, $source, $checkAuthor = false, $deleteAfterIm
 			'oldPubs' => []
         ];
 
-        $this->sectionFieldMap = $this->loadSectionFieldMap($type);
+        // $this->sectionFieldMap = $this->loadSectionFieldMap($type);
 
 		switch ($type) {
 			case 'pubmed':
@@ -210,25 +212,10 @@ function importPublications($type, $source, $checkAuthor = false, $deleteAfterIm
 				$pubsInfo = $this->importFromFile($source, $type, $pubsInfo, $checkAuthor);
 				$currentProgress = 30;
 				break;
-            case 'gscholar':
 			case 'bibtex':
-				if ($doiList) {
+				if ($doiList) 
 					$source = $this->fetchDOI($doiList);
-				} else {
-					try {
-                        $source = $source;
-
-						// $source = $this->getUploadedFilePath();
-					} catch (Exception $e) {
-                            // $rawInput = $this->getRequestParam('rawInput');
-
-                            // if (!$rawInput)
-                            // 	throw new Exception('Invalid empty file');
-
-                            // $source = $this->createSourceFile($rawInput);
-					}
-				}
-
+
 				$pubsInfo = $this->importFromFile($source, $type, $pubsInfo, $checkAuthor);
 				$currentProgress = 30;
 
@@ -238,7 +225,7 @@ function importPublications($type, $source, $checkAuthor = false, $deleteAfterIm
         }
 
 
-        $this->getOtherPubInfo($pubsInfo, $currentProgress, $duplicateCriteria);
+        // $this->getOtherPubInfo($pubsInfo, $currentProgress, $duplicateCriteria);
 
         return $pubsInfo;
 
@@ -255,7 +242,7 @@ function importFromFile($path, $type, $pubsInfo, $checkAuthor)
 
 		// Try with the old method if we run into a problem
 		if (is_null($imported)) {
-			$imp = new EndNoteImport($this->modelParams(), $this->progress, $pubsInfo);
+			$imp = new EndNoteImport($this->progress, $pubsInfo);
 			$imported = $imp->importFromFile($path, $type, $encoding, $checkAuthor);
 		}
 
@@ -801,13 +788,13 @@ static function getKeyValue($node, $key)
 
     function getHashKeys ()
     {
-        return Yaml::parseFile(self::HASH_KEYS_PATH);
+        // return Yaml::parseFile(self::HASH_KEYS_PATH);
     }
 
 
      function loadSectionFieldMap($type) 
      {
-        $fieldMap = Yaml::parseFile(self::FIELD_MAP_PATH);
+        // $fieldMap = Yaml::parseFile(self::FIELD_MAP_PATH);
         $keys = $this->getHashKeys();
 
         	// Get the UNIWeb field names

diff --git a/src/PublicationImporterCLI.php → src/PublicationFetcherCLI.php b/src/PublicationImporterCLI.php → src/PublicationFetcherCLI.php
@@ -1,15 +1,15 @@
 <?php
 
-namespace Proximify\PublicationImporter;
+namespace Proximify\PublicationFetcher;
 
-use Proximify\PublicationImporter\PublicationImporter;
+use Proximify\PublicationFetcher\PublicationFetcher;
 
 /**
  * 
  * Extend the base class in order to add an additional 
  * location for the settings folder.
  */
-class PublicationImporterCLI extends \Proximify\ForeignPackages
+class PublicationFetcherCLI extends \Proximify\ForeignPackages
 {
     const TEST_BIBTEX = __DIR__ . '/../dev/tests/assets/sample.bib';
     const TEST_GSCHOLAR = __DIR__ . '/../dev/tests/assets/sample.bib';
@@ -54,7 +54,7 @@ function outputPublicationImport($params)
             $source = $params['source'];
         }
 
-        $importer = new PublicationImporter();
+        $importer = new PublicationFetcher();
         print_r($importer->importPublications($type, $source));
     }
 

diff --git a/src/PublicationSource.php b/src/PublicationSource.php
@@ -5,7 +5,7 @@
 // UniWeb by Proximify is proprietary software.
 // ==========================================================================
 
-namespace Proximify\PublicationImporter;
+namespace Proximify\PublicationFetcher;
 
 use \Exception;
 

diff --git a/src/PubmedImport.php b/src/PubmedImport.php
@@ -4,11 +4,11 @@
 // All Rights Reserved
 // UniWeb by Proximify is proprietary software.
 // ==========================================================================
-namespace Proximify\PublicationImporter;
+namespace Proximify\PublicationFetcher;
 
-use Proximify\PublicationImporter\PublicationSource;
-use Proximify\PublicationImporter\RemoteConnection;
-use Proximify\PublicationImporter\DomWalker;
+use Proximify\PublicationFetcher\PublicationSource;
+use Proximify\PublicationFetcher\RemoteConnection;
+use Proximify\PublicationFetcher\DomWalker;
 use \Exception;
 use \DOMElement;
 

diff --git a/src/RemoteConnection.php b/src/RemoteConnection.php
@@ -5,7 +5,9 @@
 // UniWeb by Proximify is proprietary software.
 // ==========================================================================
 
-namespace Proximify\PublicationImporter;
+namespace Proximify\PublicationFetcher;
+
+use \Exception;
 
 /**
  * Connects to a remote server and fetches assets from it.