Academic Analytics Publications Import

.env.example

@@ -11,6 +11,8 @@ TESTING_MENU=true
 GOOGLE_ANALYTICS_ID=
 INFLUUENT_API_KEY=
 WOS_TOKEN=
+ORCID_TOKEN=
+ACADEMIC_ANALYTICS_KEY=
 
 DB_CONNECTION=mysql
 DB_HOST=

app/Console/Commands/AddDoiToExistingPublications.php

@@ -0,0 +1,227 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Profile;
+use App\ProfileData;
+use App\Providers\AAPublicationsApiServiceProvider;
+use Illuminate\Support\Facades\Log;
+use Illuminate\Console\Command;
+use Illuminate\Database\Eloquent\Collection;
+use Illuminate\Support\Facades\App;
+use Illuminate\Support\Facades\Cache;
+
+class AddDoiToExistingPublications extends Command
+{
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'profiles:add-doi {starting_character : The first letter of the last name of the profiles to run command for.}';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Search the DOI to add it to the existing publications for the profiles with the first letter of their last name given.';
+
+    /**
+     * Execute the console command.
+     *
+     * @return int
+     */
+    public function handle()
+    {
+        $starting_character = (string)$this->argument('starting_character');
+
+        $profiles = Cache::remember(
+            "profiles-starting-with-{$starting_character}",
+            15 * 60,
+            fn() => $this->profilesMissingDoi($starting_character)
+        );
+
+        $profiles_bar = $this->output->createProgressBar(count($profiles));
+        $profiles_bar->setFormat('debug');
+        $profiles_bar->start();
+
+        $this->lineAndLog("********** {$profiles->count()} Profiles found with publications without DOI ************ \n");
+
+        foreach ($profiles as $profile) {
+
+            $profile_publications = $profile->data;
+
+            $publications_bar = $this->output->createProgressBar(count($profile->data));
+            $publications_bar->setFormat('debug');
+            $publications_bar->start();
+
+            $pubs_service_provider = App::make(AAPublicationsApiServiceProvider::class);
+            $aa_publications = $pubs_service_provider
+                                    ->getCachedPublications($profile->id, $profile->academic_analytics_id);
+
+            $publications_found_in_url = $publications_found_in_title = $publications_found_in_aa = $doi_not_found_counter = 0;
+
+            $this->lineAndLog("********** {$profile_publications->count()} Publications found without DOI for {$profile->full_name} ************\n");
+
+            foreach ($profile_publications as $publication) {
+
+                $this->lineAndLog(  "--------- {$publication->id} -----------\n");
+
+                $doi = $aa_title = null;
+
+                    // Search in the URL
+                    if (!empty($publication->url)) {
+                        $this->lineAndLog("Searching for DOI in URL...");
+                        $doi = $this->validateDoiRegex($publication->url);
+
+                        $this->verifyAndSaveDoi($publication, $doi, 'url', $publications_found_in_url, $publications_found_in_title, $publications_found_in_aa);
+
+                    }
+
+                    // Search in the title
+                    if (is_null($doi) && !empty($publication->title)) {
+                        $this->lineAndLog("Searching for DOI in the title...");
+                        $doi = $this->validateDoiRegex(strip_tags(html_entity_decode($publication->title)));
+
+                        $this->verifyAndSaveDoi($publication, $doi, 'title', $publications_found_in_url, $publications_found_in_title, $publications_found_in_aa);
+
+                    }
+
+                    // Match the AA Publication
+                    if (is_null($doi)) {
+                        $this->lineAndLog("Searching for DOI in Academic Analytics...");
+
+                        $aa_pub_found = ProfileData::searchPublicationByTitleAndYear(
+                                                $publication->title,
+                                                $publication->year,
+                                                $aa_publications ??
+                                                $pubs_service_provider->getCachedPublications($profile->id, $profile->academic_analytics_id));
+
+                        $doi = $aa_pub_found[0];
+                        $aa_title = $aa_pub_found[1];
+
+                        $this->verifyAndSaveDoi($publication, $doi, 'Academic Analytics', $publications_found_in_url, $publications_found_in_title, $publications_found_in_aa, $aa_title);
+                    }
+
+                    if (is_null($doi)) { $doi_not_found_counter++; }
+
+                    $publications_bar->advance();
+                }
+
+                $publications_bar->finish();
+
+                $this->lineAndLogResults($publications_found_in_url, $publications_found_in_title, $publications_found_in_aa, $doi_not_found_counter, $profile->full_name);
+
+                $profiles_bar->advance();
+
+            }
+
+        $profiles_bar->finish();
+
+        return Command::SUCCESS;
+    }
+
+    /**
+     * Verify given doi. If the doi is not null, updates the profile_data record and increment the counter of doi's found.
+     */
+    public function verifyAndSaveDoi($publication, $doi, $search_field, &$publications_found_in_url, &$publications_found_in_title, &$publications_found_in_aa, $aa_title = null)
+    {
+
+        if (is_null($doi)) {
+            $this->lineAndLog("DOI not found in {$search_field}.");
+        }
+        else {
+
+            $publication->updateData(['doi' => $doi]);
+            if (!is_null($aa_title)) {
+                $publication->insertData(['aa_title' => $aa_title]);
+                $this->log("Title {$publication->title} found as {$aa_title} in Academic Analytics Publications\n.");
+            }
+
+            $publication->save();
+            $this->lineAndLog("DOI {$doi} FOUND IN {$search_field} and updated.");
+
+            switch ($search_field)
+            {
+                case 'title':
+                    ++$publications_found_in_title;
+                    break;
+                case 'url':
+                    ++$publications_found_in_url;
+                    break;
+                case 'Academic Analytics':
+                    ++$publications_found_in_aa;
+                    break;
+            }
+
+        }
+
+    }
+
+    /**
+     * Validate DOI regex
+     *
+     * @param string $doi_expression
+     * @return string|null
+     */
+    public function validateDoiRegex($doi_expression)
+    {
+        $doi_regex = config('app.doi_regex');
+
+        $doi = null;
+
+        preg_match($doi_regex, $doi_expression, $matches);
+
+        if (!empty($matches[1])) {
+            $doi = rtrim(trim($matches[1], "\xC2\xA0"), '.');
+        }
+
+        return $doi;
+    }
+
+    /**
+     * Retrieves profiles with publications that have DOI missing
+     *
+     * @param string $starting_character
+     * @return Collection
+     */
+    public function profilesMissingDoi(string $starting_character)
+    {
+        return Profile::LastNameStartWithCharacter($starting_character)
+                        ->withWhereHas('data', function($q) {
+                                      $q->where('type', 'publications')
+                                        ->whereNull('data->doi');
+        })->get();
+    }
+
+    /**
+     * Output total numbers for each profile processed to the console and log file
+     */
+    public function lineAndLogResults($publications_found_in_url, $publications_found_in_title, $publications_found_in_aa, $doi_not_found_counter, $profile_full_name): void
+    {
+        $this->lineAndLog("TOTAL:");
+        if ($publications_found_in_url > 0 ) { $this->lineAndLog("{$publications_found_in_url} DOI found by url and added successfully."); }
+        if ($publications_found_in_title > 0 ) { $this->lineAndLog("{$publications_found_in_title} DOI found by title and added successfully."); }
+        if ($publications_found_in_aa > 0 ) { $this->lineAndLog("{$publications_found_in_aa} DOI found in Academic Analytics and added successfully."); }
+        $this->lineAndLog("{$doi_not_found_counter} PUBLICATIONS NOT FOUND.", 'error');
+        $this->lineAndLog("***************** End of Report for {$profile_full_name}  ********************");
+    }
+
+    /**
+     * Output a message to the console and log file
+     */
+    public function lineAndLog(string $message, string $type = 'info'): void
+    {
+        $this->line($message, $type);
+        Log::$type($message);
+    }
+
+    /**
+     * Output a message to the log file
+     */
+    public function Log(string $message, string $type = 'info'): void
+    {
+        Log::$type($message);
+    }
+}

app/Http/Controllers/ProfilesController.php

@@ -237,7 +237,6 @@ public function edit(Profile $profile, $section)
                 ->route('profiles.show', $profile->slug)
                 ->with('flash_message', 'Publications updated via ORCID.');
         }
-
         $data = $profile->data()->$section()->get();
 
         // if no data, include one item to use as a template

app/Http/Controllers/Testing/TestingController.php

@@ -74,7 +74,7 @@ public function showLoginAsList(Request $request)
      *
      * @param Request $request
      * @param int $id
-     * @return \Illuminate\Http\RedirectResponse
+     * @return \Illuminate\Routing\Redirector|\Illuminate\Http\RedirectResponse
      */
     public function loginAs(Request $request, $id)
     {

app/Http/Livewire/PublicationsImportModal.php

@@ -0,0 +1,86 @@
+<?php
+
+namespace App\Http\Livewire;
+
+use App\Profile;
+use App\Providers\AAPublicationsApiServiceProvider;
+use Livewire\Component;
+use Livewire\WithPagination;
+use Illuminate\Support\Facades\App;
+
+class PublicationsImportModal extends Component
+{
+    use WithPagination;
+
+    protected $paginationTheme = 'bootstrap';
+    protected $listeners = ['AAPublicationsModalShown' => 'showModal', 'addToEditor', 'removeFromEditor', 'addAllToEditor', 'removeAllFromEditor'];
+    public Profile $profile;
+    public bool $modalVisible = false;
+    public bool $allChecked = false;
+    public $importedPublications = [];
+    public $perPage = 10;
+    public $allPublicationsCount;
+
+    public function showModal()
+    {
+        $this->modalVisible = true;
+    }
+
+    public function addToEditor($publicationId)
+    {
+        array_push($this->importedPublications, $publicationId);
+        $this->emit( 'alert', "Added to the Editor!", 'success');
+    }
+
+    public function removeFromEditor($publicationId)
+    {
+        if (($key = array_search($publicationId, $this->importedPublications)) !== false) {
+            unset($this->importedPublications[$key]);
+        }
+        $this->emit('alert', "Removed from the Editor!", 'success');
+    }
+
+    public function addAllToEditor()
+    {
+        $pubs_to_import = App::call([$this, 'getNewPublications'])->whereIn('imported', false);
+        $this->importedPublications = $pubs_to_import->pluck('id')->all();
+        $this->allChecked = true;
+        $this->emit('JSAddAllToEditor', $pubs_to_import);
+    }
+
+    public function removeAllFromEditor()
+    {
+        $this->reset('importedPublications');
+        $this->reset('allChecked');
+    }
+    /**
+     *
+     * @return \Illuminate\Database\Eloquent\Collection
+     */
+    public function getNewPublications(AAPublicationsApiServiceProvider $pubServiceProvider)
+    {
+        $aaPublications = $pubServiceProvider->getCachedPublications($this->profile->id, $this->profile->academic_analytics_id);
+
+        return $aaPublications
+            ->whereNotIn('doi', $this->profile->publications->pluck('data.doi')->filter()->values());
+    }
+
+    public function getPublicationsProperty()
+    {
+        $aaPublications = App::call([$this, 'getNewPublications']);
+
+        $this->allPublicationsCount = count($aaPublications);
+
+        $aaPublications
+            ->each(function($elem, $key) {
+                $elem->imported = (in_array($elem->id, $this->importedPublications));
+            });
+
+        return $aaPublications->sortByDesc('sort_order')->paginate($this->perPage);
+    }
+
+    public function render()
+    {
+        return view('livewire.publications-import-modal');
+    }
+}

app/Http/Livewire/ShowModal.php

@@ -0,0 +1,18 @@
+<?php
+
+namespace App\Http\Livewire;
+
+use App\Profile;
+use Livewire\Component;
+
+class ShowModal extends Component
+{
+    public bool $modalVisible = false;
+    public Profile $profile;
+    protected $listeners = ['showModal'];
+
+    public function showModal()
+    {
+        $this->emit('loadPublications');
+    }
+}