pkp/plagiarism#52 iThenticate API update and plugin update #57

touhidurabir · 2024-02-06T10:39:23Z

for #52 . The PR has following updates :

update of iThenticate API to latest version
EUAL confirmation process
New credentials added
Removal of previous API library and introduced new custom service class for API communication
Removal of composer dependency
Presenting the possible proper EULA as submission checklist
stamping of EULA to submission and submitter
verification of user provided ithenticate service access(API URL/KEY) before storing.
context wise EULA caching to avoid continuous data polling form API service .
allow iThenticate retry, polling, similarity score presentation for each file, refreshing similarity scores and launch similarity viewer .
Config to manage auto upload which allow iThenticate auto upload at submission time or later upload manually
Compatible with OPS

Following Issues get resolved by this PR

PlagiarismPlugin.inc.php

asmecher

Some early comments -- I'll have a look at the schema extension issue next week.

IThenticate.inc.php

PlagiarismPlugin.inc.php

asmecher

A few more changes -- I'll review these with you shortly!

IThenticate.inc.php

PlagiarismPlugin.inc.php

asmecher · 2024-02-22T16:35:51Z

PlagiarismSettingsForm.inc.php

-		);
+	public function initData() {
+		$this->_data = [
+            'ithenticateApiUrl' => $this->_plugin->getSetting($this->_contextId, 'ithenticateApiUrl'),


(spaces in with tabs)

asmecher · 2024-02-22T16:38:25Z

controllers/PlagiarismWebhookHandler.inc.php

+	}
+
+    public function handle() {
+        error_log('handle webhook request');


We probably shouldn't leave this in the distribution version of the plugin, as it's debugging/dev code. But if we did, it should be prefixed with something to indicate more about what this is, e.g. "PKP Plagiarism plugin".

we will eventually implement some functionality through webhook but probably not for stable-3.3.0 .

we initially planed not to use the webhook for 3.3.0-x but we have to as without webhook, we can not initiate the similarity report generation process .

IThenticate.inc.php

…ubmission

…d webhook registration on settings update

asmecher

A bunch more minor comments; I've mentioned a few of these before (mixed spacing/tabs and variants of EULA), so please double-check to make sure it's all cleaned up for the next round. Thanks!

asmecher · 2024-03-26T18:22:48Z

IThenticate.inc.php

+class IThenticate
+{
+    /** 
+     * The base api url in the format of schems://host


asmecher · 2024-03-26T18:23:26Z

IThenticate.inc.php

+    protected $integrationVersion;
+
+    /**
+     * The EULA(end user license agreement) that user need to confrim before making request


asmecher · 2024-03-26T18:24:36Z

IThenticate.inc.php

+    }
+
+    /**
+     * Validate the service access by retrieving the the enabled feature


asmecher · 2024-03-26T18:36:14Z

IThenticate.inc.php

+                    'Content-Type' => 'application/json'
+                ]),
+                'json' => [
+                    'owner' => $author->getId(),


Should we be using our internal IDs for owner and submitter? We use email addresses as unique account identifiers in OJS; maybe those would be more appropriate for users; we can't always count on having those for authors, though.

If this is something we can use for our own arbitrary purposes, it might be worth adding some kind of namespacing to avoid confusion -- e.g. author/54 and user/54 rather than just the numeric 54. It'll be easy to forget where we're using Users and where we're using Authors and the IDs aren't comparable. If iThenticate ever does a comparison between them for e.g. permission purposes, it'll mistakenly conclude that they're the same.

email addresses as unique account identifiers in OJS; maybe those would be more appropriate for users; we can't always count on having those for authors, though

That was my initial approach also but because an author may not have an email address and author/owner details is required, we could not use email

If this is something we can use for our own arbitrary purposes

Not actually . According to TAC developer doc, submission author/owner unique system identifier is required . The submitter information is optional but in that case owner/author must accept/confirm EULA . As in our case, the author/owner and submitter can be different and it's the submitter who confirms the EULA, we also need to pass it .

it might be worth adding some kind of namespacing to avoid confusion -- e.g. author/54 and user/54

I think that a good idea and will do it .

asmecher · 2024-03-26T18:52:10Z

IThenticate.inc.php

+
+        $response = Application::get()->getHttpClient()->request(
+            'PUT',
+            $this->getApiPath("submissions/{$submissionTacId}/original"),


Where we're building parameters into URL strings, we should probably be using rawurlencode (here and elsewhere).

Not a bad idea but then rather than using the rawurlencode directly we should let the Guzzel handle it by returning an instance of \GuzzleHttp\Psr7\Uri .

asmecher · 2024-03-26T19:27:56Z

PlagiarismPlugin.inc.php

+	public function retrieveApplicableEulaDetails($cache, $cacheId) {
+		$context = Application::get()->getRequest()->getContext();
+		$ithenticate = $this->initIthenticate(...$this->getServiceAccess($context)); /** @var \IThenticate $ithenticate */
+		$eualDetails = [];


Should be eulaDetails (here and below)

asmecher · 2024-03-26T19:29:10Z

PlagiarismPlugin.inc.php

+	 * 
+	 * @return void
+	 */
+	protected function stampEualVersionToSubmittingUser($user, $version) {


Should be Eula, not Eual.

asmecher · 2024-03-26T19:30:19Z

PlagiarismSettingsForm.inc.php

+	 * @copydoc Form::validate()
+	 */
+	public function validate($callHooks = true) {
+		$this->addCheck(


Checks should be added in the form constructor, not the call to validate.

As we need to init the ithenticate service to test the given creds, using the getData in constructor does not work and pass null . well fixed it using $request->getUserVar and moved it to constructor .

asmecher · 2024-03-26T19:33:41Z

locale/en_US/locale.po


 msgid "plugins.generic.plagiarism.manager.settings.areForced"
 msgstr "iThenticate settings were found in config.inc.php and the settings here will not be used."

 msgid "plugins.generic.plagiarism.errorMessage"
 msgstr "Upload of submission {$submissionId} to iThenticate failed with error: {$errorMessage}"
+
+msgid "plugins.generic.plagiarism.submission.checklist.eula"
+msgstr "Plagiarism EULA <a target=\"_blank\" href=\"{$localizedEulaUrl}\">link</a>"


Should be iThenticate EULA, not Plagiarism EULA, I think

asmecher · 2024-03-26T19:34:11Z

locale/en_US/locale.po

+
+msgid "plugins.generic.plagiarism.manager.settings.serviceAccessInvalid"
+msgstr ""
+"The specified API URL/KEY is invalid and can not establish connection to IThenticate API service."


Should be iThenticate, not IThenticate

touhidurabir · 2024-04-04T22:45:43Z

@asmecher ready for next review round . forced to have the vital implementation in webhook handler as no other way . Also as we get submission id from ithenticate for each submission file , moved some the association to submission file setting .

…atus

… along with user notification system on webhook handle

…as part of plugins settings

…wer launch functionality

… form

…viewer launch

asmecher · 2024-05-31T18:19:48Z

Another issue to resolve: Try editing config.inc.php and setting Installed to Off. This will cause the installation to give an error:

PHP Fatal error:  Uncaught Error: Undefined constant "SCHEMA_SUBMISSION" in /home/asmecher/git/ojs-stable-3_3_0/plugins/generic/plagiarism/PlagiarismPlugin.inc.php:95

...rather than sending the user to the installation form.

touhidurabir · 2024-06-04T06:36:15Z

Another issue to resolve: Try editing config.inc.php and setting Installed to Off. This will cause the installation to give an error:
PHP Fatal error:  Uncaught Error: Undefined constant "SCHEMA_SUBMISSION" in /home/asmecher/git/ojs-stable-3_3_0/plugins/generic/plagiarism/PlagiarismPlugin.inc.php:95
...rather than sending the user to the installation form.

@asmecher please the commit touhidurabir@6042142 . This resolve the above issue along with #49 but updated the behaviour a bit as follow

Admin must set the ithenticate to On in config.inc.php file to enable the service/plugin globally .
Admin/Journal Manager enable the plugin from plugin gallery for the given context and once it's done, the enable/disable checkbox will grey out . This also resolve issue Enabling the plugin impossible if settings are present in config file when plugin is first installed #49 .

However I still think there is room for more improvement . With our current implementation, it is impossible to disable the plugin once enabled without globally disable it by setting ithenticate to Off in config.inc.php file . This is ok for a single context based installation but does not seems flexible for a multi context based installation .

For example , in a multi context based installation, may be the JM/Admin want to disable it for one specific context for some reason but no way to do it . My proposal is to remove the plugin based implementation of getCanEnable and getCanDisable so that JM/Admin can anytime disable/enable the plugin for a given context . And if needed to disable it globally , they still has the option to do it from config.inc.php file by setting the ithenticate to Off . what you say ?

…wer launch url create process

…eved from API

…uired and validation passes

pkp#52 iThenticate API update and plugin update

7f39d43

touhidurabir mentioned this pull request Feb 6, 2024

iThenticate v2 (CrossRef similarity check) support #52

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touhidurabir commented Feb 6, 2024

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asmecher requested changes Feb 10, 2024

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touhidurabir added 3 commits February 12, 2024 12:38

pkp#52 update based on initial PR review

b51046e

pkp#52 added class doc block for Plagiarism Settings Form class

ae26048

pkp#52 fixed issue override issue

7e17e22

asmecher requested changes Feb 22, 2024

View reviewed changes

touhidurabir added 5 commits February 27, 2024 13:02

pkp#52 added eula handling and stamping to submission and submitter

26cb1d2

pkp#52 code formatting update

62ab975

pkp#52 added the handling of missing service access case

5432abe

pkp#52 added exception handling for multiple file upload for single s…

5e5622c

…ubmission

pkp#52 added ability to handle multiple file for single submission an…

eac1931

…d webhook registration on settings update

asmecher requested changes Mar 26, 2024

View reviewed changes

touhidurabir added 2 commits April 5, 2024 04:27

pkp#52 added similarity check initiation process via webhook

9740f11

pkp#52 code formatting

c22c0bd

touhidurabir added 12 commits April 6, 2024 02:53

pkp#52 code rearranged

7ca6801

pkp#52 added check to hanlde error when no ithenticate service set

f37056d

pkp#52 disable test mode by default

ff6f8e9

pkp#52 functionality added to handle EULA confirmation requirement st…

ecf0456

…atus

pkp#52 added *_permission_set for owner and submitter

d52111a

pkp#52 added SIMILARITY_COMPLETE and SIMILARITY_UPDATED event handler…

1c6adcc

… along with user notification system on webhook handle

pkp#52 added specific few similarty report generation config setting …

15ac8f8

…as part of plugins settings

pkp#52 improved workflow for eula handling

483c0b9

pkp#52 added retrying, polling, similarity score presentation and vie…

a00d5bc

…wer launch functionality

pkp#52 added missing doc blocks

4c16098

pkp#52 added confirmation checkbox on submission EULA re-confirmation…

7a7cc35

… form

pkp#52 added viewer update settings and proper handling of locale on …

43656b9

…viewer launch

pkp#52 updated readme

a08cb79

touhidurabir added 2 commits June 3, 2024 17:41

pkp#52 added exclude_small_matches validation

feac094

pkp#52 updated enable/disable behaviour to handle pkp#49

6042142

touhidurabir and others added 24 commits June 5, 2024 16:22

pkp#52 added some precautionary checks

e7375e8

pkp#52 added better enable/disable control

a0ad8d9

pkp#52 added all serach repos and removed viewer_permissions from vie…

63e783a

…wer launch url create process

pkp#52 added check before manula similarity report scheduling

9a401d3

pkp#52 translation update

2972f3d

pkp#52 added comment for issue no 49 and install mode conflict

207361b

pkp#52 readme updated

38cb063

pkp#52 existing webook delete added before registering a new one

450e03b

pkp#52 fixed webhook registration issue in settings form

a6fa2b8

pkp#52 added CLI tool update webhook on config creds change

5c493ac

Update to version 1.0.6.2

0e93569

Update to version 1.0.7.0

fda3e40

pkp#52 fixed issue with settings update

c642ad1

Update README.md

0207f2e

pkp#52 added revision files history feature

0b3fcd6

pkp#52 removed weird EULA determining from first submission and retri…

8d210b9

…eved from API

pkp#52 fixed bug preserving plagiarism history

62d3ccd

pkp#52 PHP 7.4 compatibility

e17e299

pkp#52 added error log if ithenticate creating submission failed

27b723d

pkp#52 moved default eula lang details under the checking of eula req…

c5c817e

…uired and validation passes

pkp#52 Better handling of EULA non required case

c5dae25

pkp#52 Better handling submission file name for multi lang

d859cfe

pkp#52 score value escape

a675e7b

Merge branch 'stable-3_3_0' into i52_stable_3_3_0

ce4875f

touhidurabir merged commit d6b08c5 into pkp:stable-3_3_0 Sep 30, 2024

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pkp/plagiarism#52 iThenticate API update and plugin update #57

pkp/plagiarism#52 iThenticate API update and plugin update #57

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pkp/plagiarism#52 iThenticate API update and plugin update #57

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