prechelt / ojsrqc-outdated

RQC plugin for Open Journal Systems (OJS 3)

Review Quality Collector (RQC) plugin for OJS

created 2017-08-30, Lutz Prechelt

Version 2019-11-05 Status: unfinished, not yet usable

What it is

Review Quality Collector (RQC) is an initiative for improving the quality of scientific peer review. Its core is a mechanism that supplies a reviewer with a receipt for their work for each journal year. The receipt is based on grading each review according to a journal-specific review quality definition.

This plugin is an OJS adapter for the RQC API, by which OJS reports the reviewing data of individual article submissions to RQC so that RQC can arrange the grading and add the reviews to the respective reviewers' receipts.

Find the RQC API description at https://reviewqualitycollector.org/t/api

How it works

• extends the journal master data forms by two additional fields: rqcJournalId and rqcJournalKey.
• When both are filled, they are checked against RQC whether they are a valid pair.
• If they are accepted, they are stored as additional JournalSettings.
• If these settings exist, the plugin will add a button "RQC-grade the reviews" by which editors can submit the reviewing data for a given submission to RQC in order to trigger the grading. This step is optional for the editors. Depending on how RQC is configured for that journal, the given editor may then be redirected to RQC to perform (or not) a grading rightaway.
• The plugin will also intercept the acceptance-decision-making event and send the decision and reviewing data for that submission to RQC then.
• Should the RQC service be unavailable when data is submitted automatically at decision time, the request will be stored and will be repeated once a day for several days until it goes through.

How to use it: Installation

Target audience: OJS system administrators.

• The RQC plugin requires PHP 7. It will not work with PHP 5. (PHP 5 no longer receives security updates)
• In config.inc.php, set scheduled_tasks = On.
• Make sure there is an entry in your OJS server's crontab (see "Scheduled Tasks" in the OJS docs/README) and that it includes RQC's scheduldTasks.xml besides the default one from registry. This could for instance look like this

  0 * * * *	(cd /path/to/ojs; php tools/runScheduledTasks.php registry/scheduledTasks.xml plugins/generic/reviewqualitycollector/scheduledTasks.xml)
  

• Get the RQC plugin from within OJS. This only applies if RQC has already been updated to the version of OJS that you use. When a new OJS release appears, it may take some time to update the RQC plugin and get it accepted by the OJS team. Only then does it become available in the plugins list shown at Settings->Website->Plugins->Plugin Gallery. If Review Quality Collector does not show up there, your OJS version is too new or too old. The earliest version of OJS for which RQC is available is OJS 3.2.?-?.
• Once installed, go to Settings->Website->Plugins and activate the plugin "Review Quality Collector (RQC)" in category Generic Plugins.

How to use it: Journal setup

Target audience: OJS journal managers, RQC RQGuardians.

• Read about RQC at https://reviewqualitycollector.org.
• In RQC, register an account for yourself.
• Find your publisher in the RQC publisher directory (not yet implemented!!!) and ask your publisherpersons to create an RQC section for your journal. (If needed, ask your publisher to register at RQC first.)
• Discuss review quality criteria with your co-editors. Formulate an RQC review quality definition file.
• As RQGuardian in RQC, set up your journal: review quality definition, grading parameters (which people must/should/can/cannot grade a review).
• In OJS, open the RQC plugin settings and enter your public RQC journal ID and your secret RQC journal key. To do this, you need to be journal manager for your journal in OJS.

How to use it: Daily use

• The best time to grade reviews in RQC is when you prepare the editorial decision in OJS.
• Therefore, each editor who is supposed to provide a grading should make it a habit to use the "RQC-grade reviews" button before entering their decision in OJS. This will redirect them into RQC for the grading and then back to OJS for entering the decision.
• If nobody does that (e.g. because editors are not supposed to perform review grading at your journal), OJS will submit the reviewing data to RQC when the editorial decision is entered into OJS. RQC will then remind graders via email.

---

Development notes: Development setup

• OJS installation: https://pkp.sfu.ca/wiki/index.php?title=Github_Documentation_for_PKP_Contributors
• config.inc.php: show_stacktrace = On display_errors = Off activate_developer_functions = On rqc_server = http://192.168.3.1:8000 (display_errors breaks Ajax functions when it kicks in)
• create journal rqctest: create users editor1, author1, reviewer1, reviewer2; create a submission, 2 review assignments, 2 reviews; Settings->Website->Plugins turn on RQC plugin
• tests/backup.sh backup so you can quickly restore the review case during testing
• http://localhost:8000/index.php/rqctest/rqcdevhelper/
• Perhaps apply patches to OJS codebase from ojspatches.

For running OJS with RQC in development mode:

• The OJS VM has a host-only network on 192.168.3.1/24.
  The VM is 192.168.3.6, the host is 192.168.3.1.
• For OJS to talk to RQC, start the Django dev server by python manage.py runserver 0.0.0.0:8000

(Outdated:) Branches:

• modifydecisionoptionshook (2 commits off rqcdev2: 6a275c7808 1a91b158af): PR merged 2019-09 pkp/ojs#2439 as 3c7a100610 in pkp-lib
• rqcdev2 has 4900 additional commits of very old history before the RQC commits
• rqcdev312l
• pkp-lib/robusthooks: make HookRegistry ignore non-callable callbacks: PR rejected pkp/pkp-lib#5050

Development notes: TO DO

• add the journal ID/key validation via an RQC call
• add all hooks and actual activity
• Switch to LetsEncrypt and put its root certificate into the plugin, because the Telekom certificate ends 2019-07-09 (and RQC's ends 2019-03-27!)
• elaborate on "ask your publisher" in locale.xml
• write automated tests

Development notes: RQC plugin

• Setting activate_developer_functions = On in config.inc.php enables example_request functionality in RQCPlugin::manage and ::getActions. Not yet implemented.
• See my PKP forum thread
• In particular regarding exploring the data model (qu. 5)
• settings dialog does not close after OK.
• OJS review rounds must create successive submission ids for RQC.
• SpyHandler (now DevHelperHandler) gets 8 notices a la "Undefined index: first_name in /home/vagrant/ojs/lib/pkp/classes/submission/PKPAuthorDAO.inc.php on line 127"
• Cronjob via PKPAcronPlugin?
• Delayed-call storage via Plugin::updateSchema and my own DAO?

Development notes: RQC

• resubmit elsewhere counts as reject (or is its own decision?)
• do not submit confidential comments as part of the review.
• allow a file upload instead of review text???
• submit flag that RQC should emphasize the MHS page link, because grading-relevant material is only on the MHS page.

Development notes: General OJS knowledge

• Many hooks are provided in pkp-lib like this HookRegistry::call(strtolower_codesafe(get_class($this) . '::validate') (this particular one is from classes/form/Form.inc.php)
• DAO class names are in classes/core/Application.inc.php::getDAOmap())
• Forum: create plugin and custom URL
• Control flow, dispatch, URLs: https://pkp.sfu.ca/wiki/index.php?title=Router_Architecture
• see notes in 2018.3.txt of 2018-10-02
• Editor assignment: "Can only recommend decision, authorized editor must record it."
• Settings->Website->Plugins->Plugin Gallery
• Plugins with Settings: Google Analytics (Settings fail) RQC (settings fail) Web Feed (2 radiobuttons, one with an integer textbox) Usage statistics (Sections, checkboxes, text fields, pulldown)
• Beware of the various persistent caches, e.g. for plugin settings
• LoadHandler described in OSJ2.1 TechRef p. 46
• Maybe-helpful items from the code: _callbackHandleCustomNavigationMenuItems

Development notes: OJS data model (the relevant parts)

RQC speaks of Journals, Submissions (i.e. articles), Authors, Reviewers, Reviews, Editors, EditorAssignments (which Editor has which role for which Submission). Authors, Editors, and Reviewers are all Persons.

This is how these concepts are represented in OJS (class names, other typical identifiers for such objects). OJS speaks of four "stages": submission, review, copyediting, production. RQC is concerned with the review stage only. A revised article in OJS is not a new submission but rather a new "review round" of the same submission (with new files). Most classes have a corresponding DAO (data access object, as the ORM). Accessing objects often involves retrieving them (by using the DAO) via the primary key, called the id:

• Journal: Journal; the journal is often called the context.
• Submission: Article (there is a Submission class as well: the PKP library's superclass).
• Person: User (extends Identity).
• Author: Author (but the term is oddly also used for the 'author' of a Review: the Reviewer). Inheritance: Author<--PKPAuthor<--Identity<--DataObject.
• Editor: User(?) Decision constants see EditorDecisionActionsManager. Role ID constants see Role. The handling editor is called Section Editor in OJS. StageAssignment appears to map a user ID to a stage (constants see PKPApplication, e.g. WORKFLOW_STAGE_ID_EXTERNAL_REVIEW) in a given role(?) (UserGroup(?), constants see ???).
• Reviewer: User (but usually called reviewer).
  • A ReviewAssignment connects a Reviewer to a Submission and also contains various timestamps, declined, round, reviewRoundId, reviewMethod.
  • A ReviewRound represents the version number of a manuscript: OJS could theoretically use the same Article for the, say, three versions of a manuscript until eventual acceptance or rejection and represents the versions explicitly. In contrast, RQC always uses three separate Submission objects connected more implicitly via predecessor links.
    How to get it: ReviewRoundDAO::getLastReviewRoundBySubmissionId (ReviewRoundDAO::getCurrentRoundBySubmissionId gets the round number).
  • Once the proper ReviewRound is known, get the ReviewAssignments by ReviewAssignmentDAO::getByReviewRoundId (one could also use ReviewAssignmentDAO::getBySubmissionId). This returns an array. Its indices are the review IDs!.
• Review: ReviewerSubmission, but please hold on:
  • This class extends Article, presumably because reviewers can upload annotated versions of the submission.
  • Get one by ReviewerSubmissionDAO::getReviewerSubmission($reviewId). ``
  • Attributes: timestamps, declined, reviewMethod, reviewerId, reviewId (in fact reviewAssignmentId), recommendation, decisions.
  • Recommendation constants see define('SUBMISSION_REVIEWER_RECOMMENDATION_ACCEPT', 1); define('SUBMISSION_REVIEWER_RECOMMENDATION_PENDING_REVISIONS', 2); define('SUBMISSION_REVIEWER_RECOMMENDATION_RESUBMIT_HERE', 3); define('SUBMISSION_REVIEWER_RECOMMENDATION_RESUBMIT_ELSEWHERE', 4); define('SUBMISSION_REVIEWER_RECOMMENDATION_DECLINE', 5); define('SUBMISSION_REVIEWER_RECOMMENDATION_SEE_COMMENTS', 6);
  • Also an array of SubmissionComments which represent review text. Retrieve by getMostRecentPeerReviewComment
  • SubmissionComment attributes: authorEmail, authorId, comments, commentTitle, commentType (should be 1: COMMENT_TYPE_PEER_REVIEW), timestamps, roleId, submissionId, viewable.

Development notes: phpunit and PKPTestCase/DatabaseTestCase

• Complete DB reset is available by returning PKP_TEST_ENTIRE_DB from getAffectedTables.
• Selenium test example see StaticPagesFunctionalTest.