Adds new features

[JhonathanLepidus]

This PR adds the following features:

• Annotations page, where all submissions with annotations are listed
• A new button with the number of annotations next to the PDF button in the preprint page. When this is clicked, the PDF is opened with the annotations tab opening automatically.
• The same button to the preprint item in the list of preprints

These features were discussed in the issue

[asmecher]

Thanks, @JhonathanLepidus! @defstat, would you mind taking a deeper look?

[defstat]

@JhonathanLepidus two questions on this:

I can see that the description of the issue defines

A new button with the number of annotations next to the PDF button in the preprint page.

1. I don't seem to see this button - should I do something in order to see it?
2. Does that work for OPS (because you are referring to preprints) or it should work across applications, namely OJS, OMP and OPS?

[JhonathanLepidus]

@defstat sorry for missing this information. In fact, there should be an integration with the theme plugin in order for it to work. The integration is the calling of the hook Hypothesis::annotationNumber in the place where it is intended to display the button.

For example, we did this implementation in the SciELO Preprints theme: example. It should work in other applications besides OPS.

We did it this way because it was simpler for us, but I think it can be a problem for others to use. Do you think we should change it?

[JhonathanLepidus]

We were able to identify an alternative implementation. We can change the plugin so that it uses template filters to add the button with the number of annotations next to the galley buttons.

This way, this feature could work on both platforms (OJS/OPS) without needing to be linked to a specific theme.

[defstat]

Hi @JhonathanLepidus. Thanks for that - Yes, the plugins should be "self contained", so your initial approach should be managed somehow. @jardakotesovec is a better person to talk about front end implementations, so I leave that for him.

Do you plan to migrate that change to stable-3.4 and/or main branch?

Also could you provide some screenshots on the intended end-result of the features this implementation adds?

[JhonathanLepidus]

Hi! Yes, we plan to make these features available for the version compatible with stable 3.4.0 as well. Below are some screenshots of these features.

The annotations page:

Button with annotations number on archive page

Button with annotations number on preprint page

[JhonathanLepidus]

Hi @defstat

We have updated the code in the source branch of this pull request, in order to bring the following improvements:

• Updating of the cache cointaining the submissions with annotations through a scheduled task by the Acron plugin
• The buttons with the number of annotations are now added without the use of a dependency with the theme plugin
• Minor adjustements that make the new features fully compatible with both OJS and OPS

The features have also been adapted to the version compatible with OJS/OPS 3.4.0 and are ready to be shipped at a later moment.

[defstat]

Hi @JhonathanLepidus! Thanks for all that work! It looks great, and I see that you have adapted the newer/more fluent syntax regarding

Only one question about the caching - is the caching mechanism going to affect the realtime update of the annotation display?

If you have PRs for 3.4 version, please don't hesitate to add those in #22 so that they can be reviewed also.

[JhonathanLepidus]

Hi @defstat , thanks for the feedback.

The caching mechanism does not affect the display of annotations when viewing the PDF. The cached items are only used for display on the annotations page and do not affect other parts of the application.

We will open a pull request with our contributions to 3.4.0.

Edit: PR opened

[defstat]

@JhonathanLepidus thanks for all this work. Can you share the state of this change?

[JhonathanLepidus]

HI @defstat !

The changes are ready to be merged. They're present in this pull request (for 3.3.0 version) and in this other one (for 3.4.0 version).

If you have any other doubt, please contact me.

[defstat]

Thanks @JhonathanLepidus so much for those changes, and I am sorry for delaying this. Just one or two comments here:

1. I have tried to annotate something on a PDF and then to check that annotation on the interface, but it did not seem to be visible. Maybe I am doing something wrong, but if you can, please try to test the plugin's full functionality on stable-3_3_0 branch, with PHP 7.3 which is the oldest we support on stable-3_3_0.
2. Please try the same on stable-3_4_0 for the other PR you are mentioning, and PHP 8.0 which is the oldest PHP version we support on that stable branch.

[JhonathanLepidus]

Hi @defstat , thanks for the review of these changes.

I have tested both versions of these changes in PHP 7.3 and PHP 8.0. Some fixes were needed for the first, but the second worked well.

I also fixed one bug in the 3.3.0-compatible version regarding the scheduled task and solved the problem with the runScheduledTasks tool.

I formatted the PHP code using tabs in the 3.3.0 version. However, I noticed the plugin doesn't follow the PSR-12 standard in 3.4.0, so I didn't know what to do in this case.

[defstat]

Hi @JhonathanLepidus, because I have some functionality questions regarding this, could we set-up a quick demo meeting for the new features?

[JhonathanLepidus]

Hi @defstat . Sure, I'm available for a meeting on any day of the week, except on wednesdays afternoons (considering brazilian time).

[defstat]

Thanks @JhonathanLepidus! My email is defstat@gmail.com. Send me when ever you can an email so that we can schedule something there.

[defstat]

Hi @JhonathanLepidus! do we have any development on this?

[JhonathanLepidus]

Hi @defstat ! These changes were not firstly prioritized, but I found some time to do these tests. As we discussed, I did the tests with the PKP datasets. I found two bugs on the 3.3.0 and 3.4.0 changes.

When retrieving the annotations, the submissions were divided in groups and the Hypothesis API was queried for each group (to reduce time in large databases). The bug affected the last group queried. Since the PKP dataset has only two submissions, there was only one group, which was not queried.

The second was regarding submissions with a custom URL path. This bug was present only on the 3.3.0 changes.

I still did not implement the new item for the site's navigation menu. Please, let me know if you still have problems testing these features.

[asmecher]

@defstat, I think the next step on this one is with you.

[JhonathanLepidus]

Hi @defstat

As we agreed previously, I added a new navigation menu item to ease the access of users to the annotations page. This feature is now present in both this PR and the PR for 3.4.0.