Adds new features #23

JhonathanLepidus · 2024-01-31T22:21:30Z

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

Signed-off-by: Jhon <[email protected]> Signed-off-by: Vitoria <[email protected]>

It can now request the number of annotations of a galley to the Hypothesis API Signed-off-by: Jhon <[email protected]> Signed-off-by: Vitoria <[email protected]>

Signed-off-by: Jhon <[email protected]> Signed-off-by: Vitoria <[email protected]>

Signed-off-by: Jhon <[email protected]>

Also changes some visual styling Signed-off-by: Jhon <[email protected]>

Signed-off-by: Jhon <[email protected]>

Also changes the path for annotations page Signed-off-by: Jhon <[email protected]>

Signed-off-by: Jhon <[email protected]>

Signed-off-by: Jhon <[email protected]> Signed-off-by: Richard <[email protected]>

Signed-off-by: Richard <[email protected]> Signed-off-by: Jhon <[email protected]>

Signed-off-by: Jhon <[email protected]> Signed-off-by: Richard <[email protected]>

Signed-off-by: Jhon <[email protected]>

asmecher · 2024-02-01T20:56:56Z

templates/submissionAnnotations.tpl

+			</div>
+			{/if}
+			<span class="annotation_content">
+				<blockquote>{$annotation->content}</blockquote>


I'm not sure whether annotations should be allowed to contain limited HTML, but this should probably receive at least limited escaping for XSS attacks -- and probably also the other annotation attributes (user and target) too.

Changes done!

Signed-off-by: Jhon <[email protected]>

asmecher · 2024-02-20T18:13:13Z

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

defstat · 2024-03-06T06:23:59Z

@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.

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

JhonathanLepidus · 2024-03-11T19:39:35Z

@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 · 2024-03-13T21:21:39Z

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 · 2024-03-14T05:51:51Z

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 · 2024-03-18T15:44:04Z

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

Also removes dependency for others plugins Signed-off-by: Jhon <[email protected]>

Signed-off-by: Jhon <[email protected]>

JhonathanLepidus · 2024-03-22T21:28:05Z

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 · 2024-04-02T10:42:32Z

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 · 2024-04-02T18:25:29Z

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 · 2024-09-24T10:03:48Z

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

JhonathanLepidus · 2024-09-25T18:37:21Z

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:

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.
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.

HypothesisPlugin.inc.php

Signed-off-by: Jhon <[email protected]>

JhonathanLepidus · 2024-11-08T16:33:41Z

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 · 2024-11-15T12:22:21Z

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

JhonathanLepidus · 2024-11-18T21:43:13Z

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

defstat · 2024-11-19T09:03:36Z

Thanks @JhonathanLepidus! My email is [email protected]. Send me when ever you can an email so that we can schedule something there.

defstat · 2024-12-18T10:05:22Z

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

The bugs were regarding the retrieving of a group of annotations and submissions which used custom url paths Signed-off-by: Jhon <[email protected]>

JhonathanLepidus · 2024-12-18T20:51:47Z

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.

JhonathanLepidus and others added 30 commits July 20, 2022 16:38

WIP: Get galley annotation number through Hypothesis API

1226215

Signed-off-by: Jhon <[email protected]> Signed-off-by: Vitoria <[email protected]>

Finishes HypothesisClient class

4270fca

It can now request the number of annotations of a galley to the Hypothesis API Signed-off-by: Jhon <[email protected]> Signed-off-by: Vitoria <[email protected]>

Prepares the including of custom template in preprint landing page

f91a402

Signed-off-by: Jhon <[email protected]> Signed-off-by: Vitoria <[email protected]>

Creates the template to add the annotation viewer to landing page

62a38d8

Signed-off-by: Jhon <[email protected]> Signed-off-by: Vitoria <[email protected]>

Removes left margin of annotation viewer

ea10bc6

Signed-off-by: Jhon <[email protected]>

Switch annotation viewer addin strategy

c755f8f

Signed-off-by: Jhon <[email protected]>

Removes commented code

9912be6

Signed-off-by: Jhon <[email protected]>

Brings Hypothesis API call to the template

80d50b4

Also changes some visual styling Signed-off-by: Jhon <[email protected]>

Adds Hypothesis config template

f6e5fbd

Signed-off-by: Jhon <[email protected]>

Uses load event for configuring Hypothesis client

9a1eab7

Signed-off-by: Jhon <[email protected]>

Hypothesis sidebar opens when clicking in annotation number

2b64509

Signed-off-by: Jhon <[email protected]>

Redesigns annotation viewer to use the same link of the galley

a502236

Signed-off-by: Jhon <[email protected]>

Creates HypothesisHandler class

4334c65

Signed-off-by: Jhon <[email protected]>

Adds page to list submissions with annotations

f15100b

Signed-off-by: Jhon <[email protected]>

Fixes bug occurred when galleys did not have file

4b05163

Signed-off-by: Jhon <[email protected]>

Requests Hypothesis API for annotations by submissions chunks

a118d42

Signed-off-by: Jhon <[email protected]>

Fixes problem with submissions groups annotations requests

f16d57d

Signed-off-by: Jhon <[email protected]>

Get submission object for submissions with annotations

dbf5996

Signed-off-by: Jhon <[email protected]>

Stores submissions with annotations in cache

6f11bb0

Signed-off-by: Jhon <[email protected]>

Set annotations cache to updated through scheduled task

8486eb3

Signed-off-by: Jhon <[email protected]>

Fixes bug when adding annotation number viewer

e98980b

Also changes the path for annotations page Signed-off-by: Jhon <[email protected]>

Creates page for listing of submissions with annotations

09e1351

Signed-off-by: Jhon <[email protected]>

Sets locales for annotations page

2e81266

Signed-off-by: Jhon <[email protected]>

Fix bug occurred for submissions without publications

be5214a

Signed-off-by: Jhon <[email protected]>

Handler returns submissions' annotations

45a2971

Signed-off-by: Jhon <[email protected]> Signed-off-by: Richard <[email protected]>

Sets annotations retrieving from cache

e50a87f

Signed-off-by: Jhon <[email protected]> Signed-off-by: Richard <[email protected]>

Set up the display of annotations

d8214ac

Signed-off-by: Richard <[email protected]> Signed-off-by: Jhon <[email protected]>

Adds styling for annotations

55ccaea

Signed-off-by: Jhon <[email protected]> Signed-off-by: Richard <[email protected]>

Adds Annotation class

e73ffd9

Signed-off-by: Jhon <[email protected]> Signed-off-by: Richard <[email protected]>

Retrieves annotation data from API response

8229782

Signed-off-by: Jhon <[email protected]> Signed-off-by: Richard <[email protected]>

JhonathanLepidus added 3 commits February 7, 2023 17:46

Keeps selected order through annotations pagination

27783eb

Signed-off-by: Jhon <[email protected]>

Refactors code of annotations ordering functions

58431e3

Signed-off-by: Jhon <[email protected]>

Changes default ordering to order by last annotation

ba8d71e

Signed-off-by: Jhon <[email protected]>

asmecher reviewed Feb 1, 2024

View reviewed changes

Escapes annotations content in annotations page

b7f9328

Signed-off-by: Jhon <[email protected]>

JhonathanLepidus added 2 commits March 22, 2024 15:52

Makes plugin fully compatible with OJS and OPS

3c8c56e

Also removes dependency for others plugins Signed-off-by: Jhon <[email protected]>

Minor fixes in annotations page

b98e0b6

Signed-off-by: Jhon <[email protected]>

defstat suggested changes Nov 5, 2024

View reviewed changes

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JhonathanLepidus added 4 commits November 7, 2024 17:17

Fixes error in task for updating annotations cache

dcfd8ae

Signed-off-by: Jhon <[email protected]>

Indents code using tabs instead of spaces

aaf7b86

Signed-off-by: Jhon <[email protected]>

Fixes minor leftover error in indentation

aa316ff

Signed-off-by: Jhon <[email protected]>

Fixes error when adding javascript to frontend

e87fbc7

Signed-off-by: Jhon <[email protected]>

Fixes bugs with retrieving of submissions annotations

5384163

The bugs were regarding the retrieving of a group of annotations and submissions which used custom url paths Signed-off-by: Jhon <[email protected]>

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Adds new features #23

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Adds new features #23

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Adds new features #23

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The annotations page:

Button with annotations number on archive page

Button with annotations number on preprint page

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