Annotation Management Issue

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francois maurice
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Annotation Management Issue

Post by francois maurice »

Annotation Management Issue
======================

Hi everyone, I'm not sure if this is the right place to publish this text, if not let me know.

I posted this message on many forums because I’m desperate.

I write from a researcher's point of view but I think the problem of annotations affects anyone who works extensively with annotations, even in the business community.

The problem I am raising is one of the biggest obstacle to a paperless world.

Because of this problem, it is almost impossible to work only on screen, without printing PDF files and annotation summaries. We are forced to use a mixed system: working at the same time on screen and on paper, which becomes a nightmare for medium and big research projects. It is almost worst than the old index cards system.

Most professional PDF software mixes at least two functions: 1) a PDF file editing function (rotating pages, adding or suppressing pages, cropping, etc.) and 2) an annotation function. The second function is the least well developed of the two. Given its underdevelopment, this function cannot fulfill its role properly.

In fact, the two functions can be separated in two independent software. Professionals who use the editing features of PDF files are not usually interested in annotation features and those who use annotations extensively have little interest in PDF edition. We don’t need all the PDF editing tools, which we almost never use anyway. We need powerful tools to navigate easily across all annotations in all PDF files on a device, no matter where the files are located. So, a PDF Editor is not a PDF Annotator.

Now, for annotation, most professional software offers features for Sorting, Summarizing and Searching annotations. These features are not well implemented. They are not powerful enough, not well organized, not well integrated. In short, they are not the central features of any PDF software known to me because annotations are not the focus of these software.

Usually, Sorting, Summarizing and Searching only apply to one document at a time. It is not possible to sort and summarize the annotations of a bunch of PDF files, for example all PDF files in a given directory. Many software offers advanced search features, such as searching across multiple files, but the results are awkwardly displayed and they can’t be sorted or summarized. This an example of features not well integrated. You can sort and summarize within a single file, you can search across multiple files, but you can’t do both.

So, we badly need a software to manage PDF annotations. A software that focus on annotations NOT on PDF files as a whole. The main object of a PDF Annotator is not a PDF file but a PDF annotation. The main window of a PDF Annotator has to display PDF annotations not PDF files as is the case with all PDF Viewer or Editor.

From now on:

- I will use the index card metaphor but do not worry I will not push the metaphor too far.
- I will focus on one annotation type: Highlight.
- I will give examples from PDF-XChange Editor since this is the professional PDF software I’m using
- I will discuss Qiqqa since it is the software that comes closest to a real PDF Annotator. But there are major flaws in the way Qiqqa has implemented the annotation feature.
- I will use the vocabulary from “JavaScript for Acrobat API Reference”, April 2007 (http://www.adobe.com/content/dam/acom/e ... erence.pdf).
- In what follows, we must keep in mind that many people are struggling with hundreds of PDF files that contain dozens of annotations.

There are many annotation types: Circle, FreeText, Line, etc. Maybe the most popular type is Highlight, at least in the scientific community. Each annotation type possesses some properties, many of which are common to several types and some of which are common to all types. For example, “author”, “content”, “subject” and “creationDate” are common to all annotation types. There are also properties for an entire document, such as “authors”, “creationDate”, “keywords”, “subject” and “title” which can be very useful even if an entire document is not the main object of interest. The “content” of an annotation (usually called a comment) is the text you put in the pop-up window associated with the annotation. When you highlight a portion of text you can add a comment in the pop-up window. Notice that most PDF software talk about Comments instead of Annotations.

The most important property for handling annotations (and files) is the "subject" property. As before with the old index cards, we need to create topics for our annotations so we can easily classify and find them. It is then normal to use the "subject" property to do this. Most PDF Editors allow you to write topics in the "subject" properties. But, as implemented in most software, if I write many topics in the “subject” property (let's say separated by semicolons), usually those software are unable to Sort, Summarize and Search a particular topic. For example, I enter the following topics in the “subject” property of a given annotation, an Highlight annotation in my case:

scientific method; explanation; scientific truth; testability; Karl Popper

With XChange Editor, if I sort my subjects, the sorting will be applied to the first word in the “subject” property, in this case ‘scientific’, in fact the whole string is considered a single word and if I summarize the annotations by subject, the same problem occurs, the whole string is considered a single word, not to mention that both features can only be applied to one file at a time.

Searching is a bit more powerful, at least in XChange Editor, since the Search Pane has many options to do advanced search. Contrary to the Sort and Summarize features, the whole string is NOT considered a single word. So, in the example above, I can search for “testability” only.

Besides the classic full text search, I like to be able to search within “subject” and “content” property of ALL annotations in ALL PDF files in a folder and subfolders. But since the PDF files are not indexed the search can take a very long time if you have 5 gigabytes of PDF files (which is my case), especially if the search is a full text search.

Also, the results are displayed in the already overcrowded Search Pane. The really good point is when you click on a given result the corresponding PDF file opens quickly to the right place. For example, if I do a search solely within “subject” and “content” property of all annotations in all my PDF files (not a full text search), each line in the result window in the Search Pane points to an annotation in a specific document. If I click a line, the corresponding PDF file opens where the text is highlighted. It’s good but not enough.

So, I think Searching is more powerful than Sorting and Summarizing in most PDF software. Which is why I’m using it much more than Sorting and Summarizing. However, the Search Pane in XChange Editor is all the same not a full fledge annotations management system. For example, I’m not able to have a list of all the subjects I created in the “subject” property of all my annotations!! From the example above, I’d like to have access to something like that in an alphabetical order:

explanation
Karl Popper
scientific method
scientific truth
testability

Right now, I have to keep track manually of all the subjects I created, which is an impossible task. I recall that I talk about 5 gigabytes of PDF files or hundreds of PDF files and thousands of annotations (mostly Highlight).

Now, let’s forget the Sort, Summarize and Search features as implemented by most professional PDF software. Try to think otherwise. Think about a new paradigm to manage annotations.

As I said before, the focus is on annotation not a whole PDF file and we need a way to access all annotations in all PDF files in a device based on subjects created by the users.

So, we need two main windows: a classical window or Document Window to display a PDF file (or many PDF files) and a Annotation Window to display annotations (think about index cards) based on selected subjects. As with the Document Window, it has to be possible to open many tabs in order to work on many subjects or projects on the same time.

The subjects can be listed in a Subject Pane. So the software has to maintain a subject database. From there we can select many subjects at the same time and the corresponding annotations (from all PDF files in a device) will be displayed in an Annotation Window. Of course, the Subject Pane should provide subjects management tools as renaming a subject across all annotations or across a subset of annotations or a subset of PDF files. Many more ideas come easily to mind.

When reading and annotating a PDF file, the GUI has to offer an easy way to enter or create subjects. Right now, with XChange Editor we have to open the Property Pane to get access to the “subject” property of an annotation. It has to be possible to enter or create a subject (or many subjects) directly in the pop-up window just as we fill the “content” property (usually called a comment) in the pop-up window. In addition, the field used to enter or to create a subject has to display a drop-down list of all the subjects already created so that it is possible to select topics that already exist.

It is not necessary, I think, to integrate a kind of project manager. A user has only to create special subjects for his projects. For example, the user can begin all his project names by “Project” followed by a name or a number. For example, he can enter “Project-001” or “Project-Popper and its enemies” in the “subject” property of an annotations.

Also, it is not necessary, I think, to force the user to put all is PDF files in a special folder manage by the PDF Annotator. People already manage PDF files in different ways. Most users already work with a reference manager or a sync service. Anyway, since the focus is on annotations, a PDF Annotator has only to scan a device for PDF files and annotations within those files. It does not matter if the file changes name or location, the software needs only to constantly scan the device for PDF annotations and update his subject database (and his index database for full text search).

If a user uses multiple devices, there is no need, I think, to create another synchronization service, which proliferates like plague on the Web. No matter how a user synchronizes his PDF files (Google Drive, OneDrive, Drop Box, Resilio, etc.), each copy of a PDF Annotator installed on a device works independently from each other and scans only the device on which it is installed.

Yes, I know, there is a software called PDF Annotator (http://www.pdfannotator.com). In the best case, it seems to be a PDF Presentator and in the worst case it is a toy not a tool.

Now let's talk about Qiqqa.

Qiqqa is the closest thing I saw which can be called a full fledge PDF Annotator. But there are major flaws. Take note that Qiqqa talk about tags, which is the same as the “subject” property of a PDF file.

The biggest flaw is that the main features are not PFD compliant. Annotations and tags (“subject” property) do not comply with ISO standards for PDF format. So, if Qiqqa goes bankrupt you are in big troubles. And even if Qiqqa does not go bankrupt, it's impossible to work on a device that does not have Qiqqa installed, which means you can not collaborate with colleagues who do not use Qiqqa.

Qiqqa has the right idea to focus on annotations and to use tags (“subject” property) to manage annotations (and PDF files), which is quite powerful, but the main window displays PDF files, based on selected tags (“subject” property). To see annotations based on selected tags, you have to generate a report, which is awkward. But Qiqqa is still quite powerful since you can click on an annotation in the report to open the PDF file in the right place. But, it is highly preferable, as I explained above, to have windows (or tabs) which dynamically display annotations based on selected subjects (tags in Qiqqa jargon).

Another big mistake, Qiqqa try to be a big software which can manage all the workflow of a research project. For example, it integrates a reference management system, tools to discover new papers to read and where to focus your efforts, the Expedition tool which automatically breaks your library into themes so that you can quickly get up to speed with and understand your field of research. This may be good ideas, I am not sure, but what is certain is that these functions should not interfere with the main functionality which is the management of annotations.

I hope I was clear enough. But above all, I hope someone will find these ideas interesting and potentially quite beneficial in terms of money to get into programming such a software.

I am ready to be an alpha tester or an early beta tester.


François Maurice
pdf_annotation@yahoo.com
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Re: Annotation Management Issue

Post by Sasha - Tracker Dev Team »

Hello François Maurice,

Well, something like this can be implemented as a part of the Editor or a separate product - it's not a problem from the coding part (except the consumption of the devs' time). The thing is that we do not know the scales of this scenario of usage so this will need to be discussed with our Project Director and lead devs.

Cheers,
Alex
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Re: Annotation Management Issue

Post by francois maurice »

Thanks Alex to submit the idea to your Project Director and lead devs.

As I reread my own text, I realize that the core idea is rather simple. If I can quote myself:
The subjects can be listed in a Subject Pane. So the software has to maintain a subject database. From there we can select many subjects at the same time and the corresponding annotations (from all PDF files in a device) will be displayed in an Annotation Window. Of course, the Subject Pane should provide subjects management tools as renaming a subject across all annotations or across a subset of annotations or a subset of PDF files. Many more ideas come easily to mind.

When reading and annotating a PDF file, the GUI has to offer an easy way to enter or create subjects. Right now, with XChange Editor we have to open the Property Pane to get access to the “subject” property of an annotation. It has to be possible to enter or create a subject (or many subjects) directly in the pop-up window just as we fill the “content” property (usually called a comment) in the pop-up window. In addition, the field used to enter or to create a subject has to display a drop-down list of all the subjects already created so that it is possible to select topics that already exist.
So, for the short term you can only consider adding a Subject Pane that keeps track of the topics created by the user, as well as adding a subject field in the pop-up window with a drop-down list that contains the topics already created. This field must be able to contain several topics.

Thanks,

François Maurice
PDF_Annotation@yahoo.com
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Re: Annotation Management Issue

Post by Tracker Supp-Stefan »

Hello François,

Many thanks for your detailed explanation. We are going to discuss this in a meeting this Wednesday with a very sympathetic view to seeing how we could progress this! Would you be prepared to discuss this in more detail with our team in the future and perhaps do some testing as we progress?

I've also created a feature request ticket in our internal system:
#4209: Editor FR: 'Annotations' plug-in with extended features!
So that we can keep proper track of this!

Regards,
Stefan
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Re: Annotation Management Issue

Post by francois maurice »

Hi Stefan,

I'm glad you're interested in this idea. I will be pleased to participate in the realization of an idea that I have been maintaining for a long time.

To be honest, I hope Tracker will be the first firm to offer this type of annotation management. I have been using XChange Editor for several years now for the quality of the product and the quality of the service and would like to use it again for years to come.

Do not hesitate to contact me and tell me how to proceed. I am willing to discuss and do all the appropriate tests.

Au plaisir,

François
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Re: Annotation Management Issue

Post by TrackerSupp-Daniel »

Thanks francois, Well keep you posted!
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Re: Annotation Management Issue

Post by francois maurice »

Some more ideas
===============
  • Be able to select subjects with logical criteria.
  • Update subjects in real time
  • Be able to open multiple windows to work on multiple subjects at once.
  • Make sure that all subjects are displayed in the pop-up windows, just as the comments appear completely in the pop-ups.
I will regularly post ideas on this post about annotation management.
I invite anyone interested in annotation management to post ideas on this post.
I maintain that this is an essential feature of any modern PDF software, i.e. be able to work only on screen, without printing PDF files.

François Maurice
pdf_annotation@yahoo.com

Feature request ticket in Tracker internal system:
#4209: Editor FR: 'Annotations' plug-in with extended features!
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Re: Annotation Management Issue

Post by Tracker Supp-Stefan »

Hello Francois Maurice,

Many thanks for those suggestions!
I will add them to the ticket and make sure they are taken into account when we get to this feature.
Please note that for the moment we will be dedicating a couple builds on mostly sorting out some issues, and new features will be looked at after that!

Regards,
Stefan
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Re: Annotation Management Issue

Post by francois maurice »

Hi Stefan,

you wrote:
Many thanks for those suggestions!
Tout le plaisir est pour moi. :P

Also:
Please note that for the moment we will be dedicating a couple builds on mostly sorting out some issues, and new features will be looked at after that!
I understand very well that there are priorities to manage.
I appreciate the fact that you spend time and some builds to fix problems and thus ensure the stability of XChange Editor.
This is one of the reasons I use XChange Editor Pro for several years now.
XChange Editor is lightweight, powerful and stable at a great price, not to mention the excellent support via the forum.

Now, after all these compliments, I have a favour to ask you. :D

In the very short term, I would need the most basic functionality to handle the subjects I created for my annotations.
Is it possible for you to write a small script to extract the subjects from the "subject" property field of any annotations and place them in alphabetical order in a new PDF document?
Ideally, the script should extract subjects from all annotations of all PDF files in a given folder.

With this list at least I could track the subjects I created as I inserted annotations.
This is really the bare essential to conduct a research project with PDF files without having to print everything and to avoid going back to the old index cards.

Note that I separate my subjects in the "subject" property field with semi-colons.

Thanks a lot,

François
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Re: Annotation Management Issue

Post by Patrick-Tracker Supp »

Hello François,

I am afraid that at this time we cannot write you a custom script to sort and summarize your comments by subject. It seems like a good idea for sure, so I have created a formal feature request for this. At this time, you can sort your comments by subject:
Image

I am sorry that we could not offer you an immediate solution.

Cheers!
If posting files to this forum, you must archive the files to a ZIP, RAR or 7z file or they will not be uploaded.
Thank you.

Cheers,

Patrick Charest
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Re: Annotation Management Issue

Post by francois maurice »

Hi Patrick,

Can you recommend what is necessary (books, manuals, document from the Web, etc.) on Javascript gear toward programming small scripts for manipulating PDF files and which will work with XChange Editor?

Do not be afraid, you can propose a lot. :D

Thanks,

François
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Re: Annotation Management Issue

Post by TrackerSupp-Daniel »

We support mos tof the same functions as described in the Adobe JavaScript API, so this will be the most complete are to look
https://help.adobe.com/livedocs/acrobat ... .71.1.html
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Re: Annotation Management Issue

Post by Sasha - Tracker Dev Team »

Hello François,
In the very short term, I would need the most basic functionality to handle the subjects I created for my annotations.
Is it possible for you to write a small script to extract the subjects from the "subject" property field of any annotations and place them in alphabetical order in a new PDF document?
Ideally, the script should extract subjects from all annotations of all PDF files in a given folder.
I've investigated this a little and what can be done (aside from writing to console window) is saving to the txt attachment file.
https://help.adobe.com/livedocs/acrobat ... sible=true
https://forums.adobe.com/message/3349319#3349319
The simplest thing to do though would be to copy the text from the console.

Cheers,
Alex
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Re: Annotation Management Issue

Post by francois maurice »

Thanks Alex, I'll try it and will give you feedback.
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Re: Annotation Management Issue

Post by TrackerSupp-Daniel »

Keep us posted! :)
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Re: Annotation Management Issue

Post by francois maurice »

Hi,

I would like some advice from you.

Since I need the core feature very soon, which I discussed in my post of 04 Feb 2018 17:55 in this thread and I detail below, I had the choice to either program a script myself, which may take me some time since I have to learn JavaScript before, or use a programmer.

So I started learning JavaScript and at the same time I wrote to a consultant to find out how much it would cost to program a script.

Here is what I wrote to the consultant which specify my needs:
I use extensively the annotations of PDF files, especially the Highlight type.
More precisely, I use the annotation "subject property".
I'm using it to identify each annotation with many subjects.
For example, I can write the following subjects in the subject property of a specific annotation:

scientific method; scientific truth; Karl Popper; testability; confirmation;

As you can see, I separate each subject with a semicolon and each annotation has many subjects.
Keep in mind that I work with dozens of PDF files, so I have hundreds of annotations and hundreds of topics.

The problem is that I do not know of any PDF software that can extract these topics and present them in alphabetical order so that I can track my topics. I can search within comments but it is not sufficient.
  • I need to product a list of all my subject (which are separated by semicolons in the subject property of each annotation) of all annotations within all PDF files in a given folder.
  • That list has to be in alphabetical order.
  • Subjects should appear only once in the list even if subjects appear multiple times in the annotation set.
  • In the list, each letter of the alphabet must be separated by an empty line.
  • A count of each subject must be beside each of them.
For example,

confirmation (23)
(blank line)
Karl Popper (56)
(blank line)
scientific method (103)
scientific truth (75)
(blank line)
testability (17)

So the solution, I think, would be to program a script with JavaScript which I could run from a console or from a .js file installed in a specific folder.

Can you produce that kind of script and what is your price?

I'm using XChange Editor of which a free version is available but I think that the software is fully compatible with Acrobate.

Here is the answer he gives:
what you want to do can certainly be done, but unfortunately not with a simple JavaScript. The JavaScript implementation of Adobe Acrobat and Xchange Editor are very similar, and I have programmed for the Xchange system before. However, Acrobat can be automated from the outside by using what's called the "Interapplication Communications" (or IAC for short) interface. This is not available for the XChange Editor. What we would have to do is to come up with a standalone application that can loop over all PDF files in the specified folder, extract the relevant data and then create the output file. I would use a free PDF library to do that. This saves you a lot of money, because otherwise we would have to license a library for between $300 and $1000. This free library requires that the application be written in the Java language, which will result in something that might look a little bit different than your usual Windows applications, but so far my customers have not had a problem with that.
Is it true that it is impossible to do with JavaScript alone what I specified above ?

Thank you to enlighten me,

François Maurice
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Re: Annotation Management Issue

Post by TrackerSupp-Daniel »

While I agree with him that it cannot be done with Simple JavaScript, I do want to state that It can be done with JavaScript alone. As was said it would not be simple, and I believe he is right that having an external application handle it is the best course of action. The amount of man hours you would have to put in to writing JavaScript to accomplish this kind of task would be momentous simply because of language limitations.

Conversely, if you have a development team available, I believe you could do this within our software SDK, available here:
https://www.pdf-xchange.com/product/downloads/dev

This is a free download, simply note that if you create a tool for commercial use, it will then be necessary for you to purchase a License to the SDK tools so as to avoid watermarking all your documents.
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Re: Annotation Management Issue

Post by francois maurice »

Thanks Daniel for the advice.

I will think about all that.

But can you tell me what is the difference between the list of subjects that I want and the traditional annotation summary, whose code is at this link, which seems to me to be pure JavaScript:

https://help.adobe.com/livedocs/acrobat ... ml#1516615

Thank you very well,

François
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Re: Annotation Management Issue

Post by Sasha - Tracker Dev Team »

Hello François,

You have two ways here:
1) From what I see, the JS would have a problem with reading the files from folder - you will have to store an array of the string file paths and read them one by one. The only problem here is that when you add new files to the folder, you will have to refill the array manually, so that the script would work correctly.
Other then that - there are no crucial problems and the script itself can be custom coded even by us (though again it's not a free operation - but it would be faster then 3rd party programmers as we know better how our engine works).

2) If this reading script is for you only - not for commercial usage (meaning the procedure that goes through the annotations and gives the results that you described in some text representation), then our SDK (the free version) can be used to write a small program that would do that. Unlike the JS - the SDK version of the script will have a possibility of reading from folder and will be much more versatile about the output - meaning that it can be tuned further. Again this also is not a free operation and we can develop such an application in short terms.

Cheers,
Alex
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Re: Annotation Management Issue

Post by francois maurice »

Hi everyone,

I finally found a temporary solution until Tracker implements in a future as close as possible a real annotation management system. :wink:
The solution was hint at me by Sasha.

I modified a code, "Write comments to a tab-delimited file", found in the "Batch Sequences" manual.
https://help.adobe.com/livedocs/acrobat ... ml#1516719

The code creates a file attachment in Excel and writes the subject of each annotation on a separate line (I have to modified the encoding from UTF-8 to UTF16 to take into account the French characters). In Excel, this gives something like this, where each line is the subject property of one annotation.
  • Positivisme; Réalisme; Théorie vs Pratique;
    Spontanéité; Indéterminisme; Causalité; Interprétation de Copenhague;
    Spontanéité; Indéterminisme; Causalité; Interprétation de Copenhague;
    Spontanéité; Causalité;
    Spontanéité; Causalité; Objectivisme;
As you can see I wrote many subjects for each annotation separated par semicolons.
Now I have to use VB to decompose each line into as many lines as there are topics and then delete the duplicates.

I have to do the whole process for each PDF file since it seems very difficult, if I understand, to go through each PDF file using only JavaScript.

It is very awkward but it works

Thanks to everyone for the tips and advice but especially for the excellent service and for your patience.

François :D
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Re: Annotation Management Issue

Post by Sasha - Tracker Dev Team »

Hello François,
I have to do the whole process for each PDF file since it seems very difficult, if I understand, to go through each PDF file using only JavaScript.
It's not difficult - it can be coded in a way that it would take a file path array and use it to do the operation on each of the documents. Though it will require a little more coding done.

Cheers,
Alex
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Re: Annotation Management Issue

Post by francois maurice »

Thanks Alex for this tip again.

Now I see it.

So, I'm going to code a version that will iterate through PDF files and maybe even use JS, instead of VB, to break down subjects at each semicolons; eliminate duplicates and count the number of occurrences of each subject. Wow, what a challenge to me.

It's going to take a bit of time since I need to deepen programming in JS, but I'll post the final result so that it's accessible to the community.

Thanks again,

François
Sasha - Tracker Dev Team
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Re: Annotation Management Issue

Post by Sasha - Tracker Dev Team »

:)
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