Thanks for your answer! Are you sure it's related to TinyMce because if I create a link with this url zotero://open-pdf/0_1A2B3C4D via the Inser Link icon then the href isn't removed.

If it is, do you know which file should I edit? I have looked into the zotero-master\resource\tinymce\themes\advanced\js\link.js file and found that function:

checkPrefix : function(n) {
if (n.value && Validator.isEmail(n) && !/^\s*mailto:/i.test(n.value) && confirm(tinyMCEPopup.getLang('advanced_dlg.link_is_email')))
n.value = 'mailto:' + n.value;

if (/^\s*www\./i.test(n.value) && confirm(tinyMCEPopup.getLang('advanced_dlg.link_is_external')))
n.value = 'http://' + n.value;
},

Is this the one I should edit?

I did some more testing, and apparently links like zoter://open-pdf... (notice the missing last o), zoterH://open-pdf... or zoteroA://open-pdf... are accepted, but not zotero://open-pdf.... Any random string before the :// is also accepted (except file://).

So it seems that zotero:// is intentionally forbidden (only when pasting, not when added via the Add Url icon). Any idea why? Also I still couldn't find the file causing this, so if you have any clue, that would be very welcome!

@dragonfly Thanks a lot for all this details! Finally I found the zotero.jar (it is in C:\Program Files (x86)\Zotero Standalone - I don't understand why windows didn't find it this morning...).

If I got you correctly, zotero.jar is for Zotero standalone and zotero@chnm.gmu.edu.xpi is for Zotero addons. Is that correct?

I saw your thread this morning when looking around for so direction about modifiyng TinyMce. Thanks a lot for sharing with us what you did!

Concerning the custom protocol handler, I do not often share my notes so this won't be an issue. I looked into how I should create one, apparently it's via the registry*. But I am not sure how I should implement it to my own situation, so that the custom protocol handler I am creating can redirect to the correct path zotero://open-pdf/... Let say, my protocol handler will start a python that will open my pdf. So far here is what I have:

REGEDIT4

[HKEY_CLASSES_ROOT\foo]
@="URL:Python Start Zotero Pdf Protocol"
"URL Protocol"=""

[HKEY_CLASSES_ROOT\Python Start Zotero Pdf Protocol\shell]

[HKEY_CLASSES_ROOT\Python Start Zotero Pdf Protocol\shell\open]

[HKEY_CLASSES_ROOT\Python Start Zotero Pdf Protocol\shell\open\command]
@="\"C:\\Python35\\Lib\\site-packages\\Python Start Zotero Pdf Protocol.py\" \"%1\""

Is good so far?

Also how can I use the argument %1 to be the key of the pdf (the number after the zotero://open-pdf/0_ in the actual link) so that the .py knows precisely which pdf to open?

*http://stackoverflow.com/questions/389204/how-do-i-create-my-own-url-protocol-e-g-so"

When I read about your post I didn't think it could apply to my situation... On a second thought, I think it would be difficult. Here is the whole set up. I often read pdf on my computer and as I read them I copy the interesting part and paste them in different notes. Because I am copying while I am reading and I spread the info in many different notes, the Zotfile annotation extraction tool doesn't help me much (in particular because it extracts all the highlights at once, while I just need the last one). But I also need to keep track of the source, so I made this .py to retrieve the pdf link and the page (Zotfile inspired me on that one!). So I don' really see here how adding a button to TinyMce could fit into my workflow.

Also the whole problem is about pasting the zotero://open-pdf/ in the note, so I guess even if the .py is launch from TinyMce, I will run into the same problem... well except if I can make the .py edit the source code instead of pasting in the html mode.

--

For accessing zotero.sqlite, I am doing it on a copy with shutil.copy2 of the zotero.sqlite : I tried to access the .py directly but I get an error as the file is locked because Zotero is open when I run .py. So do you thing simply copying the .sqlite can corrupt my db?


Well that's a lot of new info, just when I was running out of ideas. Thanks so much @dragonfly for your help, for writing such detailed answers and for the time you spent writing them. I really appreciate it!

If I got you correctly, zotero.jar is for Zotero standalone and zotero@chnm.gmu.edu.xpi is for Zotero addons. Is that correct?

no, that's not quite right. Both versions run essentially the same code and the Firefox add-on uses a zotero.jar , too. As bwiernik indicates in the other thread, packing and unpacking zotero.jar is a rather tedious method of trying to tweak Zotero code and the standard/recommended way would be to run the Firefox add-on straight from the github checkout, i.e. https://www.zotero.org/support/dev/source_code#working_with_git_repositories but obviously hacking straight in the .jar works. It's just a waste of time, especially if you're trying things out.

@dragonfly -- Zotfile writes this into the note directly in html using the javascript API. EnoraEdelect is trying to paste from an html clipboard to the rich text (i.e. default) view of the note, so that's a bit different.

As for editing zotero.jar -- I think I have said this before: this has nothing to do with "approved" or not. There's nothing harmful in editing the zotero.jar. I just think working with a github checkout takes 3mins to set up and then saves you a lot of time when testing code and I don't want to encourage people to use what most people would consider a far inferior setup. I'm not trying to talk you out of it, but I do discourage you from talking other people into it ;)

Just to remove some of the confusion which I helped to create.
If you are using the Firefox add-on you need to look inside zotero@chnm.gmu.edu.xpi.
If you are using Zotero standalone (as I am with Chromium connector) you need to look inside zotero.jar. I am not using Firefox at the moment.

I prefer not to post my zotero.jar as you request since it has several rough tests underway.
Instead I will post information on the steps I've taken.

Let's make a start by suggesting that you simply paste zotero://open-pdf/0_1A2B3C4D/10
into your browser URL (the example below comes from Chromium Web Browser in Ubuntu).

When you launch this URL you should see a popup window

External Protocol Request

Chromium needs to launch an external application to handle zotero: links. the link requested is zotero://open-pdf/0_1A2B3C4D/10

The following application will be launched if you accept this request.

xdg-open

Click on [ Launch Application ]

We can discuss where to go from here. So far we are not touching Zotero. Just experimenting with URL protocol handlers.

I can confirm that I can post your link zotero://open-pdf/0_1A2B3C4D/10
into tinymce 4.5.0 (it has moved on from 4.4.3).

More steps will follow.

Thanks so much for taking the time to walk me through all this.

In fact this exercise is refreshing my memory to resume some tests I've been running to capture and analyse text from collections.

Next step, I suggest that you download tinymce 4.5.0 (Community) into a folder completely divorced from zotero and begin to understand how to use it outside zotero environment. You will need to create a note.html (or index.html) file from the tinymce examples.

https://www.tinymce.com/download/

e.g. read about links here ... https://www.tinymce.com/docs/plugins/link/

Please clarify if you are testing against the default version (3.5.7) of tinymce as embedded in Zotero or if you are testing a later version of tinymce. Note that I found significant differences between tinymce 3.5.7 embedded in Zotero and tinymce 4.4.3 (or later version) fresh download.

It will help you to understand if you read default tiny_mce.js in /resource/tinymce/
You might need to "prettify" the script to make it readable.


// Contains modifications by Dan S./Zotero

(function(win) {

var whiteSpaceRe = /^\s*|\s*$/g,
undef, isRegExpBroken = 'B'.replace(/A(.)|B/, '$1') === '$1';

var tinymce = {
majorVersion : '3',
minorVersion : '5.7',
releaseDate : '2012-09-20',


If you search "zotero" through that js file there are 7 hits.
I do not know why the default tiny_mce.js was modified in this way instead of making a separate js file for the zotero modifications. Perhaps a developed zotero plugin for tinymce might make it easier to integrate. Currently v 3.5.7 makes integration of later versions of tinymce difficult to fathom out.

That is why I decided to leave this "well alone" and (for testing purposes) from note.html launch a separate instance of tinymce 4.4.3 (or now 4.5.0) just for my local experiments.

My launch window button is placed in note.html body and not in the tinymce 3.5.7 toolbar.


<body>
<button onclick="openNewTinyMCE();">launch window</button>
.... ... ...


I added a new folder "extapps" in /resources/ and in there I dropped tinymce_4.4.3 which I had downloaded.

My test script which launches a second window with second instance of tinymce is here ... placed in script tags in head of note.html


function openNewTinyMCE() {

// this test script expects /extapps/tinymce_4.4.3 folder
// to be located in /resources/ in parent zotero.jar

OpenWindow=window.open('../../extapps/tinymce_4.4.3/index.html', 'newwindow', config='height=400, width=800, toolbar=no, menubar=no, scrollbars=no, resizable=no, location=no, directories=no, status=no');

}


And an index.html has to be created in /resources/tinymce_4.4.3.
Clearly the end goal is to have only one instance of tinymce running but for my purposes I'm just testing the default note editor alongside a later version.


This may not answer your question but gives the steps I took to experiment with different versions of tinymce in an open instance of Zotero standalone. I also added svg capability but that is another story.

The version I use for the external TinyMce is 4.5.0.

I was able to follow your instructions. I now have a button in my regular Zotero note. When I click on it, a new window opens with the external 4.5.0 TinyMce. I wasn't yet able to work with the tinyMce.activeEditor.getContent. I will in more details tomorrow

There are several things that are not yet clear to me with this approach. I will only use this external editor to paste the link with href="zotero://open-pdf/0_1A2B3C4D/10" and so my workflow will generally be like: I write a couple of sentences in an already existing regular Zotero note, and then I need to add a link with this href="zotero://open-pdf/0_1A2B3C4D/10", so I will need to open the external note with tinyMce 4.5.0. I can then click on a button to close the note but at this point I would like to get back to my note (with the updated content) in the regular Zotero. I generally work on many different notes at once so the external editor can't be my by default editor (maybeit could be if I get a way to pass to it the ZoteroID of the note).

Even in this external TinyMce 4.50 note, I can't paste the href="zotero://open-pdf/0_1A2B3C4D/10". $zotero:// doesn't work (as it doesn't break the match zotero://) but something like zZotero:// or zoteroA:// work.

+++
I was also looking around for the other solution you talked about with the Protocole Handler. Does something like this will work?

REGEDIT4

[HKEY_CLASSES_ROOT\foo]
@="URL:Python Start Zotero Pdf Protocol"
"URL Protocol"=""

[HKEY_CLASSES_ROOT\Python Start Zotero Pdf Protocol\shell]

[HKEY_CLASSES_ROOT\Python Start Zotero Pdf Protocol\shell\open]

[HKEY_CLASSES_ROOT\Python Start Zotero Pdf Protocol\shell\open\command]
@="\"C:\\Program Files (x86)\\Zotero Standalone\\zotero.exe\" \"zotero://open-
pdf/0_1A2B3C4D/10\""

The trouble is to pass the argument zotero://open-
pdf/0_1A2B3C4D/10\ not to zotero but to open-pdf because zotero standalone doesn't seems to be able to open.

Also I don't really understand where I should add my custom protocol handler like if I choose "zoteroA://" where should I add it?


Thanks a lot for your help and your time!