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dwp-forge / refnotes

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config page unusable #59

Closed remygithub closed 3 years ago

remygithub commented 4 years ago

Description

Attempted use

Desired behaviour

Site configuration

Using Firefox 78.0 with nginx.

Other plugins enabled:

find -maxdepth 1 -type d
./extension
./usermanager
./wrap
./acl
./info
./upgrade
./styling
./color
./todo
./nspages
./revert
./safefnrecode
./searchindex
./imagebox
./authplain
./note
./config
./indexmenu
./move
./filelist
./tag
./simplenavi
./pagenav
./catlist
./pagelist
./bureaucracy
./sqlite
./struct
./mathpublish
./highlightparent
./edittable
./refnotes

Debugger Feedback

Debugger console output when loading Refnotes config page

Error:

Uncaught TypeError: fields.getItem(...).update is not a function
    updateFields http://127.0.1.1:XXXX/lib/plugins/refnotes/admin.js:710
    initialize http://127.0.1.1:XXXX/lib/plugins/refnotes/admin.js:632
    initialize http://127.0.1.1:XXXX/lib/plugins/refnotes/admin.js:1013
    <anonymous> http://127.0.1.1:XXXX/lib/plugins/refnotes/admin.js:1091
    jQuery 2
        e
        t

Warning:

jQuery.Deferred exception: fields.getItem(...).update is not a function updateFields@http://127.0.1.1:XXXX/lib/plugins/refnotes/admin.js:710:38
initialize@http://127.0.1.1:XXXX/lib/plugins/refnotes/admin.js:632:13
initialize@http://127.0.1.1:XXXX/lib/plugins/refnotes/admin.js:1013:20
@http://127.0.1.1:XXXX/lib/plugins/refnotes/admin.js:1091:24
e@http://127.0.1.1:XXXX/lib/exe/jquery.php?tseed=34a552433bc33cc9c3bc32527289a0b2:2:30005
l/</t<@http://127.0.1.1:XXXX/lib/exe/jquery.php?tseed=34a552433bc33cc9c3bc32527289a0b2:2:30307
 undefined
dwp-forge commented 4 years ago

I would suspect something goes wrong with deferred JS execution. Which versions of DW and RefNotes do you use?

remygithub commented 4 years ago

Running DW Release 2020-07-29 "Hogfather" and RefNotes version 2020-08-10.

I tried disabling defer_js but no change: config settings still unavailable.

Is there anything else I could try to test your hypothesis on the deferred JS execution?

dwp-forge commented 4 years ago

Given the latest versions of both DW and plugin, and the fact that defer_js had no effect (BTW, did you wipe the cache?) I would assume that deferred JS is not the issue. In #52 multiple people tried these versions and it worked okay for them. There should be something specific to your setup. I use FF 78 myself and that works fine, but maybe you could try another browser. Since we talk about JS error I doubt it makes much sense to look into server side PHP code.

If you are familiar with JS, try to add some logging around the place of the error. To start with, I would look what is field name and value returned by fields.getItem(name) right before the error.

remygithub commented 4 years ago

I tried it in Chrome -- same result.

TBH I don't have any JS or PHP experience...can't say that I understand how all of this works.

That said, I've written quite a bit of code over the past 20y and I do not mind learning new things, especially if it helps my work -- I absolutely need your plugin for a current project! I apologize for not saying it earlier: thank you for developing and sharing it!

So far I changed updateFields() (containing he first error, around line 710) as follows:

function updateFields() {
            jQuery('#name-namespaces').val(current.getName());
            jQuery('#rename-namespaces').prop('disabled', current.isReadOnly());
            jQuery('#delete-namespaces').prop('disabled', current.isReadOnly());

            console.group("Refnotes Debug");
            for (var name in fields.items) {
                console.log("\n updating field...");
                console.log(name);
                console.log("\n with item...");
                console.log(fields.getItem(name));
                fields.getItem(name).update();
            }
            console.groupEnd()
        }

Everything seems fine for fields style, font, etc. until it gets to shuffle, which does not have an update() function:

Sorry for the rudimentary debugging experience in JS. Let me know if the above is helpful or if you want me to do something else.

dwp-forge commented 4 years ago

Well, we start to get somewhere. That shuffle thing looks rather surprising as there is no such field. The fields are added to a hash map in initialize() lines 599-624. There you can see all names that should show up during updateFields() call, and shuffle is not there. BTW, congratulations on not having to deal with JS over the past 20 years ;)

image

I suspect that some other plugin injects shuffle into Array prototype, which is usually frowned upon. Try to grep your plugin directory for shuffle to see if that's the case. Temporarily disable plugin messing with the prototype if you find one to see if that helps.

remygithub commented 3 years ago

You were right about interference but it was the sprintdoc template causing the problem:

$grep -Ril shuffle lib
  lib/tpl/sprintdoc/js/base/spc.js
  lib/scripts/jquery/jquery-ui-theme/smoothness.css

In lib/tpl/sprintdoc/js/base/spc.js:

    200 // + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    201 // shuffle func for random values
    202 // + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    203 Array.prototype.shuffle = function(){
    204     var tmp, rand;
    205     for(var i =0; i < this.length; i++){
    206         rand = Math.floor(Math.random() * this.length);
    207         tmp = this[i];
    208         this[i] = this[rand];
    209         this[rand] =tmp;
    210     }
    211 };

After disabling the sprintdoc template Refnotes config worked as expected! Too bad about sprintdoc as I really liked it...

Thank you for your guidance on solving the issue! Remy

PS: what is the preferred way to get help in configuring Refnotes?

dwp-forge commented 3 years ago

If you really like that template, you can try a workaround suggested in the SO page I linked above:

Object.defineProperty(Array.prototype, 'shuffle', {
    var tmp, rand;
    for(var i =0; i < this.length; i++){
        rand = Math.floor(Math.random() * this.length);
        tmp = this[i];
        this[i] = this[rand];
        this[rand] =tmp;
    }
});

As for the configuration, you could give an example of formatting you look for. Just create some dummy DW page using whatever formatting you need. I will see how close RefNotes can get to that.

dwp-forge commented 3 years ago

Apparently, since 2009 when admin page was created there was some progress in JS. In ECMAScript 6 (released in June 2015) they got a proper Map object, so here is no need to cook-up your own implementation anymore. Also the page from which I copied HashMap updated quite a bit and doesn't use Array as a base container anymore. I guess, it's time to update that part in RefNotes as well.

remygithub commented 3 years ago

I tried the re-write of shuffle you suggested and sprintdoc does not seem to play nice.

admin.js bugs out way before reaching line 710 like before and I get the following errors:

Uncaught ReferenceError: DOKU_BASE is not defined
    sendRequest http://127.0.1.1:XXXX/lib/plugins/refnotes/admin.js:196
    loadSettings http://127.0.1.1:XXXX/lib/plugins/refnotes/admin.js:224
    initialize http://127.0.1.1:XXXX/lib/plugins/refnotes/admin.js:1024
    <anonymous> http://127.0.1.1:XXXX/lib/plugins/refnotes/admin.js:1091

Line 196 in admin.js: url : DOKU_BASE + 'lib/exe/ajax.php',

There are also weird and changing syntax errors in js.php:

That js.php script has only 490 lines but it seems to source a bunch of other scripts. The weird parts are that the template related script seems to have only comments and that the syntax errors listed above are changing when changing settings on the DW config page.

Anyway, all of the above seem related to sprintdoc and RefNote works when that template is not used.

Let me know if you want me to test anything when you decide to update admin.js

remygithub commented 3 years ago

As far as configuring Refnotes, I just want to have a Bibliography/References section that combines footnotes and citations in a format like IEEE, for example.

Here is an example for referring page:

====== Testing References ======
Testing footnote1[(Footnote_1)] and footnote2[(Footnote_2)]

Citing reference1 [(qpm_tomography:park_diffraction_2006)] and reference2 [(qpm_tomography:pan_computational_1983)].

Again citing reference1 [(qpm_tomography:park_diffraction_2006)] and reference2 [(qpm_tomography:pan_computational_1983)].

===== References =====
[(Footnote_1>FIrst footnote)]
[(Footnote_2>Second footnote)]

Bibliography page in :refnotes: namespace (sorry, I copied an existing page):

====== Initial Work On QPM Tomography ======
<refnotes qpm_tomography> inherit: :cite: </refnotes>

<code bibtex>
@Comment{refnotes,
  namespace = "qpm_tomography"
}

@article{park_diffraction_2006,
    title = {Diffraction phase and fluorescence microscopy},
    volume = {14},
    url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-14-18-8263},
    doi = {10.1364/OE.14.008263},
    number = {18},
    urldate = {2014-04-08},
    journal = {Optics Express},
    author = {Park, YongKeun and Popescu, Gabriel and Badizadegan, Kamran and Dasari, Ramachandra R. and Feld, Michael S.},
    month = sep,
    year = {2006},
    keywords = {Fluorescence microscopy, Microscopy},
    pages = {8263--8268},
    file = {oe-14-18-8263.pdf:/home/remy/Zotero/storage/B4KZFRSC/oe-14-18-8263.pdf:application/pdf;Opt. Express Snapshot:/home/remy/Zotero/storage/4EFR4AG9/abstract.html:text/html;Opt. Express Full Text PDF:/home/remy/Zotero/storage/ENH4TXIA/Park et al. - 2006 - Diffraction phase and fluorescence microscopy.pdf:application/pdf}
}

@article{pan_computational_1983,
    title = {A computational study of reconstruction algorithms for diffraction tomography: {Interpolation} versus filtered-backpropagation},
    volume = {31},
    issn = {0096-3518},
    shorttitle = {A computational study of reconstruction algorithms for diffraction tomography},
    doi = {10.1109/TASSP.1983.1164196},
    abstract = {From the standpoint of reporting a new contribution, this paper shows that by using bilinear interpolation followed by direct two-dimensional Fourier inversion, one can obtain reconstructions of quality which is comparable to that produced by the filtered-backpropagation algorithm proposed recently by Devaney. For an N × N image reconstructed from N diffracted projections, the former approach requires approximately 4N FFT's, whereas the backpropagation technique requires approximately N2FFT's. We have also taken this opportunity to present the reader with a tutorial introduction to diffraction tomography, an area that is becoming increasingly important not only in medical imaging, but also in underwater and seismic mapping with microwaves and sound. The main feature of the tutorial part is the statement of the Fourier diffraction projection theorem, which is an extension of the traditional Fourier slice theorem to the case of image formation with diffracting illumination.},
    number = {5},
    journal = {IEEE Transactions on Acoustics, Speech and Signal Processing},
    author = {Pan, S. X. and Kak, A.C.},
    year = {1983},
    keywords = {Image reconstruction, Interpolation, Tomography, Acoustic diffraction, Biomedical imaging, Reconstruction algorithms, Lighting, Backpropagation algorithms},
    pages = {1262--1275}
}
</code>

I get: DW_Refnotes_Debug_Fig1

instead of the citations section to have

[1] Y. Park, G. Popescu, K. Badizadegan, R. R. Dasari, and M. S. Feld, “Diffraction phase and fluorescence microscopy,” Opt. Express, vol. 14, no. 18, pp. 8263–8268, Sep. 2006,

[2] S. X. Pan and A. C. Kak, “A computational study of reconstruction algorithms for diffraction tomography: Interpolation versus filtered-backpropagation,” IEEE Transactions on Acoustics, Speech and Signal Processing, vol. 31, no. 5, pp. 1262–1275, 1983.

Also

Anyway the current output is not what I am used to and I find it to clutter the page. That said, it is not the end of the world.

Finally, a useful enhancement would be for the pop-up to display the title and the abstract (if available in the bibtex reference -- see above) for when an internet connection is not available.

Thanks again for helping me figure this thing out!

dwp-forge commented 3 years ago

Sorry, my bad. I missed one more layer of wrapping in that example. It should be:

Object.defineProperty(Array.prototype, 'shuffle', {
    value: function() {
        var tmp, rand;
        for(var i =0; i < this.length; i++){
            rand = Math.floor(Math.random() * this.length);
            tmp = this[i];
            this[i] = this[rand];
            this[rand] =tmp;
        }
    }
});

To get formatting closer to what you want try to inherit harvard styling for qpm_tomography namespace:

...
===== References =====
[(Footnote_1>FIrst footnote)]
[(Footnote_2>Second footnote)]

<refnotes></refnotes>

<refnotes qpm_tomography>
inherit: harvard
</refnotes>

The result:

image

remygithub commented 3 years ago

The Object.defineProperty change to lib/tpl/sprintdoc/js/base/spc.js worked: now I can use sprintdoc with refnotes!

The changes to Testing References worked out to what I wanted as well after some tuning of :harvard:.

Thank you again! Let me know if there is any way I can pay back you kindness in helping with this.

dwp-forge commented 3 years ago

You are welcome :)

dwp-forge commented 3 years ago

Migrated to ES6 Map in 20b44e6.