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issue commentnglviewer/ngl

adding a molecule to the stage disables the ability to drag/rotate proteins individual

@garyo

thank you for the quick answer. What do you mean by "in your codepen" If you mean the first codepen this is just an minimal working example to show if you set addToStage === true the molecules cannot be dragged/rotated individually any longer.

The secon pen shows our intent. The idea is to create a new stage object based on a selection

const selection = new NGL.Selection(':' + chain + ' and ' + residues)
const struc = stageObj.structure.getView(selection)
const comp = stage.addComponentFromObject(struc)

We need that new stage object and cannot simply just hide the parts of the molecules we are not interested in because we want to rotate it using principal axis. We found out if we just hide them .getPrincipalAxes() gets executed on the whole protein which leads to the "wrong" rotation.

Thus

const pa = struc.getPrincipalAxes()
comp.setRotation(pa.getRotationQuaternion())

In the end we need to show the molecule parts side by side which is also only working if we have created an new stage object. If we just hide the unwanted molecules parts we do not get the molecules evenly spaced from each other.

 const centre = comp.getCenter()
 const new_posn = [(0-centre.x)-xOffset, 0-centre.y, 0-centre.z]
 comp.setPosition(new_posn)

Everything works as expected but now we cannot drag/rotate the molecules individually any longer. https://github.com/plotly/dash-bio/pull/496#issuecomment-671076151 If you want to try it out in the python dash app: https://github.com/IvoLeist/dash_ngl

I hope this makes it more clear?

IvoLeist

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pull request commentplotly/dash-bio

add dash-ngl

Glad that you like it. Unfortunately not directly So far I only asked via filing a github issue

They merged a PR 4 days ago so it still looks maintained.

But if you have some contacts to the NGL core devs feel free to use them it might speed up things a little :crossed_fingers:

IvoLeist

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pull request commentplotly/dash-bio

add dash-ngl

@jackparmer

Just merged a quick workaround into my master

The new radio selection is connected to the react component in that way that it ether adds the structure to the stage (for the side by side view) or not (for the normal view). In the latter case the molecules can be dragged/ rotated individually by ctrl and left/right click. ! Note: it only rotates if you click on the molecule not in the box you see a mouse over if you have the molecule selected correctly.

Let me know if it works for you as well :crossed_fingers: Before adding this workaround to the PR I would wait for the answer of the guys from ngl since this hack does not feel "right". Anyway I am happy that it at least works in the not side by side view :)

dash-ngl_covid_moveIndependently

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commit sha a774b052d67f03fc665e1e969d5d4f61f85ceb85

provide the option to switch between side by side view and normal view

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issue commentYvee1/hascard

hascard: setupTerm: Couldn't look up terminfo entry "st-256color"

Hey Yvee1 I finally found the time to give it another go and yes using stack everything works as expected :)

Regarding my idea I did not found the time yet to implement that. But I let you know as soon as I have done it :nerd_face:

IvoLeist

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issue commentlilyminium/dash-ngl

join forces? Help wanted for on-going PR @dash-bio

Thank you for the kind words. Yeah, indeed !

Ok thank you lets see what I can recycle from your component ;D

Fair enough, I understand that. The same holds true for me but I spend so much time in that component / that Pull request I at one point just want to have it out there :nerd_face:

IvoLeist

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issue openednglviewer/ngl

adding a molecule to the stage disables the ability to drag/rotate proteins individual

Hello ngl maintainers,

first thank you for your work and even though your follow up molstar is already out there it is good to see that this is still maintained :)

Now to my question: At my old lab I developed and ngl component for dash which caught the interest of the dash-bio team asking me for a PR. This PR is still on going https://github.com/plotly/dash-bio/pull/496

And one of the issue we cannot seem to solve right now is why does adding a molecule to the stage disables the ability to drag/rotate proteins individually? See that codepen

//do not add to stage --> mols can be moved/rotated indepently by
// drag-ctrl+shift + right click
this.loadStructure("1blu","A","red",false)
this.loadStructure("1crn","A","blue",false)

//add to stage --> mols can only be moved/rotated together
// this.loadStructure("1blu","A","red",true)
// this.loadStructure("1crn","A","blue",true)

We are kinda forced to add them to the stage for enabling the user to see the proteins side by side. See that code pen

So what would help us: Either someone can explain how to preserve the individual protein movements although they are added to stage or an idea how we could autorotate the molecules using principal axis and show them side by side w/o adding the molecule to the stage?

Best, Ivo

created time in 2 days

pull request commentplotly/dash-bio

add dash-ngl

Used the "soft" Corona Lockdown to figure out what the difference between that codepen -> structures can be moved independently my codepen --> structures can be moved only together

My finding are summarized in this codepen

//do not add to stage --> mols can be moved indepently by
// drag-ctrl+shift + right click
this.loadStructure("1blu","A","red",false)
this.loadStructure("1crn","A","blue",false)

//add to stage --> mols can only moved together
// this.loadStructure("1blu","A","red",true)
// this.loadStructure("1crn","A","blue",true)

Why do I need to add the structures in my component to the stage?: -> In order to do the autorotation using principal components and show the proteins side by side See the codepen

Implications for the PR: To add the desired feature to move/rotate the proteins individual w/o breaking the app which already uses the component. I would suggest to add an extra button (variable in the React Component) which gives the user the option to decide if he/she wants the molecules shown side by side. Indicating that the side by side view is experimental and thus individual protein movements/rotations by mouse using drag-ctrl+shift + left/right click do not work.

IvoLeist

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issue openedlilyminium/dash-ngl

join forces? Help wanted for on-going PR @dash-bio

Hey lilyminium,

I hope you are doing well?

you might remember our cross-talk in end of January?

Thanks to twitter my dash-ngl component got recognized by the guys from plotly and since then there is a PR on-going which I had to abandon because I left the group to start my PhD in Barcelona :sunglasses:

So long story short: If you have some time and still interested in the dash-bio library and playing with NGL I would love to merge your component with mine?

Apparently they want to use it e.g. in Corona research so this could be our way to contribute to tackling that annoying virus !

Awesome to hear that you got this component working in your app! I'd love to see screenshots if you can share.

Also curious if you would like to wrap up this PR, or if you have any guidance for our team if we do.

I'm interested in making a Dash app that plots these pdb files and compares the 3 different molecule renderers in Dash Bio (dash-ngl, dash-speck, and dash-mol3D):

https://deepmind.com/research/open-source/computational-predictions-of-protein-structures-associated-with-COVID-19

Just scroll down in the PR till the very end to see in which issues you could help us.

But do not feel pressured if you do not have time or are not interested just close this issue ;D

Best, Ivo

created time in 3 days

pull request commentplotly/dash-bio

add dash-ngl

@xhlulu You were right renaming is possible but only if you hardcode it into the list. I just updated my example app accordingly: https://github.com/IvoLeist/dash_ngl/commit/a1bdd83cb7993708a040c33adc88c9d192904935

So if you pull it now and put in the show multiple structures you see that two structures. Make sure that you select for each a chain e.g. MPRO.A_NSP2.A

What I learned from this: Using an underscore to separate strings was maybe a bad idea... I wanted to use something which cannot be exploited for code injection so I refused to use $, | etc. but maybe an equal sign would be better :thinking:

To give you some context why my example is like that. In the actual app the combination of molecule chains is generated on the fly. Thus, we needed some clever way to specify which molecules/parts have to be used. And the best solution we came up with was to just sent a string from the backend to the frontend. So for testing this example app was perfect but for actual usage as a Mol3D replacement (?) I guess it would be better to use the dash multi value dropdown.

The only issue I have with that how would I "specify a chain/ residues range/ highlight chosen residues/ atoms"? Like it is done now: e.g. 6CHG.A:1-450@a50,a100,a150_3K8P.D Anyone has an idea? :thinking:

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pull request commentplotly/dash-bio

add dash-ngl

@jackparmer This is definitely possible to expose these properties to the dash component I actually did it for the x axis spacing between each molecule chain. So the user can decide on its own how much the chains should be separated from each other but doing everything with Buttons feels to hacky for me. But maybe it is still a good idea to expose that settings if user want to hardcode the positioning of several molecules (?)

I would rather suggest to look deeper into my JS coding to see what is different to the first code pen and mine. Since it works flawlessly in the one of xrobin (https://codepen.io/xrobin/pen/wXmGmm)

Since my time is right now quite limited I have asked the colleague in which app that component is working flawlessly. Maybe he can help :crossed_fingers:

IvoLeist

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pull request commentplotly/dash-bio

add dash-ngl

@xhlulu that is interesting using my upload your M_protein.pdb gets ubploaded correctly but not the whole filename get inserted in the dropdown but just protein. Looking at the code it is pretty obvious why this happens:

This part (shown below) gets the pdb_id directly from the file. Maybe this is not a a good idea if you want users to allow custom made pdb files.

pdb_id = content.split('\n')[0].split()[-1]
        if 'data_' in pdb_id:
            pdb_id = pdb_id.split('_')[1]
            ext = 'cif'

Have not tried yet what is happening if you hardcode it, will try it soon.

IvoLeist

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pull request commentplotly/dash-bio

add dash-ngl

@jackparmer In theory it should be possible see for example that code pen https://codepen.io/xrobin/pen/wXmGmm

Here using drag-ctrl+shift + right click = pans drag-ctrl+shift + left click = rotates the cylinder and structure independently but I cannot really explain why this functionality seems to be disabled in my implementation.

In my code pen they are also not independently dragable ... https://codepen.io/IvoLeist/pen/WNQEGML on a quick glance I was not able to spot the difference between this two but if you are able to modify my pen in such a way that the structures are dragable I guess it should not be difficult to change the dash-ngl component accordingly :v:

IvoLeist

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pull request commentplotly/dash-bio

add dash-ngl

@jackparmer Glad that you like it was actually quite some effort to get the orientation and the distance right for a nice side by side view. I just tried it and it seems to be that I at one point deactivated the dragging or I forgot the shortcut combination to make it draggable 😄

I just pushed the newest version (including NSP2,NSP4 etc.) to my repo: https://github.com/IvoLeist/dash_ngl Unfortunately right now only NSP2,4,6 are working since it at the moment only supports structures with the 4 letter pdb code.

For sure - actually it would be awesome! Would love to contribute in any way fighting covid / helping research in general. Let me know if you need some extra features (like the dragging) and I can see how I can support you with that

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pull request commentplotly/dash-bio

add dash-ngl

Ok I was just too intrigued by it and hat too see the structures myself. @jackparmer I made a picture for you so you understand better what the special power of my component is. You see on it how easy it is too show several protein structures (works only if you select a chain) side by side. This was not possible with any of the existing viewers. That's why I have built it on my own. For the general public this feature might be too niche and thus the whole component maybe too tailored to our specific use case. dash-ngl_covid_SideBySide

But you can also use it as normal viewer. Here the structures of NP4,NP6,NP8 are merged into one. Unfortunately they are not colored differently since this only works for chains but I guess this should not be too difficult to add that. dash-ngl_covid_merged What I would consider as a USP in comparison too the other viewers out there that mine is checking if a structure was already loaded into the frontend and if so it does not load it again from the backend but directly from the frontend.

IvoLeist

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PR merged IvoLeist/dash_ngl

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pull request commentplotly/dash-bio

add dash-ngl

@alexcjohnson @Marc-Andre-Rivet @shammamah @rpkyle Hey guys,

I am sorry that I was suddenly so silent but I was quite "spontaneously" switching my working place (CNAG) and my place to live (Barcelona 😎). In order to have a good start in my PhD I had to catch up as quickly as possible with the tools they are using there. Since I like dash I'll try to integrate in the web app I am building there but I cannot promise anything because their apps are at the moment React only but developing that component did definitely help in getting into React.

Short story short I guess I unfortunately won't find too much time to wrap up that PR. Doing only some bugfixes for my old employer. But since It works kinda flawlessly in the app of my old employee it should not be too difficult to polish to finally merge it ;D. I let you know as soon as it is published. Maybe he finds the time to finish that PR?

@jackparmer cool to hear that you show interest if it is only a short rendering of the molecule. I guess my toy app in my repo should work out of the box https://github.com/IvoLeist/dash_ngl If you have some troubles to let it run just file an issue there so we do not Spam too much into that PR. Btw. this is actually a cool idea to show the power of my component. Should have done this anyway. So I would appreciate if you fork it and show me the results would be really interested.

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pull request commentpolybar/polybar-scripts

Add keyring (un)locker

Hello x70b1

thank you for your opinion.

yes on my search for a good solution I stumbled above the pam-gnupg project. But I somehow did not managed to preset the passphrase. Whichever settings I did pass kept asking me for the pass phrase although I have seen in the gpg keylist that the pass phrase is cached.

gnome-keyring on the other hand enables me to skip the pass phrase prompt as long the keyring is unlocked.

Additionally I am reluctant to unlock my keyring with my login password thats why I use the gnome-keyring with another password.

I might be a little paranoid but since my Laptop is at the moment my only computer and thus password store for everything I just want to be on the safe side

Don't you think that gnome-keyring "workaround" is a good solution? Why would you prefer pam?

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PR opened polybar/polybar-scripts

Add keyring (un)locker

Hey polybar users

first of all thank you for maintaining this awesome collection of polybar examples. I already took many of these for my setup so now it is time for me to give something back. And since we are in Barcelona in a "lockdown" situation at the moment...

Let me know if you are interested in that module so I can clean up the code/ make the naming more consistent that it fits in your collection.

Best, Ivo

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This is a community project. We write and collect scripts for polybar!

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A small collections of scripts that (un)locks a keyring

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issue openedYvee1/hascard

hascard: setupTerm: Couldn't look up terminfo entry "st-256color"

Hello Yvee1,

first thank you for sharing that idea on reddit. I am looking for a good terminal based flashcard application for a while already to learn Spanish (recently moved to Barcelona).

Thus, I would love to give it a try but unfortunately your snap does not support the st terminal? ❯ hascard hascard: setupTerm: Couldn't look up terminfo entry "st-256color"

My idea would be to trigger your app when opening a new terminal window. Meaning I would have to solve at least one Spanish vocab / grammar question before I can use the terminal.

Best regards, Ivo

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pull request commentplotly/dash-cytoscape

Pre-v0.2.0 PR: Improve readme, clarify yarn usage in contributing, update changelog, fix emails/tagging, upgrade package versions

I actually never tried the example but directly in our web app (not yet published/ open sourced) but as soon as you have merged it I can have a try if I still have access to the project if not I have just linked that PR in our project repo

xhlulu

comment created time in a month

issue commentplotly/dash-cytoscape

Clarify usage of yarn vs npm in contributing.md

Hey @xhlulu

sorry for being so silent in the last weeks but I am right now in a job transition phase and therefore very busy with preparing a proper handover + doing all the necessary paperwork for moving to Barcelona.

Anyway long story short: I just want to give you a heads up that at least in my old project building with Yarn lead to a buggy behaviour of the compound nodes. Meaning if I dragged a compound node I would not move any longer the whole comound node but each element individually

When using npm everything worked as expected.

Best, Ivo

xhlulu

comment created time in a month

pull request commentplotly/dash-cytoscape

Pre-v0.2.0 PR: Improve readme, clarify package management in contributing, update changelog, fix emails and references

Hey @xhlulu

sorry for being so silent in the last weeks but I am right now in a job transition phase and therefore very busy with preparing a proper handover + doing all the necessary paperwork for moving to Barcelona.

Anyway long story short: I just want to give you a heads up that at least in my old project building with Yarn lead to a buggy behaviour of the compound nodes. Meaning if I dragged a compound node I would not move any longer the whole comound node but each element individually

When using npm everything worked as expected.

Best, Ivo

xhlulu

comment created time in a month

push eventIvoLeist/dash_ngl

Ivo

commit sha 7f6334683a3b564f91310578a8b30dc7710dd7c1

rebuild the component

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startedhCoV-2019/pangolin

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issue commentpaul-nameless/tg

Voice recording buggy

Using

git clone https://github.com/paul-nameless/tg.git
cd tg
PYTHONPATH=. python3 tg/main.py

Everything works as expected :)

You can close that issue

IvoLeist

comment created time in 2 months

startedmicb25/dka

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issue commentpaul-nameless/tg

Voice recording buggy

Could not check it (?)

❯ git clone git@github.com:paul-nameless/tg.git Cloning into 'tg'... git@github.com: Permission denied (publickey). fatal: Could not read from remote repository.

Please make sure you have the correct access rights and the repository exists.

I installed the app via pip install

IvoLeist

comment created time in 2 months

issue openedpaul-nameless/tg

Voice recording buggy

First of all thanks a lot for this awesome application!

Unfortunately I have some troubles with the voice recording. Not sure if I ever will use it :D but thought you might be interested.

This was my first bug: ALSA lib pcm_hw.c:1829:(_snd_pcm_hw_open) Invalid value for card [alsa @ 0x5626bffac2c0] cannot open audio device default (No such device) default: Input/output error

Fixed with adding that line to my conf.py VOICE_RECORD_CMD = "ffmpeg -f alsa -i hw:0 -c:a libopus -b:a 32k {file_path}"

But there is still another one:

Guessed Channel Layout for Input Stream #0.0 : stereo Input #0, alsa, from 'hw:0': Duration: N/A, start: 1592929738.453123, bitrate: 1536 kb/s Stream #0:0: Audio: pcm_s16le, 48000 Hz, stereo, s16, 1536 kb/s [NULL @ 0x558585020e00] Unable to find a suitable output format for '/tmp/voice-2020-06-23' /tmp/voice-2020-06-23: Invalid argument

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startedcorona-warn-app/cwa-app-android

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pull request commentplotly/dash-bio

add dash-ngl

@Marc-Andre-Rivet, @rpkyle, @shammamah, @josegonzalez sorry for pinging you all but I was not sure where/whom to ask that question.

We recently deployed this component as a part of our new app. However, for some of our test users everything worked fine while for others the component run in plenty of errors. Tracked them down I realized that they all were related to webGL being either disabled or their GPU was on the black list. Thus, setting the correct flags in chrome (Brave) or changing the about:config in firefox fixes that bug.

The current work around is a big disclaimer box explaining the user when there is no structure appearing how they do have to change the settings of their browser. Obviously, I only want to show that box if the viewer runs in a webGL error, so do you have a good idea how to catch that error?

Do you maybe have some kind of best practice for your dash-bio/dash/plotly apps for catching that?

IvoLeist

comment created time in 2 months

issue commentplotly/dash-cytoscape

ImportError: cannot import name 'utils'

@xhlulu just wanted to confirm your suggestion worked for me in a venv/conda env as well :)

IvoLeist

comment created time in 2 months

issue openedplotly/dash-cytoscape

ImportError: cannot import name 'utils'

Description

When pip installing from master and importing it an ImportError arises

Steps/Code to Reproduce

pip install git+https://github.com/plotly/dash-cytoscape.git@master

import dash_cytoscape as cyto

Expected Results

No error

Actual Results

import dash_cytoscape as cyto File "/venv/lib/python3.6/site-packages/dash_cytoscape/init.py", line 12, in <module> from . import utils ImportError: cannot import name 'utils'

Versions

Dash 1.9.1 Dash Core Components 1.0.2 Dash HTML Components 1.8.1 ! Cytoscape errors out ! import dash_renderer; print("Dash Renderer", dash_renderer.__version) AttributeError: module 'dash_renderer' has no attribute '__version'

In order to resolve the issue:

https://github.com/IvoLeist/dash-cytoscape/commit/aaed204afb88332bdd9528cddbc4abc58f98f4da#diff-2eeaed663bd0d25b7e608891384b7298

@xhlulu Should I do a short PR or do you want to quickly fix that line?

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startedplotly/dash-cytoscape

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pull request commentplotly/dash-cytoscape

Add svg image generation

@xhlulu Fine for me let's go :rocket:

IvoLeist

comment created time in 2 months

pull request commentplotly/dash-cytoscape

Add svg image generation

@xhlulu there seems to be some flakyness with ci :grimacing:

selenium.common.exceptions.WebDriverException: Message: unknown error: Chrome failed to start: crashed.
  (unknown error: DevToolsActivePort file doesn't exist)
  (The process started from chrome location /usr/bin/google-chrome is no longer running, so ChromeDriver is assuming that Chrome has crashed.)
IvoLeist

comment created time in 2 months

pull request commentplotly/dash-cytoscape

Add svg image generation

@xhlulu just added the random print statement :crossed_fingers:

I haven't used npm in a while, so i'm not totally sure when it gets created.

When I installed it the first time I used npm and was tearing my hairs out why suddenly the compounds nodes were messed up... before I finally realized that I have to use yarn :man_facepalming:

IvoLeist

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push eventIvoLeist/dash-cytoscape

Ivo

commit sha 7267497e1b7c544538ff5837a7b403e64b9c4eae

added random print statement in usage-image-export.py to pass pylint

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pull request commentplotly/dash-cytoscape

Add svg image generation

Regarding:

Also, just to make sure: Have you ran npm run build:all before committing the last changes?

You meant yarn run build:all, right? If so, yes I have done that

Regarding:

I saw that you added package-lock.json; are you perhaps using npm? At the start of the project we settled on using yarn, so it would be great if we don't have multiple lock files. Let me know if you have any question about yarn.

I removed it

IvoLeist

comment created time in 2 months

pull request commentplotly/dash-cytoscape

Add svg image generation

Hi Ivo! Thank you for not only continuing this PR, but also adding substantial changes to support exporting in SVG. This is super appreciated.

Thank you @xhlulu for the encouraging words

These should be now all required changes meaning I am ready to merge :rocket: So :crossed_fingers: that all the test are completing successfully.

IvoLeist

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Ivo

commit sha bf343f22c539189ba1f3403a9fc403e8e0a8aaa7

added usage-image-export gif to README

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Ivo

commit sha ecb7f0e6e4eeefa4b8d90f4bc341b5a83c6d8949

resolved code linting issues

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Pull request review commentplotly/dash-cytoscape

Add svg image generation

     version=package["version"],     author=package['author'],     author_email=package['author-email'],-    packages=[package_name],+    packages=[package_name,package_name+".utils"],

I reverted it to the old one. I am not sure why added +".utils" there seems to have been an import issue in the past but somehow it is now working without the +".utils".

IvoLeist

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push eventIvoLeist/dash-cytoscape

Ivo

commit sha 102bf703fbe3f5a0537c3f7380405aed7cccbf34

moved cytoscape-svg into extra_index.js

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Pull request review commentplotly/dash-cytoscape

Add svg image generation

 /**- * JavaScript Requirements: cytoscape+ * JavaScript Requirements: cytoscape, cytoscape-svg  * React.js requirements: react-cytoscapejs  */+import cytoscape from 'cytoscape';+import svg from 'cytoscape-svg';

That is a good idea, I was not aware of the exta_index.js before. I just tried to add it to extra index.js and it works as expected :)

However, following that logic I guess it would be a good idea to put the plugins in an new file. On top it kinda feels wrong to enable the svg export feature with cyto.load_extra_layouts()

Since I do not 100% understand how to implement this I just added a plugins_index.js file as a reminder.

IvoLeist

comment created time in 2 months

pull request commentplotly/dash-cytoscape

Add svg image generation

Just for the records a small disclaimer:

I have not managed to modify the react code in such a way that I was able to generate the string of the svg. Therefore, I added in usage-image-export and in Cytoscape.react.js the disclaimer that for the option 'store' only jpg and png are supported.

Maybe someone else has an idea or want to add this in a follow up release.

IvoLeist

comment created time in 3 months

pull request commentplotly/dash-cytoscape

Add svg image generation

@xhlulu These are the ones you were mentioning, right? If so I just added them.

  • [x] "In demos, it would be nice to have a usage-image-export.py example that shows how to build a simple dash app and use the image functionality in various ways."

  • [x] "Once you made that app, could you add it test_usage to make sure the app renders correctly? It should simply be 2 lines of code, since all it does is rendering (it doesn't actually test any callback)."

IvoLeist

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push eventIvoLeist/dash-cytoscape

Ivo

commit sha e55f1595b2f81542cec50fc28b0f5877bf414870

added usage-image-export.py to test_usage

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Ivo

commit sha aa5d5b96de9dc1fd39e3148c268e8f0f10a4a77f

updated comments in Cytoscape.react.js, added usage-image-export.py based on usage-event.py

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Pull request review commentplotly/dash-cytoscape

Access cytoscape.js png/jpg image generation API from dash

 class attribute).     exhaustively documented in the Cytoscape.js docs. Although methods such     as `cy.elements(...)` and `cy.filter(...)` are not available, the selector     string syntax stays the same.-- layout (dict; optional): A dictionary specifying how to set the position of the elements in your+- layout (dict; default {name: 'grid'}): A dictionary specifying how to set the position of the elements in your

Auto generated

clegaspi

comment created time in 3 months

Pull request review commentplotly/dash-cytoscape

Access cytoscape.js png/jpg image generation API from dash

 class Cytoscape(Component): - id (string; optional): The ID used to identify this component in Dash callbacks. - className (string; optional): Sets the class name of the element (the value of an element's html class attribute).-- style (dict; optional): Add inline styles to the root element.-- elements (list; optional): A list of dictionaries representing the elements of the networks.+- style (dict; default {width: '600px', height: '600px'}): Add inline styles to the root element.

Auto generated

clegaspi

comment created time in 3 months

push eventIvoLeist/dash-cytoscape

Ryan Patrick Kyle

commit sha 77e9a6ee67ed9b2a6bc8561ef6b30022bd987e74

Update dashCytoscape to v0.1.1 (#77)

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Shammamah Hossain

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Replace all instances of plot.ly with plotly.com.

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Marc-André Rivet

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Merge pull request #79 from plotly/update-plotly-url

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Xing

commit sha 8145b89e59c6913734e0896d365e170454b0ccfe

Fix failing tests (#87) * Change dragging offset to stay in screen * flake8 & pylint Also changed exit(1) to sys.exit(1) in usage-phylogeny.py

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Ivo

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fetched and merged with upstream/master

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startedvsls-contrib/codetour

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pull request commentplotly/dash-cytoscape

Add svg image generation

@alexcjohnson can you resolve these two conflicts? Or what do I have to do to resolve them?

IvoLeist

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Ivo

commit sha dbab9a3b7b6054244b3d4ef6d88bdcf829a1a263

updated changelog, moved examples into demos/, updated E-mails in package.json

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pull request commentplotly/dash-cytoscape

Access cytoscape.js png/jpg image generation API from dash

@clegaspi no worries I have already created a new PR

@alexcjohnson Done

clegaspi

comment created time in 3 months

PR opened plotly/dash-cytoscape

Add svg image generation

About

This PR is an extension of this PR which provides access to the existing Cytoscape.js image generation APIs, cy.png() and cy.jpg(), via Dash callbacks. It allows the current view of a Cytoscape graph to be saved as an image, stored as a base64 string or data URL, and/or downloaded as a file. On top it enables the generation of an .svg file using that cytoscape plugin

Description of changes

This PR adds to the generateImage and imageData properties the possibility to generate an svg image.

Pre-Merge checklist

  • [ ] The project was correctly built with yarn run build:all. !npm is buggy
  • [ ] If there was any conflict, it was solved correctly
  • [ ] All changes were documented in CHANGELOG.md.
  • [ ] All tests on CircleCI have passed.
  • [ ] All Percy visual changes have been approved.
  • [ ] Two people have :dancer:'d the pull request. You can be one of these people if you are a Dash Cytoscape core contributor.

Reference Issues

No current issues related to this PR.

Other comments

Please note that it is only building correctly if yarn is used. If you use npm and need compound nodes to be fixed at one place building dash-cytoscape with npm will result in unexpected behaviours ( = freely floating children nodes)

+14950 -595

0 comment

16 changed files

pr created time in 3 months

pull request commentplotly/dash-cytoscape

Access cytoscape.js png/jpg image generation API from dash

@alexcjohnson I tried it, but I guess @clegaspi fork does not allow pushes (?)

git push clegaspi image_download

git@github.com: Permission denied (publickey). fatal: Could not read from remote repository.

Please make sure you have the correct access rights and the repository exists.

clegaspi

comment created time in 3 months

pull request commentplotly/dash-cytoscape

Access cytoscape.js png/jpg image generation API from dash

@clegaspi would this also hold true if some one else (me) does this changes ? So my idea would be:

  • I do a PR on your fork
  • you merge it and push it to this PR
  • so @xhlulu could merge it?

Or is this too much hassle? If you do not care about being the owner of this PR I could also do another PR which includes this one giving you at least some credits in the README ;D

Btw. congrats to your new job!

clegaspi

comment created time in 3 months

pull request commentplotly/dash-cytoscape

Access cytoscape.js png/jpg image generation API from dash

@xhlulu good to see that the codebase of cytoscape is not dormant.

Is there any way to commit to an existing PR (to this one) since I would love to have also the ability to generate an .svg or should I do a new PR as soon as this is merged?

If you want to test it, see my fork and execute: https://github.com/IvoLeist/dash-cytoscape/blob/master/usage-imageDownload.py

Best, Ivo

clegaspi

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startedIvoLeist/dash_ngl

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push eventIvoLeist/dash-bio

Ivo

commit sha b6701baaf2b78241f0bd61cc444e7ae34ce023c5

added spacing after // in NglMoleculeViewer.react.js

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Ivo

commit sha ab6a80189dc5eecd40f74adfb05cc69b69431046

renamed range to aaRange to avoid confusion, changed JS vars to camelCase to comply to naming conventions

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Ivo

commit sha 011db6f8adc7e3e88b5f99502b8203f516e1ac3b

renamed range to aaRange to avoid confusion, changed all JS variables to camelCase to comply to naming conventions, replaced in the test the default dangerous value empty list with None

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issue commentmolstar/molstar

Load files remotely

Hello Caioss,

since in pandemic times speed is everything I felt so free to answer you. Disclaimer: I am not part of molstar but a user(developer) of web apps using NGL.

If you just need the basic visualization features of NGL maybe my Python Dash component could help you (?). Right now, it is based on ngl and should be part of dash-bio soonish.

But in the future I might port it to Molstar but before these issues https://github.com/molstar/molstar/issues/20, https://github.com/molstar/molstar/issues/23 need to be adressed.

Good luck with your research!

Best, Ivo

caioss

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Ivo

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removed tabbed layout

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pull request commentplotly/dash-bio

add dash-ngl

@Marc-Andre-Rivet the test 13 in ideogram is again "flaky" (?) but this time it happened in python-3.6

Results (449.03s): 69 passed 1 failed - tests/integration/test_ideogram.py:13 test_dbid001_displayed_chromosomes

Some information to the latest push: We realised in our app that once an image downloaded is selected the download handler gets triggered constantly this push fixes it. On top I added an integration test, which tests the download functionality

If you wonder why I added dash-main/ to the .gitignore: I had to update my venv with the requirements.txt from dash-main because the test rotate structure and reset it (dbn_16) was failing before. No clue which of the building dependencies caused that issue... anyway it is now working :)

IvoLeist

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Ivo

commit sha aecb08a69bda6062bb1976fac696961aadae9baf

added reset downloadImage flag to prevent constant retriggering of the download handler & integration test for downloading

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Ivo

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added reset downloadImage flag to prevent constant retriggering of the download handler

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Ivo

commit sha fb48d5a73eae10cb701eab9eda9610cb024103ea

rebuild it using yarn fixed compound nodes issue

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