janelia-flyem / dvid-console Goto Github PK

After the DAG image has been downloaded, the arrow heads in the DAG are no longer filled.

Right now, if you accidentally make two repos with the same name, the webconsole URL pattern does not serve you well as it uses the name of the repo in the URL. This can leave you without webconsole access to one or more of your repos.

(because of other reasons I need to debug I can't remove the extra repo locally ; DVID shuts down mid-API-call when I try to do so)

Add a mechanism that will enable the admin buttons in the dvid console. This should be a simple mechanism that allows someone in the know to turn the buttons on, but keep general users out of the administrative functions.

When adding a new data instance it no longer shows up on console unless you refresh/reload the page manually. This happens even if displaying all non-default data instances. Wouldn't be so bad if after adding the new data instance if it would notify you that it was successful. Instead the add data instance UI just disappears and without it updating on the list of data instances, you are kind of left hanging if it even successfully was added.

The current barebones README should be updated to reflect the new build procedure -- how one goes about getting a nice static website directory that can be used as an option to the "dvid serve" command.

When you visit a repo and see the instance list, for some types it shows their actual name (like imagetile). For others it breaks that apart into logical components (like "array" "8bit"). For none of them does it make it apparent what the parameters used to create that instance were, making it hard to look at one as a guide for how to make others. It'd be great for the WebUI to show this again (even if all it does is provide a handy link to the APIcall to get the JSON description)

(This might be an issue with my browser, rather than the viewer code.)

When evaluating a segmentation, it's sometimes important to know exactly where the superpixel/body boundaries are with pixel-level accuracy. This is hard right now because the the images appear anti-aliased in the viewer. For example:

Add the version of the console to the admin page, se we can easily tell what version of the console is being used when trying to support problems.

When on admin page and DVID server gets shutdown or restarted, an alert box appears, presumably to tell the user that the server is down. On Chrome, I see the alert box (red rectangle at top) but no text in box to say what's being alerted.

There are some bugs with the collapsing of the "_n" data instances in the console.

1. The regex is only looking for a single digit after the _ so “tiles_10" would not be hidden. Should be an easy fix, but only thought of it after deployment.
2. If you have a bunch of imageblk data instances called “testing_n” and you create an annotation called “testing_n+1” that will get hidden as well. (should be rare case)
3. The show / hide icon is now present at the top of the Data Instance column whether there is something to show or not. (Another easy fix that I thought of after deployment)

We need to add a version check on the console, so that when it starts up it checks the version of the dvid server. If the server is too old, then it should refuse to start and if the server is too new, then it should display a warning that things might be broken.

The README says I can provide a -webclient flag when I start the dvid command... But this doesn't seem to work:

dvid -verbose -webclient=/path/to/unpacked/dvid-console serve /path/to/dvid/data

When I try this, I get flag provided but not defined: -webclient

Is this an issue with dvid - where it definitely should have this flag, but it's not working - or is this README out of sync with dvid?

If dvid is fine, what's the best way to specify the web client now?

add an interface to allow people to add information to a specific node log from within the dvid console.

I tried to create a data instance with the 'versioned' checked off, but the new data instance was still versioned.

Right now, local configs are included in js/utils/config.js, which gets minified in the deployed bundle and can't be practically edited. Need to think about how to exclude this from the bundle and still reference it everywhere it needs to be referenced in the minified bundle. Also needs to be excluded from git.

When you go to the DVID landing page for a repo, the data instances are alphabetized grouped by data type (which is good). However, the data types seemed to be alphabetized into two seemingly arbitrary groups. Eg, imagetile and labelblk precede annotation, keyvalue, and labelvol. Can we get them alphabetized all together?

I tried to create an annotation data with other data instances selected in the sync list. But the new data instance is not synced correctly. Not sure if I did anything wrong.
Another suggestion: it will be appreciated that any function that does not work as expected can be removed until it's fixed. It has caused some troubles for me, at least for a couple of times.

It would be nice to have a dialog pop-up if "branch" is chosen, preferably with initial note for the newly created node.

For creating datainstances--always creates unversioned atm.

After adding a few descendent versions, I'm unable to see a commit message on mouseover of a node (f5052) on the right of the DAG for AL-7 on tem-dvid.int.janelia.org:7400. I was able to see it earlier, so not sure if this is a browser issue or problem with the code. I'm running most recent Google Chrome [Version 46.0.2490.86 (64-bit)] on Mac 10.9.5.

When navigating the DAG and doing mouse down on a node, there doesn't seem to be a way to see the "note" property attached to the node.

Currently the list of data instances is not sorted. This feature request is to alphabetically sort them, to make it faster to see if a given instance is present in the repo.

• remove border around SVG
• fix node text size and alignment

There seems to be a lag with the latest code, that is stopping the DAG from drawing correctly the first time a user switches from one repo to another. For example, switching from:

http://emdata1:8500/#/repo/99ef22cd85f143f58a623bd22aad0ef7

to

http://emdata1:8500/#/repo/0c8bc973dba74729880dd1bdfd8d0c5e

results in the incorrect DAG, but then moving to:

http://emdata1:8500/#/

and back to:

http://emdata1:8500/#/repo/0c8bc973dba74729880dd1bdfd8d0c5e

fixes the problem.

This can lead to awkward behavior when trying to drag the Z bar or dragging the region of interest in the inset ROI window.

This might be a regression bug--but either way this is a necessary feature

Seen on Mac Safari, FIrefox. The node log list depopulates when you hover over a node in the version DAG. Occasionally repopulates a single line on hover for some nodes. Specifically seen when I was looking at http://emdata2:7000/#/repo/30021a3ff14f4da5b8f455cd8d4b0be9.

To aid in navigation of the site we should add a breadcrumb trail to each page.

Please launch the viewer by choosing the center of the segmentation bounding box.

There should be a download button that will allow people to download the DAG as an SVG.

Add a button similar to the branch button that will lock the node with the commit command.

Hi,
One of my DVID installs uses nginx in front for SSL termination; the head of my config has the hostname, the httpAddress is set to 0.0.0.0:8001
I am exposing DVID over both http and https with nginx in front. My nginx config looks like this:

proxy_cache_path /var/raid/dvid/dvid-cache levels=1:2 keys_zone=dvid_cache:100m max_size=10g inactive=1h use_temp_path=off;

server {
        listen 80 default_server;
        #listen [::]:80 default_server;

        root /var/www/html;

        index index.html index.htm;
        server_name SITE;

        location / {
          proxy_ignore_headers Cache-Control;
          proxy_buffering on;
          proxy_cache_valid 200 1h;
          proxy_cache dvid_cache;
          proxy_set_header X-Real-IP $remote_addr;
          proxy_pass http://127.0.0.1:8000/;
        }

    listen 443 ssl; # managed by Certbot
    ssl_certificate /etc/letsencrypt/live/SITE/fullchain.pem; # managed by Certbot
    ssl_certificate_key /etc/letsencrypt/live/SITE/privkey.pem; # managed by Certbot
    include /etc/letsencrypt/options-ssl-nginx.conf; # managed by Certbot
    ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem; # managed by Certbot

}

The issue that I'm seeing is that when viewed over http, everything works fine (the admin page shows 1 repo, all the cores, the server uptime, and so on). When viewed over https, the console app is very confused showing "0 out of 0" cores, 0 repos, 0s server uptime, and so on. If I tell my browser to "load unsafe scripts" it works.

I believe this could be fixed by having the web app figure out whether it's talking http or https and make requests of the same sort, so as to allow for nicer SSL termination behaviour.

This isn't a major pain point for us (we rarely use the DVID console, and the DVID web API calls all work fine over https).

New version of DVID allows direct POST of image tiles into an imagetile instance, so there is no "Source" property to get voxel extents. Assume there will be a new "MaxTileCoord" property that gives you the maximum tile coord at level 0 (highest resolution):

"MaxTileCoord": [5, 5, 4]

The link of the DVID version to github is a great idea, but sometimes the build might be customized. For example, even though we check out git version 94eea of code, we might add a debug statement. This causes git to report the version as "94eea-dirty".

You could either remove any "-dirty" suffix before forming the github link, or just not provide a link since it's not exactly the version on github. I think the former is better because developers will know the dirty flag means it is "mostly" that version but there's some local changes.

We should be able to see the yz and xz planes in addition to the xy.

When I'm viewing a node in the console, I would like to be able to use the "Open Neuroglancer" button to view segmentation even if there is no grayscale data in the node. Currently, the console refuses:

It isn't actually disabled, routing is just messed up for this atm. The workaround for now: just refresh the page after adding the 'magic' parameter to the url.

Hi!! Could we add new (post-v1.14.6) releases to the tag list?

This enables downloading the tar file for specific releases.

When I click on a child UUID and then click on a data instance (e.g., a key value), data is pulled from the root node UUID.

At the moment, I can't zoom in on an image as much as I would like. For proofreading small processes or detecting tiny errors in segmentation, I need to be able to view individual pixels shown at very large scale.

The dvid-console releases page on github allows me to download zip/tar files of the source code for the most recent tag, but there is no link for the fully-packaged release bundle for distribution.

Old releases used to provide the pre-built distribution bundle. (I'm not sure how to make that appear on Github; @neomorphic could probably explain.) For reference, the most recent "complete" release was 1.14.10.

On a related note, it looks like the dist folder was accidentally committed to this repo 6 months ago. IIUC, dist is a build product and is not supposed to be committed into the repository. I suppose it ought to be removed.

The neuroglancer view does not occupy as much screen space as it could (see screenshot below). It would be nice if the neuroglancer view were full-screen, or as close to full-screen as feasible.

cc @neomorphic

When I look at the about page on the console for emdata1, I see the following:

DVID documentation can be found on githubas well as the automatically updated Go Doc documentation.

Note the lack of space between the "github" link and the following "as".

The code is here:
https://github.com/janelia-flyem/dvid-console/blob/master/js/components/About.react.js#L27

Strangely, there is some whitespace after the link tag, so is this an artifact of the minimization process?

See above image, it's definitely not a critical issue since I will just create the repo using the command line tool next, but I thought I'd let you know.

Webkit info:
WebKit version 537.36
Browser name Google Chrome 49.0.2623.110
Google Chrome version 49.0.2623.110
User Agent Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/49.0.2623.110 Safari/537.36

The UUID text label for each node is too large for the node in MB-6 (emdata1:8500). It's possible that this occured when I zoomed in to see the DAG.