Add experimental "rootless" dind variant

This is an alternative proposal to https://github.com/docker-library/docker/pull/165 + https://github.com/docker-library/docker/pull/168.
This should have roughly the same behavior as the dockerd-rootless.sh script but without the extra depdendency (and frankly I'd love to pull some official vpnkit release binaries too instead of pulling the extras bundle, but I couldn't find any official binary releases nor did it look trivial to build from source).  This allows us to iterate on this in between Docker releases as well, if necessary (like pulling in a newer rootlesskit release, for example).
I was toying with automatically adding --experimental as well, but wanted to enforce that being opt-in so that users don't switch without realizing what they're doing (since it does require some changes in usage).
Generally everything should "just work" as automatically as possible, but with the appropriate escape hatches for users who need/want to control the underlying knobs more directly.
cc @AkihiroSuda

Thanks for working on this, but I think dockerd-rootless.sh should be still kept as a separate script, so that we don't need to maintain the both upstream script and the downstream script in this repo.
Also, it is highly likely that the content of the script will differ in future revisions.

So, the reason I avoided dockerd-rootless.sh is because the entire script boiled down to setting a couple default values (based on autodetection that we can already assume based on what we include in the image) and doing a couple rm commands after running rootlesskit -- it doesn't seem worth using that script.  Do you anticipate more custom setup being required?  If so, what kinds of things do you expect and/or why can't dockerd itself perform the necessary setup?

Do you anticipate more custom setup being required?

I don't know, but something may change when we get support fo cgroup (v2).
Anyway, we can revisit this when we face some real issue.

Tested latest push via:
$ docker run -it --rm --name dind --privileged -v omg-certs:/certs/client docker:19.03-dind-rootless --experimental
...

$ docker run -it --rm --link dind:docker -v omg-certs:/certs/client docker:19.03-dind-rootless version
Client: Docker Engine - Community
 Version:           19.03.1
 API version:       1.40
 Go version:        go1.12.5
 Git commit:        74b1e89e8a
 Built:             Thu Jul 25 21:17:37 2019
 OS/Arch:           linux/amd64
 Experimental:      false

Server: Docker Engine - Community
 Engine:
  Version:          19.03.1
  API version:      1.40 (minimum version 1.12)
  Go version:       go1.12.5
  Git commit:       74b1e89e8a
  Built:            Thu Jul 25 21:27:55 2019
  OS/Arch:          linux/amd64
  Experimental:     true
 containerd:
  Version:          v1.2.6
  GitCommit:        894b81a4b802e4eb2a91d1ce216b8817763c29fb
 runc:
  Version:          1.0.0-rc8
  GitCommit:        425e105d5a03fabd737a126ad93d62a9eeede87f
 docker-init:
  Version:          0.18.0
  GitCommit:        fec3683

Hi @AkihiroSuda @tianon @yosifkit!
Could you please help me a bit to understand this pull request for my case?
In short I have a host machine with Ubuntu 18 and docker on it. In the docker I have some web service (JupyterLab) for users which can allow users to use bash thru web interface. So users can open https://host and run bash commands being inside the JupyterLab docker container. Every user in JupyterHub docker have his own home directory and without sudo.
I want to allow users to pull and run docker containers but without using host machine docker.
Could you please help me to understand this pull request and dind-rootless images:

Can I allow users to run docker inside docker using this dind-rootless?
Could you please help me to make prototype or maybe you have an articles about it? The best way for me is an example where in Ubuntu host run docker and then inside this docker run docker from user without sudo.

I'm experienced linux user but after review DinD topic in google I see this is very fresh topic with many hacks around. Please help to dive in.

If you want them to do so without using the host Docker, you're not looking
for this image (and it won't help you).
What you want is the "docker-rootless-extras" bundle from
https://download.docker.com/linux/static/ for each of your users to run
"dockerd-rootless.sh" directly (so they start their own instance).
You'll need at least Docker 19.03 and you'll need to set up subuid/subgid
ranges for each user, but all that is out of scope (and off-topic) here.

Yes,  but --privileged is needed to disable seccomp, apparmor, and masks for /proc and /sys.
https://www.slideshare.net/AkihiroSuda/dockercon-2019-hardening-docker-daemon-with-rootless-mode https://medium.com/@tonistiigi/experimenting-with-rootless-docker-416c9ad8c0d6

POC:
$ docker run -it --rm --privileged ubuntu:18.04
root@4f02dc5637d3:/# apt-get update && apt-get install -y curl uidmap iptables iproute2 kmod
root@4f02dc5637d3:/# useradd -m penguin
root@4f02dc5637d3:/# chsh -s /bin/bash penguin
root@4f02dc5637d3:/# su - penguin
penguin@4f02dc5637d3:~$ curl -fsSL https://get.docker.com/rootless | sh -

This should work, but looks like master.dockerproject.org is under outage now temporarily. Please try later.

@tianon @AkihiroSuda many thanks! I made a big step forward and now seemed I need one centimeter to success. Please assist:
This steps work as expected on Ubuntu 18 host machine:
$ docker run -it --rm --privileged ubuntu:18.04
root@4f02dc5637d3:/# apt-get update && apt-get install -y curl uidmap iptables iproute2 kmod vim
root@4f02dc5637d3:/# useradd -m penguin
root@4f02dc5637d3:/# chsh -s /bin/bash penguin
root@4f02dc5637d3:/# su - penguin

Then this command is not works properly:
penguin@4f02dc5637d3:~$ curl -fsSL https://get.docker.com/rootless | sh -

This script require changes. @AkihiroSuda told about errors with master.dockerproject.org - the download is getting error. To fix it I replace:
STATIC_RELEASE_URL="https://master.dockerproject.org/linux/x86_64/docker.tgz"
STATIC_RELEASE_ROOTLESS_URL="https://master.dockerproject.org/linux/x86_64/docker-rootless-extras.tgz"

to
STATIC_RELEASE_URL="https://download.docker.com/linux/static/stable/x86_64/docker-19.03.1.tgz"
STATIC_RELEASE_ROOTLESS_URL="https://download.docker.com/linux/static/stable/x86_64/docker-rootless-extras-19.03.1.tgz"

(Question 1): Am I right to choose the 19.03.1 version?
After it I've start rootless:
penguin@4f02dc5637d3:~$ curl -fsSL https://get.docker.com/rootless -o rl.sh && chmod +x rl.sh
penguin@4f02dc5637d3:~$ vim rl.sh
<changes>
penguin@f4e65d351f20:~$ ./rl.sh
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 60.3M  100 60.3M    0     0  56.3M      0  0:00:01  0:00:01 --:--:-- 56.3M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 17.8M  100 17.8M    0     0  35.8M      0 --:--:-- --:--:-- --:--:-- 35.7M
# systemd not detected, dockerd daemon needs to be started manually

/home/penguin/bin/dockerd-rootless.sh --experimental --storage-driver vfs

# Docker binaries are installed in /home/penguin/bin
# WARN: dockerd is not in your current PATH or pointing to /home/penguin/bin/dockerd
# Make sure the following environment variables are set (or add them to ~/.bashrc):

export XDG_RUNTIME_DIR=/tmp/docker-1000
export PATH=/home/penguin/bin:$PATH
export DOCKER_HOST=unix:///tmp/docker-1000/docker.sock

Do export and run docker manually as described:
penguin@f4e65d351f20:~$ export XDG_RUNTIME_DIR=/tmp/docker-1000
penguin@f4e65d351f20:~$ export PATH=/home/penguin/bin:$PATH
penguin@f4e65d351f20:~$ export DOCKER_HOST=unix:///tmp/docker-1000/docker.sock

penguin@f4e65d351f20:~$ /home/penguin/bin/dockerd-rootless.sh --experimental --storage-driver vfs &
----------------output------------------------
[1] 3261
penguin@f4e65d351f20:~$ + [ -w /tmp/docker-1000 ]
+ [ -w /home/penguin ]
+ rootlesskit=
+ which docker-rootlesskit
+ which rootlesskit
+ rootlesskit=rootlesskit
+ break
+ [ -z rootlesskit ]
+ :
+ :
+ net=
+ mtu=
+ [ -z ]
+ which slirp4netns
+ [ -z ]
+ which vpnkit
+ net=vpnkit
+ [ -z ]
+ mtu=1500
+ [ -z ]
+ _DOCKERD_ROOTLESS_CHILD=1
+ export _DOCKERD_ROOTLESS_CHILD
+ exec rootlesskit --net=vpnkit --mtu=1500 --disable-host-loopback --port-driver=builtin --copy-up=/etc --copy-up=/run /home/penguin/bin/dockerd-rootless.sh --experimental --storage-driver vfs
WARN[0000] "builtin" port driver is experimental
+ [ -w /tmp/docker-1000 ]
+ [ -w /home/penguin ]
+ rootlesskit=
+ which docker-rootlesskit
+ which rootlesskit
+ rootlesskit=rootlesskit
+ break
+ [ -z rootlesskit ]
+ :
+ :
+ net=
+ mtu=
+ [ -z ]
+ which slirp4netns
+ [ -z ]
+ which vpnkit
+ net=vpnkit
+ [ -z ]
+ mtu=1500
+ [ -z 1 ]
+ [ 1 = 1 ]
+ rm -f /run/docker /run/xtables.lock
+ exec dockerd --experimental --storage-driver vfs
INFO[2019-08-02T16:21:23.495120632Z] Starting up
WARN[2019-08-02T16:21:23.495180789Z] Running experimental build
WARN[2019-08-02T16:21:23.495194000Z] Running in rootless mode. Cgroups, AppArmor, and CRIU are disabled.
INFO[2019-08-02T16:21:23.495202042Z] Running with RootlessKit integration
WARN[2019-08-02T16:21:23.496421734Z] Error while setting daemon root propagation, this is not generally critical but may cause some functionality to not work or fallback to less desirable behavior  dir=/home/penguin/.local/share/docker error="error writing file to signal mount cleanup on shutdown: open /tmp/docker-1000/docker/unmount-on-shutdown: no such file or directory"
WARN[2019-08-02T16:21:23.497932662Z] could not change group /tmp/docker-1000/docker.sock to docker: group docker not found
INFO[2019-08-02T16:21:23.498815861Z] libcontainerd: started new containerd process  pid=3320
INFO[2019-08-02T16:21:23.498864189Z] parsed scheme: "unix"                         module=grpc
INFO[2019-08-02T16:21:23.498882549Z] scheme "unix" not registered, fallback to default scheme  module=grpc
INFO[2019-08-02T16:21:23.498916152Z] ccResolverWrapper: sending update to cc: {[{unix:///tmp/docker-1000/docker/containerd/containerd.sock 0  <nil>}] }  module=grpc
INFO[2019-08-02T16:21:23.498938909Z] ClientConn switching balancer to "pick_first"  module=grpc
INFO[2019-08-02T16:21:23.499008891Z] pickfirstBalancer: HandleSubConnStateChange: 0xc000795130, CONNECTING  module=grpc
INFO[2019-08-02T16:21:23.523207226Z] starting containerd                           revision=894b81a4b802e4eb2a91d1ce216b8817763c29fb version=v1.2.6
INFO[2019-08-02T16:21:23.523648846Z] loading plugin "io.containerd.content.v1.content"...  type=io.containerd.content.v1
INFO[2019-08-02T16:21:23.523775189Z] loading plugin "io.containerd.snapshotter.v1.btrfs"...  type=io.containerd.snapshotter.v1
WARN[2019-08-02T16:21:23.524170845Z] failed to load plugin io.containerd.snapshotter.v1.btrfs  error="path /home/penguin/.local/share/docker/containerd/daemon/io.containerd.snapshotter.v1.btrfs must be a btrfs filesystem to be used with the btrfs snapshotter"
INFO[2019-08-02T16:21:23.524205631Z] loading plugin "io.containerd.snapshotter.v1.aufs"...  type=io.containerd.snapshotter.v1
WARN[2019-08-02T16:21:23.525780612Z] failed to load plugin io.containerd.snapshotter.v1.aufs  error="modprobe aufs failed: "modprobe: ERROR: ../libkmod/libkmod.c:586 kmod_search_moddep() could not open moddep file '/lib/modules/4.15.0-1041-aws/modules.dep.bin'\nmodprobe: FATAL: Module aufs not found in directory /lib/modules/4.15.0-1041-aws\n": exit status 1"
INFO[2019-08-02T16:21:23.525833126Z] loading plugin "io.containerd.snapshotter.v1.native"...  type=io.containerd.snapshotter.v1
INFO[2019-08-02T16:21:23.525983008Z] loading plugin "io.containerd.snapshotter.v1.overlayfs"...  type=io.containerd.snapshotter.v1
INFO[2019-08-02T16:21:23.526244177Z] loading plugin "io.containerd.snapshotter.v1.zfs"...  type=io.containerd.snapshotter.v1
WARN[2019-08-02T16:21:23.526736258Z] failed to load plugin io.containerd.snapshotter.v1.zfs  error="path /home/penguin/.local/share/docker/containerd/daemon/io.containerd.snapshotter.v1.zfs must be a zfs filesystem to be used with the zfs snapshotter"
INFO[2019-08-02T16:21:23.526775160Z] loading plugin "io.containerd.metadata.v1.bolt"...  type=io.containerd.metadata.v1
WARN[2019-08-02T16:21:23.526867899Z] could not use snapshotter btrfs in metadata plugin  error="path /home/penguin/.local/share/docker/containerd/daemon/io.containerd.snapshotter.v1.btrfs must be a btrfs filesystem to be used with the btrfs snapshotter"
WARN[2019-08-02T16:21:23.526898990Z] could not use snapshotter aufs in metadata plugin  error="modprobe aufs failed: "modprobe: ERROR: ../libkmod/libkmod.c:586 kmod_search_moddep() could not open moddep file '/lib/modules/4.15.0-1041-aws/modules.dep.bin'\nmodprobe: FATAL: Module aufs not found in directory /lib/modules/4.15.0-1041-aws\n": exit status 1"
WARN[2019-08-02T16:21:23.526925392Z] could not use snapshotter zfs in metadata plugin  error="path /home/penguin/.local/share/docker/containerd/daemon/io.containerd.snapshotter.v1.zfs must be a zfs filesystem to be used with the zfs snapshotter"
INFO[2019-08-02T16:21:23.536210475Z] loading plugin "io.containerd.differ.v1.walking"...  type=io.containerd.differ.v1
INFO[2019-08-02T16:21:23.536270222Z] loading plugin "io.containerd.gc.v1.scheduler"...  type=io.containerd.gc.v1
INFO[2019-08-02T16:21:23.536337620Z] loading plugin "io.containerd.service.v1.containers-service"...  type=io.containerd.service.v1
INFO[2019-08-02T16:21:23.536372827Z] loading plugin "io.containerd.service.v1.content-service"...  type=io.containerd.service.v1
INFO[2019-08-02T16:21:23.536399800Z] loading plugin "io.containerd.service.v1.diff-service"...  type=io.containerd.service.v1
INFO[2019-08-02T16:21:23.536429508Z] loading plugin "io.containerd.service.v1.images-service"...  type=io.containerd.service.v1
INFO[2019-08-02T16:21:23.536458705Z] loading plugin "io.containerd.service.v1.leases-service"...  type=io.containerd.service.v1
INFO[2019-08-02T16:21:23.536491307Z] loading plugin "io.containerd.service.v1.namespaces-service"...  type=io.containerd.service.v1
INFO[2019-08-02T16:21:23.536523089Z] loading plugin "io.containerd.service.v1.snapshots-service"...  type=io.containerd.service.v1
INFO[2019-08-02T16:21:23.536546476Z] loading plugin "io.containerd.runtime.v1.linux"...  type=io.containerd.runtime.v1
INFO[2019-08-02T16:21:23.536936803Z] loading plugin "io.containerd.runtime.v2.task"...  type=io.containerd.runtime.v2
INFO[2019-08-02T16:21:23.537103742Z] loading plugin "io.containerd.monitor.v1.cgroups"...  type=io.containerd.monitor.v1
INFO[2019-08-02T16:21:23.537694622Z] loading plugin "io.containerd.service.v1.tasks-service"...  type=io.containerd.service.v1
INFO[2019-08-02T16:21:23.537753977Z] loading plugin "io.containerd.internal.v1.restart"...  type=io.containerd.internal.v1
INFO[2019-08-02T16:21:23.537820865Z] loading plugin "io.containerd.grpc.v1.containers"...  type=io.containerd.grpc.v1
INFO[2019-08-02T16:21:23.537858395Z] loading plugin "io.containerd.grpc.v1.content"...  type=io.containerd.grpc.v1
INFO[2019-08-02T16:21:23.538607799Z] loading plugin "io.containerd.grpc.v1.diff"...  type=io.containerd.grpc.v1
INFO[2019-08-02T16:21:23.538642205Z] loading plugin "io.containerd.grpc.v1.events"...  type=io.containerd.grpc.v1
INFO[2019-08-02T16:21:23.538670389Z] loading plugin "io.containerd.grpc.v1.healthcheck"...  type=io.containerd.grpc.v1
INFO[2019-08-02T16:21:23.538697814Z] loading plugin "io.containerd.grpc.v1.images"...  type=io.containerd.grpc.v1
INFO[2019-08-02T16:21:23.538726420Z] loading plugin "io.containerd.grpc.v1.leases"...  type=io.containerd.grpc.v1
INFO[2019-08-02T16:21:23.538753153Z] loading plugin "io.containerd.grpc.v1.namespaces"...  type=io.containerd.grpc.v1
INFO[2019-08-02T16:21:23.538811026Z] loading plugin "io.containerd.internal.v1.opt"...  type=io.containerd.internal.v1
WARN[2019-08-02T16:21:23.538884684Z] failed to load plugin io.containerd.internal.v1.opt  error="mkdir /opt/containerd: permission denied"
INFO[2019-08-02T16:21:23.538916666Z] loading plugin "io.containerd.grpc.v1.snapshots"...  type=io.containerd.grpc.v1
INFO[2019-08-02T16:21:23.538946394Z] loading plugin "io.containerd.grpc.v1.tasks"...  type=io.containerd.grpc.v1
INFO[2019-08-02T16:21:23.538973947Z] loading plugin "io.containerd.grpc.v1.version"...  type=io.containerd.grpc.v1
INFO[2019-08-02T16:21:23.539000971Z] loading plugin "io.containerd.grpc.v1.introspection"...  type=io.containerd.grpc.v1
INFO[2019-08-02T16:21:23.539268511Z] serving...                                    address="/tmp/docker-1000/docker/containerd/containerd-debug.sock"
INFO[2019-08-02T16:21:23.539353277Z] serving...                                    address="/tmp/docker-1000/docker/containerd/containerd.sock"
INFO[2019-08-02T16:21:23.539379019Z] containerd successfully booted in 0.017143s
INFO[2019-08-02T16:21:23.549202768Z] pickfirstBalancer: HandleSubConnStateChange: 0xc000795130, READY  module=grpc
INFO[2019-08-02T16:21:23.551666378Z] parsed scheme: "unix"                         module=grpc
INFO[2019-08-02T16:21:23.551715767Z] scheme "unix" not registered, fallback to default scheme  module=grpc
INFO[2019-08-02T16:21:23.551753658Z] ccResolverWrapper: sending update to cc: {[{unix:///tmp/docker-1000/docker/containerd/containerd.sock 0  <nil>}] }  module=grpc
INFO[2019-08-02T16:21:23.551776616Z] ClientConn switching balancer to "pick_first"  module=grpc
INFO[2019-08-02T16:21:23.551874393Z] pickfirstBalancer: HandleSubConnStateChange: 0xc0008207c0, CONNECTING  module=grpc
INFO[2019-08-02T16:21:23.552428624Z] pickfirstBalancer: HandleSubConnStateChange: 0xc0008207c0, READY  module=grpc
INFO[2019-08-02T16:21:23.553258988Z] parsed scheme: "unix"                         module=grpc
INFO[2019-08-02T16:21:23.553291601Z] scheme "unix" not registered, fallback to default scheme  module=grpc
INFO[2019-08-02T16:21:23.553335231Z] ccResolverWrapper: sending update to cc: {[{unix:///tmp/docker-1000/docker/containerd/containerd.sock 0  <nil>}] }  module=grpc
INFO[2019-08-02T16:21:23.553357346Z] ClientConn switching balancer to "pick_first"  module=grpc
INFO[2019-08-02T16:21:23.553440960Z] pickfirstBalancer: HandleSubConnStateChange: 0xc0001352f0, CONNECTING  module=grpc
INFO[2019-08-02T16:21:23.553489979Z] blockingPicker: the picked transport is not ready, loop back to repick  module=grpc
INFO[2019-08-02T16:21:23.553719439Z] pickfirstBalancer: HandleSubConnStateChange: 0xc0001352f0, READY  module=grpc
WARN[2019-08-02T16:21:23.577772929Z] Your kernel does not support swap memory limit
WARN[2019-08-02T16:21:23.577809879Z] Your kernel does not support cgroup rt period
WARN[2019-08-02T16:21:23.577829010Z] Your kernel does not support cgroup rt runtime
INFO[2019-08-02T16:21:23.578079172Z] Loading containers: start.
WARN[2019-08-02T16:21:23.579914552Z] Running modprobe bridge br_netfilter failed with message: modprobe: ERROR: ../libkmod/libkmod.c:586 kmod_search_moddep() could not open moddep file '/lib/modules/4.15.0-1041-aws/modules.dep.bin'
modprobe: WARNING: Module bridge not found in directory /lib/modules/4.15.0-1041-aws
modprobe: ERROR: ../libkmod/libkmod.c:586 kmod_search_moddep() could not open moddep file '/lib/modules/4.15.0-1041-aws/modules.dep.bin'
modprobe: WARNING: Module br_netfilter not found in directory /lib/modules/4.15.0-1041-aws
, error: exit status 1
WARN[2019-08-02T16:21:23.581070139Z] Running modprobe nf_nat failed with message: `modprobe: ERROR: ../libkmod/libkmod.c:586 kmod_search_moddep() could not open moddep file '/lib/modules/4.15.0-1041-aws/modules.dep.bin'
modprobe: WARNING: Module nf_nat not found in directory /lib/modules/4.15.0-1041-aws`, error: exit status 1
WARN[2019-08-02T16:21:23.582229493Z] Running modprobe xt_conntrack failed with message: `modprobe: ERROR: ../libkmod/libkmod.c:586 kmod_search_moddep() could not open moddep file '/lib/modules/4.15.0-1041-aws/modules.dep.bin'
modprobe: WARNING: Module xt_conntrack not found in directory /lib/modules/4.15.0-1041-aws`, error: exit status 1
INFO[2019-08-02T16:21:23.811602205Z] Default bridge (docker0) is assigned with an IP address <IP_ADDRESS>/16. Daemon option --bip can be used to set a preferred IP address
INFO[2019-08-02T16:21:24.016351027Z] Loading containers: done.
INFO[2019-08-02T16:21:24.045207655Z] Docker daemon                                 commit=74b1e89e8a graphdriver(s)=vfs version=19.03.1
INFO[2019-08-02T16:21:24.045422544Z] Daemon has completed initialization
INFO[2019-08-02T16:21:24.067357379Z] API listen on /tmp/docker-1000/docker.sock
----------------output------------------------

penguin@f4e65d351f20:~$

Now docker ps and docker images works!
penguin@f4e65d351f20:~$ docker ps
CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES

Try to run image and got warnings and nothing out:
penguin@f4e65d351f20:~$ docker run ubuntu echo test

Unable to find image 'ubuntu:latest' locally
latest: Pulling from library/ubuntu
7413c47ba209: Pull complete                                                                                0fe7e7cbb2e8: Pull complete                                                                                1d425c982345: Pull complete                                                                                344da5c95cec: Pull complete                                                                                Digest: sha256:c303f19cfe9ee92badbbbd7567bc1ca47789f79303ddcef56f77687d4744cd7a
Status: Downloaded newer image for ubuntu:latest

INFO[2019-08-02T16:23:10.852690476Z] shim containerd-shim started                  address="/containerd-shim/moby/8ac4c97499dac0863e534005ea96ff314c3adb61da1f76d96b80e5448153f5d6/shim.sock" debug=false pid=3496
WARN[2019-08-02T16:23:11.114689486Z] OOM monitoring failed                         error="cgroups: memory cgroup not supported on this system"
test
INFO[2019-08-02T16:23:11.216211230Z] shim reaped                                   id=8ac4c97499dac0863e534005ea96ff314c3adb61da1f76d96b80e5448153f5d6
INFO[2019-08-02T16:23:11.226364120Z] ignoring event                                module=libcontainerd namespace=moby topic=/tasks/delete type="*events.TaskDelete"
WARN[2019-08-02T16:23:11.342077637Z] 8ac4c97499dac0863e534005ea96ff314c3adb61da1f76d96b80e5448153f5d6 cleanup: failed to unmount IPC: umount /home/penguin/.local/share/docker/containers/8ac4c97499dac0863e534005ea96ff314c3adb61da1f76d96b80e5448153f5d6/mounts/shm, flags: 0x2: no such file or directory

(Question 2): It looks like --privileged not enough. Please help to work around.

Warning seem negligible, are you facing real issues?

@AkihiroSuda yes, with two.

Network ports issue. Example with nginx:

penguin@f4e65d351f20:~$ docker run -p 80:80 -d nginx
penguin@f4e65d351f20:~$ docker ps
CONTAINER ID        IMAGE               COMMAND                  CREATED             STATUS              PORTS                NAMES
c8eab9eab330        nginx               "nginx -g 'daemon of…"   3 minutes ago       Up 3 minutes        <IP_ADDRESS>:80->80/tcp   musing_wilbur

But:
penguin@f4e65d351f20:~$ curl <IP_ADDRESS>:80
curl: (7) Failed to connect to <IP_ADDRESS> port 80: Connection refused

If I go to the container it works:
$ docker exec -it c8eab9eab330 /bin/bash
root@c8eab9eab330:/var/log/nginx# curl <IP_ADDRESS>:80
<!DOCTYPE html>
...

How to use network ports?

Container run issue. Sometimes I've got an error when container run and container not started:

penguin@f4e65d351f20:~$ docker run -p 811:80 nginx
WARN[2019-08-02T16:55:01.051860410Z] Failed to allocate and map port 811-811: Error starting userland proxy:
WARN[2019-08-02T16:55:01.109685356Z] 2187cfeb14ea8e16fe9ae39fe31781012ea929044ec8ef72505786f2eade4ac4 cleanup: failed to unmount IPC: umount /home/penguin/.local/share/docker/containers/2187cfeb14ea8e16fe9ae39fe31781012ea929044ec8ef72505786f2eade4ac4/mounts/shm, flags: 0x2: no such file or directory
ERRO[2019-08-02T16:55:01.110705683Z] 2187cfeb14ea8e16fe9ae39fe31781012ea929044ec8ef72505786f2eade4ac4 cleanup: failed to delete container from containerd: no such container
ERRO[2019-08-02T16:55:01.110765668Z] Handler for POST /v1.40/containers/2187cfeb14ea8e16fe9ae39fe31781012ea929044ec8ef72505786f2eade4ac4/start returned error: driver failed programming external connectivity on endpoint loving_lewin (8b05abcea1381651eeaa75db3e0ffb3322ad60a7c52bb130d293a498feed0f20): Error starting userland proxy:
docker: Error response from daemon: driver failed programming external connectivity on endpoint loving_lewin (8b05abcea1381651eeaa75db3e0ffb3322ad60a7c52bb130d293a498feed0f20): Error starting userland proxy:.
ERRO[0001] error waiting for container: context canceled

(It looks like the issue appears when I try to run container immediately after stopping previous)

Port number below 1024 cannot be used without CAP_NET_BIND_SERVICE (see https://www.slideshare.net/AkihiroSuda/dockercon-2019-hardening-docker-daemon-with-rootless-mode)

So try -p 8080:80 instead please

@AkihiroSuda you rock! It works! Many thanks!

I've tried to spin up without certs per https://github.com/docker-library/docker/pull/174#issuecomment-517036465
$ docker run -it --rm --name dind --privileged docker:19.03.1-dind-rootless --experimental

I get [rootlesskit:child ] error: executing [[ip tuntap add name tap0 mode tap] [ip link set tap0 address <MAC>]]: exit status 1 on Docker Desktop for Mac <IP_ADDRESS>.

opened https://github.com/docker/for-mac/issues/3838 for Docker fo Mac issue


Add MSI Afterburner with RTSS

MSI Afterburner is the world's most recognized and widely used graphics card overclocking utility which gives you full control of your graphics cards. Works with all graphics cards vendors.

https://www.msi.com/page/afterburner

Interesting how all these download pages use only HTTP...

Yes, it is...There's alternative download server over at guru3d.com but they don't work with scoop. I tried it and if I recall correctly there was issue with Referrer header that you couldn't set in scoop.


i cant use it when i have a "non required" title :-(

Please describe - which script you are referring to?

Closing as no response.


DEVPROD-11145: Pin @leafygreen-ui/hooks to v8.1.3 for ComboBox

DEVPROD-11145

Description
The ComboBox is broken due to weird interactions with @leafygreen-ui/hooks.
You can use this CodeSandbox to verify that it doesn't work for any version after 8.1.3.

Commenting here just in case you missed the thread while you are out. The fix for this should be released as of today or tomorrow.  So we should be able to just update Combobox.


Database is not compatible with this version of eclair

I use the APK version for android. Two days ago I started the application without any problem. Now when I start and after unlocking with my fingerprint I get this error and there is no way to access the app. I have updated to the latest version and I still get the same error.

This is an old error that happens on legacy versions of the app (v1.x) that were using old channels format (and all these legacy channels have now been closed). Can you contact<EMAIL_ADDRESS>? it will be easier to debug your issue that way.

I use the APK version for android. Two days ago I started the application without any problem. Now when I start and after unlocking with my fingerprint I get this error and there is no way to access the app. I have updated to the latest version and I still get the same error.
I've just send an email to<EMAIL_ADDRESS>Thanks.


Made the footer text visible #126

I have made the text in  About us section in side the footer visible

Can you please add GSSoc Extd. and Hacktoberfest label


Windows Terminal crashing when invoking a Console request from .NET

Windows Terminal version
1.18.2310.9002
Windows build number
10.0.22621.0
Other Software
Eco (EcoServer.exe)
Steps to reproduce
Run the application without Administrator privileges.
Expected Behavior
It launches as expected.
Actual Behavior
Windows Terminal crashes resulting in a closed pipe error within .NET

This also seems to happen with the legacy applications such as cmd.exe. The issue is not consistent. However, once it starts it does not go away. We have had a few users report uninstalling Windows update KB5030649 resolves their issues.
Attempting to investigate inside the Event Viewer turns up this error
Faulting application name: OpenConsole.exe, version: 1.18.2310.9002, time stamp: 0x65248ade

Faulting module name: OpenConsole.exe, version: 1.18.2310.9002, time stamp: 0x65248ade

Exception code: 0xc0000094

Fault offset: 0x0000000000002be2

Faulting process id: 0x0xBA2C

Faulting application start time: 0x0x1DA03867118B628

Faulting application path: C:\Program Files\WindowsApps\Microsoft.WindowsTerminal_1.18.2822.0_x64__8wekyb3d8bbwe\OpenConsole.exe

Faulting module path: C:\Program Files\WindowsApps\Microsoft.WindowsTerminal_1.18.2822.0_x64__8wekyb3d8bbwe\OpenConsole.exe

Report Id: 28615991-e11f-4142-acc6-7fcfde642147

Faulting package full name: Microsoft.WindowsTerminal_1.18.2822.0_x64__8wekyb3d8bbwe

Faulting package-relative application ID: App

Alas, that Report Id didn't show up on the backend. We might need a Feedback Hub dump or a post-mortem dump to definitively ID this. Can you try following these steps to get us a dump/?
I'm guessing this is MSFT:44310564 which is #16199, but we don't really have a repro for that, just crash dumps.

Alas, that Report Id didn't show up on the backend. We might need a Feedback Hub dump or a post-mortem dump to definitively ID this. Can you try following these steps to get us a dump/?
I'm guessing this is MSFT:44310564 which is #16199, but we don't really have a repro for that, just crash dumps.

Here is the crash dump. Far as reproduction steps I wish I could be of more use. Our product is fairly sizable and the fact where it crashes vs. where Windows terminal crashes are not correlated doesn't help nailing it down. Doesn't seem to even be the same spot consistently.
What I can potentially offer and though I'd need to double check with my boss first. The game in question that is being plagued by this does offer what we call DevTier for modders which grants full source access here on Github. If its of use we can probably arrange access for the purposes of figuring this out. While its not every time, EcoServer seems to hit this issue consistently enough that is its a genuine problem.

Alas, that Report Id didn't show up on the backend. We might need a Feedback Hub dump or a post-mortem dump to definitively ID this. Can you try following these steps to get us a dump/?
I'm guessing this is MSFT:44310564 which is #16199, but we don't really have a repro for that, just crash dumps.

I've sent an email with the crash dump per the instructions. Far as reproduction unfortunately where EcoServer crashes vs when Windows Terminal crashes are not related so trying to pinpoint it is rather difficult. Only known constant is it doesn't fail in the same spot every time and running as Administrator seems to sometimes help.
What I can potentially offer though I'd need to check with my boss is giving someone on the team what we call DevTier. DevTier is normally for modders but it grants full source code access to the game on Github. While EcoServer doesn't get the issue every time, its consistent enough that its a genuine problem. If that is of interest let me know and I'll see what I can do.


Possible arbitrary code execution in create_html

https://github.com/lemystic/spylt/blob/ea057a821ab4f73c0855b4d01dfc7ddece74ff9d/spylt/builder.py#L61
Use the subprocess module instead to prevent arbitrary code execution that could occur by someone calling
create_html('hi"; rm -rf ./* #')

Here hi"; escapes the quote and ends the echo command, then rm -rf ./* is an example for aribitrary code execution and the # makes the rest of the command (npx rollup --silent...) a comment and it doesn't execute.  The command that ends up running will be
echo "hi"; rm -rf ./* #" | npx rollup --silent --config --file ./__buildcache__/bundle.js >/dev/null

This is just an example, I did not go through the code to check if the create_html function does accept user input, I am assuming it does.

I'll patch this 😅
By the way, create_html is meant to accept this code:
import App from './App.svelte';
const app = new App({ target: document.body });
export default app;

which is created by create_linker in the Module class
https://github.com/lemystic/spylt/blob/ea057a821ab4f73c0855b4d01dfc7ddece74ff9d/spylt/module.py#L32


[BUG] There was an error checking the latest version of pip

setuptools version
62.3.2
Python version
Python 3.8.10
OS
Windows 10
Additional environment information
No response
Description
Update the pip 22.1.1 and setuptools 62.3.2
Expected behavior
No warning message
How to Reproduce

Setup python-3.8.10.exe
Update setuptools 62.3.2
Update pip 22.1.1
python -m pip list
Show "WARNING: There was an error checking the latest version of pip"

Output
D:\python -m pip list
Package                   Version

nidaqmx                  0.6.2
numpy                     1.22.4
pip                           22.1.1
PyAudio                   0.2.11
pyserial                    3.5
PyVISA                     1.11.3
pywin32                   304
pywinusb                 0.4.2
scipy                        1.8.0
setuptools                62.3.2
six                            1.16.0
typing_extensions    4.2.0
wheel                       0.37.1
WARNING: There was an error checking the latest version of pip.

python -m pip install --upgrade pip
worked on mine

The cause of the warning is a bug in pip. It should be fixed by https://github.com/pypa/pip/pull/11136

python -m pip install --upgrade pip worked on mine

This eliminated the problem for me. Amazing.
Thanks buddy

Hi @J8923, I tried to replicate the problem, however I cannot simply install different versions of Python in the Windows machine I have available, so I resorted to using a Windows container.
The following script show the sequence of commands I have used trying to replicate the error you reported:
> docker run --rm -it -u ContainerAdministrator mcr.microsoft.com/powershell:lts-nanoserver-1809
# Windows containers require a Windows host correctly configured.
# The container tag version (e.g. 1809) depends on the version of the host and may require changes,
# please check https://docs.microsoft.com/en-us/virtualization/windowscontainers/deploy-containers/version-compatibility

netsh interface ip add dnsservers name="Ethernet" address=<IP_ADDRESS> index=4
# A DNS is required for downloading content from the internet.
# Please make sure `name` matches the correct adapter (a list can be found using `ipconfig /all`).

Register-PackageSource -Name nuget.org -ProviderName NuGet -Location "https://api.nuget.org/v3/index.json" -Trusted
Install-Package python -MinimumVersion 3.8.10 -MaximumVersion 3.8.10
$env:Path += ";" + (Join-Path (Split-Path (Get-Package python | % source)) "tools") + ";"

python -m pip list
# No 'error checking the latest version of pip' warning

python -m pip install -U 'setuptools==62.3.2'
python -m pip list
# No 'error checking the latest version of pip' warning

python -m pip install -U 'pip==22.1.1'
python -m pip list
# No 'error checking the latest version of pip' warning

The error does not seems to show up.
Also based on the previous reports (thank you Dominic and CanDursun), it seems that this is not a bug in setuptools, so I am inclined to close this issue soon.
Please let me know if you have a different reproducer that unequivocally associates the problem with setuptools. You can create a modified version of my script above, for example.

The error does not seems to show up. Also based on the previous reports (thank you Dominic and CanDursun), it seems that this is not a bug in setuptools, so I am inclined to close this issue soon. Please let me know if you have a different reproducer that unequivocally associates the problem with setuptools. You can create a modified version of my script above, for example.

Hi @abravalheri , I've also encountered this issue a few weeks ago after installing a requirement.txt. I'm not sure if this issue was caused by that directly, and unfortunately, I didn't keep a copy of that. But perhaps you can try some requirement texts.


Custom drop

Hello. Can you add one custom option for drop items?
Pls, add option "dropPermission".
If this option is enabled, the item will drop only to the player who has certain permission.
I hope you add this option.
Thank you in advance

won't fix for main plugin


Permission cookie

Describe the issue
I have had to rebuild my node from scratch and after sync all blockchain I have noted that I have problems with permission of .cookie file.
I have noted the following:
admin@raspibolt:~ $ ls -la /data/bitcoin/.cookie
-rw-r----- 1 bitcoin bitcoin 75 Mar 26 13:33 /data/bitcoin/.cookie
admin@raspibolt:~ $ ls -la /home/bitcoin/.bitcoin/.cookie
ls: cannot access '/home/bitcoin/.bitcoin/.cookie': Permission denied
I have checked all steps a lot of times but I don't able find my issue. I suppose that there is some related of the permission of the parents folders.
thanks for the help
Environment

Hardware platform:Raspberry Pi 4
Operating system: Raspberry Pi OS 64bit
Version: Debian GNU/Linux 12 (bookworm)

I have find the workaround in:
https://github.com/raspibolt/raspibolt/issues/1414


Success == false but OriginalException == null

I ran into a case where Success == false but OriginalException == null for a IElasticsearchResponse. This contradicts the documentation at https://github.com/elastic/elasticsearch-net/blob/develop/src/Elasticsearch.Net/Domain/Response/IElasticsearchResponse.cs#L20-L24 .
From a brief static analysis, this could be happening from a null Exception being passed into this constructor but more likely this is coming from this constructor with a 400 statusCode (which was my particular case).
So the options are: either remove that assertion from the documentation or change the code to make it comply to this assertion...

BTW I realise it would be breaking change but it would be great if this was modeled as an algebraic data type. See Sasa's Result for reference. With an ADT this cannot happen.

Thanks @mausch
In 1.x there is a code path where a bad response (400) does not actually result in an exception but still triggers an invalid response.  Will update the documentation to explicitly mention this.
For 2.0 we are actually in the process of formalising our request pipeline, what kind of exceptions it throws and how the user should handle it more sanely then in 1.x.

The idea is that you can configure the client to always throw hard exceptions on any of the immediate exit points or always return a soft error response with a guaranteed exception attached to it akin more to how 1.x. In 1.x exception behaviour is also coupled to wheter you have retries enabled and/or are using the SingleNodeConnectionPool, this is bad and we are looking to rectify this mistake in 2.0.
There are definitive up-sights to Result<>, folks who want hard exceptions simply use .Value to rethrow the original exception. Folks who want soft error responses can use .HasValue or a .Match(v=>value, error=>value_on_error) to always handle both permutations.
I need to let that idea bake in my head and also weigh its benefits against breaking 100% of the calls when folks update to NEST 2.0. NEST 2.0 is all about daring to break things where needed for the next 5 years of the client but for this one I need to regroup :+1:

Currently, when a bad response occurs, you can no longer see the actual error returned from Elasticsearch. The OriginalException is simply a WebException with a status of ProtocolError.
Is this planned to be changed?

Hey @jonyadamit assuming you're talking about 2.0?  Yes, this is planned and currently being worked on in this branch https://github.com/elastic/elasticsearch-net/tree/spike/2.0-exceptions.

:+1: :+1: That's great :-)

Closing this as non actionable, 2.0 has a much saner exception/soft error policy.
Modelling result as algebraic data type is definitely something we'll revisit when c# natively supports them (like any sane language should (roll on c# 7)).


organize metrics sidebar

🚀 Deployed on https://62f3f3d6b3377502b8d1a5b4--cozy-fox-0defec.netlify.app


Template for 'administration of substance in vivo' terms

Closes issue #1703. Creating a template (administration.tsv) for subclasses of 'administration of substance in vivo' to standardize the design pattern for terms including the route-of-administration terms requested in issue #1703 for IEDB.

I've added a few commits in which I've moved some existing administration-branch terms to the administration template. Here's a link to a ROBOT diff between the existing version (with the current terms in obi-edit) and the proposed version (with those terms in the administration module). I've included some annotations/comments about the changes made; almost all changes to logic have to do with getting rid of redundant class axioms that are already inherited from a parent class. I'm happy to talk through this on an OBI call.

This is ready for final review & merging. To be discussed in next OBI dev call.


Shift Tab doesn't work.

Tried it on both result command prompt and powershell. I can see that you are catching keys in CustomWindow.ProcessKey, but I am not sure how to tell gui.cs to go back.

Thanks, I’ve noticed this also. I’ve already fixed it once in Gui.cs (https://github.com/migueldeicaza/gui.cs/pull/110). Need to check again, and see why it’s broken again.

Should be fixed in https://github.com/migueldeicaza/gui.cs/pull/243


Appstudio update test-component-pac-xfqx

Pipelines as Code configuration proposal

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fix(MegaMenu): explicity set focus to HeaderMenu L0 item when clicked

Related Ticket(s)
[MM] My IBM maintaining focus when switching to mega menu #3617
[HP] [MM] multiple menus open at once #3731
Description
The <OverflowMenu /> component that we are using for the profile menu has logic to trap the focus when user clicks outside of the component. This affects the megamenu when user opens the profile menu, then clicks on the L0 nav item. The focus is trapped in the <OverflowMenu /> which affects the onBlur event triggered used when opening another L0 nav item.
This PR forces focus on the L0 nav item when it is clicked.
BEFORE:

AFTER:

Changelog
Changed

force focus on the HeaderMenu L0 item

@annawen1 Looks good!
I'm thinking through this, and we are already set to go as-is with what we have currently tonight, so I'm thinking of having this retargeted to a release branch for a patch release instead, so let's hold on merging this for now.

@annawen1 one other thought I have, perhaps we can target master for now so we can test around this on canary, and if we do a patch we can always cherry pick this commit. Thoughts?

@annawen1 one other thought I have, perhaps we can target master for now so we can test around this on canary, and if we do a patch we can always cherry pick this commit. Thoughts?

@jeffchew yeah sure that works


try fix travis

@defnull
remove pip install -U coverage after after python version check

failed without all your change prefer but the branch fix travis worked


boards: b_l072z_lrwan1: Move usb support to device tree

Add support for "additional functions" signals
Now that this is possible, move usb support to device tree for b_l072z_lrwan1
and remove files that are made useless following this change.

@erwango please rebase

@erwango please rebase

Done, txs


Fix solution ant bug

The solution ant now correctly uses only the pheromone values to compute its path
Removed the simulator class from the package
Better packaging and exports

Thank you for fixing this @hasnainroopawalla. I implemented a very inefficient fix for this problem (where the solution ant might either get stuck or not give the shortest path). Glad to see you implemented such a simple and elegant solution. Kudos! 👏🏾

@king-phyte please feel free to file any bugs if you come across any, thanks!


QA Pipeline Definition and Assets for Flutter projects on Google Cloud

[ ] spike Sonarqube
[ ] tarea

Needs investigation


Create a RenameKey function in qscript

Currently when qscript requests a key rename, for example in the query select foo as bar from baz the qscript will look like
MakeMap
├─ Constant(Str(bar))
╰─ ProjectField
   ├─ <src>
   ╰─ Constant(Str(foo))

This is a prescriptive approach, rather than a declarative one, describing how the connector should rename the field foo rather than declaring simply that the field should be renamed.
Instead we should introduce a RenameKey function so that the qscript can look like
RenameKey
├─ Constant(Str(foo))
├─ Constant(Str(bar))
╰─ <src>

As with all qscript, if an individual connector cannot implement RenameKey and prefers the more prescriptive approach above, then we can provide that.

This could simplify the qscript generated by the structure editor. We should consider other similar functions that represent declarative structure editor edits.


Add webpack-dev-server

It works
It working

Tested production build

This has gone stale. Deleting


[Feature Request] add support to rotate image

Allow rotating image (or optionally other elements) from within the lightbox. Also consider exposing the rotation state and method to allow changing rotation programmatically

My view is that this feature is too niche to justify the extra weight it will add to the library, so it will not be added any time soon.
Off the top of my head, the only lightbox that I know supports image rotation is lightGallery, so you might want to check that out. But be aware that it's not free for closed source projects.


std.digest should work for output ranges

lempiji reported this on 2016-12-04T13:57:08Z
Transfered from https://issues.dlang.org/show_bug.cgi?id=16947
CC List

greeenify
john.loughran.colvin

Description
The digest function calls the put function incorrectly.

This code does not work.
-----
struct MyDigest
{
    void put(ubyte data) { }
    void put(ubyte a, ubyte b) { }
    void start() { }
    ubyte[] finish() { return null; }
}

unittest
{
    writeln(isOutputRange!(MyDigest, ubyte)); //true
    writeln(isOutputRange!(MyDigest, const(ubyte)[])); //true
    writeln(isDigest!MyDigest); //true
}

unittest
{
	auto d = digest!MyDigest("test"); //compile error!
}
-----

How to fix:
-----
// https://github.com/dlang/phobos/blob/master/std/digest/digest.d#L457
hash.put(cast(const(ubyte[]))datum);
-----
.put(hash, cast(const(ubyte[]))datum);
-----

greeenify commented on 2016-12-27T10:35:24Z
>>  It probably wouldn't be a lot of work to implement, but you might be the only person for whom it's a priority...
> I would like to make a pull request when improvement is needed.

Please do so :)

lempiji commented on 2016-12-23T15:44:59Z
Thanks for the response.
I understand that this is a rare request.

I reported that it would be should to accept a general OutputRange, but I think that it is a low priority problem.

I would like to make a pull request when improvement is needed.

john.loughran.colvin commented on 2016-12-07T23:13:27Z
The documentation says that a digest must implement a put function that takes a variadic number of individual ubytes or a ubyte array. This is a stronger requirement than being an output range for ubyte and ubyte[].

It is possible to argue that std.digest should work for output ranges in general, but that's an enhancement request. It probably wouldn't be a lot of work to implement, but you might be the only person for whom it's a priority...

If you found the documentation confusing or lacking, please feel free to make a pull request to improve it.

If you found the error message confusing or lacking, that's also something that can probably be easily improved, or at least explicitly reported here.


Unable to type

Issue Type: Bug
Opening files I created on my macbook in workspace, none are allowing me to edit. I made a new file independent of the others, and it seems to work fine. How do I make the others work? I am only using scss and html files. They were working prior, and now they do not.
VS Code version: Code 1.30.1 (dea8705087adb1b5e5ae1d9123278e178656186a, 2018-12-18T18:05:00.654Z)
OS version: Darwin x64 18.0.0

System Info

Item
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CPUs
Intel(R) Core(TM) i5-5257U CPU @ 2.70GHz (4 x 2700)

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2d_canvas: enabledchecker_imaging: disabled_offflash_3d: enabledflash_stage3d: enabledflash_stage3d_baseline: enabledgpu_compositing: enabledmultiple_raster_threads: enabled_onnative_gpu_memory_buffers: enabledrasterization: enabledvideo_decode: enabledvideo_encode: enabledwebgl: enabledwebgl2: enabled

Load (avg)
2, 3, 3

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8.00GB (0.29GB free)

Process Argv

Screen Reader
no

VM
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Extensions (21)

Extension
Author (truncated)
Version

vscode-django
bat
0.17.0

vscode-markdownlint
Dav
0.22.0

python-preview
don
0.0.4

githistory
don
0.4.4

jupyter
don
1.1.4

python-extension-pack
don
1.4.0

gitlens
eam
9.2.4

MagicPython
mag
1.1.0

anaconda-extension-pack
ms-
1.0.1

python
ms-
2018.12.1

sublime-keybindings
ms-
4.0.0

team
ms-
1.144.1

vscode-yaml
red
0.2.0

live-sass
rit
3.0.0

LiveServer
rit
5.3.1

sass-indented
rob
1.5.1

python
tht
0.2.3

vscodeintellicode
Vis
1.1.2

vim
vsc
0.17.3

jinja
who
0.0.8

JavaScriptSnippets
xab
1.7.2

@Cdixon855 I'm unable to reproduce this given the information above.
What exactly do you mean by

none are allowing me to edit

I've used the following steps from a console/terminal:

touch test.html
code test.html

The file can be edited without any problems.

This has happened to me with 2 separate projects today. Keyboard shortcuts work as expected, although any files in the project do not accept keyboard inputs where the cursor is.
Following @egamma's steps did not work if that project was open (and code test.html opens in that window), however closing VS Code and executing code test.html again allows for editing that file.
Closing VS Code again, dragging the project directory onto the VS Code in macOS dock, and opening that file does not allow for editing. However, if VS Code is closed with that file as an open tab, and then the project is opened again, it allows for editing the file.
Here's a screen recording of the issue occurring.
VS Code version: Version 1.30.1 (dea8705087adb1b5e5ae1d9123278e178656186a, 2018-12-18T17:58:06.754Z)
OS version: macOS Mojave 10.14.2 (18C54)
Extensions

DavidHelmer.mavensmate
esbenp.prettier-vscode
ms-vscode.sublime-keybindings
salesforce.salesforcedx-vscode
salesforce.salesforcedx-vscode-apex
salesforce.salesforcedx-vscode-apex-debugger
salesforce.salesforcedx-vscode-apex-replay-debugger
salesforce.salesforcedx-vscode-core
salesforce.salesforcedx-vscode-lightning
salesforce.salesforcedx-vscode-visualforce
wesbos.theme-cobalt2


Security Refactor for server users

Codecov Report

:exclamation: No coverage uploaded for pull request base (develop@f0a6aea). Click here to learn what that means.
The diff coverage is 72.54%.

@@            Coverage Diff             @@
##             develop    #9160   +/-   ##
==========================================
  Coverage           ?   52.26%
  Complexity         ?    36041
==========================================
  Files              ?     2516
  Lines              ?   197355
  Branches           ?    35362
==========================================
  Hits               ?   103154
  Misses             ?    79215
  Partials           ?    14986

Impacted Files
Coverage Δ
Complexity Δ

...nologies/orient/core/security/OSecuritySystem.java
0% <ø> (ø)
0 <0> (?)

...s/orient/core/metadata/security/OSecurityUser.java
100% <ø> (ø)
0 <0> (?)

.../orient/core/metadata/security/OImmutableUser.java
57.14% <0%> (ø)
22 <0> (?)

...hnologies/orient/core/metadata/security/OUser.java
47.55% <0%> (ø)
27 <0> (?)

...orient/server/security/ODefaultServerSecurity.java
37.9% <50%> (ø)
55 <1> (?)

...ies/orient/core/metadata/security/OSystemUser.java
7.69% <75%> (ø)
1 <1> (?)

...rient/server/security/OSecurityServerExternal.java
78.57% <78.57%> (ø)
8 <8> (?)

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RetryTimeCycle gets removed, but not converted

Describe the bug
I have a service task with asyncBefore and RetryTimeCycle R4/PT10S.
Hint after conversion says:
TASK: Element 'failedJobRetryTimeCycle' was transformed, please review. Hint: Retry time cycle works different in Zeebe. Please review your implementation

But the retries on the task definition of the converted process is still empty.
Steps to reproduce
Convert a process model with a service task with async before and retryTimeCycle set.
Expected Behaviour
The retries on the converted process is set to 4.
The hint is adjusted.
Or change the hint to ' ... is removed' .
Library version
0.1.2-SNAPSHOT
Camunda version
7
Camunda Distribution
other
Other Camunda distribution
No response

After look into the code, I found that the conversion is loosely coupled.
And the amount of abstract visitors is overwhelming.
Some visitors call org.camunda.community.converter.visitor.AbstractSupportedAttributeVisitor.visitSupportedAttribute(DomElementVisitorContext, String) to return a hint.
The conversion happens as a side effect in the method by
  protected String visitSupportedAttribute(DomElementVisitorContext context, String attribute) {
    context.addConversion(
        ServiceTaskConvertible.class,
        serviceTaskConversion ->
            serviceTaskConversion.addZeebeTaskHeader(attributeLocalName(), attribute));
    context.addConversion(
        ServiceTaskConvertible.class,
        serviceTaskConversion ->
            serviceTaskConversion.getZeebeTaskDefinition().setType(CAMUNDA_7_ADAPTER));
    return "Delegate call to '"
        + attribute
        + "' was transformed to job type '"
        + CAMUNDA_7_ADAPTER
        + "'. Please review your implementation";
  }

But only some visitors implement methods that return a String as a hint to the inspected DomElement.
Which one do something, which don't? It sound like a valid request to simplify the structure.

Current Visitor structure:

more subclasses on AbstractAttributeVisitor:

more Subclasses on AbstractElementVisitor:

Was fixed in extraction of messages to properties file. The current message states:
TASK: Element 'failedJobRetryTimeCycle' cannot be transformed. The timecycle 'R5/PT10S' has to be transformed to Retries.

The value 5 is the expected value for retries.
Only the period is dropped and should be handled by the worker.


Key file from old wallet

Hello.
I am have old key file from old mintme wallet. There is no password when this created.
How do restore access to my wallet?

Windows 7, latest version of wallet, chrome browser.

Hello, for support pls write to<EMAIL_ADDRESS>or any of our Social Media channels/groups.
Thanks


Elaboration on some modules

My current module list is as this:
My questions regarding the modules are at the end.
<?xml version="1.0" encoding="utf-8"?>
<aap>
    <tasklist>

        <initialisation>
            <module><name>aamod_study_init</name></module>
        </initialisation>

        <main>

        <!-- preprocessing -->

        <module><name>aamod_structuralfromnifti</name></module>
        <module><name>aamod_reorienttomiddle_structural</name></module>

        <module><name>aamod_epifromnifti</name></module>
        <module><name>aamod_reorienttomiddle_epi</name></module>

        <module><name>aamod_realign</name></module>
        <module><name>aamod_slicetiming</name></module>
        <module><name>aamod_coreg_extended</name></module>
        <module><name>aamod_biascorrect_structural</name></module>

        <module><name>aamod_segment_structural</name></module>

        <module><name>aamod_norm_write_epi</name></module>

        <module><name>aamod_smooth</name></module>

        <!-- first-level model -->

        <module><name>aamod_firstlevel_model</name></module>
        <module><name>aamod_firstlevel_contrasts</name></module>
        <module><name>aamod_firstlevel_threshold</name></module>

        <!-- second-level model -->

        <module><name>aamod_secondlevel_model</name></module>
        <module><name>aamod_secondlevel_contrasts</name></module>
        <module><name>aamod_secondlevel_threshold</name></module>
        </main>
    </tasklist>
</aap>

SPM_CH30 tutorial module list did not have slicetiming, I added it explicitly. Is that fine?
Shall I add tsdiffana here? And I see that this module is used two times in fmri_advanced.xml. Is there a specific order of things I should follow and where I should place it? (Sorry if its a too newbie question, I haven't seen or heard of this before)
I noticed there is MVPA integration. Which MVPA toolbox does it utilize? Is it decoding toolbox or libsvm? Is it feasible to use it since the last commit on the files was 9 years ago?
MVPA has a "how to" file. Are there any example scripts for marsbar integration as well?
Does my module list do structural coregisteration? When I look at fmri_advanced.xml, I see that there are three coregisterations. Should I add them as well?
I wanted to add bias correction with aamod_biascorrect_structural but when I did that, It complained about not finding TPM.nii, which is fine, I specified it myself like this: aap.tasksettings.aamod_biascorrect_structural.tpm = fullfile(spm('dir'), 'tpm', 'TPM.nii'); But I noticed it was looking for it in Error in aamod_biascorrect_segment8_multichan (line 64) which was weird. Because I don't have that as a module. So is my current segment structural compatible with biascorrection? And also what is the difference between the two? Or am I supposed to add aamod_biascorrect_segment8_multichan instead?

I know there are a lot of questions. Thanks in advance for your answers :)

Adding slicetiming is fine, however you have to specify aap.tasksettings.aamod_slicetiming.refslice and aap.tasksettings.aamod_slicetiming.sliceorderor aap.tasksettings.aamod_slicetiming.autodetectSO. See the module header for further documentation.
tsdiffana is a fMRI QA module. You can add anywhere and anytime between aamod_reorienttomiddle_epi and aamod_firstlevel_model. I usually use twice, before and after the preprocessing.
If you mean mvpaa, then it is an obsolete and untested set of modules, and I cannot say more about it. It may work, though, but I cannot guarantee it. There are, however, newer modules integrating CoSMoMVPA and TDT toolboxes. See modules with the names of the toolboxes in them.
marsbar is not integrated, and it is not even in the plans. I usually use roiextract on firstlevel betas or contrasts to get estimates.
In your workflow, aamod_coreg_extended does structural coregistration. fmri_advanced uses a two-stage approach I described earlier
If you look at the module header of aamod_biascorrect_structural, you see that it actually calls aamod_biascorrect_segment8_multichan.m (see mfile_alias='aamod_biascorrect_segment8_multichan'). This is a common aa-practice to reuse module bodies (m-files) with different pre-specified parameters or even different streams. Also, some cases, such as bias correction, need some clean-up to remove redundancies and ambiguities. You are on the safe side as long as you follow the non-CBU examples, which are actively maintained.

Thanks for your answers. That clarifies a lot for me.

marsbar is not integrated, and it is not even in the plans. I usually use roiextract on firstlevel betas or contrasts to get estimates.

I was talking about this module when I said marsbar: https://github.com/automaticanalysis/automaticanalysis/blob/master/aa_modules/aamod_marsbar.m

Finally, what does aamod_biascorrect_meanepi do? From the header I see that it inherits from aamod_biascorrect.
I see that ds000114_motor.xml contains both structural and epi bias correction. What does the latter do? Shall I add it as well?

I forgot about the aamod_marsbar module. I have not touched it for a while, but feel free to use (and report ;)).
aamod_biascorrect_meanepi correct bias for the meanepi, as its name suggests. You may need to use if there is a considerable RF bias in your EPI, but I do not use it regularly.

Right now I am running AA on WSL to test how FSL integration works. I am particularly interested aamod_bet. The module suggests doing this somewhere between realignment and normalization. Shall I run this right before normalization, or shall I also take into account it's position in relation to bias correction and segmentation as well?

FSL is not integrated as a whole buy rather in parts. BET, for example, is integrated and used in some examples, as well.
However, you do not need BET for fMRI analysis with SPM. In fact, it sometimes makes registration/normalisation worse. I use BET mostly for DTI.

I haven't used BET myself so I asked a member in our lab who uses it.  However when you do that, apparently the skull is rendered as well so we remove the skull to visualize things better. I thought we were analyzing data on BET'ed images but it turns out this is just to visualize things.

You can add aamod_bet just before the aamod_firstlevel_threshold. Make sure you add the module which processes structural stream.

Once again, thank you so much for your answers.
I showed our preprocessing analysis pipeline to a few lab members today. So far, the approach members in the lab took for preprocessing was to use the SPM GUI using the tutorial in this youtube video.
What they claimed is, and what I also confirmed -- that overall running things with AA is slower than using the gui itself. For example, realignment or slicetiming takes about 1-2 minutes when you do it through GUI for a single subject for a single session, however when you run AA it takes much longer (5-6 minutes).
Why is it that it takes longer for the outputs to be generated, when you run AA?

aa does data management (copying and sorting the data as inputs and outputs to make sure that things work the same for 1-2-many session), sanity checks, QA (realignment plots), and provenance tracking. Because of this overhead, things are more organised, transparent, and reproducible, and you do not have to worry about e.g. filename prefixes if you change the order of realignment and slicetiming
I am not sure whether the settings for aa and the GUI were identical, i.e. you were doing the same thing. Also, if you use automaticSO for slicetiming, then aa detects the slice acquisition scheme based on JSON and set the timings accordingly; which is more precise then the default slicetiming approach.
aa main strength is that doing 10-20-100 participants does not take much longer than 1, as long as you have enough computing power

Thanks. To clarify, using AA is definitely better for me. I needed an answer for those who were complaining about speed :) Indeed when you utilize parallel computing things will become incredibly fast. I have not been able to properly utilize this just yet.

I am not sure whether the settings for aa and the GUI were identical, i.e. you were doing the same thing. Also, if you use automaticSO for slicetiming, then aa detects the slice acquisition scheme based on JSON and set the timings accordingly; which is more precise then the default slicetiming approach.

Yes. Those were same. Slicetiming and realignment are just examples, overall using GUI is much faster. For all steps.
For example, smoothing takes 2.5 minutes with GUI,
------------------------------------------------------------------------
04-Jul-2022 20:07:26 - Running job #7
------------------------------------------------------------------------
04-Jul-2022 20:07:26 - Running 'Smooth'
04-Jul-2022 20:10:56 - Done    'Smooth'

Smoothing with AA takes around 5-10 minutes. So I wanted to check why is it slower, and if there is a way to speed things up (apart from using PCT)

Also, if you use automaticSO for slicetiming, then aa detects the slice acquisition scheme based on JSON and set the timings accordingly; which is more precise then the default slicetiming approach.

I have defined slicetiming myself. My json headers are available in the script. If it is a better approach to use automaticSO I will definitely utilize this.

From where do you take your time estimates for aa?
For slicetiming: the automaticSO is more accurate than just using the sliceorder because it corrects for actual slice times and not just estimates based on TR and slice number. The difference may not be huge depending on the use case and the system. However, Siemens does not distribute slice acquisition equally within a TR, which the default (GUI-based) slicetiming assumes.

For slicetiming: the automaticSO is more accurate than just using the sliceorder because it corrects for actual slice times and not just estimates based on TR and slice number. The difference may not be huge depending on the use case and the system. However, Siemens does not distribute slice acquisition equally within a TR, which the default (GUI-based) slicetiming assumes.

Thanks. I will use that then.

From where do you take your time estimates for aa?

It is a rough guess of what I've experienced while running the scripts.
However, I tend to also look at the console output in MATLAB. For example, I am running preprocessing for a single session single participant right now.
AA output:

SPM12: spm_realign (v7141)                         20:38:26 - 04/07/2022
========================================================================
Completed                               :          20:42:18 - 04/07/2022

SPM12: spm_reslice (v7141)                         20:42:18 - 04/07/2022
========================================================================
Completed                               :          20:44:37 - 04/07/2022
Working with session 1:
 output stream epi  aamod_realign_00001 sub-01  written with 1 file(s)
Warning: Removing "C:\Program Files\MATLAB\spm12\external\fieldtrip\compat\matlablt2012a" from your path.
See http://www.fieldtriptoolbox.org/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path/
 output stream realignment_parameter  aamod_realign_00001 sub-01  written with 1 file(s)
 output stream meanepi  sub-01  written with 1 file(s)
 output stream fd  aamod_realign_00001 sub-01  written with 1 file(s)
MODULE aamod_realign COMPLETED

	 	 	 Elapsed time = 0h:6m:15s
	 	 	 ...at = 20:44:41 (4/7/2022)
MODULE aamod_slicetiming PENDING: SPM slice timing for F:\fMRI\HCFprep\results\test_2\aamod_slicetiming_00001\sub-01\done_aamod_slicetiming_00001

MODULE aamod_slicetiming RUNNING: SPM slice timing for F:\fMRI\HCFprep\results\test_2\aamod_slicetiming_00001\sub-01
 retrieving stream epi from F:\fMRI\HCFprep\results\test_2\aamod_realign_00001\sub-01 to F:\fMRI\HCFprep\results\test_2\aamod_slicetiming_00001\sub-01
 retrieving stream epi from F:\fMRI\HCFprep\results\test_2\aamod_realign_00001\sub-01 to F:\fMRI\HCFprep\results\test_2\aamod_slicetiming_00001\sub-01
 retrieving stream epi_dicom_header from F:\fMRI\HCFprep\results\test_2\aamod_epifromnifti_00001\sub-01 to F:\fMRI\HCFprep\results\test_2\aamod_slicetiming_00001\sub-01
 executing

SPM12: spm_slice_timing (v6130)                    20:44:43 - 04/07/2022
========================================================================
Number of slices is...                  :                             32
Time to Repeat (TR) is...               :                              2
Parameters are specified as...          :                  slice indices
Completed                               :          20:45:40 - 04/07/2022
 output stream epi  aamod_slicetiming_00001 sub-01  written with 1 file(s)
 output stream sliceorder  aamod_slicetiming_00001 sub-01  written with 1 file(s)
MODULE aamod_slicetiming COMPLETED

GUI output:
------------------------------------------------------------------------
04-Jul-2022 19:38:47 - Running job #3
------------------------------------------------------------------------
04-Jul-2022 19:38:47 - Running 'Realign: Estimate & Reslice'

SPM12: spm_realign (v7141)                         19:38:47 - 04/07/2022
========================================================================
Warning: Removing "C:\Program Files\MATLAB\spm12\external\fieldtrip\compat\matlablt2010b" from your path.
See http://www.fieldtriptoolbox.org/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path/
Warning: "C:\Program Files\MATLAB\spm12\external\fieldtrip\compat\matlablt2010b" not found in path.
> In rmpath (line 71)
In isrow (line 35)
In setdiff>setdiffR2012a (line 202)
In setdiff (line 157)
In matlab.graphics.illustration.Legend.autoUpdateCallback
In print (line 36)
In spm_print (line 99)
In spm_realign>plot_parameters (line 527)
In spm_realign (line 168)
In spm_run_realign (line 31)
In cfg_run_cm (line 29)
In cfg_util>local_runcj (line 1717)
In cfg_util (line 972)
In cfg_ui>MenuFileRun_Callback (line 710)
In gui_mainfcn (line 95)
In cfg_ui (line 53)
Printing 'Graphics' figure to:
  C:\Users\tamer\Desktop\study3\input\sub-01_out\spm_2022Jul04.ps
Completed                               :          19:39:43 - 04/07/2022

SPM12: spm_reslice (v7141)                         19:39:43 - 04/07/2022
========================================================================
Completed                               :          19:40:20 - 04/07/2022
04-Jul-2022 19:40:20 - Done    'Realign: Estimate & Reslice'
04-Jul-2022 19:40:20 - Done

------------------------------------------------------------------------
04-Jul-2022 19:41:31 - Running job #4
------------------------------------------------------------------------
04-Jul-2022 19:41:31 - Running 'Slice Timing'

SPM12: spm_slice_timing (v6130)                    19:41:31 - 04/07/2022
========================================================================
Number of slices is...                  :                             32
Time to Repeat (TR) is...               :                              2
Parameters are specified as...          :                  slice indices
Completed                               :          19:41:54 - 04/07/2022
04-Jul-2022 19:41:54 - Done    'Slice Timing'
04-Jul-2022 19:41:54 - Done

------------------------------------------------------------------------
04-Jul-2022 19:54:04 - Running job #5
------------------------------------------------------------------------
04-Jul-2022 19:54:04 - Running 'Coregister: Estimate & Reslice'

SPM12: spm_coreg (v7320)                           19:54:04 - 04/07/2022
========================================================================
Completed                               :          19:54:26 - 04/07/2022

SPM12: spm_reslice (v7141)                         19:54:26 - 04/07/2022
========================================================================
Completed                               :          19:54:27 - 04/07/2022
04-Jul-2022 19:54:27 - Done    'Coregister: Estimate & Reslice'
04-Jul-2022 19:54:27 - Done

Do you use 4D NIfTI (single file combining all 3d volumes for the session/run) for both cases?

I ran both of these for a single session, DICOM imported image. I did DICOM import from SPM gui.

You can switch off 4D NIfTI by aap.options.NIFTI4D = 0;

The ones I tested on SPM GUI were indeed 3D NIfTIs (it didn't occur to me that this would make a huge difference). And the ones I used with AA were 4D NIfTIs. I wasn't expecting it that to make much a huge difference. When we were comparing AA with SPM GUI I had a friend with me, he had suggested to use DICOM import because I didn't do much SPM GUI preprocessing before and he said he was unfamiliar with 4D NII's. So actually if we had used the same files, it would probably take the same time.
I will see if switching off 4D NIfTI makes any difference in terms of speed. Right now I am running it to check.

Even though you switch off 3D NIfTI, running tsdiffana or reorienttomidle etc. generates output files as a single file. So at the upcoming steps, AA deals with single image files.

aa also uses SPM 's DICOM converter when starting from DICOMs
tsdiffana does not generate EPI output
reorienttomidle uses spm_run_reorient. It is possible that it also generates 4D NIfTI as default. I have not looked into it because I prefer 4D NIfTI anyway for the abovementioned reason.
TBH, I never paid attention to speed unless for real-time application.

I agree. Speed also doesn't matter much for me. I will explain why this approach is better if anyone complains about speed.

I figured out why 3D NIfTI's were converted back to 4D. They need to be 3D from the start. I was giving them as 4D and hoping that AA would expand them once and then move on from there. That wasn't the case.
Some lab members will analyze on their own personal computers. So speed of analysis is important for those people. I noticed that add_subject accepts 3D NIfTI so I decided to give it a try. And the analysis was pretty fast. To be fair I may also want to stick to using 3D. And it may be worth looking into why it takes so long for it to process 4D NIfTI.
However, I ran into one issue. I am adding subjects like this:
aap = aas_addsubject(aap,subj,'functional',{func_files},'structural',{subject_data_anat});
func_files is a single session cell array with 3D NIfTI images:

The only issue here is that I am not sure if it is possible to provide the hdr in this setup. Is it possible? And if it is not, would it be straight forward for me to edit the code and put a PR so that hdr's can be given along with 3D files?

Okay, nevermind! I think it works fine when you put the cell array of images inside a cell array like this and then in a struct:
    tmp_struct = struct('fname',{func_files},'hdr',fullfile(func_hdr.folder,func_hdr.name));
    aap = aas_addsubject(aap,subj,'functional',{tmp_struct},'structural',{subject_data_anat});

Dear @tiborauer
autoDetectSO does not work for me.
Error using spm_slice_timing (line 125)
Input is neither slice indices nor slice times.

I only need to specify the ref slice, right?
Here's what my DICOM header looks like:
{
	"Modality": "MR",
	"MagneticFieldStrength": 3,
	"ImagingFrequency": 123.237,
	"Manufacturer": "Siemens",
	"ManufacturersModelName": "TrioTim",
	"InstitutionName": "UMRAM_AC6DEA_Ankara",
	"InstitutionalDepartmentName": "Department",
	"InstitutionAddress": "Street_StreetNo_City_District_TR_ZIP",
	"DeviceSerialNumber": "35397",
	"StationName": "MRC35397",
	"PatientPosition": "HFS",
	"ProcedureStepDescription": "AUSAF_TAMER",
	"SoftwareVersions": "syngo_MR_B17",
	"MRAcquisitionType": "2D",
	"SeriesDescription": "MoCoSeries",
	"ProtocolName": "session_1_MoCo",
	"ScanningSequence": "EP",
	"SequenceVariant": "SK_OSP",
	"ScanOptions": "FS",
	"SequenceName": "_epfid2d1_64",
	"ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM", "MOCO", "MOSAIC"],
	"SeriesNumber": 4,
	"AcquisitionTime": "18:59:54.732500",
	"AcquisitionNumber": 1,
	"ImageComments": "Reference_volume_for_motion_correction.",
	"SliceThickness": 3,
	"SpacingBetweenSlices": 3.75,
	"SAR": 0.154153,
	"EchoTime": 0.03,
	"RepetitionTime": 2,
	"FlipAngle": 78,
	"PartialFourier": 1,
	"BaseResolution": 64,
	"ShimSetting": [
		-2176,
		8069,
		2036,
		594,
		71,
		-253,
		61,
		159	],
	"TxRefAmp": 313.201,
	"PhaseResolution": 1,
	"PhaseOversampling": 0.2,
	"VendorReportedEchoSpacing": 0.00053,
	"ReceiveCoilName": "32Ch_Head",
	"CoilString": "C:HEA;HEP",
	"PulseSequenceDetails": "%SiemensSeq%_ep2d_bold",
	"PercentPhaseFOV": 100,
	"PhaseEncodingSteps": 77,
	"AcquisitionMatrixPE": 64,
	"ReconMatrixPE": 64,
	"BandwidthPerPixelPhaseEncode": 49.008,
	"ParallelReductionFactorInPlane": 2,
	"EffectiveEchoSpacing": 0.000318826,
	"DerivedVendorReportedEchoSpacing": 0.000531376,
	"TotalReadoutTime": 0.020086,
	"PixelBandwidth": 2232,
	"DwellTime": 3.5e-06,
	"PhaseEncodingDirection": "j-",
	"SliceTiming": [
		0,
		-0.0625,
		-0.1275,
		-0.19,
		-0.2525,
		-0.315,
		-0.3775,
		-0.44,
		-0.5025,
		-0.565,
		-0.6275,
		-0.69,
		-0.7525,
		-0.8175,
		-0.88,
		-0.9425,
		-1.005,
		-1.0675,
		-1.13,
		-1.1925,
		-1.255,
		-1.3175,
		-1.38,
		-1.4425,
		-1.5075,
		-1.57,
		-1.6325,
		-1.695,
		-1.7575,
		-1.82,
		-1.8825,
		-1.945	],
	"ImageOrientationPatientDICOM": [
		0.999936,
		0.003331,
		0.0108182,
		4.70324e-09,
		0.955721,
		-0.294274	],
	"InPlanePhaseEncodingDirectionDICOM": "COL",
	"ConversionSoftware": "dcm2niix",
	"ConversionSoftwareVersion": "v1.0.20181125  (JP2:OpenJPEG) GCC9.3.0"
}

This is your unprocessed DICOM headers, however, epifromnifti extends it with further info: https://github.com/automaticanalysis/automaticanalysis/blob/6377d85ca5e89e769729065f981c27590e5457ec/aa_modules/aamod_epifromnifti.m#L71-L75
You should look at the .mat file in the session folder for the aamod_slicetiming stage.
For debugging, I suggest using dbstop if error, which halts the execution if an error arises. Then you can explore the variables (at various levels) and trace back the issue.

Sliecetimes MUST always be non-negative values because they represent the time relative to the acquisition time of the volume. Descending order does not mean you go back in time. :) Your slicetime should be like this:
1.9450 1.8825 1.8200 ... 0
Have you entered these slice times manually?

Ah, I see. Sorry for my ignorance.
I did not enter these slice times manually. Please check the DICOM header in .json format I shared above. The values are negative there too.
However, could it be that this is some sort of mess up due to dcm2niix? Because I looked at the DICOM header myself using pydicom and can't get to see any slicetiming field here. What is your suggestion?
       LO: '1.0'
(0019, 100a) [NumberOfImagesInMosaic]            US: 32
(0019, 100b) [SliceMeasurementDuration]          DS: '20.0'
(0019, 100f) [GradientMode]                      SH: 'Fast*'
(0019, 1011) [FlowCompensation]                  SH: 'No'
(0019, 1012) [TablePositionOrigin]               SL: [0, 0, -1297]
(0019, 1013) [ImaAbsTablePosition]               SL: [0, 0, -1297]
(0019, 1014) [ImaRelTablePosition]               IS: [0, 0, 0]
(0019, 1015) [SlicePosition_PCS]                 FD: [-572.98795176, -585.60268331, 16.89462894]
(0019, 1016) [TimeAfterStart]                    DS: '1.945'
(0019, 1017) [SliceResolution]                   DS: '1.0'
(0019, 1018) [RealDwellTime]                     IS: '3500'
(0019, 1025) [RBMoCoTrans]                       FD: [0.0, 0.0, 0.0]
(0019, 1026) [RBMoCoRot]                         FD: [0.0, 0.0, 0.0]
(0019, 1028) [BandwidthPerPixelPhaseEncode]      FD: 49.008
(0019, 1029) [MosaicRefAcqTimes]                 FD: Array of 32 elements
(0020, 000d) Study Instance UID                  UI: <IP_ADDRESS>.1<IP_ADDRESS>.35397.30000022030109185845300000112
(0020, 000e) Series Instance UID                 UI: <IP_ADDRESS>.1<IP_ADDRESS>.35397.2022031310450158025127<IP_ADDRESS>
(0020, 0010) Study ID                            SH: '1'
(0020, 0011) Series Number                       IS: '4'
(0020, 0012) Acquisition Number                  IS: '1'
(0020, 0013) Instance Number                     IS: '1'
(0020, 0032) Image Position (Patient)            DS: [-572.98795175552, -585.60268330637, 16.894628938962]
(0020, 0037) Image Orientation (Patient)         DS: [1, -1e-016, 0, 1e-016, 0.99780146819131, -0.0662739019167]
(0020, 0052) Frame of Reference UID              UI: <IP_ADDRESS>.1<IP_ADDRESS>.35397.1.20220313103348<IP_ADDRESS>
(0020, 1040) Position Reference Indicator        LO: ''
(0020, 1041) Slice Location                      DS: '-21.952689235765'
(0020, 4000) Image Comments                      LT: Array of 39 elements
(0028, 0002) Samples per Pixel                   US: 1
(0028, 0004) Photometric Interpretation          CS: 'MONOCHROME2'
(0028, 0010) Rows                                US: 384
(0028, 0011) Columns                             US: 384
(0028, 0030) Pixel Spacing                       DS: [3, 3]
(0028, 0100) Bits Allocated                      US: 16
(0028, 0101) Bits Stored                         US: 12
(0028, 0102) High Bit                            US: 11
(0028, 0103) Pixel Representation                US: 0
(0028, 0106) Smallest Image Pixel Value          US: 0
(0028, 0107) Largest Image Pixel Value           US: 1454
(0028, 1050) Window Center                       DS: '610.0'
(0028, 1051) Window Width                        DS: '1264.0'
(0028, 1055) Window Center & Width Explanation   LO: 'Algo1'
(0029, 0010) Private Creator                     LO: 'SIEMENS CSA HEADER'
(0029, 0011) Private Creator                     LO: 'SIEMENS MEDCOM HEADER2'
(0029, 1008) [CSA Image Header Type]             CS: 'IMAGE NUM 4'
(0029, 1009) [CSA Image Header Version]          LO: '20220313'
(0029, 1010) [CSA Image Header Info]             OB: Array of 11152 elements
(0029, 1018) [CSA Series Header Type]            CS: 'MR'
(0029, 1019) [CSA Series Header Version]         LO: '20220313'
(0029, 1020) [CSA Series Header Info]            OB: Array of 89332 elements
(0029, 1160) [Series Workflow Status]            LO: 'com'
(0032, 1060) Requested Procedure Description     LO: 'AUSAF TAMER'
(0040, 0244) Performed Procedure Step Start Date DA: '20220313'
(0040, 0245) Performed Procedure Step Start Time TM: '094638.171000'
(0040, 0253) Performed Procedure Step ID         SH: 'MR20220313094638'
(0040, 0254) Performed Procedure Step Descriptio LO: 'AUSAF^TAMER'
(0051, 0010) Private Creator                     LO: 'SIEMENS MR HEADER'
(0051, 1008) [CSA Image Header Type]             CS: 'IMAGE NUM 4'
(0051, 1009) [CSA Image Header Version ??]       LO: '1.0'
(0051, 100a) [Unknown]                           LO: 'TA 00.02'
(0051, 100b) [AcquisitionMatrixText]             LO: '64*64'
(0051, 100c) [Unknown]                           LO: 'FoV 1152*1152'
(0051, 100e) [Unknown]                           LO: 'Tra>Cor(-3.8)'
(0051, 100f) [CoilString]                        LO: 'C:HEA;HEP'
(0051, 1011) [PATModeText]                       LO: 'p2'
(0051, 1012) [Unknown]                           SH: 'TP 0'
(0051, 1013) [PositivePCSDirections]             SH: '+LPH'
(0051, 1016) [Unknown]                           LO: 'p2 M/ND/NORM/MOCO/MOSAIC'
(0051, 1017) [Unknown]                           SH: 'SL 3.0'
(0051, 1019) [Unknown]                           LO: 'A1/FS'
(7fe0, 0010) Pixel Data                          OW: Array of 294912 elements

Looks like this could indeed be a dmc2niix issue. I will check with them.

The issue was due to Siemens', which messes up slice orders. dcm2niix fixes this, but only in newer versions. I solved this issue by updating dcm2niix.


feat: PAQR execution workflow

Fixes #41 #223
TODO

preprocessing
postprocessing
creation or download of poly(A) sites reference file?
cluster configs
paqr module needs samples.tsv (instead of samples.csv). Can this be overridden somehow?

Checklist

[ ] I have performed a self-review of my own code
[ ] I have commented my code, particularly in hard-to-understand areas
[ ] I have updated corresponding READMEs (if applicable)
[ ] My code follows the templates/style guidelines of the repository
[ ] In- and output formats comply with APAeval specifications
[ ] No parameters or file names are hardcoded
[ ] Results, logs or other output is not commited to the repository
[ ] I have tested my code

Hi @ninsch3000, thanks for the great work! I recognize that this is still a draft but I've got some comments.

I could not go through the test, as I got an "name 'github' is not defined" error. Not sure what the problem is, but seems like a missing import or so.
I think we decided not to have the subdirectories such as PAQR_snakemake, thus I think it can be deleted.
Include in the readme how to run the workflow, and that the current configuration is set up for the test data.
the config file seems to have parameters with similar meaning, e.g. samples table and out directory specification. I marked those I found.
some comments regarding left-overs from the template

UPDATE: actually using the bumped snakemake version helped and I don't get the "name 'github' is not defined" error anymore.
Running the testdryrun.sh works, but I get an error with run_local.sh:
ERROR  : Failed to create user namespace: user namespace disabled
which could be due to singularity.
Manually removing this from the apaeval_execution_workflows environment with conda remove singularity and instead using my locally installed Singularity (v3.5.2), the test successfully finishes.
So, maybe we need to delete the conda-based singularity (conda-forge::singularity=3.7.1) in apaeval_env.yaml? Maybe it's just not working for me because I don't have root access on my machine.

Can it be that the resulting bed files are empty?

Yes, good point! I always assumed that this would be different on real data, but always forgot to test. Just now I ran the workflow on a small C. elegans sample, and there I get some output. However, I only get 8 poly(A) sites, so that's a good reminder that the settings in config are probably not ideal yet. Have to check the publication for their defaults!

TO DO:

[ ] Check for correct chromosome naming of reference PAS (with or without "chr") and add "chr" if necessary
OR:
[ ] Remove reference PAS download from workflow and describe it and the correct chr naming necessity in README

The requirement for the same chromosome names is in a general sense right? By that I mean it's not because PAQR requires a specific naming convention (I'm pretty sure that's not the case), it's just that to match different reference files you need the same names.

PAQR requires all inputs (= PolyASite bed, gtf, bam files) to have the same chr naming, else it will not find any matches. But both, with or without "chr" are fine. But yes, PolyASite is without "chr", so we have to adjust

Thanks a lot for your thoughts @SamBryce-Smith !
I think due to lack of time we could really just add "chr" to the PolyASite bed. As I understand from the Gencode FAQs, Gencode and Ensembl are using the same genome and it's not a problem to insert or delete "chr". The conversion is needed between Ensembl and UCSC genomes though. I might be wrong however, because this topic always confuses me :stuck_out_tongue_closed_eyes:
And I agree, I'll delete the downloading of the PolyASite bed, that didn't feel right anyway.

Thanks a lot for your review @SamBryce-Smith ! Excellent points, as usual. :star_struck:
@dominikburri  and me did in fact briefly discuss the issue of the poly(A) site clusters vs. single nuc positions yesterday, but discarded it as "well, that's part of the participants algorithm/mode of function". But you are right of course, the reported intervals are already larger to begin with, which is an "advantage" for matching sites (might be a disadvantage if we're judging precision of location, or penalizing multiple overlaps between one pd and several gt sites, but as I understandm we are not with the quantification metrics. Or are we, @daneckaw ?).
However, we could then argue, that using PolyASite clusters in the first place is an advantage, because other tools might use reference PAS with only single nucleotide positions and thus have a more limited genomic range to even look for poly(A) sites. And so we're back at the old discussion about providing the same reference PAS to all participants, or using the one that the authors intended :)
That said, I'm nevertheless fine with reporting the representative sites instead of the clusters. But curious to hear @dominikburri 's opinion.


Investigate whether playouts starting at midnight is necessary

Playouts starting in the past (midnight of the current day) can be confusing to users. I believe it's currently needed to advance through the schedule items so that the correct item plays at the current time, but perhaps different logic could be used so that e.g. chronological schedules would have s01e01 "now."

Starting at midnight is required for the current playout system. Block playouts will not have this limitation.


Remove double "zoom_to_fit"

in https://github.com/KittyCAD/modeling-app/pull/3205
A hack was added to stop weird ness with zoom to fit, in that the zoom_to_fit code was duplicated so it makes the request twice in a row

This smells like a race condition, or some other client side bug, but my best theory is that it's related to  https://github.com/KittyCAD/engine/issues/2310, and that's because of some debugging code I was trying out
Explanation here:
https://github.com/user-attachments/assets/275373ca-e99a-4278-96ea-f267601a9985
But essentially the first zoom to fit looks wrong and it takes a second for it to to come good.
Other work around attempts
Don't send an empty array
https://github.com/KittyCAD/engine/issues/2310 has been difficult to replicate in the engine, so it's likely something unique about the scene when the modeling app has connected to it, it might be that there are more default planes created and they are effecting the zoom to fit, but I don't want to speculate too much. However I thought it might be worth looping over the artifactMap and sending through all of the start_path ids in object_ids the API because these become the object ids, however this had no effect.
Delete default planes for zooming
I did try
delete planes
zoom to fit
re-create planes

To make sure there wasn't anything extra in the scene but this didn't work either.

I might be wrong about the above, but it's my best theory atm, and I think the double zoom_to_fit probably needs to stay there until https://github.com/KittyCAD/engine/issues/2310 is closed out.
anyone else is welcome to look into it though ofc.

Yup we good.


feat(godeps): cleanup godeps

I just ran godep save ./... and let it cleanup some unused packages.

@Joshua-Anderson this keeps failing CI.  Mysteriously, I am unable to replicate the failure locally, but it does look related to chrootarchive  being removed from the godeps.  This also is in need of a rebase... let's rebase and let the tests have another go.

We have also updated go-etcd and removed gexpect recently, so this PR will need to catch up with those changes.

I've tried everything I can think off and can't reproduce this error locally. I even deleted the docker/docker src in my local gopath, so I know go isn't falling back on it. I updated the code to remove the latest packages. Maybe this is due to the node using a older version of godeps?

Hmm, I wonder if there's a stray Godeps directory in deis/deis/builder on that node. That could explain the failures. It passed locally for me too with a make -C builder build test-functional.


"Recently added" sort order for resources.

A "recently added" sort order provides a cheap way of knowing what is new at dohaskell by combining it with the "list all" option. Note that I implemented this in the laziest way possible -- there is no reverse "earliest added" option, and the comparison is based on mere resource ids.

Great! I haven't touched this code in over a year so it might take a bit before I can get everything pushed live (do I even have my EC2 key? ugh...).
I have one suggestion: can you go back to a full case-analysis of SortBy rather than using a catch-all? I'd rather have the duplicated RHS and the compiler error when another SortBy gets added.

can you go back to a full case-analysis of SortBy rather than using a catch-all?

Sure thing. I have amended the commit.


fix for selinux to make it work in openshift 4.X

tested in openshift 4.11.37

Thanks for opening this @bortek, I think we're going to go with a different direction and have the CSI driver set the label itself (see #105 )


Move allowsDynamicSplitting to Reader, and set it in CompressedSource.

Before the change in CompressedSource, testUnsplittable() fails in:
assertNull(reader.splitAtFraction(fractionConsumed));

R: @dhalperi

LGTM, will merge once green.


Update manifest to explicitly list installation targets

I'm using Azure DevOps Server 2019 RC1. I got an error when I install the extension. I already attached a screenshot.

Please try upgrading to 2019 Update 1: https://docs.microsoft.com/en-us/azure/devops/server/release-notes/azuredevops2019u1?view=azure-devops

Please try upgrading to 2019 Update 1: https://docs.microsoft.com/en-us/azure/devops/server/release-notes/azuredevops2019u1?view=azure-devops

Yeah, I know it. The reason for the problem is api version.  You should change to 2019 update 1 on the market place

Good point, we could update to something like:
{
    "targets": [
        {
            "id": "Microsoft.VisualStudio.Services.Cloud"
        },
        {
            "id": "Microsoft.TeamFoundation.Server",
            "version": "[15.0,)"
        }
    ]
}


[TSLA-3411] update styles to tigera design system (#165)

Cherry picking 597a57df0772e938d9e90438f181b22114266118

styling updates to Tigera design system

load font Poppins properly

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.You have signed the CLA already but the status is still pending? Let us recheck it.


MB-12189 set up fe fake data generator and factory tools

Jira ticket for this change
Summary
Is there anything you would like reviewers to give additional scrutiny?
this article explains more about the approach used.
Setup to Run Your Code

💻 You will need to use three separate terminals to test this locally.
Terminal 1
Start the Storybook locally.
make storybook

Terminal 2
Start the UI locally.
make client_run

Terminal 3
Start the Go server locally.
make server_run

Additional steps

Access the
Login as a

Verification Steps for Author
These are to be checked by the author.

[ ] Tested in the Experimental environment (for changes to containers, app startup, or connection to data stores)
[ ] Request review from a member of a different team.
[ ] Have the Jira acceptance criteria been met for this change?

Verification Steps for Reviewers
These are to be checked by a reviewer.

Frontend

[ ] User facing changes have been reviewed by design.
[ ] There are no aXe warnings for UI.
[ ] This works in Supported Browsers and their phone views (Chrome, Firefox, IE, Edge).
[ ] There are no new console errors in the browser devtools
[ ] There are no new console errors in the test output
[ ] If this PR adds a new component to Storybook, it ensures the component is fully responsive, OR if it is intentionally not, a wrapping div using the officeApp class or custom min-width styling is used to hide any states the would not be visible to the user.

Backend

[ ] Code follows the guidelines for Logging
[ ] The requirements listed in Querying the Database Safely have been satisfied.

Database
Any new migrations/schema changes:

[ ] Follows our guidelines for Zero-Downtime Deploys
[ ] Have been communicated to #g-database
[ ] Secure migrations have been tested following the instructions in our docs

Screenshots

Warnings

:warning:
This PR does not include changes to unit tests, even though it affects app code.

Messages

:book:
:link: MB-12189

  Generated by :no_entry_sign: dangerJS against 6055ab6630ceefac20541f9bf6c167ad299faf32

Request: can a link to this PR be added to the ADR for this concept?

Request: can a link to this PR be added to the ADR for this concept?

Yeah, great idea! I can open up a PR for the ADR.

Request: can a link to this PR be added to the ADR for this concept?

Yeah, great idea! I can open up a PR for the ADR.

@pearl-truss here's the other PR: https://github.com/transcom/mymove-docs/pull/205

Closing in favor of #9233


Update de.json line 28, 129 + 135-139 - [merged]

In GitLab by @markusraab78 on Jun 7, 2020, 13:12
Merges patch-1 -> master
translation of new phrases into German.
Line 28 is difficult as there is no good Dmg equivalent, Sch das not really cover it, but seems the best I can do. Maybe Karsten has an idea.

In GitLab by @Asacolips on Jun 7, 2020, 14:10
mentioned in commit 3cb882d09dc840a0d056a18c10f473cd45461348

In GitLab by @Asacolips on Jun 7, 2020, 14:10
merged

In GitLab by @Asacolips on Jun 7, 2020, 14:10
approved this merge request


update README for new Babel 6.13

no Travis I don't believe that I break anything we my markdown change 😼

This really needs to be merged because it doesn't seem to work on new babel versions without this change.

Actually, both approaches work. But I prefer the updated one so merging.


There seems to be a problem with this challenge

Challenge use-a-retina-image-for-higher-resolution-displays has an issue.
User Agent is: Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36.
Please describe how to reproduce this issue, and include links to screenshots if possible.

<style>
  img { height: 100px; width: 100px; }
</style>

<img src="https://s3.amazonaws.com/freecodecamp/FCCStickers-CamperBot200x200.jpg" alt="freeCodeCamp sticker that says 'Because CamperBot Cares'">

code doesnt seem to pass.

Thanks for looking into this! We recently fixed this (#15775), so I'm closing this issue.
Happy coding!