Questions towards using the container about distro HOT 15 CLOSED

This error is due to uploading file with a name which is already present in /images/ folder. Changing file name removes this error.

I think this should have been handled in slideuploder server which should change name of file on uploading it to server or do something similar to this.

from distro.

@zengchu2 I have not tested this on windows. However, I tried it on ubuntu 16.04 and it runs as expected.

from distro.

This is certainly concerning. Can I ask a few questions?
Do you have the body that your browser sent to try to post?
Is there anything more to the body of the 500 error? (there may not be due to what I thought was an already-reported issue about the api gateway eating errors)
Where is the slide from?

Thank you for your patience and for reporting. Our slide loading is pretty confusing at best.

from distro.

Post Slide

• The slide is selected from 'Distro/images' (re https://github.com/camicroscope/Distro/tree/master/images )

• Here are some more detailed steps I performed
  
  
  

• Here is the details of post request http://localhost:4010/data/Slide/post?:
  Header:
  POST /data/Slide/post HTTP/1.1
  Host: localhost:4010
  Connection: keep-alive
  Content-Length: 309
  DNT: 1
  User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/79.0.3945.130 Safari/537.36
  Content-Type: application/json; charset=utf-8
  Accept: /
  Origin: http://localhost:4010
  Sec-Fetch-Site: same-origin
  Sec-Fetch-Mode: cors
  Referer: http://localhost:4010/apps/loader/loader.html
  Accept-Encoding: gzip, deflate, br
  Accept-Language: en,zh-CN;q=0.9,zh;q=0.8
  Cookie: UserID=1580419694593353; lastContentInjectionMode=jquery
  Payload:
  location: "/images/sample.svs"
  mpp-x: "0.499"
  mpp-y: "0.499"
  height: "2967"
  width: "2220"
  vendor: "aperio"
  level_count: 1
  objective: 20
  md5sum: "1ad6e35c9d17e4d85fb7e3143b328efe"
  study: ""
  specimen: ""
  upload_date: "3/4/2020, 12:02:00 AM"
  name: "sample2"
  mpp: 0.499
  mpp_x: 0.499
  mpp_y: 0.499

• Here is the response for the post request above:
  {"errno":"ENOTFOUND","code":"ENOTFOUND","syscall":"getaddrinfo","hostname":"ca-data","host":"ca-data","port":"9099","__statusCode":500}

View Table

• Request http://localhost:4010/data/Template/find headers:
  GET /data/Template/find HTTP/1.1
  Host: localhost:4010
  Connection: keep-alive
  User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/79.0.3945.130 Safari/537.36
  DNT: 1
  Accept: /
  Sec-Fetch-Site: same-origin
  Sec-Fetch-Mode: cors
  Referer: http://localhost:4010/apps/table.html
  Accept-Encoding: gzip, deflate, br
  Accept-Language: en,zh-CN;q=0.9,zh;q=0.8
  Cookie: UserID=1580419694593353; lastContentInjectionMode=jquery

• Request http://localhost:4010/data/Slide/find? headers:
  GET /data/Slide/find HTTP/1.1
  Host: localhost:4010
  Connection: keep-alive
  User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/79.0.3945.130 Safari/537.36
  DNT: 1
  Accept: /
  Sec-Fetch-Site: same-origin
  Sec-Fetch-Mode: cors
  Referer: http://localhost:4010/apps/table.html
  Accept-Encoding: gzip, deflate, br
  Accept-Language: en,zh-CN;q=0.9,zh;q=0.8
  Cookie: UserID=1580419694593353; lastContentInjectionMode=jquery

Thanks for your patience.

from distro.

Thanks @vikasgola, but how about the error of showing 'No Data'. According the doc, I should be fine just simply lanuching the app using command docker-compose -f caMicroscope.yml up right @birm ?

from distro.

Yes; I wonder what's wrong with ca-data. Can I get more diagonistic information; namely, if you replicate this, run docker ps in another terminal?

from distro.

@zengchu2 are you using windows?

from distro.

Yes, and I am using powershell to build docker container.

from distro.

Yes; I wonder what's wrong with ca-data. Can I get more diagonistic information; namely, if you replicate this, run docker ps in another terminal?

I did not setup docker stuff on the embedded system Ubuntu, I just get a 'Cannot connect to the daemon at tcp://localhost:2375. Is this docker daemon running?'

from distro.

Hi all, here is what I get under Ubuntu 18.04 LTS

Logs:
zengchu2@DESKTOP-9AMNB8N:/mnt/h/gsoc/Distro$ docker-compose -f caMicroscope.yml up
ca-mongo is up-to-date
ca-load is up-to-date
ca-auth is up-to-date
ca-iip is up-to-date
ca-security is up-to-date
Starting ca-front ...
Starting ca-data ... error
Starting ca-idx ...

ERROR: for ca-data Cannot start service bindaas: OCI runtime create failed: container_linux.go:346: starting container process caused "process_linux.go:449: container init caused "rootfs_linux.go:58: mounting \"/mnt/h/gsoc/Distro/config/bindaas.config.json\" to rootfs \"/var/lib/docker/overlay2/8facbc375c88c3319c5d906d6854d0d88faf50d3df056b52832d60443432ac7f/merged\" at \"/var/lib/docker/overlay2/8facbc375c88c3319c5d906d6854d0d88faf50d3df056b52832d6Starting ca-front ... error
: unknown: Are you trying to mount a directory onto a file (or vice-versa)? Check if the specified host path exists and is the expected type

ERROR: for ca-front Cannot start service viewer: OCI runtime create failed: container_linux.go:346: starting container process caused "process_linux.go:449: container init caused "rootfs_linux.go:58: mounting \"/mnt/h/gsoc/Distro/config/login.html\" to rootfs \"/var/lib/docker/overlay2/07a37e85341dae5c4e6f8ccfebb8cac45cea695424a93ea32d494a6c404cd178/merged\" at \"/var/lib/docker/overlay2/07a37e85341dae5c4e6f8ccfebb8cac45cea695424a93ea32d494a6c404cd178/merged/var/www/html/login.html\" caused \"not a directory\""": unknown: Are you trying to mount a directory onto a file (or vice-versa)? Check if the specified host path existsStarting ca-idx ... done

ERROR: for viewer Cannot start service viewer: OCI runtime create failed: container_linux.go:346: starting container process caused "process_linux.go:449: container init caused "rootfs_linux.go:58: mounting \"/mnt/h/gsoc/Distro/config/login.html\" to rootfs \"/var/lib/docker/overlay2/07a37e85341dae5c4e6f8ccfebb8cac45cea695424a93ea32d494a6c404cd178/merged\" at \"/var/lib/docker/overlay2/07a37e85341dae5c4e6f8ccfebb8cac45cea695424a93ea32d494a6c404cd178/merged/var/www/html/login.html\" caused \"not a directory\""": unknown: Are you trying to mount a directory onto a file (or vice-versa)? Check if the specified host path exists and is the expected type

ERROR: for bindaas Cannot start service bindaas: OCI runtime create failed: container_linux.go:346: starting container process caused "process_linux.go:449: container init caused "rootfs_linux.go:58: mounting \"/mnt/h/gsoc/Distro/config/bindaas.config.json\" to rootfs \"/var/lib/docker/overlay2/8facbc375c88c3319c5d906d6854d0d88faf50d3df056b52832d60443432ac7f/merged\" at \"/var/lib/docker/overlay2/8facbc375c88c3319c5d906d6854d0d88faf50d3df056b52832d60443432ac7f/merged/root/bindaas/bin/bindaas.config.json\" caused \"not a directory\""": unknown: Are you trying to mount a directory onto a file (or vice-versa)? Check if the specified host path exists and is the expected type
ERROR: Encountered errors while bringing up the project.

from distro.

@zengchu2 are you trying to run it on Windows 10 WSL?

from distro.

I'm getting this error as well. Uploads are successful, but nothing showing up in the data table viewer

from distro.

I think there are at least three different issues floating about here.

If you're getting something about ca-data's mounts failing i.e. "Are you trying to mount a directory onto a file" please let me know more about your system (docker version, compose version, os, etc). I have a windows machine, but not one which supports docker, so I have to admit that that's undertested on windows (not that it should matter, but windows is always a bit of a pain for compatibility; maybe we'll add appveyor or something.)

If you're not noticing the mounting issue, and are feeling especially inquisitive, either use the develop.yml config or remove the logging driver none for the ca-data (bindaas) container. Maybe something else is up with bindaas for one of these issues.

If you're getting an issue about a https handler not being found, then let's put that in a new issue. I think that's more of a docker issue than a camic issue, but we can still troubleshoot.

I'm hoping that #96 will resolve this, though I'm sure we'll have entirely new quirks as a result.

Thanks for your patience. Let's figure out what's up!

from distro.

@birm , I have created a separate issue for htpps handler not being found : #107 .

from distro.

I think this has been resolved since we no longer mount in files directly.

from distro.