I tried to install pgadmin4 on my system in several ways, but each time I was defeated by the intricacies of the install. Luckily I discovered a Dockerfile (dpage/pgadmin4) and that worked out of the box. In my docker-compose.yml I added a volume statement
volumes:
- /var/lib/pgadmin4:/var/lib/pgadmin
In order to preserve the pgadmin data over successive runs. pgadmin4 is accessible from 0.0.0.0:5050 and all works fine.
However, I cannot access the files from my local file system with the query tool, this is all hidden in the docker file system. Fortunately that is in the /var/lib/pgadmin4 system on my local machine. In that directory there is a directory storage and that contains the id I use to login as the name of a directory: the ID x#y.z becomes directory x_y.z and that contains the files and folders I had created from my browser as a test. I tried to change this in the pgadmin4 options to /home/user/development but that path is not recognized because it is not in x_y.z.
Question: how can I change pgadmin4's path from /var/lib/pgadmin4/storage/x_y.z into /home/user/development?
Update
I tried to link a part of my home directory into /var/lib/pgadmin4/storage/x_y.z as a symbolic link:
sudo ln -s /home/user/Documents
After that command there exists a linked directory /var/lib/pgadmin4/storage/x_y.z/Documents with uid:gid being root:root and 777 permission. When I next start the query toolbox and click at open the open box appears and I get 4 identical error messages:
Error: [Errno 2] No such file or directory: /var/lib/pgadmin4/storage/x_y.z/Documents
I have changed the owner:group to the relevant ones I could think of:
1000:1000 (me as user)
root:root
5050:5050 (pgadmin uid and gid)
In all three cases I got this error. What is wrong here?
You override paths in config_local.py (you can create it if not exists already).
STORAGE_DIR = os.path.join(DATA_DIR, 'storage')
to
STORAGE_DIR = '/home/user/Documents'
Restart pgAdmin4.
Ref: https://www.pgadmin.org/docs/pgadmin4/4.22/config_py.html
Related
I'm trying to setup a singularity container for an image processing application, and I need it to be able to save images to a specified directory. I had originally tried using a straight -B flag, but that seems to mount a directory as read only if the container wasn't being run as root. Is there a way to either make a bind r/w for any user, or would I need to use some sort of scratch directory or fusemount?
The write permissions for the bound directory match those on the host system. If you want anyone to be able to write to a given directory, set permissions on the host with chmod 777 dir_name. Keep in mind this will allow anyone to read, write and delete files in the directory. Consider adding users to a shared group and using group permissions (chmod g+rwX dir_name) if there are people using the server who should not have access.
If the directory has the right permissions but you still can't write to it when it's bound, you may want to use singularity --debug exec ... to see that everything is being correctly bound to the container.
I am trying to execute the below docker command where I am trying to get the 'Orthanc.json" file to my system folder which is "orthanc".
docker run --rm --entrypoint=cat jodogne/orthanc /etc/orthanc/orthanc.json >
orthanc/orthanc.json
under /etc/orthanc/orthanc.json - It is a directory and not a file - Am not able to use vim editor to read/open the file. - This is a public one. Anyone can access using this link Orthanc link
I get the below error message, Can you please help me understand what is the issue?
-bash: /orthanc/orthanc.json: Is a directory
orthanc.json should be a file but why does it treat it as a directory?
when I use vim orthanc.json, it throws an error message that it's a directory.
What should I be doing to see this as a config file as I have to make changes to it?
You've somehow already got a directory named /orthanc/orthanc.json on your host system. Remove it and try again.
rmdir /orthanc/orthanc.json # if empty
rm -rf /orthanc/orthanc.json # if not empty -- but see what's in there first!
I am sharing a docker-compose file with a team member to easily build our app. We're both on OSX and it works fine from my machine, but my colleague is getting the following error:
ERROR: for backend Cannot start service backend: b'Mounts denied: \r\nThe path /usr/bin/docker\r\nis not shared from OS X and is not known to Docker.\r\nYou can configure shared paths from Docker -> Preferences... -> File Sharing.\r\nSee https://docs.docker.com/docker-for-mac/osxfs/#namespaces for more info.\r\n.'
I assume it is due to the following statement in the docker-compose.yaml.
volumes:
- "/usr/bin/docker:/usr/bin/docker"
I didn't have to alter my docker-> preferences-> file sharing to make this work. I only have the default dirs shared: /Users, /Volumes, /tmp, /private.
How come it isn't working on his machine? Does he have to add the /usr dir as a shared dir? If so, how come I don't have to?
UPDATE
The problem was that the docker executable was located in /usr/local/bin/ rather than /usr/bin. I have no idea why docker installed the executable differently despite both machines being OSX.
That's a misleading error, should have asked you to check if the path /usr/bin/docker exists on the host machine. Docker (at least on Mac) will attempt to create a directory if it doesn't exist. Apparently, your team mate isn't logged in with sufficient privileges to create /usr/bin/docker.
I am running Docker Toolbox v. 1.13.1a on Windows 7 Pro Service pack 1 x64OS.
with Virtual Box Version 5.1.14 r112924
when I try to run any docker image e.g. official postgres image from Docker Hub with volumes disabled, it works fine!
But when I enable the volumes it fails.
I tried all official documentations
The VM has shared folder as required and has full access to it also
shared folder screenshot
In case of my example of postgresql it crashes with following log
The files belonging to this database system will be owned by user "postgres".
This user must also own the server process.
The database cluster will be initialized with locale "en_US.utf8".
The default database encoding has accordingly been set to "UTF8".
The default text search configuration will be set to "english".
Data page checksums are disabled.
fixing permissions on existing directory /var/lib/postgresql/data ... ok
creating subdirectories ... ok
selecting default max_connections ... 100
selecting default shared_buffers ... 128MB
selecting dynamic shared memory implementation ... posix
selecting default max_connections ... 100
selecting default shared_buffers ... 128MB
selecting dynamic shared memory implementation ... posix
creating configuration files ... ok
running bootstrap script ... LOG: could not link file "pg_xlog/xlogtemp.27" to "pg_xlog/000000010000000000000001": Operation not permitted
FATAL: could not open file "pg_xlog/000000010000000000000001": No such file or directory
child process exited with exit code 1
initdb: removing contents of data directory "/var/lib/postgresql/data"
I know its the problem with folder permissions. But kinda stuck!
A ton of thanks in advance
I've been busy with this problem all day and my conclusion that it's currently simply not possible to run postgresql inside a docker container while keeping your data persistent in a separate volume.
I even tried running the container without linking to a volume and copying the data that was originally in /var/lib/postgresql into a folder of my host OS (Windows 10 Home), then copy that into the folder that got then linked to the container itself.
Alas, I got the next error:
FATAL: data directory "/var/lib/postgresql/data/pgadmin" has wrong ownership
HINT: The server must be started by the user that owns the data directory.
In conclusion: There's something going wrong with the ownership and the correct user owning it and to be able to fix it, you'll need a unix commandline on Windows that is able to run docker (something currently not possible with Bash on Ubuntu on Windows that is running using Ubuntu 16.04 binaries).
Maybe, in the future, you'll be able to run the needed commands (found here, under Arbitrary --user Notes), but these are *nix commands and powershell (started by Kitematic) can't run those. Bash for Ubuntu for Windows could run those, but that shell has no connection to the docker daemon/service on windows...
TL;DR: Lost a day of work: It is currently impossible on Windows.
I have been trying to fix this issue also ..
At first I thought it was a symlink problem (because the first error fails on " could not link .. operation not permitted)
To be sure symlink is permitted you have to :
share a folder in virtualbox
run virtualbox as administrator (if you account is in administrator group) Right click virtualbox.exe and select run as Administrator
if your account is not administrator, add the symlink privilege with secpol.msc > "Local Policies-User Rights Assignments" add your user to "Create symbolic links"
enable symlink for your shared folder in virtualbox :
VBoxManage setextradata VM_NAME VBoxInternal2/SharedFoldersEnableSymlinksCreate/SHARED_FOLDER_NAME 1
Alternatively you can also use the c:\User\username folder which is shared and symlink enabled by default dockertools installation
Now I can create symlinks in the shared folder from the docker container .. but I still have the same error "could not link ... operation not permitted"
So the reason must be somewhere else ... in the file permissions as you said but I do not see why ?
I'm having an issue with docker-compose where I'm passing a file into the container when it's run. The issue is that it doesn't seem to recognize when the file has been changed and serves the saved result back indefinitely until I change the name of the file.
An example (modified names for brevity):
jono#macbook:~/myProj% docker-compose run vpn conf.opvn
Options error: Unrecognized option or missing parameter(s) in conf.opvn:71: AXswRE+
5aN64mYiPSatOACC6+bISv8RcDPX/lMYdLwe8zQY6qWtbrjFXrp2 (2.3.8)
Then I change the file, save it, and run the command again - exact same output.
Then without changing anything I do this:
jono#macbook:~/myProj% cp conf.opvn newconf.opvn
And when I run $ docker-compose run vpn newconf.opvn it works. Seems really silly.
I'm working with Tmux and Mac if there is some way that affects it. Is this the expected behaviour? I couldn't find anything documenting this on the docker-compose homepage.
EDIT:
Specifically I'm using this repo from the amazing Jess.
The image you are using is using volume in order to mount your current directory. Basically the file conf.opvn is copied to the docker container.
When you change the file, the container doesn't see that change, but it does pick up the rename (which the container sees as a new file). This most probably is due to user rights of the file and the user rights of the folder in the docker container where this file is mounted. Try changing the file's permissions to 777 before beginning the process and check again.
You can find a discussion about this in the official forum of docker