I made the Dockerfile for making Docker image that runnable from AWS Batch, contains multiple layers, copy files to '/opt', which I set it as WORKDIR.
I have to run a program called 'BLAST', which is a single .exe program, requires several parameters including the location of DB.
When I run the image, the error comes out with it cannot find the mounted DB location. Full error message is b'BLAST Database error: No alias or index file found for nucleotide database [/mnt/fsx/ntdb/nt] in search path [/opt:/fsx/ntdb:]\n'] where /mnt/fsx/ntdb/nt is the DB path.
The only assumption is because I gave WORKDIR in my Dockerfile so the default workspace is set as '/opt:'.
I wonder how should I fix this issue. By removing WORKDIR ? or something else?
My Dockerfile looks like below
# Set Work dir
ARG FUNCTION_DIR="/opt"
# Get layers
FROM (aws-account).dkr.ecr.(aws-region).amazonaws.com/uclust AS layer_1
FROM (aws-account).dkr.ecr.(aws-region).amazonaws.com/blast AS layer_2
FROM public.ecr.aws/lambda/python:3.9
# Copy arg and set work dir
ARG FUNCTION_DIR
COPY . ${FUNCTION_DIR}
WORKDIR ${FUNCTION_DIR}
# Copy from layers
COPY --from=layer_1 /opt/ .
RUN true
COPY --from=layer_2 /opt/ .
RUN true
COPY . ${FUNCTION_DIR}/
RUN true
# Copy and Install required libraries
COPY requirements.txt .
RUN true
RUN pip3 install -r requirements.txt
# To run lambda handler
RUN pip install \
--target "${FUNCTION_DIR}" \
awslambdaric
# To run blast
RUN yum -y install libgomp
# See files inside image
RUN dir -s
# Get permissions for files
RUN chmod +x /opt/main.py
RUN chmod +x /opt/mode/submit/main.py
# Set Entrypoint and CMD
ENTRYPOINT [ "python3" ]
CMD [ "-m", "awslambdaric", "main.lambda_handler" ]
Edit: Further info I found, When looking at the error, the BLAST program trying to search db at the path /opt:/fsx/ntdb:, which is the combination of path set as WORKDIR in Dockerfile and BLASTDB path set by os.environ.['BLASTDB'] (os.environ['BLASTDB'] description.).
Figured out the problem after many debug trials. So the problem was neither WORKDIR nor os.environ.['BLASTDB']. The paths were correctly defined, and the BLAST program searching [/opt:/fsx/ntdb:] was correct way according to what is says in here
Current working directory (*)
User's HOME directory (*)
Directory specified by the NCBI environment variable
The standard system directory (“/etc” on Unix-like systems, and given by the environment variable SYSTEMROOT on Windows)
The actual solution was checking whether file system is correctly mounted or not and the permission of the files inside the file system. Initially I thought file system was mounted correctly since I already tested from other Batch submit job many times, but only the mount folder is created, files were not exist. Therefore, even though the program tried to find the index file, it could not find any so the error came out.
New to Docker here. I'm trying to create a basic Dockerfile where I run a python script that runs some queries in postgres through psycopg2. I currently have a pgpass file setup in my environment variables so that I can run these tools without supplying a password in the code. I'm trying to replicate this in Docker. I have windows on my local.
FROM datascienceschool/rpython as base
RUN mkdir /test
WORKDIR /test
COPY requirements.txt requirements.txt
RUN pip install -r requirements.txt
COPY main_airflow.py /test
RUN cp C:\Users\user.name\AppData\Roaming\postgresql\pgpass.conf /test
ENV PGPASSFILE="test/pgpass.conf"
ENV PGUSER="user"
ENTRYPOINT ["python", "/test/main_airflow.py"]
This is what I've tried in my Dockerfile. I've tried to copy over my pgpassfile and set it as my environment variable. Apologies if I have a forward/backslashes wrong, or syntax. I'm very new to Docker, Linux, etc.
Any help or alternatives would be appreciated
It's better to pass your secrets into the container at runtime than it is to include the secret in the image at build-time. This means that the Dockerfile doesn't need to know anything about this value.
For example
$ export PGPASSWORD=<postgres password literal>
$ docker run -e PGPASSWORD <image ref>
Now in that example, I've used PGPASSWORD, which is an alternative to PGPASSFILE. It's a little more complicated to do this same if you're using a file, but that would be something like this:
The plan will be to mount the credentials as a volume at runtime.
FROM datascienceschool/rpython as base
RUN mkdir /test
WORKDIR /test
COPY requirements.txt requirements.txt
RUN pip install -r requirements.txt
COPY main_airflow.py /test
ENV PGPASSFILE="/credentials/pgpass.conf"
ENV PGUSER="user"
ENTRYPOINT ["python", "/test/main_airflow.py"]
As I said above, we don't want to include the secrets in the image. We are going to indicate where the file will be in the image, but we don't actually include it yet.
Now, when we start the image, we'll mount a volume containing the file at the location specified in the image, /credentials
$ docker run --mount src="<host path to directory>",target="/credentials",type=bind <image ref>
I haven't tested this so you may need to adjust the exact paths and such, but this is the idea of how to set sensitive values in a docker container
How can I include files from outside of Docker's build context using the "ADD" command in the Docker file?
From the Docker documentation:
The path must be inside the context of the build; you cannot ADD
../something/something, because the first step of a docker build is to
send the context directory (and subdirectories) to the docker daemon.
I do not want to restructure my whole project just to accommodate Docker in this matter. I want to keep all my Docker files in the same sub-directory.
Also, it appears Docker does not yet (and may not ever) support symlinks: Dockerfile ADD command does not follow symlinks on host #1676.
The only other thing I can think of is to include a pre-build step to copy the files into the Docker build context (and configure my version control to ignore those files). Is there a better workaround for than that?
The best way to work around this is to specify the Dockerfile independently of the build context, using -f.
For instance, this command will give the ADD command access to anything in your current directory.
docker build -f docker-files/Dockerfile .
Update: Docker now allows having the Dockerfile outside the build context (fixed in 18.03.0-ce). So you can also do something like
docker build -f ../Dockerfile .
I often find myself utilizing the --build-arg option for this purpose. For example after putting the following in the Dockerfile:
ARG SSH_KEY
RUN echo "$SSH_KEY" > /root/.ssh/id_rsa
You can just do:
docker build -t some-app --build-arg SSH_KEY="$(cat ~/file/outside/build/context/id_rsa)" .
But note the following warning from the Docker documentation:
Warning: It is not recommended to use build-time variables for passing secrets like github keys, user credentials etc. Build-time variable values are visible to any user of the image with the docker history command.
I spent a good time trying to figure out a good pattern and how to better explain what's going on with this feature support. I realized that the best way to explain it was as follows...
Dockerfile: Will only see files under its own relative path
Context: a place in "space" where the files you want to share and your Dockerfile will be copied to
So, with that said, here's an example of the Dockerfile that needs to reuse a file called start.sh
Dockerfile
It will always load from its relative path, having the current directory of itself as the local reference to the paths you specify.
COPY start.sh /runtime/start.sh
Files
Considering this idea, we can think of having multiple copies for the Dockerfiles building specific things, but they all need access to the start.sh.
./all-services/
/start.sh
/service-X/Dockerfile
/service-Y/Dockerfile
/service-Z/Dockerfile
./docker-compose.yaml
Considering this structure and the files above, here's a docker-compose.yml
docker-compose.yaml
In this example, your shared context directory is the runtime directory.
Same mental model here, think that all the files under this directory are moved over to the so-called context.
Similarly, just specify the Dockerfile that you want to copy to that same directory. You can specify that using dockerfile.
The directory where your main content is located is the actual context to be set.
The docker-compose.yml is as follows
version: "3.3"
services:
service-A
build:
context: ./all-service
dockerfile: ./service-A/Dockerfile
service-B
build:
context: ./all-service
dockerfile: ./service-B/Dockerfile
service-C
build:
context: ./all-service
dockerfile: ./service-C/Dockerfile
all-service is set as the context, the shared file start.sh is copied there as well the Dockerfile specified by each dockerfile.
Each gets to be built their own way, sharing the start file!
On Linux you can mount other directories instead of symlinking them
mount --bind olddir newdir
See https://superuser.com/questions/842642 for more details.
I don't know if something similar is available for other OSes.
I also tried using Samba to share a folder and remount it into the Docker context which worked as well.
If you read the discussion in the issue 2745 not only docker may never support symlinks they may never support adding files outside your context. Seems to be a design philosophy that files that go into docker build should explicitly be part of its context or be from a URL where it is presumably deployed too with a fixed version so that the build is repeatable with well known URLs or files shipped with the docker container.
I prefer to build from a version controlled source - ie docker build
-t stuff http://my.git.org/repo - otherwise I'm building from some random place with random files.
fundamentally, no.... -- SvenDowideit, Docker Inc
Just my opinion but I think you should restructure to separate out the code and docker repositories. That way the containers can be generic and pull in any version of the code at run time rather than build time.
Alternatively, use docker as your fundamental code deployment artifact and then you put the dockerfile in the root of the code repository. if you go this route probably makes sense to have a parent docker container for more general system level details and a child container for setup specific to your code.
I believe the simpler workaround would be to change the 'context' itself.
So, for example, instead of giving:
docker build -t hello-demo-app .
which sets the current directory as the context, let's say you wanted the parent directory as the context, just use:
docker build -t hello-demo-app ..
You can also create a tarball of what the image needs first and use that as your context.
https://docs.docker.com/engine/reference/commandline/build/#/tarball-contexts
This behavior is given by the context directory that the docker or podman uses to present the files to the build process.
A nice trick here is by changing the context dir during the building instruction to the full path of the directory, that you want to expose to the daemon.
e.g:
docker build -t imageName:tag -f /path/to/the/Dockerfile /mysrc/path
using /mysrc/path instead of .(current directory), you'll be using that directory as a context, so any files under it can be seen by the build process.
This example you'll be exposing the entire /mysrc/path tree to the docker daemon.
When using this with docker the user ID who triggered the build must have recursively read permissions to any single directory or file from the context dir.
This can be useful in cases where you have the /home/user/myCoolProject/Dockerfile but want to bring to this container build context, files that aren't in the same directory.
Here is an example of building using context dir, but this time using podman instead of docker.
Lets take as example, having inside your Dockerfile a COPY or ADDinstruction which is copying files from a directory outside of your project, like:
FROM myImage:tag
...
...
COPY /opt/externalFile ./
ADD /home/user/AnotherProject/anotherExternalFile ./
...
In order to build this, with a container file located in the /home/user/myCoolProject/Dockerfile, just do something like:
cd /home/user/myCoolProject
podman build -t imageName:tag -f Dockefile /
Some known use cases to change the context dir, is when using a container as a toolchain for building your souce code.
e.g:
podman build --platform linux/s390x -t myimage:mytag -f ./Dockerfile /tmp/mysrc
or it can be a path relative, like:
podman build --platform linux/s390x -t myimage:mytag -f ./Dockerfile ../../
Another example using this time a global path:
FROM myImage:tag
...
...
COPY externalFile ./
ADD AnotherProject ./
...
Notice that now the full global path for the COPY and ADD is omitted in the Dockerfile command layers.
In this case the contex dir must be relative to where the files are, if both externalFile and AnotherProject are in /opt directory then the context dir for building it must be:
podman build -t imageName:tag -f ./Dockerfile /opt
Note when using COPY or ADD with context dir in docker:
The docker daemon will try to "stream" all the files visible on the context dir tree to the daemon, which can slowdown the build. And requires the user to have recursively permission from the context dir.
This behavior can be more costly specially when using the build through the API. However,with podman the build happens instantaneously, without needing recursively permissions, that's because podman does not enumerate the entire context dir, and doesn't use a client/server architecture as well.
The build for such cases can be way more interesting to use podman instead of docker, when you face such issues using a different context dir.
Some references:
https://docs.docker.com/engine/reference/commandline/build/
https://docs.podman.io/en/latest/markdown/podman-build.1.html
As is described in this GitHub issue the build actually happens in /tmp/docker-12345, so a relative path like ../relative-add/some-file is relative to /tmp/docker-12345. It would thus search for /tmp/relative-add/some-file, which is also shown in the error message.*
It is not allowed to include files from outside the build directory, so this results in the "Forbidden path" message."
Using docker-compose, I accomplished this by creating a service that mounts the volumes that I need and committing the image of the container. Then, in the subsequent service, I rely on the previously committed image, which has all of the data stored at mounted locations. You will then have have to copy these files to their ultimate destination, as host mounted directories do not get committed when running a docker commit command
You don't have to use docker-compose to accomplish this, but it makes life a bit easier
# docker-compose.yml
version: '3'
services:
stage:
image: alpine
volumes:
- /host/machine/path:/tmp/container/path
command: bash -c "cp -r /tmp/container/path /final/container/path"
setup:
image: stage
# setup.sh
# Start "stage" service
docker-compose up stage
# Commit changes to an image named "stage"
docker commit $(docker-compose ps -q stage) stage
# Start setup service off of stage image
docker-compose up setup
Create a wrapper docker build shell script that grabs the file then calls docker build then removes the file.
a simple solution not mentioned anywhere here from my quick skim:
have a wrapper script called docker_build.sh
have it create tarballs, copy large files to the current working directory
call docker build
clean up the tarballs, large files, etc
this solution is good because (1.) it doesn't have the security hole from copying in your SSH private key (2.) another solution uses sudo bind so that has another security hole there because it requires root permission to do bind.
I think as of earlier this year a feature was added in buildx to do just this.
If you have dockerfile 1.4+ and buildx 0.8+ you can do something like this
docker buildx build --build-context othersource= ../something/something .
Then in your docker file you can use the from command to add the context
ADD –from=othersource . /stuff
See this related post https://www.docker.com/blog/dockerfiles-now-support-multiple-build-contexts/
Workaround with links:
ln path/to/file/outside/context/file_to_copy ./file_to_copy
On Dockerfile, simply:
COPY file_to_copy /path/to/file
I was personally confused by some answers, so decided to explain it simply.
You should pass the context, you have specified in Dockerfile, to docker when
want to create image.
I always select root of project as the context in Dockerfile.
so for example if you use COPY command like COPY . .
first dot(.) is the context and second dot(.) is container working directory
Assuming the context is project root, dot(.) , and code structure is like this
sample-project/
docker/
Dockerfile
If you want to build image
and your path (the path you run the docker build command) is /full-path/sample-project/,
you should do this
docker build -f docker/Dockerfile .
and if your path is /full-path/sample-project/docker/,
you should do this
docker build -f Dockerfile ../
An easy workaround might be to simply mount the volume (using the -v or --mount flag) to the container when you run it and access the files that way.
example:
docker run -v /path/to/file/on/host:/desired/path/to/file/in/container/ image_name
for more see: https://docs.docker.com/storage/volumes/
I had this same issue with a project and some data files that I wasn't able to move inside the repo context for HIPAA reasons. I ended up using 2 Dockerfiles. One builds the main application without the stuff I needed outside the container and publishes that to internal repo. Then a second dockerfile pulls that image and adds the data and creates a new image which is then deployed and never stored anywhere. Not ideal, but it worked for my purposes of keeping sensitive information out of the repo.
In my case, my Dockerfile is written like a template containing placeholders which I'm replacing with real value using my configuration file.
So I couldn't specify this file directly but pipe it into the docker build like this:
sed "s/%email_address%/$EMAIL_ADDRESS/;" ./Dockerfile | docker build -t katzda/bookings:latest . -f -;
But because of the pipe, the COPY command didn't work. But the above way solves it by -f - (explicitly saying file not provided). Doing only - without the -f flag, the context AND the Dockerfile are not provided which is a caveat.
How to share typescript code between two Dockerfiles
I had this same problem, but for sharing files between two typescript projects. Some of the other answers didn't work for me because I needed to preserve the relative import paths between the shared code. I solved it by organizing my code like this:
api/
Dockerfile
src/
models/
index.ts
frontend/
Dockerfile
src/
models/
index.ts
shared/
model1.ts
model2.ts
index.ts
.dockerignore
Note: After extracting the shared code into that top folder, I avoided needing to update the import paths because I updated api/models/index.ts and frontend/models/index.ts to export from shared: (eg export * from '../../../shared)
Since the build context is now one directory higher, I had to make a few additional changes:
Update the build command to use the new context:
docker build -f Dockerfile .. (two dots instead of one)
Use a single .dockerignore at the top level to exclude all node_modules. (eg **/node_modules/**)
Prefix the Dockerfile COPY commands with api/ or frontend/
Copy shared (in addition to api/src or frontend/src)
WORKDIR /usr/src/app
COPY api/package*.json ./ <---- Prefix with api/
RUN npm ci
COPY api/src api/ts*.json ./ <---- Prefix with api/
COPY shared usr/src/shared <---- ADDED
RUN npm run build
This was the easiest way I could send everything to docker, while preserving the relative import paths in both projects. The tricky (annoying) part was all the changes/consequences caused by the build context being up one directory.
One quick and dirty way is to set the build context up as many levels as you need - but this can have consequences.
If you're working in a microservices architecture that looks like this:
./Code/Repo1
./Code/Repo2
...
You can set the build context to the parent Code directory and then access everything, but it turns out that with a large number of repositories, this can result in the build taking a long time.
An example situation could be that another team maintains a database schema in Repo1 and your team's code in Repo2 depends on this. You want to dockerise this dependency with some of your own seed data without worrying about schema changes or polluting the other team's repository (depending on what the changes are you may still have to change your seed data scripts of course)
The second approach is hacky but gets around the issue of long builds:
Create a sh (or ps1) script in ./Code/Repo2 to copy the files you need and invoke the docker commands you want, for example:
#!/bin/bash
rm -r ./db/schema
mkdir ./db/schema
cp -r ../Repo1/db/schema ./db/schema
docker-compose -f docker-compose.yml down
docker container prune -f
docker-compose -f docker-compose.yml up --build
In the docker-compose file, simply set the context as Repo2 root and use the content of the ./db/schema directory in your dockerfile without worrying about the path.
Bear in mind that you will run the risk of accidentally committing this directory to source control, but scripting cleanup actions should be easy enough.
I have a Python script, python_script.py, that reads an HDF5 file, hdf_file.h5, on my local machine. The directory path to the files is
folder1
folder2
python_script.py
hdf_file.h5
I have the following sample code:
from pandas import read_hdf
df = read_hdf('hdf_file.h5')
When I run this code on my local machine, it works fine.
However, I need to place the Python script inside a Docker container, keep the HDF file out of the container, and have the code read the file. I want to have something like the following directory path for the container:
folder1
folder2
hdf_file.h5
docker-folder
python_script.py
requirements.txt
Dockerfile
I use the following Dockerfile:
FROM python:3
WORKDIR /project
COPY ./requirements.txt /project/requirements.txt
RUN pip install -r requirements.txt
COPY . /project
CMD [ "python", "python_script.py" ]
I am new to Docker and am having a lot of trouble figuring out how to get a Python script inside a container to read a file outside the container. What commands do I use or code changes do I make to be able to do this?
It seems you need to use docker volumes (https://docs.docker.com/storage/volumes/).
Try the following:
docker run -v path/where/lives/hdf5/:path/to/your/project/folder/your_image your_docker_image:your_tag
Where the first part before the : refers to host machine and after, the container.
Hope it helps!
I have a simple Python program that I want to run in IBM Cloud functions. Alas it needs two libraries (O365 and PySnow) so I have to Dockerize it and it needs to be able to accept a Json feed from STDIN. I succeeded in doing this:
FROM python:3
ADD requirements.txt ./
RUN pip install -r requirements.txt
ADD ./main ./main
WORKDIR /main
CMD ["python", "main.py"]
This runs with: cat env_var.json | docker run -i f9bf70b8fc89
I've added the Docker container to IBM Cloud Functions like this:
ibmcloud fn action create e2t-bridge --docker [username]/e2t-bridge
However when I run it, it times out.
Now I did see a possible solution route, where I dockerize it as an Openwhisk application. But for that I need to create a binary from my Python application and then load it into a rather complicated Openwhisk skeleton, I think?
But having a file you can simply run was is the whole point of my Docker, so to create a binary of an interpreted language and then adding it into a Openwhisk docker just feels awfully clunky.
What would be the best way to approach this?
It turns out you don't need to create a binary, you just need to edit the OpenWhisk skeleton like so:
# Dockerfile for example whisk docker action
FROM openwhisk/dockerskeleton
ENV FLASK_PROXY_PORT 8080
### Add source file(s)
ADD requirements.txt /action/requirements.txt
RUN cd /action; pip install -r requirements.txt
# Move the file to
ADD ./main /action
# Rename our executable Python action
ADD /main/main.py /action/exec
CMD ["/bin/bash", "-c", "cd actionProxy && python -u actionproxy.py"]
And make sure that your Python code accepts a Json feed from stdin:
json_input = json.loads(sys.argv[1])
The whole explaination is here: https://github.com/iainhouston/dockerPython