For getpapers:- "Dockerfile: cannot find the file specified."

[Priya-Jk-15]

I am trying to install getpapers via Docker in Windows 10 Pro. I have installed Docker desktop successfully.
For installing getpapers, I have created a Dockerfile with respective commands as below:

Then in command prompt, I gave the command docker build -t get_paper . but got the following output:

unable to prepare context: unable to evaluate symlinks in Dockerfile path: CreateFile C:\Users\laksm\OneDrive\Desktop\Dockerfile: The system cannot find the file specified.

I tried the command docker build -t get_paper -f Dockerfile . but got the same output:

unable to prepare context: unable to evaluate symlinks in Dockerfile path: CreateFile C:\Users\laksm\OneDrive\Desktop\Dockerfile: The system cannot find the file specified.

I created the Dockerfile in desktop and executed the command there.
Is there anything else should be done before using Dockerfile like switching to the Windows containers..? Kindly guide me.

[bauhuasbadguy]

It looks like you named your Dockerfile, paper_getter. It needs to be named Dockerfile or else have the extension .Dockerfile. The . at the end of the command is telling docker to look for the file called Dockerfile in the current directory

[Priya-Jk-15]

Now, I created the Dockerfile again in desktop and renamed the file as Dockerfile

and tried the above commands docker build -t get_paper . and docker build -t get_paper -f Dockerfile . but got the same output

unable to prepare context: unable to evaluate symlinks in Dockerfile path: CreateFile C:\Users\laksm\OneDrive\Desktop\Dockerfile: The system cannot find the file specified.

[bauhuasbadguy]

You don't need to write the full path. If your in the same repo you can just use . and Docker will search for the file called Dockerfile. So you would only need:

docker build -t paper_getter .

To build the docker image

[Priya-Jk-15]

I tried only the command docker build -t paper_getter . but got the same output

unable to prepare context: unable to evaluate symlinks in Dockerfile path: CreateFile C:\Users\laksm\OneDrive\Desktop\Dockerfile: The system cannot find the file specified.

Does 'if in the same repo' mean the same directory(Desktop) or the cloned openVirus repo?

[bauhuasbadguy]

No, the same directory as the Dockerfile

[bauhuasbadguy]

Can you try using the modified version of the get_papers repo?

https://github.com/bauhuasbadguy/getpapers

[Priya-Jk-15]

Can you please explain the process? I'm unable to understand.

[bauhuasbadguy]

The project structure should be:

|
|- Dockerfile
|- run.sh
| -- results

You then build your image by running the Dockerfile using the command

docker build -t paper_getter .

In the same folder as the Dockerfile. This will build the image and tag it as paper_getter. This seems to be the part you are having trouble with.

Once this is solved the next part is to run the image in a container.

###################################################

To run the image paper_getter we use the command:-

docker run -it paper_getter

In the example shell script I have added a few things to this docker run command.

First is the flag --rm. This will remove the container once it has done its job,

Second is the volume mount -v $(pwd)/xml_results:/xml_results. This connects the folder xml_results outside the container to the folder xml_results inside the container. Allowing the results to be stored.

Finally I have added the command to be run by the get_papers container. In the example this is

getpapers -p -x -o /xml_results --query 'chloroquine'

The final run command being

docker run -it --rm --name get-papers \
 -v $(pwd)/xml_results:/xml_results \
 paper_getter \
getpapers -p -x -o /xml_results --query 'chloroquine'

[Priya-Jk-15]

Thank you for the explanation. I can understand the process now.
Yes, as you said I'm having problem in building the dockerfile. I have no idea what should I do to get the output. Should I switch to Windows containers or anything else?

[bauhuasbadguy]

I'm not sure how docker for windows differs from the linux version. It was my understanding that docker for windows ran in a shell.
Are you using the command line version of docker? Did you get the hello-world example to work?

[Priya-Jk-15]

Yes, I'm using the command line to run the commands.

Yes, the hello-world example worked. This was the output gained.

C:\Users\laksm\OneDrive\Desktop>docker pull hello-world
Using default tag: latest
latest: Pulling from library/hello-world
0e03bdcc26d7: Pull complete
Digest: sha256:4cf9c47f86df71d48364001ede3a4fcd85ae80ce02ebad74156906caff5378bc
Status: Downloaded newer image for hello-world:latest
docker.io/library/hello-world:latest

C:\Users\laksm\OneDrive\Desktop>docker run hello-world

Hello from Docker!
This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:
 1. The Docker client contacted the Docker daemon.
 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
    (amd64)
 3. The Docker daemon created a new container from that image which runs the
    executable that produces the output you are currently reading.
 4. The Docker daemon streamed that output to the Docker client, which sent it
    to your terminal.

To try something more ambitious, you can run an Ubuntu container with:
 $ docker run -it ubuntu bash

Share images, automate workflows, and more with a free Docker ID:
 https://hub.docker.com/

For more examples and ideas, visit:
 https://docs.docker.com/get-started/

[bauhuasbadguy]

Just checking you have capitalized the D in dockerfile? Can you send me the result of ls in the directory you are building in?

[Priya-Jk-15]

I'm in Windows, so I used the command dir instead of ls. The output of the directory:

C:\Users\laksm\OneDrive\Desktop>dir
 Volume in drive C is OS
 Volume Serial Number is 845F-351F

 Directory of C:\Users\laksm\OneDrive\Desktop

09/30/2020  06:38 PM    <DIR>          .
09/30/2020  06:38 PM    <DIR>          ..
08/24/2020  11:51 AM    <DIR>          class
09/30/2020  06:38 PM             2,148 Docker Desktop.lnk
09/22/2020  10:32 AM                72 Dockerfile.txt
09/29/2020  03:44 PM               808 GE_lab_exp2b.txt
10/01/2020  03:53 PM    <DIR>          github
08/06/2020  10:38 PM             1,450 Microsoft Edge.lnk
09/25/2020  12:36 PM             2,368 Microsoft Teams.lnk
09/15/2020  10:57 AM             1,442 Modifying enzyme for rDNA technique.txt
08/30/2020  04:46 PM             2,471 Personal - Edge.lnk
09/12/2020  08:26 AM             2,209 Slack.lnk
09/25/2020  10:35 PM    <DIR>          SRF reports
08/19/2020  11:10 PM               554 step21.txt
08/06/2020  10:55 PM               727 Windows 10 Update Assistant.lnk
              10 File(s)         14,249 bytes
               5 Dir(s)  123,297,308,672 bytes free

[bauhuasbadguy]

1. Is your dockerfile called Dockerfile.txt? It should be simply called Dockerfile with no extension.
2. I would do all this stuff in a dedicated folder to keep everything separate.
3. You should be able to use ls if your using the docker client since the docker client creates a Linux VM

[Priya-Jk-15]

1. I created a Dockerfile using notepad and I'm not sure if its name is with the extension as Dockerfile.txt. Please check the properties of the Dockerfile.

2. I created a separate folder named docker to keep the docker-related works separate.

3. I was not able to use ls command

C:\Users\laksm\OneDrive\Desktop\docker>ls
'ls' is not recognized as an internal or external command,
operable program or batch file.

Does this mean I'm not using the docker client?