Merge pull request #351 from incf-nidash/cleanup-docker

Clean up Docker-related files

docker/Dockerfile

@@ -1,37 +1,9 @@
-FROM ubuntu:18.04
-
-RUN apt-get update &&  \
-    apt-get install -y git python3 graphviz python3-pip ssh mercurial python-setuptools zip
-
-RUN python3 -m pip install --upgrade pip && \
-    pip3 install rdflib requests rapidfuzz fuzzywuzzy pygithub pybids duecredit setuptools \
-                 python-Levenshtein pytest graphviz prov pydot validators ontquery \
-                 click rdflib-jsonld pyld pytest-cov tabulate joblib
-
-
-
+FROM python:3.11
+RUN apt-get update && apt-get install -y graphviz
 WORKDIR /opt
-
-RUN wget https://files.pythonhosted.org/packages/af/1c/7e4c25d5539ac8979d633afe03d16ddb01716c6cde97ebea33a6659ea9c6/Owlready2-0.24.tar.gz&& \
-    tar -xzf Owlready2-0.24.tar.gz && \
-    cd Owlready2-0.24 && \
-    python setup.py build && \
-    python setup.py install
-
 ENV LC_ALL=C.UTF-8
 ENV LANG=C.UTF-8
-RUN update-alternatives --remove python /usr/bin/python2 && \
-    update-alternatives --install /usr/bin/python python /usr/bin/python3 10 && \
-    update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10
-
-RUN cd / && \
-    git clone https://github.com/incf-nidash/PyNIDM.git && \
-    mv PyNIDM PyNIDM-snapshot && \
-    cd PyNIDM-snapshot && \
-    pip install -e .
-
-RUN git config --global user.name "docker user" && git config --global user.email "docker@example.com"
-
-ENV TMPDIR=/opt/project/cache
-
-COPY . .
+RUN pip install git+https://github.com/incf-nidash/PyNIDM.git
+RUN git config --global user.name "docker user" && \
+    git config --global user.email "docker@example.com"
+CMD ["/bin/bash"]

docker/Dockerfile-rest

@@ -1,6 +1,5 @@
 FROM pynidm:latest
-
-RUN pip3 install flask flask_restful flask-cors
-
+RUN pip install flask flask_restful flask-cors
 EXPOSE 5000
-CMD ["python", "/opt/project/rest-server.py"]
+COPY rest-server.py /usr/src/
+CMD ["python", "/usr/src/rest-server.py"]

docker/README.md

@@ -1,45 +1,47 @@
 # Docker and REST API
 
-This dockerfile can be used to create a development docker container suitable for both
-interactive use and also as a proof of concept REST API server.
+This Dockerfile can be used to create a development Docker container suitable
+for both interactive use and also as a proof-of-concept REST API server.
 
-#Build the container
+## Build the container
 
-These instructions assume you have the PyNIDM source code in ~/PyNIDM.
-To build the container, start in this directory and use the command:
+To build the container, start in this directory and run the commands:
 
 ```
-./build.sh
+docker build -f Dockerfile -t pynidm .
+docker build -f Dockerfile-rest -t pynidm-rest .
 ```
 
 ## Interactive
 
-You can then run the container interactively with:
+You can then run the container interactively with a command like:
+
 ```
-./rundocker.sh
+docker run -it -v ~/PyNIDM:/opt/project pynidm
 ```
 
-This will make a live mount of the files in ~/PyNIDM on your host system
-in the directory /opt/PyNIDM in the container.
+This will make a live mount of the files in `~/PyNIDM` on your host system in
+the directory `/opt/project` in the container.
 
 ## REST Server
 
-This section assumes you have the PyNIDM source code in ~/PyNIDM. You should
-also put any NIDM ttl files you want the REST s     erver to process somewhere under the
-~/PyNIDM/ttl directory.  Once you have done those things, use the command:
+This section assumes you have any NIDM ttl files you want the REST server to
+process stored under `ttl/` in the current directory.  Then, use the command:
+
 ```
-./runrest.sh
+docker run -it -p 5000:5000 -v "$PWD/ttl":/opt/project/ttl pynidm-rest
 ```
 
-This should start a HTTP server that is listening on port 5000 of your
+This should start an HTTP server that is listening on port 5000 of your
 local system.  You should be able to connect to the following routes:
+
 ```
 http://localhost:5000/projects
 http://localhost:5000/projects/[Project-UUID]
 http://localhost:5000/projects/[Project-UUID]/subjects
 http://localhost:5000/projects/[Project-UUID]/subjects/[Subject-UUID]
 ```
 
-After the server is started you can continue to modify the files in your
-~/PyNIDM/ttl directory and those changes will immediately be reflected in the
-REST API results.
+After the server is started you can continue to modify the files in your `ttl/`
+directory, and those changes will immediately be reflected in the REST API
+results.