Discrepancy between Python in docker-compose and independent container with same image - python-2.7

Question

In my project, I have a dockerized microservice based off of ubuntu:trusty which I wanted to update to python 2.7.13 from the standard apt-get 2.7.6 version. In doing so, I ran into some module import issues. Since then, I've added to the beginning of my pythonpath python2.7/dist-packages, which contains all of the modules I'm concerned with.
I built my microservice images using docker-compose build, but here's the issue: When I run docker-compose up, this microservice fails on importing all non-standard modules, yet when I create my own container from the same image using docker run -it image_id /bin/bash and then subsequently run a python shell and import any of the said modules, everything works perfectly. Even when I run the same python script, it gets past all of these import statements (but fails for other issues due to being run in isolation without proper linking).
I've asserted that python 2.7.13 is running on both docker-compose up and when I run my own container. I've cleared all of my containers, images, and cache and have rebuilt with no progress. The command being run at the end of the docker file is CMD python /filename/file.py.
Any ideas what could cause such a discrepancy?
EDIT:
As requested, here's the Dockerfile. The file structure is simply a project folder with subfolders, each being their own dockerized microservice. The one of concern here is called document_analyzer and following is the relevant section of the docker-compose file. Examples of the files that aren't properly installing are PyPDF2, pymongo, boto3.
FROM ubuntu:trusty
# Built using PyImageSearch guide:
# http://www.pyimagesearch.com/2015/06/22/install-opencv-3-0-and-python-2-7-on-ubuntu/
# Install dependencies
RUN \
apt-get -qq update && apt-get -qq upgrade -y && \
apt-get -qq install -y \
wget \
unzip \
libtbb2 \
libtbb-dev && \
apt-get -qq install -y \
build-essential \
cmake \
git \
pkg-config \
libjpeg8-dev \
libtiff4-dev \
libjasper-dev \
libpng12-dev \
libgtk2.0-dev \
libavcodec-dev \
libavformat-dev \
libswscale-dev \
libv4l-dev \
libatlas-base-dev \
gfortran \
libhdf5-dev \
libreadline-gplv2-dev \
libncursesw5-dev \
libssl-dev \
libsqlite3-dev \
tk-dev \
libgdbm-dev \
libc6-dev \
libbz2-dev \
libxml2-dev \
libxslt-dev && \
wget https://www.python.org/ftp/python/2.7.13/Python-2.7.13.tgz && \
tar -xvf Python-2.7.13.tgz && \
cd Python-2.7.13 && \
./configure && \
make && \
make install && \
apt-get install -y python-dev python-setuptools && \
easy_install pip && \
pip install numpy==1.12.0 && \
apt-get autoclean && apt-get clean && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
# Download OpenCV 3.2.0 and install
# step 10
RUN \
cd ~ && \
wget https://github.com/Itseez/opencv/archive/3.2.0.zip && \
unzip 3.2.0.zip && \
mv ~/opencv-3.2.0/ ~/opencv/ && \
rm -rf ~/3.2.0.zip && \
cd ~ && \
wget https://github.com/opencv/opencv_contrib/archive/3.2.0.zip -O 3.2.0-contrib.zip && \
unzip 3.2.0-contrib.zip && \
mv opencv_contrib-3.2.0 opencv_contrib && \
rm -rf ~/3.2.0-contrib.zip && \
cd /root/opencv && \
mkdir build && \
cd build && \
cmake -D CMAKE_BUILD_TYPE=RELEASE \
-D CMAKE_INSTALL_PREFIX=/usr/local \
-D INSTALL_C_EXAMPLES=OFF \
-D INSTALL_PYTHON_EXAMPLES=ON \
-D OPENCV_EXTRA_MODULES_PATH=~/opencv_contrib/modules \
-D BUILD_EXAMPLES=ON .. && \
cd ~/opencv/build && \
make -j $(nproc) && \
make install && \
ldconfig && \
# clean opencv repos
rm -rf ~/opencv/build && \
rm -rf ~/opencv/3rdparty && \
rm -rf ~/opencv/doc && \
rm -rf ~/opencv/include && \
rm -rf ~/opencv/platforms && \
rm -rf ~/opencv/modules && \
rm -rf ~/opencv_contrib/build && \
rm -rf ~/opencv_contrib/doc
RUN mkdir ~/.aws/ && touch ~/.aws/config && touch ~/.aws/credentials && \
echo "[default]" > ~/.aws/credentials && \
echo "AWS_ACCESS_KEY_ID=xxxxxxx" >> ~/.aws/credentials && \
echo "AWS_SECRET_ACCESS_KEY=xxxxxxx" >> ~/.aws/credentials && \
echo "[default]" > ~/.aws/config && \
echo "output = json" >> ~/.aws/config && \
echo "region = us-east-1" >> ~/.aws/config
RUN apt-get update && \
apt-get -y install bcrypt \
libssl-dev \
libffi-dev \
libpq-dev \
vim \
redis-server \
rsyslog \
imagemagick \
libmagickcore-dev \
libmagickwand-dev \
libmagic-dev \
curl
RUN pip install pyopenssl ndg-httpsclient pyasn1
WORKDIR /document_analyzer
# Add requirements and install
COPY . /document_analyzer
RUN pip install -r /document_analyzer/requirements.txt && \
pip install -Iv https://pypi.python.org/packages/f5/1f/2d7579a6d8409a61b6b8e84ed02ca9efae8b51fd6228e24be88588fac255/tika-1.14.1.tar.gz#md5=aa7d77a4215e252f60243d423946de8d && \
pip install awscli
ENV PYTHONPATH="/usr/local/lib/python2.7/dist-packages/:${PYTHONPATH}"
CMD python /document_analyzer/api.py
Docker-compose:
document_analyzer:
environment:
- IP=${IP}
extends:
file: common.yml
service: microservice
build: document_analyzer
ports:
- "5001:5001"
volumes:
- ./document_analyzer:/document_analyzer
- .:/var/lib/
environment:
- PYTHONPATH=$PYTHONPATH:/var/lib
links:
- redis
- rabbit
- ocr_runner
- tika
- document_envelope
- converter
restart: on-failure

Answer 1

You have this work being done during the build phase:
WORKDIR /document_analyzer
# Add requirements and install
COPY . /document_analyzer
RUN pip install -r /document_analyzer/requirements.txt && \
pip install -Iv https://pypi.python.org/packages/f5/1f/2d7579a6d8409a61b6b8e84ed02ca9efae8b51fd6228e24be88588fac255/tika-1.14.1.tar.gz#md5=aa7d77a4215e252f60243d423946de8d && \
pip install awscli
And at runtime you do this in the compose yaml file:
volumes:
- ./document_analyzer:/document_analyzer
That volume mount will override everything you did in /document_analyzer during the build. Only what is in the directory outside the container will now be available at /document_analyzer inside the container. Whatever was at /document_analyzer before, from the build phase, is now hidden by this mount and not available.
The difference when you use docker run is that you did not create this mount.