I'm trying to connect a pyodbc python script running in a docker container to login to a MSSQL database I have tried all sorts of docker files, but not been able to make the connection (fails when bulding the docker or when python tries to connect), Does anyone have a working dockerfile, using pyodbc:
Dockerfile:
# Use an official Python runtime as a parent image
FROM python:2.7-slim
# Set the working directory to /app
WORKDIR /app
# Copy the current directory contents into the container at /app
ADD . /app
# Install any needed packages specified in requirements.txt
RUN pip install -r requirements.txt
# Run app.py when the container launches
CMD ["python", "App.py"]
requirements.TXT
pyodbc
App.Py
import pyodbc
connection = pyodbc.connect('Driver={SQL Server};'
'Server=xxxx;'
'Database=xxx;'
'UID=xxxx;'
'PWD=xxxx')
cursor = connection.cursor()
cursor.execute("SELECT [Id],[Name] FROM [DCMM].[config].[Models]")
for row in cursor.fetchall():
print(row.Name)
connection.close()
Bulding the container
docker build -t sqltest .
Output:
Sending build context to Docker daemon 4.096kB
Step 1/5 : FROM python:2.7-slim
---> 426d65ab9a72
Step 2/5 : WORKDIR /app
---> Using cache
---> 725f35122880
Step 3/5 : ADD . /app
---> 3feb8b7744f7
Removing intermediate container 4214091a111a
Step 4/5 : RUN pip install -r requirements.txt
---> Running in 27aa4dcfe738
Collecting pyodbc (from -r requirements.txt (line 1))
Downloading pyodbc-4.0.17.tar.gz (196kB)
Building wheels for collected packages: pyodbc
Running setup.py bdist_wheel for pyodbc: started
Running setup.py bdist_wheel for pyodbc: finished with status 'error'
Failed building wheel for pyodbc
Complete output from command /usr/local/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-EfWsmy/pyodbc/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/tmpa3S13tpip-wheel- --python-tag cp27:
running bdist_wheel
running build
running build_ext
building 'pyodbc' extension
creating build
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPYODBC_VERSION=4.0.17 -DSQL_WCHART_CONVERT=1 -I/usr/local/include/python2.7 -c src/cursor.cpp -o build/temp.linux-x86_64-2.7/src/cursor.o -Wno-write-strings
unable to execute 'gcc': No such file or directory
error: command 'gcc' failed with exit status 1
----------------------------------------
Running setup.py clean for pyodbc
Failed to build pyodbc
Installing collected packages: pyodbc
Running setup.py install for pyodbc: started
Running setup.py install for pyodbc: finished with status 'error'
Complete output from command /usr/local/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-EfWsmy/pyodbc/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-BV4sRM-record/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_ext
building 'pyodbc' extension
creating build
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPYODBC_VERSION=4.0.17 -DSQL_WCHART_CONVERT=1 -I/usr/local/include/python2.7 -c src/cursor.cpp -o build/temp.linux-x86_64-2.7/src/cursor.o -Wno-write-strings
unable to execute 'gcc': No such file or directory
error: command 'gcc' failed with exit status 1
----------------------------------------
Command "/usr/local/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-EfWsmy/pyodbc/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-BV4sRM-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-EfWsmy/pyodbc/
The command '/bin/sh -c pip install -r requirements.txt' returned a non-zero code: 1
Need to Run:
sudo apt-get install gcc
need to add a odbcinst.ini file containing:
[FreeTDS]Description=FreeTDS Driver Driver=/usr/lib/x86_64-linux-gnu/odbc/libtdsodbc.so Setup=/usr/lib/x86_64-linux-gnu/odbc/libtdsS.so
need to add folowing to docker file
ADD odbcinst.ini /etc/odbcinst.ini
RUN apt-get update
RUN apt-get install -y tdsodbc unixodbc-dev
RUN apt install unixodbc-bin -y
RUN apt-get clean -y
need to change connection in .py to
connection = pyodbc.connect('Driver={FreeTDS};'
'Server=xxxxx;'
'Database=DCMM;'
'UID=xxxxx;'
'PWD=xxxxx')
Now the container compiles, and gets data from SQL server
Running through this recently I found it was necessary to additionally include the following line (note that it did not build without this step):
RUN apt-get install --reinstall build-essential -y
The full Dockerfile looks as follows:
# parent image
FROM python:3.7-slim
# install FreeTDS and dependencies
RUN apt-get update \
&& apt-get install unixodbc -y \
&& apt-get install unixodbc-dev -y \
&& apt-get install freetds-dev -y \
&& apt-get install freetds-bin -y \
&& apt-get install tdsodbc -y \
&& apt-get install --reinstall build-essential -y
# populate "ocbcinst.ini"
RUN echo "[FreeTDS]\n\
Description = FreeTDS unixODBC Driver\n\
Driver = /usr/lib/x86_64-linux-gnu/odbc/libtdsodbc.so\n\
Setup = /usr/lib/x86_64-linux-gnu/odbc/libtdsS.so" >> /etc/odbcinst.ini
# install pyodbc (and, optionally, sqlalchemy)
RUN pip install --trusted-host pypi.python.org pyodbc==4.0.26 sqlalchemy==1.3.5
# run app.py upon container launch
CMD ["python", "app.py"]
Here's one way to then actually establish the connection inside app.py, via sqlalchemy (and assuming port 1433):
import sqlalchemy as sa
args = (username, password, server, database)
connstr = "mssql+pyodbc://{}:{}#{}/{}?driver=FreeTDS&port=1433&odbc_options='TDS_Version=8.0'"
engine = sa.create_engine(connstr.format(*args))
Based on Kåre Rasmussen's answer, here's a complete dockerfile for further use.
Make sure to edit the last two lines according to your architecture! They should reflect the actual paths to libtdsodbc.so and libtdsS.so.
If you're not sure about the paths to libtdsodbc.so and libtdsS.so, try dpkg --search libtdsodbc.so and dpkg --search libtdsS.so.
FROM python:3
#Install FreeTDS and dependencies for PyODBC
RUN apt-get update && apt-get install -y tdsodbc unixodbc-dev \
&& apt install unixodbc-bin -y \
&& apt-get clean -y
RUN echo "[FreeTDS]\n\
Description = FreeTDS unixODBC Driver\n\
Driver = /usr/lib/arm-linux-gnueabi/odbc/libtdsodbc.so\n\
Setup = /usr/lib/arm-linux-gnueabi/odbc/libtdsS.so" >> /etc/odbcinst.ini
Afterwards, install PyODBC, COPY your app and run it.
I was unable to use all of the above resolutions, I was keeping al kind of errors relating to the pyodbc package, in particular:
ImportError: libodbc.so.2: cannot open shared object file: No such file or directory.
I ended up with another resolution which defines the ODBC SQL Server Driver specifically for an Ubuntu 18.04 Docker image, in this case ODBC Driver 17 for SQL Server. In my specific use case I needed to make the connection to my MySQL database server on Azure via Flask SQLAlchemy, but the latter is not a necessity for the Docker configuration.
Dockerfile, with most important part adding the Microsoft repository and installing msodbcsql17 and unixodbc-dev:
# Ubuntu 18.04 base with Python runtime and pyodbc to connect to SQL Server
FROM ubuntu:18.04
WORKDIR /app
# apt-get and system utilities
RUN apt-get update && apt-get install -y \
curl apt-utils apt-transport-https debconf-utils gcc build-essential g++-5\
&& rm -rf /var/lib/apt/lists/*
# adding custom Microsoft repository
RUN curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add -
RUN curl https://packages.microsoft.com/config/ubuntu/18.04/prod.list > /etc/apt/sources.list.d/mssql-release.list
# install SQL Server drivers
RUN apt-get update && ACCEPT_EULA=Y apt-get install -y msodbcsql17 unixodbc-dev
# install SQL Server tools
RUN apt-get update && ACCEPT_EULA=Y apt-get install -y mssql-tools
RUN echo 'export PATH="$PATH:/opt/mssql-tools/bin"' >> ~/.bashrc
RUN /bin/bash -c "source ~/.bashrc"
# python libraries
RUN apt-get update -y && \
apt-get install -y python3-pip python3-dev
# install necessary locales, this prevents any locale errors related to Microsoft packages
RUN apt-get update && apt-get install -y locales \
&& echo "en_US.UTF-8 UTF-8" > /etc/locale.gen \
&& locale-gen
# copy requirements and install packages, I added this for general use
COPY ./requirements.txt > ./requirements.txt
RUN pip3 install -r ./requirements.txt
# you can also use regular install of the packages
RUN pip3 install pyodbc SQLAlchemy
# and if you are also planning to use Flask and Flask-SQLAlchemy
Run pip3 install Flask Flask-SQLAlchemy
COPY ..
# run your app via entrypoint or change the CMD command to your regular command
COPY docker-entrypoint.sh wsgi.py ./
CMD ["./docker-entrypoint.sh"]
This should build without any errors in Docker.
My database url looked like this:
import urllib.parse
# name the sepcific ODBC driver by version number, we installed msodbcsql17
params = urllib.parse.quote_plus("DRIVER={ODBC Driver 17 for SQL Server};SERVER=<your.database.windows.net>;DATABASE=<your-db-name>;UID=<username>;PWD=<password>")
db_uri = "mssql+pyodbc:///?odbc_connect={PARAMS}".format(PARAMS=params)
And for the bonus if you are using Flask-SQLAlchemy, your app config should contain something like this:
app.config["SQLALCHEMY_TRACK_MODIFICATIONS"] = False
app.config["SQLALCHEMY_DATABASE_URI"] = db_uri # from above
Happy coding!
How to install the necessary dependencies for pyodbc is related to the linux distribution and its version (in docker case, that is the base image of your docker image). If none of the above work for you, you can figure out the commands by trying in the docker container instance.
First, exec into the docker container
docker exec -it <container id> bash
Try various ways to get the distribution name and version of your linux. Then try different instructions in Install the Microsoft ODBC driver for SQL Server (Linux)
Here is a working example for Debian 9 based images, deriving exactly as the document instructions.
# Install pyodbc dependencies
RUN curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add -
RUN curl https://packages.microsoft.com/config/debian/9/prod.list > /etc/apt/sources.list.d/mssql-release.list
RUN apt-get update
RUN ACCEPT_EULA=Y apt-get -y install msodbcsql17
RUN apt-get -y install unixodbc-dev
RUN pip install pyodbc
For me to solve this issue I also had to add the following 2 lines in the dockerfile:
RUN echo MinProtocol = TLSv1.0 >> /etc/ssl/openssl.cnf
RUN echo CipherString = DEFAULT#SECLEVEL=1 >> /etc/ssl/openssl.cnf
For those who wanted to do official microsoft approach to install odbc driver and use python:slim docker image, you can use this as DockerFile:
FROM python:3.9-slim
RUN apt-get -y update && apt-get install -y curl gnupg
RUN curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add -
# download appropriate package for the OS version
# Debian 11
RUN curl https://packages.microsoft.com/config/debian/11/prod.list \
> /etc/apt/sources.list.d/mssql-release.list
RUN exit
RUN apt-get -y update
RUN ACCEPT_EULA=Y apt-get install -y msodbcsql18
Then for sqlalchemy's this can be called:
con_str = f"mssql+pyodbc://{username}:{password}#{host}/{db}?" \
"driver=ODBC+Driver+18+for+SQL+Server&TrustServerCertificate=yes"
engine = create_engine(con_str)
I created a Gist on GitHub on how to do this. I hope it helps. I had to piece things together from what I found on different resources.
https://gist.github.com/joshatxantie/4bcf5d0243fba63845fce7cc40365a3a
Goodluck!
I fixed this problem by using pypyodbc instead of pyodbc.
pip install pypyodbc==1.3.5
https://pypi.org/project/pypyodbc/
Found the hint here:
https://github.com/Azure/azure-functions-python-worker/issues/249
For not more problem use library for python
pymssql this not need install driver
pip install pymssql
import pymssql
conn = pymssql.connect(server, user, password, "tempdb")
cursor = conn.cursor(as_dict=True)
cursor.execute('SELECT * FROM persons WHERE salesrep=%s', 'John Doe')
for row in cursor:
print("ID=%d, Name=%s" % (row['id'], row['name']))
conn.close()
and work in docker
Related
I am using Poetry to install a python project using Poetry in a Docker container. Below you can find my Docker file, which used to work fine until recently when I switched to a new version of Poetry (1.2.1) and the new recommended Poetry installer:
# pull official base image
FROM ubuntu:20.04
ENV PATH = "${PATH}:/home/poetry/bin"
ENV APP_HOME=/home/app/web
RUN apt-get -y update && \
apt upgrade -y && \
apt-get install -y \
python3-pip \
curl \
netcat \
gunicorn && \
rm -fr /var/lib/apt/lists
# alias python2 to python3
RUN ln -s /usr/bin/python3 /usr/bin/python
# Install Poetry
RUN mkdir -p /home/poetry && \
curl -sSL https://install.python-poetry.org | POETRY_HOME=/home/poetry python -
# Cleanup
RUN apt-get remove -y curl && \
apt-get clean
RUN pip install --upgrade pip && \
pip install cryptography && \
pip install psycopg2-binary
# create directory for the app user
# create the app user
# create the appropriate directories
RUN adduser --system --group app && \
mkdir -p $APP_HOME/static-incdtim && \
mkdir -p $APP_HOME/mediafiles
# copy project
COPY . $APP_HOME
WORKDIR $APP_HOME
# Install Python packages
RUN poetry config virtualenvs.create false
RUN poetry install --only main
# copy entrypoint-prod.sh
COPY ./entrypoint.incdtim.prod.sh $APP_HOME/entrypoint.sh
RUN chmod a+x $APP_HOME/entrypoint.sh
# chown all the files to the app user
RUN chown -R app:app $APP_HOME
# change to the app user
USER app
# run entrypoint.prod.sh
ENTRYPOINT ["/home/app/web/entrypoint.sh"]
The poetry install works fine, I attached to a running container and run it myself and found that it works without problems. However, when I open a Python console and try to import a module (django) which is installed by the Poetry project, the module is not found. Please note that I am installing my project in the system environment (poetry config virtualenvs.create false). I verified, and there is only one version of python installed in the docker container. The specific error I get when trying to import a python module installed by Poetry is: ModuleNotFoundError: No module named xxxx
Although this is not an answer, it is too long to fit within the comment section. It is rather a piece of advice:
declare your ENV at the top of the Dockerfile to make it easier to read.
merge the multiple RUN commands together to avoid creating useless intermediate layers. In the particular case of apt-get install, this will also prevent you from installing a package which dates back from the first "apt-get update". Indeed, since the command line has not changed Docker will not re-execute the command and thus not refresh the package list..
avoid making a copy of all the files in "." when you previously copy some specific files to specific places..
Here, you Dockerfile could rather look like:
# pull official base image
FROM ubuntu:20.04
ENV PATH = "${PATH}:/home/poetry/bin"
ENV HOME=/home/app
ENV APP_HOME=/home/app/web
RUN apt-get -y update && \
apt upgrade -y && \
apt-get install -y \
python3-pip \
curl \
netcat \
gunicorn && \
rm -fr /var/lib/apt/lists
# alias python2 to python3
RUN ln -s /usr/bin/python3 /usr/bin/python
# Install Poetry
RUN mkdir -p /home/poetry && \
curl -sSL https://install.python-poetry.org | POETRY_HOME=/home/poetry python -
# Cleanup
RUN apt-get remove -y \
curl && \
apt-get clean
RUN pip install --upgrade pip && \
pip install cryptography && \
pip install psycopg2-binary
# create directory for the app user
# create the app user
# create the appropriate directories
RUN mkdir -p /home/app && \
adduser --system --group app && \
mkdir -p $APP_HOME/static-incdtim && \
mkdir -p $APP_HOME/mediafiles
WORKDIR $APP_HOME
# copy project
COPY . $APP_HOME
# Install Python packages
RUN poetry config virtualenvs.create false && \
poetry install --only main
# copy entrypoint-prod.sh
RUN cp $APP_HOME/entrypoint.incdtim.prod.sh $APP_HOME/entrypoint.sh && \
chmod a+x $APP_HOME/entrypoint.sh && \
chown -R app:app $APP_HOME
# change to the app user
USER app
# run entrypoint.prod.sh
ENTRYPOINT ["/home/app/web/entrypoint.sh"]
UPDATE:
Let's get back to your question. Having your program running okay when you "run it yourself" does not mean all the dependencies are met. Indeed, this can mean that your module has not been imported yet (and thus has not triggered the ModuleNotFoundError exception yet).
In order to validate this theory, you can either:
create a simple application which imports the failing module and then quits. If the import succeeds then there is something weird indeed.
list the installed modules with poetry show --latest. If the package is listed, then there is something weird indeed.
If none of the above indicates the module is installed, that just means the module is not installed and you should update your Dockerfile to install it.
NOTE: I do not know much about poetry, but you may want to have a list external dependencies to be met for your application. In the case of pip3, the list is expressed as a file named requirement.txt and can be installed with pip3 install -r requirement.txt.
It turns out this is known a bug in Poetry: https://github.com/python-poetry/poetry/issues/6459
I've got a small Dockerfile where I'm trying to get to a point where I can RUN pip3 bdist_wheel successfully. That is, without getting this error:
unknown command "bdist_wheel" - maybe you meant "wheel"
I've tried installing everything mentioned in this answer, but no luck.
Minimal repro Dockerfile and docker build output:
FROM ubuntu:18.04
RUN apt-get update \
&& apt-get install -qyy -o APT::Install-Recommends=false -o APT::Install-Suggests=false \
file \
gcc \
python3 \
python3-dev \
python3-pip \
python3-setuptools \
python3-venv \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN pip3 install --cache-dir=/tmp/pipcache --upgrade pip && rm -rf /tmp/pipcache
RUN pip install --cache-dir=/tmp/pipcache poetry && rm -rf /tmp/pipcache
WORKDIR /src/app
RUN poetry new .
RUN poetry add gevent
The most relevant part of the output is of course
error: invalid command 'bdist_wheel'
First, some notes to the error: invalid command 'bdist_wheel' output. When running pip install <pkgname>, pip will try to find a prebuilt wheel that matches your target platform. If it doesn't find one, it tries to build a wheel itself -- the source dist is downloaded and pip wheel is run to produce the wheel. On success, the built wheel is installed. On any failure (the wheel package not installed, python setup.py bdist_wheel failed or whatever), pip will fallback to the second option, which is the distutils installation method: running python setup.py install over the unpacked source dist. This is what you can observe in the log you posted:
Failed building wheel for gevent
...
Running setup.py install for gevent: started
Only when the setup.py install also fails, the installation is failed unconditionally. So while pip can't indeed build the wheel b/c the wheel package is not installed, it is not an issue for the failing installation. You can fix this by adding wheel to development packages:
RUN poetry add --dev wheel
RUN poetry add gevent
but this is an optional thing and won't affect the build result.
Now, to the real error:
Running '(cd "/tmp/pip-build-ek9pxyw2/gevent/deps/libev" && sh ./configure -C > configure-output.txt )' in /tmp/pip-build-ek9pxyw2/gevent
config.status: error: in `/tmp/pip-build-ek9pxyw2/gevent/deps/libev':
config.status: error: Something went wrong bootstrapping makefile fragments
for automatic dependency tracking. Try re-running configure with the
'--disable-dependency-tracking' option to at least be able to build
the package (albeit without support for automatic dependency tracking).
See `config.log' for more details
Something went wrong bootstrapping makefile fragments usually means that you're missing make. Install it in addition to the rest:
RUN apt install -y make
After doing that and rerunning the build, I've got the last error
error: src/gevent/libev/corecext.c: No such file or directory
This is because gevent needs Cython for generating the C extension sources. Install it before installing gevent:
RUN poetry add --dev cython
RUN poetry add gevent
The complete Dockerfile for reference, changes in bold:
FROM ubuntu:18.04
RUN apt-get update \
&& apt-get install -qyy -o APT::Install-Recommends=false -o APT::Install-Suggests=false \
file \
gcc \
python3 \
python3-dev \
python3-pip \
python3-setuptools \
python3-venv \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN pip3 install --cache-dir=/tmp/pipcache --upgrade pip && rm -rf /tmp/pipcache
RUN pip install --cache-dir=/tmp/pipcache poetry && rm -rf /tmp/pipcache
WORKDIR /src/app
RUN poetry new .
RUN apt update
RUN apt install -y make
RUN poetry add --dev wheel cython
RUN poetry add gevent
Neither wheel nor cython are required to actually run gevent, so they can be safely uninstalled afterwards to reduce the image size.
My Dockerfile using a pypy base fails with FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config' when installing llvmlite, a dependency of numba which is listed in my requirements.txt
I tried to follow and update the instructions here
Python numba / llvmlite on Debian 8 - i can't build llvmlite
My error in more detail:
Building wheels for collected packages: llvmlite
Building wheel for llvmlite (setup.py): started
Building wheel for llvmlite (setup.py): finished with status 'error'
ERROR: Command errored out with exit status 1:
command: /usr/local/bin/pypy3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ux49fegr/llvmlite/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ux49fegr/llvmlite/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-8s6wwump --python-tag pp371
cwd: /tmp/pip-install-ux49fegr/llvmlite/
Complete output (26 lines):
running bdist_wheel
/usr/local/bin/pypy3 /tmp/pip-install-ux49fegr/llvmlite/ffi/build.py
LLVM version... Traceback (most recent call last):
File "/tmp/pip-install-ux49fegr/llvmlite/ffi/build.py", line 105, in main_posix
out = subprocess.check_output([llvm_config, '--version'])
File "/usr/local/lib-python/3/subprocess.py", line 336, in check_output
**kwargs).stdout
File "/usr/local/lib-python/3/subprocess.py", line 403, in run
with Popen(*popenargs, **kwargs) as process:
File "/usr/local/lib-python/3/subprocess.py", line 722, in __init__
restore_signals, start_new_session)
File "/usr/local/lib-python/3/subprocess.py", line 1354, in _execute_child
raise child_exception_type(errno_num, err_msg)
FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config'
I don't want the heavy weight of a conda installation. Is there a way to achieve a numba install for pypy without it?
FROM pypy:3.6-slim-stretch
RUN apt-get update && apt-get install -y gnupg wget software-properties-common
RUN wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | apt-key add - 15CF4D18AF4F7421
RUN apt-add-repository "deb http://apt.llvm.org/stretch/ llvm-toolchain-stretch-6.0 main"
RUN apt-get update
RUN apt-get -y install cython python-llvm build-essential libedit-dev
RUN apt-get -y install libllvm6.0 llvm-6.0-dev llvm-dev
RUN pip install enum34
ENV LLVM_CONFIG=/usr/lib/llvm-6.0-dev/bin/llvm-config pip install llvmlite
ENV LLVM_CONFIG=/usr/lib/llvm-6.0-dev/bin/llvm-config pip install numba
# ENV LD_LIBRARY_PATH /usr/lib/llvm-6.0-dev/lib/
#... other stuff
RUN apt-get clean && apt-get -y update
RUN apt-get -y install python3-dev \
&& apt-get -y install build-essential
# Add requirements
COPY requirements.txt /tmp/
# Install sphinx first as it does not work inside requirements
RUN pip install -U pip && pip install -U sphinx && pip install numpy && pip install cython && \
pip install -r /tmp/requirements.txt
I expect a clean build of the docker image with numba on pypy
WORKAROUND If the error appeared after April the 17th (they released a new version, see history).
As a workaround try installing a previous version
pip3 install llvmlite==0.31.0
At the moment numba won't install on python 3.9.
I changed my base docker image from python:3.9-slim to python:3.8-slim and then pip install numba succeeded
This fixed it for me -
RUN echo "deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-8 main" >> /etc/apt/sources.list
RUN echo "deb-src http://apt.llvm.org/xenial/ llvm-toolchain-xenial-8 main" >> /etc/apt/sources.list
RUN apt-get install -y --no-install-recommends libedit-dev build-essential
RUN apt-get install -y --no-install-recommends llvm-8 llvm-8-dev
RUN LLVM_CONFIG=/usr/bin/llvm-config-8 pip3 install enum34 llvmlite numba
Used version 8, because got an error with the latest llvm version -
RuntimeError: Building llvmlite requires LLVM 7.0.x, 7.1.x or 8.0.x, got '3.7.1'
Reference - https://apt.llvm.org/
The "real" solution would be to encourage llvmlite and/or numba to release a wheel for pypy. But for the immediate problem...
Somehow you are missing an llvm installation, at least according to apt-file:
$ apt-file find llvm-config |grep llvm-6
llvm-6.0: /usr/bin/llvm-config-6.0
llvm-6.0: /usr/lib/llvm-6.0/bin/llvm-config
llvm-6.0: /usr/share/man/man1/llvm-config-6.0.1.gz
For installing numba on Python 3.9 on macOS, the following works:
# install llvm using MacPorts
sudo port install llvm-10
sudo port install llvm_select
sudo port select --set llvm mp-llvm-10
# set environment variable used when building `llvmlite`
export LLVM_CONFIG=/opt/local/bin/llvm-config
# clone, build, and install `llvmlite`
# http://llvmlite.pydata.org/en/latest/admin-guide/install.html#compiling-llvmlite
git clone git#github.com:numba/llvmlite.git
cd llvmlite
python setup.py build
python runtests.py
python setup.py install
cd ..
# clone, build, and install `numba`
# https://numba.readthedocs.io/en/stable/user/installing.html#installing-from-source
git clone git#github.com:numba/numba.git
cd numba
export PATH=/usr/bin/:$PATH # use clang, same as used for building Python 3.9
pip install -v .
cd ..
The above are with:
llvmlite at commit 334411cf638c8e06ba19bfda16b07dd64e9dac3c, and
numba at commit ca8132ba5e43fc3f79767046ed55217aeeabb35e.
according to https://askubuntu.com/questions/1286131/how-do-i-install-llvm-10-on-ubuntu-18-04
I added to Dockerfile the lines
RUN apt-get -y install llvm-10*
RUN rm -f /usr/bin/llvm-config
RUN ln -s /usr/bin/llvm-config-10 /usr/bin/llvm-config
and It worked (llvmlite installed)
This is the solution, obtained from this github issues thread, that worked for me! Essentially, pip just needed an upgrade in the Dockerfile before installing libraries. All I needed to do was add this line in my Dockerfile:
--upgrade pip \
Here is the sample of my Dockerfile:
# Docker commands here ...
RUN APT_INSTALL="apt-get install -y " && \
PIP_INSTALL="python3 -m pip install " && \
apt-get update && \
# more docker commands here ...
DEBIAN_FRONTEND=noninteractive $APT_INSTALL \
python3.6 \
python3.6-dev \
python3-distutils-extra \
python3-pip && \
ln -s /usr/bin/python3.6 /usr/local/bin/python3 && \
$PIP_INSTALL \
--upgrade pip \ # adding this line was my solution
setuptools \
&& \
$PIP_INSTALL \
numpy==1.18.5 \
# more docker commands here...
This is for python 3.6
I currently have the following Dockerfile to create my Docker image.
FROM python:3.6.6-alpine3.8
# Add dependencies for Python packages pandas, numpy and pyodbc
RUN apk add --no-cache curl gcc g++ unixodbc-dev
RUN ln -s /usr/include/locale.h /usr/include/xlocale.h
# Project files
ARG PROJECT_DIR=/srv/scripts
RUN mkdir -p $PROJECT_DIR
WORKDIR $PROJECT_DIR
COPY requirements.txt ./
# Install Python dependencies
RUN pip install --upgrade pip
RUN pip install -r requirements.txt
I would like to include various ODBC drivers in this image so that I can use them to connect to different databases from the Python program running in my container.
The Python program is using Pyodbc to connect to databases.
The ODBC drivers I need to install are:
PostgreSQL
MySQL
Ms SQL Server
Teradata
Oracle
Hive
Impala
I wanted to start with PostgreSQL thinking it would be the easiest one but I could not find any package on the Alpine Linux Package manager. Do you have any idea how I should install such a driver?
I was facing the same issue. I solved this issue by adding RUN apk update before RUN apk add commands.(I was using python:3.6-alpine)
Dockerfile
FROM python:3.6-alpine
RUN apk update
RUN apk add gcc libc-dev g++ libffi-dev libxml2 unixodbc-dev mariadb-dev postgresql-dev
As the OP ended moving away from Alpine- to a Debian-base image, and another answer has a small snapshot of a working Dockerfile, I will flesh out a full Dockerfile that builds SQL Server ODBC Driver 17 into a Debian-base image.
# load python 3.8 dependencies using slim debian 10 image.
FROM python:3.8-slim-buster
# build variables.
ENV DEBIAN_FRONTEND noninteractive
# install Microsoft SQL Server requirements.
ENV ACCEPT_EULA=Y
RUN apt-get update -y && apt-get update \
&& apt-get install -y --no-install-recommends curl gcc g++ gnupg unixodbc-dev
# Add SQL Server ODBC Driver 17 for Ubuntu 18.04
RUN curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add - \
&& curl https://packages.microsoft.com/config/debian/10/prod.list > /etc/apt/sources.list.d/mssql-release.list \
&& apt-get update \
&& apt-get install -y --no-install-recommends --allow-unauthenticated msodbcsql17 mssql-tools \
&& echo 'export PATH="$PATH:/opt/mssql-tools/bin"' >> ~/.bash_profile \
&& echo 'export PATH="$PATH:/opt/mssql-tools/bin"' >> ~/.bashrc
# upgrade pip and install requirements.
COPY /requirements.txt /requirements.txt
RUN pip install --upgrade pip
RUN pip install -r /requirements.txt
# clean the install.
RUN apt-get -y clean
# copy all files to /app directory and move into directory.
COPY . /app
WORKDIR /app
ENTRYPOINT ["some", "python", "command"]
if keeping it lightweight is your concerns, specifically in case of odbc, i recommend using debian:stretch image.
Docker Codes
# Import Ubuntu image to Docker
docker pull ubuntu:16.04
docker run -it ubuntu:16.04
# Instsall Python3 and pip3
apt-get update
apt-get install -y python3 python3-pip
# Install Selenium
pip3 install selenium
# Install BeautifulSoup4
pip3 install beautifulsoup4
# Install library for PhantomJS
apt-get install -y wget libfontconfig
# Downloading and installing binary
mkdir -p /home/root/src && cd &_
tar jxvf phantomjs-2.1.1-linux-x86_64.tar.bz2
cd phantomjs-2.1.1-linux-x86_64/bin/
cp phantomjs /usr/local/bin/
# Installing font
apt-get install -y fonts-nanum*
Question
I am trying to import Ubuntu image to docker and install serveral packages inscluding python3, pip3, bs4, and PhantomJs. Then I want to save all this configurations in Docker as "ubuntu-phantomjs". As I am currently on Ubuntu image, anything that starts with 'docker' command do not work. How could I save my image?
Here is the dockerfile:
# Import Ubuntu image to Docker
FROM ubuntu:16.04
# Install Python3, pip3, library and fonts
RUN apt-get update && apt-get install -y \
python3 \
python3-pip \
wget libfontconfig \
fonts-nanum*
&& rm -rf /var/lib/apt/lists/*
RUN pip3 install selenium beautifulsoup4
# Downloading and installing binary
RUN mkdir -p /home/root/src && cd &_ tar jxvf phantomjs-2.1.1-linux-x86_64.tar.bz2 && cd phantomjs-2.1.1-linux-x86_64/bin/ && cp phantomjs /usr/local/bin/
Now after saving the code in file named dockerfile, open a terminal in the same directory as the one where file is stored, and run following command:
$ docker build -t ubuntu-phantomjs .
-t means that the target is ubuntu-phantomjs and . means that the context for docker is the current directory. The above dockerfile is not a standard one, and does not follow all good practices mentioned here. You can change this file according to your needs, read the documentations for more help.