Merge pull request #71 from hydroshare/bullseye-py39-dj32-upgrade

Base image update: Debian buster, Python3.9

Dockerfile

@@ -1,33 +1,34 @@
-FROM python:3.6-jessie
-MAINTAINER Michael J. Stealey <[email protected]>
-
+FROM python:3.9-buster
 
 ENV DEBIAN_FRONTEND noninteractive
 ENV PY_SAX_PARSER=hs_core.xmlparser
 
-RUN printf "deb http://deb.debian.org/debian/ jessie main\ndeb http://security.debian.org jessie/updates main" > /etc/apt/sources.list
+RUN printf "deb http://deb.debian.org/debian/ buster main\ndeb http://security.debian.org/debian-security buster/updates main" > /etc/apt/sources.list
 
 RUN apt-get update && apt-get install -y \
     apt-transport-https \
     ca-certificates \
-    sudo \
-    && apt-key adv --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys 58118E89F3A912897C070ADBF76221572C52609D
+    curl \
+    lsb-release \
+    sudo
+
+RUN sudo mkdir -p /etc/apt/keyrings
+RUN curl -fsSL https://download.docker.com/linux/debian/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg
 
-RUN curl -sL https://deb.nodesource.com/setup_7.x | sudo -E bash -
+RUN echo \
+  "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/debian \
+  $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
 
-# Add docker.list and requirements.txt - using /tmp to keep hub.docker happy
-COPY . /tmp
-RUN cp /tmp/docker.list /etc/apt/sources.list.d/ \
-    && cp /tmp/requirements.txt /requirements.txt
+RUN curl -sL https://deb.nodesource.com/setup_lts.x | sudo -E bash -
 
+COPY docker.list /etc/apt/sources.list.d/
 RUN sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 7EA0A9C3F273FCD8
 
-RUN sudo sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt/ `lsb_release -cs`-pgdg main" >> /etc/apt/sources.list.d/pgdg.list' \
-    && wget -q https://www.postgresql.org/media/keys/ACCC4CF8.asc -O - | sudo apt-key add -
+RUN sudo sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt $(lsb_release -cs)-pgdg main" > /etc/apt/sources.list.d/pgdg.list'
+RUN wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
 
 RUN apt-get update && apt-get install -y --fix-missing --no-install-recommends \
     apt-utils \
-    docker-ce \
     libfuse2 \
     libjpeg62-turbo \
     libjpeg62-turbo-dev \
@@ -36,9 +37,8 @@ RUN apt-get update && apt-get install -y --fix-missing --no-install-recommends \
     gdal-bin \
     build-essential \
     libgdal-dev \
-    libgdal1h \
-    postgresql-9.4 \
-    postgresql-client-9.4 \
+    postgresql-15 \
+    postgresql-client-15 \
     git \
     rsync \
     openssh-client \
@@ -50,21 +50,14 @@ RUN npm install -g phantomjs-prebuilt
 
 WORKDIR /
 
-#install numpy before matplotlib
-RUN pip install 'numpy==1.16.0'
-
-RUN pip install git+https://github.com/sblack-usu/defusedexpat.git
-
-# Install pip based packages (due to dependencies some packages need to come first)
 RUN export CPLUS_INCLUDE_PATH=/usr/include/gdal 
 RUN export C_INCLUDE_PATH=/usr/include/gdal 
 RUN export GEOS_CONFIG=/usr/bin/geos-config 
 RUN HDF5_INCDIR=/usr/include/hdf5/serial 
 RUN pip install --upgrade pip 
-RUN pip install -r requirements.txt
+RUN pip install 'setuptools<58.0.0'
 
-# Install GDAL 2.4.1 from source
-RUN wget http://download.osgeo.org/gdal/2.4.1/gdal-2.4.1.tar.gz \
+RUN wget https://ftp.osuosl.org/pub/osgeo/download/gdal/2.4.1/gdal-2.4.1.tar.gz \
     && tar -xzf gdal-2.4.1.tar.gz \
     && rm gdal-2.4.1.tar.gz
 
@@ -75,19 +68,30 @@ RUN ./configure --with-python --with-geos=yes \
     && sudo ldconfig
 WORKDIR /
 
+# TODO: iROds 4.2.x is holding us to Debian Buster which is EOL. It also requires libssl1.0.0 which is obsolete
+# we should upgrade to iRods 4.3, Debian Bullseye, etc but this will require at a minimum, changes to our iinit use in HS
+RUN wget http://snapshot.debian.org/archive/debian/20190501T215844Z/pool/main/g/glibc/multiarch-support_2.28-10_amd64.deb
+RUN sudo dpkg -i multiarch-support*.deb
+RUN wget http://snapshot.debian.org/archive/debian/20170705T160707Z/pool/main/o/openssl/libssl1.0.0_1.0.2l-1%7Ebpo8%2B1_amd64.deb
+RUN sudo dpkg -i libssl1.0.0*.deb
+
 # Install iRODS
 RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add - \
-    && echo "deb [arch=amd64] https://packages.irods.org/apt/ trusty main" | \
+    && echo "deb [arch=amd64] https://packages.irods.org/apt/ bionic main" | \
     sudo tee /etc/apt/sources.list.d/renci-irods.list \
     && sudo apt-get update && sudo apt-get install -y \
     apt-transport-https \
-    irods-runtime \
-    irods-icommands
+    irods-runtime=4.2.10 \
+    irods-icommands=4.2.10
+
+# Removed defusedexpat (as part of upgrade to python 3.9)
+# Added defusedxml
+# https://docs.python.org/3.9/library/xml.html?highlight=xml#the-defusedxml-package
+# https://github.com/python/cpython/issues/82766
 
-# inplaceedit in pip doesn't seem compatible with Django 1.11 yet...
-RUN pip install git+https://github.com/theromis/django-inplaceedit.git@e6fa12355defedf769a5f06edc8fc079a6e982ec
-# foresite-toolkit in pip isn't compatible with python3
-RUN pip install git+https://github.com/sblack-usu/foresite-toolkit.git#subdirectory=foresite-python/trunk
+# Install pip based packages (due to dependencies some packages need to come first)
+COPY ./requirements.txt /requirements.txt
+RUN pip install -r requirements.txt
 
 # Install SSH for remote PyCharm debugging
 RUN mkdir /var/run/sshd

docker.list

@@ -1 +1 @@
-deb https://download.docker.com/linux/debian jessie stable
+deb https://download.docker.com/linux/debian buster stable

requirements.txt

@@ -1,110 +1,182 @@
-amqp==2.5.2
+# generated using pipdeptree https://github.com/tox-dev/pipdeptree
+# pipdeptree -f | sed 's/ //g' | sort -u > requirements.txt
+aiohttp==3.8.3
+amqp==2.6.1
 anyjson==0.3.3
 arrow==0.7.0
+asgiref==3.5.2
+astroid==1.4.9
+attrs==22.1.0
 autopep8==1.2.2
+Babel==2.11.0
 bagit==1.5.4
-celery==4.4.0
-cffi==1.11.5
-click==6.7
+bcrypt==4.0.1
+beautifulsoup4==4.11.1
+billiard==3.6.4.0
+bleach==4.1.0
+celery==4.4.7
+certifi==2022.12.7
+cffi==1.15.1
+cftime==1.6.2
+chardet==5.1.0
+charset-normalizer==2.0.12
+click==8.1.3
+colorama==0.4.6
 coreapi==2.3.3
-coverage==4.0.3
+coreschema==0.0.4
+coverage==6.5.0
+cryptography==38.0.4
 cycler==0.10.0
-#defusedexpat==0.4
-defusedxml==0.4.1
-Django==1.11.29
-django-appconf==1.0.2
-django-autocomplete-light==2.3.3
-django-braces==1.9.0
-django-compressor==2.2
-django-contrib-comments==1.9.0
-django-cors-headers==2.4.0
-django-crispy-forms==1.7.2
-django-debug-toolbar==1.9.1
+debugpy==1.6.4
+deepdiff==1.7.0
+defusedxml==0.7.1
+Deprecated==1.2.13
+Django==3.2.15
+django-appconf==1.0.5
+django-autocomplete-light==2.3.6
+django-braces==1.15.0
+django-compressor==4.1
+django-contrib-comments==2.2.0
+django-cors-headers==3.10.1
+django-crispy-forms==1.13.0
+django-debug-toolbar==3.2.4
 django-freshly==0.1.2
-django-haystack==2.8.1
+django-haystack==3.1.1
 django-heartbeat==2.0.2
 django-ipware==2.1.0
-django-jsonfield==1.0.1
+django-jsonfield==1.4.1
 django-modeltranslation==0.12.2
 django-nose==1.4.5
-django-oauth-toolkit==1.1.0
-django-robots==2.0
-django-security==0.9.3
+django-oauth-toolkit==2.1.0
+djangorestframework==3.12.4
+django-robots==4.0
+django-security==0.12.0
 django-test-without-migrations==0.6
 django-timedeltafield==0.7.10
 django-widget-tweaks==1.4.1
-djangorestframework==3.11.0
+dnspython==2.2.1
 docker-py==1.7.2
 dominate==2.4.0
 DoubleMetaphone==0.1
-drf-haystack==1.8.5
-drf-yasg==1.17.1
-ecdsa==0.13.3
-enum34==1.1.6
-filebrowser-safe==0.5.0
-flake8==3.5.0
+drf-haystack==1.8.11
+drf-yasg==1.20.0
+ecdsa==0.18.0
+email-validator==1.3.0
+exceptiongroup==1.0.4
+filebrowser-safe==1.1.1
+flake8==6.0.0
 flex==6.14.1
 flower==0.9.3
+foresite@git+https://github.com/sblack-usu/foresite-toolkit.git@94c0c2a8e21a922caa1df6cc412d5dc1a7adb189#subdirectory=foresite-python/trunk
 funcsigs==1.0.2
-#functools32==3.2.3.post2
 future==0.16.0
+GDAL==2.4.1
+geographiclib==1.52
 geojson==1.3.2
 geopy==1.16.0
-gevent==1.4.0
-grappelli-safe==0.5.1
-gunicorn==19.6.0
+gevent==22.10.2
+grappelli-safe==1.1.1
+greenlet==2.0.1
+gunicorn==20.1.0
+hsmodels@git+https://github.com/hydroshare/hsmodels.git@3197b512d2764e2a4772596fe6c288331e53223e
 html5lib==0.9999999
+idna==3.4
 inflection==0.3.1
+iniconfig==1.1.1
+ipaddress==1.0.22
 isodate==0.5.4
+itypes==1.2.0
 Jinja2==2.10.1
 jsonpointer==1.14
 jsonschema==2.6.0
+jwcrypto==1.4.2
 keepalive==0.5
-kombu==4.6.7
+kiwisolver==1.4.4
+kombu==4.6.11
+lazy-object-proxy==1.8.0
 lxml==4.4.0
-#mapnik==0.1
 Markdown==3.0.1
-MarkupSafe==1.0
+MarkupSafe==2.0.1
 matplotlib==3.1.2
-mccabe==0.6.1
-Mezzanine==4.3.1
+mccabe==0.7.0
+Mezzanine==5.1.4
 mock==1.3.0
 nameparser==0.5.7
-netCDF4==1.5.1.2 
+netCDF4==1.5.1.2
 nose==1.3.7
-nose-timer>=0.7.4,<1.0.0
+nose-timer==0.7.6
+numpy==1.16.6
 oauthlib==3.1.0
 OWSLib==0.10.3
-paramiko==2.4.2
+packaging==21.3
+paramiko==2.12.0
 pbr==1.10.0
 pep8==1.7.0
+Pillow==9.3.0
+pip==22.3.1
+pluggy==1.0.0
 prettytable==0.7.2
+probableparsing==0.0.1
 probablepeople==0.5.4
-psycopg2==2.8.2
-ipaddress==1.0.22
+psutil==4.0.0
+psycopg2==2.9.5
 pyasn1==0.4.4
-pycodestyle==2.3.1
+pycodestyle==2.10.0
+pycparser==2.21
 PyCRS==1.0.1
-pyflakes==1.6.0
+pydantic==1.10.2
+pydebug==1.0.3
+pyflakes==3.0.1
+PyLD==2.0.3
 pylint==1.5.5
-pyproj==1.9.5.1
-pysolr==3.4.0
-pysqlite3==0.2.1
-pytest-django>=3.4.7, <4.0.0
-python-crfsuite==0.9.6
-python-dateutil==2.5.3
-python-irodsclient==0.8.1 
-pytz==2016.3
+PyNaCl==1.5.0
+pyparsing==3.0.9
+pyproj==3.4.0
+pysolr==3.9.0
+pytest==7.2.0
+pytest-cov==4.0.0
+pytest-django==4.5.2
+python-crfsuite==0.9.8
+python-dateutil==2.8.0
+python-irodsclient==0.8.1
+pytz==2022.6
+pytz-deprecation-shim==0.1.0.post0
 PyYAML==5.3
-rcssmin==1.0.6
-rdflib==4.0.1
+rcssmin==1.1.0
+rdflib==5.0.0
 redis==2.10.5
-requests==2.20.0
+requests==2.28.1
+requests-oauthlib==1.3.1
 rfc3987==1.3.8
+rjsmin==1.2.0
 robot-detection==0.4
+ruamel.yaml==0.17.21
+ruamel.yaml.clib==0.2.7
 selenium==3.0.2
+setuptools==57.5.0
+six==1.16.0
+sorl-thumbnail==12.8.0
+soupsieve==2.3.2.post1
+sqlparse==0.4.3
+strict-rfc3339==0.7
 suds-jurko==0.6
 timeago==1.0.10
+tomli==2.0.1
+tornado==5.1.1
+typing_extensions==4.4.0
+tzdata==2022.7
+tzlocal==4.2
+ua-parser==0.16.1
 uritemplate==3.0.0
+urllib3==1.26.13
+validate-email==1.3
+vine==1.3.0
 virtualenv==15.0.2
+webencodings==0.5.1
+websocket-client==1.4.2
+wheel==0.38.4
+wrapt==1.14.1
+xmlrunner==1.7.7
 xmltodict==0.10.2
+zope.event==4.5.0
+zope.interface==5.5.2