Support #380 by undoing all of the upgrades from #374

EDRN · Nov 15, 2024 · a6fbd4d · a6fbd4d
1 parent b438ae2
commit a6fbd4d
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diff --git a/.github/workflows/delivery.yaml b/.github/workflows/delivery.yaml
@@ -18,7 +18,7 @@ on:
     push:
         branches:
             -   main
-            -   i374
+            -   i380
         paths:
             -   'src/**'
             -   'docker/Dockerfile'

diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -15,7 +15,7 @@
 # `numpy-gitpod` and `numpy-dev`—and I'm not going to use a `-dev` image in production.) See the `py_deps`
 # below.
 
-FROM alpine:3.19
+FROM alpine:3.18
 
 
 # Configurable Arguments
@@ -58,8 +58,8 @@ RUN \
     :
 
 RUN \
-    build_deps="automake bzip2-dev cyrus-sasl-dev git g++ gcc libffi-dev libjpeg-turbo-dev libwebp-dev libxml2-dev libxslt-dev make musl-dev openjpeg-dev openldap-dev openssl-dev pcre-dev python3-dev postgresql-dev su-exec tiff-dev zlib-dev py3-pip" &&\
-    run_deps="curl krb5-libs libgcc libjpeg-turbo libldap libpq libsasl libstdc++ libwebp libxml2 libxslt netcat-openbsd openjpeg python3 rsync tiff tidyhtml py3-gunicorn py3-flask" &&\
+    build_deps="automake bzip2-dev cyrus-sasl-dev git g++ gcc libffi-dev libjpeg-turbo-dev libwebp-dev libxml2-dev libxslt-dev make musl-dev openjpeg-dev openldap-dev openssl-dev pcre-dev python3-dev postgresql-dev su-exec tiff-dev zlib-dev" &&\
+    run_deps="curl krb5-libs libgcc libjpeg-turbo libldap libpq libsasl libstdc++ libwebp libxml2 libxslt netcat-openbsd openjpeg python3 rsync tiff tidyhtml" &&\
     py_deps="py3-numpy py3-pandas py3-pillow py3-psycopg2 py3-biopython" &&\
     /sbin/apk update --quiet &&\
     /sbin/apk add --no-progress --quiet --virtual /edrn-build $build_deps &&\
@@ -69,21 +69,31 @@ RUN \
 
 # Over on GitHub Actions, we need to fail fast and not hit the six hour run limit, so make sure we got it right
 
-RUN echo `/usr/bin/python3 --version` | grep -q '^Python 3\.11\.'
-RUN echo `/usr/bin/python3 -c 'import numpy; print(numpy.__version__)'` | grep -q '^1\.25\.'
-RUN echo `/usr/bin/python3 -c 'import pandas; print(pandas.__version__)'` | grep -q '^2\.0\.'
-RUN echo `/usr/bin/python3 -c 'import PIL; print(PIL.__version__)'` | grep -q '^10\.3\.'
-RUN echo `/usr/bin/python3 -c 'import psycopg2; print(psycopg2.__version__)'` | grep -q '^2\.9\.'
+RUN [ "`/usr/bin/python3 --version`" = "Python 3.11.10" ]
+RUN [ "`/usr/bin/python3 -c 'import numpy; print(numpy.__version__)'`" = "1.24.4" ]
+RUN [ "`/usr/bin/python3 -c 'import pandas; print(pandas.__version__)'`" = "1.5.3" ]
+RUN [ "`/usr/bin/python3 -c 'import PIL; print(PIL.__version__)'`" = "9.5.0" ]
+RUN [ "`/usr/bin/python3 -c 'import psycopg2; print(psycopg2.__version__)'`" = "2.9.6 (dt dec pq3 ext lo64)" ]
+RUN [ "`/usr/bin/python3 -c 'import Bio; print(Bio.__version__)'`" = "1.81" ]
+
+# RUN echo `/usr/bin/python3 --version` | grep -q '^Python 3\.11\.'
+# RUN echo `/usr/bin/python3 -c 'import numpy; print(numpy.__version__)'` | grep -q '^1\.25\.'
+# RUN echo `/usr/bin/python3 -c 'import pandas; print(pandas.__version__)'` | grep -q '^2\.0\.'
+# RUN echo `/usr/bin/python3 -c 'import PIL; print(PIL.__version__)'` | grep -q '^10\.3\.'
+# RUN echo `/usr/bin/python3 -c 'import psycopg2; print(psycopg2.__version__)'` | grep -q '^2\.9\.'
 # Note that Biopython does not use MAJOR.MINOR.MICRO versions so there's no trailing dot here
-RUN echo `/usr/bin/python3 -c 'import Bio; print(Bio.__version__)'` | grep -q '^1\.81'
+# RUN echo `/usr/bin/python3 -c 'import Bio; print(Bio.__version__)'` | grep -q '^1\.81'
 
 RUN \
     : See https://github.com/python-ldap/python-ldap/issues/432 for workaround to Python LDAP vs OpenLDAP 2.5 issue &&\
     echo 'INPUT ( libldap.so )' > /usr/lib/libldap_r.so &&\
-    /usr/bin/python3 -m venv --system-site-packages --upgrade-deps /app &&\
-    /usr/bin/install -o edrn -g edrn -d /app/media /app/static /app/wheels &&\
+    /usr/bin/python3 -m ensurepip --upgrade &&\
+    /usr/bin/pip3 install --quiet --progress-bar off --upgrade pip setuptools wheel &&\
+    /usr/bin/pip3 install gunicorn==20.1.0 &&\
+    /usr/bin/install -o edrn -g edrn -d /app /app/media /app/static /app/wheels &&\
     :
 
+
 COPY --chown=edrn:edrn ./dist/*.whl /app/wheels/
 
 # Normally a single RUN would work fine:
@@ -103,30 +113,32 @@ COPY --chown=edrn:edrn ./dist/*.whl /app/wheels/
 # Except the Docker plugin for Jenkins at CBIIT chokes with an HTTP 400 error because apparently
 # the single layer made above is too big. So, we have to do these in separate RUNs:
 
-RUN /app/bin/pip3 install --progress-bar off /app/wheels/edrnsite.controls-*.whl
-RUN /app/bin/pip3 install --progress-bar off /app/wheels/edrnsite.streams-*.whl
-RUN /app/bin/pip3 install --progress-bar off /app/wheels/edrnsite.content-*.whl
-RUN /app/bin/pip3 install --progress-bar off /app/wheels/edrn.collabgroups-*.whl
-RUN /app/bin/pip3 install --progress-bar off /app/wheels/edrn.theme-*.whl
-RUN /app/bin/pip3 install --progress-bar off /app/wheels/edrnsite.ploneimport-*.whl
-RUN /app/bin/pip3 install --progress-bar off /app/wheels/eke.geocoding-*.whl
-RUN /app/bin/pip3 install --progress-bar off /app/wheels/eke.knowledge-*.whl
-RUN /app/bin/pip3 install --progress-bar off /app/wheels/eke.biomarkers-*.whl
-RUN /app/bin/pip3 install --progress-bar off /app/wheels/edrnsite.search-*.whl
-RUN /app/bin/pip3 install --progress-bar off /app/wheels/edrn.metrics-*.whl
-RUN /app/bin/pip3 install --progress-bar off /app/wheels/edrnsite.policy-*.whl
+RUN /usr/bin/pip3 install --progress-bar off /app/wheels/edrnsite.controls-*.whl
+RUN /usr/bin/pip3 install --progress-bar off /app/wheels/edrnsite.streams-*.whl
+RUN /usr/bin/pip3 install --progress-bar off /app/wheels/edrnsite.content-*.whl
+RUN /usr/bin/pip3 install --progress-bar off /app/wheels/edrn.collabgroups-*.whl
+RUN /usr/bin/pip3 install --progress-bar off /app/wheels/edrn.theme-*.whl
+RUN /usr/bin/pip3 install --progress-bar off /app/wheels/edrnsite.ploneimport-*.whl
+RUN /usr/bin/pip3 install --progress-bar off /app/wheels/eke.geocoding-*.whl
+RUN /usr/bin/pip3 install --progress-bar off /app/wheels/eke.knowledge-*.whl
+RUN /usr/bin/pip3 install --progress-bar off /app/wheels/eke.biomarkers-*.whl
+RUN /usr/bin/pip3 install --progress-bar off /app/wheels/edrnsite.search-*.whl
+RUN /usr/bin/pip3 install --progress-bar off /app/wheels/edrn.metrics-*.whl
+RUN /usr/bin/pip3 install --progress-bar off /app/wheels/edrnsite.policy-*.whl
 
 # And this too:
 
 RUN \
     cd /app &&\
     : Get the static files ready &&\
-    /sbin/su-exec edrn /usr/bin/env LDAP_BIND_PASSWORD=unused SIGNING_KEY=unused /app/bin/django-admin collectstatic --settings edrnsite.policy.settings.ops --no-input --clear --link &&\
+    /sbin/su-exec edrn /usr/bin/env LDAP_BIND_PASSWORD=unused SIGNING_KEY=unused /usr/bin/django-admin collectstatic --settings edrnsite.policy.settings.ops --no-input --clear --link &&\
     : Clean up clean up everybody everywhere &&\
+    : PrismaCloud does not like pip to be in the image &&\
+    /usr/bin/pip3 uninstall --yes --quiet pip &&\
     /sbin/apk del --quiet /edrn-build &&\
     /bin/rm -rf /app/wheels &&\
     /bin/rm -rf /var/cache/apk/* &&\
-    /bin/chown -R edrn:edrn /app/lib/python3.*/site-packages &&\
+    /bin/chown -R edrn:edrn /usr/lib/python3.*/site-packages &&\
     :
 
 COPY --chown=edrn:edrn docker/*.py /app/
@@ -141,7 +153,7 @@ EXPOSE      8000
 VOLUME      ["/app/media"]
 USER        edrn
 WORKDIR     /app
-ENTRYPOINT  ["/app/bin/python3"]
+ENTRYPOINT  ["/usr/bin/python3"]
 CMD         ["/usr/bin/gunicorn", "-c", "/app/gunicorn.conf.py"]
 HEALTHCHECK --interval=5m --timeout=2m --start-period=10m CMD /usr/bin/curl --fail --retry 6 --max-time 5 --retry-delay 10 --retry-max-time 60 http://127.0.0.1:8000/ || /bin/sh -c 'killall5 -TERM && (/bin/sleep 10; killall5 -KILL)'
 

diff --git a/docker/docker-compose.yaml b/docker/docker-compose.yaml
@@ -124,7 +124,7 @@ services:
     #
     # Port 6379, not published.
     cache:
-        image: redis:7.4.1-alpine3.20
+        image: redis:7.0.11-alpine3.18
         networks:
             -   lattice
         restart: on-failure
@@ -174,7 +174,7 @@ services:
     # Worker processes run Django functions so it needs all the same env vars as `portal`.
     worker:
         image: ${EDRN_IMAGE_OWNER-edrndocker/}edrn-portal:${EDRN_VERSION:-6.3.0-uid26013}
-        entrypoint: ['/app/bin/django-admin', 'worker', '--verbosity', '2']
+        entrypoint: ['/usr/bin/django-admin', 'worker', '--verbosity', '2']
         volumes:
             -
                 type: bind

diff --git a/src/edrn.collabgroups/setup.cfg b/src/edrn.collabgroups/setup.cfg
@@ -17,8 +17,8 @@ package_dir =
 packages = find_namespace:
 python_requires = >= 3.9
 install_requires =
-    django  < 6
-    wagtail < 6
+    django  < 5, > 4
+    wagtail < 6, > 5
     edrnsite.streams
     edrnsite.content
 

diff --git a/src/edrn.metrics/setup.cfg b/src/edrn.metrics/setup.cfg
@@ -18,8 +18,8 @@ packages = find_namespace:
 python_requires = >= 3.9
 install_requires =
     edrn.auth
-    django  < 6
-    wagtail < 6
+    django  < 5, > 4
+    wagtail < 6, > 5
 
 
 [options.packages.find]

diff --git a/src/edrn.theme/setup.cfg b/src/edrn.theme/setup.cfg
@@ -20,8 +20,8 @@ python_requires = >= 3.9
 install_requires =
     edrn.auth
     edrnsite.controls
-    django  <  6
-    wagtail <  6
+    django  <  5, > 4
+    wagtail <  6, > 5
 
 
 [options.packages.find]

diff --git a/src/edrnsite.content/setup.cfg b/src/edrnsite.content/setup.cfg
@@ -18,13 +18,13 @@ packages = find_namespace:
 python_requires = >= 3.9
 install_requires =
     edrnsite.streams
-    django  < 6
-    wagtail < 6
+    django  < 5, > 4
+    wagtail < 6, > 5
     django-widget-tweaks ~= 1.4.12
     wagtail-django-recaptcha ~= 1.0
     django-recaptcha ~= 3.0.0
     gdown ~= 4.7.1
-    pandas ~= 2.0.3   # Must match py3-pandas package in Dockerfile
+    pandas ~= 1.5.3   # Must match py3-pandas package in Dockerfile
 
 
 # A couple of the forms in this package actually depend on eke.knowledge, but eke.knowledge depends on

diff --git a/src/edrnsite.controls/setup.cfg b/src/edrnsite.controls/setup.cfg
@@ -17,8 +17,8 @@ package_dir =
 packages = find:
 python_requires = >= 3.9
 install_requires =
-    django  < 6
-    wagtail < 6
+    django  < 5, > 4
+    wagtail < 6, > 5
 
 
 [options.packages.find]

diff --git a/src/edrnsite.ploneimport/setup.cfg b/src/edrnsite.ploneimport/setup.cfg
@@ -17,8 +17,8 @@ package_dir =
 packages = find_namespace:
 python_requires = >= 3.9
 install_requires =
-    django  < 6
-    wagtail < 6
+    django  < 5, > 4
+    wagtail < 6, > 5
 
 
 [options.packages.find]

diff --git a/src/edrnsite.policy/setup.cfg b/src/edrnsite.policy/setup.cfg
@@ -27,21 +27,21 @@ install_requires =
     edrnsite.ploneimport
     eke.biomarkers
     edrn.metrics
-    edrn.auth             ~= 2.0.1
-    celery[redis]         ~= 5.4.0
+    edrn.auth             ~= 2.0.0
+    celery[redis]         ~= 5.2.7
     dj-database-url       ~= 2.1.0
-    django                ~= 5.0.9
-    django-auth-ldap      ~= 5.1.0
+    django                ~= 4.2.9
+    django-auth-ldap      ~= 4.1.0
     django-celery-results ~= 2.5.1
     django-redis          ~= 5.4.0
-    pillow                ~= 10.3.0        # Must match py3-pillow package installed in Dockerfile
-    psycopg2              ~= 2.9.9         # Must match py3-pyscopg2 package installed in Dockerfile
+    pillow                == 9.5.0        # Must match py3-pillow package installed in Dockerfile
+    psycopg2              == 2.9.6        # Must match py3-pyscopg2 package installed in Dockerfile
     pymemcache            ~= 3.5.2
-    wagtail               == 5.2.6
+    wagtail               == 5.2.3
     wagtail-favicon       ~= 0.3.0
     wagtail-metadata      ~= 5.0.0
-    tzdata                == 2024.2
-    wagtailmenus          ~= 4.0.1
+    tzdata                == 2022.1
+    wagtailmenus          ~= 3.1.9
     wagtail-robots        @ git+https://github.com/unexceptable/wagtail-robots.git@9a47b6c09bec120bd5a85f4c7c1856cdc7f71f51
 
 

diff --git a/src/edrnsite.policy/src/edrnsite/policy/settings/ops.py b/src/edrnsite.policy/src/edrnsite/policy/settings/ops.py
@@ -9,11 +9,11 @@
 # Debug Mode
 # ----------
 #
-# This had better be off!
+# This had better be off! TURN THIS BACK TO FALSE!!!
 #
 # 🔗 https://docs.djangoproject.com/en/3.2/ref/settings/#debug
 
-DEBUG = True
+DEBUG = False
 
 
 # Secret Key

diff --git a/src/edrnsite.search/setup.cfg b/src/edrnsite.search/setup.cfg
@@ -18,8 +18,8 @@ packages = find_namespace:
 python_requires = >= 3.9
 install_requires =
     edrnsite.controls
-    django < 6
-    wagtail < 6
+    django < 5, > 4
+    wagtail < 6, > 5
     elasticsearch == 7.13.4
 
 

diff --git a/src/edrnsite.streams/setup.cfg b/src/edrnsite.streams/setup.cfg
@@ -17,8 +17,8 @@ package_dir =
 packages = find_namespace:
 python_requires = >= 3.9
 install_requires =
-    django < 6
-    wagtail < 6
+    django < 5, > 4
+    wagtail < 6, > 5
 
 
 [options.packages.find]

diff --git a/src/edrnsite.test/setup.cfg b/src/edrnsite.test/setup.cfg
@@ -20,8 +20,8 @@ install_requires =
     selenium ~= 4.9.1
     edrnsite.controls
     edrnsite.content
-    django  < 6
-    wagtail < 6
+    django  < 5, > 4
+    wagtail < 6, > 5
 
 
 [options.packages.find]

diff --git a/src/eke.biomarkers/setup.cfg b/src/eke.biomarkers/setup.cfg
@@ -21,14 +21,14 @@ install_requires =
     eke.knowledge
     edrnsite.content
     edrn.auth
-    biopython          ~= 1.81    # Must mathc py3-biopython package in Dockerfile
-    django             <  6
+    biopython          == 1.81    # Must mathc py3-biopython package in Dockerfile
+    django             <  5, > 4
     django_plotly_dash == 1.7.1
-    numpy              ~= 1.25.2  # Must match py3-numpy package in Dockerfile
-    pandas             ~= 2.0.3   # Must match py3-pandas package in Dockerfile
+    numpy              == 1.24.4  # Must match py3-numpy package in Dockerfile
+    pandas             == 1.5.3   # Must match py3-pandas package in Dockerfile
     rdflib             ~= 6.1.1   # Regression in 6.2.0, see https://github.com/RDFLib/rdflib/issues/2120
     sortedcontainers   ~= 2.4.0
-    wagtail            <  6
+    wagtail            <  6, > 5
     Werkzeug           == 2.0.3   # django_plotly_dash fails with 2.1
 
 

diff --git a/src/eke.geocoding/setup.cfg b/src/eke.geocoding/setup.cfg
@@ -19,9 +19,9 @@ packages = find_namespace:
 python_requires = >= 3.9
 install_requires =
     boto3    ~= 1.24.75
-    django   <  6
+    django   <  5, > 4
     geocoder ~= 1.38.1
-    wagtail  <  6
+    wagtail  <  6, > 5
 
 
 [options.packages.find]

diff --git a/src/eke.knowledge/setup.cfg b/src/eke.knowledge/setup.cfg
@@ -22,19 +22,19 @@ install_requires =
     edrnsite.controls
     edrn.collabgroups
     eke.geocoding
-    biopython                       ~= 1.81    # Must match py3-biopython package in Dockerfile
+    biopython                       == 1.81    # Must match py3-biopython package in Dockerfile
     boto3                           ~= 1.24.75
-    celery                          ~= 5.4.0
+    celery                          ~= 5.2.7
     dash-dangerously-set-inner-html ~= 0.0.2
-    django                          <  6
+    django                          <  5, > 4
     django_plotly_dash              == 1.7.1
     humanize                        ~= 4.3.0
     libgravatar                     ~= 1.0.4
-    numpy                           ~= 1.25.2  # Must match py3-numpy package in Dockerfile
-    pandas                          ~= 2.0.3   # Must match py3-pandas package in Dockerfile
+    numpy                           == 1.24.4  # Must match py3-numpy package in Dockerfile
+    pandas                          == 1.5.3   # Must match py3-pandas package in Dockerfile
     rdflib                          == 6.1.1   # Regression in 6.2.0, see https://github.com/RDFLib/rdflib/issues/2120
     sortedcontainers                ~= 2.4.0
-    wagtail                         <  6
+    wagtail                         <  6, > 5
     Werkzeug                        == 2.0.3   # django_plotly_dash fails with 2.1
 
 [options.packages.find]

diff --git a/src/eke.knowledge/src/eke/knowledge/sciencedata.py b/src/eke.knowledge/src/eke/knowledge/sciencedata.py
@@ -277,6 +277,8 @@ def faceted_markup(self, request):
         return ''.join(rows)
 
     def get_context(self, request: HttpRequest, *args, **kwargs) -> dict:
+        app = DjangoDash('ScienceDataDashboard')  # ← referenced in data-collection-index.html
+
         context = super().get_context(request, *args, **kwargs)
         context['statistics'] = DataStatistic.objects.child_of(self).order_by('title')
         matches = context['knowledge_objects']
@@ -317,7 +319,6 @@ def get_context(self, request: HttpRequest, *args, **kwargs) -> dict:
         cats_figure.update_layout(showlegend=False, margin=dict(l=20, r=20, t=40, b=20))
         cats_legend = ghetto_plotly_legend([i[0] for i in c.most_common()], palette)
 
-        app = DjangoDash('ScienceDataDashboard')  # ← referenced in data-collection-index.html
         app.layout = html.Div(className='container', children=[
             html.Div(className='row', children=[
                 html.Div(className='col-md-4', children=[

diff --git a/support/cbiit-deploy-prod.sh b/support/cbiit-deploy-prod.sh
@@ -129,10 +129,10 @@ bzip2 --decompress --stdout /local/content/edrn/database-access/edrn.sql.bz2 | \
 echo ""
 echo "📀 Initial database setup"
 ssh -q $USER@$WEBSERVER "cd $WEBROOT ; \
-docker compose --project-name edrn exec portal /app/bin/django-admin makemigrations &&\
-docker compose --project-name edrn exec portal /app/bin/django-admin migrate &&\
-docker compose --project-name edrn exec portal /app/bin/django-admin fixtree &&\
-docker compose --project-name edrn exec portal /app/bin/django-admin collectstatic --no-input --clear" || exit 1
+docker compose --project-name edrn exec portal /usr/bin/django-admin makemigrations &&\
+docker compose --project-name edrn exec portal /usr/bin/django-admin migrate &&\
+docker compose --project-name edrn exec portal /usr/bin/django-admin fixtree &&\
+docker compose --project-name edrn exec portal /usr/bin/django-admin collectstatic --no-input --clear" || exit 1
 
 echo ""
 echo "🤷‍♀️ Restarting the portal and stopping search engine"
@@ -145,7 +145,7 @@ docker compose --project-name edrn start portal" || exit 1
 echo ""
 echo "🆙 Applying upgrades"
 ssh -q $USER@$WEBSERVER "cd $WEBROOT ; \
-docker compose --project-name edrn exec portal /app/bin/django-admin copy_daily_hits_from_wagtailsearch" || exit 1
+docker compose --project-name edrn exec portal /usr/bin/django-admin copy_daily_hits_from_wagtailsearch" || exit 1
 
 echo ""
 echo "🤷‍♀️ Final portal restart and restart of search engine"