From 2ca42a9579aa2978093f834ef20385316a13dd36 Mon Sep 17 00:00:00 2001
From: Sean Kelly <kelly@seankelly.biz>
Date: Fri, 22 Nov 2024 14:35:33 -0600
Subject: [PATCH] Upgrade Plone to 5.2.14

---
 Dockerfile                           |   2 +-
 etc/versions/dists.cfg               |   4 +-
 etc/versions/known-good-versions.cfg | 527 +--------------------------
 3 files changed, 21 insertions(+), 512 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 36d863b..174bfb0 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -3,7 +3,7 @@
 #
 # Defines the image for the CancerDataExpo
 
-FROM plone:5.2.9
+FROM plone:5.2.14
 
 ENV numpy=1.23.4
 
diff --git a/etc/versions/dists.cfg b/etc/versions/dists.cfg
index 1fcd4f6..a5b0d50 100644
--- a/etc/versions/dists.cfg
+++ b/etc/versions/dists.cfg
@@ -10,11 +10,11 @@
 # Here we specify extensions of "known good sets" of software we need,
 # including:
 #
-# • Plone 5.2.2
+# • Plone 5.2.14
 #
 # That's it (for now).
 [buildout]
-extends = https://dist.plone.org/release/5.2.9/versions.cfg
+extends = https://dist.plone.org/release/5.2.14/versions.cfg
 
 
 # Software Distributions to Compile/Make/Install
diff --git a/etc/versions/known-good-versions.cfg b/etc/versions/known-good-versions.cfg
index de84e0d..76e7df6 100644
--- a/etc/versions/known-good-versions.cfg
+++ b/etc/versions/known-good-versions.cfg
@@ -1,509 +1,18 @@
 [versions]
 
-# Added by buildout at 2021-01-05 17:23:43.130315
-biothings-client = 0.2.3
-collective.recipe.backup = 4.1.1
-isort = 5.7.0
-modernize = 0.8.0
-mr.scripty = 1.0
-unittest2 = 1.1.0
-
-# Required by:
-# unittest2==1.1.0
-argparse = 1.4.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-biopython = 1.78
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-collective.autopermission = 1.0b2
-
-# Required by:
-# modernize==0.8.0
-fissix = 20.8.0
-
-# Required by:
-# rdflib==4.2.2
-isodate = 0.6.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-jsonlib-python3 = 1.6.1
-
-# Required by:
-# traceback2==1.4.0
-linecache2 = 1.0.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-mygene = 3.1.0
-
-# Required by:
-# biopython==1.78
-numpy = 1.19.3
-
-# Required by:
-# edrn.rdf==1.3.8
-pysolr = 3.9.0
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-suds2 = 0.7.1
-
-# Required by:
-# unittest2==1.1.0
-traceback2 = 1.4.0
-
-# Added by buildout at 2021-01-27 14:37:21.534916
-biothings-client = 0.2.3
-collective.recipe.backup = 4.1.1
-isort = 5.7.0
-modernize = 0.8.0
-mr.scripty = 1.0
-unittest2 = 1.1.0
-
-# Required by:
-# unittest2==1.1.0
-argparse = 1.4.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-biopython = 1.78
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-collective.autopermission = 1.0b2
-
-# Required by:
-# modernize==0.8.0
-fissix = 20.8.0
-
-# Required by:
-# rdflib==4.2.2
-isodate = 0.6.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-jsonlib-python3 = 1.6.1
-
-# Required by:
-# traceback2==1.4.0
-linecache2 = 1.0.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-mygene = 3.1.0
-
-# Required by:
-# biopython==1.78
-numpy = 1.19.3
-
-# Required by:
-# edrn.rdf==1.3.8
-pysolr = 3.9.0
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-suds2 = 0.7.1
-
-# Required by:
-# unittest2==1.1.0
-traceback2 = 1.4.0
-
-# Added by buildout at 2022-07-06 09:13:55.535085
-biothings-client = 0.2.6
-collective.recipe.backup = 4.2.0
-isort = 5.10.1
-modernize = 0.8.0
-mr.scripty = 1.0
-unittest2 = 1.1.0
-
-# Required by:
-# unittest2==1.1.0
-argparse = 1.4.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-biopython = 1.79
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-collective.autopermission = 1.0b2
-
-# Required by:
-# modernize==0.8.0
-fissix = 21.11.13
-
-# Required by:
-# rdflib==4.2.2
-isodate = 0.6.1
-
-# Required by:
-# edrn.summarizer==0.0.8
-jsonlib-python3 = 1.6.1
-
-# Required by:
-# traceback2==1.4.0
-linecache2 = 1.0.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-mygene = 3.2.2
-
-# Required by:
-# edrn.rdf==1.3.8
-pysolr = 3.9.0
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-suds2 = 0.7.1
-
-# Required by:
-# unittest2==1.1.0
-traceback2 = 1.4.0
-
-# Added by buildout at 2022-07-06 09:46:04.546661
-biothings-client = 0.2.3
-collective.recipe.backup = 4.1.1
-isort = 5.7.0
-modernize = 0.8.0
-mr.scripty = 1.0
-unittest2 = 1.1.0
-
-# Required by:
-# unittest2==1.1.0
-argparse = 1.4.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-biopython = 1.79
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-collective.autopermission = 1.0b2
-
-# Required by:
-# modernize==0.8.0
-fissix = 20.8.0
-
-# Required by:
-# rdflib==4.2.2
-isodate = 0.6.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-jsonlib-python3 = 1.6.1
-
-# Required by:
-# traceback2==1.4.0
-linecache2 = 1.0.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-mygene = 3.1.0
-
-# Required by:
-# edrn.rdf==1.3.8
-pysolr = 3.9.0
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-suds2 = 0.7.1
-
-# Required by:
-# unittest2==1.1.0
-traceback2 = 1.4.0
-
-# Added by buildout at 2022-12-05 16:58:47.176461
-biothings-client = 0.2.6
-collective.recipe.backup = 4.2.0
-isort = 5.10.1
-modernize = 0.8.0
-mr.scripty = 1.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-biopython = 1.80
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-collective.autopermission = 1.0b2
-
-# Required by:
-# modernize==0.8.0
-fissix = 21.11.13
-
-# Required by:
-# rdflib==4.2.2
-isodate = 0.6.1
-
-# Required by:
-# edrn.summarizer==0.0.8
-mygene = 3.2.2
-
-# Required by:
-# edrn.rdf==1.3.8
-pysolr = 3.9.0
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-suds2 = 0.7.1
-
-# Required by:
-# python-dotenv==0.15.0
-typing = 3.10.0.0
-
-# Added by buildout at 2022-12-05 17:12:03.918426
-biothings-client = 0.2.6
-collective.recipe.backup = 4.2.0
-isort = 5.10.1
-modernize = 0.8.0
-mr.scripty = 1.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-biopython = 1.80
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-collective.autopermission = 1.0b2
-
-# Required by:
-# modernize==0.8.0
-fissix = 21.11.13
-
-# Required by:
-# rdflib==4.2.2
-isodate = 0.6.1
-
-# Required by:
-# edrn.summarizer==0.0.8
-mygene = 3.2.2
-
-# Required by:
-# edrn.rdf==1.3.8
-pysolr = 3.9.0
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-suds2 = 0.7.1
-
-# Added by buildout at 2022-12-06 09:35:44.943510
-biothings-client = 0.2.6
-collective.recipe.backup = 4.2.0
-isort = 5.10.1
-modernize = 0.8.0
-mr.scripty = 1.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-biopython = 1.80
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-collective.autopermission = 1.0b2
-
-# Required by:
-# modernize==0.8.0
-fissix = 21.11.13
-
-# Required by:
-# rdflib==6.2.0
-isodate = 0.6.1
-
-# Required by:
-# edrn.summarizer==0.0.8
-mygene = 3.2.2
-
-# Required by:
-# edrn.rdf==1.3.8
-pysolr = 3.9.0
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-suds2 = 0.7.1
-
-# Added by buildout at 2022-12-06 09:44:08.666120
-biothings-client = 0.2.6
-collective.recipe.backup = 4.2.0
-isort = 5.10.1
-modernize = 0.8.0
-mr.scripty = 1.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-biopython = 1.80
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-collective.autopermission = 1.0b2
-
-# Required by:
-# modernize==0.8.0
-fissix = 21.11.13
-
-# Required by:
-# rdflib==5.0.0
-isodate = 0.6.1
-
-# Required by:
-# edrn.summarizer==0.0.8
-mygene = 3.2.2
-
-# Required by:
-# edrn.rdf==1.3.8
-pysolr = 3.9.0
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-suds2 = 0.7.1
-
-# Added by buildout at 2022-12-06 10:22:10.706859
-biothings-client = 0.2.6
-collective.recipe.backup = 4.2.0
-isort = 5.10.1
-modernize = 0.8.0
-mr.scripty = 1.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-biopython = 1.80
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-collective.autopermission = 1.0b2
-
-# Required by:
-# modernize==0.8.0
-fissix = 21.11.13
-
-# Required by:
-# rdflib==6.2.0
-isodate = 0.6.1
-
-# Required by:
-# edrn.summarizer==0.0.8
-mygene = 3.2.2
-
-# Required by:
-# edrn.rdf==1.3.8
-pysolr = 3.9.0
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-suds2 = 0.7.1
-
-# Added by buildout at 2023-04-04 13:19:04.283913
-biothings-client = 0.2.6
-collective.recipe.backup = 4.2.0
-dnspython = 2.3.0
-isort = 5.10.1
-modernize = 0.8.0
-mr.scripty = 1.0
-
-# Required by:
-# edrn.summarizer==0.0.8
-biopython = 1.80
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-collective.autopermission = 1.0b2
-
-# Required by:
-# modernize==0.8.0
-fissix = 21.11.13
-
-# Required by:
-# rdflib==6.2.0
-isodate = 0.6.1
-
-# Required by:
-# edrn.summarizer==0.0.8
-mygene = 3.2.2
-
-# Required by:
-# edrn.rdf==1.3.8
-pysolr = 3.9.0
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-suds2 = 0.7.1
-
-# Added by buildout at 2023-04-05 15:42:08.530170
-biothings-client = 0.2.6
-collective.recipe.backup = 4.2.0
-dnspython = 2.3.0
-email-validator = 1.3.1
-isort = 5.10.1
-modernize = 0.8.0
-mr.scripty = 1.0
-rfc3986-validator = 0.1.1
-
-# Required by:
-# edrn.summarizer==0.0.8
-biopython = 1.80
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-collective.autopermission = 1.0b2
-
-# Required by:
-# modernize==0.8.0
-fissix = 21.11.13
-
-# Required by:
-# rdflib==6.2.0
-isodate = 0.6.1
-
-# Required by:
-# edrn.summarizer==0.0.8
-mygene = 3.2.2
-
-# Required by:
-# edrn.rdf==1.3.8
-pysolr = 3.9.0
-
-# Required by:
-# edrn.rdf==1.3.8
-# edrn.summarizer==0.0.8
-suds2 = 0.7.1
-
-# Added by buildout at 2023-06-21 17:46:16.940244
-biothings-client = 0.2.6
-collective.recipe.backup = 4.2.0
-dnspython = 2.3.0
+# Added by buildout at 2024-11-22 14:17:52.591203
+biothings-client = 0.3.1
+collective.recipe.backup = 5.0.0
+dnspython = 2.6.1
 email-validator = 1.3.1
-isort = 5.10.1
+isort = 5.13.2
 modernize = 0.8.0
 mr.scripty = 1.0
 rfc3986-validator = 0.1.1
 
 # Required by:
 # edrn.summarizer==0.0.8
-biopython = 1.80
+biopython = 1.83
 
 # Required by:
 # edrn.rdf==1.3.8
@@ -512,11 +21,11 @@ collective.autopermission = 1.0b2
 
 # Required by:
 # modernize==0.8.0
-fissix = 21.11.13
+fissix = 24.4.24
 
 # Required by:
 # rdflib==6.2.0
-isodate = 0.6.1
+isodate = 0.7.2
 
 # Required by:
 # edrn.summarizer==0.0.8
@@ -524,26 +33,26 @@ mygene = 3.2.2
 
 # Required by:
 # edrn.rdf==1.3.8
-pysolr = 3.9.0
+pysolr = 3.10.0
 
 # Required by:
 # edrn.rdf==1.3.8
 # edrn.summarizer==0.0.8
 suds2 = 0.7.1
 
-# Added by buildout at 2023-06-21 17:47:56.860527
-biothings-client = 0.2.6
-collective.recipe.backup = 4.2.0
-dnspython = 2.3.0
+# Added by buildout at 2024-11-22 14:32:25.365038
+biothings-client = 0.3.1
+collective.recipe.backup = 5.0.0
+dnspython = 2.6.1
 email-validator = 1.3.1
-isort = 5.10.1
+isort = 5.13.2
 modernize = 0.8.0
 mr.scripty = 1.0
 rfc3986-validator = 0.1.1
 
 # Required by:
 # edrn.summarizer==0.0.8
-biopython = 1.80
+biopython = 1.83
 
 # Required by:
 # edrn.rdf==1.3.8
@@ -552,11 +61,11 @@ collective.autopermission = 1.0b2
 
 # Required by:
 # modernize==0.8.0
-fissix = 21.11.13
+fissix = 24.4.24
 
 # Required by:
 # rdflib==6.2.0
-isodate = 0.6.1
+isodate = 0.7.2
 
 # Required by:
 # edrn.summarizer==0.0.8
@@ -564,7 +73,7 @@ mygene = 3.2.2
 
 # Required by:
 # edrn.rdf==1.3.8
-pysolr = 3.9.0
+pysolr = 3.10.0
 
 # Required by:
 # edrn.rdf==1.3.8