Patch PyPDF2

PyPDF2 overwrites `warning.showwarning` and this is already confirmed as a major flaw: https://github.com/mstamy2/PyPDF2/issues/67#issuecomment-34387142

But, this is never applied in PyPDF2.

To fix this issue in ERP5, we will copy the patch to our stack and apply it.

See merge request !746

component/egg-patch/PyPDF2/0001-Custom-implementation-of-warnings.formatwarning-remo.patch

+From f8ef2a193edf565d61aa628232f0e46e55a6aa6f Mon Sep 17 00:00:00 2001
+From: Pavel Brych <pavel@brych.cz>
+Date: Thu, 3 Sep 2015 08:04:53 +0200
+Subject: [PATCH] Custom implementation of warnings.formatwarning removed
+
+---
+ PyPDF2/pdf.py   | 15 ++-------------
+ PyPDF2/utils.py |  6 ------
+ 2 files changed, 2 insertions(+), 19 deletions(-)
+
+diff --git a/PyPDF2/pdf.py b/PyPDF2/pdf.py
+index f54680a..3554f40 100644
+--- a/PyPDF2/pdf.py
++++ b/PyPDF2/pdf.py
+@@ -63,7 +63,7 @@ import warnings
+ import codecs
+ from .generic import *
+ from .utils import readNonWhitespace, readUntilWhitespace, ConvertFunctionsToVirtualList
+-from .utils import isString, b_, u_, ord_, chr_, str_, formatWarning
++from .utils import isString, b_, u_, ord_, chr_, str_
+ 
+ if version_info < ( 2, 4 ):
+    from sets import ImmutableSet as frozenset
+@@ -1039,18 +1039,7 @@ class PdfFileReader(object):
+         ``warnings.py`` module with a custom implementation (defaults to
+         ``True``).
+     """
+-    def __init__(self, stream, strict=True, warndest = None, overwriteWarnings = True):
+-        if overwriteWarnings:
+-            # have to dynamically override the default showwarning since there are no
+-            # public methods that specify the 'file' parameter
+-            def _showwarning(message, category, filename, lineno, file=warndest, line=None):
+-                if file is None:
+-                    file = sys.stderr
+-                try:
+-                    file.write(formatWarning(message, category, filename, lineno, line))
+-                except IOError:
+-                    pass
+-            warnings.showwarning = _showwarning
++    def __init__(self, stream, strict=True):
+         self.strict = strict
+         self.flattenedPages = None
+         self.resolvedObjects = {}
+diff --git a/PyPDF2/utils.py b/PyPDF2/utils.py
+index 718a875..7bcb9ce 100644
+--- a/PyPDF2/utils.py
++++ b/PyPDF2/utils.py
+@@ -64,12 +64,6 @@ def isBytes(b):
+     return isinstance(b, bytes_type)
+ 
+ 
+-#custom implementation of warnings.formatwarning
+-def formatWarning(message, category, filename, lineno, line=None):
+-    file = filename.replace("/", "\\").rsplit("\\", 1)[1] # find the file name
+-    return "%s: %s [%s:%s]\n" % (category.__name__, message, file, lineno)
+-
+-
+ def readUntilWhitespace(stream, maxchars=None):
+     """
+     Reads non-whitespace characters and returns them.
+-- 
+2.23.0
+

software/slapos-sr-testing/software.cfg

@@ -198,6 +198,11 @@ scripts =
 interpreter=
   python_for_test
 
+# patches for eggs
+patch-binary = ${patch:location}/bin/patch
+PyPDF2-patches = ${:_profile_base_location_}/../../component/egg-patch/PyPDF2/0001-Custom-implementation-of-warnings.formatwarning-remo.patch#d25bb0f5dde7f3337a0a50c2f986f5c8
+PyPDF2-patch-options = -p1
+
 [git-clone-repository]
 recipe = slapos.recipe.build:gitclone
 git-executable = ${git:location}/bin/git
@@ -265,6 +270,9 @@ requests-toolbelt = 0.8.0
 selenium = 3.141.0
 slapos.recipe.template = 4.4
 
+# Patched eggs
+PyPDF2 = 1.26.0+SlapOSPatched001
+
 # modern versions for SSL fixed support
 requests = 2.20.0
 certifi = 2018.10.15
@@ -291,7 +299,6 @@ backports.lzma = 0.0.13
 mock = 2.0.0
 testfixtures = 6.11
 funcsigs = 1.0.2
-PyPDF2 = 1.26.0
 mysqlclient = 1.3.12
 pexpect = 4.8.0
 ptyprocess = 0.6.0

stack/erp5/buildout.cfg

@@ -410,7 +410,7 @@ eggs = ${neoppod:eggs}
   paramiko
   ply
   pyflakes
-  pypdf2
+  PyPDF2
   python-magic
   python-memcached
   pytz
@@ -528,6 +528,8 @@ extra-paths =
 
 # patches for eggs
 patch-binary = ${patch:location}/bin/patch
+PyPDF2-patches = ${:_profile_base_location_}/../../component/egg-patch/PyPDF2/0001-Custom-implementation-of-warnings.formatwarning-remo.patch#d25bb0f5dde7f3337a0a50c2f986f5c8
+PyPDF2-patch-options = -p1
 Acquisition-patches = ${:_profile_base_location_}/../../component/egg-patch/Acquisition/aq_dynamic.patch#1d9a56e9af4371f5b6951ebf217a15d7
 Acquisition-patch-options = -p1
 Products.DCWorkflow-patches = ${:_profile_base_location_}/../../component/egg-patch/Products.DCWorkflow/workflow_method.patch#975b49e96bae33ac8563454fe5fa9899
@@ -576,6 +578,7 @@ ocropy = 1.0+SlapOSPatched001
 pysvn = 1.7.10+SlapOSPatched002
 python-ldap = 2.4.32+SlapOSPatched001
 python-magic = 0.4.12+SlapOSPatched001
+PyPDF2 = 1.26.0+SlapOSPatched001
 ## https://lab.nexedi.com/nexedi/slapos/merge_requests/648
 pylint = 1.4.4
 
@@ -623,7 +626,6 @@ Products.MimetypesRegistry = 2.0.10
 Products.PluginRegistry = 1.4
 Products.TIDStorage = 5.5.0
 pyPdf = 1.13
-PyPDF2 = 1.26.0
 PyStemmer = 1.3.0
 PyXML = 0.8.5
 Pympler = 0.4.3