From 176068fb5ec2350e0b034c233e878c80bf6b2de2 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Thu, 11 May 2023 16:48:45 +0200
Subject: [PATCH] fix: SCHWED-5913 support bad OST_ROOT
---
modules/base/pymod/__init__.py.in | 33 ++++++++++++++++++++++++++++---
1 file changed, 30 insertions(+), 3 deletions(-)
diff --git a/modules/base/pymod/__init__.py.in b/modules/base/pymod/__init__.py.in
index 2d6f85a73..3043b7d56 100644
--- a/modules/base/pymod/__init__.py.in
+++ b/modules/base/pymod/__init__.py.in
@@ -32,6 +32,14 @@ class StreamLogSink(LogSink):
self._stream.write(message)
+def _GetPrefixFromPythonPath():
+ """Get the prefix from this file's path"""
+ prefix_path = __file__
+ for _ in range(5):
+ prefix_path = os.path.dirname(prefix_path)
+ return prefix_path
+
+
def _SetupOstPrefix():
""" This function attempts to set the OST prefix path if $OST_ROOT was not
set already.
@@ -44,12 +52,11 @@ def _SetupOstPrefix():
try:
# $OST_ROOT was set
+ # Note: this doesn't mean set to a valid prefix
GetPrefixPath()
except RuntimeError:
# Setup from this file's path
- prefix_path = __file__
- for _ in range(5):
- prefix_path = os.path.dirname(prefix_path)
+ prefix_path = _GetPrefixFromPythonPath()
SetPrefixPath(prefix_path)
@@ -71,6 +78,8 @@ def _SetupCompoundsLib():
1. The $OST_COMPOUNDS_CHEMLIB environment variable
2. The 'compounds.chemlib' file in the shared path under the folder pointed
by the $OST_ROOT environment variable
+ 3. The 'compounds.chemlib' file in the shared path under the OST prefix where
+ the ost python module is installed.
If no compound library can be loaded with any of these strategies, a warning
message is issued.
@@ -94,6 +103,24 @@ def _SetupCompoundsLib():
else:
return
+ # If OST_ROOT was pointing to a root with no compound lib or to an invalid
+ # root, try
+ try:
+ old_prefix = GetPrefixPath() # This is set by now and won't raise
+ prefix_path = _GetPrefixFromPythonPath()
+ SetPrefixPath(prefix_path)
+ compound_lib_path = os.path.join(GetSharedDataPath(), 'compounds.chemlib')
+ _TrySetCompoundsLib(compound_lib_path)
+ except (RuntimeError, ValueError):
+ SetPrefixPath(old_prefix)
+ else:
+ # If we're here, OST root was set but the prefix did not contain a compound
+ # lib, but the root obtained from the python path contained one.
+ # Most likely OST_ROOT was set incorrectly
+ LogWarning("$OST_ROOT is pointing to an invalid OST prefix: '%s'" % (
+ os.getenv("OST_ROOT")))
+ return
+
LogWarning("Compound library not available. Some functionality may not " \
"work as expected.")
--
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