From 46213f56db37daa1fa160cba6fe4f2a86fad352d Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 2 Oct 2014 11:44:26 +0200
Subject: [PATCH] Started helper module
---
actions/pm-build-rawmodel | 7 +++++--
core/doc/CMakeLists.txt | 1 +
core/doc/helper.rst | 36 ++++++++++++++++++++++++++++++++++++
core/doc/index.rst | 5 ++++-
core/pymod/CMakeLists.txt | 2 +-
core/pymod/core/argcheck.py | 16 ++++++++--------
core/pymod/core/helper.py | 27 +++++++++++++++++++++++++++
doc/conf.py.in | 10 ++++++++--
8 files changed, 90 insertions(+), 14 deletions(-)
create mode 100644 core/doc/helper.rst
create mode 100644 core/pymod/core/helper.py
diff --git a/actions/pm-build-rawmodel b/actions/pm-build-rawmodel
index aed752bc..29486cf6 100755
--- a/actions/pm-build-rawmodel
+++ b/actions/pm-build-rawmodel
@@ -1,8 +1,8 @@
#!/usr/bin/env ost
-import argparse
+import os, argparse
from promod3 import meld
-from promod3.core import argcheck
+from promod3.core import argcheck, helper
### CHANGELOG - START
# 2013-11-07 - created
@@ -13,6 +13,7 @@ from promod3.core import argcheck
# 2 - template structure file has unsupported file extension
# 3 - alignment file does not exist
# 4 - alignment file has unsupported file extension
+# 5 - failed to write results to file
### EXIT STATUS - END
### SETUP - START
@@ -69,6 +70,8 @@ aln = io.LoadAlignment(opts.alignment_file)
aln.AttachView(1, tpl.CreateFullView())
result = meld.BuildRawModel(aln)
io.SavePDB(result.model, opts.model_file)
+if not os.path.isfile(opts.model_file):
+ helper.MsgErrorAndExit("Failed to write model file '%s'." % opts.model_file, 5)
### MAIN - END
diff --git a/core/doc/CMakeLists.txt b/core/doc/CMakeLists.txt
index 9e2491f7..9097ded5 100644
--- a/core/doc/CMakeLists.txt
+++ b/core/doc/CMakeLists.txt
@@ -1,6 +1,7 @@
set(CORE_RST
index.rst
argcheck.rst
+helper.rst
)
add_doc_source(NAME core RST ${CORE_RST})
diff --git a/core/doc/helper.rst b/core/doc/helper.rst
new file mode 100644
index 00000000..c790f0ab
--- /dev/null
+++ b/core/doc/helper.rst
@@ -0,0 +1,36 @@
+:mod:`~promod3.core.helper` - Shared functionality for the everything
+================================================================================
+
+.. currentmodule:: promod3.core.helper
+
+Introduction
+--------------------------------------------------------------------------------
+
+We collect functions here, which should be useful in many places but would make
+rather empty modules left alone.
+
+
+Messages
+--------------------------------------------------------------------------------
+
+.. testcode:: helper
+ :hide:
+
+ from promod3.core import helper
+
+ try:
+ helper.MsgErrorAndExit("Something failed!", 1)
+ except SystemExit, e:
+ if e.code == 1:
+ pass
+ else:
+ raise
+
+.. doctest:: helper
+
+ from promod3.core import helper
+
+ helper.MsgErrorAndExit("Something failed!", 1)
+
+.. autofunction:: MsgErrorAndExit
+
diff --git a/core/doc/index.rst b/core/doc/index.rst
index 4ec3a445..896ac2e6 100644
--- a/core/doc/index.rst
+++ b/core/doc/index.rst
@@ -4,11 +4,14 @@
.. module:: promod3.core
:synopsis: Basic functionality, supporting standard tasks in your code.
-This module gathers functions and classes which are not devoted to homology modeling per se but cover standard programming issues.
+This module gathers functions and classes which are not devoted to homology
+modeling per se but cover standard programming issues.
.. toctree::
:maxdepth: 2
argcheck
+ helper
+
.. LocalWords: promod se toctree maxdepth argcheck
diff --git a/core/pymod/CMakeLists.txt b/core/pymod/CMakeLists.txt
index d1400c33..8a6a110f 100644
--- a/core/pymod/CMakeLists.txt
+++ b/core/pymod/CMakeLists.txt
@@ -1,4 +1,4 @@
-set(PROMOD3_CORE_FILES __init__.py argcheck.py)
+set(PROMOD3_CORE_FILES __init__.py argcheck.py helper.py)
pymod(NAME core PY ${PROMOD3_CORE_FILES} IN_DIR core
__init__.py
OUTPUT_DIR "promod3")
diff --git a/core/pymod/core/argcheck.py b/core/pymod/core/argcheck.py
index 86cff3c7..8907d413 100644
--- a/core/pymod/core/argcheck.py
+++ b/core/pymod/core/argcheck.py
@@ -4,10 +4,7 @@ Basic helpers for arguments.
import os, sys
import ost
-
-def _MsgErrorAndExit(msg, exit_status):
- ost.LogError(msg)
- sys.exit(exit_status)
+import helper
def FileExists(prefix, exit_status, file):
'''
@@ -29,7 +26,7 @@ def FileExists(prefix, exit_status, file):
missing.
'''
if not os.path.exists(file):
- _MsgErrorAndExit('%s file does not exist: %s\n' % (prefix, file),
+ helper.MsgErrorAndExit('%s file does not exist: %s\n' % (prefix, file),
exit_status)
def FileExtension(prefix, exit_status, file, extensions, gz=False):
@@ -74,14 +71,16 @@ def FileExtension(prefix, exit_status, file, extensions, gz=False):
filename, fileext = os.path.splitext(filename)
if not gz:
extension_string = ', '.join(extensions)
- _MsgErrorAndExit('%s file extension not supported: %s. ' % (prefix, file)+
+ helper.MsgErrorAndExit('%s file extension not supported: %s. ' % (prefix,
+ file)+
'Allowed extensions are: %s\n' % extension_string,
exit_status)
if fileext == '':
extension_string = ', '.join(extensions)
if gz:
extension_string += ', ' + '.gz, '.join(extensions) + '.gz'
- _MsgErrorAndExit('%s file extension not supported: %s. ' % (prefix, file)+
+ helper.MsgErrorAndExit('%s file extension not supported: %s. ' % (prefix,
+ file)+
'Allowed extensions are: %s\n' % extension_string,
exit_status)
fileext = fileext[1:].lower()
@@ -94,7 +93,8 @@ def FileExtension(prefix, exit_status, file, extensions, gz=False):
extension_string = ', '.join(extensions)
if gz:
extension_string += ', ' + '.gz, '.join(extensions) + '.gz'
- _MsgErrorAndExit('%s file extension not supported: %s. ' % (prefix, file)+
+ helper.MsgErrorAndExit('%s file extension not supported: %s. ' % (prefix,
+ file)+
'Allowed extensions are: %s\n' % extension_string,
exit_status)
diff --git a/core/pymod/core/helper.py b/core/pymod/core/helper.py
new file mode 100644
index 00000000..7f5871d5
--- /dev/null
+++ b/core/pymod/core/helper.py
@@ -0,0 +1,27 @@
+"""
+Uncategorised functions which may come handy at several places.
+"""
+
+import sys
+import ost
+
+def MsgErrorAndExit(msg, exit_status):
+ '''
+ Send a messages to the |ost_s| :ost_docs:`error log <base/logging/>` and exit
+ the Python interpreter.
+
+ :param msg: The message.
+ :type msg: :class:`str`
+
+ :param exit_status: Exit code, ends up in ``$?`` in the shell. ``0`` is
+ traditionally reserved to successful commands.
+ :type exit_status: :class:`int`
+
+ :returns: No return value, exits script with value ``exit_status``.
+ '''
+ ost.LogError(msg)
+ sys.exit(exit_status)
+
+__all__ = (
+ 'MsgErrorAndExit',
+)
diff --git a/doc/conf.py.in b/doc/conf.py.in
index 79fcf5ce..1cc6b9e8 100644
--- a/doc/conf.py.in
+++ b/doc/conf.py.in
@@ -29,7 +29,11 @@ sys.path.insert(1, '@OST_ROOT@/@LIB_DIR@/python@PYTHON_VERSION@/site-packages')
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', 'sphinx.ext.extlinks']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest',
+ 'sphinx.ext.intersphinx', 'sphinx.ext.todo',
+ 'sphinx.ext.coverage', 'sphinx.ext.pngmath',
+ 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode',
+ 'sphinx.ext.extlinks']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
@@ -252,7 +256,9 @@ intersphinx_mapping = {'python': ('@PYTHON_DOC_URL@', None),
# -- ProMod3 specific configuration --------------------------------------------
extlinks = {'py_docs' : ('@PYTHON_DOC_URL@/%s',
- 'Python documentation')}
+ 'Python documentation'),
+ 'ost_docs' : ('@OST_DOC_URL@/%s',
+ 'OpenStructure documentation')}
# The _nameattr is a bit ugly: we want to have __name__ formatted as Python
# attribute but Sphinx does not go with calling :attr: inside extlinks. To keep
# the Python url prefix, we define sth here.
--
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