34 add file selector utility (#35)

* - Adds a utility to get the caller's module
- Adds file-Utils to allow selection of packaged files
  (based on module name)

* - pick_sdf now exposes `namespace`

* - file -> filename

* - Moved Python 3 files to new test directory

* - An attempt to fix the Python 2.7 tests

* - Separated tests that need Python3

* - Adds missing files

* - Refactored

* - removed unused requirements

* - Fixed travis.yml

* - Experiment with file-encoding

* - Removed back-ticks

* - Removed back-ticks

* - Removing file

* - File returned

* - Moved test_utils to python3

* - Now just the base file is returned in the SDF picker

* - pick now returns module and its full path

* - Minor typo

* - Adjusted for Python 2 tests

* - Now returns full path

Author: Alan B. Christie

.travis.yml

@@ -32,7 +32,6 @@ branches:
 # Installation steps.
 # We have more than one requirements file.
 install:
-- pip install -r requirements.txt
 - pip install -r package-requirements.txt
 
 # Test/build execution steps...

requirements.txt

@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+
+# Copyright 2018 Informatics Matters Ltd.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import print_function
+import os
+from . import utils
+
+# Files are normally located in sub-directories of the pipeline module path.
+# For example a pipeline module 'pipeline_a.py'  that expects to use a file
+# or SDF picker would place its files in the directory
+# 'pipelines/demo/pipeline_a'.
+
+
+def pick(filename, directory=None):
+    """Returns the named file. If directory is not specified the file is
+    expected to be located in a sub-directory whose name matches
+    that of the calling module otherwise the file is expected to be found in
+    the named directory.
+
+    :param filename: The file, whose path is required.
+    :type filename: ``str``
+    :param directory: An optional directory.
+                      If not provided it is calculated automatically.
+    :type directory: ``str``
+    :return: The full path to the file, or None if it does not exist
+    :rtype: ``str``
+    """
+    if directory is None:
+        directory = utils.get_undecorated_calling_module()
+        # Remove the CWD and the anticipated '/' from the front of the module
+        directory = directory[len(os.getcwd()) + 1:]
+
+    file_path = os.path.join(directory, filename)
+    return file_path if os.path.isfile(file_path) else None
+
+
+def pick_sdf(filename, directory=None):
+    """Returns a full path to the chosen SDF file. The supplied file
+    is not expected to contain a recognised SDF extension, this is added
+    automatically.
+    If a file with the extension `.sdf.gz` or `.sdf` is found the path to it
+    (excluding the extension) is returned. If this fails, `None` is returned.
+
+    :param filename: The SDF file basename, whose path is required.
+    :type filename: ``str``
+    :param directory: An optional directory.
+                      If not provided it is calculated automatically.
+    :type directory: ``str``
+    :return: The full path to the file without extension,
+             or None if it does not exist
+    :rtype: ``str``
+    """
+    if directory is None:
+        directory = utils.get_undecorated_calling_module()
+        # Remove the CWD and the anticipated '/' from the front of the module
+        directory = directory[len(os.getcwd()) + 1:]
+
+    file_path = os.path.join(directory, filename)
+    if os.path.isfile(file_path + '.sdf.gz'):
+        return file_path + '.sdf.gz'
+    elif os.path.isfile(file_path + '.sdf'):
+        return file_path + '.sdf'
+    # Couldn't find a suitable SDF file
+    return None

src/python/pipelines_utils/file_utils.py

@@ -15,7 +15,7 @@
 # limitations under the License.
 
 from __future__ import print_function
-import sys, gzip, json, uuid
+import inspect, os, sys, gzip, json, uuid
 from math import log10, floor
 from pipelines_utils.BasicObjectWriter import BasicObjectWriter
 from pipelines_utils.TsvWriter import TsvWriter
@@ -132,7 +132,7 @@ def write_metrics(baseName, values):
 
 def generate_molecule_object_dict(source, format, values):
     """Generate a dictionary that represents a Squonk MoleculeObject when
-    writen as JSON
+    written as JSON
 
     :param source: Molecules in molfile or smiles format
     :param format: The format of the molecule. Either 'mol' or 'smiles'
@@ -142,3 +142,20 @@ def generate_molecule_object_dict(source, format, values):
     if values:
         m["values"] = values
     return m
+
+
+def get_undecorated_calling_module():
+    """Returns the module name of the caller's calling module.
+    If a.py makes a call to b() in b.py, b() can get the name of the
+    calling module (i.e. a) by calling get_undecorated_calling_module().
+
+    The module also includes its full path.
+
+    As the name suggests, this does not work for decorated functions.
+    """
+    frame = inspect.stack()[2]
+    module = inspect.getmodule(frame[0])
+    # Return the module's file and its path
+    # and omit the extension...
+    # so /a/c.py becomes /a/c
+    return module.__file__.rsplit('.', 1)[0]

src/python/pipelines_utils/utils.py

@@ -5,15 +5,24 @@
 #
 # Jan 2018
 
+import platform
 from setuptools import setup, find_packages
 
+# By default the test suite is the root test suite.
+# Unless it's Python 2.
+_TEST_SUITE = 'test'
+if int(platform.python_version_tuple()[0]) == 2:
+    _TEST_SUITE = 'test.python2_3'
+
+
 def get_long_description():
     return open('README.rst').read()
 
+
 setup(
 
     name='im-pipelines-utils',
-    version='2.2.2',
+    version='2.3.0',
     author='Alan Christie',
     author_email='[email protected]',
     url='https://github.com/InformaticsMatters/pipelines-utils',
@@ -48,7 +57,7 @@ def get_long_description():
     ],
 
     # Root of the test suite
-    test_suite = 'test',
+    test_suite=_TEST_SUITE,
 
     zip_safe=False,
 

src/python/setup.py

@@ -0,0 +1,5 @@
+# python2_3
+A directory of unit tests that are happy on Python 2.
+All tests would normally go in here unless they have
+specific needs for Python 3 (where they can be put in
+the python3 directory)