- Further work restructuring

- Preparing for version 2.2.0
- Adds a few simple file-based tests

Author: Alan Christie

src/python/pipelines_utils/BasicObjectWriter.py

@@ -50,5 +50,3 @@ def write(self, dictOfValues, objectUUID=None):
     def close(self):
         if self.file:
             self.file.close()
-
-

src/python/pipelines_utils/TsvWriter.py

@@ -50,7 +50,3 @@ def writeFooter(self):
     def close(self):
         if self.file:
             self.file.close()
-
-
-
-

src/python/pipelines_utils/parameter_utils.py

@@ -21,6 +21,31 @@
 """
 
 
+def add_default_input_args(parser):
+    parser.add_argument('-i', '--input',
+                        help="Input file, if not defined the STDIN is used")
+    parser.add_argument('-if', '--informat', choices=['sdf', 'json'],
+                        help="Input format."
+                             " When using STDIN this must be specified.")
+
+
+def add_default_output_args(parser):
+    parser.add_argument('-o', '--output',
+                        help="Base name for output file (no extension)."
+                             " If not defined then SDTOUT is used for the"
+                             " structures and output is used as base name"
+                             " of the other files.")
+    parser.add_argument('-of', '--outformat', choices=['sdf', 'json'],
+                        help="Output format. Defaults to 'sdf'.")
+    parser.add_argument('--meta', action='store_true',
+                        help='Write metadata and metrics files')
+
+
+def add_default_io_args(parser):
+    add_default_input_args(parser)
+    add_default_output_args(parser)
+
+
 def splitValues(textStr):
     """Splits a comma-separated number sequence into a list (of floats).
     """

src/python/pipelines_utils/utils.py

@@ -14,57 +14,22 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 from __future__ import print_function
 import sys, gzip, json, uuid
 from math import log10, floor
 from pipelines_utils.BasicObjectWriter import BasicObjectWriter
 from pipelines_utils.TsvWriter import TsvWriter
 
+
 def log(*args, **kwargs):
-    """
-    Log output to STDERR
+    """Log output to STDERR
     """
     print(*args, file=sys.stderr, **kwargs)
 
+
 def round_sig(x, sig):
     """Round the number to the specified number of significant figures"""
-    return round(x, sig - int(floor(log10(abs(x))))-1)
-
-def add_default_input_args(parser):
-    parser.add_argument('-i', '--input', help="Input file, if not defined the STDIN is used")
-    parser.add_argument('-if', '--informat', choices=['sdf', 'json'], help="Input format. When using STDIN this must be specified.")
-
-def add_default_output_args(parser):
-    parser.add_argument('-o', '--output', help="Base name for output file (no extension). If not defined then SDTOUT is used for the structures and output is used as base name of the other files.")
-    parser.add_argument('-of', '--outformat', choices=['sdf', 'json'], help="Output format. Defaults to 'sdf'.")
-    parser.add_argument('--meta', action='store_true', help='Write metadata and metrics files')
-
-def add_default_io_args(parser):
-    add_default_input_args(parser)
-    add_default_output_args(parser)
-
-
-def default_open_input_output(inputDef, inputFormat, outputDef, defaultOutput, outputFormat, thinOutput=False, valueClassMappings=None,
-                              datasetMetaProps=None, fieldMetaProps=None):
-    """Default approach to handling the inputs and outputs"""
-    input, suppl = default_open_input(inputDef, inputFormat)
-    output,writer,outputBase = default_open_output(outputDef, defaultOutput, outputFormat, thinOutput=thinOutput,
-                                                   valueClassMappings=valueClassMappings, datasetMetaProps=datasetMetaProps, fieldMetaProps=fieldMetaProps)
-    return input,output,suppl,writer,outputBase
-
-
-def default_open_input(inputDef, inputFormat):
-    if not inputDef and not inputFormat:
-        raise ValueError('Must specify either an input file name or an input format (or both)')
-    elif inputFormat == 'sdf' or (inputDef and (inputDef.lower().endswith('.sdf') or inputDef.lower().endswith('.sdf.gz'))):
-        input, suppl = default_open_input_sdf(inputDef)
-    elif inputFormat == 'json' or (inputDef and (inputDef.lower().endswith('.data') or inputDef.lower().endswith('.data.gz'))):
-        input, suppl = default_open_input_json(inputDef)
-    else:
-        raise ValueError('Unsupported input format')
-
-    return input, suppl
+    return round(x, sig - int(floor(log10(abs(x)))) - 1)
 
 
 def open_file(filename):
@@ -75,18 +40,20 @@ def open_file(filename):
         return open(filename, 'r')
 
 
-def create_simple_writer(outputDef, defaultOutput, outputFormat, fieldNames, compress=True, valueClassMappings=None, datasetMetaProps=None, fieldMetaProps=None):
-    """Create a simple writer suitable for writing flat data e.g. as BasicObject or TSV"""
+def create_simple_writer(outputDef, defaultOutput, outputFormat, fieldNames,
+                         compress=True, valueClassMappings=None,
+                         datasetMetaProps=None, fieldMetaProps=None):
+    """Create a simple writer suitable for writing flat data
+    e.g. as BasicObject or TSV."""
 
     if not outputDef:
         outputBase = defaultOutput
     else:
         outputBase = outputDef
 
     if outputFormat == 'json':
-
-        write_squonk_datasetmetadata(outputBase, True, valueClassMappings, datasetMetaProps, fieldMetaProps)
-
+        write_squonk_datasetmetadata(outputBase, True, valueClassMappings,
+                                     datasetMetaProps, fieldMetaProps)
         return BasicObjectWriter(open_output(outputDef, 'data', compress)), outputBase
 
     elif outputFormat == 'tsv':
@@ -95,6 +62,7 @@ def create_simple_writer(outputDef, defaultOutput, outputFormat, fieldNames, com
     else:
         raise ValueError("Unsupported format: " + outputFormat)
 
+
 def open_output(basename, ext, compress):
     if basename:
         fname = basename + '.' + ext
@@ -110,6 +78,7 @@ def open_output(basename, ext, compress):
         else:
             return sys.stdout
 
+
 def write_squonk_datasetmetadata(outputBase, thinOutput, valueClassMappings, datasetMetaProps, fieldMetaProps):
     """This is a temp hack to write the minimal metadata that Squonk needs.
     Will needs to be replaced with something that allows something more complete to be written.
@@ -150,7 +119,8 @@ def write_squonk_datasetmetadata(outputBase, thinOutput, valueClassMappings, dat
 def write_metrics(baseName, values):
     """Write the metrics data
 
-    :param baseName: The base name of the output files. e.g. extensions will be appended to this base name
+    :param baseName: The base name of the output files.
+                     e.g. extensions will be appended to this base name
     :param values dictionary of values to write
     """
     m = open(baseName  + '_metrics.txt', 'w')
@@ -161,7 +131,8 @@ 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
+    """Generate a dictionary that represents a Squonk MoleculeObject when
+    writen as JSON
 
     :param source: Molecules in molfile or smiles format
     :param format: The format of the molecule. Either 'mol' or 'smiles'

src/python/setup.py

@@ -13,7 +13,7 @@ def get_long_description():
 setup(
 
     name='im-pipelines-utils',
-    version='2.1.0',
+    version='2.2.0',
     author='Alan Christie',
     author_email='[email protected]',
     url='https://github.com/InformaticsMatters/pipelines-utils',

src/python/test/pipelines_utils/test_utils.py

@@ -1,5 +1,7 @@
 import unittest
 
+import os
+
 from pipelines_utils import utils
 
 
@@ -19,11 +21,51 @@ def test_round_sig(self):
     def test_create_simple_writer_for_json(self):
         """Just check the very basics
         """
-        writer = utils.create_simple_writer('experiment', None, 'json', None)
+        json_base = 'test_json'
+        json_files = [json_base + '.metadata', json_base + '.data.gz']
+
+        writer = utils.create_simple_writer(json_base, None, 'json', None)
+
         self.assertTrue(writer is not None)
+        # Check files and clean-up
+        for json_file in json_files:
+            self.assertTrue(os.path.exists(json_file))
+            os.remove(json_file)
 
     def test_create_simple_writer_for_tsv(self):
         """Just check the very basics
         """
-        writer = utils.create_simple_writer('experiment', None, 'tsv', None)
+        tsv_base = 'test_tsv'
+        tsv_files = [tsv_base + '.tsv.gz']
+
+        writer = utils.create_simple_writer('test_tsv', None, 'tsv', None)
+
         self.assertTrue(writer is not None)
+        # Check files and clean-up
+        for tsv_file in tsv_files:
+            self.assertTrue(os.path.exists(tsv_file))
+            os.remove(tsv_file)
+
+    def test_write_metrics(self):
+        """Checks metrics are written.
+        """
+        m_base = 'test_utils'
+        m_filename = m_base + '_metrics.txt'
+
+        utils.write_metrics('test_utils', {'key_a': 'value_a',
+                                           'key_b': 'value_b'})
+
+        # Read back...
+        self.assertTrue(os.path.exists(m_filename))
+        metrics = open(m_filename, 'r')
+        found_a = False
+        found_b = False
+        for line in metrics.readlines():
+            if line.strip() == 'key_a=value_a':
+                found_a = True
+            elif line.strip() == 'key_b=value_b':
+                found_b = True
+        metrics.close()
+        os.remove(m_filename)
+        self.assertTrue(found_a)
+        self.assertTrue(found_b)