ex-183 (jebene) pushed column specification file validation upstream to

validate_args

jacquard/expand.py

@@ -25,23 +25,14 @@
                                "or this expression may be irrelevant.")
 
 def _read_col_spec(col_spec):
-    if not os.path.isfile(col_spec):
-        raise utils.UsageError(("The column specification file [{}] could "
-                                "not be read. "
-                                "Review inputs/usage and try again."),
-                               col_spec)
-
     spec_file = open(col_spec, "r")
     columns = []
-
     for line in spec_file:
         columns.append(line.rstrip())
-
     spec_file.close()
 
     return columns
 
-
 ##TODO: hook this idea up -- change method
 def _disambiguate_column_names(column_header, info_header):
     overlap = 0
@@ -128,8 +119,15 @@ def get_required_input_output_types():
     return ("file", "file")
 
 #TODO (cgates): Validate should actually validate
-def validate_args(dummy):
-    pass
+def validate_args(args):
+    if args.column_specification:
+        if not os.path.isfile(args.column_specification):
+            raise utils.UsageError(("The column specification file [{}] could "
+                                    "not be read. Review inputs/usage and "
+                                    "try again."),
+                                    args.column_specification)
+
+        _read_col_spec(args.column_specification)
 
 def execute(args, dummy_execution_context):
     #for the moment, there is no good place to put the execution context

test/expand_test.py

@@ -2,16 +2,20 @@
 #pylint: disable=global-statement, star-args, too-few-public-methods, invalid-name
 #pylint: disable=too-many-public-methods
 from __future__ import absolute_import
+
 from argparse import Namespace
-from test.vcf_test import MockVcfReader
+import os
+
 from testfixtures import TempDirectory
+
 import jacquard.expand as expand
 import jacquard.logger
 import jacquard.utils as utils
 import jacquard.vcf as vcf
-import os
 import test.mock_logger
 import test.test_case as test_case
+from test.vcf_test import MockVcfReader
+
 
 class ExpandTestCase(test_case.JacquardBaseTestCase):
     def setUp(self):
@@ -223,43 +227,28 @@ def test_predict_output(self):
             self.assertEquals(expected_desired_output_files,
                               desired_output_files)
 
-
-    def test_execute_colSpecValid(self):
-        with TempDirectory() as input_dir,\
-             TempDirectory() as output_dir,\
-             TempDirectory() as col_spec_dir:
-            col_spec_dir.write("col_spec.txt", "foo\nbar")
+    def test_validate_args_colSpecValid(self):
+        with TempDirectory() as col_spec_dir:
+            col_spec_dir.write("col_spec.txt", "chrom\npos\ninfo")
             col_spec_file = os.path.join(col_spec_dir.path, "col_spec.txt")
-            input_dir.write("summarized.vcf", "##source=strelka\n#foo")
-            input_file = os.path.join(input_dir.path, "summarized.vcf")
-            output_file = os.path.join(output_dir.path, "expanded.txt")
-            args = Namespace(input=input_file,
-                             original_output=output_file,
-                             output=output_file,
-                             column_specification=col_spec_file)
 
-            expand.execute(args, ["extra_header1", "extra_header2"])
+            args = Namespace(input="input.txt",
+                             output="expanded.txt",
+                             column_specification=col_spec_file)
+            expand.validate_args(args)
             self.ok()
 
-    def test_execute_colSpecInvalid(self):
-        with TempDirectory() as input_dir,\
-             TempDirectory() as output_dir,\
-             TempDirectory() as col_spec_dir:
-            col_spec_dir.write("col_spec.txt", "foo\nbar")
-            input_dir.write("summarized.vcf", "##source=strelka\n#foo")
-            input_file = os.path.join(input_dir.path, "summarized.vcf")
-            output_file = os.path.join(output_dir.path, "expanded.txt")
-            args = Namespace(input=input_file,
-                             output=output_file,
-                             column_specification=col_spec_dir.path)
+    def test_validate_args_colSpecInvalid(self):
+        with TempDirectory() as col_spec_dir:
+            col_spec_dir.write("col_spec.txt", "chrom\npos\ninfo")
 
+            args = Namespace(input="input.txt",
+                             output="expanded.txt",
+                             column_specification=col_spec_dir.path)
             self.assertRaisesRegexp(utils.UsageError,
-                                    "The column specification file .* could "
-                                    "not be read. Review inputs/usage and "
-                                    "try again",
-                                    expand.execute,
-                                    args,
-                                    ["extra_header1", "extra_header2"])
+                                    "The column specification file .* could not be read. Review inputs/usage and try again",
+                                    expand.validate_args,
+                                    args)
 
 class ExpandFunctionalTestCase(test_case.JacquardBaseTestCase):
     def test_expand(self):