ex-279 (cgates/dkriti): Adjust expand to give friendly error message if

input not VCF.

jacquard/expand.py

@@ -168,8 +168,21 @@ def validate_args(args):
                                     "not be read. Review inputs/usage and "
                                     "try again."),
                                     args.selected_columns_file)
+        columns = None
+        try:
+            columns = _read_col_spec(args.selected_columns_file)
+        except:
+            pass
+        if not columns:
+            raise utils.UsageError("The selected_columns_file .* has no rows. Review inputs/usage and try again")
+
+    try:
+        vcf.VcfReader(vcf.FileReader(args.input))
+    except:
+        raise utils.UsageError(("The expand command requires a VCF file as an "
+                               "input, but the specified input [{}] contains no VCF "
+                               "metaheaders. Review inputs and try again.").format(args.input))
 
-        _read_col_spec(args.selected_columns_file)
 
 def _get_actual_columns(vcf_reader, col_spec):
     columns  = _create_potential_column_list(vcf_reader)

test/expand_test.py

@@ -18,6 +18,14 @@
 from test.utils.vcf_test import MockVcfReader, MockFileWriter
 
 
+_VALID_VCF_CONTENT = ('''##source=strelka
+##INFO=<ID=SOMATIC,Number=1,Description="foo">
+##FORMAT=<ID=GT,Number=1,Description="bar">
+#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|NORMAL|TUMOR
+chr1|1|.|A|C|.|.|SOMATIC|GT|0/1|0/1
+chr2|1|.|A|C|.|.|SOMATIC|GT|0/1|0/1
+''').replace('|', "\t")
+
 class ExpandTestCase(test_case.JacquardBaseTestCase):
     def setUp(self):
         super(ExpandTestCase, self).setUp()
@@ -209,16 +217,8 @@ def test_disambiguate_column_names(self):
         self.assertEquals(expected, actual)
 
     def test_execute(self):
-        vcf_content = ('''##source=strelka
-##INFO=<ID=SOMATIC,Number=1,Description="foo">
-##FORMAT=<ID=GT,Number=1,Description="bar">
-#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|NORMAL|TUMOR
-chr1|1|.|A|C|.|.|SOMATIC|GT|0/1|0/1
-chr2|1|.|A|C|.|.|SOMATIC|GT|0/1|0/1
-''').replace('|', "\t")
-
         with TempDirectory() as input_dir, TempDirectory() as output_dir:
-            input_dir.write("P1.vcf", vcf_content.encode("utf8"))
+            input_dir.write("P1.vcf", _VALID_VCF_CONTENT.encode("utf8"))
             input_file = os.path.join(input_dir.path, "P1.vcf")
             output_file = os.path.join(output_dir.path, "P1.txt")
             args = Namespace(input=input_file,
@@ -250,17 +250,19 @@ def test_predict_output(self):
                               desired_output_files)
 
     def test_validate_args_colSpecValid(self):
-        with TempDirectory() as col_spec_dir:
-            col_spec_dir.write("col_spec.txt", b"chrom\npos\ninfo")
-            col_spec_file = os.path.join(col_spec_dir.path, "col_spec.txt")
-
-            args = Namespace(input="input.txt",
+        with TempDirectory() as input_dir:
+            input_dir.write("input.vcf", _VALID_VCF_CONTENT.encode("utf8"))
+            input_file = os.path.join(input_dir.path, "input.vcf")
+            input_dir.write("col_spec.txt", b"chrom\npos\ninfo")
+            col_spec_file = os.path.join(input_dir.path, "col_spec.txt")
+
+            args = Namespace(input=input_file,
                              output="expanded.txt",
                              selected_columns_file=col_spec_file)
             expand.validate_args(args)
             self.ok()
 
-    def test_validate_args_colSpecInvalid(self):
+    def test_validate_args_colSpecIsNotAFile(self):
         with TempDirectory() as col_spec_dir:
             col_spec_dir.write("col_spec.txt", b"chrom\npos\ninfo")
 
@@ -272,6 +274,36 @@ def test_validate_args_colSpecInvalid(self):
                                     expand.validate_args,
                                     args)
 
+    def test_validate_args_colSpecIsEmpty(self):
+        with TempDirectory() as col_spec_dir:
+            col_spec_dir.write("col_spec.txt", b"")
+            col_spec_filename = os.path.join(col_spec_dir.path, "col_spec.txt")
+
+            args = Namespace(input="input.txt",
+                             output="expanded.txt",
+                             selected_columns_file=col_spec_filename)
+            self.assertRaisesRegexp(utils.UsageError,
+                                    "The selected_columns_file .* has no rows. Review inputs/usage and try again",
+                                    expand.validate_args,
+                                    args)
+
+    def test_validate_args_checkInputIfVCF(self):
+        with TempDirectory() as input_dir:
+            input_dir.write("input.vcf", b"123")
+            input_filename = os.path.join(input_dir.path, "input.vcf")
+            args = Namespace(input=input_filename,
+                             output="expanded.txt",
+                             selected_columns_file=None)
+            self.assertRaisesRegexp(utils.UsageError,
+                                    ("The expand command requires a VCF file "
+                                     "as an input, but the specified input "
+                                     "\[.*input.vcf\] contains no VCF "
+                                     "metaheaders. Review inputs and try "
+                                     "again."),
+                                    expand.validate_args,
+                                    args)
+
+
     def test_create_glossary_entry(self):
         header = '##INFO=<ID=SOMATIC,Number=1,Description="foo">'
         actual_line = expand._create_glossary_entry(header)