Raise an error if timeline values are duplicated

scripts/importer/validateData.py

@@ -3492,6 +3492,10 @@ class TimelineValidator(Validator):
     REQUIRE_COLUMN_ORDER = True
     ALLOW_BLANKS = True
 
+    def __init__(self, *args, **kwargs):
+        super(TimelineValidator, self).__init__(*args, **kwargs)
+        self.timeline_entries = {}
+
     def checkLine(self, data):
         super(TimelineValidator, self).checkLine(data)
         # TODO check the values
@@ -3522,6 +3526,17 @@ def checkLine(self, data):
                         extra={'line_number': self.line_number,
                                'column_number': col_index + 1,
                                'cause': value})
+        # validate the uniqueness of timeline records
+        timeline_entry = ", ".join(data)
+        if timeline_entry in self.timeline_entries:
+            self.logger.error(
+                'Duplicate entry in timeline data',
+                extra = {'line_number': self.line_number,
+                         'cause': '%s (already defined on line %d)' % (
+                             timeline_entry,
+                             self.timeline_entries[timeline_entry])})
+        else:
+            self.timeline_entries[timeline_entry] = self.line_number
 
 class CancerTypeValidator(Validator):
 

tests/test_data/data_timeline_duplicated.txt

@@ -0,0 +1,5 @@
+PATIENT_ID	START_DATE	STOP_DATE	EVENT_TYPE	SPECIMEN_SITE	SPECIMEN_TYPE	SOURCE
+TCGA-BH-A18K	20	60	SPECIMEN	test_specimen_site_1	test_specimen_type	test_source_3
+TCGA-BH-A18K	20	60	SPECIMEN	test_specimen_site_1	test_specimen_type	test_source_3
+TCGA-BH-A18K	10	20	STATUS			test_source_4
+TCGA-BH-NEW	100	200	STATUS			test_source_1

tests/unit_tests_validate_data.py

@@ -498,6 +498,19 @@ def test_start_date_validation_TimelineValidator(self):
             self.assertEqual("ERROR", error.levelname)
             self.assertIn("Invalid START_DATE", error.getMessage())
 
+    def test_duplicated_timeline_lines(self):
+        """Raise an error if timeline lines are duplicated.
+        """
+        # set level according to this test case:
+        self.logger.setLevel(logging.ERROR)
+        record_list = self.validate('data_timeline_duplicated.txt',
+                                    validateData.TimelineValidator)
+        self.assertEqual(1, len(record_list))
+        for error in record_list:
+            self.assertEqual("ERROR", error.levelname)
+            self.assertIn("Duplicate entry in timeline data", error.getMessage())
+
+
 
 # TODO: make tests in this testcase check the number of properly defined types
 class CancerTypeFileValidationTestCase(DataFileTestCase):