Merge pull request #76 from ypriverol/master

bug fix when only one factor value is provided

sdrf_pipelines/openms/openms.py

@@ -132,13 +132,12 @@ def openms_convert(self, sdrf_file: str = None, keep_raw: bool = False, one_tabl
                     c.startswith('comment[modification parameters')]  # columns with modification parameters
 
         if not split_by_columns:
-            # get factor columns (except constant ones)
+
             factor_cols = [c for ind, c in enumerate(sdrf) if
-                           c.startswith('factor value[') and len(sdrf[c].unique()) > 1]
+                           c.startswith('factor value[') and len(sdrf[c].unique()) >= 1]
 
-            # get characteristics columns (except constant ones)
             characteristics_cols = [c for ind, c in enumerate(sdrf) if
-                                    c.startswith('characteristics[') and len(sdrf[c].unique()) > 1]
+                                    c.startswith('characteristics[') and len(sdrf[c].unique()) >= 1]
             # and remove characteristics columns already present as factor
             characteristics_cols = self.removeRedundantCharacteristics(characteristics_cols, sdrf, factor_cols)
             print('Factor columns: ' + str(factor_cols))
@@ -358,7 +357,7 @@ def removeRedundantCharacteristics(self, characteristics_cols, sdrf, factor_cols
     def reportWarnings(self, sdrf_file):
         if len(self.warnings) != 0:
             for k, v in self.warnings.items():
-                print('WARNING: "' + k + '" occured ' + str(v) + ' times.')
+                print('WARNING: "' + k + '" occurred ' + str(v) + ' times.')
         print("SUCCESS (WARNINGS=" + str(len(self.warnings)) + "): " + sdrf_file)
 
     def writeTwoTableExperimentalDesign(self, output_filename, sdrf, file2technical_rep, source_name_list,

sdrf_pipelines/tests/sdrfchecker_tests.py

@@ -6,7 +6,6 @@
 
 def test_validate_srdf():
   """
-  Test the default behaviour of the vcf-to-proteindb tool
   :return:
   """
   runner = CliRunner()
@@ -17,11 +16,10 @@ def test_validate_srdf():
 
 def test_convert_openms():
   """
-    Test the default behaviour of the vcf-to-proteindb tool
     :return:
     """
   runner = CliRunner()
-  result = runner.invoke(cli, ['convert-openms', '-t2', '-l', '-s', 'testdata/sdrf.tsv'])
+  result = runner.invoke(cli, ['convert-openms', '-t2', 'l', '-s', 'testdata/sdrf.tsv'])
   print('convert to openms' + result.output)
   assert 'ERROR' not in result.output
 

setup.py

@@ -6,7 +6,7 @@
 
 setup(
   name="sdrf-pipelines",
-  version="0.0.12",
+  version="0.0.13",
   author="BigBio Team",
   author_email="ypriverol@gmail.com",
   description="Translate, convert SDRF to configuration pipelines",