EBI submission only uploads the samples present in the prep template - and added a test for this

Author: josenavas

qiita_ware/ebi.py

@@ -838,9 +838,9 @@ def add_samples_from_templates(self, sample_template, prep_template,
                                  library_construction_protocol,
                                  **prep)
 
-        # to_remove = set(self.samples).difference(prep_template_samples)
-        # for sample in to_remove:
-        #     del self.samples[sample]
+        to_remove = set(self.samples).difference(prep_template_samples)
+        for sample in to_remove:
+            del self.samples[sample]
 
     @classmethod
     def from_templates_and_per_sample_fastqs(cls, preprocessed_data_id,

qiita_ware/test/test_ebi.py

@@ -386,6 +386,25 @@ def test_add_samples_from_templates(self):
         with self.assertRaises(KeyError):
             submission.samples['nothere']
 
+    def test_add_samples_from_templates_filter_samples(self):
+        sample_template = StringIO(EXP_SAMPLE_TEMPLATE)
+        prep_template = StringIO(EXP_PREP_TEMPLATE_FILTERED)
+        submission = EBISubmission('001', 'teststudy', 'test asbstract',
+                                   investigation_type='Other',
+                                   new_investigation_type='metagenome')
+        submission.add_samples_from_templates(sample_template, prep_template,
+                                              self.path)
+        self.assertTrue('sample1' in submission.samples)
+        self.assertTrue('sample2' in submission.samples)
+        self.assertFalse('sample3' in submission.samples)
+        self.assertEqual(submission.samples['sample2']['prep']['platform'],
+                         'ILLUMINA')
+        self.assertEqual(
+            submission.samples['sample2']['prep']['file_path'],
+            self.sample2_fp)
+        with self.assertRaises(KeyError):
+            submission.samples['nothere']
+
     def test_add_samples_from_templates_error(self):
         sample_template = StringIO(SAMPLE_TEMPLATE_ERROR)
         prep_template = StringIO(EXP_PREP_TEMPLATE)
@@ -695,5 +714,14 @@ def test_generate_curl_command(self):
     "sample3\tANL\tTest Project\t2\t1\tValue for sample 2"
     "\tILLUMINA\texp design\tlib protocol\n")
 
+EXP_PREP_TEMPLATE_FILTERED = (
+    "sample_name\tcenter_name\tcenter_project_name\tdata_type_id\t"
+    "temp_status_id\tstr_column\tplatform\texperiment_design_description"
+    "\tlibrary_construction_protocol"
+    "\nsample1\tANL\tTest Project\t2\t1\tValue for sample 3"
+    "\tILLUMINA\texp design\tlib protocol\n"
+    "sample2\tANL\tTest Project\t2\t1\tValue for sample 1"
+    "\tILLUMINA\texp design\tlib protocol\n")
+
 if __name__ == "__main__":
     main()