Fix for generating failed_samples.html reporting. (#99)

Author: charles-cowart

qp_klp/StandardMetagenomicWorkflow.py

@@ -175,6 +175,8 @@ def execute_pipeline(self):
         # prep is pointing to.
         self.load_preps_into_qiita()
 
+        self.fsr.generate_report()
+
         self.update_status("Generating packaging commands", 8, 9)
         self.generate_commands()
 

qp_klp/StandardMetatranscriptomicWorkflow.py

@@ -176,6 +176,8 @@ def execute_pipeline(self):
         # prep is pointing to.
         self.load_preps_into_qiita()
 
+        self.fsr.generate_report()
+
         self.update_status("Generating packaging commands", 8, 9)
         self.generate_commands()
 

qp_klp/TellseqMetagenomicWorkflow.py

@@ -173,6 +173,8 @@ def execute_pipeline(self):
         # prep is pointing to.
         self.load_preps_into_qiita()
 
+        self.fsr.generate_report()
+
         self.update_status("Generating packaging commands", 8, 9)
         self.generate_commands()
 

qp_klp/tests/test_workflows.py

@@ -437,6 +437,16 @@ def test_partial_metagenomic_pipeline(self):
 
         # NuQCJob successful.
 
+        # we have specific code to test FailedSamplesReport() itself. All
+        # we need to do here is confirm that the workflow used has
+        # instantiated a valid FailedSamplesReport() object, attached it to
+        # wf.fsr, generate_report() can be run, and that the following two
+        # files were generated at the location below.
+        wf.fsr.generate_report()
+
+        self.assertTrue(exists(join(self.output_dir, 'failed_samples.json')))
+        self.assertTrue(exists(join(self.output_dir, 'failed_samples.html')))
+
     def test_partial_metatranscriptomic_pipeline(self):
         # Tests convert_raw_to_fastq() and quality_control() steps of
         # StandardMetatranscriptomicWorkflow(), which in turn exercises