Ensure run_and_print prints in one case

Convert some run_and_print calls to run since we're not using nose anymore

test/integration/snake.py

@@ -123,4 +123,4 @@ def run(self, rules=None):
         cmd = ['snakemake', '--verbose', '--reason', '--printshellcmds']
         if rules:
             cmd.extend(rules)
-        res = util.misc.run_and_print(cmd, check=True, cwd=self.workdir)
+        res = util.misc.run(cmd, check=True, cwd=self.workdir)

test/unit/test_tools_kraken.py

@@ -17,9 +17,6 @@ class TestToolKrakenMocked(TestCaseWithTmp):
     def setUp(self):
         super().setUp()
 
-        patcher = mock.patch('util.misc.run_and_print', autospec=True)
-        self.addCleanup(patcher.stop)
-        self.mock_run_and_print = patcher.start()
         patcher = mock.patch('util.misc.run', autospec=True)
         self.addCleanup(patcher.stop)
         self.mock_run = patcher.start()

test/unit/test_tools_krona.py

@@ -17,7 +17,7 @@ def setUp(self):
         self.krona = tools.krona.Krona()
         self.krona.install()
 
-        patcher = patch('util.misc.run_and_print', autospec=True)
+        patcher = patch('subprocess.check_call', autospec=True)
         self.addCleanup(patcher.stop)
         self.mock_run = patcher.start()
 

tools/kraken.py

@@ -53,7 +53,7 @@ def build(self, db, options=None, option_string=None):
         '''
         self.execute('kraken-build', db, db, options=options,
                             option_string=option_string)
-    
+
     def classify(self, inBam, db, outReads, numThreads=None):
         """Classify input reads (bam)
 
@@ -88,13 +88,13 @@ def classify(self, inBam, db, outReads, numThreads=None):
         res = self.execute('kraken', db, outReads, args=[tmp_fastq1, tmp_fastq2], options=opts)
         os.unlink(tmp_fastq1)
         os.unlink(tmp_fastq2)
-        
+
     def filter(self, inReads, db, outReads, filterThreshold):
         """Filter Kraken hits
         """
         self.execute('kraken-filter', db, outReads, args=[inReads],
                             options={'--threshold': filterThreshold})
-    
+
     def report(self, inReads, db, outReport):
         """Convert Kraken read-based output to summary reports
         """
@@ -133,13 +133,12 @@ def execute(self, command, db, output, args=None, options=None,
         elif command == 'kraken-build':
             jellyfish_path = Jellyfish().install_and_get_path()
             env = os.environ.copy()
-            env['PATH'] = ':'.join([os.path.dirname(jellyfish_path),
-                                   env['PATH']])
-            util.misc.run_and_print(cmd, env=env, check=True, silent=False)
+            env['PATH'] = ':'.join([os.path.dirname(jellyfish_path), env['PATH']])
+            subprocess.check_call(cmd, env=env)
         else:
             with util.file.open_or_gzopen(output, 'w') as of:
-                util.misc.run(cmd, stdout=of, stderr=subprocess.PIPE,
-                              check=True)
+                util.misc.run(cmd, stdout=of, stderr=subprocess.PIPE, check=True)
+
 
 @tools.skip_install_test(condition=tools.is_osx())
 class Jellyfish(Kraken):

tools/krona.py

@@ -2,7 +2,6 @@
 import os.path
 import subprocess
 from os.path import join
-import util.misc
 from builtins import super
 
 TOOL_NAME = 'krona'
@@ -55,7 +54,7 @@ def import_taxonomy(self,
             cmd.append('-k')
         cmd.extend(input_tsvs)
 
-        util.misc.run_and_print(cmd, env=env, check=True)
+        subprocess.check_call(cmd, env=env, check=True)
 
     def create_db(self, db_dir):
         """Caution - this deletes the original .dmp files."""
@@ -65,4 +64,4 @@ def create_db(self, db_dir):
 
         sh = join(self.opt, 'updateTaxonomy.sh')
         cmd = [sh, '--only-build', os.path.abspath(db_dir)]
-        util.misc.run_and_print(cmd, env=env, check=True)
+        subprocess.check_call(cmd, env=env, check=True)

util/misc.py

@@ -209,9 +209,21 @@ def run_and_print(args, stdout=None, stderr=None,
     if not buffered:
         if check and not silent:
             try:
-                result = run(args, stdin=stdin, stdout=subprocess.PIPE,
-                           stderr=subprocess.STDOUT, env=env, cwd=cwd,
-                           timeout=timeout, check=check)
+                result = run(
+                    args,
+                    stdin=stdin,
+                    stdout=subprocess.PIPE,
+                    stderr=subprocess.STDOUT,
+                    env=env,
+                    cwd=cwd,
+                    timeout=timeout,
+                    check=check
+                )
+                print(result.stdout.decode('utf-8'))
+                try:
+                    print(result.stderr.decode('utf-8'))
+                except AttributeError:
+                    pass
             except subprocess.CalledProcessError as e:
                 if loglevel:
                     try: