From ba2b501022fd0975389cd49f0cbc1e2e2b04b272 Mon Sep 17 00:00:00 2001
From: Vince <vince.reuter@gmail.com>
Date: Wed, 19 Jun 2019 23:27:28 -0400
Subject: [PATCH] first pass at print-only behavior for PM; #4

---
 pypiper/manager.py | 20 +++++++++++++-------
 pypiper/utils.py   | 11 +++++++++--
 2 files changed, 22 insertions(+), 9 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 25be0109..414519e1 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -124,7 +124,9 @@ def __init__(
             'config_file': config_file,
             'output_parent': output_parent,
             'cores': cores,
-            'mem': mem}
+            'mem': mem,
+            'testmode': False
+        }
 
         # Transform the command-line namespace into a Mapping.
         args_dict = vars(args) if args else dict()
@@ -168,6 +170,7 @@ def __init__(
         self.dirty = params['dirty']
         self.cores = params['cores']
         self.output_parent = params['output_parent']
+        self.testmode = params['testmode']
 
         # Keep track of an ID for the number of processes attempted
         self.proc_count = 0
@@ -794,9 +797,12 @@ def checkprint(self, cmd, shell=None, nofail=False):
         :param bool nofail: Should the pipeline bail on a nonzero return from a process? Default: False
             Nofail can be used to implement non-essential parts of the pipeline; if these processes fail,
             they will not cause the pipeline to bail out.
+        :return str: text output by the executed subprocess (check_output)
         """
 
         self._report_command(cmd)
+        if self.testmode:
+            return ""
 
         likely_shell = check_shell(cmd, shell)
 
@@ -874,10 +880,6 @@ def get_mem_child_sum(proc):
         def display_memory(memval):
             return None if memval < 0 else "{}GB".format(round(memval, 3))
 
-        def make_dict(command):
-            a, s = (command, True) if check_shell(command, shell) else (shlex.split(command), False)
-            return dict(args=a, stdout=subprocess.PIPE, shell=s)
-
         def make_hash(o):
             """
             Convert the object to string and hash it, return None in case of failure
@@ -893,6 +895,10 @@ def make_hash(o):
         if container:
             cmd = "docker exec " + container + " " + cmd
 
+        if self.testmode:
+            self._report_command(cmd)
+            return 0, 0
+
         param_list = parse_cmd(cmd, shell)
         proc_name = get_proc_name(cmd)
 
@@ -929,7 +935,7 @@ def make_hash(o):
             print("</pre>")
             ids = [x.pid for x in processes]
             print ("Not waiting for subprocesses: " + str(ids))
-            return [0, -1]
+            return 0, -1
 
         def proc_wrapup(i):
             """
@@ -1307,7 +1313,7 @@ def _report_command(self, cmd, procs=None):
         :param str | list[str] procs: process numbers for processes in the command
         """
         if isinstance(procs, list):
-            procs = ",".join(map(str,procs))
+            procs = ",".join(map(str, procs))
         if procs:
             line = "\n> `{cmd}` ({procs})\n".format(cmd=str(cmd), procs=procs)
         else:
diff --git a/pypiper/utils.py b/pypiper/utils.py
index 4a4397d8..6e4a912e 100644
--- a/pypiper/utils.py
+++ b/pypiper/utils.py
@@ -222,6 +222,7 @@ def check_shell_asterisk(cmd):
     """
     return r"*" in cmd
 
+
 def split_by_pipes_nonnested(cmd):
     """
     Split the command by shell pipes, but preserve contents in 
@@ -235,8 +236,10 @@ def split_by_pipes_nonnested(cmd):
     r = re.compile(r'(?:[^|(]|\([^)]*\)+|\{[^}]*\})')
     return r.findall(cmd)
 
+
 # cmd="a | b | { c | d } ABC | { x  | y } hello '( () e |f )"
 
+
 def split_by_pipes(cmd):
     """
     Split the command by shell pipes, but preserve contents in 
@@ -303,6 +306,7 @@ def strip_braced_txt(cmd):
 
     return cmd
 
+
 def check_shell_redirection(cmd):
     """
     Determine whether a command appears to contain shell redirection symbol outside of curly brackets
@@ -399,7 +403,7 @@ def get_first_value(param, param_pools, on_missing=None, error=True):
         if param in pool:
             return pool[param]
 
-    # Raise error if unfound and no strategy or value is provided or handling
+    # Raise error if not found and no strategy or value is provided or handling
     # unmapped parameter requests.
     if error and on_missing is None:
         raise KeyError("Unmapped parameter: '{}'".format(param))
@@ -691,7 +695,7 @@ def _determine_args(argument_groups, arguments, use_all_args=False):
 
     # Define the argument groups.
     args_by_group = {
-        "pypiper": ["recover", "new-start", "dirty", "force-follow"],
+        "pypiper": ["recover", "new-start", "dirty", "force-follow", "testmode"],
         "config": ["config"],
         "checkpoint": ["stop-before", "stop-after"],
         "resource": ["mem", "cores"],
@@ -763,6 +767,9 @@ def _add_args(parser, args, required):
 
     # Define the arguments.
     argument_data = {
+        "testmode":
+            ("-T", {"action": "store_true",
+                    "help": "Only print commands, don't run"}),
         "recover":
             ("-R", {"action": "store_true",
                     "help": "Overwrite locks to recover from previous failed run"}),