use command callability from ubiquerg; generalize identical logic/flo…

…w across data structures

docs/changelog.md

@@ -1,8 +1,12 @@
 # Changelog
 
+## [0.23.0] - Unreleased
+### Changed
+- Remove `is_command_callable` from `utils` module; instead, refer to [`ubiquerg`](https://pypi.org/project/ubiquerg/).
+
 ## [0.22.2] - 2019-06-20
 ### Changed
-- Remove `ngstk` requirement
+- Remove `ngstk` requirement.
 
 ## [0.22.1] - 2019-06-19
 ### Changed

peppy/_version.py

@@ -1 +1 @@
-__version__ = "0.22.2"
+__version__ = "0.23.0-dev"

peppy/utils.py

@@ -1,23 +1,23 @@
 """ Helpers without an obvious logical home. """
 
-from collections import Counter, defaultdict, Iterable, Sized
+from collections import Counter, defaultdict, Iterable, Mapping, Sized
 import contextlib
 import logging
 import os
 import random
 import string
 import yaml
 from .const import SAMPLE_INDEPENDENT_PROJECT_SECTIONS
-from ubiquerg import is_collection_like
+from ubiquerg import is_collection_like, is_command_callable
 
 
 _LOGGER = logging.getLogger(__name__)
 
 
 __all__ = [
     "CommandChecker", "add_project_sample_constants", "count_repeats",
-    "get_logger", "fetch_samples", "grab_project_data",
-    "has_null_value", "is_command_callable", "type_check_strict"
+    "get_logger", "fetch_samples", "grab_project_data", "has_null_value",
+    "type_check_strict"
 ]
 
 
@@ -450,38 +450,20 @@ def __init__(self, path_conf_file,
                              s, self.path)
                 continue
             # Test each of the section's commands.
-            try:
-                # Is section's data a mapping?
-                commands_iter = section_data.items()
-                self._logger.debug("Processing section '%s' data "
-                                   "as mapping", s)
-                for name, command in commands_iter:
-                    failed = self._store_status(section=s, command=command,
-                                                name=name)
-                    self._logger.debug("Command '%s': %s", command,
-                                       "FAILURE" if failed else "SUCCESS")
-            except AttributeError:
-                self._logger.debug("Processing section '%s' data as list", s)
-                commands_iter = conf_data[s]
-                for cmd_item in commands_iter:
-                    # Item is K-V pair?
-                    try:
-                        name, command = cmd_item
-                    except ValueError:
-                        # Treat item as command itself.
-                        name, command = "", cmd_item
-                    success = self._store_status(section=s, command=command,
-                                                 name=name)
-                    self._logger.debug("Command '%s': %s", command,
-                                       "SUCCESS" if success else "FAILURE")
-
-    def _store_status(self, section, command, name):
+            cmds = list(section_data.values()) if isinstance(section_data, Mapping) \
+                else [c[1] if isinstance(c, (tuple, list)) else c for c in section_data]
+            for command in cmds:
+                succ = self._store_status(section=s, command=command)
+                self._logger.debug("Command '%s': %s", command,
+                                   "SUCCESS" if succ else "FAILURE")
+
+    def _store_status(self, section, command):
         """
         Based on new command execution attempt, update instance's
         data structures with information about the success/fail status.
         Return the result of the execution test.
         """
-        succeeded = is_command_callable(command, name)
+        succeeded = is_command_callable(command)
         # Store status regardless of its value in the instance's largest DS.
         self.section_to_status_by_command[section][command] = succeeded
         if not succeeded:
@@ -505,23 +487,3 @@ def failed(self):
         if not self.section_to_status_by_command:
             raise ValueError("No commands validated")
         return 0 == len(self.failures)
-
-
-def is_command_callable(command, name=""):
-    """
-    Check if command can be called.
-
-    :param str command: actual command to call
-    :param str name: nickname/alias by which to reference the command, optional
-    :return bool: whether given command's call succeeded
-    """
-
-    # Use `command` to see if command is callable, store exit code
-    code = os.system(
-        "command -v {0} >/dev/null 2>&1 || {{ exit 1; }}".format(command))
-
-    if code != 0:
-        alias_value = " ('{}') ".format(name) if name else " "
-        _LOGGER.debug("Command '{0}' is not callable: {1}".
-                      format(alias_value, command))
-    return not bool(code)

requirements/requirements-all.txt

@@ -3,4 +3,4 @@ pandas>=0.20.2
 pyyaml>=5
 divvy>=0.3.2
 logmuse>=0.2
-ubiquerg>=0.4.3
+ubiquerg>=0.4.5