From 8a608e0a0fd4b6a987e5eedeb953b44de3ca5157 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 22 Jun 2017 14:06:11 -0400
Subject: [PATCH] Normalize special handling for galaxy_root in ~/.planemo.yml.

---
 planemo/config.py        | 16 ++++++++++------
 planemo/galaxy/config.py |  2 --
 planemo/options.py       |  3 +++
 3 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/planemo/config.py b/planemo/config.py
index a39376708..85b588eee 100644
--- a/planemo/config.py
+++ b/planemo/config.py
@@ -19,7 +19,7 @@
 
 
 def _default_callback(
-    default, use_global_config=False, resolve_path=False,
+    default, use_global_config=False, resolve_path=False, extra_global_config_vars=[],
 ):
 
     def callback(ctx, param, value):
@@ -33,6 +33,7 @@ def callback(ctx, param, value):
                 planemo_ctx,
                 param,
                 use_global_config=use_global_config,
+                extra_global_config_vars=extra_global_config_vars,
             )
 
         if result is VALUE_UNSET:
@@ -51,13 +52,14 @@ def callback(ctx, param, value):
     return callback
 
 
-def _find_default(ctx, param, use_global_config):
+def _find_default(ctx, param, use_global_config, extra_global_config_vars):
     if use_global_config:
         global_config = ctx.global_config
-        global_config_key = "default_%s" % param.name
-        if global_config_key in global_config:
-            default_value = global_config[global_config_key]
-            return default_value, OptionSource.global_config
+        global_config_keys = ["default_%s" % param.name] + extra_global_config_vars
+        for global_config_key in global_config_keys:
+            if global_config_key in global_config:
+                default_value = global_config[global_config_key]
+                return default_value, OptionSource.global_config
 
     return VALUE_UNSET, None
 
@@ -73,6 +75,7 @@ def planemo_option(*args, **kwargs):
     option_type = kwargs.get("type", None)
     use_global_config = kwargs.pop("use_global_config", False)
     use_env_var = kwargs.pop("use_env_var", False)
+    extra_global_config_vars = kwargs.pop("extra_global_config_vars", [])
 
     default_specified = "default" in kwargs
     default = None
@@ -87,6 +90,7 @@ def callback(ctx, param, value):
             result = _default_callback(
                 default,
                 use_global_config=use_global_config,
+                extra_global_config_vars=extra_global_config_vars,
                 resolve_path=resolve_path,
             )(ctx, param, value)
 
diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py
index 530127a71..6e41eebee 100644
--- a/planemo/galaxy/config.py
+++ b/planemo/galaxy/config.py
@@ -977,8 +977,6 @@ def _find_galaxy_root(ctx, **kwds):
     galaxy_root = kwds.get(root_prop, None)
     if galaxy_root:
         return galaxy_root
-    elif ctx.global_config.get(root_prop, None):
-        return ctx.global_config[root_prop]
     else:
         par_dir = os.getcwd()
         while True:
diff --git a/planemo/options.py b/planemo/options.py
index e95dfe318..1afd9a107 100644
--- a/planemo/options.py
+++ b/planemo/options.py
@@ -122,6 +122,7 @@ def galaxy_root_option():
     return planemo_option(
         "--galaxy_root",
         use_global_config=True,
+        extra_global_config_vars=["galaxy_root"],
         use_env_var=True,
         type=click.Path(exists=True, file_okay=False, resolve_path=True),
         help="Root of development galaxy directory to execute command with.",
@@ -143,6 +144,8 @@ def galaxy_cwl_root_option():
     return planemo_option(
         "--cwl_galaxy_root",
         use_global_config=True,
+        extra_global_config_vars=["cwl_galaxy_root"],
+        use_env_var=True,
         type=click.Path(exists=True, file_okay=False, resolve_path=True),
         help=("Root of development galaxy directory to execute command with"
               " (must be branch of Galaxy with CWL support, this option"