Fix #331.

jmchilton · jmchilton · commit 19900a6f61b4 · 2015-10-22T10:28:26.000+01:00
- Fully resolve report paths before passing to Galaxy, this used to be done by click before I wanted fancier defaults (falling back to .planemo.yml for instance).
 - Make warning about Galaxy version more clear.
diff --git a/planemo/config.py b/planemo/config.py
@@ -6,15 +6,18 @@
 }
 
 
-def get_default_callback(default, name=None):
+def get_default_callback(default, name=None, resolve_path=False):
 
     def callback(ctx, param, value):
         planemo_ctx = ctx.obj
         config_name = name
         if config_name is None:
             config_name = param.name
 
-        return _default_option(planemo_ctx, config_name, value, default)
+        result = _default_option(planemo_ctx, config_name, value, default)
+        if resolve_path and result:
+            result = os.path.abspath(result)
+        return result
 
     return callback
 
diff --git a/planemo/galaxy_test/structures.py b/planemo/galaxy_test/structures.py
@@ -7,6 +7,8 @@
 import json
 import xml.etree.ElementTree as ET
 
+from planemo.io import error
+
 RUN_TESTS_CMD = (
     "sh run_tests.sh --report_file %s %s %s %s"
 )
@@ -62,7 +64,7 @@ def __init__(self, json_path):
                 structured_data = json.load(output_json_f)
                 structured_data_tests = structured_data["tests"]
         except Exception:
-            print("Warning: Targetting older Galaxy which did not "
+            error("Warning: Targetting older Galaxy which did not "
                   "produce a structured test results files.")
             structured_data = {}
             structured_data_tests = {}
diff --git a/planemo/options.py b/planemo/options.py
@@ -585,37 +585,39 @@ def test_options():
         click.option(
             "--test_output",
             type=click.Path(file_okay=True, resolve_path=True),
-            callback=get_default_callback("tool_test_output.html"),
+            callback=get_default_callback("tool_test_output.html",
+                                          resolve_path=True),
             help=("Output test report (HTML - for humans) defaults to "
                   "tool_test_output.html."),
             default=None,
         ),
         click.option(
             "--test_output_text",
             type=click.Path(file_okay=True, resolve_path=True),
-            callback=get_default_callback(None),
+            callback=get_default_callback(None, resolve_path=True),
             help=("Output test report (Basic text - for display in CI)"),
             default=None,
         ),
         click.option(
             "--test_output_markdown",
             type=click.Path(file_okay=True, resolve_path=True),
-            callback=get_default_callback(None),
+            callback=get_default_callback(None, resolve_path=True),
             help=("Output test report (Markdown style - for humans & "
                   "computers)"),
             default=None,
         ),
         click.option(
             "--test_output_xunit",
             type=click.Path(file_okay=True, resolve_path=True),
-            callback=get_default_callback(None),
+            callback=get_default_callback(None, resolve_path=True),
             help="Output test report (xUnit style - for computers).",
             default=None,
         ),
         click.option(
             "--test_output_json",
             type=click.Path(file_okay=True, resolve_path=True),
-            callback=get_default_callback("tool_test_output.json"),
+            callback=get_default_callback("tool_test_output.json",
+                                          resolve_path=True),
             help=("Output test report (planemo json) defaults to "
                   "tool_test_output.json."),
             default=None,
