Fix shed_test and shed_serve for test/local tool sheds.

jmchilton · jmchilton · commit f3cafaa1f3be · 2015-05-21T21:10:18.000-04:00
diff --git a/planemo/galaxy_config.py b/planemo/galaxy_config.py
@@ -20,6 +20,7 @@
 from planemo.io import write_file
 from planemo.io import kill_pid_file
 from planemo import git
+from planemo.shed import tool_shed_url
 from planemo.bioblend import (
     galaxy,
     ensure_module,
@@ -73,6 +74,11 @@
 </dependency_resolvers>
 """
 
+TOOL_SHEDS_CONF = """<tool_sheds>
+  <tool_shed name="Target Shed" url="${shed_target_url}" />
+</tool_sheds>
+"""
+
 # Provide some shortcuts for simple/common dependency resolutions strategies.
 STOCK_DEPENDENCY_RESOLUTION_STRATEGIES = {
     "brew_dependency_resolution": BREW_DEPENDENCY_RESOLUTION_CONF,
@@ -128,6 +134,9 @@ def config_join(*args):
         tool_conf = config_join("tool_conf.xml")
         database_location = config_join("galaxy.sqlite")
         shed_tools_path = config_join("shed_tools")
+        sheds_config_path = _configure_sheds_config_file(
+            config_directory, **kwds
+        )
         preseeded_database = True
         master_api_key = kwds.get("master_api_key", "test_key")
         dependency_dir = os.path.join(config_directory, "deps")
@@ -166,6 +175,7 @@ def config_join(*args):
             file_path="${temp_directory}/files",
             new_file_path="${temp_directory}/tmp",
             tool_config_file=tool_config_file,
+            tool_sheds_config_file=sheds_config_path,
             check_migrate_tools="False",
             manage_dependency_relationships="False",
             job_working_directory="${temp_directory}/job_working_directory",
@@ -431,6 +441,17 @@ def _search_tool_path_for(path, target, extra_paths=[]):
     return None
 
 
+def _configure_sheds_config_file(config_directory, **kwds):
+    if "shed_target" not in kwds:
+        kwds = kwds.copy()
+        kwds["shed_target"] = "toolshed"
+    shed_target_url = tool_shed_url(kwds)
+    contents = _sub(TOOL_SHEDS_CONF, {"shed_target_url": shed_target_url})
+    tool_sheds_conf = os.path.join(config_directory, "tool_sheds_conf.xml")
+    write_file(tool_sheds_conf, contents)
+    return tool_sheds_conf
+
+
 def _tool_conf_entry_for(tool_paths):
     tool_definitions = ""
     for tool_path in tool_paths:
diff --git a/planemo/shed/__init__.py b/planemo/shed/__init__.py
@@ -322,7 +322,7 @@ def tool_shed_client(ctx=None, **kwds):
     def prop(key):
         return kwds.get("shed_%s" % key, None) or shed_config.get(key, None)
 
-    url = _tool_shed_url(kwds)
+    url = tool_shed_url(kwds)
     if read_only:
         key = None
         email = None
@@ -608,7 +608,7 @@ def shed_repo_type(config, name):
     return repo_type
 
 
-def _tool_shed_url(kwds):
+def tool_shed_url(kwds):
     url = kwds.get("shed_target")
     if url in SHED_SHORT_NAMES:
         url = SHED_SHORT_NAMES[url]
@@ -1217,6 +1217,7 @@ class RealizationException(Exception):
     'for_each_repository',
     'api_exception_to_message',
     'tool_shed_client',
+    'tool_shed_url',
     'diff_repo',
     'download_tarball',
     'shed_init',
diff --git a/tests/test_shed_test.py b/tests/test_shed_test.py
@@ -12,7 +12,7 @@
 class ShedTestTestCase(CliTestCase):
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
-    def test_serve(self):
+    def test_shed_test(self):
         fastqc_path = os.path.join(TEST_REPOS_DIR, "fastqc")
         test_cmd = [
             "shed_test",
