Merge pull request #7167 from mvdbeek/verify_tool_improvements

Remote tool testing enhancements

lib/galaxy/tools/verify/interactor.py

@@ -12,6 +12,7 @@ from collections import OrderedDict
 from json import dumps
 from logging import getLogger
 
+from packaging.version import parse as parse_version, Version
 try:
     from nose.tools import nottest
 except ImportError:
@@ -98,9 +99,20 @@ class GalaxyInteractorApi(object):
         if kwds.get('user_api_key_is_admin_key', False):
             self.master_api_key = self.api_key
         self.keep_outputs_dir = kwds["keep_outputs_dir"]
+        self._target_galaxy_version = None
 
         self.uploads = {}
 
+    @property
+    def target_galaxy_version(self):
+        if self._target_galaxy_version is None:
+            self._target_galaxy_version = parse_version(self._get('version').json()['version_major'])
+        return self._target_galaxy_version
+
+    @property
+    def supports_test_data_download(self):
+        return self.target_galaxy_version >= Version("19.01")
+
     def __get_user_key(self, user_key, admin_key, test_user=None):
         if not test_user:
             test_user = "test@bx.psu.edu"
@@ -259,16 +271,29 @@ class GalaxyInteractorApi(object):
 
     @nottest
     def test_data_download(self, tool_id, filename, mode='file'):
-        response = self._get("tools/%s/test_data_download?filename=%s" % (tool_id, filename), admin=True)
-        assert response.status_code == 200
-        if mode == 'file':
-            return response.content
-        elif mode == 'directory':
-            prefix = os.path.basename(filename)
-            path = tempfile.mkdtemp(prefix=prefix)
-            with tarfile.open(fileobj=BytesIO(response.content)) as tar_contents:
-                tar_contents.extractall(path=path)
-            return path
+        if self.supports_test_data_download:
+            response = self._get("tools/%s/test_data_download?filename=%s" % (tool_id, filename), admin=True)
+            assert response.status_code == 200
+            if mode == 'file':
+                return response.content
+            elif mode == 'directory':
+                prefix = os.path.basename(filename)
+                path = tempfile.mkdtemp(prefix=prefix)
+                with tarfile.open(fileobj=BytesIO(response.content)) as tar_contents:
+                    tar_contents.extractall(path=path)
+                return path
+        else:
+            # We can only use local data
+            response = self._get("tools/%s/test_data_path?filename=%s" % (tool_id, filename), admin=True)
+            assert response.status_code == 200
+            file_name = response.json()
+            if mode == 'file':
+                return open(file_name, mode='rb')
+            elif mode == 'directory':
+                # Make a copy, since we are going to clean up the returned path
+                path = tempfile.mkdtemp()
+                shutil.copytree(file_name, path)
+                return path
 
     def __output_id(self, output_data):
         # Allow data structure coming out of tools API - {id: <id>, output_name: <name>, etc...}
@@ -677,7 +702,7 @@ def _verify_extra_files_content(extra_files, hda_id, dataset_fetcher, test_data_
             shutil.rmtree(path)
 
 
-def verify_tool(tool_id, galaxy_interactor, resource_parameters=None, register_job_data=None, test_index=0, tool_version=None, quiet=False):
+def verify_tool(tool_id, galaxy_interactor, resource_parameters=None, register_job_data=None, test_index=0, tool_version=None, quiet=False, test_history=None):
     if resource_parameters is None:
         resource_parameters = {}
     tool_test_dicts = galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version)
@@ -686,7 +711,8 @@ def verify_tool(tool_id, galaxy_interactor, resource_parameters=None, register_j
 
     _handle_def_errors(testdef)
 
-    test_history = galaxy_interactor.new_history()
+    if test_history is None:
+        test_history = galaxy_interactor.new_history()
 
     stage_data_in_history(galaxy_interactor, tool_id, testdef.test_data(), test_history)
 

test/api/test_galaxy_interactor.py

@@ -0,0 +1,13 @@
+# Test galaxy interactor
+
+from packaging.version import Version
+
+from base import api   # noqa: I100,I202
+
+
+class GalaxyInteractorBackwardCompatTestCase(api.ApiTestCase):
+
+    def test_local_test_data_download(self):
+        self.galaxy_interactor._target_galaxy_version = Version("18.09")
+        assert self.galaxy_interactor.supports_test_data_download is False
+        assert self.galaxy_interactor.test_data_download(tool_id='cat1', filename='1.bed').readline().startswith('chr1\t147962192\t147962580')