Integration tests for remote_files API endpoint.

lib/galaxy/webapps/galaxy/api/remote_files.py

@@ -32,17 +32,18 @@ def index(self, trans, **kwd):
 
         Displays remote files.
 
-        :param  target:      target to load available datasets from, defaults to ftp
-            possible values: ftp, userdir, importdir
+        :param  target:      target to load available datasets from, defaults to ftpdir
+            possible values: ftpdir, userdir, importdir
         :type   target:      str
 
         :param  format:      requested format of data, defaults to flat
-            possible values: flat, jstree, ajax
+            possible values: flat, jstree
 
         :returns:   list of available files
         :rtype:     list
         """
-        target = kwd.get('target', None)
+        # If set, target must be one of 'ftpdir' (default), 'userdir', 'importdir'
+        target = kwd.get('target', 'ftpdir')
         format = kwd.get('format', None)
 
         if target == 'userdir':
@@ -94,7 +95,7 @@ def index(self, trans, **kwd):
                 except Exception:
                     log.exception('Could not get user import files')
                     raise exceptions.InternalServerError('Could not get the files from your import directory folder.')
-        else:
+        elif target == 'ftpdir':
             user_ftp_base_dir = trans.app.config.ftp_upload_dir
             if user_ftp_base_dir is None:
                 raise exceptions.ConfigDoesNotAllowException('The configuration of this Galaxy instance does not allow upload from FTP directories.')
@@ -108,6 +109,8 @@ def index(self, trans, **kwd):
             except Exception:
                 log.warning('Could not get ftp files', exc_info=True)
                 return None
+        else:
+            raise exceptions.RequestParameterInvalidException("Invalid target parameter supplied [%s]" % target)
         return response
 
     def __load_all_filenames(self, directory, allowlist=None):

lib/galaxy_test/base/api_asserts.py

@@ -44,4 +44,12 @@ def assert_error_code_is(response, error_code):
     assert err_code == int(error_code), ASSERT_FAIL_ERROR_CODE % (err_code, int(error_code))
 
 
+def assert_error_message_contains(response, expected_contains):
+    if hasattr(response, "json"):
+        response = response.json()
+    assert_has_keys(response, "err_msg")
+    err_msg = response["err_msg"]
+    assert expected_contains in err_msg
+
+
 assert_has_key = assert_has_keys

test/integration/test_remote_files.py

@@ -0,0 +1,126 @@
+import operator
+import os
+from tempfile import mkdtemp
+
+from galaxy.exceptions import error_codes
+from galaxy_test.base.api_asserts import assert_error_code_is, assert_error_message_contains
+from galaxy_test.driver import integration_util
+
+SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
+FILE_SOURCES_JOB_CONF = os.path.join(SCRIPT_DIRECTORY, "file_sources_conf.yml")
+
+USERNAME = 'user--bx--psu--edu'
+USER_EMAIL = '[email protected]'
+
+
+class RemoteFilesIntegrationTestCase(integration_util.IntegrationTestCase):
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        root = os.path.realpath(mkdtemp())
+        cls._test_driver.temp_directories.append(root)
+        cls.root = root
+        cls.library_dir = os.path.join(root, "library")
+        cls.user_library_dir = os.path.join(root, "user_library")
+        cls.ftp_upload_dir = os.path.join(root, "ftp")
+        config["library_import_dir"] = cls.library_dir
+        config["user_library_import_dir"] = cls.user_library_dir
+        config["ftp_upload_dir"] = cls.ftp_upload_dir
+        config["ftp_upload_site"] = "ftp://cow.com"
+
+        for d in [cls.library_dir, cls.user_library_dir, cls.ftp_upload_dir]:
+            os.mkdir(d)
+
+    def test_index(self):
+        index = self.galaxy_interactor.get("remote_files?target=importdir").json()
+        self._assert_index_empty(index)
+
+        _write_file_fixtures(self.root, self.library_dir)
+        index = self.galaxy_interactor.get("remote_files?target=importdir").json()
+        self._assert_index_matches_fixtures(index)
+
+        # Get a 404 if the directory doesn't exist.
+        index = self.galaxy_interactor.get("remote_files?target=userdir").json()
+        assert_error_code_is(index, error_codes.USER_OBJECT_NOT_FOUND)
+
+        users_dir = os.path.join(self.user_library_dir, USER_EMAIL)
+        os.mkdir(users_dir)
+
+        index = self.galaxy_interactor.get("remote_files?target=userdir").json()
+        self._assert_index_empty(index)
+
+        _write_file_fixtures(self.root, users_dir)
+
+        index = self.galaxy_interactor.get("remote_files?target=userdir").json()
+        self._assert_index_matches_fixtures(index)
+
+        index = self.galaxy_interactor.get("remote_files?target=userdir&format=jstree").json()
+        self._assert_index_matches_fixtures_jstree(index)
+
+    def _assert_index_empty(self, index):
+        assert len(index) == 0
+
+    def _assert_index_matches_fixtures(self, index):
+        paths = map(operator.itemgetter("path"), index)
+        assert "a" in paths
+        assert "subdir1/c" in paths
+
+    def _assert_index_matches_fixtures_jstree(self, index):
+        a_file = index[0]
+        assert a_file["li_attr"]["full_path"] == "a"
+        subdir1 = index[1]
+        assert subdir1["type"] == "folder"
+        assert subdir1["state"]["disabled"]
+        assert subdir1["li_attr"]["full_path"] == "subdir1"
+        subdir1_children = subdir1["children"]
+        assert len(subdir1_children) == 2
+        c = subdir1_children[0]
+        assert c["li_attr"]["full_path"] == "subdir1/c"
+
+
+class RemoteFilesNotConfiguredIntegrationTestCase(integration_util.IntegrationTestCase):
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["library_import_dir"] = None
+        config["user_library_import_dir"] = None
+        config["ftp_upload_dir"] = None
+
+    def test_configuration_statuses(self):
+        importfiles = self.galaxy_interactor.get("remote_files?target=importdir")
+        assert_error_code_is(importfiles, error_codes.CONFIG_DOES_NOT_ALLOW)
+        assert_error_message_contains(importfiles, 'import directory')
+
+        importfiles = self.galaxy_interactor.get("remote_files?target=ftpdir")
+        assert_error_code_is(importfiles, error_codes.CONFIG_DOES_NOT_ALLOW)
+        assert_error_message_contains(importfiles, 'FTP directories')
+
+        importfiles = self.galaxy_interactor.get("remote_files?target=userdir")
+        assert_error_code_is(importfiles, error_codes.CONFIG_DOES_NOT_ALLOW)
+        assert_error_message_contains(importfiles, 'user directories')
+
+        # invalid request parameter waitwhat...
+        importfiles = self.galaxy_interactor.get("remote_files?target=waitwhat")
+        assert_error_code_is(importfiles, error_codes.USER_REQUEST_INVALID_PARAMETER)
+
+
+def _write_file_fixtures(tmp, root):
+    if not os.path.exists(root):
+        os.mkdir(root)
+    os.symlink(os.path.join(tmp, "b"), os.path.join(root, "unsafe"))
+    with open(os.path.join(root, "a"), "w") as f:
+        f.write("a\n")
+    with open(os.path.join(tmp, "b"), "w") as f:
+        f.write("b\n")
+
+    subdir1 = os.path.join(root, "subdir1")
+    os.mkdir(subdir1)
+    with open(os.path.join(subdir1, "c"), "w") as f:
+        f.write("c\n")
+
+    subdir2 = os.path.join(subdir1, "subdir2")
+    os.mkdir(subdir2)
+    with open(os.path.join(subdir2, "d"), "w") as f:
+        f.write("d\n")
+
+    return tmp, root