Added support for illumina basespace filesource

Author: nuwang

lib/galaxy/dependencies/__init__.py

@@ -241,6 +241,9 @@ def check_fs_gcsfs(self):
     def check_fs_onedatafs(self):
         return 'onedata' in self.file_sources
 
+    def check_fs_basespace(self):
+        return 'basespace' in self.file_sources
+
     def check_watchdog(self):
         install_set = {'auto', 'True', 'true', 'polling', True}
         return (self.config['watch_tools'] in install_set

lib/galaxy/dependencies/conditional-requirements.txt

@@ -23,6 +23,7 @@ fs.anvilfs # type: anvil
 fs.googledrivefs # type: googledrive
 fs-gcsfs # type: googlecloudstorage
 fs-onedatafs # type: onedata
+fs-basespace # type: basespace
 
 # Chronos client
 chronos-python==1.2.1

lib/galaxy/files/sources/basespace.py

@@ -0,0 +1,20 @@
+try:
+    from fs_basespace import BASESPACEFS
+except ImportError:
+    BASESPACEFS = None
+
+from ._pyfilesystem2 import PyFilesystem2FilesSource
+
+
+class BaseSpaceFilesSource(PyFilesystem2FilesSource):
+    plugin_type = 'basespace'
+    required_module = BASESPACEFS
+    required_package = "fs-basespace"
+
+    def _open_fs(self, user_context):
+        props = self._serialization_props(user_context)
+        handle = BASESPACEFS(**props)
+        return handle
+
+
+__all__ = ('BaseSpaceFilesSource',)

test/unit/files/_util.py

@@ -63,6 +63,9 @@ def user_context_fixture(user_ftp_dir=None, role_names=None, group_names=None, i
             'googlecloudstorage|bucket_name': 'genomics-public-data',
             'onedata|provider_host': os.environ.get('GALAXY_TEST_ONEDATA_PROVIDER_HOST'),
             'onedata|access_token': os.environ.get('GALAXY_TEST_ONEDATA_ACCESS_TOKEN'),
+            'basespace|client_id': os.environ.get('GALAXY_TEST_ONEDATA_CLIENT_ID'),
+            'basespace|client_secret': os.environ.get('GALAXY_TEST_ONEDATA_CLIENT_SECRET'),
+            'basespace|access_token': os.environ.get('GALAXY_TEST_ONEDATA_ACCESS_TOKEN'),
         },
         role_names=role_names or set(),
         group_names=group_names or set(),

test/unit/files/basespace_file_sources_conf.yml

@@ -0,0 +1,7 @@
+- type: basespace
+  id: test1
+  doc: Test access to Illumina BaseSpace
+  basespace_server: https://api.basespace.illumina.com
+  client_id: ${user.preferences['basespace|client_id']}
+  client_secret: ${user.preferences['basespace|client_secret']}
+  access_token: ${user.preferences['basespace|access_token']}

test/unit/files/test_basespace.py

@@ -0,0 +1,41 @@
+import os
+
+import pytest
+
+from galaxy.files import ConfiguredFileSources, ConfiguredFileSourcesConfig
+from ._util import (
+    assert_realizes_as,
+    find,
+    user_context_fixture,
+)
+SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
+FILE_SOURCES_CONF = os.path.join(SCRIPT_DIRECTORY, "basespace_file_sources_conf.yml")
+
+skip_if_no_basespace_access_token = pytest.mark.skipif(
+    not os.environ.get('GALAXY_TEST_BASESPACE_CLIENT_ID')
+    and not os.environ.get('GALAXY_TEST_BASESPACE_CLIENT_SECRET')
+    and not os.environ.get('GALAXY_TEST_BASESPACE_ACCESS_TOKEN')
+    and not os.environ.get('GALAXY_TEST_BASESPACE_TEST_FILE_PATH'),
+    reason="GALAXY_TEST_BASESPACE_CLIENT_ID and related vars not set"
+)
+
+
+@skip_if_no_basespace_access_token
+def test_file_source():
+    user_context = user_context_fixture()
+    file_sources = _configured_file_sources()
+    file_source_pair = file_sources.get_file_source_path("gxfiles://test1")
+
+    assert file_source_pair.path == "/"
+    file_source = file_source_pair.file_source
+    test_file = os.environ.get('GALAXY_TEST_BASESPACE_TEST_FILE_PATH')
+    res = file_source.list(os.path.dirname(test_file), recursive=False, user_context=user_context)
+    a_file = find(res, class_="File", name=os.path.basename(test_file))
+    assert a_file
+
+    assert_realizes_as(file_sources, a_file['uri'], "a\n", user_context=user_context)
+
+
+def _configured_file_sources(conf_file=FILE_SOURCES_CONF):
+    file_sources_config = ConfiguredFileSourcesConfig()
+    return ConfiguredFileSources(file_sources_config, conf_file=conf_file)