Merge pull request #349 from genestack/master

Merge master to the stable for the release

ChangeLog

@@ -1,3 +1,6 @@
+* 0.35.0
+    * Genestack host is now mandatory when setting up the Genestack user, default host has been removed
+
 * 0.34.0
     * Initial Python 3 support
     * Implement auto checking for common sub-URLs (no explicit `/frontend`
@@ -9,7 +12,7 @@
       * `normalised_input` argument for ExpressionNavigator applications
       * `Connection.open` method
       * `CLApplication.rename_file` method
-      * `DataImporter.create_owl_ontology` method
+      * `DataImporter`: `create_owl_ontology` and `create_pathway_database` methods
       * `FilesUtil`: `create_dataset`, `get_groups_to_share`, `share_files`,
                      `share_folder` methods
       * `TaskLogViewer.view_log` method

genestack_client/data_importer.py

@@ -740,39 +740,3 @@ def create_microarray_annotation(self, annotation_type, parent=None,
         self.__add_to_metainfo(metainfo, Metainfo.NAME, name, StringValue, required=True)
         self.__add_to_metainfo(metainfo, BioMetaKeys.DATA_LINK, url, ExternalLink, required=True)
         return self.__invoke_loader(parent, annotation_type, metainfo)
-
-    def create_pathway_database(
-            self, db_name=None, version=None, parent=None, url=None, name=None, metainfo=None
-    ):
-        """
-        Create a Pathway Database file from a local or remote BioPAX archive.
-        ``name`` and ``url` are required fields.
-        They can be specified through the arguments or
-        via a :py:class:`~genestack_client.Metainfo` instance.
-
-        :param db_name: pathway database name (e.g. 'Reactome')
-        :type db_name: str
-        :param version: pathway database version (e.g. 'v50')
-        :type version: str
-        :param parent: accession of parent folder
-            (if not provided, files will be created in the ``Imported files`` folder)
-        :type parent: str
-        :param url: URL of a BioPAX archive
-        :type url: str
-        :param name: name of the created Genestack file
-        :type name: str
-        :param metainfo: metainfo of the created Genestack file
-        :type metainfo: Metainfo
-        :return: file accession
-        :rtype: str
-        """
-        metainfo = DataImporter._copy_metainfo(metainfo)
-        self.__add_to_metainfo(metainfo, Metainfo.NAME, name, StringValue, required=True)
-        self.__add_to_metainfo(metainfo, BioMetaKeys.DATA_LINK, url, ExternalLink, required=True)
-        self.__add_to_metainfo(
-            metainfo, 'genestack.bio:pathwayDatabaseName', db_name, StringValue, required=True
-        )
-        self.__add_to_metainfo(
-            metainfo, 'genestack.bio:pathwayDatabaseVersion', version, StringValue, required=True
-        )
-        return self.__invoke_loader(parent, 'pathwayDatabase', metainfo)

genestack_client/scripts/genestack_user_setup.py

@@ -7,6 +7,7 @@
 from __future__ import unicode_literals
 
 from future import standard_library
+
 standard_library.install_aliases()
 from builtins import input
 from builtins import *
@@ -19,13 +20,18 @@
 
 from genestack_client import GenestackAuthenticationException
 from genestack_client.genestack_shell import Command, GenestackShell
-from genestack_client.settings import DEFAULT_HOST, User, config
+from genestack_client.settings import User, config
 from genestack_client.utils import interactive_select
 
 
 def input_host():
-    host = input('host [%s]: ' % DEFAULT_HOST).strip()
-    return host or DEFAULT_HOST
+    print('Please input Genestack host address')
+    while True:
+        host = input('host: ').strip()
+        if not host:
+            print('Host can not be empty')
+            continue
+        return host
 
 
 def validate_alias(alias):
@@ -335,9 +341,8 @@ def get_command_parser(self, parser=None):
         parser.description = self.DESCRIPTION
         group = parser.add_argument_group('command arguments')
         self.update_parser(group)
-        group.add_argument('-H', '--host', default=DEFAULT_HOST,
-                           help='Genestack host, '
-                                'change it to connect somewhere else than %s' % DEFAULT_HOST,
+        group.add_argument('-H', '--host',
+                           help='Genestack host address',
                            metavar='<host>')
         return parser
 
@@ -388,16 +393,21 @@ class UserManagement(GenestackShell):
     prompt = 'user_setup> '
 
     def set_shell_user(self, args):
+        if not args.host:
+            sys.stderr.write("Genestack host is mandatory. Please specify the host using the -H flag")
+            sys.exit(1)
+
         config_path = config.get_settings_file()
         if not os.path.exists(config_path):
             print('No config file was found, creating one interactively')
-            self.process_command(Init(), ['--host', args.host or DEFAULT_HOST], False)
+            self.process_command(Init(), ['--host', args.host], False)
             args.host = None  # do not provide host for future use of arguments
 
 
 def main():
     shell = UserManagement()
     shell.cmdloop()
 
+
 if __name__ == '__main__':
     main()

genestack_client/settings/__init__.py

@@ -8,6 +8,6 @@
 standard_library.install_aliases()
 from builtins import *
 from genestack_client.settings.genestack_config import config
-from genestack_client.settings.genestack_user import DEFAULT_HOST, User
+from genestack_client.settings.genestack_user import User
 
 

genestack_client/settings/genestack_user.py

@@ -6,6 +6,7 @@
 from __future__ import unicode_literals
 
 from future import standard_library
+
 standard_library.install_aliases()
 from builtins import input
 from builtins import *
@@ -18,8 +19,6 @@
 from genestack_client import Connection, GenestackAuthenticationException, GenestackException
 from genestack_client.utils import isatty, interactive_select
 
-DEFAULT_HOST = 'platform.genestack.org'
-
 
 def _get_server_url(host):
     split_host = urlsplit(host)
@@ -62,7 +61,6 @@ def __init__(self, email, alias=None, host=None, password=None, token=None):
         """
         All fields are optional.
         If ``alias`` is None it will be the same as ``email``.
-        If no ``host`` is specified, the ``DEFAULT_HOST`` be used.
 
         If you login interactively, no ``email`` or ``password`` is required.
         The alias is used to find the matching user in :py:func:`~genestack_client.get_user`
@@ -76,7 +74,7 @@ def __init__(self, email, alias=None, host=None, password=None, token=None):
         :param password: password
         :type password: str
         """
-        self.host = host or DEFAULT_HOST
+        self.host = host
         self.email = email
         self.password = password  # TODO make property
         self.alias = alias or email
@@ -87,7 +85,6 @@ def get_connection(self, interactive=True, debug=False, show_logs=False):
         Return a logged-in connection for current user.
         If ``interactive`` is ``True`` and the password or email are unknown,
         they will be asked in interactive mode.
-        If no host is specified, the ``DEFAULT_HOST`` will be used.
 
         :param interactive: ask email and/or password interactively.
         :type interactive: bool

genestack_client/version.py

@@ -1 +1 @@
-__version__ = '0.34.0'
+__version__ = '0.35.0'

test/test_arguments.py

@@ -17,7 +17,7 @@
 
 sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
 from genestack_client import get_user, make_connection_parser
-from genestack_client.settings.genestack_user import User, DEFAULT_HOST
+from genestack_client.settings.genestack_user import User
 
 
 def test_parse_default_user():
@@ -100,7 +100,6 @@ def test_token_without_username():
     args = parser.parse_args(['--token', some_token])
     user = get_user(args)
     assert user.token == some_token
-    assert user.host == DEFAULT_HOST
 
 
 if __name__ == '__main__':