Merge pull request #44 from Sage-Bionetworks/update-login

Create login utility function

README.md

@@ -41,4 +41,4 @@ RetrieveCls = create.SynapseCreation(syn, only_get=True)
 ```
 
 ## Contributing
-Please view our [contributing guide](CONTRIBUTING.md)
+Please view our [contributing guide](CONTRIBUTING.md)

requirements.txt

@@ -1,3 +1,3 @@
 click
-synapseclient==2.3.0
+synapseclient==2.4.0
 pyyaml

setup.py

@@ -25,7 +25,7 @@
     python_requires='>=3.6',
     entry_points={'console_scripts': ['synapseformation = synapseformation.__main__:cli']},
     install_requires=['click',
-                      'synapseclient>=2.0.0',
+                      'synapseclient>=2.4.0',
                       'pyyaml'],
     project_urls={
         "Documentation": "https://github.com/Sage-Bionetworks/synapseformation",

synapseformation/__main__.py

@@ -1,8 +1,10 @@
 """synapseformation command line client"""
 import click
+
 import synapseclient
 
 from .client import create_synapse_resources
+from .utils import synapse_login
 from .__version__ import __version__
 
 
@@ -37,11 +39,13 @@ def cli():
 
 @cli.command()
 @click.option('--template_path', help='Template path', type=click.Path())
-def create(template_path):
-    """Creates Synapse Resources"""
-    # syn = utils.synapse_login()
-    # syn = synapseclient.login()
-    create_synapse_resources(template_path)
+@click.option('-c', '--config_path', help='Synapse configuration file',
+              type=click.Path(), show_default=True,
+              default=synapseclient.client.CONFIG_FILE)
+def create(template_path, config_path):
+    """Creates Synapse Resources given a yaml or json"""
+    syn = synapse_login(synapse_config=config_path)
+    create_synapse_resources(syn=syn, template_path=template_path)
 
 
 if __name__ == "__main__":

synapseformation/client.py

@@ -94,10 +94,8 @@ def _create_synapse_resources(config_list: List[dict],
                                           parentid=parent_id)
 
 
-def create_synapse_resources(template_path: str):
+def create_synapse_resources(syn: synapseclient.Synapse, template_path: str):
     """Creates synapse resources from template"""
-    # TODO: abstract out login function
-    syn = synapseclient.login()
     # Function will attempt to read template as yaml then try to read in json
     config = utils.read_config(template_path)
     # Expands shortended configuration into full configuration.  This should

synapseformation/utils.py

@@ -1,50 +1,49 @@
 """Utility functions"""
 import yaml
 
+import synapseclient
+from synapseclient.core.exceptions import (
+    SynapseNoCredentialsError,
+    SynapseAuthenticationError,
+)
 
-# def read_yaml_config(template_path: str) -> dict:
-#     """Get yaml synapse formation template
 
-#     Args:
-#         template_path: Path to yaml synapse formation template
+def read_config(template_path: str) -> dict:
+    """Read in yaml or json configuration
 
-#     Returns:
-#         dict for synapse configuration
-#     """
-#     with open(template_path, "r") as template_f:
-#         template = yaml.safe_load(template_f)
-#     return template
+    Args:
+        template_path: Path to yaml or json configuration
 
-
-# def read_json_config(template_path):
-#     """Get json synapse formation template
-
-#     Args:
-#         template_path: Path to yaml synapse formation template
-
-#     Returns:
-#         dict for synapse configuration
-#     """
-#     with open(template_path, "r") as template_f:
-#         template = json.load(template_f)
-#     return template
-
-
-def read_config(template_path: str):
-    """Read in yaml or json configuration"""
+    Returns:
+        Configuration
+    """
     # JSON is technically yaml but not the other way around.
     # yaml.safe_load can actually read in json files.
     with open(template_path, "r") as template_f:
         config = yaml.safe_load(template_f)
     return config
 
-# class Ref(yaml.YAMLObject):
-#     yaml_loader = yaml.SafeLoader
-#     yaml_tag = '!Ref'
-#     def __init__(self, val):
-#         self.val = val
 
-#     @classmethod
-#     def from_yaml(cls, loader, node):
-#         return cls(node.value)
-# # yaml.safe_load('Foo: !Ref bar')
+def synapse_login(synapse_config=synapseclient.client.CONFIG_FILE):
+    """Login to Synapse
+
+    Args:
+        synapse_config: Path to synapse configuration file.
+                        Defaults to ~/.synapseConfig
+
+    Returns:
+        Synapse connection
+    """
+    try:
+        syn = synapseclient.Synapse(configPath=synapse_config)
+        syn.login(silent=True)
+    except (SynapseNoCredentialsError, SynapseAuthenticationError):
+        raise ValueError(
+            "Login error: please make sure you have correctly "
+            "configured your client.  Instructions here: "
+            "https://help.synapse.org/docs/Client-Configuration.1985446156.html. "
+            "You can also create a Synapse Personal Access Token and set it "
+            "as an environmental variable: "
+            "SYNAPSE_AUTH_TOKEN='<my_personal_access_token>'"
+        )
+    return(syn)

tests/test_utils.py

@@ -0,0 +1,73 @@
+"""Test utility functions"""
+import json
+import tempfile
+from unittest import mock
+from unittest.mock import patch, Mock
+
+import pytest
+import synapseclient
+from synapseclient.core.exceptions import (
+    SynapseAuthenticationError,
+    SynapseNoCredentialsError,
+)
+
+from synapseformation import utils
+
+
+def test_read_config_yaml():
+    """Test reading in yaml configuration"""
+    test_yaml = "Test:\n  name: foo\n  test: bar"
+    expected = {'Test': {'name': 'foo', 'test': 'bar'}}
+    mock_open = mock.mock_open(read_data=test_yaml)
+    with mock.patch("builtins.open", mock_open):
+        yaml_dict = utils.read_config('file')
+        assert yaml_dict == expected
+
+
+def test_read_config_json():
+    """Test JSON config can be read with yaml.safe_load"""
+    expected = {'Test': {'name': 'foo', 'test': 'bar'}}
+    mock_open = mock.mock_open(read_data=json.dumps(expected))
+    with mock.patch("builtins.open", mock_open):
+        json_dict = utils.read_config('file')
+        assert json_dict == expected
+
+
+def test_synapse_login_default():
+    """Test default synapse login config path"""
+    syn = Mock()
+    with patch.object(synapseclient, "Synapse",
+                      return_value=syn) as patch_synapse,\
+         patch.object(syn, "login") as patch_login:
+        syn_conn = utils.synapse_login()
+        assert syn_conn == syn
+        patch_synapse.assert_called_once_with(
+            configPath=synapseclient.client.CONFIG_FILE
+        )
+        patch_login.assert_called_once()
+
+
+def test_synapse_login_specify():
+    """Test default synapse login config path"""
+    syn = Mock()
+    temp_config = tempfile.NamedTemporaryFile()
+    with patch.object(synapseclient, "Synapse",
+                      return_value=syn) as patch_synapse:
+        syn_conn = utils.synapse_login(synapse_config=temp_config.name)
+        assert syn_conn == syn
+        patch_synapse.assert_called_once_with(
+            configPath=temp_config.name
+        )
+    temp_config.close()
+
+
+@pytest.mark.parametrize("error", [SynapseAuthenticationError,
+                                   SynapseNoCredentialsError])
+def test_synapse_login_error(error):
+    """Test default synapse login config path"""
+    syn = Mock()
+    with patch.object(synapseclient, "Synapse", return_value=syn),\
+         patch.object(syn, "login", side_effect=error),\
+         pytest.raises(ValueError,
+                       match=r"Login error: please make sure you .*"):
+        utils.synapse_login()