diff --git a/README.md b/README.md index 04e7c2e..1a425c9 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,39 @@ # DataSHIELD Interface Python This DataSHIELD Client Interface is a Python port of the original DataSHIELD Client Interface written in R ([DSI](https://github.com/datashield/DSI)). The provided interface can be implemented for accessing a data repository supporting the DataSHIELD infrastructure: controlled R commands to be executed on the server side are garanteeing that non disclosive information is returned to client side. + +## Configuration + +The search path for the DataSHIELD configuration file is the following: + +1. User general location: `~/.config/datashield/config.yaml` +2. Current project specific location: `./.datashield/config.yaml` + +The configurations are merged: any existing entry is replaced by the new one (for instance server names must be unique). + +The format of the DataSHIELD configuration file is: + +```yaml +servers: + - name: server1 + url: https://opal-demo.obiba.org + user: dsuser + password: P@ssw0rd + - name: server2 + url: https://opal.example.org + token: your-access-token-here + profile: default + - name: server3 + url: https://study.example.org/opal + user: dsuser + password: P@ssw0rd + profile: custom + driver: datashield_opal.OpalDriver +``` + +Each server entry in the list must have: +- `name`: Unique identifier for the server +- `url`: The server URL +- Authentication: Either `user` and `password`, or `token` (recommended) +- `profile`: DataSHIELD profile name (optional, defaults to "default") +- `driver`: Connection driver class name (optional, defaults to "datashield_opal.OpalDriver") \ No newline at end of file diff --git a/datashield/__init__.py b/datashield/__init__.py index 0874d1e..25c7dbe 100644 --- a/datashield/__init__.py +++ b/datashield/__init__.py @@ -1,5 +1,6 @@ from datashield.interface import ( DSConnection as DSConnection, + DSConfig as DSConfig, DSLoginInfo as DSLoginInfo, DSDriver as DSDriver, DSError as DSError, diff --git a/datashield/api.py b/datashield/api.py index f41c839..b2cf4b6 100644 --- a/datashield/api.py +++ b/datashield/api.py @@ -3,7 +3,7 @@ """ import logging -from datashield.interface import DSLoginInfo, DSConnection, DSDriver, DSError +from datashield.interface import DSConfig, DSLoginInfo, DSConnection, DSDriver, DSError import time @@ -12,8 +12,24 @@ class DSLoginBuilder: Helper class to formalize DataSHIELD login arguments for a set of servers. """ - def __init__(self): + def __init__(self, names: list[str] = None): + """Create a builder, optionally loading login information from configuration files + for the specified server names. + + :param names: The list of server names to load from configuration files, if any. If not defined, + no login information will be loaded from configuration files. + """ self.items: list[DSLoginInfo] = [] + # load login information from configuration files, in order of precedence + if names is not None and len(names) > 0: + config = DSConfig.load() + name_set = set(names) + if config.servers: + items = [x for x in config.servers if x.name in name_set] + if len(items) == 0: + logging.warning(f"No matching server names found in configuration for: {', '.join(names)}") + else: + self.items.extend(items) def add( self, @@ -46,7 +62,9 @@ def add( raise ValueError(f"Server name must be unique: {name}") if user is None and token is None: raise ValueError("Either user or token must be provided") - self.items.append(DSLoginInfo(name, url, user, password, token, profile, driver)) + self.items.append( + DSLoginInfo(name=name, url=url, user=user, password=password, token=token, profile=profile, driver=driver) + ) return self def remove(self, name: str): @@ -109,7 +127,7 @@ def open(self, restore: str = None, failSafe: bool = False) -> None: raise e if self.has_errors(): for name in self.errors: - print(f"Connection to {name} has failed") + logging.error(f"Connection to {name} has failed") def close(self, save: str = None) -> None: """ diff --git a/datashield/interface.py b/datashield/interface.py index c2a45dc..084d741 100644 --- a/datashield/interface.py +++ b/datashield/interface.py @@ -3,31 +3,97 @@ """ import importlib +import logging +import os +import yaml +from pydantic import BaseModel, Field, model_validator +# Default configuration file paths to look for DataSHIELD login information, in order of precedence +CONFIG_FILES = ["~/.config/datashield/config.yaml", "./.datashield/config.yaml"] -class DSLoginInfo: + +class DSLoginInfo(BaseModel): """ Helper class with DataSHIELD login details. """ - def __init__( - self, - name: str, - url: str, - user: str = None, - password: str = None, - token: str = None, - profile: str = "default", - driver: str = "datashield_opal.OpalDriver", - ): - self.items = [] - self.name = name - self.url = url - self.user = user - self.password = password - self.token = token - self.profile = profile if profile is not None else "default" - self.driver = driver if driver is not None else "datashield_opal.OpalDriver" + name: str + url: str + user: str | None = None + password: str | None = None + token: str | None = None + profile: str = "default" + driver: str = "datashield_opal.OpalDriver" + + model_config = {"extra": "forbid"} + + @model_validator(mode="after") + def validate_credentials(self) -> "DSLoginInfo": + if self.user is None and self.token is None: + raise ValueError("Either user or token must be provided") + return self + + +class DSConfig(BaseModel): + """ + Helper class with DataSHIELD configuration details. + """ + + servers: list[DSLoginInfo] = Field(default_factory=list) + + model_config = {"extra": "forbid"} + + @classmethod + def load(cls) -> "DSConfig": + """ + Load the DataSHIELD configuration from the default configuration files. + Each file must contain a list of servers with their login details. + All readable configuration files listed in ``CONFIG_FILES`` are processed in + order. Their configurations are merged, with servers identified by their + ``name`` field. If the same server name appears in multiple files, the + definition from the later file in the list takes precedence and replaces + the earlier one. Servers that are only present in earlier files are kept. + + :return: The DataSHIELD configuration object + """ + merged_config = None + for config_file in CONFIG_FILES: + try: + # check file exists and is readable, if not, silently ignore + path = os.path.expanduser(config_file) + if not os.path.exists(path): + continue + if not os.access(path, os.R_OK): + continue + config = cls.load_from_file(path) + if merged_config is None: + merged_config = config + else: + # merge servers by name, new ones replacing existing ones, and keep the rest of existing ones + existing_servers = {x.name: x for x in merged_config.servers} + for server in config.servers: + existing_servers[server.name] = server + merged_config.servers = list(existing_servers.values()) + except Exception: + # log and ignore errors, e.g. file not found or invalid format + logging.error(f"Failed to load login information from {config_file}") + return merged_config if merged_config else cls() + + @classmethod + def load_from_file(cls, file: str) -> "DSConfig": + """ + Load the DataSHIELD configuration from a YAML file. The file must contain a list of servers with their login details. + + :param file: The path to the YAML file containing the DataSHIELD configuration + :return: The DataSHIELD configuration object + """ + with open(file) as f: + config_data = yaml.safe_load(f) + + if config_data is None: + config_data = {} + + return cls.model_validate(config_data) class DSResult: @@ -409,7 +475,7 @@ def new_connection(cls, args: DSLoginInfo, restore: str = None) -> DSConnection: raise NotImplementedError("DSConnection function not available") @classmethod - def load_class(cls, name: str) -> any: + def load_class(cls, name: str) -> type["DSDriver"]: """ Load a class from its fully qualified name (dot separated). diff --git a/pyproject.toml b/pyproject.toml index 0a2d8cb..f893173 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "datashield" -version = "0.2.0" +version = "0.3.0" description = "DataSHIELD Client Interface in Python." authors = [ {name = "Yannick Marcon", email = "yannick.marcon@obiba.org"} @@ -22,7 +22,10 @@ classifiers = [ "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13", ] -dependencies = [] +dependencies = [ + "pydantic>=2.0", + "PyYAML>=6.0", +] [project.optional-dependencies] test = [ diff --git a/tests/test_config.py b/tests/test_config.py new file mode 100644 index 0000000..ce040da --- /dev/null +++ b/tests/test_config.py @@ -0,0 +1,465 @@ +""" +Test loading configuration from YAML file using Pydantic. +""" + +import os +import tempfile +import pytest +from pydantic import ValidationError +from datashield import DSConfig, DSLoginInfo + + +def test_load_config_from_yaml(): + """Test loading a configuration from a YAML file.""" + yaml_content = """ +servers: + - name: server1 + url: https://opal-demo.obiba.org + user: dsuser + password: your-password-here + - name: server2 + url: https://opal.example.org + token: your-access-token-here + profile: default + - name: server3 + url: https://study.example.org/opal + user: dsuser + password: your-password-here + profile: custom + driver: datashield_opal.OpalDriver +""" + + # Create a temporary file + with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as f: + f.write(yaml_content) + temp_file = f.name + + try: + # Load the configuration + config = DSConfig.load_from_file(temp_file) + + # Verify the configuration + assert config is not None + assert len(config.servers) == 3 + + # Check server1 + assert config.servers[0].name == "server1" + assert config.servers[0].url == "https://opal-demo.obiba.org" + assert config.servers[0].user == "dsuser" + assert config.servers[0].password == "your-password-here" + assert config.servers[0].token is None + assert config.servers[0].profile == "default" + assert config.servers[0].driver == "datashield_opal.OpalDriver" + + # Check server2 + assert config.servers[1].name == "server2" + assert config.servers[1].url == "https://opal.example.org" + assert config.servers[1].user is None + assert config.servers[1].password is None + assert config.servers[1].token == "your-access-token-here" + assert config.servers[1].profile == "default" + assert config.servers[1].driver == "datashield_opal.OpalDriver" + + # Check server3 + assert config.servers[2].name == "server3" + assert config.servers[2].url == "https://study.example.org/opal" + assert config.servers[2].user == "dsuser" + assert config.servers[2].password == "your-password-here" + assert config.servers[2].token is None + assert config.servers[2].profile == "custom" + assert config.servers[2].driver == "datashield_opal.OpalDriver" + + finally: + # Clean up + os.unlink(temp_file) + + +def test_load_config_with_defaults(): + """Test that default values are applied when not specified in YAML.""" + yaml_content = """ +servers: + - name: minimal + url: https://example.org + user: testuser + password: testpass +""" + + with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as f: + f.write(yaml_content) + temp_file = f.name + + try: + config = DSConfig.load_from_file(temp_file) + + assert config is not None + assert len(config.servers) == 1 + assert config.servers[0].name == "minimal" + assert config.servers[0].url == "https://example.org" + assert config.servers[0].user == "testuser" + assert config.servers[0].password == "testpass" + assert config.servers[0].profile == "default" + assert config.servers[0].driver == "datashield_opal.OpalDriver" + + finally: + os.unlink(temp_file) + + +def test_load_empty_config(): + """Test loading an empty configuration file.""" + yaml_content = "" + + with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as f: + f.write(yaml_content) + temp_file = f.name + + try: + config = DSConfig.load_from_file(temp_file) + + assert config is not None + assert len(config.servers) == 0 + + finally: + os.unlink(temp_file) + + +def test_load_config_no_servers(): + """Test loading a configuration file without a 'servers' key.""" + yaml_content = """ +other_key: value +""" + + with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as f: + f.write(yaml_content) + temp_file = f.name + + try: + # This should raise a validation error because 'other_key' is not allowed + with pytest.raises(ValidationError) as exc_info: + DSConfig.load_from_file(temp_file) + + # Check that the error is about extra fields + assert "extra" in str(exc_info.value).lower() or "forbidden" in str(exc_info.value).lower() + + finally: + os.unlink(temp_file) + + +def test_pydantic_validation_missing_required_fields(): + """Test that Pydantic validates required fields.""" + yaml_content = """ +servers: + - name: incomplete +""" + + with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as f: + f.write(yaml_content) + temp_file = f.name + + try: + # Should raise validation error for missing 'url' field + with pytest.raises(ValidationError) as exc_info: + DSConfig.load_from_file(temp_file) + + # Check that the error mentions the missing field + assert "url" in str(exc_info.value).lower() + + finally: + os.unlink(temp_file) + + +def test_create_dslogininfo_directly(): + """Test creating DSLoginInfo objects directly with Pydantic.""" + login = DSLoginInfo(name="test", url="https://example.org", user="testuser", password="testpass") + + assert login.name == "test" + assert login.url == "https://example.org" + assert login.user == "testuser" + assert login.password == "testpass" + assert login.profile == "default" + assert login.driver == "datashield_opal.OpalDriver" + + +def test_create_dslogininfo_requires_user_or_token(): + """Test that DSLoginInfo requires at least one credential method.""" + with pytest.raises(ValidationError) as exc_info: + DSLoginInfo(name="test", url="https://example.org") + + assert "either user or token must be provided" in str(exc_info.value).lower() + + +def test_create_dsconfig_directly(): + """Test creating DSConfig objects directly with Pydantic.""" + login1 = DSLoginInfo(name="server1", url="https://example1.org", user="user1", password="pass1") + login2 = DSLoginInfo(name="server2", url="https://example2.org", token="token123") + + config = DSConfig(servers=[login1, login2]) + + assert len(config.servers) == 2 + assert config.servers[0].name == "server1" + assert config.servers[1].name == "server2" + + +def test_pydantic_extra_fields_forbidden(): + """Test that extra fields in server configuration are rejected.""" + yaml_content = """ +servers: + - name: server1 + url: https://example.org + user: testuser + password: testpass + extra_field: should_fail +""" + + with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as f: + f.write(yaml_content) + temp_file = f.name + + try: + # Should raise validation error for extra field + with pytest.raises(ValidationError) as exc_info: + DSConfig.load_from_file(temp_file) + + assert "extra_field" in str(exc_info.value).lower() or "extra" in str(exc_info.value).lower() + + finally: + os.unlink(temp_file) + + +def test_model_serialization(): + """Test that Pydantic models can be serialized to dict.""" + login = DSLoginInfo(name="test", url="https://example.org", user="testuser", password="testpass") + + # Test model_dump (Pydantic v2 method) + data = login.model_dump() + assert data["name"] == "test" + assert data["url"] == "https://example.org" + assert data["user"] == "testuser" + assert data["password"] == "testpass" + assert data["profile"] == "default" + assert data["driver"] == "datashield_opal.OpalDriver" + + +def test_load_no_config_files(monkeypatch): + """Test loading configuration when no config files exist.""" + # Mock the CONFIG_FILES to point to non-existent paths + monkeypatch.setattr( + "datashield.interface.CONFIG_FILES", ["/nonexistent/path/config.yaml", "/another/nonexistent/path/config.yaml"] + ) + + config = DSConfig.load() + + assert config is not None + assert len(config.servers) == 0 + + +def test_load_from_first_config_file(monkeypatch): + """Test loading configuration from the first config file found.""" + yaml_content = """ +servers: + - name: server1 + url: https://example1.org + user: user1 + password: pass1 +""" + + with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as f: + f.write(yaml_content) + first_config_file = f.name + + try: + # Mock CONFIG_FILES to use our temporary file + monkeypatch.setattr("datashield.interface.CONFIG_FILES", [first_config_file, "/nonexistent/second/config.yaml"]) + + config = DSConfig.load() + + assert config is not None + assert len(config.servers) == 1 + assert config.servers[0].name == "server1" + assert config.servers[0].url == "https://example1.org" + assert config.servers[0].user == "user1" + + finally: + os.unlink(first_config_file) + + +def test_load_from_second_config_file(monkeypatch): + """Test loading configuration from the second config file if first doesn't exist.""" + yaml_content = """ +servers: + - name: server2 + url: https://example2.org + user: user2 + token: token123 +""" + + with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as f: + f.write(yaml_content) + second_config_file = f.name + + try: + # Mock CONFIG_FILES to use our temporary file as second option + monkeypatch.setattr("datashield.interface.CONFIG_FILES", ["/nonexistent/first/config.yaml", second_config_file]) + + config = DSConfig.load() + + assert config is not None + assert len(config.servers) == 1 + assert config.servers[0].name == "server2" + assert config.servers[0].url == "https://example2.org" + assert config.servers[0].token == "token123" + + finally: + os.unlink(second_config_file) + + +def test_load_merge_multiple_config_files(monkeypatch): + """Test merging configurations from multiple config files.""" + yaml_content1 = """ +servers: + - name: server1 + url: https://example1.org + user: user1 + password: pass1 + - name: server2 + url: https://example2.org + user: user2 + password: pass2 +""" + + yaml_content2 = """ +servers: + - name: server2 + url: https://example2-updated.org + user: user2_updated + password: pass2_updated + - name: server3 + url: https://example3.org + token: token123 +""" + + with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as f1: + f1.write(yaml_content1) + first_config_file = f1.name + + with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as f2: + f2.write(yaml_content2) + second_config_file = f2.name + + try: + # Mock CONFIG_FILES to use both our temporary files + monkeypatch.setattr("datashield.interface.CONFIG_FILES", [first_config_file, second_config_file]) + + config = DSConfig.load() + + assert config is not None + assert len(config.servers) == 3 + + # Check server1 (from first file, unchanged) + server1 = next(s for s in config.servers if s.name == "server1") + assert server1.url == "https://example1.org" + assert server1.user == "user1" + + # Check server2 (from first file, but updated by second file) + server2 = next(s for s in config.servers if s.name == "server2") + assert server2.url == "https://example2-updated.org" + assert server2.user == "user2_updated" + assert server2.password == "pass2_updated" + + # Check server3 (from second file only) + server3 = next(s for s in config.servers if s.name == "server3") + assert server3.url == "https://example3.org" + assert server3.token == "token123" + + finally: + os.unlink(first_config_file) + os.unlink(second_config_file) + + +def test_load_handles_invalid_yaml_silently(monkeypatch): + """Test that load() silently handles invalid YAML files.""" + invalid_yaml_content = """ +servers: + - name: server1 + url: https://example.org + invalid: yaml: content: +""" + + valid_yaml_content = """ +servers: + - name: server2 + url: https://example2.org + user: user2 + password: pass2 +""" + + with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as f1: + f1.write(invalid_yaml_content) + invalid_config_file = f1.name + + with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as f2: + f2.write(valid_yaml_content) + valid_config_file = f2.name + + try: + # Mock CONFIG_FILES with invalid file first, then valid file + monkeypatch.setattr("datashield.interface.CONFIG_FILES", [invalid_config_file, valid_config_file]) + + # Should not raise an exception, but load from the valid file + config = DSConfig.load() + + assert config is not None + assert len(config.servers) == 1 + assert config.servers[0].name == "server2" + assert config.servers[0].url == "https://example2.org" + + finally: + os.unlink(invalid_config_file) + os.unlink(valid_config_file) + + +def test_load_handles_permission_denied_silently(monkeypatch): + """Test that load() silently handles files without read permissions.""" + yaml_content1 = """ +servers: + - name: server1 + url: https://example1.org + user: user1 + password: pass1 +""" + + yaml_content2 = """ +servers: + - name: server2 + url: https://example2.org + user: user2 + password: pass2 +""" + + with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as f1: + f1.write(yaml_content1) + no_read_file = f1.name + + with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as f2: + f2.write(yaml_content2) + readable_file = f2.name + + try: + # Remove read permissions from first file + os.chmod(no_read_file, 0o000) + + # Mock CONFIG_FILES with unreadable file first, then readable file + monkeypatch.setattr("datashield.interface.CONFIG_FILES", [no_read_file, readable_file]) + + # Should not raise an exception, but load from the readable file + config = DSConfig.load() + + assert config is not None + assert len(config.servers) == 1 + assert config.servers[0].name == "server2" + assert config.servers[0].url == "https://example2.org" + + finally: + # Restore permissions to allow cleanup + os.chmod(no_read_file, 0o644) + os.unlink(no_read_file) + os.unlink(readable_file) diff --git a/uv.lock b/uv.lock index 41bf396..4f7a97e 100644 --- a/uv.lock +++ b/uv.lock @@ -2,6 +2,15 @@ version = 1 revision = 3 requires-python = ">=3.10" +[[package]] +name = "annotated-types" +version = "0.7.0" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/ee/67/531ea369ba64dcff5ec9c3402f9f51bf748cec26dde048a2f973a4eea7f5/annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89", size = 16081, upload-time = "2024-05-20T21:33:25.928Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/78/b6/6307fbef88d9b5ee7421e68d78a9f162e0da4900bc5f5793f6d3d0e34fb8/annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53", size = 13643, upload-time = "2024-05-20T21:33:24.1Z" }, +] + [[package]] name = "colorama" version = "0.4.6" @@ -13,8 +22,12 @@ wheels = [ [[package]] name = "datashield" -version = "0.2.0" +version = "0.3.0" source = { 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