Merge pull request #256 from FAIRDataPipeline/feature/address_on_local

Feature/address on local

.gitignore

@@ -157,4 +157,10 @@ token.txt
 !/.github/*
 
 # data_store
-/data_store 
+/data_store 
+
+# Mac OS
+.DS_Store
+
+# Coverage
+cov.xml

fair/cli.py

@@ -324,14 +324,16 @@ def install(debug: bool, force: bool, directory: str, version: str):
 @registry.command()
 @click.option("--debug/--no-debug", help="Run in debug mode", default=False)
 @click.option("--port", help="port on which to run registry", default=8000)
-def start(debug: bool, port: int) -> None:
+@click.option("--address", help="Address on which to run registry", default="127.0.0.1")
+def start(debug: bool, port: int, address: str) -> None:
     """Start the local registry server"""
     try:
         fdp_session.FAIR(
             os.getcwd(),
             server_mode=fdp_svr.SwitchMode.USER_START,
             debug=debug,
             server_port=port,
+            server_address=address
         )
     except fdp_exc.FAIRCLIException as e:
         if debug:

fair/common.py

@@ -38,12 +38,15 @@
 import enum
 import os
 import pathlib
+import logging
 
 import git
 import yaml
 
 import fair.exceptions as fdp_exc
 
+_logger = logging.getLogger("FAIRDataPipeline.Common")
+
 USER_FAIR_DIR = os.path.join(pathlib.Path.home(), ".fair")
 FAIR_CLI_CONFIG = "cli-config.yaml"
 USER_CONFIG_FILE = "config.yaml"
@@ -145,6 +148,23 @@ def registry_session_port_file(registry_dir: str = None) -> str:
         registry_dir = registry_home()
     return os.path.join(registry_dir, "session_port.log")
 
+def registry_session_address_file(registry_dir: str = None) -> str:
+    """Retrieve the location of the registry session port file
+
+    Parameters
+    ----------
+    registry_dir : str, optional
+        registry directory, by default None
+
+    Returns
+    -------
+    str
+        path to registry port session file
+    """
+    if not registry_dir:
+        registry_dir = registry_home()
+    return os.path.join(registry_dir, "session_address.log")
+
 
 def registry_session_port(registry_dir: str = None) -> int:
     """Retrieve the registry session port
@@ -164,6 +184,33 @@ def registry_session_port(registry_dir: str = None) -> int:
     """
     return int(open(registry_session_port_file(registry_dir)).read().strip())
 
+def registry_session_address(registry_dir: str = None) -> str:
+    """Retrieve the registry session address
+
+    Unlike 'get_local_address' within the configuration module, this retrieves the
+    port number from the file generated by the registry itself
+
+    Parameters
+    ----------
+    registry_dir : str, optional
+        registry directory, by default None
+
+    Returns
+    -------
+    str
+        current/most recent address used to launch the registry
+    """
+    if not os.path.exists(registry_session_address_file(registry_dir)):
+        _logger.warning("Session Address file not found, please make sure your registry is up-to-date")
+        _logger.info("Using 127.0.0.1")
+        return "127.0.0.1"
+
+    _address = open(registry_session_address_file(registry_dir)).read().strip()
+    if _address != "0.0.0.0":
+        return _address
+    else:
+        return "127.0.0.1"
+
 
 def staging_cache(user_loc: str) -> str:
     """Location of staging cache for the given repository"""

fair/configuration/__init__.py

@@ -438,18 +438,10 @@ def get_local_port(local_uri: str = None) -> int:
 
 def update_local_port() -> str:
     """Updates the local port in the global configuration from the session port file"""
-    # If the global configuration does not exist or is empty do nothing
-    if (
-        not os.path.exists(fdp_com.global_fdpconfig())
-        or not read_global_fdpconfig()
-    ):
-        _local_uri = fdp_com.DEFAULT_LOCAL_REGISTRY_URL
-    else:
-        _local_uri = get_local_uri()
-    _old_local_port = get_local_port()
     _current_port = fdp_com.registry_session_port()
+    _current_address = fdp_com.registry_session_address()
 
-    _new_url = _local_uri.replace(f":{_old_local_port}", f":{_current_port}")
+    _new_url = f'http://{_current_address}:{_current_port}/api/'
 
     if os.path.exists(fdp_com.global_fdpconfig()) and read_global_fdpconfig():
         _glob_conf = read_global_fdpconfig()

fair/identifiers.py

@@ -28,13 +28,11 @@
 ID_URIS = {
     "orcid": "https://orcid.org/",
     "ror": "https://ror.org/",
-    "grid": "https://www.grid.ac/institutes/",
 }
 
 QUERY_URLS = {
     "orcid": "https://pub.orcid.org/v2.0/",
     "ror": "https://api.ror.org/organizations?query=",
-    "grid": "https://www.grid.ac/institutes/",
 }
 
 
@@ -89,29 +87,15 @@ def check_ror(ror: str) -> typing.Dict:
         metadata from the given ID
     """
 
-    _url = f"{QUERY_URLS['ror']}{ror}"
-    _response = requests.get(_url)
-
-    _result_dict: typing.Dict[str, typing.Any] = {}
-
-    if _response.status_code != 200:
-        return _result_dict
-
-    if _response.json()["number_of_results"] == 0:
-        return _result_dict
-
-    _name = _response.json()["items"][0]["name"]
-    _result_dict["name"] = _name
-    _result_dict["family_name"] = _name
-    _result_dict["given_names"] = None
-    _result_dict["ror"] = ror
-    _result_dict["uri"] = f'{ID_URIS["ror"]}{ror}'
+    _result_dict = _check_generic_ror(ror)
+    if _result_dict:
+        _result_dict["ror"] = ror
 
     return _result_dict
 
 
 def check_grid(grid_id: str) -> typing.Dict:
-    """Checks if valid GRID ID using GRID public api
+    """Checks if valid GRID ID using ROR (https://ror.org/) public api
     Parameters
     ----------
     grid_id : str
@@ -121,21 +105,43 @@ def check_grid(grid_id: str) -> typing.Dict:
     typing.Dict
         metadata from the given ID
     """
-    _header = {"Accept": "application/json"}
-    _response = requests.get(f'{QUERY_URLS["grid"]}{grid_id}', headers=_header)
+    _result_dict = _check_generic_ror(f'"{grid_id}"')
+    if _result_dict:
+        _result_dict["grid"] = grid_id
+
+    return _result_dict
+
+def _check_generic_ror(id: str) -> typing.Dict:
+    """Checks if valid ROR using ROR public api
+
+    Parameters
+    ----------
+    ror : str
+        ROR to be checked
+
+    Returns
+    -------
+    typing.Dict
+        metadata from the given ID
+    """
+
+    _url = f"{QUERY_URLS['ror']}{id}"
+    _response = requests.get(_url)
 
     _result_dict: typing.Dict[str, typing.Any] = {}
 
     if _response.status_code != 200:
         return _result_dict
 
-    _name = _response.json()["institute"]["name"]
+    if _response.json()["number_of_results"] == 0:
+        return _result_dict
 
+    _id = _response.json()["items"][0]["id"]
+    _name = _response.json()["items"][0]["name"]
     _result_dict["name"] = _name
     _result_dict["family_name"] = _name
     _result_dict["given_names"] = None
-    _result_dict["grid"] = grid_id
-    _result_dict["uri"] = f'{ID_URIS["grid"]}{grid_id}'
+    _result_dict["uri"] = _id
 
     return _result_dict
 

fair/registry/server.py

@@ -95,7 +95,7 @@ def check_server_running(local_uri: str = None) -> bool:
 
 
 def launch_server(
-    port: int = 8000, registry_dir: str = None, verbose: bool = False
+    port: int = 8000, registry_dir: str = None, verbose: bool = False, address: str = "127.0.0.1"
 ) -> int:
     """Start the registry server.
 
@@ -122,7 +122,9 @@ def launch_server(
             " is the FAIR data pipeline properly installed on this system?"
         )
 
-    _cmd = [_server_start_script, "-p", f"{port}"]
+    _cmd = [_server_start_script, "-p", f"{port}", "-a", f"{address}"]
+
+    os.environ["FAIR_ALLOWED_HOSTS"] = address if not "FAIR_ALLOWED_HOSTS" in os.environ else os.environ["FAIR_ALLOWED_HOSTS"] + f",{address}"
 
     logger.debug("Launching server with command '%s'", " ".join(_cmd))
 
@@ -345,7 +347,7 @@ def install_registry(
 
     logger.debug("Using reference '%s' for registry checkout", reference)
 
-    _candidates = [t.name for t in _repo.tags + _repo.heads]
+    _candidates = [t.name for t in _repo.tags + _repo.heads + _repo.remote().refs]
 
     if reference not in _candidates:
         raise fdp_exc.RegistryError(

fair/session.py

@@ -80,6 +80,7 @@ def __init__(
         debug: bool = False,
         server_mode: fdp_serv.SwitchMode = fdp_serv.SwitchMode.NO_SERVER,
         server_port: int = 8000,
+        server_address: str = "127.0.0.1",
         allow_dirty: bool = False,
         testing: bool = False,
         local: bool = False,
@@ -177,7 +178,7 @@ def __init__(
 
         self._load_configurations()
 
-        self._setup_server(server_port)
+        self._setup_server(server_port, server_address)
 
     def purge(
         self,
@@ -242,15 +243,15 @@ def purge(
             if os.path.exists(_global_dirs):
                 shutil.rmtree(_global_dirs)
 
-    def _setup_server(self, port: int) -> None:
+    def _setup_server(self, port: int, address: str) -> None:
         """Start or stop the server if required"""
         self._logger.debug(
             f"Running server setup for run mode {self._run_mode}"
         )
         if self._run_mode == fdp_serv.SwitchMode.CLI:
-            self._setup_server_cli_mode(port)
+            self._setup_server_cli_mode(port, address)
         elif self._run_mode == fdp_serv.SwitchMode.USER_START:
-            self._setup_server_user_start(port)
+            self._setup_server_user_start(port, address)
         elif self._run_mode in [
             fdp_serv.SwitchMode.USER_STOP,
             fdp_serv.SwitchMode.FORCE_STOP,
@@ -278,7 +279,7 @@ def _stop_server(self) -> None:
             force=self._run_mode == fdp_serv.SwitchMode.FORCE_STOP,
         )
 
-    def _setup_server_cli_mode(self, port: int) -> None:
+    def _setup_server_cli_mode(self, port: int, address: str) -> None:
         self.check_is_repo()
         _cache_addr = os.path.join(
             fdp_com.session_cache_dir(), f"{self._session_id}.run"
@@ -288,7 +289,7 @@ def _setup_server_cli_mode(self, port: int) -> None:
         # If there are no session cache files start the server
         if not glob.glob(os.path.join(fdp_com.session_cache_dir(), "*.run")):
             self._logger.debug("No sessions found, launching server")
-            fdp_serv.launch_server(port=port)
+            fdp_serv.launch_server(port=port, address=address)
 
         self._logger.debug(f"Creating new session #{self._session_id}")
 
@@ -301,7 +302,7 @@ def _setup_server_cli_mode(self, port: int) -> None:
         # Create new session cache file
         pathlib.Path(_cache_addr).touch()
 
-    def _setup_server_user_start(self, port: int) -> None:
+    def _setup_server_user_start(self, port: int, address: str) -> None:
         if not os.path.exists(fdp_com.session_cache_dir()):
             os.makedirs(fdp_com.session_cache_dir())
 
@@ -319,7 +320,7 @@ def _setup_server_user_start(self, port: int) -> None:
             )
         click.echo("Starting local registry server")
         pathlib.Path(_cache_addr).touch()
-        fdp_serv.launch_server(port=port, verbose=True)
+        fdp_serv.launch_server(port=port, verbose=True, address=address)
 
     def _pre_job_setup(self, remote: str = None) -> None:
         self._logger.debug("Running pre-job setup")

tests/test_identifiers.py

@@ -12,20 +12,28 @@ def test_check_orcid():
     assert _data["orcid"] == "0000-0002-6773-1049"
     assert not fdp_id.check_orcid("notanid!")
 
+@pytest.mark.faircli_ids
+def test_check_generic_ror():
+    _data = fdp_id._check_generic_ror("049s0ch10")
+    assert _data["name"] == "Rakon (France)" == _data["family_name"]
+    assert not "ror" in _data
+    assert not "grid" in _data
+    assert not fdp_id.check_ror("notanid!")
 
 @pytest.mark.faircli_ids
 def test_check_ror():
     _data = fdp_id.check_ror("049s0ch10")
     assert _data["name"] == "Rakon (France)" == _data["family_name"]
     assert _data["ror"] == "049s0ch10"
-    assert not fdp_id.check_grid("notanid!")
-
+    assert _data['uri'] == "https://ror.org/049s0ch10"
+    assert not fdp_id.check_ror("notanid!")
 
 @pytest.mark.faircli_ids
 def test_check_grid():
     _data = fdp_id.check_grid("grid.438622.9")
     assert _data["name"] == "Rakon (France)" == _data["family_name"]
     assert _data["grid"] == "grid.438622.9"
+    assert _data['uri'] == "https://ror.org/049s0ch10"
     assert not fdp_id.check_grid("notanid!")