Source code for openghg.objectstore._local_store

import glob
import json
import os
import threading
import warnings
from pathlib import Path
import shutil
from typing import Dict, List, Optional, Union
from uuid import uuid4
import logging
import pyvis
from openghg.types import ObjectStoreError

rlock = threading.RLock()

__all__ = [

logger = logging.getLogger("openghg.objectstore")
logger.setLevel(logging.DEBUG)  # Have to set level for logger as well as handler

[docs]def get_tutorial_store_path() -> Path: """Get the path to the local tutorial store Returns: pathlib.Path: Path of tutorial store """ return get_local_objectstore_path() / "tutorial_store"
# @lru_cache
[docs]def get_local_objectstore_path() -> Path: """Read Returns: pathlib.Path: Path of object store """ from openghg.util import read_local_config config = read_local_config() object_store_path = Path(config["object_store"]["local_store"]) return object_store_path
[docs]def get_all_object_names(bucket: str, prefix: Optional[str] = None, without_prefix: bool = False) -> List: """Returns the names of all objects in the passed bucket Args: bucket: Bucket path prefix: Prefix for keys without_prefix: If True don't use prefix Returns: list: List of object names """ root = bucket if prefix is not None: root = f"{bucket}/{prefix}" root_len = len(bucket) + 1 if without_prefix is not None: prefix_len = len(str(prefix)) subdir_names = glob.glob(f"{root}*") object_names = [] while True: names = subdir_names subdir_names = [] for name in names: if name.endswith("._data"): # remove the ._data at the end name = name[root_len:-6] while name.endswith("/"): name = name[0:-1] if without_prefix: name = name[prefix_len:] while name.startswith("/"): name = name[1:] if len(name) > 0: object_names.append(name) elif os.path.isdir(name): subdir_names += glob.glob(f"{name}/*") if len(subdir_names) == 0: break return object_names
[docs]def delete_object(bucket: str, key: str) -> None: """Remove object at key in bucket Args: bucket: Bucket path key: Key to data in bucket Returns: None """ key = f"{bucket}/{key}._data" try: os.remove(key) except FileNotFoundError: pass
[docs]def get_object_names(bucket: str, prefix: Optional[str] = None) -> List[str]: """List all the keys in the object store Args: bucket: Bucket containing data Returns: list: List of keys in object store """ return get_all_object_names(bucket=bucket, prefix=prefix)
[docs]def get_object(bucket: str, key: str) -> bytes: """Gets the object at key in the passed bucket Args: bucket: Bucket containing data key: Key for data in bucket Returns: bytes: Binary data from the store """ with rlock: filepath = Path(f"{bucket}/{key}._data") if filepath.exists(): return filepath.read_bytes() else: raise ObjectStoreError(f"No object at key '{key}'")
[docs]def set_object(bucket: str, key: str, data: bytes) -> None: """Store data in bucket at key Args: bucket: Bucket path key: Key to store data in bucket data: Data in string form Returns: None """ filename = f"{bucket}/{key}._data" with rlock: try: with open(filename, "wb") as f: f.write(data) except FileNotFoundError: dir = "/".join(filename.split("/")[0:-1]) os.makedirs(dir, exist_ok=True) with open(filename, "wb") as f: f.write(data)
[docs]def set_object_from_json(bucket: str, key: str, data: Union[str, Dict]) -> None: """Set JSON data in the object store Args: bucket: Bucket for data storage key: Key for data in bucket data: JSON serialised data string Returns: None """ data_bytes = json.dumps(data).encode("utf-8") set_object(bucket=bucket, key=key, data=data_bytes)
[docs]def set_object_from_file(bucket: str, key: str, filename: Union[str, Path]) -> None: """Set the contents of file at filename to key in bucket Args: bucket: Bucket path key: Key to for data filename (str, pathlib.Path): Filename/path Returns: None """ set_object(bucket=bucket, key=key, data=open(filename, "rb").read())
[docs]def get_object_from_json(bucket: str, key: str) -> Dict[str, Union[str, Dict]]: """Return an object constructed from JSON stored at key. Args: bucket: Bucket containing data key: Key for data in bucket Returns: dict: Dictionary """ data: Union[str, bytes] = get_object(bucket, key).decode("utf-8") data_dict: Dict = json.loads(data) return data_dict
[docs]def exists(bucket: str, key: str) -> bool: """Checks if there is an object in the object store with the given key Args: bucket: Bucket containing data key: Prefix for key in object store Returns: bool: True if key exists in store """ names = get_all_object_names(bucket=bucket, prefix=key) return len(names) > 0
[docs]def get_bucket() -> str: """Find and return the local object store path (bucket) Returns: str: Path to object store """ import os tutorial_store = os.getenv("OPENGHG_TUT_STORE") if tutorial_store is not None: return str(get_tutorial_store_path()) openghg_env = os.getenv("OPENGHG_PATH") if openghg_env is not None: warnings.warn( "Use of the OPENGHG_PATH environment variable is deprecated and will be ignored in coming versions." + "If you want to set a specific object" + " store path please use the configuration file. See", category=DeprecationWarning, ) return openghg_env local_store = get_local_objectstore_path() return str(local_store)
def clear_object_store() -> None: """Delete the object store. This will only delete a local object store and not a group level or other store. You will be asked for input to confirm the path. Returns: None """ local_store = str(get_local_objectstore_path()) logger.warning(f"You have requested to delete {local_store}.") confirmed_path = input("Please enter the full path of the store: ") if confirmed_path == local_store: shutil.rmtree(local_store, ignore_errors=True) else: logger.warning("Cannot delete object store.")
[docs]def query_store() -> Dict: """Create a dictionary that can be used to visualise the object store Returns: dict: Dictionary for data to be shown in force graph """ from import ObsSurface from import Datasource obs = ObsSurface.load() datasource_uuids = obs.datasources() datasources = (Datasource.load(uuid=uuid, shallow=True) for uuid in datasource_uuids) data = {} for d in datasources: metadata = d.metadata() result = { "site": metadata["site"], "species": metadata["species"], "instrument": metadata.get("instrument", "Unknown"), "network": metadata.get("network", "Unknown"), "inlet": metadata.get("inlet", "Unknown"), } data[d.uuid()] = result return data
[docs]def visualise_store() -> """View the object store using a pyvis force graph. This function should only be called from within a notebook Returns: """ raise NotImplementedError from addict import Dict as aDict data = query_store() net ="800px", "100%", notebook=True) net.force_atlas_2based() # Create the ObsSurface node net.add_node(0, label="Surface Observations", color="#4e79a7", value=5000) network_split = aDict() for key, value in data.items(): # Iterate over Datasources to select the networks network = value["network"] site = value["site"] inlet = value["inlet"] network_split[network][site][inlet][key] = value for network, sites in network_split.items(): network_name = network.upper() net.add_node(network, label=network_name, color="#59a14f", value=2500) net.add_edge(source=0, to=network) # Then we want a subnode for each site for site, site_data in sites.items(): # Don't want to use a site here as a site might be in multiple networks site_name = site.upper() site_id = str(uuid4()) net.add_node(site_id, label=site_name, color="#e15759", value=1000) net.add_edge(source=network, to=site_id) for inlet, inlet_data in site_data.items(): inlet_name = str(inlet).lower() inlet_id = str(uuid4()) net.add_node(n_id=inlet_id, label=inlet_name, color="#808080", value=500) net.add_edge(source=site_id, to=inlet_id) # Now for each site create the datasource nodes for uid, datasource in inlet_data.items(): species = datasource["species"] instrument = datasource["instrument"].upper() label = f"{species.upper()} {instrument}" title = "\n".join( [ f"Site: {site.upper()}", f"Species : {species.upper()}", f"Instrument: {instrument}", ] ) net.add_node(n_id=uid, label=label, title=title, color="#f28e2b", value=100) net.add_edge(source=inlet_id, to=uid) return"openghg_objstore.html")