diff --git a/.gitignore b/.gitignore index 41e29a2..8d8939a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,6 @@ +# OpenSAMPL data paths +archive/ +ntp-snapshots/ # Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] diff --git a/README.md b/README.md index f67f9ae..aaddde5 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,7 @@ python tools for adding clock data to a timescale db. ### Installation -1. Ensure you have Python 3.9 or higher installed +1. Ensure you have Python 3.10 or higher installed 2. Pip install the latest version of opensampl: ```bash pip install opensampl @@ -234,4 +234,3 @@ adva_mask_margin: 0 # Mask margin - Table relationships are maintained through UUID references - Geographic coordinates use WGS84 projection (SRID 4326) by default - Boolean fields (public) are optional and can be null - diff --git a/docs/getting-started/installation.md b/docs/getting-started/installation.md index 982c177..c74d434 100644 --- a/docs/getting-started/installation.md +++ b/docs/getting-started/installation.md @@ -2,7 +2,7 @@ ## Installation for Users -1. Ensure you have Python 3.9 or higher installed +1. Ensure you have Python 3.10 or higher installed 2. Pip install the latest version of openSAMPL: ```bash pip install opensampl diff --git a/opensampl/cli.py b/opensampl/cli.py index 91f2369..3137c44 100644 --- a/opensampl/cli.py +++ b/opensampl/cli.py @@ -9,7 +9,7 @@ import os import sys from pathlib import Path -from typing import Literal, Optional, Union +from typing import Literal import click import yaml @@ -35,7 +35,7 @@ """ -def load_config(env_file: Optional[str] = None) -> CLIConfig: +def load_config(env_file: str | None = None) -> CLIConfig: """ Load the configuration settings @@ -64,7 +64,7 @@ def load_config(env_file: Optional[str] = None) -> CLIConfig: class CaseInsensitiveGroup(click.Group): """Defines Click group options as case-insensitive. By default, click groups are case-sensitive.""" - def get_command(self, ctx: click.Context, cmd_name: str) -> Optional[click.Command]: # noqa: ARG002 + def get_command(self, ctx: click.Context, cmd_name: str) -> click.Command | None: # noqa: ARG002 """Normalize command name to lower case""" cmd_name = cmd_name.lower() # Match against lowercased command names @@ -200,7 +200,7 @@ def collect(): collect.add_command(_vend.get_collect_cli_command(), name=vendor.name) -def path_or_string(value: str) -> Union[dict, list]: +def path_or_string(value: str) -> dict | list: """Get content from a file or use the string directly""" # Get content - either from file or use the string directly content = value @@ -236,9 +236,7 @@ def path_or_string(value: str) -> Union[dict, list]: ) @click.argument("table_name", type=click.Choice(get_table_names())) @click.argument("filepath", type=path_or_string) -def table_load( - filepath: Union[dict, list], table_name: str, if_exists: Literal["update", "error", "replace", "ignore"] -): +def table_load(filepath: dict | list, table_name: str, if_exists: Literal["update", "error", "replace", "ignore"]): r""" Perform a Table load into the database. diff --git a/opensampl/collect/cli.py b/opensampl/collect/cli.py index e65df6e..6a07e69 100644 --- a/opensampl/collect/cli.py +++ b/opensampl/collect/cli.py @@ -1,7 +1,7 @@ """Consolidated CLI entry point for opensampl.collect tools.""" import sys -from typing import Literal, Optional +from typing import Literal import click from loguru import logger @@ -84,8 +84,8 @@ def tp4100( port: int, output_dir: str, duration: int, - channels: Optional[list[str]], - metrics: Optional[list[str]], + channels: list[str] | None, + metrics: list[str] | None, method: Literal["chart_data", "download_file"], save_full_status: bool, verbose: bool, diff --git a/opensampl/collect/microchip/tp4100/__init__.py b/opensampl/collect/microchip/tp4100/__init__.py index d2434d0..9246439 100644 --- a/opensampl/collect/microchip/tp4100/__init__.py +++ b/opensampl/collect/microchip/tp4100/__init__.py @@ -7,7 +7,7 @@ """ from dataclasses import dataclass -from typing import ClassVar, Optional +from typing import ClassVar @dataclass @@ -76,7 +76,7 @@ class MonitoringConfig: channel_str: str ids: list[int] metrics: list[MetricInfo] - default_download: Optional[dict] = None + default_download: dict | None = None @property def download_path(self): @@ -90,7 +90,7 @@ def download_path(self): return f"perfmon_{self.channel_str}_stat" def download_payload( - self, download: Optional[dict] = None, which_id: int = 1, down_metric: MetricInfo = MONITOR_METRIC.TE + self, download: dict | None = None, which_id: int = 1, down_metric: MetricInfo = MONITOR_METRIC.TE ): """ Generate payload for data download requests. diff --git a/opensampl/collect/microchip/tp4100/collect_4100.py b/opensampl/collect/microchip/tp4100/collect_4100.py index f3de6ba..20de8f4 100644 --- a/opensampl/collect/microchip/tp4100/collect_4100.py +++ b/opensampl/collect/microchip/tp4100/collect_4100.py @@ -11,7 +11,7 @@ from datetime import datetime, timezone from pathlib import Path from pprint import pformat -from typing import Any, Literal, Optional +from typing import Any, Literal import pandas as pd import requests @@ -44,8 +44,8 @@ def __init__( port: int = 443, output_dir: str = "./output", duration: int = 600, - channels: Optional[list[str]] = None, - metrics: Optional[list[str]] = None, + channels: list[str] | None = None, + metrics: list[str] | None = None, method: Literal["chart_data", "download_file"] = "chart_data", save_full_status: bool = False, ): @@ -171,7 +171,7 @@ def collect_readings(self): elif self.method == "download_file": self.download_files(request_tpl) - def get_filename(self, detail: Optional[str] = None, extension: str = ".txt"): + def get_filename(self, detail: str | None = None, extension: str = ".txt"): """ Generate timestamped filename for probe connection @@ -194,7 +194,7 @@ def get_filename(self, detail: Optional[str] = None, extension: str = ".txt"): return filename def collect_chart_data( - self, request_key: tuple[MonitoringConfig, int, MetricInfo], download_dict: Optional[dict[str, Any]] = None + self, request_key: tuple[MonitoringConfig, int, MetricInfo], download_dict: dict[str, Any] | None = None ): """ Collect chart data for a specific metric and channel. @@ -271,7 +271,7 @@ def format_utc_second(tai_sec: str, utc_offset: str) -> datetime: df.to_csv(new_file, mode="a", index=False) def download_files( - self, request_key: tuple[MonitoringConfig, int, MetricInfo], download_dict: Optional[dict[str, Any]] = None + self, request_key: tuple[MonitoringConfig, int, MetricInfo], download_dict: dict[str, Any] | None = None ): """ Download data files directly from the device. @@ -341,8 +341,8 @@ def main( port: int = 443, output_dir: str = "./output", duration: int = 600, - channels: Optional[list[str]] = None, - metrics: Optional[list[str]] = None, + channels: list[str] | None = None, + metrics: list[str] | None = None, method: Literal["chart_data", "download_file"] = "chart_data", save_full_status: bool = False, ): diff --git a/opensampl/collect/microchip/twst/context.py b/opensampl/collect/microchip/twst/context.py index 688a39e..3d4f2fc 100644 --- a/opensampl/collect/microchip/twst/context.py +++ b/opensampl/collect/microchip/twst/context.py @@ -9,7 +9,7 @@ import textwrap from datetime import datetime, timezone from types import SimpleNamespace -from typing import Any, Optional +from typing import Any import yaml from loguru import logger @@ -54,7 +54,7 @@ def finished_ok(line: str) -> bool: return re.match(r"^\[OK\]", line) is not None @staticmethod - def finished_error(line: str) -> tuple[bool, Optional[str]]: + def finished_error(line: str) -> tuple[bool, str | None]: """ Check if a command completed with an error. diff --git a/opensampl/collect/microchip/twst/generate_twst_files.py b/opensampl/collect/microchip/twst/generate_twst_files.py index 5f145dc..da15612 100644 --- a/opensampl/collect/microchip/twst/generate_twst_files.py +++ b/opensampl/collect/microchip/twst/generate_twst_files.py @@ -24,7 +24,6 @@ import csv import time from pathlib import Path -from typing import Optional from loguru import logger @@ -57,7 +56,7 @@ def collect_files( status_port: int = 1900, output_dir: str = "./output", dump_interval: int = 300, - total_duration: Optional[int] = None, + total_duration: int | None = None, ): """ Continuously collect blocks of modem measurements and save to timestamped CSV files. diff --git a/opensampl/collect/microchip/twst/readings.py b/opensampl/collect/microchip/twst/readings.py index 622cce3..02fb712 100644 --- a/opensampl/collect/microchip/twst/readings.py +++ b/opensampl/collect/microchip/twst/readings.py @@ -6,7 +6,6 @@ """ import asyncio -from typing import Optional from loguru import logger @@ -23,7 +22,7 @@ class ModemStatusReader(ModemReader): status readings over a specified duration. """ - def __init__(self, host: str, duration: int = 60, keys: Optional[list[str]] = None, port: int = 1900): + def __init__(self, host: str, duration: int = 60, keys: list[str] | None = None, port: int = 1900): """ Initialize ModemStatusReader. diff --git a/opensampl/collect/modem.py b/opensampl/collect/modem.py index 95b62cc..d602aa0 100644 --- a/opensampl/collect/modem.py +++ b/opensampl/collect/modem.py @@ -5,9 +5,9 @@ for interfacing with modems via telnet. """ +from collections.abc import Callable from contextlib import asynccontextmanager from functools import wraps -from typing import Callable, Optional from loguru import logger @@ -36,7 +36,7 @@ def require_conn(method: Callable): """ @wraps(method) - async def wrapper(self: "ModemReader", *args: list, **kwargs: dict) -> Optional[Callable]: + async def wrapper(self: "ModemReader", *args: list, **kwargs: dict) -> Callable | None: if not getattr(self, "open", False): raise RuntimeError( "Telnet connection not active: reader/writer cannot be used outside of 'async with connect()'" @@ -72,8 +72,8 @@ def __init__( self.host = host self.port = port self.encoding = encoding - self.reader: Optional[telnetlib3.TelnetReader] = None - self.writer: Optional[telnetlib3.TelnetWriter] = None + self.reader: telnetlib3.TelnetReader | None = None + self.writer: telnetlib3.TelnetWriter | None = None self.open: bool = False @asynccontextmanager diff --git a/opensampl/config/base.py b/opensampl/config/base.py index aa2af28..145b1f5 100644 --- a/opensampl/config/base.py +++ b/opensampl/config/base.py @@ -6,7 +6,7 @@ """ from pathlib import Path -from typing import Any, Optional +from typing import Any from dotenv import set_key from loguru import logger @@ -28,21 +28,27 @@ class BaseConfig(BaseSettings): ROUTE_TO_BACKEND: bool = Field( False, description="URL of the backend service when routing is enabled", alias="ROUTE_TO_BACKEND" ) - BACKEND_URL: Optional[str] = Field( + BACKEND_URL: str | None = Field( None, description="URL of the backend service when routing is enabled", alias="BACKEND_URL" ) - DATABASE_URL: Optional[str] = Field(None, description="URL for direct database connections", alias="DATABASE_URL") + DATABASE_URL: str | None = Field(None, description="URL for direct database connections", alias="DATABASE_URL") ARCHIVE_PATH: Path = Field( Path("archive"), description="Default path that files are moved to after they have been processed", alias="ARCHIVE_PATH", ) LOG_LEVEL: str = Field("INFO", description="Log level for opensampl cli", alias="LOG_LEVEL") - API_KEY: Optional[str] = Field(None, description="Access key for interacting with the backend", alias="API_KEY") + API_KEY: str | None = Field(None, description="Access key for interacting with the backend", alias="API_KEY") INSECURE_REQUESTS: bool = Field( False, description="Allow insecure requests to be made to the backend", alias="INSECURE_REQUESTS" ) + ENABLE_GEOLOCATE: bool = Field( + False, + description="Enable geolocate features which extract a location from ip addresses", + alias="ENABLE_GEOLOCATE", + ) + @field_serializer("ARCHIVE_PATH") def convert_to_str(self, v: Path) -> str: """Convert archive path to a string for serialization""" @@ -111,7 +117,7 @@ def set_by_name(self, name: str, value: Any): set_key(self.env_file, name, str(value)) - def save_config(self, values: Optional[list[str]] = None): + def save_config(self, values: list[str] | None = None): """ Save the current env configuration. diff --git a/opensampl/config/server.py b/opensampl/config/server.py index 6478145..16d061b 100644 --- a/opensampl/config/server.py +++ b/opensampl/config/server.py @@ -5,11 +5,12 @@ configuration validation, and settings management. """ +from __future__ import annotations + import shlex from importlib.resources import as_file, files from pathlib import Path -from types import ModuleType -from typing import Any, Union +from typing import TYPE_CHECKING, Any from dotenv import dotenv_values, set_key from loguru import logger @@ -20,8 +21,11 @@ from opensampl.config.base import BaseConfig from opensampl.server import check_command +if TYPE_CHECKING: + from types import ModuleType + -def get_resolved_resource_path(pkg: Union[str, ModuleType], relative_path: str) -> str: +def get_resolved_resource_path(pkg: str | ModuleType, relative_path: str) -> str: """Retrieve the resolved path to a resource in a package.""" resource = files(pkg).joinpath(relative_path) with as_file(resource) as real_path: @@ -35,6 +39,8 @@ class ServerConfig(BaseConfig): COMPOSE_FILE: str = Field(default="", description="Fully resolved path to the Docker Compose file.") + OVERRIDE_FILE: str | None = Field(default=None, description="Override for the compose file") + DOCKER_ENV_FILE: str = Field(default="", description="Fully resolved path to the Docker .env file.") docker_env_values: dict[str, Any] = Field(default_factory=dict, init=False) @@ -54,7 +60,7 @@ def _ignore_in_set(self) -> list[str]: return ignored @model_validator(mode="after") - def get_docker_values(self) -> "ServerConfig": + def get_docker_values(self) -> ServerConfig: """Get the values that the docker containers will use on startup""" self.docker_env_values = dotenv_values(self.DOCKER_ENV_FILE) return self @@ -67,6 +73,14 @@ def resolve_compose_file(cls, v: Any) -> str: return get_resolved_resource_path(opensampl.server, "docker-compose.yaml") return str(Path(v).expanduser().resolve()) + @field_validator("OVERRIDE_FILE", mode="before") + @classmethod + def resolve_override_file(cls, v: Any) -> str: + """Resolve the provided compose file for docker to use, or default to the docker-compose.yaml provided""" + if v: + return str(Path(v).expanduser().resolve()) + return v + @field_validator("DOCKER_ENV_FILE", mode="before") @classmethod def resolve_docker_env_file(cls, v: Any) -> str: @@ -89,6 +103,8 @@ def build_docker_compose_base(self): compose_command = self.get_compose_command() command = shlex.split(compose_command) command.extend(["--env-file", self.DOCKER_ENV_FILE, "-f", self.COMPOSE_FILE]) + if self.OVERRIDE_FILE: + command.extend(["-f", self.OVERRIDE_FILE]) return command def set_by_name(self, name: str, value: Any): diff --git a/opensampl/create/create_vendor.py b/opensampl/create/create_vendor.py index 5663759..0a8d0d6 100644 --- a/opensampl/create/create_vendor.py +++ b/opensampl/create/create_vendor.py @@ -14,7 +14,7 @@ from pathlib import Path from pprint import pformat from string import Template -from typing import Any, Optional, Union +from typing import Any import yaml from loguru import logger @@ -36,8 +36,8 @@ class MetadataField(BaseModel): """ name: str - sqlalchemy_type: Optional[str] = Field(default="Text") - primary_key: Optional[bool] = False + sqlalchemy_type: str | None = Field(default="Text") + primary_key: bool | None = False class DEFAULT_METADATA: # noqa N801 @@ -70,7 +70,7 @@ class VendorConfig(VendorType): metadata_fields: list[MetadataField] @classmethod - def from_config_file(cls, config_path: Union[str, Path]) -> "VendorConfig": + def from_config_file(cls, config_path: str | Path) -> "VendorConfig": """ Convert file config into Config object. diff --git a/opensampl/create/templates/collect_mixin_template.txt b/opensampl/create/templates/collect_mixin_template.txt index 8983309..65b8670 100644 --- a/opensampl/create/templates/collect_mixin_template.txt +++ b/opensampl/create/templates/collect_mixin_template.txt @@ -30,7 +30,7 @@ class $parser_class(BaseProbe, CollectMixin): def __init__(self, input_file: str, **kwargs): """Initialize $parser_class from input file""" - super().__init__(input_file) + super().__init__(input_file, **kwargs) # TODO: parse self.input_file contents or file name to extract ip_address and id to self.probe_key # self.probe_key = ProbeKey(probe_id=..., ip_address=...) diff --git a/opensampl/create/templates/parser_template.txt b/opensampl/create/templates/parser_template.txt index 04be83a..648c618 100644 --- a/opensampl/create/templates/parser_template.txt +++ b/opensampl/create/templates/parser_template.txt @@ -13,7 +13,7 @@ class $parser_class(BaseProbe): def __init__(self, input_file: str, **kwargs): """Initialize $parser_class from input file""" - super().__init__(input_file) + super().__init__(input_file, **kwargs) # TODO: parse self.input_file contents or file name to extract ip_address and id to self.probe_key # self.probe_key = ProbeKey(probe_id=..., ip_address=...) diff --git a/opensampl/db/access_orm.py b/opensampl/db/access_orm.py index 715b6f1..e07f052 100644 --- a/opensampl/db/access_orm.py +++ b/opensampl/db/access_orm.py @@ -3,7 +3,7 @@ import secrets import uuid from datetime import datetime, timezone -from typing import Optional, Union +from typing import Optional from sqlalchemy import Column, DateTime, ForeignKey, Integer, String, Text from sqlalchemy.orm import Session, declarative_base, relationship @@ -53,7 +53,7 @@ class Views(Base): name = Column(Text) @staticmethod - def get_view_by_name(session: Session, name: str) -> Optional[type["Views"]]: + def get_view_by_name(session: Session, name: str) -> type["Views"] | None: """ Get view by name. @@ -81,7 +81,7 @@ class Roles(Base): view_id = Column(Text, ForeignKey("views.view_id")) @staticmethod - def get_role_by_name(session: Session, name: str) -> Optional[type["Roles"]]: + def get_role_by_name(session: Session, name: str) -> type["Roles"] | None: """ Get role by name. @@ -135,7 +135,7 @@ class UserRole(Base): role_id = Column(Text, ForeignKey("roles.role_id"), primary_key=True) -def add_user_role(emails: Union[str, list[str]], role_name: str, session: Session): +def add_user_role(emails: str | list[str], role_name: str, session: Session): """ Add user role to the database. diff --git a/opensampl/db/orm.py b/opensampl/db/orm.py index ee6b374..2e104e6 100644 --- a/opensampl/db/orm.py +++ b/opensampl/db/orm.py @@ -2,7 +2,7 @@ import uuid from datetime import datetime -from typing import Any, Optional +from typing import Any from geoalchemy2 import Geometry, WKTElement from geoalchemy2.shape import to_shape @@ -43,7 +43,7 @@ def convert_value(value: Any) -> Any: return {c.name: convert_value(getattr(self, c.name)) for c in self.__table__.columns} @classmethod - def identifiable_constraint(cls) -> Optional[str]: + def identifiable_constraint(cls) -> str | None: """ Get the name of the unique constraint used for identification. @@ -57,7 +57,7 @@ def identifiable_constraint(cls) -> Optional[str]: """ return None - def resolve_references(self, session: Optional[Session] = None) -> None: # noqa: ARG002 + def resolve_references(self, session: Session | None = None) -> None: # noqa: ARG002 """ Resolve UUIDs for other entries in the database given a unique constraint. @@ -181,6 +181,7 @@ class ProbeMetadata(Base): adva_metadata = relationship("AdvaMetadata", back_populates="probe", uselist=False) microchip_twst_metadata = relationship("MicrochipTWSTMetadata", back_populates="probe", uselist=False) microchip_tp4100_metadata = relationship("MicrochipTP4100Metadata", back_populates="probe", uselist=False) + ntp_metadata = relationship("NtpMetadata", back_populates="probe", uselist=False) # --- CUSTOM PROBE METADATA RELATIONSHIP --- @@ -202,7 +203,7 @@ def __init__(self, **kwargs: Any): self._test_name = test_name @classmethod - def identifiable_constraint(cls) -> Optional[str]: + def identifiable_constraint(cls) -> str | None: """ Get the name of the unique constraint used for identification. @@ -212,7 +213,7 @@ def identifiable_constraint(cls) -> Optional[str]: """ return "uq_probe_metadata_ipaddress_probeid" - def resolve_references(self, session: Optional[Session] = None): + def resolve_references(self, session: Session | None = None): """ Resolve references to location and/or test entries when given just the name. @@ -433,8 +434,30 @@ class MicrochipTP4100Metadata(Base): probe = relationship("ProbeMetadata", back_populates="microchip_tp4100_metadata") +class NtpMetadata(Base): + """NTP Clock Probe specific metadata""" + + __tablename__ = "ntp_metadata" + + probe_uuid = Column(String, ForeignKey("probe_metadata.uuid"), primary_key=True) + mode = Column(Text) + reference = Column(Boolean, comment="Is used as a reference for other probes") + target_host = Column(Text) + target_port = Column(Integer) + sync_status = Column(Text) + leap_status = Column(Text) + reference_id = Column(Text) + observation_sources = Column(JSONB) + collection_id = Column(Text) + collection_ip = Column(Text) + timeout = Column(Float) + additional_metadata = Column(JSONB) + probe = relationship("ProbeMetadata", back_populates="ntp_metadata") + + # --- CUSTOM TABLES --- !! Do not remove line, used as reference when inserting metadata table + # --- TABLE FUNCTIONS --- diff --git a/opensampl/helpers/geolocator.py b/opensampl/helpers/geolocator.py new file mode 100644 index 0000000..adf2be4 --- /dev/null +++ b/opensampl/helpers/geolocator.py @@ -0,0 +1,124 @@ +"""Associate NTP probes with ``castdb.locations`` for the geospatial Grafana dashboard.""" + +from __future__ import annotations + +import ipaddress +import json +import os +import socket +import urllib.request +from typing import TYPE_CHECKING + +from loguru import logger + +from opensampl.load.table_factory import TableFactory + +if TYPE_CHECKING: + from sqlalchemy.orm import Session + + +_GEO_CACHE: dict[str, tuple[float, float, str]] = {} + + +def _env_bool(name: str, default: bool) -> bool: + v = os.getenv(name) + if v is None: + return default + return v.strip().lower() in ("1", "true", "yes", "on") + + +def _default_lab_coords() -> tuple[float, float]: + lat = float(os.getenv("DEFAULT_LAT", "35.9312")) + lon = float(os.getenv("DEFAULT_LON", "-84.3101")) + return lat, lon + + +def _is_private_or_loopback(ip: str) -> bool: + try: + addr = ipaddress.ip_address(ip) + except ValueError: + return True + return bool(addr.is_private or addr.is_loopback or addr.is_link_local or addr.is_reserved) + + +def _lookup_geo_ipapi(ip: str) -> tuple[float, float, str] | None: + if ip in _GEO_CACHE: + return _GEO_CACHE[ip] + url = f"http://ip-api.com/json/{ip}?fields=status,lat,lon,city,country" + try: + with urllib.request.urlopen(url, timeout=4.0) as resp: # noqa: S310 + body = json.loads(resp.read().decode("utf-8")) + except Exception as e: + logger.warning("ip-api geolocation failed for {}: {}", ip, e) + return None + + if body.get("status") != "success" or body.get("lat") is None or body.get("lon") is None: + logger.warning("ip-api returned no coordinates for {}", ip) + return None + + city = body.get("city") or "" + country = body.get("country") or "" + label = ", ".join(x for x in (city, country) if x) + out = (float(body["lat"]), float(body["lon"]), label or ip) + _GEO_CACHE[ip] = out + return out + + +def create_location(session: Session, geolocate_enabled: bool, ip_address: str, geo_override: dict) -> str | None: + """ + Set probe ``name``, ``public``, and ``location_uuid`` on NTP metadata before ``probe_metadata`` insert. + + Uses ``additional_metadata.geo_override`` when present (lat/lon/label). Otherwise resolves the remote + host, uses RFC1918/loopback defaults from env, or ip-api.com for public IPs (HTTP, no API key). + """ + lat: float | None = None + lon: float | None = None + name: str | None = None + + if geo_override.get("lat") is not None and geo_override.get("lon") is not None: + lat = float(geo_override["lat"]) + lon = float(geo_override["lon"]) + + name = geo_override.get("name") + + if geolocate_enabled and lat is None and lon is None: + ip_for_geo = ip_address + try: + ip_for_geo = socket.gethostbyname(ip_address) + except OSError as e: + logger.debug("Could not resolve {}: {}", ip_address, e) + + if _is_private_or_loopback(ip_for_geo): + lat, lon = _default_lab_coords() + else: + geo = _lookup_geo_ipapi(ip_for_geo) + if geo: + lat, lon, _name = geo + name = name or _name + else: + lat, lon = _default_lab_coords() + + loc_factory = TableFactory("locations", session=session) + loc = None + if name: + loc = loc_factory.find_existing({"name": name}) + + if loc is None: + if any(x is None for x in [lat, lon, name]): + logger.warning( + "Skipping location creation for {}: insufficient location data (name={!r}, lat={!r}, lon={!r})", + ip_address, + name, + lat, + lon, + ) + return None + + loc = loc_factory.write( + {"name": name, "lat": lat, "lon": lon, "public": True}, + if_exists="ignore", + ) + + if loc: + return loc.uuid + return None diff --git a/opensampl/load/data.py b/opensampl/load/data.py index 591fb5b..18d8ab2 100644 --- a/opensampl/load/data.py +++ b/opensampl/load/data.py @@ -1,6 +1,6 @@ """Data Factory for defining the unique probe/metric/reference combination to use for Data readings""" -from typing import Any, Optional +from typing import Any from loguru import logger from sqlalchemy.inspection import inspect @@ -25,11 +25,11 @@ class DataFactory: object will also have the database object for any compound references filled as well. """ - probe: Optional[DBProbe] = None - metric: Optional[DBMetricType] = None - db_ref_type: Optional[DBReferenceType] = None - reference: Optional[DBReference] = None - db_compound_reference: Optional[Base] = None + probe: DBProbe | None = None + metric: DBMetricType | None = None + db_ref_type: DBReferenceType | None = None + reference: DBReference | None = None + db_compound_reference: Base | None = None def __init__( self, @@ -37,7 +37,7 @@ def __init__( metric_type: MetricType, reference_type: ReferenceType, session: Session, - compound_key: Optional[dict[str, Any]] = None, + compound_key: dict[str, Any] | None = None, strict: bool = True, ): """ diff --git a/opensampl/load/routing.py b/opensampl/load/routing.py index c1205df..2e602d5 100644 --- a/opensampl/load/routing.py +++ b/opensampl/load/routing.py @@ -1,8 +1,9 @@ """Decorator which ensures we are routing our db operations through a backend if configured, or directly if not.""" import json +from collections.abc import Callable from functools import wraps -from typing import Callable, Literal, Optional +from typing import Literal import requests import requests.exceptions @@ -45,7 +46,7 @@ def decorator(func: Callable) -> Callable: """ @wraps(func) - def wrapper(*args: list, **kwargs: dict) -> Optional[Callable]: + def wrapper(*args: list, **kwargs: dict) -> Callable | None: """ Handle the actual routing logic. diff --git a/opensampl/load/table_factory.py b/opensampl/load/table_factory.py index 0f4a791..f2d9002 100644 --- a/opensampl/load/table_factory.py +++ b/opensampl/load/table_factory.py @@ -1,6 +1,6 @@ """Database table factory for handling CRUD operations with conflict resolution.""" -from typing import Any, Literal, Optional, Union +from typing import Any, Literal from loguru import logger from sqlalchemy import UniqueConstraint, and_, inspect, select @@ -89,7 +89,7 @@ def create_col_filter(self, data: dict[str, Any], cols: list[str]): logger.debug(f"some or all columns from {cols} missing in data") return None - def print_filter_debug(self, filter_expr: Optional[Union[BinaryExpression, BooleanClauseList]], label: str): + def print_filter_debug(self, filter_expr: BinaryExpression | BooleanClauseList | None, label: str): """ Print debug information for a filter expression. @@ -102,7 +102,7 @@ def print_filter_debug(self, filter_expr: Optional[Union[BinaryExpression, Boole compiled = filter_expr.compile(dialect=postgresql.dialect(), compile_kwargs={"literal_binds": True}) logger.debug(f"{label}: {compiled}") - def find_existing(self, data: dict[str, Any]) -> Optional[Base]: + def find_existing(self, data: dict[str, Any]) -> Base | None: """ Find an existing record that matches the provided data. diff --git a/opensampl/load_data.py b/opensampl/load_data.py index f427167..d21f5ce 100644 --- a/opensampl/load_data.py +++ b/opensampl/load_data.py @@ -1,7 +1,7 @@ """Main functionality for loading data into the database""" import json -from typing import Any, Literal, Optional +from typing import Any, Literal import pandas as pd from loguru import logger @@ -10,6 +10,7 @@ from opensampl.config.base import BaseConfig from opensampl.db.orm import Base, ProbeData +from opensampl.helpers.geolocator import create_location from opensampl.load.routing import route from opensampl.load.table_factory import TableFactory from opensampl.metrics import MetricType @@ -25,7 +26,7 @@ def write_to_table( data: dict[str, Any], _config: BaseConfig, if_exists: conflict_actions = "update", - session: Optional[Session] = None, + session: Session | None = None, ): """ Write object to table with configurable behavior for handling conflicts. @@ -79,9 +80,9 @@ def load_time_data( reference_type: ReferenceType, data: pd.DataFrame, _config: BaseConfig, - compound_key: Optional[dict[str, Any]] = None, + compound_key: dict[str, Any] | None = None, strict: bool = True, - session: Optional[Session] = None, + session: Session | None = None, ): """ Write time data to probe_data table @@ -125,9 +126,9 @@ def load_time_data( strict=strict, session=session, ) + probe = data_definition.probe # ty: ignore[possibly-unbound-attribute] probe_readable = ( - data_definition.probe.name # ty: ignore[possibly-unbound-attribute] - or f"{data_definition.probe.ip_address} ({data_definition.probe.probe_id})" # ty: ignore[possibly-unbound-attribute] + probe.name or f"{probe.ip_address} ({probe.probe_id})" # ty: ignore[possibly-unbound-attribute] ) if any(x is None for x in [data_definition.probe, data_definition.metric, data_definition.reference]): @@ -156,11 +157,13 @@ def load_time_data( total_rows = len(records) inserted = result.rowcount # ty: ignore[unresolved-attribute] excluded = total_rows - inserted - - logger.warning( - f"Inserted {inserted}/{total_rows} rows for {probe_readable}; " - f"{excluded}/{total_rows} rejected due to conflicts" - ) + if excluded > 0: + logger.warning( + f"Inserted {inserted}/{total_rows} rows for {probe_readable}; " + f"{excluded}/{total_rows} rejected due to conflicts" + ) + else: + logger.info(f"Inserted {inserted}/{total_rows} rows for {probe_readable}") except Exception as e: # In case of an error, roll back the session @@ -181,7 +184,7 @@ def load_probe_metadata( probe_key: ProbeKey, data: dict[str, Any], _config: BaseConfig, - session: Optional[Session] = None, + session: Session | None = None, ): """Write object to table""" if _config.ROUTE_TO_BACKEND: @@ -199,6 +202,19 @@ def load_probe_metadata( pm_cols = {col.name for col in pm_factory.inspector.columns} probe_info = {k: data.pop(k) for k in list(data.keys()) if k in pm_cols} + location_name = probe_info.pop("location_name", None) + geolocation = ({"name": location_name} if location_name else {}) | probe_info.pop("geolocation", {}) + + if geolocation or _config.ENABLE_GEOLOCATE: + location_uuid = create_location( + session, + geolocate_enabled=_config.ENABLE_GEOLOCATE, + geo_override=geolocation, + ip_address=probe_key.ip_address, + ) + if location_uuid: + probe_info.update({"location_uuid": location_uuid}) + probe_info.update({"probe_id": probe_key.probe_id, "ip_address": probe_key.ip_address, "vendor": vendor.name}) probe = pm_factory.write(data=probe_info, if_exists="update") @@ -214,7 +230,7 @@ def load_probe_metadata( @route("create_new_tables", method="GET") -def create_new_tables(*, _config: BaseConfig, create_schema: bool = True, session: Optional[Session] = None): +def create_new_tables(*, _config: BaseConfig, create_schema: bool = True, session: Session | None = None): """Use the ORM definition to create all tables, optionally creating the schema as well""" if _config.ROUTE_TO_BACKEND: return {"create_schema": create_schema} @@ -227,6 +243,7 @@ def create_new_tables(*, _config: BaseConfig, create_schema: bool = True, sessio session.execute(text(f"CREATE SCHEMA IF NOT EXISTS {Base.metadata.schema}")) session.commit() Base.metadata.create_all(session.bind) + session.commit() except Exception as e: session.rollback() logger.error(f"Error writing to table: {e}") diff --git a/opensampl/metrics.py b/opensampl/metrics.py index 8cc1418..27b6b8a 100644 --- a/opensampl/metrics.py +++ b/opensampl/metrics.py @@ -62,5 +62,70 @@ class METRICS: unit="unknown", value_type=object, ) + DELAY = MetricType( + name="Delay", + description=( + "Round-trip delay (RTD) or Round-Trip Time (RTT). The time in seconds it takes for a data signal to " + "travel from a source to a destination and back, including acknowledgement." + ), + unit="s", + value_type=float, + ) + JITTER = MetricType( + name="Jitter", + description=("Jitter or offset variation in delay in seconds. Represents inconsistent response times."), + unit="s", + value_type=float, + ) + STRATUM = MetricType( + name="Stratum", + description=( + 'Stratum level. Hierarchical layer defining the distance (or "hops") between device and reference.' + ), + unit="level", + value_type=int, + ) + REACHABILITY = MetricType( + name="Reachability", + description=( + "Reachability register (0-255) as a scalar for plotting. Ability of a source node to communicate " + "with a target node." + ), + unit="count", + value_type=float, + ) + DISPERSION = MetricType( + name="Dispersion", + description="Uncertainty in a clock's time relative to its reference source in seconds", + unit="s", + value_type=float, + ) + NTP_ROOT_DELAY = MetricType( + name="NTP Root Delay", + description=( + "Total round-trip network delay from the local system" + " all the way to the primary reference clock (stratum 0)" + ), + unit="s", + value_type=float, + ) + NTP_ROOT_DISPERSION = MetricType( + name="NTP Root Dispersion", + description="The total accumulated clock uncertainty from the local system back to the primary reference clock", + unit="s", + value_type=float, + ) + POLL_INTERVAL = MetricType( + name="Poll Interval", + description="Time between requests sent to a time server in seconds", + unit="s", + value_type=float, + ) + SYNC_HEALTH = MetricType( + name="Sync Health", + description="1.0 if synchronized/healthy, 0.0 otherwise (probe-defined)", + unit="ratio", + value_type=float, + ) # --- CUSTOM METRICS --- !! Do not remove line, used as reference when inserting metric diff --git a/opensampl/mixins/collect.py b/opensampl/mixins/collect.py index 91da293..c7b93d6 100644 --- a/opensampl/mixins/collect.py +++ b/opensampl/mixins/collect.py @@ -2,9 +2,10 @@ import json from abc import ABC, abstractmethod +from collections.abc import Callable from datetime import datetime, timezone from pathlib import Path -from typing import Any, Callable, Optional +from typing import Any import click import pandas as pd @@ -27,15 +28,15 @@ class DataArtifact(BaseModel): value: pd.DataFrame metric: MetricType = METRICS.UNKNOWN reference_type: ReferenceType = REF_TYPES.UNKNOWN - compound_reference: Optional[dict[str, Any]] = None + compound_reference: dict[str, Any] | None = None model_config = ConfigDict(arbitrary_types_allowed=True) class CollectArtifact(BaseModel): """Model for a single probe's collected data""" data: list["CollectMixin.DataArtifact"] - probe_key: Optional[ProbeKey] = None - metadata: Optional[dict] = Field(default_factory=dict) + probe_key: ProbeKey | None = None + metadata: dict | None = Field(default_factory=dict) model_config = ConfigDict(arbitrary_types_allowed=True) @property @@ -58,13 +59,13 @@ class CollectConfig(BaseModel): Attributes: output_dir: When provided, will save collected data as a file to provided directory. - Filename will be automatically generated as {ip_address}_{probe_id}_{vendor}_{timestamp}.txt + Filename will be automatically generated as {vendor}_{ip_address}_{probe_id}_{vendor}_{timestamp}.txt load: Whether to load collected data directly to the database duration: Number of seconds to collect data for """ - output_dir: Optional[Path] = None + output_dir: Path | None = None load: bool = False duration: int = 300 @@ -144,7 +145,7 @@ def _collect_and_save(cls, collect_config: CollectConfig) -> None: @classmethod def filter_files(cls, files: list[Path]) -> list[Path]: """Filter the files found in the input directory when loading this vendor's data files""" - return [f for f in files if f.name.startswith(f"{cls.vendor.parser_class}_") and f.stem == ".txt"] + return [f for f in files if f.name.startswith(f"{cls.vendor.parser_class}_") and f.suffix == ".txt"] @classmethod def load_metadata(cls, probe_key: ProbeKey, metadata: dict) -> None: diff --git a/opensampl/mixins/random_data.py b/opensampl/mixins/random_data.py index 3929e85..99c5f40 100644 --- a/opensampl/mixins/random_data.py +++ b/opensampl/mixins/random_data.py @@ -2,9 +2,10 @@ import random from abc import abstractmethod +from collections.abc import Callable from datetime import datetime, timedelta, timezone from pathlib import Path -from typing import Any, Callable, Optional, Union +from typing import Any import click import numpy as np @@ -25,7 +26,7 @@ class RandomDataConfig(BaseModel): # General configuration num_probes: int = 1 duration_hours: float = 1.0 - seed: Optional[int] = None + seed: int | None = None # Time series parameters sample_interval: float = 1 @@ -37,10 +38,10 @@ class RandomDataConfig(BaseModel): outlier_multiplier: float = 10.0 # Start time (computed at runtime if None) - start_time: Optional[datetime] = None + start_time: datetime | None = None - probe_id: Union[str, None] = None - probe_ip: Optional[str] = None + probe_id: str | None = None + probe_ip: str | None = None @classmethod def _generate_random_ip(cls) -> str: @@ -267,7 +268,7 @@ def _extract_random_data_config(cls, kwargs: dict) -> RandomDataConfig: return cls.RandomDataConfig(**kwargs) @classmethod - def _setup_random_seed(cls, seed: Optional[int]) -> None: + def _setup_random_seed(cls, seed: int | None) -> None: """Set up random seed for reproducible data generation.""" if seed is not None: random.seed(seed) diff --git a/opensampl/server/backend/main.py b/opensampl/server/backend/main.py index a53c5a4..87d3783 100644 --- a/opensampl/server/backend/main.py +++ b/opensampl/server/backend/main.py @@ -5,8 +5,9 @@ import os import sys import time +from collections.abc import Callable from datetime import UTC, datetime, timedelta -from typing import Any, Callable, Optional +from typing import Any import pandas as pd import psycopg2 @@ -102,13 +103,23 @@ def get_keys(): return [] -def validate_api_key(api_key: str = Security(api_key_header)): - """Validate provided API key""" - if not USE_API_KEY: - return None # Security is disabled - if api_key not in get_keys(): - raise HTTPException(status_code=403, detail="Invalid or missing API key") - return api_key +def require_api_key(bootstrap: bool = False): + """Return function to validate api key with or without bootstrap.""" + + def validate_api_key(api_key: str = Security(api_key_header)) -> str | None: + """Validate provided API key""" + if not USE_API_KEY: + return None # Security is disabled + + keys = get_keys() + if not keys and bootstrap: + logger.warning("No API keys configured; allowing bootstrap API key generation") + return None + if api_key not in keys: + raise HTTPException(status_code=403, detail="Invalid or missing API key") + return api_key + + return validate_api_key def get_db(): @@ -145,7 +156,7 @@ async def docs_redirect(): @app.get("/setloglevel") -def set_log_level(newloglevel: str, api_key: str = Depends(validate_api_key)): +def set_log_level(newloglevel: str, api_key: str = Depends(require_api_key())): """Change visible log level in backend container""" newloglevel = newloglevel.upper() logger.configure(handlers=[{"sink": sys.stderr, "level": newloglevel}]) @@ -153,7 +164,7 @@ def set_log_level(newloglevel: str, api_key: str = Depends(validate_api_key)): @app.get("/checkloglevel") -def check_log_level(api_key: str = Depends(validate_api_key)): +def check_log_level(api_key: str = Depends(require_api_key())): """Check which log levels are visible in backend container""" logger.debug("Debug test") logger.info("Info test") @@ -165,7 +176,7 @@ def check_log_level(api_key: str = Depends(validate_api_key)): @app.post("/write_to_table") def write_to_table( - payload: WriteTablePayload, api_key: str = Depends(validate_api_key), session: Session = Depends(get_db) + payload: WriteTablePayload, api_key: str = Depends(require_api_key()), session: Session = Depends(get_db) ): """Write given data to specified table""" try: @@ -190,11 +201,11 @@ def write_to_table( @app.post("/load_time_data") async def load_time_data( # noqa: PLR0912, C901 probe_key_str: str = Form(...), - metric_type_str: Optional[str] = Form(None), - reference_type_str: Optional[str] = Form(None), - compound_key_str: Optional[str] = Form(None), + metric_type_str: str | None = Form(None), + reference_type_str: str | None = Form(None), + compound_key_str: str | None = Form(None), file: UploadFile = File(...), - api_key: str = Depends(validate_api_key), + api_key: str = Depends(require_api_key()), session: Session = Depends(get_db), ): """Load provided data for given probe""" @@ -258,7 +269,7 @@ async def load_time_data( # noqa: PLR0912, C901 @app.post("/load_probe_metadata") def load_probe_metadata( - payload: ProbeMetadataPayload, api_key: str = Depends(validate_api_key), session: Session = Depends(get_db) + payload: ProbeMetadataPayload, api_key: str = Depends(require_api_key()), session: Session = Depends(get_db) ): """Load metadata for given probe""" logger.debug(f"Received payload: {payload.model_dump()}") @@ -289,7 +300,7 @@ def load_probe_metadata( @app.get("/create_new_tables") def create_new_tables( - create_schema: bool = True, api_key: str = Depends(validate_api_key), session: Session = Depends(get_db) + create_schema: bool = True, api_key: str = Depends(require_api_key()), session: Session = Depends(get_db) ): """Update DB based on ORM Tables""" try: @@ -307,7 +318,11 @@ def create_new_tables( @app.get("/gen_api_key") -def generate_api_key(expire_after: Optional[int] = None, session: Session = Depends(get_db)): +def generate_api_key( + expire_after: int | None = None, + api_key: str | None = Depends(require_api_key(bootstrap=True)), + session: Session = Depends(get_db), +): """Generate new API key in the database""" try: new_key = APIAccessKey() diff --git a/opensampl/server/grafana/grafana-dashboards/ntp_dash.json b/opensampl/server/grafana/grafana-dashboards/ntp_dash.json new file mode 100644 index 0000000..345fd8c --- /dev/null +++ b/opensampl/server/grafana/grafana-dashboards/ntp_dash.json @@ -0,0 +1,1412 @@ +{ + "annotations": { + "list": [ + { + "builtIn": 1, + "datasource": { + "type": "grafana", + "uid": "-- Grafana --" + }, + "enable": true, + "hide": true, + "iconColor": "rgba(0, 211, 255, 1)", + "name": "Annotations & Alerts", + "type": "dashboard" + } + ] + }, + "description": "NTP reference path: measurements are relative to OpenSAMPL’s configured default reference (UNKNOWN type) unless you add GNSS-backed probes; timing vs GNSS is not implied for these series.", + "editable": true, + "fiscalYearStartMonth": 0, + "graphTooltip": 0, + "id": 0, + "links": [], + "panels": [ + { + "collapsed": false, + "gridPos": { + "h": 1, + "w": 24, + "x": 0, + "y": 0 + }, + "id": 52, + "panels": [], + "title": "All Probes", + "type": "row" + }, + { + "datasource": { + "type": "datasource", + "uid": "-- Dashboard --" + }, + "fieldConfig": { + "defaults": { + "color": { + "mode": "palette-classic" + }, + "custom": { + "axisBorderShow": false, + "axisCenteredZero": false, + "axisColorMode": "text", + "axisLabel": "", + "axisPlacement": "auto", + "barAlignment": 0, + "barWidthFactor": 0.6, + "drawStyle": "line", + "fillOpacity": 0, + "gradientMode": "none", + "hideFrom": { + "legend": false, + "tooltip": false, + "viz": false + }, + "insertNulls": false, + "lineInterpolation": "linear", + "lineWidth": 1, + "pointSize": 5, + "scaleDistribution": { + "type": "linear" + }, + "showPoints": "auto", + "showValues": false, + "spanNulls": false, + "stacking": { + "group": "A", + "mode": "none" + }, + "thresholdsStyle": { + "mode": "off" + } + }, + "mappings": [], + "thresholds": { + "mode": "absolute", + "steps": [ + { + "color": "green", + "value": 0 + }, + { + "color": "red", + "value": 80 + } + ] + }, + "unit": "ns" + }, + "overrides": [] + }, + "gridPos": { + "h": 9, + "w": 12, + "x": 0, + "y": 1 + }, + "id": 1, + "options": { + "legend": { + "calcs": [], + "displayMode": "list", + "placement": "bottom", + "showLegend": true + }, + "tooltip": { + "hideZeros": false, + "mode": "single", + "sort": "none" + } + }, + "pluginVersion": "12.2.1", + "targets": [ + { + "datasource": { + "type": "datasource", + "uid": "-- Dashboard --" + }, + "panelId": 51, + "refId": "A" + } + ], + "title": "NTP phase offset (Phase Offset metric)", + "transformations": [ + { + "id": "organize", + "options": { + "excludeByName": { + "jitter": true, + "metric_type_uuid": true, + "probe_uuid": true, + "reference_uuid": true, + "stratum": true, + "sync_health": true + }, + "includeByName": {}, + "indexByName": { + "metric_type_uuid": 5, + "probe_name": 0, + "probe_uuid": 3, + "reference_uuid": 4, + "time": 1, + "value": 2 + }, + "renameByName": { + "probe_name": "" + } + } + }, + { + "id": "groupingToMatrix", + "options": { + "columnField": "probe_name", + "rowField": "time", + "valueField": "phase_offset" + } + }, + { + "id": "prepareTimeSeries", + "options": { + "format": "multi" + } + } + ], + "type": "timeseries" + }, + { + "datasource": { + "type": "datasource", + "uid": "-- Dashboard --" + }, + "description": "Remote single-packet paths use a conservative jitter estimate from delay and root dispersion when peer RMS jitter is unavailable; local chrony/ntpq snapshots may supply measured jitter.", + "fieldConfig": { + "defaults": { + "color": { + "mode": "palette-classic" + }, + "custom": { + "axisBorderShow": false, + "axisCenteredZero": false, + "axisColorMode": "text", + "axisLabel": "", + "axisPlacement": "auto", + "barAlignment": 0, + "barWidthFactor": 0.6, + "drawStyle": "line", + "fillOpacity": 0, + "gradientMode": "none", + "hideFrom": { + 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"P55EB97F79F5EB88E" + }, + "fieldConfig": { + "defaults": { + "color": { + "mode": "thresholds" + }, + "custom": { + "align": "auto", + "cellOptions": { + "type": "auto" + }, + "footer": { + "reducers": [] + }, + "hideFrom": { + "viz": false + }, + "inspect": false + }, + "mappings": [], + "thresholds": { + "mode": "absolute", + "steps": [ + { + "color": "green", + "value": 0 + }, + { + "color": "red", + "value": 80 + } + ] + } + }, + "overrides": [] + }, + "gridPos": { + "h": 9, + "w": 24, + "x": 0, + "y": 96 + }, + "id": 51, + "options": { + "cellHeight": "sm", + "frameIndex": 1, + "showHeader": true + }, + "pluginVersion": "12.2.1", + "targets": [ + { + "dataset": "castdb", + "editorMode": "code", + "format": "table", + "rawQuery": true, + "rawSql": "WITH probe_ref AS (\n SELECT\n uuid,\n COALESCE(pm.name, CONCAT(pm.ip_address, ' ', pm.probe_id)) AS probe_name\n FROM castdb.probe_metadata pm\n)\nSELECT\n time_bucket('1 minute'::interval, pd.time AT TIME ZONE 'UTC') AS time,\n pd.probe_uuid,\n pr.probe_name,\n pd.reference_uuid,\n AVG(pd.value::float * 1e9) FILTER (WHERE lower(m.name) = 'phase offset') AS phase_offset,\n AVG(pd.value::float * 1e9) FILTER (WHERE lower(m.name) = 'jitter') AS jitter,\n AVG((pd.value)::float) FILTER (WHERE lower(m.name) = 'stratum') AS stratum,\n AVG((pd.value)::float) FILTER (WHERE lower(m.name) = 'sync health') AS sync_health\nFROM castdb.probe_data pd\nJOIN probe_ref pr\n ON pd.probe_uuid = pr.uuid\nJOIN castdb.metric_type m\n ON pd.metric_type_uuid = m.uuid\nWHERE pd.probe_uuid = ANY(ARRAY[${ntp_probe:sqlstring}]::text[]) AND $__timeFilter(pd.time)\nGROUP BY 1, 2, 3, 4\nORDER BY\n 1, 3;", + "refId": "A", + "sql": { + "columns": [ + { + "parameters": [], + "type": "function" + } + ], + "groupBy": [ + { + "property": { + "type": "string" + }, + "type": "groupBy" + } + ], + "limit": 50 + } + } + ], + "title": "source_panel", + "type": "table" + } + ], + "title": "Reference & source metadata", + "type": "row" + } + ], + "preload": false, + "refresh": "30s", + "schemaVersion": 42, + "tags": [ + "ntp", + "opensampl", + "reference" + ], + "templating": { + "list": [ + { + "current": { + "text": [ + "All" + ], + "value": [ + "$__all" + ] + }, + "datasource": { + "type": "grafana-postgresql-datasource", + "uid": "castdb-datasource" + }, + "definition": "SELECT pm.uuid::text AS __value, COALESCE(pm.name, CONCAT(pm.ip_address, ' ', pm.probe_id)) AS __text FROM castdb.probe_metadata pm WHERE pm.vendor = 'NTP' ORDER BY 2", + "includeAll": true, + "multi": true, + "name": "ntp_probe", + "options": [], + "query": "SELECT pm.uuid::text AS __value, COALESCE(pm.name, CONCAT(pm.ip_address, ' ', pm.probe_id)) AS __text FROM castdb.probe_metadata pm WHERE pm.vendor = 'NTP' ORDER BY 2", + "refresh": 1, + "regex": "", + "sort": 1, + "type": "query" + }, + { + "current": { + "text": "All", + "value": [ + "$__all" + ] + }, + "datasource": { + "type": "grafana-postgresql-datasource", + "uid": "castdb-datasource" + }, + "definition": "SELECT pm.reference_uuid::text AS __value, COALESCE(pm.name, CONCAT(pm.ip_address, ' ', pm.probe_id)) AS __text FROM castdb.reference_probe_metadata pm WHERE pm.vendor = 'NTP' \nUNION ALL\nSELECT r.uuid::text AS __value, rt.\"name\" AS __text FROM castdb.reference r JOIN castdb.reference_type rt ON r.reference_type_uuid = rt.\"uuid\" WHERE rt.\"name\" = 'UNKNOWN';", + "includeAll": true, + "multi": true, + "name": "ntp_reference", + "options": [], + "query": "SELECT pm.reference_uuid::text AS __value, COALESCE(pm.name, CONCAT(pm.ip_address, ' ', pm.probe_id)) AS __text FROM castdb.reference_probe_metadata pm WHERE pm.vendor = 'NTP' \nUNION ALL\nSELECT r.uuid::text AS __value, rt.\"name\" AS __text FROM castdb.reference r JOIN castdb.reference_type rt ON r.reference_type_uuid = rt.\"uuid\" WHERE rt.\"name\" = 'UNKNOWN';", + "refresh": 1, + "regex": "", + "sort": 1, + "type": "query" + } + ] + }, + "time": { + "from": "now-6h", + "to": "now" + }, + "timepicker": {}, + "timezone": "utc", + "title": "NTP probes (NTP server reference path)", + "uid": "ntp-opensampl", + "version": 17 +} \ No newline at end of file diff --git a/opensampl/server/grafana/grafana-dashboards/public-timing-dashboard.json b/opensampl/server/grafana/grafana-dashboards/public-timing-dashboard.json index 687ceae..24b7a6f 100644 --- a/opensampl/server/grafana/grafana-dashboards/public-timing-dashboard.json +++ b/opensampl/server/grafana/grafana-dashboards/public-timing-dashboard.json @@ -338,7 +338,7 @@ "group": [], "metricColumn": "none", "rawQuery": true, - "rawSql": "select\n pm.name as \"Clock\",\n l.name as \"Location Name\",\n l.latitude,\n l.longitude,\n l.campus\nfrom castdb.campus_locations l left join castdb.probe_metadata pm on l.uuid = pm.location_uuid\nwhere pm.uuid in (${clock_name:sqlstring});", + "rawSql": "select\n pm.name as \"Clock\",\n l.name as \"Location Name\",\n l.latitude,\n l.longitude,\n l.campus\nfrom castdb.campus_locations l left join castdb.probe_metadata pm on l.uuid = pm.location_uuid\nwhere (trim('${clock_name:csv}') = '' OR pm.uuid = ANY(string_to_array(trim('${clock_name:csv}'), ',')));", "refId": "ClockProbes", "select": [ [ @@ -379,13 +379,13 @@ { "datasource": { "type": "grafana-postgresql-datasource", - "uid": "P55EB97F79F5EB88E" + "uid": "castdb-datasource" }, "editorMode": "code", "format": "table", "hide": false, "rawQuery": true, - "rawSql": "SELECT\n l.latitude,\n l.longitude,\n l.campus,\n sum(\n CASE\n when pm.public = True and pm.vendor in ('ADVA', 'MicrochipTP4100') then 1 else 0\n end \n ) as visible_clocks,\n sum(\n CASE\n when pm.uuid in (${clock_name:sqlstring}) then 1 else 0\n end \n ) as selected_clocks\n from castdb.campus_locations l left join castdb.probe_metadata pm on l.uuid = pm.location_uuid\n where l.public = True\n group by\n l.latitude, l.longitude, l.campus;", + "rawSql": "SELECT\n l.latitude,\n l.longitude,\n l.campus,\n sum(\n CASE\n when pm.public = True and pm.vendor in ('ADVA', 'MicrochipTP4100', 'NTP') then 1 else 0\n end \n ) as visible_clocks,\n sum(\n CASE\n when (trim('${clock_name:csv}') = '' OR pm.uuid = ANY(string_to_array(trim('${clock_name:csv}'), ','))) then 1 else 0\n end \n ) as selected_clocks\n from castdb.campus_locations l left join castdb.probe_metadata pm on l.uuid = pm.location_uuid\n where l.public = True\n group by\n l.latitude, l.longitude, l.campus;", "refId": "A", "sql": { "columns": [ @@ -465,7 +465,7 @@ }, "format": "table", "rawQuery": true, - "rawSql": "SELECT COUNT(*) as \"Total Clock Probes\" FROM castdb.probe_metadata where uuid in ($clock_name)", + "rawSql": "SELECT COUNT(*)::bigint AS \"Total Clock Probes\" FROM castdb.probe_metadata pm WHERE pm.vendor IN ('ADVA', 'MicrochipTP4100', 'NTP') AND coalesce(pm.public, true) AND (trim('${clock_name:csv}') = '' OR pm.uuid = ANY(string_to_array(trim('${clock_name:csv}'), ',')))", "refId": "A" } ], @@ -539,7 +539,7 @@ "editorMode": "code", "format": "table", "rawQuery": true, - "rawSql": "SELECT \n coalesce(pm.name, concat(pm.ip_address, 'Inteface', pm.probe_id)) as \"Clock Probe\", \n COUNT(*) as \"Total Records\" \nFROM castdb.probe_data pd\njoin castdb.probe_metadata pm on pd.probe_uuid = pm.uuid \nwhere pm.uuid in (${clock_name:sqlstring})\nAND pd.\"time\" >= $__timeFrom()\nAND pd.\"time\" <= $__timeTo()\ngroup by pm.uuid, pm.name, pm.ip_address, pm.probe_id;", + "rawSql": "SELECT \n coalesce(pm.name, concat(pm.ip_address, ' Interface ', pm.probe_id)) AS \"Clock Probe\", \n COUNT(*)::bigint AS \"Total Records\" \nFROM castdb.probe_data pd\nJOIN castdb.probe_metadata pm ON pd.probe_uuid = pm.uuid \nWHERE pm.vendor IN ('ADVA', 'MicrochipTP4100', 'NTP')\n AND coalesce(pm.public, true)\n AND (trim('${clock_name:csv}') = '' OR pm.uuid = ANY(string_to_array(trim('${clock_name:csv}'), ',')))\n AND pd.\"time\" >= $__timeFrom()\n AND pd.\"time\" <= $__timeTo()\nGROUP BY pm.uuid, pm.name, pm.ip_address, pm.probe_id;", "refId": "A", "sql": { "columns": [ @@ -568,7 +568,7 @@ "type": "grafana-postgresql-datasource", "uid": "castdb-datasource" }, - "description": "Average time error \n(averaged on selected resolution)", + "description": "Average time error vs stored reference (resolution as selected). GNSS-specific labeling applies only when the probe/reference model is GNSS-backed.", "fieldConfig": { "defaults": { "color": { @@ -650,7 +650,7 @@ "editorMode": "code", "format": "time_series", "rawQuery": true, - "rawSql": "SELECT \n time_bucket(${resolution:sqlstring}, pd.time AT TIME ZONE 'UTC') AS time,\n coalesce(pm.name, concat(pm.ip_address, ' Interface ', pm.probe_id)),\n AVG(pd.value::FLOAT) * 1e9 AS value\nFROM castdb.probe_data pd join castdb.probe_metadata pm on pd.probe_uuid = pm.uuid\nWHERE\n $__timeFilter(pd.time)\n AND pd.probe_uuid IN (${clock_name:sqlstring})\nGROUP BY \n time_bucket(${resolution:sqlstring}, pd.time AT TIME ZONE 'UTC'),\n pd.probe_uuid,\n pm.name,\n pm.ip_address,\n pm.probe_id\nORDER BY \n time_bucket(${resolution:sqlstring}, pd.time AT TIME ZONE 'UTC')\n", + "rawSql": "SELECT \n time_bucket(${resolution:sqlstring}, pd.time AT TIME ZONE 'UTC') AS time,\n coalesce(pm.name, concat(pm.ip_address, ' Interface ', pm.probe_id)),\n AVG(pd.value::FLOAT) * 1e9 AS value\nFROM castdb.probe_data pd JOIN castdb.probe_metadata pm ON pd.probe_uuid = pm.uuid\nWHERE\n $__timeFilter(pd.time)\n AND pm.vendor IN ('ADVA', 'MicrochipTP4100', 'NTP')\n AND coalesce(pm.public, true)\n AND (trim('${clock_name:csv}') = '' OR pd.probe_uuid = ANY(string_to_array(trim('${clock_name:csv}'), ',')))\nGROUP BY \n time_bucket(${resolution:sqlstring}, pd.time AT TIME ZONE 'UTC'),\n pd.probe_uuid,\n pm.name,\n pm.ip_address,\n pm.probe_id\nORDER BY \n time_bucket(${resolution:sqlstring}, pd.time AT TIME ZONE 'UTC')\n", "refId": "A", "sql": { "columns": [ @@ -671,7 +671,7 @@ } } ], - "title": "Time Error - Clock Time vs GNSS", + "title": "Time Error - Clock Time vs Reference", "transformations": [ { "id": "prepareTimeSeries", @@ -776,7 +776,7 @@ "editorMode": "code", "format": "time_series", "rawQuery": true, - "rawSql": "SELECT \n time_bucket(${resolution:sqlstring}, pd.time AT TIME ZONE 'UTC') AS time,\n COALESCE(name, CONCAT(ip_address, ' Interface ', probe_id)),\n (MAX(pd.value::FLOAT) - MIN(pd.value::FLOAT)) * 1e9 AS value\nFROM castdb.probe_data pd join castdb.probe_metadata pm on pd.probe_uuid = pm.uuid\nWHERE\n $__timeFilter(pd.time)\n AND pd.probe_uuid in (${clock_name:sqlstring})\nGROUP BY \n time_bucket(${resolution:sqlstring}, pd.time AT TIME ZONE 'UTC'),\n pd.probe_uuid,\n pm.name,\n pm.ip_address,\n pm.probe_id\nORDER BY \n time_bucket(${resolution:sqlstring}, pd.time AT TIME ZONE 'UTC')\n", + "rawSql": "SELECT \n time_bucket(${resolution:sqlstring}, pd.time AT TIME ZONE 'UTC') AS time,\n COALESCE(pm.name, CONCAT(pm.ip_address, ' Interface ', pm.probe_id)),\n (MAX(pd.value::FLOAT) - MIN(pd.value::FLOAT)) * 1e9 AS value\nFROM castdb.probe_data pd JOIN castdb.probe_metadata pm ON pd.probe_uuid = pm.uuid\nWHERE\n $__timeFilter(pd.time)\n AND pm.vendor IN ('ADVA', 'MicrochipTP4100', 'NTP')\n AND coalesce(pm.public, true)\n AND (trim('${clock_name:csv}') = '' OR pd.probe_uuid = ANY(string_to_array(trim('${clock_name:csv}'), ',')))\nGROUP BY \n time_bucket(${resolution:sqlstring}, pd.time AT TIME ZONE 'UTC'),\n pd.probe_uuid,\n pm.name,\n pm.ip_address,\n pm.probe_id\nORDER BY \n time_bucket(${resolution:sqlstring}, pd.time AT TIME ZONE 'UTC')\n", "refId": "A", "sql": { "columns": [ @@ -797,7 +797,7 @@ } } ], - "title": "Maximum Time Interval Error VS GNSS", + "title": "Maximum Time Interval Error vs Reference", "transformations": [ { "id": "prepareTimeSeries", @@ -834,7 +834,7 @@ "type": "grafana-postgresql-datasource", "uid": "castdb-datasource" }, - "description": "Average time error \n(averaged on selected resolution)", + "description": "Average time error vs stored reference (resolution as selected). GNSS-specific labeling applies only when the probe/reference model is GNSS-backed.", "fieldConfig": { "defaults": { "color": { @@ -937,7 +937,7 @@ } } ], - "title": "Time Error - Clock Time vs GNSS", + "title": "Time Error - Clock Time vs Reference", "type": "timeseries" }, { @@ -1048,14 +1048,44 @@ } } ], - "title": "Maximum Time Interval Error", + "title": "Maximum Time Interval Error vs Reference", "type": "timeseries" + }, + { + "collapsed": true, + "gridPos": {"h": 1, "w": 24, "x": 0, "y": 29}, + "id": 101, + "panels": [ + { + "datasource": {"type": "grafana-postgresql-datasource", "uid": "castdb-datasource"}, + "description": "Rows reflect stored `probe_metadata`, `ntp_metadata` (when vendor is NTP), `locations`, and one sample `reference`/`reference_type` from `probe_data` per probe.", + "fieldConfig": {"defaults": {}, "overrides": []}, + "gridPos": {"h": 10, "w": 24, "x": 0, "y": 0}, + "id": 100, + "options": {"cellHeight": "sm", "showHeader": true}, + "pluginVersion": "12.0.0", + "targets": [ + { + "datasource": {"type": "grafana-postgresql-datasource", "uid": "castdb-datasource"}, + "editorMode": "code", + "format": "table", + "rawQuery": true, + "rawSql": "SELECT\n COALESCE(pm.name, CONCAT(pm.ip_address, ' ', pm.probe_id)) AS probe,\n pm.vendor,\n COALESCE(rt.name, '') AS reference_type,\n COALESCE(nm.target_host::text, '') AS ntp_server,\n COALESCE(nm.mode::text, '') AS ntp_mode,\n COALESCE(nm.reference_id::text, '') AS ntp_ref_id,\n COALESCE(l.name, '') AS location,\n COALESCE(pm.public::text, '') AS public\nFROM castdb.probe_metadata pm\nLEFT JOIN castdb.ntp_metadata nm ON nm.probe_uuid = pm.uuid\nLEFT JOIN castdb.locations l ON l.uuid = pm.location_uuid\nLEFT JOIN LATERAL (\n SELECT pd.reference_uuid FROM castdb.probe_data pd WHERE pd.probe_uuid = pm.uuid LIMIT 1\n) rp ON true\nLEFT JOIN castdb.reference r ON r.uuid = rp.reference_uuid\nLEFT JOIN castdb.reference_type rt ON rt.uuid = r.reference_type_uuid\nWHERE pm.vendor IN ('ADVA', 'MicrochipTP4100', 'NTP')\n AND coalesce(pm.public, true)\n AND (trim('${clock_name:csv}') = '' OR pm.uuid = ANY(string_to_array(trim('${clock_name:csv}'), ',')))\nORDER BY 1;", + "refId": "A" + } + ], + "title": "Probe reference & source (stored metadata)", + "type": "table" + } + ], + "title": "Reference & source metadata", + "type": "row" } ], "preload": false, "refresh": "", "schemaVersion": 41, - "tags": [], + "tags": ["opensampl", "reference", "geospatial"], "templating": { "list": [ { @@ -1067,12 +1097,12 @@ "type": "grafana-postgresql-datasource", "uid": "castdb-datasource" }, - "definition": "SELECT uuid AS __value, COALESCE(name, CONCAT(ip_address, ' Interface ', probe_id)) AS __text FROM castdb.probe_metadata WHERE vendor in ('ADVA', 'MicrochipTP4100') and public;", + "definition": "SELECT pm.uuid::text AS __value, COALESCE(pm.name, CONCAT(pm.ip_address, ' Interface ', pm.probe_id)) AS __text FROM castdb.probe_metadata pm WHERE pm.vendor in ('ADVA', 'MicrochipTP4100', 'NTP') AND coalesce(pm.public, true) ORDER BY 2;", "includeAll": true, "multi": true, "name": "clock_name", "options": [], - "query": "SELECT uuid AS __value, COALESCE(name, CONCAT(ip_address, ' Interface ', probe_id)) AS __text FROM castdb.probe_metadata WHERE vendor in ('ADVA', 'MicrochipTP4100') and public;", + "query": "SELECT pm.uuid::text AS __value, COALESCE(pm.name, CONCAT(pm.ip_address, ' Interface ', pm.probe_id)) AS __text FROM castdb.probe_metadata pm WHERE pm.vendor in ('ADVA', 'MicrochipTP4100', 'NTP') AND coalesce(pm.public, true) ORDER BY 2;", "refresh": 1, "regex": "", "type": "query" @@ -1130,7 +1160,8 @@ }, "timepicker": {}, "timezone": "utc", - "title": "Public Geospatial and Timing Combined Dashboard", + "description": "Geospatial views use stored `locations` geometry. Timing series are relative to each probe\u2019s stored reference (OpenSAMPL `reference` / `reference_type`) and are **not** GNSS-truth unless a GNSS-backed probe supplies that semantics.", + "title": "Public Geospatial and Timing (Reference)", "uid": "public-geospatial-dashboard", "version": 10 } \ No newline at end of file diff --git a/opensampl/server/migrations/_migrations/versions/2026_04_17_1243_add_ntp_values.py b/opensampl/server/migrations/_migrations/versions/2026_04_17_1243_add_ntp_values.py new file mode 100644 index 0000000..4cd6b14 --- /dev/null +++ b/opensampl/server/migrations/_migrations/versions/2026_04_17_1243_add_ntp_values.py @@ -0,0 +1,159 @@ +"""add ntp values + +Revision ID: 5665e5902905 +Revises: d419cac01df2 +Create Date: 2026-04-17 12:43:23.711453 + +""" +from typing import Sequence, Union +import uuid +from sqlalchemy.dialects import postgresql +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '5665e5902905' +down_revision: Union[str, None] = 'd419cac01df2' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + +SCHEMA = 'castdb' + +def upgrade() -> None: + op.create_table( + "ntp_metadata", + sa.Column( + "probe_uuid", + sa.String(), + sa.ForeignKey(f"{SCHEMA}.probe_metadata.uuid"), + primary_key=True, + nullable=False, + ), + sa.Column("mode", sa.Text(), nullable=True), + sa.Column( + "reference", + sa.Boolean(), + nullable=True, + comment="Is used as a reference for other probes", + ), + sa.Column("target_host", sa.Text(), nullable=True), + sa.Column("target_port", sa.Integer(), nullable=True), + sa.Column("sync_status", sa.Text(), nullable=True), + sa.Column("leap_status", sa.Text(), nullable=True), + sa.Column("reference_id", sa.Text(), nullable=True), + sa.Column("observation_sources", postgresql.JSONB(astext_type=sa.Text()), nullable=True), + sa.Column("collection_id", sa.Text(), nullable=True), + sa.Column("collection_ip", sa.Text(), nullable=True), + sa.Column("timeout", sa.Float(), nullable=True), + sa.Column("additional_metadata", postgresql.JSONB(astext_type=sa.Text()), nullable=True), + schema=SCHEMA, + if_not_exists=True, + comment="NTP Clock Probe specific metadata" + ) + + metric_type_table = sa.table('metric_type', + sa.column('uuid', sa.String), + sa.column('name', sa.String), + sa.column('description', sa.Text), + sa.column('unit', sa.String), + sa.column('value_type', sa.String), + schema=SCHEMA + ) + new_metrics = [ + dict(uuid=str(uuid.uuid4()), + name="Delay", + description=( + "Round-trip delay (RTD) or Round-Trip Time (RTT). The time in seconds it takes for a data signal to " + "travel from a source to a destination and back, including acknowledgement." + ), + unit="s", + value_type='float', + ), + dict(uuid=str(uuid.uuid4()), + name="Jitter", + description=("Jitter or offset variation in delay in seconds. Represents inconsistent response times."), + unit="s", + value_type='float', + ), + dict(uuid=str(uuid.uuid4()), + name="Stratum", + description=( + 'Stratum level. Hierarchical layer defining the distance (or "hops") between device and reference.' + ), + unit="level", + value_type='int', + ), + dict(uuid=str(uuid.uuid4()), + name="Reachability", + description=( + "Reachability register (0-255) as a scalar for plotting. Ability of a source node to communicate " + "with a target node." + ), + unit="count", + value_type='float', + ), + dict(uuid=str(uuid.uuid4()), + name="Dispersion", + description="Uncertainty in a clock's time relative to its reference source in seconds", + unit="s", + value_type='float', + ), + dict(uuid=str(uuid.uuid4()), + name="NTP Root Delay", + description=( + "Total round-trip network delay from the local system" + " all the way to the primary reference clock (stratum 0)" + ), + unit="s", + value_type='float' + ), + dict(uuid=str(uuid.uuid4()), + name="NTP Root Dispersion", + description="The total accumulated clock uncertainty from the local system back to the primary reference clock", + unit="s", + value_type='float', + ), + dict(uuid=str(uuid.uuid4()), + name="Poll Interval", + description="Time between requests sent to a time server in seconds", + unit="s", + value_type='float', + ), + dict(uuid=str(uuid.uuid4()), + name="Sync Health", + description="1.0 if synchronized/healthy, 0.0 otherwise (probe-defined)", + unit="ratio", + value_type='float', + ) + ] + op.bulk_insert(metric_type_table, new_metrics) + + + + +def downgrade() -> None: + op.drop_table('ntp_metadata', schema=SCHEMA, if_exists=True) + metric_type = sa.sql.table( + "metric_type", + sa.column("name", sa.String), + schema=SCHEMA, + ) + + op.execute( + metric_type.delete().where( + metric_type.c.name.in_( + [ + "Delay", + "Jitter", + "Stratum", + "Reachability", + "Dispersion", + "NTP Root Delay", + "NTP Root Dispersion", + "Poll Interval", + "Sync Health", + ] + ) + ) + ) diff --git a/opensampl/server/migrations/_migrations/versions/2026_04_17_1254_add_reference_view.py b/opensampl/server/migrations/_migrations/versions/2026_04_17_1254_add_reference_view.py new file mode 100644 index 0000000..8cbb326 --- /dev/null +++ b/opensampl/server/migrations/_migrations/versions/2026_04_17_1254_add_reference_view.py @@ -0,0 +1,56 @@ +"""add reference view + +Revision ID: c95e49e551be +Revises: 5665e5902905 +Create Date: 2026-04-17 12:54:27.037125 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = 'c95e49e551be' +down_revision: Union[str, None] = '5665e5902905' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + +SCHEMA = 'castdb' + +CREATE_VIEW_SQL = f""" +CREATE VIEW {SCHEMA}.reference_probe_metadata +AS WITH probe_references AS ( + SELECT r.uuid, + r.reference_type_uuid, + r.compound_reference_uuid + FROM {SCHEMA}.reference r + JOIN {SCHEMA}.reference_type rt ON r.reference_type_uuid::text = rt.uuid::text + WHERE rt.name::text = 'PROBE'::text + ) + SELECT pm.uuid, + pm.probe_id, + pm.ip_address, + pm.vendor, + pm.model, + pm.name, + pm.public, + pm.location_uuid, + pm.test_uuid, + pr.uuid AS reference_uuid + FROM probe_references pr + JOIN {SCHEMA}.probe_metadata pm ON pr.compound_reference_uuid::text = pm.uuid::text; +""" + +DROP_VIEW_SQL = f""" +DROP VIEW IF EXISTS {SCHEMA}.reference_probe_metadata""" + +def upgrade() -> None: + # Drop the view first, just to be extra safe. + op.execute(DROP_VIEW_SQL) + op.execute(CREATE_VIEW_SQL) + + +def downgrade() -> None: + op.execute(DROP_VIEW_SQL) diff --git a/opensampl/vendors/adva.py b/opensampl/vendors/adva.py index 5ea9808..1d6ed36 100644 --- a/opensampl/vendors/adva.py +++ b/opensampl/vendors/adva.py @@ -5,7 +5,7 @@ import re from datetime import datetime, timezone from pathlib import Path -from typing import ClassVar, TextIO, Union +from typing import ClassVar, TextIO import click import pandas as pd @@ -63,9 +63,9 @@ def get_random_data_cli_options(cls) -> list: ] return base_options + vendor_options - def __init__(self, input_file: Union[str, Path]): + def __init__(self, input_file: str | Path, **kwargs: dict): """Initialize AdvaProbe object give input_file and determines probe identity from filename""" - super().__init__(input_file=input_file) + super().__init__(input_file=input_file, **kwargs) self.probe_key, self.timestamp = self.parse_file_name(self.input_file) @classmethod @@ -95,7 +95,7 @@ def parse_file_name(cls, file_name: Path) -> tuple[ProbeKey, datetime]: return ProbeKey(probe_id=probe_id, ip_address=ip_address), timestamp raise ValueError(f"Could not parse file name {file_name} into probe key and timestamp for ADVA probe") - def _open_file(self) -> Union[TextIO, gzip.GzipFile]: + def _open_file(self) -> TextIO | gzip.GzipFile: """Open the input file, handling both .txt and .txt.gz formats""" if self.input_file.name.endswith(".gz"): return gzip.open(self.input_file, "rt") diff --git a/opensampl/vendors/base_probe.py b/opensampl/vendors/base_probe.py index 1253844..f2188ce 100644 --- a/opensampl/vendors/base_probe.py +++ b/opensampl/vendors/base_probe.py @@ -4,11 +4,12 @@ import shutil from abc import ABC, abstractmethod +from collections.abc import Callable from concurrent.futures import ThreadPoolExecutor from contextlib import contextmanager from datetime import datetime, timezone from pathlib import Path -from typing import TYPE_CHECKING, Any, Callable, ClassVar, TypeVar +from typing import TYPE_CHECKING, Any, ClassVar, TypeVar import click import psycopg2.errors @@ -461,16 +462,16 @@ def ip_address(self): return self.probe_key.ip_address @abstractmethod - def process_time_data(self) -> pd.DataFrame: + def process_time_data(self) -> None: """ - Process time series data. + Parse and load time series data from self.input_file. - Returns - ------- - pd.DataFrame: DataFrame with columns: + Use either send_time_data (which prefills METRICS.PHASE_OFFSET) + or send_data and provide alternative METRICS type. + Both require a df as follows: + pd.DataFrame with columns: - time (datetime64[ns]): timestamp for each measurement - value (float64): measured value at each timestamp - """ @dualmethod @@ -483,13 +484,13 @@ def send_data( probe_key: ProbeKey | None = None, ) -> None: """Ingests data into the database""" - if isinstance(self, BaseProbe): + if isinstance(self, BaseProbe) and probe_key is None: probe_key = self.probe_key if probe_key is None: raise ValueError("send data must be called with probe_key if used as class method") - if self.chunk_size: + if hasattr(self, "chunk_size") and self.chunk_size: for chunk_start in range(0, len(data), self.chunk_size): chunk = data.iloc[chunk_start : chunk_start + self.chunk_size] load_time_data( diff --git a/opensampl/vendors/constants.py b/opensampl/vendors/constants.py index 4725b05..b5b7bdd 100644 --- a/opensampl/vendors/constants.py +++ b/opensampl/vendors/constants.py @@ -70,6 +70,14 @@ class VENDORS: metadata_orm="MicrochipTP4100Metadata", ) + NTP = VendorType( + name="NTP", + parser_class="NtpProbe", + parser_module="ntp", + metadata_table="ntp_metadata", + metadata_orm="NtpMetadata", + ) + # --- CUSTOM VENDORS --- !! Do not remove line, used as reference when inserting vendor # --- VENDOR FUNCTIONS --- diff --git a/opensampl/vendors/microchip/tp4100.py b/opensampl/vendors/microchip/tp4100.py index 09b0d4d..e6d2f31 100644 --- a/opensampl/vendors/microchip/tp4100.py +++ b/opensampl/vendors/microchip/tp4100.py @@ -2,7 +2,7 @@ import random from pathlib import Path -from typing import ClassVar, Optional, Union +from typing import ClassVar import click import pandas as pd @@ -30,13 +30,13 @@ class RandomDataConfig(RandomDataMixin.RandomDataConfig): """Model for storing random data generation configurations as provided by CLI or YAML""" # Time series parameters - base_value: Optional[float] = Field( + base_value: float | None = Field( default_factory=lambda: random.uniform(-5e-7, 5e-7), description="random.uniform(-5e-7, 5e-7)" ) - noise_amplitude: Optional[float] = Field( + noise_amplitude: float | None = Field( default_factory=lambda: random.uniform(1e-8, 5e-8), description="random.uniform(1e-8, 5e-8)" ) - drift_rate: Optional[float] = Field( + drift_rate: float | None = Field( default_factory=lambda: random.uniform(-1e-10, 1e-10), description="random.uniform(-1e-10, 1e-10)" ) @@ -59,9 +59,9 @@ def get_random_data_cli_options(cls) -> list: ] return base_options + vendor_options - def __init__(self, input_file: Union[str, Path]): + def __init__(self, input_file: str | Path, **kwargs: dict): """Initialize MicrochipTP4100 object given input_file and determines probe identity from file headers""" - super().__init__(input_file=input_file) + super().__init__(input_file=input_file, **kwargs) self.header = self.get_header() self.probe_key = ProbeKey( ip_address=self.header.get("host"), probe_id=self.header.get("probe_id", None) or "1-1" diff --git a/opensampl/vendors/microchip/twst.py b/opensampl/vendors/microchip/twst.py index bf91f5b..2ead581 100644 --- a/opensampl/vendors/microchip/twst.py +++ b/opensampl/vendors/microchip/twst.py @@ -4,7 +4,7 @@ import re from datetime import timedelta from pathlib import Path -from typing import ClassVar, Optional, Union +from typing import ClassVar import click import numpy as np @@ -34,23 +34,23 @@ class RandomDataConfig(RandomDataMixin.RandomDataConfig): """Model for storing random data generation configurations as provided by CLI or YAML""" # Time series parameters - base_value: Optional[float] = Field( + base_value: float | None = Field( default_factory=lambda: random.uniform(-1e-8, 1e-8), description="random.uniform(-1e-8, 1e-8)" ) - noise_amplitude: Optional[float] = Field( + noise_amplitude: float | None = Field( default_factory=lambda: random.uniform(1e-10, 1e-9), description="random.uniform(1e-10, 1e-9)" ) - drift_rate: Optional[float] = Field( + drift_rate: float | None = Field( default_factory=lambda: random.uniform(-1e-12, 1e-12), description="random.uniform(-1e-12, 1e-12)" ) - ebno_base_value: Optional[float] = Field( + ebno_base_value: float | None = Field( default_factory=lambda: random.uniform(10.0, 20.0), description="random.uniform(10.0, 20.0)" ) - ebno_noise_amplitude: Optional[float] = Field( + ebno_noise_amplitude: float | None = Field( default_factory=lambda: random.uniform(0.5, 2.0), description="random.uniform(0.5, 2.0)" ) - ebno_drift_rate: Optional[float] = Field( + ebno_drift_rate: float | None = Field( default_factory=lambda: random.uniform(-0.01, 0.01), description="random.uniform(-0.01, 0.01)" ) @@ -123,9 +123,9 @@ def get_random_data_cli_options(cls) -> list: ] return vendor_options + base_options - def __init__(self, input_file: Union[str, Path]): + def __init__(self, input_file: str | Path, **kwargs: dict): """Initialize MicrochipTWST object give input_file and determines probe identity from filename""" - super().__init__(input_file=input_file) + super().__init__(input_file=input_file, **kwargs) self.header = self.get_header() self.probe_key = ProbeKey(probe_id="modem", ip_address=self.header["local"]["ip"]) diff --git a/opensampl/vendors/ntp.py b/opensampl/vendors/ntp.py new file mode 100644 index 0000000..52cbb90 --- /dev/null +++ b/opensampl/vendors/ntp.py @@ -0,0 +1,772 @@ +"""Probe implementation for NTP vendor""" + +from __future__ import annotations + +import contextlib +import random +import re +import shutil +import socket +import subprocess +import textwrap +import time +from datetime import datetime, timedelta, timezone +from io import StringIO +from typing import TYPE_CHECKING, Any, ClassVar, Literal, TypeVar + +import click +import numpy as np +import pandas as pd +import psycopg2.errors +import requests +import yaml +from loguru import logger +from pydanclick import from_pydantic +from pydantic import BaseModel, ConfigDict, Field +from sqlalchemy.exc import IntegrityError + +from opensampl.load_data import load_probe_metadata +from opensampl.metrics import METRICS, MetricType +from opensampl.mixins.collect import CollectMixin +from opensampl.mixins.random_data import RandomDataMixin +from opensampl.references import REF_TYPES, ReferenceType +from opensampl.vendors.base_probe import BaseProbe +from opensampl.vendors.constants import VENDORS, ProbeKey + +T = TypeVar("T") + +if TYPE_CHECKING: + from collections.abc import Callable + from pathlib import Path + + +def _merge(a: T | None, b: T | None) -> T | None: + return a if a is not None else b + + +class NTPCollector(BaseModel): + """Base class for NTP Collector, for specific implementations to inherit.""" + + mode: ClassVar[Literal["remote", "local"]] + metric_map: ClassVar[dict[str, MetricType]] = { + "phase_offset_s": METRICS.PHASE_OFFSET, + "delay_s": METRICS.DELAY, + "jitter_s": METRICS.JITTER, + "stratum": METRICS.STRATUM, + "reachability": METRICS.REACHABILITY, + "dispersion_s": METRICS.DISPERSION, + "root_delay_s": METRICS.NTP_ROOT_DELAY, + "root_dispersion_s": METRICS.NTP_ROOT_DISPERSION, + "poll_interval_s": METRICS.POLL_INTERVAL, + "sync_health": METRICS.SYNC_HEALTH, + } + + target_host: str + + sync_status: str = Field("unknown") + sync_health: float | None = Field(None, json_schema_extra={"metric": True}) + + stratum: int | None = Field(None, json_schema_extra={"metric": True}) + reachability: int | None = Field(None, json_schema_extra={"metric": True}) + offset_s: float | None = Field(None, serialization_alias="phase_offset_s", json_schema_extra={"metric": True}) + delay_s: float | None = Field(None, json_schema_extra={"metric": True}) + jitter_s: float | None = Field(None, json_schema_extra={"metric": True}) + reference_id: str | None = None + observation_sources: list[str] = Field(default_factory=list) + collection_id: str + collection_ip: str + probe_id: str | None = None + + extras: dict = Field(default_factory=dict, serialization_alias="additional_metadata") + model_config = ConfigDict(serialize_by_alias=True) + + def collect(self): + """Collect a single NTP Reading""" + raise NotImplementedError + + def export_data(self) -> list[CollectMixin.DataArtifact]: + """ + Export the data from the NTP Collection to a list of DataArtifacts + + Each distinct metric type will get it's own data artifact + """ + now = datetime.now(tz=timezone.utc) + include_list = { + f + for f, field_info in type(self).model_fields.items() + if field_info.json_schema_extra and field_info.json_schema_extra.get("metric", False) + } + reference_type, compound_reference = self.determine_reference() + metric_values = self.model_dump(include=include_list, exclude_none=True) + + artifacts: list[CollectMixin.DataArtifact] = [] + for m, v in metric_values.items(): + metric = self.metric_map.get(m, None) + if metric is None: + metric = MetricType( + name=m, + description=f"Automatically generated metric type for {m}", + value_type=object, + unit="unknown", + ) + logger.warning(f"Generated new metric type for {m}") + value = pd.DataFrame([(now, v)], columns=["time", "value"]) + value["time"] = pd.to_datetime(value["time"]) + + artifacts.append( + CollectMixin.DataArtifact( + metric=metric, reference_type=reference_type, compound_reference=compound_reference, value=value + ) + ) + return artifacts + + def export_metadata(self) -> dict[str, Any]: + """Export the metadata from the NTP Collection to a dict""" + include_list = { + f + for f, field_info in type(self).model_fields.items() + if not field_info.json_schema_extra or not field_info.json_schema_extra.get("metric", False) + } + meta = self.model_dump(include=include_list, exclude_none=True) + meta["mode"] = self.mode + return meta + + def export(self) -> CollectMixin.CollectArtifact: + """Export the data + metadata for the NTP Collection to a CollectArtifact""" + meta = self.export_metadata() + + artifacts: list[CollectMixin.DataArtifact] = self.export_data() + + return CollectMixin.CollectArtifact(data=artifacts, metadata=meta) + + @classmethod + def invert_metric_map(cls) -> dict[str, str]: + """Invert metric map to go from MetricType.name to string""" + return {v.name: k for k, v in cls.metric_map.items()} + + def determine_reference(self) -> tuple[ReferenceType, None | dict[str, Any]]: + """Get the reference type and compound reference details""" + return REF_TYPES.PROBE, {"ip_address": self.collection_ip, "probe_id": self.collection_id} + + +class NTPLocalCollector(NTPCollector): + """Collector model for taking NTP readings from local device""" + + mode: ClassVar[Literal["remote", "local"]] = "local" + + @staticmethod + def _run(cmd: list[str], timeout: float = 8.0) -> str | None: + """Run command; return stdout or None if missing/failed.""" + bin0 = cmd[0] + if shutil.which(bin0) is None: + logger.debug(f"ntp local: command {bin0!r} not found") + return None + try: + proc = subprocess.run( # noqa: S603 + cmd, + capture_output=True, + text=True, + timeout=timeout, + check=False, + ) + except (OSError, subprocess.SubprocessError) as e: + logger.debug(f"ntp local: command {cmd!r} failed: {e}") + return None + if proc.returncode != 0: + logger.debug(f"ntp local: {cmd!r} exit {proc.returncode}: {proc.stderr!r}") + return None + logger.debug(f"ntp local: {cmd!r} exit {proc.stdout}") + return proc.stdout or "" + + def _parse_chronyc_tracking(self, text: str) -> None: + """Parse `chronyc tracking` key: value output.""" + out: dict[str, Any] = {} + for l in text.splitlines(): + line = l.strip() + if not line or ":" not in line: + continue + key, _, rest = line.partition(":") + key = key.strip().lower().replace(" ", "_") + val = rest.strip() + out[key] = val + + # Last offset : +0.000000123 seconds + m = re.search(r"last offset\s*:\s*([+-]?[\d.eE+-]+)\s*seconds?", text, re.IGNORECASE) + if m: + with contextlib.suppress(ValueError): + self.offset_s = _merge(self.offset_s, float(m.group(1))) + + m = re.search(r"rms offset\s*:\s*([+-]?[\d.eE+-]+)\s*seconds?", text, re.IGNORECASE) + if m: + with contextlib.suppress(ValueError): + self.jitter_s = _merge(self.jitter_s, float(m.group(1))) + + m = re.search(r"stratum\s*:\s*(\d+)", text, re.IGNORECASE) + if m: + with contextlib.suppress(ValueError): + self.stratum = _merge(self.stratum, int(m.group(1))) + + m = re.search(r"reference id\s*:\s*(\S+)(?:\s*\(([^)]+)\))?", text, re.IGNORECASE) + if m: + self.reference_id = (m.group(2) or m.group(1)) or self.reference_id + + self.sync_status = "unsynchronized" + if "normal" in text.lower() or self.offset_s is not None: + self.sync_status = "tracking" + self.extras["chronyc_raw_tracking"] = out + self.observation_sources.append("chronyc_tracking") + + def _parse_chronyc_sources(self, text: str) -> None: + """Parse `chronyc sources` for reach and selected source.""" + reach: int | None = None + selected: str | None = None + for l in text.splitlines(): + line = l.strip() + if not line or line.startswith(("MS", "=")): + continue + # ^* or ^+ prefix indicates selected/accepted + if line.startswith(("*", "+")): + parts = line.split() + if len(parts) >= 7: + try: + reach = int(parts[5], 8) if parts[5].startswith("0") else int(parts[5]) + except ValueError: + with contextlib.suppress(ValueError): + reach = int(parts[5]) + selected = parts[1] + break + # Fallback: last column often reach (octal) + parts = line.split() + if len(parts) >= 7 and parts[0] in ("^*", "^+", "*", "+"): + # already handled + pass + if reach is None: + # Try any line with 377 octal style + m = re.search(r"\b([0-7]{3})\b", text) + if m: + with contextlib.suppress(ValueError): + reach = int(m.group(1), 8) + + self.reachability = self.reachability or reach + self.reference_id = self.reference_id or selected + self.observation_sources.append("chronyc_sources") + + def _parse_ntpq(self, text: str) -> None: + """Parse `ntpq -p` / `ntpq -pn` output.""" + offset_s: float | None = None + delay_s: float | None = None + jitter_s: float | None = None + stratum: int | None = None + reach: int | None = None + ref = None + for l in text.splitlines(): + line = l.strip() + if not line or line.startswith(("remote", "=")): + continue + if line.startswith(("*", "+", "-")): + parts = line.split() + # remote refid st t when poll reach delay offset jitter + if len(parts) >= 10: + with contextlib.suppress(ValueError): + stratum = int(parts[2]) + + try: + delay_s = float(parts[7]) / 1000.0 # ms -> s + offset_s = float(parts[8]) / 1000.0 + jitter_s = float(parts[9]) / 1000.0 + except (ValueError, IndexError): + pass + try: + reach = int(parts[6], 8) if parts[6].startswith("0") else int(parts[6]) + except ValueError: + with contextlib.suppress(ValueError): + reach = int(parts[6]) + + ref = parts[1] + break + sync_status = "synced" if offset_s is not None else "unknown" + + self.offset_s = self.offset_s or offset_s + self.delay_s = self.delay_s or delay_s + self.jitter_s = self.jitter_s or jitter_s + self.stratum = self.stratum or stratum + self.reachability = self.reachability or reach + self.reference_id = self.reference_id or ref + self.sync_status = sync_status or self.sync_status + self.observation_sources.append("ntpq") + + def _parse_timedatectl(self, text: str) -> None: + """Parse `timedatectl status` / `show-timesync --all`.""" + sync = None + for line in text.splitlines(): + low = line.lower() + if "system clock synchronized" in low or "ntp synchronized" in low: + if "yes" in low: + sync = True + elif "no" in low: + sync = False + sync_status = "unknown" + if sync is True: + sync_status = "synchronized" + elif sync is False: + sync_status = "unsynchronized" + + if self.sync_status == "unknown": + self.sync_status = sync_status or self.sync_status + self.observation_sources.append("timedatectl") + self.extras["timedatectl"] = text[:2000] + + def _parse_systemctl_show(self, text: str) -> None: + """Parse `systemctl show` / `systemctl status` for systemd-timesyncd.""" + active = None + for line in text.splitlines(): + if line.strip().lower().startswith("activestate="): + active = line.split("=", 1)[1].strip().lower() == "active" + break + if active is None and "active (running)" in text.lower(): + active = True + sync_status = "unknown" + if active is True: + sync_status = "service_active" + elif active is False: + sync_status = "service_inactive" + + if self.sync_status == "unknown": + self.sync_status = sync_status or self.sync_status + self.extras["systemctl"] = text[:2000] + self.observation_sources.append("systemctl_timesyncd") + + def collect(self): + """Collect local NTP readings using various tools""" + t = self._run(["chronyc", "tracking"]) + if t: + self._parse_chronyc_tracking(t) + + t = self._run(["chronyc", "sources", "-v"]) or self._run(["chronyc", "sources"]) + if t: + self._parse_chronyc_sources(t) + + if self.offset_s is None and self.stratum is None: + t = self._run(["ntpq", "-pn"]) or self._run(["ntpq", "-p"]) + if t: + self._parse_ntpq(t) + + t = self._run(["timedatectl", "show-timesync", "--all"]) or self._run(["timedatectl", "status"]) + if t: + self._parse_timedatectl(t) + + t = self._run(["systemctl", "show", "systemd-timesyncd", "--property=ActiveState"]) + if not t: + t = self._run(["systemctl", "status", "systemd-timesyncd", "--no-pager"]) + + if t: + self._parse_systemctl_show(t) + + if not self.observation_sources: + self.observation_sources = ["none"] + + self.sync_health = 1.0 if self.sync_status in ("tracking", "synchronized", "synced") else 0.0 + + if self.probe_id is None: + self.probe_id = "ntp-local" + + +class NTPRemoteCollector(NTPCollector): + """Collector model for taking readings from remote NTP Server.""" + + mode: ClassVar[Literal["remote", "local"]] = "remote" + + target_port: int + timeout: float = 3.0 + + root_delay_s: float | None = Field(None, json_schema_extra={"metric": True}) + root_dispersion_s: float | None = Field(None, json_schema_extra={"metric": True}) + poll_interval_s: float | None = Field(None, json_schema_extra={"metric": True}) + leap_status: str = "unknown" + + def configure_failure(self, e: Exception) -> None: + """Set all metric and metadata values to reflect failure to connect""" + self.sync_status = "unreachable" + self.sync_health = 0 + self.extras["error"] = str(e) + self.observation_sources.append("ntplib") + self.observation_sources.append("error") + + def _estimate_jitter_s(self) -> None: + """ + Single NTP client response does not include RFC5905 peer jitter (that needs multiple samples). + + Emit a conservative positive bound from round-trip delay and root dispersion so downstream + ``NTP Jitter`` metrics and dashboards have a value; chrony/ntpq local paths still supply + true jitter when available. + """ + if self.delay_s is None and self.root_dispersion_s is None: + return + d = float(self.delay_s) if self.delay_s is not None else 0.0 + r = float(self.root_dispersion_s) if self.root_dispersion_s is not None else 0.0 + est = 0.05 * d + 0.25 * r + if est > 0: + self.jitter_s = est + return + + def collect(self): + """Collect readings from a single ping against a remote NTP server.""" + try: + import ntplib # type: ignore[import-untyped] + except ImportError as e: + raise ImportError( + "Remote NTP collection requires the 'ntplib' package (install opensampl[collect])." + ) from e + client = ntplib.NTPClient() + try: + resp = client.request(self.target_host, port=self.target_port, version=3, timeout=self.timeout) + except Exception as e: + logger.warning(f"NTP request to {self.target_host}:{self.target_port} failed: {e}") + self.configure_failure(e) + return + leap = int(resp.leap) + leap_map = {0: "no_warning", 1: "add_second", 2: "del_second", 3: "alarm"} + self.leap_status = leap_map.get(leap, str(leap)) + + stratum = int(resp.stratum) + + try: + self.poll_interval_s = float(2 ** int(resp.poll)) + except (TypeError, ValueError, OverflowError): + logger.debug("No poll interval determined") + + self.root_delay_s = float(resp.root_delay) if resp.root_delay is not None else None + self.root_dispersion_s = float(resp.root_dispersion) if resp.root_dispersion is not None else None + self.delay_s = float(resp.delay) if resp.delay is not None else None + self.offset_s = float(resp.offset) if resp.offset is not None else None + + ref_id = getattr(resp, "ref_id", None) + if hasattr(ref_id, "decode"): + try: + ref_id = ref_id.decode("ascii", errors="replace") + except Exception: + ref_id = str(ref_id) + self.reference_id = str(ref_id) if ref_id is not None else None + + sync_ok = stratum < 16 and self.offset_s is not None + self.observation_sources.append("ntplib") + self.sync_status = "synchronized" if sync_ok else "unsynchronized" + self.sync_health = 1.0 if sync_ok else 0.0 + self._estimate_jitter_s() + + self.extras["version"] = getattr(resp, "version", None) + + if self.probe_id is None: + self.probe_id = f"remote:{self.target_port}" + + +def collect_ip_factory() -> str: + """Get ip address for collection host using socket (default to 127.0.0.1)""" + s = None + try: + s = socket.socket(socket.AF_INET, socket.SOCK_DGRAM) + s.connect(("8.8.8.8", 80)) # doesn't actually send data + v = s.getsockname()[0] + except Exception: + v = "127.0.0.1" + finally: + if s: + s.close() + return v + + +def collect_id_factory() -> str: + """Get humanreadable host name for collection host using socket (default to collection-host)""" + try: + return socket.gethostname() or "collection-host" + except Exception: + return "collection-host" + + +class NtpProbe(BaseProbe, CollectMixin, RandomDataMixin): + """Probe parser for NTP vendor data files""" + + vendor = VENDORS.NTP + + class CollectConfig(CollectMixin.CollectConfig): + """ + Configuration for Collecting NTP Readings + + Attributes: + probe_id: stable probe_id slug (e.g. local-chrony) + ip_address: Host or IP address for Probe (default '127.0.0.1') + port: UDP port for remote mode (use high ports for lab mocks) + output_dir: When provided, will save collected data as a file to provided directory. Filename will be + automatically generated as NTP_{ip_address}_{probe_id}_{vendor}_{timestamp}.txt + load: Whether to load collected data directly to the database + duration: Number of seconds to collect data for + mode: Collect remote or local NTP. Default is 'local'. + interval: Seconds between samples; 0 = single sample and exit + duration: Samples to collect when interval > 0 + timeout: UDP request timeout for remote mode(seconds) default: 3.0 + collection_ip: Override for the IP address of device collecting readings. Will attempt to resolve a local + network IP using socket and fall back to '127.0.0.1' + collection_id: Override for the Probe ID of the device collecting readings. Will attempt to resolve using + socket.gethostname and fall back to 'collection-host' + + """ + + ip_address: str = "127.0.0.1" + port: int = 123 + mode: Literal["remote", "local"] = "local" + interval: float = Field(0.0, ge=0.0) + duration: int = Field(1, ge=1) + timeout: float = 3.0 + collection_ip: str = Field(default_factory=collect_ip_factory) + collection_id: str = Field(default_factory=collect_id_factory) + + @classmethod + def get_collect_cli_options(cls) -> list[Callable]: + """Get the decorators to generate collection options for CLI""" + return [ + from_pydantic(cls.CollectConfig, rename={"ip_address": "host", "duration": "count"}), + click.pass_context, + ] + + class RandomDataConfig(RandomDataMixin.RandomDataConfig): + """Random NTP-like test data.""" + + base_value: float = Field( + default_factory=lambda: random.uniform(-1e-4, 1e-4), + description="random.uniform(-1e-4, 1e-4)", + ) + noise_amplitude: float = Field( + default_factory=lambda: random.uniform(1e-9, 1e-7), + description="random.uniform(1e-9, 1e-7)", + ) + drift_rate: float = Field( + default_factory=lambda: random.uniform(-1e-12, 1e-12), + description="random.uniform(-1e-12, 1e-12)", + ) + + def __init__(self, input_file: str | Path, **kwargs: dict): + """Initialize NtpProbe from input file""" + super().__init__(input_file=input_file, **kwargs) + self.collection_probe = None + + def process_metadata(self) -> dict: + """ + Parse and return probe metadata from input file. + + Returns: + dict with metadata field names as keys + + """ + if not self.metadata_parsed: + header_lines = [] + with self.input_file.open() as f: + for line in f: + if line.startswith("#"): + header_lines.append(line[2:]) + else: + break + + header_str = "".join(header_lines) + self.metadata = yaml.safe_load(header_str) + self.collection_probe = ProbeKey( + ip_address=self.metadata.get("collection_ip"), probe_id=self.metadata.get("collection_id") + ) + load_probe_metadata(vendor=self.vendor, probe_key=self.collection_probe, data={"reference": True}) + self.probe_key = ProbeKey( + ip_address=self.metadata.get("target_host"), probe_id=self.metadata.get("probe_id") + ) + self.metadata_parsed = True + + return self.metadata + + @classmethod + def load_metadata(cls, probe_key: ProbeKey, metadata: dict) -> None: + """ + Parse and return probe metadata from input file. + + Returns: + dict with metadata field names as keys + + """ + collection_probe = ProbeKey(ip_address=metadata.get("collection_ip"), probe_id=metadata.get("collection_id")) + load_probe_metadata(vendor=cls.vendor, probe_key=collection_probe, data={"reference": True}) + load_probe_metadata(vendor=cls.vendor, probe_key=probe_key, data=metadata) + + def process_time_data(self) -> None: + """ + Parse and load time series data from self.input_file. + + Use either send_time_data (which prefills METRICS.PHASE_OFFSET) + or send_data and provide alternative METRICS type. + Both require a df as follows: + pd.DataFrame with columns: + - time (datetime64[ns]): timestamp for each measurement + - value (float64): measured value at each timestamp + + """ + raw_df = pd.read_csv( + self.input_file, + comment="#", + ) + self.process_metadata() + + reference_type = REF_TYPES.PROBE + grouped_dfs: dict[str, pd.DataFrame] = { + str(metric): group.reset_index(drop=True) for metric, group in raw_df.groupby("metric") + } + for metr, df in grouped_dfs.items(): + metric = NTPCollector.metric_map.get(metr) + if not metric: + logger.warning(f"Metric {metr} is not supported for NTP. Will not ingest {len(df)} rows") + continue + try: + self.send_data( + data=df, + metric=metric, + reference_type=reference_type, + compound_reference=self.collection_probe.model_dump(), + ) + except requests.HTTPError as e: + resp = e.response + if resp is None: + raise + status_code = resp.status_code + if status_code == 409: + logger.info(f"{metr} against {self.collection_probe} already loaded for time frame, continuing..") + continue + raise + except IntegrityError as e: + if isinstance(e.orig, psycopg2.errors.UniqueViolation): # ty: ignore[unresolved-attribute] + logger.info( + f"{metr} against {self.collection_probe} already loaded for time " + f"frame already loaded for time frame, continuing.." + ) + + @classmethod + def collect(cls, collect_config: CollectConfig) -> CollectMixin.CollectArtifact: + """Collect readings for an NTP probe according to collect_config.""" + collector_overrides = collect_config.model_dump( + include=["collection_ip", "collection_id", "probe_id"], exclude_none=True + ) + + def collect_once() -> CollectMixin.CollectArtifact: + collector = None + if collect_config.mode == "local": + collector = NTPLocalCollector(target_host=collect_config.ip_address, **collector_overrides) + elif collect_config.mode == "remote": + collector = NTPRemoteCollector( + target_host=collect_config.ip_address, + target_port=collect_config.port, + timeout=collect_config.timeout, + **collector_overrides, + ) + if collector is None: + raise ValueError("Could not determine mode from collect_config") + collector.collect() + + return collector.export() + + if collect_config.interval <= 0: + return collect_once() + + artifact = None + sample_count = max(collect_config.duration, 1) + for sample_idx in range(sample_count): + newer = collect_once() + if artifact is None: + artifact = newer + else: + artifact.data.extend(newer.data) + artifact.metadata |= newer.metadata + + if sample_idx < sample_count - 1: + time.sleep(collect_config.interval) + + return artifact + + @classmethod + def create_file_content(cls, collected: CollectMixin.CollectArtifact) -> str: + """Create the content of a file from the CollectArtifacts""" + metric_names = NTPCollector.invert_metric_map() + dfs = [] + for d in collected.data or []: + df = d.value + df["metric"] = metric_names.get(d.metric.name, d.metric.name.lower().replace(" ", "_")) + dfs.append(df) + value_df = pd.concat(dfs) if dfs else None + + header = yaml.dump(collected.metadata, sort_keys=False) + header = textwrap.indent(header, prefix="# ") + buffer = StringIO() + buffer.write(header) + buffer.write("\n") + + if value_df is not None: + # write dataframe + value_df.to_csv(buffer, index=False) + + return buffer.getvalue() + + @classmethod + def generate_random_data( + cls, + config: RandomDataConfig, + probe_key: ProbeKey, + ) -> ProbeKey: + """Generate synthetic NTP-like metrics for testing.""" + cls._setup_random_seed(config.seed) + logger.info(f"Generating random NTP data for {probe_key}") + + meta = { + "mode": "random", + "name": f"Random NTP {probe_key}", + "target_host": "", + "target_port": 0, + "sync_status": "tracking", + "leap_status": "no_warning", + "observation_sources": ["random"], + "additional_metadata": {"test_data": True}, + } + cls._send_metadata_to_db(probe_key, meta) + + total_seconds = config.duration_hours * 3600 + num_samples = int(total_seconds / config.sample_interval) + times = [] + metric_maps = { + "offset": {"metric": METRICS.PHASE_OFFSET, "values": []}, + "delay_s": {"metric": METRICS.DELAY, "values": []}, + "jitter_s": {"metric": METRICS.JITTER, "values": []}, + "stratum": {"metric": METRICS.STRATUM, "values": []}, + "sync_health": {"metric": METRICS.SYNC_HEALTH, "values": []}, + } + + for i in range(num_samples): + sample_time = config.start_time + timedelta(seconds=i * config.sample_interval) + times.append(sample_time) + time_offset = i * config.sample_interval + drift_component = config.drift_rate * time_offset + noise = float(np.random.normal(0, config.noise_amplitude)) + offset = config.base_value + drift_component + noise + if random.random() < config.outlier_probability: + offset += float(np.random.normal(0, config.noise_amplitude * config.outlier_multiplier)) + + delay_s = 0.02 + abs(0.0001 * random.random()) + jitter_s = abs(float(config.noise_amplitude * 5)) + stratum = 2 + (1 if random.random() < 0.05 else 0) + sync_health = 1.0 + metric_maps["offset"]["values"].append(offset) + metric_maps["delay_s"]["values"].append(delay_s) + metric_maps["jitter_s"]["values"].append(jitter_s) + metric_maps["stratum"]["values"].append(stratum) + metric_maps["sync_health"]["values"].append(sync_health) + + for metric in metric_maps.values(): + cls.send_data( + probe_key=probe_key, + metric=metric.get("metric"), + reference_type=REF_TYPES.UNKNOWN, + data=pd.DataFrame({"time": times, "value": metric.get("values")}), + ) + + logger.info(f"Finished random NTP generation for {probe_key}") + return probe_key diff --git a/pyproject.toml b/pyproject.toml index d297b5d..acfd712 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,10 +18,11 @@ classifiers = [ "License :: OSI Approved :: MIT License", "Natural Language :: English", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", "Operating System :: OS Independent", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Physics", @@ -37,7 +38,7 @@ classifiers = [ "Framework :: Pydantic", "Framework :: Pydantic :: 2" ] -requires-python = ">=3.9,<3.13" +requires-python = ">=3.10,<3.15" dependencies = [ "pydantic>=2.10.3,<3", "pydantic-settings>=2.9.0", @@ -54,7 +55,7 @@ dependencies = [ "loguru>=0.7.0,<0.8", "psycopg2-binary>=2.9.0,<3", "python-dotenv", - "python-multipart>=0.0.20,<0.0.21", + "python-multipart>=0.0.26,<0.0.27", "astor", "libcst", "jinja2>=3.1.6", @@ -77,7 +78,10 @@ backend = [ "uvicorn", "prometheus-client", ] -collect = ["telnetlib3==2.0.4"] +collect = [ + "telnetlib3==2.0.4", + "ntplib>=0.4.0,<0.5" +] [project.scripts] opensampl = "opensampl.cli:cli" @@ -97,6 +101,8 @@ dev = [ "mkdocs-gen-files", "mkdocs-material", "mkdocs-click", + "psycopg[binary]", + "pytest-postgresql" ] [tool.hatch.build.targets.sdist] @@ -131,7 +137,7 @@ build-backend = "hatchling.build" [tool.ruff] line-length = 120 -exclude = [".git", "__pycache__", "venv", "env", ".venv", ".env", "build", "dist", "docs", "opensampl/server/migrations/**/*.py",] +exclude = [".git", "__pycache__", "venv", "env", ".venv", ".env", "build", "dist", "docs", "opensampl/server/migrations/**/*.py"] include = ["opensampl/**/*.py"] [tool.ruff.lint] @@ -141,12 +147,13 @@ select = ["F", "E", "W", "C", "I", "D", "N", "B", "ERA", "ANN", "S", "A", "COM", "FLY", "PERF", "PL", "UP", "FURB", "RUF", "TRY"] ignore = ["D203", "D212", "D400", "D415", "ANN401", "S101", "PLR2004", "COM812", "ANN201", "B011", "EM102", "TRY003", "ANN204", "FA100", "PIE790", "EM101", - "PLC0415"] + "PLC0415", 'E741'] [tool.ruff.lint.per-file-ignores] "opensampl/vendors/**/*.py" = ['S311'] # we want to ignore the errors about random "opensampl/server/backend/main.py" = ['B008', 'ARG001'] #ignore complaints about calling functions in args "opensampl/mixins/random_data.py" = ['S311'] + [tool.ruff.lint.pylint] max-args = 10 diff --git a/tests/integration/__init__.py b/tests/integration/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/integration/conftest.py b/tests/integration/conftest.py new file mode 100644 index 0000000..1ccf890 --- /dev/null +++ b/tests/integration/conftest.py @@ -0,0 +1,332 @@ +""" +tests/conftest.py + +Shared pytest fixtures for openSAMPL integration tests. + +Prerequisites +------------- +- PostgreSQL with PostGIS extension available +- pytest-postgresql installed: + uv add --group dev pytest-postgresql +- On macOS (Homebrew): + brew install postgresql postgis + +pytest-postgresql will locate pg_ctl automatically from your PATH. If you +have multiple Postgres versions installed, point it at the right one via +pytest.ini or pyproject.toml: + + [tool.pytest.ini_options] + postgresql_exec = "/opt/homebrew/opt/postgresql@16/bin/pg_ctl" +""" + +import pytest +from pytest_postgresql import factories as pg_factories +from sqlalchemy import create_engine, text +from sqlalchemy.orm import Session, sessionmaker + +from opensampl.db.orm import Base +from opensampl.db.orm import Defaults as DBDefaults +from opensampl.db.orm import MetricType as DBMetricType +from opensampl.db.orm import Reference as DBReference +from opensampl.db.orm import ReferenceType as DBReferenceType +from opensampl.metrics import METRICS, MetricType +from opensampl.references import REF_TYPES, ReferenceType + + +# --------------------------------------------------------------------------- +# pytest-postgresql process fixture +# +# postgresql_proc manages the Postgres server lifetime (session-scoped). +# We deliberately avoid the postgresql connection fixture so we have no +# dependency on a specific psycopg version — the project already has +# psycopg2-binary, and SQLAlchemy handles the connection from here. +# --------------------------------------------------------------------------- + +postgresql_proc = pg_factories.postgresql_proc() + + +# --------------------------------------------------------------------------- +# Helpers: introspect METRICS / REF_TYPES the same way VENDORS.all() does +# --------------------------------------------------------------------------- + +def _all_metrics() -> list[MetricType]: + """All MetricType instances defined on the METRICS class.""" + return [v for v in METRICS.__dict__.values() if isinstance(v, MetricType)] + + +def _all_ref_types() -> list[ReferenceType]: + """All ReferenceType instances defined on REF_TYPES (includes CompoundReferenceType).""" + return [v for v in REF_TYPES.__dict__.values() if isinstance(v, ReferenceType)] + + +# --------------------------------------------------------------------------- +# Session-scoped engine +# Schema, tables, seed data, and the get_default_uuid_for stub are all +# created once per test session. +# --------------------------------------------------------------------------- + +@pytest.fixture(scope="session") +def db_engine(postgresql_proc): + """ + Session-scoped SQLAlchemy engine pointed at the pytest-postgresql instance. + + Connects using psycopg2-binary (already a project dependency) so there is + no dependency on psycopg3. Creates the opensampl_test database on first + run via a temporary autocommit connection to the default 'postgres' database. + + Lifecycle: + 1. Create the opensampl_test database. + 2. Install PostGIS and create the castdb schema. + 3. Create all ORM tables via Base.metadata.create_all(). + 4. Seed metric_type, reference_type, reference, and defaults tables. + 5. Install the get_default_uuid_for() PL/pgSQL stub. + """ + # postgresql_proc exposes plain attributes — no psycopg version dependency + host = postgresql_proc.host + port = postgresql_proc.port + user = postgresql_proc.user + test_dbname = "opensampl_test" + + # Connect to the default 'postgres' db to create our test database. + # Must use isolation_level=AUTOCOMMIT because CREATE DATABASE cannot run + # inside a transaction block. + bootstrap_url = f"postgresql+psycopg2://{user}@{host}:{port}/postgres" + bootstrap_engine = create_engine(bootstrap_url, isolation_level="AUTOCOMMIT") + with bootstrap_engine.connect() as conn: + exists = conn.execute( + text("SELECT 1 FROM pg_database WHERE datname = :dbname"), + {"dbname": test_dbname}, + ).fetchone() + if not exists: + conn.execute(text(f'CREATE DATABASE "{test_dbname}"')) + bootstrap_engine.dispose() + + db_url = f"postgresql+psycopg2://{user}@{host}:{port}/{test_dbname}" + engine = create_engine(db_url, echo=False) + + with engine.begin() as conn: + # PostGIS is required by the Locations.geom column (GeoAlchemy2) + conn.execute(text("CREATE EXTENSION IF NOT EXISTS postgis")) + conn.execute(text(f"CREATE SCHEMA IF NOT EXISTS {Base.metadata.schema}")) + + Base.metadata.create_all(engine) + _seed_lookup_tables(engine) + _install_default_uuid_stub(engine) + + yield engine + + engine.dispose() + + +# --------------------------------------------------------------------------- +# Seeding helpers (called once from db_engine, not exposed as fixtures) +# --------------------------------------------------------------------------- + +def _seed_lookup_tables(engine) -> None: + """ + Populate metric_type, reference_type, reference, and defaults tables. + + Reads directly from the METRICS and REF_TYPES Python definitions so the + test DB always matches what the application expects — no hardcoded values. + After inserting the lookup rows, seeds the defaults table with the UUIDs + of the UNKNOWN rows, mirroring how production initialises get_default_uuid_for(). + """ + SessionLocal = sessionmaker(bind=engine) + session = SessionLocal() + + try: + # --- metric_type --- + for metric in _all_metrics(): + data = metric.model_dump() # value_type serialised to str by field_serializer + if not session.query(DBMetricType).filter_by(name=data["name"]).first(): + session.add(DBMetricType(**data)) + + # --- reference_type --- + # CompoundReferenceType.model_dump() includes reference_table; the column is nullable so plain + # ReferenceType rows (no reference_table) are stored with NULL, which is correct. + for ref_type in _all_ref_types(): + data = ref_type.model_dump() + if not session.query(DBReferenceType).filter_by(name=data["name"]).first(): + session.add(DBReferenceType(**data)) + + session.flush() + + # --- reference: one default UNKNOWN row -------------------------- + # get_default_uuid_for('reference') needs at least one reference row to + # point at. We use the UNKNOWN reference type with no compound target. + unknown_ref_type = session.query(DBReferenceType).filter_by(name=REF_TYPES.UNKNOWN.name).one() + default_reference = session.query(DBReference).filter_by( + reference_type_uuid=unknown_ref_type.uuid, + compound_reference_uuid=None, + ).first() + if not default_reference: + default_reference = DBReference( + reference_type_uuid=unknown_ref_type.uuid, + compound_reference_uuid=None, + ) + session.add(default_reference) + + session.flush() + + # --- defaults table --------------------------------------------- + # Maps table/category names to the UUID that get_default_uuid_for() + # should return. Mirrors what the production TimescaleDB init does. + unknown_metric = session.query(DBMetricType).filter_by(name=METRICS.UNKNOWN.name).one() + + for table_name, uuid_value in [ + ("metric_type", unknown_metric.uuid), + ("reference", default_reference.uuid), + ]: + if not session.query(DBDefaults).filter_by(table_name=table_name).first(): + session.add(DBDefaults(table_name=table_name, uuid=uuid_value)) + + session.commit() + + except Exception: + session.rollback() + raise + finally: + session.close() + + +def _install_default_uuid_stub(engine) -> None: + """ + Install the get_default_uuid_for() PL/pgSQL stub. + + Rather than hardcoding UUIDs, the stub queries the defaults table — the + same approach the production TimescaleDB function uses. This means it + automatically returns whatever was seeded above. + """ + schema = Base.metadata.schema + + with engine.begin() as conn: + conn.execute(text(f""" + CREATE OR REPLACE FUNCTION get_default_uuid_for(entity_type TEXT) + RETURNS TEXT AS $$ + DECLARE + result_uuid TEXT; + BEGIN + SELECT uuid + INTO result_uuid + FROM {schema}.defaults + WHERE table_name = entity_type; + + RETURN result_uuid; + END; + $$ LANGUAGE plpgsql; + """)) + + +# --------------------------------------------------------------------------- +# Per-test session — savepoint rollback keeps tests isolated +# --------------------------------------------------------------------------- + +@pytest.fixture +def db_session(db_engine) -> Session: + """ + Function-scoped database session backed by a savepoint. + + Every test starts with the full seeded dataset intact. Any rows inserted + or updated during the test are rolled back when the test ends without + disturbing the seeded rows, and without the cost of recreating the schema. + + Usage:: + + def test_something(db_session): + factory = TableFactory("locations", db_session) + factory.write({"name": "test-loc", "lat": 35.9, "lon": -84.3}) + result = db_session.query(Locations).filter_by(name="test-loc").one() + assert result.name == "test-loc" + # row is gone after the test + """ + connection = db_engine.connect() + outer_transaction = connection.begin() + session = Session(bind=connection) + session.begin_nested() # SAVEPOINT — inner rollback target + + yield session + + session.close() + outer_transaction.rollback() # wipes everything written during the test + connection.close() + + +# --------------------------------------------------------------------------- +# Seeded UUIDs — expose the canonical lookup UUIDs tests may need directly +# --------------------------------------------------------------------------- + +@pytest.fixture(scope="session") +def seeded_uuids(db_engine) -> dict: + """ + Session-scoped dict of UUIDs inserted during seed, keyed by logical name. + + Useful when a test needs to construct ORM objects by hand (e.g. ProbeData) + and must reference real FK values. + + Keys + ---- + metric_type. — UUID from the metric_type table + reference_type. — UUID from the reference_type table + reference.unknown — UUID of the default UNKNOWN reference row + default.metric_type — what get_default_uuid_for('metric_type') returns + default.reference — what get_default_uuid_for('reference') returns + + Example:: + + def test_probe_data(db_session, seeded_uuids): + phase_offset_uuid = seeded_uuids["metric_type.Phase Offset"] + """ + SessionLocal = sessionmaker(bind=db_engine) + session = SessionLocal() + + try: + uuids: dict = {} + + for row in session.query(DBMetricType).all(): + uuids[f"metric_type.{row.name}"] = row.uuid + + for row in session.query(DBReferenceType).all(): + uuids[f"reference_type.{row.name}"] = row.uuid + + unknown_ref_type = session.query(DBReferenceType).filter_by(name=REF_TYPES.UNKNOWN.name).one() + unknown_ref = session.query(DBReference).filter_by( + reference_type_uuid=unknown_ref_type.uuid, + compound_reference_uuid=None, + ).one() + uuids["reference.unknown"] = unknown_ref.uuid + + for row in session.query(DBDefaults).all(): + uuids[f"default.{row.table_name}"] = row.uuid + + return uuids + + finally: + session.close() + + +# --------------------------------------------------------------------------- +# Routing environment — patch BaseConfig for @route-decorated functions +# --------------------------------------------------------------------------- + +@pytest.fixture +def db_env(db_engine, monkeypatch) -> None: + """ + Set env vars so that BaseConfig routes directly to the test DB. + + Any test that calls a @route-decorated function (write_to_table, + load_time_data, load_probe_metadata, create_new_tables) must include + this fixture. Pass session=db_session explicitly so the route wrapper + uses your test session rather than opening a new one. + + Usage:: + + def test_write_to_table(db_env, db_session): + write_to_table( + "locations", + {"name": "test-loc", "lat": 35.9, "lon": -84.3}, + session=db_session, + ) + """ + monkeypatch.setenv("ROUTE_TO_BACKEND", "false") + monkeypatch.setenv("DATABASE_URL", str(db_engine.url)) + monkeypatch.delenv("BACKEND_URL", raising=False) \ No newline at end of file diff --git a/tests/integration/test_db_setup.py b/tests/integration/test_db_setup.py new file mode 100644 index 0000000..6f1f542 --- /dev/null +++ b/tests/integration/test_db_setup.py @@ -0,0 +1,106 @@ +""" +tests/integration/test_db_setup.py + +Smoke tests to verify the test database spun up and seeded correctly. +""" + +import pytest +from sqlalchemy import text + +from opensampl.db.orm import Defaults as DBDefaults +from opensampl.db.orm import MetricType as DBMetricType +from opensampl.db.orm import Reference as DBReference +from opensampl.db.orm import ReferenceType as DBReferenceType +from opensampl.metrics import METRICS, MetricType +from opensampl.references import REF_TYPES, ReferenceType + + +def test_schema_exists(db_session): + """castdb schema was created.""" + result = db_session.execute( + text("SELECT schema_name FROM information_schema.schemata WHERE schema_name = 'castdb'") + ).scalar() + assert result == "castdb" + + +def test_postgis_installed(db_session): + """PostGIS extension is available (required for Locations.geom).""" + result = db_session.execute(text("SELECT extname FROM pg_extension WHERE extname = 'postgis'")).scalar() + assert result == "postgis" + + +def test_all_metrics_seeded(db_session): + """Every MetricType defined on METRICS is present in the metric_type table.""" + expected = {v.name for v in METRICS.__dict__.values() if isinstance(v, MetricType)} + seeded = {row.name for row in db_session.query(DBMetricType).all()} + assert expected == seeded + + +def test_all_reference_types_seeded(db_session): + """Every ReferenceType defined on REF_TYPES is present in the reference_type table.""" + expected = {v.name for v in REF_TYPES.__dict__.values() if isinstance(v, ReferenceType)} + seeded = {row.name for row in db_session.query(DBReferenceType).all()} + assert expected == seeded + + +def test_default_reference_row_exists(db_session): + """A default UNKNOWN reference row exists for get_default_uuid_for('reference').""" + unknown_ref_type = db_session.query(DBReferenceType).filter_by(name=REF_TYPES.UNKNOWN.name).one() + ref = db_session.query(DBReference).filter_by( + reference_type_uuid=unknown_ref_type.uuid, + compound_reference_uuid=None, + ).first() + assert ref is not None + + +def test_defaults_table_seeded(db_session): + """defaults table has entries for both metric_type and reference.""" + rows = {row.table_name for row in db_session.query(DBDefaults).all()} + assert "metric_type" in rows + assert "reference" in rows + + +def test_get_default_uuid_for_metric_type(db_session): + """Stub function returns the UUID of the UNKNOWN metric type.""" + result = db_session.execute(text("SELECT get_default_uuid_for('metric_type')")).scalar() + expected = db_session.query(DBMetricType.uuid).filter_by(name=METRICS.UNKNOWN.name).scalar() + assert result == expected + + +def test_get_default_uuid_for_reference(db_session): + """Stub function returns the UUID of the default UNKNOWN reference row.""" + result = db_session.execute(text("SELECT get_default_uuid_for('reference')")).scalar() + unknown_ref_type = db_session.query(DBReferenceType).filter_by(name=REF_TYPES.UNKNOWN.name).one() + expected = db_session.query(DBReference.uuid).filter_by( + reference_type_uuid=unknown_ref_type.uuid, + compound_reference_uuid=None, + ).scalar() + assert result == expected + + +def test_seeded_uuids_fixture(seeded_uuids): + """seeded_uuids convenience fixture has the expected keys.""" + assert f"metric_type.{METRICS.UNKNOWN.name}" in seeded_uuids + assert f"metric_type.{METRICS.PHASE_OFFSET.name}" in seeded_uuids + assert f"reference_type.{REF_TYPES.UNKNOWN.name}" in seeded_uuids + assert "reference.unknown" in seeded_uuids + assert "default.metric_type" in seeded_uuids + assert "default.reference" in seeded_uuids + + +def test_session_rollback_isolation(db_session, db_engine): + """Writes in one session do not leak — the savepoint rolls back cleanly.""" + from opensampl.db.orm import TestMetadata + + db_session.add(TestMetadata(name="rollback-canary")) + db_session.flush() + + # Row is visible within this session + assert db_session.query(TestMetadata).filter_by(name="rollback-canary").one() + + # After the test ends the fixture rolls back, but we can verify the + # mechanism works by checking a fresh session sees nothing yet + from sqlalchemy.orm import Session + with Session(bind=db_engine) as fresh: + result = fresh.query(TestMetadata).filter_by(name="rollback-canary").first() + assert result is None, 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