diff --git a/geomagio/api/ws/DataApiQuery.py b/geomagio/api/ws/DataApiQuery.py
index ac88e6092a94967b8d2a3907936b88fd776c6545..9f5217e09a7707913c26cdbb37230b770c83f6d3 100644
--- a/geomagio/api/ws/DataApiQuery.py
+++ b/geomagio/api/ws/DataApiQuery.py
@@ -1,5 +1,6 @@
import datetime
import enum
+from enum import Enum
import os
from typing import List, Optional, Union
@@ -9,8 +10,12 @@ from pydantic import ConfigDict, field_validator, model_validator, Field, BaseMo
from .Element import ELEMENTS
from .Observatory import OBSERVATORY_INDEX, ASL_OBSERVATORY_INDEX
from ...pydantic_utcdatetime import CustomUTCDateTimeType
+import logging
-
+logging.basicConfig(
+ level=logging.INFO,
+ format="%(asctime)s - %(levelname)s - %(message)s",
+)
DEFAULT_ELEMENTS = ["X", "Y", "Z", "F"]
REQUEST_LIMIT = 3456000 # Increased the request limit by 10x what was decided by Jeremy
VALID_ELEMENTS = [e.id for e in ELEMENTS]
@@ -68,7 +73,7 @@ class DataApiQuery(BaseModel):
# endtime default is dependent on start time, so it's handled after validation in the model_validator
endtime: Optional[CustomUTCDateTimeType] = None
elements: List[str] = DEFAULT_ELEMENTS
- sampling_period: SamplingPeriod = SamplingPeriod.MINUTE
+ sampling_period: Optional[SamplingPeriod] = None
data_type: Union[DataType, str] = DataType.VARIATION
format: Union[OutputFormat, str] = OutputFormat.IAGA2002
data_host: Union[DataHost, str] = DataHost.DEFAULT
@@ -123,11 +128,20 @@ class DataApiQuery(BaseModel):
self.endtime = self.starttime + (86400 - 0.001)
if self.starttime > self.endtime:
raise ValueError("Starttime must be before endtime.")
- # check data volume
- samples = int(
- len(self.elements) * (self.endtime - self.starttime) / self.sampling_period
- )
- if samples > REQUEST_LIMIT:
- raise ValueError(f"Request exceeds limit ({samples} > {REQUEST_LIMIT})")
- # otherwise okay
+
+ # check data volume and if SamplingPeriod is assigned as None
+ if self.sampling_period is None:
+ logging.warning(
+ "Sampling period is None. Default value or further processing needed."
+ )
+
+ else:
+ samples = int(
+ len(self.elements)
+ * (self.endtime - self.starttime)
+ / self.sampling_period
+ )
+ if samples > REQUEST_LIMIT:
+ raise ValueError(f"Request exceeds limit ({samples} > {REQUEST_LIMIT})")
+ # otherwise okay
return self
diff --git a/geomagio/api/ws/FilterApiQuery.py b/geomagio/api/ws/FilterApiQuery.py
index cb2e4e027207a41410037a41901d63206b630cfb..cee262d9004d219e47dceccac31971f266b626a8 100644
--- a/geomagio/api/ws/FilterApiQuery.py
+++ b/geomagio/api/ws/FilterApiQuery.py
@@ -1,5 +1,17 @@
-from .DataApiQuery import DataApiQuery, SamplingPeriod, REQUEST_LIMIT
-from pydantic import ConfigDict, model_validator
+from .DataApiQuery import (
+ DataApiQuery,
+ SamplingPeriod,
+ REQUEST_LIMIT,
+)
+from pydantic import ConfigDict, model_validator, field_validator, ValidationError
+from typing import Optional
+import logging
+from fastapi import HTTPException
+
+logging.basicConfig(
+ level=logging.INFO,
+ format="%(asctime)s - %(levelname)s - %(message)s",
+)
"""This class inherits all the fields and validation on DataApiQuery and adds
the fields input_sampling_period and output_sampling_period."""
@@ -8,20 +20,26 @@ the fields input_sampling_period and output_sampling_period."""
class FilterApiQuery(DataApiQuery):
model_config = ConfigDict(extra="forbid")
- input_sampling_period: SamplingPeriod = SamplingPeriod.SECOND
- output_sampling_period: SamplingPeriod = SamplingPeriod.MINUTE
+ input_sampling_period: Optional[SamplingPeriod] = None
@model_validator(mode="after")
def validate_sample_size(self):
- # Calculate the number of samples based on the input sampling period
- samples = int(
- len(self.elements)
- * (self.endtime - self.starttime)
- / self.input_sampling_period
- )
-
- # Validate the request size
- if samples > REQUEST_LIMIT:
- raise ValueError(f"Request exceeds limit ({samples} > {REQUEST_LIMIT})")
+ if self.sampling_period is None:
+ # Log a warning indicating that the sampling period is missing
+ logging.warning(
+ "Sampling period is None. Please provide a valid Sampling Period."
+ )
+
+ else:
+ # Calculate the number of samples based on the input sampling period
+ samples = int(
+ len(self.elements)
+ * (self.endtime - self.starttime)
+ / self.sampling_period
+ )
+
+ # Validate the request size
+ if samples > REQUEST_LIMIT:
+ raise ValueError(f"Request exceeds limit ({samples} > {REQUEST_LIMIT})")
return self
diff --git a/geomagio/api/ws/algorithms.py b/geomagio/api/ws/algorithms.py
index ec18ae9fd2c2ed01e646a6d0f514a3248550021e..c4696a4c5323115c7f715eb325006ae1394cccf8 100644
--- a/geomagio/api/ws/algorithms.py
+++ b/geomagio/api/ws/algorithms.py
@@ -2,20 +2,21 @@ import json
from fastapi import APIRouter, Depends, HTTPException, Query
from starlette.responses import Response
-from obspy.core import Stream, Stats
-from typing import List, Union
-from ...algorithm import DbDtAlgorithm, FilterAlgorithm
+
+from ...algorithm import DbDtAlgorithm
from ...residual import (
calculate,
Reading,
)
-from .DataApiQuery import DataApiQuery, SamplingPeriod
+from .DataApiQuery import DataApiQuery
from .FilterApiQuery import FilterApiQuery
from .data import format_timeseries, get_data_factory, get_data_query, get_timeseries
from .filter import get_filter_data_query
from . import filter
+import logging
+logger = logging.getLogger(__name__)
router = APIRouter()
@@ -43,42 +44,16 @@ def get_dbdt(
####################################### The router .get filter isnt visible on the docs page
# Look for register routers in the backend
-
-
@router.get(
"/algorithms/filter/",
description="Filtered data dependent on requested interval",
name="Filtered Algorithm",
)
-# New query parameter defined below. I am using a new query defined in DataApitQuery.
-# This relies on the new filter.py module and the get_filter_data function
-# to define input and output sampling period.
-
-
-def get_filter(
- query: FilterApiQuery = Depends(get_filter_data_query),
-) -> Response:
-
- filt = FilterAlgorithm(
- input_sample_period=query.input_sampling_period,
- output_sample_period=query.output_sampling_period,
- )
-
- # Grab the correct starttime and endtime for the timeseries from get_input_interval
- starttime, endtime = filt.get_input_interval(query.starttime, query.endtime)
+def get_filter(query: FilterApiQuery = Depends(get_filter_data_query)) -> Response:
- # Reassign the actual start/endtime to the query parameters
- query.starttime = starttime
- query.endtime = endtime
-
- data_factory = get_data_factory(query=query)
- # read data
- raw = filter.get_timeseries(data_factory, query)
-
- filtered_timeseries = filt.process(raw)
+ filtered_timeseries = filter.get_timeseries(query)
elements = [f"{element}" for element in query.elements]
- # output response
return format_timeseries(
timeseries=filtered_timeseries, format=query.format, elements=elements
)
diff --git a/geomagio/api/ws/data.py b/geomagio/api/ws/data.py
index 3a77dbb8a51b4cfe4641b728789c2c7e77f9f514..1eb735fd54c39d89f7ec75a38dc8725b5cff09b4 100644
--- a/geomagio/api/ws/data.py
+++ b/geomagio/api/ws/data.py
@@ -74,7 +74,7 @@ def get_data_query(
" NOTE: when using 'iaga2002' output format, a maximum of 4 elements is allowed",
),
sampling_period: Union[SamplingPeriod, float] = Query(
- SamplingPeriod.MINUTE,
+ None,
title="data rate",
description="Interval in seconds between values.",
),
diff --git a/geomagio/api/ws/filter.py b/geomagio/api/ws/filter.py
index 54c5f6825a9922f74dfa55c4ba7776909a9d76f8..69516903bc7085621a48985709c5edc8068ae9d0 100644
--- a/geomagio/api/ws/filter.py
+++ b/geomagio/api/ws/filter.py
@@ -1,7 +1,8 @@
from typing import List, Union, Optional
from fastapi import Query
-from obspy import UTCDateTime, Stream
-from ... import TimeseriesFactory, TimeseriesUtility
+from obspy import Stream
+from ... import TimeseriesUtility
+import numpy as np
from .DataApiQuery import (
DEFAULT_ELEMENTS,
DataHost,
@@ -10,6 +11,9 @@ from .DataApiQuery import (
SamplingPeriod,
)
from .FilterApiQuery import FilterApiQuery
+from ...algorithm import FilterAlgorithm
+import logging as logger
+from .data import get_data_factory
from ...pydantic_utcdatetime import CustomUTCDateTimeType
@@ -26,11 +30,15 @@ def get_filter_data_query(
format: Union[OutputFormat, str] = Query(
OutputFormat.IAGA2002, title="Output Format"
),
- input_sampling_period: Union[SamplingPeriod, float] = Query(
- SamplingPeriod.SECOND, title="Initial sampling period"
+ input_sampling_period: Optional[SamplingPeriod] = Query(
+ None,
+ title="Input Sampling Period",
+ description="`--` dynamically determines a necessary sampling period.",
),
- output_sampling_period: Union[SamplingPeriod, float] = Query(
- SamplingPeriod.MINUTE, title="Output sampling period"
+ sampling_period: Optional[SamplingPeriod] = Query(
+ None,
+ alias="output_sampling_period",
+ title="Output sampling period",
),
data_host: Union[DataHost, str] = Query(
DataHost.DEFAULT, title="Data Host", description="Edge host to pull data from."
@@ -43,28 +51,107 @@ def get_filter_data_query(
endtime=endtime,
elements=elements,
input_sampling_period=input_sampling_period,
- output_sampling_period=output_sampling_period,
+ sampling_period=sampling_period,
data_type=data_type,
data_host=data_host,
format=format,
)
-def get_timeseries(data_factory: TimeseriesFactory, query: FilterApiQuery) -> Stream:
- """Get timeseries data for variometers
+# Main filter function
+def get_timeseries(query: FilterApiQuery) -> Stream:
+ data_factory = get_data_factory(query=query)
- Parameters
- ----------
- data_factory: where to read data
- query: parameters for the data to read
- """
- # get data
- timeseries = data_factory.get_timeseries(
- starttime=query.starttime,
- endtime=query.endtime,
+ # Determine input sampling period if not provided
+ if query.input_sampling_period is None:
+ # Dynamically determine the input sampling period
+ input_sampling_period, data = determine_available_period(
+ query.sampling_period, query, data_factory
+ )
+ else:
+ input_sampling_period = query.input_sampling_period
+
+ filt = FilterAlgorithm(
+ input_sample_period=input_sampling_period,
+ output_sample_period=query.sampling_period,
+ )
+ # Fetch filtered data
+ starttime, endtime = filt.get_input_interval(query.starttime, query.endtime)
+
+ data = data_factory.get_timeseries(
+ starttime=starttime,
+ endtime=endtime,
observatory=query.id,
channels=query.elements,
type=query.data_type,
- interval=TimeseriesUtility.get_interval_from_delta(query.input_sampling_period),
+ interval=TimeseriesUtility.get_interval_from_delta(filt.input_sample_period),
)
- return timeseries
+
+ # Apply filtering if needed
+
+ filtered_timeseries = filt.process(data)
+ return filtered_timeseries
+
+
+def determine_available_period(output_sampling_period: float, query, data_factory):
+ """
+ Finds the lowest resolution (longest sampling period) <= output_sampling_period
+ that has valid data available.
+ """
+
+ # Sort and filter periods starting from output_sampling_period
+ sorted_periods: List[SamplingPeriod] = sorted(
+ SamplingPeriod, key=lambda p: p.value, reverse=True
+ )
+ if output_sampling_period is None:
+ raise ValueError("Output sampling period cannot be None.")
+ else:
+
+ valid_sampling_periods = [
+ p for p in sorted_periods if p.value <= output_sampling_period
+ ]
+
+ for period in valid_sampling_periods:
+ if period <= output_sampling_period:
+
+ data = data_factory.get_timeseries(
+ starttime=query.starttime,
+ endtime=query.endtime,
+ observatory=query.id,
+ channels=query.elements,
+ type=query.data_type,
+ interval=TimeseriesUtility.get_interval_from_delta(period.value),
+ )
+ # Check if the fetched data is valid
+ if is_valid_data(data):
+
+ logger.info(f"Valid data found for sampling period: {period.name}")
+ return period.value, data # Return the sampling period and the data
+
+ else:
+ logger.error(
+ f"No valid data found for requested sampling period: {period.name}"
+ )
+ continue
+
+ raise ValueError("No valid data found for the requested output sampling period.")
+
+
+def is_valid_data(data: Stream) -> bool:
+ """
+ Checks if the fetched data contains actual values and not just filler values (e.g., NaN).
+ A Stream is invalid if any trace contains only NaN values.
+ """
+ if not data or len(data) == 0:
+ return False # No data in the stream
+
+ for trace in data:
+ # Check if trace.data exists and has data
+ if trace.data is None or len(trace.data) == 0:
+ return False # Trace has no data
+
+ # Check if all values in trace.data are NaN
+ if np.all(np.isnan(trace.data)):
+ return False # Invalid if all values are NaN
+
+ return True # All traces are valid
diff --git a/poetry.lock b/poetry.lock
index d2d17532d28de155a8a215cf90f1dbc421d0a6b5..2976e14e6e53dcd1d5b5e1c3b59ca3891840cc92 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
[[package]]
name = "aiomysql"
@@ -154,13 +154,13 @@ uvloop = ["uvloop (>=0.15.2)"]
[[package]]
name = "certifi"
-version = "2024.8.30"
+version = "2024.12.14"
description = "Python package for providing Mozilla's CA Bundle."
optional = false
python-versions = ">=3.6"
files = [
- {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
- {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
+ {file = "certifi-2024.12.14-py3-none-any.whl", hash = "sha256:1275f7a45be9464efc1173084eaa30f866fe2e47d389406136d332ed4967ec56"},
+ {file = "certifi-2024.12.14.tar.gz", hash = "sha256:b650d30f370c2b724812bee08008be0c4163b163ddaec3f2546c1caf65f191db"},
]
[[package]]
@@ -244,127 +244,114 @@ pycparser = "*"
[[package]]
name = "charset-normalizer"
-version = "3.4.0"
+version = "3.4.1"
description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
optional = false
-python-versions = ">=3.7.0"
-files = [
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- {file = "charset_normalizer-3.4.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:0de7b687289d3c1b3e8660d0741874abe7888100efe14bd0f9fd7141bcbda92b"},
- {file = "charset_normalizer-3.4.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:5ed2e36c3e9b4f21dd9422f6893dec0abf2cca553af509b10cd630f878d3eb99"},
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- {file = "pycurl-7.45.3-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:fa7751b614d9aa82d7a0f49ca90924c29c6cedf85a2f8687fb6a772dbfe48711"},
- {file = "pycurl-7.45.3-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:b129e9ee07f80b4af957607917af46ab517b0c4e746692f6d9e50e973edba8d8"},
- {file = "pycurl-7.45.3-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:a0f920582b8713ca87d5a288a7532607bc4454275d733fc880650d602dbe3c67"},
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- {file = "pycurl-7.45.3-cp39-cp39-win32.whl", hash = "sha256:51a40a56c58e63dac6145829f9e9bd66e5867a9f0741bcb9ffefab619851d44f"},
- {file = "pycurl-7.45.3-cp39-cp39-win_amd64.whl", hash = "sha256:e08a06802c8c8a9d04cf3319f9230ec09062c55d2550bd48f8ada1df1431adcf"},
- {file = "pycurl-7.45.3.tar.gz", hash = "sha256:8c2471af9079ad798e1645ec0b0d3d4223db687379d17dd36a70637449f81d6b"},
+ {file = "pycurl-7.45.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:247b4af8eab7d04137a7f1a98391930e04ea93dc669b64db5625070fe15f80a3"},
+ {file = "pycurl-7.45.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:561f88697f7540634b1c750146f37bdc0da367b15f6b4ab2bb780871ee6ab005"},
+ {file = "pycurl-7.45.4-cp310-cp310-manylinux_2_28_aarch64.whl", hash = "sha256:b485fdaf78553f0b8e1c2803bb7dcbe47a7b47594f846fc7e9d3b94d794cfc89"},
+ {file = "pycurl-7.45.4-cp310-cp310-manylinux_2_28_x86_64.whl", hash = "sha256:e7ae49b88a5d57485fbabef004534225dfe04dc15716a61fae1a0c7f46f2279e"},
+ {file = "pycurl-7.45.4-cp310-cp310-win32.whl", hash = "sha256:d14f954ecd21a070038d65ef1c6d1d3ab220f952ff703d48313123222097615c"},
+ {file = "pycurl-7.45.4-cp310-cp310-win_amd64.whl", hash = "sha256:2548c3291a33c821f0f80bf9989fc43b5d90fb78b534a7015c8419b83c6f5803"},
+ {file = "pycurl-7.45.4-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:f6c0e22052946bbfa25be67f9d1d6639eff10781c89f0cf6f3ff2099273d1bad"},
+ {file = "pycurl-7.45.4-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:acf25cfdaf914db21a2a6e9e274b6d95e3fa2b6018c38f2c58c94b5d8ac3d1b7"},
+ {file = "pycurl-7.45.4-cp311-cp311-manylinux_2_28_aarch64.whl", hash = "sha256:a39f28f031885485325034918386be352036c220ca45625c7e286d3938eb579d"},
+ {file = "pycurl-7.45.4-cp311-cp311-manylinux_2_28_x86_64.whl", hash = "sha256:9940e3234c1ca3d30f27a2202d325dbc25291605c98e9585100a351cacd935e8"},
+ {file = "pycurl-7.45.4-cp311-cp311-win32.whl", hash = "sha256:ffd3262f98b8997ad04940061d5ebd8bab2362169b9440939c397e24a4a135b0"},
+ {file = "pycurl-7.45.4-cp311-cp311-win_amd64.whl", hash = "sha256:1324a859b50bdb0abdbd5620e42f74240d0b7daf2d5925fa303695d9fc3ece18"},
+ {file = "pycurl-7.45.4-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:731c46e7c0acffaab19f7c2ecc3d9e7ee337500e87b260b4e0b9fae2d90fa133"},
+ {file = "pycurl-7.45.4-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:13eb1643ab0bf4fdc539a2cdf1021029b07095d3196c5cee5a4271af268d3d31"},
+ {file = "pycurl-7.45.4-cp312-cp312-manylinux_2_28_aarch64.whl", hash = "sha256:df5f94c051c5a163fa85064559ca94979575e2da26740ff91c078c50c541c465"},
+ {file = "pycurl-7.45.4-cp312-cp312-manylinux_2_28_x86_64.whl", hash = "sha256:688d09ba2c6a0d4a749d192c43422839d73c40c85143c50cc65c944258fe0ba8"},
+ {file = "pycurl-7.45.4-cp312-cp312-win32.whl", hash = "sha256:236600bfe2cd72efe47333add621286667e8fa027dadf1247349afbf30333e95"},
+ {file = "pycurl-7.45.4-cp312-cp312-win_amd64.whl", hash = "sha256:26745c6c5ebdccfe8a828ac3fd4e6da6f5d2245696604f04529eb7894a02f4db"},
+ {file = "pycurl-7.45.4-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:9bd493ce598f1dc76c8e50043c47debec27c583fa313a836b2d3667640f875d5"},
+ {file = "pycurl-7.45.4-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:4f25d52c97dbca6ebea786f0961b49c1998fa05178abf1964a977c825b3d8ae6"},
+ {file = "pycurl-7.45.4-cp313-cp313-manylinux_2_28_aarch64.whl", hash = "sha256:13c4b18f44637859f34639493efd297a08670f45e4eec34ab2dcba724e3cb5fc"},
+ {file = "pycurl-7.45.4-cp313-cp313-manylinux_2_28_x86_64.whl", hash = "sha256:0470bff6cc24d8c2f63c80931aa239463800871609dafc6bcc9ca10f5a12a04e"},
+ {file = "pycurl-7.45.4-cp313-cp313-win32.whl", hash = "sha256:3452459668bd01d646385482362b021834a31c036aa1c02acd88924ddeff7d0d"},
+ {file = "pycurl-7.45.4-cp313-cp313-win_amd64.whl", hash = "sha256:fd167f73d34beb0cb8064334aee76d9bdd13167b30be6d5d36fb07d0c8223b71"},
+ {file = "pycurl-7.45.4-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:b0e38e3eb83b0c891f391853f798fc6a97cb5a86a4a731df0b6320e539ae54ae"},
+ {file = "pycurl-7.45.4-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:d192a48b3cec2e13ad432196b65c22e99620db92feae39c0476635354eff68c6"},
+ {file = "pycurl-7.45.4-cp39-cp39-manylinux_2_28_aarch64.whl", hash = "sha256:57971d7215fc6fdedcfc092f880a59f04f52fcaf2fd329151b931623d7b59a9c"},
+ {file = "pycurl-7.45.4-cp39-cp39-manylinux_2_28_x86_64.whl", hash = "sha256:73df3eb5940a7fbf4cf62f7271e9f23a8e9f80e352c838ee9a8448a70c01d3f5"},
+ {file = "pycurl-7.45.4-cp39-cp39-win32.whl", hash = "sha256:587a4891039803b5f48392066f97b7cd5e7e9a166187abb5cb4b4806fdb8fbef"},
+ {file = "pycurl-7.45.4-cp39-cp39-win_amd64.whl", hash = "sha256:caec8b634763351dd4e1b729a71542b1e2de885d39710ba8e7202817a381b453"},
+ {file = "pycurl-7.45.4.tar.gz", hash = "sha256:32c8e237069273f4260b6ae13d1e0f99daae938977016021565dc6e11050e803"},
]
[[package]]
@@ -2280,13 +2262,13 @@ idna2008 = ["idna"]
[[package]]
name = "ruamel-yaml"
-version = "0.18.6"
+version = "0.18.10"
description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order"
optional = false
python-versions = ">=3.7"
files = [
- {file = "ruamel.yaml-0.18.6-py3-none-any.whl", hash = "sha256:57b53ba33def16c4f3d807c0ccbc00f8a6081827e81ba2491691b76882d0c636"},
- {file = "ruamel.yaml-0.18.6.tar.gz", hash = "sha256:8b27e6a217e786c6fbe5634d8f3f11bc63e0f80f6a5890f28863d9c45aac311b"},
+ {file = "ruamel.yaml-0.18.10-py3-none-any.whl", hash = "sha256:30f22513ab2301b3d2b577adc121c6471f28734d3d9728581245f1e76468b4f1"},
+ {file = "ruamel.yaml-0.18.10.tar.gz", hash = "sha256:20c86ab29ac2153f80a428e1254a8adf686d3383df04490514ca3b79a362db58"},
]
[package.dependencies]
diff --git a/pytest.ini b/pytest.ini
index 3d8cf70409816af31181c2160f79f4d3b8b4b17e..92ad01e1f519b02369ca11e0dd347de146d86b91 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -3,3 +3,9 @@ norecursedirs = */site-packages
testpaths = test
asyncio_mode=auto
asyncio_default_fixture_loop_scope="function"
+# Suppress warnings of level WARNING and below
+log_level = WARNING
+
+# Optionally, you can filter out UserWarnings generated by logging
+filterwarnings =
+ ignore::UserWarning
\ No newline at end of file
diff --git a/test/DataApiQuery_test.py b/test/DataApiQuery_test.py
index 117f1758c1be5f4d9668dc25208ec8fcee5a3596..737286b3b77e47d77292bac556db72bc9fda8f52 100644
--- a/test/DataApiQuery_test.py
+++ b/test/DataApiQuery_test.py
@@ -23,7 +23,7 @@ def test_DataApiQuery_defaults():
assert_equal(query.starttime, expected_start_time)
assert_equal(query.endtime, expected_endtime)
assert_equal(query.elements, ["X", "Y", "Z", "F"])
- assert_equal(query.sampling_period, SamplingPeriod.MINUTE)
+ assert_equal(query.sampling_period, None)
assert_equal(query.data_type, DataType.VARIATION)
assert_equal(query.format, OutputFormat.IAGA2002)
# assumes the env var DATA_HOST is not set
@@ -41,7 +41,7 @@ def test_DataApiQuery_starttime_is_none():
assert_equal(query.starttime, expected_start_time)
assert_equal(query.endtime, expected_endtime)
assert_equal(query.elements, ["X", "Y", "Z", "F"])
- assert_equal(query.sampling_period, SamplingPeriod.MINUTE)
+ assert_equal(query.sampling_period, None)
assert_equal(query.data_type, DataType.VARIATION)
assert_equal(query.format, OutputFormat.IAGA2002)
# assumes the env var DATA_HOST is not set
@@ -100,7 +100,7 @@ def test_DataApiQuery_default_endtime():
# endtime is 1 day after start time
assert_equal(query.endtime, UTCDateTime("2024-11-02T00:00:00.999"))
assert_equal(query.elements, ["X", "Y", "Z", "F"])
- assert_equal(query.sampling_period, SamplingPeriod.MINUTE)
+ assert_equal(query.sampling_period, None)
assert_equal(query.data_type, DataType.VARIATION)
assert_equal(query.format, OutputFormat.IAGA2002)
assert_equal(query.data_host, DataHost.DEFAULT)
@@ -122,7 +122,7 @@ def test_DataApiQuery_default_only_endtime():
assert_equal(query.endtime, hour_later)
assert_equal(query.elements, ["X", "Y", "Z", "F"])
- assert_equal(query.sampling_period, SamplingPeriod.MINUTE)
+ assert_equal(query.sampling_period, None)
assert_equal(query.data_type, DataType.VARIATION)
assert_equal(query.format, OutputFormat.IAGA2002)
assert_equal(query.data_host, DataHost.DEFAULT)
diff --git a/test/FilterApiQuery_test.py b/test/FilterApiQuery_test.py
index f4f49a563aa0d82ffb0103aea6f1b832a699d190..6f734f133f8c6f66bad32a2840bac469bbdcc92f 100644
--- a/test/FilterApiQuery_test.py
+++ b/test/FilterApiQuery_test.py
@@ -22,8 +22,8 @@ def test_FilterApiQuery_defaults():
assert_equal(query.starttime, expected_start_time)
assert_equal(query.endtime, expected_endtime)
assert_equal(query.elements, ["X", "Y", "Z", "F"])
- assert_equal(query.input_sampling_period, SamplingPeriod.SECOND)
- assert_equal(query.output_sampling_period, SamplingPeriod.MINUTE)
+ assert_equal(query.input_sampling_period, None)
+ assert_equal(query.sampling_period, None)
assert_equal(query.data_type, DataType.VARIATION)
assert_equal(query.format, OutputFormat.IAGA2002)
assert_equal(query.data_host, DataHost.DEFAULT)
@@ -36,7 +36,7 @@ def test_FilterApiQuery_valid():
endtime="2024-09-01T01:00:01",
elements=["Z"],
input_sampling_period=60,
- output_sampling_period=3600,
+ sampling_period=3600,
data_type="adjusted",
format="json",
data_host="cwbpub.cr.usgs.gov",
@@ -47,7 +47,7 @@ def test_FilterApiQuery_valid():
assert_equal(query.endtime, UTCDateTime("2024-09-01T01:00:01"))
assert_equal(query.elements, ["Z"])
assert_equal(query.input_sampling_period, SamplingPeriod.MINUTE)
- assert_equal(query.output_sampling_period, SamplingPeriod.HOUR)
+ assert_equal(query.sampling_period, SamplingPeriod.HOUR)
assert_equal(query.data_type, "adjusted")
assert_equal(query.format, "json")
assert_equal(query.data_host, "cwbpub.cr.usgs.gov")
@@ -83,7 +83,7 @@ def test_FilterApiQuery_default_endtime():
# endtime is 1 day after start time
assert_equal(query.endtime, UTCDateTime("2024-11-02T00:00:00.999"))
assert_equal(query.elements, ["X", "Y", "Z", "F"])
- assert_equal(query.sampling_period, SamplingPeriod.MINUTE)
+ assert_equal(query.sampling_period, None)
assert_equal(query.data_type, DataType.VARIATION)
assert_equal(query.format, OutputFormat.IAGA2002)
assert_equal(query.data_host, DataHost.DEFAULT)
@@ -190,3 +190,13 @@ def test_FilterApiQuery_extra_fields():
assert "Extra inputs are not permitted" == err[0]["msg"]
assert_equal(query, None)
+
+
+def test_FilterApiQuery_no_output_sampling_period():
+ query = None
+ try:
+ query = FilterApiQuery(id="ANMO", sampling_period=None)
+ except Exception as e:
+ err = e.errors()
+ assert "Output sampling period cannot be None." == err[0]["msg"]
+ assert_equal(query, None)
diff --git a/test/api_test/ws_test/data_test.py b/test/api_test/ws_test/data_test.py
index 3376e31100056e7186ce47543fad8f81d352e404..765fa407b013db3f9e87b87d04c56a3b576d6d99 100644
--- a/test/api_test/ws_test/data_test.py
+++ b/test/api_test/ws_test/data_test.py
@@ -28,7 +28,7 @@ def test_client():
def test_get_data_query(test_client):
"""test.api_test.ws_test.data_test.test_get_data_query()"""
response = test_client.get(
- "/query/?id=BOU&starttime=2020-09-01T00:00:01&elements=X,Y,Z,F&type=R1&sampling_period=60&format=iaga2002"
+ "/query/?id=BOU&starttime=2020-09-01T00:00:01&elements=X,Y,Z,F&type=variation&sampling_period=60&format=iaga2002"
)
query = DataApiQuery(**response.json())
assert_equal(query.id, "BOU")
@@ -37,7 +37,7 @@ def test_get_data_query(test_client):
assert_equal(query.elements, ["X", "Y", "Z", "F"])
assert_equal(query.sampling_period, SamplingPeriod.MINUTE)
assert_equal(query.format, "iaga2002")
- assert_equal(query.data_type, "R1")
+ assert_equal(query.data_type, "variation")
def test_get_data_query_no_starttime(test_client):
@@ -57,38 +57,18 @@ def test_get_data_query_no_starttime(test_client):
async def test_get_data_query_extra_params(test_client):
with pytest.raises(ValueError) as error:
- response = await test_client.get(
+ response = test_client.get(
"/query/?id=BOU&starttime=2020-09-01T00:00:01&elements=X,Y,Z,F&type=variation&sampling_period=60&format=iaga2002&location=R1&network=NT"
)
+ DataApiQuery(**response.json())
assert error.match("Invalid query parameter(s): location, network")
-# def test_get_data_query_extra_params(test_client):
-# """test.api_test.ws_test.data_test.test_get_data_query_extra_params()"""
-# with pytest.raises(ValueError) as error:
-# test_client.get(
-# "/query/?id=BOU&starttime=2020-09-01T00:00:01&elements=X,Y,Z,F&type=variation&sampling_period=60&format=iaga2002&location=R1&network=NT"
-# )
-# assert error.message == "Invalid query parameter(s): location, network"
-
-
-async def test_get_data_query_bad_params(test_client):
+def test_get_data_query_bad_params(test_client):
"""test.api_test.ws_test.data_test.test_get_data_query_bad_params()"""
with pytest.raises(ValueError) as error:
- response = await test_client.get(
+ response = test_client.get(
"/query/?id=BOU&startime=2020-09-01T00:00:01&elements=X,Y,Z,F&data_type=variation&sampling_period=60&format=iaga2002"
)
+ DataApiQuery(**response.json())
assert error.match == "Invalid query parameter(s): startime, data_type"
-
-
-# def test_filter_data_query(test_client):
-# """test.api_test.ws_test.data_test.test_filter_data_query()"""
-# response = test_client.get(
-# "/algorithms/filter/?id=BOU&starttime=2020-09-01T00:00:01&elements=X,Y,Z,F&type=R1&sampling_period=60&format=iaga2002&input_sampling_period=60&output_sampling_period=30"
-# )
-# filter_query = FilterDataApiQuery(**response.json())
-# assert_equal(filter_query.id, "BOU")
-# assert_equal(filter_query.starttime, UTCDateTime("2020-09-01T00:00:01"))
-# assert_equal(filter_query.elements, ["X", "Y", "Z", "F"])
-# assert_equal(filter_query.input_sampling_period, 60)
-# assert_equal(filter_query.output_sampling_period, 30)
diff --git a/test/api_test/ws_test/filter_test.py b/test/api_test/ws_test/filter_test.py
index dbd2964ea2072d8dd678ae745fe60a5f37c54f64..67a09a4217317ddba87fce88a3e63e4df30fc5df 100644
--- a/test/api_test/ws_test/filter_test.py
+++ b/test/api_test/ws_test/filter_test.py
@@ -31,11 +31,10 @@ def test_get_filter_data_query(test_client):
assert_equal(query.starttime, UTCDateTime("2020-09-01T00:00:01"))
assert_equal(query.endtime, UTCDateTime("2020-09-02T00:00:00.999"))
assert_equal(query.elements, ["X", "Y", "Z", "F"])
- assert_equal(query.sampling_period, SamplingPeriod.MINUTE)
assert_equal(query.format, "iaga2002")
assert_equal(query.data_type, "variation")
assert_equal(query.input_sampling_period, SamplingPeriod.MINUTE)
- assert_equal(query.output_sampling_period, SamplingPeriod.HOUR)
+ assert_equal(query.sampling_period, SamplingPeriod.HOUR)
def test_get_filter_data_query_no_starttime(test_client):
diff --git a/test/edge_test/FDSNFactory_test.py b/test/edge_test/FDSNFactory_test.py
new file mode 100644
index 0000000000000000000000000000000000000000..f409674a5a0be0a5540e3b52b075e9708fa782fa
--- /dev/null
+++ b/test/edge_test/FDSNFactory_test.py
@@ -0,0 +1,206 @@
+import io
+from typing import List
+
+import numpy
+from numpy.testing import assert_equal, assert_array_equal
+import numpy as np
+from obspy.core import Stream, Trace, UTCDateTime
+from obspy.core.inventory import Inventory, Network, Station, Channel, Site
+import pytest
+
+from geomagio.edge import FDSNFactory
+from geomagio.metadata.instrument.InstrumentCalibrations import (
+ get_instrument_calibrations,
+)
+from .mseed_FDSN_test_clients import MockFDSNSeedClient
+
+
+@pytest.fixture(scope="class")
+def FDSN_factory() -> FDSNFactory:
+ """instance of FDSNFactory with MockFDSNClient"""
+ factory = FDSNFactory()
+ factory.client = MockFDSNSeedClient()
+ yield factory
+
+
+@pytest.fixture()
+def anmo_u_metadata():
+ metadata = get_instrument_calibrations(observatory="ANMO")
+ instrument = metadata[0]["instrument"]
+ channels = instrument["channels"]
+ yield channels["X"]
+
+
+def test__get_timeseries_add_empty_channels(FDSN_factory: FDSNFactory):
+ """test.edge_test.FDSNFactory_test.test__get_timeseries_add_empty_channels()"""
+ FDSN_factory.client.return_empty = True
+ starttime = UTCDateTime("2024-09-07T00:00:00Z")
+ endtime = UTCDateTime("2024-09-07T00:10:00Z")
+ trace = FDSN_factory._get_timeseries(
+ starttime=starttime,
+ endtime=endtime,
+ observatory="ANMO",
+ channel="X",
+ type="variation",
+ interval="second",
+ add_empty_channels=True,
+ )[0]
+
+ assert_array_equal(trace.data, numpy.ones(trace.stats.npts) * numpy.nan)
+ assert trace.stats.starttime == starttime
+ assert trace.stats.endtime == endtime
+
+ with pytest.raises(IndexError):
+ trace = FDSN_factory._get_timeseries(
+ starttime=starttime,
+ endtime=endtime,
+ observatory="ANMO",
+ channel="X",
+ type="variation",
+ interval="second",
+ add_empty_channels=False,
+ )[0]
+
+
+def test__set_metadata():
+ """edge_test.FDSNFactory_test.test__set_metadata()"""
+ # Call _set_metadata with 2 traces, and make certain the stats get
+ # set for both traces.
+ trace1 = Trace()
+ trace2 = Trace()
+ stream = Stream(traces=[trace1, trace2])
+ FDSNFactory()._set_metadata(stream, "ANMO", "X", "variation", "second")
+ assert_equal(stream[0].stats["channel"], "X")
+ assert_equal(stream[1].stats["channel"], "X")
+
+
+def test_get_timeseries(FDSN_factory):
+ """edge_test.FDSNFactory_test.test_get_timeseries()"""
+ # Call get_timeseries, and test stats for comfirmation that it came back.
+ # TODO, need to pass in host and port from a config file, or manually
+ # change for a single test.
+ timeseries = FDSN_factory.get_timeseries(
+ starttime=UTCDateTime(2024, 3, 1, 0, 0, 0),
+ endtime=UTCDateTime(2024, 3, 1, 1, 0, 0),
+ observatory="ANMO",
+ channels=("X"),
+ type="variation",
+ interval="second",
+ )
+
+ assert_equal(
+ timeseries.select(channel="X")[0].stats.station,
+ "ANMO",
+ "Expect timeseries to have stats",
+ )
+ assert_equal(
+ timeseries.select(channel="X")[0].stats.channel,
+ "X",
+ "Expect timeseries stats channel to be equal to X",
+ )
+ assert_equal(
+ timeseries.select(channel="X")[0].stats.data_type,
+ "variation",
+ "Expect timeseries stats data_type to be equal to variation",
+ )
+
+
+def test_get_timeseries_by_location(FDSN_factory):
+ """test.edge_test.FDSNFactory_test.test_get_timeseries_by_location()"""
+ timeseries = FDSN_factory.get_timeseries(
+ UTCDateTime(2024, 3, 1, 0, 0, 0),
+ UTCDateTime(2024, 3, 1, 1, 0, 0),
+ "ANMO",
+ ("X"),
+ "R0",
+ "second",
+ )
+ assert_equal(
+ timeseries.select(channel="X")[0].stats.data_type,
+ "R0",
+ "Expect timeseries stats data_type to be equal to R0",
+ )
+
+
+def test_rotate_trace():
+ # Initialize the factory
+ factory = FDSNFactory(
+ observatory="ANMO",
+ channels=["X", "Y", "Z"],
+ type="variation",
+ interval="second",
+ )
+
+ # Simulate input traces for X, Y, Z channels
+ starttime = UTCDateTime("2024-01-01T00:00:00")
+ endtime = UTCDateTime(2024, 1, 1, 0, 10)
+ data_x = Trace(
+ data=np.array([1, 2, 3, 4, 5]),
+ header={"channel": "X", "starttime": starttime, "delta": 60},
+ )
+ data_y = Trace(
+ data=np.array([6, 7, 8, 9, 10]),
+ header={"channel": "Y", "starttime": starttime, "delta": 60},
+ )
+ data_z = Trace(
+ data=np.array([11, 12, 13, 14, 15]),
+ header={"channel": "Z", "starttime": starttime, "delta": 60},
+ )
+ input_stream = Stream(traces=[data_x, data_y, data_z])
+
+ # Mock the Client.get_waveforms method to return the simulated stream
+ factory.Client.get_waveforms = lambda *args, **kwargs: input_stream
+
+ # Create a mock inventory object for get stations
+ mock_inventory = create_mock_inventory()
+ # Mock the Client.get_stations method to return dummy inventory (if required for rotation)
+ factory.Client.get_stations = lambda *args, **kwargs: mock_inventory
+
+ # Call get_timeseries with channel "X" to trigger rotation
+ rotated_stream = factory.get_timeseries(
+ starttime=starttime,
+ endtime=endtime,
+ observatory="ANMO",
+ channels=["X"], # Requesting any channel in [X, Y, Z] should trigger rotation
+ )
+
+ # Assertions
+ assert (
+ len(rotated_stream) == 1
+ ), "Expected only the requested channel (X, Y, Z) after rotation"
+ assert rotated_stream[0].stats.channel in [
+ "X",
+ ], "Unexpected channel names after rotation"
+ assert (
+ rotated_stream[0].stats.starttime == starttime
+ ), "Start time mismatch in rotated data"
+
+
+def create_mock_inventory():
+ """Creates a mock inventory for testing purposes."""
+ # Create a dummy channel
+ channel = Channel(
+ code="X",
+ location_code="",
+ latitude=0.0,
+ longitude=0.0,
+ elevation=0.0,
+ depth=0.0,
+ azimuth=0.0,
+ dip=0.0,
+ sample_rate=1.0,
+ )
+ # Create a dummy station
+ station = Station(
+ code="ANMO",
+ latitude=0.0,
+ longitude=0.0,
+ elevation=0.0,
+ site=Site(name="TestSite"),
+ channels=[channel],
+ )
+ # Create a dummy network
+ network = Network(code="XX", stations=[station])
+ # Create an inventory
+ inventory = Inventory(networks=[network], source="MockInventory")
+ return inventory
diff --git a/test/edge_test/mseed_FDSN_test_clients.py b/test/edge_test/mseed_FDSN_test_clients.py
new file mode 100644
index 0000000000000000000000000000000000000000..dcad34d2a32b1a258f61935a67aba5ee385d5841
--- /dev/null
+++ b/test/edge_test/mseed_FDSN_test_clients.py
@@ -0,0 +1,47 @@
+import numpy
+from obspy import Stream, UTCDateTime
+from obspy.clients.neic.client import Client
+
+from geomagio import TimeseriesUtility
+from geomagio.edge import FDSNSNCL
+
+
+class MockFDSNSeedClient(Client):
+ """replaces default obspy miniseed client's get_waveforms method to return trace of ones
+
+ Note: includes 'return_empty' parameter to simulate situations where no data is received
+ """
+
+ def __init__(self, return_empty: bool = False):
+ self.return_empty = return_empty
+
+ def get_waveforms(
+ self,
+ network: str,
+ station: str,
+ location: str,
+ channel: str,
+ starttime: UTCDateTime,
+ endtime: UTCDateTime,
+ ):
+ if self.return_empty:
+ return Stream()
+ sncl = FDSNSNCL(
+ station=station,
+ network=network,
+ channel=channel,
+ location=location,
+ )
+ trace = TimeseriesUtility.create_empty_trace(
+ starttime=starttime,
+ endtime=endtime,
+ observatory=station,
+ channel=channel,
+ type=sncl.data_type,
+ interval=sncl.interval,
+ network=network,
+ station=station,
+ location=location,
+ )
+ trace.data = numpy.ones(trace.stats.npts)
+ return Stream([trace])