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Merge pull request #523 from TRI-AMDD/fix_auto_load_bug_schema
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Fix bug with loading processed file from a different environment
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patrickherring-TRI authored Jan 24, 2022
2 parents a0d6fd0 + e2d6fba commit 8588736
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Showing 3 changed files with 12 additions and 0 deletions.
2 changes: 2 additions & 0 deletions beep/structure/base.py
Original file line number Diff line number Diff line change
Expand Up @@ -200,6 +200,8 @@ def __init__(self, raw_data, metadata, paths=None, schema=None, impute_missing=T

if os.path.exists(abs_schema):
self.schema = abs_schema
elif os.path.exists(os.path.join(VALIDATION_SCHEMA_DIR, os.path.split(schema)[-1])):
self.schema = os.path.join(VALIDATION_SCHEMA_DIR, os.path.split(schema)[-1])
else:
raise FileNotFoundError(f"The schema file specified for validation could not be found: {schema}.")

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9 changes: 9 additions & 0 deletions beep/structure/tests/test_base.py
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,8 @@
from beep.structure.base_eis import EIS, BEEPDatapathWithEIS
from beep.structure.maccor import MaccorDatapath
from beep.tests.constants import TEST_FILE_DIR, BIG_FILE_TESTS, SKIP_MSG
from beep.structure.cli import auto_load_processed
from beep import VALIDATION_SCHEMA_DIR


class TestBEEPDatapath(unittest.TestCase):
Expand Down Expand Up @@ -203,6 +205,13 @@ def test_serialization(self):
if os.path.exists(fname):
os.remove(fname)

# Test to address bug where schema_path is absolute but is created in a different environment
def test_reloading_new(self):
test_file = os.path.join(TEST_FILE_DIR, "PredictionDiagnostics_000107_0001B9_structure_short.json")
struct = auto_load_processed(test_file)
self.assertEqual(struct.schema,
os.path.join(VALIDATION_SCHEMA_DIR, "schema-maccor-2170.yaml"))

# based on RCRT.test_serialization
def test_serialization_legacy(self):
test_file = os.path.join(
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{"@module": "beep.structure.maccor", "@class": "MaccorDatapath", "metadata": {"_today_datetime": "10/10/2019", "start_datetime": "10/10/2019", "filename": "C:\\Users\\Maccor Tester User\\Documents\\Backup\\STANFORD LOANER #1\\STANFORD LOANER #2\\PredictionDiagnostics_000107_0001B9.008", "protocol": "PredictionDiagnostics_000107.000", "barcode": "0001B9", "channel_id": 8}, "paths": {"raw": "/home/beep_ep/s3TempInput/d3Batt/maccor/PredictionDiagnostics_000107_0001B9.008", "metadata": "/home/beep_ep/s3TempInput/d3Batt/maccor/PredictionDiagnostics_000107_0001B9.008", "protocol_parameters": "/home/beep_ep/s3TempInput/d3Batt/raw/parameters", "structured": "/Users/patrickherring/Code/beep/beep/tests/test_files/PredictionDiagnostics_000107_0001B9_structure.json"}, "barcode": "0001B9", "protocol": "PredictionDiagnostics_000107.000", "channel_id": 8, "summary": {"cycle_index": [0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65], "discharge_capacity": [4.7429470283, 3.7637790322, 3.756532646, 3.7511818379, 3.7448093907, 3.737966022, 3.7311903633, 3.7209321978, 3.7091684939, 3.6966655858, 3.6805860329, 3.6634045815, 3.6433727175, 3.6208399825, 3.5947986286, 3.5680178022, 3.5354423527, 3.5000435887, 3.4617545879, 3.4201041346, 3.3750660296, 3.3274330199, 3.2790473634, 3.2267761145, 3.1735504482, 3.1196928626, 3.0667359153, 3.0105391165, 2.9566144172, 2.7804007973, 2.7265431563, 3.4520609992, 3.3674969851, 3.277097879, 3.1898986782, 3.1070821482, 3.0269545396, 2.9502417239, 2.7586613775, 2.686304516, 2.6173489497, 2.5519025018, 2.488338201, 2.4279063567, 2.3689803031, 2.3095434532, 2.248883065, 2.1884107404, 2.1275893721, 2.0685554907, 2.008406061, 1.951779001, 1.8944797144, 1.8405682695, 1.9521080644, 4.3877135163], "charge_capacity": [3.8534094846999998, 3.7158041116, 3.7584523385, 3.7537525266, 3.7486121774, 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NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN], "temperature_average": [NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN], "temperature_minimum": [NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN], "date_time_iso": ["2019-10-11T01:14:37+00:00", "2019-10-16T05:32:35+00:00", "2019-10-16T08:04:09+00:00", "2019-10-16T10:36:38+00:00", "2019-10-16T13:08:55+00:00", "2019-10-16T15:40:57+00:00", 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"schema_path": "/Users/patrickherring/Code/beep/beep/validation_schemas/schema-maccor-2170.yaml"}

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