From f73fd94c9e6de3e12a9f068b9003263dee98c495 Mon Sep 17 00:00:00 2001
From: Maeva Pourpoint <maeva@passcal.nmt.edu>
Date: Wed, 6 Jul 2022 12:47:49 -0600
Subject: [PATCH] Rename populate and init methods
---
lemi2seed/lemi_metadata.py | 34 +++++-----
tests/test_lemi_metadata.py | 120 ++++++++++++++++++------------------
2 files changed, 77 insertions(+), 77 deletions(-)
diff --git a/lemi2seed/lemi_metadata.py b/lemi2seed/lemi_metadata.py
index 313acca..4318065 100644
--- a/lemi2seed/lemi_metadata.py
+++ b/lemi2seed/lemi_metadata.py
@@ -117,7 +117,7 @@ class LemiMetadata():
"file!".format(filename))
return sheet_type
- def init_run_md_props(self) -> List[Run]:
+ def init_run_props(self) -> List[Run]:
"""
Instantiate Run data class object and initialize non-user defined
properties.
@@ -133,7 +133,7 @@ class LemiMetadata():
runs.append(run)
return runs
- def init_cha_md_props(self, cha_type: str, run_id: str) -> DCS_SUB_EMA:
+ def init_cha_props(self, cha_type: str, run_id: str) -> DCS_SUB_EMA:
"""
Create instances of Elec, Mag or Aux data class and
initialize properties inherited from the BaseSta and BaseChannel
@@ -194,7 +194,7 @@ class LemiMetadata():
if isinstance(mprop, list):
if cat == 'Run':
if not mprop:
- mprop = self.init_run_md_props()
+ mprop = self.init_run_props()
for ind, dc in enumerate(mprop):
key = f'Run_{self.run_list[ind]}'
output[cat][key] = LemiMetadata.dc2dict(dc)
@@ -202,7 +202,7 @@ class LemiMetadata():
for run_id in self.run_list:
chas = self.filter_cha('elec', run_id)
if not chas:
- cha = self.init_cha_md_props('elec', run_id)
+ cha = self.init_cha_props('elec', run_id)
chas = [LemiMetadata.update_cha_num(cha, f'E{ind + 1}') # type: ignore
for ind in range(NUM_E_CHA_MAX)] # type: ignore
for ind in range(NUM_E_CHA_MAX):
@@ -212,7 +212,7 @@ class LemiMetadata():
for run_id in self.run_list:
chas = self.filter_cha('mag', run_id)
if not chas:
- dc = self.init_cha_md_props('mag', run_id)
+ dc = self.init_cha_props('mag', run_id)
else:
dc = chas[0]
key = f'Run_{run_id}_Mag'
@@ -354,7 +354,7 @@ class LemiMetadata():
else:
cat.md_missing.discard(key)
- def populate_net_md_props(self, md_fields_n: Dict) -> None:
+ def populate_net_props(self, md_fields_n: Dict) -> None:
"""
Populate properties of Network data class based on user inputs from
the field sheets and/or GUI.
@@ -362,7 +362,7 @@ class LemiMetadata():
self.populate(self.net, md_fields_n)
LemiMetadata.flag_md_missing(self.net)
- def populate_sta_md_props(self, md_fields_s: Dict) -> None:
+ def populate_sta_props(self, md_fields_s: Dict) -> None:
"""
Populate properties of Sta data class based on user inputs from
the field sheets and/or GUI.
@@ -371,13 +371,13 @@ class LemiMetadata():
self.sta.run_list = ', '.join(self.run_list)
LemiMetadata.flag_md_missing(self.sta)
- def populate_run_md_props(self, md_fields_r: Dict) -> None:
+ def populate_run_props(self, md_fields_r: Dict) -> None:
"""
Populate properties of run data class based on user inputs from
the field sheets and/or GUI.
"""
if not self.run:
- self.run.extend(self.init_run_md_props())
+ self.run.extend(self.init_run_props())
for ind, run in enumerate(self.run):
run_id = self.run_list[ind]
name = f'Run_{run_id}'
@@ -486,7 +486,7 @@ class LemiMetadata():
elec = [c for c in self.elec if c.run_id == run_id and c.cha_num == key]
elec[0].loc_code = e_loc.get(key, '')
- def populate_elec_md_props(self, md_fields_e: Dict, num_e_pairs: Optional[Dict] = None) -> Tuple[Dict, Dict]:
+ def populate_elec_props(self, md_fields_e: Dict, num_e_pairs: Optional[Dict] = None) -> Tuple[Dict, Dict]:
"""
Populate properties of Elec data class based on user inputs from
the field sheets and/or GUI.
@@ -498,7 +498,7 @@ class LemiMetadata():
if not e_comps:
continue
if not self.filter_cha('elec', run_id):
- cha = self.init_cha_md_props('elec', run_id)
+ cha = self.init_cha_props('elec', run_id)
self.elec.extend([LemiMetadata.update_cha_num(cha, f'E{i+1}') # type: ignore
for i in range(NUM_E_CHA_MAX)]) # type: ignore
num_e_pairs_run = (int(num_e_pairs.get(run_id) or len(e_comps))
@@ -541,7 +541,7 @@ class LemiMetadata():
tmp.cha_name = CHA_NAMING_CONV[tmp.comp]
return tmp
- def populate_mag_md_props(self, md_fields_m: Dict) -> None:
+ def populate_mag_props(self, md_fields_m: Dict) -> None:
"""
Populate properties of Mag data class based on user inputs from the
field sheets and/or GUI.
@@ -552,7 +552,7 @@ class LemiMetadata():
if not m_comps:
continue
if not self.filter_cha('mag', run_id):
- cha = self.init_cha_md_props('mag', run_id)
+ cha = self.init_cha_props('mag', run_id)
# Use deepcopy here so that any changes made to the copy object
# do not reflect in the original object.
self.mag.extend([copy.deepcopy(cha) for i in range(len(CHA_TYPES['mag']))]) # type: ignore
@@ -567,14 +567,14 @@ class LemiMetadata():
comp = CHA_TYPES['mag'][ind]
self.mag[cha_ind] = LemiMetadata.update_comp_cha_name(cha, comp) # type: ignore
- def populate_aux_md_props(self) -> None:
+ def populate_aux_props(self) -> None:
"""
Populate properties of Aux data class based on user inputs from
the field sheets and/or GUI.
"""
for ind_run, run_id in enumerate(self.run_list):
if not self.filter_cha('aux', run_id):
- cha = self.init_cha_md_props('aux', run_id)
+ cha = self.init_cha_props('aux', run_id)
# Use deepcopy here so that any changes made to the copy object
# do not reflect in the original object.
self.aux.extend([copy.deepcopy(cha) for i in range(len(CHA_TYPES['aux']))]) # type: ignore
@@ -588,14 +588,14 @@ class LemiMetadata():
comp = CHA_TYPES['aux'][ind]
self.aux[cha_ind] = LemiMetadata.update_comp_cha_name(cha, comp) # type: ignore
- def populate_md_props(self, md_fields: Dict) -> None:
+ def populate_props(self, md_fields: Dict) -> None:
"""
Populate metadata properties based on user inputs from the field sheets
and/or GUI.
"""
for cat in self.cats:
md_fields_ = md_fields.get(cat)
- populate_method = f'populate_{cat.lower()}_md_props'
+ populate_method = f'populate_{cat.lower()}_props'
if md_fields_:
methodcaller(populate_method, md_fields_)(self)
else:
diff --git a/tests/test_lemi_metadata.py b/tests/test_lemi_metadata.py
index 1a4859b..759379c 100644
--- a/tests/test_lemi_metadata.py
+++ b/tests/test_lemi_metadata.py
@@ -147,9 +147,9 @@ class TestLemiMetadata(unittest.TestCase):
"""Test basic functionality of from_field_sheets"""
self.assertDictEqual(self.md.from_field_sheets, self.md_fields)
- def test_populate_net_md_props(self):
- """Test basic functionality of populate_net_md_props."""
- self.md.populate_net_md_props(self.md_fields['Net'])
+ def test_populate_net_props(self):
+ """Test basic functionality of populate_net_props."""
+ self.md.populate_net_props(self.md_fields['Net'])
self.assertSetEqual(self.md.net.md_missing,
{'geo_name', 'start', 'project', 'name'})
self.assertSetEqual(self.md.net.md_invalid, {'start'})
@@ -158,9 +158,9 @@ class TestLemiMetadata(unittest.TestCase):
self.assertEqual(getattr(self.md.net, key), val)
self.assertIsNone(self.md.net.start)
- def test_populate_sta_md_props(self):
- """Test basic functionality of populate_sta_md_props."""
- self.md.populate_sta_md_props(self.md_fields['Sta'])
+ def test_populate_sta_props(self):
+ """Test basic functionality of populate_sta_props."""
+ self.md.populate_sta_props(self.md_fields['Sta'])
self.assertSetEqual(self.md.sta.md_missing,
{'end', 'elev', 'lon', 'start', 'geo_name'})
self.assertSetEqual(self.md.sta.md_invalid, {'elev', 'lon', 'start'})
@@ -171,8 +171,8 @@ class TestLemiMetadata(unittest.TestCase):
self.assertIsNone(self.md.sta.elev)
self.assertIsNone(self.md.sta.start)
- def test_init_run_md_props(self):
- """Test basic functionality of init_run_md_props."""
+ def test_init_run_props(self):
+ """Test basic functionality of init_run_props."""
time_period_starts = [UTCDateTime(2020, 9, 30, 21, 5),
UTCDateTime(2020, 9, 30, 21, 12),
UTCDateTime(2020, 9, 30, 21, 14),
@@ -181,15 +181,15 @@ class TestLemiMetadata(unittest.TestCase):
UTCDateTime(2020, 9, 30, 21, 13, 45),
UTCDateTime(2020, 9, 30, 21, 27, 59),
UTCDateTime(2020, 10, 1, 0, 5, 59)]
- self.md.init_run_md_props()
+ self.md.init_run_props()
for ind, run in enumerate(self.md.run):
self.assertEqual(run.start, time_period_starts[ind])
self.assertEqual(run.end, time_period_ends[ind])
self.assertEqual(run.resource_id, 'mt.run.id:' + self.md.run_list[ind])
- def test_populate_run_md_props(self):
- """Test basic functionality of populate_run_md_props."""
- self.md.populate_run_md_props(self.md_fields['Run'])
+ def test_populate_run_props(self):
+ """Test basic functionality of populate_run_props."""
+ self.md.populate_run_props(self.md_fields['Run'])
self.assertEqual(self.md.run[0].comps_rec, 'E1, E2, E3, E4, Hx, Hy, Hz')
self.assertEqual(self.md.run[0].datalogger_sn, 110)
self.assertSetEqual(self.md.run[0].md_missing, set())
@@ -200,45 +200,45 @@ class TestLemiMetadata(unittest.TestCase):
self.assertSetEqual(run.md_missing, {'datalogger_sn', 'comps_rec'})
self.assertSetEqual(run.md_invalid, {'datalogger_sn', 'comps_rec'})
- def test_init_cha_md_props_elec(self):
- """Test basic functionality of init_cha_md_props."""
- cha = self.md.init_cha_md_props('elec', 'a')
+ def test_init_cha_props_elec(self):
+ """Test basic functionality of init_cha_props."""
+ cha = self.md.init_cha_props('elec', 'a')
self.assertIsInstance(cha, Elec)
self.assertEqual(cha.elev, round(self.md.data_stats['elev'], 3))
self.assertEqual(cha.lat, round(self.md.data_stats['lat'], 3))
self.assertEqual(cha.lon, round(self.md.data_stats['lon'], 3))
self.assertEqual(cha.run_id, 'a')
- def test_init_cha_md_props_mag(self):
- """Test basic functionality of init_cha_md_props."""
- cha = self.md.init_cha_md_props('mag', 'a')
+ def test_init_cha_props_mag(self):
+ """Test basic functionality of init_cha_props."""
+ cha = self.md.init_cha_props('mag', 'a')
self.assertIsInstance(cha, Mag)
self.assertEqual(cha.elev, round(self.md.data_stats['elev'], 3))
self.assertEqual(cha.lat, round(self.md.data_stats['lat'], 3))
self.assertEqual(cha.lon, round(self.md.data_stats['lon'], 3))
self.assertEqual(cha.run_id, 'a')
- def test_init_cha_md_props_aux(self):
- """Test basic functionality of init_cha_md_props."""
- cha = self.md.init_cha_md_props('aux', 'a')
+ def test_init_cha_props_aux(self):
+ """Test basic functionality of init_cha_props."""
+ cha = self.md.init_cha_props('aux', 'a')
self.assertIsInstance(cha, Aux)
self.assertEqual(cha.elev, round(self.md.data_stats['elev'], 3))
self.assertEqual(cha.lat, round(self.md.data_stats['lat'], 3))
self.assertEqual(cha.lon, round(self.md.data_stats['lon'], 3))
self.assertEqual(cha.run_id, 'a')
- def test_populate_elec_md_props_one_run_set(self):
- """Test basic functionality of populate_elec_md_props."""
- self.md.populate_run_md_props(self.md_fields['Run'])
- self.md.populate_elec_md_props(self.md_fields['Elec'])
+ def test_populate_elec_props_one_run_set(self):
+ """Test basic functionality of populate_elec_props."""
+ self.md.populate_run_props(self.md_fields['Run'])
+ self.md.populate_elec_props(self.md_fields['Elec'])
file_ = self.path2md.joinpath('electric_metadata_properties_1.pkl')
with open(file_, 'rb') as fin:
expected = pickle.load(fin)
self.assertListEqual(self.md.elec, expected)
- def test_populate_elec_md_props_two_runs_set(self):
- """Test basic functionality of populate_elec_md_props."""
- self.md.populate_run_md_props(self.md_fields['Run'])
+ def test_populate_elec_props_two_runs_set(self):
+ """Test basic functionality of populate_elec_props."""
+ self.md.populate_run_props(self.md_fields['Run'])
self.md.run[1].comps_rec = 'E1, E2, Hx, Hy, Hz'
specs = 'Borin STELTH 4 - Silver-Silver Chloride'
self.md_fields['Elec']['Run_b_Elec_Pair_1']['cha_num'] = 'E1'
@@ -247,37 +247,37 @@ class TestLemiMetadata(unittest.TestCase):
self.md_fields['Elec']['Run_b_Elec_Pair_4']['cha_num'] = 'E4'
self.md_fields['Elec']['Run_b_Elec_Pair_1']['inst_specs'] = specs
self.md_fields['Elec']['Run_b_Elec_Pair_2']['inst_specs'] = specs
- self.md.populate_elec_md_props(self.md_fields['Elec'])
+ self.md.populate_elec_props(self.md_fields['Elec'])
file_ = self.path2md.joinpath('electric_metadata_properties_2.pkl')
with open(file_, 'rb') as fin:
expected = pickle.load(fin)
self.assertListEqual(self.md.elec, expected)
- def test_populate_mag_md_props_one_run_set(self):
- """Test basic functionality of populate_mag_md_props."""
- self.md.populate_run_md_props(self.md_fields['Run'])
- self.md.populate_mag_md_props(self.md_fields['Mag'])
+ def test_populate_mag_props_one_run_set(self):
+ """Test basic functionality of populate_mag_props."""
+ self.md.populate_run_props(self.md_fields['Run'])
+ self.md.populate_mag_props(self.md_fields['Mag'])
file_ = self.path2md.joinpath('magnetic_metadata_properties_1.pkl')
with open(file_, 'rb') as fin:
expected = pickle.load(fin)
self.assertListEqual(self.md.mag, expected)
- def test_populate_mag_md_props_two_runs_set(self):
- """Test basic functionality of populate_mag_md_props."""
- self.md.populate_run_md_props(self.md_fields['Run'])
+ def test_populate_mag_props_two_runs_set(self):
+ """Test basic functionality of populate_mag_props."""
+ self.md.populate_run_props(self.md_fields['Run'])
self.md.run[1].comps_rec = 'E1, E2, Hx, Hy, Hz'
specs = 'LEMI-039'
self.md_fields['Mag']['Run_b_Mag']['inst_specs'] = specs
- self.md.populate_mag_md_props(self.md_fields['Mag'])
+ self.md.populate_mag_props(self.md_fields['Mag'])
file_ = self.path2md.joinpath('magnetic_metadata_properties_2.pkl')
with open(file_, 'rb') as fin:
expected = pickle.load(fin)
self.assertListEqual(self.md.mag, expected)
- def test_populate_aux_md_props_one_run_set(self):
- """Test basic functionality of populate_aux_md_props."""
- self.md.populate_run_md_props(self.md_fields['Run'])
- self.md.populate_aux_md_props()
+ def test_populate_aux_props_one_run_set(self):
+ """Test basic functionality of populate_aux_props."""
+ self.md.populate_run_props(self.md_fields['Run'])
+ self.md.populate_aux_props()
file_ = self.path2md.joinpath('auxiliary_metadata_properties.pkl')
with open(file_, 'rb') as fin:
expected = pickle.load(fin)
@@ -290,7 +290,7 @@ class TestLemiMetadata(unittest.TestCase):
def test_filter_cha_cha_populated_for_given_run(self):
"""Test basic functionality of filter_cha."""
cha_names = ['LEH', 'LKH', 'LKF', 'GNS', 'GST', 'LCE']
- self.md.populate_md_props(self.md_fields)
+ self.md.populate_props(self.md_fields)
cha_filtered = self.md.filter_cha('aux', 'a')
self.assertEqual(len(cha_filtered), 6)
for ind, cha in enumerate(cha_filtered):
@@ -302,7 +302,7 @@ class TestLemiMetadata(unittest.TestCase):
def test_get_cha_inds_cha_populated_for_given_run(self):
"""Test basic functionality of get_cha_inds."""
- self.md.populate_md_props(self.md_fields)
+ self.md.populate_props(self.md_fields)
cha_inds = self.md.get_cha_inds('aux', 'a')
self.assertListEqual(cha_inds, [0, 1, 2, 3, 4, 5])
@@ -311,7 +311,7 @@ class TestLemiMetadata(unittest.TestCase):
type_ = 'E'
cha_type = 'electric field'
run_id = 'b'
- self.md.populate_run_md_props(self.md_fields['Run'])
+ self.md.populate_run_props(self.md_fields['Run'])
with self.assertLogs(logger, level='WARNING') as cmd:
self.md.get_comps_rec(type_, run_id)
msg = (f"No {cha_type} data recorded for run '{run_id}'. If you "
@@ -325,7 +325,7 @@ class TestLemiMetadata(unittest.TestCase):
type_ = 'E'
cha_type = 'electric field'
run_id = 'b'
- self.md.populate_run_md_props(self.md_fields['Run'])
+ self.md.populate_run_props(self.md_fields['Run'])
self.md.run[1].comps_rec = 'Hx, Hy, Hz'
with self.assertLogs(logger, level='WARNING') as cmd:
self.md.get_comps_rec(type_, run_id)
@@ -339,7 +339,7 @@ class TestLemiMetadata(unittest.TestCase):
"""Test basic functionality of get_comps_rec."""
type_ = 'E'
run_id = 'a'
- self.md.populate_run_md_props(self.md_fields['Run'])
+ self.md.populate_run_props(self.md_fields['Run'])
comps = self.md.get_comps_rec(type_, run_id)
self.assertEqual(comps, ['E1', 'E2', 'E3', 'E4'])
@@ -348,7 +348,7 @@ class TestLemiMetadata(unittest.TestCase):
type_ = 'H'
cha_type = 'magnetic field'
run_id = 'b'
- self.md.populate_run_md_props(self.md_fields['Run'])
+ self.md.populate_run_props(self.md_fields['Run'])
self.md.run[1].comps_rec = 'Hx, Hy'
with self.assertLogs(logger, level='WARNING') as cmd:
self.md.get_comps_rec(type_, run_id)
@@ -362,7 +362,7 @@ class TestLemiMetadata(unittest.TestCase):
"""Test basic functionality of get_comps_rec."""
type_ = 'H'
run_id = 'a'
- self.md.populate_run_md_props(self.md_fields['Run'])
+ self.md.populate_run_props(self.md_fields['Run'])
comps = self.md.get_comps_rec(type_, run_id)
self.assertEqual(comps, ['Hx', 'Hy', 'Hz'])
@@ -370,7 +370,7 @@ class TestLemiMetadata(unittest.TestCase):
"""Test basic functionality of match_num_e_pairs."""
comps = ['E1', 'E2', 'E3', 'E4']
run_id = 'a'
- self.md.populate_md_props(self.md_fields)
+ self.md.populate_props(self.md_fields)
with self.assertLogs(logger, level='ERROR') as cmd:
self.md.match_num_e_pairs(comps, run_id, 2)
msg = (f"Invalid number of electrode pairs (run '{run_id}')! The "
@@ -388,7 +388,7 @@ class TestLemiMetadata(unittest.TestCase):
"""Test basic functionality of match_comps_rec."""
comps = ['E1', 'E2']
run_id = 'a'
- self.md.populate_md_props(self.md_fields)
+ self.md.populate_props(self.md_fields)
with self.assertLogs(logger, level='ERROR') as cmd:
self.md.match_comps_rec(self.md.elec, comps, run_id)
msg = (f"Invalid electric channel numbers (run '{run_id}')! The "
@@ -400,14 +400,14 @@ class TestLemiMetadata(unittest.TestCase):
def test_update_cha_num(self):
"""Test basic functionality of update_cha_num."""
- cha = self.md.init_cha_md_props('elec', 'a')
+ cha = self.md.init_cha_props('elec', 'a')
self.assertIsNone(cha.cha_num)
updated_cha = LemiMetadata.update_cha_num(cha, 'E1')
self.assertEqual(updated_cha.cha_num, 'E1')
def test_update_comp_cha_name(self):
"""Test basic functionality of update_comp_cha_name."""
- cha = self.md.init_cha_md_props('mag', 'a')
+ cha = self.md.init_cha_props('mag', 'a')
self.assertIsNone(cha.cha_name)
self.assertIsNone(cha.comp)
updated_cha = LemiMetadata.update_comp_cha_name(cha, 'Hx')
@@ -417,12 +417,12 @@ class TestLemiMetadata(unittest.TestCase):
def test_get_e_infos(self):
"""Test basic functionality of get_e_infos."""
comps = ['Ex', 'Ey', 'Ex', 'Ey', 'Ex', 'Ey']
- self.md.populate_run_md_props(self.md_fields['Run'])
+ self.md.populate_run_props(self.md_fields['Run'])
self.md.run[1].comps_rec = 'E1, E2, Hx, Hy, Hz'
- cha = self.md.init_cha_md_props('elec', 'a')
+ cha = self.md.init_cha_props('elec', 'a')
self.md.elec.extend([self.md.update_cha_num(cha, f'E{i+1}')
for i in range(4)])
- cha = self.md.init_cha_md_props('elec', 'b')
+ cha = self.md.init_cha_props('elec', 'b')
self.md.elec.extend([self.md.update_cha_num(cha, f'E{i+1}')
for i in range(2)])
for ind, elec in enumerate(self.md.elec):
@@ -436,8 +436,8 @@ class TestLemiMetadata(unittest.TestCase):
"""Test basic functionality of update_location."""
comps = ['Ex', 'Ey', 'Ex', 'Ey']
location_codes = ['00', '00', '01', '01']
- self.md.populate_run_md_props(self.md_fields['Run'])
- cha = self.md.init_cha_md_props('elec', 'a')
+ self.md.populate_run_props(self.md_fields['Run'])
+ cha = self.md.init_cha_props('elec', 'a')
self.md.elec.extend([self.md.update_cha_num(cha, f'E{i+1}') for i in range(4)])
for ind, elec in enumerate(self.md.elec):
elec.comp = comps[ind]
@@ -461,7 +461,7 @@ class TestLemiMetadata(unittest.TestCase):
def test_dc2dict(self):
"""Test basic functionality of dc2dict."""
- cha = self.md.init_cha_md_props('elec', 'a')
+ cha = self.md.init_cha_props('elec', 'a')
self.assertDictEqual(self.md.dc2dict(cha),
{'elev': 2201.725,
'lat': 34.048,
@@ -493,7 +493,7 @@ class TestLemiMetadata(unittest.TestCase):
def test_for_gui_md_populated(self):
"""Test basic functionality of for_gui."""
- self.md.populate_md_props(self.md_fields)
+ self.md.populate_props(self.md_fields)
file_ = self.path2md.joinpath('gui_metadata_populated.pkl')
with open(file_, 'rb') as fin:
expected = pickle.load(fin)
@@ -519,7 +519,7 @@ class TestLemiMetadata(unittest.TestCase):
def test_update_azimuth_tilt(self):
"""Test basic functionality of update_azimuth_tilt."""
- self.md.populate_md_props(self.md_fields)
+ self.md.populate_props(self.md_fields)
self.md.update_azimuth_tilt()
for cha in self.md.filter_cha('mag', 'a'):
if cha.comp == 'Hx':
--
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