fgreg closed pull request #4: SDAP-33 New Processor for adding Global Attributes
URL: https://github.com/apache/incubator-sdap-ningesterpy/pull/4
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diff --git a/sdap/processors/__init__.py b/sdap/processors/__init__.py
index 8a48500..6d4a679 100644
--- a/sdap/processors/__init__.py
+++ b/sdap/processors/__init__.py
@@ -56,6 +56,7 @@ def process_nexus_tile(self, nexus_tile):
from sdap.processors.emptytilefilter import EmptyTileFilter
from sdap.processors.kelvintocelsius import KelvinToCelsius
from sdap.processors.normalizetimebeginningofmonth import
NormalizeTimeBeginningOfMonth
+from sdap.processors.promotevariabletoglobalattribute import
PromoteVariableToGlobalAttribute
from sdap.processors.regrid1x1 import Regrid1x1
from sdap.processors.subtract180longitude import Subtract180Longitude
from sdap.processors.tilereadingprocessor import GridReadingProcessor,
SwathReadingProcessor, TimeSeriesReadingProcessor
@@ -70,6 +71,7 @@ def process_nexus_tile(self, nexus_tile):
"EmptyTileFilter": EmptyTileFilter,
"KelvinToCelsius": KelvinToCelsius,
"NormalizeTimeBeginningOfMonth": NormalizeTimeBeginningOfMonth,
+ "PromoteVariableToGlobalAttribute": PromoteVariableToGlobalAttribute,
"Regrid1x1": Regrid1x1,
"Subtract180Longitude": Subtract180Longitude,
"GridReadingProcessor": GridReadingProcessor,
diff --git a/sdap/processors/processorchain.py
b/sdap/processors/processorchain.py
index 6a68b04..82bad8e 100644
--- a/sdap/processors/processorchain.py
+++ b/sdap/processors/processorchain.py
@@ -14,6 +14,7 @@
# limitations under the License.
import inspect
+import re
import sdap.processors
@@ -51,18 +52,37 @@ def __init__(self, processor_list, *args, **kwargs):
except KeyError as e:
raise ProcessorNotFound(processor['name']) from e
+ processor_config = dict(**processor['config'])
+
missing_args = []
for arg in
inspect.signature(processor_constructor).parameters.keys():
if arg in ['args', 'kwargs']:
continue
- if arg not in processor['config']:
+ if arg not in processor_config:
missing_args.append(arg)
+ # Need to check for list type args
+ list_pattern = re.compile('\.\d+$')
+ list_args = [k for k in processor_config if list_pattern.search(k)]
+ if list_args:
+ import itertools
+ grouped = itertools.groupby(list_args, key=lambda k:
k.split('.')[0])
+ for group, grouped_args in grouped:
+ for list_arg in grouped_args:
+ key, idx = list_arg.split('.')
+ if group not in processor_config:
+ processor_config[group] = []
+
+ processor_config[group].insert(int(idx),
processor_config[list_arg])
+ del(processor_config[list_arg])
+
+ # Check if the list args satisfied the
+ missing_args = list(filter(lambda a: a not in
processor_config.keys(), missing_args))
if missing_args:
raise MissingProcessorArguments(processor['name'],
missing_args)
if 'config' in processor.keys():
- processor_instance =
processor_constructor(**processor['config'])
+ processor_instance = processor_constructor(**processor_config)
else:
processor_instance = processor_constructor()
diff --git a/sdap/processors/promotevariabletoglobalattribute.py
b/sdap/processors/promotevariabletoglobalattribute.py
new file mode 100644
index 0000000..11fa9d8
--- /dev/null
+++ b/sdap/processors/promotevariabletoglobalattribute.py
@@ -0,0 +1,49 @@
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import nexusproto.DataTile_pb2
+from netCDF4 import Dataset
+
+from sdap.processors import NexusTileProcessor
+
+
+class PromoteVariableToGlobalAttribute(NexusTileProcessor):
+
+ def __init__(self, attribute_name, variable_name, dimensioned_by, *args,
**kwargs):
+ super().__init__(*args, **kwargs)
+
+ self.attribute_name = attribute_name
+ self.variable_name = variable_name
+ self.dimensioned_by = dimensioned_by
+
+ def process_nexus_tile(self, nexus_tile):
+ output_tile = nexusproto.DataTile_pb2.NexusTile()
+ output_tile.CopyFrom(nexus_tile)
+
+ file_path = output_tile.summary.granule
+ file_path = file_path[len('file:'):] if file_path.startswith('file:')
else file_path
+
+ dimtoslice = {}
+ for dimension in output_tile.summary.section_spec.split(','):
+ name, start, stop = dimension.split(':')
+ dimtoslice[name] = slice(int(start), int(stop))
+
+ with Dataset(file_path) as ds:
+ new_attr = output_tile.summary.global_attributes.add()
+ new_attr.name = self.attribute_name
+ new_attr.values.extend(
+ [str(v) for v in ds[self.variable_name][[dimtoslice[dim] for
dim in self.dimensioned_by]]])
+
+ yield output_tile
diff --git a/tests/datafiles/not_empty_wswm.nc
b/tests/datafiles/not_empty_wswm.nc
index 772bbcb..ce0ebcc 100644
Binary files a/tests/datafiles/not_empty_wswm.nc and
b/tests/datafiles/not_empty_wswm.nc differ
diff --git a/tests/processorchain_test.py b/tests/processorchain_test.py
index 7657ba6..26f2e52 100644
--- a/tests/processorchain_test.py
+++ b/tests/processorchain_test.py
@@ -21,6 +21,63 @@
from sdap.processors.processorchain import ProcessorChain
+class TestConstructChain(unittest.TestCase):
+
+ def test_construct_chain_with_list_config(self):
+ processor_list = [
+ {'name': 'TimeSeriesReadingProcessor',
+ 'config': {'latitude': 'lat',
+ 'longitude': 'lon',
+ 'time': 'time',
+ 'variable_to_read': 'Qout'}},
+ {'name': 'EmptyTileFilter', 'config': {}},
+ {'name': 'PromoteVariableToGlobalAttribute',
+ 'config': {
+ 'attribute_name': 'rivid_i',
+ 'variable_name': 'rivid',
+ 'dimensioned_by.0': 'rivid',
+ 'dimensioned_by.1': 'other'
+ }},
+ {'name': 'TileSummarizingProcessor', 'config': {}}
+ ]
+
+ processorchain = ProcessorChain(processor_list)
+
+ self.assertIsNotNone(processorchain)
+
+ def test_construct_chain_with_multiple_list_config(self):
+ processor_list = [
+ {'name': 'PromoteVariableToGlobalAttribute',
+ 'config': {
+ 'attribute_name': 'rivid_i',
+ 'variable_name': 'rivid',
+ 'dimensioned_by.0': 'rivid',
+ 'dimensioned_by.1': 'other',
+ 'unused.0': 'list',
+ 'unused.1': 'second'
+ }}
+ ]
+
+ processorchain = ProcessorChain(processor_list)
+
+ self.assertIsNotNone(processorchain)
+
+ def test_construct_chain_with_list_config_bad_index(self):
+ processor_list = [
+ {'name': 'PromoteVariableToGlobalAttribute',
+ 'config': {
+ 'attribute_name': 'rivid_i',
+ 'variable_name': 'rivid',
+ 'dimensioned_by.0': 'rivid',
+ 'dimensioned_by.10': 'other'
+ }}
+ ]
+
+ processorchain = ProcessorChain(processor_list)
+
+ self.assertIsNotNone(processorchain)
+
+
class TestRunChainMethod(unittest.TestCase):
def test_run_chain_read_filter_all(self):
processor_list = [
@@ -29,7 +86,7 @@ def test_run_chain_read_filter_all(self):
'longitude': 'lon',
'time': 'time',
'variable_to_read': 'analysed_sst'}},
- {'name': 'EmptyTileFilter'}
+ {'name': 'EmptyTileFilter', 'config': {}}
]
processorchain = ProcessorChain(processor_list)
@@ -52,7 +109,7 @@ def test_run_chain_read_filter_none(self):
'longitude': 'lon',
'time': 'time',
'variable_to_read': 'analysed_sst'}},
- {'name': 'EmptyTileFilter'}
+ {'name': 'EmptyTileFilter', 'config': {}}
]
processorchain = ProcessorChain(processor_list)
@@ -75,9 +132,9 @@ def test_run_chain_read_filter_kelvin_summarize(self):
'longitude': 'lon',
'time': 'time',
'variable_to_read': 'analysed_sst'}},
- {'name': 'EmptyTileFilter'},
- {'name': 'KelvinToCelsius'},
- {'name': 'TileSummarizingProcessor'}
+ {'name': 'EmptyTileFilter', 'config': {}},
+ {'name': 'KelvinToCelsius', 'config': {}},
+ {'name': 'TileSummarizingProcessor', 'config': {}}
]
processorchain = ProcessorChain(processor_list)
@@ -100,9 +157,9 @@ def test_run_chain_partial_empty(self):
'longitude': 'lon',
'time': 'time',
'variable_to_read': 'analysed_sst'}},
- {'name': 'EmptyTileFilter'},
- {'name': 'KelvinToCelsius'},
- {'name': 'TileSummarizingProcessor'}
+ {'name': 'EmptyTileFilter', 'config': {}},
+ {'name': 'KelvinToCelsius', 'config': {}},
+ {'name': 'TileSummarizingProcessor', 'config': {}}
]
processorchain = ProcessorChain(processor_list)
@@ -130,6 +187,39 @@ def test_run_chain_partial_empty(self):
self.assertEqual(0, len(results))
+ def test_run_chain_promote_var(self):
+ processor_list = [
+ {'name': 'GridReadingProcessor',
+ 'config': {'latitude': 'lat',
+ 'longitude': 'lon',
+ 'time': 'time',
+ 'variable_to_read': 'analysed_sst'}},
+ {'name': 'EmptyTileFilter', 'config': {}},
+ {'name': 'KelvinToCelsius', 'config': {}},
+ {'name': 'PromoteVariableToGlobalAttribute',
+ 'config': {
+ 'attribute_name': 'time_i',
+ 'variable_name': 'time',
+ 'dimensioned_by.0': 'time'
+ }},
+ {'name': 'TileSummarizingProcessor', 'config': {}}
+ ]
+ processorchain = ProcessorChain(processor_list)
+
+ test_file = path.join(path.dirname(__file__), 'datafiles',
'partial_empty_mur.nc4')
+
+ input_tile = nexusproto.NexusTile()
+ tile_summary = nexusproto.TileSummary()
+ tile_summary.granule = "file:%s" % test_file
+ tile_summary.section_spec = "time:0:1,lat:489:499,lon:0:10"
+ input_tile.summary.CopyFrom(tile_summary)
+
+ results = list(processorchain.process(input_tile))
+
+ self.assertEqual(1, len(results))
+ tile = results[0]
+ self.assertEqual("1104483600",
tile.summary.global_attributes[0].values[0])
+
if __name__ == '__main__':
unittest.main()
diff --git a/tests/promotevariabletoglobalattribute_test.py
b/tests/promotevariabletoglobalattribute_test.py
new file mode 100644
index 0000000..1fbe21d
--- /dev/null
+++ b/tests/promotevariabletoglobalattribute_test.py
@@ -0,0 +1,38 @@
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+import unittest
+
+from os import path
+
+import sdap.processors
+import nexusproto.DataTile_pb2
+
+
+class TestReadWSWMData(unittest.TestCase):
+
+ def test_read_not_empty_wswm(self):
+ test_file = path.join(path.dirname(__file__), 'datafiles',
'not_empty_wswm.nc')
+
+ promoter = sdap.processors.PromoteVariableToGlobalAttribute('rivid_i',
'rivid', ('rivid',))
+
+ input_tile = nexusproto.DataTile_pb2.NexusTile()
+ tile_summary = nexusproto.DataTile_pb2.TileSummary()
+ tile_summary.granule = "file:%s" % test_file
+ tile_summary.section_spec = "time:0:5832,rivid:0:1"
+ input_tile.summary.CopyFrom(tile_summary)
+
+ results = list(promoter.process(input_tile))
+
+ print(results)
\ No newline at end of file
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