Remove libsonata hidden API and add Sonata error

BlueBrain · Jul 7, 2020 · 0dd7b00 · 0dd7b00
1 parent 7870430
commit 0dd7b00
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Showing 4 changed files with 32 additions and 14 deletions.
diff --git a/bluepysnap/frame_report.py b/bluepysnap/frame_report.py
@@ -21,7 +21,7 @@
 from pathlib2 import Path
 import numpy as np
 import pandas as pd
-from libsonata import ElementReportReader
+from libsonata import ElementReportReader, SonataError
 
 import bluepysnap._plotting
 from bluepysnap.exceptions import BluepySnapError
@@ -98,11 +98,13 @@ def get(self, group=None, t_start=None, t_stop=None):
         Returns:
             pandas.DataFrame: frame as columns indexed by timestamps.
         """
-        ids = [] if group is None else self._resolve(group).tolist()
-        t_start = -1 if t_start is None else t_start
-        t_stop = -1 if t_stop is None else t_stop
+        ids = self._resolve(group).tolist()
+
+        try:
+            view = self._frame_population.get(node_ids=ids, tstart=t_start, tstop=t_stop)
+        except SonataError as e:
+            raise BluepySnapError(e)
 
-        view = self._frame_population.get(node_ids=ids, tstart=t_start, tstop=t_stop)
         if len(view.ids) == 0:
             return pd.DataFrame()
         res = pd.DataFrame(data=view.data,

diff --git a/bluepysnap/spike_report.py b/bluepysnap/spike_report.py
@@ -22,14 +22,14 @@
 from cached_property import cached_property
 import pandas as pd
 import numpy as np
+from libsonata import SpikeReader, SonataError
 
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.utils import fix_libsonata_empty_list
 import bluepysnap._plotting
 
 
 def _get_reader(spike_report):
-    from libsonata import SpikeReader
     path = str(Path(spike_report.config["output_dir"]) / spike_report.config["spikes_file"])
     return SpikeReader(path)
 
@@ -101,12 +101,14 @@ def get(self, group=None, t_start=None, t_stop=None):
         Returns:
             pandas.Series: return spiking node_ids indexed by sorted spike time.
         """
-        node_ids = [] if group is None else self._resolve_nodes(group).tolist()
+        node_ids = self._resolve_nodes(group).tolist()
 
-        t_start = -1 if t_start is None else t_start
-        t_stop = -1 if t_stop is None else t_stop
         series_name = "ids"
-        res = self._spike_population.get(node_ids=node_ids, tstart=t_start, tstop=t_stop)
+        try:
+            res = self._spike_population.get(node_ids=node_ids, tstart=t_start, tstop=t_stop)
+        except SonataError as e:
+            raise BluepySnapError(e)
+
         if not res:
             return pd.Series(data=[], index=pd.Index([], name="times"), name=series_name)
 

diff --git a/tests/test_frame_report.py b/tests/test_frame_report.py
@@ -214,8 +214,6 @@ def test_get(self):
         pdt.assert_frame_equal(
             self.test_obj.get([2, 1], t_start=0.2, t_stop=0.8), self.df.iloc[2:9].loc[:, [1, 2]])
 
-        pdt.assert_frame_equal(self.test_obj.get([0, 2], t_start=15), pd.DataFrame())
-
         pdt.assert_frame_equal(
             self.test_obj.get(group={Cell.MTYPE: "L6_Y"}, t_start=0.2, t_stop=0.8),
             self.df.iloc[2:9].loc[:, [1, 2]])
@@ -226,6 +224,15 @@ def test_get(self):
         pdt.assert_frame_equal(
             self.test_obj.get(group="Layer23"), self.df.loc[:, [0]])
 
+        with pytest.raises(BluepySnapError):
+            self.test_obj.get(-1, t_start=0.2)
+
+        with pytest.raises(BluepySnapError):
+            self.test_obj.get(0, t_start=-1)
+
+        with pytest.raises(BluepySnapError):
+            self.test_obj.get([0, 2], t_start=15)
+
         with pytest.raises(BluepySnapError):
             self.test_obj.get(4)
 

diff --git a/tests/test_spike_report.py b/tests/test_spike_report.py
@@ -157,8 +157,6 @@ def test_get(self):
         pdt.assert_series_equal(self.test_obj.get([2, 1], t_start=0.2, t_stop=0.8),
                                 _create_series([1, 2], [0.3, 0.7]))
 
-        pdt.assert_series_equal(self.test_obj.get([0, 2], t_start=12), _create_series([], []))
-
         pdt.assert_series_equal(
             self.test_obj.get(group={Cell.MTYPE: "L6_Y"}, t_start=0.2, t_stop=0.8),
             _create_series([1, 2], [0.3, 0.7]))
@@ -169,6 +167,15 @@ def test_get(self):
         pdt.assert_series_equal(
             self.test_obj.get(group="Layer23"), _create_series([0, 0], [0.2, 1.3]))
 
+        with pytest.raises(BluepySnapError):
+            self.test_obj.get([-1], t_start=0.2)
+
+        with pytest.raises(BluepySnapError):
+            self.test_obj.get([0, 2], t_start=-1)
+
+        with pytest.raises(BluepySnapError):
+            self.test_obj.get([0, 2], t_start=12)
+
         with pytest.raises(BluepySnapError):
             self.test_obj.get(4)