Added a script to try loading Neo test data from GIN

test/test_gin.py

@@ -0,0 +1,241 @@
+"""
+
+"""
+
+import os
+from os.path import join
+from collections import defaultdict
+from urllib.parse import urlencode
+from datetime import datetime
+from time import time
+import pickle
+from importlib import import_module
+import unittest
+import requests
+from neo.test.rawiotest.common_rawio_test import BaseTestRawIO
+
+modules_to_test = [
+    "neuroshare",
+    "winedr",
+    "stimfit",
+    "openephys",
+    "axograph",
+    "axon",
+    "nix",
+    "plexon",
+    "rawbinarysignal",
+    "neohdf5",
+    "elphy",
+    "brainwaref32",
+    "tdt",
+    "klustakwik",
+    "asciisignal",
+    "neuroscope",
+    "neuroexplorer",
+    "alphaomega",
+    "blackrock",
+    "rawmcs",
+    "kwik",
+    "micromed",
+    "igor",
+    "brainvision",
+    "asciispiketrain",
+    "winwcp",
+    "brainwaredam",
+    "brainwaresrc",
+    "intan",
+    "nest",
+    "spike2",
+    "bci2000",
+    "elan",
+    "neuralynx",
+]
+
+# base_data_url = "https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/"
+base_data_url = "https://gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/"
+neo_viewer_url = "https://neo-viewer-staging.brainsimulation.eu/api/"
+
+responses = defaultdict(dict)
+
+start_time = time()
+for iomodule in modules_to_test:
+    try:
+        test_module = import_module("neo.test.iotest.test_{}io".format(iomodule))
+    except ImportError:
+        pass  # print("Unable to import {}".format(iomodule))
+    else:
+        for name, obj in test_module.__dict__.items():
+            if (
+                isinstance(obj, type)
+                and issubclass(obj, unittest.TestCase)
+                and not issubclass(obj, BaseTestRawIO)
+            ):
+                if hasattr(obj, "ioclass") and obj.entities_to_test:
+                    assert iomodule in obj.ioclass.__module__
+                    for filename in obj.entities_to_test:
+                        assert iomodule in filename
+                        data_url = join(base_data_url, filename)
+                        block_url = (
+                            neo_viewer_url
+                            + "blockdata/?"
+                            + urlencode(
+                                {
+                                    "format": "json",
+                                    "url": data_url,
+                                    "type": obj.ioclass.__name__,
+                                }
+                            )
+                        )
+                        response = requests.get(block_url)
+                        block_status_code = response.status_code
+                        if response.status_code == 200:
+                            segment_url = (
+                                neo_viewer_url
+                                + "segmentdata/?"
+                                + urlencode(
+                                    {
+                                        "format": "json",
+                                        "url": data_url,
+                                        "segment_id": "0",
+                                        "type": obj.ioclass.__name__,
+                                    }
+                                )
+                            )
+                            response2 = requests.get(segment_url)
+                            segment_status_code = response2.status_code
+                            if response2.status_code == 200:
+                                signal_url = (
+                                    neo_viewer_url
+                                    + "analogsignaldata/?"
+                                    + urlencode(
+                                        {
+                                            "format": "json",
+                                            "url": data_url,
+                                            "segment_id": "0",
+                                            "analog_signal_id": "0",
+                                            "type": obj.ioclass.__name__,
+                                        }
+                                    )
+                                )
+                                response3 = requests.get(signal_url)
+                                signal_status_code = response3.status_code
+                            else:
+                                signal_status_code = "-"
+                        else:
+                            segment_status_code = "-"
+                            signal_status_code = "-"
+                        print(
+                            data_url,
+                            time() - start_time,
+                            block_status_code,
+                            segment_status_code,
+                            signal_status_code,
+                        )
+                        responses[response.status_code][filename] = response
+
+print("Status code counts")
+for key in responses:
+    print(key, len(responses[key]))
+
+for name, r in responses[500].items():
+    print(name, r.content.split(b"\n\n")[0])
+
+timestamp = datetime.now().strftime("%Y%m%d-%H%M%S")
+with open(f"results_gin_{timestamp}.pkl", "wb") as fp:
+    pickle.dump(responses, fp)
+
+
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/winedr/File_WinEDR_1.EDR', 343.57470703125, 200, 200, 200)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/winedr/File_WinEDR_2.EDR', 406.673837184906, 200, 200, 504)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/winedr/File_WinEDR_3.EDR', 430.24066615104675, 200, 200, 200)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/stimfit/File_stimfit_1.h5', 431.99944615364075, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/stimfit/File_stimfit_2.h5', 433.46491503715515, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/stimfit/File_stimfit_3.h5', 434.542622089386, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/stimfit/File_stimfit_4.h5', 435.75226616859436, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/stimfit/File_stimfit_5.h5', 436.8318700790405, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/stimfit/File_stimfit_6.h5', 437.87960505485535, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/openephys/OpenEphys_SampleData_1', 438.46606516838074, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/axograph/File_axograph.axgd', 439.87526512145996, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/axon/File_axon_1.abf', 502.08061814308167, 200, 200, 504)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/axon/File_axon_2.abf', 566.5939300060272, 200, 200, 504)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/axon/File_axon_3.abf', 584.4787490367889, 200, 200, 200)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/axon/File_axon_4.abf', 646.7802860736847, 200, 200, 504)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/axon/File_axon_5.abf', 704.5435080528259, 200, 200, 200)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/axon/File_axon_6.abf', 726.445855140686, 200, 200, 200)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/axon/File_axon_7.abf', 729.8017871379852, 200, 200, 200)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/plexon/File_plexon_1.plx', 734.0235509872437, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/plexon/File_plexon_2.plx', 794.4063730239868, 504, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/plexon/File_plexon_3.plx', 857.6411371231079, 504, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/rawbinarysignal/File_rawbinary_10kHz_2channels_16bit.raw', 959.683207988739, 200, 200, 200)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/elphy/ElphyExample.DAT', 960.313395023346, 415, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/elphy/ElphyExample_Mode1.dat', 961.3540730476379, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/elphy/ElphyExample_Mode2.dat', 962.2745161056519, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/elphy/ElphyExample_Mode3.dat', 963.3444330692291, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaref32/block_300ms_4rep_1clust_part_ch1.f32', 965.9617831707001, 200, 200, 500)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaref32/block_500ms_5rep_empty_fullclust_ch1.f32', 967.713632106781, 200, 200, 500)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaref32/block_500ms_5rep_empty_partclust_ch1.f32', 969.5349810123444, 200, 200, 500)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaref32/interleaved_500ms_5rep_ch2.f32', 972.4128661155701, 200, 200, 500)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaref32/interleaved_500ms_5rep_nospikes_ch1.f32', 977.4060971736908, 200, 200, 500)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaref32/multi_500ms_mulitrep_ch1.f32', 981.3215980529785, 200, 200, 500)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaref32/random_500ms_12rep_noclust_part_ch2.f32', 984.5162370204926, 200, 200, 500)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaref32/sequence_500ms_5rep_ch2.f32', 986.464928150177, 200, 200, 500)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/tdt/aep_05', 987.6529760360718, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/klustakwik/test2/base', 988.7491271495819, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/klustakwik/test2/base2', 989.4053881168365, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/asciisignal/File_asciisignal_2.txt', 990.8959012031555, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/asciisignal/File_asciisignal_3.txt', 992.1295230388641, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/neuroscope/test1/test1.xml', 992.6065061092377, 415, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/neuroexplorer/File_neuroexplorer_1.nex', 993.705087184906, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/neuroexplorer/File_neuroexplorer_2.nex', 995.6957621574402, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/alphaomega/File_AlphaOmega_1.map', 997.8663520812988, 200, 200, 500)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/alphaomega/File_AlphaOmega_2.map', 1000.752032995224, 200, 200, 500)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/blackrock/FileSpec2.3001', 1001.2958881855011, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/rawmcs/raw_mcs_with_header_1.raw', 1002.829537153244, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/kwik/neo.kwik', 1004.6954171657562, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/micromed/File_micromed_1.TRC', 1005.2305672168732, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/igor/mac-version2.ibw', 1006.4016361236572, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/igor/win-version2.ibw', 1007.6389729976654, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainvision/File_brainvision_1.vhdr', 1011.5036389827728, 200, 200, 200)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainvision/File_brainvision_2.vhdr', 1015.6663680076599, 200, 200, 200)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainvision/File_brainvision_3_float32.vhdr', 1022.631028175354, 200, 200, 200)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainvision/File_brainvision_3_int16.vhdr', 1028.212128162384, 200, 200, 200)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainvision/File_brainvision_3_int32.vhdr', 1032.7176032066345, 200, 200, 200)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/asciispiketrain/File_ascii_spiketrain_1.txt', 1034.4098720550537, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/winwcp/File_winwcp_1.wcp', 1052.7634761333466, 200, 200, 200)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaredam/block_300ms_4rep_1clust_part_ch1.dam', 1053.8219740390778, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaredam/interleaved_500ms_5rep_ch2.dam', 1055.050096988678, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaredam/long_170s_1rep_1clust_ch2.dam', 1056.5989110469818, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaredam/multi_500ms_mulitrep_ch1.dam', 1060.3307621479034, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaredam/random_500ms_12rep_noclust_part_ch2.dam', 1061.9835941791534, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaredam/sequence_500ms_5rep_ch2.dam', 1062.8565120697021, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaresrc/block_300ms_4rep_1clust_part_ch1.src', 1063.730674982071, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaresrc/block_500ms_5rep_empty_fullclust_ch1.src', 1064.8823781013489, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaresrc/block_500ms_5rep_empty_partclust_ch1.src', 1066.0766310691833, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaresrc/interleaved_500ms_5rep_ch2.src', 1067.140293121338, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaresrc/interleaved_500ms_5rep_nospikes_ch1.src', 1068.1508340835571, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaresrc/interleaved_500ms_7rep_noclust_ch1.src', 1069.9386990070343, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaresrc/long_170s_1rep_1clust_ch2.src', 1077.4439430236816, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaresrc/multi_500ms_mulitrep_ch1.src', 1081.4652621746063, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaresrc/random_500ms_12rep_noclust_part_ch2.src', 1084.2070090770721, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/brainwaresrc/sequence_500ms_5rep_ch2.src', 1085.260073184967, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/intan/intan_rhs_test_1.rhs', 1108.6231281757355, 200, 200, 200)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/intan/intan_rhd_test_1.rhd', 1114.6307561397552, 200, 200, 200)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/spike2/File_spike2_1.smr', 1115.134532213211, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/spike2/File_spike2_2.smr', 1116.1406362056732, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/spike2/File_spike2_3.smr', 1116.9410290718079, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/spike2/130322-1LY.smr', 1118.949949979782, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/spike2/multi_sampling.smr', 1120.2054960727692, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/elan/File_elan_1.eeg', 1184.0774340629578, 200, 200, 504)
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/neuralynx/Cheetah_v5.5.1/original_data', 1184.6444220542908, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/neuralynx/Cheetah_v5.6.3/original_data', 1185.4696061611176, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/neuralynx/Cheetah_v5.7.4/original_data', 1186.1286251544952, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/neuralynx/Cheetah_v5.5.1/original_data', 1187.8566591739655, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/neuralynx/Cheetah_v5.6.3/original_data', 1188.3791670799255, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/neuralynx/Cheetah_v5.7.4/original_data', 1189.5361762046814, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/neuralynx/Cheetah_v5.5.1/original_data', 1189.9167890548706, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/neuralynx/Cheetah_v5.6.3/original_data', 1190.379625082016, 500, '-', '-')
+# ('https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/neuralynx/Cheetah_v5.7.4/original_data', 1190.9355380535126, 500, '-', '-')
+# (200, 30)
+# (504, 2)
+# (500, 50)
+# (415, 2)