From c74c800fb1b4003fe213fa15cf4e9ce636feb744 Mon Sep 17 00:00:00 2001 From: CodyCBakerPhD Date: Tue, 14 Sep 2021 12:39:26 -0400 Subject: [PATCH 1/5] generalized get_source_schema() across all interfaces --- nwb_conversion_tools/basedatainterface.py | 3 ++- .../datainterfaces/behavior/movie/moviedatainterface.py | 4 ---- .../ecephys/baserecordingextractorinterface.py | 5 ----- .../datainterfaces/ecephys/basesortingextractorinterface.py | 5 ----- .../datainterfaces/ophys/baseimagingextractorinterface.py | 4 ---- .../ophys/basesegmentationextractorinterface.py | 4 ---- 6 files changed, 2 insertions(+), 23 deletions(-) diff --git a/nwb_conversion_tools/basedatainterface.py b/nwb_conversion_tools/basedatainterface.py index bf95e0c5b..9fb86ba74 100644 --- a/nwb_conversion_tools/basedatainterface.py +++ b/nwb_conversion_tools/basedatainterface.py @@ -6,9 +6,10 @@ class BaseDataInterface(ABC): + @classmethod def get_source_schema(cls): - return get_base_schema() + return get_schema_from_method_signature(cls.__init__) @classmethod def get_conversion_options_schema(cls): diff --git a/nwb_conversion_tools/datainterfaces/behavior/movie/moviedatainterface.py b/nwb_conversion_tools/datainterfaces/behavior/movie/moviedatainterface.py index 8208e9c62..d458eae3e 100644 --- a/nwb_conversion_tools/datainterfaces/behavior/movie/moviedatainterface.py +++ b/nwb_conversion_tools/datainterfaces/behavior/movie/moviedatainterface.py @@ -42,10 +42,6 @@ def __init__(self, file_paths: list): assert HAVE_OPENCV, INSTALL_MESSAGE super().__init__(file_paths=file_paths) - @classmethod - def get_source_schema(cls): - return get_schema_from_method_signature(cls.__init__) - def run_conversion( self, nwbfile: NWBFile, diff --git a/nwb_conversion_tools/datainterfaces/ecephys/baserecordingextractorinterface.py b/nwb_conversion_tools/datainterfaces/ecephys/baserecordingextractorinterface.py index fd88dc8d1..6f852ab68 100644 --- a/nwb_conversion_tools/datainterfaces/ecephys/baserecordingextractorinterface.py +++ b/nwb_conversion_tools/datainterfaces/ecephys/baserecordingextractorinterface.py @@ -23,11 +23,6 @@ class BaseRecordingExtractorInterface(BaseDataInterface, ABC): RX = None - @classmethod - def get_source_schema(cls): - """Compile input schema for the RecordingExtractor.""" - return get_schema_from_method_signature(cls.__init__) - def __init__(self, **source_data): super().__init__(**source_data) self.recording_extractor = self.RX(**source_data) diff --git a/nwb_conversion_tools/datainterfaces/ecephys/basesortingextractorinterface.py b/nwb_conversion_tools/datainterfaces/ecephys/basesortingextractorinterface.py index 553b3599d..fa2c0fb55 100644 --- a/nwb_conversion_tools/datainterfaces/ecephys/basesortingextractorinterface.py +++ b/nwb_conversion_tools/datainterfaces/ecephys/basesortingextractorinterface.py @@ -16,11 +16,6 @@ class BaseSortingExtractorInterface(BaseDataInterface, ABC): SX = None - @classmethod - def get_source_schema(cls): - """Compile input schema for the SortingExtractor.""" - return get_schema_from_method_signature(cls.__init__) - def __init__(self, **source_data): super().__init__(**source_data) self.sorting_extractor = self.SX(**source_data) diff --git a/nwb_conversion_tools/datainterfaces/ophys/baseimagingextractorinterface.py b/nwb_conversion_tools/datainterfaces/ophys/baseimagingextractorinterface.py index e2543d64f..7c48eeec8 100644 --- a/nwb_conversion_tools/datainterfaces/ophys/baseimagingextractorinterface.py +++ b/nwb_conversion_tools/datainterfaces/ophys/baseimagingextractorinterface.py @@ -16,10 +16,6 @@ class BaseImagingExtractorInterface(BaseDataInterface): IX = None - @classmethod - def get_source_schema(cls): - return get_schema_from_method_signature(cls.__init__) - def __init__(self, **source_data): super().__init__(**source_data) self.imaging_extractor = self.IX(**source_data) diff --git a/nwb_conversion_tools/datainterfaces/ophys/basesegmentationextractorinterface.py b/nwb_conversion_tools/datainterfaces/ophys/basesegmentationextractorinterface.py index db36d1181..9443857a2 100644 --- a/nwb_conversion_tools/datainterfaces/ophys/basesegmentationextractorinterface.py +++ b/nwb_conversion_tools/datainterfaces/ophys/basesegmentationextractorinterface.py @@ -18,10 +18,6 @@ class BaseSegmentationExtractorInterface(BaseDataInterface, ABC): SegX = None - @classmethod - def get_source_schema(cls): - return get_schema_from_method_signature(cls.__init__) - def __init__(self, **source_data): super().__init__(**source_data) self.segmentation_extractor = self.SegX(**source_data) From 206fa055914350e2abc049107684a8e64aa13c1e Mon Sep 17 00:00:00 2001 From: Cody Baker Date: Mon, 27 Sep 2021 19:31:23 +0000 Subject: [PATCH 2/5] Automated changes --- nwb_conversion_tools/basedatainterface.py | 1 - 1 file changed, 1 deletion(-) diff --git a/nwb_conversion_tools/basedatainterface.py b/nwb_conversion_tools/basedatainterface.py index 9fb86ba74..9c7acbeb9 100644 --- a/nwb_conversion_tools/basedatainterface.py +++ b/nwb_conversion_tools/basedatainterface.py @@ -6,7 +6,6 @@ class BaseDataInterface(ABC): - @classmethod def get_source_schema(cls): return get_schema_from_method_signature(cls.__init__) From bdb0a355a76c09b8ba638e9fa912257c46b36482 Mon Sep 17 00:00:00 2001 From: Cody Baker Date: Mon, 27 Sep 2021 17:06:20 -0400 Subject: [PATCH 3/5] debug CI --- tests/test_converter.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tests/test_converter.py b/tests/test_converter.py index 13ee437ea..e347752e9 100644 --- a/tests/test_converter.py +++ b/tests/test_converter.py @@ -21,6 +21,9 @@ def test_converter(): nwbfile_path = str(test_dir / "extension_test.nwb") class NdxEventsInterface(BaseDataInterface): + def __init__(self): + super().__init__() + def run_conversion(self, nwbfile: NWBFile, metadata: dict): events = LabeledEvents( name="LabeledEvents", From 30ac86945b12c076b1b97d03974e99356ee95a85 Mon Sep 17 00:00:00 2001 From: Cody Baker Date: Tue, 28 Sep 2021 08:55:43 -0400 Subject: [PATCH 4/5] altered debug --- nwb_conversion_tools/basedatainterface.py | 2 +- tests/test_converter.py | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/nwb_conversion_tools/basedatainterface.py b/nwb_conversion_tools/basedatainterface.py index 9c7acbeb9..1dc5df470 100644 --- a/nwb_conversion_tools/basedatainterface.py +++ b/nwb_conversion_tools/basedatainterface.py @@ -8,7 +8,7 @@ class BaseDataInterface(ABC): @classmethod def get_source_schema(cls): - return get_schema_from_method_signature(cls.__init__) + return get_schema_from_method_signature(cls.__init__, exclude=["source_data"]) @classmethod def get_conversion_options_schema(cls): diff --git a/tests/test_converter.py b/tests/test_converter.py index e347752e9..4b534aaea 100644 --- a/tests/test_converter.py +++ b/tests/test_converter.py @@ -21,8 +21,6 @@ def test_converter(): nwbfile_path = str(test_dir / "extension_test.nwb") class NdxEventsInterface(BaseDataInterface): - def __init__(self): - super().__init__() def run_conversion(self, nwbfile: NWBFile, metadata: dict): events = LabeledEvents( From d1cb8b11b9794bb1cc432013ad903be7170a6fc1 Mon Sep 17 00:00:00 2001 From: Cody Baker Date: Tue, 28 Sep 2021 12:57:29 +0000 Subject: [PATCH 5/5] Automated changes --- tests/test_converter.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/test_converter.py b/tests/test_converter.py index 4b534aaea..13ee437ea 100644 --- a/tests/test_converter.py +++ b/tests/test_converter.py @@ -21,7 +21,6 @@ def test_converter(): nwbfile_path = str(test_dir / "extension_test.nwb") class NdxEventsInterface(BaseDataInterface): - def run_conversion(self, nwbfile: NWBFile, metadata: dict): events = LabeledEvents( name="LabeledEvents",