diff --git a/q2_amr/amrfinderplus/types/__init__.py b/q2_amr/amrfinderplus/types/__init__.py index 5a6cbb9..f94c621 100644 --- a/q2_amr/amrfinderplus/types/__init__.py +++ b/q2_amr/amrfinderplus/types/__init__.py @@ -6,7 +6,7 @@ # The full license is in the file LICENSE, distributed with this software. # ---------------------------------------------------------------------------- from q2_amr.amrfinderplus.types._format import ( - AMRFinderPlusDatabaseDirectoryFormat, + AMRFinderPlusDatabaseDirFmt, ARMFinderPlusAnnotationDirFmt, ARMFinderPlusAnnotationFormat, ARMFinderPlusAnnotationsDirFmt, @@ -15,7 +15,7 @@ ) __all__ = [ - "AMRFinderPlusDatabaseDirectoryFormat", + "AMRFinderPlusDatabaseDirFmt", "ARMFinderPlusAnnotationFormat", "ARMFinderPlusAnnotationsDirFmt", "ARMFinderPlusAnnotationDirFmt", diff --git a/q2_amr/amrfinderplus/types/_format.py b/q2_amr/amrfinderplus/types/_format.py index ac1ba7d..0b7c7e1 100644 --- a/q2_amr/amrfinderplus/types/_format.py +++ b/q2_amr/amrfinderplus/types/_format.py @@ -24,7 +24,7 @@ def _validate_(self, level): pass -class AMRFinderPlusDatabaseDirectoryFormat(model.DirectoryFormat): +class AMRFinderPlusDatabaseDirFmt(model.DirectoryFormat): amr_lib = model.File("AMR.LIB", format=TextFormat) amr_lib_comp = model.FileCollection(r"^AMR\.LIB\.h3.$", format=BinaryFormat) amrprot = model.File("AMRProt", format=ProteinFASTAFormat) diff --git a/q2_amr/amrfinderplus/types/tests/test_types_formats_transformers.py b/q2_amr/amrfinderplus/types/tests/test_types_formats_transformers.py index 9ea964b..3674ab7 100644 --- a/q2_amr/amrfinderplus/types/tests/test_types_formats_transformers.py +++ b/q2_amr/amrfinderplus/types/tests/test_types_formats_transformers.py @@ -11,7 +11,7 @@ from qiime2.plugin.testing import TestPluginBase from q2_amr.amrfinderplus.types._format import ( - AMRFinderPlusDatabaseDirectoryFormat, + AMRFinderPlusDatabaseDirFmt, ARMFinderPlusAnnotationDirFmt, ARMFinderPlusAnnotationFormat, ARMFinderPlusAnnotationsDirFmt, @@ -22,9 +22,7 @@ class TestAMRFinderPlusTypesAndFormats(TestPluginBase): package = "q2_amr.amrfinderplus.types.tests" def test_amrfinderplus_database_directory_format_validate_positive(self): - format = AMRFinderPlusDatabaseDirectoryFormat( - self.get_data_path("database"), mode="r" - ) + format = AMRFinderPlusDatabaseDirFmt(self.get_data_path("database"), mode="r") format.validate() def test_amrfinderplus_annotation_format_validate_positive(self): diff --git a/q2_amr/plugin_setup.py b/q2_amr/plugin_setup.py index e6f0095..b4f763a 100644 --- a/q2_amr/plugin_setup.py +++ b/q2_amr/plugin_setup.py @@ -30,7 +30,7 @@ from q2_amr import __version__ from q2_amr.amrfinderplus.types._format import ( - AMRFinderPlusDatabaseDirectoryFormat, + AMRFinderPlusDatabaseDirFmt, ARMFinderPlusAnnotationDirFmt, ARMFinderPlusAnnotationFormat, ARMFinderPlusAnnotationsDirFmt, @@ -1124,7 +1124,7 @@ ) plugin.register_semantic_type_to_format( AMRFinderPlusDatabase, - artifact_format=AMRFinderPlusDatabaseDirectoryFormat, + artifact_format=AMRFinderPlusDatabaseDirFmt, ) plugin.register_semantic_type_to_format( SampleData[ARMFinderPlusAnnotations], @@ -1158,7 +1158,7 @@ CARDReadsKmerAnalysisJSONFormat, CARDReadsGeneKmerAnalysisDirectoryFormat, CARDReadsAlleleKmerAnalysisDirectoryFormat, - AMRFinderPlusDatabaseDirectoryFormat, + AMRFinderPlusDatabaseDirFmt, TextFormat, BinaryFormat, ARMFinderPlusAnnotationFormat,