Merge branch '80_amrfinder_database_type' into 77_amrfinder_ncbi_data…

…base

q2_amr/amrfinderplus/types/_format.py

@@ -19,10 +19,6 @@ def _validate_(self, level):
         pass
 
 
-def _path_maker(name):
-    return str(name)
-
-
 class AMRFinderPlusDatabaseDirFmt(model.DirectoryFormat):
     amr_lib = model.File("AMR.LIB", format=TextFormat)
     amr_lib_comp = model.FileCollection(r"^AMR\.LIB\.h3.$", format=BinaryFormat)
@@ -46,10 +42,26 @@ class AMRFinderPlusDatabaseDirFmt(model.DirectoryFormat):
     amr_cds_comp = model.FileCollection(r"^AMR_CDS\.n..$", format=BinaryFormat)
     amr_cds = model.File("AMR_CDS", format=MixedCaseDNAFASTAFormat)
 
-    def __init__(self, path, mode):
-        super().__init__(path, mode)
+    @amr_lib_comp.set_path_maker
+    def amr_lib_comp_path_maker(self):
+        return r"^AMR\.LIB\.h3.$"
+
+    @amrprot_blast.set_path_maker
+    def amrprot_blast_path_maker(self):
+        return r"^AMRProt\.p..$"
+
+    @amr_dna.set_path_maker
+    def amr_dna_path_maker(self):
+        return r"^AMR_DNA-[a-zA-Z_]+$"
+
+    @amr_dna_comp.set_path_maker
+    def amr_dna_comp_path_maker(self):
+        return r"^AMR_DNA-[a-zA-Z_]+\.n..$"
+
+    @amr_cds_comp.set_path_maker
+    def amr_cds_comp_path_maker(self):
+        return r"^AMR_CDS\.n..$"
 
-        # Overwrite path maker methods for all file collections
-        for var_name, var_value in vars(self.__class__).items():
-            if isinstance(var_value, model.FileCollection):
-                var_value.set_path_maker(_path_maker)
+    @amr_dna_tab.set_path_maker
+    def amr_dna_tab_path_maker(self):
+        return r"^AMR_DNA-[a-zA-Z_]+\.tab$"