[MRG] Refactor the database loading code in sourmash_args (#1373)

* refactor return signature of load_dbs_and_sigs

* more refactor - filename stuff

* add 'location' to SBT objects

* finish removing filename

* Update src/sourmash/sbt.py

Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>

Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>

src/sourmash/sbt.py

@@ -183,6 +183,7 @@ def __init__(self, factory, *, d=2, storage=None, cache_size=None):
         if cache_size is None:
             cache_size = sys.maxsize
         self._nodescache = _NodesCache(maxsize=cache_size)
+        self._location = None
 
     def signatures(self):
         for k in self.leaves():
@@ -389,7 +390,7 @@ def search(self, query, *args, **kwargs):
             # tree search should always/only return matches above threshold
             assert similarity >= threshold
 
-            results.append((similarity, leaf.data, None))
+            results.append((similarity, leaf.data, self.location))
 
         return results
 
@@ -435,7 +436,7 @@ def gather(self, query, *args, **kwargs):
             containment = query.minhash.contained_by(leaf_mh, True)
 
             assert containment >= threshold, "containment {} not below threshold {}".format(containment, threshold)
-            results.append((containment, leaf.data, None))
+            results.append((containment, leaf.data, self.location))
 
         results.sort(key=lambda x: -x[0])
 
@@ -758,7 +759,9 @@ def load(cls, location, *, leaf_loader=None, storage=None, print_version_warning
             elif storage is None:
                 storage = klass(**jnodes['storage']['args'])
 
-        return loader(jnodes, leaf_loader, dirname, storage, print_version_warning=print_version_warning, cache_size=cache_size)
+        obj = loader(jnodes, leaf_loader, dirname, storage, print_version_warning=print_version_warning, cache_size=cache_size)
+        obj.location = location
+        return obj
 
     @staticmethod
     def _load_v1(jnodes, leaf_loader, dirname, storage, *, print_version_warning=True, cache_size=None):

src/sourmash/search.py

@@ -29,12 +29,13 @@ def search_databases(query, databases, threshold, do_containment, best_only,
                      ignore_abundance, unload_data=False):
     results = []
     found_md5 = set()
-    for (obj, filename, filetype) in databases:
-        search_iter = obj.search(query, threshold=threshold,
+    for db in databases:
+        search_iter = db.search(query, threshold=threshold,
                                  do_containment=do_containment,
                                  ignore_abundance=ignore_abundance,
                                  best_only=best_only,
                                  unload_data=unload_data)
+
         for (similarity, match, filename) in search_iter:
             md5 = match.md5sum()
             if md5 not in found_md5:
@@ -84,8 +85,8 @@ def _find_best(dblist, query, threshold_bp):
     threshold_bp = int(threshold_bp / query_scaled) * query_scaled
 
     # search across all databases
-    for (obj, filename, filetype) in dblist:
-        for cont, match, fname in obj.gather(query, threshold_bp=threshold_bp):
+    for db in dblist:
+        for cont, match, fname in db.gather(query, threshold_bp=threshold_bp):
             assert cont                   # all matches should be nonzero.
 
             # note, break ties based on name, to ensure consistent order.
@@ -94,9 +95,7 @@ def _find_best(dblist, query, threshold_bp):
                 # update best match.
                 best_cont = cont
                 best_match = match
-
-                # some objects may not have associated filename (e.g. SBTs)
-                best_filename = fname or filename
+                best_filename = fname
 
     if not best_match:
         return None, None, None

src/sourmash/sourmash_args.py

@@ -256,6 +256,8 @@ def load_dbs_and_sigs(filenames, query, is_similarity_query, *, cache_size=None)
     Load one or more SBTs, LCAs, and/or signatures.
 
     Check for compatibility with query.
+
+    This is basically a user-focused wrapping of _load_databases.
     """
     query_ksize = query.minhash.ksize
     query_moltype = get_moltype(query)
@@ -281,7 +283,7 @@ def load_dbs_and_sigs(filenames, query, is_similarity_query, *, cache_size=None)
             siglist = _select_sigs(db, moltype=query_moltype, ksize=query_ksize)
             siglist = filter_compatible_signatures(query, siglist, 1)
             linear = LinearIndex(siglist, filename=filename)
-            databases.append((linear, filename, False))
+            databases.append(linear)
 
             n_signatures += len(linear)
 
@@ -291,7 +293,7 @@ def load_dbs_and_sigs(filenames, query, is_similarity_query, *, cache_size=None)
                                             is_similarity_query):
                 sys.exit(-1)
 
-            databases.append((db, filename, 'SBT'))
+            databases.append(db)
             notify('loaded SBT {}', filename, end='\r')
             n_databases += 1
 
@@ -304,7 +306,7 @@ def load_dbs_and_sigs(filenames, query, is_similarity_query, *, cache_size=None)
             notify('loaded LCA {}', filename, end='\r')
             n_databases += 1
 
-            databases.append((db, filename, 'LCA'))
+            databases.append(db)
 
         # signature file
         elif dbtype == DatabaseType.SIGLIST:
@@ -316,7 +318,7 @@ def load_dbs_and_sigs(filenames, query, is_similarity_query, *, cache_size=None)
                 sys.exit(-1)
 
             linear = LinearIndex(siglist, filename=filename)
-            databases.append((linear, filename, 'signature'))
+            databases.append(linear)
 
             notify('loaded {} signatures from {}', len(linear),
                    filename, end='\r')