add DirectoryIndex

src/sourmash/index.py

@@ -449,8 +449,9 @@ class LazyLinearIndex(Index):
     * this class stores the provided index 'db' in memory. If you need
       a class that does lazy loading of signatures from disk and does not
       store signatures in memory, see LazyLoadedIndex.
-    * if you want efficient in-memory manifest-based selection, consider
-      LazyMultiIndex.
+    * if you want efficient manifest-based selection, consider
+      MultiIndex (signatures in memory) and LazyMultiIndex (signatures loaded
+      upon request).
     """
 
     def __init__(self, db, selection_dict={}):
@@ -895,9 +896,18 @@ def sigloc_iter():
         return cls(manifest, parent=parent)
 
     @classmethod
-    def load_from_directory(cls, pathname, force=False):
+    def load_from_directory(cls, pathname, *, force=False):
+        """Create a MultiIndex from a directory.
+
+        Takes directory path plus optional boolean 'force'. Attempts to
+        load all files ending in .sig or .sig.gz, by default; if 'force' is
+        True, will attempt to load _all_ files, ignoring errors.
+        """
         from .sourmash_args import traverse_find_sigs
 
+        if not os.path.isdir(pathname):
+            raise ValueError(f"'{pathname}' must be a directory.")
+
         index_list = []
         source_list = []
 
@@ -980,6 +990,56 @@ def select(self, **kwargs):
         return MultiIndex(new_manifest, parent=self.parent)
 
 
+class DirectoryIndex(Index):
+    """
+    Notes:
+    * Lazy - loads signatures only when requested
+    """
+    def __init__(self, parent, manifest):
+        self.parent = parent
+        self.manifest = manifest
+
+    @classmethod
+    def load(cls, pathname):
+        "Create a DirectoryIndex from a directory with an existing manifest."
+        if not os.path.isdir(pathname):
+            raise ValueError(f"'{pathname}' must be a directory.")
+
+        manifest_path = os.path.join(pathname, "SOURMASH-MANIFEST.csv")
+        if not os.path.exists(manifest_path):
+            raise ValueError(f"Cannot find manifest '{manifest_path}'")
+
+        with open(manifest_path, newline="") as csvfp:
+            manifest = CollectionManifest.load_from_csv(csvfp)
+
+        return cls(pathname, manifest)
+
+    def signatures(self):
+        for ss, _ in self.signatures_with_location():
+            yield ss
+
+    def signatures_with_location(self):
+        for location in self.manifest.locations():
+            fullpath = os.path.join(self.parent, location)
+            for ss in load_signatures(fullpath):
+                if ss in self.manifest:
+                    yield ss, fullpath
+
+    def __len__(self):
+        return len(self.manifest)
+
+    def insert(self, *args):
+        raise NotImplementedError
+
+    def save(self, *args):
+        raise NotImplementedError
+
+    def select(self, **kwargs):
+        "Run 'select' on the manifest."
+        new_manifest = self.manifest.select_to_manifest(**kwargs)
+        return DirectoryIndex(self.parent, new_manifest)
+
+
 class LazyLoadedIndex(Index):
     """Given an index location and a manifest, do select only on the manifest
     until signatures are actually requested, and only then load the index.
@@ -991,7 +1051,6 @@ class LazyLoadedIndex(Index):
     from disk every time they are needed (e.g. 'find(...)', 'signatures()').
 
     Can be used with LazyMultiIndex to support many such indices at once.
-
     """
     def __init__(self, filename, manifest):
         "Create an Index with given filename and manifest."