Add forgotten db.py

cuburn/genome/db.py

@@ -0,0 +1,46 @@
+import os
+import json
+
+class GenomeDB(object):
+    """
+    Abstract base class for accessing genomes by ID. This is likely to be
+    extended in the future.
+    """
+    def __init__(self):
+        self.stashed = {}
+    def _get(self, id):
+        raise NotImplementedError()
+    def get(self, id):
+        if id in self.stashed:
+            return self.stashed[id]
+        return self._get(id)
+    def stash(self, id, gnm):
+        self.stashed[id] = gnm
+
+class OneFileDB(object):
+    def __init__(self, dct):
+        assert dct.get(type) == 'onefiledb', "Doesn't look like a OneFileDB."
+        self.dct = dct
+
+    @classmethod
+    def read(cls, path):
+        with open(path) as fp:
+            return cls(json.load(fp))
+
+    def get(self, id):
+        return self.dct[id]
+
+class FilesystemDB(object):
+    def __init__(self, path):
+        self.path = path
+
+    def get(self, id):
+        if not id.endswith('.json'):
+            id += '.json'
+        with open(os.path.join(self.path, id)) as fp:
+            return json.load(fp)
+
+def connect(path):
+    if os.path.isfile(path):
+        return OneFileDB.read(path)
+    return FilesystemDB(path)