link result view and source view

int2intmap.py

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+import math
+import os
+from logging import exception
+from typing import Optional
+
+
+class Int2IntMap():
+    """
+    A file used to map byte numbers of the filter view to byte numbers in the original file.
+    Each line contains the two integers separated by a comma.
+    The first column is sorted ascending. This allows us to do binary searches.
+    The file uses 4kb blocks. That means we add fill bytes (newlines) if a line would cross a 4kb block boundary.
+    """
+    blocksize = 4096
+
+    def __init__(self, file):
+        self._file = file
+        self._handle = open(file, "w+t")
+        self._buffer = ""
+
+    def close(self):
+        if not self._handle.closed:
+            self._handle.close()
+
+    def reset(self):
+        self._handle.truncate(0)
+
+    def add(self, key: int, val: int):
+        line = "%d,%d\n" % (key, val)
+        length = len(line)
+        offset = self._handle.tell() + len(self._buffer)
+        if offset % self.blocksize + length > self.blocksize:
+            # end of block: fill block
+            fill_bytes = self.blocksize - offset % self.blocksize
+            self._buffer = self._buffer + ("\n" * fill_bytes)
+        self._buffer = self._buffer + line
+        if len(self._buffer) > self.blocksize * 100:
+            self._flush_buffer()
+
+    def _flush_buffer(self):
+        self._handle.write(self._buffer)
+        self._buffer = ""
+        self._handle.flush()
+
+    def find(self, key: int) -> Optional[int]:
+        if (len(self._buffer)) > 0:
+            self._flush_buffer()
+        size = os.stat(self._file).st_size
+        if size == 0:
+            return None
+        total_blocks = math.ceil(size / self.blocksize)
+        l = 0
+        r = total_blocks - 1
+        while r >= l:
+            mid = l + math.floor((r - l) / 2)
+            offset = mid * self.blocksize
+
+            self._handle.seek(offset)
+            block = self._handle.read(self.blocksize)
+            lines = block.split("\n")
+            is_before = None
+            for line in lines:
+                if len(line) == 0:
+                    continue
+                token = line.split(",")
+                k = int(token[0])
+                val = int(token[1])
+
+                if key == k:
+                    return val
+                tmp = key < k
+                if is_before is not None and tmp != is_before:
+                    return None
+                else:
+                    is_before = tmp
+
+            if is_before:
+                r = mid - 1
+            else:
+                l = mid + 1
+        return None
+
+    def total_blocks(self) -> int:
+        size = os.stat(self._file).st_size
+        return math.ceil(size / self.blocksize)