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SequenceSearchDef: report file search progress on debug log #16

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SequenceSearchDef: report file search progress on debug log #16

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18 changes: 15 additions & 3 deletions searchkit/search.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,8 @@
import threading
import time
import uuid
import json
from pathlib import Path
from functools import cached_property
from collections import namedtuple, UserDict, UserList

Expand Down Expand Up @@ -1112,16 +1114,26 @@ def _run_search(self, fd):
sequence_results = SequenceSearchResults()
search_ids = set([s.id for s in self.search_defs]) # noqa, pylint: disable=R1718
offset = self.constraints_manager.apply_global(search_ids, fd)
log.debug("starting search of %s (offset=%s, pos=%s)", fd.name, offset,
fd.tell())
log.debug("starting search of %s (offset=%s, pos=%s) for tags [%s]",
fd.name, offset, fd.tell(),
json.dumps([s.tag for s in self.search_defs], indent=2))

# Get the total file size (needed for calculating the search progress)
before_pos = fd.tell()
fd.seek(0, 2)
eof_offset = fd.tell()
fd.seek(before_pos)

runnable = {s.id: _runnable
for s, _runnable in self.search_defs.items()}
ln = 0
filename_short = Path(*Path(fd.name).parts[-2:])
# NOTE: line numbers start at 1 hence offset + 1
for ln, line in enumerate(fd, start=offset + 1):
# This could be helpful to show progress for large files
if ln % 100000 == 0:
log.debug("%s lines searched in %s", ln, fd.name)
log.debug("%s lines searched in %s (%.3f%%)",
ln, filename_short, (fd.tell() / eof_offset) * 100.0)

self.stats['lines_searched'] += 1
line = line.decode("utf-8", **self.decode_kwargs)
Expand Down