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The pod restarted spontaneously mid-search (no liveness probe is set, so it was the kernel OOM-killer against the 1Gi limit). Cause: search_bot built its work queue with maxsize 35_500_000. The producers stream the WHOLE DOI database (tens of millions of lines across chunks) into it while a few consumers drain, so the queue could buffer gigabytes of lines - blowing the 1Gi container and taking the whole in-flight search with it. Bound the queue (default 100k lines, env CONJURER_LIBRARIAN_WORKQ_SIZE), so producers backpressure to consumers and RAM stays in the low MB. Because a bounded queue means a producer can now block on a FULL queue, make the producer's put timeout-poll the TERM sentinel, so a full queue whose consumers have already finished (all DOIs found) can never deadlock it. New test pins that: tiny queue + target on line 1 + thousands of trailing decoys still terminates and finds the target. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
301 lines
12 KiB
Python
301 lines
12 KiB
Python
"""
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This module contains functions for searching for DOI (Digital Object Identifier)
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in a list of live results.
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It includes a producer-consumer pattern implementation using threads and queues.
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Functions:
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- producer: Reads lines from a file and puts them into an output queue.
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- consumer: Consumes items from an input queue and checks if DOI exists in the live results list.
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- search_for_doi: Searches for DOI in live results using the producer-consumer pattern.
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Global Variables:
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- MAXTHREADS: Maximum number of worker threads.
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- DATABASE_PATH: Path to the database files.
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- ENCODING: Encoding of the database files.
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- CHUNK: File name pattern for the database files.
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- _sentinel: Sentinel object used to signal termination.
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- result_list: List to store the search results.
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- WORK_Q_SIZE: Maximum size of the work queue.
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"""
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# TODO: Wpiemdolić to wszystko w klasę z loggerem przysłanym z góry
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import os
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import re
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from queue import Empty, Full, Queue
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from threading import Thread
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import time
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q = Queue()
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#TODO: Count number of lines in files and print to approximate on which part of the file search is
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# Deployment data is environment-overridable so the local DOI database can live
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# on a mounted volume (Docker/Linux) instead of the hardcoded Windows path.
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DATABASE_PATH = os.getenv("CONJURER_LIBRARIAN_DB_PATH", r"C:\\Database\\chunks\\")
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ENCODING = os.getenv("CONJURER_ENCODING", "utf-8")
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CHUNK = os.getenv("CONJURER_LIBRARIAN_CHUNK", "_chunk.txt")
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# DEPRECATED. The chunk files are now auto-discovered from DATABASE_PATH, so the
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# thread count and the termination threshold both derive from what is actually
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# on disk. This used to be BOTH "how many chunk files to read" AND "how many
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# sentinels to wait for", which had to match exactly: set too low it silently
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# skipped trailing chunks, set too high it referenced a nonexistent file whose
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# producer crashed, starving the sentinel count and hanging the search forever.
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# Kept only so old env files / references don't break; it no longer gates logic.
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MAXTHREADS = int(os.getenv("CONJURER_LIBRARIAN_MAXTHREADS", "0"))
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_sentinel = object()
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# BOUNDED work queue. The producers stream the WHOLE DOI database (potentially
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# tens of millions of lines across chunks) into this queue; the previous cap of
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# 35_500_000 items was effectively unbounded (~3.5 GB of buffered lines), which
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# OOM-killed the 1 GiB container mid-search. A small bound makes the producers
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# backpressure to the consumers, keeping RAM to a few MB. The producer put below
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# stays responsive to the TERM sentinel so a full queue can never deadlock it.
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WORK_Q_SIZE = int(os.getenv("CONJURER_LIBRARIAN_WORKQ_SIZE", "100000"))
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# Idle backstop: after this many consecutive empty seconds a consumer assumes
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# the producers are done (or dead) and exits, so the search can never hang even
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# if a sentinel were somehow lost. The primary, correct termination is still the
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# sentinel count reaching the number of producers actually started.
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EMPTY_LIMIT = 30
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# Chunk files are named "<n>_chunk.txt" (suffix from CHUNK).
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_CHUNK_RE = re.compile(r"^(\d+)" + re.escape(CHUNK) + r"$")
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def discover_chunk_files(_logger):
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"""Return the ``<n>_chunk.txt`` files present in DATABASE_PATH, numeric order.
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Reading what exists (rather than files 0..MAXTHREADS-1) removes both historic
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failure modes at once: no trailing chunk is ever silently skipped, and no
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producer is ever pointed at a missing file, so it cannot crash before
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emitting its sentinel and deadlock the consumers.
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"""
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try:
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names = os.listdir(DATABASE_PATH)
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except OSError as exc:
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_logger.error("Cannot list DOI database dir %s: %s", DATABASE_PATH, exc)
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return []
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indexed = []
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for name in names:
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match = _CHUNK_RE.match(name)
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if match:
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indexed.append((int(match.group(1)), name))
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indexed.sort()
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ordered = [name for _, name in indexed]
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_logger.info("Discovered %d chunk files in %s", len(ordered), DATABASE_PATH)
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return ordered
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def producer(out_q, control_q, filename, _logger):
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"""
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Produces items from the output queue and puts them into the control queue.
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Args:
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out_q (Queue): Output queue.
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control_q (Queue): Control queue.
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filename (str): Name of the file.
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_logger: Logger object for logging.
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"""
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try:
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# errors="replace" so a stray non-UTF-8 byte in a chunk (they happen in
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# scraped DOI dumps) becomes U+FFFD instead of raising UnicodeDecodeError
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# mid-file. Without it the readline() below would blow up, killing the
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# producer partway and leaving every DOI after the bad byte unsearched.
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# DOIs are ASCII, so a replaced byte can only affect junk, never a match.
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with open(DATABASE_PATH + filename, "r", encoding=ENCODING, errors="replace") as operated_file:
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print(f"Worker {filename} ")
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line_no = 0
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while True:
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line = operated_file.readline()
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line_no += 1
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print(f"\t \t \t \t \t \t W{filename}{line_no}\r", end="")
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if not line:
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print(f"EOF {filename}")
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break
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# Backpressure-safe put onto the BOUNDED queue: wait for room,
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# but keep polling the TERM sentinel so a full queue whose
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# consumers have already finished can never deadlock us here.
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stopped = False
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while True:
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try:
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out_q.put(line, timeout=1)
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break
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except Full:
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try:
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if control_q.get(block=False) is _sentinel:
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control_q.put(_sentinel)
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stopped = True
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break
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except Empty:
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pass
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if stopped:
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print("TERM signal received (queue full)")
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break
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try:
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check = control_q.get(block=False)
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except Empty:
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check = False
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if check is _sentinel:
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print("TERM signal received")
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control_q.put(check)
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break
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print(f"Worker finished: {filename}")
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except Exception as exc: # pylint: disable=broad-except
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# No per-file error (missing/unreadable chunk, a decode edge case that
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# slips past errors="replace", anything unforeseen) may take the whole
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# search down or crash the thread with a traceback. Log it and move on;
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# the sentinel below still fires (finally), so the consumers' count stays
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# correct and nothing deadlocks or silently loses a producer.
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_logger.warning("Chunk %s failed, skipping rest of it: %s", filename, exc)
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print(f"Worker {filename} failed: {exc}")
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finally:
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# ALWAYS emit exactly one sentinel per producer, on every exit path (EOF,
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# early TERM, or crash). This is what lets the consumers count producers
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# deterministically instead of hanging on a lost sentinel.
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out_q.put(_sentinel)
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# IMPORTANT!!! ONLY ONE CONSUMER THREAD AS WE ARE NOT PUTTING SENTINELS BACK
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def consumer(in_q, control_q, doi, live_results, result_list, control_dict, expected_sentinels, no, _logger):
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"""
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Consumes items from an input queue and checks if DOI exists in the live results list.
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Args:
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in_q (Queue): Input queue.
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control_q (Queue): Control queue.
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doi (list): List of DOI to search for.
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live_results (list): List to store the search results.
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_logger: Logger object for logging.
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"""
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print(f"Consumer thread started: {no} no")
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empty_counter = 0
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alive_no = 0
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# DOI -> result item, so a line is matched with one O(1) dict lookup instead
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# of scanning every queried DOI. Items are shared with result_list, so
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# setting exists here is seen by everyone.
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doi_index = {item["DOI"]: item for item in result_list}
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while True:
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try:
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data = in_q.get(block=True, timeout = 1)
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if data is _sentinel:
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control_dict["sentinels"] += 1
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print(f"Workers finished: {control_dict['sentinels']} reported by consumer {no}")
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else:
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empty_counter = 0
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alive_no += 1
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print(f"C{no}__{alive_no}\r", end="")
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# Each DB line is a DOI (optionally followed by metadata). Match
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# the WHOLE first token exactly - the old `item["DOI"] in data`
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# was a substring test, so a DOI that is a prefix of a longer one
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# (10.1/1 vs 10.1/12) produced a false 'exists' hit.
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parts = data.split()
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line_doi = parts[0] if parts else ""
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item = doi_index.get(line_doi)
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if item is not None and not item["exists"]:
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print(f"HIT in {no}: {line_doi}")
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_logger.info("HIT %s", line_doi)
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item["exists"] = True
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live_results.append(item)
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# All found? Signal producers to stop early (rare -> cheap).
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if all(it["exists"] for it in result_list):
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control_q.put(_sentinel)
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except Empty:
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empty_counter += 1
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time.sleep(1)
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print(f"Consumer {no} empty")
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# Order matters: the >EMPTY_LIMIT break must be checked BEFORE the
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# lesser threshold, otherwise (as in the original) the first branch
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# always wins and the break is dead code, leaving the sentinel count
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# as the only exit - which is exactly what used to hang the search.
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if empty_counter > EMPTY_LIMIT:
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print(f"Consumer thread finished {no} (idle backstop)")
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break
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if empty_counter > 5:
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print(f"Consumer {no} empty lvl 2")
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time.sleep(2)
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if control_dict["sentinels"] >= expected_sentinels:
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_logger.info(f"All workers finished {no}")
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break
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def search_for_doi(doi, live_results, _logger):
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"""
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Search for DOI in live_results using _logger for logging.
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Args:
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doi (list): List of DOI to search for.
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live_results (list): List to store the search results.
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_logger: Logger object for logging.
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"""
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control_dict = {"sentinels":0}
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result_list = []
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threads = []
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work_q = Queue(maxsize=WORK_Q_SIZE)
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control_q = Queue()
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for item in doi:
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result_list.append({"DOI": item[0], "exists": False, "data": item[1]})
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# One producer per chunk file that actually exists; the sentinel threshold is
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# that same count, so the two can never drift apart the way MAXTHREADS did.
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chunk_files = discover_chunk_files(_logger)
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expected = len(chunk_files)
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if expected == 0:
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_logger.error(
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"No '<n>%s' chunk files in %s - DOI search cannot run", CHUNK, DATABASE_PATH
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)
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return result_list
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for i in range (0, (len(doi)//1000)+2):
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t_cons = Thread(
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target=consumer,
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args=(work_q, control_q, doi, live_results, result_list, control_dict, expected, i, _logger),
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)
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_logger.info("Consumer thread created")
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threads.append(t_cons)
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for filename in chunk_files:
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_logger.info("Creating worker thread for %s", filename)
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threads.append(
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Thread(target=producer, args=(work_q, control_q, filename, _logger))
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)
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for worker in threads:
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worker.start()
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for worker in threads:
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worker.join()
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return result_list
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if __name__ == "__main__":
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import logging
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logger = logging.getLogger()
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logger.setLevel("DEBUG")
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h1 = logging.StreamHandler()
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logger.addHandler(h1)
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logger.info("TEST RUN")
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live_result = []
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logger.info(
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search_for_doi(
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[
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("10.1002/9781118786352.wbieg0998.pub2", "DATA"),
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("10.1002/j.2050-0416.2002.tb00563.x", "DATA"),
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("10.1111/j.1365-2958.1994.tb00448.x", "DATA"),
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("10.2165/00128415-200309690-00017", "DATA"),
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("10.5772/48313", "DATA"),
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("10.15803/ijnc.7.2_419", "DATA"),
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("10.1051/0004-6361/201321596e", "DATA"),
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("10.2307/40835941", "DATA"),
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],
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live_result,
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logger,
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)
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)
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logger.info(live_result)
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