New deasrc

conjurer_librarian/conjurer_librarian.py

@@ -26,6 +26,7 @@ from queue import Queue
 import requests
 import scrape_bot
 import search_bot
+#import search_bot2 as search_bot
 from flask import Flask, jsonify, request
 from habanero import Crossref
 from waitress import serve
@@ -37,7 +38,10 @@ PORT_ADDRESS = 5001
 MAIN_BOT_ADDRESS = "http://192.168.1.191:5000"
 SEND_RESULTS = "/conjurer"
 BDSM_UUID_TEST = "96b7f85a-1142-4908-8986-62a2ea25a147"
-MAX_CR_RESULTS = 7000
+
+MAX_CR_RESULTS = 1000
+#TEST PURPOSES ONLY!
+#MAX_CR_RESULTS = 5
 
 ENCODING = "utf-8"
 
@@ -114,14 +118,15 @@ class Librarian(object):
         self.app.logger.info("STARTED SEARCH")
         
         if not deep_search:
-            cr_result = self.cr.works(query=query, limit=1000)
+            query_limit = MAX_CR_RESULTS if MAX_CR_RESULTS < 1000 else 1000
+            cr_result = self.cr.works(query=query, limit=query_limit)
             self.search_result_from_cr.update(cr_result)
             self.total = cr_result["message"]["total-results"]
             self.fetched += len(cr_result["message"]["items"])
             self.app.logger.info(self.total)
             self.app.logger.info(self.fetched)
             while self.total > self.fetched and self.limit > self.fetched:
-                tmp_result = self.cr.works(query=query, limit=1000, offset=self.fetched)
+                tmp_result = self.cr.works(query=query, limit=query_limit, offset=self.fetched)
                 cr_result["message"]["items"].extend(tmp_result["message"]["items"])
                 self.total = tmp_result["message"]["total-results"]
                 self.fetched = len(cr_result["message"]["items"])
@@ -130,7 +135,7 @@ class Librarian(object):
                 time.sleep(0.1)
 
         else:
-            cr_result = self.cr.works(query=query, cursor_max=10000, cursor='*', progress_bar = True)
+            cr_result = self.cr.works(query=query, cursor_max=15000, cursor='*', progress_bar = True)
             result = cr_result[0]
             for item in cr_result[1:]:
                 result["message"]["items"].extend(item["message"]["items"])

conjurer_librarian/scrape_bot.py

@@ -33,12 +33,14 @@ def load_ndb_to_q(logger):
             try:
                 ndb_database = json.load(ndb_file)
                 for _ in range (1,10):
+                    try:
                         key = next(iter(ndb_database))
-                    item = ndb_database.pop(key)
+                        _ = ndb_database.pop(key)
                         logger.info(key)
                         url = f"https://sci-hub.se/{key}"
-                    WORK_Q.put([item, url, False])
+                        WORK_Q.put([key, url, False])
-
+                    except StopIteration:
+                        break
                 ndb_file.truncate(0)
                 ndb_file.seek(0)
                 json.dump(ndb_database, ndb_file, indent=4)

conjurer_librarian/search_bot.py

@@ -21,7 +21,7 @@ Global Variables:
 # TODO: Wpiemdolić to wszystko w klasę z loggerem przysłanym z góry
 from queue import Empty, Queue
 from threading import Thread
-
+import time
 q = Queue()
 
 # DATA FOR TEST ONLY
@@ -49,9 +49,17 @@ def producer(out_q, control_q, filename, _logger):
         _logger: Logger object for logging.
     """
     with open(DATABASE_PATH + filename, "r+", encoding=ENCODING) as operated_file:
-        _logger.info(f"Worker {filename} ")
+        print(f"Worker {filename} ")
+        line_no = 0
         while True:
             line = operated_file.readline()
+            line_no += 1
+            print(f"\t \t \t \t \t \t W{filename}{line_no}\r", end="")
+
+            if not line:
+                print(f"EOF {filename}")
+                break
+
             if not line:
                 break
             out_q.put(line)
@@ -59,11 +67,12 @@ def producer(out_q, control_q, filename, _logger):
                 check = control_q.get(block=False)
             except Empty:
                 check = False
+
             if check is _sentinel:
-                _logger.info("TERM signal received")
+                print("TERM signal received")
                 control_q.put(check)
                 break
-        _logger.info(f"Worker finished: {filename}")
+        print(f"Worker finished: {filename}")
         out_q.put(_sentinel)
 
 
@@ -79,19 +88,25 @@ def consumer(in_q, control_q, doi, live_results, result_list, control_dict, no,
         live_results (list): List to store the search results.
         _logger: Logger object for logging.
     """
-    _logger.info("Consumer thread started:%s", no)
+    print(f"Consumer thread started: {no} no")
-    for item in doi:
+    empty_counter = 0
-        result_list.append({"DOI": item[0], "exists": False, "data": item[1]})
+    alive_no = 0
     while True:
         done_check = True
         try:
-            data = in_q.get(block=False)
+            data = in_q.get(block=True, timeout = 1)
             if data is _sentinel:
-                _logger.info("Worker finished")
                 control_dict["sentinels"] += 1
+                print(f"Workers finished: {control_dict['sentinels']} reported by consumer {no}")
+
             else:
+                empty_counter = 0
+                alive_no += 1
+                print(f"C{no}__{alive_no}\r", end="")
+
                 for item in result_list:
                     if item["DOI"] in data and not item["exists"]:
+                        print(f"HIT in {no} content {data[0]} line {data[1]} file {data[2]} {item["exists"]}")
                         _logger.info(data)
                         _logger.info("HIT")
                         item["exists"] = True
@@ -100,9 +115,18 @@ def consumer(in_q, control_q, doi, live_results, result_list, control_dict, no,
                 if done_check:
                     control_q.put(_sentinel)
         except Empty:
-            pass
+            empty_counter += 1
+            time.sleep(1)
+            print(f"Consumer {no} empty")
+            if empty_counter > 5:
+                print("Consumer %s empty lvl 2", no)
+                time.sleep(2)
+            elif empty_counter > 10:
+                print(f"Consumer thread finished {no}")
+                break
+
         if control_dict["sentinels"] >= MAXTHREADS:
-            _logger.info("All workers finished")
+            _logger.info(f"All workers finished {no}")
             break
 
 
@@ -121,6 +145,10 @@ def search_for_doi(doi, live_results, _logger):
     threads = []
     work_q = Queue(maxsize=WORK_Q_SIZE)
     control_q = Queue()
+
+    for item in doi:
+        result_list.append({"DOI": item[0], "exists": False, "data": item[1]})
+
     for i in range (0, (len(doi)//1000)+2):
         t_cons = Thread(
             target=consumer, args=(work_q, control_q, doi, live_results, result_list, control_dict, i, _logger)

conjurer_librarian/search_bot2.py

@@ -0,0 +1,206 @@
+"""
+This module contains functions for searching for DOI (Digital Object Identifier)
+in a list of live results.
+It includes a producer-consumer pattern implementation using threads and queues.
+
+Functions:
+- producer: Reads lines from a file and puts them into an output queue.
+- consumer: Consumes items from an input queue and checks if DOI exists in the live results list.
+- search_for_doi: Searches for DOI in live results using the producer-consumer pattern.
+
+Global Variables:
+- MAXTHREADS: Maximum number of worker threads.
+- DATABASE_PATH: Path to the database files.
+- ENCODING: Encoding of the database files.
+- CHUNK: File name pattern for the database files.
+- _sentinel: Sentinel object used to signal termination.
+- result_list: List to store the search results.
+- WORK_Q_SIZE: Maximum size of the work queue.
+"""
+
+# TODO: Wpiemdolić to wszystko w klasę z loggerem przysłanym z góry
+from multiprocessing import Manager, Process, Queue
+from queue import Empty, Full
+import time
+
+# DATA FOR TEST ONLY
+#MAXTHREADS = 6
+#DATABASE_PATH = r'C:\\Database\\chunks_1\\'
+
+# DEPLOYMENT DATA
+MAXTHREADS = 41
+DATABASE_PATH = r"C:\\Database\\chunks\\"
+
+ENCODING = "utf-8"
+CHUNK = "_chunk.txt"
+_sentinel = None
+WORK_Q_SIZE = 355000
+
+
+def producer(out_q, control_q, filename, _logger):
+    """
+    Produces items from the output queue and puts them into the control queue.
+
+    Args:
+        out_q (Queue): Output queue.
+        control_q (Queue): Control queue.
+        filename (str): Name of the file.
+        _logger: Logger object for logging.
+    """
+    with open(DATABASE_PATH + filename, "r+", encoding=ENCODING) as operated_file:
+        print(f"Worker {filename} ")
+        line_no = 0
+        while True:
+            line = operated_file.readline()
+            line_no += 1
+            print(f"\t \t \t W{filename}{line_no}\r", end="")
+
+            if not line:
+                print(f"EOF {filename}")
+                break
+            try:
+                out_q.put([line, line_no, filename], block = True, timeout = 60)
+            except Full:
+                print("queue fulll")
+            try:
+                check = control_q.get(block=False)
+            except Empty:
+                check = False
+            if check is None:
+                print(f"TERM signal received {filename}")
+                control_q.put(check)
+                control_q.close()
+                break
+        print(f"Worker finished: {filename}")
+        out_q.put(_sentinel)
+        out_q.close()
+
+
+
+# IMPORTANT!!! ONLY ONE CONSUMER THREAD AS WE ARE NOT PUTTING SENTINELS BACK
+def consumer(in_q, control_q, doi, live_results, result_list, control_dict, no, _logger):
+    """
+    Consumes items from an input queue and checks if DOI exists in the live results list.
+
+    Args:
+        in_q (Queue): Input queue.
+        control_q (Queue): Control queue.
+        doi (list): List of DOI to search for.
+        live_results (list): List to store the search results.
+        _logger: Logger object for logging.
+    """
+    print(f"Consumer thread started: {no} no")
+    empty_counter = 0
+    alive_no = 0
+    while True:
+        done_check = True
+        try:
+            data = in_q.get(block=True, timeout = 1)
+            empty_counter = 0
+            if data is None:
+                control_dict["sentinels"] += 1
+                print(f"Workers finished: {control_dict['sentinels']} reported by consumer {no}")
+            else:
+                empty_counter = 0
+                if alive_no > 9:
+                    alive_no = 0
+                alive_no += 1
+                print(f"C{no}{alive_no}\r", end="")
+                for item in result_list:
+                    if item["DOI"] in data[0] and not item["exists"]:
+                        print(f"HIT in {no} content {data[0]} line {data[1]} file {data[2]} {item["exists"]}")
+                        item["exists"] = True
+                        live_results.append(item)
+                    done_check = done_check and item["exists"]
+                if done_check:
+                    control_q.put(_sentinel)
+        except Empty:
+            empty_counter += 1
+            time.sleep(1)
+            print(f"Consumer {no} empty")
+            if empty_counter > 5:
+                print("Consumer %s empty lvl 2", no)
+                time.sleep(2)
+            elif empty_counter > 10:
+                print(f"Consumer thread finished {no}")
+                break
+        if control_dict["sentinels"] >= MAXTHREADS:
+            print(f"All workers finished killing {no}")
+            break
+    print("Consumer thread finished %s",no )
+    control_q.close()
+
+
+def search_for_doi(doi, live_results, _logger):
+    """
+    Search for DOI in live_results using _logger for logging.
+
+    Args:
+        doi (list): List of DOI to search for.
+        live_results (list): List to store the search results.
+        _logger: Logger object for logging.
+    """
+    with Manager() as manager:
+        control_dict = manager.dict()
+        control_dict["sentinels"] = 0
+        result_list = []
+        for item in doi:
+            result_list.append({"DOI": item[0], "exists": False, "data": item[1]})
+        result_list_proxy = manager.list(result_list)
+
+        threads = []
+        work_q = Queue(maxsize=WORK_Q_SIZE)
+        control_q = Queue()
+        for i in range(0, MAXTHREADS):
+            # TEST DATA
+            #filename = "test" + str(i) + CHUNK
+            # DEPLOYMENT DATA
+            filename = str(i) + CHUNK
+            print(f"Creating worker thread no: {i}")
+            threads.append(
+                Process(target=producer, args=(work_q, control_q, filename, _logger))
+            )
+        for i in range (0, (len(doi)//1000)+5):
+            t_cons = Process(
+                target=consumer, args=(work_q, control_q, doi, live_results, result_list_proxy, control_dict, i, _logger)
+            )
+            print("Consumer thread created")
+            threads.append(t_cons)
+
+        for worker in threads:
+            worker.start()
+        for worker in threads:
+            worker.join()
+        result_list = list(result_list_proxy)
+        for worker in threads:
+            worker.close()
+        return result_list
+
+
+if __name__ == "__main__":
+    import logging
+
+    logger = logging.getLogger()
+    logger.setLevel("DEBUG")
+    h1 = logging.StreamHandler()
+    logger.addHandler(h1)
+    print("TEST RUN")
+    live_result = []
+    print(
+        search_for_doi(
+            [
+                ("10.1002/9781118786352.wbieg0998.pub2", "DATA"),
+                ("10.1002/j.2050-0416.2002.tb00563.x", "DATA"),
+                ("10.1111/j.1365-2958.1994.tb00448.x", "DATA"),
+                ("10.2165/00128415-200309690-00017", "DATA"),
+                ("10.5772/48313", "DATA"),
+                ("10.15803/ijnc.7.2_419", "DATA"),
+                ("10.1051/0004-6361/201321596e", "DATA"),
+                ("10.2307/40835941", "DATA"),
+                ("NOT_ON_LIST", "DATA"),
+            ],
+            live_result,
+            logger,
+        )
+    )
+    print(live_result)