Add the pdfCoverageEvaluator software.
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Copyright 2024 OpenAIRE AMKE
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@ -0,0 +1,26 @@
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# PDF-coverage-evaluator
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This python-3 script checks each PID from a given collection, against the pdf-aggregation-service-DB,
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in order to find whether that PID exists in the aggregator's DB and has full-text coverage.
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<br>
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In detail, it does the following:
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- extracts the pids from a json-file (DOIs and PMIDs)
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- if a "previous-results" file is provided, extracts the pid from there as well and reduced the original input to the pids which have not been processed before.
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- splits them in batches and for each batch it submits each pid-evaluation-job to a "ThreadPoolExecutor", which uses 12 threads.
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- for each one of the PID-pairs, makes a query with Impala, to quickly acquire the following: "dedupid", "id", "pid", "pid_type", "fulltext_url", "location"
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- saves the results in a json-file, including the pid for which it made the check (for example in case a record has both "doi" and "pmid" and a fulltext was detected for the "doi" (at least), then the output-record has the "doi" as its PID)
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## Install & Run:
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```python3 --version; sudo apt install -y python3 python3-pip; sudo pip3 install --upgrade pip; cd pdfCoverageEvaluator; sudo pip3 install -r requirements.txt; python3 pdfCoverageEvaluator.py ${input_file_path} ${max_num_to_process} ${previous_results_file_path}```
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### Install & run, using the provided scripts
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1) **transferToRemoteMachineAndExecute.sh**: this script transfers the project to the defined location on a remote machine, replaces the project-files there and executes the software it inside a screen,
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in order to not lose the execution in case the session is closed before the software finishes.
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2) **transferToRemoteMachine.sh**: this script just transfers the project to the defined location on a remote machine and replaces the project-files there.
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### Checking the logs
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The log file is located inside the project's directory and has this name: "pdfCoverageEvaluator.log"
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import sys
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import threading
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from impala.dbapi import connect
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import numpy as np
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from time import perf_counter
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from concurrent.futures import ThreadPoolExecutor
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import json
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import logging
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from _datetime import datetime
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# Configure logging.
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targets = logging.StreamHandler(sys.stdout), logging.FileHandler('pdfCoverageEvaluator.log')
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logging_level = logging.INFO
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logging.basicConfig(format='%(asctime)s %(threadName)s %(levelname)s %(filename)s:%(funcName)s(@%(lineno)d) %(message)s', datefmt='%Y-%m-%d %H:%M:%S %Z', level=logging_level,
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handlers=targets)
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logger = logging.getLogger()
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input_file_path = "pids_to_check.json" # Default value. The user has to provide the path nevertheless (in the cmd-args).
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max_num_records_to_process = -1 # The default is to process all records.
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previous_results_file = None # This is rarely used.
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impala_host = "impala-gw.openaire.eu"
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db = "pdfaggregation_i"
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cur_time = datetime.now().strftime('%Y-%m-%d__%H-%M-%S')
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results_json_file_path = "results__" + cur_time + ".json"
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number_of_threads = 12 # The target machine is a 2-core, 4-threads CPU. This script runs faster with 12 threads in parallel, in that machine.
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# I tested 100 pids with 8, 10, 12, 16, and 20 threads. The number "12" was the best.
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def getCursorForImpala():
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global impala_host
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conn = connect(host=impala_host, port=21050)
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return conn.cursor()
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def testImpalaConnection():
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global db
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logging.info("Going to test the connections with Impala..")
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cursor = getCursorForImpala()
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result_data = {}
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try:
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cursor.execute(
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'select * from ' + db + '.publication_pids limit 1') # Test the "publication" table instead of the "payload" view, in order to avoid catching the tables of that view in a "merging-state".
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result_row = cursor.fetchone()
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logging.info("result_row: " + str(result_row))
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if result_row:
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logging.info("The testing of the connection with Impala succeeded! Test results from \"publication_pids\" table:")
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for i, col in enumerate(cursor.description):
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logging.info(str(col[0]) + " = '" + str(result_row[i]) + "'")
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result_data[col[0]] = str(result_row[i])
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logging.info("result_data: " + str(result_data))
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return True
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else:
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logging.error("No data was retrieved during testing!")
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return False
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except Exception as e:
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logging.error(e)
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return False
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def load_json_records(json_file_path, max_num_records_to_process):
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json_records = []
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try:
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with open(json_file_path) as json_file:
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for counter, line in enumerate(json_file):
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line = line.strip()
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if len(line) > 0 and (max_num_records_to_process == -1 or counter < max_num_records_to_process): # "counter" starts from 0
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json_records.append(json.loads(line))
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except Exception as e:
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logging.error("Problem when opening file: " + json_file_path, e)
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return None
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return json_records
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def extract_PIDs(json_records):
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# Get only the pids, in a dictionary, having both the doi and the pmid (if available)
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pids = []
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for record in json_records:
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pids_or_record = {}
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try:
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doi = record["doi"]
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if doi:
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pids_or_record['doi'] = doi
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except KeyError:
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pass
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try:
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pmid = record["pmid"]
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if pmid:
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pids_or_record['pmid'] = pmid
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except KeyError:
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pass
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if pids_or_record: # If not empty.
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pids.append(pids_or_record)
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return pids
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def extract_PIDs_from_previous_results(json_records):
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pids = set()
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for record in json_records:
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try:
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pid = record["pid"]
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if pid:
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pids.add(pid)
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except KeyError:
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pass
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return pids
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def reduce_to_unprocessed_records(json_records_to_be_processed, pids_of_previous_records):
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unprocessed_records = []
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for record in json_records_to_be_processed:
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doi = None
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try:
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doi = record["doi"]
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except KeyError:
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pass
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|
|
||||||
|
pmid = None
|
||||||
|
try:
|
||||||
|
pmid = record["pmid"]
|
||||||
|
except KeyError:
|
||||||
|
pass
|
||||||
|
|
||||||
|
# Skip if no pid exists
|
||||||
|
if (doi is None or not doi) and (pmid is None or not pmid):
|
||||||
|
continue
|
||||||
|
|
||||||
|
# Skip if pid has given a result before.
|
||||||
|
if (doi is not None and doi and doi in pids_of_previous_records) or (pmid is not None and pmid and pmid in pids_of_previous_records):
|
||||||
|
continue
|
||||||
|
|
||||||
|
unprocessed_record = {}
|
||||||
|
if doi is not None and doi:
|
||||||
|
unprocessed_record['doi'] = doi
|
||||||
|
if pmid is not None and pmid:
|
||||||
|
unprocessed_record['pmid'] = pmid
|
||||||
|
|
||||||
|
if unprocessed_record:
|
||||||
|
unprocessed_records.append(unprocessed_record)
|
||||||
|
|
||||||
|
return unprocessed_records
|
||||||
|
|
||||||
|
|
||||||
|
def get_empty_result(doi, pmid):
|
||||||
|
result_data = {'dedupid': 'None', 'id': 'None'}
|
||||||
|
if doi is not None:
|
||||||
|
result_data['pid'] = doi
|
||||||
|
result_data['pid_type'] = 'doi'
|
||||||
|
else:
|
||||||
|
result_data['pid'] = pmid
|
||||||
|
result_data['pid_type'] = 'pmid'
|
||||||
|
result_data['fulltext_url'] = 'None'
|
||||||
|
result_data['location'] = 'None'
|
||||||
|
return result_data
|
||||||
|
|
||||||
|
|
||||||
|
def get_query_to_check_coverage_for_record(doi, pmid):
|
||||||
|
# Check that we have at least one file-location associated with one of the pids of this record.
|
||||||
|
|
||||||
|
predicate = '0' # Control value to match nothing.
|
||||||
|
if doi is not None:
|
||||||
|
predicate = "ppid.pid = '" + doi + "'"
|
||||||
|
if pmid is not None:
|
||||||
|
predicate += " or ppid.pid = '" + pmid + "'"
|
||||||
|
elif pmid is not None:
|
||||||
|
predicate = "ppid.pid = '" + pmid + "'"
|
||||||
|
# Else no pid is available. This is already caught by the caller method.
|
||||||
|
|
||||||
|
return "select pu.dedupid, pu.id, ppid.pid, ppid.type as pid_type, p.actual_url as fulltext_url, p.`location` from " + db + ".publication_pids ppid\n" + \
|
||||||
|
" join " + db + ".publication pu on pu.id = ppid.id\n" + \
|
||||||
|
" left outer join " + db + ".payload p on p.id = ppid.id\n" + \
|
||||||
|
"where " + predicate + \
|
||||||
|
"\norder by coalesce(fulltext_url, 'z')" + \
|
||||||
|
"\nlimit 1;" # Order alphabetically, ascending. This is important, so that the pdf-results are preferred over the non-pdf-results.
|
||||||
|
# We use "left outer join" for "payload", in order to retrieve results also for non-pdf-covered PIDs.
|
||||||
|
|
||||||
|
|
||||||
|
thread_local_var = threading.local()
|
||||||
|
|
||||||
|
num_of_pids_covered = 0 # integer variable shared between threads
|
||||||
|
lock = threading.Lock() # lock object, used to safely increment the above variable
|
||||||
|
|
||||||
|
|
||||||
|
def get_coverage_for_record(pids_of_record, retry_count):
|
||||||
|
global num_of_pids_covered
|
||||||
|
|
||||||
|
if retry_count > 10:
|
||||||
|
logging.warning("Could not find the requested payload-type table in an non-merging state, after " + (retry_count - 1) + " retries!")
|
||||||
|
return None
|
||||||
|
|
||||||
|
if not hasattr(thread_local_var, 'cursor'): # If this is the first time this thread accesses its "thread-local" variable, introduce and assign the cersor attribute."
|
||||||
|
thread_local_var.__setattr__('cursor', getCursorForImpala())
|
||||||
|
|
||||||
|
doi = None
|
||||||
|
try:
|
||||||
|
doi = pids_of_record['doi']
|
||||||
|
except KeyError:
|
||||||
|
pass # The "doi" does not exist. Let's hope the "pmid" exists.
|
||||||
|
|
||||||
|
pmid = None
|
||||||
|
try:
|
||||||
|
pmid = pids_of_record['pmid']
|
||||||
|
except KeyError:
|
||||||
|
pass # The "pmid" does not exist (it's common).
|
||||||
|
|
||||||
|
if (doi is None or not doi) and (pmid is None or not pmid):
|
||||||
|
logging.warning("Current record has no pid: " + str(pids_of_record))
|
||||||
|
return None
|
||||||
|
|
||||||
|
result_data = {}
|
||||||
|
try:
|
||||||
|
thread_local_var.cursor.execute(get_query_to_check_coverage_for_record(doi, pmid))
|
||||||
|
result_row = thread_local_var.cursor.fetchone()
|
||||||
|
if result_row:
|
||||||
|
if logger.isEnabledFor(logging.DEBUG):
|
||||||
|
logging.debug("result_row: " + str(result_row)) # DEBUG!
|
||||||
|
for i, col in enumerate(thread_local_var.cursor.description):
|
||||||
|
if logger.isEnabledFor(logging.DEBUG):
|
||||||
|
logging.debug(str(col[0]) + " = '" + str(result_row[i]) + "'") # DEBUG!
|
||||||
|
result_data[str(col[0])] = str(result_row[i])
|
||||||
|
|
||||||
|
if result_data['location'] != 'None':
|
||||||
|
logging.info("PDF-coverage for record with pid: \"" + result_data['pid'] + "\" of type \"" + result_data['pid_type'] + "\" and location: \"" + result_data[
|
||||||
|
'location'] + "\".")
|
||||||
|
with lock:
|
||||||
|
num_of_pids_covered += 1
|
||||||
|
else:
|
||||||
|
logging.info("No coverage! Record with doi: \"" + str(doi) + "\" and pmid: \"" + str(pmid) + "\"")
|
||||||
|
|
||||||
|
if logger.isEnabledFor(logging.DEBUG):
|
||||||
|
logging.debug("result_data: " + str(result_data)) # DEBUG!
|
||||||
|
|
||||||
|
return result_data
|
||||||
|
else:
|
||||||
|
logging.warning("Not in DB! Record with doi: \"" + str(doi) + "\" and pmid: \"" + str(pmid) + "\"")
|
||||||
|
return get_empty_result(doi, pmid)
|
||||||
|
except Exception as e:
|
||||||
|
ex_msg = str(e)
|
||||||
|
if "Could not resolve table reference" in ex_msg or "Could not open HDFS file" in ex_msg:
|
||||||
|
if logger.isEnabledFor(logging.DEBUG):
|
||||||
|
logging.debug("One of the tables is in a merging-state!") # DEBUG!
|
||||||
|
return get_coverage_for_record(pids_of_record, (++retry_count))
|
||||||
|
else:
|
||||||
|
logging.error("Error when querying for 'doi': '" + str(doi) + "' and 'pmid': '" + str(pmid) + "'\n", type(e).__name__, e)
|
||||||
|
return get_empty_result(doi, pmid)
|
||||||
|
|
||||||
|
|
||||||
|
pids_per_batch = 1_000
|
||||||
|
|
||||||
|
|
||||||
|
def check_pids_against_pdf_aggregation_db_and_write_results(pids_of_records):
|
||||||
|
global num_of_pids_covered
|
||||||
|
|
||||||
|
num_of_batches = int(len(pids_of_records) / pids_per_batch)
|
||||||
|
if num_of_batches == 0:
|
||||||
|
num_of_batches = 1
|
||||||
|
|
||||||
|
num_of_batches_str = str(num_of_batches)
|
||||||
|
|
||||||
|
# Split the pids into multiple batches (sub-lists) of < pids_per_batch > elements each,
|
||||||
|
chunked_arrays = np.array_split(np.array(pids_of_records), num_of_batches)
|
||||||
|
pids_of_records_sublists = [list(array) for array in chunked_arrays]
|
||||||
|
|
||||||
|
start = perf_counter()
|
||||||
|
|
||||||
|
num_of_all_records = len(pids_of_records)
|
||||||
|
|
||||||
|
logging.info(
|
||||||
|
"Submitting the " + str(num_of_all_records) + " tasks to the 'ThreadPoolExecutor', in " + num_of_batches_str + " batches of " + str(len(pids_of_records_sublists[0]))
|
||||||
|
+ " elements each.")
|
||||||
|
|
||||||
|
with ThreadPoolExecutor(max_workers=number_of_threads) as executor:
|
||||||
|
|
||||||
|
for batch_counter, pids_of_records_batch in enumerate(pids_of_records_sublists):
|
||||||
|
result_futures = []
|
||||||
|
for count, pids_of_record in enumerate(pids_of_records_batch):
|
||||||
|
if pids_of_record:
|
||||||
|
result_futures.append(executor.submit(get_coverage_for_record, pids_of_record, 0))
|
||||||
|
|
||||||
|
batch_counter_str = str(batch_counter)
|
||||||
|
logging.info("Finished submitting the tasks for batch_" + batch_counter_str + " (out of " + num_of_batches_str + "), will wait for them to finish executing..")
|
||||||
|
# After all tasks for this batch have been submitted. Iterate through the futures and wait for all of them to finish and use their results.
|
||||||
|
results_data = []
|
||||||
|
for count, result_future in enumerate(result_futures):
|
||||||
|
try:
|
||||||
|
result_data = result_future.result()
|
||||||
|
if result_data is not None:
|
||||||
|
results_data.append(result_data)
|
||||||
|
|
||||||
|
except Exception as e:
|
||||||
|
logging.error("Error when checking a future's result for batch_" + batch_counter_str, e)
|
||||||
|
|
||||||
|
if len(results_data) > 0:
|
||||||
|
logging.info("Writing " + str(len(results_data)) + " results (from batch_" + batch_counter_str + ") to the output file..")
|
||||||
|
try:
|
||||||
|
with open(results_json_file_path, "a") as outfile:
|
||||||
|
for result in results_data:
|
||||||
|
outfile.write(json.dumps(result) + "\n")
|
||||||
|
except Exception as e:
|
||||||
|
logging.critical("Error when writing to output-file: " + results_json_file_path, e)
|
||||||
|
# It's very serious to lose results, but it may be a temporal error, appearing in the middle of the execution. So, we should not stop the whole execution.
|
||||||
|
else:
|
||||||
|
logging.info("Batch_" + batch_counter_str + " gave no results.")
|
||||||
|
|
||||||
|
finish = perf_counter()
|
||||||
|
|
||||||
|
elapsed_time = finish - start
|
||||||
|
if elapsed_time >= 3600:
|
||||||
|
elapsed_time = elapsed_time / 3600
|
||||||
|
time_message = "Finished in " + str(round(elapsed_time, 2)) + " hours. "
|
||||||
|
elif elapsed_time >= 60:
|
||||||
|
elapsed_time = elapsed_time / 60
|
||||||
|
time_message = "Finished in " + str(round(elapsed_time, 2)) + " minutes. "
|
||||||
|
else:
|
||||||
|
time_message = "Finished in " + str(round(elapsed_time, 2)) + " seconds. "
|
||||||
|
|
||||||
|
logging.info(time_message + str(num_of_pids_covered) + " out of " + str(num_of_all_records) + " pids had coverage.")
|
||||||
|
|
||||||
|
|
||||||
|
def print_records(json_records):
|
||||||
|
records_to_print = ''
|
||||||
|
for record in json_records:
|
||||||
|
records_to_print += str(record) + "\n"
|
||||||
|
logging.info(records_to_print)
|
||||||
|
|
||||||
|
|
||||||
|
if __name__ == '__main__':
|
||||||
|
args = sys.argv
|
||||||
|
num_args = len(args)
|
||||||
|
if num_args < 2 or num_args > 4: # (the 1st arg is the script's name)
|
||||||
|
logging.critical("Wrong number of argument given (" + str(
|
||||||
|
num_args - 1) + ")! Should give between 1 and 3 arguments, in that order: <input_file> , <max_num_records_to_process> , <previous_results_file_path>")
|
||||||
|
sys.exit(1)
|
||||||
|
elif num_args == 2:
|
||||||
|
input_file_path = args[1]
|
||||||
|
max_num_records_to_process = -1
|
||||||
|
elif num_args == 3:
|
||||||
|
input_file_path = args[1]
|
||||||
|
max_num_records_to_process = int(args[2])
|
||||||
|
if max_num_records_to_process == 0:
|
||||||
|
max_num_records_to_process = -1
|
||||||
|
elif num_args == 4:
|
||||||
|
input_file_path = args[1]
|
||||||
|
max_num_records_to_process = int(args[2])
|
||||||
|
if max_num_records_to_process == 0:
|
||||||
|
max_num_records_to_process = -1
|
||||||
|
previous_results_file = args[3]
|
||||||
|
|
||||||
|
if not testImpalaConnection():
|
||||||
|
logging.info("Exiting!")
|
||||||
|
exit(2)
|
||||||
|
|
||||||
|
if max_num_records_to_process == -1:
|
||||||
|
logging.info("Going to process all available pid-records..")
|
||||||
|
else:
|
||||||
|
logging.info("Going to process at most " + str(max_num_records_to_process) + " pid-records..")
|
||||||
|
|
||||||
|
json_records_to_be_processed = load_json_records(input_file_path, max_num_records_to_process)
|
||||||
|
logging.info("Loaded " + str(len(json_records_to_be_processed)) + " json-records from input_file: " + input_file_path)
|
||||||
|
|
||||||
|
if not json_records_to_be_processed:
|
||||||
|
logging.critical("No json-records were found in the input! Exiting...")
|
||||||
|
exit(3)
|
||||||
|
|
||||||
|
# print_records(json_records_to_be_processed)
|
||||||
|
|
||||||
|
pids_of_records = extract_PIDs(json_records_to_be_processed)
|
||||||
|
num_pid_records_str = str(len(pids_of_records))
|
||||||
|
logging.info("Extracted " + num_pid_records_str + " pid-records from input_file: " + input_file_path)
|
||||||
|
|
||||||
|
if not pids_of_records:
|
||||||
|
logging.critical("No pids were extracted from the input json-records! Exiting...")
|
||||||
|
exit(4)
|
||||||
|
|
||||||
|
json_records_previously_processed = None
|
||||||
|
if previous_results_file is not None:
|
||||||
|
logging.info("Going to check the input-records if they were previously processed..")
|
||||||
|
|
||||||
|
json_records_previously_processed = load_json_records(previous_results_file, -1)
|
||||||
|
logging.info("Loaded " + str(len(json_records_previously_processed)) + " json-records from input_file: " + previous_results_file)
|
||||||
|
|
||||||
|
if json_records_previously_processed:
|
||||||
|
pids_of_previous_records = extract_PIDs_from_previous_results(json_records_previously_processed)
|
||||||
|
logging.info("Extracted " + str(len(pids_of_previous_records)) + " pid-records from previous_results_input_file: " + previous_results_file)
|
||||||
|
|
||||||
|
if pids_of_previous_records:
|
||||||
|
unprocessed_records = reduce_to_unprocessed_records(json_records_to_be_processed, pids_of_previous_records)
|
||||||
|
logging.info("Reduced the " + num_pid_records_str + " pid-records to " + str(len(unprocessed_records)) + " after checking if they have been processed before.")
|
||||||
|
pids_of_records = unprocessed_records
|
||||||
|
else:
|
||||||
|
logging.error("No pids were extracted from the previous-results-input! Continue by checking all selected pids from input..")
|
||||||
|
else:
|
||||||
|
logging.warning("No json-records were found in the previous-results-input! Continue by checking all selected pids from input..")
|
||||||
|
|
||||||
|
# if logger.isEnabledFor(logging.DEBUG):
|
||||||
|
# logging.info(pids_of_records)
|
||||||
|
|
||||||
|
check_pids_against_pdf_aggregation_db_and_write_results(pids_of_records)
|
||||||
|
|
||||||
|
exit(0)
|
||||||
|
|
@ -0,0 +1,2 @@
|
||||||
|
impyla~=0.19.0
|
||||||
|
numpy~=1.19.5
|
||||||
|
|
@ -0,0 +1,11 @@
|
||||||
|
# We can only connect to Impala from authorized IPs, so we have to transfer this python-project-directory to such a machine.
|
||||||
|
|
||||||
|
remote_user_with_ip='<USER>@<IP>' # Fill this information as needed.
|
||||||
|
|
||||||
|
echo -e "Removing remote directory.."
|
||||||
|
ssh -t ${remote_user_with_ip} "rm -rf pdfCoverageEvaluator"
|
||||||
|
|
||||||
|
cd ../
|
||||||
|
scp -r -C pdfCoverageEvaluator ${remote_user_with_ip}:.
|
||||||
|
|
||||||
|
ssh -t ${remote_user_with_ip} "python3 --version; sudo apt install -y python3-pip; sudo pip3 install -r ./pdfCoverageEvaluator/requirements.txt"
|
||||||
|
|
@ -0,0 +1,18 @@
|
||||||
|
# We can only connect to Impala from authorized IPs, so we have to transfer this python-project-directory to such a machine.
|
||||||
|
|
||||||
|
remote_user_with_ip='<USER>@<IP>' # Fill this information as needed.
|
||||||
|
|
||||||
|
echo -e "Removing remote directory.."
|
||||||
|
ssh -t ${remote_user_with_ip} "rm -rf pdfCoverageEvaluator"
|
||||||
|
|
||||||
|
cd ../
|
||||||
|
scp -r -C pdfCoverageEvaluator ${remote_user_with_ip}:.
|
||||||
|
|
||||||
|
input_file_path='pids_to_check.json'
|
||||||
|
max_num_to_process=-1 # -1 == All records
|
||||||
|
#previous_results_file_path='previous_results.json' # Uncomment this, if you want to exclude the pids from the input which have already been processed and gave a result in a previous run.
|
||||||
|
|
||||||
|
ssh -t ${remote_user_with_ip} "python3 --version; sudo apt install -y python3 python3-pip; sudo pip3 install --upgrade pip; cd pdfCoverageEvaluator; sudo pip3 install -r requirements.txt; (screen -d -m python3 pdfCoverageEvaluator.py ${input_file_path} ${max_num_to_process} ${previous_results_file_path} && screen -r); tail -n 100 pdfCoverageEvaluator.log"
|
||||||
|
|
||||||
|
# In case the program fails and the screen terminates without logs, use the following command to debug (without the screen):
|
||||||
|
#ssh -t ${remote_user_with_ip} "python3 --version; sudo apt install -y python3 python3-pip; sudo pip3 install --upgrade pip; cd pdfCoverageEvaluator; sudo pip3 install -r requirements.txt; python3 pdfCoverageEvaluator.py ${input_file_path} ${max_num_to_process}" # ${previous_results_file_path}"
|
||||||
Loading…
Reference in New Issue