path: root/please

#!/usr/bin/env python3
"""
Helper script for running Sandcrawler (journal pipeline) tasks in production.

This is basically a Makefile. If you edit this file, be sure to only use
python3 standard library modules, so there are no dependencies.
"""

import sys
import argparse
import subprocess
from datetime import datetime

HDFS_DIR = "hdfs:///user/bnewbold/sandcrawler"
HBASE_HOST = "wbgrp-svc263.us.archive.org"
ZOOKEEPER_HOSTS = "mtrcs-zk1.us.archive.org:2181"
GROBID_URI = "http://wbgrp-svc096.us.archive.org:8070"

def rebuild_python():
    print("Rebuilding python venv...")
    cmd = """cd python;
        export PIPENV_VENV_IN_PROJECT=1;
        pipenv install --deploy
        tar -czf venv-current.tar.gz -C .venv ."""
    subprocess.call(cmd, shell=True)

def rebuild_scalding():
    print("Rebuilding scalding jar...")
    cmd = """cd scalding; sbt assembly"""
    subprocess.call(cmd, shell=True)

def run_backfill(args):
    if args.rebuild:
        rebuild_python()
    print("Starting backfill job...")
    output = "{}/output-{}/{}-backfill".format(
        HDFS_DIR,
        args.env,
        datetime.strftime(datetime.now(), "%Y-%m-%d-%H%M.%S"))
    cmd = """cd python;
        pipenv run ./backfill_hbase_from_cdx.py \
            --hbase-host {hbase_host} \
            --hbase-table wbgrp-journal-extract-0-{env} \
            -r hadoop \
            -c mrjob.conf \
            --archive venv-current.tar.gz#venv \
            {input_cdx}
            """.format(hbase_host=HBASE_HOST, env=args.env,
                input_cdx=args.input_cdx)
    subprocess.call(cmd, shell=True)

def run_extract(args):
    if args.rebuild:
        rebuild_python()
    print("Starting extract job...")
    output = "{}/output-{}/{}-extract".format(
        HDFS_DIR,
        args.env,
        datetime.strftime(datetime.now(), "%Y-%m-%d-%H%M.%S"))
    cmd = """cd python;
        pipenv run ./extraction_cdx_grobid.py \
            --hbase-host {hbase_host} \
            --hbase-table wbgrp-journal-extract-0-{env} \
            --grobid-uri {grobid_uri} \
            -r hadoop \
            -c mrjob.conf \
            --output-dir {output} \
            --no-output \
            --archive venv-current.tar.gz#venv \
            --jobconf mapred.line.input.format.linespermap=8000 \
            --jobconf mapreduce.job.queuename=extraction \
            --jobconf mapred.task.timeout=3600000 \
            {input_cdx}
            """.format(hbase_host=HBASE_HOST, env=args.env,
                output=output,
                input_cdx=args.input_cdx,
                grobid_uri=GROBID_URI)
    subprocess.call(cmd, shell=True)

def run_extract_ungrobided(args):
    if args.rebuild:
        rebuild_python()
    print("Starting extractungrobided job...")
    output = "{}/output-{}/{}-extract-ungrobided".format(
        HDFS_DIR,
        args.env,
        datetime.strftime(datetime.now(), "%Y-%m-%d-%H%M.%S"))
    cmd = """cd python;
        pipenv run ./extraction_ungrobided.py \
            --hbase-host {hbase_host} \
            --hbase-table wbgrp-journal-extract-0-{env} \
            --grobid-uri {grobid_uri} \
            -r hadoop \
            -c mrjob.conf \
            --output-dir {output} \
            --no-output \
            --archive venv-current.tar.gz#venv \
            --jobconf mapred.line.input.format.linespermap=8000 \
            --jobconf mapreduce.job.queuename=extraction \
            --jobconf mapred.task.timeout=3600000 \
            {input_ungrobided}
            """.format(hbase_host=HBASE_HOST, env=args.env,
                input_ungrobided=args.input_ungrobided,
                output=output,
                grobid_uri=GROBID_URI)
    subprocess.call(cmd, shell=True)

def run_rowcount(args):
    if args.rebuild:
        rebuild_scalding()
    print("Starting rowcount job...")
    output = "{}/output-{}/{}-rowcount".format(
        HDFS_DIR,
        args.env,
        datetime.strftime(datetime.now(), "%Y-%m-%d-%H%M.%S"))
    cmd = """hadoop jar \
        scalding/target/scala-2.11/sandcrawler-assembly-0.2.0-SNAPSHOT.jar \
        com.twitter.scalding.Tool sandcrawler.HBaseRowCountJob \
        --hdfs \
        --app.conf.path scalding/ia_cluster.conf \
        --hbase-table wbgrp-journal-extract-0-{env} \
        --zookeeper-hosts {zookeeper_hosts} \
        --output {output}""".format(
            output=output,
            zookeeper_hosts=ZOOKEEPER_HOSTS,
            env=args.env)
    subprocess.call(cmd, shell=True)

def run_statuscodecount(args):
    if args.rebuild:
        rebuild_scalding()
    print("Starting statuscodecount job...")
    output = "{}/output-{}/{}-statuscodecount".format(
        HDFS_DIR,
        args.env,
        datetime.strftime(datetime.now(), "%Y-%m-%d-%H%M.%S"))
    cmd = """hadoop jar \
        scalding/target/scala-2.11/sandcrawler-assembly-0.2.0-SNAPSHOT.jar \
        com.twitter.scalding.Tool sandcrawler.HBaseStatusCodeCountJob \
        --hdfs \
        --app.conf.path scalding/ia_cluster.conf \
        --hbase-table wbgrp-journal-extract-0-{env} \
        --zookeeper-hosts {zookeeper_hosts} \
        --output {output}""".format(
            output=output,
            zookeeper_hosts=ZOOKEEPER_HOSTS,
            env=args.env)
    subprocess.call(cmd, shell=True)

def run_statuscount(args):
    if args.rebuild:
        rebuild_scalding()
    print("Starting statuscount job...")
    output = "{}/output-{}/{}-statuscount".format(
        HDFS_DIR,
        args.env,
        datetime.strftime(datetime.now(), "%Y-%m-%d-%H%M.%S"))
    cmd = """hadoop jar \
        scalding/target/scala-2.11/sandcrawler-assembly-0.2.0-SNAPSHOT.jar \
        com.twitter.scalding.Tool sandcrawler.HBaseStatusCountJob \
        --hdfs \
        --app.conf.path scalding/ia_cluster.conf \
        --hbase-table wbgrp-journal-extract-0-{env} \
        --zookeeper-hosts {zookeeper_hosts} \
        --output {output}""".format(
            output=output,
            zookeeper_hosts=ZOOKEEPER_HOSTS,
            env=args.env)
    subprocess.call(cmd, shell=True)

def run_matchcrossref(args):
    if args.rebuild:
        rebuild_scalding()
    print("Starting matchcrossref job...")
    output = "{}/output-{}/{}-matchcrossref".format(
        HDFS_DIR,
        args.env,
        datetime.strftime(datetime.now(), "%Y-%m-%d-%H%M.%S"))
    if args.fatcat_insertable:
        jobclass = "ScoreInsertableJob"
    else:
        jobclass = "ScoreJob"
    # Notes: -D options must come after Tool but before class name
    # https://github.com/twitter/scalding/wiki/Frequently-asked-questions#how-do-i-pass-parameters-to-my-hadoop-job-number-of-reducers--memory-options--etc-
    # Compression: changed due to errors in production
    # https://stackoverflow.com/a/11336820/4682349
    cmd = """hadoop jar \
        scalding/target/scala-2.11/sandcrawler-assembly-0.2.0-SNAPSHOT.jar \
        com.twitter.scalding.Tool \
        -Dmapred.reduce.tasks={reducers} \
        -Dcascading.spill.list.threshold=500000 \
        -D mapred.output.compress=false \
        -Dmapred.compress.map.output=true\
        sandcrawler.{jobclass} \
        --hdfs \
        --app.conf.path scalding/ia_cluster.conf \
        --hbase-table wbgrp-journal-extract-0-{env} \
        --zookeeper-hosts {zookeeper_hosts} \
        --crossref-input {crossref_input} \
        --output {output}""".format(
            output=output,
            jobclass=jobclass,
            zookeeper_hosts=ZOOKEEPER_HOSTS,
            env=args.env,
            reducers=args.reducers,
            crossref_input=args.crossref_input)
    subprocess.call(cmd, shell=True)

def run_grobidscorabledump(args):
    if args.rebuild:
        rebuild_scalding()
    print("Starting grobid-scorable-dump job...")
    output = "{}/output-{}/{}-grobidscorabledump".format(
        HDFS_DIR,
        args.env,
        datetime.strftime(datetime.now(), "%Y-%m-%d-%H%M.%S"))
    cmd = """hadoop jar \
        scalding/target/scala-2.11/sandcrawler-assembly-0.2.0-SNAPSHOT.jar \
        com.twitter.scalding.Tool sandcrawler.GrobidScorableDumpJob \
        --hdfs \
        --app.conf.path scalding/ia_cluster.conf \
        --hbase-table wbgrp-journal-extract-0-{env} \
        --zookeeper-hosts {zookeeper_hosts} \
        --output {output}""".format(
            output=output,
            zookeeper_hosts=ZOOKEEPER_HOSTS,
            env=args.env)
    subprocess.call(cmd, shell=True)

def run_dumpfilemeta(args):
    if args.rebuild:
        rebuild_scalding()
    print("Starting dumpfilemeta job...")
    output = "{}/output-{}/{}-dumpfilemeta".format(
        HDFS_DIR,
        args.env,
        datetime.strftime(datetime.now(), "%Y-%m-%d-%H%M.%S"))
    cmd = """hadoop jar \
        scalding/target/scala-2.11/sandcrawler-assembly-0.2.0-SNAPSHOT.jar \
        com.twitter.scalding.Tool sandcrawler.DumpFileMetaJob \
        --hdfs \
        --app.conf.path scalding/ia_cluster.conf \
        --hbase-table wbgrp-journal-extract-0-{env} \
        --zookeeper-hosts {zookeeper_hosts} \
        --output {output}""".format(
            output=output,
            zookeeper_hosts=ZOOKEEPER_HOSTS,
            env=args.env)
    subprocess.call(cmd, shell=True)

def run_colcount(args):
    if args.rebuild:
        rebuild_scalding()
    print("Starting colcount job...")
    output = "{}/output-{}/{}-colcount-{}".format(
        HDFS_DIR,
        args.env,
        datetime.strftime(datetime.now(), "%Y-%m-%d-%H%M.%S"),
        args.column.replace(':', '_'))
    cmd = """hadoop jar \
        scalding/target/scala-2.11/sandcrawler-assembly-0.2.0-SNAPSHOT.jar \
        com.twitter.scalding.Tool sandcrawler.HBaseColCountJob \
        --hdfs \
        --app.conf.path scalding/ia_cluster.conf \
        --hbase-table wbgrp-journal-extract-0-{env} \
        --zookeeper-hosts {zookeeper_hosts} \
        --column {column} \
        --output {output}""".format(
            column=args.column,
            output=output,
            zookeeper_hosts=ZOOKEEPER_HOSTS,
            env=args.env)
    subprocess.call(cmd, shell=True)

def run_matchbenchmark(args):
    if args.rebuild:
        rebuild_scalding()
    print("Starting matchbenchmark job...")
    cmd = """./pig/deps/hadoop/bin/hadoop jar \
        scalding/target/scala-2.11/sandcrawler-assembly-0.2.0-SNAPSHOT.jar \
        com.twitter.scalding.Tool \
        sandcrawler.MatchBenchmarkJob \
        --local \
        --app.conf.path scalding/ia_cluster.conf \
        --left-bibjson {left_bibjson} \
        --right-bibjson {right_bibjson} \
        --output {output}""".format(
            output=args.output,
            left_bibjson=args.left_bibjson,
            right_bibjson=args.right_bibjson)
    subprocess.call(cmd, shell=True)

def run_keysmissingcol(args):
    if args.rebuild:
        rebuild_scalding()
    print("Starting keysmissingcol job...")
    output = "{}/output-{}/{}-keysmissingcol-{}".format(
        HDFS_DIR,
        args.env,
        datetime.strftime(datetime.now(), "%Y-%m-%d-%H%M.%S"),
        args.column.replace(":", "_"))
    cmd = """hadoop jar \
        scalding/target/scala-2.11/sandcrawler-assembly-0.2.0-SNAPSHOT.jar \
        com.twitter.scalding.Tool sandcrawler.MissingColumnDumpJob \
        --hdfs \
        --app.conf.path scalding/ia_cluster.conf \
        --hbase-table wbgrp-journal-extract-0-{env} \
        --zookeeper-hosts {zookeeper_hosts} \
        --column {column} \
        --output {output}""".format(
            output=output,
            zookeeper_hosts=ZOOKEEPER_HOSTS,
            column=args.column,
            env=args.env)
    subprocess.call(cmd, shell=True)

def run_dumpungrobided(args):
    if args.rebuild:
        rebuild_scalding()
    print("Starting dumpungrobided job...")
    output = "{}/output-{}/{}-dumpungrobided".format(
        HDFS_DIR,
        args.env,
        datetime.strftime(datetime.now(), "%Y-%m-%d-%H%M.%S"))
    cmd = """hadoop jar \
        scalding/target/scala-2.11/sandcrawler-assembly-0.2.0-SNAPSHOT.jar \
        com.twitter.scalding.Tool sandcrawler.DumpUnGrobidedJob \
        --hdfs \
        --app.conf.path scalding/ia_cluster.conf \
        --hbase-table wbgrp-journal-extract-0-{env} \
        --zookeeper-hosts {zookeeper_hosts} \
        --output {output}""".format(
            output=output,
            zookeeper_hosts=ZOOKEEPER_HOSTS,
            env=args.env)
    subprocess.call(cmd, shell=True)

def main():
    parser = argparse.ArgumentParser()

    parser.add_argument('--prod',
        help="run against prod HBase table",
        action='store_true')
    parser.add_argument('--qa',
        help="run against qa HBase table",
        action='store_true')
    parser.add_argument('--rebuild',
        help="rebuild whatever artifact gets sent",
        action='store_true')
    subparsers = parser.add_subparsers()

    sub_backfill = subparsers.add_parser('backfill')
    sub_backfill.set_defaults(func=run_backfill)
    sub_backfill.add_argument('input_cdx',
        help="full HDFS path of CDX file to backfill")

    sub_extract = subparsers.add_parser('extract')
    sub_extract.set_defaults(func=run_extract)
    sub_extract.add_argument('input_cdx',
        help="full HDFS path of CDX file to extract")

    sub_extractungrobided = subparsers.add_parser('extract-ungrobided')
    sub_extractungrobided.set_defaults(func=run_extract_ungrobided)
    sub_extractungrobided.add_argument('input_ungrobided',
        help="full HDFS path of 'ungrobided' file to extract")

    sub_rowcount = subparsers.add_parser('row-count')
    sub_rowcount.set_defaults(func=run_rowcount)

    sub_statuscount = subparsers.add_parser('status-count')
    sub_statuscount.set_defaults(func=run_statuscount)

    sub_statuscodecount = subparsers.add_parser('status-code-count')
    sub_statuscodecount.set_defaults(func=run_statuscodecount)

    sub_matchcrossref = subparsers.add_parser('match-crossref')
    sub_matchcrossref.set_defaults(func=run_matchcrossref)
    sub_matchcrossref.add_argument('crossref_input',
        help="full HDFS path of Crossref JSON dump")
    sub_matchcrossref.add_argument('--reducers',
        help="number of reducers to run",
        type=int, default=200)
    sub_matchcrossref.add_argument('--fatcat-insertable',
        help="whether to include CDX and other metadata in output",
        action='store_true')

    sub_grobidscorabledump = subparsers.add_parser('grobid-scorable-dump')
    sub_grobidscorabledump.set_defaults(func=run_grobidscorabledump)

    sub_dumpfilemeta = subparsers.add_parser('dump-file-meta')
    sub_dumpfilemeta.set_defaults(func=run_dumpfilemeta)

    sub_colcount = subparsers.add_parser('col-count')
    sub_colcount.set_defaults(func=run_colcount)
    sub_colcount.add_argument('column',
        help="column name to use in count")

    sub_matchbenchmark = subparsers.add_parser('match-benchmark')
    sub_matchbenchmark.set_defaults(func=run_matchbenchmark)
    sub_matchbenchmark.add_argument('left_bibjson',
        help="First bibjson file")
    sub_matchbenchmark.add_argument('right_bibjson',
        help="Second bibjson file")
    sub_matchbenchmark.add_argument('output',
        help="where to write output")

    sub_keysmissingcol = subparsers.add_parser('keys-missing-col')
    sub_keysmissingcol.set_defaults(func=run_keysmissingcol)
    sub_keysmissingcol.add_argument('column',
        help="column to SCAN for missing keys")

    sub_dumpungrobided = subparsers.add_parser('dump-ungrobided')
    sub_dumpungrobided.set_defaults(func=run_dumpungrobided)

    args = parser.parse_args()
    if not args.__dict__.get("func"):
        print("tell me what to do! (try --help)")
        sys.exit(-1)
    if not (args.prod or args.qa) or (args.prod and args.qa):
        print("must pass one of --prod or --qa")
        sys.exit(-1)
    if args.prod:
        args.env = "prod"
    if args.qa:
        args.env = "qa"

    args.func(args)

if __name__ == '__main__':
    main()