From: Nate E TeBlunthuis Date: Wed, 12 Aug 2020 05:37:36 +0000 (-0700) Subject: Update submissions to parse using the backfill queue. X-Git-Url: https://code.communitydata.science/cdsc_reddit.git/commitdiff_plain/2d425600a813e2fb280023a5a870b5660c36ea22?ds=inline;hp=-c Update submissions to parse using the backfill queue. --- 2d425600a813e2fb280023a5a870b5660c36ea22 diff --git a/comments_2_parquet.sh b/comments_2_parquet.sh index 096fa06..9233138 100755 --- a/comments_2_parquet.sh +++ b/comments_2_parquet.sh @@ -1,5 +1,9 @@ +## needs to be run by hand since i don't have a nice way of waiting on a parallel-sql job to complete + #!/usr/bin/env bash + + echo "#!/usr/bin/bash" > job_script.sh echo "source $(pwd)/../bin/activate" >> job_script.sh echo "python3 $(pwd)/comments_2_parquet_part1.py" >> job_script.sh diff --git a/submissions_2_parquet.sh b/submissions_2_parquet.sh index 4ec4354..f133069 100644 --- a/submissions_2_parquet.sh +++ b/submissions_2_parquet.sh @@ -1,10 +1,8 @@ -#!/usr/bin/env bash +## this should be run manually since we don't have a nice way to wait on parallel_sql jobs -echo "!#/usr/bin/bash" > job_script.sh -echo "source $(pwd)/../bin/activate" >> job_script.sh -echo "python3 $(pwd)/submissions_2_parquet_part1.py" >> job_script.sh +#!/usr/bin/env bash -srun -p comdata -A comdata --nodes=1 --mem=120G --time=48:00:00 job_script.sh +./parse_submissions.sh start_spark_and_run.sh 1 $(pwd)/submissions_2_parquet_part2.py diff --git a/submissions_2_parquet_part1.py b/submissions_2_parquet_part1.py index 23b1200..16d1988 100755 --- a/submissions_2_parquet_part1.py +++ b/submissions_2_parquet_part1.py @@ -4,7 +4,6 @@ # 1. from gz to arrow parquet (this script) # 2. from arrow parquet to spark parquet (submissions_2_parquet_part2.py) -import json from datetime import datetime from multiprocessing import Pool from itertools import islice @@ -12,19 +11,23 @@ from helper import find_dumps, open_fileset import pandas as pd import pyarrow as pa import pyarrow.parquet as pq +import simdjson +import fire +import os +parser = simdjson.Parser() def parse_submission(post, names = None): if names is None: names = ['id','author','subreddit','title','created_utc','permalink','url','domain','score','ups','downs','over_18','has_media','selftext','retrieved_on','num_comments','gilded','edited','time_edited','subreddit_type','subreddit_id','subreddit_subscribers','name','is_self','stickied','quarantine','error'] try: - post = json.loads(post) - except (json.decoder.JSONDecodeError, UnicodeDecodeError) as e: + post = parser.parse(post) + except (ValueError) as e: # print(e) # print(post) row = [None for _ in names] - row[-1] = "json.decoder.JSONDecodeError|{0}|{1}".format(e,post) + row[-1] = "Error parsing json|{0}|{1}".format(e,post) return tuple(row) row = [] @@ -55,55 +58,61 @@ def parse_submission(post, names = None): row.append(post[name]) return tuple(row) -dumpdir = "/gscratch/comdata/raw_data/reddit_dumps/submissions" - -files = list(find_dumps(dumpdir)) - -pool = Pool(28) - -stream = open_fileset(files) - -N = 100000 - -rows = pool.imap_unordered(parse_submission, stream, chunksize=int(N/28)) - -schema = pa.schema([ - pa.field('id', pa.string(),nullable=True), - pa.field('author', pa.string(),nullable=True), - pa.field('subreddit', pa.string(),nullable=True), - pa.field('title', pa.string(),nullable=True), - pa.field('created_utc', pa.timestamp('ms'),nullable=True), - pa.field('permalink', pa.string(),nullable=True), - pa.field('url', pa.string(),nullable=True), - pa.field('domain', pa.string(),nullable=True), - pa.field('score', pa.int64(),nullable=True), - pa.field('ups', pa.int64(),nullable=True), - pa.field('downs', pa.int64(),nullable=True), - pa.field('over_18', pa.bool_(),nullable=True), - pa.field('has_media',pa.bool_(),nullable=True), - pa.field('selftext',pa.string(),nullable=True), - pa.field('retrieved_on', pa.timestamp('ms'),nullable=True), - pa.field('num_comments', pa.int64(),nullable=True), - pa.field('gilded',pa.int64(),nullable=True), - pa.field('edited',pa.bool_(),nullable=True), - pa.field('time_edited',pa.timestamp('ms'),nullable=True), - pa.field('subreddit_type',pa.string(),nullable=True), - pa.field('subreddit_id',pa.string(),nullable=True), - pa.field('subreddit_subscribers',pa.int64(),nullable=True), - pa.field('name',pa.string(),nullable=True), - pa.field('is_self',pa.bool_(),nullable=True), - pa.field('stickied',pa.bool_(),nullable=True), - pa.field('quarantine',pa.bool_(),nullable=True), - pa.field('error',pa.string(),nullable=True)]) - -with pq.ParquetWriter("/gscratch/comdata/output/reddit_submissions.parquet_temp",schema=schema,compression='snappy',flavor='spark') as writer: - while True: - chunk = islice(rows,N) - pddf = pd.DataFrame(chunk, columns=schema.names) - table = pa.Table.from_pandas(pddf,schema=schema) - if table.shape[0] == 0: - break - writer.write_table(table) - - writer.close() - +def parse_dump(partition): + + N=10000 + stream = open_fileset([f"/gscratch/comdata/raw_data/reddit_dumps/submissions/{partition}"]) + rows = map(parse_submission,stream) + schema = pa.schema([ + pa.field('id', pa.string(),nullable=True), + pa.field('author', pa.string(),nullable=True), + pa.field('subreddit', pa.string(),nullable=True), + pa.field('title', pa.string(),nullable=True), + pa.field('created_utc', pa.timestamp('ms'),nullable=True), + pa.field('permalink', pa.string(),nullable=True), + pa.field('url', pa.string(),nullable=True), + pa.field('domain', pa.string(),nullable=True), + pa.field('score', pa.int64(),nullable=True), + pa.field('ups', pa.int64(),nullable=True), + pa.field('downs', pa.int64(),nullable=True), + pa.field('over_18', pa.bool_(),nullable=True), + pa.field('has_media',pa.bool_(),nullable=True), + pa.field('selftext',pa.string(),nullable=True), + pa.field('retrieved_on', pa.timestamp('ms'),nullable=True), + pa.field('num_comments', pa.int64(),nullable=True), + pa.field('gilded',pa.int64(),nullable=True), + pa.field('edited',pa.bool_(),nullable=True), + pa.field('time_edited',pa.timestamp('ms'),nullable=True), + pa.field('subreddit_type',pa.string(),nullable=True), + pa.field('subreddit_id',pa.string(),nullable=True), + pa.field('subreddit_subscribers',pa.int64(),nullable=True), + pa.field('name',pa.string(),nullable=True), + pa.field('is_self',pa.bool_(),nullable=True), + pa.field('stickied',pa.bool_(),nullable=True), + pa.field('quarantine',pa.bool_(),nullable=True), + pa.field('error',pa.string(),nullable=True)]) + + if not os.path.exists("/gscratch/comdata/output/temp/reddit_submissions.parquet/"): + os.mkdir("/gscratch/comdata/output/temp/reddit_submissions.parquet/") + + with pq.ParquetWriter(f"/gscratch/comdata/output/temp/reddit_submissions.parquet/{partition}",schema=schema,compression='snappy',flavor='spark') as writer: + while True: + chunk = islice(rows,N) + pddf = pd.DataFrame(chunk, columns=schema.names) + table = pa.Table.from_pandas(pddf,schema=schema) + if table.shape[0] == 0: + break + writer.write_table(table) + + writer.close() + +def gen_task_list(dumpdir="/gscratch/comdata/raw_data/reddit_dumps/submissions"): + files = list(find_dumps(dumpdir,base_pattern="RS_20*.*")) + with open("parse_submissions_task_list",'w') as of: + for fpath in files: + partition = os.path.split(fpath)[1] + of.write(f'python3 submissions_2_parquet_part1.py parse_dump {partition}\n') + +if __name__ == "__main__": + fire.Fire({'parse_dump':parse_dump, + 'gen_task_list':gen_task_list}) diff --git a/submissions_2_parquet_part2.py b/submissions_2_parquet_part2.py index b88764b..3a58617 100644 --- a/submissions_2_parquet_part2.py +++ b/submissions_2_parquet_part2.py @@ -17,7 +17,7 @@ conf = conf.set('spark.sql.crossJoin.enabled',"true") conf = conf.set('spark.debug.maxToStringFields',200) sqlContext = pyspark.SQLContext(sc) -df = spark.read.parquet("/gscratch/comdata/output/reddit_submissions_by_subreddit.parquet") +df = spark.read.parquet("/gscratch/comdata/output/temp/reddit_submissions.parquet/") df = df.withColumn("subreddit_2", f.lower(f.col('subreddit'))) df = df.drop('subreddit') @@ -32,13 +32,11 @@ df = df.withColumn("subreddit_hash",f.sha2(f.col("subreddit"), 256)[0:3]) df = df.repartition("subreddit") df2 = df.sort(["subreddit","CreatedAt","id"],ascending=True) df2 = df.sortWithinPartitions(["subreddit","CreatedAt","id"],ascending=True) -df2.write.parquet("/gscratch/comdata/output/reddit_submissions_by_subreddit.parquet2", mode='overwrite',compression='snappy') +df2.write.parquet("/gscratch/comdata/output/temp/reddit_submissions_by_subreddit.parquet2", mode='overwrite',compression='snappy') # # we also want to have parquet files sorted by author then reddit. df = df.repartition("author") df3 = df.sort(["author","CreatedAt","id"],ascending=True) df3 = df.sortWithinPartitions(["author","CreatedAt","id"],ascending=True) -df3.write.parquet("/gscratch/comdata/output/reddit_submissions_by_author.parquet2", mode='overwrite',compression='snappy') - -os.remove("/gscratch/comdata/output/reddit_submissions.parquet_temp") +df3.write.parquet("/gscratch/comdata/output/temp/reddit_submissions_by_author.parquet2", mode='overwrite',compression='snappy')