Added mode parameter to PySparkS3Dataset

This parameter allows for filtering out VisitIds that are part of
`incompleted_visits` or that had a command with a command_status other than
"ok" since users probably shouldn't consider them for analysis

This filtering functionality is extracted into the TableFilter class to
be reused by other Datasets.

Author: vringar

openwpm_utils/crawlhistory.py

@@ -0,0 +1,28 @@
+import pyspark.sql.functions as F
+from pyspark.sql.types import StringType
+
+reduce_to_worst_command_status = (
+    F.when(F.array_contains("command_status", "critical"), "critical")
+    .when(F.array_contains("command_status", "error"), "error")
+    .when(F.array_contains("command_status", "neterror"), "neterror")
+    .when(F.array_contains("command_status", "timeout"), "timeout")
+    .otherwise("ok")
+    .alias("worst_status")
+)
+
+
+reduce_to_best_command_status = (
+    F.when(F.array_contains("command_status", "ok"), "ok")
+    .when(F.array_contains("command_status", "timeout"), "timeout")
+    .when(F.array_contains("command_status", "neterror"), "neterror")
+    .when(F.array_contains("command_status", "error"), "error")
+    .otherwise("critical")
+    .alias("best_status")
+)
+
+
+def get_worst_status_per_visit_id(crawl_history):
+    """Adds column `worst_status`"""
+    return (crawl_history.groupBy("visit_id")
+            .agg(F.collect_list("command_status").alias("command_status"))
+            .withColumn("worst_status",reduce_to_worst_command_status))

openwpm_utils/dataquality.py

@@ -1,5 +1,9 @@
-from pyspark.sql.functions import countDistinct, col, isnan, lit, sum, count, when
+import pyspark.sql.functions as F
 from pyspark.mllib.stat import Statistics
+from pyspark.sql.dataframe import DataFrame
+from pyspark.sql.functions import col, count, countDistinct, isnan, lit, sum, when
+
+from openwpm_utils.crawlhistory import get_worst_status_per_visit_id
 
 
 def count_not_null(c, nan_as_null=False):
@@ -53,3 +57,23 @@ def check_df(df, skip_null_check=True):
         "\nNumber of records with visit_id == -1: %d"
         % df.where(df.visit_id == -1).count()
     )
+
+
+class TableFilter:
+    def __init__(self, incomplete_visits: DataFrame, crawl_history: DataFrame) -> None:
+        self._incomplete_visit_ids = incomplete_visits.select("visit_id")
+        self._failed_visit_ids = (
+            get_worst_status_per_visit_id(crawl_history)
+            .where(F.col("worst_status") != "ok")
+            .select("visit_id")
+        )
+
+    def clean_table(self, table: DataFrame) -> DataFrame:
+        return table.join(self._failed_visit_ids, "visit_id", how="leftanti").join(
+            self._incomplete_visit_ids, "visit_id", how="leftanti"
+        )
+
+    def dirty_table(self, table: DataFrame) -> DataFrame:
+        return table.join(self._failed_visit_ids, "visit_id", how="inner").union(
+            table.join(self._incomplete_visit_ids, "visit_id", how="inner")
+        )

openwpm_utils/s3.py

@@ -1,15 +1,22 @@
 import gzip
+from typing import List
 
 import boto3
 import jsbeautifier
 import pyarrow.parquet as pq
+import pyspark.sql.functions as F
 import s3fs
 from botocore.exceptions import ClientError
 from pyarrow.filesystem import S3FSWrapper  # noqa
-from pyspark.sql import SQLContext
+from pyspark import SparkContext
+from pyspark.sql import DataFrame, SQLContext
 
-class S3Dataset:
-    def __init__(self, s3_directory, s3_bucket='openwpm-crawls'):
+from openwpm_utils.crawlhistory import get_worst_status_per_visit_id
+from openwpm_utils.dataquality import TableFilter
+
+
+class S3Dataset(object):
+    def __init__(self, s3_directory, s3_bucket="openwpm-crawls"):
         """Helper class to load OpenWPM datasets from S3 using pandas
 
         This dataset wrapper is safe to use by spark worker processes, as it
@@ -38,30 +45,33 @@ def read_table(self, table_name, columns=None):
         columns : list of strings
             The set of columns to filter the parquet dataset by
         """
-        return pq.ParquetDataset(
-            self._s3_table_loc % table_name,
-            filesystem=self._s3fs,
-            metadata_nthreads=4
-        ).read(use_pandas_metadata=True, columns=columns).to_pandas()
+        return (
+            pq.ParquetDataset(
+                self._s3_table_loc % table_name,
+                filesystem=self._s3fs,
+                metadata_nthreads=4,
+            )
+            .read(use_pandas_metadata=True, columns=columns)
+            .to_pandas()
+        )
 
     def collect_content(self, content_hash, beautify=False):
         """Collect content by directly connecting to S3 via boto3"""
-        s3 = boto3.client('s3')
+        s3 = boto3.client("s3")
         try:
             obj = s3.get_object(
-                Bucket=self._s3_bucket,
-                Key=self._content_key % content_hash
+                Bucket=self._s3_bucket, Key=self._content_key % content_hash
             )
             body = obj["Body"]
             compressed_content = body.read()
             body.close()
         except ClientError as e:
-            if e.response['Error']['Code'] != 'NoSuchKey':
+            if e.response["Error"]["Code"] != "NoSuchKey":
                 raise
             else:
                 return None
 
-        with gzip.GzipFile(fileobj=compressed_content, mode='r') as f:
+        with gzip.GzipFile(fileobj=compressed_content, mode="r") as f:
             content = f.read()
 
         if content is None or content == "":
@@ -74,9 +84,11 @@ def collect_content(self, content_hash, beautify=False):
                 pass
         return content
 
+
 class PySparkS3Dataset(S3Dataset):
-    def __init__(self, spark_context, s3_directory,
-                 s3_bucket='openwpm-crawls'):
+    def __init__(
+        self, spark_context, s3_directory: str, s3_bucket: str = "openwpm-crawls"
+    ):
         """Helper class to load OpenWPM datasets from S3 using PySpark
 
         Parameters
@@ -89,16 +101,17 @@ def __init__(self, spark_context, s3_directory,
         s3_bucket : string, optional
             The bucket name on S3. Defaults to `openwpm-crawls`.
         """
-        self._s3_bucket = s3_bucket
-        self._s3_directory = s3_directory
+        super().__init__(s3_directory, s3_bucket)
         self._spark_context = spark_context
         self._sql_context = SQLContext(spark_context)
-        self._s3_table_loc = "s3a://%s/%s/visits/%%s/" % (
-            s3_bucket, s3_directory)
-        self._s3_content_loc = "s3a://%s/%s/content/%%s.gz" % (
-            s3_bucket, s3_directory)
+        self._s3_table_loc = f"s3a://{self._s3_table_loc}"
+        incomplete_visits = self.read_table("incomplete_visits", mode="all")
+        crawl_history = self.read_table("crawl_history", mode="all")
+        self._filter = TableFilter(incomplete_visits, crawl_history)
 
-    def read_table(self, table_name, columns=None):
+    def read_table(
+        self, table_name: str, columns: List[str] = None, mode: str = "successful"
+    ):
         """Read `table_name` from OpenWPM dataset into a pyspark dataframe.
 
         Parameters
@@ -107,8 +120,26 @@ def read_table(self, table_name, columns=None):
             OpenWPM table to read
         columns : list of strings
             The set of columns to filter the parquet dataset by
+        mode : string
+            The valid values are "successful", "failed", "all"
+            Success is determined per visit_id. A visit_id is failed
+            if one of it's commands failed or if it's in the interrupted table
         """
         table = self._sql_context.read.parquet(self._s3_table_loc % table_name)
+
+        if mode == "all":
+            table = table
+        elif mode == "failed":
+            table = self._filter.dirty_table(table)
+        elif mode == "successful":
+            table = self._filter.clean_table(table)
+        else:
+            raise AssertionError(
+                f"Mode was ${mode},"
+                "allowed modes are 'all', 'failed' and 'successful'"
+            )
+
         if columns is not None:
-            return table.select(columns)
+            table = table.select(columns)
+
         return table

setup.py

@@ -11,7 +11,7 @@
     name='openwpm-utils',
     license='MPL 2.0',
     url='https://github.com/mozilla/openwpm-utils',
-    version='0.2.0',
+    version='0.3.0',
     packages=['openwpm_utils'],
 
     # Dependencies