Apache Drill 1.15.0 + sergeant 0.8.0 = pcapng Support, Proper Column Types & Mounds of New Metadata

January 2, 2019
By

(This article was first published on R – rud.is, and kindly contributed to R-bloggers)

Apache Drill is an innovative distributed SQL engine designed to enable data exploration and analytics on non-relational datastores […] without having to create and manage schemas. […] It has a schema-free JSON document model similar to MongoDB and Elasticsearch; [a plethora of APIs, including] ANSI SQL, ODBC/JDBC, and HTTP[S] REST; [is] extremely user and developer friendly; [and, has a] pluggable architecture enables connectivity to multiple datastores.

To ring in the new year the Drill team knocked out a new 1.15.0 release with a cadre of new functionality including:

One super-helpful new feature of the REST API is that it now returns query results metadata along with the query results themselves. This means REST API endpoints finally know both column order and column type. This gave me cause to re-visit the sergeant package [GL|GH] and make some accommodations for some of these new features.

Ushering In A New Order

Drill REST API queries return a "columns" field and "metadata" field with the data itself. We can use that to force an order to the columns as well as mostly use proper types (vs JSON-parsed/guessed types). I say mostly since the package still uses jsonlite to parse the results and there’s no support for 64-bit integers in jsonlite (more on this later).

We’ll use the example from DRILL-6847 and use the example provided by Charles Givre in his Jira issue since it will let me demonstrate more of that “mostly” comment and show off another new feature:

library(sergeant) # 0.8.0 branch of sergeant on gitlab or github
library(tidyverse)

con <- src_drill("localhost")

x <- tbl(con, "cp.`employee.json`")

mutate(x, employee_id = as.integer64(employee_id)) %>% 
  mutate(position_id = as.integer64(position_id)) %>% 
  select(
    employee_id, full_name, first_name, last_name, 
    position_id, position_title
  ) -> bigint_result

The above is (logically):

SELECT 
  CAST (employee_id AS INT) AS employee_id,
  full_name,
  first_name, 
  last_name, 
  CAST (position_id AS BIGINT) AS position_id, 
  position_title 
FROM cp.`employee.json`

What do we get when we take a preview of the result?

bigint_result
## # Source:   lazy query [?? x 6]
## # Database: DrillConnection
##    employee_id full_name  first_name last_name position_id position_title 
##                                             
##  1           1 Sheri Now… Sheri      Nowmer              1 President      
##  2           2 Derrick W… Derrick    Whelply             2 VP Country Man…
##  3           4 Michael S… Michael    Spence              2 VP Country Man…
##  4           5 Maya Guti… Maya       Gutierrez           2 VP Country Man…
##  5           6 Roberta D… Roberta    Damstra             3 VP Information…
##  6           7 Rebecca K… Rebecca    Kanagaki            4 VP Human Resou…
##  7           8 Kim Brunn… Kim        Brunner            11 Store Manager  
##  8           9 Brenda Bl… Brenda     Blumberg           11 Store Manager  
##  9          10 Darren St… Darren     Stanz               5 VP Finance     
## 10          11 Jonathan … Jonathan   Murraiin           11 Store Manager  
## # ... with more rows
Warning message:
One or more columns are of type BIGINT. The sergeant package currently uses jsonlite::fromJSON()
to process Drill REST API result sets. Since jsonlite does not support 64-bit integers BIGINT 
columns are initially converted to numeric since that's how jsonlite::fromJSON() works. This is
problematic for many reasons, including trying to use 'dplyr' idioms with said converted 
BIGINT-to-numeric columns. It is recommended that you 'CAST' BIGINT columns to 'VARCHAR' prior to
working with them from R/'dplyr'.

If you really need BIGINT/integer64 support, consider using the R ODBC interface to Apache Drill 
with the MapR ODBC drivers.

This informational warning will only be shown once per R session and you can disable them from 
appearing by setting the 'sergeant.bigint.warnonce' option to 'FALSE' 
(i.e. options(sergeant.bigint.warnonce = FALSE)). 

The first thing sergeant users will notice is proper column order (before it just returned the columns in the order they came back in the JSON rows[] structure). The second thing is that we didn’t get integer64s back. Instead, we got doubles plus an information warning about why and what you can do about it. Said warning only displays once per-session and can be silenced with the option sergeant.bigint.warnonce. i.e. just put:

options(sergeant.bigint.warnonce = FALSE)

in your script or ~/.Rprofile and you won’t hear from it again.

The as.integer64() we used is not from the bit64 package but an internal sergeant package function that knows how to translate said operation to, e.g. CAST( employee_id AS BIGINT ).

You can use the ODBC drivers to gain BIGINT support and there are plans for the 0.8.0 branch to eventually use rapidjsonr at the C++-level to provide direct in-package support for BIGINTs as well.

Better Error Messages

Drill query errors that the sergeant package bubbled up through its various interfaces have not been pretty or all that useful. This has changed with the 0.8.0 branch. Let’s take a look:

tbl(con, "cp.employees.json")
## # Source:   table [?? x 4]
## # Database: DrillConnection
Warning message:
VALIDATION ERROR: From line 2, column 6 to line 2, column 24: Object 'cp.employees.json' not found

Original Query:

  1: SELECT *
  2: FROM `cp.employees.json`
  3: LIMIT 10

Query Profile Error Link:
http://localhost:8047/profiles/079fc8cf-19c6-4c78-95a9-0b949a3ecf4c 

As you can see in the above output, you now get a highly-formatted return value with the original SQL query broken into lines (with line numbers) and a full link to the Drill query profile so you can dig in to the gnarly details of complex query issues. As you work with this and find edge cases I missed for messages, drop an issue on your social-coding site of choice.

SUPPORT ALL THE PCAPs!

Drill has had packet capture (PCAP) file support for a while now and 1.15.0 adds support for the more modern/rich pcapng format. To enable support for this you need to add "pcapng": {"type": "pcapng", "extensions": ["pcapng"] }, to the "formats" section of your storage plugins and also configure a workspace directory to use that as the default (the principle of which is covered here).

We’ll use one of the Wireshark example captures to demonstrate:

pcaps <- tbl(con, "dfs.caps.`*.pcapng`")

glimpse(pcaps)
## Observations: ??
## Variables: 25
## $ tcp_flags_ece_ecn_capable             0, 0, 0, 0, 0, 0, 0, 0, 0...
## $ tcp_flags_ece_congestion_experienced  0, 0, 0, 0, 0, 0, 0, 0, 0...
## $ tcp_flags_psh                         0, 0, 0, 0, 0, 0, 0, 0, 0...
## $ type                                  "TCP", "TCP", "TCP", "TCP...
## $ tcp_flags_cwr                         0, 0, 0, 0, 0, 0, 0, 0, 0...
## $ dst_ip                                "74.125.28.139", "10.254....
## $ src_ip                                "10.254.157.208", "74.125...
## $ tcp_flags_fin                         1, 1, 0, 0, 0, 0, 0, 0, 0...
## $ tcp_flags_ece                         0, 0, 0, 0, 0, 0, 0, 0, 0...
## $ tcp_flags                             17, 17, 16, 16, 16, 0, 0,...
## $ tcp_flags_ack                         1, 1, 1, 1, 1, 0, 0, 0, 0...
## $ src_mac_address                       "00:05:9A:3C:7A:00", "00:...
## $ tcp_flags_syn                         0, 0, 0, 0, 0, 0, 0, 0, 0...
## $ tcp_flags_rst                         0, 0, 0, 0, 0, 0, 0, 0, 0...
## $ timestamp                             2015-04-14 07:19:25, 201...
## $ tcp_session                           8.353837e+17, 8.353837e+1...
## $ packet_data                           "\"3DU... "ACK|FIN", "ACK|FIN", "AC...
## $ tcp_flags_ns                          0, 0, 0, 0, 0, 0, 0, 0, 0...
## $ src_port                              60268, 443, 60268, 58382,...
## $ packet_length                         54, 54, 54, 55, 66, 78, 7...
## $ tcp_flags_urg                         0, 0, 0, 0, 0, 0, 0, 0, 0...
## $ tcp_ack                               662445631, 1496589825, 66...
## $ dst_port                              443, 60268, 443, 29216, 5...
## $ dst_mac_address                       "00:11:22:33:44:55", "00:...

count(pcaps, src_ip, dst_ip, sort=TRUE)
## # Source:     lazy query [?? x 3]
## # Database:   DrillConnection
## # Groups:     src_ip
## # Ordered by: desc(n)
##    src_ip         dst_ip             n
##                        
##  1 10.254.157.208 10.254.158.25    298
##  2 10.254.158.25  10.254.157.208   204
##  3 174.137.42.81  10.254.157.208    76
##  4 10.254.157.208 10.254.158.8      54
##  5 10.254.158.8   10.254.157.208    49
##  6 74.125.28.102  10.254.157.208    49
##  7 10.254.157.208 74.125.28.102     44
##  8 10.254.157.208 174.137.42.81     41
##  9 54.84.98.25    10.254.157.208    25
## 10 157.55.56.168  10.254.157.208    25
## # ... with more rows

More work appears to be planned by the Drill team to enable digging into the packet (binary) contents.

Drill Metadata As Data

Drill has provided ways to lookup Drill operational information as actual tables but the Drill team has added support for even more metadata-as-data queries.

First up is finally having better access to filesystem information. Prior to 1.15.0 one could get file and path attributes as part of other queries, but now we can treat filesystems as actual data. Let’s list all the PCAPs in the above workspace:

tbl(con, "information_schema.`schemata`") %>% 
  filter(SCHEMA_NAME == "dfs.caps") %>% 
  print() %>% 
  pull(SCHEMA_NAME) -> pcap_schema
## # Source:   lazy query [?? x 9]
## # Database: DrillConnection
##   CATALOG_NAME SCHEMA_NAME SCHEMA_OWNER TYPE  IS_MUTABLE
##                                
## 1 DRILL        dfs.caps          file  NO

tbl(con, "information_schema.`files`") %>% 
  filter(schema_name == pcap_schema) %>% 
  glimpse()
## Observations: ??
## Variables: 13
## $ SCHEMA_NAME        "dfs.caps"
## $ ROOT_SCHEMA_NAME   "dfs"
## $ WORKSPACE_NAME     "caps"
## $ FILE_NAME          "dof-short-capture.pcapng"
## $ RELATIVE_PATH      "dof-short-capture.pcapng"
## $ IS_DIRECTORY       FALSE
## $ IS_FILE            TRUE
## $ LENGTH             634280
## $ OWNER              "hrbrmstr"
## $ GROUP              "staff"
## $ PERMISSION         "rw-r--r--"
## $ ACCESS_TIME        1969-12-31 19:00:00
## $ MODIFICATION_TIME  2019-01-01 19:12:17

The Drill system options table now has full descriptions for the options and also provides a new table that knows about all of Drills functions and all your custom UDFs. drill_opts() and drill_functions() return a data frame of all this info and have an optional browse parameter which, if set to TRUE, will show a DT interactive data table for them. I find this especially handy when I forget something like regexp_like syntax (I use alot of back-ends and many are wildly different) and can now do this:

FIN

Keep on the lookout for the rapidjsonr/BIGINT integration and more new features of the sergeant package. NOTE: The better error messages have been ported over to the sergeant.caffeinated package (the RJDBC interface) and the other niceties will make their way into that package soon as well.

So, make sure you’re using the 0.8.0 GL / GH, kick the tyres, file issues where you’re most comfortable working.

May your queries all be optimized and results sets complete in the new year!

To leave a comment for the author, please follow the link and comment on their blog: R – rud.is.

R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...



If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Comments are closed.

Search R-bloggers


Sponsors

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)