R / R News

Updates to the sergeant (Apache Drill connector) Package & a look at Apache Drill 1.14.0 release

by hrbrmstr · August 16, 2018

This article is originally published at https://rud.is/b

Apache Drill 1.14.0 was recently released, bringing with it many new features and a temporary incompatibility with the current rev of the MapR ODBC drivers. The Drill community expects new ODBC drivers to arrive shortly. The sergeant is an alternative to ODBC for R users as it provides a dplyr interface to the REST API along with a JDBC interface and functions to work directly with the REST API in a more programmatic fashion.

First-class dplyr-citizen support for the sergeant JDBC interface

I’ve been primarily using the ODBC interface for a while, now, since it’s dead simple to use it with dplyr (as has been noted in my still-unfinished, short cookbook on wiring up Drill and R). The ODBC incompatibility is pretty severe since it’s at the protobuf-level, but sergeant::src_drill() is an easy swap out and does not have any issues since it works against the REST API. Unfortunately, the query endpoint of the REST API mangles the field order when it returns query results. This really isn’t too painful since it’s easy to add in a select() call after gathering query results to reorder things. However, it’s painful enough that it facilitated rounding out some of the corners to the JDBC interface.

sergeant::drill_jdbc() now returns a <DrillJDBCConnection> object which was necessary to add dplyr classes for just enough bits to enable smooth operation with the tbl() function (without breaking all your other RJDBC usage in the same session). The next blog section will use the new JDBC interface with dplyr as it introduces one of Drill’s new features.

Query Image Metadata with Apache Drill 1.14.0

There are quite a few R packages for reading image/media metadata. Since that seems to be en vogue, R folks might be interested in Drill’s new image metadata format plugin. Just point drill to a directory of files and you can use a familiar dplyr interface to get the deets on your ~~pirated torrent archive~~family photo inventory.

You first need to follow the directions at the aforelinked resource and add the following format to the formats: section.

formats: {
     "image": {
       "type": "image",
       "extensions": [
         "jpg", "jpeg", "jpe", "tif", "tiff", "dng", "psd", "png", "bmp", "gif",
         "ico", "pcx", "wav", "wave", "avi", "webp", "mov", "mp4", "m4a", "m4p",
         "m4b", "m4r", "m4v", "3gp", "3g2", "eps", "epsf", "epsi", "ai", "arw",
         "crw", "cr2", "nef", "orf", "raf", "rw2", "rwl", "srw", "x3f"
       ],
       "fileSystemMetadata": true,
       "descriptive": true,
       "timeZone": null
     }  
   }

Note that the configuration snippet on Drill’s site (as of the date-stamp on this post) did not have a , after the ] for the extensions array, so copy this one instead.

I created a media workspace and set the defaultInputFormat to image. Here’s a naive first look at what you can get back from a simple query to a jpg directory under it (using the new JDBC interface and dplyr):

library(sergeant)
library(tidyverse)

(con < - drill_jdbc("bigd:2181"))
## 

tbl(con, "dfs.media.`/jpg/*`") %>%
  glimpse()
## Observations: ??
## Variables: 28
## $ FileSize         "4412686 bytes", "4737696 bytes", "4253912 byt...
## $ FileDateTime     "Thu Aug 16 03:04:16 -04:00 2018", "Thu Aug 16...
## $ Format           "JPEG", "JPEG", "JPEG", "JPEG", "JPEG", "JPEG"...
## $ PixelWidth       "4032", "4032", "4032", "4032", "4032", "4032"...
## $ PixelHeight      "3024", "3024", "3024", "3024", "3024", "3024"...
## $ BitsPerPixel     "24", "24", "24", "24", "24", "24", "24", "24"...
## $ DPIWidth         "72", "72", "72", "72", "72", "72", "72", "72"...
## $ DPIHeight        "72", "72", "72", "72", "72", "72", "72", "72"...
## $ Orientaion       "Unknown (0)", "Unknown (0)", "Unknown (0)", "...
## $ ColorMode        "RGB", "RGB", "RGB", "RGB", "RGB", "RGB", "RGB...
## $ HasAlpha         "false", "false", "false", "false", "false", "...
## $ Duration         "00:00:00", "00:00:00", "00:00:00", "00:00:00"...
## $ VideoCodec       "Unknown", "Unknown", "Unknown", "Unknown", "U...
## $ FrameRate        "0", "0", "0", "0", "0", "0", "0", "0", "0", "...
## $ AudioCodec       "Unknown", "Unknown", "Unknown", "Unknown", "U...
## $ AudioSampleSize  "0", "0", "0", "0", "0", "0", "0", "0", "0", "...
## $ AudioSampleRate  "0", "0", "0", "0", "0", "0", "0", "0", "0", "...
## $ JPEG             "{\"CompressionType\":\"Baseline\",\"DataPreci...
## $ JFIF             "{\"Version\":\"1.1\",\"ResolutionUnits\":\"no...
## $ ExifIFD0         "{\"Make\":\"Apple\",\"Model\":\"iPhone 7 Plus...
## $ ExifSubIFD       "{\"ExposureTime\":\"1/2227 sec\",\"FNumber\":...
## $ AppleMakernote   "{\"UnknownTag(0x0001)\":\"5\",\"UnknownTag(0x...
## $ GPS              "{\"GPSLatitudeRef\":\"N\",\"GPSLatitude\":\"4...
## $ XMP              "{\"XMPValueCount\":\"4\",\"Photoshop\":{\"Dat...
## $ Photoshop        "{\"CaptionDigest\":\"48 89 11 77 33 105 192 3...
## $ IPTC             "{\"CodedCharacterSet\":\"UTF-8\",\"Applicatio...
## $ Huffman          "{\"NumberOfTables\":\"4 Huffman tables\"}", "...
## $ FileType         "{\"DetectedFileTypeName\":\"JPEG\",\"Detected...

That’s quite a bit of metadata, but the Drill format plugin page kinda fibs a bit about column types since we see many chrs there. You may be quick to question the sergeant package but this isn’t using the REST interface and we can use DBI calls to ask Drill what’s it’s sending us:

dbSendQuery(con, "SELECT * FROM dfs.media.`/jpg/*`") %>%
  dbColumnInfo()
##         field.name        field.type data.type            name
## 1         FileSize CHARACTER VARYING character        FileSize
## 2     FileDateTime CHARACTER VARYING character    FileDateTime
## 3           Format CHARACTER VARYING character          Format
## 4       PixelWidth CHARACTER VARYING character      PixelWidth
## 5      PixelHeight CHARACTER VARYING character     PixelHeight
## 6     BitsPerPixel CHARACTER VARYING character    BitsPerPixel
## 7         DPIWidth CHARACTER VARYING character        DPIWidth
## 8        DPIHeight CHARACTER VARYING character       DPIHeight
## 9       Orientaion CHARACTER VARYING character      Orientaion
## 10       ColorMode CHARACTER VARYING character       ColorMode
## 11        HasAlpha CHARACTER VARYING character        HasAlpha
## 12        Duration CHARACTER VARYING character        Duration
## 13      VideoCodec CHARACTER VARYING character      VideoCodec
## 14       FrameRate CHARACTER VARYING character       FrameRate
## 15      AudioCodec CHARACTER VARYING character      AudioCodec
## 16 AudioSampleSize CHARACTER VARYING character AudioSampleSize
## 17 AudioSampleRate CHARACTER VARYING character AudioSampleRate
## 18            JPEG               MAP character            JPEG
## 19            JFIF               MAP character            JFIF
## 20        ExifIFD0               MAP character        ExifIFD0
## 21      ExifSubIFD               MAP character      ExifSubIFD
## 22  AppleMakernote               MAP character  AppleMakernote
## 23             GPS               MAP character             GPS
## 24             XMP               MAP character             XMP
## 25       Photoshop               MAP character       Photoshop
## 26            IPTC               MAP character            IPTC
## 27         Huffman               MAP character         Huffman
## 28        FileType               MAP character        FileType

We can still work with the results, but there’s also a pretty key element missing: the media filename. The reason it’s not in the listing is that filename is an implicit column that we have to ask for. So, we need to modify our query to be something like this:

tbl(con, sql("SELECT filename AS fname, * FROM dfs.media.`/jpg/*`")) %>%
  glimpse()
## Observations: ??
## Variables: 29
## $ fname            "IMG_0778.jpg", "IMG_0802.jpg", "IMG_0793.jpg"...
## $ FileSize         "4412686 bytes", "4737696 bytes", "4253912 byt...
## $ FileDateTime     "Thu Aug 16 03:04:16 -04:00 2018", "Thu Aug 16...
## $ Format           "JPEG", "JPEG", "JPEG", "JPEG", "JPEG", "JPEG"...
## $ PixelWidth       "4032", "4032", "4032", "4032", "4032", "4032"...
## $ PixelHeight      "3024", "3024", "3024", "3024", "3024", "3024"...
## $ BitsPerPixel     "24", "24", "24", "24", "24", "24", "24", "24"...
## $ DPIWidth         "72", "72", "72", "72", "72", "72", "72", "72"...
## $ DPIHeight        "72", "72", "72", "72", "72", "72", "72", "72"...
## $ Orientaion       "Unknown (0)", "Unknown (0)", "Unknown (0)", "...
## $ ColorMode        "RGB", "RGB", "RGB", "RGB", "RGB", "RGB", "RGB...
## $ HasAlpha         "false", "false", "false", "false", "false", "...
## $ Duration         "00:00:00", "00:00:00", "00:00:00", "00:00:00"...
## $ VideoCodec       "Unknown", "Unknown", "Unknown", "Unknown", "U...
## $ FrameRate        "0", "0", "0", "0", "0", "0", "0", "0", "0", "...
## $ AudioCodec       "Unknown", "Unknown", "Unknown", "Unknown", "U...
## $ AudioSampleSize  "0", "0", "0", "0", "0", "0", "0", "0", "0", "...
## $ AudioSampleRate  "0", "0", "0", "0", "0", "0", "0", "0", "0", "...
## $ JPEG             "{\"CompressionType\":\"Baseline\",\"DataPreci...
## $ JFIF             "{\"Version\":\"1.1\",\"ResolutionUnits\":\"no...
## $ ExifIFD0         "{\"Make\":\"Apple\",\"Model\":\"iPhone 7 Plus...
## $ ExifSubIFD       "{\"ExposureTime\":\"1/2227 sec\",\"FNumber\":...
## $ AppleMakernote   "{\"UnknownTag(0x0001)\":\"5\",\"UnknownTag(0x...
## $ GPS              "{\"GPSLatitudeRef\":\"N\",\"GPSLatitude\":\"4...
## $ XMP              "{\"XMPValueCount\":\"4\",\"Photoshop\":{\"Dat...
## $ Photoshop        "{\"CaptionDigest\":\"48 89 11 77 33 105 192 3...
## $ IPTC             "{\"CodedCharacterSet\":\"UTF-8\",\"Applicatio...
## $ Huffman          "{\"NumberOfTables\":\"4 Huffman tables\"}", "...
## $ FileType         "{\"DetectedFileTypeName\":\"JPEG\",\"Detected...

We could work with the “map” columns with Drill’s SQL, but this is just metadata and even if there are many files, most R folks have sufficient system memory these days to collect it all and work with it locally. There’s nothing stopping you from working on the SQL side, though, and it may be a better choice if you’ll be using this to process huge archives. But, we’ll do this in R and convert a bunch of field types along the way:

from_map < - function(x) { map(x, jsonlite::fromJSON)}

tbl(con, sql("SELECT filename AS fname, * FROM dfs.media.`/jpg/*`")) %>%
  collect() %>%
  mutate_at(
    .vars = vars(
      JPEG, JFIF, ExifSubIFD, AppleMakernote, GPS, XMP, Photoshop, IPTC, Huffman, FileType
    ),
    .funs=funs(from_map)
  ) %>%
  mutate_at(
    .vars = vars(
      PixelWidth, PixelHeight, DPIWidth, DPIHeight, FrameRate, AudioSampleSize, AudioSampleRate
    ),
    .funs=funs(as.numeric)
  ) %>%
  glimpse() -> media_df
## Observations: 11
## Variables: 29
## $ fname            "IMG_0778.jpg", "IMG_0802.jpg", "IMG_0793.jpg"...
## $ FileSize         "4412686 bytes", "4737696 bytes", "4253912 byt...
## $ FileDateTime     "Thu Aug 16 03:04:16 -04:00 2018", "Thu Aug 16...
## $ Format           "JPEG", "JPEG", "JPEG", "JPEG", "JPEG", "JPEG"...
## $ PixelWidth       4032, 4032, 4032, 4032, 4032, 4032, 3024, 4032...
## $ PixelHeight      3024, 3024, 3024, 3024, 3024, 3024, 4032, 3024...
## $ BitsPerPixel     "24", "24", "24", "24", "24", "24", "24", "24"...
## $ DPIWidth         72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72
## $ DPIHeight        72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72
## $ Orientaion       "Unknown (0)", "Unknown (0)", "Unknown (0)", "...
## $ ColorMode        "RGB", "RGB", "RGB", "RGB", "RGB", "RGB", "RGB...
## $ HasAlpha         "false", "false", "false", "false", "false", "...
## $ Duration         "00:00:00", "00:00:00", "00:00:00", "00:00:00"...
## $ VideoCodec       "Unknown", "Unknown", "Unknown", "Unknown", "U...
## $ FrameRate        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
## $ AudioCodec       "Unknown", "Unknown", "Unknown", "Unknown", "U...
## $ AudioSampleSize  0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
## $ AudioSampleRate  0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
## $ JPEG             [["Baseline", "8 bits", "3024 pixels", "4032 ...
## $ JFIF             [["1.1", "none", "72 dots", "72 dots", "0", "...
## $ ExifIFD0         "{\"Make\":\"Apple\",\"Model\":\"iPhone 7 Plus...
## $ ExifSubIFD       [["1/2227 sec", "f/1.8", "Program normal", "2...
## $ AppleMakernote   [["5", "[558 values]", "[104 values]", "1", "...
## $ GPS              [["N", "44° 19' 6.3\"", "W", "-68° 11' 22.39\...
## $ XMP              [["4", ["2017-06-22T14:28:04"], ["2017-06-22T...
## $ Photoshop        [["48 89 11 77 33 105 192 33 170 252 63 34 43...
## $ IPTC             [["UTF-8", "2", "14:28:04", "2017:06:22", "20...
## $ Huffman          [["4 Huffman tables"], ["4 Huffman tables"], ...
## $ FileType         [["JPEG", "Joint Photographic Experts Group",...

Now, we can do anything with the data, including getting the average file size:

mutate(media_df, FileSize = str_replace(FileSize, " bytes", "") %>% as.numeric()) %>%
  summarise(mean(FileSize))
## # A tibble: 1 x 1
##   `mean(FileSize)`
##              
## 1         3878963.

FIN

The enhancements to the JDBC interface have only been given a light workout but seem to be doing well so-far. Kick the tyres and file an issue if you have any problems. ODBC users should not have to wait long for new drivers and src_drill() aficionados can keep chugging along as before without issue.

For those new to Apache Drill, there’s now an official Docker image for it so you can get up and running without adding too much cruft to your local systems. I may add support for spinning up and managing a Drill container to the sergeant package, so keep your eyes on pushes to the repo.

Also keep an eye on the mini-cookbook as I’ll be modifying to to account for the new package changes and introduce additional, new Drill features.

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This article is originally published at https://rud.is/b
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Updates to the sergeant (Apache Drill connector) Package & a look at Apache Drill 1.14.0 release

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Updates to the sergeant (Apache Drill connector) Package & a look at Apache Drill 1.14.0 release

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