datagristle 0.2.2

A toolbox and library of ETL, data quality, and data analysis tools

Introduction

Datagristle is a toolbox of tough and flexible command line tools for working with data. It’s kind of an interactive mix between ETL and data analysis optimized for rapid analysis and manipulation of a wide variety of data at the command line.

More info is on the DataGristle wiki here: wiki

And examples of all csv utilities can be found here: examples

Installation

• Using pip:

  $ pip install datagristle

Dependencies

• Python 3.8
• or Python 3.9

CSV Utilities provided in this release:

• gristle_differ
  • Allows two identically-structured files to be compared by key columns and split into same, inserts, deletes, chgold and chgnew files.
  • The user can configure which columns are included in the comparison.
  • Post delta transformations can include assign sequence numbers, copying field values, etc.
• gristle_converter (was: gristle_file_converter)
  • Converts an input file with one csv dialect into an output file with another.
• gristle_freaker
  • Produces a frequency distribution of multiple columns from input file.
• gristle_profiler (was: gristle_determinator)
  • Identifies file formats, generates metadata, prints file analysis report
  • This is the most mature - and also used by the other utilities so that you generally do not need to enter file structure info.
• gristle_slicer
  • Used to extract a subset of columns and rows out of an input file.
• gristle_sorter
  • CSV-aware sort utility that handles data that breaks unix sorts.
• gristle_validator
  • Validates csv files by confirming that all records have the right number of fields, and by apply a json schema full of requirements to each record.
• gristle_viewer
  • Shows one record from a file at a time - formatted based on metadata.

File and Directory Utilities provided in this release:

• gristle_dir_merger
  • Used to consolidate large directories with options to control matching criteria as well as matching actions.
• gristle_processor
  • Used to apply actions, like delete, compress, etc, to files based on very flexible criteria.

gristle_slicer

Extracts subsets of input files based on user-specified columns and rows.
The input csv file can be piped into the program through stdin or identified
via a command line option.  The output will default to stdout, or redirected
to a filename via a command line option.
The columns and rows are specified using python list slicing syntax -
so individual columns or rows can be listed as can ranges.   Inclusion
or exclusion logic can be used - and even combined.
Examples:
$ gristle_slicer -i sample.csv
Prints all rows and columns
$ gristle_slicer -i sample.csv -c":5, 10:15, dept" -C 13
Prints columns 0-4 and 10,11,12,14, and the col associated
with the header field 'dept' for all records
$ gristle_slicer -i sample.csv -C:-1
Prints all columns except for the last for all records
$ gristle_slicer -i sample.csv -c:5 -r-100
Prints columns 0-4 for the last 100 records
$ gristle_slicer -i sample.csv -c:5 -r-100 -d'|' --quoting=quote_all
Prints columns 0-4 for the last 100 records, csv
dialect info (delimiter, quoting) provided manually)
$ cat sample.csv | gristle_slicer -c:5 -r-100 -d'|' --quoting=quote_all
Prints columns 0-4 for the last 100 records, csv
dialect info (delimiter, quoting) provided manually)
Many more examples can be found here:
https://github.com/kenfar/DataGristle/tree/master/examples/gristle_slicer

gristle_freaker

Creates a frequency distribution of values from columns of the input file
and prints it out in columns - the first being the unique key and the last
being the count of occurances.
Examples:
$ gristle_freaker -i sample.csv -c 0
Creates two columns from the input - the first with
unique keys from column 0, the second with a count of
how many times each exists.
$ gristle_freaker -i sample.csv -c home_state
This is the same as the previous example - but in this case
the column reference uses the name of the field from the
file header.
$ gristle_freaker -i sample.csv -d '|'  -c 0 --sortcol 1 --sortorder forward --writelimit 25
In addition to what was described in the first example,
this example adds sorting of the output by count ascending
and just prints the first 25 entries.
$ gristle_freaker -i sample.csv -d '|'  -c 0,1
Creates three columns from the input - the first two
with unique key combinations from columns 0 & 1, the
third with the number of times each combination exists.
Many more examples can be found here:
https://github.com/kenfar/DataGristle/tree/master/examples/gristle_freaker

gristle_sorter

Provides a csv dialect-aware sort that can safely handle delimiters, quotes, and newlines
within fields.
Examples:
$ gristle_sorter -i sample.csv -k 0sf -D
Sort file by the 0-position string column in forward (ascending) direction,
dedupes the results and writes them to stdout.  The csv dialect is auto-
detected.
$ gristle_sorter -i sample.csv -k 0sf dept-s-r -D
This example uses the optional tildes to separate the parts of the key,
and uses a fieldname reference from the file header (dept) rather than a
numeric field position.
$ gristle_sorter -i sample.csv --keys 0sf 3ir --outfile sample_out.csv
Sorts file by the 0-position column string in forward direction followed
by the position 3 column integer in reverse direction.  The output is not
deduped, but is written to a file.  The csv dialect is auto-detected.
$ gristle_sorter -i sample.csv -k 0sf -d '|' -q quote_all --doublequote --has-header
Sort file by the 0-position string column in forward (ascending) direction,
specifies the csv dialect explicitly, including that the file has a header
that will be written to the top of the output file.
Many more examples can be found here:
https://github.com/kenfar/DataGristle/tree/master/examples/gristle_sorter

gristle_profiler

Analyzes the structures and contents of csv files in the end producing a
report of its findings.  It is intended to speed analysis of csv files by
automating the most common and frequently-performed analysis tasks.  It's
useful in both understanding the format and data and quickly spotting issues.
Examples:
$ gristle_profiler --infiles japan_station_radiation.csv
This command will analyze a file with radiation measurements
from various Japanese radiation stations.
File Structure:
format type:       csv
field cnt:         4
record cnt:        100
has header:        True
delimiter:
csv quoting:       False
skipinitialspace:  False
quoting:           QUOTE_NONE
doublequote:       False
quotechar:         "
lineterminator:    '\n'
escapechar:        None

Field Analysis Progress:
Analyzing field: 0
Analyzing field: 1
Analyzing field: 2
Analyzing field: 3

Fields Analysis Results:

    ------------------------------------------------------
    Name:             station_id
    Field Number:     0
    Wrong Field Cnt:  0
    Type:             timestamp
    Min:              1010000001
    Max:              1140000006
    Unique Values:    99
    Known Values:     99
    Top Values not shown - all values are unique

    ------------------------------------------------------
    Name:             datetime_utc
    Field Number:     1
    Wrong Field Cnt:  0
    Type:             timestamp
    Min:              2011-02-28 15:00:00
    Max:              2011-02-28 15:00:00
    Unique Values:    1
    Known Values:     1
    Top Values:
        2011-02-28 15:00:00                      x 99 occurrences

    ------------------------------------------------------
    Name:             sa
    Field Number:     2
    Wrong Field Cnt:  0
    Type:             integer
    Min:              -999
    Max:              52
    Unique Values:    35
    Known Values:     35
    Mean:             2.45454545455
    Median:           38.0
    Variance:         31470.2681359
    Std Dev:          177.398613681
    Top Values:
        41                                       x 7 occurrences
        42                                       x 7 occurrences
        39                                       x 6 occurrences
        37                                       x 5 occurrences
        46                                       x 5 occurrences
        17                                       x 4 occurrences
        38                                       x 4 occurrences
        40                                       x 4 occurrences
        45                                       x 4 occurrences
        44                                       x 4 occurrences

    ------------------------------------------------------
    Name:             ra
    Field Number:     3
    Wrong Field Cnt:  0
    Type:             integer
    Min:              -888
    Max:              0
    Unique Values:    2
    Known Values:     2
    Mean:             -556.121212121
    Median:           -888.0
    Variance:         184564.833792
    Std Dev:          429.610095077
    Top Values:
        -888                                     x 62 occurrences
        0                                        x 37 occurrences

Many more examples can be found here:
https://github.com/kenfar/DataGristle/tree/master/examples/gristle_profiler

gristle_converter

Converts a file from one csv dialect to another
Examples:
$ gristle_converter -i foo.csv -o bar.csv 

--delimiter=',' --has-header --quoting=quote-all doublequote 

--out-delimiter='|'  --out-has-no-header --out-quoting quote_none --out-escapechar=''
Copies input file to output while completely changing every aspect
of the csv dialect.
Many more examples can be found here:
https://github.com/kenfar/DataGristle/tree/master/examples/gristle_converter

gristle_validator

Splits a csv file into two separate files based on how records pass or fail
validation checks:
   - Field count - checks the number of fields in each record against the
     number required.  The correct number of fields can be provided in an
     argument or will default to using the number from the first record.
   - Schema - uses csv file requirements defined in a json-schema file for
     quality checking.  These requirements include the number of fields,
     and for each field - the type, min & max length, min & max value,
     whether or not it can be blank, existance within a list of valid
     values, and finally compliance with a regex pattern.
The output can just be the return code (0 for success, 1+ for errors), can
be some high level statistics, or can be the csv input records split between
good and erroneous files.  Output can also be limited to a random subset.
Examples:
$ gristle_validator  -i sample.csv -f 3
Prints all valid input rows to stdout, prints all records with
other than 3 fields to stderr along with an extra final field that
describes the error.
$ gristle_validator  -i sample.csv
Prints all valid input rows to stdout, prints all records with
other than the same number of fields found on the first record to
stderr along with an extra final field that describes the error.
$ gristle_validator  -i sample.csv  -d '|' --has-header
Same comparison as above, but in this case the file was too small
or complex for the pgm to automatically determine csv dialect, so
we had to explicitly give that info to program.
$ gristle_validator  -i sample.csv -o sample_good.csv --outerr sample_err.csv
Same comparison as above, but explicitly splits good and bad data
into separate files.
$ gristle_validator  -i sample.csv --randomout 1
Same comparison as above, but only writes a random 1% of data out.
$ gristle_validator  -i sample.csv --silent
Same comparison as above, but writes nothing out.  Exit code can be
used to determine if any bad records were found.
$ gristle_validator  -i sample.csv --validschema sample_schema.csv
The above command checks both field count as well as validations
described in the sample_schema.csv file.  Here's an example of what
that file might look like:
items:
- title:            rowid
blank:            False
required:         True
dg_type:          integer
dg_minimum:       1
dg_maximum:       60
- title:            start_date
blank:            False
minLength:        8
maxLength:        10
pattern:          '[0-9]/[0-9]/[1-2][0-9][0-9][0-9]'
- title:            location
blank:            False
minLength:        2
maxLength:        2
enum:             ['ny','tx','ca','fl','wa','ga','al','mo']

gristle_viewer

Displays a single record of a file, one field per line, with field names
displayed as labels to the left of the field values.  Also allows simple
navigation between records.
Examples:
$ gristle_viewer -i sample.csv -r 3
Presents the third record in the file with one field per line
and field names from the header record as labels in the left
column.
$ gristle_viewer -i sample.csv -r 3  -d '|' -q quote_none
In addition to what was described in the first example this
adds explicit csv dialect overrides.
Many more examples can be found here:
https://github.com/kenfar/DataGristle/tree/master/examples/gristle_viewer

gristle_differ

gristle_differ compares two files, typically an old and a new file, based
on explicit keys in a way that is far more accurate than diff.  It can also
compare just subsets of columns, and perform post-delta transforms to
populate fields with static values, values from other fields, variables
from the command line, or incrementing sequence numbers.
More info on the wiki here:  https://github.com/kenfar/DataGristle/wiki/gristle_differ
Examples:
$ gristle_differ --infiles file0.dat file1.dat --key-cols 0 2 --ignore_cols  19 22 33
    - Sorts both files on columns 0 & 2
    - Dedupes both files on column 0
    - Compares all fields except fields 19,22, and 23
    - Automatically determines the csv dialect
    - Produces the following files:
       - file1.dat.insert
       - file1.dat.delete
       - file1.dat.same
       - file1.dat.chgnew
       - file1.dat.chgold

$ gristle_differ --infiles file0.dat file1.dat --key-cols 0 --compare-cols 1 2 3 4 5 6 7  -d '|'
    - Sorts both files on columns 0
    - Dedupes both files on column 0
    - Compares fields 1,2,3,4,5,6,7
    - Uses '|' as the field delimiter
    - Produces the same output file names as example 1.

$ gristle_differ --infiles file0.dat file1.dat --config-fn ./foo.yml  

--variables batchid:919 --variables pkid:82304
    - Produces the same output file names as example 1.
    - But in this case it gets the majority of its configuration items from
      the config file ('foo.yml').  This could include key columns, comparison
      columns, ignore columns, post-delta transformations, and other information.
    - The two variables options are used to pass in user-defined variables that
      can be referenced by the post-delta transformations.  The batchid will get
      copied into a batch_id column for every file, and the pkid is a sequence
      that will get incremented and used for new rows in the insert, delete and
      chgnew files.

Many more examples can be found here:
https://github.com/kenfar/DataGristle/tree/master/examples/gristle_differ

gristle_metadata

Gristle_metadata provides a command-line interface to the metadata database.
It's mostly useful for scripts, but also useful for occasional direct
command-line access to the metadata.
Examples:
$ gristle_metadata --table schema --action list
Prints a list of all rows for the schema table.
$ gristle_metadata --table element --action put --prompt
Allows the user to input a row into the element table and
prompts the user for all fields necessary.

gristle_md_reporter

Gristle_md_reporter allows the user to create data dictionary reports that
combine information about the collection and fields along with field value
descriptions and frequencies.
Examples:
$ gristle_md_reporter --report datadictionary --collection_id 2
Prints a data dictionary report of collection_id 2.
$ gristle_md_reporter --report datadictionary --collection_name presidents
Prints a data dictionary report of the president collection.
$ gristle_md_reporter --report datadictionary --collection_id 2 --field_id 3
Prints a data dictionary report of the president collection,
only shows field-level information for field_id 3.

gristle_dir_merger

Gristle_dir_merger consolidates directory structures of files.  Is both fast
and flexible with a variety of options for choosing which file to use based
on full (name and md5) and partial matches (name only) .
Examples
$ gristle_dir_merger /tmp/foo /data/foo
- Compares source of /tmp/foo to dest of /data/foo.
- Files will be consolidated into /data/foo, and deleted from /tmp/foo.
- Comparison will be: match-on-name-and-md5 (default)
- Full matches will use: keep_dest (default)
- Partial matches will use: keep_newest (default)
- Bottom line: this is what you normally want.
$ gristle_dir_merger /tmp/foo /data/foo --dry-run
- Same as the first example - except it only prints what it would do
without actually doing it.
- Bottom line: this is a good step to take prior to running it for real.
$ gristle_dir_merger /tmp/foo /data/foo -r
- Same as the first example - except it runs recursively through
the directories.
$ gristle_dir_merger /tmp/foo /data/foo --on-partial-match keep-biggest
- Comparison will be: match-on-name-and-md5 (default)
- Full matches will use: keep_dest (default)
- Partial matches will use: keep_biggest (override)
- Bottom line: this is a good combo if you know that some files
have been modified on both source & dest, and newest isn't the best.
$ gristle_dir_merger /tmp/foo /data/foo --match-on-name-only --on-full-match keep-source
- Comparison will be: match-on-name-only (override)
- Full matches will use: keep_source (override)
- Bottom line: this is a good way to go if you have
files that have changed in both directories, but always want to
use the source files.

Licensing

• Gristle uses the BSD license - see the separate LICENSE file for further information

Copyright

• Copyright 2011-2021 Ken Farmer

V0.2.2 - 2021-05

• Improvement: the field-names from headers can now be used instead of column offsets for gristle_sorter, gristle_freaker, gristle_profiler, and gristle_slicer.

• Improvement: The use of the header now follows four simple rules:

  • It can be referred to as row 0 when it makes sense - like with gristle_slicer & gristle_viewer.
  • It will be passed through when it makes sense - like with gristle_sorter.
  • It will be used to translate field names to offsets for configuration.
  • But will otherwise be ignored.

• Bug Fix: gristle_freaker was failing with 0-length files when using col-type=each

• Bug Fix: gristle_sorter was failing with some multi-directional sorts

V0.2.1 - 2021-04

• Improvement: added gristle_sorter as a script to install in the system so that it is available to users.

V0.2.0 - 2021-04

• Improvement: Now supports python versions 3.8 and 3.9.

• Improvement: All csv programs now support envvars and config files for input and can generate config files.

• Improvement: Programs always autodetect file csv dialect before applying user overrides - except for piped-in data.

• BREAKING CHANGE: dropped support for python version 3.7

• BREAKING CHANGES to all csv programs:

  • Various changes to names of options for consistency, with older versions caught with an error msg to provides new name.
  • Various changes to csv dialect handling for consistency and correct handling of escapechar, doublequoting, skipinitialspace.

v0.1.7 - 2020-07

• Improvement: now supports python versions 3.7 and 3.8

• BREAKING CHANGE: dropped support for python version 3.6

• Bumped versions on dependent modules to eliminate vulnerabilities

• gristle_differ

  • BREAKING CHANGE: col_names renamed to col-names for consistency
  • Fixes –already-unix option bug with file parsing
  • Fixes –stats bug with empty files
  • Improvement: added ability to use column names from file headers
  • Improvement: if a key-col is in the ignore-cols - it will simply be ignored, and the program will continue processing.
  • Improvement: if a key-col is in the compare-cols - it will simply be ignored, and the program will continue processing.
  • Improvement: if neither compare or ignore cols are provided it will use all cols as compare-cols and continue processing.
  • Improvement: CLI help is updated to provide more details and accurate examples of these options.

v0.1.6 - 2019-02

• upgraded to support python3.7

v0.1.5 - 2018-05

• fixed setup.py bug in which pip10 no longer includes req module

v0.1.4 - 2017-12

• fixed gristle_validator bug in which checks on dg_maximum were not being run

v0.1.3 - 2017-08

• additional improvements to code quality, but with some breaking changes

• changed argument handling for multiple utilities to simplify code and get more consistency.

  • affects: gristle_freaker, gristle_slicer, and gristle_viewer
  • This means words are separated by hyphens, not underscores. –sortorder is –sort-order.

• changed file handling for multiple utilities to simplify code and get more consistency.

  • affects: gristle_freaker, gristle_slicer, gristle_validator, and gristle_viewer
  • This means that behavior in handling multiple files, piped input, and other edge cases is more consistent between utilities.

v0.1.2 - 2017-06

• long-overdue code quality updates

v0.1.1 - 2017-05

• upgraded to use python3.6
• changed versioning format, which has broken pypy for history

v0.59 - 2016-11

• gristle_differ

  • totally rewritten. Can now handle very large files, perform post-transform transformations, handle more complex comparisons, and use column names rather than just positions.

• gristle_determinator

  • added read-limit argument. This allows the tool to be easily run against a subset of a very large input file.

• gristle_scalar

  • removed from toolkit. There are better tools in other solutions can be used instead. This tool may come back again later, but only if enormously rewritten.

• gristle_filter

  • removed from toolkit. There are better tools in other solutions can be used instead. This tool may come back again later, but only if enormously rewritten.

• minor:

  • gristle_md_reporter - slight formatting change: text descriptions of fields are now included, and column widths were tweaked.
  • all utilities - a substantial performance improvement for large files when quoting information is not provided.

v0.58 - 2014-08

• gristle_dir_merger

  • initial addition to toolkit. Merges directories of files using a variety of matching criteria and matching actions.

v0.57 - 2014-07

• gristle_processor

  • initial addition to toolkit. Provides ability to scan through directory structure recursively, and delete files that match config criteria.

v0.56 - 2014-03

• gristle_determinator

  • added hasnoheader arg
  • fixed problem printing top_values on empty file with header

• gristle_validator

  • added hasnoheader arg

• gristle_freaker

  • added hasnoheader arg

v0.55 - 2014-02

• gristle_determinator - fixed a few problems:

  • the ‘Top Values not shown - all unique’ message being truncated
  • floats not handled correctly for stddev & variance
  • quoted ints & floats not handled

v0.54 - 2014-02

• gristle_validator - major updates to allow validation of csv files based on the json schema standard, with help from the Validictory module.

v0.53 - 2014-01

• gristle_freaker - major updates to enable distributes on all columns to be automatically gathered through either (all or each) args. ‘All’ combines all columns into a single tuple prior to producing distribution. ‘Each’ creates a separate distribution for every column within the csv file.
• travisci - added support and started using this testing service.