jsonextended

JSON Extended

A module to extend the python json package functionality:

• Treat a directory structure like a nested dictionary:
  • lightweight plugin system: define bespoke classes for parsing different file extensions (in-the-box: .json, .csv, .hdf5) and encoding/decoding objects
  • lazy loading: read files only when they are indexed into
  • tab completion: index as tabs for quick exploration of data
• Manipulation of nested dictionaries:
  • enhanced pretty printer
  • Javascript rendered, expandable tree in the Jupyter Notebook
  • functions including; filter, merge, flatten, unflatten, diff
  • output to directory structure (of n folder levels)
• On-disk indexing option for large json files (using the ijson package)
• Units schema concept to apply and convert physical units (using the pint package)

Documentation: https://jsonextended.readthedocs.io

Contents

• JSON Extended
  • Contents
  • Installation
  • Basic Example
  • Creating and Loading Plugins
    • Interface specifications
  • Extended Examples
    • Data Folders JSONisation
    • Nested Dictionary Manipulation
    • Units Schema

Installation

From Conda (recommended):

conda install -c conda-forge jsonextended

From PyPi:

pip install jsonextended

jsonextended has no import dependancies, on Python 3.x and only pathlib2 on 2.7 but, for full functionallity, it is advised to install the following packages:

conda install -c conda-forge ijson numpy pint h5py pandas

Basic Example

from jsonextended import edict, plugins, example_mockpaths

Take a directory structure, potentially containing multiple file types:

datadir = example_mockpaths.directory1
print(datadir.to_string(indentlvl=3,file_content=True))

Folder("dir1")
   File("file1.json") Contents:
    {"key2": {"key3": 4, "key4": 5}, "key1": [1, 2, 3]}
   Folder("subdir1")
     File("file1.csv") Contents:
       # a csv file
      header1,header2,header3
      val1,val2,val3
      val4,val5,val6
      val7,val8,val9
     File("file1.literal.csv") Contents:
       # a csv file with numbers
      header1,header2,header3
      1,1.1,string1
      2,2.2,string2
      3,3.3,string3
   Folder("subdir2")
     Folder("subsubdir21")
       File("file1.keypair") Contents:
         # a key-pair file
        key1 val1
        key2 val2
        key3 val3
        key4 val4

Plugins can be defined for parsing each file type (see Creating Plugins section):

plugins.load_builtin_plugins('parsers')
plugins.view_plugins('parsers')

{'csv.basic': 'read *.csv delimited file with headers to {header:[column_values]}',
 'csv.literal': 'read *.literal.csv delimited files with headers to {header:column_values}, with number strings converted to int/float',
 'hdf5.read': 'read *.hdf5 (in read mode) files using h5py',
 'json.basic': 'read *.json files using json.load',
 'keypair': "read *.keypair, where each line should be; '<key> <pair>'"}

LazyLoad then takes a path name, path-like object or dict-like object, which will lazily load each file with a compatible plugin.

lazy = edict.LazyLoad(datadir)
lazy

{file1.json:..,subdir1:..,subdir2:..}

Lazyload can then be treated like a dictionary, or indexed by tab completion:

list(lazy.keys())

['subdir1', 'subdir2', 'file1.json']

lazy[['file1.json','key1']]

[1, 2, 3]

lazy.subdir1.file1_literal_csv.header2

[1.1, 2.2, 3.3]

For pretty printing of the dictionary:

edict.pprint(lazy,depth=2)

file1.json:
  key1: [1, 2, 3]
  key2: {...}
subdir1:
  file1.csv: {...}
  file1.literal.csv: {...}
subdir2:
  subsubdir21: {...}

Numerous functions exist to manipulate the nested dictionary:

edict.flatten(lazy.subdir1)

{('file1.csv', 'header1'): ['val1', 'val4', 'val7'],
 ('file1.csv', 'header2'): ['val2', 'val5', 'val8'],
 ('file1.csv', 'header3'): ['val3', 'val6', 'val9'],
 ('file1.literal.csv', 'header1'): [1, 2, 3],
 ('file1.literal.csv', 'header2'): [1.1, 2.2, 3.3],
 ('file1.literal.csv', 'header3'): ['string1', 'string2', 'string3']}

LazyLoad parses the plugins.decode function to parser plugin's read_file method (keyword 'object_hook'). Therefore, bespoke decoder plugins can be set up for specific dictionary key signatures:

print(example_mockpaths.jsonfile2.to_string())

File("file2.json") Contents:
{"key1":{"_python_set_": [1, 2, 3]},"key2":{"_numpy_ndarray_": {"dtype": "int64", "value": [1, 2, 3]}}}

edict.LazyLoad(example_mockpaths.jsonfile2).to_dict()

{u'key1': {u'_python_set_': [1, 2, 3]},
 u'key2': {u'_numpy_ndarray_': {u'dtype': u'int64', u'value': [1, 2, 3]}}}

plugins.load_builtin_plugins('decoders')
plugins.view_plugins('decoders')

{'decimal.Decimal': 'encode/decode Decimal type',
 'numpy.ndarray': 'encode/decode numpy.ndarray',
 'pint.Quantity': 'encode/decode pint.Quantity object',
 'python.set': 'decode/encode python set'}

dct = edict.LazyLoad(example_mockpaths.jsonfile2).to_dict()
dct

{u'key1': {1, 2, 3}, u'key2': array([1, 2, 3])}

This process can be reversed, using encoder plugins:

plugins.load_builtin_plugins('encoders')
plugins.view_plugins('encoders')

{'decimal.Decimal': 'encode/decode Decimal type',
 'numpy.ndarray': 'encode/decode numpy.ndarray',
 'pint.Quantity': 'encode/decode pint.Quantity object',
 'python.set': 'decode/encode python set'}

import json
json.dumps(dct,default=plugins.encode)

'{"key2": {"_numpy_ndarray_": {"dtype": "int64", "value": [1, 2, 3]}}, "key1": {"_python_set_": [1, 2, 3]}}'

Creating and Loading Plugins

from jsonextended import plugins, utils

Plugins are recognised as classes with a minimal set of attributes matching the plugin category interface:

plugins.view_interfaces()

{'decoders': ['plugin_name', 'plugin_descript', 'dict_signature'],
 'encoders': ['plugin_name', 'plugin_descript', 'objclass'],
 'parsers': ['plugin_name', 'plugin_descript', 'file_regex', 'read_file']}

plugins.unload_all_plugins()
plugins.view_plugins()

{'decoders': {}, 'encoders': {}, 'parsers': {}}

For example, a simple parser plugin would be:

class ParserPlugin(object):
    plugin_name = 'example'
    plugin_descript = 'a parser for *.example files, that outputs (line_number:line)'
    file_regex = '*.example'
    def read_file(self, file_obj, **kwargs):
        out_dict = {}
        for i, line in enumerate(file_obj):
            out_dict[i] = line.strip()
        return out_dict

Plugins can be loaded as a class:

plugins.load_plugin_classes([ParserPlugin],'parsers')
plugins.view_plugins()

{'decoders': {},
 'encoders': {},
 'parsers': {'example': 'a parser for *.example files, that outputs (line_number:line)'}}

Or by directory (loading all .py files):

fobj = utils.MockPath('example.py',is_file=True,content="""
class ParserPlugin(object):
    plugin_name = 'example.other'
    plugin_descript = 'a parser for *.example.other files, that outputs (line_number:line)'
    file_regex = '*.example.other'
    def read_file(self, file_obj, **kwargs):
        out_dict = {}
        for i, line in enumerate(file_obj):
            out_dict[i] = line.strip()
        return out_dict
""")
dobj = utils.MockPath(structure=[fobj])
plugins.load_plugins_dir(dobj,'parsers')
plugins.view_plugins()

{'decoders': {},
 'encoders': {},
 'parsers': {'example': 'a parser for *.example files, that outputs (line_number:line)',
  'example.other': 'a parser for *.example.other files, that outputs (line_number:line)'}}

For a more complex example of a parser, see jsonextended.complex_parsers

Interface specifications

• Parsers:
  • file_regex attribute, a str denoting what files to apply it to. A file will be parsed by the longest regex it matches.
  • read_file method, which takes an (open) file object and kwargs as parameters
• Decoders:
  • dict_signature attribute, a tuple denoting the keys which the dictionary must have, e.g. dict_signature=('a','b') decodes {'a':1,'b':2}
  • from_... method(s), which takes a dict object as parameter. The plugins.decode function will use the method denoted by the intype parameter, e.g. if intype='json', then from_json will be called.
• Encoders:
  • objclass attribute, the object class to apply the encoding to, e.g. objclass=decimal.Decimal encodes objects of that type
  • to_... method(s), which takes a dict object as parameter. The plugins.encode function will use the method denoted by the outtype parameter, e.g. if outtype='json', then to_json will be called.

Extended Examples

For more information, all functions contain doc-strings with tested examples.

Data Folders JSONisation

from jsonextended import ejson, edict, utils

path = utils.get_test_path()
ejson.jkeys(path)

['dir1', 'dir2', 'dir3']

jdict1 = ejson.to_dict(path)
edict.pprint(jdict1,depth=2)

dir1:
  dir1_1: {...}
  file1: {...}
  file2: {...}
dir2:
  file1: {...}
dir3:

edict.to_html(jdict1,depth=2)

To try the rendered JSON tree, output in the Jupyter Notebook, go to : https://chrisjsewell.github.io/

Nested Dictionary Manipulation

jdict2 = ejson.to_dict(path,['dir1','file1'])
edict.pprint(jdict2,depth=1)

initial: {...}
meta: {...}
optimised: {...}
units: {...}

filtered = edict.filter_keys(jdict2,['vol*'],use_wildcards=True)
edict.pprint(filtered)

initial:
  crystallographic:
    volume: 924.62752781
  primitive:
    volume: 462.313764
optimised:
  crystallographic:
    volume: 1063.98960509
  primitive:
    volume: 531.994803

edict.pprint(edict.flatten(filtered))

(initial, crystallographic, volume):   924.62752781
(initial, primitive, volume):          462.313764
(optimised, crystallographic, volume): 1063.98960509
(optimised, primitive, volume):        531.994803

Units Schema

from jsonextended.units import apply_unitschema, split_quantities
withunits = apply_unitschema(filtered,{'volume':'angstrom^3'})
edict.pprint(withunits)

initial:
  crystallographic:
    volume: 924.62752781 angstrom ** 3
  primitive:
    volume: 462.313764 angstrom ** 3
optimised:
  crystallographic:
    volume: 1063.98960509 angstrom ** 3
  primitive:
    volume: 531.994803 angstrom ** 3

newunits = apply_unitschema(withunits,{'volume':'nm^3'})
edict.pprint(newunits)

initial:
  crystallographic:
    volume: 0.92462752781 nanometer ** 3
  primitive:
    volume: 0.462313764 nanometer ** 3
optimised:
  crystallographic:
    volume: 1.06398960509 nanometer ** 3
  primitive:
    volume: 0.531994803 nanometer ** 3

edict.pprint(split_quantities(newunits),depth=4)

initial:
  crystallographic:
    volume:
      magnitude: 0.92462752781
      units:     nanometer ** 3
  primitive:
    volume:
      magnitude: 0.462313764
      units:     nanometer ** 3
optimised:
  crystallographic:
    volume:
      magnitude: 1.06398960509
      units:     nanometer ** 3
  primitive:
    volume:
      magnitude: 0.531994803
      units:     nanometer ** 3