chemdataextractor¶
.config¶
Config file reader/writer.
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chemdataextractor.config.
construct_yaml_str
(self, node)[source]¶ Override the default string handling function to always return unicode objects.
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class
chemdataextractor.config.
Config
(path=None)[source]¶ Bases:
collections.abc.MutableMapping
Read and write to config file.
A config object is essentially a string key-value store that can be treated like a dictionary:
c = Config() c['foo'] = 'bar' print c['foo']
The file location may be specified:
c = Config('~/matt/anotherconfig.yml') c['where'] = 'in a different file'
If no location is specified, the environment variable CHEMDATAEXTRACTOR_CONFIG is checked and used if available. Otherwise, a standard config location is used, which varies depending on the operating system. You can check the location using the
path
property. For more information see https://github.com/ActiveState/appdirsIt is possible to edit the file by hand with a text editor. It is in YAML format.
Warning: multiple instances of Config() pointing to the same file will not see each others’ changes, and will overwrite the entire file when any key is changed.
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path
¶ The path to the config file.
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chemdataextractor.config.
config
= <Config: /home/docs/.config/ChemDataExtractor/chem...¶ Global config instance.
.data¶
Tools for loading and caching data files.
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class
chemdataextractor.data.
Package
(path, server_root=None, remote_path=None, unzip=False, untar=False, custom_download=None)[source]¶ Bases:
object
Data package.
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__init__
(path, server_root=None, remote_path=None, unzip=False, untar=False, custom_download=None)[source]¶ - Parameters:
path (str) – The path to where this package will be located under ChemDataExtractor’s default data directory.
(optional) server_root (str) – The root path for the server. If you do not supply the remote_path parameter, this will be used to find the remote path for the package.
(optional) remote_path (str) – The remote path for the package.
(optional) unzip (bool) – Whether the package should be unzipped after download. You should only ever set this or untar to True.
(optional) untar (bool) – Whether the package should be untarred after download. You should only ever set this or unzip to True.
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remote_path
¶
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local_path
¶
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chemdataextractor.data.
find_data
(path, warn=True, get_data=True)[source]¶ Return the absolute path to a data file within the data directory.
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chemdataextractor.data.
load_model
(path)[source]¶ Load a model from a pickle file in the data directory. Cached so model is only loaded once.
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chemdataextractor.data.
PACKAGES
= [<Package: models/cem_crf-1.0.pickle>, <Package: m...¶ Current active data packages
.errors¶
Error classes for ChemDataExtractor.
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exception
chemdataextractor.errors.
ChemDataExtractorError
[source]¶ Bases:
Exception
Base ChemDataExtractor exception.
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exception
chemdataextractor.errors.
ReaderError
[source]¶ Bases:
chemdataextractor.errors.ChemDataExtractorError
Raised when a reader is unable to read a document.
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exception
chemdataextractor.errors.
ModelNotFoundError
[source]¶ Bases:
chemdataextractor.errors.ChemDataExtractorError
Raised when a model file could not be found.
.utils¶
Miscellaneous utility functions.
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chemdataextractor.utils.
memoize
(obj)[source]¶ Decorator to create memoized functions, methods or classes.
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chemdataextractor.utils.
python_2_unicode_compatible
(klass)[source]¶ Fix __str__, __unicode__ and __repr__ methods under Python 2.