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A generic TSV-style format based intermodular communication framework and REST API

Project description

xtsv – A generic TSV-style format based intermodular communication framework and REST API implemented in Python

  • inter-module communication via a TSV-style format
    • processing can be started or stopped at any module
    • module dependency checks before processing
    • easy to add new modules
    • multiple alternative modules for some tasks
  • easy to use command-line interface
  • convenient REST API with simple web frontend
  • Python library API
  • Can be turned into a docker image and runnable docker form

If a bug is found please leave feedback with the exact details.

Citing and License

xtsv is licensed under the LGPL 3.0 license. The submodules have their own license.

We are currently working on a paper which should be cited when xtsv is used.

Requirements

  • Python 3.5 <=
  • [Optional, if required by any module] PyJNIus and OpenJDK 8 JDK (we are transitioning to OpenJDK 11)

API documentation

  • ModuleError: The exception thrown when something bad happened to the modules (e.g. the module could not be found or the ordering of the modules is not feasible because of the required and supplied fields)
  • HeaderError: The exception thrown when the input could not satisfy the required fields in its header
  • jnius_config: Set JAVA VM options and CLASSPATH for the PyJNIus library
  • build_pipeline(inp_data, used_tools, available_tools, presets, conll_comments=False) -> iterator_on_output_lines: Build the current pipeline from the input data (stream, iterable or string), the list of the elements of the desired pipeline chosen from the available tools and presets returning an output iterator
  • pipeline_rest_api(name, available_tools, presets, conll_comments, singleton_store=None, form_title, doc_link) -> app: Create a Flask application with the REST API and web frontend on the available initialised tools and presets with the desired name. Run with a wsgi server or Flask's built-in server with with app.run() (see REST API section)
  • singleton_store_factory() -> singleton: Singletons can be used for initialisation of modules (eg. when the application is restarted frequently and not all modules are used between restarts)
  • process(stream, initialised_app, conll_comments=False) -> iterator_on_output_lines: A low-level API to run a specific member of the pipeline on a specific input stream, returning an output iterator
  • parser_skeleton(...) -> argparse.ArgumentParser(...): A CLI argument parser skeleton can be further customized when needed
  • add_bool_arg(parser, name, help_text, default=False, has_negative_variant=True): A helper function to easily add BOOL arguments to the ArgumentParser class
  • download(available_models=None, required_models=None): Download all (or a subset of) large model files specified in models.yaml (filename can be changed in the first parameter)

To be defined by the actual pipeline:

  • tools: The list of tools (see configuration for details)
  • presets: The dictionary of shorthands for tasks which are defined as list of tools to be run in a pipeline (see configuration for details)

Data format

The input and output can be one of the following:

  • Free form text file
  • TSV file with fixed column order and without header (like CoNLL-U)
  • TSV file with arbitrary column order where the columns are identified by the TSV header (main format of xtsv)

The TSV files are formatted as follows (closely resembling the CoNLL-U, vertical format):

  • The first line is the header (when the column order is not fixed, therefore the next module identifies columns by their names)
  • Columns are separated by TAB characters
  • One token per line (one column), the other columns contain the information (stem, POS-tag, etc.) of that individual token
  • Sentences are separated by emtpy lines
  • If allowed by settings, zero or more comment lines (e.g. lines starting with hashtag and space) immediately precede the sentences

The fields (represented by TSV columns) are identified by the header in the first line of the input. Each module can (but does not necessarily have to) define:

  • A set of source fields which is required to present in the input
  • A list of target fields which are to be generated to the output in order
    • Newly generated fields are started from the right of the rightmost column, the existing columns should not be modified at all

The following types of modules can be defined by their input and output format requirements:

  • Tokeniser: No source fields, no header, has target fields, free-format text as input, TSV+header output
  • Internal module: Has source fields, has header, has target fields, TSV+header input, TSV+header output
  • Finalizer: Has source fields, no header, no target fields, TSV+header input, free-format text as output
  • Fixed-order TSV importer: No source fields, no header, has target fields, Fixed-order TSV w/o header as input, TSV+header output
  • Fixed-order TSV processor: No source fields, no header, no target fields, Fixed-order TSV w/o header as input, Fixed-order TSV w/o header as output

Creating a module that can be used with xtsv

The following requirements apply for a new module:

  1. It must provide (at least) the mandatory API (see emDummy for a well-documented example)
  2. It must conform to the (to be defined) field-name conventions and the format conventions
  3. It must have an LGPL 3.0 compatible license

The following steps are needed to insert the new module into the pipeline:

  1. Add the new module as submodule to the repository

  2. Insert the configuration in config.py:

    # Setup the tuple:
    #   module name (ending with the filename the class defined in),
    #   class,
    #   friendly name,
    #   args (tuple),
    #   kwargs (dict)
    em_dummy = (
        'emdummy.dummytagger',
        'DummyTagger',
        'EXAMPLE (The friendly name of DummyTagger used in REST API form)',
        ('Params', 'goes', 'here'),
        {
            'source_fields': {'Source field names'},
            'target_fields': ['Target field names']
        }
    )
    
  3. Add the new module to tools list in config.py, optionally also to presets dictionary

    tools = [
        ...,
        (em_dummy, ('dummy-tagger', 'emDummy')),
    ]
    
  4. Test, commit and push

Installation

  • Can be installed as pip package: pip3 install xtsv
  • Or by using the git repository as submodule for another git repository

Usage

Here we present the usage scenarios.

To extend the toolchain with new modules, just add new modules to config.py.

Some examples of the realised applications:

Command-line interface

  • Multiple modules at once (not necessarily starting with raw text):

    echo "Input text." | python3 ./main.py modules,separated,by,comas
    
  • Modules glued together one by one with the standard *nix pipelines where users can interact with the data between the modules:

    echo "Input text." | \
        python3 main.py module | \
        python3 main.py separated | \
        python3 main.py by | \
        python3 main.py comas
    
  • Independently from the other options, xtsv can also be used with input or output streams redirected or with string input (this applies to the runnable docker form as well):

    python3 ./main.py modules,separated,by,comas -i input.txt -o output.txt
    python3 ./main.py modules,separated,by,comas --text "Input text."
    

Docker image

With the appropriate Dockerfile xtsv can be used as follows:

  • Runnable docker form (CLI usage of docker image):

    cat input.txt | docker run -i xtsv-docker task,separated,by,comas > output.txt
    
  • As service through Rest API (docker container)

    docker run --rm -p5000:5000 -it xtsv-docker  # REST API listening on http://0.0.0.0:5000
    

REST API

Server:

  • Docker image (see above)

  • Any wsgi server (uwsgi, gunicorn, waitress, etc.) can be configured to run with a prepared wsgi file .

  • Debug server (Flask) only for development (single threaded, one request at a time):

    When the server outputs a message like * Running on then it is ready to accept requests on http://127.0.0.1:5000. (We do not recommend using this method in production as it is built atop of Flask debug server! Please consider using the Docker image for REST API in production!)

  • Any wsgi server (uwsgi, gunicorn, waitress, etc.) can be configured to run with a prepared wsgi file .

  • Docker image (see above)

Client:

  • Web fronted provided by xtsv

  • From Python (the URL contains the tools to be run separated by /):

    >>> import requests
    >>> # With input file
    >>> r = requests.post('http://127.0.0.1:5000/tools/separated/by/slashes', files={'file': open('input.file', encoding='UTF-8')})
    >>> print(r.text)
    ...
    >>> # With input text
    >>> r = requests.post('http://127.0.0.1:5000/tools/separated/by/slashes', data={'text': 'Input text.'})
    >>> print(r.text)
    ...
    >>> # CoNLL style comments can be enabled per request (disabled by default):
    >>> r = requests.post('http://127.0.0.1:5000/tools/separated/by/slashes', files={'file':open('input.file', encoding='UTF-8')}, data={'conll_comments': True})
    >>> print(r.text)
    ...
    

    The server checks whether the module order is feasible, and returns an error message if there are any problems.

As Python Library

TODO

  1. Install xtsv in xtsv directory or make sure the emtsv installation is in the PYTHONPATH environment variable.

  2. import xtsv

  3. Example:

    import sys
    from xtsv import build_pipeline, jnius_config, process, pipeline_rest_api, singleton_store_factory
    
    jnius_config.classpath_show_warning = False  # To suppress warning
    
    tools = ...
    presets = ...
    
    # Imports end here. Must do only once per Python session
    
    # Set input from any stream or iterable and output stream...
    input_data = sys.stdin
    output_iterator = sys.stdout
    # Raw, or processed TSV input list and output file...
    # input_data = iter(['A kutya', 'elment sétálni.'])  # Raw text line by line
    # Processed data: header and the token POS-tag pairs line by line
    # input_data = iter([['form', 'xpostag'], ['A', '[/Det|Art.Def]'], ['kutya', '[/N][Nom]'], ['elment', '[/V][Pst.NDef.3Sg]'], ['sétálni', '[/V][Inf]'], ['.', '.']])
    # output_iterator = open('output.txt', 'w', encoding='UTF-8')  # File
    # input_data = 'A kutya elment sétálni.'  # Or raw string in any acceptable format.
    
    # Select a predefined task to do or provide your own list of pipeline
    # elements
    used_tools = ['tools', 'in', 'a', 'list']
    
    conll_comments = True  # Enable the usage of CoNLL comments
    
    # Run the pipeline on input and write result to the output...
    output_iterator.writelines(build_pipeline(input_data, used_tools, tools, presets, conll_comments))
    
    # Alternative: Run specific tool for input streams (still in emtsv format).
    # Useful for training a module (see Huntag3 for details):
    output_iterator.writelines(process(sys.stdin, an_inited_tool))
    
    # Or process individual tokens further... WARNING: The header will be the
    # first item in the iterator!
    for tok in build_pipeline(input_data, used_tools, tools, presets, conll_comments):
        if len(tok) > 1:  # Empty line (='\n') means end of sentence
            form, xpostag, *rest = tok.strip().split('\t')  # Split to the expected columns
    
    # Alternative2: Flask application (REST API)
    singleton_store = singleton_store_factory()
    app = application = pipeline_rest_api(name='e-magyar-tsv', available_tools=tools, presets=presets,
                                conll_comments=conll_comments, singleton_store=singleton_store,
                                form_title='e-magyar text processing system',
                                doc_link='https://github.com/dlt-rilmta/emtsv')
    # And run the Flask debug server separately
    app.run()
    

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