csv-reconcile 0.3.2
OpenRefine reconciliation service backed by csv resource
License: MIT
Requires Python: >=3.7,<4.0
Keywords: OpenRefine,reconcile,fuzzy search

-   <a href="#csv-reconcile" id="toc-csv-reconcile">CSV Reconcile</a>
    -   <a href="#quick-start" id="toc-quick-start">Quick start</a>
    -   <a href="#poetry" id="toc-poetry">Poetry</a>
        -   <a href="#prerequesites" id="toc-prerequesites">Prerequesites</a>
        -   <a href="#running" id="toc-running">Running</a>
        -   <a href="#building" id="toc-building">Building</a>
    -   <a href="#description" id="toc-description">Description</a>
    -   <a href="#usage" id="toc-usage">Usage</a>
        -   <a href="#initialization" id="toc-initialization">Initialization</a>
        -   <a href="#running-the-service" id="toc-running-the-service">Running the
            service</a>
        -   <a href="#deprecated" id="toc-deprecated">Deprecated</a>
    -   <a href="#common-configuration" id="toc-common-configuration">Common
        configuration</a>
    -   <a href="#built-in-preview-service"
        id="toc-built-in-preview-service">Built-in preview service</a>
    -   <a href="#scoring-plugins" id="toc-scoring-plugins">Scoring plugins</a>
        -   <a href="#implementing" id="toc-implementing">Implementing</a>
        -   <a href="#installing" id="toc-installing">Installing</a>
        -   <a href="#using" id="toc-using">Using</a>
        -   <a href="#known-plugins" id="toc-known-plugins">Known plugins</a>
    -   <a href="#testing" id="toc-testing">Testing</a>
        -   <a href="#tests-layout" id="toc-tests-layout">Tests layout</a>
        -   <a href="#running-tests" id="toc-running-tests">Running tests</a>
    -   <a href="#future-enhancements" id="toc-future-enhancements">Future
        enhancements</a>

# CSV Reconcile

A [reconciliation service](https://github.com/reconciliation-api/specs)
for [OpenRefine](https://openrefine.org/) based on a CSV file similar to
[reconcile-csv](http://okfnlabs.org/reconcile-csv/). This one is written
in Python and has some more configurability.

## Quick start

-   Clone this repository

-   Run the service

        $ python -m venv venv                                             # create virtualenv
        $ venv/bin/pip install csv-reconcile                              # install package
        $ source venv/bin/activate                                        # activate virtual environment
        (venv) $ csv-reconcile init sample/reps.tsv item itemLabel        # initialize the service
        (venv) $ csv-reconcile serve                                      # run the service
        (venv) $ deactivate                                               # remove virtual environment

The service is run at <http://127.0.0.1:5000/reconcile>. You can point
at a different host:port by adding
[SERVER\_NAME](https://flask.palletsprojects.com/en/0.12.x/config/) to
the sample.cfg. Since this is running from a virtualenv, you can simply
delete the whole lot to clean up.

If you have a C compiler installed you may prefer to install the sdist
`dist/csv-reconcile-0.1.0.tar.gz` which will build a
[Cython](https://cython.readthedocs.io/en/latest/) version of the
computationally intensive fuzzy match routine for speed. With `pip` add
the option `--no-binary csv-reconcile`.

## Poetry

### Prerequesites

You'll need to have both [poetry](https://python-poetry.org/docs/) and
[poethepoet](https://pypi.org/project/poethepoet/0.0.3/) installed. For
publishing to [PyPI](https://pypi.org/) [pandoc](https://pandoc.org/) is
required.

### Running

This is packaged with [poetry](https://python-poetry.org/docs/), so you
can use those commands if you have it installed.

    $ poe install
    $ poetry run csv-reconcile init sample/reps.tsv item itemLabel
    $ poetry run csv-reconcile serve

### Building

Because this package uses a `README.org` file and `pip` requires a
`README.md`, there are extra build steps beyond what `poetry` supplies.
These are managed using
[poethepoet](https://pypi.org/project/poethepoet/0.0.3/). Thus building
is done as follows:

    $ poe build

If you want to build a platform agnostic wheel, you'll have to comment
out the `build =
    "build.py"` line from `pyproject.toml` until `poetry` supports
[selecting build
platform](https://github.com/python-poetry/poetry/issues/3594).

## Description

This reconciliation service uses [Dice coefficient
scoring](https://en.wikipedia.org/wiki/S%C3%B8rensen%E2%80%93Dice_coefficient)
to reconcile values against a given column in a
[CSV](https://en.wikipedia.org/wiki/Comma-separated_values) file. The
CSV file must contain a column containing distinct values to reconcile
to. We'll call this the *id column*. We'll call the column being
reconciled against the *name column*.

For performance reasons, the *name column* is preprocessed to normalized
values which are stored in an
[sqlite](https://www.sqlite.org/index.html) database. This database must
be initialized at least once by running the init sub-command. Once
initialized this need not be run for subsequent runs.

Note that the service supplies all its data with a dummy *type* so there
is no reason to reconcile against any particular *type*.

In addition to reconciling against the *name column*, the service also
functions as a [data extension
service](https://reconciliation-api.github.io/specs/latest/#data-extension-service),
which offers any of the other columns of the CSV file.

Note that Dice coefficient scoring is agnostic to word ordering.

## Usage

Basic usage involves two steps:

-   initialization
-   running the service

Initialization primes the database with the data processed from the CSV
file with the `init` subcommand. There are several options for running
the service as described below.

### Initialization

Basic usage of the `init` sub-command requires passing the name of the
CSV file, the *id column* and the *name column*.

    (venv) $ csv-reconcile --help
    Usage: csv-reconcile [OPTIONS] COMMAND [ARGS]...

    Options:
      --help  Show this message and exit.

    Commands:
      init
      run
      serve
    (venv) $ csv-reconcile init --help
    Usage: csv-reconcile init [OPTIONS] CSVFILE IDCOL NAMECOL

    Options:
      --config TEXT  config file
      --scorer TEXT  scoring plugin to use
      --help         Show this message and exit.
    (venv) $ poetry run csv-reconcile serve --help
    Usage: csv-reconcile serve [OPTIONS]

    Options:
      --help         Show this message and exit.
    (venv) $

The `--config` option is used to point to a configuration file. The file
is a [Flask
configuration](https://flask.palletsprojects.com/en/1.1.x/config/) and
hence is Python code though most configuration is simply setting
variables to constant values.

### Running the service

The simplest way to run the service is to use Flask's built-in web
server with the `serve` subcommand which takes no arguments. However, as
mentioned in the [Flask
documentation](https://flask.palletsprojects.com/en/2.0.x/deploying/),
this server is not suitable for production purposes.

For a more hardened service, you can use one of the other deployment
options mentioned in that documentation. For example, gunicorn can be
run as follows:

    (venv) $ gunicorn -w 4 'csv_reconcile:create_app()'
    1-11-16 17:40:20 +0900] [84625] [INFO] Starting gunicorn 20.1.0
    1-11-16 17:40:20 +0900] [84625] [INFO] Listening at: http://127.0.0.1:8000 (84625)
    1-11-16 17:40:20 +0900] [84625] [INFO] Using worker: sync
    1-11-16 17:40:20 +0900] [84626] [INFO] Booting worker with pid: 84626
    1-11-16 17:40:20 +0900] [84627] [INFO] Booting worker with pid: 84627
    1-11-16 17:40:20 +0900] [84628] [INFO] Booting worker with pid: 84628
    1-11-16 17:40:20 +0900] [84629] [INFO] Booting worker with pid: 84629
    ...

One thing to watch out for is that the default manifest points the
extension service to port 5000, the default port for the Flask built-in
web server. If you want to use the extension service when deploying to a
different port, you'll want to be sure to override that part of the
manifest in your config file. You'll need something like the following:

    MANIFEST = {
        "extend": {
            "propose_properties": {
                "service_url": "http://localhost:8000",
                "service_path": "/properties"
            }
        }
    }

Note also that the configuration is saved during the `init` step. If you
change the config, you'll need to re-run that step. You may also need to
delete and re-add the service in OpenRefine.

### Deprecated

The `run` subcommand mimics the old behavior which combined the
initialization step with the running of the service. This may be removed
in a future release.

## Common configuration

-   `SERVER_NAME` - The host and port the service is bound to. e.g.
    `SERVER_NAME=localhost:5555`. ( Default localhost:5000 )
-   `CSVKWARGS` - Arguments to pass to
    [csv.reader](https://docs.python.org/3/library/csv.html). e.g.
    `CSVKWARGS={'delimiter': ',', 'quotechar': '"'}` for comma delimited
    files using `"` as quote character.
-   `CSVENCODING` - Encoding of the CSV file. e.g.
    `CSVENCODING="utf-8-sig"` is the encoding used for data downloaded
    from
    [GNIS](https://www.usgs.gov/core-science-systems/ngp/board-on-geographic-names/download-gnis-data).
-   `SCOREOPTIONS` - Options passed to scoring plugin during
    normalization. e.g.
    `SCOREOPTIONS={'stopwords':['lake','reservoir']}`
-   `LIMIT` - The maximum number of reonciliation candidates returned
    per entry. ( Default 10 ) e.g. `LIMIT=10`
-   `THRESHOLD` - The minimum score for returned reconciliation
    candidates. ( Default 30.0 ) e.g. `THRESHOLD=80.5`
-   `DATABASE` - The name of the generated sqlite database containing
    pre-processed values. (Default `csvreconcile.db`) e.g.
    `DATABASE='lakes.db'` You may want to change the name of the
    database if you regularly switch between databases being used.
-   `MANIFEST` - Overrides for the service manifest. e.g.
    `MANIFEST={"name": "My service"}` sets the name of the service to
    "My service".

This last is most interesting. If your data is coming from
[Wikidata](https://www.wikidata.org) and your *id column* contains [Q
values](https://www.wikidata.org/wiki/Help:Items), then a manifest like
the following will allow your links to be clickable inside OpenRefine.

    MANIFEST = {
      "identifierSpace": "http://www.wikidata.org/entity/",
      "schemaSpace": "http://www.wikidata.org/prop/direct/",
      "view": {"url":"https://www.wikidata.org/wiki/{{id}}"},
      "name": "My reconciliation service"
    }

If your CSV is made up of data taken from another [reconciliation
service](https://reconciliation-api.github.io/testbench/), you may
similiarly copy parts of their manifest to make use of their features,
such as the [preview
service](https://reconciliation-api.github.io/specs/latest/#preview-service).
See the reconciliation spec for details.

## Built-in preview service

There is a preview service built into the tool. (Thanks
[b2m](https://github.com/b2m)!) You can turn it on by adding the
following to your manifest:

    "preview": {
       "url": "http://localhost:5000/preview/{{id}}",
       "width": 400,
       "height": 300
    }

Note that if you reconcile against a service with a preview service
enabled, a link to the service becomes part of the project. Thus if you
bring the service down, your project will have hover over pop-ups to an
unavailable service. One way around this is to copy the `recon.match.id`
to a new column which can be re-reconciled to the column by id if you
bring the service back up again whether or not you have preview service
enabled. (Perhaps OpenRefine could be smarter about enabling this
pop-ups only when the service is active.)

## Scoring plugins

As mentioned above the default scoring method is to use [Dice
coefficient
scoring](https://en.wikipedia.org/wiki/S%C3%B8rensen%E2%80%93Dice_coefficient),
but this method can be overridden by implementing a
`cvs_reconcile.scorers` plugin.

### Implementing

A plugin module may override any of the methods in the
`csv_reconcile.scorers` module by simply implementing a method of the
same name with the decorator `@cvs_reconcile.scorer.register`.

See `csv_reconcile_dice` for how Dice coefficient scoring is
implemented.

The basic hooks are as follows:

-   `normalizedWord(word, **scoreOptions)` preprocesses values to be
    reconciled to produce a tuple used in fuzzy match scoring. The value
    of `SCOREOPTIONS` in the configuration will be passed in to allow
    configuration of this preprocessing. This hook is required.
-   `normalizedRow(word, row, **scoreOptions)` preprocesses values to be
    reconciled against to produce a tuple used in fuzzy match scoring.
    Note that both the reconciled column and the entire row is available
    for calculating the normalized value and that the column reconciled
    against is required even when not used. The value of `SCOREOPTIONS`
    in the configuration will be passed in to allow configuration of
    this preprocessing. This defaults to calling
    normalizeWord(word,\*\*scoreOptions).
-   `getNormalizedFields()` returns a tuple of names for the columns
    produced by `normalizeWord()`. The length of the return value from
    both functions must match. This defaults to calling
    normalizeWord(word,\*\*scoreOptions). This hook is required.
-   `processScoreOptions(options)` is passed the value of `SCOREOPTIONS`
    to allow it to be adjusted prior to being used. This can be used for
    adding defaults and/or validating the configuration. This hook is
    optional
-   `scoreMatch(left, right, **scoreOptions)` gets passed two tuples as
    returned by `normalizedWord()`. The `left` value is the value being
    reconciled and the `right` value is the value being reconciled
    against. The value of `SCOREOPTIONS` in the configuration will be
    passed in to allow configuration of this preprocessing. Returning a
    score of `None` will not add tested value as a candidate. This hook
    is required.
-   `valid(normalizedFields)` is passed the normalized tuple prior to
    being scored to make sure it's appropriate for the calculation. This
    hook is optional.
-   `features(word, row, **scoreOptions)` calculates
    [features](https://reconciliation-api.github.io/specs/latest/#reconciliation-query-responses)
    using the query string and the normalized row. By default
    calculating features is disabled. Implementions of this hook are
    automatically enabled. This hook is optional.

### Installing

Hooks are automatically discovered as long as they provide a
`csv_reconcile.scorers` [setuptools entry
point](https://setuptools.readthedocs.io/en/latest/userguide/entry_point.html).
Poetry supplies a
[plugins](https://python-poetry.org/docs/pyproject/#plugins)
configuration which wraps the setuptools funtionality.

The default Dice coefficent scoring is supplied via the following
snippet from `pyproject.toml` file.

    [tool.poetry.plugins."csv_reconcile.scorers"]
    "dice" = "csv_reconcile_dice"

Here `dice` becomes the name of the scoring option and
`csv_reconcile_dice` is the package implementing the plugin.

### Using

If there is only one scoring plugin available, that plugin is used. If
there are more than one available, you will be prompted to pass the
`--scorer` option to select among the scoring options.

### Known plugins

See [wiki](https://github.com/gitonthescene/csv-reconcile/wiki) for list
of known plugins.

## Testing

Though I long for the old days when a unit test was a unit test, these
days things are a bit more complicated with various versions of `Python`
and installation of plugins to manage. Now we have to wrestle with
[virtual environments](https://docs.python.org/3/tutorial/venv.html).
`poetry` handles the virtual environment for developing, but testing
involves covering more options.

### Tests layout

The tests directory structure is the following:

    tests
        main
        plugins
            geo

Tests for the main package are found under `main` and don't require
installing any other packages whereas tests under `plugins` require the
installation of the given plugin.

### Running tests

1.  Basic tests

    These tests are written with
    [pytest](https://docs.pytest.org/en/6.2.x/contents.html) and can be
    running through `poetry` as follows:

        $ poetry run pytest

    To avoid the complications that come from installing plugins, there
    is a `poe` script for running only the tests under main which can be
    invoked as follows:

        $ poe test

    For steady state developing this is probably the command you'll use
    most often.

2.  Build matrices

    The GitHub Actions for this project currently use a [build
    matrix](https://docs.github.com/en/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix)
    across a couple of architectures and several versions of `Python`,
    but a similar effect can be achieved using
    [nox](https://nox.thea.codes/en/stable/tutorial.html).

    `nox` manages the creation of various virtual environments in what
    they call "sessions", from which various commands can be run. This
    project's `noxfile.py` manages the installation of the
    `csv-reconcile-geo` plugin for the plugin tests as well as running
    across several versions of `Python`. See the `nox` documentation for
    detail.

    Some versions of this command you're likely to run are as follows:

        $ nox      # Run all the tests building virtual environemnts from scratch
        $ nox -r   # Reuse previously built virtual environments for speed
        $ nox -s test_geo  # Run only the tests for the csv-reconcile-geo plugin
        $ nox -s test_main -p 3.8   # Run only the main tests with Python3.8

    Eventually, the GitHub Actions may be changed to use
    [setup-nox](https://github.com/marketplace/actions/setup-nox).

## Future enhancements

It would be nice to add support for using
[properties](https://reconciliation-api.github.io/specs/latest/#structure-of-a-reconciliation-query)
as part of the scoring, so that more than one column of the csv could be
taken into consideration.