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.. include:: ../global.inc
.. _decorators.collate_ex:
.. index::
pair: @collate (Advanced Usage); Syntax
pair: @collate, inputs(...); Syntax
pair: @collate, add_inputs(...); Syntax
.. role:: raw-html(raw)
:format: html
:raw-html:`<style> .red {color:red} </style>`
.. role:: red
.. seealso::
* :ref:`@collate <new_manual.collate>` in the **Ruffus** Manual
* :ref:`Use of add_inputs(...) | inputs(...) <new_manual.inputs>` in the **Ruffus** Manual
* :ref:`Decorators <decorators>` for more decorators
.. |input| replace:: `input`
.. _input: `decorators.collate_ex.input`_
.. |extras| replace:: `extras`
.. _extras: `decorators.collate_ex.extras`_
.. |output| replace:: `output`
.. _output: `decorators.collate_ex.output`_
.. |filter| replace:: `filter`
.. _filter: `decorators.collate_ex.filter`_
.. |matching_regex| replace:: `matching_regex`
.. _matching_regex: `decorators.collate_ex.matching_regex`_
.. |matching_formatter| replace:: `matching_formatter`
.. _matching_formatter: `decorators.collate_ex.matching_formatter`_
.. |replace_inputs| replace:: `replace_inputs`
.. _replace_inputs: `decorators.collate_ex.replace_inputs`_
.. |add_inputs| replace:: `add_inputs`
.. _add_inputs: `decorators.collate_ex.add_inputs`_
################################################################################################################################################
@collate( |input|_, |filter|_, |replace_inputs|_ | |add_inputs|_, |output|_, [|extras|_,...] )
################################################################################################################################################
**Purpose:**
Use |filter|_ to identify common sets of |input|_\s which are to be grouped or collated together:
Each set of |input|_\ s which generate identical |output|_ and |extras|_ using the
:ref:`formatter<decorators.formatter>` or :ref:`regex<decorators.regex>` (regular expression)
filters are collated into one job.
This variant of ``@collate`` allows additional inputs or dependencies to be added
dynamically to the task, with optional string substitution.
:ref:`add_inputs<decorators.add_inputs>` nests the the original input parameters in a list before adding additional dependencies.
:ref:`inputs<decorators.inputs>` replaces the original input parameters wholescale.
This is a **many to fewer** operation.
Only out of date jobs (comparing input and output files) will be re-run.
**Example of** :ref:`add_inputs<decorators.add_inputs>`
``regex(r".*(\..+)"), "\1.summary"`` creates a separate summary file for each suffix.
But we also add date of birth data for each species::
animal_files = "tuna.fish", "shark.fish", "dog.mammals", "cat.mammals"
# summarise by file suffix:
@collate(animal_files, regex(r".+\.(.+)$"), add_inputs(r"\1.date_of_birth"), r'\1.summary')
def summarize(infiles, summary_file):
pass
This results in the following equivalent function calls::
summarize([ ["shark.fish", "fish.date_of_birth" ],
["tuna.fish", "fish.date_of_birth" ] ], "fish.summary")
summarize([ ["cat.mammals", "mammals.date_of_birth"],
["dog.mammals", "mammals.date_of_birth"] ], "mammals.summary")
**Example of** :ref:`add_inputs<decorators.inputs>`
using ``inputs(...)`` will summarise only the dates of births for each species group::
animal_files = "tuna.fish", "shark.fish", "dog.mammals", "cat.mammals"
# summarise by file suffix:
@collate(animal_files, regex(r".+\.(.+)$"), inputs(r"\1.date_of_birth"), r'\1.summary')
def summarize(infiles, summary_file):
pass
This results in the following equivalent function calls::
summarize(["fish.date_of_birth" ], "fish.summary")
summarize(["mammals.date_of_birth"], "mammals.summary")
**Parameters:**
.. _decorators.collate_ex.input:
* **input** = *tasks_or_file_names*
can be a:
#. Task / list of tasks.
File names are taken from the output of the specified task(s)
#. (Nested) list of file name strings (as in the example above).
File names containing ``*[]?`` will be expanded as a |glob|_.
E.g.:``"a.*" => "a.1", "a.2"``
.. _decorators.collate_ex.filter:
.. _decorators.collate_ex.matching_regex:
* **filter** = *matching_regex*
is a python regular expression string, which must be wrapped in
a :ref:`regex<decorators.regex>` indicator object
See python `regular expression (re) <http://docs.python.org/library/re.html>`_
documentation for details of regular expression syntax
.. _decorators.collate_ex.matching_formatter:
* **filter** = *matching_formatter*
a :ref:`formatter<decorators.formatter>` indicator object containing optionally
a python `regular expression (re) <http://docs.python.org/library/re.html>`_.
.. _decorators.collate_ex.add_inputs:
.. _decorators.collate_ex.replace_inputs:
* **add_inputs** = *add_inputs*\ (...) or **replace_inputs** = *inputs*\ (...)
Specifies the resulting |input|_\ (s) to each job.
Positional parameters must be disambiguated by wrapping the values in :ref:`inputs(...)<decorators.inputs>` or an :ref:`add_inputs(...)<decorators.add_inputs>`.
Named parameters can be passed the values directly.
Takes:
#. Task / list of tasks.
File names are taken from the output of the specified task(s)
#. (Nested) list of file name strings.
Strings will be subject to substitution.
File names containing ``*[]?`` will be expanded as a |glob|_.
E.g. ``"a.*" => "a.1", "a.2"``
.. _decorators.collate_ex.output:
* **output** = *output*
Specifies the resulting output file name(s).
.. _decorators.collate_ex.extras:
* **extras** = *extras*
Any extra parameters are passed verbatim to the task function
If you are using named parameters, these can be passed as a list, i.e. ``extras= [...]``
See :ref:`@collate <decorators.collate>` for more straightforward ways to use collate.
|
