Fixed an issue with the MP Pipeline (#295)

nlpie · Apr 17, 2023 · 18d0170 · 18d0170
1 parent 4132717
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diff --git a/python/docs/conf.py b/python/docs/conf.py
@@ -32,10 +32,10 @@
 import sys
 import re
 
-sys.path.insert(0, os.path.abspath('../'))
-
 import mtap
 
+sys.path.insert(0, os.path.abspath('../'))
+
 # -- Project information -----------------------------------------------------
 
 project = 'MTAP'

diff --git a/python/docs/deployment.rst b/python/docs/deployment.rst
@@ -1,7 +1,10 @@
+***************
 mtap.deployment
-===============
-Deployment
-----------
+***************
+
+Deploying Processors
+====================
+
 .. automodule:: mtap.deployment
 .. autoclass:: Deployment
    :members:

diff --git a/python/docs/index.rst b/python/docs/index.rst
@@ -6,8 +6,11 @@ Welcome to MTAP's documentation!
    :caption: Contents:
 
    mtap
+   processing
    deployment
+   pipeline
    serialization
+   metrics
 
 Overview
 ========

diff --git a/python/docs/metrics.rst b/python/docs/metrics.rst
@@ -0,0 +1,9 @@
+************
+mtap.metrics
+************
+
+Computing Metrics using processing
+----------------------------------
+
+.. automodule:: mtap.metrics
+   :members:
diff --git a/python/docs/mtap.rst b/python/docs/mtap.rst
@@ -5,11 +5,8 @@ mtap
 
 .. contents::
 
-Command-Line Utility
---------------------
-
 Running Events Service
-^^^^^^^^^^^^^^^^^^^^^^
+======================
 
 usage:
 
@@ -30,136 +27,42 @@ usage:
   --config CONFIG, -c CONFIG
                         path to config file
 
-API Documentation
-=================
 
 Events service client, documents
---------------------------------
-.. autoclass:: EventsClient
+================================
+.. autofunction:: events_client
+.. autoclass:: mtap.types.EventsClient
+   :show-inheritance:
+   :members:
 .. autoclass:: Event
    :members:
 .. autoclass:: Document
    :members:
-.. autoclass:: mtap.data.Labeler
-   :members:
-.. autoclass:: mtap.data.LabelIndexInfo
-   :members:
-.. autoclass:: mtap.data.LabelIndexType
+.. autoclass:: mtap.types.Labeler
    :members:
 
 Labels
-------
-.. autoclass:: mtap.data.Label
+======
+.. autoclass:: mtap.types.Label
    :members:
-.. autoclass:: mtap.data.Location
+.. autoclass:: Location
    :members:
 .. autofunction:: label
 .. autoclass:: GenericLabel
    :members:
    :show-inheritance:
 
 Label Indices
--------------
-.. autofunction:: label_index
-.. autoclass:: mtap.data.LabelIndex
-   :members:
-
-Custom Label Types
-------------------
-.. autoclass:: mtap.data.ProtoLabelAdapter
-   :members:
-
-Creating Processors
--------------------
-.. autoclass:: mtap.processing.Processor
-   :members:
-.. autoclass:: EventProcessor
-   :members:
-   :show-inheritance:
-.. autoclass:: DocumentProcessor
-   :members:
-   :show-inheritance:
-.. autoclass:: mtap.processing.Stopwatch
-   :members:
-
-Processor Description Decorators
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. autofunction:: processor
-.. automodule:: mtap.processing.descriptions
-   :members:
-   :no-inherited-members:
-   :exclude-members: processor
-
-Running Services
-----------------
-.. module:: mtap
-   :noindex:
-.. autofunction:: processor_parser
-.. autofunction:: run_processor
-
-Running a pipeline
-------------------
-.. autoclass:: Pipeline
-   :members:
-   :show-inheritance:
-.. autoclass:: mtap.processing.MpConfig
-   :members:
-.. autoclass:: mtap.processing.ComponentDescriptor
-.. autoclass:: RemoteProcessor
-   :show-inheritance:
-.. autoclass:: LocalProcessor
-   :show-inheritance:
-
-Pipeline Document Sources
-^^^^^^^^^^^^^^^^^^^^^^^^^
-.. module:: mtap.processing
-   :noindex:
-.. autoclass:: ProcessingSource
-   :members:
-.. autoclass:: FilesInDirectoryProcessingSource
-   :members:
-   :show-inheritance:
+=============
+Label indices are normally retrieved via the :attr:`~mtap.Document.labels` property, but
+they can be created independently of documents as well.
 
-Pipeline Results
-^^^^^^^^^^^^^^^^
-.. autoclass:: BatchPipelineResult
-.. autoclass:: PipelineResult
-.. autoclass:: ComponentResult
-.. autoclass:: TimerStats
-.. autoclass:: AggregateTimingInfo
-   :members:
-
-Pipeline Error Handling
-^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: mtap.processing._error_handling
-   :no-members:
-.. module:: mtap.processing
-.. autoclass:: ProcessingErrorHandler
-.. autoclass:: ErrorInfo
-.. autoclass:: ErrorOrigin
-   :members:
-.. autoclass:: StopProcessing
-.. autoclass:: SuppressError
-.. autoclass:: ErrorHandlerRegistry
-   :members:
-.. autoclass:: SimpleErrorHandler
-   :members:
-   :show-inheritance:
-.. autoclass:: TerminationErrorHandler
-   :members:
-   :show-inheritance:
-.. autoclass:: LoggingErrorHandler
-   :members:
-   :show-inheritance:
-.. autoclass:: ErrorsDirectoryErrorHandler
-   :members:
-   :show-inheritance:
-.. autoclass:: SuppressAllErrorsHandler
+.. autofunction:: label_index
+.. autoclass:: mtap.types.LabelIndex
    :members:
-   :show-inheritance:
 
 Configuration
--------------
+=============
 .. module:: mtap
    :noindex:
 .. autoclass:: Config
diff --git a/python/docs/pipeline.rst b/python/docs/pipeline.rst
@@ -0,0 +1,71 @@
+*************
+mtap.pipeline
+*************
+.. module:: mtap.pipeline
+
+
+Running a pipeline
+==================
+.. autoclass:: Pipeline
+   :members:
+   :show-inheritance:
+.. autoclass:: MpConfig
+   :members:
+.. autoclass:: ComponentDescriptor
+.. autoclass:: RemoteProcessor
+   :show-inheritance:
+.. autoclass:: LocalProcessor
+   :show-inheritance:
+
+Pipeline Document Sources
+=========================
+.. autoclass:: ProcessingSource
+   :members:
+.. autoclass:: FilesInDirectoryProcessingSource
+   :members:
+   :show-inheritance:
+
+Pipeline Results
+================
+.. autoclass:: BatchPipelineResult
+   :members:
+.. autoclass:: PipelineResult
+   :members:
+.. autoclass:: mtap.processing.results.ComponentResult
+   :members:
+.. autoclass:: mtap.processing.results.TimerStats
+   :members:
+.. autoclass:: mtap.processing.results.AggregateTimingInfo
+   :members:
+
+Pipeline Error Handling
+=======================
+.. automodule:: mtap.pipeline._error_handling
+   :no-members:
+.. module:: mtap.pipeline
+   :noindex:
+.. autoclass:: ProcessingErrorHandler
+   :members:
+.. autoclass:: mtap.processing.ErrorInfo
+   :members:
+.. autoclass:: mtap.processing.ErrorOrigin
+   :members:
+.. autoclass:: StopProcessing
+.. autoclass:: SuppressError
+.. autoclass:: ErrorHandlerRegistry
+   :members:
+.. autoclass:: SimpleErrorHandler
+   :members:
+   :show-inheritance:
+.. autoclass:: TerminationErrorHandler
+   :members:
+   :show-inheritance:
+.. autoclass:: LoggingErrorHandler
+   :members:
+   :show-inheritance:
+.. autoclass:: ErrorsDirectoryErrorHandler
+   :members:
+   :show-inheritance:
+.. autoclass:: SuppressAllErrorsHandler
+   :members:
+   :show-inheritance:
diff --git a/python/docs/processing.rst b/python/docs/processing.rst
@@ -0,0 +1,44 @@
+***************
+mtap.processing
+***************
+
+.. module:: mtap.processing
+
+Processor Abstract Classes
+==========================
+
+.. autoclass:: Processor
+   :members:
+.. autoclass:: mtap.EventProcessor
+   :members:
+   :show-inheritance:
+.. autoclass:: mtap.DocumentProcessor
+   :members:
+   :show-inheritance:
+
+Processor Utilities
+===================
+
+.. autoclass:: Stopwatch
+   :members:
+
+Processor Description Decorators
+================================
+.. automodule:: mtap.descriptors
+.. autofunction:: processor
+.. autofunction:: parameter
+.. autofunction:: labels
+.. autofunction:: label_property
+.. autoclass:: ProcessorDescriptor
+   :members:
+.. autoclass:: ParameterDescriptor
+   :members:
+.. autoclass:: LabelIndexDescriptor
+   :members:
+.. autoclass:: LabelPropertyDescriptor
+   :members:
+
+Running Services
+================
+.. autofunction:: mtap.processor_parser
+.. autofunction:: mtap.run_processor
diff --git a/python/docs/serialization.rst b/python/docs/serialization.rst
@@ -10,17 +10,16 @@ Serialization
    :members:
 
 Built-In Serializers
-^^^^^^^^^^^^^^^^^^^^
+--------------------
 .. autodata:: JsonSerializer
    :no-value:
 .. autodata:: YamlSerializer
    :no-value:
 .. autodata:: PickleSerializer
    :no-value:
-.. autofunction:: get_serializer
 
 Helpers
-^^^^^^^
+-------
 .. autofunction:: event_to_dict
 .. autofunction:: dict_to_event
 .. autofunction:: document_to_dict

diff --git a/python/mtap/__init__.py b/python/mtap/__init__.py
@@ -14,28 +14,29 @@
 """Public API and access points for the MTAP Framework."""
 
 from mtap._config import Config
-from mtap._events_service import EventsServer
-from mtap.data import (
-    Document,
-    Event,
-    EventsClient,
-    GenericLabel,
-    label,
-    label_index,
-    Location,
-)
+from mtap._document import Document
+from mtap._event import Event
+from mtap._events_client import events_client
+from mtap._labels import GenericLabel, label, Location
+from mtap._label_indices import label_index
+
 from mtap.processing import (
     DocumentProcessor,
     EventProcessor,
-    Pipeline,
-    ProcessorServer,
-    descriptions,
-    processor,
     processor_parser,
-    run_processor,
-    RemoteProcessor,
+    run_processor
+)
+
+from mtap.descriptors import (
+    processor
+)
+
+from mtap.pipeline import (
+    Pipeline,
     LocalProcessor,
+    RemoteProcessor,
 )
+
 from mtap.version import (
     __version__,
     __version_tuple__,