(#10) adding makeflow parser

Author: rafaelfsilva

docs/source/dev_api_generator.rst

@@ -85,7 +85,7 @@ workflowhub.generator.workflow.soykb\_recipe
    :noindex:
 
 workflowhub.generator.workflow.srasearch\_recipe
---------------------------------------------
+------------------------------------------------
 
 .. automodule:: workflowhub.generator.workflow.srasearch_recipe
    :members:

docs/source/dev_api_trace.rst

@@ -2,7 +2,7 @@ workflowhub.trace
 =================
 
 workflowhub.trace.schema
----------------------------------
+------------------------
 
 .. automodule:: workflowhub.trace.schema
    :members:
@@ -40,8 +40,18 @@ workflowhub.trace.logs.abstract\_logs\_parser
    :private-members:
    :noindex:
 
+workflowhub.trace.logs.makeflow
+-------------------------------
+
+.. automodule:: workflowhub.trace.logs.makeflow
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :private-members:
+   :noindex:
+
 workflowhub.trace.logs.pegasus
----------------------------------------------
+------------------------------
 
 .. automodule:: workflowhub.trace.logs.pegasus
    :members:

docs/source/parsing_logs.rst

@@ -7,11 +7,47 @@ The most common way for obtaining traces from actual workflow executions is to p
 execution logs. As part of the WorkflowHub project, we are constantly developing
 parsers for commonly used workflow management systems.
 
-Each parser class is derived from the :class:`~workflowhub.trace.logs.abstract_logs_parser.LogsParser`
-class. Thus, each parser provides a
+Each parser class is derived from the abstract
+:class:`~workflowhub.trace.logs.abstract_logs_parser.LogsParser` class. Thus, each
+parser provides a
 :meth:`~workflowhub.trace.logs.abstract_logs_parser.LogsParser.build_workflow`
 method.
 
+Makeflow
+--------
+
+`Makeflow <http://ccl.cse.nd.edu/software/makeflow/>`_ is a workflow system for
+executing large complex workflows on clusters, clouds, and grids. The Makeflow
+language is similar to traditional Make, so if you can write a Makefile, then you
+can write a Makeflow. A workflow can be just a few commands chained together, or
+it can be a complex application consisting of thousands of tasks. It can have an
+arbitrary DAG structure and is not limited to specific patterns. Makeflow is used
+on a daily basis to execute complex scientific applications in fields such as data
+mining, high energy physics, image processing, and bioinformatics. It has run on
+campus clusters, the Open Science Grid, NSF XSEDE machines, NCSA Blue Waters, and
+Amazon Web Services. Makeflow logs provide time-stamped event traces from these
+executions. The following example shows the analysis of Makeflow execution logs,
+stored in a local folder (execution dir), for a workflow execution using the
+:class:`~workflowhub.trace.logs.makeflow.MakeflowLogsParser` class: ::
+
+    from workflowhub.trace import MakeflowLogsParser
+
+    # creating the parser for the Makeflow workflow
+    parser = MakeflowLogsParser(execution_dir='/path/to/makeflow/execution/dir/blast/chameleon-small-001/'
+                                resource_monitor_logs_dir='/path/to/makeflow/resource/monitor/logs/dir')
+
+    # generating the workflow trace object
+    workflow = parser.build_workflow('workflow-test')
+
+    # writing the workflow trace to a JSON file
+    workflow.write_json('workflow.json')
+
+.. note::
+    The :class:`~workflowhub.trace.logs.makeflow.MakeflowLogsParser` class requires
+    that Makeflow workflows to run with the
+    `Resource Monitor <https://cctools.readthedocs.io/en/latest/resource_monitor/>`_
+    tool (e.g., execute the workflow using the :code:`--monitor=logs`).
+
 Pegasus WMS
 -----------
 
@@ -39,9 +75,8 @@ class: ::
     # writing the workflow trace to a JSON file
     workflow.write_json('workflow.json')
 
-.. note::
-
+.. warning::
     By default, the :class:`~workflowhub.trace.logs.pegasus.PegasusLogsParser`
-    class assumes that the submit dir is from a Pegasus execution with version 5.0 or later.
-    To enable parsing of Pegasus execution logs from version 4.9 or earlier, the option
-    :code:`legacy=True` should be used.
+    class assumes that the submit dir is from a Pegasus execution with **version 5.0**
+    or later. To enable parsing of Pegasus execution logs from version 4.9 or earlier,
+    the option :code:`legacy=True` should be used.

docs/source/quickstart_installation.rst

@@ -10,23 +10,22 @@ Requirements
 Graphviz
 ^^^^^^^^
 
-WorkflowHub uses `pygraphviz <https://pygraphviz.github.io/documentation/latest/install.html>`_ and thus needs the `graphviz <https://www.graphviz.org/>`_ package installed (version 2.16 or later).
-You can install graphviz easily on Linux with your favorite package manager,
+WorkflowHub uses `pygraphviz <https://pygraphviz.github.io/documentation/latest/install.html>`_
+and thus needs the `graphviz <https://www.graphviz.org/>`_ package installed (version 2.16
+or later). You can install graphviz easily on Linux with your favorite package manager,
 for example for Debian-based distributions:
 
 .. code-block:: bash
 
     $ sudo apt-get install graphviz libgraphviz-dev
 
-
 and for RedHat-based distributions:
 
 .. code-block:: bash
 
     $ sudo yum install python-devel graphviz-devel
 
-
-On macOS you can use :code:`brew` package manager:
+On macOS you can use the :code:`brew` package manager:
 
 .. code-block:: bash
 

docs/source/user_api_generator.rst

@@ -63,7 +63,7 @@ workflowhub.generator.workflow.soykb\_recipe
    :show-inheritance:
 
 workflowhub.generator.workflow.srasearch\_recipe
---------------------------------------------
+------------------------------------------------
 
 .. automodule:: workflowhub.generator.workflow.srasearch_recipe
    :members:

docs/source/user_api_trace.rst

@@ -17,8 +17,16 @@ workflowhub.trace.trace\_analyzer
    :undoc-members:
    :show-inheritance:
 
+workflowhub.trace.logs.makeflow
+-------------------------------
+
+.. automodule:: workflowhub.trace.logs.makeflow
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 workflowhub.trace.logs.pegasus
----------------------------------
+------------------------------
 
 .. automodule:: workflowhub.trace.logs.pegasus
    :members:

workflowhub/trace/__init__.py

@@ -1,14 +1,14 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020 The WorkflowHub Team.
+# Copyright (c) 2020-2021 The WorkflowHub Team.
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
 
-from .logs import PegasusLogsParser
+from .logs import MakeflowLogsParser, PegasusLogsParser
 from .schema import SchemaValidator
 from .trace import Trace
 from .trace_analyzer import TraceAnalyzer, TraceElement

workflowhub/trace/logs/__init__.py

@@ -8,4 +8,5 @@
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
 
+from .makeflow import MakeflowLogsParser
 from .pegasus import PegasusLogsParser

workflowhub/trace/logs/abstract_logs_parser.py

@@ -20,16 +20,31 @@
 class LogsParser(ABC):
     """An abstract class of logs parser for creating workflow traces.
 
+    :param wms_name: Name of the workflow system.
+    :type wms_name: str
+    :param wms_url: URL for the workflow system.
+    :type wms_url: str
     :param description: Workflow trace description.
     :type description: str
     :param logger: The logger where to log information/warning or errors (optional).
     :type logger: Logger
     """
 
-    def __init__(self, description: Optional[str] = None, logger: Optional[Logger] = None) -> None:
+    def __init__(self,
+                 wms_name: str,
+                 wms_url: Optional[str] = None,
+                 description: Optional[str] = None,
+                 logger: Optional[Logger] = None) -> None:
         """Create an object of the logs parser."""
         self.logger = logging.getLogger(__name__) if logger is None else logger
         self.description = description
+        self.wms_name = wms_name
+        self.wms_url = wms_url
+        self.workflow = None
+        self.workflow_name = None
+        self.schema_version = None
+        self.executed_at = None
+        self.makespan = None
 
     @abstractmethod
     def build_workflow(self, workflow_name: Optional[str] = None) -> Workflow: