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.gitignore

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+*.pyc

README.md

@@ -1,9 +1,7 @@
-# MuGtoolAPI
-A first attempt at outlining the main structures related to the tools section of the VRE.
+# mg-tool-api
 
 ## Introduction
-This is a first attempt at outlining the main structures related to the
-tools section of the VRE. It implements the specifications detailed in the
+This library implements the specifications detailed in the
 current version (23/09/2016) of the Deliverable 6.1 document: "Design of
 computational architecture of software modules" (http://bit.ly/MuGD6_1). It
 extends the above document with the aim to provide a simple programming
@@ -30,31 +28,29 @@ data retrieval; this also makes changes in the DMP transparent to the tools.
 straightforward to combine them in workflows, using COMPSs "task" decorator and
 the COMPSs runtime as the workflow scheduler. 
 
-## Objective
-
-This code is intended as a first draft to fuel discussions among all
-involved parties (in particular WP4, WP5 and WP6) about the precise details of
-the software architecture of the VRE, and as such won't run as valid Python
-code out of the box. Please note that the scientific relevance of this is
-limited to providing an example of usage of the class structure proposed.
-
 ## Implementation overview
-
-1. Resource:
-     It is the general container for all data that is exchanged within the
-     VRE. Subclasses, such as the examples outlined below, should deal with the
-     details of making the resource available from the various data storage
-     facilities defined in the DMP. There should be at least one subclass per
-     storage class in the DMP. Every Resource instance is defined by its data
-     type, which is immutable. In fact, Resources should probably be immutable
-     altogether (in the following they are, but aren't forced to be).  
-2. Tool:
-     It is the top-level wrapper for tools within the VRE; each tool is defined
-     by its input and output formats, and by its specific requirements on the
-     execution environment. Tools should implement a "run" method, that defines
-     operations needed to get from input to output. Decorating the "run" method
-     with "@constraints" allows developers to define the execution environment,
-     while decorating with "@task" makes the tool workflow-ready.
+1. Tool:
+	Is the top-level wrapper for tools within the VRE; each tool is defined
+	by its input and output formats, and by its specific requirements on the
+	execution environment. Tools should implement a "run" method, that defines
+	operations needed to get from input to output. The "run" method calls other
+	methods which are decorated using PyCOMPSs "@task" and "@constraints",
+	allowing tool developers to define the workflow and execution environment.
+2. App:
+	Is the main entry point to the tools layer of the VRE; it deals with heterogeneity
+	in the way Tools are run, in terms of filesystem access, runtime environment,
+	error reporting, and more. Therefore, Apps are compatible with all Tools.
+	Apps implement a "launch" method, which prepares and runs a single instance of Tool. 
+	The "apps" module provides some example Apps for straightforward cases:
+
+	- *LocalApp*: uses the MuG DMP API to retrieve file names that are assumed
+	to be locally accessible;
+
+	- *PyCOMPSsApp*: specific for Tools using PyCOMPSs;
+
+	- *WorkflowApp*: inherits from both of the above, and implements the ability
+	to unstage intermediate outputs.
+
 3. mug_datatypes:
      A repository of all data types available in MuG; it should closely mirror
      the contents of the DMP. 
@@ -68,17 +64,10 @@ limited to providing an example of usage of the class structure proposed.
      others not related to the Tool should not be caught. The Tool also takes
      care of attaching error information to the output resource.
 
-## Examples
+See the documentation for the classes for more information.
 
-The "example_docking_workflow.py" contains a minimal implementation of a few 
-simple example tools in order to perform:
+## Examples
 
-a. Ab-initio predict the structure of a protein given its sequence;
-b. Ab-initio predict the structure of a DNA oligomer given its sequence;
-c. Rigid-body dock two molecules given their 3D structure.
+The "examples" module contains usage examples.
 
-These tools wrap external resources, Python libraries, binary executables or 
-REST APIs, to perform their task; in this example these are not implemented,
-but may be replaced with existing tools in the future. Finally, an example
-simple workflow is outlined to generate a protein-DNA complex given the
-sequence of the two partners using the tools defined above.
+The "summer.py" example implements a workflow using PyCOMPSs.

__init__.py

@@ -1,50 +1,19 @@
-if __name__ == "__main__":
-
-    ## Mock the MuG library
-    class datatypes(object):
-        Sequence = 0
-        PDBStructure = 1
-
-    class conversion(object):
-        def mol_to_pdb(molfile, pdbfile):
-            pass
-
-    class mug(object):
-        datatypes = datatypes
-        conversion = conversion
-
-    import sys
-    sys.modules["mug"] = mug
-
-
-    ## Mock pycompss
-    class parameter(object):
-        IN=0
-        OUT=1
-        #...
-
-    class task(object):
-        @staticmethod
-        def task(**kwargs):
-            return lambda x:x
-
-    class constraint(object):
-        @staticmethod
-        def constraint(**kwargs):
-            return lambda x:x
-
-    import sys
-    sys.modules["pycompss"] = object()
-    sys.modules["pycompss.api"] = object()
-    sys.modules["pycompss.api.task"] = task
-    sys.modules["pycompss.api.constraint"] = constraint
-    sys.modules["pycompss.api.parameter"] = parameter
-
-    ## Import and execute workflow
-    sys.path.append("/Users/marco/sci/MuG/src/D6.1")
-    from MuGtoolAPI import tool, example_docking_workflow, resource
-
-    protein_sequence = resource.Resource(mug.datatypes.Sequence)
-    dna_sequence = resource.Resource(mug.datatypes.Sequence)
-    example_docking_workflow.DockingWorkflow().run(
-        protein_sequence, dna_sequence)
+"""
+Copyright (C) 2016 Marco Pasi <mf.pasi@gmail.com>
+
+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 2 of the License, or
+(at your option) any later version.
+"""
+
+from app import App
+from metadata import Metadata
+from tool import Tool
+from workflow import Workflow
+import apps
+import examples
+
+__author__ = 'Marco Pasi, Javier Conejero'
+__version__ = '0.3'
+__license__ = 'GPL v2'