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.. _chap-webservices:
************************
Example: Web Services
************************
A *web service* grants you programmatic access to an online data source
via a straightforward API. In this chapter, you will learn how to invoke web
services from within |vistrails| workflows. We will build a simple workflow that
invokes a web service and generates an HTML table with the results. Our current
example is intentionally simple; for more in-depth examples, please refer to
the |vistrails| website.
**Where we're going in this chapter:** The European Bioinformatics Institute maintains ChEBI, [#]_ a database of over 15,000 chemical
compounds. Each entity is referenced by a unique ID number, called
its *chebiID*. To see an example of the kind of queries we will build in
this example, go to http://www.ebi.ac.uk/chebi/webServices.do and scroll
down until you find the web form labeled "getCompleteEntity."
(Figure :ref:`fig-webservices_webform1`). If you type 15357 into the text
field, it will return a long string of data in XML format about this
chemical. We learn, among other things, that this chemical's name
is *acetylenedicarboxylate(-2)*.
To try another query, scroll down to the area labeled "getOntologyChildren"
and type 15357 into the text field. This returns an XML representation of this
chemical's ontology children. In this case, the result is a single
chemical, *acetylenedicarboxylate(-1)*, whose chebiID is 30782
(Figure :ref:`fig-webservices_webform2`).
.. _fig-webservices_webform:
.. _fig-webservices_webform1:
.. figure:: figures/example_webservices/webservices_webform.png
:width: 3.2in
:align: center
\(a\) Web browser interface for the ChEBI database
.. _fig-webservices_webform2:
.. figure:: figures/example_webservices/webservices_webform_result.png
:width: 3.2in
:align: center
\(b\) Results from a "getOntologyChildren" query
In this example, we will build a workflow that accesses a web service to
perform the second of these two queries. Because we're using a web service, we
don't need a browser --- we will perform this query programmatically
within |vistrails|.
Enabling the SUDSWebServices Package
====================================
In order to use web services in |vistrails|, you need to ensure that the ``SUDSWebServices`` package is enabled in the ``Preferences``
dialog. (Please refer to Chapter :ref:`chap-packages` for more information on enabling packages.)
Adding Web Service Packages
===========================
Within the ``Module Packages`` tab of the ``Preferences`` dialog, click the ``Configure`` button to open the configuration dialog for this package (``SUDSWebServices``). Select the ``wsdlList`` and click on the ``Value`` field. This is where you will enter the URL(s) of the web service(s) you wish to access. If there is more than one URL, place a semicolon (;) between each URL, but *not* after the final URL. In other words, the URLs must be semicolon-delimited, but not semicolon-terminated.
For our example, we need the following URL:
``http://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl``
After closing the dialog, you need to reload the ``SUDSWebServices`` package in order to load the changes. Then, close the ``Preferences`` dialog. A new package will be created for each URL provided.
Alternatively, you may add a web service package by clicking the secondary mouse button on the "SUDS Web Services" package in the module palette and entering the corresponding URL. You may remove a web service by clicking the secondary mouse button on the corresponding package in the module palette and selecting ``Remove this Web Service``.
.. _fig-webservices_preferences:
.. figure:: figures/example_webservices/modules_list.png
:align: center
:height: 3in
The available modules in the ``webServices`` module are shown in the ``Modules`` panel.
Creating a new vistrail
=======================
After configuring the ``SUDSWebServices`` package properly, there
will be a ``SUDSWebServices`` entry in your ``Modules``
panel.
The ``SUDSWebServices`` package will generate a module for each
published method in a web service.
.. %Figure TODO.
Start with a new empty workflow in the ``Pipeline`` view, and drag
the following modules to the canvas.
.. index::
pair: modules; adding
* ``String`` (under "Basic Modules")
* ``getOntologyChildren`` (under "Methods" for the current web service)
* ``getOntologyChildrenResponse`` (under "Types" for the current web service)
* ``OntologyDataItemList`` (under "Types" for the current web service)
* ``PythonSource`` (under "Basic Modules")
* ``RichTextCell`` (under "Spreadsheet")
As discussed in Chapter :ref:`chap-creating`, ``PythonSource`` has no
input and output ports by default; we need to create some. Open the
configuration dialog for ``PythonSource`` by selecting this module in
the pipeline canvas and typing 'Ctrl-E'. Add a new input port
named "ontologyDataItemList" of type ``List``, and a new
output port named "outfile" of type ``File``. (Please refer
to Chapter :ref:`chap-creating` for more information about configuring and using
the ``PythonSource`` module.)
We will now add some Python code to this module. This code generates a simple
HTML table based on the information retrieved from the web service query. Type
or paste the following source code into the ``PythonSource``
configuration dialog:
.. code-block:: python
dataitemlist = self.get_input("ontologyDataItemList")
output1 = self.interpreter.filePool.create_file()
f1 = open(str(output1.name), "w")
text = "<HTML><TITLE>Chebi WebService</TITLE><BODY BGCOLOR=#FFFFFF>"
f1.write(text)
text = "<H2>getOntologyChildren Query</H2><BR>"
f1.write(text)
text = "<CENTER><table border = 1><tr><TH>ChebiId</TH> <TH>ChebiName</TH>"
text += "<TH>Comments</TH> <TH>Type</TH> <TH>Status</TH>"
text += "<TH>CyclicRelationship</TH></tr>"
f1.write(text)
for element in dataitemlist:
if not hasattr(element,'Comments') or str(element.Comments) == '[]':
comment = ""
else:
comment = str(element.Comments)
line = "<tr><td>" + str(element.chebiId) + "</td><td>" + str(element.chebiName)
line += "</td><td>" + comment + "</td><td>" + str(element.type) + "</td><td>"
line += str(element.status) + "</td><td>" + str(element.cyclicRelationship)
line += "</td></tr>"
f1.write(line)
text = "</table></CENTER></BODY></HTML>"
f1.write(text)
self.set_output("outfile",output1)
f1.close()
Close the dialog. One of the ports we need to use is an optional port. Select the ``OntologyDataItemList`` module and select the ``Outputs`` tab from the ``Module Information`` panel. Click in the left column next to ``ListElement`` so the eye icon appears. Now connect the modules together as shown in Figure :ref:`fig-chebi_pipeline_screenshot`.
.. _fig-chebi_pipeline_screenshot:
.. figure:: figures/example_webservices/only_modules.png
:align: center
:width: 2.5in
Our example pipeline
Our workflow is now complete except for one crucial element: the starting point. We need to pass a chebiID string to the workflow in order to look up information about a chemical. We do this by assigning a chebiID string to the ``String`` module at the top of the pipeline. Highlight the ``String`` module in the canvas, then in the ``Module Information`` panel on the right, make sure the ``Inputs`` tab is selected and click on ``value`` and type ``CHEBI:15357`` into the ``String`` input box that comes up.
Executing the workflow
======================
.. index::
pair: spreadsheet; RichTextCell
The workflow is now ready to be visualized. Click the ``Execute``
button to send the current pipeline with the current parameters to
a ``RichTextCell`` within the |vistrails|
Spreadsheet. Your result should resemble
Figure :ref:`fig-webservices_spreadsheet`. As you can see,
the "ontology children" query returns the same information as before,
but without the use of a web browser. In addition, we used a small Python
program (via the ``PythonSource`` module) to transform the raw XML into
a readable HTML table.
.. _fig-webservices_spreadsheet:
.. figure:: figures/example_webservices/ws_spreadsheet.png
:align: center
:height: 2.5in
The HTML table generated by our workflow
.. rubric:: Footnotes
.. [#] ChEBI is an acronym for Chemical Entities of Biological Interest.
|
