2014 Taverna tutorial Shims and Beanshell scripts

Shim (Helper) Services
and Beanshell Services
Stian Soiland-Reyes and Christian Brenninkmeijer
University of Manchester
materials by Katy Wolstencroft and Aleksandra Pawlik
http://orcid.org/0000-0001-9842-9718
Bonn University, 2014-09-01
http://www.taverna.org.uk/
This work is licensed under a
Creative Commons Attribution 3.0 Unported License

Taverna Tutorial
Building a simple workflow
Stian Soiland-Reyes and Christian Brennikmeijer
University of Manchester
materials by Katy Wolstencroft and Aleksandra Pawlik
Bonn University, 2014-09-01
http://www.taverna.org.uk/
This work is licensed under a
Creative Commons Attribution 3.0 Unported License

 Taverna is good way to access lots of
globally distributed services out there on
the Web
 This saves you the considerable trouble of
installing stuff (e.g. databases, tools etc)
on your personal machine or laboratory
server

 Provided by third parties:
 EMBOSS / SOAPlab - UK
 BioMOBY -
Canada/Germany/Australi
a etc
 BioMART / EBI - UK
 NCBI and PathPort - US
 KEGG - Japan
 SeqHound / BIND –
Canada
 The catch – services are
not designed to work
together

A two-stage process
1. Assembly – identifying services that perform
the scientific functions needed for the
experiment
2. Gluing – identifying how (or more usually, if)
theses services are compatible
If they are incompatible – we need services
that convert data formats and act as
connectors – we call these services Shims (or
helper services)

 Lots of services don’t match: A into B doesn’t go
 Lots of services are poorly described – can you
even tell if A goes into B?

UniProt record
Match
Mismatch
protein_sequence Shim

DNA fasta
Match
Mismatch
DNA embl Shim

 If you’re lucky someone will have already created a
service that does what you want and will have
described / annotated it in a way that lets you find it
 …if no service exists, one way to solve the problem
is to create a lightweight BeanShell script
(essentially a “lighter” version of Java) that runs on
your local machine (not on a server like the services
do)
 These come in two flavours: Ready made “Local
Java Widgets” and roll-your-own “Local Services’’,

 BioCatalogue – some shims are regular WSDL
or REST services
 myExperiment – look for all workflows
containing the scientific services. Has anyone
linked them together before?

Exploring Shims
 A shim is a service that doesn’t perform an experimental
function, but acts as a connector, or glue, when 2
experimental services have incompatible outputs and
inputs
 A shim can be any type of service – WSDL, soaplab etc.
Many are simple Beanshell scripts
 We have already used many shims in these exercises

Shims for Data Input
 We will use the simple workflow that we build in the introductory
tutorial
 So far, we have only added a few input values to our workflows.
Normally, you would have a much larger data set. The
“GetProteinFasta” activity can only handle one ID at a time.

 You can add a list of IDs by configuring the input port
 Right-click on the ID input and select ‘Edit workflow input port’ and
change the depth to 1 (a list).
 Now, when you run the workflow, you can add multiple ID values

 Try running it with 215422388 and 1220173
 Press “Add value” to add each new value.
 If you have hundreds of IDs, however, this is not very practical.
Instead, we need an extra service to split a list of data items into
individual values

 In the services panel, search for “split”
 Select “Split string into string list by regular expression”
(a purple local java service) and drag it into the workflow
 Delete the data link between the “ID” input and
“GetProteinFasta” by selecting and right-clicking on the
diagram
 Connect “ID” to the “string” port of the new “split” activity
 Hint: Press To Display all Service ports
 Add “n” as a constant value to the “regex” input on
“split…” by right-clicking and selecting “Set constant
value”

 In the services panel, search for “split”
 Select
“split_string_into_string_list_by_regular_expression” (a
purple local java service) and drag it into the workflow

 Delete the data link between the “ID” input and
“GetProteinFasta” by selecting and right-clicking on the diagram
 Connect “ID” to the “string” port of the new “split” activity
 Hint: If you don’t see the “string” port press the “Display all
Service ports” button

 Add a text constant. (Hint rightclick a blank part of the workflow
and select “Text constant”)
 Set the value to “n” and press “Apply” and “Close”
 Rename the service “regex_value” (Hint: rightclick the
Text_constant” service and select Rename Service)

Shims for viewing data
 Connect the “regex_value” to
the “regex” port.
 Connect the “split” output port to
Get_protein_Fasta (“ID” input
port)

 Run the workflow
 This time, instead of adding individual IDs add a file of
IDs. If you don’t have one to hand, there is one to
download here:
 http://www.myexperiment.org/files/1267/download
 You can download and add the file, or you can add the
URL from the input window
 As the workflow runs, you will see it iterate over the IDs
in the file

Pre-configured Shims
 The local workers are ‘pre-configured’ shims. Have a
look at the different categories on offer.

Writing your own shim services -
Beanshells
 Many shims are actually Beanshell scripts.
 Beanshell scripts allow you to add simple data
transformation steps into your workflow in an easy way.
 We will take a brief look at writing Beanshells

Writing your Own Beanshell
 Create a new workflow by
selecting ‘file’ and ‘New
Workflow’
 Add a new Beanshell
 Hint (right click on blank part
of the workflow)
 A configure window will pop-up

 Create 2 input ports named: “myName” and mySurname
 Hint: Press “Add Port” after selecting the ‘Input Ports’ tab
 Cretate 1 output port named: myFullname

 Select the script tab and Paste
the following script
 myFullname = myName + "t"
+ mySurname
 The variable names must
match exactly the names of
the input and output ports
 Hint: They are shown in purple
when correctly matching
 Then “Apply” and “Close” the
“Beanshell” Window

 Create 2 workflow inputs and 1 workflow output and
connect them to the configured beanshell service.
 Hint: The names of the input and output ports do not need to
be the same as the names used in the script.

 Run the workflow
 You should get your full name printed in the output.
This is a very simple example of using helper services to
format results from your workflow

2014 Taverna tutorial Shims and Beanshell scripts

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2014 Taverna tutorial Shims and Beanshell scripts