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genotoul-bioinfo
jflow
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480aa4c4
Commit
480aa4c4
authored
Aug 31, 2015
by
Jerome Mariette
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communication/Bioinformatics/jflow_BIOINF.tex
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480aa4c4
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@@ -29,7 +29,7 @@ web portals in which they can upload and analyze their files. Providing such
tools requires to mask the complexity induced by the needed High Performance
Computing (HPC) environment. The connexion between interface and computing
infrastructure is usually specific to each portal. With Jflow, we introduce
a Workflow Management System (WMS), composed of
Jq
uery plug-ins which can easily
a Workflow Management System (WMS), composed of
jQ
uery plug-ins which can easily
be
embedded in any web application and a Python library providing all requested
features to setup, run and monitor workflows.
...
...
@@ -65,13 +65,13 @@ but they do not provide a user interface, enable component and workflow
definition or check file formats.
To our knowledge, Jflow, presented in this article, is the only WMS designed to
be embedded in any web application, thanks to its organization as five
Jq
uery
be embedded in any web application, thanks to its organization as five
jQ
uery
(http://jquery.com/) plug-ins.
\section
{
Methods
}
Jflow user interface gathers five
Jq
uery plug-ins providing user oriented views.
Jflow user interface gathers five
jQ
uery plug-ins providing user oriented views.
\begin{itemize}
\item
\textit
{
availablewf
}
lists all runnable workflows accessible to users,
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@@ -85,12 +85,12 @@ Jflow user interface gathers five Jquery plug-ins providing user oriented views.
plug-in (Lopes et al., 2010).
\end{itemize}
The plug
ins give access to multiple communication methods and events. They
The plug
-
ins give access to multiple communication methods and events. They
interact with the server side through Jflow's REST API, running under a cherrypy
(http://www.cherrypy.org/) web server. The included server uses the JSONP
communication technique enabling cross-domain requests.
To be available from the different
Jq
uery plug-ins, the workflows have to be
To be available from the different
jQ
uery plug-ins, the workflows have to be
implemented using the Jflow API. A Jflow component is in charge of an execution
step. Adding a component to the system requires to write a Python
\textit
{
Component
}
subclass. In Jflow, different solutions are available to ease
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@@ -153,7 +153,7 @@ launch each sample processing.
\caption
{
\textbf
{
Jflow integration:
}
(a) A piece of the NG6 HTML code source in
which is positioned an empty div to build the
\textit
{
activewf
}
plug-in
and a
modal box for the
\textit
{
wfstatus
}
plug-in. (b) The
Jq
uery code in
modal box for the
\textit
{
wfstatus
}
plug-in. (b) The
jQ
uery code in
charge to
build Jflow plug-ins and manage user action. When the
\textit
{
select.activewf
}
...
...
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