+1 (binding)


On Oct 16, 2014, at 12:42 PM, Andy Seaborne <a...@apache.org> wrote:

> On 16/10/14 18:47, sebb wrote:
>> Apart from the typo, I thought it was necessary for the VOTE thread to
>> contain the full text of the proposal.
>> This has been the case for (almost) all previous acceptance votes.
> The Lens one I copied from didn't :-)
> Version static link:
> https://wiki.apache.org/incubator/TavernaProposal?rev=10
> and copied below.
>       Andy
>> I assume the text is required so the mail archives have a full record
>> of what was actually voted on.
>> The Wiki page might subsequently change or be deleted.
> Abstract
> Taverna is an open source and domain-independent suite of tools used to
> design and execute data-driven workflows.
> Proposal
> The Taverna suite includes:
> * Taverna Workbench, a desktop application written in Java for graphically
>  composing, editing and executing workflows composed of distributed Web
>  services and local tools
> * Taverna Command Line Tool, which allows execution of workflows from a 
> command line
> * Taverna Server, which provides a REST and SOAP API for executing workflows
> * Taverna Player, a Web interface the Taverna Server written in Ruby
>  towards, providing a high-level view of workflow executions and their
>  results and allowing further integrations with other Ruby on Rails
>  applications
> Taverna allows browsing through and combining different service types in
> workflows, allowing them to integrate steps of arbitrary REST and SOAP Web
> services with command line tools (local and via SSH), scripts (Beanshell,
> R, Jython), and finally to visualize the results.
> The goal of the Taverna suite is to help researchers to access distributed
> datasets and processing capabilities by the construction of (data)
> pipelines, and also to simplify the execution of these pipelines in various
> environments.
> The Taverna suite of products is already successful and in wide use across
> different domains. The software is currently licensed as LGPL 2.1, with
> copyright owned by the University of Manchester. External contributors have
> all signed Apache-like CLAs.
> Background
> Taverna workflows coordinate inputs and outputs between computational
> processes and Web services. The workflow is designed in a graphical
> interface which shows the workflow as a series of boxes connected with
> arrows representing processes (i.e. executable services) and their data
> connections. Different processes in a workflow can be command line tools,
> REST and WSDL Web services; which are used for combining steps such as data
> acquisition, filtering, cleaning, integrating, analysis and
> visualization. Taverna calls these processes "services", as they generally
> are provided by remote (third-party) servers.These kind of computational
> workflows, also known as pipelines or dataflows, focus on the movement of
> data rather than the execution order of the underlying processes. Features
> such as implicit iterations (where an input list of values causes multiple
> process executions) and parallel invocations (independent processes are
> executed as soon as their data is available) are intrinsic to a dataflow
> system, not requiring any particular constructs by the workflow designer.As
> a visual programming environment, workflows aids collaboration and reuse of
> workflows. At the highest level, a workflow represents the conceptual level
> of an analysis, allowing understanding, discussion and communication of the
> overall analysis protocol. More detail can be revealed and modified for
> individual steps. At the individual process level, the workflow defines
> execution specifics such as operations, parameters and command line
> tools.Sharing of the workflow definitions allows re-use and re-purposing of
> the computational analysis. During workflow execution, provenance can be
> collected from every step, allowing deep inspection of intermediate values
> for the purpose of debugging and validation.
> Rationale
> There is a strong need to lower the barrier of entry to datasets and
> computational resources widely available on the Internet, to increase their
> use by researchers who understand the computational steps needed to produce
> their results, but who are not necessarily expert programmers. Taverna has
> already shown its success and popularity in a wide range of scientific
> disciplines.
> Initial Goals
>    Transition mailing lists to Apache (keep existing subscribers, but invite 
> more)
>    Taverna developer workshop (2014-10-30)
>    Fully investigate/resolve incompatibly licensed dependencies
>    Stage git repositories for move at https://github.com/taverna-incubator :
>        Update headers/metadata to indicate Apache License 2.0
>        Restructure git repositories (to ~ 10 repos?)
>        Rename Maven groupIds to org.apache.taverna.*
>        Rename packages to org.apache.taverna.*
>    Move staged Github repositories to Apache git
>    Automated builds in Apache's Jenkins
>    Update to latest releases of Apache dependencies
>    Propose updated release and testing procedure under Apache
>    Moved Website and documentation
> We intend to only release the current development version Taverna 3 under
> the Apache umbrella. 3.0 is not yet officially released - however the
> Taverna 3.0 Command Line can be released almost "as-is" after
> migration. The Taverna 3.0 Server is at beta quality, while the Taverna 3.0
> Workbench is at alpha stage and would need to be stabilized to an initial
> beta release.
>    Before first release: Maven Central releases of Taverna support libraries 
> (e.g. taverna-scufl2 and taverna-databundle)
>    First release: Apache Taverna Command Line 3.0 (OSGi-based)
>    Release: Apache Taverna Server 3.0
>    Release: Apache Taverna Workbench 3.0 beta
>    Provenance exchange with relevant Apache products (e.g. Apache 
> CXF->Taverna->CouchDB)
>    Release: Apache Taverna Workbench 3.0
> It is not yet decided if the current Workbench Editions will be carried
> over to Taverna 3, or if this can be solved by having a "Install extra
> plugin" step on first start-up of Apache Taverna. In any case, we imagine
> that some of these specializing editions will be maintained outside (but in
> collaboration with) the Apache project. This is particularly the case for
> the Astronomy edition as it depends on several LGPL/GPL libraries and is
> maintained by the AstroTaverna team.
> Current Status
> Meritocracy
> Taverna was initially created by the myGrid consortium in 2003. Since 2006,
> the majority of contributions to Taverna's core code-base, its architecture
> and direction have been led by staff at Tthe University of Manchester and
> the European Bioinformatics Institute (EMBL-EBI).
> The project have benefited of a high-degree of extensions and integrations
> by other developers - but mainly in the form of plugins and integrations,
> including Taverna Online.
> Taverna's developer community have unfortunately not had a culture of
> submitting patches that would warrant later commit access - perhaps due to
> its background in the science community. However contributors have been
> added as committers when the plugin becomes a part of the core distribution
> (e.g. External Tool plugin by Möller and Krabbenhöft and AstroTaverna by
> Garrido), or when their development has required patches to the existing
> code base.
> Community
> Taverna has an active community of plug-in developers and users. The
> developer mailing list ( taverna-hack...@lists.sourceforge.net ) has 248
> members, the user mailing list ( taverna-us...@lists.sourceforge.net ) has
> 370 members.
> 1500 users have registered as of 19 August 2014. Total downloads of all
> products since version 2.1 (released December 2009) is 35000.
> Them Taverna Developers Workshop is being arranged for 30 October 2014 to
> bring together developers and integrators of Taverna. We want to encourage
> plug-in developers to participate further in the core development of
> Taverna as well, by introducing them to the code base and how to
> contribute.
> Active steps to grow the communities of users and developers by targeting
> specific research domains such as the work by Kevin Benson on Taverna's use
> in the Heliophysics and Astrophysics community. Susheel Varma is helping
> increase the usage of Taverna within the Biomedical domain. Julián Garrido
> and his work on AstroTaverna is promoting Taverna within the IVOA Virtual
> Astronomy community. Sonja Holl and Björn Hagemeier's are targeting high
> performance computing.
> Core Developers
> What we currently consider to be the core Taverna Team is (in alphabetical 
> order):
>    Christian Brenninkmeijer (University of Manchester)
>    Donal Fellows (University of Manchester)
>    Robert Haines (University of Manchester)
>    Aleksandra Nenadic (University of Manchester)
>    Dmitry Repchevsky (Barcelona Supercomputing Center)
>    Stian Soiland-Reyes (University of Manchester)
>    Shoaib Sufi (University of Manchester)
>    Vadim Surpin (Institute for Information Transmission Problems in Moscow)
>    Alan Williams (University of Manchester)
> The team consists of experienced developers who have worked on a multitude
> projects, particular within writing software for supporting scientists. The
> committers list (see below) includes additionally plugin developers whose
> contributions have become part of Taverna. Part of our desire to join the
> Apache Foundation is to recognise their effort and promote them into also
> being "core developers".
> Alignment
> Taverna dependencies include Apache Commons, Axis, Abdera, Batik, CXF,
> Derby, Felix, HttpComponents, Jena, log4j, Maven, POI, Velocity, Xerces,
> XMLBeans, Xalan, We use Tomcat for testing and deployment of the Taverna
> Server.As part of moving to Apache-compatible dependencies, Taverna will
> probably adopt OpenJPA to replace (LGPL) Hibernate.
> Known Risks
> Orphaned products
> Most of the core developers are from the myGrid team at the University of
> Manchester, but are funded through a series of projects. Many of these
> projects incorporate Taverna, so the effort from Manchester is partially
> based on direct project requirements, but also partially on a volunteer
> effort for project maintenance and general development. The myGrid team has
> guaranteed funding until 2017.
> The developers that are outside Manchester are generally funded for other
> activities, and so their effort to Taverna is to a greater extent a
> volunteer effort - although again project-specific requirements steer their
> effort (e.g. for a new Taverna plugin).
> One of the reasons for our desire to move to the Apache Foundation is to
> formalise this volunteering/contribution effort so that it becomes obvious
> that it is not just the University of Manchester that is contributing to
> the core code base - and therefore reducing the impression that Taverna is
> vulnerable to Manchester’s future funding and projects.
> Inexperience with Open Source
> Taverna has been an open-source project since its first release in
> 2003. Most of the contributors also have experience with working with and
> contributing to other open source projects (e.g. TCL, CXF, Jena),
> particularly as Taverna strongly relies on other open source tools. Most of
> the research projects which the myGrid members have participated in
> produces open-source software.
> Homogeneous Developers
> The committers' list includes many people from the myGrid group from the
> University of Manchester in United Kingdom - but these developers have been
> working on a range of distributed and European projects in the field of
> scientific software.
> The other developers on the committers' list come from many different
> projects and institutions across the world, e.g. Russia, Canada, Germany
> and Spain.
> Reliance on Salaried Developers
> Development of Taverna is mainly performed as part of the developers'
> salaried work, but funded through many different projects at several
> institutions (see above). These projects do not generally have "contribute
> to Taverna" as their main goals - so therefore in many ways the effort is
> still volunteer-based - contributing to Taverna as a way to support one's
> own work.
> From our experience of running Taverna over the last 10 years, new 
> contributors will continue to join as Taverna becomes an ingredient in new 
> projects, while existing contributors more slowly fade out of their 
> involvement. Often existing contributors and users gives the personal link to 
> the new contributors.
> Relationships with Other Apache Products
> Apache already contains projects that seem relevant to Taverna.
> Apache Airavata http://airavata.apache.org/ is a software framework for
> executing and managing computational jobs and workflows on distributed
> computing resources. Taverna's concern is not as much job coordination, but
> more of a data flow between services. Airavata's XBaya Workflow Suite can
> export workflows in Taverna 1 format SCUFL, but could be updated to work
> with Taverna 3's SCUFL2 format.
> Apache ODE https://ode.apache.org/ is a WS-BPEL workflow engine. BPEL as a
> workflow language is quite verbose compared to dataflow languages like
> Taverna, and is additionally bound to a particular protocol
> (SOAP). Nevertheless, a sub-section of Taverna workflows could in theory
> run on the Apache ODE engine - and the Taverna 3 Platform API has
> facilities for plugging in alternative workflow engines. We have previously
> considered Apache Hadoop as one such alternate engine for executing a
> different subset of workflows with local command line tools.
> Apache OODT http://oodt.apache.org is a scientific data processing and data
> management system. OODT has a workflow manager, a file manager, and a
> resource manager, along with client-side frameworks including an automatic
> remote file acquisition system; automated crawler, and science algorithm
> wrapping facility. OODT and Taverna could benefit from cross pollination.
> Apache Pig https://pig.apache.org/ is a high-level language for creating
> Map-Reduce programs for Apache Hadoop. There already exists third-party
> efforts to convert Taverna Workflows to Hadoop and Pig -
> https://github.com/umaqsud/taverna-to-pig
> https://github.com/schenck/taverna-to-hadoop (thus making a graphical
> interface for building Apache Pig workflows) - and part of the Apache
> Taverna effort would be to invite these to join the project.
> Apache Storm http://storm.incubator.apache.org/ is a distributed real-time
> computation framework. Experiments are under development to use Taverna as
> a front-end for creating Apache Storm workflows -
> http://markmail.org/message/zg5ylo2aucpwfc5j
> Apache has several popular frameworks for building REST/SOAP web services
> (Apache CXF, Apache Clerezza), data services (Apache Jena, Apache Hive,
> Apache CouchDB) and specific workflow engines (Apache Oozie for Hadoop,
> Apache ODE for WS-BPEL). Taverna as a general REST and SOAP service client
> can be used for combining, testing and demonstrating such services.
> An Excessive Fascination with the Apache Brand
> Taverna is a long-running project (since 2003) with an existing user- and
> developer base across the academic world. Our main motivation for moving to
> Apache is to further encourage an open development process and engage
> existing and new developers to contribute to the core code base. We also
> want to ensure long-term continuity of the Taverna products, and for its
> future directions to be decided by the whole Taverna community rather than
> one of the parties involved.
> Documentation
> Taverna's documentation is available from
> http://www.taverna.org.uk/documentation/taverna-2-x/, including the
> extensive user manual, tutorials and videos.
> The developer documentation includes developer tutorials for working with
> Taverna's source code and creating plugins.
> Initial Source
> Taverna's source code is available from the 'taverna' github team account:
> https://github.com/taverna/. These 85 git repositories reflect the current
> modules of Taverna's plugin system after recently transitioning from Google
> Code SVN at http://taverna.googlecode.com/svn/taverna/. The history of
> Taverna's code base goes back to being hosted in CVS at SourceForge
> http://taverna.cvs.sourceforge.net/, transitioned as of
> http://taverna.googlecode.com/svn/archived/cvs2svn-2008-09-25/. Note that
> reasonable steps have been made to preserve commit history when moving
> between version control system, this has not always been achieved when
> moving between modules and refactoring larger Java packages. Some source
> files might therefore in git have initial commits like "Moved from
> /taverna/utils/trunk" referring to SVN paths.
> One of the reason for many repositories is that we rely on Apache Maven and
> a plugin system (since Taverna 3 OSGi-based) where different modules have
> different version numbers and release cycles (e.g. tags/branches). This is
> essential for the plug-in support of Taverna as the plug-ins depend on the
> semantic versioning of the APIs and required implementations.
> It is however in our current plans to merge repositories that have similar
> release cycles and greatly reduce the number of repositories, to about 10
> repositories that would be imported to Apache's Git server.
> We suggest that this would be the first phase of the incubator project, to
> prepare and stage the merged repositories to
> https://github.com/taverna-incubator
> Taverna source code uses the package names (and children packages):
>    net.sf.taverna - since Taverna 2
>    uk.org.taverna - new from Taverna 3
>    org.taverna (sic) - Taverna Server
> Some contributed code uses package names depending on their originating 
> projects:
>    org.purl.wf4ever.provtaverna
>    org.biomart.martservice
> We intend to release only the upcoming Taverna 3.0 version under the Apache
> umbrella (not 2.x) - therefore, according to semantic versioning rules
> http://semver.org/, the transition period of the Apache Incubator would be
> the best (and possibly only) chance to rename Java packages and Maven
> groupIDs to org.apache.taverna.* Under OSGi the packaging and JAR goes
> hand-in-hand (several JARs don't normally provide the same package), and
> therefore any package rename would be done together with the repository
> restructuring.
> Source and Intellectual Property Submission Plan
>    Taverna source code from http://github.com/taverna/ (to be staged as a 
> reduced list of repositories at https://github.com/taverna-incubator )
>        (c) University of Manchester.
>        Signed Apache-like CLAs for all external contributors.
>        Current license is LGPL 2.1 (and GPL3 for one domain-specific 
> download), as sole copyright holder Manchester will change this to Apache 
> License 2.0
>        Check-out-all-and-build meta project - 
> https://github.com/taverna/taverna-build
>    taverna.org.uk domain - registrant University of Manchester
>    http://www.taverna.org.uk/ content (c) University of Manchester
>    http://dev.mygrid.org.uk/wiki/display/tav250/ Confluence wiki content (c) 
> University of Manchester
>    http://dev.mygrid.org.uk/wiki/display/developer Confluence wiki content 
> (c) University of Manchester
> The details of intellectual property submission will be worked out together
> with myGrid project manager Shoaib Sufi and the University of Manchester's
> Contracts Office.
> As University of Manchester is the copyright holder of all the Taverna
> Source code (either directly or through signed CLAs), we are able to change
> the license to Apache License 2.0 wholesale.
> External Dependencies
> Taverna, as an integrating workflow system, has a fairly large number of
> dependencies - the latest 2.5.0 Core Workbench distribution has 517 JARs
> (although many of those are duplicates in different versions)
> We are intending for our first Apache-based release to be Taverna 3, which
> has already reduced this dependency list.
> We have performed an analysis of Taverna 3 dependencies - this list should
> be complete for the dependencies (and their transitive dependencies) of
> Taverna Workbench.
> The internal dependencies that are managed by Taverna/myGrid would need to
> be part of the transition to Apache so that their license can change from
> LGPL 2.1 to Apache License 2.0. As we will change groupId at the same time
> to org.apache.taverna, it should be fairly trivial to ensure that no JARs
> from the original Taverna repositories are included in the first Apache
> releases, as
>    They are only available from the Taverna Maven repository
>    Their groupId (net.sf.taverna/uk.org.mygrid/uk.org.taverna) would be
>    easy to identify in the distribution folder.
> We know that some of the external dependencies are licensed as LGPL, and
> for AstroTaverna, some dependencies are licensed as LGPL. As Apache License
> is incompatible with *GPL (but not vice versa), the general solution we
> suggest for this is to either:
>    Try to use alternative non-LGPL dependencies, aka. Apache JPA instead
>    of Hibernate
>    Keep module that requires LGPL dependency as a separate Taverna plugin,
>    maintained and published independently at Github
>    (e.g. https://github.com/wf4ever/astrotaverna ).
> In our analysis of Taverna's third party licenses we have identified the
> incompatible GPL/LGPL dependencies and suggested a resolution that will be
> performed as part of incubation.
> We found a list of dependencies with unknown licences (not declared through
> Maven). Part of incubation is to fully resolve this list as it could be
> hiding additional incompatible dependencies. (In many cases, simply using a
> newer version will include licensing information.)
> Cryptography
> Taverna uses these cryptography dependencies:
>    BouncyCastle
>    OpenJDK builds with the default JCE full/strong encryption policy (bundled 
> in installer)
> Taverna utilise these to form of an encrypted keystore (storing
> username/password and client certificates for third-party services accessed
> by the designed workflow) with corresponding user interface, and
> additionally binds to Java's SSL support to provide UI and command line
> options for security interactions, e.g. accepting new server certificates,
> or asking for username/passwords for HTTP Basic Authentication (which can
> then be stored in the keystore).
> Required Resources
> Taverna currently relies on a mixture of infrastructure hosted for free by
> third-parties (e.g. Github, SourceForge, GoogleCode, Launchpad, Bitbucket)
> and infrastructure hosted by the myGrid group at the University of
> Manchester (Jenkins, Jira, Confluence, Wordpress).
> Mailing lists
> Existing mailing lists for Taverna are hosted at Sourceforge with archives
> at markmail. See http://www.taverna.org.uk/about/
>    comm...@taverna.incubator.apache.org (replacing 
> taverna-...@lists.sourceforge.net )
>    priv...@taverna.incubator.apache.org (replacing supp...@mygrid.org.uk - to 
> a lesser degree as we would want to encourage openness)
>    d...@taverna.incubator.apache.org (replacing 
> taverna-hack...@lists.sourceforge.net , 240 members)
>    us...@taverna.incubator.apache.org (replacing 
> taverna-us...@lists.sourceforge.net , 370 members)
> Git repositories
> The Taverna community would prefer to keep using git and Github, and we
> would request for experimental writable git repositories
> http://www.apache.org/dev/writable-git with mirroring to Github.
> The repositories would be named taverna-*, as the current repositories on
> the github team: https://github.com/taverna/. This repository organization
> is styled equivalent to the git repositories of cordova-* and couchdb-*.
> Exactly how repositories are split/merged is open for discussion - it is
> part of our current plan to reduce the number of repositories by merging
> common modules with a similar release cycle - this could be done at an
> early phase of the incubation period.
> Issue Tracking
> JIRA Taverna (TAV)
> Existing issues in Taverna 3's current JIRA -
> http://dev.mygrid.org.uk/issues/browse/T3 - should be imported - but its
> current list of Modules should be further agreed.
> Other Resources
>    Wiki spaces in Confluence https://cwiki.apache.org/confluence -
>    importing the most recent Taverna-related spaces and documentation from
>    http://dev.mygrid.org.uk/wiki/spacedirectory/view.action?startIndex=24
>    Jenkins - replacing myGrid Jenkins at http://build.mygrid.org.uk/ci/
>    Maven repository at https://repository.apache.org/ - replacing myGrid
>    artifactory http://repository.mygrid.org.uk/
>    File-based Web space for Plugin Update Site - replacing
>    http://updates.taverna.org.uk/ and
>    http://www.mygrid.org.uk/taverna/updates/
>    Home pages - to be transitioned from from http://www.taverna.org.uk/ 
> (Wordpress)
>    Binary distribution download hosting, about ~8 GB pr release, replacing
>    http://www.taverna.org.uk/download/ (currently downloads are hosted by
>    http://launchpad.net/ and https://bitbucket.org/)
> Initial Committers
> The initial list of committers reflect the current list of active
> developers at the Github team: https://github.com/orgs/taverna/people (Note
> that not all of these have made their membership public on Github)
> Alan R Williams
> alan.r.willi...@manchester.ac.uk
> Aleksandra Nenadic
> a.nena...@manchester.ac.uk
> Christian Y. Brenninkmeijer
> brenn...@cs.man.ac.uk
> David Withers
> david.with...@gmail.com
> Dmitriy Repchevsky
> dmitry.repchev...@bsc.es
> Donal K. Fellows
> donal.k.fell...@manchester.ac.uk
> Finn Bacall
> finn.bac...@manchester.ac.uk
> Hajo Nils Krabbenhöft
> h...@krabbenhoeft.de
> Ian Dunlop
> ian.dun...@manchester.ac.uk
> Ingo Wassink
> i.h.c.wass...@ewi.utwente.nl
> Julián Garrido
> jgarr...@iaa.es
> Mark Wilkinson
> ma...@illuminae.com
> Luke McCarthy
> elmccar...@gmail.com
> Robert Haines
> rhai...@manchester.ac.uk
> Shoaib Sufi
> shoaib.s...@manchester.ac.uk
> Steffen Möller
> moel...@inb.uni-luebeck.de
> Stian Soiland-Reyes
> st...@soiland-reyes.com
>       (ICLA on file.)
> Stuart Owen
> so...@cs.manchester.ac.uk
> In addition to the Core Team (mentioned earlier), this list also reflects
> Taverna's existing meritocracy as it includes plugin developers whose
> contributions have been merged into the main code base. We acknowledge that
> not all of these are likely to continue as "Core" developers, but would
> like to encourage that during the Incubating process.
> Affiliations
> The majority of the initial committers are employed by University of
> Manchester as part of the myGrid team, including responsibilities for
> contributing to and supporting
> Taverna. http://www.mygrid.org.uk/about-us/people/core-mygrid-team/.
> Dmitriy Repchevsky is employed by the Barcelona Supercomputing Center,
> including responsibilities for contributing to Taverna. Steffen Möller is
> employed by University of Lübeck. Julián Garrido is employed by Instituto
> de Astrofísica de Andalucía.
> Sponsor Champion
> Andy Seaborne
> Nominated Mentors
>    Andy Seaborne
>    Chris Mattmann
>    Suresh Srinivas
>    Suresh Marru
>    Marlon Pierce
> Offers of participation, not formally a mentor:
>    Michael Joyce
> Sponsoring Entity
> The Incubator.
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