Taverna Workflow Bundle

The archive must be a ZIP file, and should have the file extension .wfbundle. Some situations might require treating the workflow bundle as an unpacked set of folders. In this case the top folder should still have the file extension .wfbundle.

According to the Adobe UCF specifications, the mimetype file must be the first file in the folder, and must be stored without compression, encryption or permission attributes, to support detection by mimemagic and similar.

The file META-INF/manifest.xml - if present - must list every non-META-INF file and folder in the archive, including the root folder. It should provide the mime-type - if known - for individual files. The root folder should have the same mime type as in the mimetype file - application/vnd.taverna.scufl2.workflow-bundle.

The file META-INF/container.xml - if present - should point to the 'root' workflow bundle document. One and only one entry which must be of the mime type application/rdf+xml, and this entry must be called workflowBundle.rdf. Alternative representation of the workflow bundle root document can be included in other formats, there's no similar restriction on their filenames, although it is recommended they match the RDF/XML filename, for instance workflowBundle.html, workflowBundle.json, etc.

The folder workflow contain each of the workflow definitions as Workflow Documents. One of these is typically the main workflow while the others are nested workflows, but there is no requirement that the workflows included are to be included as a nested workflow or a main workflow. Such 'dangling workflows' can be considered to be only declared workflows - they might be there for historical reasons or because the workflow bundle is at an early stage of development when there is no main workflow yet.

The execution details of workflows (such as activity choice, configuration) are described in the profile folder, one Profile Document per possible execution binding. (For instance, one profile for the graphical Workbench, one for the Taverna Server and one for the Taverna Portal.). One profile document can include execution details for several workflows, but there could also be workflows which don't have any execution details in any profile - these can be considered abstract workflows.

workflowBundle.rdf¶

The workflow bundle document workflowBundle.rdf should list each of these workflows and profiles, and should suggest the main workflow and main profile.

mimetype¶

This file is required, as a guide for mime magic and similar tools that guess the type of the archive. Therefore it must be added as the first file to the archive, uncompressed, so that its content is available in cleartext in the first bytes of the ZIP archive.

The file must be in ASCII and not contain any line feeds. If the archive is a Taverna Workflow Bundle, the mime type should be application/vnd.taverna.scufl2.workflow-bundle. If META-INF/manifest.xml is present, this mime type must match the mime type of "/" in the manifest.

To add the file mimetype as the first uncompressed file, followed by the rest of the bundle (excluding the mimetype file), try using InfoZip:

$ zip -0 -X ../example.wfbundle mimetype
  adding: mimetype (stored 0%)

$ zip -X -r ../example.wfbundle . -x mimetype
  adding: workflowBundle.rdf (deflated 74%)
  adding: workflow/ (stored 0%)
  adding: workflow/HelloWorld.rdf (stored 0%)
..
  adding: META-INF/ (stored 0%)
  adding: META-INF/manifest.xml (deflated 78%)
  adding: META-INF/container.xml (deflated 50%)

To verify:

$ unzip -lv ../example.wfbundle
Archive:  ../example.wfbundle
 Length   Method    Size  Cmpr    Date    Time   CRC-32   Name
--------  ------  ------- ---- ---------- ----- --------  ----
      35  Stored       35   0% 2010-10-11 16:44 8373c7d8  mimetype
    3047  Defl:N      786  74% 2010-10-13 09:40 743ecfe4  workflowBundle.rdf
       0  Stored        0   0% 2010-10-06 14:57 00000000  workflow/
...

$ python -c "print open ('../example.wfbundle').read(128)[38:84]"
print("code sample");`application/vnd.taverna.scufl2.workflow-bundle

META-INF/manifest.xml¶

This file, if exists, should follow the OpenDocument container format, and list every file in the bundle (except for the META-INF files). The main functionality provided by the manifest is to give the mime-type of additional resources. As a minimum the mime-type should distinguish between text/plain (UTF-8 text) and application/octet-stream (binary). If a mime-magick like tool has guessed a more detailed mime type, it can also be provided here.

Additionally the manifest may specify the file sizes, cccin general this can be useful when inspecting a larger workflow bundle remotely (exposed as a RESTful folder or similar).

The folder / represents the bundle itself, and must have the same mime type as in the file mimetype, ie. application/vnd.taverna.scufl2.workflow-bundle. A different mime type might be used if the primary purpose of the archive is different from being a workflow bundle, for instance being a Taverna Data Bundle.

The workflowBundle.rdf file must be listed in the manifest, and it must be listed with the application/rdf+xml mime type. Any alternative representations must also be listed, and their mime type must match those in META-INF/container.xml (see below).

The other folders are not required to have a mimetype.

If there is no manifest in the workflow bundle, all data value files should be treated to be binary application/octet-stream, unless they have one of these file extensions:

• *.txt is text/plain in UTF-8 character set
• *.rdf is application/rdf+xml

Example manifest:

<?xml version="1.0" encoding="UTF-8"?>
<manifest:manifest xmlns:manifest="urn:oasis:names:tc:opendocument:xmlns:manifest:1.0">
 <manifest:file-entry manifest:media-type="application/vnd.taverna.scufl2.workflow-bundle" manifest:full-path="/"/>

 <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="workflowBundle.rdf"/>
 <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="workflow/HelloWorld.rdf"/>
 <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="annotation/workflow/HelloWorld.rdf"/>
 <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="annotation/workflowBundle.rdf"/>
 <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="profile/tavernaWorkbench.rdf"/>
 <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="profile/tavernaServer.rdf"/>

 <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="workflowBundle.ttl"/>
 <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="workflow/HelloWorld.ttl"/>
 <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="annotation/workflow/HelloWorld.ttl"/>
 <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="annotation/workflowBundle.ttl"/>
 <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="profile/tavernaWorkbench.ttl"/>
 <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="profile/tavernaServer.ttl"/>

 <manifest:file-entry manifest:media-type="image/svg+xml" manifest:full-path="Thumbnails/thumbnail.svg"/>
 <manifest:file-entry manifest:media-type="image/png" manifest:full-path="Thumbnails/thumbnail.png"/>

 <manifest:file-entry manifest:media-type="image/svg+xml" manifest:full-path="diagram/workflow/HelloWorld.svg"/>
 <manifest:file-entry manifest:media-type="image/png" manifest:full-path="diagram/workflow/HelloWorld.png"/>
</manifest:manifest>

META-INF/container.xml¶

This file, if present, should point to the root workflow bundle document, which in an application/vnd.taverna.scufl2.workflow-bundle must be workflowBundle.rdf. Alternative representation of the same file are permitted, but SCUFL2 compliant tools are only required to understand the application/rdf+xml representations described here.

The Adobe UCF specification defines the format of this container file.

XML namespace in container.xml

Adobe UCF have used the XML namespace `urn:oasis:names:tc:opendocument:xmlns:container` although this format

is not defined by OASIS or the Open Document specification.

SCUFL2 compliant tools should therefore parse `container.xml` ignoring any default namespaces, and write using the default name

space and <container xmlns="urn:oasis:names:tc:opendocument:xmlns:container" as the root element.

If the archive is of the mime type application/vnd.taverna.scufl2.workflow-bundle and contains other representations of the workflow bundle (for instance: JSON, Turtle, t2flow) then the bundle must have a container file and list these representations in addition to workflowBundle.rdf. Derived representations such as SVG diagrams and HTML reports should generally not be listed as 'root files' unless they can be considered to 'fully represent the workflow bundle', for instance by using RDFa.

A SCUFL2 compliant parser can assume that an archive which is not of the mime type application/vnd.taverna.scufl2.workflow-bundle, but does contain a META-INF/container.xml-listed root file named workflowBundle.rdf, that file can be read as an RDF/XML representation of a workflow bundle document, even if it is not declared as having the application/rdf+xml mime type. This enables any future extensions superseeding this application/vnd.taverna.scufl2.workflow-bundle format.

All rootfiles must be equivalent and describe the same workflow structure, although additional formats can include more or less information than the required format. There should be only one rootfile per media-type, and there must be a rootfile for the media type application/rdf+xml.

Example:

<?xml version="1.0"?>
<container version="1.0"
    xmlns="urn:oasis:names:tc:opendocument:xmlns:container">
    <rootfiles>
        <rootfile full-path="workflowBundle.ttl"
         media-type="text/turtle" /> 
        <rootfile full-path="workflowBundle.rdf"
         media-type="application/rdf+xml" /> 
    </rootfiles>
    <relationships>
        <relationship type="metadata" target="/annotation/$dir/$filename.$ext" />
    </relationships>
</container>

Unknown files and file types¶

Any other files in workflow and profile should be ignored by SCUFL2 compliant parsers, regardless of if they have the application/rdf+xml mime type or not. When a SCUFL2 compliant tool has modified an existing Workflow Bundle, it should remove such unknown files from workflow and profile when saving, unless it has the capabilities to also update these. These files would typically be representations in other formats which would be out of date after the editing. On the other hand, if the tool has not structurally modified a workflow or profile, the tool should not remove unknown files from workflow and profile.

On removal of files, the tool should also remove them from META-INF/manifest.xml and if necessary from META-INF/container.xml.

Additional resources¶

The workflow bundle format is an open-ended specification, so the archive can include additional resources not described here.

For instance the bundle can include:

• Thumbnail of bundle (mini-diagram) (Recommendation: META-INF/Thumbnails/thumbnail.png and Thumbnails/thumbnail.svg)
• Ontologies referenced from RDF/XML files, in particular from configurations (Recommendation: ontology/taverna2.2/beanshell.rdf)
• Diagrams of workflows (Recommendation: diagram/workflow/HelloWorld.svg and .png)
• Alternative representations (RDF, JSON) (Recommendation: Same naming conventions with different extensions)
• Annotations (Recommendation: under annotations/ in RDF/XML format) - one file per annotation source, like `myExperiment.rdf)
• Resources/binaries/data needed by workflow (Recommendation: under resources/
• Example input and output data (Recommendation: as in data bundle)
• Provenance and data of one or more workflow runs (Recommendation: under run/

A workflow bundle can also play 'double roles' by being other bundles, like a data bundle. It is the mimetype and root file that determines what is the "main function" of the bundle, suggesting which tool should primarily open the bundle. One can for instance imagine an UCF archive which primarily is an Adobe PDFXML file for a published paper (see: Mars project) and should be opened in Adobe Acrobat Reader. However, it can also contain workflowBundle.rdf, workflow/importantResearch.rdf, and could therefore also be opened using SCUFL2 tools.