Skip to end of metadata
Go to start of metadata

Please have a look at the alpha release to the Stilts based Table Tool plugin.

Plugin base: http://ondex2.cs.man.ac.uk/repository/net/sf/taverna/t2/activities/stilts/

Code: hhttps://github.com/taverna/table-activity

Known Bugs

Activity hangs if not configured correctly

  • This is caused by Stilts being a CommandLine tool
  • Workaround appeared to work in unit tests
  • Do not understand the File / String / URL choice
  • Delete column(s) does not always terminate
  • Add column configuration is extremely confusing / broken
  • Port names should not have spaces
  • Service names should not contain punctuation
  • Need consistent capitalization e.g. "reformat" v "Sort rows"
  • reformat does not work for comma to tab separated conversion. It returned
    • C:\Users\alanrw\AppData\Local\Temp\astro2085142791920992086.tmp

      # Attempted guesses about identity of columns in the table.
      # These have been inferred from column UCDs and/or names
      # in the original table data.
      # The algorithm which identifies these columns is not particularly reliable,
      # so it is possible that these are incorrect.
      id_col: 27
      ra_col: -1
      dec_col: -1

      # This TST file generated by STIL v3.0-3

      authorship genusPart infragenericEpithet specificEpithet infraspecificEpithet nameComplete uninomial taxonName occurrenceID decimalLatitude decimalLongitude earliestDateCollected latestDateCollected coordinateUncertaintyInMeters country collector fieldNotes locality maximumDepthInMeters maximumElevationInMeters minimumDepthInMeters minimumElevationInMeters value dataProviderName dataResourceName dataResourceRights dataResourceCitation Index
      ---------- --------- ------------------- --------------- -------------------- ------------ --------- --------- ------------ --------------- ---------------- --------------------- ------------------- ----------------------------- ------- --------- ---------- -------- -------------------- ------------------------ -------------------- ------------------------ ----- ---------------- ---------------- ------------------ -------------------- -----
      japonica Tapes japonica Tapes japonica 38983410 Hawaiian Islands; Oahu; Pearl Harbor Bernice Pauahi Bishop Museum Bishop Museum Natural Sciences Data BPBM data records may be used by individual researchers or research groups, but they may not be repackaged, resold, or redistributed in any form without the express written consent of a curatorial staff member of the BPBM. If any of these records are used in an analysis or report, the provenance of the original data must be acknowledged and the BPBM notified. The Bernice P. Bishop Museum and its staff are not responsible for damages, injury or loss due to the use of these data. Bishop Museum Natural History Data 1
      japonica Tapes japonica Tapes japonica 40833298 35.4492 139.642 Japan Kanagawa Prefectural Office Marine Science Institute, UCSB Paleobiology Database Varied sources. Individual references may be obtained from website (paleodb.org) 2
      japonica Tapes japonica Tapes japonica 147680709 USA Vokes, H. E. R-0276 Florida Museum of Natural History Malacology specimens In progress In progress 3
      japonica Tapes japonica Tapes japonica 147680711 Canada Vokes R-0404 Florida Museum of Natural History Malacology specimens In progress In progress 4
      japonica Tapes japonica Tapes japonica 147680710 Canada Kocurko, J. R-0402 Florida Museum of Natural History Malacology specimens In progress In progress 5
      [EOD]


  • Need spell check - "Keeap", "comannd"
  • Select rows configuration is extremely confusing / broken
  • Sort rows configuration - ticking the ascending box makes the sort into descending
  • The icon is messy and looks like a GPU bug (smile)
  • Need colour for activity

General

  1. Need to have an icon for Stilts - at the moment uses black cog
    1. Addressed for Service panel but not for Workflow Explorer as of course they don't pick up icons in the same way.
  2. The names of the services are inconsistent in their capitalisation
    1. Fixed
  3. Alan thinks you could use some hierarchy e.g. Stilts Tools -> Add Column -> Fully Configurable
    1. Improved
  4. The different variants of Add Column are confusing
    1. Replaced different versions with a command wizard for building the equation
  5. Using "Stilts Tools" as the name is not a good idea. This is similar to the discussion of Sardine v WebDAV, Should say what it gives the user not what the underlying technology is
    1. Changed to "Table processing tools"
  6. Need descriptions of the services
    1. Added
  7. You can only configure from the Details panel. There must be a contextual menu entry. This would also get the "select and press return" trick to work
    1. Jumped through all the hoops to get a configuration on right click.
  8. Do the services make sense without configuration? If not, then you need to make the configuration pop up when they are added to the workflow
    1. Configuration opens during drag and drop.
  9. Need to look at overlap with the spreadsheet service.
    1. Note done!
  10. Need to check the spelling. For example, in the configuration of Keep Column(s) it has "Seperaated by a space".
    1. Fixed a few but spelling is not by Stong point.

Details panel

  1. The UI has to be changed to have normal Taverna look
    1. Done
  2. Lots of strange and (to me) meaningless information - it needs to be userrelevant
    1. Many improved
  3. Details has heading "Test" - should be something better e.g. "Table service"
    1. Fixed

Configuration Panel Recommendations

  1. For preprocessing only hide the fact it depends on "Simple Piping Tool"
    1. Done
  2. Reconfigure configuration gui to standard Taverna table look
    1. Highly improved
  3. Split tool tips over various lines
    1. Done
  4. In the list of formats, the entries need to be ordered. At the moment they appear to be random.
    1. Changed from Stilts order to user based one.

Additional Functionality Desired

 

Labels
  • None