Interface Requirements for Workflow Manager-20091202

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					Interface Requirements for Workflow Manager


    wwPDB Common D & A project

            Annotation team
                 November 2009




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Jasmine/Jawahar                     Interface requirements for workflow manager                             Nov 2009



                       Interface Requirements for Workflow Manager


1. Login based on username and password. Login determines SITE identifier and the role assigned to the person logging
   on to the WF manager for the SITE.

2. User group dependent interface

3. User groups: accessibility to read and write at various interfaces is user group dependent. The public view
   (depositors) TBD.

    System Admin
    Lead Annotators/Coordinators
    Annotators
    Depositors

4. The privilege at each interface is site dependent. For example, annotator group may have write access for assignment
   and re-assignment at PDBe; Only lead annotator or coordinator has write access for assignment and reassignment at
   RCSB. This should ideally be tunable and set using a preferences panel available to the Lead Annotator/Coordinator
   for all user levels below the Lead Annotator.

5. Each task interface should display tree level (like bread crumbs) and allow annotators to switch from one workflow to
   another at different interface without interrupting each workflow. For example, from ligand processing of one PDB entry
   to external sequence alignment of another PDB entry. (This could require going up the tree as WF Manager -> Entry -
   > Workflow Details -> Ligand analysis, so switching from one to another would merely require a click on the WF
   manager in the bread crumbs and going down another WF).

6. Both stop (stop after finishing current task) and kill (immediate) should be made available at both workflow manager
   and task interfaces levels. The kill command should have pop up for confirmation. (Zukang has concern on the kill
   requirement- the cost is too high.)

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Jasmine/Jawahar                       Interface requirements for workflow manager                               Nov 2009


7. The level 2 workflow interface should be domain dependent (EM, BMRB, PDB).

8. During testing period, there should be a help button at every interface page for reporting bug on a particular task. The
   help button can be reduced to one page after fully tested. Choosing the help should transfer current state snapshot to
   the developers for debugging purposes.

9. Some workflow tasks can be hidden as default- Display only on demand. Filter options must be provided for
   annotators to select/screen what kind of information to be shown. For example, a lead annotator may wish to only view
   a particular task or a particular deposition if an annotator asks lead to take a look at a difficult case (read & write
   access), or to only view overall unassigned depositions across sites (read access only), or to only make assignment
   for his/her site (read & write access).

    Filter    Site     Status      Accession id   PDB id         Deposition data set id   Annotator initials
    options
              RCSB     PROC                       Multiple ids
              PDBe     WAIT
              PDBj     AUTH
              BMRB     HPUB
                       HOLD
                       POLC
                       REPL
                       WDRN
                       REL


10. A simplified table of Annotation Status from level 1 should be always visible on the top of every task interface. This is
    very useful when one annotator processes multiple entries at the same time; he/she is able to monitor the status of all
    the tasks and able to switch between tasks efficiently.

11. Common data items should be defined (see wwPDB D&A Mar 09 Annotation Summary) and should be automatically
    updated to multiple annotation workflows which are either from the same deposition data set or are related
    depositions. For example, one workflow is processing EM coordinate file, while the same time the other workflow is
    processing EM map. Author’s names are shared common data. If author’s name gets updated during EM coordinate
    processing workflow, then the updated information should also reflect in the EM map processing workflow.

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Jasmine/Jawahar                             Interface requirements for workflow manager                                             Nov 2009


12. Regarding immediate & remote modes, workflow tasks should be defined as optional vs mandatory (by demand vs
    automatic); the view and actions should be tunable based on this and is site dependent.

Note: The tables which list all the requirements are for data content purpose, not for the interface design.



Level 1- Lead Annotator Administrative
             a. Default view: Overall view of the deposition site activity. All open tickets, issues requiring attention with
                annotator and entry details.
             b. Actions could include assign, reassign etc.
             c. If statistics are necessary to be shown, then it must be on request and not a default view (a work practice
                issue).
             d. A calendar access very useful indicating holidays, absences etc.
Tasks

Assignments      Annotator    Deposition    PDB    Accession    Exp method          Deposition   Title          Author’s          Action:
                 initials     data set id   id     code                             site                        names             Assign
                                                                                                                                  Re-assign
                                                                                                                                  De-assign
Annotation       Annotator    Deposition    PDB    Task id      Task         Task   Action:
status           initials     data set id   id                  status       name   View task
                                                                                    details
Entry status     Annotator    Deposition    PDB    Process      Exp       Coord     Deposition   Initial     title     Author’s   Action: View
                 initials     data set id   id     site         data      status    date         process               names      Author’s
                                                                status                           date                             Correspondence
*Processing      Annotator    Start         End    # of         # of entries on     # of         # of entries Weekly or           Action:
Statistics       initials     Date          date   entries on   WAIT                entries on   processed       monthly          Run query
                                                   Proc                             AUTH                         average
                                                                                                                 On
                                                                                                                 processed
                                                                                                                 entries
*Deposition      Deposition   Deposition    PDB    Country of   Accession code      Start        End date        Number of        Action:
Statistics       site         data set id   id     the                              date                         entries          Run query
                                                   depositors                                                    deposited



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Jasmine/Jawahar                     Interface requirements for workflow manager                              Nov 2009


Highlighted ones are for input. The start and end dates are both inputs and are refreshed upon run action.

*Note: We understand that this workflow manager may not be suitable for querying statistics, but we need a place holder
for such tasks.




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Jasmine/Jawahar                    Interface requirements for workflow manager   Nov 2009



Level 1- Annotator view
      The individual tasks could be shown in the form of a flow diagram:




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Jasmine/Jawahar                              Interface requirements for workflow manager                                      Nov 2009


The following two sections details what the WF manager interface could look like at PDBe and RCSB. Ideally, we see it as
two sides of the same interface, where upon the settings can be setup such that each site could configure the local look-
and-feel of the WF manager (locked down vs unlocked etc). Essentially a tabular form with data.

PDBe

   a. Show unactioned assigned items, items requiring attention and open tickets (unassigned items)
   b. Assignments are not owner locked and annotators may self-assign tasks from the open tickets to themselves.
      Annotators may de-assign tasks after certain action back to open items. This is well in keeping with our work
      practice here and works best for our organizational structure. One of the actions for the annotator view could be de-
      assign or reassign.
   c. If it is necessary to have so many attributes to every entry, then it should be possible to fine tune what fields one
      wants to see (much like in Thunderbird or iTunes!). There will have to be some mandatory items
   d. Filter to see other annotator assignment within the same site.
   e. Filter to see other site (basic information only, no details on annotator for reasons of privacy etc).
   f. If statistics are necessary to be shown, then it must be on request and not a default view (again a work practice
      issue).
   g. Useful to have access to a calendar indicating holidays, absences etc.
   h. Action: View Details/Contact Depositor/De-assign

RCSB

*Annotation   Deposition    PDB     Annotator    Task id   Task      Task         Action:
status        data set id   id      initials               status    name         View
                                                                                  details
**Entry       Deposition    PDB     Coord        Exp       Process   Annotator    Deposition     Initial   title   Author’s    Action:
status        data set id   id      status       data      site      initials     date           process           names       View author correspondence
                                                 status                                          date                          Contact depositor
                                                                                                                               Request Re-assign
Processing    Annotator     Start   End date     # of      # of      # of         # of entries   Weekly/monthly       Action: Run query
Statistics    initials      date                 entries   entries   entries on   processed      average              Read only and accessible by annotator
                                                 on Proc   on        AUTH                        On processed         initials
                                                           WAIT                                  entries
*Note: Entry status and processing statistics are shown by demand. Default should only be Annotation status and should
only list the ongoing process entries owned by the login annotator. Others can be shown only by demand.

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Jasmine/Jawahar                       Interface requirements for workflow manager                            Nov 2009


**Note: List of entry status should be screened (by status, by initials, by site or by any combinations).

Level 2- Annotator view/ Annotation status details
       Each Circle is a process in the workflow as detailed in the table above. Greens indicate that the task has completed
       successfully, orange could indicate process completed but a warning was issued (not disastrous) or manual input
       needed, Red (process stuck due to error). White not yet done. There could be automatic steps in these (as above)
       as well as manual steps where the WF will pause and indicate manual input is required.

       Clicking on any of the circles should provide the log file output of that process with accompanying actions: Re-run,
       Stop, Retrieve Version, Report Bug, Bypass etc.




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 Jasmine/Jawahar                        Interface requirements for workflow manager                                    Nov 2009


 Details of a particular workflow is listed in the below table

Annotation   Deposit    PDB   Accessi   Task   Annotato     Task name                                 Date   version   action
status       ion data   id    on id     id     r initials                                             &
details      set id                                                                                   time
                                                            Format Checking                                            Retrieve version
                                                            *Text Editing**                                            Stop
                                                            *Ligand Analysis                                           Re-run
                                                                                                                       View log file
                                                            *Internal sequence alignment                               Report bug
                                                            *External sequence alignment                               Bypass
                                                            Verification of source organism                            Edit
                                                            Build sequence/coordinate relationship                     Download files
                                                            Entity Integration Check                                   View files
                                                            Various Corrections
                                                            Calculation of Derived data
                                                            *Prediction of Biological Assembly
                                                            Validation
                                                            Generation of Files
                                                            *Send Files/reports to author
                                                            Merge new coordinates
                                                            Merge new refinement statistics & other
                                                            Update citation
                                                            *Release
                                                            Update status
                                                            *Load to database
 *Note: Most of the tasks should be automatic without annotator’s intervention during the workflow except the marked
 ones.

 **Note: One of the workflow should allow annotator to do text editing, for example, change title or author’s name. The
 actions should include download entire cif or pdb file to local machine for review or list entire file for review. Download
 option is very important in the case where a structure is too complicated for system to handle and annotator should be
 able to escape the workflow and process it on the command line.

 EM and BMRB interface requirements TBD.

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Jasmine/Jawahar                      Interface requirements for workflow manager                              Nov 2009



Level 1- Depositor view*
PDB id   Coord    Exp      Process   Title    Author’s
         status   data     site               names
                  status
*Assuming that post processed full reports will be made available at deposition site for author’s review & feedback. This is
merely for authors to check status during processing. But the question would then be, do we want authors to see “live”
status or to see weekly updated status from public website?




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