Business logic for annotation workflow

Tom OldfieldJuly 21, 2010

Glossary• Deposition Business workflow: the over arching workflow that the server-engine manages during the

deposition process. This workflow includes all of the component modules as well as the initiation and closure functions: eg. login/deposition/submit

• Annotation Business workflow: The over arching workflow that the server-engine manages during the annotation process. This workflow includes all of the component modules as well as the initiation and closure functions: eg. login/deposition/annotation/release

• Module workflow: The individual workflow that does a “component” of work : eg. sequence annotation. It is controlled by the sequence XML file

• Server Engine: A copy of the workflow engine that runs multiple workflow-engine children that do module

WF. It divides up work on multiple computers. Its action is controlled by the business workflow XML.

Deposition AnnotationLogin ReleaseBusiness logic(server engine)

SequenceModules: A big bit of work – sequence annotation

Task : basic unit of work : blast alignment/ sequence interface

General system requirements1. The Deposition business workflow is started when a depositor goes to

the wwPDB deposition site -> deposition proceeds automatically -> Depositor hits - [submit]

2. The Annotation business workflow is started when the depositor presses [submit]

3. The Annotation business workflow starts automatically, reads through the deposition report and if all criteria is met the system will proceeds through the prescribed tasks. Starting with the Ligand module.

4. The resulting “data” is prepared “offline” -> the annotator does nothing until “waiting” appears on the WFM screen.

5. When the Ligand module completes it’s processing the server engine would automatically run the next module -> sequence module

6. It would be expected that an annotator would arrive in the morning with a list of entries at various stages of “waiting” representing process module interfaces in need of annotator input, as well as, a list of “finished” for depositions that have completed the process without incident.

Introduction to “Level 2”

• The business logic for the annotation workflow is controlled by a workflow XML file.

• This business workflow (Workflow execution) runs the module workflows.

• It checks that each workflow ran correctly and then runs the next step in the business flow.

• It manages goback, stop, start, kill, restart

Workflow Management – A parallel process

• Business Workflow Execution: the WF manages/invokes the business rules (logic) to run the workflow which consists of the modules that make up the full business process: sequence, ligand, validation....

• Workflow Monitor: The business workflow contains a monitor task that communicates with other components of the system. This is a single infinite task (?)Please give a simple examples of this.

Workflow ExecutionOption #1 Pre-defined Sequential pipeline.

– This is the simple option where the modules are run in a pre-defined order

– This represents the default path, through which we expect that 80% of the depositions will conform.

– In the event of “special case” entries or an “exception” occurs the annotator will direct the deposition out of this path into Option #2.

validation Ligand Sequence

Direct/Monitor/Alert

Business workflow of modules Option #2 – Annotator directed path. • This option enables the processing annotator to order the annotation

path by choosing which module to run

Interface(O) – Sequence(O) – validation(O) – ligand

Sequence

Ligand

Validation

AutoDone all ?

NO

YES

Default business logicThis is our understanding of the default business logic – This maps to the business process map of

annotation (with chopper added) that we developed over a year ago – see next 2 slides. We should have the group sign off on this

1. Start with Ligand module2. If no ligand is found, go to sequence

processing3. If Ligand – then process ligand first4. If Ligand contains a sequence (inhibitor

example) invoke chopper, complete ligand.5. Once ligand complete go to Sequence

Processing

Release ProcessingRelease Processing

Calculated annotations(Bio Assem)

Calculated annotations(Bio Assem)

Corrections (water trans, pro-chiral ck)

Corrections (water trans, pro-chiral ck)

Geometry CKValidationGeometry CKValidation

User InterfaceWFE/WFM/API

Requirements

Design

LigandProcessingLigandProcessing

Progress Tracking/ Status

Progress Tracking/ Status

Sequence ProcessingModule

4.1, 4.24.34.44.5

DeliveredMay 6, 2010

Annotation Pipeline

LigandChop-per

LigandChop-per

FunctionalCode Dev.

Production Annotation: All Experimental Methods Updated Nov 18, 2008

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wwPDB Data Model Concept Team Mtg November 6,7, 2008

22.0 Integrate all data, create

summary report

Depositor information· Method type· Experimental Data· Derived Data· Added value Annot.· Outstanding issues

report

Captured at Deposition

25.0 Create Author Annotation Report

15.0, 16.0, 17.0, 18.0, 19.0 Domain specific validation processes (super

#5, #9)1. Address remaining depo. Issues, ensure file completeness and consistency with controlled vocab.2. External Ref. Check, ie. Fit to experiment, Assembly, Active Site

21.3 Integrate with external DB

Ie. UniProt, Taxid

21.2 Calculation engines

Ie. MSDfold

21.1 Integrate with comparative

measure against DBIe. Z values

Standard uncertainty

24.0 create all data files in

required formats

21.0 create value added data

18.0 Ligand processing

Ligand?

no

Existing ligand?

yes

23.0 Final expert review

and valiadtion

OK

yes

OK

no

5.0 / 7.0 or direct communication

14.1Data Inventory check based on

method

EM maps Process (19.0)

NMR Chem Shift Process (19.0)

XYZ coor. (15.0)

yes

yes

Update cross ref. Ligand Data

Load sharing?

Xray SF (16.0)

Load sharing?

NMR MR (17.0)

no

20.0 Annotator Review

no

Quality Validation Processes: TBD Validation Task

Force

File ok no5.0 / 7.0 or direct communication

14.0 “Splitter” 14.2

We may want to update this map – sequence processing is the first “validation” step. I will take a first pass with Jasmine. Step 4 in the previous slide pertains to breakdown of step 15 on this one

The business workflow is : Level 2

• The annotator staff see this workflow as the Level 2 view in the WFM

• The monitor process : clicking this will show the business workflow (in level 3)

• The following slide shows sequential order of modules.– TBD : the ability to render complex workflow

diagram on level 2 (ie non-sequential.)– Not for August.

Level 2 : Business workflow

(a) GoBack

(b) Insert new data/restart here

(c) Return to interface

(d) Data in/out

Arrows, boxes and buttons are active and do things when clicked

Click boxes to go to Level 3

I believe based on the process maps that we need to flip these two. Also we need sign off by the annotators on the UI layout