Business logic for annotation workflow Tom Oldfield July 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. DepositionAnnotationLoginRelease Business logic (server engine) Sequence Modules: A big bit of work – sequence annotation Task : basic unit of work : blast alignment/ sequence interface

General system requirements 1.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 Execution Option #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. validationLigandSequence 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 Auto Done all ? NO YES

Default business logic This 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 module 2.If no ligand is found, go to sequence processing 3.If Ligand – then process ligand first 4.If Ligand contains a sequence (inhibitor example) invoke chopper, complete ligand. 5.Once ligand complete go to Sequence Processing

Release Processing Calculated annotations (Bio Assem) Calculated annotations (Bio Assem) Corrections (water trans, pro-chiral ck) Geometry CK Validation Geometry CK Validation User Interface WFE/WFM/API Requirements Design Ligand Processing Ligand Processing Progress Tracking/ Status Sequence Processing Module 4.1, Delivered May 6, 2010 Annotation Pipeline Ligand Chop- per Ligand Chop- per Functional Code Dev.

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