business logic for annotation workflow tom oldfield july 21, 2010
TRANSCRIPT
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