API.md

 [[_TOC_]]
 
 ### Assertion API
-Assertion API endpoint for computing variant pathogenicity given a set of evidence counts and the specification to use. The specification used here is based on _Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology_.  Richards _et.al_ (https://pubmed.ncbi.nlm.nih.gov/25741868/). For ClinGen VCEP specific assertion criteria refer the CSpec Registry - https://cspec.genome.network
 
-**Summary of Sequence Variant Interpretation Reasoner service route which interprets a variant pathogenicity  assertion from Evidence and [Criteria Specification](https://cspec.genome.network)**
- 1. Request to the engine service _assertion_ route.
- 
- > **Route** for the assertion engine is  - https://cspec.genome.network/cspec/eng/svi/assertion.  This is a GET route with a payload (see next).
+Assertion API endpoint for computing variant pathogenicity given a set of evidence counts and assertion criteria. The specification used here is based on _Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology_. Richards _et.al_ (<https://pubmed.ncbi.nlm.nih.gov/25741868/>). For ClinGen VCEP specific assertion criteria refer the CSpec Registry - <https://cspec.genome.network>
 
->  A **payload** contains two required fields - evidence and cspecRuleSetUrl. 
->    An example of a payload object is given below:
-> 
-> ```
+**Summary of Sequence Variant Interpretation Reasoner service route which interprets a variant pathogenicity assertion from Evidence and** [**Criteria Specification**](https://cspec.genome.network)
+
+1. Request to the engine service _assertion_ route.
+
+> **Route** for the assertion engine is - <https://cspec.genome.network/cspec/eng/svi/assertion>. This is a GET route with a payload (see next).
+
+> A **payload** contains two required fields - evidence and cspecRuleSetUrl. An example of a payload object is given below:
+>
+> ```plaintext
 > let payload = { 
->   cspecRuleSetUrl: 'https://cspec.genome.network/cspec/RuleSet/id//643243101',
->   evidence:    { 
+>   cspecRuleSetUrl: 'https://cspec.genome.network/cspec/RuleSet/id/643243101',
+>   evidence: { 
 >     'Pathogenic.Moderate': 2,
 >     'Pathogenic.Strong': 1,
->     'Pathogenic.Supporting': 1
+>     'Pathogenic.Supporting': 1,
+>     'Pathogenic.Very Strong': 1 
 >    }
 >  }
 > ```
 
+A.4) Example of how the route works:
 
-   A.4) Example of how the route works:
-```
+```plaintext
 const SimpleJsonReq = require( "@brl/brl-gb/client/simple/simpleJsonReq" ).SimpleJsonReq
 let baseUrl = "https://cspec.genome.network/cspec/eng/svi"
 let clientOpts = { timeout: 600000 }
@@ -36,53 +38,15 @@ let reqConfig = {
   data: payload
 }
 resp = await jsClient.doGet('/assertion', reqConfig)
-> let engRespObj = global.brl.dot.pick('data', resp.data)
-undefined
-> engRespObj
-{ 
-  comment: 'As the rules only suggest one assertion that is Likely Pathogenic, the final assertion is Likely Pathogenic',
-  finalCall: 'Likely Pathogenic',
-  rules: // List of rules that are satisfied
-   [ { _conditions: [Array],
-       _inference: 'Likely Pathogenic',
-       _name: 'Rule20',
-       _satisfied: true,
-       _statement: 'Pathogenic.Strong ==1 & Pathogenic.Moderate ==2' } ],
-  statusObj: { // statusObj with status and name 
-    name: 'assertion computed', 
-    status: 'ok' 
-  } 
-```
-}
-   A.5. The SVI ENGINE helper classes - making an assertion interpretation with evidence and rules
-     A.5.1) Separate classes for Rule, MetRule, Interpretation and Condition are implemented.
-     A.5.2) Example of how it works
-//get cspec rules and metarules by making a request to the cspec service as shown below
-const BrlGbApp = require( "@brl/brl-gb/app/brlGbApp" )
-BrlGbApp.globalPrep()
-const SimpleJsonReq = require( "@brl/brl-gb/client/simple/simpleJsonReq" ).SimpleJsonReq
-let clientOpts = { timeout: 600000 }
-let baseUrl = 'https://cspec.genome.network/cspec'
-let jsClient = new SimpleJsonReq( baseUrl, clientOpts )
-jsClient = new SimpleJsonReq( baseUrl, clientOpts )
-let resp
-resp = await jsClient.doGet('/SequenceVariantInterpretation/id/GN006', {serverCertCheck:false})
-
-// run the assertion engine
-const Interpretation = require ('@brl/cspec-eng-svi/helpers/reasoner/interpretation').Interpretation
-let guidelineMetaRules = resp.data.data.entContent.guidelineMetaRules
-let evidence = { 'Pathogenic.Moderate': 2, 'Pathogenic.Strong': 1, 'Pathogenic.Supporting': 1 }
-const int = new Interpretation(evidence, guidelineMetaRules)
-resp = await int.makeInterpretation()
-console.log(resp)
-{ rules:
-   [ Rule {
-       _conditions: [Array],
-       _inference: 'Likely Pathogenic',
-       _name: 'Rule20',
-       _satisfied: true,
-       _statement: 'Pathogenic.Strong ==1 & Pathogenic.Moderate ==2' } ],
-  finalCall: 'Likely Pathogenic',
-  comment:
-   'As the rules only suggest one assertion that is Likely Pathogenic, the final assertion is Likely Pathogenic',
-  statusObj: { status: 'ok', name: 'assertion computed' } }
\ No newline at end of file
+> global.brl.dot.pick('data', resp.data)
+{ comment:
+   'Two assertions: Pathogenic and Likely Pathogenic were made. In such case the final call is the highest strength call, hence the allele is Pathogenic',
+  finalCall: 'Pathogenic',
+  rules:
+   [ { conditions: [Array], inference: 'Pathogenic', rule: 'Rule1' },
+     { conditions: [Array], inference: 'Pathogenic', rule: 'Rule2' },
+     { conditions: [Array],
+       inference: 'Likely Pathogenic',
+       rule: 'Rule20' } ],
+  statusObj: { name: 'assertion computed', status: 'ok' } }
+```
\ No newline at end of file