API.md

+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).
+
+>  A **payload** contains two required fields - evidence and cspecRuleSetUrl. 
+>    An example of a payload object is given below:
+> 
+> ```
+> let payload = { 
+>   cspecRuleSetUrl: 'https://cspec.genome.network/cspec/RuleSet/id//643243101',
+>   evidence:    { 
+>     'Pathogenic.Moderate': 2,
+>     'Pathogenic.Strong': 1,
+>     'Pathogenic.Supporting': 1
+>    }
+>  }
+> ```
+
+
+   A.4) Example of how the route works:
+```
+const SimpleJsonReq = require( "@brl/brl-gb/client/simple/simpleJsonReq" ).SimpleJsonReq
+let baseUrl = "https://cspec.genome.network/cspec/eng/svi"
+let clientOpts = { timeout: 600000 }
+let jsClient = undefined
+let resp = undefined
+jsClient = new SimpleJsonReq( baseUrl, clientOpts )
+let reqConfig = {
+  serverCertCheck : false, 
+  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' } }
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