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Eric Prud'hommeauxclaude
Eric Prud'hommeaux
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claude
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+ evidence-dnf: abstracted DNF rule engine + compiler mode-toggle tests
An evidence-appraisal abstraction of a production rule engine (components -> evidence; component types -> observational/rnc study types; diameterInInches -> pValue; material -> effectMeasure with OddsRatio/AdjustedOddsRatio/HazardRatio values; study-sounding names throughout; the recommendation UNION arm and its data omitted): tests/Algae3/evidence-dnf.rq + data/evidence{,-groups,-rules}.ttl, structurally identical to the source (same selectors/disjuncts/conjuncts, polarities and olo:index ordering) - two rules fire with the same shape of per-level logs. Compiler mode-toggle coverage: - evidence-dnf.{topdown,bottomup}.a3: committed sparql-to-a3.js outputs (regen + self-check: tests/Algae3/regen-compiled.mjs, needs node). - test_Algae3 evaluates both against one golden and re-runs each under both engine modes (the workaround-style query is well-designed, so all four combinations agree). - sparql-to-a3.js: SPARQL query blank nodes now compile as ?_bn_* variables - they are BGP-scoped existentials (SPARQL 4.1.4) and a3 blank nodes do not join across '.' boundaries; this fixes a cross-join of every rule with every message. - engine load: pseudo-absolute file:/rel paths (from a bare BASE <file:>) retry relative to the script directory. All 22 suites pass. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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‎lib/Algae3.cpp‎

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@@ -630,9 +630,17 @@ namespace a3 {
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if (!path.empty() && path[0] != '/' && !e.baseDir.empty())
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path = e.baseDir + "/" + path;
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std::ifstream check(path.c_str());
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if (!check.good())
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if (!check.good() && path[0] == '/' && !e.baseDir.empty()) {
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/* a bare `file:` base yields pseudo-absolute /rel paths;
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* retry relative to the script directory */
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std::string rel = e.baseDir + path;
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std::ifstream retry(rel.c_str());
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if (retry.good())
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path = rel;
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}
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std::ifstream check2(path.c_str());
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if (!check2.good())
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throw std::string("load: cannot open \"") + path + "\"";
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check.close();
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IStreamContext istr(path, IStreamContext::FILE);
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/* a fresh driver per load: its private bnode map standardizes
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* blank nodes apart, making load a graph MERGE; `as` leaves the

‎sparql-to-a3.js‎

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@@ -25,7 +25,10 @@ function term(t) {
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switch (t.termType) {
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case "NamedNode": return "<" + t.value + ">";
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case "Variable": return "?" + t.value;
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case "BlankNode": return "_:" + t.value.replace(/[^A-Za-z0-9_]/g, "_");
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case "BlankNode": /* query blank nodes are existential variables scoped to
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the BGP (SPARQL 4.1.4); Algae 3 blank nodes do not join across `.`
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boundaries, so compile them as variables with a reserved prefix */
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return "?_bn_" + t.value.replace(/[^A-Za-z0-9_]/g, "_");
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case "Literal": {
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const lex = '"' + t.value.replace(/\\/g, "\\\\").replace(/"/g, '\\"') + '"';
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const dt = t.datatype?.value;

‎tests/Algae3/data/evidence-groups.ttl‎

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# Evidence groups (abstracted from component groups).
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PREFIX ex: <http://a.example/ns#>
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PREFIX ev: <http://a.example/evidence#>
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PREFIX evgrp: <http://a.example/evgrp/>
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evgrp:MetaAnalyses1 a ex:Group ;
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ex:name "MetaAnalyses1(?)" ;
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ex:member [ ex:evidence ev:MA-1 ] .
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evgrp:RecentCohorts a ex:Group ;
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ex:name "cohorts started within 2y" ;
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ex:member
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<#RecentCohorts_OBS-2214> ,
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<#RecentCohorts_DOES_NOT_EXIST> .
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<#RecentCohorts_OBS-2214> ex:evidence ev:OBS-2214 .
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<#RecentCohorts_DOES_NOT_EXIST> ex:evidence ev:DOES_NOT_EXIST .
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evgrp:PeerReviewedCohorts a ex:Group ;
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ex:name "peer-reviewed cohorts" ;
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ex:member
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[ ex:evidence ev:OBS-0999 ] ,
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[ ex:evidence ev:OBS-2214 ] .
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evgrp:ConfoundedStudies a ex:Group ;
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ex:name "confounding-prone studies" ;
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ex:member
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[ ex:evidence ev:OBS-2214 ] ,
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[ ex:evidence ev:OBS-0990 ] .
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evgrp:PreregisteredStudies a ex:Group ;
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ex:name "preregistered studies" ;
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# does NOT include ev:OBS-2214
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ex:member [ ex:evidence ev:OBS-0990 ] .
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evgrp:PeerReviewedCohortsEXCLUDED a ex:Group ;
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ex:name "peer-reviewed cohorts" ;
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ex:member
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[ ex:evidence ev:OBS-0999EXCLUDED ] ,
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[ ex:evidence ev:OBS-2214EXCLUDED ] .
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evgrp:ConfoundedStudiesEXCLUDED a ex:Group ;
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ex:name "confounded studies" ;
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ex:member
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[ ex:evidence ev:OBS-2214EXCLUDED ] ,
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[ ex:evidence ev:OBS-0990EXCLUDED ] .

‎tests/Algae3/data/evidence-rules.ttl‎

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# Evidence-appraisal rules in DNF (abstracted from a production rule set;
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# same selectors/disjuncts/conjuncts, polarities and olo:index ordering).
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@prefix evgrp: <http://a.example/evgrp/> .
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@prefix ex: <http://a.example/ns#> .
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@prefix olo: <http://purl.org/ontology/olo/core#> .
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@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
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<#pubbias> a ex:CorroborationRule,
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ex:Rule ;
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ex:action <#pubbias_action0> ;
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ex:label "publication-bias" ;
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ex:selector <#pubbias_selector0>,
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<#pubbias_selector1> .
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<#confound> a ex:Rule,
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ex:SingleEvidenceRule ;
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ex:action <#confound_action0> ;
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ex:label "confound-sensitive" ;
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ex:selector <#confound_selector0> .
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<#underpow> a ex:CorroborationRule,
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ex:Rule ;
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ex:action <#underpow_action0> ;
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ex:label "underpowered" ;
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ex:selector <#underpow_selector0>,
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<#underpow_selector1> .
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<#pubbias_action0> ex:message "publication-bias" ;
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ex:severity ex:Critical .
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<#pubbias_selector0> ex:or <#pubbias_selector0_or0>,
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<#pubbias_selector0_or1> ;
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olo:index 0 .
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<#pubbias_selector0_or0> ex:and <#pubbias_selector0_or0_and0>,
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<#pubbias_selector0_or0_and2>,
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<#pubbias_selector0_or0_and3> ;
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olo:index 0 .
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<#pubbias_selector0_or0_and0> ex:evidenceGroup evgrp:RecentCohorts ;
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ex:polarity ex:pos ;
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olo:index 0 .
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<#pubbias_selector0_or0_and2> ex:attribute ex:effectMeasure ;
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ex:eq ex:OddsRatio ;
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ex:polarity ex:pos ;
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olo:index 2 .
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<#pubbias_selector0_or0_and3> ex:attribute ex:effectMeasure ;
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ex:eq ex:AdjustedOddsRatio ;
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ex:polarity ex:neg ;
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olo:index 3 .
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<#pubbias_selector0_or1> ex:and <#pubbias_selector0_or1_and0>,
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<#pubbias_selector0_or1_and2> ;
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olo:index 1 .
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<#pubbias_selector0_or1_and0> ex:evidenceGroup evgrp:PeerReviewedCohorts ;
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ex:polarity ex:pos ;
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olo:index 0 .
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<#pubbias_selector0_or1_and2> ex:attribute ex:effectMeasure ;
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ex:eq ex:OddsRatio ;
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ex:polarity ex:pos ;
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olo:index 2 .
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<#pubbias_selector1> ex:or <#pubbias_selector1_or0> ;
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olo:index 1 .
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<#pubbias_selector1_or0> ex:and <#pubbias_selector1_or0_and0> ;
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olo:index 0 .
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<#pubbias_selector1_or0_and0> ex:attribute ex:pValue ;
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ex:ge 0.5 ;
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ex:polarity ex:pos ;
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olo:index 0 .
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<#confound_action0> ex:message "confound-sensitive" ;
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ex:severity ex:Critical .
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<#confound_selector0> ex:or <#confound_selector0_or0>,
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<#confound_selector0_or1> ;
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olo:index 0 .
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<#confound_selector0_or0> ex:and <#confound_selector0_or0_and0>,
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<#confound_selector0_or0_and1>,
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<#confound_selector0_or0_and2>,
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<#confound_selector0_or0_and3> ;
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ex:description """
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RecentCohorts
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∧ in ConfoundedStudies
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∧ effectMeasure=OddsRatio
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∧ ¬effectMeasure=HazardRatio
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""" ;
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olo:index 0 .
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<#confound_selector0_or0_and0> ex:evidenceGroup evgrp:RecentCohorts ;
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ex:polarity ex:pos ;
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olo:index 0 .
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<#confound_selector0_or0_and1> ex:evidenceGroup evgrp:ConfoundedStudies ;
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ex:polarity ex:pos ;
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olo:index 1 .
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<#confound_selector0_or0_and2> ex:attribute ex:effectMeasure ;
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ex:eq ex:OddsRatio ;
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ex:polarity ex:pos ;
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olo:index 2 .
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<#confound_selector0_or0_and3> ex:attribute ex:effectMeasure ;
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ex:eq ex:HazardRatio ;
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ex:polarity ex:neg ;
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olo:index 3 .
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<#confound_selector0_or1> ex:and <#confound_selector0_or1_and0>,
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<#confound_selector0_or1_and1>,
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<#confound_selector0_or1_and2> ;
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ex:description """
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PeerReviewedCohorts
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∧ in ConfoundedStudies
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∧ effectMeasure=OddsRatio
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""" ;
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olo:index 1 .
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<#confound_selector0_or1_and0> ex:evidenceGroup evgrp:PeerReviewedCohorts ;
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ex:polarity ex:pos ;
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olo:index 0 .
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<#confound_selector0_or1_and1> ex:evidenceGroup evgrp:ConfoundedStudies ;
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ex:polarity ex:pos ;
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olo:index 1 .
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<#confound_selector0_or1_and2> ex:attribute ex:effectMeasure ;
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ex:eq ex:OddsRatio ;
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ex:polarity ex:pos ;
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olo:index 2 .
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<#underpow_action0> ex:message "underpowered" ;
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ex:severity ex:Critical .
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<#underpow_selector0> ex:or <#underpow_selector0_or0>,
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<#underpow_selector0_or1> ;
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olo:index 0 .
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<#underpow_selector0_or0> ex:and <#underpow_selector0_or0_and0>,
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<#underpow_selector0_or0_and1>,
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<#underpow_selector0_or0_and2>,
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<#underpow_selector0_or0_and3> ;
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olo:index 0 .
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<#underpow_selector0_or0_and0> ex:evidenceGroup evgrp:RecentCohorts ;
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ex:polarity ex:pos ;
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olo:index 0 .
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<#underpow_selector0_or0_and1> ex:evidenceGroup evgrp:ConfoundedStudies ;
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ex:polarity ex:pos ;
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olo:index 1 .
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<#underpow_selector0_or0_and2> ex:attribute ex:effectMeasure ;
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ex:eq ex:OddsRatio ;
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ex:polarity ex:pos ;
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olo:index 2 .
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<#underpow_selector0_or0_and3> ex:attribute ex:effectMeasure ;
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ex:eq ex:HazardRatio ;
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ex:polarity ex:neg ;
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olo:index 3 .
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<#underpow_selector0_or1> ex:and <#underpow_selector0_or1_and0>,
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<#underpow_selector0_or1_and1>,
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<#underpow_selector0_or1_and2>,
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<#underpow_selector0_or1_and3> ;
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olo:index 1 .
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<#underpow_selector0_or1_and0> ex:evidenceGroup evgrp:PeerReviewedCohorts ;
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ex:polarity ex:pos ;
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olo:index 0 .
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<#underpow_selector0_or1_and1> ex:evidenceGroup evgrp:ConfoundedStudies ;
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ex:polarity ex:pos ;
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olo:index 1 .
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<#underpow_selector0_or1_and2> ex:attribute ex:effectMeasure ;
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ex:eq ex:OddsRatio ;
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ex:polarity ex:pos ;
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olo:index 2 .
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<#underpow_selector0_or1_and3> ex:evidenceGroup evgrp:PreregisteredStudies ;
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ex:polarity ex:neg ;
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olo:index 3 .
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<#underpow_selector1> ex:or <#underpow_selector1_or0> ;
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olo:index 1 .
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<#underpow_selector1_or0> ex:and <#underpow_selector1_or0_and0> ;
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olo:index 0 .
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<#underpow_selector1_or0_and0> ex:attribute ex:pValue ;
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ex:lt 0.25 ;
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ex:polarity ex:pos ;
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olo:index 0 .
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‎tests/Algae3/data/evidence.ttl‎

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# Evidence-appraisal instance data (abstracted from a production component
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# catalog: components -> evidence, Film -> Observational, Port -> Rnc,
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# diameterInInches -> pValue, material -> effectMeasure).
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PREFIX ex: <http://a.example/ns#>
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PREFIX ev: <http://a.example/evidence#>
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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ex:Observational rdfs:subClassOf ex:Evidence .
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ex:Rnc rdfs:subClassOf ex:Evidence .
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## Pooled analyses
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ev:MA-1 a ex:PooledAnalysis ;
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ex:onObservational ev:OBS-2214 ;
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ex:onRnc ev:RNC-0859.1 .
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## Observational studies
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ev:OBS-2214 a ex:Observational ;
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ex:registryId "OBS-2214" ;
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ex:name "Cohort of 2214 adults" ;
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ex:effectMeasure ex:OddsRatio .
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## Randomized controlled trials (one family, four arms)
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ev:RNC-0859.1 a ex:Rnc ;
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ex:trialFamily "RNC-0859" ;
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ex:pValue .15625 ;
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ex:name "multi-arm trial (arm 1)" .
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ev:RNC-0859.2 a ex:Rnc ;
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ex:trialFamily "RNC-0859" ;
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ex:pValue .25 ;
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ex:name "multi-arm trial (arm 2)" .
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ev:RNC-0859.3 a ex:Rnc ;
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ex:trialFamily "RNC-0859" ;
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ex:pValue .375 ;
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ex:name "multi-arm trial (arm 3)" .
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ev:RNC-0859.4 a ex:Rnc ;
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ex:trialFamily "RNC-0859" ;
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ex:pValue .5 ;
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ex:name "multi-arm trial (arm 4)" .

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