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by default dont calculate scores of potential matche's potential matches generating new certificates
mherman22 · May 10, 2022 · 27369c4 · 27369c4
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Showing 17 changed files with 23,642 additions and 4,384 deletions.
diff --git a/server/clientCertificates/openmrs.p12 b/server/clientCertificates/openmrs.p12
diff --git a/server/clientCertificates/openmrs_cert.pem b/server/clientCertificates/openmrs_cert.pem
@@ -1,22 +1,22 @@
 -----BEGIN CERTIFICATE-----
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 -----END CERTIFICATE-----
diff --git a/server/clientCertificates/openmrs_csr.pem b/server/clientCertificates/openmrs_csr.pem
@@ -1,26 +1,26 @@
 -----BEGIN CERTIFICATE REQUEST-----
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 -----END CERTIFICATE REQUEST-----
diff --git a/server/clientCertificates/openmrs_key.pem b/server/clientCertificates/openmrs_key.pem
@@ -1,52 +1,52 @@
 -----BEGIN PRIVATE KEY-----
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 -----END PRIVATE KEY-----
diff --git a/server/config/config_development_template.json b/server/config/config_development_template.json
@@ -31,7 +31,8 @@
   },
   "matching": {
     "tool": "elasticsearch",
-    "autoMatchPatientWithHumanAdjudTag": false
+    "autoMatchPatientWithHumanAdjudTag": false,
+    "resolvePotentialOfPotentials": false
   },
   "codes": {
     "goldenRecord": "5c827da5-4858-4f3d-a50c-62ece001efea"

diff --git a/server/config/config_docker_template.json b/server/config/config_docker_template.json
@@ -37,7 +37,9 @@
       "reportRelationship": "patientreport"
     },
     "matching": {
-      "tool": "elasticsearch"
+      "tool": "elasticsearch",
+      "autoMatchPatientWithHumanAdjudTag": false,
+      "resolvePotentialOfPotentials": false
     },
     "clients": [
       {

diff --git a/server/config/config_production_template.json b/server/config/config_production_template.json
@@ -31,7 +31,8 @@
   },
   "matching": {
     "tool": "elasticsearch",
-    "autoMatchPatientWithHumanAdjudTag": false
+    "autoMatchPatientWithHumanAdjudTag": false,
+    "resolvePotentialOfPotentials": false
   },
   "codes": {
     "goldenRecord": "5c827da5-4858-4f3d-a50c-62ece001efea"

diff --git a/server/config/config_test_template.json b/server/config/config_test_template.json
@@ -31,7 +31,8 @@
   },
   "matching": {
     "tool": "elasticsearch",
-    "autoMatchPatientWithHumanAdjudTag": false
+    "autoMatchPatientWithHumanAdjudTag": false,
+    "resolvePotentialOfPotentials": false
   },
   "codes": {
     "goldenRecord": "5c827da5-4858-4f3d-a50c-62ece001efea"

diff --git a/server/config/decisionRules.json b/server/config/decisionRules.json
@@ -58,8 +58,8 @@
         "espath": "art"
       }
     },
-    "potentialMatchThreshold": 4,
-    "autoMatchThreshold": 6,
+    "potentialMatchThreshold": 1,
+    "autoMatchThreshold": 9,
     "filters": {
       "gender": {
         "fhirpath": "gender",

diff --git a/server/lib/esMatching.js b/server/lib/esMatching.js
@@ -8,6 +8,7 @@ const fhirWrapper = require('./fhir')();
 const logger = require('./winston');
 const config = require('./config');
 const generalMixin = require('./mixins/generalMixin');
+const axios = require('axios');
 const fhir = new Fhir();
 
 const refreshIndex = (callback) => {
@@ -186,6 +187,70 @@ const buildQuery = (sourceResource, decisionRule) => {
   return esquery;
 };
 
+const getESDocument = (query, callback) => {
+  let error = false;
+  let documents = [];
+  if(!query) {
+    query = {};
+  }
+  let url = URI(config.get('elastic:server'))
+    .segment(config.get('elastic:index'))
+    .segment('_search')
+    .addQuery('scroll', '1m')
+    .addQuery('size', 1000)
+    .toString();
+  let scroll_id = null;
+  async.doWhilst(
+    (callback) => {
+      axios({
+        method: 'POST',
+        url,
+        data: query,
+        auth: {
+          username: config.get('elastic:username'),
+          password: config.get('elastic.password'),
+        }
+      }).then((response) => {
+        if(response.data.hits && response.data.hits.hits && Array.isArray(response.data.hits.hits)) {
+          documents = documents.concat(response.data.hits.hits);
+        }
+        if(response.data.hits.hits.length === 0 || response.data.hits.total.value == documents.length || !response.data._scroll_id) {
+          scroll_id = null;
+        } else {
+          scroll_id = response.data._scroll_id;
+          url = URI(config.get('elastic:server'))
+            .segment('_search')
+            .segment('scroll')
+            .toString();
+          query = {
+            scroll: '1m',
+            scroll_id: scroll_id
+          };
+        }
+        return callback(null);
+      }).catch((err) => {
+        if(err.response && err.response.status === 429) {
+          logger.warn('ES is overloaded with too many requests, delaying for 2 seconds');
+          setTimeout(() => {
+            return callback(null);
+          }, 2000);
+        } else {
+          error = err;
+          logger.error(err);
+          scroll_id = null;
+          return callback(null);
+        }
+      });
+    },
+    (callback) => {
+      return callback(null, scroll_id !== null);
+    },
+    () => {
+      return callback(error, documents);
+    }
+  );
+};
+
 const performMatch = ({
   sourceResource,
   currentGoldenLink,
@@ -216,27 +281,14 @@ const performMatch = ({
       if (Object.keys(esquery).length === 0) {
         return callback(true);
       }
-      const url = URI(config.get('elastic:server'))
-        .segment(config.get('elastic:index'))
-        .segment('_search')
-        .toString();
-      const options = {
-        url,
-        auth: {
-          username: config.get('elastic:username'),
-          password: config.get('elastic.password'),
-        },
-        json: esquery,
-      };
-      request.get(options, (err, res, body) => {
-        if (!body || !body.hits || !body.hits.hits || !Array.isArray(body.hits.hits)) {
-          logger.error(JSON.stringify(body, 0, 2));
+      getESDocument(esquery, (err, documents) => {
+        if(documents.length === 0) {
           return nxtRule();
         }
         const potentialHits = [];
         const autoHits = [];
         const conflictsHits = [];
-        for (const hit of body.hits.hits) {
+        for (const hit of documents) {
           const id = hit['_id'];
           if (ignoreList.includes(id)) {
             continue;