fix valueset expansion

src/fhir/terminology.coffee

@@ -1,4 +1,5 @@
 utils = require('../core/utils')
+compat = require('../compat')
 outcome = require('./outcome')
 
 exports.fhir_expand_valueset = (plv8, query)->
@@ -124,6 +125,17 @@ exports.fhir_valueset_after_changed = (plv8, resource)->
   for inc in  ((resource.compose && resource.compose.include) || [])
     for concept in (inc.concept || [])
       _create_concept(plv8, acc, {valueset_id: resource.id, system: inc.system}, {}, concept)
+    if inc.system
+      plv8.debug = true
+      syst = utils.exec plv8,
+        select: [':*']
+        from: ':codesystem'
+        where: ['$eq', ":resource->>'url'", inc.system]
+        limit: 1
+      syst_res = (syst[0] && syst[0].resource && JSON.parse(syst[0].resource))
+      for concept in ((syst_res && syst_res.concept) || [])
+        _create_concept(plv8, acc, {valueset_id: resource.id, system: inc.system}, {}, concept)
+      plv8.debug = false
 
   res = plv8.execute """
     INSERT INTO _valueset_expansion

test/fhir/terminology_spec.coffee

@@ -1,5 +1,6 @@
 term = require('../../src/fhir/terminology')
 crud = require('../../src/fhir/crud')
+schema = require('../../src/core/schema')
 test = require('../helpers.coffee')
 plv8 = require('../../plpl/src/plv8')
 
@@ -8,6 +9,19 @@ log = (x)-> console.log(JSON.stringify(x, null, " "))
 
 expand = (q)-> term.fhir_expand_valueset(plv8, q)
 
+TEST_CS = {
+  id: 'mytestvs'
+  url: '/mycodesystem'
+  resourceType: 'CodeSystem'
+  concept: [
+    {
+      code: 'b'
+      display: 'b'
+      concept: [{code: 'b1', display: 'b1'}]
+    }
+  ]
+}
+
 TEST_VS = {
   id: 'mytestvs'
   resourceType: 'ValueSet'
@@ -34,18 +48,23 @@ TEST_VS = {
          {code: 'a31', display: 'A31'}
          {code: 'a32', display: 'A32'}]
       }
+      {system: '/mycodesystem'}
     ]
 }
 
+
 big_valueset = require('./fixtures/valueset-ucum-common.json')
 big_valueset.id = 'bigone'
 
 describe "terminology", ->
   @timeout(50000)
 
   before (done)->
+    schema.fhir_create_storage(plv8, {resourceType: 'CodeSystem'})
     crud.fhir_terminate_resource(plv8, {resourceType: 'ValueSet', id: TEST_VS.id})
     crud.fhir_terminate_resource(plv8, {resourceType: 'ValueSet', id: big_valueset.id})
+    crud.fhir_terminate_resource(plv8, {resourceType: 'CodeSystem', id: TEST_CS.id})
+    crud.fhir_create_resource(plv8, {resourceType: 'CodeSystem', allowId: true, resource: TEST_CS})
     crud.fhir_create_resource(plv8, {resourceType: 'ValueSet', allowId: true, resource: TEST_VS})
     done()
 
@@ -61,7 +80,7 @@ describe "terminology", ->
   it "custom vs", ->
     vs =  expand(id: "mytestvs")
     res = vs.expansion.contains.map((x)-> x.code).sort()
-    assert.deepEqual([ 'a1', 'a21', 'a22', 'a31', 'a32', 'nested' ], res)
+    assert.deepEqual([ 'a1', 'a21', 'a22', 'a31', 'a32', 'b', 'b1', 'nested' ], res)
 
     vs =  expand(id: "mytestvs", filter: '32')
     res = vs.expansion.contains
@@ -75,6 +94,11 @@ describe "terminology", ->
     res = vs.expansion.contains
     assert.equal(res.length, 1)
 
+    vs =  expand(id: "mytestvs", filter: 'b1')
+    res = vs.expansion.contains
+    console.log(res)
+    assert.equal(res.length, 1)
+
     crud.fhir_update_resource plv8,
       resource:
         resourceType: 'ValueSet'

utils/generate_migrations.coffee

@@ -45,6 +45,7 @@ output  schema.fhir_create_storage_sql(plv8, resourceType: 'SearchParameter')
 output  schema.fhir_create_storage_sql(plv8, resourceType: 'OperationDefinition')
 output  schema.fhir_create_storage_sql(plv8, resourceType: 'ValueSet')
 output  schema.fhir_create_storage_sql(plv8, resourceType: 'ConceptMap')
+output  schema.fhir_create_storage_sql(plv8, resourceType: 'CodeSystem')
 output  schema.fhir_create_storage_sql(plv8, resourceType: 'NamingSystem')
 
 bundles = [
@@ -100,7 +101,7 @@ console.log """
   );
 """
 
-for tp in ['StructureDefinition', 'SearchParameter', 'OperationDefinition', 'ValueSet', 'ConceptMap', 'NamingSystem']
+for tp in ['StructureDefinition', 'SearchParameter', 'OperationDefinition', 'ValueSet', 'ConceptMap', 'NamingSystem', 'CodeSystem']
   console.log """
     INSERT INTO #{tp.toLowerCase()} (id, version_id, resource)
     SELECT m.resource->>'id', m.resource->>'id' || '-#{VERSION}' , resource

utils/patch_3.sql

@@ -57,6 +57,14 @@ DO $JS$
                 for(var j = 0; j < (include.concept && include.concept.length) || 0; j++){
                     expand_concept(acc, props, {}, include.concept[j]);
                 }
+                var syst = plv8.execute("SELECT * FROM codesystem WHERE resource->>'url' = $1 LIMIT 1", include.system);
+                var syst_res = syst && syst[0] && syst[0].resource && parse(syst[0].resource);
+                /* if(syst_res && syst_res.concept.length > 0){ */
+                /*   log("+ " + include.system + '  (' + syst_res.concept.length + ')'); */
+                /* } */
+                for(var j = 0; j < (syst_res && syst_res.concept.length) || 0; j++){
+                  expand_concept(acc, props, {}, syst_res.concept[j]);
+                }
             }
         }
         return acc;
@@ -74,15 +82,16 @@ DO $JS$
    var cursor = plan.cursor();
    var row = null;
    while (row = cursor.fetch()) {
-     var res = expand(parse(row.resource))
-     if(res.length > 0){
-        log('expand valueset: ' + row.resource.id + ' (' + res.length + ')')
+     var res = parse(row.resource)
+     var items = expand(res);
+     if(items.length > 0){
+        log('expand valueset: ' + res.id + ' (' + items.length + ')')
         plv8.execute(
             "INSERT INTO _valueset_expansion" +
             "(valueset_id, system, parent_code, code, display, abstract, definition, designation, extension) " +
             "SELECT x->>'valueset_id', x->>'system', x->>'parent_code', x->>'code', x->>'display', (x->>'abstract')::boolean, x->>'definition', (x->'designation')::jsonb, (x->'extension')::jsonb " +
             "FROM json_array_elements($1::json) x"
-        , JSON.stringify(res))
+        , JSON.stringify(items))
      }
    }
    cursor.close();