From 9bf0ef5c2f883a860868bd68b1d65d64270060f6 Mon Sep 17 00:00:00 2001
From: Bruno Pacheco <brunopacheco1@yahoo.com>
Date: Thu, 14 Nov 2024 15:40:39 +0100
Subject: [PATCH] feat: align beacon filters with Beacon Network options

---
 .../META-INF/resources/beacon-filters.json    | 199 +++++++++++++-----
 .../quarkus/RetrieveFiltersTest.java          |  11 +-
 2 files changed, 145 insertions(+), 65 deletions(-)

diff --git a/src/main/resources/META-INF/resources/beacon-filters.json b/src/main/resources/META-INF/resources/beacon-filters.json
index dde25d5..ebbb908 100644
--- a/src/main/resources/META-INF/resources/beacon-filters.json
+++ b/src/main/resources/META-INF/resources/beacon-filters.json
@@ -2,16 +2,24 @@
   {
     "source": "beacon",
     "type": "DROPDOWN",
-    "key": "ncit",
-    "label": "National Cancer Institute Thesaurus",
+    "key": "diseases",
+    "label": "Diseases",
     "values": [
       {
-        "value": "NCIT:C25179",
-        "label": "Hospitalization"
+        "value": "NCIT:C4349",
+        "label": "Colon adenocarcinoma"
       },
       {
-        "value": "NCIT:C171454",
-        "label": "Intensive Care Unit Stay"
+        "value": "NCIT:C7966",
+        "label": "Mucinous Adenocarcinoma of the Colon and Rectum"
+      },
+      {
+        "value": "NCIT:C9383",
+        "label": "Rectal Adenocarcinoma"
+      },
+      {
+        "value": "MONDO:0100096",
+        "label": "COVID-19"
       },
       {
         "value": "NCIT:C14139",
@@ -37,6 +45,10 @@
         "value": "NCIT:C15289",
         "label": "Organ Transplantation"
       },
+      {
+        "value": "NCIT:C3117",
+        "label": "Hypertension"
+      },
       {
         "value": "NCIT:C3080",
         "label": "Congestive Heart Failure"
@@ -61,91 +73,162 @@
   },
   {
     "source": "beacon",
-    "type": "FREE_TEXT",
-    "key": "BMI",
-    "label": "BMI in Kilograms per Square Meter",
-    "operators": [
-      "=",
-      "!=",
-      ">",
-      "<",
-      "%"
+    "type": "DROPDOWN",
+    "key": "histopathology",
+    "label": "Histopathology",
+    "values": [
+      {
+        "value": "ICD10:C18.2",
+        "label": "Ascending colon"
+      },
+      {
+        "value": "ICD10:C18.6",
+        "label": "Descending colon"
+      },
+      {
+        "value": "ICD10:C18.4",
+        "label": "Transverse colon"
+      },
+      {
+        "value": "ICD10:C18.3",
+        "label": "Hepatic flexure"
+      },
+      {
+        "value": "ICD10:C18.5",
+        "label": "Splenic flexure"
+      },
+      {
+        "value": "ICD10:C18.7",
+        "label": "Sigmoid colon"
+      },
+      {
+        "value": "ICD10:C18.0",
+        "label": "Caecum"
+      },
+      {
+        "value": "NCIT:C27966",
+        "label": "Stage I"
+      },
+      {
+        "value": "NCIT:C28054",
+        "label": "Stage II"
+      },
+      {
+        "value": "NCIT:C27970",
+        "label": "Stage III"
+      },
+      {
+        "value": "NCIT:C27971",
+        "label": "Stage IV"
+      }
     ]
   },
   {
     "source": "beacon",
-    "type": "FREE_TEXT",
-    "key": "Height-standing",
-    "label": "Height-standing in Centimeters",
-    "operators": [
-      "=",
-      "!=",
-      ">",
-      "<",
-      "%"
+    "type": "DROPDOWN",
+    "key": "treatment",
+    "label": "Treatment",
+    "values": [
+      {
+        "value": "NCIT:C15313",
+        "label": "Radiation Therapy"
+      },
+      {
+        "value": "NCIT:C15632",
+        "label": "Chemotherapy"
+      },
+      {
+        "value": "NCIT:C505",
+        "label": "Fluorouracil"
+      },
+      {
+        "value": "NCIT:C1181",
+        "label": "Oxaliplatin"
+      },
+      {
+        "value": "NCIT:C1699",
+        "label": "Zoledronic Acid"
+      },
+      {
+        "value": "NCIT:C62040",
+        "label": "Irinotecan"
+      }
     ]
   },
   {
     "source": "beacon",
-    "type": "ENTRIES",
-    "key": "gene+aminoacid",
-    "label": "Mutations in:",
-    "entries": [
+    "type": "DROPDOWN",
+    "key": "intervention",
+    "label": "Intervention",
+    "values": [
       {
-        "key": "geneId",
-        "label": "gene"
+        "value": "NCIT:C25179",
+        "label": "Hospitalization"
       },
       {
-        "key": "aminoacidChange",
-        "label": "aminoacid"
+        "value": "NCIT:C171454",
+        "label": "Intensive Care Unit Stay"
+      },
+      {
+        "value": "SNOMED:52765003",
+        "label": "Intubation (procedure)"
+      },
+      {
+        "value": "SNOMED:371907003",
+        "label": "Oxygen administration by nasal cannula"
       }
     ]
   },
   {
     "source": "beacon",
-    "type": "ENTRIES",
-    "key": "gene",
-    "label": "Mutations in:",
-    "entries": [
+    "type": "DROPDOWN",
+    "key": "sex",
+    "label": "Sex",
+    "values": [
       {
-        "key": "geneId",
-        "label": "gene"
+        "value": "NCIT:C16576",
+        "label": "Female"
+      },
+      {
+        "value": "NCIT:C20197",
+        "label": "Male"
       }
     ]
   },
+  {
+    "source": "beacon",
+    "type": "FREE_TEXT",
+    "key": "diseases.ageOfOnset.iso8601duration",
+    "label": "Age",
+    "operators": [
+      "=",
+      "!=",
+      ">",
+      "<",
+      "%"
+    ]
+  },
   {
     "source": "beacon",
     "type": "ENTRIES",
-    "key": "bases",
-    "label": "Mutations in:",
+    "key": "genetic_mutation",
+    "label": "Genetic Mutation",
     "entries": [
       {
-        "key": "alternateBases",
-        "label": "alternateBases"
-      },
-      {
-        "key": "referenceBases",
-        "label": "referenceBases"
-      },
-      {
-        "key": "start",
-        "label": "start"
-      },
-      {
-        "key": "end",
-        "label": "end"
+        "key": "geneId",
+        "label": "gene"
       },
       {
-        "key": "variantType",
-        "label": "type"
+        "key": "aminoacidChange",
+        "label": "aminoacid"
       }
     ]
   },
   {
     "source": "beacon",
     "type": "ENTRIES",
-    "key": "bases+assembly",
-    "label": "Mutations in:",
+    "key": "genetic_variation",
+    "label": "Genetic Variation",
     "entries": [
       {
         "key": "alternateBases",
diff --git a/src/test/java/io/github/genomicdatainfrastructure/discovery/filters/infrastructure/quarkus/RetrieveFiltersTest.java b/src/test/java/io/github/genomicdatainfrastructure/discovery/filters/infrastructure/quarkus/RetrieveFiltersTest.java
index cb298d7..b1901a1 100644
--- a/src/test/java/io/github/genomicdatainfrastructure/discovery/filters/infrastructure/quarkus/RetrieveFiltersTest.java
+++ b/src/test/java/io/github/genomicdatainfrastructure/discovery/filters/infrastructure/quarkus/RetrieveFiltersTest.java
@@ -47,12 +47,8 @@ void shouldRetrieveAllFilters_WhenAuthenticated() {
                 .get("/api/v1/filters")
                 .then()
                 .statusCode(200)
-                .body("", hasSize(12))
                 .body("find { it.source == 'ckan' }.values", hasSize(greaterThan(0)))
-                .body("find { it.source == 'beacon' }.values", hasSize(greaterThan(0)))
-                .body("find { it.label == 'National Cancer Institute Thesaurus' }.values", hasSize(
-                        greaterThan(
-                                0)));
+                .body("find { it.source == 'beacon' }.values", hasSize(greaterThan(0)));
     }
 
     @Test
@@ -76,8 +72,9 @@ void shouldRetrievesBeaconFilteringTerms_WhenAuthenticated() {
 
             assertThat(actual)
                     .containsExactlyInAnyOrder(
-                            "ncit", "BMI", "Height-standing", "bases", "bases+assembly", "gene",
-                            "gene+aminoacid"
+                            "treatment", "genetic_variation", "sex", "histopathology", "diseases",
+                            "intervention",
+                            "diseases.ageOfOnset.iso8601duration", "genetic_mutation"
                     );
         } catch (Exception e) {
             throw new RuntimeException(e);