Merge pull request #634 from helxplatform/update-data-for-name-lookup

Change Name-Lookup to use the new synonym format

helm/name-lookup/Chart.yaml

@@ -14,11 +14,11 @@ type: application
 
 # This is the chart version. This version number should be incremented each time you make changes
 # to the chart and its templates, including the app version.
-version: 0.3.0
+version: 0.4.0
 
 # This is the version number of the application being deployed. This version number should be
 # incremented each time you make changes to the application.
 # 
 # NameRes versions are based on the version of the NameRes Docker image concatenated with the
 # Babel release date.
-appVersion: 1.2.0_2022dec2-2
+appVersion: 1.3.4_2023jul9

helm/name-lookup/ncats-images-meta.yaml

@@ -1,10 +1,10 @@
 nameLookup:
-  image: "ghcr.io/translatorsri/nameresolution"
-  version: "v1.2.0"
+  image: ghcr.io/translatorsri/nameresolution
+  version: v1.3.4
 solr:
-  image: "solr"
-  version: "8.11.1"
+  image: solr
+  version: 9.1.0
 
 busyBox:
-  image: "busybox"
-  version: "stable"
+  image: busybox
+  version: "1.35"

helm/name-lookup/templates/scripts-config-map.yaml

@@ -82,26 +82,71 @@ data:
         --header='Content-Type:application/json' \
         -O- ${SOLR_SERVER}/solr/${COLLECTION_NAME}/schema
     sleep 1
+    # exactish type taken from https://stackoverflow.com/a/29105025/27310
+    wget --post-data '{
+              "add-field-type" : {
+                  "name": "exactish",
+                  "class": "solr.TextField",
+                  "analyzer": {
+                      "tokenizer": {
+                          "class": "solr.KeywordTokenizerFactory"
+                      },
+                      "filters": [{
+                          "class": "solr.LowerCaseFilterFactory"
+                      }]
+                  }
+              }}' \
+        --header='Content-Type:application/json' \
+        -O- ${SOLR_SERVER}/solr/${COLLECTION_NAME}/schema
+    sleep 1
     wget --post-data '{
                 "add-field": [
                     {
-                        "name":"name",
+                        "name":"names",
                         "type":"LowerTextField",
-                        "stored":true
-                    },
-                    {
-                        "name":"length",
-                        "type":"plong",
-                        "stored":true
+                        "stored": true,
+                        "multiValued": true
                     },
                     {
                         "name":"curie",
                         "type":"string",
                         "stored":true
+                    },
+                    {
+                        "name": "preferred_name",
+                        "type": "LowerTextField",
+                        "stored": true
+                    },
+                    {
+                        "name": "preferred_name_exactish",
+                        "type": "exactish",
+                        "indexed": true,
+                        "stored": false,
+                        "multiValued": false
+                    },
+                    {
+                        "name": "types",
+                        "type": "string",
+                        "stored": true,
+                        "multiValued": true
+                    },
+                    {
+                        "name": "shortest_name_length",
+                        "type": "pint",
+                        "stored": true
                     }
                 ]
             }' \
           --header='Content-Type:application/json' \
           -O- ${SOLR_SERVER}/solr/${COLLECTION_NAME}/schema
     sleep 1
+    wget --post-data '{
+              "add-copy-field" : {
+                "source": "preferred_name",
+                "dest": "preferred_name_exactish"
+              }}' \
+        --header='Content-Type:application/json' \
+        -O- ${SOLR_SERVER}/solr/${COLLECTION_NAME}/schema
+    sleep 1
+ 
     exit 0

helm/name-lookup/templates/solr-deployment.yaml

@@ -77,4 +77,4 @@ spec:
         accessModes: [ "ReadWriteOnce" ]
         resources:
           requests:
-            storage: 100Gi
+            storage: {{ .Values.solr.storage }}

helm/name-lookup/values.yaml

@@ -13,15 +13,15 @@ webServer:
   port: 2433
   image:
     repository: ghcr.io/translatorsri/nameresolution
-    tag: "v1.2.0"
+    tag: v1.3.4
 
-dataUrl: "https://stars.renci.org/var/babel_outputs/2022dec2-2/solr/snapshot.backup.tar.gz"
+dataUrl: "https://stars.renci.org/var/babel_outputs/2023jul13/solr/snapshot.backup.tar.gz"
 forceRun: false
 
 busybox:
   image:
     repository: busybox
-    tag: stable
+    tag: "1.35"
 
 # busybox:
 #   image:
@@ -34,22 +34,26 @@ solr:
     type: ClusterIP
   # container port
   port: 8983
-  heap_mem: "-Xms4000m -Xmx4000m"
+  heap_mem: "-Xms58G -Xmx58G"
   image:
     repository: solr
-    tag: latest
+    tag: 9.1
   resources:
     requests:
-      memory: "5Gi"
+      memory: "64Gi"
     limits:
-      memory: "5Gi"
+      memory: "64Gi"
+  # As of Babel 2023may18, we need 128G to store the
+  # backup + uncompressed backup + Solr database
+  # So 500Gi should be enough for the time being.
+  storage: 500Gi
 
   initresources:
     requests:
-      memory: 5Gi
+      memory: 32Gi
       cpu: 1000m
     limits:
-      memory: 10Gi
+      memory: 64Gi
       cpu: 1000m
 
 nameOverride: ""