Merge branch 'main' of https://github.com/biothings/biothings_explorer …

…into dev
biothings · Oct 19, 2023 · 68beede · 68beede
2 parents 61ec856 + 2e7f73d
commit 68beede
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Showing 6 changed files with 47 additions and 8 deletions.
diff --git a/deploy/Chart.yaml b/deploy/Chart.yaml
@@ -15,7 +15,7 @@ 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.
 # Versions are expected to follow Semantic Versioning (https://semver.org/)
-version: 0.1.0
+version: 0.1.1
 
 # This is the version number of the application being deployed. This version number should be
 # incremented each time you make changes to the application. Versions are not expected to

diff --git a/deploy/templates/deployment.yaml b/deploy/templates/deployment.yaml
@@ -19,6 +19,10 @@ spec:
       serviceAccountName: {{ include "bte.serviceAccountName" . }}
       containers:
         - name: {{ .Chart.Name }}
+          {{- with .Values.resources }}
+          resources:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
           imagePullPolicy: {{ .Values.image.pullPolicy }}
           ports:

diff --git a/deploy/values.yaml b/deploy/values.yaml
@@ -19,13 +19,14 @@ serviceAccount:
   name: ""
 
 service:
-  type: NodePort
+  type: ClusterIP
   port: 80
 
 ingress:
   annotations: 
     kubernetes.io/ingress.class: alb
     alb.ingress.kubernetes.io/scheme: internet-facing
+    alb.ingress.kubernetes.io/target-type: ip
     alb.ingress.kubernetes.io/tags: Name=BTE_ALB_TAG_VALUE,Environment=ENVIRONMENT_TAG_VALUE
     alb.ingress.kubernetes.io/load-balancer-attributes: idle_timeout.timeout_seconds=660
     alb.ingress.kubernetes.io/security-groups: translator-ci-alb-http-sg
@@ -52,7 +53,7 @@ env:
 # toleration to node taint such that this deployment can be scheduled on the tainted node while others without the toleration can not
 tolerations: 
 - key      : "transltr"
-  value    : "bte"
+  value    : "managed-app"
   operator : "Equal"
   effect   : "NoSchedule"
 
@@ -66,7 +67,7 @@ affinity:
         - key: application
           operator: In
           values:
-          - bte
+          - managed-app
   # this ensures only ONE pod will run on each node
   podAntiAffinity:
     requiredDuringSchedulingIgnoredDuringExecution:
@@ -75,5 +76,12 @@ affinity:
         - key: app.kubernetes.io/name
           operator: In
           values:
-          - bte
+          - managed-app
       topologyKey: "kubernetes.io/hostname"
+resources:
+  requests:
+    memory: 56Gi
+    cpu: 13000m
+  limits:
+    memory: 58Gi
+    cpu: 14000m 
diff --git a/docs/INSTALLATION.md b/docs/INSTALLATION.md
@@ -207,6 +207,10 @@ This repository intentionally includes a set of VSCode task and debug configs fo
 
 If you want to run BTE with debug logging and async support, with VSCode's debugger attaching to BTE so you can set breakpoints, catch on errors, etc., Use "Run and Debug" > "Build w/ Cache" and hit the play button. A number of other configurations are supplied, you can explore them in [the launch.json file.](../.vscode/launch.json)
 
+### Updating
+In this base package (biothings_explorer), run the command `npm run pull`, which will pull the latest code from this module and all submodules. Note any warnings or errors in the console logs.
+
+
 ## Usage
 
 Now that you have an instance of BTE up and running, you can POST queries to `http://<HOST>:3000/v1/query`. See [Usage](./USAGE.md) for more information.

diff --git a/examples/v1.1/inferred_query_drug_treats_disease.json b/examples/v1.1/inferred_query_drug_treats_disease.json
@@ -0,0 +1,23 @@
+{
+    "message": {
+        "query_graph": {
+            "nodes": {
+                "n0": {
+                    "categories": ["biolink:ChemicalEntity"]
+                },
+                "n1": {
+                    "categories": ["biolink:Disease"],
+                    "ids": ["MONDO:0800044"]
+                }
+            },
+            "edges": {
+                "e01": {
+                    "subject": "n0",
+                    "object": "n1",
+                    "predicates": ["biolink:treats"],
+                    "knowledge_type": "inferred"
+                }
+            }
+        }
+    }
+}
diff --git a/src/web-app/src/stores/examples.js b/src/web-app/src/stores/examples.js
@@ -194,12 +194,12 @@ export const useExamplesStore = defineStore({
         store.loading = false;
         console.log(res.data)
         self.jobs.unshift({
-          'id': res.data.id,
+          'id': res.data.job_id,
           'date': this.getDateRightNow(),
-          'url': res.data.url,
+          'url': res.data.job_url,
           'description': description
         });
-        self.message = `A new job ID has been created: ${res.data.id} `
+        self.message = `A new job ID has been created: ${res.data.job_id} `
         self.updateJobs();
       }).catch(err=>{
         store.loading = false;