Merge pull request #421 from NCEAS/bugfix-postgres-connections

Ensure postgres connections are closed properly and other minor changes
NCEAS · May 3, 2024 · 2773529 · 2773529
2 parents 47667aa + a114df9
commit 2773529
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Showing 25 changed files with 868 additions and 736 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -75,7 +75,7 @@ jobs:
 
   docker-publish:
     name: Docker Build and Publish
-    if: github.ref_name == 'develop' || startsWith(github.ref, 'refs/tags/v') || startsWith(github.ref_name, 'feature')
+    if: github.ref_name == 'develop' || startsWith(github.ref, 'refs/tags/v') || startsWith(github.ref_name, 'bugfix')
     needs: maven-build
     runs-on: ubuntu-latest
     permissions:

diff --git a/Docker/metadig-worker/Dockerfile b/Docker/metadig-worker/Dockerfile
@@ -34,6 +34,7 @@ ENV PATH="$PATH:$JAVA_HOME/bin"
 RUN echo 'options(repos = c(CRAN = "http://cran.rstudio.com"))' >> /usr/lib/R/etc/Rprofile.site
 RUN Rscript -e "install.packages(c('remotes', 'stringr', 'jsonlite'))"
 RUN Rscript -e "remotes::install_github('NCEAS/metadig-r', ref = 'v.0.2.0')"
+RUN Rscript -e "remotes::install_github('NCEAS/metadig-rake', ref = 'develop')"
 
 # DataONE indexer prints copious error msgs if these files don't exist
 RUN mkdir -p /etc/dataone/index && touch /etc/dataone/index/d1client.properties && touch /etc/dataone/node.properties && touch /etc/dataone/index/cn-index-processor.properties

diff --git a/helm/metadig-controller/Chart.yaml b/helm/metadig-controller/Chart.yaml
@@ -15,10 +15,10 @@ 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: 1.0.4
+version: 1.0.5
 
 # 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
 # follow Semantic Versioning. They should reflect the version the application is using.
 # It is recommended to use it with quotes.
-appVersion: "3.0.0"
+appVersion: "3.0.1-SNAPSHOT"
diff --git a/helm/metadig-controller/values.yaml b/helm/metadig-controller/values.yaml
@@ -7,7 +7,7 @@ replicaCount: 1
 image:
   repository: ghcr.io/nceas/metadig-controller
   pullPolicy: Always
-  tag: "v.3.0.0"
+  tag: "bugfix-postgres-connections"
 
 
 imagePullSecrets: []

diff --git a/helm/metadig-postgres/Chart.yaml b/helm/metadig-postgres/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: 1.0.0
+version: 1.0.1
 
 # 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/helm/metadig-postgres/config/pgbouncer.ini b/helm/metadig-postgres/config/pgbouncer.ini
@@ -198,7 +198,7 @@ max_client_conn = 200
 ; default pool size.  20 is good number when transaction pooling
 ; is in use, in session pooling it needs to be the number of
 ; max clients you want to handle at any moment
-default_pool_size = 50
+default_pool_size = 200
 
 ;; Minimum number of server connections to keep in pool.
 ;min_pool_size = 0
@@ -213,7 +213,7 @@ default_pool_size = 50
 ;max_db_connections = 0
 ;max_user_connections = 0
 
-max_db_connections = 90
+max_db_connections = 220
 #max_user_connections = 100
 max_user_connections = 200
 

diff --git a/helm/metadig-scheduler/Chart.yaml b/helm/metadig-scheduler/Chart.yaml
@@ -15,10 +15,10 @@ 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: 1.0.4
+version: 1.0.5
 
 # 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
 # follow Semantic Versioning. They should reflect the version the application is using.
 # It is recommended to use it with quotes.
-appVersion: "3.0.0"
+appVersion: "3.0.1-SNAPSHOT"
diff --git a/helm/metadig-scheduler/values.yaml b/helm/metadig-scheduler/values.yaml
@@ -7,7 +7,7 @@ replicaCount: 1
 image:
   repository: ghcr.io/nceas/metadig-scheduler
   pullPolicy: Always
-  tag: "v.3.0.0"
+  tag: "bugfix-postgres-connections"
 
 imagePullSecrets: []
 nameOverride: ""

diff --git a/helm/metadig-scorer/Chart.yaml b/helm/metadig-scorer/Chart.yaml
@@ -15,10 +15,10 @@ 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: 1.0.4
+version: 1.0.5
 
 # 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
 # follow Semantic Versioning. They should reflect the version the application is using.
 # It is recommended to use it with quotes.
-appVersion: "3.0.0"
+appVersion: "3.0.0-SNAPSHOT"
diff --git a/helm/metadig-scorer/values.yaml b/helm/metadig-scorer/values.yaml
@@ -7,7 +7,7 @@ replicaCount: 1
 image:
   repository: ghcr.io/nceas/metadig-scorer
   pullPolicy: Always
-  tag: "v.3.0.0"
+  tag: "bugfix-postgres-connections"
 
 
 imagePullSecrets: []

diff --git a/helm/metadig-worker/Chart.yaml b/helm/metadig-worker/Chart.yaml
@@ -15,10 +15,10 @@ 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: 1.0.4
+version: 1.0.5
 
 # 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
 # follow Semantic Versioning. They should reflect the version the application is using.
 # It is recommended to use it with quotes.
-appVersion: "3.0.0"
+appVersion: "3.0.1-SNAPSHOT"
diff --git a/helm/metadig-worker/templates/deployment.yaml b/helm/metadig-worker/templates/deployment.yaml
@@ -27,6 +27,8 @@ spec:
       serviceAccountName: {{ include "metadig-worker.serviceAccountName" . }}
       securityContext:
         {{- toYaml .Values.podSecurityContext | nindent 8 }}
+      topologySpreadConstraints:
+        {{- toYaml .Values.topologySpreadConstraints | nindent 8}}
       containers:
         - name: {{ .Chart.Name }}
           securityContext:
@@ -60,14 +62,6 @@ spec:
           defaultMode: 0644
       restartPolicy: Always
       {{- with .Values.nodeSelector }}
-      nodeSelector:
-        {{- toYaml . | nindent 8 }}
-      {{- end }}
-      {{- with .Values.affinity }}
-      affinity:
-        {{- toYaml . | nindent 8 }}
-      {{- end }}
-      {{- with .Values.tolerations }}
       tolerations:
         {{- toYaml . | nindent 8 }}
       {{- end }}

diff --git a/helm/metadig-worker/values.yaml b/helm/metadig-worker/values.yaml
@@ -4,10 +4,13 @@
 
 replicaCount: 1
 
+labels:
+  app: metadig-worker
+
 image:
   repository: ghcr.io/nceas/metadig-worker
   pullPolicy: Always
-  tag: "v.3.0.0"
+  tag: "bugfix-postgres-connections"
 
 imagePullSecrets: []
 nameOverride: ""
@@ -38,6 +41,14 @@ podAnnotations: {}
 podSecurityContext: {}
   # fsGroup: 2000
 
+topologySpreadConstraints:
+  - maxSkew: 10
+    topologyKey: kubernetes.io/hostname
+    whenUnsatisfiable: ScheduleAnyway
+    labelSelector:
+      matchLabels:
+        app: metadig-worker
+
 securityContext: {}
   # capabilities:
   #   drop:

diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>edu.ucsb.nceas</groupId>
   <artifactId>metadig-engine</artifactId>
-  <version>3.0.0</version>
+  <version>3.0.1-SNAPSHOT</version>
   <packaging>jar</packaging>
   <name>metadig-engine</name>
   <description>MetaDIG library for running metadata quality tests</description>

diff --git a/src/main/java/edu/ucsb/nceas/mdqengine/Worker.java b/src/main/java/edu/ucsb/nceas/mdqengine/Worker.java
@@ -451,7 +451,6 @@ private void returnReport(String metadataPid, String suiteId, QueueEntry qEntry,
                 try {
                     log.info("Resetting RabbitMQ queues and resending completed report...");
                     // destroy channel before setting up queues again
-                    RabbitMQchannel.close();
                     RabbitMQconnection.close();
                     // setup queues
                     this.setupQueues();