Trying to fix tooltip on measurement value charts

.circleci/config.yml

@@ -2,7 +2,7 @@ version: 2.1
 
 defaults: &defaults
   docker:
-    - image: us.gcr.io/broad-dsp-gcr-public/workbench:buildimage-0.0.28
+    - image: us.gcr.io/broad-dsp-gcr-public/workbench:buildimage-0.0.29
   working_directory: ~/data-browser
 java_defaults: &java_defaults
   <<: *defaults
@@ -51,7 +51,7 @@ commands:
 jobs:
   public-api-local-test:
     docker:
-      - image: us.gcr.io/broad-dsp-gcr-public/workbench:buildimage-0.0.28
+      - image: us.gcr.io/broad-dsp-gcr-public/workbench:buildimage-0.0.29
       - image: mysql:5.7
         environment:
           - MYSQL_ROOT_PASSWORD=ubuntu

ci/Dockerfile.circle_build

@@ -19,7 +19,7 @@ FROM cimg/openjdk:17.0-browsers
 
 USER circleci
 
-ENV CLOUD_SDK_VERSION 471.0.0
+ENV CLOUD_SDK_VERSION 503.0.0
 
 RUN cd && \
   wget https://dl.google.com/dl/cloudsdk/channels/rapid/downloads/google-cloud-sdk-${CLOUD_SDK_VERSION}-linux-x86_64.tar.gz -O gcloud.tgz && \
@@ -53,7 +53,7 @@ RUN cd /tmp && \
 
 ENV PATH=/home/circleci/node/bin:/home/circleci/google-cloud-sdk/bin:$PATH
 
-RUN curl https://dl.google.com/cloudsql/cloud_sql_proxy.linux.amd64 > /tmp/cloud_sql_proxy \
+RUN curl -o /tmp/cloud_sql_proxy https://storage.googleapis.com/cloud-sql-connectors/cloud-sql-proxy/v2.14.2/cloud-sql-proxy.linux.amd64 \
   && sudo mv /tmp/cloud_sql_proxy /usr/local/bin && sudo chmod +x /usr/local/bin/cloud_sql_proxy
 
 # It never makes sense for Gradle to run a daemon within a docker container.

deploy/Dockerfile

@@ -28,29 +28,30 @@ RUN n 22
 # Install openapi-generator-cli
 RUN npm install @openapitools/openapi-generator-cli -g
 
-ENV CLOUD_SDK_VERSION 471.0.0
+ENV CLOUD_SDK_VERSION 503.0.0
 
 WORKDIR /root
-RUN wget https://dl.google.com/dl/cloudsdk/channels/rapid/downloads/google-cloud-sdk-${CLOUD_SDK_VERSION}-linux-x86_64.tar.gz -O gcloud.tgz && \
+RUN curl -o gcloud.tgz https://dl.google.com/dl/cloudsdk/channels/rapid/downloads/google-cloud-sdk-${CLOUD_SDK_VERSION}-linux-x86_64.tar.gz && \
   tar -xf gcloud.tgz && \
   ./google-cloud-sdk/install.sh  --quiet && \
   ./google-cloud-sdk/bin/gcloud components install app-engine-java && \
   rm -rf gcloud.tgz
 
 ENV PATH=~/node/bin:~/google-cloud-sdk/bin:$PATH
 
-RUN wget https://dl.google.com/cloudsql/cloud_sql_proxy.linux.amd64 -O /tmp/cloud_sql_proxy \
+RUN curl -o /tmp/cloud_sql_proxy https://storage.googleapis.com/cloud-sql-connectors/cloud-sql-proxy/v2.14.2/cloud-sql-proxy.linux.amd64 \
   && mv /tmp/cloud_sql_proxy /usr/local/bin && chmod +x /usr/local/bin/cloud_sql_proxy
 
 # It never makes sense for Gradle to run a daemon within a docker container.
 ENV GRADLE_OPTS="-Dorg.gradle.daemon=false"
 
 ENV GRADLE_VERSION 7.6.1
 
-RUN wget "https://services.gradle.org/distributions/gradle-${GRADLE_VERSION}-bin.zip" -O /tmp/gradle.zip \
+RUN curl -L -o /tmp/gradle.zip https://services.gradle.org/distributions/gradle-${GRADLE_VERSION}-bin.zip \
   && unzip /tmp/gradle.zip -d /opt/gradle
 ENV PATH="/opt/gradle/gradle-${GRADLE_VERSION}/bin:${PATH}"
 
-# Force a lower concurrent-ruby version, as we only have Ruby 2.3.
-RUN gem install activesupport -v 6.1.4.6
+RUN gem install logger
+RUN  gem install concurrent-ruby -v 1.3.4
+RUN gem install activesupport -v 6.1.4.6 --conservative
 RUN gem install jira-ruby

deploy/docker-compose.yaml

@@ -1,4 +1,3 @@
-version: "3"
 services:
   deploy:
     build:

deploy/libproject/deploy.rb

@@ -1,5 +1,6 @@
 require "open3"
 require "set"
+require "logger"
 require_relative "../../aou-utils/serviceaccounts"
 require_relative "../../aou-utils/utils/common"
 require_relative "../../aou-utils/workbench"

public-api/config/cdr_config_prod.json

@@ -105,6 +105,6 @@
     "creationTime": "2023-12-19 15:55:44Z",
     "releaseNumber": 15,
     "numParticipants": 633540,
-    "publicDbName": "p_2024q3_18"
+    "publicDbName": "p_2024q3_21"
   }
 ]

public-api/config/cdr_config_stable.json

@@ -106,6 +106,6 @@
     "creationTime": "2023-12-19 15:55:44Z",
     "releaseNumber": 15,
     "numParticipants": 633540,
-    "publicDbName": "p_2024q3_18"
+    "publicDbName": "p_2024q3_21"
   }
 ]

public-api/config/cdr_config_staging.json

@@ -107,6 +107,6 @@
     "creationTime": "2023-12-19 15:55:44Z",
     "releaseNumber": 15,
     "numParticipants": 633540,
-    "publicDbName": "p_2024q3_18"
+    "publicDbName": "p_2024q3_21"
   }
 ]

public-api/config/cdr_config_test.json

@@ -125,6 +125,6 @@
     "creationTime": "2023-12-19 15:55:44Z",
     "releaseNumber": 15,
     "numParticipants": 633540,
-    "publicDbName": "p_2024q3_18"
+    "publicDbName": "p_2024q3_21"
   }
 ]

public-api/db-cdr/generate-cdr/csv/survey_module.csv

@@ -3,7 +3,7 @@ concept_id,"name","description",question_count,participant_count,order_number
 1333342,"COVID-19 Participant Experience (COPE)","This survey asks about the impact of COVID-19 on a participant’s mental health, well-being, and everyday life. This survey was administered to participants multiple times from May 2020 to March 2021.",176,100220,7
 1585710,"Overall Health","This survey collects information about a participant’s overall health including general health, daily activities, and women’s health topics.",21,412220,2
 1585855,"Lifestyle","This survey asks about a participant’s use of tobacco, alcohol, and recreational drugs.",26,412220,3
-1586134,"The Basics","This core survey asks basic demographic questions, including questions about a participant’s work and home. Participants must complete this survey before responding to additional surveys.",28,413360,1
+1586134,"The Basics","This core survey asks basic demographic questions, including questions about a participant’s work and home. Participants must complete this survey before responding to additional surveys.",25,413360,1
 40192389,"Social Determinants of Health","This survey asks about the social determinants of health, including a participant’s neighborhood, social life, stress, and feelings about everyday life.",80,117800,9
 43528895,"Health Care Access And Utilization","This survey asks questions about a participant’s access to and use of health care.",57,190220,5
 43529712,"Personal and Family Health History","This survey includes information about past medical history, including medical conditions and approximate age of diagnosis. Multiple versions of this survey have been offered at different times. All survey questions are presented together on this page. Further breakdown by survey type can be performed within the Research Workbench. The layout of each survey version can be viewed in the linked PDFs.",604,185240,6

public-api/libproject/cloudsqlproxycontext.rb

@@ -6,11 +6,13 @@ class CloudSqlProxyContext < ServiceAccountContext
   def run()
     # TODO(dmohs): An error here does not cause the main thread to die.
     super do
+      instance = "#{@project}:us-central1:databrowsermaindb"
       @ps = fork do
         exec(*%W{
           cloud_sql_proxy
-            -instances #{@project}:us-central1:databrowsermaindb=tcp:0.0.0.0:3307
-            -credential_file=#{@path}
+            --port 3307
+            #{instance}
+            --credentials-file=#{@path}
         })
       end
       begin

public-api/src/dev/server/Dockerfile

@@ -26,7 +26,7 @@ RUN apt-get update && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-ENV CLOUD_SDK_VERSION 471.0.0
+ENV CLOUD_SDK_VERSION 503.0.0
 
 ENV PATH /google-cloud-sdk/bin:$PATH
 

public-ui/src/app/data-browser/charts/chart-measurement-values/chart-value-react.component.tsx

@@ -23,13 +23,15 @@ interface Props {
 }
 
 export class ValueReactChartComponent extends React.Component<Props, State> {
+  chartRef: React.RefObject<any>;
   constructor(props) {
     super(props);
     this.state = {
       options: null,
       pageX: 0,
       pageY: 0,
     };
+    this.chartRef = React.createRef();
   }
 
   componentDidMount() {
@@ -169,12 +171,24 @@ export class ValueReactChartComponent extends React.Component<Props, State> {
         useHTML: true,
       };
     }
+
     newBaseOptions.tooltip.positioner = (width, height, point) => {
-      return {
-        x: this.state.pageX - 144,
-        y: this.state.pageY - 90,
-      };
+      const chart = this.chartRef.current?.chart; // Access chart via ref
+      if (!chart) return { x: 0, y: 0 };
+
+      const chartWidth = chart.chartWidth;
+      const chartHeight = chart.chartHeight;
+
+      const xPos = point.plotX + chart.plotLeft + point.shapeArgs.width;
+      const yPos = point.plotY + chart.plotTop - height / 2;
+
+      // Ensure the tooltip stays within chart bounds
+      const adjustedX = Math.max(0, Math.min(chartWidth - width, xPos));
+      const adjustedY = Math.max(0, Math.min(chartHeight - height, yPos));
+
+      return { x: adjustedX, y: adjustedY };
     };
+
     this.setState({ options: newBaseOptions });
   }
 

public-ui/src/app/data-browser/views/genomic-view/genomic-view.component.tsx

@@ -733,16 +733,13 @@ export const GenomicViewComponent = withRouteData(
       window.addEventListener("beforeunload", this.componentCleanup);
       const { search } = urlParamsStore.getValue();
       const currentUrl = window.location.href;
-      console.log(currentUrl);
-      console.log(currentUrl.includes('variants'));
-      console.log(currentUrl.includes('structural-variants'));
 
       if (search) {
           if (currentUrl.includes('structural-variants')) {
               this.setState({ svSearchTerm: search }, () => {
                 this.getSVVariantSearch(search);
               });
-          } else if (currentUrl.includes('variants')) {
+          } else if (currentUrl.includes('snvsindels')) {
               this.setState({ searchTerm: search }, () => {
                 this.getVariantSearch(search);
               });