try again to fix server

.github/workflows/prepare-release.yml

@@ -8,7 +8,7 @@
 #
 # Othewise the pull can never be merged because no status check runs.
 # This is described here: https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/defining-the-mergeability-of-pull-requests/troubleshooting-required-status-checks#handling-skipped-but-required-checks
-name: Prepare to release nlp-insights 
+name: Prepare to release nlp-insights
 on:
   pull_request:
     types: [opened, synchronize, labeled, reopened]
@@ -65,7 +65,7 @@ jobs:
              UPDATES=$(.github/workflows/scripts/update_files_with_version.sh \
               --project_dir=. \
               --version=${{ env.VERSION }} \
-              --docker_org=${{ env.docker_org }} \
+              --docker_org=${{ env.docker_server }}/${{ env.docker_org }} \
               --docker_repo=${{ env.docker_repo}})
 
              >&2 echo "${UPDATES} changes were made to update the release to ${{ env.VERSION }}"
@@ -89,7 +89,7 @@ jobs:
       - name: Validate Documentation
         run: |
              pip install --upgrade pip && pip install mkdocs mkdocs-gen-files pymdown-extensions
-             mkdocs build -s      
+             mkdocs build -s
       - name: Push Docker Image
         run: |
              ./gradlew dockerPush -PdockerUser=${{ env.docker_server }}/${{ env.docker_org }}
@@ -111,7 +111,7 @@ jobs:
              BUILD_URL="${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID}"
              sha=$(git rev-parse HEAD)
              obj="{\"state\" : \"success\", \"context\" : \"Prepare release\", \"target_url\": \"${BUILD_URL}\" }"
- 
+
              curl -X POST "${GITHUB_API_URL}/repos/${GITHUB_REPOSITORY}/statuses/${sha}"  \
                   -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
                   -H "Accept: application/vnd.github.v3+json" \

.github/workflows/scripts/update_files_with_version.sh

@@ -43,7 +43,7 @@ last_org=`echo $last_org | sed -e 's/^[[:space:]]*//'`
 
 if [ "${DOCKER_ORG}" != "${last_org}" ]; then
   >&2 echo "Updating ${values_yaml} to org = ${DOCKER_ORG}/${DOCKER_REPO}"
-  sed -i -e 's/\(\s*repository:\).*/\1 '${DOCKER_ORG}'\/'${DOCKER_REPO}'/' ${values_yaml}
+  sed -i -e 's_\(\s*repository:\).*_\1 '${DOCKER_ORG}'\/'${DOCKER_REPO}'_' ${values_yaml}
   updates=$((updates+1))
 fi
 
@@ -105,4 +105,4 @@ if [[ ${last_gradle_tag} != ${VERSION} ]]; then
 fi
 
 echo $updates
-exit 0 
+exit 0

build.gradle

@@ -16,7 +16,7 @@ ext {
   production_pkgs = [
     'ibm-whcs-sdk:1.9.0',
     'fhir.resources:6.1.0',
-    'flask:2.0.1'
+    'flask:2.1.1'
   ]
 
   dev_pkgs = [
@@ -351,7 +351,7 @@ task docTestSource(type: PythonTask) {
     "--doctest-modules",
     "--junit-xml=${pyDocTestXmlFile}"
   ]
-  
+
 }
 
 
@@ -379,11 +379,11 @@ task flake8(type: Exec) {
   ignoreExitValue=true
   workingDir = "${project.buildDir}"
   commandLine "${buildVenv}/bin/flake8", "${pySrcDir}/py", "--format=junit-xml", "--config=setup.cfg"
-  
+
   doLast {
     outputs.files.singleFile.text = standardOutput.toString()
   }
-  
+
 }
 
 
@@ -445,8 +445,8 @@ task checkSource {
   group 'quality'
   dependsOn project.tasks.lint
   dependsOn project.tasks.test
-  
-  
+
+
   doLast {
     groovy.xml.XmlSlurper slurper = new groovy.xml.XmlSlurper();
 
@@ -484,12 +484,12 @@ task checkSource {
       count += v.size()
       message.append("${fname} : ${v.size()} warnings\n")
     }
-    
+
     if (count && !project.hasProperty("noFailForSourceProblems")) {
       System.err.println(message)
       throw new GradleException("Build Failed with ${count} source code issues!")
     }
-    
+
     println(message)
   }
 }
@@ -522,7 +522,7 @@ docker {
 
   name dockerUser + "/${project.name}:" + version
   dockerfile file('Dockerfile')
-  
+
 }
 
 dockerPush {}
@@ -542,4 +542,3 @@ tasks.each {
     it.mustRunAfter clean
   }
 }
-

chart/Chart.yaml

@@ -15,12 +15,12 @@ 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: 0.1.3
+version: 0.1.6
 
 # 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.
-appVersion: 0.1.3
+appVersion: 0.1.6
 
 keywords:
   - ibm

chart/values.yaml

@@ -5,9 +5,9 @@
 replicaCount: 1
 
 image:
-  repository: alvearie/nlp-insights
+  repository: quay.io/alvearie/nlp-insights
   pullPolicy: Always
-  tag: 0.1.3
+  tag: 0.1.6
   pullSecret:
 
 service:

docs/charts/index.yaml

@@ -1,9 +1,28 @@
 apiVersion: v1
 entries:
   nlp-insights:
+  - apiVersion: v2
+    appVersion: 0.1.6
+    created: "2022-04-05T19:48:28.912139714Z"
+    description: A Helm Chart to deploy the NLP Insights service.
+    digest: 05802701a78468728d4b7ef01cf1afa09fc2e6ec3a6674c1bb0bdc0b7288f46e
+    home: https://github.com/LinuxForHealth/nlp-insights
+    keywords:
+    - ibm
+    - alvearie
+    - nlp
+    - insights
+    maintainers:
+    - email: ntl@us.ibm.com
+      name: Nicholas T. Lawrence
+    name: nlp-insights
+    type: application
+    urls:
+    - nlp-insights-0.1.6.tgz
+    version: 0.1.6
   - apiVersion: v2
     appVersion: 0.1.3
-    created: "2022-03-09T20:39:30.438685533Z"
+    created: "2022-04-05T19:48:28.911731108Z"
     description: A Helm Chart to deploy the NLP Insights service.
     digest: 286099b95180065ebe50b78cf2f5daa8d2d76a4fa51f46ad16e834332db9e902
     home: https://github.com/LinuxForHealth/nlp-insights
@@ -22,7 +41,7 @@ entries:
     version: 0.1.3
   - apiVersion: v2
     appVersion: 0.1.2
-    created: "2022-03-09T20:39:30.437815031Z"
+    created: "2022-04-05T19:48:28.911383003Z"
     description: A Helm Chart to deploy the NLP Insights service.
     digest: 42bed86de1f193821ca0a58269a44bdfa575d258be5b1b3950d0c64d9d5aa25a
     home: https://github.com/LinuxForHealth/nlp-insights
@@ -41,7 +60,7 @@ entries:
     version: 0.1.2
   - apiVersion: v2
     appVersion: 0.0.1
-    created: "2022-03-09T20:39:30.437242729Z"
+    created: "2022-04-05T19:48:28.911002398Z"
     description: A Helm Chart to deploy the NLP Insights service.
     digest: 0f23831266fa1c80fe75cc2cd8b35bb9325d047ac6470843d8624568ba73f7c7
     home: https://github.com/Alvearie/health-patterns/tree/main/services/nlp-insights
@@ -58,4 +77,4 @@ entries:
     urls:
     - nlp-insights-0.1.0.tgz
     version: 0.1.0
-generated: "2022-03-09T20:39:30.435180423Z"
+generated: "2022-04-05T19:48:28.91039589Z"

gradle.properties

@@ -5,7 +5,7 @@ reportsDir = reports
 pyDistDir = dist
 dockerUser=
 # Version is set by github actions during the build
-version=0.1.3
+version=0.1.6
 dockerLocalPort=5000
 # The python version number needs to be in sync with DockerFile
 # For example if the DockerFile has "FROM python:3.9-slim-buster"

requirements_dev.txt

@@ -13,7 +13,7 @@
 ### Production Dependencies
 ibm-whcs-sdk==1.9.0
 fhir.resources==6.1.0
-flask==2.0.1
+flask==2.1.1
 
 ### Development Dependencies
 pytest==6.2.5