Merge pull request #11 from qbicsoftware/release/1.0.0

## 1.0.0 (2022-01-28) * Add first working implementation to report updates based on a point in time. * The application fails when any problems arise retrieving samples
qbicsoftware · Feb 2, 2022 · 928b842 · 928b842
2 parents 328e40d + c5c7545
commit 928b842
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diff --git a/.github.settings.xml b/.github.settings.xml
@@ -0,0 +1,14 @@
+<settings>
+  <servers>
+    <server>
+      <id>nexus-snapshots</id>
+      <username>${env.MAVEN_REPO_USERNAME}</username>
+      <password>${env.MAVEN_REPO_PASSWORD}</password>
+    </server>
+    <server>
+      <id>nexus-releases</id>
+      <username>${env.MAVEN_REPO_USERNAME}</username>
+      <password>${env.MAVEN_REPO_PASSWORD}</password>
+    </server>
+  </servers>
+</settings>
diff --git a/.github/workflows/build_package.yml b/.github/workflows/build_package.yml
@@ -1,6 +1,6 @@
 name: Build Maven Package
 
-on: [push]
+on: [ push ]
 
 jobs:
   build:

diff --git a/.github/workflows/changelog-update.yml b/.github/workflows/changelog-update.yml
@@ -1,7 +1,7 @@
 name: "Changelog update"
 on:
   pull_request:
-    types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+    types: [ opened, synchronize, reopened, ready_for_review, labeled, unlabeled ]
 
 jobs:
   # Enforces the update of a changelog file on every pull request

diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -37,47 +37,47 @@ jobs:
         # Learn more about CodeQL language support at https://git.io/codeql-language-support
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v2
-    - name: Set up JDK 1.17
-      uses: actions/setup-java@v1
-      with:
-        java-version: 1.17
-        settings-path: ${{ github.workspace }}
+      - name: Checkout repository
+        uses: actions/checkout@v2
+      - name: Set up JDK 1.17
+        uses: actions/setup-java@v1
+        with:
+          java-version: 1.17
+          settings-path: ${{ github.workspace }}
 
-    - name: Load local Maven repository cache
-      uses: actions/cache@v2
-      with:
-        path: ~/.m2/repository
-        key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
-        restore-keys: |
-          ${{ runner.os }}-maven-
+      - name: Load local Maven repository cache
+        uses: actions/cache@v2
+        with:
+          path: ~/.m2/repository
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: |
+            ${{ runner.os }}-maven-
 
-    # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
-      with:
-        languages: ${{ matrix.language }}
-        # If you wish to specify custom queries, you can do so here or in a config file.
-        # By default, queries listed here will override any specified in a config file.
-        # Prefix the list here with "+" to use these queries and those in the config file.
-        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v1
+        with:
+          languages: ${{ matrix.language }}
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
+          # queries: ./path/to/local/query, your-org/your-repo/queries@main
 
-    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
-    # If this step fails, then you should remove it and run the build manually (see below)
-    - name: Autobuild
-      uses: github/codeql-action/autobuild@v1
+      # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+      # If this step fails, then you should remove it and run the build manually (see below)
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v1
 
-    # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 https://git.io/JvXDl
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 https://git.io/JvXDl
 
-    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
-    #    and modify them (or add more) to build your code if your project
-    #    uses a compiled language
+      # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+      #    and modify them (or add more) to build your code if your project
+      #    uses a compiled language
 
-    #- run: |
-    #   make bootstrap
-    #   make release
+      #- run: |
+      #   make bootstrap
+      #   make release
 
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v1
diff --git a/.github/workflows/generate-reports.yml b/.github/workflows/generate-reports.yml
@@ -5,7 +5,7 @@ name: Generate reports and API documentation
 
 on:
   release:
-    types: [created]
+    types: [ created ]
   push:
     branches:
       - development
@@ -20,10 +20,10 @@ jobs:
       - name: Install git
         run: sudo apt-get install git
 
-      - name: Set up JDK 1.11
+      - name: Set up JDK 1.17
         uses: actions/setup-java@v1
         with:
-          java-version: 1.11
+          java-version: 1.17
           server-id: github # Value of the distributionManagement/repository/id field of the pom.xml
           settings-path: ${{ github.workspace }}
 
@@ -44,15 +44,15 @@ jobs:
           path: ~/.m2/repository
           key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
           restore-keys: |
-              ${{ runner.os }}-maven-
+            ${{ runner.os }}-maven-
 
       - name: Maven generate reports
         run: mvn --activate-profiles !development-build,!release-build --settings .github.settings.xml site
 
       - name: Set up git
         run: |
-            git config --global user.email "[email protected]"
-            git config --global user.name "JohnnyQ5"
+          git config --global user.email "[email protected]"
+          git config --global user.name "JohnnyQ5"
 
       - name: Publish reports
         run: |

diff --git a/.github/workflows/groovy_checkstyle.yml b/.github/workflows/groovy_checkstyle.yml
@@ -1,6 +1,6 @@
 name: Groovy Checkstyle
 
-on: [push]
+on: [ push ]
 
 jobs:
   build:

diff --git a/.github/workflows/nexus-publish-release.yml b/.github/workflows/nexus-publish-release.yml
@@ -6,38 +6,38 @@ name: Nexus Package
 
 on:
   release:
-    types: [created]
+    types: [ created ]
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up JDK 1.17
-      uses: actions/setup-java@v1
-      with:
-        java-version: 1.17
-        server-id: github # Value of the distributionManagement/repository/id field of the pom.xml
-        settings-path: ${{ github.workspace }}
-
-    -   name: Load local Maven repository cache
+      - uses: actions/checkout@v2
+      - name: Set up JDK 1.17
+        uses: actions/setup-java@v1
+        with:
+          java-version: 1.17
+          server-id: github # Value of the distributionManagement/repository/id field of the pom.xml
+          settings-path: ${{ github.workspace }}
+
+      - name: Load local Maven repository cache
         uses: actions/cache@v2
         with:
-            path: ~/.m2/repository
-            key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
-            restore-keys: |
-                ${{ runner.os }}-maven-
+          path: ~/.m2/repository
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: |
+            ${{ runner.os }}-maven-
 
-    -   name: Remove snapshot tags
-        run:  mvn versions:set -DremoveSnapshot
+      - name: Remove snapshot tags
+        run: mvn versions:set -DremoveSnapshot
 
-    -   name: Build with Maven
+      - name: Build with Maven
         run: mvn -B package --file pom.xml
 
-    -   name: Publish artefact to QBiC Nexus Repository
+      - name: Publish artefact to QBiC Nexus Repository
         run: mvn --quiet --activate-profiles !development-build,release-build --settings $GITHUB_WORKSPACE/.github.settings.xml deploy
         env:
-            MAVEN_REPO_USERNAME: ${{ secrets.NEXUS_USERNAME }}
-            MAVEN_REPO_PASSWORD: ${{ secrets.NEXUS_PASSWORD }}
+          MAVEN_REPO_USERNAME: ${{ secrets.NEXUS_USERNAME }}
+          MAVEN_REPO_PASSWORD: ${{ secrets.NEXUS_PASSWORD }}
diff --git a/.github/workflows/nexus-publish.yml b/.github/workflows/nexus-publish.yml
@@ -21,7 +21,7 @@ jobs:
         with:
           java-version: 1.17
           settings-path: ${{ github.workspace }}
-      
+
       - name: Load local Maven repository cache
         uses: actions/cache@v2
         with:

diff --git a/.github/workflows/pr_to_master_from_hotfix_release_only.yml b/.github/workflows/pr_to_master_from_hotfix_release_only.yml
@@ -3,7 +3,7 @@ name: PR to master/main branch from patch/release branch only
 on:
   pull_request:
     branches:
-    - main
+      - main
 
 jobs:
   test:

diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -1,6 +1,6 @@
 name: Run Maven Tests
 
-on: [push]
+on: [ push ]
 
 jobs:
   build:

diff --git a/.gitignore b/.gitignore
@@ -27,7 +27,9 @@ hs_err_pid*
 
 # misc
 *.DS_STORE
+/target/
+/bin/
 
 # IntelliJ
 
-.idea
+.idea
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,10 @@
+# Changelog
+
+This project adheres to [Semantic Versioning](https://semver.org/).
+
+## 1.0.0 (2022-01-28)
+
+* Add first working implementation to report updates based on a point in time.
+* The application fails when any problems arise retrieving samples 
+
+
diff --git a/HELP.md b/HELP.md
@@ -1,11 +1,14 @@
 # Read Me First
+
 The following was discovered as part of building this project:
 
-* The original package name 'life.qbic.spring-minimal-template' is invalid and this project uses 'life.qbic.springminimaltemplate' instead.
+* The original package name 'life.qbic.spring-minimal-template' is invalid and this project uses '
+  life.qbic.springminimaltemplate' instead.
 
 # Getting Started
 
 ### Reference Documentation
+
 For further reference, please consider the following sections:
 
 * [Official Apache Maven documentation](https://maven.apache.org/guides/index.html)

diff --git a/README.md b/README.md
@@ -1,34 +1,43 @@
-# LIMS Sample Status Reporter 
+# LIMS Sample Status Reporter
+
 [![CodeQL](https://github.com/qbicsoftware/sample-status-reporter/actions/workflows/codeql-analysis.yml/badge.svg?branch=main)](https://github.com/qbicsoftware/sample-status-reporter/actions/workflows/codeql-analysis.yml)
 [![Latest Release ](https://img.shields.io/github/v/release/qbicsoftware/sample-status-reporter.svg)](https://github.com/qbicsoftware/sample-status-reporter/releases)
 ![Groovy Language](https://img.shields.io/badge/language-groovy-blue.svg)
 
-The LIMS Sample status reporter application is used to report changes in the status of a sample set in the LIMS environment to Sample Tracking Service. 
-
-Overview:
-
-- [Requirements](#requirements)
-- [Run the app](#run-the-app)
-- [App structure](#app-structure)
-
-# Requirements
-
-To run this app, you need to have version 17 of a **Java JRE** or **JDK** installed (e.g. **Zulu**).
+## System setup
+
+For this application to be run the following environment variables need to be set:
+
+| Name                                | Description                                                            |
+|-------------------------------------|------------------------------------------------------------------------|
+| `LAST_UPDATE_FILE`                  | A path to a persistent file. The last successful run is stored here.   |
+| `LIMS_PASSWORD`                     | The password to access the OpenBiS LIMS                                |
+| `LIMS_SERVER_URL`                   | The URL to the OpenBiS LIMS API                                        |
+| `LIMS_USER`                         | The user to access the OpenBiS LIMS                                    |
+| `SAMPLE_TRACKING_AUTH_PASSWORD`     | The password for the sample tracking user                              |
+| `SAMPLE_TRACKING_AUTH_USER`         | The username for the sample tracking service                           |
+| `SAMPLE_TRACKING_LOCATION_ENDPOINT` | The endpoint to list all locations. This does not contain the base url |
+| `SAMPLE_TRACKING_LOCATION_USER`     | The sample tracking user currently using the application               |
+| `SAMPLE_TRACKING_URL`               | The base URL for the sample tracking service                           |
+| `USER_DB_DIALECT`                   | The database dialect of the user database                              |
+| `USER_DB_DRIVER`                    | The database driver for the user database                              |
+| `USER_DB_HOST`                      | The URL to the host of the user database containing the database name  |
+| `USER_DB_USER_NAME`                 | The database user name                                                 |
+| `USER_DB_USER_PW`                   | The database user password                                             |
 
 ## Run the app
 
 Checkout the latest code from `main` and run the Maven goal `spring-boot:run`:
 
 ```
-mvn spring-boot:run
+mvn spring-boot:run [-Dspring-boot.run.arguments=[-hV],[-t=<timePoint>]]
+  -h, --help      Show this help message and exit.
+  -t, --time-point=<timePoint>
+                  Point in time from where to search for updates e.g. '2022-01-01T00:00:00Z'.
+                  Defaults to the last successful run. 
+                  If never run successfully defaults to the same time yesterday.
+  -V, --version   Print version information and exit.
 ```
 
 
-## App structure
-
-The preliminary app structure is outlined in this UML diagram:
-![Bioinformatics Analysis Result Set ER](./docs/Spring%20Boot%20Starter%20Template%20UML.jpg)
-
-
-
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,7 +3,7 @@ name: PR to master/main branch from patch/release branch only @@
     on:
       pull_request:
         branches:
-        - main
+          - main
     jobs:
       test:
@@ Expand Down @@