Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

AMT V4 Flatfile generation #1

Open
wants to merge 36 commits into
base: master
Choose a base branch
from
Open

AMT V4 Flatfile generation #1

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
36 commits
Select commit Hold shift + click to select a range
478891d
Updates to work with AMT v3 and AMT v4 - still more work required
dionmcm Apr 12, 2023
9ee1866
Updates to work with AMT v3 and AMT v4 - still more work required
dionmcm Jul 19, 2023
fa0bb1f
Add back Junit XML generation
edeati Jul 20, 2023
a62496a
Forgot pom.xml from previous commit
edeati Jul 20, 2023
f26dc53
Initial checkin of AMTv4 changes
edeati Jul 25, 2023
fc9d26f
Speed up the V4 flat file generation
edeati Jul 26, 2023
260eb82
Change plugin version
edeati Jul 26, 2023
856ea00
Add Deployment details
edeati Jul 26, 2023
353b7ce
Change java to 17
edeati Jul 26, 2023
e5b0ae5
Change java version for compiler
edeati Jul 26, 2023
1d517af
Change Java to 11
edeati Jul 26, 2023
ded159f
Add application/java-archive to the allowed zip file input
edeati Jul 26, 2023
9bb4c08
AMT V3 backward compatible now
edeati Jul 27, 2023
7775eb9
Re-add tests
edeati Jul 27, 2023
9756627
Fix content test
edeati Jul 27, 2023
07ace3b
Remove extra stuff not needed
edeati Jul 27, 2023
ae2194d
Create parent directory for junit file if it doesn't exist
edeati Jul 27, 2023
657a7da
My, oh my. You cannot delete artefacts from Azure Devops repo. If you…
edeati Jul 27, 2023
517161d
AMT V4 TP is not a parent of TPUU but a HAS_PRODUCT_NAME - test error…
edeati Jul 28, 2023
86c8019
updated allowed file size
dionmcm Aug 10, 2023
9818c8d
updated allowed file size
dionmcm Aug 10, 2023
039d525
need to cache more now that the AMT module is gone
dionmcm Aug 20, 2023
844ab01
updated to account for case change in en-AU to en-au matching SNOMED …
dionmcm Feb 15, 2024
ad6946f
Add handling for active ingredients in Concept class
dionmcm Mar 28, 2024
62c82d3
Works on experimental files too
edeati May 7, 2024
4b408fe
Add TSV file generation and fix tests
edeati May 8, 2024
8da9a8b
Throw exception if there are duplicated testcases in the file
edeati May 8, 2024
46f9d47
Fix logging
edeati May 9, 2024
08e382b
Update src/main/java/au/gov/digitalhealth/terminology/amtflatfile/Amt…
dionmcm Jun 7, 2024
85b1e4d
Update src/main/java/au/gov/digitalhealth/terminology/amtflatfile/Amt…
dionmcm Jun 7, 2024
94cc144
Merge pull request #11 from aehrc/feature/amt-v4
dionmcm Jun 7, 2024
6cc6a71
Fix field quoting for TSV format
dionmcm Aug 28, 2024
5783983
Merge pull request #2 from AuDigitalHealth/feature/amt-v4
dionmcm Aug 28, 2024
5ebbb52
Replace newLine() with write("\r\n") and refactor tests
dionmcm Sep 3, 2024
ef0ec24
Refactor code, add lombok annotations, and simplify logging
dionmcm Sep 3, 2024
cfb5648
Merge branch 'AuDigitalHealth:feature/amt-v4' into feature/amt-v4
dionmcm Sep 3, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
.vscode
target/
1 change: 1 addition & 0 deletions .java-version
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
11
2 changes: 1 addition & 1 deletion README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@ An example execution is
<artifactId>amt-to-flat-file</artifactId>
<configuration>
<inputZipFilePath>NCTS_SCT_RF2_DISTRIBUTION_32506021000036107-XXX-SNAPSHOT.zip</inputZipFilePath>
<outputFilePath>amt-flat-file.csv</outputFilePath>
<outputFilePath>amt-flat-file</outputFilePath>
</configuration>
<plugin>
<plugins>
Expand Down
26 changes: 26 additions & 0 deletions azure-pipelines.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
trigger:
branches:
include:
- '*'
pool:
vmImage: ubuntu-latest

steps:

- task: MavenAuthenticate@0
inputs:
artifactsFeeds: 'amtv4'

- task: Maven@3
displayName: Build and Deploy on NCTS Devops
inputs:
mavenPomFile: 'pom.xml'
mavenOptions: '-Xmx3072m'
options: '-B'
javaHomeOption: 'JDKVersion'
jdkVersionOption: '1.11'
jdkArchitectureOption: 'x64'
publishJUnitResults: false
testResultsFiles: '**/surefire-reports/TEST-*.xml'
mavenAuthenticateFeed: true
goals: 'deploy'
104 changes: 89 additions & 15 deletions pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<groupId>au.gov.digitalhealth.terminology</groupId>
<artifactId>amt-to-flat-file</artifactId>

<version>master-SNAPSHOT</version>
<version>amt-v4-SNAPSHOT</version>
<name>AMT flat file generator</name>
<description>Generates an "AMT Flat File" from a Snapshot SNOMED CT-AU release</description>

Expand All @@ -17,53 +17,81 @@
<url>https://github.com/AuDigitalHealth/amt-flat-file-generator.git</url>
</scm>

<properties>
<java.version>11</java.version>
<deployment.repo.id>amtv4</deployment.repo.id>
<deployment.repo.url>https://pkgs.dev.azure.com/OD225632-NCTS-ContentAndTooling/OD225632-NCTS-ContentAndTooling/_packaging/amtv4/maven/v1</deployment.repo.url>
</properties>

<dependencies>
<dependency>
<groupId>org.openmbee.junit</groupId>
<artifactId>junit-xml-parser</artifactId>
<version>1.0.0</version>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
<version>4.0.0</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>4.0.0</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
<version>1.18.28</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.13.2</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.13.0</version>
</dependency>
<dependency>
<groupId>org.apache.maven</groupId>
<artifactId>maven-plugin-api</artifactId>
<version>3.0</version>
<version>3.9.0</version>
</dependency>
<dependency>
<groupId>org.apache.maven.plugin-tools</groupId>
<artifactId>maven-plugin-annotations</artifactId>
<version>3.4</version>
<version>3.8.1</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.jgrapht</groupId>
<artifactId>jgrapht-core</artifactId>
<version>1.3.0</version>
<version>1.5.1</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.4</version>
<version>1.5.0</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.5</version>
<version>3.12.0</version>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.9.8</version>
<version>7.7.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.maven.wagon</groupId>
<artifactId>wagon-http</artifactId>
<version>3.2.0</version>
<version>3.5.3</version>
</dependency>
<dependency>
<groupId>org.apache.tika</groupId>
<artifactId>tika-core</artifactId>
<version>1.22</version>
<version>2.7.0</version>
</dependency>
</dependencies>

Expand All @@ -76,8 +104,8 @@
<artifactId>maven-compiler-plugin</artifactId>
<version>3.7.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<source>${java.version}</source>
<target>${java.version}</target>
</configuration>
</plugin>
<plugin>
Expand All @@ -95,7 +123,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-plugin-plugin</artifactId>
<version>3.3</version>
<version>3.8.1</version>
<configuration>
<goalPrefix>amt-to-flat-file</goalPrefix>
<skipErrorNoDescriptorsFound>true</skipErrorNoDescriptorsFound>
Expand Down Expand Up @@ -149,4 +177,50 @@
</plugin>
</plugins>
</build>

<repositories>
<repository>
<id>spring-releases</id>
<url>https://repo.spring.io/release</url>
</repository>
<repository>
<id>${deployment.repo.id}</id>
<url>${deployment.repo.url}</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
</repositories>
<pluginRepositories>
<pluginRepository>
<id>${deployment.repo.id}</id>
<url>${deployment.repo.url}</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</pluginRepository>
</pluginRepositories>
<distributionManagement>
<repository>
<id>${deployment.repo.id}</id>
<url>${deployment.repo.url}</url>
<name>Maven Release Feed</name>
<layout>default</layout>
<uniqueVersion>true</uniqueVersion>
</repository>
<snapshotRepository>
<id>${deployment.repo.id}</id>
<url>${deployment.repo.url}</url>
<name>Maven Snapshot Release Feed</name>
<layout>default</layout>
<uniqueVersion>true</uniqueVersion>
</snapshotRepository>
</distributionManagement>

</project>
Loading