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Test pr #1

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ed9e146
Create Jenkinsfile
automation555 Aug 5, 2021
5e5861e
Update Jenkinsfile
automation555 Aug 5, 2021
96788d0
Create .gammascan.json
automation555 Sep 6, 2021
397291a
Update repository-configuration.json
automation555 Feb 4, 2022
708a0ef
Create embold.yaml
automation555 Mar 15, 2022
0e7523e
Update embold.yaml
automation555 Mar 15, 2022
222ae83
Update HmmerDemo.java
automation555 Jun 15, 2022
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89 changes: 89 additions & 0 deletions .gammascan.json
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{
"gammaAccess": {
"url": "",
"userName": "",
"password": ""
},
"repositories": [
{
"dataDir": "%WORKSPACE%/temp",
"repository": {
"uid": "cc796041d00be75d0ea1a2dc8b3e705e",
"projectName": "githubdemo_jenkins",
"languages": [
"JAVA"
],
"sources": {
"baseDir": "%WORKSPACE%",
"exclusions": []
}
},
"settings": {
"additionalOptions": [],
"includePaths": []
},
"modules": {
"codeissues": [
{
"name": "gamma_java",
"enabled": true,
"config": {
"rules": [],
"options": []
}
}
],
"unittest": [
{
"name": "junit",
"enabled": true,
"config": {
"rules": [],
"options": [
{
"name": "reportDir",
"type": "upload",
"value": "",
"required": true
}
]
}
}
],
"coverage": [
{
"name": "jacoco",
"enabled": true,
"config": {
"rules": [],
"options": [
{
"name": "binaryReportPath",
"type": "upload",
"value": "",
"required": false
},
{
"name": "xmlReportPath",
"type": "upload",
"value": "",
"required": true
}
]
}
}
],
"relevance": [
{
"name": "relevance",
"enabled": true,
"config": {
"rules": [],
"options": []
}
}
]
}
}
]
}
14 changes: 14 additions & 0 deletions Jenkinsfile
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pipeline {
agent any
stages {
stage('build') {
steps {
sh 'mvn clean install'
sh 'echo $GIT_COMMIT'
sh 'echo $GIT_PREVIOUS_SUCCESSFUL_COMMIT'
sh "git diff --name-only --oneline $GIT_PREVIOUS_SUCCESSFUL_COMMIT $GIT_COMMIT > result2.txt"
sh '/var/jenkins_home/corona_wrap/bin/embold-ci-cd-wrapper -c $WORKSPACE/repository-configuration.json -lf result2.txt'
}
}
}
}
4 changes: 2 additions & 2 deletions biojava-ws/src/main/java/demo/HmmerDemo.java
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Expand Up @@ -44,7 +44,7 @@ public static void main(String[] args) throws Exception {
// first we get a UniProt sequence
String uniProtID = "P08487";
ProteinSequence seq = getUniprot(uniProtID);

int i=0;

// now we submit this sequence to the Hmmer web site
RemoteHmmerScan hmmer = new RemoteHmmerScan();
Expand All @@ -58,7 +58,7 @@ public static void main(String[] args) throws Exception {

int counter = 0;
for (HmmerResult hmmerResult : results) {
//System.out.println(hmmerResult);
System.out.println(hmmerResult);

for ( HmmerDomain domain : hmmerResult.getDomains()) {
counter++;
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38 changes: 38 additions & 0 deletions embold.yaml
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version: 1

# Please visit https://docs.embold.io/v2-quick-start-guide/#default-configurations
# to know more about configurations available

sources:
#Files or Directories to be Excluded are mentioned in exclusions
exclusions:
- 'test'
- 'biojava-ws'
- 'mock'
- 'thirdparty'
- 'third-party'
- '3rd-party'
- '3rdparty'
- 'external'
- 'build'
- 'node_modules'
- 'assets'
- 'gulp'
- 'grunt'
- 'library'
- '.git'

# Specify the languages you would like to Scan. Default is all Detected
languages: 'JAVA'


# Define modules one would like to run or disable. This is enough for Basic Users
# Get List of Modules (Which are Default Enabled/Disabled) at the documentation link above
#modules:
# - name: pmd
# enabled: true
# - name: gamma_cxx
# enabled: false
# - name: jshint
# enabled: true

2 changes: 1 addition & 1 deletion repository-configuration.json
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Expand Up @@ -8,7 +8,7 @@
{
"dataDir": "%WORKSPACE%/temp",
"repository": {
"uid": "cc796041d00be75d0ea1a2dc8b3e705e",
"uid": "0e1c3665863ee85b18f357d364109e35",
"projectName": "githubdemo_jenkins",
"languages": [
"JAVA"
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