From bca38d58387124883451807ff90a159e9d2190a8 Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Fri, 21 Feb 2025 18:31:34 +0000
Subject: [PATCH] Began Jenkinsfile pipeline writing

---
 .gitignore                                    |  4 +--
 Jenkinsfile                                   | 27 +++++++++++++++++++
 autobigs-cli.xml                              | 18 ++++++++++---
 ...is.fasta => tohama_I_bpertussis_wgs.fasta} |  0
 ....csv => tohama_I_bpertussis_wgs_typed.csv} |  0
 5 files changed, 43 insertions(+), 6 deletions(-)
 create mode 100644 Jenkinsfile
 rename test-data/{tohama_I_bpertussis.fasta => tohama_I_bpertussis_wgs.fasta} (100%)
 rename test-data/{results.csv => tohama_I_bpertussis_wgs_typed.csv} (100%)

diff --git a/.gitignore b/.gitignore
index 291190e..95cf782 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,2 @@
-autobigs-cli_test_report.html
-galaxy-server/**
\ No newline at end of file
+galaxy-server/**
+test_results
diff --git a/Jenkinsfile b/Jenkinsfile
new file mode 100644
index 0000000..0feccd8
--- /dev/null
+++ b/Jenkinsfile
@@ -0,0 +1,27 @@
+pipeline {
+    agent {
+        kubernetes {
+            cloud 'rsys-devel'
+            defaultContainer 'pip'
+        }
+    }
+    stages {
+        stage ("install") {
+            steps {
+                sh 'pip install -r requirements.txt'
+            }
+        }
+        stage ("lint") {
+            steps {
+                sh "planemo lint autobigs-cli.xml"
+            }
+        }
+        stage ("test") {
+            steps {
+                sh 'mkdir test_results'
+                sh "planemo test autobigs-cli.xml --test_output_junit test_results/junit_results.xml --test_output_json test_results/results.json --test_output test_results/human.html"
+                xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results/junit_report.xml', stopProcessingIfError: true)]
+            }
+        }
+    }
+}
\ No newline at end of file
diff --git a/autobigs-cli.xml b/autobigs-cli.xml
index 17866d6..5598a5b 100644
--- a/autobigs-cli.xml
+++ b/autobigs-cli.xml
@@ -54,19 +54,29 @@
 	</inputs>
 	<outputs>
 		<data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv">
-			<filter>mode.operation == "st"</filter>
+			<filter>mode['operation'] == "st"</filter>
 		</data>
 		<data name="info_out" label="${tool.name} supported databases/schemas" format="csv">
-			<filter>mode.operation == "info"</filter>
+			<filter>mode['operation'] == "info"</filter>
 		</data>
 	</outputs>
     <tests>
         <test expect_num_outputs="1">
             <param name="operation" value="st" />
-            <param name="fastas" value="tohama_I_bpertussis.fasta" />
+            <param name="fastas" value="tohama_I_bpertussis_wgs.fasta" />
             <param name="seqdefdb" value="pubmlst_bordetella_seqdef" />
             <param name="schema" value="3" />
-            <output name="mlst_profiles_output" file="results.csv" ftype="csv" />
+            <output name="mlst_profiles_output" file="tohama_I_bpertussis_wgs_typed.csv" ftype="csv" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="operation" value="info" />
+            <param name="retrieved" value="databases" />
+            <output name="info_out">
+				<assert_contents>
+					<has_line line="BIGSdb Names,Source"/>
+					<has_line line="pubmlst_bordetella_seqdef,https://bigsdb.pasteur.fr/api"/>
+				</assert_contents>
+			</output>
         </test>
     </tests>
 	<help><![CDATA[
diff --git a/test-data/tohama_I_bpertussis.fasta b/test-data/tohama_I_bpertussis_wgs.fasta
similarity index 100%
rename from test-data/tohama_I_bpertussis.fasta
rename to test-data/tohama_I_bpertussis_wgs.fasta
diff --git a/test-data/results.csv b/test-data/tohama_I_bpertussis_wgs_typed.csv
similarity index 100%
rename from test-data/results.csv
rename to test-data/tohama_I_bpertussis_wgs_typed.csv