diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
new file mode 100644
index 0000000..b72aac3
--- /dev/null
+++ b/.github/workflows/ci.yaml
@@ -0,0 +1,27 @@
+name: CI
+
+on:
+ push:
+ branches:
+ - '**'
+ pull_request:
+ branches:
+ - '**'
+
+jobs:
+ build:
+ runs-on: ubuntu-latest
+
+ steps:
+ - name: Checkout code
+ uses: actions/checkout@v4
+
+ - name: Set up JDK 21
+ uses: actions/setup-java@v4
+ with:
+ distribution: 'temurin'
+ java-version: '21'
+ cache: maven
+
+ - name: Build and run tests with Maven
+ run: mvn clean compile test
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index 81293fb..fcf72c6 100644
--- a/pom.xml
+++ b/pom.xml
@@ -18,6 +18,7 @@
21
UTF-8
2025-01-02T12:10:36+01:00
+ 5.15.2
@@ -25,16 +26,10 @@
org.springframework.boot
spring-boot-starter-web
-
- org.springframework.boot
- spring-boot-starter-test
- test
-
-
- org.springframework.boot
- spring-boot-starter-validation
-
-
+
+
+
+
org.springdoc
springdoc-openapi-starter-webmvc-ui
@@ -46,11 +41,11 @@
jackson-databind-nullable
0.2.6
-
- com.google.code.gson
- gson
- 2.11.0
-
+
+
+
+
+
org.openscience.cdk
cdk-bundle
@@ -63,11 +58,11 @@
main-6a6cddc02c-1
-
- org.apache.commons
- commons-configuration2
- 2.11.0
-
+
+
+
+
+
edu.ucdavis.fiehnlab.splash
core
@@ -116,6 +111,12 @@
protobuf-java
4.28.2
+
+ org.mockito
+ mockito-core
+ ${mockito.version}
+ test
+
@@ -161,35 +162,12 @@
- org.codehaus.mojo
- build-helper-maven-plugin
- 3.6.0
-
-
- add-source
- generate-sources
-
- add-source
-
-
-
- target/generated-sources/openapi/src/main/java
-
-
-
-
- add-test-source
- generate-test-sources
-
- add-test-source
-
-
-
- target/generated-sources/openapi/src/main/java
-
-
-
-
+ org.apache.maven.plugins
+ maven-surefire-plugin
+ 3.5.2
+
+ -javaagent:${settings.localRepository}/org/mockito/mockito-core/${mockito.version}/mockito-core-${mockito.version}.jar
+
diff --git a/src/test/java/ExportServiceControllerTest.java b/src/test/java/ExportServiceControllerTest.java
index b9b4e14..f0225fd 100644
--- a/src/test/java/ExportServiceControllerTest.java
+++ b/src/test/java/ExportServiceControllerTest.java
@@ -23,14 +23,78 @@ public void testGetVersion() throws Exception {
.andExpect(jsonPath("$").value(startsWith("export service ")));
}
+ String nist_msp = """
+Name: Rutin
+Synon: 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-[[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxymethyl]oxan-2-yl]oxychromen-4-one
+DB#: MSBNK-IPB_Halle-PB001341
+InChIKey: IKGXIBQEEMLURG-NVPNHPEKSA-N
+InChI: InChI=1S/C27H30O16/c1-8-17(32)20(35)22(37)26(40-8)39-7-15-18(33)21(36)23(38)27(42-15)43-25-19(34)16-13(31)5-10(28)6-14(16)41-24(25)9-2-3-11(29)12(30)4-9/h2-6,8,15,17-18,20-23,26-33,35-38H,7H2,1H3/t8-,15+,17-,18+,20+,21-,22+,23+,26+,27-/m0/s1
+SMILES: C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)OC[C@@H]2[C@H]([C@@H]([C@H]([C@@H](O2)OC3=C(OC4=CC(=CC(=C4C3=O)O)O)C5=CC(=C(C=C5)O)O)O)O)O)O)O)O
+Precursor_type: [M+H]+
+Spectrum_type: MS2
+Instrument_type: LC-ESI-QTOF
+Instrument: API QSTAR Pulsar i
+Ion_mode: POSITIVE
+Collision_energy: 10 eV
+Formula: C27H30O16
+MW: 610
+ExactMass: 610.15338
+Comments: Parent=-1
+Splash: splash10-0wmi-0009506000-98ca7f7c8f3072af4481
+Num Peaks: 5
+147.063 11
+303.050 999
+449.108 64
+465.102 587
+611.161 669
+
+""";
+
@Test
- public void testCreateConversionTask() throws Exception {
+ public void testCreateConversionTaskNistMSP() throws Exception {
String requestBody = "{ \"record_list\": [\"MSBNK-IPB_Halle-PB001341\"], \"format\": \"nist_msp\" }";
mockMvc.perform(post("/convert")
.contentType("application/json")
.content(requestBody))
.andExpect(status().isOk())
- .andExpect(content().contentType("application/octet-stream"));
+ .andExpect(content().contentType("application/octet-stream"))
+ .andExpect(content().string(nist_msp));
+ }
+
+ String riken_msp = """
+NAME : Rutin
+PRECURSORMZ:\s
+PRECURSORTYPE: [M+H]+
+FORMULA: C27H30O16
+INCHIKEY: IKGXIBQEEMLURG-NVPNHPEKSA-N
+INCHI: InChI=1S/C27H30O16/c1-8-17(32)20(35)22(37)26(40-8)39-7-15-18(33)21(36)23(38)27(42-15)43-25-19(34)16-13(31)5-10(28)6-14(16)41-24(25)9-2-3-11(29)12(30)4-9/h2-6,8,15,17-18,20-23,26-33,35-38H,7H2,1H3/t8-,15+,17-,18+,20+,21-,22+,23+,26+,27-/m0/s1
+SMILES: C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)OC[C@@H]2[C@H]([C@@H]([C@H]([C@@H](O2)OC3=C(OC4=CC(=CC(=C4C3=O)O)O)C5=CC(=C(C=C5)O)O)O)O)O)O)O)O
+RETENTIONTIME: 0
+INSTRUMENTTYPE: LC-ESI-QTOF
+INSTRUMENT: API QSTAR Pulsar i
+IONMODE: Positive
+LINKS: INCHIKEY:IKGXIBQEEMLURG-NVPNHPEKSA-N; KEGG:C05625; PUBCHEM:CID:5280805; COMPTOX:DTXSID3022326
+Comment: DB#=MSBNK-IPB_Halle-PB001341; origin=MassBank; IPB_RECORD: 541; Annotation confident structure
+Splash: splash10-0wmi-0009506000-98ca7f7c8f3072af4481
+Num Peaks: 5
+147.063 121.684
+303.050 10000.000
+449.108 657.368
+465.102 5884.210
+611.161 6700.000
+
+""";
+
+ @Test
+ public void testCreateConversionTaskRikenMSP() throws Exception {
+ String requestBody = "{ \"record_list\": [\"MSBNK-IPB_Halle-PB001341\"], \"format\": \"riken_msp\" }";
+
+ mockMvc.perform(post("/convert")
+ .contentType("application/json")
+ .content(requestBody))
+ .andExpect(status().isOk())
+ .andExpect(content().contentType("application/octet-stream"))
+ .andExpect(content().string(riken_msp));
}
}
\ No newline at end of file