Finish test code and add CI workflow

MassBank · Jan 8, 2025 · 767455a · 767455a
1 parent f930050
commit 767455a
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diff --git a/.github/workflows/ci.yaml 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
diff --git a/pom.xml b/pom.xml
@@ -18,23 +18,18 @@
         <java.version>21</java.version>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 	    <timestamp>2025-01-02T12:10:36+01:00</timestamp>
+        <mockito.version>5.15.2</mockito.version>
     </properties>
 
     <dependencies>
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-web</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-test</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-validation</artifactId>
-        </dependency>
-
+<!--        <dependency>-->
+<!--            <groupId>org.springframework.boot</groupId>-->
+<!--            <artifactId>spring-boot-starter-validation</artifactId>-->
+<!--        </dependency>-->
         <dependency>
             <groupId>org.springdoc</groupId>
             <artifactId>springdoc-openapi-starter-webmvc-ui</artifactId>
@@ -46,11 +41,11 @@
             <artifactId>jackson-databind-nullable</artifactId>
             <version>0.2.6</version>
         </dependency>
-        <dependency>
-            <groupId>com.google.code.gson</groupId>
-            <artifactId>gson</artifactId>
-            <version>2.11.0</version>
-        </dependency>
+<!--        <dependency>-->
+<!--            <groupId>com.google.code.gson</groupId>-->
+<!--            <artifactId>gson</artifactId>-->
+<!--            <version>2.11.0</version>-->
+<!--        </dependency>-->
         <dependency>
             <groupId>org.openscience.cdk</groupId>
             <artifactId>cdk-bundle</artifactId>
@@ -63,11 +58,11 @@
 <!--            <version>2.4.2</version>-->
             <version>main-6a6cddc02c-1</version>
         </dependency>
-        <dependency>
-            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-configuration2</artifactId>
-            <version>2.11.0</version>
-        </dependency>
+<!--        <dependency>-->
+<!--            <groupId>org.apache.commons</groupId>-->
+<!--            <artifactId>commons-configuration2</artifactId>-->
+<!--            <version>2.11.0</version>-->
+<!--        </dependency>-->
         <dependency>
             <groupId>edu.ucdavis.fiehnlab.splash</groupId>
             <artifactId>core</artifactId>
@@ -116,6 +111,12 @@
                 <artifactId>protobuf-java</artifactId>
                 <version>4.28.2</version>
             </dependency>
+            <dependency>
+                <groupId>org.mockito</groupId>
+                <artifactId>mockito-core</artifactId>
+                <version>${mockito.version}</version>
+                <scope>test</scope>
+            </dependency>
         </dependencies>
     </dependencyManagement>
 
@@ -161,35 +162,12 @@
                 </executions>
             </plugin>
             <plugin>
-                <groupId>org.codehaus.mojo</groupId>
-                <artifactId>build-helper-maven-plugin</artifactId>
-                <version>3.6.0</version>
-                <executions>
-                    <execution>
-                        <id>add-source</id>
-                        <phase>generate-sources</phase>
-                        <goals>
-                            <goal>add-source</goal>
-                        </goals>
-                        <configuration>
-                            <sources>
-                                <source>target/generated-sources/openapi/src/main/java</source>
-                            </sources>
-                        </configuration>
-                    </execution>
-                    <execution>
-                        <id>add-test-source</id>
-                        <phase>generate-test-sources</phase>
-                        <goals>
-                            <goal>add-test-source</goal>
-                        </goals>
-                        <configuration>
-                            <sources>
-                                <source>target/generated-sources/openapi/src/main/java</source>
-                            </sources>
-                        </configuration>
-                    </execution>
-                </executions>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>3.5.2</version>
+                <configuration>
+                    <argLine>-javaagent:${settings.localRepository}/org/mockito/mockito-core/${mockito.version}/mockito-core-${mockito.version}.jar</argLine>
+                </configuration>
             </plugin>
         </plugins>
     </build>

diff --git 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));
     }
 }