Add test code and infrastructure

MassBank · Jan 7, 2025 · f930050 · f930050
1 parent 45a1450
commit f930050
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diff --git a/pom.xml b/pom.xml
@@ -25,6 +25,11 @@
             <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>
@@ -55,6 +60,7 @@
         <dependency>
             <groupId>com.github.petitparser.java-petitparser</groupId>
             <artifactId>petitparser-core</artifactId>
+<!--            <version>2.4.2</version>-->
             <version>main-6a6cddc02c-1</version>
         </dependency>
         <dependency>
@@ -120,6 +126,12 @@
                 <filtering>true</filtering>
             </resource>
         </resources>
+        <testResources>
+            <testResource>
+                <directory>src/test/resources</directory>
+                <filtering>true</filtering>
+            </testResource>
+        </testResources>
         <plugins>
             <plugin>
                 <groupId>org.springframework.boot</groupId>
@@ -148,6 +160,37 @@
                     </execution>
                 </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>
+            </plugin>
         </plugins>
     </build>
 

diff --git a/src/main/resources/openapi.yaml b/src/main/resources/openapi.yaml
@@ -66,7 +66,4 @@ components:
         record_list:
           $ref: "#/components/schemas/record_list"
         format:
-          $ref: "#/components/schemas/format"
-#      allOf:
-#        - $ref: "#/components/schemas/record_list"
-#        - $ref: "#/components/schemas/format"
+          $ref: "#/components/schemas/format"
diff --git a/src/test/java/ExportServiceControllerTest.java b/src/test/java/ExportServiceControllerTest.java
@@ -0,0 +1,36 @@
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.test.web.servlet.MockMvc;
+
+import static org.hamcrest.Matchers.startsWith;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+
+@SpringBootTest(classes = org.openapitools.OpenApiGeneratorApplication.class)
+@AutoConfigureMockMvc
+public class ExportServiceControllerTest {
+
+    @Autowired
+    private MockMvc mockMvc;
+
+    @Test
+    public void testGetVersion() throws Exception {
+        mockMvc.perform(get("/version"))
+            .andExpect(status().isOk())
+            .andExpect(content().contentType("application/json"))
+            .andExpect(jsonPath("$").value(startsWith("export service ")));
+    }
+
+    @Test
+    public void testCreateConversionTask() 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"));
+    }
+}
diff --git a/src/test/resources/MassBank-data-test/IPB_Halle/MSBNK-IPB_Halle-PB000122.txt b/src/test/resources/MassBank-data-test/IPB_Halle/MSBNK-IPB_Halle-PB000122.txt
@@ -0,0 +1,33 @@
+ACCESSION: MSBNK-IPB_Halle-PB000122
+RECORD_TITLE: Naringenin; LC-ESI-QTOF; MS2; CE:15 eV; [M+H]+
+DATE: 2016.01.19 (Created 2008.01.02, modified 2013.06.04)
+AUTHORS: Boettcher C, Institute of Plant Biochemistry, Halle, Germany
+LICENSE: CC BY-SA
+COMMENT: IPB_RECORD: 83
+COMMENT: CONFIDENCE confident structure
+CH$NAME: Naringenin
+CH$NAME: 5,7-dihydroxy-2-(4-hydroxyphenyl)chroman-4-one
+CH$COMPOUND_CLASS: Natural Product; Flavanone
+CH$FORMULA: C15H12O5
+CH$EXACT_MASS: 272.06847
+CH$SMILES: C1[C@H](OC2=CC(=CC(=C2C1=O)O)O)C3=CC=C(C=C3)O
+CH$IUPAC: InChI=1S/C15H12O5/c16-9-3-1-8(2-4-9)13-7-12(19)15-11(18)5-10(17)6-14(15)20-13/h1-6,13,16-18H,7H2/t13-/m0/s1
+CH$LINK: INCHIKEY FTVWIRXFELQLPI-ZDUSSCGKSA-N
+CH$LINK: KEGG C00509
+CH$LINK: PUBCHEM CID:439246
+CH$LINK: COMPTOX DTXSID1022392
+AC$INSTRUMENT: API QSTAR Pulsar i
+AC$INSTRUMENT_TYPE: LC-ESI-QTOF
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+AC$MASS_SPECTROMETRY: COLLISION_ENERGY 15 eV
+AC$MASS_SPECTROMETRY: IONIZATION ESI
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+PK$SPLASH: splash10-00di-0090000000-ed08d01208992e5a7a9f
+PK$NUM_PEAK: 4
+PK$PEAK: m/z int. rel.int.
+  147.044 218.845 20
+  153.019 316.545 30
+  273.076 10000.000 999
+  274.083 318.003 30
+//
diff --git a/src/test/resources/MassBank-data-test/IPB_Halle/MSBNK-IPB_Halle-PB000123.txt b/src/test/resources/MassBank-data-test/IPB_Halle/MSBNK-IPB_Halle-PB000123.txt
@@ -0,0 +1,41 @@
+ACCESSION: MSBNK-IPB_Halle-PB000123
+RECORD_TITLE: Naringenin; LC-ESI-QTOF; MS2; CE:25 eV; [M+H]+
+DATE: 2016.01.19 (Created 2008.01.02, modified 2013.06.04)
+AUTHORS: Boettcher C, Institute of Plant Biochemistry, Halle, Germany
+LICENSE: CC BY-SA
+COMMENT: IPB_RECORD: 83
+COMMENT: CONFIDENCE confident structure
+CH$NAME: Naringenin
+CH$NAME: 5,7-dihydroxy-2-(4-hydroxyphenyl)chroman-4-one
+CH$COMPOUND_CLASS: Natural Product; Flavanone
+CH$FORMULA: C15H12O5
+CH$EXACT_MASS: 272.06847
+CH$SMILES: C1[C@H](OC2=CC(=CC(=C2C1=O)O)O)C3=CC=C(C=C3)O
+CH$IUPAC: InChI=1S/C15H12O5/c16-9-3-1-8(2-4-9)13-7-12(19)15-11(18)5-10(17)6-14(15)20-13/h1-6,13,16-18H,7H2/t13-/m0/s1
+CH$LINK: INCHIKEY FTVWIRXFELQLPI-ZDUSSCGKSA-N
+CH$LINK: KEGG C00509
+CH$LINK: PUBCHEM CID:439246
+CH$LINK: COMPTOX DTXSID1022392
+AC$INSTRUMENT: API QSTAR Pulsar i
+AC$INSTRUMENT_TYPE: LC-ESI-QTOF
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+AC$MASS_SPECTROMETRY: COLLISION_ENERGY 25 eV
+AC$MASS_SPECTROMETRY: IONIZATION ESI
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+PK$SPLASH: splash10-0uka-0920000000-39d4e97d34abae145e72
+PK$NUM_PEAK: 12
+PK$PEAK: m/z int. rel.int.
+  119.051 467.616 45
+  123.044 370.662 36
+  147.044 6078.145 606
+  148.048 113.113 10
+  151.039 125.695 11
+  153.018 10000.000 999
+  154.023 270.265 26
+  179.036 141.192 13
+  189.058 176.358 16
+  255.067 169.007 15
+  273.076 5286.093 527
+  274.081 246.689 23
+//
diff --git a/src/test/resources/MassBank-data-test/IPB_Halle/MSBNK-IPB_Halle-PB000124.txt b/src/test/resources/MassBank-data-test/IPB_Halle/MSBNK-IPB_Halle-PB000124.txt
@@ -0,0 +1,41 @@
+ACCESSION: MSBNK-IPB_Halle-PB000124
+RECORD_TITLE: Naringenin; LC-ESI-QTOF; MS2; CE:40 eV; [M+H]+
+DATE: 2016.01.19 (Created 2008.01.02, modified 2013.06.04)
+AUTHORS: Boettcher C, Institute of Plant Biochemistry, Halle, Germany
+LICENSE: CC BY-SA
+COMMENT: IPB_RECORD: 83
+COMMENT: CONFIDENCE confident structure
+CH$NAME: Naringenin
+CH$NAME: 5,7-dihydroxy-2-(4-hydroxyphenyl)chroman-4-one
+CH$COMPOUND_CLASS: Natural Product; Flavanone
+CH$FORMULA: C15H12O5
+CH$EXACT_MASS: 272.06847
+CH$SMILES: C1[C@H](OC2=CC(=CC(=C2C1=O)O)O)C3=CC=C(C=C3)O
+CH$IUPAC: InChI=1S/C15H12O5/c16-9-3-1-8(2-4-9)13-7-12(19)15-11(18)5-10(17)6-14(15)20-13/h1-6,13,16-18H,7H2/t13-/m0/s1
+CH$LINK: INCHIKEY FTVWIRXFELQLPI-ZDUSSCGKSA-N
+CH$LINK: KEGG C00509
+CH$LINK: PUBCHEM CID:439246
+CH$LINK: COMPTOX DTXSID1022392
+AC$INSTRUMENT: API QSTAR Pulsar i
+AC$INSTRUMENT_TYPE: LC-ESI-QTOF
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+AC$MASS_SPECTROMETRY: COLLISION_ENERGY 40 eV
+AC$MASS_SPECTROMETRY: IONIZATION ESI
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+PK$SPLASH: splash10-0udi-0900000000-69d64a193ad59cc8263f
+PK$NUM_PEAK: 12
+PK$PEAK: m/z int. rel.int.
+  67.019 186.967 17
+  68.998 126.366 11
+  69.036 97.117 8
+  91.054 732.733 72
+  95.050 204.264 19
+  97.029 119.880 10
+  107.051 222.102 21
+  119.050 3386.787 337
+  123.044 394.715 38
+  147.044 2275.676 226
+  153.018 10000.000 999
+  154.023 356.697 34
+//
diff --git a/src/test/resources/MassBank-data-test/IPB_Halle/MSBNK-IPB_Halle-PB000125.txt b/src/test/resources/MassBank-data-test/IPB_Halle/MSBNK-IPB_Halle-PB000125.txt
@@ -0,0 +1,58 @@
+ACCESSION: MSBNK-IPB_Halle-PB000125
+RECORD_TITLE: Naringenin; LC-ESI-QTOF; MS2; CE:55 eV; [M+H]+
+DATE: 2016.01.19 (Created 2008.01.02, modified 2013.06.04)
+AUTHORS: Boettcher C, Institute of Plant Biochemistry, Halle, Germany
+LICENSE: CC BY-SA
+COMMENT: IPB_RECORD: 83
+COMMENT: CONFIDENCE confident structure
+CH$NAME: Naringenin
+CH$NAME: 5,7-dihydroxy-2-(4-hydroxyphenyl)chroman-4-one
+CH$COMPOUND_CLASS: Natural Product; Flavanone
+CH$FORMULA: C15H12O5
+CH$EXACT_MASS: 272.06847
+CH$SMILES: C1[C@H](OC2=CC(=CC(=C2C1=O)O)O)C3=CC=C(C=C3)O
+CH$IUPAC: InChI=1S/C15H12O5/c16-9-3-1-8(2-4-9)13-7-12(19)15-11(18)5-10(17)6-14(15)20-13/h1-6,13,16-18H,7H2/t13-/m0/s1
+CH$LINK: INCHIKEY FTVWIRXFELQLPI-ZDUSSCGKSA-N
+CH$LINK: KEGG C00509
+CH$LINK: PUBCHEM CID:439246
+CH$LINK: COMPTOX DTXSID1022392
+AC$INSTRUMENT: API QSTAR Pulsar i
+AC$INSTRUMENT_TYPE: LC-ESI-QTOF
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+AC$MASS_SPECTROMETRY: COLLISION_ENERGY 55 eV
+AC$MASS_SPECTROMETRY: IONIZATION ESI
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+PK$SPLASH: splash10-0gbc-9800000000-79055ba218dabe14501d
+PK$NUM_PEAK: 29
+PK$PEAK: m/z int. rel.int.
+  53.037 111.391 10
+  55.017 718.038 70
+  65.038 1125.168 111
+  67.018 1665.237 165
+  68.997 2395.872 238
+  69.035 1956.044 194
+  77.039 605.468 59
+  79.018 331.546 32
+  81.034 135.272 12
+  83.014 471.723 46
+  85.030 98.767 8
+  91.054 7753.953 774
+  92.058 168.025 15
+  92.999 114.286 10
+  95.050 921.201 91
+  97.029 914.232 90
+  107.049 644.063 63
+  111.011 382.203 37
+  115.054 299.384 28
+  119.050 5392.656 538
+  120.054 146.851 13
+  123.044 249.397 23
+  125.022 186.626 17
+  128.060 202.332 19
+  147.043 597.159 58
+  152.060 313.053 30
+  153.018 10000.000 999
+  154.024 440.901 43
+  157.068 101.153 9
+//
diff --git a/src/test/resources/MassBank-data-test/IPB_Halle/MSBNK-IPB_Halle-PB000126.txt b/src/test/resources/MassBank-data-test/IPB_Halle/MSBNK-IPB_Halle-PB000126.txt
@@ -0,0 +1,32 @@
+ACCESSION: MSBNK-IPB_Halle-PB000126
+RECORD_TITLE: Naringenin chalcone; LC-ESI-QTOF; MS2; CE:15 eV; [M+H]+
+DATE: 2016.01.19 (Created 2008.01.02, modified 2013.06.04)
+AUTHORS: Boettcher C, Institute of Plant Biochemistry, Halle, Germany
+LICENSE: CC BY-SA
+COMMENT: IPB_RECORD: 101
+COMMENT: CONFIDENCE confident structure
+CH$NAME: Naringenin chalcone
+CH$NAME: 3-(4-hydroxyphenyl)-1-(2,4,6-trihydroxyphenyl)prop-2-en-1-one
+CH$COMPOUND_CLASS: Natural Product; Chalcone
+CH$FORMULA: C15H12O5
+CH$EXACT_MASS: 272.06847
+CH$SMILES: C1=CC(=CC=C1/C=C/C(=O)C2=C(C=C(C=C2O)O)O)O
+CH$IUPAC: InChI=1S/C15H12O5/c16-10-4-1-9(2-5-10)3-6-12(18)15-13(19)7-11(17)8-14(15)20/h1-8,16-17,19-20H/b6-3+
+CH$LINK: INCHIKEY YQHMWTPYORBCMF-ZZXKWVIFSA-N
+CH$LINK: KEGG C06561
+CH$LINK: PUBCHEM CID:5280960
+AC$INSTRUMENT: API QSTAR Pulsar i
+AC$INSTRUMENT_TYPE: LC-ESI-QTOF
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+AC$MASS_SPECTROMETRY: COLLISION_ENERGY 15 eV
+AC$MASS_SPECTROMETRY: IONIZATION ESI
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+PK$SPLASH: splash10-00di-0090000000-f174e512861692b4e263
+PK$NUM_PEAK: 4
+PK$PEAK: m/z int. rel.int.
+  147.044 302.770 29
+  153.018 409.695 39
+  273.076 10000.000 999
+  274.084 213.352 20
+//
diff --git a/src/test/resources/MassBank-data-test/IPB_Halle/MSBNK-IPB_Halle-PB000127.txt b/src/test/resources/MassBank-data-test/IPB_Halle/MSBNK-IPB_Halle-PB000127.txt
@@ -0,0 +1,38 @@
+ACCESSION: MSBNK-IPB_Halle-PB000127
+RECORD_TITLE: Naringenin chalcone; LC-ESI-QTOF; MS2; CE:25 eV; [M+H]+
+DATE: 2016.01.19 (Created 2008.01.02, modified 2013.06.04)
+AUTHORS: Boettcher C, Institute of Plant Biochemistry, Halle, Germany
+LICENSE: CC BY-SA
+COMMENT: IPB_RECORD: 101
+COMMENT: CONFIDENCE confident structure
+CH$NAME: Naringenin chalcone
+CH$NAME: 3-(4-hydroxyphenyl)-1-(2,4,6-trihydroxyphenyl)prop-2-en-1-one
+CH$COMPOUND_CLASS: Natural Product; Chalcone
+CH$FORMULA: C15H12O5
+CH$EXACT_MASS: 272.06847
+CH$SMILES: C1=CC(=CC=C1/C=C/C(=O)C2=C(C=C(C=C2O)O)O)O
+CH$IUPAC: InChI=1S/C15H12O5/c16-10-4-1-9(2-5-10)3-6-12(18)15-13(19)7-11(17)8-14(15)20/h1-8,16-17,19-20H/b6-3+
+CH$LINK: INCHIKEY YQHMWTPYORBCMF-ZZXKWVIFSA-N
+CH$LINK: KEGG C06561
+CH$LINK: PUBCHEM CID:5280960
+AC$INSTRUMENT: API QSTAR Pulsar i
+AC$INSTRUMENT_TYPE: LC-ESI-QTOF
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+AC$MASS_SPECTROMETRY: COLLISION_ENERGY 25 eV
+AC$MASS_SPECTROMETRY: IONIZATION ESI
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+PK$SPLASH: splash10-0udj-0920000000-1bfd55f600a901a79c87
+PK$NUM_PEAK: 10
+PK$PEAK: m/z int. rel.int.
+  107.051 123.057 11
+  119.051 510.497 50
+  123.045 397.422 38
+  147.044 6132.597 612
+  151.040 135.138 12
+  153.018 10000.000 999
+  154.022 137.643 12
+  179.038 144.125 13
+  189.058 175.654 16
+  273.076 4416.206 440
+//