Updated swagger config and README.

lifs-tools · Aug 7, 2019 · fc95118 · fc95118
1 parent b163de7
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Showing 8 changed files with 33 additions and 23 deletions.
diff --git a/README.adoc b/README.adoc
@@ -6,6 +6,11 @@ image:https://img.shields.io/github/release/lifs-tools/jmzTab-m-webapp.svg["Late
 
 This project provides a validator implementation for the mzTab 1.0 standard and for the current draft 2.0 standard for metabolomics.
 
+== Using the LIFS Web application
+
+The mzTab validator webapplication is hosted https://apps.lifs.isas.de/mztabvalidator[here]. 
+For programmatic usage of the validation service, the REST API description is available https://apps.lifs.isas.de/mztabvalidator/swagger-ui.html[here].
+
 == Building the project from the command-line
 
 In order to build the project and run the unit tests, execute the following command from a terminal:

diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>de.isas.mztab</groupId>
     <artifactId>mztab-validator-webapp</artifactId>
-    <version>1.0.22-SNAPSHOT</version>
+    <version>1.0.22</version>
     <packaging>jar</packaging>
     <description>A web-based validator for mzTab format version 1.0 onwards.</description>
     <name>MzTab validator webapplication.</name>	

diff --git a/src/main/java/de/isas/lipidomics/mztab/validator/webapp/controller/ValidationController.java b/src/main/java/de/isas/lipidomics/mztab/validator/webapp/controller/ValidationController.java
@@ -17,33 +17,30 @@
 
 import de.isas.lipidomics.mztab.validator.webapp.ExampleFileConfig;
 import de.isas.lipidomics.mztab.validator.webapp.domain.AppInfo;
-import de.isas.lipidomics.mztab.validator.webapp.domain.ValidationStatistics;
 import de.isas.lipidomics.mztab.validator.webapp.domain.Page;
 import de.isas.lipidomics.mztab.validator.webapp.domain.ToolResult;
 import de.isas.lipidomics.mztab.validator.webapp.domain.ToolResult.Keys;
-import de.isas.lipidomics.mztab.validator.webapp.domain.ValidationForm;
-import de.isas.lipidomics.mztab.validator.webapp.service.StorageService;
-import de.isas.lipidomics.mztab.validator.webapp.service.ValidationService;
-import de.isas.lipidomics.mztab.validator.webapp.service.storage.StorageFileNotFoundException;
 import de.isas.lipidomics.mztab.validator.webapp.domain.UserSessionFile;
+import de.isas.lipidomics.mztab.validator.webapp.domain.ValidationForm;
 import de.isas.lipidomics.mztab.validator.webapp.domain.ValidationLevel;
 import de.isas.lipidomics.mztab.validator.webapp.domain.ValidationResult;
+import de.isas.lipidomics.mztab.validator.webapp.domain.ValidationStatistics;
 import de.isas.lipidomics.mztab.validator.webapp.service.SessionIdGenerator;
+import de.isas.lipidomics.mztab.validator.webapp.service.StorageService;
 import de.isas.lipidomics.mztab.validator.webapp.service.StorageService.SLOT;
 import de.isas.lipidomics.mztab.validator.webapp.service.ToolResultService;
+import de.isas.lipidomics.mztab.validator.webapp.service.ValidationService;
 import de.isas.lipidomics.mztab.validator.webapp.service.ValidationService.Status;
 import de.isas.lipidomics.mztab.validator.webapp.service.storage.StorageException;
-import java.io.File;
+import de.isas.lipidomics.mztab.validator.webapp.service.storage.StorageFileNotFoundException;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.nio.file.Path;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
 import java.util.EnumMap;
 import java.util.List;
 import java.util.Map;
-import java.util.Optional;
 import java.util.UUID;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpSession;

diff --git a/...de/isas/lipidomics/mztab/validator/webapp/service/execution/DefaultToolResultService.java b/...de/isas/lipidomics/mztab/validator/webapp/service/execution/DefaultToolResultService.java
@@ -29,7 +29,7 @@
 @Service
 public class DefaultToolResultService implements ToolResultService {
 
-    private ConcurrentHashMap<UUID, ToolResult> sessionToToolResultMap = new ConcurrentHashMap<>();
+    private final ConcurrentHashMap<UUID, ToolResult> sessionToToolResultMap = new ConcurrentHashMap<>();
 
     @Override
     public ToolResult getOrCreateResultFor(UUID sessionId) {
@@ -43,14 +43,7 @@ public ToolResult getOrCreateResultFor(UUID sessionId) {
 
     @Override
     public void addResultFor(UUID sessionId, ToolResult result) {
-//        if(sessionToToolResultMap.containsKey(sessionId)) {
-//            sessionToToolResultMap.get(sessionId).setException(result.getException());
-//            sessionToToolResultMap.get(sessionId).setStatus(result.getStatus());
-//            sessionToToolResultMap.get(sessionId).getMessages().addAll(result.getMessages());
-//            sessionToToolResultMap.get(sessionId).getParameters().putAll(result.getParameters());
-//        } else {
         sessionToToolResultMap.put(sessionId, result);
-//        }
     }
 
     @Override

diff --git a/src/main/java/de/isas/mztab2/server/api/ValidateApi.java b/src/main/java/de/isas/mztab2/server/api/ValidateApi.java
@@ -39,7 +39,7 @@
 @javax.annotation.Generated(value = "io.swagger.codegen.languages.SpringCodegen",
     date = "2018-01-11T19:50:29.849+01:00")
 
-@Api(value = "validate", description = "the validate API")
+@Api(value = "validate", description = "The validation API for mzTab-m documents in JSON or XML format.", tags = {"validate"})
 @RequestMapping(path = "/rest/v2")
 public interface ValidateApi {
 

diff --git a/src/main/java/de/isas/mztab2/server/api/ValidatePlainApi.java b/src/main/java/de/isas/mztab2/server/api/ValidatePlainApi.java
@@ -34,7 +34,7 @@
 @javax.annotation.Generated(value = "io.swagger.codegen.languages.SpringCodegen",
     date = "2018-01-11T19:50:29.849+01:00")
 
-@Api(value = "validatePlain", description = "the validatePlain API")
+@Api(value = "validatePlain", description = "The validation API for mzTab-m documents in plaintext / tsv format.", tags = {"validatePlain"})
 @RequestMapping(path = "/rest/v2")
 public interface ValidatePlainApi {
 
@@ -179,7 +179,8 @@ default Optional<StorageService> getStorageService() {
         method = RequestMethod.POST)
     default ResponseEntity<List<ValidationMessage>> validatePlainMzTabFile(
         @ApiParam(value = "mzTab file that should be validated.",
-            required = true, examples = @Example({@ExampleProperty(mediaType = "text/plain", value=GCGCMS_EXAMPLE),@ExampleProperty(mediaType = "text/tab-separated-values", value=GCGCMS_EXAMPLE)})) @Valid @RequestBody String mztabfile,
+            required = true, 
+            examples = @Example(value={@ExampleProperty(mediaType = "text/plain", value=GCGCMS_EXAMPLE),@ExampleProperty(mediaType = "text/tab-separated-values", value=GCGCMS_EXAMPLE)})) @Valid @RequestBody String mztabfile,
         @RequestParam(
             value = "The level of errors that should be reported, one of error, warn, info.",
             defaultValue = "info",

diff --git a/src/main/java/io/swagger/configuration/SwaggerDocumentationConfig.java b/src/main/java/io/swagger/configuration/SwaggerDocumentationConfig.java
@@ -19,12 +19,12 @@ public class SwaggerDocumentationConfig {
     ApiInfo apiInfo() {
         return new ApiInfoBuilder()
             .title("mzTab validation API.")
-            .description("This is an mzTab validation service.")
+            .description("This is the mzTab validation service.")
             .license("Apache 2.0")
             .licenseUrl("http://www.apache.org/licenses/LICENSE-2.0.html")
-            .termsOfServiceUrl("")
+            .termsOfServiceUrl("https://lifs.isas.de/imprint-privacy-policy.html")
             .version("2.0.0")
-            .contact(new Contact("","", "nils.hoffmann@isas.de"))
+            .contact(new Contact("LIFS-Tools jmzTab-m-webapp","https://github.com/lifs-tools/jmzTab-m-webapp", "lifs-support@isas.de"))
             .build();
     }
 

diff --git a/src/main/resources/static/css/site.css b/src/main/resources/static/css/site.css
@@ -18,4 +18,18 @@
 .form-row {
     margin-bottom: 5px;
 }
+/*
+#metaDataRowsTable > tbody:nth-child(2) {
+    background-color: #ebf0f5;
+}
 
+#summaryDataRowsTable > tbody:nth-child(2) {
+    background-color: #ebf6ea;
+}
+#featureDataRowsTable > tbody:nth-child(2) {
+    background-color: #fff5e1;
+}
+#evidenceDataRowsTable > tbody:nth-child(2) {
+    background-color: #ffe9e1;
+}
+*/