diff --git a/README.adoc b/README.adoc
index 89690ed..152097c 100644
--- 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
index ba39f1f..2ef4ea0 100644
--- a/pom.xml
+++ b/pom.xml
@@ -3,7 +3,7 @@
4.0.0
de.isas.mztab
mztab-validator-webapp
- 1.0.22-SNAPSHOT
+ 1.0.22
jar
A web-based validator for mzTab format version 1.0 onwards.
MzTab validator webapplication.
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
index de6e9d6..b2ff55e 100644
--- 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/src/main/java/de/isas/lipidomics/mztab/validator/webapp/service/execution/DefaultToolResultService.java b/src/main/java/de/isas/lipidomics/mztab/validator/webapp/service/execution/DefaultToolResultService.java
index 7ff580b..6470b37 100644
--- a/src/main/java/de/isas/lipidomics/mztab/validator/webapp/service/execution/DefaultToolResultService.java
+++ b/src/main/java/de/isas/lipidomics/mztab/validator/webapp/service/execution/DefaultToolResultService.java
@@ -29,7 +29,7 @@
@Service
public class DefaultToolResultService implements ToolResultService {
- private ConcurrentHashMap sessionToToolResultMap = new ConcurrentHashMap<>();
+ private final ConcurrentHashMap 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
index 7683579..db5d1f3 100644
--- 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
index 6ddff25..c1c1aa4 100644
--- 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 getStorageService() {
method = RequestMethod.POST)
default ResponseEntity> 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
index 674adbf..594fab1 100644
--- 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
index fff224f..7c6ff5d 100644
--- 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;
+}
+*/
\ No newline at end of file