Fixed problem with title

maximiliani · maximiliani · commit 4a7a149ac11b · 2022-09-16T13:47:35.000+02:00
some cleanup
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/MappingServiceApplication.java b/src/main/java/edu/kit/datamanager/mappingservice/MappingServiceApplication.java
@@ -55,14 +55,7 @@ public static void main(String[] args) {
         SpringApplication.run(MappingServiceApplication.class, args);
         System.out.println("Mapping service is running! Access it at http://localhost:8095");
 
-//        PluginManager.reloadPlugins();
-
         PluginManager.soleInstance().getListOfAvailableValidators().forEach(System.out::println);
         PythonRunnerUtil.printPythonVersion();
-//        try {
-//            ShellRunnerUtil.run(new String[]{"ls", "-la"});
-//        } catch (MappingPluginException e) {
-//            e.printStackTrace();
-//        }
     }
 }
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/configuration/ApplicationProperties.java b/src/main/java/edu/kit/datamanager/mappingservice/configuration/ApplicationProperties.java
@@ -41,17 +41,17 @@ public class ApplicationProperties extends GenericPluginProperties {
     @Value("${mapping-service.pythonLocation}")
     private URL pythonLocation;
 
-    /**
-     * The path to the gemma mapping script 'mapping_single.py'
-     */
-    @edu.kit.datamanager.annotations.LocalFileURL
-    @Value("${mapping-service.gemmaLocation}")
-    private URL gemmaLocation;
+//    /**
+//     * The path to the gemma mapping script 'mapping_single.py'
+//     */
+//    @edu.kit.datamanager.annotations.LocalFileURL
+//    @Value("${mapping-service.gemmaLocation}")
+//    private URL gemmaLocation;
 
     /**
      * The absolute path where the mappings are stored.
      */
     @edu.kit.datamanager.annotations.LocalFolderURL
-    @Value("${mapping-service.mappingsLocation}")
+    @Value("${mapping-service.mappingSchemasLocation}")
     private URL mappingsLocation;
 }
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/domain/MappingRecord.java b/src/main/java/edu/kit/datamanager/mappingservice/domain/MappingRecord.java
@@ -42,17 +42,27 @@ public class MappingRecord implements EtagSupport, Serializable {
     public final static MediaType MAPPING_RECORD_MEDIA_TYPE = MediaType.valueOf("application/vnd.datamanager.mapping-record+json");
 
     @Id
-//  @NotBlank(message = "The unique identify of the record.")
+    @NotNull(message = "The unique identify of the record.")
     private String mappingId;
+
     @Id
-//  @NotBlank(message = "Type of the mapping, e.g. GEMMA, XSLT, handlebars, ....")
+    @NotNull(message = "Type of the mapping, e.g. GEMMA, XSLT, handlebars, ....")
     private String mappingType;
+
+    @NotNull(message = "Title of the mapping.")
+    private String title;
+
+    @NotNull(message = "Description of the mapping.")
+    private String description;
+
     @NotNull(message = "A list of access control entries for resticting access.")
     @OneToMany(cascade = javax.persistence.CascadeType.ALL, orphanRemoval = true)
     private final Set<AclEntry> acl = new HashSet<>();
-    //  @NotBlank(message = "The metadata document uri, e.g. pointing to a local file.")
+
+    @NotNull(message = "The metadata document uri, e.g. pointing to a local file.")
     private String mappingDocumentUri;
-    //  @NotBlank(message = "The SHA-1 hash of the associated metadata file. The hash is used for comparison while updating.")
+
+    @NotNull(message = "The SHA-1 hash of the associated metadata file. The hash is used for comparison while updating.")
     private String documentHash;
 
     /**
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/impl/MappingService.java b/src/main/java/edu/kit/datamanager/mappingservice/impl/MappingService.java
@@ -79,7 +79,7 @@ public void createMapping(String content, MappingRecord mappingRecord) throws IO
         Iterable<MappingRecord> findMapping = mappingRepo.findByMappingIdInOrMappingTypeIn(Arrays.asList(mappingRecord.getMappingId()), Arrays.asList((String) null));
         if (findMapping.iterator().hasNext()) {
             mappingRecord = findMapping.iterator().next();
-            throw new MappingException("Error: Mapping '" + mappingRecord.getMappingId() + "/" + mappingRecord.getMappingType() + "' already exists!");
+            throw new MappingException("Error: Mapping '" + mappingRecord.getMappingType() + "_" + mappingRecord.getMappingId() + "' already exists!");
         }
         saveMappingFile(content, mappingRecord);
         mappingRepo.save(mappingRecord);
@@ -94,7 +94,7 @@ public void createMapping(String content, MappingRecord mappingRecord) throws IO
     public void updateMapping(String content, MappingRecord mappingRecord) throws IOException {
         Optional<MappingRecord> findMapping = mappingRepo.findByMappingIdAndMappingType(mappingRecord.getMappingId(), mappingRecord.getMappingType());
         if (!findMapping.isPresent()) {
-            throw new MappingException("Error: Mapping '" + mappingRecord.getMappingId() + "/" + mappingRecord.getMappingType() + "' doesn't exist!");
+            throw new MappingException("Error: Mapping '" + mappingRecord.getMappingType() + "_" + mappingRecord.getMappingId() + "' doesn't exist!");
         }
         mappingRecord.setMappingDocumentUri(findMapping.get().getMappingDocumentUri());
         saveMappingFile(content, mappingRecord);
@@ -109,7 +109,7 @@ public void updateMapping(String content, MappingRecord mappingRecord) throws IO
     public void deleteMapping(MappingRecord mappingRecord) throws IOException {
         Optional<MappingRecord> findMapping = mappingRepo.findByMappingIdAndMappingType(mappingRecord.getMappingId(), mappingRecord.getMappingType());
         if (!findMapping.isPresent()) {
-            throw new MappingException("Error: Mapping '" + mappingRecord.getMappingId() + "/" + mappingRecord.getMappingType() + "' doesn't exist!");
+            throw new MappingException("Error: Mapping '" + mappingRecord.getMappingType() + "_" + mappingRecord.getMappingId() + "' doesn't exist!");
         }
         mappingRecord = findMapping.get();
         deleteMappingFile(mappingRecord);
@@ -187,8 +187,6 @@ public List<Path> executeMapping(URI contentUrl, String mappingId) throws Mappin
      */
     private void init(ApplicationProperties applicationProperties) throws URISyntaxException {
         if ((applicationProperties != null) && (applicationProperties.getMappingsLocation() != null)) {
-            PluginManager.reloadPlugins();
-//            mappingUtil = new MappingUtil(applicationProperties);
             try {
                 mappingsDirectory = Files.createDirectories(new File(applicationProperties.getMappingsLocation().getPath()).getAbsoluteFile().toPath());
             } catch (IOException e) {
@@ -212,7 +210,6 @@ private void saveMappingFile(String content, MappingRecord mapping) throws IOExc
             LOGGER.debug("Storing mapping file with id '{}' and type '{}'", mapping.getMappingId(), mapping.getMappingType());
             LOGGER.trace("Content of mapping: '{}'", content);
             try {
-//                Mapping.valueOf(mapping.getMappingType());
                 // 'delete' old file
                 deleteMappingFile(mapping);
                 newMappingFile = Paths.get(mappingsDirectory.toString(), mapping.getMappingId() + "_" + mapping.getMappingType() + ".mapping");
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/rest/impl/MappingAdministrationController.java b/src/main/java/edu/kit/datamanager/mappingservice/rest/impl/MappingAdministrationController.java
@@ -358,6 +358,7 @@ public ResponseEntity reloadAllAvailableMappingTypes(WebRequest wr, HttpServletR
         PluginManager.reloadPlugins();
         return ResponseEntity.noContent().build();
     }
+
     /**
      * Get the record of given id / type.
      *
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/util/FileUtil.java b/src/main/java/edu/kit/datamanager/mappingservice/util/FileUtil.java
@@ -21,6 +21,7 @@
 import org.apache.commons.io.FilenameUtils;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.http.MediaType;
@@ -182,6 +183,8 @@ public static void cloneGitRepository(String repositoryUrl, String targetDirecto
         target.mkdirs();
         try {
             Git.cloneRepository().setURI(repositoryUrl).setBranch(branch).setDirectory(target).call();
+        } catch (JGitInternalException e){
+            LOGGER.info(e.getMessage());
         } catch (GitAPIException ex) {
             throw new MappingException("Error cloning git repository '" + repositoryUrl + "' to '" + targetDirectory + "'!", ex);
         }
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/util/PythonRunnerUtil.java b/src/main/java/edu/kit/datamanager/mappingservice/util/PythonRunnerUtil.java
@@ -40,6 +40,7 @@ public PythonRunnerUtil(ApplicationProperties configuration) {
 
     public static void printPythonVersion() {
         try {
+            LOGGER.info("Configured Python version:");
             ShellRunnerUtil.run(new String[]{configuration.getPythonLocation().getPath(), "--version"}, new LoggerOutputStream(LOGGER, LoggerOutputStream.Level.INFO), new LoggerOutputStream(LOGGER, LoggerOutputStream.Level.WARN));
         } catch (MappingPluginException e) {
             e.printStackTrace();
@@ -56,6 +57,7 @@ public static MappingPluginState runPythonScript(String script, String... args)
     }
 
     public static MappingPluginState runPythonScript(String script, OutputStream output, OutputStream error, String... args) throws MappingPluginException {
+        if (configuration == null || configuration.getPythonLocation() == null) return MappingPluginState.UNKNOWN_ERROR;
         ArrayList<String> command = new ArrayList<>();
         command.add(configuration.getPythonLocation().getPath());
         command.add(script);
diff --git a/src/main/java/edu/kit/datamanager/mappingservice/util/ShellRunnerUtil.java b/src/main/java/edu/kit/datamanager/mappingservice/util/ShellRunnerUtil.java
@@ -21,7 +21,6 @@
 import org.slf4j.LoggerFactory;
 
 import java.io.*;
-import java.util.Arrays;
 import java.util.List;
 import java.util.concurrent.*;
 import java.util.stream.Collectors;
@@ -54,7 +53,7 @@ public static MappingPluginState run(String[] command, OutputStream output, Outp
         ExecutorService pool = Executors.newSingleThreadExecutor();
         int result;
         MappingPluginState returnValue = MappingPluginState.SUCCESS;
-        Arrays.stream(command).toList().forEach(LOGGER::info);
+//        Arrays.stream(command).toList().forEach(LOGGER::info);
 
         try {
             ProcessBuilder pb = new ProcessBuilder(command);
diff --git a/src/main/resources/application.properties b/src/main/resources/application.properties
@@ -42,9 +42,6 @@ repo.auth.jwtSecret:test123
 #mapping-service.pythonLocation:file:///usr/bin/python3
 mapping-service.pythonLocation=file:///opt/homebrew/bin/python3
 
-# Absolute path to the local gemma mapping script mapping_single.py'
-mapping-service.gemmaLocation:file:src/test/resources/python/mapping_single.py
-
 # Absolute path to the local gemma mappings folder
-#metastore.indexer.mappingsLocation:file:src/test/resources/mapping/gemma
-mapping-service.mappingsLocation:file:///tmp/mapping-service/
+#mapping-service.mappingsLocation:file://tmp/mappings
+mapping-service.mappingSchemasLocation:file:///Users/maximilian/mappingSchemas
diff --git a/src/main/resources/static/JS/addScheme.js b/src/main/resources/static/JS/addScheme.js
@@ -12,15 +12,22 @@ let isEdit = false
 let aclEdit
 let data
 let selectedType = null
+let isJSONInput = true
 load()
 
 function loadFile() {
     const reader = new FileReader();
     reader.onload = (event) => {
-        const obj = JSON.parse(event.target.result);
-        console.log(obj)
-        editor.set(obj)
-        editor.expandAll()
+        try {
+            const obj = JSON.parse(event.target.result);
+            console.log(obj)
+            editor.set(obj)
+            editor.expandAll()
+        } catch (e) {
+            console.log("Error parsing JSON: " + e)
+            editor.set({})
+            isJSONInput = false
+        }
     };
     reader.readAsText(document.getElementById("schema").files[0]);
 }
@@ -43,6 +50,8 @@ function load() {
             document.getElementById("id").value = data.record.mappingId
             // document.getElementById("type").value = data.record.mappingType
             selectType(data.record.mappingType)
+            document.getElementById("title").value = data.record.title
+            document.getElementById("descr").value = data.record.description
             for (let i = 0; i < data.record.acl.length; i++) {
                 acl.push({
                     "id": data.record.acl[i].id,
@@ -122,8 +131,10 @@ function deleteACL(index) {
 function createMapping() {
     const id = document.getElementById("id").value
     const type = selectedType
+    const title = document.getElementById("title").value
+    const description = document.getElementById("descr").value
     const file = document.getElementById("schema").files[0]
-    if (editor.getText() === "{}") {
+    if (editor.getText() === "{}" && isJSONInput) {
         document.getElementById("errorMessage").textContent = "Please define a schema document."
         document.getElementById("errorMessage").hidden = false
         return
@@ -136,10 +147,14 @@ function createMapping() {
     const record = {
         "mappingId": id,
         "mappingType": type,
+        "title": title,
+        "description": description,
         "acl": resultACLs
     }
     const recordBlob = new Blob([JSON.stringify(record)], {type: "application/json"});
-    const documentBlob = new Blob([editor.getText()], {type: "application/json"})
+    let documentBlob
+    if(isJSONInput) documentBlob = new Blob([editor.getText()], {type: "application/json"})
+    else documentBlob = file
 
     console.log("Sending record:" + JSON.stringify(record))
     console.log("Sending document:" + editor.getText())
@@ -156,14 +171,6 @@ function createMapping() {
         document.getElementById("submit").disabled = false
         if (http.status <= 300) {
             document.getElementById("errorMessage").hidden = true
-            // const element = document.createElement('a');
-            // element.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(editor.getText()));
-            // if (file != null) element.setAttribute('download', file.name);
-            // else element.setAttribute('download', id + "_schema.json");
-            // element.style.display = 'none';
-            // document.body.appendChild(element);
-            // element.click();
-            // document.body.removeChild(element);
             document.getElementById("successDisplay").hidden = false
             setTimeout(() => {
                 clearForm()
@@ -195,6 +202,8 @@ function createMapping() {
 function updateMapping() {
     const id = document.getElementById("id").value
     const type = selectedType
+    const title = document.getElementById("title").value
+    const description = document.getElementById("descr").value
     const file = document.getElementById("schema").files[0]
     if (editor.getText() === "{}") {
         document.getElementById("errorMessage").textContent = "Please define a schema document."
@@ -209,6 +218,8 @@ function updateMapping() {
     const record = {
         "mappingId": id,
         "mappingType": type,
+        "title": title,
+        "description": description,
         "acl": resultACLs
     }
     const recordBlob = new Blob([JSON.stringify(record)], {type: "application/json"});
@@ -271,6 +282,7 @@ function clearForm() {
     document.getElementById("successDisplay").hidden = true
     document.getElementById("editSuccessDisplay").hidden = true
     document.getElementById("errorMessage").hidden = true
+    unselect()
     acl.forEach((value, key) => {
         deleteACL(key)
     })
diff --git a/src/main/resources/static/JS/listSchemes.js b/src/main/resources/static/JS/listSchemes.js
@@ -40,7 +40,7 @@ function getRecords() {
                     "ETAG": ETAG
                 })
                 console.log(records)
-                addListElement(results[i].mappingId, results[i].mappingType, schema.title, schema.description)
+                addListElement(results[i].mappingId, results[i].mappingType, results[i].title, results[i].description)
             }
         }
         document.getElementById("progress").hidden = true
diff --git a/src/main/resources/static/addScheme.html b/src/main/resources/static/addScheme.html

Original file line number	Diff line number	Diff line change
`@@ -55,14 +55,7 @@ public static void main(String[] args) {`
`55`	`55`	`SpringApplication.run(MappingServiceApplication.class, args);`
`56`	`56`	`System.out.println("Mapping service is running! Access it at http://localhost:8095");`
`57`	`57`
`58`		`-// PluginManager.reloadPlugins();`
`59`		`-`
`60`	`58`	`PluginManager.soleInstance().getListOfAvailableValidators().forEach(System.out::println);`
`61`	`59`	`PythonRunnerUtil.printPythonVersion();`
`62`		`-// try {`
`63`		`-// ShellRunnerUtil.run(new String[]{"ls", "-la"});`
`64`		`-// } catch (MappingPluginException e) {`
`65`		`-// e.printStackTrace();`
`66`		`-// }`
`67`	`60`	`}`
`68`	`61`	`}`
Original file line number	Diff line number	Diff line change
`@@ -358,6 +358,7 @@ public ResponseEntity reloadAllAvailableMappingTypes(WebRequest wr, HttpServletR`
`358`	`358`	`PluginManager.reloadPlugins();`
`359`	`359`	`return ResponseEntity.noContent().build();`
`360`	`360`	`}`
	`361`	`+`
`361`	`362`	`/**`
`362`	`363`	`* Get the record of given id / type.`
`363`	`364`	`*`