PR for v1.0.2

.github/workflows/CI.yml

@@ -48,7 +48,7 @@ jobs:
         run: ./gradlew build -DapplicationProperties="src/test/resources/test-config/application-test.properties" -DpythonLocation=`which python3`
       - name: Generate report
         run: ./gradlew jacocoTestReport
-      - name: Codecov
-        uses: codecov/codecov-action@v1
-        with:
-          files: ./build/reports/jacoco/test/jacocoTestReport.xml
+#      - name: Codecov
+#        uses: codecov/codecov-action@v1
+#        with:
+#          files: ./build/reports/jacoco/test/jacocoTestReport.xml

echo.bat

@@ -1 +1 @@
-echo @1
+echo %* 

src/main/java/edu/kit/datamanager/mappingservice/plugins/PluginLoader.java

@@ -128,7 +128,7 @@ private static List<Class<IMappingPlugin>> extractClassesFromJAR(File jar, Class
     private static boolean isPluggableClass(Class<?> cls) {
         for (Class<?> i : cls.getInterfaces()) {
             LOG.trace("Checking {} against {}.", i, IMappingPlugin.class);
-LOG.trace("ASSIGN {}", IMappingPlugin.class.isAssignableFrom(cls));
+            LOG.trace("ASSIGN {}", IMappingPlugin.class.isAssignableFrom(cls));
             if (i.equals(IMappingPlugin.class)) {
                 LOG.trace("IMappingPlugin interface found.");
                 return true;

src/main/java/edu/kit/datamanager/mappingservice/plugins/impl/GemmaPlugin.java

@@ -0,0 +1,87 @@
+/*
+ * Copyright 2023 Karlsruhe Institute of Technology.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package edu.kit.datamanager.mappingservice.plugins.impl;
+
+import edu.kit.datamanager.mappingservice.plugins.*;
+import edu.kit.datamanager.mappingservice.util.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.util.MimeType;
+import org.springframework.util.MimeTypeUtils;
+import java.nio.file.Path;
+
+public class GemmaPlugin implements IMappingPlugin {
+
+    private final Logger LOGGER = LoggerFactory.getLogger(GemmaPlugin.class);
+    private static final String GEMMA_REPOSITORY = "https://github.com/kit-data-manager/gemma.git";
+    private static final String GEMMA_BRANCH = "master";
+    private static Path gemmaDir;
+    private boolean initialized = false;
+
+    @Override
+    public String name() {
+        return "GEMMA";
+    }
+
+    @Override
+    public String description() {
+        return "GEMMA is a tool written in Python that allows to map from JSON and XML to JSON. Furthermore, it allows to map with a mapping schema.";
+    }
+
+    @Override
+    public String version() {
+        return "1.0.0";
+    }
+
+    @Override
+    public String uri() {
+        return "https://github.com/kit-data-manager/gemma";
+    }
+
+    @Override
+    public MimeType[] inputTypes() {
+        return new MimeType[]{MimeTypeUtils.APPLICATION_JSON, MimeTypeUtils.APPLICATION_XML};
+    }
+
+    @Override
+    public MimeType[] outputTypes() {
+        return new MimeType[]{MimeTypeUtils.APPLICATION_JSON};
+    }
+
+    @Override
+    public void setup() {
+        LOGGER.info("Checking and installing dependencies for Gemma: gemma, xmltodict, wget");
+        try {
+            PythonRunnerUtil.runPythonScript("-m", "pip", "install", "xmltodict", "wget");
+            PythonRunnerUtil.runPythonScript("-m", new LoggerOutputStream(LOGGER, LoggerOutputStream.Level.DEBUG), new LoggerOutputStream(LOGGER, LoggerOutputStream.Level.DEBUG), "pip", "install", "xmltodict", "wget");
+            gemmaDir = FileUtil.cloneGitRepository(GEMMA_REPOSITORY, GEMMA_BRANCH);
+            initialized = true;
+        } catch (MappingPluginException e) {
+            LOGGER.error("Failed to setup plugin '" + name() + "' " + version() + ".", e);
+        }
+    }
+
+    @Override
+    public MappingPluginState mapFile(Path mappingFile, Path inputFile, Path outputFile) throws MappingPluginException {
+        if (initialized) {
+            LOGGER.trace("Run gemma on '{}' with mapping '{}' -> '{}'", inputFile, mappingFile, outputFile);
+            return PythonRunnerUtil.runPythonScript(gemmaDir + "/mapping_single.py", mappingFile.toString(), inputFile.toString(), outputFile.toString());
+        } else {
+            LOGGER.error("Plugin '" + name() + "' " + version() + " not initialized. Returning EXECUTION_ERROR.");
+            return MappingPluginState.EXECUTION_ERROR;
+        }
+    }
+}

src/main/java/edu/kit/datamanager/mappingservice/plugins/impl/IdentifyPlugin.java

@@ -1,14 +1,24 @@
 /*
- * Click nbfs://nbhost/SystemFileSystem/Templates/Licenses/license-default.txt to change this license
- * Click nbfs://nbhost/SystemFileSystem/Templates/Classes/Class.java to edit this template
+ * Copyright 2023 Karlsruhe Institute of Technology.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  */
 package edu.kit.datamanager.mappingservice.plugins.impl;
 
 import edu.kit.datamanager.mappingservice.plugins.IMappingPlugin;
 import edu.kit.datamanager.mappingservice.plugins.MappingPluginException;
 import edu.kit.datamanager.mappingservice.plugins.MappingPluginState;
 import edu.kit.datamanager.mappingservice.util.ShellRunnerUtil;
-import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.nio.file.Path;

src/main/java/edu/kit/datamanager/mappingservice/plugins/impl/TestPlugin.java

@@ -1,6 +1,17 @@
 /*
- * Click nbfs://nbhost/SystemFileSystem/Templates/Licenses/license-default.txt to change this license
- * Click nbfs://nbhost/SystemFileSystem/Templates/Classes/Class.java to edit this template
+ * Copyright 2023 Karlsruhe Institute of Technology.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  */
 package edu.kit.datamanager.mappingservice.plugins.impl;
 

src/main/java/edu/kit/datamanager/mappingservice/rest/impl/MappingAdministrationController.java

@@ -219,8 +219,12 @@ public ResponseEntity getMappingDocumentById(
             LOG.trace("Mapping document at path {} either does not exist or is no file or is not readable. Returning HTTP INTERNAL_SERVER_ERROR.", mappingDocumentPath);
             return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR).body("Metadata document on server either does not exist or is no file or is not readable.");
         }
+
+        LOG.trace("Get ETag of MappingRecord.");
+        String etag = record.getEtag();
+
         LOG.trace("Mapping document found. Returning result.");
-        return ResponseEntity.ok().header(HttpHeaders.CONTENT_LENGTH, String.valueOf(mappingDocumentPath.toFile().length())).body(new FileSystemResource(mappingDocumentPath.toFile()));
+        return ResponseEntity.ok().eTag("\"" + etag + "\"").header(HttpHeaders.CONTENT_LENGTH, String.valueOf(mappingDocumentPath.toFile().length())).body(new FileSystemResource(mappingDocumentPath.toFile()));
     }
 
     @Override

src/main/java/edu/kit/datamanager/mappingservice/util/FileUtil.java

@@ -292,7 +292,8 @@ public static Path cloneGitRepository(String repositoryUrl, String branch) {
     }
 
     /**
-     * This method clones a git repository into the 'lib' folder.
+     * This method clones a git repository into the 'lib' folder. If the folder
+     * already exists, a pull is performed.
      *
      * @param repositoryUrl the url of the repository to clone
      * @param branch the branch to clone
@@ -301,17 +302,24 @@ public static Path cloneGitRepository(String repositoryUrl, String branch) {
      */
     public static Path cloneGitRepository(String repositoryUrl, String branch, String targetFolder) {
         File target = new File(targetFolder);
-        target.mkdirs();
+        if (target.exists()) {
+            try {
+                Git.open(target).pull().call();
+            } catch (IOException | JGitInternalException | GitAPIException e) {
+                LOGGER.error("Error pulling git repository at '" + target + "'!", e);
+                throw new MappingException("Error pulling git repository at '" + target + "'!", e);
+            }
+        } else {
+            target.mkdirs();
 
-        LOGGER.info("Cloning branch '{}' of repository '{}' to '{}'", branch, repositoryUrl, target.getPath());
-        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 '" + target + "'!", ex);
+            LOGGER.info("Cloning branch '{}' of repository '{}' to '{}'", branch, repositoryUrl, target.getPath());
+            try {
+                Git.cloneRepository().setURI(repositoryUrl).setBranch(branch).setDirectory(target).call();
+            } catch (JGitInternalException | GitAPIException e) {
+                LOGGER.error("Error cloning git repository '" + repositoryUrl + "' to '" + target + "'!", e);
+                throw new MappingException("Error cloning git repository '" + repositoryUrl + "' to '" + target + "'!", e);
+            }
         }
-
         return target.toPath();
     }
 }

src/main/resources/static/JS/listSchemes.js

@@ -7,59 +7,60 @@ function getRecords() {
     http.open("GET", apiUrl);
     http.send();
     http.onprogress = () => {
-        document.getElementById("progress").hidden = false
-    }
+        document.getElementById("progress").hidden = false;
+    };
     http.onload = (e) => {
         const results = JSON.parse(http.responseText);
         if (results.length > 0) {
             document.getElementById("nothingHere").hidden = true;
-            document.getElementById("progress").hidden = true
+            document.getElementById("progress").hidden = true;
         }
         for (let i = 0; i < results.length; i++) {
-            document.getElementById("progress").hidden = false
-            console.log(results[i].mappingId)
-            const schemaHttp = new XMLHttpRequest()
-            var schema
+            document.getElementById("progress").hidden = false;
+            console.log(results[i].mappingId);
+            const schemaHttp = new XMLHttpRequest();
+            //var schema
             var ETAG
 
-            schemaHttp.open("GET", apiUrl + results[i].mappingId)
-            schemaHttp.setRequestHeader("Content-Type", "application/json")
-            schemaHttp.send()
+            schemaHttp.open("GET", apiUrl + results[i].mappingId);
+            schemaHttp.setRequestHeader("Accept", "application/vnd.datamanager.mapping-record+json");
+            schemaHttp.send();
             schemaHttp.onload = (e) => {
-                schema = JSON.parse(schemaHttp.responseText)
-                ETAG = '"' + schemaHttp.getResponseHeader("If-Match") + '"'
-                console.log("Received Data:" + {
+              //  schema = JSON.parse(schemaHttp.responseText);
+                ETAG = schemaHttp.getResponseHeader("ETag");
+                console.log("Received Data:");
+                console.log({
                     "record": results[i],
-                    "schema": schema,
+                    //"schema": schema,
                     "ETAG": ETAG
-                })
+                });
                 records.set(results[i].mappingId, {
                     "record": results[i],
-                    "schema": schema,
+                    //"schema": schema,
                     "ETAG": ETAG
                 })
-                console.log(records)
-                addListElement(results[i].mappingId, results[i].mappingType, results[i].title, results[i].description)
-            }
+                console.log(records);
+                addListElement(results[i].mappingId, results[i].mappingType, results[i].title, results[i].description);
+            };
         }
-        document.getElementById("progress").hidden = true
-    }
-    document.getElementById("progress").hidden = true
+        document.getElementById("progress").hidden = true;
+    };
+    document.getElementById("progress").hidden = true;
 }
 
 function mapWithMapping(id) {
     const data = {
         id: id,
         type: records.get(id).record.mappingType
-    }
-    window.sessionStorage.setItem("data", JSON.stringify(data))
-    window.location = "mapDocument.html"
+    };
+    window.sessionStorage.setItem("data", JSON.stringify(data));
+    window.location = "mapDocument.html";
 }
 
 function editMapping(id) {
     let sessionData = JSON.stringify(records.get(id))
     window.sessionStorage.setItem("data", sessionData)
-    window.location = "./addScheme.html"
+    window.location = "./addScheme.html";
 }
 
 function downloadMapping(id) {
@@ -74,22 +75,23 @@ function downloadMapping(id) {
         document.body.appendChild(element);
         element.click();
         document.body.removeChild(element);
-    }
+    };
 }
 
 function deleteMapping(id) {
     let mapEntry = records.get(id);
-    if (mapEntry != null && mapEntry.record.mappingId === id) {
+    console.log("Deleting mapping with id " + id);
+    if (mapEntry !== null && mapEntry.record.mappingId === id) {
         const http = new XMLHttpRequest();
-        http.open("DELETE", apiUrl + id)
-        http.setRequestHeader("If-Match", mapEntry.ETAG)
+        http.open("DELETE", apiUrl + id);
+        http.setRequestHeader("If-Match", mapEntry.ETAG);
         http.send();
         http.onload = (e) => {
-            records.delete(id)
-            document.getElementById(id).remove()
+            records.delete(id);
+            document.getElementById(id).remove();
             if (records.size < 1) document.getElementById("nothingHere").hidden = false;
-            console.log("Successfully deleted mapping with id " + id)
-        }
+            console.log("Successfully deleted mapping with id " + id);
+        };
     }
 }