Changed: Replace RequestBody Class with ImportPathBody, CreateProject…

…Body, CsvDatasource, Csv DatasourceTable and changed ViewFactory to JSONFactory
samply · Dec 25, 2024 · 7204c22 · 7204c22
1 parent f1d8428
commit 7204c22
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Showing 9 changed files with 171 additions and 83 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -69,6 +69,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 - OPAL CSV (replacement of quotes with escape charachters)
 - Replaced Python commands in OpalEngine with WebClient request
 - waitUntilTaskIsFinished Method in OpalEngine
+- Replace RequestBody Class with ImportPathBody, CreateProjectBody, CsvDatasource, Csv DatasourceTable
+- Changed ViewFactory to JSONFactory
 
 
 ### Removed

diff --git a/src/main/java/de/samply/opal/CsvToOpalConverter.java b/src/main/java/de/samply/opal/CsvToOpalConverter.java
@@ -1,5 +1,6 @@
 package de.samply.opal;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
 import de.samply.converter.Format;
 import de.samply.converter.TargetConverterImpl;
 import de.samply.exporter.ExporterConst;
@@ -55,6 +56,8 @@ private void sendPathToOpal(Path input, Session session) {
             opalEngine.sendPathToOpal(input, session);
         } catch (OpalEngineException e) {
             logger.error(ExceptionUtils.getStackTrace(e));
+        } catch (JsonProcessingException e) {
+            throw new RuntimeException(e);
         }
     }
 
@@ -70,6 +73,8 @@ private void createProjectIfNotExists(Session session) {
             opalEngine.createProjectIfNotExists(session);
         } catch (OpalEngineException e) {
             throw new RuntimeException(e);
+        } catch (JsonProcessingException e) {
+            throw new RuntimeException(e);
         }
     }
 

diff --git a/...main/java/de/samply/opal/ViewFactory.java → ...main/java/de/samply/opal/JSONFactory.java b/...main/java/de/samply/opal/ViewFactory.java → ...main/java/de/samply/opal/JSONFactory.java
@@ -5,10 +5,7 @@
 import com.fasterxml.jackson.databind.SerializationFeature;
 import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
 import de.samply.exporter.ExporterConst;
-import de.samply.opal.model.Attribute;
-import de.samply.opal.model.MagmaView;
-import de.samply.opal.model.Variable;
-import de.samply.opal.model.View;
+import de.samply.opal.model.*;
 import de.samply.template.AttributeTemplate;
 import de.samply.template.ContainerTemplate;
 
@@ -17,14 +14,25 @@
 import java.util.List;
 import java.util.concurrent.atomic.AtomicInteger;
 
-public class ViewFactory {
-
+public class JSONFactory {
     private final static ObjectMapper objectMapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT)
             .registerModule(new JavaTimeModule());
 
 
     public static String createViewAndSerializeAsJson(Session session, ContainerTemplate containerTemplate) throws JsonProcessingException {
-        return objectMapper.writeValueAsString(ViewFactory.createView(session, containerTemplate));
+        return objectMapper.writeValueAsString(JSONFactory.createView(session, containerTemplate));
+    }
+
+    public static String createBodyAndSerializeAsJson(Session session, ContainerTemplate containerTemplate, String data, String separator) throws JsonProcessingException {
+        return objectMapper.writeValueAsString(JSONFactory.createCSVDatasourceBody(session, containerTemplate, data, separator));
+    }
+
+    public static String createBodyAndSerializeAsJson(String projectName, String database) throws JsonProcessingException {
+        return objectMapper.writeValueAsString(JSONFactory.createProjectBody(projectName, database));
+    }
+
+    public static String createBodyAndSerializeAsJson(Session session, ContainerTemplate template, String transientUid) throws JsonProcessingException {
+        return objectMapper.writeValueAsString(JSONFactory.createPathBody(session, template, transientUid));
     }
 
     public static View createView(Session session, ContainerTemplate containerTemplate) {
@@ -35,6 +43,46 @@ public static View createView(Session session, ContainerTemplate containerTempla
         return view;
     }
 
+    public static CsvDatasource createCSVDatasourceBody(Session session, ContainerTemplate containerTemplate, String data, String separator) {
+        CsvDatasource body = new CsvDatasource();
+        CsvDatasource.Params params = new CsvDatasource.Params();
+        params.setCharacterSet("UTF-8");
+        params.setFirstRow(1);
+        params.setQuote("\"");
+        params.setSeparator(separator);
+        params.setDefaultValueType("text");
+        params.setTables(List.of(createCSVDatasourceTable(session, containerTemplate, data)));
+        body.setParams(params);
+        return body;
+    }
+
+    public static CreateProjectBody createProjectBody(String projectName, String database) {
+        CreateProjectBody body = new CreateProjectBody();
+        body.setName(projectName);
+        body.setTitle(projectName);
+        body.setDescription("");
+        body.setDatabase(database);
+        body.setVcfStoreService(null);
+        body.setExportFolder("");
+        return body;
+    }
+
+    public static ImportPathBody createPathBody(Session session, ContainerTemplate containerTemplate, String transientUid) {
+        ImportPathBody body = new ImportPathBody();
+        body.setDestination(session.fetchProject());
+        body.setTables(new String[]{transientUid + "." + containerTemplate.getOpalTable()});
+        return body;
+    }
+
+    public static CsvDatasourceTable createCSVDatasourceTable(Session session, ContainerTemplate containerTemplate, String data) {
+        CsvDatasourceTable table = new CsvDatasourceTable();
+        table.setName(containerTemplate.getOpalTable());
+        table.setData(data);
+        table.setEntityType(containerTemplate.getOpalEntityType());
+        table.setRefTable(session.fetchProject() + "." + containerTemplate.getOpalTable());
+        return table;
+    }
+
     private static List<String> fetchViewFrom(Session session, ContainerTemplate containerTemplate) {
         return Arrays.asList(session.fetchProject() + '.' + containerTemplate.getOpalTable());
     }

diff --git a/src/main/java/de/samply/opal/OpalEngine.java b/src/main/java/de/samply/opal/OpalEngine.java
@@ -31,7 +31,7 @@ public OpalEngine(OpalServer opalServer) {
         this.webClient = opalServer.createWebClient();
     }
 
-    public void sendPathToOpal(Path path, Session session) throws OpalEngineException {
+    public void sendPathToOpal(Path path, Session session) throws OpalEngineException, JsonProcessingException {
         ContainerTemplate containerTemplate = session.getContainerTemplate(
                 path.getFileName().toString());
         if (containerTemplate != null) {
@@ -44,7 +44,7 @@ public void sendPathToOpal(Path path, Session session) throws OpalEngineExceptio
         }
     }
 
-    public void createProjectIfNotExists(Session session) throws OpalEngineException {
+    public void createProjectIfNotExists(Session session) throws OpalEngineException, JsonProcessingException {
         if (!existsProject(session)) {
             createProject(session);
             createProjectPermissions(session);
@@ -69,20 +69,13 @@ private boolean existsProject(Session session) {
                 .block());
     }
 
-    private void createProject(Session session) {
+    private void createProject(Session session) throws JsonProcessingException {
         String projectName = session.fetchProject();
         logger.info("Create Project " + projectName);
         webClient.post()
                 .uri(ExporterConst.OPAL_PROJECT_WS + ExporterConst.PROJECTS_OPAL)
                 .headers(headers -> headers.set(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE))
-                .bodyValue("{\n" +
-                        "    \"name\": \"" + projectName + "\",\n" +
-                        "    \"title\": \"" + projectName + "\",\n" +
-                        "    \"description\": \"\",\n" +
-                        "    \"database\": \"" + opalServer.getDatabase() + "\",\n" +
-                        "    \"vcfStoreService\": null,\n" +
-                        "    \"exportFolder\": \"\"\n" +
-                        "}")
+                .bodyValue(JSONFactory.createBodyAndSerializeAsJson(projectName, opalServer.getDatabase()))
                 .retrieve()
                 .onStatus(HttpStatusCode::is4xxClientError, this::handleError)
                 .onStatus(HttpStatusCode::is5xxServerError, this::handleError)
@@ -141,7 +134,7 @@ private void deletePath(Path path, Session session) {
         logger.info("File successfully deleted.");
     }
 
-    private String importPathTransient(Path path, Session session, ContainerTemplate template) throws OpalEngineException {
+    private String importPathTransient(Path path, Session session, ContainerTemplate template) throws OpalEngineException, JsonProcessingException {
         logger.info("Import started for: " + template.getOpalTable() + " in Project " + session.fetchProject());
         Map<String, Object> response = webClient.post()
                 .uri(uriBuilder -> uriBuilder
@@ -152,19 +145,9 @@ private String importPathTransient(Path path, Session session, ContainerTemplate
                     headers.set(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE);
                     headers.set(HttpHeaders.ACCEPT, MediaType.APPLICATION_JSON_VALUE);
                 })
-                .bodyValue(new RequestBody(
-                        "UTF-8",
-                        1,
-                        "\"",
-                        normalizeSepartor(session.getConverterTemplate().getCsvSeparator()),
-                        "text",
-                        List.of(RequestBody.createTable(
-                                template.getOpalTable(),
-                                session.fetchOpalProjectDirectoryPath(opalServer.getFilesDirectory(), path),
-                                template.getOpalEntityType(),
-                                session.fetchProject() + "." + template.getOpalTable()
-                        ))
-                ).getRequestMap())
+                .bodyValue(JSONFactory.createBodyAndSerializeAsJson(session, template,
+                        session.fetchOpalProjectDirectoryPath(opalServer.getFilesDirectory(), path),
+                        normalizeSepartor(session.getConverterTemplate().getCsvSeparator())))
                 .retrieve()
                 .onStatus(HttpStatusCode::is4xxClientError, this::handleError)
                 .onStatus(HttpStatusCode::is5xxServerError, this::handleError)
@@ -183,14 +166,11 @@ private String importPathTransient(Path path, Session session, ContainerTemplate
         return transientUid;
     }
 
-    private String importPath(Session session, ContainerTemplate template, String transientUid) {
+    private String importPath(Session session, ContainerTemplate template, String transientUid) throws JsonProcessingException {
         return webClient.post()
                 .uri(ExporterConst.OPAL_PROJECT + session.fetchProject() + ExporterConst.OPAL_PROJECT_IMPORT)
                 .headers(headers -> headers.set(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE))
-                .bodyValue(Map.of(
-                        "destination", session.fetchProject(),
-                        "tables", new String[]{transientUid + "." + template.getOpalTable()}
-                ))
+                .bodyValue(JSONFactory.createBodyAndSerializeAsJson(session, template, transientUid))
                 .retrieve()
                 .onStatus(HttpStatusCode::is4xxClientError, this::handleError)
                 .onStatus(HttpStatusCode::is5xxServerError, this::handleError)
@@ -253,13 +233,6 @@ public void waitUntilTaskIsFinished(String taskId) throws OpalEngineException {
         }
     }
 
-    private String extractErrorMessage(List<Map<String, Object>> messages) {
-        return messages.stream()
-                .map(msg -> (String) msg.get("msg"))
-                .reduce((first, second) -> first + "; " + second)
-                .orElse("No specific message found");
-    }
-
     private void createView(Session session, ContainerTemplate containerTemplate)
             throws OpalEngineException {
         try {
@@ -270,7 +243,7 @@ private void createView(Session session, ContainerTemplate containerTemplate)
     }
 
     private void createViewWithoutExceptionHandling(Session session, ContainerTemplate containerTemplate) throws JsonProcessingException {
-        String view = ViewFactory.createViewAndSerializeAsJson(session, containerTemplate);
+        String view = JSONFactory.createViewAndSerializeAsJson(session, containerTemplate);
         logger.info("Create View");
         logger.info("Request body: " + view);
         webClient.post()
@@ -285,7 +258,6 @@ private void createViewWithoutExceptionHandling(Session session, ContainerTempla
                 .onStatus(HttpStatusCode::is5xxServerError, this::handleError)
                 .bodyToMono(String.class)
                 .block();
-
     }
 
     private String normalizeSepartor(String separator) {
@@ -300,4 +272,4 @@ private Mono<? extends Throwable> handleError(ClientResponse clientResponse) {
                 });
     }
 
-}
+}
diff --git a/src/main/java/de/samply/opal/RequestBody.java b/src/main/java/de/samply/opal/RequestBody.java
diff --git a/src/main/java/de/samply/opal/model/CreateProjectBody.java b/src/main/java/de/samply/opal/model/CreateProjectBody.java
@@ -0,0 +1,23 @@
+package de.samply.opal.model;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import lombok.Data;
+
+@Data
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class CreateProjectBody {
+
+    @JsonProperty(value = "name")
+    private String name;
+    @JsonProperty(value = "title")
+    private String title;
+    @JsonProperty(value = "description")
+    private String description;
+    @JsonProperty(value = "database")
+    private String database;
+    @JsonProperty(value = "vcfStoreService")
+    private String vcfStoreService;
+    @JsonProperty(value = "exportFolder")
+    private String exportFolder;
+}
diff --git a/src/main/java/de/samply/opal/model/CsvDatasource.java b/src/main/java/de/samply/opal/model/CsvDatasource.java
@@ -0,0 +1,37 @@
+package de.samply.opal.model;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import lombok.Data;
+
+import java.util.List;
+
+@Data
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class CsvDatasource {
+
+    @JsonProperty("Magma.CsvDatasourceFactoryDto.params")
+    private Params params;
+
+    @Data
+    @JsonInclude(JsonInclude.Include.NON_NULL)
+    public static class Params {
+        @JsonProperty("characterSet")
+        private String characterSet;
+
+        @JsonProperty("firstRow")
+        private int firstRow;
+
+        @JsonProperty("quote")
+        private String quote;
+
+        @JsonProperty("separator")
+        private String separator;
+
+        @JsonProperty("defaultValueType")
+        private String defaultValueType;
+
+        @JsonProperty("tables")
+        private List<CsvDatasourceTable> tables;
+    }
+}
diff --git a/src/main/java/de/samply/opal/model/CsvDatasourceTable.java b/src/main/java/de/samply/opal/model/CsvDatasourceTable.java
@@ -0,0 +1,22 @@
+package de.samply.opal.model;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import lombok.Data;
+
+@Data
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class CsvDatasourceTable {
+
+    @JsonProperty("name")
+    private String name;
+
+    @JsonProperty("data")
+    private String data;
+
+    @JsonProperty("entityType")
+    private String entityType;
+
+    @JsonProperty("refTable")
+    private String refTable;
+}
diff --git a/src/main/java/de/samply/opal/model/ImportPathBody.java b/src/main/java/de/samply/opal/model/ImportPathBody.java
@@ -0,0 +1,15 @@
+package de.samply.opal.model;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import lombok.Data;
+
+@Data
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class ImportPathBody {
+
+    @JsonProperty(value = "destination")
+    private String destination;
+    @JsonProperty(value = "tables")
+    private String[] tables;
+}