From 60844997ffd403f715078e686dcd110e6fb34a24 Mon Sep 17 00:00:00 2001
From: jcorvi <javier.corvi@bsc.es>
Date: Tue, 8 Feb 2022 15:07:15 +0100
Subject: [PATCH 1/2] add execution information

---
 pom.xml                                       |  5 ++
 .../es/bsc/inb/importjson/mongo/main/App.java | 48 ++++++++++++++++++-
 2 files changed, 51 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index 7b046ad..c718fb1 100644
--- a/pom.xml
+++ b/pom.xml
@@ -32,6 +32,11 @@
 		    <artifactId>mongo-java-driver</artifactId>
 		    <version>3.10.2</version>
 		</dependency>
+		<dependency>
+		    <groupId>org.json</groupId>
+		    <artifactId>json</artifactId>
+		    <version>20211205</version>
+		</dependency>
   	</dependencies>
 
   <build>
diff --git a/src/main/java/es/bsc/inb/importjson/mongo/main/App.java b/src/main/java/es/bsc/inb/importjson/mongo/main/App.java
index abac2bf..d446ff7 100644
--- a/src/main/java/es/bsc/inb/importjson/mongo/main/App.java
+++ b/src/main/java/es/bsc/inb/importjson/mongo/main/App.java
@@ -3,6 +3,8 @@ package es.bsc.inb.importjson.mongo.main;
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Paths;
+import java.text.SimpleDateFormat;
+import java.util.Date;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
@@ -13,6 +15,7 @@ import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.FileUtils;
 import org.bson.Document;
+import org.json.JSONObject;
 
 import com.mongodb.MongoClient;
 import com.mongodb.MongoClientURI;
@@ -106,7 +109,8 @@ public class App {
         try {
         	MongoClient mongoClient = new MongoClient(uri);
         	MongoDatabase db = mongoClient.getDatabase(mongoDatabaseStr);
-    	    process(inputFilePath, workdirPath, db, collection_prefixStr);
+    	    Integer total_processed = process(inputFilePath, workdirPath, db, collection_prefixStr);
+    	    addExecution(db,collection_prefixStr, total_processed);
     	    mongoClient.close();
     	}catch(Exception e) {
     		System.out.println("ERROR: App ");
@@ -120,8 +124,9 @@ public class App {
 	 * @param properties_parameters_path
      * @throws IOException 
 	 */
-	public static void process(String inputDirectoryPath, String workdir, MongoDatabase mongoDB, String collection_prefixStr) throws IOException {
+	public static Integer process(String inputDirectoryPath, String workdir, MongoDatabase mongoDB, String collection_prefixStr) throws IOException {
     	System.out.println("App::processTagger :: INIT ");
+    	Integer total_processed = 0;
 		if (java.nio.file.Files.isDirectory(Paths.get(inputDirectoryPath))) {
 			File inputDirectory = new File(inputDirectoryPath);
 			String collection = "documents"; 
@@ -141,6 +146,7 @@ public class App {
 							collection = collection_prefixStr + "_" + collection;
 						}
 						processDocument(file, mongoDB, collection);
+						total_processed = total_processed + 1;
 					} catch (MongoTimeoutException e) {
 						System.out.println("App::process :: MongoTimeoutException ERROR " + file.getAbsolutePath());
 						System.out.println("App::process :: Please review the connection ");
@@ -160,7 +166,10 @@ public class App {
 		}else {
 			System.out.println("App::process :: No directory :  " + inputDirectoryPath);
 		}
+		total_processed = total_processed / 2;
+		System.out.println("App::process :: TOTAL FILES PROCESSED : " + total_processed );
 		System.out.println("App::process :: END ");
+		return total_processed;
 	}
 	
 	/**
@@ -183,4 +192,39 @@ public class App {
 		coll=null;
 		
 	}
+	
+	/**
+	 * Execute process in a document
+	 * @param inputFile
+	 * @param outputGATEFile
+	 * @throws ResourceInstantiationException
+	 * @throws IOException 
+	 * @throws JsonGenerationException 
+	 * @throws InvalidOffsetException
+	 */
+	private static void addExecution(MongoDatabase mongoDB, String collection_prefixStr, Integer total_processed) throws IOException{
+		String collection = "execution";
+		if(collection_prefixStr!=null && !collection_prefixStr.equals("")) {
+			collection = collection_prefixStr + "_" + collection;
+		}
+		Date date = new Date();  
+	    SimpleDateFormat formatter = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");  
+	    String strDate= formatter.format(date);  
+		MongoCollection<Document> coll = mongoDB.getCollection(collection);
+		String jsonString = new JSONObject()
+                .put("date", strDate)
+                .put("comment", "DEBBIE Pipeline execution")
+                .put("abstracts_processed", total_processed)
+                .toString();
+		Document doc = Document.parse(jsonString);
+		coll.insertOne(doc);
+		jsonString=null;
+		doc.clear();
+		doc=null;
+		coll=null;
+		
+	}
+	
+	
+	
 }
-- 
GitLab


From 8f64220ef2afbd2d76c6a44296ccf5973d75e2b6 Mon Sep 17 00:00:00 2001
From: jcorvi <javier.corvi@bsc.es>
Date: Tue, 8 Feb 2022 15:18:50 +0100
Subject: [PATCH 2/2] gitlab pipeline

---
 .gitlab-ci.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index adaee4e..414b52b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -5,8 +5,6 @@ stages:
   - build
 build_docker_image:
   stage: build
-  only:
-    - tags
   script:
      - docker login -u gitlab-ci-token -p $CI_BUILD_TOKEN $DOCKER_REGISTRY
      - docker build -t $IMAGE_FULL_PATH .
-- 
GitLab