From 7c899dd1334b956c3bfc523140e37a18367498f7 Mon Sep 17 00:00:00 2001
From: gaellafond <g.lafond@aims.gov.au>
Date: Tue, 21 Mar 2023 11:02:49 +0800
Subject: [PATCH] Version 0.7.1 DownloadManager: - Added support for manually
 specify a list of files to download. - Minor typo fixes in comments.

---
 pom.xml                                       |  2 +-
 .../ereefs/bean/download/DownloadBean.java    | 46 ++++++++++++++++++-
 .../aims/ereefs/database/DatabaseClient.java  |  6 +--
 3 files changed, 49 insertions(+), 5 deletions(-)

diff --git a/pom.xml b/pom.xml
index f71b945..29dc7ac 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>au.gov.aims</groupId>
     <artifactId>ereefs-database</artifactId>
-    <version>0.7.0</version>
+    <version>0.7.1</version>
 
     <!--
         *** IMPORTANT ***
diff --git a/src/main/java/au/gov/aims/ereefs/bean/download/DownloadBean.java b/src/main/java/au/gov/aims/ereefs/bean/download/DownloadBean.java
index 47abb6d..e566aa2 100644
--- a/src/main/java/au/gov/aims/ereefs/bean/download/DownloadBean.java
+++ b/src/main/java/au/gov/aims/ereefs/bean/download/DownloadBean.java
@@ -10,12 +10,14 @@
 import org.json.JSONObject;
 
 import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 import java.util.regex.Pattern;
 
 /**
  * This is a simple bean, used with the {@code ereefs-download-manager} project.
- * It represent the documents found in the MongoDB collection {@code download}.
+ * It represents the documents found in the MongoDB collection {@code download}.
  * It's describing a Download definition for a THREDDS catalogue.
  */
 public class DownloadBean extends AbstractBean {
@@ -26,6 +28,7 @@ public class DownloadBean extends AbstractBean {
 
     private String filenameTemplate;
     private String filenameRegexStr;
+    private Set<String> files;
 
     // List of catalogue URLs.
     // NOTE: Download definitions usually contain only one catalogue URL.
@@ -66,6 +69,7 @@ public DownloadBean(JSONObject jsonDownload) {
             this.catalogueUrls = null;
             this.addCatalogueUrl(jsonDownload.optString("catalogueUrl", null), null);
             this.addCatalogueUrls(jsonDownload.optJSONArray("catalogueUrls"));
+            this.addFiles(jsonDownload.optJSONArray("files"));
             this.setOutput(jsonDownload.optJSONObject("output"));
         }
     }
@@ -387,6 +391,46 @@ public void addCatalogueUrls(JSONArray catalogueUrlsArray) {
         }
     }
 
+    /**
+     * Get the manually provided list of files to download.
+     * This list will be null or empty unless it has been manually set by the user.
+     * @return list of files, specified as a {@code JSONArray}.
+     */
+    public Set<String> getFiles() {
+        return this.files;
+    }
+
+    /**
+     * Manually specify a list of files to be downloaded from the catalogue.
+     *
+     * @param jsonFiles list of files, specified as a {@code JSONArray}.
+     */
+    public void addFiles(JSONArray jsonFiles) {
+        if (jsonFiles != null && !jsonFiles.isEmpty()) {
+            for (int i=0; i<jsonFiles.length(); i++) {
+                this.addFile(jsonFiles.optString(i, null));
+            }
+        }
+    }
+
+    /**
+     * Add a file to be downloaded from the catalogue.
+     * NOTE: Adding a file will prevent the DownloadManager from downloading
+     *     the other files listed in the catalogue.
+     * @param fileStr file to download, as listed the catalogue.
+     */
+    public void addFile(String fileStr) {
+        if (fileStr != null) {
+            fileStr = fileStr.trim();
+            if (!fileStr.isEmpty()) {
+                if (this.files == null) {
+                    this.files = new HashSet<String>();
+                }
+                this.files.add(fileStr);
+            }
+        }
+    }
+
     /**
      * Return the {@link OutputBean} which describe where the files are downloaded.
      * @return the {@link OutputBean}.
diff --git a/src/main/java/au/gov/aims/ereefs/database/DatabaseClient.java b/src/main/java/au/gov/aims/ereefs/database/DatabaseClient.java
index e940146..e9e1b83 100644
--- a/src/main/java/au/gov/aims/ereefs/database/DatabaseClient.java
+++ b/src/main/java/au/gov/aims/ereefs/database/DatabaseClient.java
@@ -40,12 +40,12 @@ public class DatabaseClient {
     private static final String AUTHENTICATION_SOURCE = "admin";
     private static final String VARIABLE_STORE_PREFIX_ENVIRONMENT_VARIABLE = "EXECUTION_ENVIRONMENT";
 
-    // NOTE: The database is not 100% reliable. Sometime it disconnect (example: during server backups).
+    // NOTE: The database is not 100% reliable. Sometimes it disconnect (example: during server backups).
     //     Each method that access the DB is in a loop that try to re-establish a connection to the DB
-    //     when it fail, up to X number of times, with a sufficient delay between retry to give a chance
+    //     when it fails, up to X number of times, with a sufficient delay between retry to give a chance
     //     to the DB to recover / restart.
     // 10 attempts = 10 seconds + 2*10 seconds + ... + 15*10 seconds = 1200 seconds
-    //     = 20 minutes (without considering timeout / running time of each attempts)
+    //     = 20 minutes (without considering timeout / running time of each attempt)
     private static final int DEFAULT_DB_RETRY_ATTEMPTS = 15;
     private static final int DEFAULT_DB_INITIAL_DELAY_BETWEEN_ATTEMPT = 10; // in seconds