From 99f5213954080c20bdc3a756cb6c52c60a5dbd33 Mon Sep 17 00:00:00 2001
From: Erhun Giray TUNCAY <giray.tuncay@tib.eu>
Date: Tue, 20 Aug 2024 09:03:31 +0000
Subject: [PATCH] Fully removed kohsuke dependency and upgraded
 springfox-swagger2 to 2.9.1 to Resolve "Some dependencies fail"

---
 ols-web/pom.xml                               |  7 --
 .../spot/ols/service/RepoMetadataService.java | 91 -------------------
 ontology-tools/pom.xml                        |  4 +-
 3 files changed, 2 insertions(+), 100 deletions(-)

diff --git a/ols-web/pom.xml b/ols-web/pom.xml
index 31c0ccd6..db550c94 100644
--- a/ols-web/pom.xml
+++ b/ols-web/pom.xml
@@ -169,13 +169,6 @@
             <artifactId>spring-boot-starter-cache</artifactId>
         </dependency>
         
-        <!-- https://mvnrepository.com/artifact/org.kohsuke/github-api -->
-        <dependency>
-            <groupId>org.kohsuke</groupId>
-            <artifactId>github-api</artifactId>
-            <version>1.70</version>
-        </dependency>
-        
         <dependency>
             <groupId>org.json</groupId>
             <artifactId>json</artifactId>
diff --git a/ols-web/src/main/java/uk/ac/ebi/spot/ols/service/RepoMetadataService.java b/ols-web/src/main/java/uk/ac/ebi/spot/ols/service/RepoMetadataService.java
index 276d3dc3..6b41fe38 100644
--- a/ols-web/src/main/java/uk/ac/ebi/spot/ols/service/RepoMetadataService.java
+++ b/ols-web/src/main/java/uk/ac/ebi/spot/ols/service/RepoMetadataService.java
@@ -22,12 +22,6 @@
 import org.apache.http.util.EntityUtils;
 import org.json.JSONArray;
 import org.json.JSONObject;
-import org.kohsuke.github.GHContent;
-import org.kohsuke.github.GHRelease;
-import org.kohsuke.github.GHRepository;
-import org.kohsuke.github.GHTag;
-import org.kohsuke.github.GitHub;
-import org.kohsuke.github.GitHubBuilder;
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.core.io.ClassPathResource;
 import org.springframework.stereotype.Service;
@@ -66,91 +60,6 @@ public static String removePrefix(String s, String prefix)
         return s;
     }
 
-	 public static GHContent traverse (GHContent ghc, String keyword, GHTag tag, GHRepository repo, GHRelease ghr, Set<String> downloadUrls) {
-
-		 if (ghc.isFile()) {
-					try {
-						downloadUrls.add(repo.getFileContent(ghc.getPath(), tag.getCommit().getSHA1()).getDownloadUrl());  ;
-					} catch (IOException e) {
-						// TODO Auto-generated catch block
-						e.printStackTrace();
-					}
-		 } else if (ghc.isDirectory()) {
-			 try {
-				for (GHContent ghc2 : repo.getDirectoryContent(ghc.getPath(),ghr.getTagName())) {
-					 traverse(ghc2,keyword, tag, repo, ghr, downloadUrls);
-				 }
-			} catch (IOException e) {
-				// TODO Auto-generated catch block
-				e.printStackTrace();
-			}
-		 }
-
-		 return null;
-	 }
-
-	@Cacheable(value = "releases", key="#repoUrl.concat('-').concat('kohsuke').concat('-').concat(#filter).concat('-').concat(#keyword)")
-	public List<Release> releasesKohsuke(String repoUrl, String externalToken, RepoFilterEnum filter, String keyword) {
-	    String userName = "";
-	    String personalAccessToken = "";
-
-	    if(externalToken != null)
-			if (externalToken.length() >= 1)
-				personalAccessToken = externalToken;
-		if(externalToken == null || externalToken.length() < 1) {
-	        try {
-	        	// reads from src/main/resource
-				InputStream is = new ClassPathResource("/github.com.token.txt").getInputStream();
-				try {
-				    String contents = new String(FileCopyUtils.copyToByteArray(is), StandardCharsets.UTF_8);
-				    System.out.println(contents);
-				    personalAccessToken = contents.split("\n")[0];
-				    userName = contents.split("\n")[1];
-				} catch (IOException e) {
-				    e.printStackTrace();
-				} finally {
-				    if (is != null) {
-				        is.close();
-				    }
-				}
-			} catch (IOException e) {
-				// TODO Auto-generated catch block
-				e.printStackTrace();
-			}
-		}
-
-		List<Release> releasesWithRawUrls = new ArrayList<Release>();
-		try {
-			GitHub github = new GitHubBuilder().withOAuthToken(personalAccessToken, userName).build();
-			GHRepository repo = null;
-			if(repoUrl.startsWith("https://github.com/"))
-				repo = github.getRepository(removePrefix(repoUrl,"https://github.com/"));
-			else if (repoUrl.startsWith("http://github.com/"))
-				repo = github.getRepository(removePrefix(repoUrl,"http://github.com/"));
-			if(repo != null) {
-				List<GHTag> tags = repo.listTags().asList();
-				List<GHRelease> releases = repo.getReleases();
-				for(GHRelease ghr : releases) {
-					Set<String> downloadUrls = new HashSet<String>();
-
-					for (GHTag tag : tags) {
-						if(tag.getName().equals(ghr.getTagName())) {
-							for (GHContent ghc : repo.getDirectoryContent("",ghr.getTagName())) {
-								traverse(ghc,keyword, tag, repo, ghr, downloadUrls);
-							}
-						}
-					}
-					releasesWithRawUrls.add(addRelease(ghr.getName(), ghr.getHtmlUrl().toString(), ghr.getCreatedAt().toString(),downloadUrls,  filter, keyword));
-				}
-			}
-
-		} catch (IOException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-		return releasesWithRawUrls;
-	}
-
 	@Cacheable(value = "releases", key="#repoUrl.concat('-').concat('github').concat('-').concat('rest').concat('-').concat(#filter).concat('-').concat(#keyword)")
 	public List<Release> releasesGithubREST(String repoUrl, String externalToken, RepoFilterEnum filter, String keyword){
 	    StringBuilder token = new StringBuilder();
diff --git a/ontology-tools/pom.xml b/ontology-tools/pom.xml
index dc471b9f..bfa864df 100644
--- a/ontology-tools/pom.xml
+++ b/ontology-tools/pom.xml
@@ -86,13 +86,13 @@
         <dependency>
             <groupId>io.springfox</groupId>
             <artifactId>springfox-swagger2</artifactId>
-            <version>2.9.0</version>
+            <version>2.9.1</version>
         </dependency>
 
         <dependency>
             <groupId>io.springfox</groupId>
             <artifactId>springfox-swagger-ui</artifactId>
-            <version>2.9.0</version>
+            <version>2.9.1</version>
         </dependency>
         
     </dependencies>