From eaaeb3ded4cb7bf6293e06a5ddd00fb38e68b5aa Mon Sep 17 00:00:00 2001
From: Jorge Ejarque <jorgee@users.noreply.github.com>
Date: Mon, 11 Nov 2024 12:19:54 +0100
Subject: [PATCH] Fix overlapping file lock exception (#5489) [ci fast]

Signed-off-by: jorgee <jorge.ejarque@seqera.io>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../groovy/nextflow/conda/CondaCache.groovy   | 23 +++++++++++++------
 .../nextflow/conda/CondaCacheTest.groovy      | 10 ++++----
 2 files changed, 22 insertions(+), 11 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy b/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy
index 7d1ff901f5..17c605f19b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy
@@ -22,6 +22,7 @@ import java.nio.file.Path
 import java.nio.file.Paths
 import java.util.concurrent.ConcurrentHashMap
 
+import com.google.common.hash.Hashing
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
@@ -32,7 +33,6 @@ import nextflow.file.FileMutex
 import nextflow.util.CacheHelper
 import nextflow.util.Duration
 import nextflow.util.Escape
-import org.yaml.snakeyaml.Yaml
 /**
  * Handle Conda environment creation and caching
  *
@@ -166,6 +166,18 @@ class CondaCache {
         str.endsWith('.txt') && !str.contains('\n')
     }
 
+    static protected String sipHash(CharSequence data) {
+        Hashing
+            .sipHash24()
+            .newHasher()
+            .putUnencodedChars(data)
+            .hash()
+            .toString()
+    }
+
+    static protected String sipHash(Path path) {
+        sipHash(path.toAbsolutePath().normalize().toString())
+    }
 
     /**
      * Get the path on the file system where store a Conda environment
@@ -188,11 +200,8 @@ class CondaCache {
             try {
                 final path = condaEnv as Path
                 content = path.text
-                final yaml = (Map)new Yaml().load(content)
-                if( yaml.name )
-                    name = yaml.name
-                else
-                    name = path.baseName
+                name = 'env-' + sipHash(path)
+
             }
             catch( NoSuchFileException e ) {
                 throw new IllegalArgumentException("Conda environment file does not exist: $condaEnv")
@@ -205,7 +214,7 @@ class CondaCache {
             try {
                 final path = condaEnv as Path
                 content = path.text
-                name = path.baseName
+                name = 'env-' + sipHash(path)
             }
             catch( NoSuchFileException e ) {
                 throw new IllegalArgumentException("Conda environment file does not exist: $condaEnv")
diff --git a/modules/nextflow/src/test/groovy/nextflow/conda/CondaCacheTest.groovy b/modules/nextflow/src/test/groovy/nextflow/conda/CondaCacheTest.groovy
index 637ae5623a..9a8baf952c 100644
--- a/modules/nextflow/src/test/groovy/nextflow/conda/CondaCacheTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/conda/CondaCacheTest.groovy
@@ -89,6 +89,7 @@ class CondaCacheTest extends Specification {
         def cache = Spy(CondaCache)
         def BASE = Paths.get('/conda/envs')
         def ENV = folder.resolve('foo.yml')
+        def hash = CondaCache.sipHash(ENV)
         ENV.text = '''
             channels:
               - bioconda
@@ -99,13 +100,12 @@ class CondaCacheTest extends Specification {
               - bwa=0.7.15        
             '''
             .stripIndent(true)  // https://issues.apache.org/jira/browse/GROOVY-9423
-
         when:
         def prefix = cache.condaPrefixPath(ENV.toString())
         then:
         1 * cache.isYamlFilePath(ENV.toString())
         1 * cache.getCacheDir() >> BASE
-        prefix.toString() == '/conda/envs/foo-9416240708c49c4e627414b46a743664'
+        prefix.toString() == "/conda/envs/env-${hash}-9416240708c49c4e627414b46a743664"
 
         cleanup:
         folder?.deleteDir()
@@ -118,6 +118,7 @@ class CondaCacheTest extends Specification {
         def cache = Spy(CondaCache)
         def BASE = Paths.get('/conda/envs')
         def ENV = Files.createTempFile('test','.yml')
+        def hash = CondaCache.sipHash(ENV)
         ENV.text = '''  
             name: my-env-1.1
             channels:
@@ -135,7 +136,7 @@ class CondaCacheTest extends Specification {
         then:
         1 * cache.isYamlFilePath(ENV.toString())
         1 * cache.getCacheDir() >> BASE
-        prefix.toString() == '/conda/envs/my-env-1.1-e7fafe40ca966397a2c0d9bed7181aa7'
+        prefix.toString() == "/conda/envs/env-${hash}-e7fafe40ca966397a2c0d9bed7181aa7"
 
     }
 
@@ -146,6 +147,7 @@ class CondaCacheTest extends Specification {
         def cache = Spy(CondaCache)
         def BASE = Paths.get('/conda/envs')
         def ENV = folder.resolve('bar.txt')
+        def hash = CondaCache.sipHash(ENV)
         ENV.text = '''
                 star=2.5.4a
                 bwa=0.7.15   
@@ -159,7 +161,7 @@ class CondaCacheTest extends Specification {
         1 * cache.isYamlFilePath(ENV.toString())
         1 * cache.isTextFilePath(ENV.toString())
         1 * cache.getCacheDir() >> BASE
-        prefix.toString() == '/conda/envs/bar-8a4aa7db8ddb8ce4eb4d450d4814a437'
+        prefix.toString() == "/conda/envs/env-${hash}-8a4aa7db8ddb8ce4eb4d450d4814a437"
 
         cleanup:
         folder?.deleteDir()