feat: feed all lifebit related changes to this version from 21.04.1

.github/CODEOWNERS

@@ -0,0 +1,3 @@
+# Core analyses is the default owner for this repo.
+* @lifebit-ai/core-analyses
+* @lifebit-ai/tre-batch-analysis

buildSrc/build.gradle

@@ -11,7 +11,7 @@ version = "1.0.1"
 group = "io.nextflow"
 
 dependencies {
-    implementation ('com.amazonaws:aws-java-sdk-s3:1.11.542')
+    implementation ('com.amazonaws:aws-java-sdk-s3:1.12.129')
     implementation 'com.google.code.gson:gson:2.9.0'
 }
 

modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy

@@ -286,6 +286,7 @@ class BashWrapperBuilder {
         binding.fix_ownership = fixOwnership() ? "[ \${NXF_OWNER:=''} ] && chown -fR --from root \$NXF_OWNER ${workDir}/{*,.*} || true" : null
 
         binding.trace_script = isTraceRequired() ? getTraceScript(binding) : null
+        binding.temp_dir = "\${1:-${copyStrategy.getTempDir(workDir)}}"
 
         return binding
     }

modules/nextflow/src/main/groovy/nextflow/executor/ScriptFileCopyStrategy.groovy

@@ -86,4 +86,9 @@ interface ScriptFileCopyStrategy {
      */
     String getEnvScript(Map environment, boolean container)
 
+    /**
+     * @param targetDir The directory where output files need to be unstaged ie. stored
+     * @return the path string for the temp directory
+     */
+    String getTempDir( Path targetDir )
 }

modules/nextflow/src/main/groovy/nextflow/executor/SimpleFileCopyStrategy.groovy

@@ -415,4 +415,9 @@ class SimpleFileCopyStrategy implements ScriptFileCopyStrategy {
         }
     }
 
+    @Override
+    String getTempDir( Path workDir ) {
+        return "/tmp"
+    }
+
 }

modules/nextflow/src/main/resources/nextflow/cloud/aws/cloud-boot.txt

@@ -31,13 +31,25 @@ region="${zone::-1}"
 #
 [[ '!{dockerPull}' ]] && for x in '!{dockerPull}'; do docker pull $x || true; done
 
+#
+# Mount fsx file systems if provided
+#
+mountCommandsString="!{fsxFileSystemsMountCommands}"
+IFS=';' read -ra mountCommandsArray <<< "$mountCommandsString"
+[[ '!{fsxFileSystemsMountCommands}' ]] && for fsxMountCommand in "${mountCommandsArray[@]}"; do $fsxMountCommand || true; done
+
 #
 # Install NEXTFLOW and launch it
 #
-version="v!{nextflow.version}"
+if [[ '!{customNextflowBinaryUrl}' ]]; then
 curl -fsSL http://www.nextflow.io/releases/${version}/nextflow  > $HOME/nextflow
+  curl -s https://get.nextflow.io --output nextflow
 chmod +x $HOME/nextflow
+  NXF_PACK="all" NXF_URL="!{customNextflowBinaryUrl}" NXF_VER=${version} NXF_MODE="ignite" NXF_EXECUTOR="ignite" bash nextflow info
 $HOME/nextflow -download
+  chmod +x $HOME/nextflow
+  $HOME/nextflow -download
+fi
 
 # pull the nextflow pipeline repo
 [[ '!{nextflow.pull}' ]] && $HOME/nextflow pull '!{nextflow.pull}'

modules/nextflow/src/main/resources/nextflow/executor/command-run.txt

@@ -1,4 +1,4 @@
-##
+    ##
 ##  Copyright 2020-2022, Seqera Labs
 ##  Copyright 2013-2019, Centre for Genomic Regulation (CRG)
 ##
@@ -64,7 +64,7 @@ nxf_kill() {
 }
 
 nxf_mktemp() {
-    local base=${1:-/tmp}
+    local base={{temp_dir}}
     mkdir -p "$base"
     if [[ $(uname) = Darwin ]]; then mktemp -d $base/nxf.XXXXXXXXXX
     else TMPDIR="$base" mktemp -d -t nxf.XXXXXXXXXX

plugins/nf-amazon/src/main/nextflow/cloud/aws/AmazonClientFactory.groovy

@@ -17,10 +17,12 @@
 
 package nextflow.cloud.aws
 
+import com.amazonaws.AmazonClientException
 import com.amazonaws.auth.AWSCredentials
 import com.amazonaws.auth.AWSStaticCredentialsProvider
 import com.amazonaws.auth.BasicAWSCredentials
 import com.amazonaws.auth.BasicSessionCredentials
+import com.amazonaws.regions.InstanceMetadataRegionProvider
 import com.amazonaws.regions.Region
 import com.amazonaws.regions.RegionUtils
 import com.amazonaws.services.batch.AWSBatchClient
@@ -29,6 +31,8 @@ import com.amazonaws.services.ecs.AmazonECS
 import com.amazonaws.services.ecs.AmazonECSClientBuilder
 import com.amazonaws.services.logs.AWSLogs
 import com.amazonaws.services.logs.AWSLogsAsyncClientBuilder
+import com.amazonaws.services.securitytoken.AWSSecurityTokenServiceClientBuilder
+import com.amazonaws.services.securitytoken.model.GetCallerIdentityRequest
 import groovy.transform.CompileStatic
 import groovy.transform.Memoized
 import groovy.util.logging.Slf4j
@@ -136,35 +140,19 @@ class AmazonClientFactory {
      */
     protected String fetchIamRole() {
         try {
-            def role = getUrl('http://169.254.169.254/latest/meta-data/iam/security-credentials/').readLines()
-            if( role.size() != 1 )
-                throw new IllegalArgumentException("Not a valid EC2 IAM role")
-            return role.get(0)
+            def stsClient = AWSSecurityTokenServiceClientBuilder.defaultClient();
+            def roleArn = stsClient.getCallerIdentity(new GetCallerIdentityRequest()).getArn()
+            if(roleArn){
+                return roleArn.split('/')[-2]
+            }
+            return null
         }
-        catch( IOException e ) {
+        catch( AmazonClientException e ) {
             log.trace "Unable to fetch IAM credentials -- Cause: ${e.message}"
             return null
         }
     }
 
-    /**
-     * Fetch a remote URL resource text content
-     *
-     * @param path
-     *      A valid http/https resource URL
-     * @param timeout
-     *      Max connection timeout in millis
-     * @return
-     *      The resource URL content
-     */
-    protected String getUrl(String path, int timeout=150) {
-        final url = new URL(path)
-        final con = url.openConnection()
-        con.setConnectTimeout(timeout)
-        con.setReadTimeout(timeout)
-        return con.getInputStream().text.trim()
-    }
-
     /**
      * Retrieve the AWS region from the EC2 instance metadata.
      * See http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/ec2-instance-metadata.html
@@ -175,10 +163,9 @@ class AmazonClientFactory {
      */
     protected String fetchRegion() {
         try {
-            def zone = getUrl('http://169.254.169.254/latest/meta-data/placement/availability-zone')
-            zone ? zone.substring(0,zone.length()-1) : null
+            return new InstanceMetadataRegionProvider().getRegion()
         }
-        catch (IOException e) {
+        catch (AmazonClientException e) {
             log.debug "Cannot fetch AWS region", e
             return null
         }

plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchExecutor.groovy

@@ -108,11 +108,13 @@ class AwsBatchExecutor extends Executor implements ExtensionPoint {
 
     protected void validateWorkDir() {
         /*
-         * make sure the work dir is a S3 bucket
+         * make sure the work dir is a S3 bucket and if we are not usign lustre fsx
          */
-        if( !(workDir instanceof S3Path) ) {
+        def isUsingLustre = session.config.navigate('cloud.fsxFileSystemsMountCommands')
+        log.debug "Checking workdir validation, isUsingLustre $isUsingLustre"
+        if( !(workDir instanceof S3Path) && !isUsingLustre ) {
             session.abort()
-            throw new AbortOperationException("When using `$name` executor an S3 bucket must be provided as working directory using either the `-bucket-dir` or `-work-dir` command line option")
+            throw new AbortOperationException("When using `$name` executor and we are not using Lustre storage a S3 bucket must be provided as working directory either using -bucket-dir or -work-dir command line option")
         }
     }
 
@@ -259,6 +261,19 @@ class AwsBatchExecutor extends Executor implements ExtensionPoint {
     @PackageScope
     ThrottlingExecutor getReaper() { reaper }
 
+    String getInstanceIdByQueueAndTaskArn(String queue, String taskArn) {
+        try {
+            return helper?.getInstanceIdByQueueAndTaskArn(queue, taskArn)
+        }
+        catch ( AccessDeniedException e ) {
+            log.warn "Unable to retrieve AWS Batch instance Id | ${e.message}"
+            return null
+        }
+        catch( Exception e ) {
+            log.warn "Unable to retrieve AWS batch instance id for queue=$queue; task=$taskArn | ${e.message}", e
+            return null
+        }
+    }
 
     CloudMachineInfo getMachineInfoByQueueAndTaskArn(String queue, String taskArn) {
         try {
@@ -299,13 +314,4 @@ class AwsBatchExecutor extends Executor implements ExtensionPoint {
         ThreadPoolHelper.await(reaper, Duration.of('60min'), waitMsg, exitMsg, )
     }
 
-}
-
-
-
-
-
-
-
-
-
+}

plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategy.groovy

@@ -70,8 +70,13 @@ class AwsBatchFileCopyStrategy extends SimpleFileCopyStrategy {
             copy.remove('PATH')
         // when a remote bin directory is provide managed it properly
         if( opts.remoteBinDir ) {
-            result << "${opts.getAwsCli()} s3 cp --recursive --only-show-errors s3:/${opts.remoteBinDir} \$PWD/nextflow-bin\n"
-            result << "chmod +x \$PWD/nextflow-bin/* || true\n"
+            final isUsingLustreFsx = !opts.getFsxFileSystemsMountCommands().isEmpty()
+            final copyCommandWhenUsingLustre = "cp -r ${opts.remoteBinDir} \$PWD/nextflow-bin\n"
+            final copyCommandWhenUsingS3 = "${opts.getAwsCli()} s3 cp --recursive --only-show-errors s3:/${opts.remoteBinDir} \$PWD/nextflow-bin\n"
+            final copyCommand = isUsingLustreFsx ? copyCommandWhenUsingLustre : copyCommandWhenUsingS3
+
+            result << copyCommand
+            result << "chmod +x \$PWD/nextflow-bin/*\n"
             result << "export PATH=\$PWD/nextflow-bin:\$PATH\n"
         }
         // finally render the environment
@@ -83,6 +88,11 @@ class AwsBatchFileCopyStrategy extends SimpleFileCopyStrategy {
 
     @Override
     String getStageInputFilesScript(Map<String,Path> inputFiles) {
+        final isUsingLustreFsx = !opts.getFsxFileSystemsMountCommands().isEmpty()
+        if( isUsingLustreFsx ) {
+            log.trace "[USING LUSTRE FSX] stage_inputs."
+            return super.getStageInputFilesScript(inputFiles) + '\n'
+        }
         def result = 'downloads=(true)\n'
         result += super.getStageInputFilesScript(inputFiles) + '\n'
         result += 'nxf_parallel "${downloads[@]}"\n'
@@ -94,6 +104,10 @@ class AwsBatchFileCopyStrategy extends SimpleFileCopyStrategy {
      */
     @Override
     String stageInputFile( Path path, String targetName ) {
+        final isUsingLustreFsx = !opts.getFsxFileSystemsMountCommands().isEmpty()
+        if( isUsingLustreFsx ) {
+            return "cp -r ${Escape.path(path)} ${Escape.path(targetName)}"
+        }
         // third param should not be escaped, because it's used in the grep match rule
         def stage_cmd = opts.maxTransferAttempts > 1 && !opts.retryMode
                 ? "downloads+=(\"nxf_cp_retry nxf_s3_download s3:/${Escape.path(path)} ${Escape.path(targetName)}\")"
@@ -118,6 +132,20 @@ class AwsBatchFileCopyStrategy extends SimpleFileCopyStrategy {
         for( String it : patterns )
             escape.add( Escape.path(it) )
 
+        def isUsingLustreFsx = !opts.getFsxFileSystemsMountCommands().isEmpty()
+        if ( isUsingLustreFsx ) {
+            log.trace "[USING LUSTRE FSX] unstage_outputs."
+            return """\
+            uploads=()
+            IFS=\$'\\n'
+            for name in \$(eval "ls -1d ${escape.join(' ')}" | sort | uniq); do
+                uploads+=("cp -r '\$name' ${Escape.path(targetDir)}")
+            done
+            unset IFS
+            nxf_parallel "\${uploads[@]}"
+            """.stripIndent(true)
+        }
+
         return """\
             uploads=()
             IFS=\$'\\n'
@@ -134,7 +162,11 @@ class AwsBatchFileCopyStrategy extends SimpleFileCopyStrategy {
      */
     @Override
     String touchFile( Path file ) {
-        "echo start | nxf_s3_upload - s3:/${Escape.path(file)}"
+        def encryption = opts.storageEncryption ? "--sse $opts.storageEncryption " : ''
+        final isUsingLustreFsx = !opts.getFsxFileSystemsMountCommands().isEmpty()
+        final touchCommandWhenUsingLustre = "echo start > ${Escape.path(file)}"
+        final touchCommandWhenUsingS3 = "echo start | nxf_s3_upload - s3:/${Escape.path(file)}"
+        return isUsingLustreFsx ? touchCommandWhenUsingLustre : touchCommandWhenUsingS3
     }
 
     /**
@@ -150,7 +182,10 @@ class AwsBatchFileCopyStrategy extends SimpleFileCopyStrategy {
      */
     @Override
     String copyFile( String name, Path target ) {
-        "nxf_s3_upload ${Escape.path(name)} s3:/${Escape.path(target.getParent())}"
+        final isUsingLustreFsx = !opts.getFsxFileSystemsMountCommands().isEmpty()
+        final copyCommandWhenUsingLustre = "cp -r ${Escape.path(name)} ${Escape.path(target.getParent())}"
+        final copyCommandWhenUsingS3 = "nxf_s3_upload ${Escape.path(name)} s3:/${Escape.path(target.getParent())}"
+        return isUsingLustreFsx ? copyCommandWhenUsingLustre : copyCommandWhenUsingS3
     }
 
     static String uploadCmd( String source, Path target ) {
@@ -161,7 +196,11 @@ class AwsBatchFileCopyStrategy extends SimpleFileCopyStrategy {
      * {@inheritDoc}
      */
     String exitFile( Path path ) {
-        "| nxf_s3_upload - s3:/${Escape.path(path)} || true"
+        def encryption = opts.storageEncryption ? "--sse $opts.storageEncryption " : ''
+        final isUsingLustreFsx = !opts.getFsxFileSystemsMountCommands().isEmpty()
+        final exitCommandWhenUsingLustre = "> ${Escape.path(path)}"
+        final exitCommandWhenUsingS3 = "| nxf_s3_upload - s3:/${Escape.path(path)} || true"
+        return isUsingLustreFsx ? exitCommandWhenUsingLustre : exitCommandWhenUsingS3
     }
 
     /**
@@ -171,4 +210,10 @@ class AwsBatchFileCopyStrategy extends SimpleFileCopyStrategy {
     String pipeInputFile( Path path ) {
         " < ${Escape.path(path.getFileName())}"
     }
+
+    @Override
+    String getTempDir( Path targetDir ) {
+        final isUsingLustreFsx = !opts.getFsxFileSystemsMountCommands().isEmpty()
+        return isUsingLustreFsx ? "${Escape.path(targetDir)}" : super.getTempDir(targetDir)
+    }
 }

plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchHelper.groovy

@@ -219,5 +219,20 @@ class AwsBatchHelper {
         return result.toString()
     }
 
+    private String getInstanceIdByClusterAndTaskArn(String clusterArn, String taskArn) {
+        final containerId = getContainerIdByClusterAndTaskArn(clusterArn, taskArn)
+        return containerId ? getInstanceIdByClusterAndContainerId(clusterArn, containerId) : null
+    }
+
+    String getInstanceIdByQueueAndTaskArn(String queue, String taskArn) {
+        final clusterArnList = getClusterArnByBatchQueue(queue)
+        for (String cluster : clusterArnList) {
+            final result = getInstanceIdByClusterAndTaskArn(cluster, taskArn)
+            if (result)
+                return result
+        }
+        return null
+    }
+
 }
 

plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy

@@ -248,6 +248,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         final job = describeJob(jobId)
         final done = job?.status in ['SUCCEEDED', 'FAILED']
         if( done ) {
+            log.trace "[AWS BATCH] Completed task: jobId=$jobId"
             // finalize the task
             task.exitStatus = readExitFile()
             task.stdout = outputFile
@@ -622,7 +623,17 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         final sse = opts.storageEncryption ? " --sse $opts.storageEncryption" : ''
         final kms = opts.storageKmsKeyId ? " --sse-kms-key-id $opts.storageKmsKeyId" : ''
         final aws = "$cli s3 cp --only-show-errors${sse}${kms}${debug}"
-        final cmd = "trap \"{ ret=\$?; $aws ${TaskRun.CMD_LOG} s3:/${getLogFile()}||true; exit \$ret; }\" EXIT; $aws s3:/${getWrapperFile()} - | bash 2>&1 | tee ${TaskRun.CMD_LOG}"
+        def isUsingLustreFsx = !opts.getFsxFileSystemsMountCommands().isEmpty()
+        def logCopyCommand = isUsingLustreFsx
+                ? "trap \"{ ret=\$?; cp ${TaskRun.CMD_LOG} ${getLogFile()} 2> /dev/null; exit \$ret; }\" EXIT; "
+                : "trap \"{ ret=\$?; $aws --request-payer ${TaskRun.CMD_LOG} s3:/${getLogFile()}||true; exit \$ret; }\" EXIT; "
+        // Note(ruben): Since we do not download the .command.run from s3 bucket and due the fact that is auto imported
+        // through the link capacity of fsx when mounting we have already access to the file. So, we just need to make it
+        // executable and run it
+        def runCopyCommand = isUsingLustreFsx
+                ? "chmod +x ${getWrapperFile()}; ${getWrapperFile()} 2>&1 | tee ${TaskRun.CMD_LOG}"
+                : "$aws --request-payer s3:/${getWrapperFile()} - | bash 2>&1 | tee ${TaskRun.CMD_LOG}"
+        def cmd = "${logCopyCommand}${runCopyCommand}"
         return ['bash','-o','pipefail','-c', cmd.toString()]
     }
 
@@ -777,7 +788,8 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
             return machineInfo
         if( queueName && taskArn && executor.awsOptions.fetchInstanceType ) {
             machineInfo = executor.getMachineInfoByQueueAndTaskArn(queueName, taskArn)
-            log.trace "[AWS BATCH] jobId=$jobId; queue=$queueName; task=$taskArn => machineInfo=$machineInfo"
+            def instanceId = executor.getInstanceIdByQueueAndTaskArn(queueName, taskArn)
+            log.trace "[AWS BATCH] jobId=$jobId; queue=$queueName; task=$taskArn => machineInfo=$machineInfo; instanceId=$instanceId\""
         }
         return machineInfo
     }