Add support for conda lock file

src/main/groovy/io/seqera/wave/controller/BuildController.groovy

@@ -21,6 +21,7 @@ package io.seqera.wave.controller
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import io.micronaut.core.annotation.Nullable
+import io.micronaut.http.HttpHeaders
 import io.micronaut.http.HttpResponse
 import io.micronaut.http.MediaType
 import io.micronaut.http.annotation.Controller
@@ -32,6 +33,7 @@ import io.micronaut.scheduling.annotation.ExecuteOn
 import io.seqera.wave.api.BuildStatusResponse
 import io.seqera.wave.exception.BadRequestException
 import io.seqera.wave.service.builder.ContainerBuildService
+import io.seqera.wave.service.conda.CondaLockService
 import io.seqera.wave.service.logs.BuildLogService
 import io.seqera.wave.service.mirror.ContainerMirrorService
 import io.seqera.wave.service.mirror.MirrorRequest
@@ -58,6 +60,9 @@ class BuildController {
  @Nullable
  BuildLogService logService
 
+ @Inject
+ CondaLockService condaLockService
+
  @Get("/v1alpha1/builds/{buildId}")
  HttpResponse<WaveBuildRecord> getBuildRecord(String buildId) {
  final record = buildService.getBuildRecord(buildId)
@@ -85,6 +90,18 @@ class BuildController {
  : HttpResponse.<BuildStatusResponse>notFound()
  }
 
+ @Produces(MediaType.TEXT_PLAIN)
+ @Get(value="/v1alpha1/builds/{buildId}/condalock")
+ HttpResponse<StreamedFile> getCondaLock(String buildId){
+ if( condaLockService==null )
+ throw new IllegalStateException("Build Logs service not configured")
+ final condaLock = condaLockService.fetchCondaLock(buildId)
+ return condaLock
+ ? HttpResponse.ok(condaLock)
+ .header(HttpHeaders.CONTENT_DISPOSITION, "attachment; filename=\"" + buildId + ".lock\"")
+ : HttpResponse.<StreamedFile>notFound()
+ }
+
  protected BuildStatusResponse buildResponse0(String buildId) {
  if( !buildId )
  throw new BadRequestException("Missing 'buildId' parameter")
@@ -100,4 +117,5 @@ class BuildController {
  ?.toStatusResponse()
  }
  }
+
 }

src/main/groovy/io/seqera/wave/controller/ViewController.groovy

@@ -33,6 +33,7 @@ import io.micronaut.scheduling.annotation.ExecuteOn
 import io.micronaut.views.View
 import io.seqera.wave.exception.NotFoundException
 import io.seqera.wave.service.builder.ContainerBuildService
+import io.seqera.wave.service.conda.CondaLockService
 import io.seqera.wave.service.inspect.ContainerInspectService
 import io.seqera.wave.service.logs.BuildLogService
 import io.seqera.wave.service.persistence.PersistenceService
@@ -68,6 +69,9 @@ class ViewController {
  @Nullable
  private BuildLogService buildLogService
 
+ @Inject
+ private CondaLockService condaLockService
+
  @Inject
  private ContainerInspectService inspectService
 
@@ -152,6 +156,10 @@ class ViewController {
  binding.build_log_truncated = buildLog?.truncated
  binding.build_log_url = "$serverUrl/v1alpha1/builds/${result.buildId}/logs"
  }
+ //configure conda lock file when available
+ if( condaLockService && result.condaFile ) {
+ binding.build_conda_lock_url = "$serverUrl/v1alpha1/builds/${result.buildId}/condalock"
+ }
  // result the main object
  return binding
  }

src/main/groovy/io/seqera/wave/service/conda/Conda.groovy

@@ -0,0 +1,13 @@
+package io.seqera.wave.service.conda
+
+/**
+ * Interface for Conda constants
+ *
+ * @author Munish Chouhan <[email protected]>
+ */
+interface Conda {
+
+ String CONDA_LOCK_START = "conda_lock_start"
+ String CONDA_LOCK_END = "conda_lock_end"
+
+}

src/main/groovy/io/seqera/wave/service/conda/CondaLockService.groovy

@@ -0,0 +1,34 @@
+/*
+ * Wave, containers provisioning service
+ * Copyright (c) 2024, Seqera Labs
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package io.seqera.wave.service.conda
+
+import io.micronaut.http.server.types.files.StreamedFile
+
+/**
+ * Service to manage conda lock files
+ *
+ * @author Munish Chouhan <[email protected]>
+ */
+interface CondaLockService {
+
+ void storeCondaLock(String buildId, String condaLock)
+
+ StreamedFile fetchCondaLock(String buildId)
+
+}

src/main/groovy/io/seqera/wave/service/conda/impl/CondaLockServiceImpl.groovy

@@ -0,0 +1,103 @@
+/*
+ * Wave, containers provisioning service
+ * Copyright (c) 2024, Seqera Labs
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package io.seqera.wave.service.conda.impl
+
+import io.micronaut.http.MediaType
+import io.micronaut.http.server.types.files.StreamedFile
+import io.seqera.wave.service.conda.CondaLockService
+
+import java.nio.charset.StandardCharsets
+import java.util.concurrent.CompletableFuture
+import java.util.concurrent.ExecutorService
+
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+import io.micronaut.runtime.event.annotation.EventListener
+import io.micronaut.scheduling.TaskExecutors
+import io.seqera.wave.service.builder.BuildEvent
+import io.seqera.wave.service.persistence.PersistenceService
+import io.seqera.wave.service.persistence.WaveCondaLockRecord
+import jakarta.inject.Inject
+import jakarta.inject.Named
+import jakarta.inject.Singleton
+import static io.seqera.wave.service.conda.Conda.CONDA_LOCK_END
+import static io.seqera.wave.service.conda.Conda.CONDA_LOCK_START
+/**
+ * Implements Service to manage conda lock files from an Object store
+ *
+ * @author Munish Chouhan <[email protected]>
+ */
+@Slf4j
+@Singleton
+@CompileStatic
+class CondaLockServiceImpl implements CondaLockService {
+
+ @Inject
+ @Named(TaskExecutors.IO)
+ private volatile ExecutorService ioExecutor
+
+ @Inject
+ PersistenceService persistenceService
+
+ @EventListener
+ void onBuildEvent(BuildEvent event) {
+ if ( event.request.condaFile ) {
+ CompletableFuture.supplyAsync(() -> storeCondaLock(event.result.id, event.result.logs), ioExecutor)
+ }
+ }
+
+ @Override
+ void storeCondaLock(String buildId, String logs) {
+ if( !logs ) return
+ try {
+ String condaLock = extractCondaLockFile(logs)
+ if (condaLock){
+ log.debug "Storing condalock for buildId: $buildId"
+ def record = new WaveCondaLockRecord(buildId, condaLock.getBytes(StandardCharsets.UTF_8))
+ persistenceService.saveCondaLock(record)
+ }
+ }
+ catch (Exception e) {
+ log.warn "Unable to store condalock for buildId: $buildId - reason: ${e.message}", e
+ }
+ }
+
+ @Override
+ StreamedFile fetchCondaLock(String buildId) {
+ if( !buildId )
+ return null
+ def condaLock = persistenceService.loadCondaLock(buildId)?.condaLockFile
+ if( !condaLock )
+ return null
+ def inputStream = new ByteArrayInputStream(condaLock)
+ return new StreamedFile(inputStream, MediaType.APPLICATION_OCTET_STREAM_TYPE)
+
+ }
+
+ protected static extractCondaLockFile(String logs) {
+ try {
+ return logs.substring(logs.lastIndexOf(CONDA_LOCK_START) + CONDA_LOCK_START.length(), logs.lastIndexOf(CONDA_LOCK_END))
+ .replaceAll(/#\d+ \d+\.\d+\s*/, '')
+ } catch (Exception e) {
+ log.warn "Unable to extract conda lock file from logs - reason: ${e.message}", e
+ return null
+ }
+ }
+
+}

src/main/groovy/io/seqera/wave/service/logs/BuildLogServiceImpl.groovy

@@ -41,6 +41,9 @@ import jakarta.inject.Inject
 import jakarta.inject.Named
 import jakarta.inject.Singleton
 import org.apache.commons.io.input.BoundedInputStream
+import static org.apache.commons.lang3.StringUtils.strip
+import static io.seqera.wave.service.conda.Conda.CONDA_LOCK_END
+import static io.seqera.wave.service.conda.Conda.CONDA_LOCK_START
 /**
  * Implements Service to manage logs from an Object store
  *
@@ -83,7 +86,7 @@ class BuildLogServiceImpl implements BuildLogService {
  return null
  if( !prefix )
  return buildId + '.log'
- final base = org.apache.commons.lang3.StringUtils.strip(prefix, '/')
+ final base = strip(prefix, '/')
  return "${base}/${buildId}.log"
  }
 
@@ -97,6 +100,7 @@ class BuildLogServiceImpl implements BuildLogService {
  @Override
  void storeLog(String buildId, String content){
  try {
+ content = removeCondaLockFile(content)
  log.debug "Storing logs for buildId: $buildId"
  final uploadRequest = UploadRequest.fromBytes(content.getBytes(), logKey(buildId))
  objectStorageOperations.upload(uploadRequest)
@@ -125,4 +129,11 @@ class BuildLogServiceImpl implements BuildLogService {
  final logs = new BoundedInputStream(result.getInputStream(), maxLength).getText()
  return new BuildLog(logs, logs.length()>=maxLength)
  }
+
+ protected static removeCondaLockFile(String logs) {
+ if(logs.indexOf(CONDA_LOCK_START) < 0 ) {
+ return logs
+ }
+ return logs.replaceAll(/(?s)\n?#\d+ \d+\.\d+ $CONDA_LOCK_START.*?$CONDA_LOCK_END\n?/, '\n')
+ }
 }

src/main/groovy/io/seqera/wave/service/persistence/PersistenceService.groovy

@@ -111,6 +111,22 @@ interface PersistenceService {
  */
  WaveScanRecord loadScanRecord(String scanId)
 
+ /**
+ * Store a condaLock for buildId in the underlying persistence layer.
+ *
+ *
+ * @param build A {@link WaveBuildRecord} object
+ */
+ void saveCondaLock(WaveCondaLockRecord condaLock)
+
+ /**
+ * Retrieve a condaLock for the given build id
+ *
+ * @param buildId
+ * @return The corresponding condaLock file as a string
+ */
+ WaveCondaLockRecord loadCondaLock(String buildId)
+
  /**
  * Load a mirror state record
  *

src/main/groovy/io/seqera/wave/service/persistence/WaveCondaLockRecord.groovy

@@ -0,0 +1,43 @@
+/*
+ * Wave, containers provisioning service
+ * Copyright (c) 2024, Seqera Labs
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package io.seqera.wave.service.persistence
+
+import groovy.transform.CompileStatic
+import groovy.transform.EqualsAndHashCode
+import groovy.transform.ToString
+
+/**
+ * Model a Wave conda lock record
+ *
+ * @author Munish Chouhan <[email protected]>
+ */
+@ToString
+@CompileStatic
+@EqualsAndHashCode
+class WaveCondaLockRecord {
+ String buildId
+ byte[] condaLockFile
+
+ WaveCondaLockRecord() {}
+
+ WaveCondaLockRecord(String buildId, byte[] condaLockFile) {
+ this.buildId = buildId
+ this.condaLockFile = condaLockFile
+ }
+}

src/main/groovy/io/seqera/wave/service/persistence/impl/LocalPersistenceService.groovy

@@ -23,6 +23,7 @@ import io.seqera.wave.core.ContainerDigestPair
 import io.seqera.wave.service.mirror.MirrorEntry
 import io.seqera.wave.service.persistence.PersistenceService
 import io.seqera.wave.service.persistence.WaveBuildRecord
+import io.seqera.wave.service.persistence.WaveCondaLockRecord
 import io.seqera.wave.service.persistence.WaveContainerRecord
 import io.seqera.wave.service.persistence.WaveScanRecord
 import jakarta.inject.Singleton
@@ -38,9 +39,12 @@ class LocalPersistenceService implements PersistenceService {
  private Map<String,WaveBuildRecord> buildStore = new HashMap<>()
 
  private Map<String,WaveContainerRecord> requestStore = new HashMap<>()
+
  private Map<String,WaveScanRecord> scanStore = new HashMap<>()
  private Map<String, MirrorEntry> mirrorStore = new HashMap<>()
 
+ private Map<String,WaveCondaLockRecord> condaLockStore = new HashMap<>()
+
  @Override
  void saveBuild(WaveBuildRecord record) {
  buildStore[record.buildId] = record
@@ -98,6 +102,16 @@ class LocalPersistenceService implements PersistenceService {
  scanStore.get(scanId)
  }
 
+ @Override
+ void saveCondaLock(WaveCondaLockRecord condaLock) {
+ condaLockStore.put(condaLock.buildId, condaLock)
+ }
+
+ @Override
+ WaveCondaLockRecord loadCondaLock(String buildId) {
+ return condaLockStore.get(buildId)
+ }
+
  MirrorEntry loadMirrorEntry(String mirrorId) {
  mirrorStore.get(mirrorId)
  }