DataBiosphere / azul

Metadata indexer and query service used for AnVIL, HCA, LungMAP, and CGP
Apache License 2.0
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Update PyCharm base image to bookworm #6575

Open hannes-ucsc opened 3 days ago

hannes-ucsc commented 3 days ago

Most of the new Hs are Linux kernel. The PyCharm image in which most of these occur is based on bullseye which has been superseded by bookworm. When we update to PyCharm 3.12 we should also update to the -slim-bookworm image, from the -slim-bullseye one.

Originally posted by @hannes-ucsc in https://github.com/DataBiosphere/azul/issues/6537#issuecomment-2354397961

achave11-ucsc commented 2 days ago

The following updates are compatible with Azul, this updates the azul-docker-pycharm base image to use bookworm:

Index: .github/workflows/docker-publish.yml
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml
--- a/.github/workflows/docker-publish.yml  (revision e3f0ebc534c36385c058b236d80aa97a56a74ee2)
+++ b/.github/workflows/docker-publish.yml  (date 1726609551020)
@@ -21,7 +21,7 @@
   # value isn't reflected in the tag for this image, you also need to bump the
   # internal version below when changing this variable.
   #
-  azul_docker_pycharm_base_image_tag: bullseye-20240904
+  azul_docker_pycharm_base_image_tag: bookworm-20240904

   # The version of PyCharm to install in this image.
   #
@@ -31,7 +31,7 @@
   # upstream image followed by the value of this variable. Increment this value
   # to update the OS packages installed in the image.
   #
-  azul_docker_pycharm_internal_version: 33
+  azul_docker_pycharm_internal_version: 34

 jobs:
   build:
Tested successfully by running: `azul_docker_registry="" make format` ``` azul_docker_registry="" make format docker run \ --rm \ --volume $(python scripts/resolve_container_path.py /Users/achave11/Pycharm/Azul/azul.sc):/home/developer/azul \ --workdir /home/developer/azul \ $(AZUL_DEBUG=0 python -m azul 'docker.resolve_docker_image_for_launch("pycharm")') \ /opt/pycharm/bin/format.sh -r -settings .pycharm.style.xml -mask '*.py' src scripts test lambdas/layer/app.py lambdas/indexer/app.py lambdas/service/app.py .flake8/azul_flake8.py environment.py deployments/abrahamsc.local/environment.py deployments/achave.local/environment.py deployments/anvilbox/environment.py deployments/anvildev.browser/environment.py deployments/anvildev.gitlab/environment.py deployments/anvildev.shared/environment.py deployments/anvildev/environment.py deployments/anvilprod.browser/environment.py deployments/anvilprod.gitlab/environment.py deployments/anvilprod.shared/environment.py deployments/anvilprod/environment.py deployments/dev.browser/environment.py deployments/dev.gitlab/environment.py deployments/dev.shared/environment.py deployments/dev/environment.py deployments/gitlab.local/environment.py deployments/hammerbox/environment.py deployments/prod.gitlab/environment.py deployments/prod.shared/environment.py deployments/prod/environment.py deployments/sandbox/environment.py deployments/tempdev.browser/environment.py deployments/tempdev.gitlab/environment.py deployments/tempdev.shared/environment.py deployments/tempdev/environment.py .github/workflows/schedule.py terraform/backend.tf.json.template.py terraform/common.tf.json.template.py terraform/step_function.tf.json.template.py terraform/lambda_layer.tf.json.template.py terraform/dynamo.tf.json.template.py terraform/cloudwatch.tf.json.template.py terraform/elasticsearch.tf.json.template.py terraform/api_gateway.tf.json.template.py terraform/providers.tf.json.template.py terraform/authentication.tf.json.template.py terraform/sqs.tf.json.template.py terraform/s3.tf.json.template.py terraform/gitlab/gitlab.tf.json.template.py terraform/shared/shared.tf.json.template.py terraform/browser/browser.tf.json.template.py lambdas/indexer/.chalice/config.json.template.py lambdas/service/.chalice/config.json.template.py .github/pull_request_template.md.template.py envhook.py: Warning: azul_docker_registry is '' but should be '122796619775.dkr.ecr.us-east-1.amazonaws.com/', you must run `source environment` envhook.py: Warning: AZUL_DEBUG is '0' but should be '1', you must run `source environment` envhook.py: Warning: azul_docker_registry is '' but should be '122796619775.dkr.ecr.us-east-1.amazonaws.com/', you must run `source environment` 2024-09-17 15:01:52,099 INFO MainThread azul.docker: Resolving 'pycharm' image TagImageRef(registry='localhost:5000', username='docker.io', repository=('ucscgi', 'azul-pycharm'), tag='2024.2.1-34') … 2024-09-17 15:01:52,100 INFO MainThread azul.docker: Resolved 'pycharm' image to DigestImageRef(registry='localhost:5000', username='docker.io', repository=('ucscgi', 'azul-pycharm'), digest='sha256:e31a93d76cddfcc147ffc8c3954660e02cbc2c3b8798490d0017dacd2f27c8f2') 2024-09-17 15:01:52,100 INFO MainThread azul.docker: Pulling image DigestImageRef(registry='localhost:5000', username='docker.io', repository=('ucscgi', 'azul-pycharm'), digest='sha256:e31a93d76cddfcc147ffc8c3954660e02cbc2c3b8798490d0017dacd2f27c8f2') … 2024-09-17 15:01:52,154 INFO MainThread azul.docker: Pulled image DigestImageRef(registry='localhost:5000', username='docker.io', repository=('ucscgi', 'azul-pycharm'), digest='sha256:e31a93d76cddfcc147ffc8c3954660e02cbc2c3b8798490d0017dacd2f27c8f2') Sep 17, 2024 10:01:52 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. PyCharm 2024.2.1, build PC-242.21829.153 Formatter 2024-09-17 22:01:53,118 [ 535] SEVERE - #c.i.o.f.i.FileTypeManagerImpl - org.jetbrains.plugins.textmate.TextMateFileType PluginClassLoader(plugin=PluginDescriptor(name=TextMate Bundles, id=org.jetbrains.plugins.textmate, descriptorPath=plugin.xml, path=/opt/pycharm/plugins/textmate, version=242.21829.153, package=null, isBundled=true), packagePrefix=null, state=active, parents=, ) java.lang.ClassNotFoundException: org.jetbrains.plugins.textmate.TextMateFileType PluginClassLoader(plugin=PluginDescriptor(name=TextMate Bundles, id=org.jetbrains.plugins.textmate, descriptorPath=plugin.xml, path=/opt/pycharm/plugins/textmate, version=242.21829.153, package=null, isBundled=true), packagePrefix=null, state=active, parents=, ) at com.intellij.serviceContainer.ComponentManagerImplKt.doLoadClass(ComponentManagerImpl.kt:1464) at com.intellij.serviceContainer.ComponentManagerImplKt.doLoadClass$default(ComponentManagerImpl.kt:1460) at com.intellij.serviceContainer.ComponentManagerImpl.loadClass(ComponentManagerImpl.kt:887) at com.intellij.openapi.fileTypes.impl.FileTypeManagerImpl.instantiateFileTypeBean(FileTypeManagerImpl.java:519) at com.intellij.openapi.fileTypes.impl.FileTypeManagerImpl.mergeOrInstantiateFileTypeBean(FileTypeManagerImpl.java:483) at com.intellij.openapi.fileTypes.impl.FileTypeManagerImpl.instantiatePendingFileTypes(FileTypeManagerImpl.java:476) at com.intellij.openapi.fileTypes.impl.FileTypeManagerImpl.initializeComponent(FileTypeManagerImpl.java:653) at com.intellij.configurationStore.ComponentStoreImpl.initComponent(ComponentStoreImpl.kt:172) at com.intellij.configurationStore.ComponentStoreWithExtraComponents.initComponent(ComponentStoreWithExtraComponents.kt:46) at com.intellij.serviceContainer.ComponentManagerImpl.initializeService$intellij_platform_serviceContainer(ComponentManagerImpl.kt:651) at com.intellij.serviceContainer.ServiceInstanceInitializer.createInstance$suspendImpl(ServiceInstanceInitializer.kt:70) at com.intellij.serviceContainer.ServiceInstanceInitializer.createInstance(ServiceInstanceInitializer.kt) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder$initialize$1$1.invokeSuspend(LazyInstanceHolder.kt:162) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder$initialize$1$1.invoke(LazyInstanceHolder.kt) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder$initialize$1$1.invoke(LazyInstanceHolder.kt) at kotlinx.coroutines.intrinsics.UndispatchedKt.startUndispatchedOrReturn(Undispatched.kt:62) at kotlinx.coroutines.BuildersKt__Builders_commonKt.withContext(Builders.common.kt:163) at kotlinx.coroutines.BuildersKt.withContext(Unknown Source) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder$initialize$1.invokeSuspend(LazyInstanceHolder.kt:160) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder$initialize$1.invoke(LazyInstanceHolder.kt) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder$initialize$1.invoke(LazyInstanceHolder.kt) at kotlinx.coroutines.intrinsics.UndispatchedKt.startCoroutineUndispatched(Undispatched.kt:27) at kotlinx.coroutines.CoroutineStart.invoke(CoroutineStart.kt:90) at kotlinx.coroutines.AbstractCoroutine.start(AbstractCoroutine.kt:123) at kotlinx.coroutines.BuildersKt__Builders_commonKt.launch(Builders.common.kt:52) at kotlinx.coroutines.BuildersKt.launch(Unknown Source) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder.initialize(LazyInstanceHolder.kt:145) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder.access$initialize(LazyInstanceHolder.kt:13) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder.tryInitialize(LazyInstanceHolder.kt:135) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder.getInstance(LazyInstanceHolder.kt:95) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder.getInstance$suspendImpl(LazyInstanceHolder.kt:83) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder.getInstance(LazyInstanceHolder.kt) at com.intellij.platform.instanceContainer.internal.InstanceContainerImpl.instance(InstanceContainerImpl.kt:68) at com.intellij.serviceContainer.ComponentManagerImpl.getServiceAsync(ComponentManagerImpl.kt:694) at com.intellij.platform.ide.bootstrap.AppServicePreloadingKt$postAppRegistered$1$fileTypeManagerJob$1.invokeSuspend(appServicePreloading.kt:145) at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33) at kotlinx.coroutines.DispatchedTask.run(DispatchedTask.kt:104) at kotlinx.coroutines.scheduling.CoroutineScheduler.runSafely(CoroutineScheduler.kt:608) at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.executeTask(CoroutineScheduler.kt:873) at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.runWorker(CoroutineScheduler.kt:763) at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.run(CoroutineScheduler.kt:750) 2024-09-17 22:01:53,122 [ 539] SEVERE - #c.i.o.f.i.FileTypeManagerImpl - PyCharm 2024.2.1 Build #PC-242.21829.153 2024-09-17 22:01:53,122 [ 539] SEVERE - #c.i.o.f.i.FileTypeManagerImpl - JDK: 21.0.3; VM: OpenJDK 64-Bit Server VM; Vendor: JetBrains s.r.o. 2024-09-17 22:01:53,122 [ 539] SEVERE - #c.i.o.f.i.FileTypeManagerImpl - OS: Linux 2024-09-17 22:01:53,123 [ 540] SEVERE - #c.i.o.f.i.FileTypeManagerImpl - Last Action: 2024-09-17 22:01:53,437 [ 854] WARN - #c.i.s.ComponentManagerImpl - `preload=TRUE` must be used only for core services (service=com.intellij.cwm.plugin.users.BackendUserManager, plugin=com.jetbrains.codeWithMe) 2024-09-17 22:01:53,437 [ 854] WARN - #c.i.s.ComponentManagerImpl - `preload=TRUE` must be used only for core services (service=com.intellij.cwm.plugin.ports.CwmPortForwardingToolWindowManager, plugin=com.jetbrains.codeWithMe) 2024-09-17 22:01:53,437 [ 854] WARN - #c.i.s.ComponentManagerImpl - `preload=TRUE` must be used only for core services (service=com.intellij.cwm.plugin.users.BackendCWMUserFocusHost, plugin=com.jetbrains.codeWithMe) 2024-09-17 22:01:53,437 [ 854] WARN - #c.i.s.ComponentManagerImpl - `preload=TRUE` must be used only for core services (service=com.intellij.cwm.plugin.following.FollowMeManagerService, plugin=com.jetbrains.codeWithMe) 2024-09-17 22:01:53,437 [ 854] WARN - #c.i.s.ComponentManagerImpl - `preload=TRUE` must be used only for core services (service=com.intellij.cwm.plugin.following.BackendProjectViewSync, plugin=com.jetbrains.codeWithMe) 2024-09-17 22:01:53,437 [ 854] WARN - #c.i.s.ComponentManagerImpl - `preload=TRUE` must be used only for core services (service=com.intellij.cwm.plugin.following.BackendFollowMeEditorsHost, plugin=com.jetbrains.codeWithMe) 2024-09-17 22:01:53,437 [ 854] WARN - #c.i.s.ComponentManagerImpl - `preload=TRUE` must be used only for core services (service=com.intellij.cwm.plugin.following.BackendFollowMeDebuggerHost, plugin=com.jetbrains.codeWithMe) 2024-09-17 22:01:53,437 [ 854] WARN - #c.i.s.ComponentManagerImpl - `preload=TRUE` must be used only for core services (service=com.intellij.cwm.plugin.following.FollowMeLookupSynchronizer, plugin=com.jetbrains.codeWithMe) 2024-09-17 22:01:53,627 [ 1044] SEVERE - #c.i.o.f.i.FileTypeManagerImpl - org.jetbrains.plugins.textmate.TextMateFileType PluginClassLoader(plugin=PluginDescriptor(name=TextMate Bundles, id=org.jetbrains.plugins.textmate, descriptorPath=plugin.xml, path=/opt/pycharm/plugins/textmate, version=242.21829.153, package=null, isBundled=true), packagePrefix=null, state=active, parents=, ) java.lang.ClassNotFoundException: org.jetbrains.plugins.textmate.TextMateFileType PluginClassLoader(plugin=PluginDescriptor(name=TextMate Bundles, id=org.jetbrains.plugins.textmate, descriptorPath=plugin.xml, path=/opt/pycharm/plugins/textmate, version=242.21829.153, package=null, isBundled=true), packagePrefix=null, state=active, parents=, ) at com.intellij.serviceContainer.ComponentManagerImplKt.doLoadClass(ComponentManagerImpl.kt:1464) at com.intellij.serviceContainer.ComponentManagerImplKt.doLoadClass$default(ComponentManagerImpl.kt:1460) at com.intellij.serviceContainer.ComponentManagerImpl.loadClass(ComponentManagerImpl.kt:887) at com.intellij.openapi.fileTypes.impl.FileTypeManagerImpl.instantiateFileTypeBean(FileTypeManagerImpl.java:519) at com.intellij.openapi.fileTypes.impl.FileTypeManagerImpl.mergeOrInstantiateFileTypeBean(FileTypeManagerImpl.java:483) at com.intellij.openapi.fileTypes.impl.FileTypeManagerImpl.instantiatePendingFileTypes(FileTypeManagerImpl.java:476) at com.intellij.openapi.fileTypes.impl.FileTypeManagerImpl.getRegisteredFileTypes(FileTypeManagerImpl.java:1026) at com.intellij.util.indexing.IndexInfrastructureVersionBase.getAllStubFileElementTypes(IndexInfrastructureVersionBase.java:171) at com.intellij.util.indexing.IndexInfrastructureVersionBase.stubFileElementTypeVersions(IndexInfrastructureVersionBase.java:152) at com.intellij.indexing.shared.platform.api.IdeSharedIndexesState.getIndexVersion(IdeSharedIndexesState.java:68) at com.intellij.indexing.shared.platform.api.SharedIndexInfrastructureVersion.getIdeVersion(SharedIndexInfrastructureVersion.java:68) at com.intellij.indexing.shared.platform.impl.SharedIndexStorageUtil.openFileBasedIndexChunks(SharedIndexStorageUtil.java:54) at com.intellij.indexing.shared.platform.impl.SharedIndexChunkConfigurationImpl.openFileBasedIndexChunk(SharedIndexChunkConfigurationImpl.java:657) at com.intellij.indexing.shared.platform.impl.SharedIndexChunkConfigurationImpl.registerChunk(SharedIndexChunkConfigurationImpl.java:618) at com.intellij.indexing.shared.platform.impl.SharedIndexChunkConfigurationImpl.openChunkForProject(SharedIndexChunkConfigurationImpl.java:484) at com.intellij.indexing.shared.platform.impl.SharedIndexChunkConfigurationImpl.attachExistingChunk(SharedIndexChunkConfigurationImpl.java:456) at com.intellij.indexing.shared.platform.impl.BundledSharedIndexPostStartupActivity$execute$2.invoke(SharedIndexZipBundledStorage.kt:184) at com.intellij.indexing.shared.platform.impl.BundledSharedIndexPostStartupActivity$execute$2.invoke(SharedIndexZipBundledStorage.kt:182) at com.intellij.openapi.progress.CoroutinesKt.blockingContextInner(coroutines.kt:339) at com.intellij.openapi.progress.CoroutinesKt$blockingContext$2.invokeSuspend(coroutines.kt:232) at com.intellij.openapi.progress.CoroutinesKt$blockingContext$2.invoke(coroutines.kt) at com.intellij.openapi.progress.CoroutinesKt$blockingContext$2.invoke(coroutines.kt) at kotlinx.coroutines.intrinsics.UndispatchedKt.startUndispatchedOrReturn(Undispatched.kt:62) at kotlinx.coroutines.CoroutineScopeKt.coroutineScope(CoroutineScope.kt:261) at com.intellij.openapi.progress.CoroutinesKt.blockingContext(coroutines.kt:231) at com.intellij.indexing.shared.platform.impl.BundledSharedIndexPostStartupActivity.execute(SharedIndexZipBundledStorage.kt:182) at com.intellij.ide.startup.impl.StartupManagerImplKt$launchActivity$1.invokeSuspend(StartupManagerImpl.kt:496) at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33) at kotlinx.coroutines.DispatchedTask.run(DispatchedTask.kt:104) at kotlinx.coroutines.scheduling.CoroutineScheduler.runSafely(CoroutineScheduler.kt:608) at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.executeTask(CoroutineScheduler.kt:873) at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.runWorker(CoroutineScheduler.kt:763) at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.run(CoroutineScheduler.kt:750) 2024-09-17 22:01:53,628 [ 1045] SEVERE - #c.i.o.f.i.FileTypeManagerImpl - PyCharm 2024.2.1 Build #PC-242.21829.153 2024-09-17 22:01:53,628 [ 1045] SEVERE - #c.i.o.f.i.FileTypeManagerImpl - JDK: 21.0.3; VM: OpenJDK 64-Bit Server VM; Vendor: JetBrains s.r.o. 2024-09-17 22:01:53,628 [ 1045] SEVERE - #c.i.o.f.i.FileTypeManagerImpl - OS: Linux 2024-09-17 22:01:53,629 [ 1046] SEVERE - #c.i.o.f.i.FileTypeManagerImpl - Last Action: Formatting /home/developer/azul/src/humancellatlas/data/metadata/lookup.py...OK Formatting /home/developer/azul/src/humancellatlas/data/metadata/api.py...OK Formatting /home/developer/azul/src/humancellatlas/data/metadata/age_range.py...OK Formatting /home/developer/azul/src/humancellatlas/data/metadata/datetime.py...OK Formatting /home/developer/azul/src/humancellatlas/data/metadata/helpers/staging_area.py...OK Formatting /home/developer/azul/src/humancellatlas/data/metadata/helpers/json.py...OK Formatting /home/developer/azul/src/humancellatlas/data/metadata/helpers/schema_validation.py...OK Formatting /home/developer/azul/src/azul/doctests.py...OK Formatting /home/developer/azul/src/azul/uuids.py...OK Formatting /home/developer/azul/src/azul/auth.py...OK Formatting /home/developer/azul/src/azul/time.py...OK Formatting /home/developer/azul/src/azul/azulclient.py...OK Formatting /home/developer/azul/src/azul/logging.py...OK Formatting /home/developer/azul/src/azul/files.py...OK Formatting /home/developer/azul/src/azul/enums.py...OK Formatting /home/developer/azul/src/azul/queues.py...OK Formatting /home/developer/azul/src/azul/terraform.py...OK Formatting /home/developer/azul/src/azul/deployment.py...OK Formatting /home/developer/azul/src/azul/oauth2.py...OK Formatting /home/developer/azul/src/azul/plugins/repository/tdr_anvil/__init__.py...OK Formatting /home/developer/azul/src/azul/plugins/repository/tdr_hca/__init__.py...OK Formatting /home/developer/azul/src/azul/plugins/repository/canned/__init__.py...OK Formatting /home/developer/azul/src/azul/plugins/repository/__init__.py...OK Formatting /home/developer/azul/src/azul/plugins/repository/dss/__init__.py...OK Formatting /home/developer/azul/src/azul/plugins/repository/tdr.py...OK Formatting /home/developer/azul/src/azul/plugins/__init__.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/hca/bundle.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/hca/__init__.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/hca/service/aggregation.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/hca/service/__init__.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/hca/service/response.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/hca/service/contributor_matrices.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/hca/service/filter.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/hca/indexer/aggregate.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/hca/indexer/__init__.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/hca/indexer/transform.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/__init__.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/anvil/bundle.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/anvil/__init__.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/anvil/service/aggregation.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/anvil/service/__init__.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/anvil/service/response.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/anvil/service/filter.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/anvil/indexer/aggregate.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/anvil/indexer/__init__.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/anvil/indexer/transform.py...OK Formatting /home/developer/azul/src/azul/plugins/metadata/anvil/schema.py...OK Formatting /home/developer/azul/src/azul/health.py...OK Formatting /home/developer/azul/src/azul/bigquery.py...OK Formatting /home/developer/azul/src/azul/__init__.py...OK Formatting /home/developer/azul/src/azul/types.py...OK Formatting /home/developer/azul/src/azul/lambda_layer.py...OK Formatting /home/developer/azul/src/azul/openapi/params.py...OK Formatting /home/developer/azul/src/azul/openapi/responses.py...OK Formatting /home/developer/azul/src/azul/openapi/__init__.py...OK Formatting /home/developer/azul/src/azul/openapi/spec.py...OK Formatting /home/developer/azul/src/azul/openapi/schema.py...OK Formatting /home/developer/azul/src/azul/compliance/fedramp_inventory_service.py...OK Formatting /home/developer/azul/src/azul/compliance/__init__.py...OK Formatting /home/developer/azul/src/azul/docker.py...OK Formatting /home/developer/azul/src/azul/terra.py...OK Formatting /home/developer/azul/src/azul/threads.py...OK Formatting /home/developer/azul/src/azul/changelog.py...OK Formatting /home/developer/azul/src/azul/caching.py...OK Formatting /home/developer/azul/src/azul/collections.py...OK Formatting /home/developer/azul/src/azul/http.py...OK Formatting /home/developer/azul/src/azul/chalice.py...OK Formatting /home/developer/azul/src/azul/iterators.py...OK Formatting /home/developer/azul/src/azul/es.py...OK Formatting /home/developer/azul/src/azul/template.py...OK Formatting /home/developer/azul/src/azul/args.py...OK Formatting /home/developer/azul/src/azul/vendored/frozendict/__init__.py...OK Formatting 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/home/developer/azul/deployments/tempdev.browser/environment.py...OK Formatting /home/developer/azul/deployments/tempdev.gitlab/environment.py...OK Formatting /home/developer/azul/deployments/tempdev.shared/environment.py...OK Formatting /home/developer/azul/deployments/tempdev/environment.py...OK Formatting /home/developer/azul/.github/workflows/schedule.py...OK Formatting /home/developer/azul/terraform/backend.tf.json.template.py...OK Formatting /home/developer/azul/terraform/common.tf.json.template.py...OK Formatting /home/developer/azul/terraform/step_function.tf.json.template.py...OK Formatting /home/developer/azul/terraform/lambda_layer.tf.json.template.py...OK Formatting /home/developer/azul/terraform/dynamo.tf.json.template.py...OK Formatting /home/developer/azul/terraform/cloudwatch.tf.json.template.py...OK Formatting /home/developer/azul/terraform/elasticsearch.tf.json.template.py...OK Formatting /home/developer/azul/terraform/api_gateway.tf.json.template.py...OK Formatting /home/developer/azul/terraform/providers.tf.json.template.py...OK Formatting /home/developer/azul/terraform/authentication.tf.json.template.py...OK Formatting /home/developer/azul/terraform/sqs.tf.json.template.py...OK Formatting /home/developer/azul/terraform/s3.tf.json.template.py...OK Formatting /home/developer/azul/terraform/gitlab/gitlab.tf.json.template.py...OK Formatting /home/developer/azul/terraform/shared/shared.tf.json.template.py...OK Formatting /home/developer/azul/terraform/browser/browser.tf.json.template.py...OK Formatting /home/developer/azul/lambdas/indexer/.chalice/config.json.template.py...OK Formatting /home/developer/azul/lambdas/service/.chalice/config.json.template.py...OK Formatting /home/developer/azul/.github/pull_request_template.md.template.py...OK 254 file(s) scanned. 254 file(s) formatted. 2024-09-17 22:02:00,003 [ 7420] WARN - #c.i.n.i.NotificationGroupManagerImpl - Cannot create notification group: NotificationGroupEP{id='TextMate Bundles', displayType=BALLOON, isLogByDefault=true, toolWindowId='null', bundle='messages.TextMateBundle', key='notification.group.textmate.bundles', notificationIds='null', pluginDescriptor=PluginDescriptor(name=TextMate Bundles, id=org.jetbrains.plugins.textmate, descriptorPath=plugin.xml, path=/opt/pycharm/plugins/textmate, version=242.21829.153, package=null, isBundled=true)} java.util.MissingResourceException: Can't find bundle for base name messages.TextMateBundle, locale en_US at java.base/java.util.ResourceBundle.throwMissingResourceException(ResourceBundle.java:2059) at java.base/java.util.ResourceBundle.getBundleImpl(ResourceBundle.java:1697) at java.base/java.util.ResourceBundle.getBundleImpl(ResourceBundle.java:1600) at java.base/java.util.ResourceBundle.getBundle(ResourceBundle.java:1283) at com.intellij.AbstractBundle$Companion.resolveResourceBundleWithFallback(AbstractBundle.kt:85) at com.intellij.DynamicBundle.resolveResourceBundle(DynamicBundle.java:308) at com.intellij.DynamicBundle.lambda$getResourceBundle$4(DynamicBundle.java:277) at java.base/java.util.concurrent.ConcurrentMap.computeIfAbsent(ConcurrentMap.java:330) at com.intellij.DynamicBundle.getResourceBundle(DynamicBundle.java:277) at com.intellij.notification.impl.NotificationGroupEP.getDisplayName(NotificationGroupEP.java:117) at com.intellij.notification.impl.NotificationGroupManagerImplKt.registerNotificationGroup(NotificationGroupManagerImpl.kt:82) at com.intellij.notification.impl.NotificationGroupManagerImplKt.access$registerNotificationGroup(NotificationGroupManagerImpl.kt:1) at com.intellij.notification.impl.NotificationGroupManagerImplKt$computeGroups$1.invoke(NotificationGroupManagerImpl.kt:61) at com.intellij.notification.impl.NotificationGroupManagerImplKt$computeGroups$1.invoke(NotificationGroupManagerImpl.kt:60) at com.intellij.openapi.extensions.impl.ExtensionPointImpl.processWithPluginDescriptor(ExtensionPointImpl.kt:1086) at com.intellij.openapi.extensions.ExtensionPointName.processWithPluginDescriptor(ExtensionPointName.kt:143) at com.intellij.notification.impl.NotificationGroupManagerImplKt.computeGroups(NotificationGroupManagerImpl.kt:60) at com.intellij.notification.impl.NotificationGroupManagerImplKt.access$computeGroups(NotificationGroupManagerImpl.kt:1) at com.intellij.notification.impl.NotificationGroupManagerImpl.(NotificationGroupManagerImpl.kt:16) at com.intellij.platform.instanceContainer.instantiation.InstantiateKt$instantiate$2.invoke(instantiate.kt:45) at com.intellij.platform.instanceContainer.instantiation.InstantiateKt$instantiate$2.invoke(instantiate.kt:42) at com.intellij.platform.instanceContainer.instantiation.InstantiateKt.instantiate(instantiate.kt:313) at com.intellij.platform.instanceContainer.instantiation.InstantiateKt.instantiate(instantiate.kt:42) at com.intellij.serviceContainer.ServiceInstanceInitializer.createInstance$suspendImpl(ServiceInstanceInitializer.kt:31) at com.intellij.serviceContainer.ServiceInstanceInitializer.createInstance(ServiceInstanceInitializer.kt) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder$initialize$1$1.invokeSuspend(LazyInstanceHolder.kt:162) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder$initialize$1$1.invoke(LazyInstanceHolder.kt) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder$initialize$1$1.invoke(LazyInstanceHolder.kt) at kotlinx.coroutines.intrinsics.UndispatchedKt.startUndispatchedOrReturn(Undispatched.kt:62) at kotlinx.coroutines.BuildersKt__Builders_commonKt.withContext(Builders.common.kt:163) at kotlinx.coroutines.BuildersKt.withContext(Unknown Source) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder$initialize$1.invokeSuspend(LazyInstanceHolder.kt:160) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder$initialize$1.invoke(LazyInstanceHolder.kt) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder$initialize$1.invoke(LazyInstanceHolder.kt) at kotlinx.coroutines.intrinsics.UndispatchedKt.startCoroutineUndispatched(Undispatched.kt:27) at kotlinx.coroutines.CoroutineStart.invoke(CoroutineStart.kt:90) at kotlinx.coroutines.AbstractCoroutine.start(AbstractCoroutine.kt:123) at kotlinx.coroutines.BuildersKt__Builders_commonKt.launch(Builders.common.kt:52) at kotlinx.coroutines.BuildersKt.launch(Unknown Source) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder.initialize(LazyInstanceHolder.kt:145) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder.access$initialize(LazyInstanceHolder.kt:13) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder.tryInitialize(LazyInstanceHolder.kt:135) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder.getInstance(LazyInstanceHolder.kt:95) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder.getInstanceInCallerContext$suspendImpl(LazyInstanceHolder.kt:87) at com.intellij.platform.instanceContainer.internal.LazyInstanceHolder.getInstanceInCallerContext(LazyInstanceHolder.kt) at com.intellij.serviceContainer.ComponentManagerImplKt$doGetOrCreateInstanceBlocking$1.invokeSuspend(ComponentManagerImpl.kt:1568) at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33) at kotlinx.coroutines.DispatchedTask.run(DispatchedTask.kt:104) at kotlinx.coroutines.EventLoopImplBase.processNextEvent(EventLoop.common.kt:277) at kotlinx.coroutines.BlockingCoroutine.joinBlocking(Builders.kt:111) at kotlinx.coroutines.BuildersKt__BuildersKt.runBlocking$BuildersKt__BuildersKt(Builders.kt:84) at kotlinx.coroutines.BuildersKt__BuildersKt.runBlocking(Builders.kt:52) at kotlinx.coroutines.BuildersKt.runBlocking(Unknown Source) at com.intellij.serviceContainer.ComponentManagerImplKt$runBlockingInitialization$1.invoke(ComponentManagerImpl.kt:1686) at com.intellij.serviceContainer.ComponentManagerImplKt$runBlockingInitialization$1.invoke(ComponentManagerImpl.kt:1677) at com.intellij.openapi.progress.ContextKt.prepareThreadContext(context.kt:85) at com.intellij.serviceContainer.ComponentManagerImplKt.runBlockingInitialization(ComponentManagerImpl.kt:1677) at com.intellij.serviceContainer.ComponentManagerImplKt.doGetOrCreateInstanceBlocking(ComponentManagerImpl.kt:1567) at com.intellij.serviceContainer.ComponentManagerImplKt.getOrCreateInstanceBlocking(ComponentManagerImpl.kt:1562) at com.intellij.serviceContainer.ComponentManagerImpl.doGetService(ComponentManagerImpl.kt:746) at com.intellij.serviceContainer.ComponentManagerImpl.getService(ComponentManagerImpl.kt:690) at com.intellij.notification.NotificationGroupManager.getInstance(NotificationGroupManager.java:19) at com.intellij.platform.execution.dashboard.RunDashboardCheckerActivity$RunDashboardListener.createNotification(RunDashboardCheckerActivity.kt:119) at com.intellij.platform.execution.dashboard.RunDashboardCheckerActivity$RunDashboardListener.isEnabled(RunDashboardCheckerActivity.kt:69) at com.intellij.platform.execution.dashboard.RunDashboardCheckerActivity.execute(RunDashboardCheckerActivity.kt:43) at com.intellij.ide.startup.impl.StartupManagerImplKt$launchActivity$1.invokeSuspend(StartupManagerImpl.kt:496) at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33) at kotlinx.coroutines.DispatchedTask.run(DispatchedTask.kt:104) at kotlinx.coroutines.scheduling.CoroutineScheduler.runSafely(CoroutineScheduler.kt:608) at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.executeTask(CoroutineScheduler.kt:873) at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.runWorker(CoroutineScheduler.kt:763) at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.run(CoroutineScheduler.kt:750) 2024-09-17 22:02:00,341 [ 7758] SEVERE - #c.i.o.v.n.RefreshQueue - null org.jetbrains.concurrency.AsyncPromise$Companion$CANCELED$1 2024-09-17 22:02:00,341 [ 7758] SEVERE - #c.i.o.v.n.RefreshQueue - PyCharm 2024.2.1 Build #PC-242.21829.153 2024-09-17 22:02:00,341 [ 7758] SEVERE - #c.i.o.v.n.RefreshQueue - JDK: 21.0.3; VM: OpenJDK 64-Bit Server VM; Vendor: JetBrains s.r.o. 2024-09-17 22:02:00,341 [ 7758] SEVERE - #c.i.o.v.n.RefreshQueue - OS: Linux ```
Initially, the command return a non-zero exit status while still succeeding in formating the files. Then it ran successfully with warnings (as in the details above). ``` Formatting /home/developer/azul/lambdas/service/.chalice/config.json.template.py...OK Formatting /home/developer/azul/.github/pull_request_template.md.template.py...OK 254 file(s) scanned. 254 file(s) formatted. **Start Failed** Internal error java.lang.RuntimeException: Cannot write /tmp/PyCharmCore.format.75c34d84-b8c2-41d7-bd66-4514688e1b82.tmp/.idea/.idea/workspace.xml at com.intellij.configurationStore.FileBasedStorageKt.writeFile(FileBasedStorage.kt:348) at com.intellij.configurationStore.FileBasedStorage$FileSaveSessionProducer.saveLocally(FileBasedStorage.kt:117) at com.intellij.configurationStore.XmlElementStorage$XmlElementStorageSaveSessionProducer$XmlSaveSession.doSave(XmlElementStorage.kt:282) at com.intellij.configurationStore.XmlElementStorage$XmlElementStorageSaveSessionProducer$XmlSaveSession.access$doSave(XmlElementStorage.kt:253) at com.intellij.configurationStore.XmlElementStorage$XmlElementStorageSaveSessionProducer$XmlSaveSession$save$2.invoke(XmlElementStorage.kt:258) at com.intellij.configurationStore.XmlElementStorage$XmlElementStorageSaveSessionProducer$XmlSaveSession$save$2.invoke(XmlElementStorage.kt:258) at com.intellij.openapi.progress.CoroutinesKt.blockingContextInner(coroutines.kt:339) at com.intellij.openapi.progress.CoroutinesKt$blockingContext$2.invokeSuspend(coroutines.kt:232) at com.intellij.openapi.progress.CoroutinesKt$blockingContext$2.invoke(coroutines.kt) at com.intellij.openapi.progress.CoroutinesKt$blockingContext$2.invoke(coroutines.kt) at kotlinx.coroutines.intrinsics.UndispatchedKt.startUndispatchedOrReturn(Undispatched.kt:62) at kotlinx.coroutines.CoroutineScopeKt.coroutineScope(CoroutineScope.kt:261) at com.intellij.openapi.progress.CoroutinesKt.blockingContext(coroutines.kt:231) at com.intellij.configurationStore.XmlElementStorage$XmlElementStorageSaveSessionProducer$XmlSaveSession.save(XmlElementStorage.kt:258) at com.intellij.configurationStore.SaveSessionProducerManager.saveSessions(SaveSessionProducerManager.kt:70) at com.intellij.configurationStore.ProjectSaveSessionProducerManager.saveAndValidate(ProjectSaveSessionProducerManager.kt:15) at com.intellij.configurationStore.ProjectStoreImpl$doSave$2$1.invokeSuspend(ProjectStoreImpl.kt:376) at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33) at kotlinx.coroutines.DispatchedTask.run(DispatchedTask.kt:104) at kotlinx.coroutines.scheduling.CoroutineScheduler.runSafely(CoroutineScheduler.kt:608) at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.executeTask(CoroutineScheduler.kt:873) at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.runWorker(CoroutineScheduler.kt:763) at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.run(CoroutineScheduler.kt:750) Caused by: java.nio.file.FileSystemException: /tmp/PyCharmCore.format.75c34d84-b8c2-41d7-bd66-4514688e1b82.tmp/.idea/.idea: No space left on device at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100) at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106) at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111) at java.base/sun.nio.fs.UnixFileSystemProvider.createDirectory(UnixFileSystemProvider.java:438) at java.base/java.nio.file.Files.createDirectory(Files.java:699) at com.intellij.openapi.util.io.NioFiles.tryCreateDirectory(NioFiles.java:96) at com.intellij.openapi.util.io.NioFiles.createDirectories(NioFiles.java:89) at com.intellij.openapi.util.io.NioFiles.createParentDirectories(NioFiles.java:111) at com.intellij.util.io.PathKt.createParentDirectories(path.kt:27) at com.intellij.util.io.PathKt.safeOutputStream(path.kt:41) at com.intellij.configurationStore.DataWriter.writeTo(DataWriter.kt:24) at com.intellij.configurationStore.FileBasedStorageKt.writeFile(FileBasedStorage.kt:342) ... 22 more ----- JRE: 21.0.3+13-b509.11 aarch64 (JetBrains s.r.o.) /opt/pycharm/jbr 2024-09-17 21:58:23,708 [ 7877] WARN - java.util.prefs - Couldn't flush user prefs: java.util.prefs.BackingStoreException: /home/developer/.java/.userPrefs/jetbrains create failed. make: *** [format] Error 3 ```
❯ docker scout quickview localhost:5000/docker.io/ucscgi/azul-pycharm:2024.2.1-34
    i New version 1.13.0 available (installed version is 1.11.0) at https://github.com/docker/scout-cli
    ✓ Image stored for indexing
    ✓ Indexed 380 packages
    ✓ Provenance obtained from attestation

  Target             │  localhost:5000/docker.io/ucscgi/azul-pycharm:2024.2.1-34  │    3C     0H     1M    67L   
    digest           │  0c9f88af5dcc                                              │                              
  Base image         │  debian:bookworm-20240904                                  │    0C     0H     0M    23L   
  Updated base image │  debian:stable-20240904-slim                               │    0C     0H     0M    23L   
                     │                                                            │                              

What's next:
    View vulnerabilities → docker scout cves localhost:5000/docker.io/ucscgi/azul-pycharm:2024.2.1-34
    View base image update recommendations → docker scout recommendations localhost:5000/docker.io/ucscgi/azul-pycharm:2024.2.1-34
    Include policy results in your quickview by supplying an organization → docker scout quickview localhost:5000/docker.io/ucscgi/azul-pycharm:2024.2.1-34 --org <organization>