There was no fonts in Linux version

From @JamesMung on October 23, 2018 3:54
JDK Version ; jdk8u181-b13
When I use jasper print PDF in Windows is fine, but for Linux found the error as follow:
Caused by: net.sf.jasperreports.engine.JRRuntimeException: java.io.IOException: Problem reading font data.
        at net.sf.jasperreports.engine.fonts.SimpleFontFace.<init>(SimpleFontFace.java:108)
        at net.sf.jasperreports.engine.fonts.SimpleFontFace.<init>(SimpleFontFace.java:128)
        at net.sf.jasperreports.engine.fonts.SimpleFontFace.getInstance(SimpleFontFace.java:67)
        at net.sf.jasperreports.engine.fonts.SimpleFontFamily.setNormal(SimpleFontFamily.java:99)
        at net.sf.jasperreports.engine.fonts.SimpleFontExtensionHelper.parseFontFamily(SimpleFontExtensionHelper.java:261)
        at net.sf.jasperreports.engine.fonts.SimpleFontExtensionHelper.parseFontFamilies(SimpleFontExtensionHelper.java:232)
        at net.sf.jasperreports.engine.fonts.SimpleFontExtensionHelper.loadFontFamilies(SimpleFontExtensionHelper.java:193)
        at net.sf.jasperreports.engine.fonts.SimpleFontExtensionHelper.loadFontFamilies(SimpleFontExtensionHelper.java:162)
        at net.sf.jasperreports.engine.fonts.FontExtensionsRegistry.getExtensions(FontExtensionsRegistry.java:56)
        at net.sf.jasperreports.extensions.DefaultExtensionsRegistry.getExtensions(DefaultExtensionsRegistry.java:110)
        at net.sf.jasperreports.engine.util.JRStyledTextParser.<clinit>(JRStyledTextParser.java:83)
        ... 73 more
Caused by: java.io.IOException: Problem reading font data.
        at java.awt.Font.createFont0(Font.java:1000)
        at java.awt.Font.createFont(Font.java:877)
        at net.sf.jasperreports.engine.fonts.SimpleFontFace.<init>(SimpleFontFace.java:100)
        ... 83 more

Can you help for solve this problem in current version ? And please fix it in future version.
Copied from original issue: AdoptOpenJDK/openjdk8-releases#16

HI @JamesMung - I haven't used jasper before - do you have a quick set of instructions to reproduce the error? Also which Linux distribution are you using (it's unclear if this is a JDK issue or something that's supposed to be on the underlying OS).

Hi @sxa555, I tried to use Oracle JDK of Linux version and it's no problem to print PDF. So I compare between Windows and Linux version. I found Windows version has fonts and config in jre directory. But I can't found it from Linux version. So I think this is the problem.
And I tried to copy the font and config from Oracle JDK to Adopt JDK. but it's not work. Can you kindly give the solution to solve it ? And please fix it in further versions.
Distribution : jdk8u181-b13 Linux x64

Hi there, our team hit this problem on various Linux distributions too. (Ubuntu, Centos, Debian etc)
JDK version: jdk8u181-b13
We hit this problem even at a very early phase, when installing our product using installer4j, stack trace as follows:
java.lang.NullPointerException     at sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1264)     at sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:219)     at sun.awt.FontConfiguration.init(FontConfiguration.java:107)     at sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:774)     at sun.font.SunFontManager$2.run(SunFontManager.java:431)     at java.security.AccessController.doPrivileged(Native Method)     at sun.font.SunFontManager.<init>(SunFontManager.java:376)     at sun.awt.FcFontManager.<init>(FcFontManager.java:35)     at sun.awt.X11FontManager.<init>(X11FontManager.java:57)     at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)     at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)     at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)     at java.lang.reflect.Constructor.newInstance(Constructor.java:423)     at java.lang.Class.newInstance(Class.java:442)     at sun.font.FontManagerFactory$1.run(FontManagerFactory.java:83)     at java.security.AccessController.doPrivileged(Native Method)     at sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)     at sun.font.SunFontManager.getInstance(SunFontManager.java:250)     at sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:264)     at sun.swing.SwingUtilities2.getFontMetrics(SwingUtilities2.java:1113)     at javax.swing.JComponent.getFontMetrics(JComponent.java:1626)     at javax.swing.text.WrappedPlainView.updateMetrics(WrappedPlainView.java:318)     at javax.swing.text.WrappedPlainView.updateChildren(WrappedPlainView.java:297)     at javax.swing.text.WrappedPlainView.insertUpdate(WrappedPlainView.java:463)     at javax.swing.plaf.basic.BasicTextUI$RootView.insertUpdate(BasicTextUI.java:1610)     at javax.swing.plaf.basic.BasicTextUI$UpdateHandler.insertUpdate(BasicTextUI.java:1869)     at javax.swing.text.AbstractDocument.fireInsertUpdate(AbstractDocument.java:201)     at javax.swing.text.AbstractDocument.handleInsertString(AbstractDocument.java:748)     at javax.swing.text.AbstractDocument.insertString(AbstractDocument.java:707)     at javax.swing.text.PlainDocument.insertString(PlainDocument.java:130)     at javax.swing.text.DefaultEditorKit.read(DefaultEditorKit.java:273)     at javax.swing.JEditorPane.setText(JEditorPane.java:1416)     at javax.swing.JEditorPane.<init>(JEditorPane.java:290)     at com.install4j.runtime.installer.frontend.headless.AbstractHeadlessScreenExecutor.init(AbstractHeadlessScreenExecutor.java:68)     at com.install4j.runtime.installer.frontend.headless.ConsoleScreenExecutor.<init>(ConsoleScreenExecutor.java:24)     at com.install4j.runtime.installer.frontend.headless.InstallerConsoleScreenExecutor.<init>(InstallerConsoleScreenExecutor.java:6)     at com.install4j.runtime.installer.Installer.getScreenExecutor(Installer.java:88)     at com.install4j.runtime.installer.Installer.runInProcess(Installer.java:57)     at com.install4j.runtime.installer.Installer.main(Installer.java:45)     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)     at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)     at java.lang.reflect.Method.invoke(Method.java:498)     at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:85)     at com.install4j.runtime.launcher.UnixLauncher.main(UnixLauncher.java:62)
Currently we use a workaround to install font dependency by
apt install fontconfig
However, this workaround will change behaviour when our customer switches from Oracle jdk to AdoptOpenJDK, and remains a compatibility issue for us.
Would the team consider bundle the font config in the JDK and help fix it in further versions?
Cheers,

Hi @xinyi9, Thanks for your solution. BTW, @sxa555 I tried use these code in my program :
try {
	GraphicsEnvironment ge = GraphicsEnvironment.getLocalGraphicsEnvironment();
	File fontsDir = new File(System.getProperty("user.home") + "/fonts"); // fonts dir (*.ttf)
	if(fontsDir.isDirectory()){
		for(File file : fontsDir.listFiles()){
			ge.registerFont(Font.createFont(Font.TRUETYPE_FONT, file));

			if(logger.isInfoEnabled()) {
				logger.info("Load font " + file.getName());
			}
		}
	}
} catch (Exception e) {
	e.printStackTrace();
}

And it appear NullPointerException same as @xinyi9 provided. I wish it would helpful for you.
Distribution : jdk8u181-b13 Linux x64

The fonts in jre/lib/fonts directory are taken from closed code in Oracle JDK and missing from openJDK. We need to understand why it is failing only on Linux and not on Windows. Which fonts were trying to create when the failure occurred. @mbvreddy FYI

We also ran into this problem today with JDK 11.0.1 and it affects at least the Linux version, but not the Windows version of AdoptOpenJDK.
The NullPointerException in FontConfiguration.java:1264 is caused by a missing font configuration file, which is not included with the Linux version of AdoptOpenJDK. It is important to notice that the direct cause of the exception is a missing configuration file and not that actual font files are missing.
When the AWT font subsystem is initialized, it will look for a font configuration file in $JAVA_HOME/lib following a naming scheme and priority as described here: https://docs.oracle.com/javase/8/docs/technotes/guides/intl/fontconfig.html
Even if no fonts are provided by the JDK and use of OS provided fonts is not intented or configured, a minimal configuration is required by the AWT font subsystem to initialize without throwing exceptions. Providing a fontconfiguration.properties file in $JAVA_HOME/lib with the following two lines will at least, to start with, mitigate the problem with the NullPointerException:
version=1
sequence.allfonts=default

Since we are only using fonts bundled with our application, this is a feasible workaround in our situation. It allows the font subsystem to initialize and we can later without issues load our own fonts from the classpath. I am not sure what happens and YMMV if you try to run an application, which relies on the JDK to provide actual fonts, either as bundled with the JDK or as provided by the operating system.

Initially commented on issue 693, but also relevant here:
The NullPointerException in FontConfiguration.java:1264 is caused by a missing font configuration file, which is not included with the Linux version of AdoptOpenJDK. It is important to notice that the direct cause of the exception is a missing configuration file and not that actual font files are missing.
When the AWT font subsystem is initialized, it will look for a font configuration file in $JAVA_HOME/lib following a naming scheme and priority as described here: https://docs.oracle.com/javase/8/docs/technotes/guides/intl/fontconfig.html
Even if no fonts are provided by the JDK and use of OS provided fonts is not intented or configured, a minimal configuration is required by the AWT font subsystem to initialize without throwing exceptions. Providing a fontconfiguration.properties file in $JAVA_HOME/lib with the following two lines will at least, to start with, mitigate the problem with the NullPointerException:
version=1
sequence.allfonts=default

Since we are only using fonts bundled with our application, this is a feasible workaround in our situation. It allows the font subsystem to initialize and we can later without issues load our own fonts from the classpath. I am not sure what happens and YMMV if you try to run an application, which relies on the JDK to provide actual fonts, either as bundled with the JDK or as provided by the operating system.

Just to add to the list of people who have experienced this, I hit this issue when using Apache POI (which uses fonts in the background to size Excel columns etc) on a headless server. In essence jarnbjo is right - the cause of the exception shown in the issue is the lack of the fontconfig.properties file, as described here: https://docs.oracle.com/javase/8/docs/technotes/guides/intl/fontconfig.html
In my case this alone wasn't sufficient to remove the issue. For any task that needs an actual font to be present you need two things:

The JDK/the system to have some way of finding fonts.
At least one font to find - this is where I had additional problems.

No. 1 can be provided by the Java fontconfig.properties system, or (on Linux) by the fontconfig package - both seem to work. Solving no. 2 means actually having a font file somewhere that your solution to no. 1 can find it. Solution that worked for me (on Centos 6/7) was installing the fontconfig and liberation-sans-fonts packages (the choice of font is arbitrary, any worked, including manual installs).
Ideally (for my purposes) the JDK distribution would include the Java fontconfig.properties and at least one default font, just like the Sun distribution does (maybe some more open font to replace Lucidia if licensing is the issue). If that were the case then my code would run with Adopt OJDK out of the box, whereas at the moment there are "hidden" dependencies on bare-bones Linux distributions.

I was struggling with this until I downloaded Adopt JDK8 with the OpenJ9 JVM.  The Hotspot version does not work and that solved my problems. I wasn't getting many errors at all so finally started from scratch and noticed this.

Does anyone know the progress of this issue? I see in the migration guide that "Relicensed Lucidia Fonts" are "coming soon". It also states Q2 2019.
How is the progress on that? Is it planned to be part of the next Java 8 Update? Is there still potential to slip out of Q2 or is it basically already finished?

@maxpg we have the May 2019 milestone label which means it's in the bucket of things that we want to look at next (May is false in terms of timing though). It's an unassigned issue so unless a volunteer picks it up beforehand we won't tackle it until some other priorities get sorted first.

@karianna The issue is a major one if you want to ship your (on-premise) application with AdoptOpenJDK as the application may not work correctly on some Linux distributions. Considering this, I hope that you can give the issue a higher priority and a reliable milestone (waiting half a year because your page states "expected to complete in 2Q 2019" just to see that the issue is still unassigned is somewhat disappointing).

@karianna The issue is a major one if you want to ship your (on-premise) application with AdoptOpenJDK as the application may not work correctly on some Linux distributions. Considering this, I hope that you can give the issue a higher priority and a reliable milestone (waiting half a year because your page states "expected to complete in 2Q 2019" just to see that the issue is still unassigned is somewhat disappointing).

We do our best to prioritize issues that impact the most folks, but this is a community/volunteer project.  If you'd like this particular issue looked at more quickly then we're always looking for more help and/or there are support options listed at adoptopenjdk.net/support.html

We're having issues here as well (on AdoptOpenJDK10):
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.GeneratedConstructorAccessor9.newInstance(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:488)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 32 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1288)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:765)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:440)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:385)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 36 more

It happens for us on vanilla Fedora 30 (just boot the live CD). Whenever AWT or Swing is used, things go bad... I have no idea what the problem is, libfontconfig.so.1 is present, so I guess it must be something else...
I did test this with the reference build as well (https://jdk.java.net/java-se-ri/10), and this works. So it must be something with AdoptOpenJDK builds... but what?

I upgraded to AdoptOpenJDK 11, and this fixed the issue for Fedora 30. I can confirm that fonts work out of the box where they did not with JDK10. We were unable to upgrad to 11 previously due to jersey not supporting it, but now it works :)
openjdk version "11.0.4" 2019-07-16
OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.4+11)
OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.4+11, mixed mode)

OK so it sounds like this is still an issue for AdoptOpenJDK 8 but not 11 (potentially)

Adding this info in hopes it might help someone or provide some clues, although the exact scenario is a little different than above:
Context:
My application uses a PDF generation tool (Crystal Reports) to generate PDFs.  This runs in a Windows 10 environment.
Short Story:
My issues go away when I create a JAVA_HOME/jre/lib/fonts and add ANY single ttf font that is installed on my system.
Long Story:
On Amazon Corretto 8 or AdoptOpenJDK 8, I get an NPE when Crystal Reports (thrown from its OpenTypeFontManager) is generating a PDF.  Like many people, I tried copying Oracle's font folder to JAVA_HOME/jre/lib/fonts.  In Corretto I get 'java.lang.UnsatisfiedLinkError: \jre\bin\fontmanager.dll: Can't find dependent libraries', and in AdoptOpenJDK the PDF would generate but with no text, and a few special symbols sprinkled on the page.
I deleted the contents of the 'fonts' folder and copied a single TTF font (webdings.ttf, which is not even used by the PDF) and things worked in both Corretto and AdoptOpenJDK.
I then also added back all of the Oracle fonts (LucidaBrightDemiBold, LucidaBrightDemiItalic, LucidaBrightItalic, LucidaBrightRegular, LucidaSansDemiBold, LucidaTypewriterBold, LucidaTypewriterRegular, LucidaSansRegular) and things failed again.  I then deleted each Oracle font one by one until I discovered that deleting LucidaSansRegular alone was enough to make things work.
Summary:
Copying over the Oracle fonts and deleting LucidaSansRegular OR creating an empty 'fonts' directory and copying one of the OS fonts, made things work in Corretto and AdoptOpenJDK.

Having this issue on Debian 10 while trying to run Jenkins 1.204.1
The @jarnbjo solution worked for me.
I use linux binaries and install them in /usr/share/java/{java_version}. Creating /usr/share/java/jdk-11.0.5+10/lib/fontconfig.properties with the following content allowed jenkins to start:
version=1
sequence.allfonts=default

@lumpfish is this related to what you were working on recently?

Some of it, yes.  I was looking for any progress on the The AdoptOpenJDK migration guide (https://adoptopenjdk.net/MigratingtoAdoptOpenJDKfromOracleJava.pdf) statement "The Lucida fonts that are available in Oracle JDK 8 have a proprietary 3rd party license. AdoptOpenJDK intends to provide relicensed Lucida fonts. Work is ongoing to minimize any display issues when these fonts are rendered by Freetype and are expected to complete in 2Q2019."
From this I deduce it is still unresolved.
What needs to be done to "provide relicensed Lucida fonts"?


[RUNTIME] Add min_repeat_ms to time_evaluator

min_repeat_ms sets the minimum duration of a measurement and has been used in autotvm for measurement.
As it is a useful feature to make measurement accurate and smart, we'd better move it to general API time_evaluator and encourage people to use it.
cc @eqy @tqchen   @sgrechanik-h

@merrymercy what is the status of this PR?

@eqy please review again

ping @eqy @sgrechanik-h please take another look, if there is no further comments in 24 hours, we can go ahead and merge this PR in

Thanks, @merrymercy @eqy @sgrechanik-h , this is merged


Remove winds

After making all changes to the cask:

[x] brew cask audit --download {{cask_file}} is error-free.
[x] brew cask style --fix {{cask_file}} left no offenses.
[x] The commit message includes the cask’s name and version.

Thanks!

Re-added in https://github.com/Homebrew/homebrew-cask/pull/48699 with less wall.


have to keep scrolling down when I add rename an item or edit a path

solution is just to keep a way for the list to stay where the current thing is


Task Orchestration != Task Execution

Migrated from GitLab: https://gitlab.com/meltano/meltano/-/issues/3193
Originally created by @kgpayne on 2022-01-31 15:03:58

Note: this issue is a written record of thoughts and experiences to serve as background to specific proposals. It need not be read unless i) it is linked to and relevant to a specific proposal you are evaluating, or ii) you are especially curious about the specifics of data task orchestration and execution and have time to spend reading.
tldr; today we expect that to run data tasks at all in production, we need to deploy an 'orchestrator'. This need not be the case, and is even contrary to the intent and design of the data worlds most popular orchestrator - Airflow. We need more and better execution options, not more orchestrators.
Historical Context
I use Airflow as the base example for this issue as it is widely understood and also served as the inspiration for later orchestrators. In the 'Current State of the Art' section below I endeavour to cite similarities and differences from other popular orchestrators.
Airflow, developed internally at AirBnb, was announced and Open Sourced in June of 2015 and has since become a core part of many organisations data infrastructure. From the very beginning Airflow was built to "author, schedule, and monitor data pipelines", but not execute the tasks in those pipelines. Back in 2015 AirBnb highlighted the Extensibility of the Airflow tool, through the use of Hooks, Operators and Executors:

Hooks are defined as external systems abstraction and share a homogenous interface. Hooks use a centralized vault that abstracts host/port/login/password information and exposes methods to interact with these system.
Operators leverage hooks to generate a certain type of task that become nodes in workflows when instantiated. All operators derive from BaseOperator and inherit a rich set of attributes and methods.
Executors implement an interface that allow Airflow components (CLI, scheduler, web server) to run jobs jobs remotely. Airflow currently ships with a SequentialExecutor (for testing purposes), a threaded LocalExecutor, and a CeleryExecutor that leverages Celery, an excellent asynchronous task queue based on distributed message passing. We are also planning on sharing a YarnExecutor in the near future.

Core to Airflows model then is an explicit design decision to "run jobs remotely" - to separate orchestration from execution. 9 months later, AirBnb shared details about how Airflow is used within their wider Data Infrastructure:

Scheduling of jobs happens through Airflow, a platform to programmatically author, schedule, and monitor data pipelines that can run jobs on Hive, Presto, Spark, MySQL, and more — note that we logically share Airflow across clusters, but physically the Airflow jobs run on the appropriate sets of clusters, machines, and workers. We built Airflow and open sourced it, as well. The Spark cluster is another processing tool favoured heavily by engineers and data scientists working on machine learning, and is useful for stream processing.

The team who conceived of and built the first iterations of Airflow emphasise over and over that "we logically share Airflow across clusters, but physically the Airflow jobs run on the appropriate sets of clusters, machines, and workers."
Fast forward a few years and it becomes clear this advice was not heeded. With convenient facilities to run arbitrary code within the Airflow execution environment (using the bulit-in BashOperator and PythonOperator operators, or by subclassing the BaseOperator directly), 1000's of companies not running AirBnb-scale workloads on Hive/Presto/Spark implemented their tasks directly in Airflow. Whilst convenient to begin with, this soon became problematic. Anyone working on an Airflow project created before 2019 is likely to have come across dependency tree and resource isolation issues that result from 'doing work' in Airflows execution environment:

Dependency tree issues: All 3 of the offending operators execute within the same environment as Airflow itself. This means that any task dependencies (e.g. Pandas, AWS SDK, other 3rd Party SaaS clients) must not conflict with each other or Airflow. I personally remember the AWS case being particularly painful, with many SDK's using various versions of botocore to interact with common AWS integration points such as S3. Meltano, with our creation and management of virtualenvs, goes some way in alleviating this pain point, however we don't directly address resource isolation.

Resource isolation issues: Another consequence of running arbitrary code and tasks within the same environment is the "noisy neighbours" effect. Airflows parallel execution strategy (when using the threaded LocalExecutor and the CeleryExecutor) is optimistic; Executors will execute tasks up to the configured parallelism (for LocalExecutor) or worker_concurrency (for CeleryExecutor) without any additional control or consideration for resource consumption. This core execution strategy is 'good enough' when job execution is offloaded onto "appropriate sets of clusters, machines, and workers"; all the workers are doing is polling an external job runner (such as Spark) to retrieve status and log information. However optimistic execution fails miserably when two Network-intensive (e.g. Extract-Load) or CPU-intensive (e.g. Transform) jobs are run concurrently directly on the Airflow workers. Jobs begin to hang or fail at random due to "transient" resource issues, affecting overall stability of users pipelines.

In summary, managing dependency and resource constraints of arbitrary data tasks in Airflow is not easy by design, as these use cases (however common) fall outside of Airflows intended use as a "job scheduler" not a "job runner".
Current 'State of the Art'
So how do people manage today? After a concerted campaign in the Airflow community to extricate tools from the Airflow environment, we have arrived at the KubernetesPodOperator (and equivalents for other managed Docker execution platforms such as the EcsOperator) as a Best Practice. This approach directs users to wrap tasks in separate Docker images and to launch them onto Docker-compatible clusters like Kubernetes or ECS using the provided operators. This solves the two problems stated above; dependency-isolation is managed using separate Docker images for each task (or task type), and Docker-compatible clusters have native constructs for specifying the resources required by those launched Dockerized tasks (CPU, memory, volume-mounts, secrets etc). Huzzah!
This shift to 'Dockerizing' tasks for execution is so successful that it is supported out-of-the-box by all of the 'second wave' orchestrators:

Dagster
Architecture

Supported Executors
Example executors include:

in_process_executor: Execution plan executes serially within the run worker itself.
multiprocess_executor: Each step executes within its own spawned process. Has configurable level of parallelism.
dask_executor: Executes each step within a dask task.
celery_executor: Executes each step within a celery task.
docker_executor: Executes each step within a Docker container.
k8s_job_executor: Executes each step within an ephemeral kubernetes pod.
celery_k8s_job_executor: Executes each step within a ephemeral kubernetes pod, using celery as a control plane for prioritization and queuing.
celery_docker_executor: Executes each step within a Docker container, using celery as a control plane for prioritization and queueing.

Prefect
Architecture

Supported Agents
Prefect supports several different agent types for deploying on different platforms.

Local: The Local Agent executes flow runs as local processes.
Docker: The Docker Agent executes flow runs in docker containers.
Kubernetes: The Kubernetes Agent executes flow runs as Kubernetes Jobs.
GCP Vertex: The Vertex Agent executes flow runs as Vertex Custom Jobs.
AWS ECS: The ECS Agent executes flow runs as AWS ECS tasks (on either ECS or Fargate).

Limitations of the Current State
Whilst new Dockerized execution patterns alleviate the issues of dependency tree and resource isolation issues of Airflows' past, they are not without their own challenges nor do they yet meet the aspirations of "jobs run on the appropriate sets of clusters, machines, and workers".

Cluster managers expose centralised resources, a pattern that is adequate for deploying web services but that is often not fit for the distributed nature of the data world. Using a single cluster for all the tasks in a DAG assumes all of the external service dependencies (e.g. APIs, databases, filestores etc.) of each Task in that DAG are met. For even a simple ELT pipeline, this assumes source and target are both accessible on the same network as the cluster. In a world of microservices, multi-VPC and multi-Account architecture patterns, this is a fragile assumption, and when false it forces teams to build and maintain complex network bridges to provide centralised access to those disparate services. Whilst it is possible to run two different DAGs (or their equivalent in the newer orchestrators) on two separate clusters, it is not readily possible to run two separate Tasks in the same DAG on separate clusters, nor is it attractive to run multiple clusters (with all the overhead that entails).

Docker and available cluster management tooling (such as Kubernetes) can be a high price to pay for the benefits derived. It imposes a steep learning curve and administrative burden on data teams that is only partially mitigated by paid managed offerings.

Taking a direct dependency on a cluster manager for the execution of DAGs compromises the local development experience (even as containerisation makes it easier to test individual Tasks). To execute a DAG made of KubernetesPodOperator tasks locally you must have a Kuberentes cluster deployed and available locally, with resources (such as volumes, secrets etc.) closely matching the configuration in production. This is not a simple task to set up or maintain.

Whilst it is natural to build Spark apps in the Spark framework, for remote execution on a Spark cluster, expressing other kinds of Tasks in standalone Docker containers negates the benefits offered by Task definition decorators and base classes included with the major Orchestrators. No general-purpose Task definition SDK has achieved broad adoption, nor is there yet a standalone Task 'app store' for reuse of common Tasks. Defining and containerising Tasks is left as an exercise for the end-user. More on this in Task Orchestration != Task Implementation.

Consequences for Meltano
By wrapping an Orchestrator as a proxy for providing Execution (i.e. meltano invoke airflow for Airflow to call meltano elt ...), we inherit the limitations of that Orchestrator. However, if we acknowledge that Orchestration != Execution, we can choose to reverse the relationship by providing our own Execution paradigm for Orchestrators (current and future) to integrate with, providing a Task Execution Framework (rather than a Task Orchestration Framework) performing a function equivalent to Spark in the big-data ecosystem. This idea is proposed in #3139.

View 2 previous comments from the original issue on GitLab

@kgpayne feel free to re-open as discussion if needed!


python3Packages.mocket: 3.10.1 -> 3.10.2

Motivation for this change
https://github.com/mindflayer/python-mocket/releases/tag/3.10.2
Things done

Built on platform(s)

[x] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

[ ] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[ ] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
22.05 Release Notes (or backporting 21.11 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module
[ ] (Release notes changes) Ran nixos/doc/manual/md-to-db.sh to update generated release notes

[x] Fits CONTRIBUTING.md.

Result of nixpkgs-review pr 152528 run on x86_64-linux 1

17 packages built:

ansible (python39Packages.ansible-core)
ansible-lint (python39Packages.ansible-lint)
ansible_2_10 (python39Packages.ansible-base)
ansible_2_11
python38Packages.ansible-base
python38Packages.ansible-core
python38Packages.ansible-lint
python38Packages.geoip2
python38Packages.mocket
python38Packages.parsedmarc
python38Packages.sopel
python38Packages.ttp
python39Packages.geoip2
python39Packages.mocket
python39Packages.parsedmarc
python39Packages.sopel
ttp (python39Packages.ttp)

@ofborg eval


Tofu appears in UTF-8-encoded Markdown README

Describe the bug
My README.md contains non-ASCII characters. When rendered on PyPI they appear as tofu.
Expected behavior
These characters should be rendered normally.
To Reproduce

See README.md, pyproject.toml
Run pdm publish

My Platform

Occurs in Firefox, GNOME Web and Chrome. I do not see tofu on other pages (link below), so I don't think this is a browser issue.
PDM 2.1.2, installed via pipx 1.0.0, running Python 3.10.4

Additional context

On my machine file --mime README.md returns README.md: text/plain; charset=utf-8 so I believe the file encoding is correct before upload.
I believe I have declared the readme field correctly, see pyproject.toml above.
READMEs for other packages render correctly, for example epitran contains a variety of non-ASCII characters for various alphabets.

This is likely an issue with pdm. The raw value that PyPI was provided for the Description metadata field includes TOFU:
warehouse=> select raw from release_descriptions where id = 'e092febc-d162-4e7d-80fd-6565d2d24201';
                                                                                raw
--------------------------------------------------------------------------------------------------------------------------------------------------------------------
 # Samosa (���������������)                                                                                +
                                                                                +
 Enforce a triangular Git workflow. If this is not possible, explain why.                                                                                +

However it's clear that the actual value in the distribution does not contain TOFU: https://inspector.pypi.io/project/samosa/0.1.2/packages/f5/02/d6fa62fc59eca0d52c4043e215ec4ee7f0590ae6592403e2b211c670cae3/samosa-0.1.2.tar.gz/samosa-0.1.2/PKG-INFO#line.10
Because PyPI does zero introspection of the artifact and depends on the metadata provided at upload time instead, this means that when the uploader was preparing the metadata to provide along with the artifact, it incorrectly read this field from the distribution artifact.
Can you confirm that a) that you're using the latest version of pdm and b) that this issue does not occur when you publish with https://pypi.org/p/twine/ instead?

(Actually, I can determine that you used pdm 2.1.2, which is the current latest)

Thanks for the info! This was indeed a PDM bug, now fixed in 2.1.3 https://github.com/pdm-project/pdm/commit/7ade7625194fa99596551f43782e2c43c3099cc5


Resolved Issues with CRC Encoder/Decoder and Built Test Functions

Please checkout changes and run the test_crc.py file to verify that all checks pass.

You should also modify the code in the test function to flip some bits and see that checks fail. No need to push your changes since it would just be a sanity check.


This is on Windows 10 Home 21H2:

God do I love Microsoft.
Apparently it now returns the relevant Version in relations to the programs Manifest, which we don't have.
Sooo.... I know that Source has an internhal helper function to identify the relevant OS Version, surely Respawn didn't gut it and replace it with their own hacky solution, right? :clueless:
Their method (found in engine.dll) does nonsense checks that at the end just return Windows 8.1.
Annoying

The only good replacement i found is RtlGetVersion

Yep, that seems to be the best alternative.
Since this is a one-time thing, going kernel space should have practically no impact at all.

Implemented it similar to how the wine callbacks are done, as suggested by this SO Answer https://stackoverflow.com/a/48749703/6331425
Needs re-testing

Works fine on Gentoo with NorthstarProton 8.1.1
[21:57:37] [NORTHSTAR] [info] NorthstarLauncher version: <IP_ADDRESS>+dev
[21:57:37] [NORTHSTAR] [info] Command line: "Z:\home\noah\.local\share\Steam\steamapps\common\Titanfall2\Titanfall2.exe"   -noborder -windowed -northstar --use-gl=osmesa
[21:57:37] [NORTHSTAR] [info] Using profile: R2Northstar
[21:57:37] [NORTHSTAR] [info] Operating System: Linux (Wine)
[21:57:37] [NORTHSTAR] [info] Wine build: wine-8.1.r0.gdde73435 ( TkG Staging Esync Fsync )
[21:57:37] [NORTHSTAR] [info] Proton build: NorthstarProton-8.1-1
[21:57:37] [NORTHSTAR] [info] Enabling hook _GetCommandLineA


Firestore Fatal Exception: [FSTImmutableSortedDictionary documentDictionary]: unrecognized selector sent to class

Enviornment

Xcode version: 9.3
Firebase SDK version: 5.0.1 (Carthage)
Firebase Component: Firestore
Component version: 5.0.1

Steps to reproduce:

Try a basic query of a collection (see Relevant Code):

After calling getDocuments, the app will experience a fatal exception.
Console Output:
2018-05-28 03:44:39.558364-0500 AppName[99307:5274217] 5.0.0 - [Firebase/Core][I-COR000022] Firebase Analytics is not available.
2018-05-28 03:44:39.559563-0500 AppName[99307:5274217] 5.0.0 - [Firebase/Core][I-COR000025] FIRAuth getUID implementation wasn't set.
got here!
firebaseDatabase: <FIRFirestore: 0x6040000da6a0>
collection: characteristics
2018-05-28 03:44:39.596419-0500 AppName[99307:5274217] +[FSTImmutableSortedDictionary documentDictionary]: unrecognized selector sent to class 0x104663d00
2018-05-28 03:44:39.600865-0500 AppName[99307:5274217] *** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '+[FSTImmutableSortedDictionary documentDictionary]: unrecognized selector sent to class 0x104663d00'
*** First throw call stack:
(
	0   CoreFoundation                      0x00000001063be1e6 __exceptionPreprocess + 294
	1   libobjc.A.dylib                     0x0000000105a53031 objc_exception_throw + 48
	2   CoreFoundation                      0x000000010643f6c4 +[NSObject(NSObject) doesNotRecognizeSelector:] + 132
	3   CoreFoundation                      0x0000000106340898 ___forwarding___ + 1432
	4   CoreFoundation                      0x0000000106340278 _CF_forwarding_prep_0 + 120
	5   AppName              0x00000001043c30db -[FSTLevelDBRemoteDocumentCache documentsMatchingQuery:] + 56
	6   AppName              0x00000001043c6740 -[FSTLocalDocumentsView documentsMatchingCollectionQuery:] + 167
	7   AppName              0x00000001043c64cd -[FSTLocalDocumentsView documentsMatchingQuery:] + 115
	8   AppName              0x00000001043cd96f -[FSTLocalStore executeQuery:] + 184
	9   AppName              0x00000001043fdd4d -[FSTSyncEngine listenToQuery:] + 280
	10  AppName              0x00000001043aa427 -[FSTEventManager addListener:] + 486
	11  AppName              0x00000001043b2104 __64-[FSTFirestoreClient listenToQuery:options:viewSnapshotHandler:]_block_invoke + 62
	12  AppName              0x00000001043a3e49 -[FSTDispatchQueue enterCheckedOperation:] + 79
	13  libdispatch.dylib                   0x000000010b204807 _dispatch_call_block_and_release + 12
	14  libdispatch.dylib                   0x000000010b205848 _dispatch_client_callout + 8
	15  libdispatch.dylib                   0x000000010b20dc41 _dispatch_queue_serial_drain + 1305
	16  libdispatch.dylib                   0x000000010b20e556 _dispatch_queue_invoke + 328
	17  libdispatch.dylib                   0x000000010b20a3a0 _dispatch_queue_override_invoke + 726
	18  libdispatch.dylib                   0x000000010b2113c8 _dispatch_root_queue_drain + 664
	19  libdispatch.dylib                   0x000000010b2110d2 _dispatch_worker_thread3 + 132
	20  libsystem_pthread.dylib             0x000000010b72b169 _pthread_wqthread + 1387
	21  libsystem_pthread.dylib             0x000000010b72abe9 start_wqthread + 13
)
libc++abi.dylib: terminating with uncaught exception of type NSException
(lldb)

Relevant Code:
        FirebaseApp.configure()

        let firestore = Firestore.firestore()
        let settings = firestore.settings
        settings.areTimestampsInSnapshotsEnabled = true
        firestore.settings = settings

        firestore.collection("cities").getDocuments { (querySnapshot, error) in
            // crash happens before this line
            print("querySnapshot: \(querySnapshot) error: \(error)")
        }

Looks like that's crashing on this line, which shouldn't ever crash.
@wilhuff was this code changed recently?

Nearly everything has had some minor modifications lately, but overall this code is not moving fast.

@mpaulsonco, can you share a project that's causing this crash? Is it consistently reproducible, or does it only happen sporadically?

I had the same issue and for some reason adding $(inherited) to the other linker flags of my target seems to fix the issue. What is weird is that there are no flags in my project settings.

@mpaulsonco, I'm closing this issue as it hasn't seen any activity lately and we don't have a solid repro case. Please open this if you have an example to share.

The issue can be reproduced consistently using this test app. The thing that triggers this seems to be the fact that Podfile is configured to fetch Firestore and FirebaseCore from Git (just using the default pod for FirebaseCore "fixes" it). I have found this out accidentally while trying out my branch, which is the branch I'm using. It looks like FSTDocumentDictionary is somehow not linked properly.
The original post mentioned using Carthage, so perhaps the Carthage configuration file is (or was) somehow broken.

-ObjC is not getting added to the OTHER_LDFLAGS setting. Adding it manually is a workaround.  I suspect something about one of the pods is messing with the typical CocoaPods install behavior.

@var-const Thanks for finding the root cause. The CocoaPods bug fix is now merged into master and will be part of the CocoaPods 1.6.0 release.  In the meantime, the workaround is to add -ObjC to OTHER_LDFLAGS.


Add something like lxc.start.auto = 1

I'm not using Openstack but i have my management stuff which will be my openstack replacement inside a lxd container, which means i need lxd to autostart at least the management containers with lxd.
Also i want to start them in a particular order so i need something like lxc.start.order and lxc.start.delay.
I'm sure i'm not the only one needing something like that, others also asking for it here

Ok, so I think there are a few things we want to do here:

Remove the power_state column from the containers table
Introduce a new volatile.last_state config key which is used as an equivalent to power_state. On clean shutdown, set to whatever state the container is in. On next startup, bring things back up and clear the key.
Introduce a new boot.autostart key that can be set to 1 to always cause the container to start on LXD startup.
Introduce a new boot.autostart.delay key that can be set to a number of seconds to wait after the container has been started before attempting to start the next one.
Introduce a new boot.autostart.order key that can be set to an integer used to sort the containers to start in the right order.

For now that's pretty much equivalent to what we have in LXC. At some point later we may be able to introduce an alternative to the delay option which would instead use some kind of signal over the /dev/lxd socket.

Changed above comment from volatile.last_state to volatile.last_state.power as we'll need a volatile.last_state.idmap for #787

@pcdummy any interest in working on this?

I may take a stab at this one on my flight to Seattle.


ci: change git-secrets branch

ci: change git-secrets branch
Description
awslabs/git-secrets does not use a 'main' branch yet.
Checklist:

[ ] I have tested my changes. No regression in existing tests.
[ ] My code is Linted.

By submitting this pull request, I confirm that you can use, modify, copy, and redistribute this contribution, under the terms of your choice.

/bot run checks

/bot run checks


OptionBuildAddressables does not call IDataBuilder.ClearCachedData

Addressables can generate data that's useful during the build, but not afterwards. This data can then be cleared with the IDataBuilder.ClearCachedData method. It can be called via a menu item in the editor, but it can be called in scripts as well.
I'd like Trimmer's OptionBuildAddressables to optionally call this method after a build. I say optionally because if the build goes wrong, these intermediate files can help with debugging.

 The code I submitted, as written, will likely delete the runtime Addressables directory. My bad. I'm fixing this now.


Kiki's P1 (at the top) - Flag for tutorial writer to choose default to read [More...] or [Less...]

Right now, instructions default to expanded, but in a world of detailed instructions, that's too much.  If we default to closed instructions, it will be inconvenient for tutorials already created.  A flag will leave existing things be while I'm able to progress in a way requested by users.

@shakao  @riknoll  @abchatra
We're going to start a user study with students in a couple of weeks.  Is there any chance of sneaking this feature in by then?

I agree that the default More/Less buttons are not great.  They clutter up the tutorial area, and most times, you want the instructions fully expanded.  I think this is something we can test with users (Kiki, let's include it as a hypothesis).

@shakao do you have a quick estimate on how much is the work to make the   configurable through markdown? Is that the right design?

i think adding it as a flag is fine if we are using it only for internal experimentation, i'm more hesitant to add it if we expose/document for external content creators. implementation should be straightforward, less than a day to add!

Ok. Not sure I understand, why are you hesitant to document it?

i think it's ok for kiki/jacqueline to use to test, but we haven't received requests for "tutorial step closed by default" from other content creators and we have so many metadata flags already, i don't want to keep adding them if they aren't really neccessary

Sounds good to me. Lets keep as internal until someone external asks for the same.

Fixed


HA PoC : Test MultiCloud functionality in HA mode.

Issue/Feature Description:
Test scale out / scale in.
Test node down / node addition.
Test Client failure scenarios.
Why this issue to fixed / feature is needed(give scenarios or use cases):
How to reproduce, in case of a bug:
Other Notes /  Environment Information: (Please give the env information, log link or any useful information for this issue)

Basic Installation and Dashboard Testing was done

More Testing to be done as indicated in the Task Above..

Merged in : #1189

Completed in I Release


unify bagua package name with CUDA version

Would be possible to unify the package name and Cuda-version have in a version like PT, for example, torch==1.11.0+cu113 instead of bagua-cuda113==0.9.0?
https://github.com/PyTorchLightning/pytorch-lightning/pull/12723

won't fix


Lua Pit Stop Race

Feature Summary
Using Lua, create a milestone race with 5-6 contacts or phone boxes that you must click on before proceeding to the next "pit stop". Your time to reach each pitstop would be recorded, and at the end you'd receive a Souvenir based upon your speed (bronze, silver, gold).
Could even spawn the pit stop NPCs at badge locations, or simply use phone call boxes, or maybe a combination of both. I think 4-6 "stops" is probably enough.
Bonus points if you can make the /kiosk home home city info terminals show a leader board

Closed by #770


basic setup and minimal working example

Bazel setup and world's simplest rendezvous instruction generator, with tests.

Looks great! thanks for setting this up!


Mocking XORM

Is there a mocking library that works well with XORM. I've been trying to get gopkg.in/DATA-DOG/go-sqlmock.v1 to work but it's such a hassle to even get it running. When I try to mock complicated queries it just blows up and it's saying the sql string doesn't match despite it matching... Basically, I'm wondering what other people are doing to test without actually having to spin up a test database. That just seems wrong. Thanks!

Gitea are using xorm and use gopkg.in/testfixtures.v2 to do the unit tests. Maybe that will help you.


The element that matches the specified selector is not visible - But button is visible

Are you requesting a feature or reporting a bug?
Maybe a bug
What is the current behavior?
Cannot click a button that is in my site and do not gets manipulated at any time.
In the command line I get the following message shown:

The test breaks after this message:

What is the expected behavior?
Button click should work like on all other pages I use for the tests.
How would you reproduce the current behavior (if this is a bug)?
It can not be reproduced, since on every other site the .click function works without any problems.
Provide the test code and the tested page URL (if applicable)
Tested page URL: -
Test code
const submitOrderBtn = Selector('button[type="submit"].btn-success');
//also tried with this:
//const submitOrderBtn = Selector('#confirmation-submit');
// and this:
//const submitOrderBtn = Selector('button').withText('order now');

const agbBtn = Selector("#conditions_accepted5");
const wiederrufsrechtBtn = Selector("#rescission_accepted6");

fixture `shop a product`
     .page `http://dev.local/checkout`;

test('complete order', async t =>{
     await t
          //some other actions for the process. Alle the stuff below is on the same page:
          .click(paymentSubmitBtn)
	  .click(agbBtn);
     console.log("[DEBUG], Trying to click submit button");
     await t
          .click(paymentSubmitBtn)
	  .click(agbBtn)
          .click(submitOrderBtn)

This is what the button looks in the html code:
<button id="confirmation-submit" type="submit" class="btn btn-success pull-right hidden-xs">

     order now
</button>

Specify your

operating system: Windows 10
testcafe version: 0.8.15
node.js version: 8.9.0

Hello @Hack4Life!
Unfortunately, it's hard to say something without the full page source code. If you concern about privacy, you can send a link/source through private messages on our forum: https://testcafe-discuss.devexpress.com/ to me, Helen Dikareva or Alexander Moskovkin.
If you can't share your code, could you please try to write minimal reproducible example, please?
TestCafe will consider element visibile if its width or height have a non-zero value. In your case #confirmation-button might be an invisible button hidden somewhere in an actual visible element.
Also, you can try to resize browser window using resizeWindow action. It may help if your layout is adaptive or it is a scrolling issue.

Thanks for your reply @AndreyBelym!
Your hint with resizeWindow helped me. I completely overlooked that another submit button is hidden on desktops and only visible on smaller devices. Since the first step in my tests is always .maximizeWindow() I have not thought that this could be the problem.
I will close this issue since it was just me overlooking a html piece of code.

@Hack4Life Did you maximize the window again, after resizing it? or continued the test execution in the resized window?


Add support for Python 3.13

Python 3.13 finalised the "dead batteries" deprecations, so there are some modules that no longer exist.
Temporarily disabling the binary modules so that the 3.13 tests will pass.
This also drops Python 3.8 support, and makes some minor project format changes for recent Briefcase releases.
PR Checklist:

[x] All new features have been tested
[x] All new features have been documented
[x] I have read the CONTRIBUTING.md file
[x] I will abide by the code of conduct

See the Briefcase PR for details on the merge strategy for this template change.

I've reverted the changes related to Android; this PR is now "no worse than it was before" regarding Android support. When wheels for Cryptography on 3.11+ are available, we can push an update to - at this point, we might as well wait until we have full 3.13 support for Android.
Binary package support for iOS has also been removed; again, we can restore that in a separate PR once the wheels are available.


27 current logic to quit game causes simharness vectorized environment setup to crash

This PR adds

num_active_games class variable to the simfire.game.Game class
minor updates to simfire/utils/layers.py that update the retrieval of landfire tif data (used to build the LandfireLatLongBox). The updates help ensure that if the respective output path exists but does not contain any .tif files, the tif data will be pulled as if the directory did not exist.

The addition of 2. resolves #26, which I added to this PR since it was already a very small amount of changes.

@doyled-it this PR is ready to go, please review at your leisure.


multiple hits for plasmid description in NCBI

I love your tool.  Thanks for making it.
I am using it with a collection of WGS Shigella isolates and some of the plasmid descriptions have multiple hits on NCBI.  Is there a way I can figure out which of the plasmids it is?  Are all of them in your collection?   The plasmids in your database are binary files.
Here are the two examples:
Shigella flexneri 1a strain 0228 plasmid, complete sequence (There are four of that name CP012736.1, CP012734.1, CP012733.1 and CP012732.1)
Escherichia coli   O104:H4 str. C227-11 plasmid, complete sequence (There are six CP011332.1 to CP011337.1)
Also, this one doesn't appear to be in NCBI at all:
Xuhuaishuia manganoxidans strain DY6-4 plasmid sequence
Thanks,
Adam Waalkes
Research Scientist
UWMC

You can download the FASTA file of all plasmids used to build the latest database.
Here: https:/bioinfo.ut.ee/plasmidseeker/plasmidseeker_db_w20_fna_Nov-2021.tar.gz
This may help to track down the actual identity of hits.

Thanks, that helps a lot.  It appears though that the numbering system between the .list files and the .fna is not consistent.
PlasmidSeeker output:
K-mers found  Total kmers     %Kmers found(F) Copy number     P-value Plasmid ID      Coverage        List file
MinP 80
Estimated bacteria isolate median coverage 94
Number of tests: 16   Significant p-value (initial 0.05) with correction: 0.003125

    PLASMID CLUSTER 1

149428  166885  89.54%  1.12    0       Shigella flexneri 2002017 plasmid pSFxv_1, complete sequence    105     /mnt/disk4/labs/salipante/programs/PlasmidSeeker/db_w20/plasmid_3951.fna_20.list
yet when I look at plasmid_3951.fna it is not the same:
tron:/mnt/disk4/labs/salipante/programs/PlasmidSeeker/db_w20_fna $ head -n 1 plasmid_3951.fna

NZ_CP028268.1 Pediococcus pentosaceus strain SRCM102739 plasmid unnamed2, complete sequence

Is this by design?  Both lists seem to contain the same number of plasmids so I assume I have the same db versions.
tron:/mnt/disk4/labs/salipante/programs/PlasmidSeeker $ ls -l db_w20/.list | wc -l
19782
tron:/mnt/disk4/labs/salipante/programs/PlasmidSeeker $ ls -l db_w20_fna/.fna | wc -l
19782
tron:/mnt/disk4/labs/salipante/programs/PlasmidSeeker $


Jar task CopySpec is ignored

This plugin hardcodes the content of the produced jar.
For example only the main source set is considered when gathering sources & "resources".
See https://github.com/TomDmitriev/gradle-bundle-plugin/blob/master/src/main/groovy/org/dm/gradle/plugins/bundle/BundleUtils.groovy#L73-L84
If supplementary source sets are added to the Jar, by e.g. jarTask.from sourceSets.another.output, then this plugin ignores that.
The Jar task defines a CopySpec that specifies it's intended content, build authors and other plugins will add to this CopySpec. This plugin should honor this instead of hardcoding what will be packaged in the resulting Jar.
Fixing this will allow usage of this plugin alongside other plugins that contribute content to the Jar like for example any source code generation plugin.

Hi @TomDmitriev, i am the original creator of the referenced ticket on the gradle side (https://github.com/gradle/gradle/issues/1046).
I tried to fix the problem in your plugin and propose a PR by changing the lines at https://github.com/TomDmitriev/gradle-bundle-plugin/blob/master/src/main/groovy/org/dm/gradle/plugins/bundle/BundleUtils.groovy#L73-L84.
However, as written in the gradle ticket linked above, i wrestled more with unexpected Gradle Errors (yes, StackOverflowErrors..) than with anything else.
I guess its easier for you to pick up the suggestions mentioned by @eskatos and apply them to your plugin. A fix would be highly appreciated!
I'd be happy to supply more suggestions and test the fix.
Enjoy, Toni

Hi @tonit,
What part of BundleUtils did you try to alter? When it comes to building a jar using bndtools, which is what this plugin essentially does, the resources are usually added using instruction -includeresource, i.e.:
bundle {
    instruction '-includeresource', '${resource1Path},${resource2Path}'
}

As for the sources, I don't see any way to specify them using an instruction. Also, I think it's impossible to distinguish between source files and any other files using the API of JarTask. The solution that comes to my mind is to add a new property, sourceSets to BundleExtension, which by default would point to the main sourceSet only, and get the files from this property. Will it work for you?

Hi @tonit,
What part of BundleUtils did you try to alter? When it comes to building a jar using bndtools, which is what this plugin essentially does, the resources are usually added using instruction -includeresource, i.e.:
bundle {
    instruction '-includeresource', '${resource1Path},${resource2Path}'
}

As for the sources, I don't see any way to specify them using an instruction. Also, I think it's impossible to distinguish between source files and any other files using the API of JarTask. The solution that comes to my mind is to add a new property, sourceSets to BundleExtension, which by default would point to the main sourceSet only, and get the files from this property. Will it work for you?

Thanks Tom for your quick reply.
I am aware of bnds endless amount of tricks and macros. Thats not the question here.
Its really about setting better defaults so that this plugin works seemlessly with other tools.
See, in line https://github.com/TomDmitriev/gradle-bundle-plugin/blob/master/src/main/groovy/org/dm/gradle/plugins/bundle/BundleUtils.groovy#L80 you specifically add the main sourceSet. However, the JarTaks allows to add additional sourceSets to be included as "resources". Other plugins build on that, but in your plugin you pick a single "default". I'd imagine that jarTask.from sourceSets.* gives you a list of all sourceSets configured. By default you still will only get "main" but in more complex cases you get more.
So, this is really about being a good gradle citizen, not that its impossible to do with bnds macros.
Your suggestion would be a good "workaround" but it does not make it much better I'd say. I still need to manually add the extra sourceSet in your Extension. Not better than adding a bnd instruction in my .bnd file.
Anyway, thanks for picking this up. My main concern is that the simple solution i described in the linked gradle ticket raises a StackOverflow. Gradle guys say the plugin is not a good citizen. So I'd like to help but after been a very long Maven citizen, my 'gradle' is not good enough, yet.
Happy New Year, Tom! ;)

Thanks Tom for your quick reply.
I am aware of bnds endless amount of tricks and macros. Thats not the question here.
Its really about setting better defaults so that this plugin works seemlessly with other tools.
See, in line https://github.com/TomDmitriev/gradle-bundle-plugin/blob/master/src/main/groovy/org/dm/gradle/plugins/bundle/BundleUtils.groovy#L80 you specifically add the main sourceSet. However, the JarTaks allows to add additional sourceSets to be included as "resources". Other plugins build on that, but in your plugin you pick a single "default". I'd imagine that jarTask.from sourceSets.* gives you a list of all sourceSets configured. By default you still will only get "main" but in more complex cases you get more.
So, this is really about being a good gradle citizen, not that its impossible to do with bnds macros.
Your suggestion would be a good "workaround" but it does not make it much better I'd say. I still need to manually add the extra sourceSet in your Extension. Not better than adding a bnd instruction in my .bnd file.
Anyway, thanks for picking this up. My main concern is that the simple solution i described in the linked gradle ticket raises a StackOverflow. Gradle guys say the plugin is not a good citizen. So I'd like to help but after been a very long Maven citizen, my 'gradle' is not good enough, yet.
Happy New Year, Tom! ;)

Happy New Year, Toni!
Could you please check out branch issue-68 and test if the changes work for you? If they do, I will roll them out as a new release.

A first test looks good! However, we face an integration problem with IntelliJ now. When referencing that bundle project via compile project(":otherBundleProject") it appears to not pick the bundle as created by bnd but.. only the "main" source output?
I still need to digg deeper. First guess is that your change is good! Maybe you also use IntelliJ and can reproduce?

This issue only appears when configuring intellij to do "create separate module per source set". If i deactivate it, its looks wonderful

Great, thanks, @TomDmitriev


Nat.Pow is no longer in Mathlib4

Trying chapter 1:
stderr:
error: 'Mathlib.Data.Nat.Pow': no such file or directory (error code: 2)
  file: ./.lake/packages/mathlib/././Mathlib/Data/Nat/Pow.lean

It appears Nat.Pow is no longer in Mathlib4.

Thanks for trying this. I will do a rebase with up-to-date Mathlib soon.

bump complete: https://github.com/mo271/formal_book/commit/d3dc53e36cca085106c592e04d7dddb7db638fa0
Should now be in sync with current Mathlib


[All hosts](community call agenda)

Clearing agenda.

Docs Build status updates of commit cb8def5:
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Note: Broken links written as relative paths are included in the above build report. For broken links written as absolute paths or external URLs, see the broken link report.
For any questions, please:Try searching the docs.microsoft.com contributor guidesPost your question in the Docs support channel


Bump versions of node modules automatically upon release

ATM we don't automatically update them. We need to plugin pre-release and post release hooks for maven release plugin. Furthermore we need to fix this along with gradle build.

Moved to https://github.com/wso2/ballerina-plugin-vscode/issues/18


Improve BD_InitShpDerJaco unit test

Use a 3 node element rather than 2 node
Deallocate variables after use

Currently, this unit test has memory management issues which cause test failures intermittently. This pull request fixes the memory problem and, as of openfast/dev, executes successfully every time.

The unit test has also been modified to test functionalities added to the function after commit #114


New package: PLists v1.1.1

Registering package: PLists
Repository: https://github.com/ordovician/PLists.jl
Created by: @translusion
Version: v1.1.1
Commit: 59b4da580c26e663ac9995de535bf32b7353a5d0
Git reference: master
Release notes:

Basic package with no dependencies for reading and writing XML, ASCII and XML PList files.

Line 133 says: ERROR: LoadError: RegistryCI.AutoMerge.AutoMergeGuidelinesNotMet("The automerge guidelines were not met.")
However there is only a stack backtrace and no clear explanation of what exactly I am missing to get accepted.


Herring case study with SDTool to reduce the number of trips, reduce the number of ages (BioSim/SampleOptim) (probably by the begginning of May)

It is completed


WebSocket connection to 'ws://localhost:4000/ws' failed

I don't know what is happening or where this is coming from but the client is constantly trying to connect to this web socket and failing ...

There is a placeholder for websockets (in apiCore) but I'm not sure what could be calling it. So ... it's probably not the stack.
What it could be is the hot-reload in the Nuxt dev environment which does use sockets to check for code changes. You might want to try refreshing your Nuxt / yarn install (delete the .nuxt and node_modules folders in frontend and then yarn install again).

Thanks, it was something nuxt related so I fixed it by putting watch: false, inside the nuxt.config.ts/content dict


Wrong MODEL writing PDB file

The fields should foolw:
pdb formats              1         2         3
123456789012345678901234567890
model          = "MODEL     {0:4d}"
atom           = "ATOM  {0:5d} {1:^4s}{2:1s}{3:3s} {4:1s}{5:4d}{6:1s}   {7:8.3f}{8:8.3f}{9:8.3f}{10:6.2f}{11:6.2f}          {12:>2s}{13:2s}"
ter            = "TER   {0:5d}      {1:3s} {2:1s}{3:4d}{4:1s}"
https://github.com/Matheus-Mello/NDB-Converters/blob/master/ndb2pdb.py

Fixed in the last version.


Clean description

We must strip :space: because meta-tags won't stlip spaces like nbsp.

This is サイコー！


Gmail (and other Google Auth apps) authorization error

I heard the news and replaced my old station client with the new open-source version.
Now I'm trying to get setup again and connecting my Gmail account but I can't make it work. No matter how often I try, I always get the same error message:

Does anyone have the same issue or knows how to fix that? Thanks in advance.

Details:
I'm on macOS Big Sure 11.4 and I installed the newest version of Station, which was linked in the email (v2.0.9)

I'm experiencing the same issue on the windows version (v2.0.9 - linked in the email.)
I've also noticed I encounter the same error when trying to authenticate in Google Keep.

Same issue for macOS Big Sure 11.4 and macOS Sierra - also Google log-in  issue with Trello which thinks the browser is unsafe

Same issue on macOS Big Sure 11.2, no access to Google tools.

Same issue here, macOS 10.14.6

Same issue here. Windows 10 1909.

A temporary work around for this is to create your own custom app and use the following URL:
https://mail.google.com/mail/u/0/#inbox
How to do it:

Click on the + icon in the bottom left
Select My Custom Apps from the left hand menu
Click on Add a custom app in the top right.
Give it a name like Gmail.
Click on the add button.
Enter a colour hex code you like. e.g. #000000 for black.
Select a logo like the mail logo.
Enter the following URL: https://mail.google.com/mail/u/0/#inbox
Click the add button.
Click the install now button.
Click on the app icon you selected from the left hand menu and log in with google account.

That should work until a fix can be sorted out.

Same issue here, thanks for the temp workaround!

Somehow it does work on the old version that I use
Station Canary version 0.19.131

A temporary work around for this is to create your own custom app and use the following URL:
https://mail.google.com/mail/u/0/#inbox
How to do it:

Click on the + icon in the bottom left
Select My Custom Apps from the left hand menu
Click on Add a custom app in the top right.
Give it a name like Gmail.
Click on the add button.
Enter a colour hex code you like. e.g. #0 for black.
Select a logo like the mail logo.
Enter the following URL: https://mail.google.com/mail/u/0/#inbox
Click the add button.
Click the install now button.
Click on the app icon you selected from the left hand menu and log in with google account.

That should work until a fix can be sorted out. It only works for one account at a time though.

Didn't work for me unfortunately. Google told me the browser I'm using is unsafe and refused to log me in.

This has probably something to do with this issue here: https://github.com/getstation/desktop-app/issues/9 but who knows--with such complexity--when this will be fixed

It looks like the Client Id is not filled in the url. Incase that helps, I have the url that is missing client_id value. @ssandison
accounts.google.com/signin/v2/identifier?continue=https%3A%2F%2Faccounts.google.com%2Fo%2Foauth2%2Fv2%2Fauth%3Faccess_type%3Doffline%26scope%3Dhttps%253A%252F%252Fwww.googleapis.com%252Fauth%252Fplus.me%2520profile%2520email%26redirect_uri%3Dhttp%253A%252F%252F<IP_ADDRESS>%253A42813%252Fcallback%26response_type%3Dcode%26client_id%3D&flowName=GlifWebSignIn&flowEntry=AddSession

For now, I've reverted back to the old version 1.65.0 which I found here:
https://www.macupdate.com/app/mac/60202/station
https://mac.softpedia.com/get/Internet-Utilities/getStation.shtml
Note, 1.65.0 will stop working on 8.31

@krunk4ever very helpful, thanks! Will need to find another solution after end of August.

A temporary work around for this is to create your own custom app and use the following URL:
https://mail.google.com/mail/u/0/#inbox
How to do it:

Click on the + icon in the bottom left
Select My Custom Apps from the left hand menu
Click on Add a custom app in the top right.
Give it a name like Gmail.
Click on the add button.
Enter a colour hex code you like. e.g. #0 for black.
Select a logo like the mail logo.
Enter the following URL: https://mail.google.com/mail/u/0/#inbox
Click the add button.
Click the install now button.
Click on the app icon you selected from the left hand menu and log in with google account.

That should work until a fix can be sorted out. It only works for one account at a time though.

This worked for me, Calendar still does not work

@Joshstomp For Calendar, you can do the same thing and just use this URL: https://calendar.google.com/calendar/u/0/r

Any workarounds to have more than one Gmail account logged in at the same time?

Having same issue, not being able to use Gmail accounts at all. I have several and station has been the "email" client for me.
Have to look some other ways, maybe just create own iframe style html file with the accounts as tabs and use through normal browser instance.

Same issue  --  haven't found a workaround yet for multiple accounts :(

I (quite innocently) tried to edit the authorization link by pasting the Client ID for the previous version — 3D382046058303-cghjkl19vsm6deuc9cc336fdpev5f7jt.apps.googleusercontent.com — in the place where the current Client ID should be.
Authorization went through, and it even called back the app, but the authorized account wasn't recognized by Station.
I guess, then, a really easy temporary fix would be for the devs to provide us with the Client ID for the current version.
I don't know if it is a problem, as I'm just a beginner. Well established companies have disclosed their Client IDs, but I don't really know the impact of this decision on a small open source project.

Same issue here, is there any update?

Same issue here, is there any update?

This is dead. Probably is an abandoned project, I would look for an alternative like pinning tabs in edge. Good luck!

Don't know about that. Last release was just a month ago. Let's hope the developers are just too busy to answer hahaha

I don't think they can fix it. The reason being you need a client ID from
Google to access the APIs. Previously Station were presumably using their
account to get the keys for the API for the app. Now they have open sourced
it, they have removed their keys. Some of these Google APIs cost money
based on the amount of requests. Really they should have provided a way for
people to add their own API keys into the settings at the very least.
On Wed, 25 Aug 2021 at 19:19, Tuba @.***> wrote:

Same issue here, is there any update?
This is dead. Probably is an abandoned project, I would look for an
alternative like pinning tabs in edge. Good luck!
Don't know about that. Last release was just a month ago. Let's hope the
developers are just too busy to answer hahaha
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One thing I discovered to enable other google apps is to use the nine dots app icon inside gmail to access drive, calendar etc.
it will open a new station tab with the correct app logged in.

Station, Any update here? This is a major issue.

I think people have given up and switched to something like Stack. That’s what I’ve done and the experience is pretty similar.

On 15 Jan 2022, at 14:38, Smithbc @.***> wrote:

Station, Any update here? This is a major issue.
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Is Stack open source?
On January 15, 2022 at 8:43:39 AM, ssandison @.***)
wrote:

I think people have given up and switched to something like Stack. That’s
what I’ve done and the experience is pretty similar.

On 15 Jan 2022, at 14:38, Smithbc @.***> wrote:

Station, Any update here? This is a major issue.
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I don’t think so. Station was opened source because it’s been abandoned. If you want to stick with it you will probably need to get an account for the google APIs that it needs to use and generate keys to connect to the APIs. I think that’s why it no longer works. It’s a lot of hassle if you’re just wanting something that works rather than to maintain it yourself.

On 16 Jan 2022, at 04:16, Smithbc @.***> wrote:

Is Stack open source?
On January 15, 2022 at 8:43:39 AM, ssandison @.***)
wrote:

I think people have given up and switched to something like Stack. That’s
what I’ve done and the experience is pretty similar.

On 15 Jan 2022, at 14:38, Smithbc @.***> wrote:

Station, Any update here? This is a major issue.
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Not open source but completely free for all users. You can donate money if
you want but they’re not needed! Give it a go :)
On Sun, 16 Jan 2022 at 05:16, Smithbc @.***> wrote:

Is Stack open source?
On January 15, 2022 at 8:43:39 AM, ssandison @.***)
wrote:

I think people have given up and switched to something like Stack. That’s
what I’ve done and the experience is pretty similar.

On 15 Jan 2022, at 14:38, Smithbc @.***> wrote:

Station, Any update here? This is a major issue.
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Here your open source alternative. Works great without affecting the pc performance.
Rambox: https://rambox.app/#home

Here your open source alternative. Works great without affecting the pc performance. Rambox: https://rambox.app/#home

Rambox is not Open Source any more

There is always the Community Edition for that https://github.com/ramboxapp/community-edition

Here your open source alternative. Works great without affecting the pc performance. Rambox: https://rambox.app/#home

Rambox is not Open Source any more

There is always the Community Edition for that https://github.com/ramboxapp/community-edition

Fixed in 2.1.0


Raise isDisposed from AbstractMesh class to Node class

Hi,
The isDisposed() public method (and the _isDisposed private property) is declared in the AbstractMesh class.
Considering the public method dispose() can be called on any Node instance, is there a reason not to move isDisposed() at the Node class level ?
Thanks !

No problem:)

Thanks a lot !


Error Fix for OOOr client - OpenERB database wrong error

Fixing error shown below when OpenERP database name supplied is wrong to OOOr client
Added a validate method with more informative stack trace.

ERROR BELOW  -
/home/kannan/.rvm/gems/ruby-2.2.1/gems/ooor-2.1.0/lib/ooor/services.rb:51:in login': undefined method []' for nil:NilClass (NoMethodError)
from /home/kannan/.rvm/gems/ruby-2.2.1/gems/ooor-2.1.0/lib/ooor/services.rb:85:in object_service' 	from /home/kannan/.rvm/gems/ruby-2.2.1/gems/ooor-2.1.0/lib/ooor/session.rb:98:in read_model_data'
from /home/kannan/.rvm/gems/ruby-2.2.1/gems/ooor-2.1.0/lib/ooor/session.rb:84:in load_models' 	from /home/kannan/.rvm/gems/ruby-2.2.1/gems/ooor-2.1.0/lib/ooor/session.rb:47:in global_login'
from /home/kannan/.rvm/gems/ruby-2.2.1/gems/ooor-2.1.0/lib/ooor/railtie.rb:15:in block in <class:Railtie>' 	from /home/kannan/.rvm/gems/ruby-2.2.1/gems/railties-4.2.0/lib/rails/initializable.rb:30:in instance_exec'
from /home/kannan/.rvm/gems/ruby-2.2.1/gems/railties-4.2.0/lib/rails/initializable.rb:30:in run' 	from /home/kannan/.rvm/gems/ruby-2.2.1/gems/railties-4.2.0/lib/rails/initializable.rb:55:in block in run_initializers'
from /home/kannan/.rvm/rubies/ruby-2.2.1/lib/ruby/2.2.0/tsort.rb:226:in block in tsort_each' 	from /home/kannan/.rvm/rubies/ruby-2.2.1/lib/ruby/2.2.0/tsort.rb:348:in block (2 levels) in each_strongly_connected_component'
from /home/kannan/.rvm/rubies/ruby-2.2.1/lib/ruby/2.2.0/tsort.rb:429:in each_strongly_connected_component_from' 	from /home/kannan/.rvm/rubies/ruby-2.2.1/lib/ruby/2.2.0/tsort.rb:347:in block in each_strongly_connected_component'
from /home/kannan/.rvm/rubies/ruby-2.2.1/lib/ruby/2.2.0/tsort.rb:345:in each' 	from /home/kannan/.rvm/rubies/ruby-2.2.1/lib/ruby/2.2.0/tsort.rb:345:in call'
from /home/kannan/.rvm/rubies/ruby-2.2.1/lib/ruby/2.2.0/tsort.rb:345:in each_strongly_connected_component' 	from /home/kannan/.rvm/rubies/ruby-2.2.1/lib/ruby/2.2.0/tsort.rb:224:in tsort_each'
from /home/kannan/.rvm/rubies/ruby-2.2.1/lib/ruby/2.2.0/tsort.rb:203:in tsort_each' 	from /home/kannan/.rvm/gems/ruby-2.2.1/gems/railties-4.2.0/lib/rails/initializable.rb:54:in run_initializers'
from /home/kannan/.rvm/gems/ruby-2.2.1/gems/railties-4.2.0/lib/rails/application.rb:352:in initialize!' 	from /home/kannan/Documents/7NODES/external-projects/Metawarelabs-projects/pands/config/environment.rb:5:in <top (required)>'
from /home/kannan/.rvm/gems/ruby-2.2.1/gems/activesupport-4.2.0/lib/active_support/dependencies.rb:274:in require' 	from /home/kannan/.rvm/gems/ruby-2.2.1/gems/activesupport-4.2.0/lib/active_support/dependencies.rb:274:in block in require'
from /home/kannan/.rvm/gems/ruby-2.2.1/gems/activesupport-4.2.0/lib/active_support/dependencies.rb:240:in load_dependency' 	from /home/kannan/.rvm/gems/ruby-2.2.1/gems/activesupport-4.2.0/lib/active_support/dependencies.rb:274:in require'
from /home/kannan/.rvm/gems/ruby-2.2.1/gems/spring-1.2.0/lib/spring/application.rb:92:in preload' 	from /home/kannan/.rvm/gems/ruby-2.2.1/gems/spring-1.2.0/lib/spring/application.rb:143:in serve'
from /home/kannan/.rvm/gems/ruby-2.2.1/gems/spring-1.2.0/lib/spring/application.rb:131:in block in run' 	from /home/kannan/.rvm/gems/ruby-2.2.1/gems/spring-1.2.0/lib/spring/application.rb:125:in loop'
from /home/kannan/.rvm/gems/ruby-2.2.1/gems/spring-1.2.0/lib/spring/application.rb:125:in run' 	from /home/kannan/.rvm/gems/ruby-2.2.1/gems/spring-1.2.0/lib/spring/application/boot.rb:18:in <top (required)>'
from /home/kannan/.rvm/rubies/ruby-2.2.1/lib/ruby/site_ruby/2.2.0/rubygems/core_ext/kernel_require.rb:54:in require' 	from /home/kannan/.rvm/rubies/ruby-2.2.1/lib/ruby/site_ruby/2.2.0/rubygems/core_ext/kernel_require.rb:54:in require'
from -e:1:in `'

Coverage decreased (-42.12%) to 48.69% when pulling 2a4322cf7ef0cfa8fa90d4294eec11513343420f on kannancet:error_service_fix into 8393f12f264af79703844d5cf9ddd039a5fe3061 on akretion:master.


[WIP] GDScript: Disable LSP if either jsonrpc or websocket are disabled

Follow-up to #29780, solves this comment: https://github.com/godotengine/godot/pull/29780#discussion_r318520008
CC @Geequlim @ankitpriyarup

Wait that's likely not enough as things get registered in the base module too.

Should be ready for review.


Identifiers declared in super types spec

There's ambiguity in whether we should allow a class to override an identifying field declared in a super type.
For example, this code is currently disabled:
https://github.com/hyperledger/composer-concerto/blob/master/lib/introspect/classdeclaration.js#L201

Do we actually allow override at all?! With what semantic?


{prefix}servers and {prefix}server id

error code is
{prefix}servers
message.client.guilds.cache.array is not a function
at module.exports.run  (/home/runner/boltza/src/commands/owner/servers.js:16:49)
at module.exports.runCommand (/home/runner/boltza/src/events/message/messageCreate.js:307:19)
at module.exports.run (/home/runner/boltza/src/events/message/messageCreate.js:281:20)
{prefix}server id

has a different error
Cannot read properties of undefined (reading 'user')

fixed in https://github.com/Pogy-Bot/Pogy/commit/9dfca80a74fee2289ad17f201e511c3a27d1da4c
I recommend you delete your old src folder and update.


Rfc5737

I think there are still some prefixes which could be updated but thought i would send this early in case there is no desire to switch.  Should probably also switch to rfc5398 ASN's

I don't have objections. Especially for the documentation, I should have done it in the first place. I'm scared about the tests, but should not be impossible to change them, as long as they maintain the ip version, the perfix length, and in some cases the hierarchy among each other (in some tests less/more specifics are important). Alternatively, we can start only with the documentation.

cool, ill try and tidy this up a bit next week, its definitely not a big issue, it just looked odd when i was looking at the logs and forgot i had run with --test :) e.g.
2022-01-11T19:08:05+00:00 verbose: type:announcement timestamp:1641928085841 prefix:2a00:5884::/32 peer:<IP_ADDRESS> path:[1,2,3,204092] nextHop:<IP_ADDRESS> aggregator:null

a simpler fix may be to add some "test" annotation to theses log lines


util: cli: Unify configuration

Right now the code for parsing command line arguments in dffml/base.py and dffml/util/cli/. We should get rid of the arg_ notation when defining CLI commands and replace it with the CONFIG = ExampleConfig style syntax (#164). This will probably involve moving that config parsing code from dffml/base.py into util, somewhere like dffml/util/config.py (or something), and then using it in dffml/util/cli/.

After we merge this we'll want to get rid of position, because we realized that the information on position is just the same as the index of the field within the config class.


docker镜像seataio/seata-server:latest里有xstream-1.4.17.jar，有很多安全漏洞

[x] I have searched the issues of this repository and believe that this is not a duplicate.

Ⅰ. Issue Description
➜  ~ docker run -ti --rm --entrypoint sh seataio/seata-server
# ls -l /seata-server/libs/ | grep xstream
-rw-r--r-- 1 root root  629806 Jan  1  1970 xstream-1.4.17.jar

https://x-stream.github.io/security.html
xstream 1.4.17 和 1.4.18 有以下漏洞

Version 1.4.18

CVE-2021-43859
XStream can cause a Denial of Service by injecting highly recursive collections or maps.

Version 1.4.17

CVE-2021-39139
XStream is vulnerable to an Arbitrary Code Execution attack.

CVE-2021-39140
XStream can cause a Denial of Service.

CVE-2021-39141
XStream is vulnerable to an Arbitrary Code Execution attack.

CVE-2021-39144
XStream is vulnerable to a Remote Command Execution attack.

CVE-2021-39145
XStream is vulnerable to an Arbitrary Code Execution attack.

CVE-2021-39146
XStream is vulnerable to an Arbitrary Code Execution attack.

CVE-2021-39147
XStream is vulnerable to an Arbitrary Code Execution attack.

CVE-2021-39148
XStream is vulnerable to an Arbitrary Code Execution attack.

CVE-2021-39149
XStream is vulnerable to an Arbitrary Code Execution attack.

CVE-2021-39150
A Server-Side Forgery Request can be activated unmarshalling with XStream to access data streams from an arbitrary URL referencing a resource in an intranet or the local host.

CVE-2021-39151
XStream is vulnerable to an Arbitrary Code Execution attack.

CVE-2021-39152
A Server-Side Forgery Request can be activated unmarshalling with XStream to access data streams from an arbitrary URL referencing a resource in an intranet or the local host.

CVE-2021-39153
XStream is vulnerable to an Arbitrary Code Execution attack.

CVE-2021-39154
XStream is vulnerable to an Arbitrary Code Execution attack.

Ⅱ. Describe what happened
If there is an exception, please attach the exception trace:
Just paste your stack trace here!

Ⅲ. Describe what you expected to happen
Ⅳ. How to reproduce it (as minimally and precisely as possible)

xxx
xxx
xxx

Ⅴ. Anything else we need to know?
Ⅵ. Environment:

JDK version :
Seata version:
OS :
Others:

plz assign to me


Error on Safari: ReferenceError: Can't find variable: BigUint64Array

Currently the examples don't work for me on Safari 14.0.3 (latest currently available): https://flatgeobuf.org/examples/leaflet/index.html
Console output:
[Error] ReferenceError: Can't find variable: BigUint64Array
	(anonymous function) (flatgeobuf-geojson.min.js:1:19960)
	(anonymous function) (flatgeobuf-geojson.min.js:1:142)
	Global Code (flatgeobuf-geojson.min.js:1:212)
[Error] Unhandled Promise Rejection: TypeError: flatgeobuf.deserialize is not a function. (In 'flatgeobuf.deserialize(response.body, undefined, handleHeaderMeta)', 'flatgeobuf.deserialize' is undefined)
	handleResponse (index.js:22)
	promiseReactionJob

BigUint64Array is not currently supported on Safari (including iOS): https://caniuse.com/?search=BigUint64Array

Apparently this is implemented, but not yet released:
Implement BigInt64Array and BigUint64Array:
https://bugs.webkit.org/show_bug.cgi?id=190800
committed:
https://trac.webkit.org/changeset/272170/webkit
The good news is that I just tried it in https://developer.apple.com/safari/technology-preview/ and it works. I don't know when this will reach mainline though, and even when it is released, it'll be a while before it rolls out to users. It'd be nice if there were some kind of fallback for older Safari/iOS.

Thanks for reporting, I was not aware and would like to find out why it is used. But perhaps it can be polyfilled?

It looks like it's only used in https://github.com/flatgeobuf/flatgeobuf/blob/ee6548d/src/ts/ColumnMeta.ts#L12
const arrayTypeMap = {
    [ColumnType.Byte]: Uint8Array,
    [ColumnType.UByte]: Uint8Array,
    [ColumnType.Bool]: Uint8Array,
    [ColumnType.Short]: Uint16Array,
    [ColumnType.UShort]: Uint16Array,
    [ColumnType.Int]: Uint32Array,
    [ColumnType.UInt]: Uint32Array,
    # Used here
    [ColumnType.Long]: BigUint64Array,
    # Used here
    [ColumnType.ULong]: BigUint64Array,
    [ColumnType.Float]: Float64Array,
    [ColumnType.Double]: Float64Array,
    [ColumnType.String]: String,
    [ColumnType.Json]: String,
    [ColumnType.DateTime]: String,
    [ColumnType.Binary]: String
}

I think this means, if your feature data includes Long/ULong, it's mapped to this type.

There is a pure-js implementation of BigNum which might be useful.
https://github.com/GoogleChromeLabs/jsbi/issues/4
Only problem is it also seems to not implement 64bit handling 😓, but there is a (stalled?) PR which seems to work towards that:
https://github.com/GoogleChromeLabs/jsbi/pull/18

Hmm funky.. I've completely forgot what I'm using that array type for. 😆

Hmm I made use of it when refactoring property encoding in https://github.com/flatgeobuf/flatgeobuf/pull/63. I wanted to avoid having to preallocate... the complexity of it is a bit too much though now that I look at it again. But not sure if I can figure out a better approach.

Reworked with https://github.com/flatgeobuf/flatgeobuf/commit/08f85cff7811259e2ea33c43a155f3bf789fd13f so that it could be removed with https://github.com/flatgeobuf/flatgeobuf/commit/c57150181ea148199fbeba131d0bb7f40cc5a588.

Verified that this fixes things for me. Thanks!