GLUE | linked unified embedding for single-cell multi | Genomics library
kandi X-RAY | GLUE Summary
kandi X-RAY | GLUE Summary
Graph-linked unified embedding for single-cell multi-omics data integration. For more details, please check out our preprint.
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QUESTION
my lambda function triggers glue job by boto3 glue.start_job_run
and here is my glue job script
...ANSWER
Answered 2022-Mar-20 at 13:58You can't define schema types using toDF()
. By using toDF()
method, we don't have the control over schema customization. Having said that, using createDataFrame()
method we have complete control over the schema customization.
See below logic -
QUESTION
When switching from Glue 2.0 to 3.0, which means also switching from Spark 2.4 to 3.1.1, my jobs start to fail when processing timestamps prior to 1900 with this error:
...ANSWER
Answered 2022-Feb-10 at 13:45I made it work by setting --conf
to spark.sql.legacy.parquet.int96RebaseModeInRead=CORRECTED --conf spark.sql.legacy.parquet.int96RebaseModeInWrite=CORRECTED --conf spark.sql.legacy.parquet.datetimeRebaseModeInRead=CORRECTED --conf spark.sql.legacy.parquet.datetimeRebaseModeInWrite=CORRECTED
.
This is a workaround though and Glue Dev team is working on a fix, although there is no ETA.
Also this is still very buggy. You can not call .show()
on a DynamicFrame
for example, you need to call it on a DataFrame
. Also all my jobs failed where I call data_frame.rdd.isEmpty()
, don't ask me why.
Update 24.11.2021: I reached out to the Glue Dev Team and they told me that this is the intended way of fixing it. There is a workaround that can be done inside of the script though:
QUESTION
I've created a dynamic column name w/ dplyr::mutate() based on this thread Use dynamic variable names in `dplyr` and now I want to sort the new column.... but I'm not correctly passing the column name
...ANSWER
Answered 2022-Feb-07 at 07:47Unfortunately I don't know if any way to use that nice glue syntax with anything that's not on the left side of a :=
. That's there the magic happens. You can get something to work if you take care of the explicity conversion to sumbol your self and do the string building manually. It's not pretty, but this works
QUESTION
I would like to change the values in a specific column to include information from another column using the glue
function.
I do it normally like this:
...ANSWER
Answered 2021-Aug-02 at 15:36Another option could be:
QUESTION
I am having a lot of issues handling concurrent runs of a StateMachine (Step Function) that does have a GlueJob task in it.
The state machine is initiated by a Lambda that gets trigger by a FIFO SQS queue.
The lambda gets the message, checks how many of state machine instances are running and if this number is below the GlueJob concurrent runs threshold, it starts the State Machine.
The problem I am having is that this check fails most of the time. The state machine starts although there is not enough concurrency available for my GlueJob. Obviously, the message the SQS queue passes to lambda gets processed, so if the state machine fails for this reason, that message is gone forever (unless I catch the exception and send back a new message to the queue).
I believe this behavior is due to the speed messages gets processed by my lambda (although it's a FIFO queue, so 1 message at a time), and the fact that my checker cannot keep up.
I have implemented some time.sleep() here and there to see if things get better, but no substantial improvement.
I would like to ask you if you have ever had issues like this one and how you got them programmatically solved.
Thanks in advance!
This is my checker:
...ANSWER
Answered 2022-Jan-22 at 14:39You are going to run into problems with this approach because the call to start a new flow may not immediately cause the list_executions()
to show a new number. There may be some seconds between requesting that a new workflow start, and the workflow actually starting. As far as I'm aware there are no strong consistency guarantees for the list_executions()
API call.
You need something that is strongly consistent, and DynamoDB atomic counters is a great solution for this problem. Amazon published a blog post detailing the use of DynamoDB for this exact scenario. The gist is that you would attempt to increment an atomic counter in DynamoDB, with a limit
expression that causes the increment to fail if it would cause the counter to go above a certain value. Catching that failure/exception is how your Lambda function knows to send the message back to the queue. Then at the end of the workflow you call another Lambda function to decrement the counter.
QUESTION
I am working on Glue in AWS and trying to test and debug in local dev. I follow the instruction here https://aws.amazon.com/blogs/big-data/developing-aws-glue-etl-jobs-locally-using-a-container/ to develop Glue job locally. On that post, they use Glue 1.0 image for testing and it works as it should be. However when I load and try to dev by Glue 3.0 version; I follow the guidance steps but, I can't open Jupyter notebook on :8888 like the post said even every step seems correct.
here my cmd to start a Jupyter notebook on Glue 3.0 container
...ANSWER
Answered 2022-Jan-16 at 11:25It seems that GLUE 3.0 image has some issues with SSL. A workaround for working locally is to disable SSL (you also have to change the script paths as documentation is not updated).
QUESTION
This question is somehow related but not depending to this Can you color an adjacent cell in gt table in r?:
I am explicitly looking for the modification of the part of my code!
I have this example dataset with colors of the background of mpg
column depending on the values applied with html.
ANSWER
Answered 2022-Jan-16 at 09:28One option would be prismatic::best_contrast
. By default it will not use pure white
so we have to set the colors:
QUESTION
There are a number of different Q/A's regarding this topic on SO, but none that I have been able to find that fit my use-case. I am also very surprised that RStudio / the Shiny developers themselves have not come out with some documentation on how to do this. Regardless, take this example application:
...ANSWER
Answered 2021-Dec-16 at 23:55A few things edited and it's working:
- using
dir
instead ofls
inside thezip::zip
call to show the contents of the temp directory (ls
lists R environment rather than directory contents) - as a further suggestion: making a new, unique folder inside
tempdir()
to ensure only relevant files are added.
QUESTION
I followed this doc to call JavaScript function from my C# script in Unity to make a WebGL game.
But there is a problem if the js code contains async/await, for example:
C# script:
...ANSWER
Answered 2021-Nov-11 at 09:27tl;dr: This is how. c#
doesn't need to be aware of the async
and it should work.
I just made a little test using
Assets/Plugins/mylib.jslib
QUESTION
I'm trying to nest a function that glues together two strings within a function that uses the combined string to name a column of a dataframe. However, the problem seems to be that the glue expression is not evaluated to a string early enough. Can (and should) I force the expression to be evaluated before it is being passed on as an argument to another function?
...ANSWER
Answered 2021-Oct-29 at 23:37name
is not a symbol. Try:
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