GLUE | linked unified embedding for single-cell multi | Genomics library

 by   gao-lab Python Version: v0.3.2 License: MIT

kandi X-RAY | GLUE Summary

kandi X-RAY | GLUE Summary

GLUE is a Python library typically used in Artificial Intelligence, Genomics applications. GLUE has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install GLUE' or download it from GitHub, PyPI.

Graph-linked unified embedding for single-cell multi-omics data integration. For more details, please check out our preprint.
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              GLUE has a low active ecosystem.
              It has 249 star(s) with 37 fork(s). There are 5 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 11 open issues and 62 have been closed. On average issues are closed in 15 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of GLUE is v0.3.2

            kandi-Quality Quality

              GLUE has 0 bugs and 0 code smells.

            kandi-Security Security

              GLUE has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              GLUE code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              GLUE is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              GLUE releases are available to install and integrate.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.

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            GLUE Key Features

            No Key Features are available at this moment for GLUE.

            GLUE Examples and Code Snippets

            No Code Snippets are available at this moment for GLUE.

            Community Discussions

            QUESTION

            Can I convert RDD to DataFrame in Glue?
            Asked 2022-Mar-20 at 13:58

            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 13:58

            You 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 -

            Source https://stackoverflow.com/questions/71547278

            QUESTION

            Problems when writing parquet with timestamps prior to 1900 in AWS Glue 3.0
            Asked 2022-Feb-10 at 13:45

            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 13:45

            I 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:

            Source https://stackoverflow.com/questions/68891312

            QUESTION

            How to pass a dynamic column name in a pipe in custom function in R
            Asked 2022-Feb-07 at 08:03

            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 07:47

            Unfortunately 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

            Source https://stackoverflow.com/questions/71014763

            QUESTION

            Mutate using glue in a user defined function
            Asked 2022-Feb-06 at 13:15

            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 15:36

            Another option could be:

            Source https://stackoverflow.com/questions/68623850

            QUESTION

            AWS Checking StateMachines/StepFunctions concurrent runs
            Asked 2022-Feb-03 at 10:41

            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 14:39

            You 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.

            Source https://stackoverflow.com/questions/70813239

            QUESTION

            AWS Glue 3.0 container not working for Jupyter notebook local development
            Asked 2022-Jan-16 at 11:25

            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 11:25

            It 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).

            Source https://stackoverflow.com/questions/70491686

            QUESTION

            How to use INLINE HTML to make text white on dark background automatically after setting background from palette
            Asked 2022-Jan-16 at 09:28

            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 09:28

            One option would be prismatic::best_contrast. By default it will not use pure white so we have to set the colors:

            Source https://stackoverflow.com/questions/70728687

            QUESTION

            How to download multiple files from R/Shiny app?
            Asked 2021-Dec-16 at 23:55

            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 23:55

            A few things edited and it's working:

            • using dir instead of ls inside the zip::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.

            Source https://stackoverflow.com/questions/70386165

            QUESTION

            How to call async/await JavaScript function in Unity/C# WebGL platform?
            Asked 2021-Nov-11 at 18:39

            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 09:27

            tl;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

            Source https://stackoverflow.com/questions/69923986

            QUESTION

            How to evaluate a glue expression in a nested function?
            Asked 2021-Oct-30 at 07:03

            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 23:37

            name is not a symbol. Try:

            Source https://stackoverflow.com/questions/69775343

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install GLUE

            The scglue package can be installed either via conda:. Installing within a conda environment is recommended.

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            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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