pype | An interactive python driven filter for processing files | Genomics library
kandi X-RAY | pype Summary
kandi X-RAY | pype Summary
Pipe files to python.
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QUESTION
I am using docudmentDB(version 3.6) in AWS. I use a python lambda in AWS for this task. The task is to rename a field that is in an array. Here is the sample JSON document I have. Here I need to rename 'version' to 'label'.
...ANSWER
Answered 2021-May-13 at 21:12Amazon DocumentDB does not support $map. For the complete list of APIs that DocumentDB supports, refer to https://docs.aws.amazon.com/documentdb/latest/developerguide/mongo-apis.html.
We are constantly working backwards from the APIs our customers are looking to use. You can keep an eye on our future launches here https://aws.amazon.com/documentdb/resources/
QUESTION
I am currently working on a project where I need to create multiple fork who read from different pipe until the pipe closed. The issue here is that if I create more than one pipe, even if I close both side of all the pipe the child are still stuck on read.
Here is a simplify version of my code with the same issue:
...ANSWER
Answered 2021-Mar-18 at 15:33So thanks to Bodo I found the issue Here is a correct version of the code:
QUESTION
I'm working with a module called VMTK to build scripts for analyzing vascular models. They have a tutorial for writing these scripts so they're easily identifiable by the system allowing you to pipe scripts together known as PypeS. I've followed the tutorial exactly as shown and end up with the same "No module named: vmtk.name_of_script" error.
What I've tried:
- Putting the script in the same directory as all the preloaded scripts provided by the module so
__init__.py
could catch it - Copy-pasting the code from the website into my editor so I'm sure there are no errors in what I've written
- Submitting the question directly onto the forum meant for questions about VMTK, with no responses for the past week and a half
- Changing my Python interpreter to the one within the VMTK directory
The tutorial says you can put the custom script anywhere in your filesystem, but the issue arises no matter what. I'm currently using Python 3.6.10 through Anaconda and a binary install of VMTK (as opposed to building from source) on MacOS High Sierra.
I really don't want to have to build from source, as I only need the preloaded scripts and ability to write new scripts, as opposed to using the C++ files that the scripts are built from. I've been stuck for so long and am not at all sure what the issue is. The closest thing I found was an SO question addressing this problem, but the OP simply said the problem had been resolved and provided no other information.
Here's the aforementioned code:
...ANSWER
Answered 2020-Jul-29 at 02:50The solution I found after a week of trying and searching:
git clone
the vmtk repo onto your computer and follow the VMTK download instructions on how to build it from source. It will absolutely feel like a headache and be a long process; just wait it out.- If you don't have cmake installed on your computer, they offer a GUI version on their website. I'm not sure how it would work for Windows, but it definitely works for Mac.
Once you've built it, make sure that each terminal instance of VMTK you set
source vmtk_env.sh
from the path where that file is. This will allow you to use the VMTK environment.After writing the custom script, making sure to follow all the directions in the tutorial (assuming this is the first time), make sure to save it in the "site-packages" folder in the build folder. The path for me is "vmtk-build/lib/python-2.7/site-packages/vmtk/". I'm currently looking to update the version of Python it's using, but that's not the point.
Once that's done, navigate to that folder from within terminal and run
chmod u+x name_of_script.py
(if you're in a Unix-based operating system). This will allow you to execute the file with./name_of_script.py
.I believe it was due to the version of Python VMTK is using, but I had two "No module named" errors come up, each one a separate time: one for
tkinter
and one forjoblib
.The
tkinter
issue is one that can be resolved by going into the file where the import is, I believevmtkscripts.py
, and changing all instances oftkinter
toTkinter
(capital T). This is because they changed the name of the module from Python 2 to 3, so in newer versions of Python it would betkinter
. That fixed the first error.When I attempted to fix the
joblib
issue, I saw that the other version of Python available on my system already had it, thus I couldn't install it through pip. Instead, you can dopython-2.7 -m pip install joblib
to install it for a specific version of Python. Although I did uninstalljoblib
as a whole from my computer before doing that.
That should fix everything. The next time I attempted to run my script, it ran without any errors.
Extra: I wasn't using any Anaconda environment for this. Might go back and try to set that up, but I'm just glad I got it to work. Additionally, I deleted the binary install of VMTK from my computer. No need to keep it around if you're just going to build it from source. You can run VMTK through the terminal after setting source vmtk_env.sh
by running the vmtk
command.
QUESTION
While writing PDF file to HTML file format using the code below...
...ANSWER
Answered 2018-Oct-27 at 10:22Please update to the latest version of the jbig2 decoder, which is 3.0.2. The jbig2 decoder is now a part of Apache PDFBox, thanks to levigo solutions GmbH. For maven, use this:
QUESTION
When writing data exceeding 4096 bytes to Cmd.StdinPipe
in Go, program processing stops on Windows. This phenomenon does not occur when the same code running on Linux, or when writing process using goroutine.
Processing will not proceed from _, err = in.Write ([] byte {'0'})
(4097 bytes) in the code shown below. Why is this?
Why does not it occur with goroutine or on Linux?
*** Golang reference describes Cmd.StdinPipe using goroutine as an example, and my problem has also been solved. This question arises from curiosity about Go.
...ANSWER
Answered 2018-May-01 at 14:58Writing only blocks if no more space is in the pipe. While the size of the pipe in Windows might be 4k it is much larger in Linux. From pipe(7):
... Since Linux 2.6.11, the pipe capacity is 16 pages (i.e., 65,536 bytes in a system with a page size of 4096 bytes)...
Thus, you will probably get the same result on Linux as on Windows when writing into a pipe where nobody is reading but you need to write way more data into the pipe until you reach this situation.
QUESTION
I'm trying to create aliases that I can use in Vagrant any time I run the VM. I've found several sources on the web about it, but can't get it working. I tried making a .bash_profile in my synced folder, but that didn't work. I noticed if I run the command alias name="command" this will work, but only for the current session. Anyone know how to do this? I'm using macOS. Thanks for your help!
Here is my Vagrantfile:
...ANSWER
Answered 2017-Oct-23 at 23:53The details depend on the specific of the guest being run, but some notes:
- Assuming the default user account is active for
vagrant ssh
, ensure that any dotfiles you wish to override are copied to/home/vagrant
. - If overriding
.bashrc
, ensure that the remote shell is started with the interactive flag (if this is true,echo $-
will includei
). - If overriding
.bash_profile
, ensure that the remote shell is started as a login shell (if this is true,echo $-
will includel
).
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Install pype
You can use pype like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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