text:
unable to run multiple times

problem
Works fine the first call but calling consecutive times results in an error. Restarting the node process results in the call working but again just the one time.
Does not matter if the cloned repo is deleted or not, consecutive calls never work.
expected
Should be able to call the function repeatedly and get the same result
error
RangeError: path should be a `path.relative()`d string, but got "../repos-e709b5ad-83c9-439a-ad0c-22d3a1193cc1KMhgcm"
    at throwError (/app/node_modules/ignore/index.js:364:9)
    at checkPath (/app/node_modules/ignore/index.js:383:12)
    at Ignore._test (/app/node_modules/ignore/index.js:504:5)
    at Ignore.test (/app/node_modules/ignore/index.js:562:17)
    at analyse (/app/node_modules/linguist-js/dist/index.js:89:47)
    at runMicrotasks (<anonymous>)
    at processTicksAndRejections (node:internal/process/task_queues:96:5)
    at async Object.self.techStack (/app/src/lib.js:34:19)
    at async techStack (/app/src/controller.js:32:19)
2022-03-19T11:23:17.012Z error: uncaughtException: path should be a `path.relative()`d string, but got "../repos-e709b5ad-83c9-439a-ad0c-22d3a1193cc1KMhgcm"
RangeError: path should be a `path.relative()`d string, but got "../repos-e709b5ad-83c9-439a-ad0c-22d3a1193cc1KMhgcm"
    at throwError (/app/node_modules/ignore/index.js:364:9)
    at checkPath (/app/node_modules/ignore/index.js:383:12)
    at Ignore._test (/app/node_modules/ignore/index.js:504:5)
    at Ignore.test (/app/node_modules/ignore/index.js:562:17)
    at analyse (/app/node_modules/linguist-js/dist/index.js:89:47)
    at runMicrotasks (<anonymous>)
    at processTicksAndRejections (node:internal/process/task_queues:96:5)
    at async Object.self.techStack (/app/src/lib.js:34:19)
    at async techStack (/app/src/controller.js:32:19)

code
  const linguist = require('linguist-js');

  const fs = require('fs').promises;
  const path = require('path');
  const os = require('os');
  const { v4: uuid } = require('uuid');

  const tmpDir = () => fs.mkdtemp(path.join(os.tmpdir(), `repos-${uuid()}`));

  const run = async ({ org, repo, user, token }) => {
    const git = SimpleGit();
    const dir = await tmpDir();

    await git.clone(`https://${user}:${token}@github.com/${org}/${repo}.git`, dir);

    const stack = await linguist(dir, {
      categories: ['data', 'markup', 'programming', 'prose'],
      ignore: [
        'yarn.lock',
        'package-lock.json',
      ],
    });
  };

I've debugged the folder I pass to linguist "getting dir:..." and then at this line debugged what is being processed
Even though the second time passing a different folder, the first folder is some how being processed.
Seems to me the walk is cached or something?
first run
// path requested
Getting dir: /tmp/repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ

// contents of /tmp - note there are many other dirs from previous runs
[
  'repos-0a67eea0-9eda-4c26-93a9-f32b9766adffLmcAob',
  'repos-105be0e8-d125-41e8-bff5-7f4a79140901JijchF',
  'repos-21ae90ce-eb50-4ae6-95d8-bf6296a9f5a7iHmHEc',
  'repos-ba83e13b-b50a-490f-8e20-3b3080d61bfafAIOhl',
  'repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ', // <-- new one
  'v8-compile-cache-0',
  'yarn--1647698425451-0.859800277564736'
]
// line 50 of index.ts
resolvedInput [ '/tmp/repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ' ]
// line 51 or index.tx
commonRoot /tmp/repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ

// resolved dirs from walk
[
  '/tmp/repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ',
  '/tmp/repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ/.devcontainer',
  '/tmp/repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ/.github',
  '/tmp/repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ/.github/ISSUE_TEMPLATE',
  '/tmp/repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ/.github/workflows',
  ...
  .. 234 more items

Second run
// path requested - note it is different to last path
Getting dir: /tmp/repos-f6cf1998-0a1d-4318-ae5e-74faaa73f782cmIIii

// contents of /tmp
[
  'repos-0a67eea0-9eda-4c26-93a9-f32b9766adffLmcAob',
  'repos-105be0e8-d125-41e8-bff5-7f4a79140901JijchF',
  'repos-21ae90ce-eb50-4ae6-95d8-bf6296a9f5a7iHmHEc',
  'repos-ba83e13b-b50a-490f-8e20-3b3080d61bfafAIOhl',
  'repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ',
  'repos-f6cf1998-0a1d-4318-ae5e-74faaa73f782cmIIii', // <-- new one
  'v8-compile-cache-0',
  'yarn--1647698425451-0.859800277564736'
]
// line 50 of index.ts - note it is what was passed in so correct.
resolvedInput [ '/tmp/repos-f6cf1998-0a1d-4318-ae5e-74faaa73f782cmIIii' ]

// line 51, again correct
commonRoot /tmp/repos-f6cf1998-0a1d-4318-ae5e-74faaa73f782cmIIii

// resolved dirs from walk - Wrong values, contains last run
[
  '/tmp/repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ',
  '/tmp/repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ/.devcontainer',
  '/tmp/repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ/.github',
  '/tmp/repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ/.github/ISSUE_TEMPLATE',
  '/tmp/repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ/.github/workflows',

// error due to wrong path
2022-03-19T14:05:02.125Z error: uncaughtException: path should be a `path.relative()`d string, but got "../repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ"
RangeError: path should be a `path.relative()`d string, but got "../repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ"
    ...
2022-03-19T14:05:02.125Z error: uncaughtException: path should be a `path.relative()`d string, but got "../repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ"
RangeError: path should be a `path.relative()`d string, but got "../repos-f44970fe-ab18-4c05-a6c3-8905f8a53812jNbNMJ"
    ...

Seems it is here.

Thanks a lot for the debugging! I'll make a patch release for that today.

Should be fixed in 2.4.2

Confirmed working 🥇

source: gharchive/issue

repo: Nixinova/Linguist

license: ISC


text:
updated the db.json file with some new acronyms

updated the db.json file with some new acronyms, making use of the website to avoid duplicates.

Fixes Issue

Changes proposed

Check List (Check all the applicable boxes)

[ ] My code follows the code style of this project.
[ ] My change requires changes to the documentation.
[ ] I have updated the documentation accordingly.
[ ] All new and existing tests passed.
[ ] This PR does not contain plagiarized content.
[ ] The title of my pull request is a short description of the requested changes.

Screenshots

Note to reviewers

Brother write the acronyms you have added in the db.json file. It would be nice for the reviewer to check the deployment without looking at the code.

@theselaw how is this coming along?

Hello @theselaw are you still up for updating this? You'll have to check the abbreviations again because many of them have changed, and also the README because the method of adding abbreviations has also changed. If this PR stands for too long, I'll have to close it.

I'm sorry but I will have to close this PR. I has been stagnating for a while. Feel free to checkout more issues you may want to work on. Thank you nonetheless for your contribution.

source: gharchive/pull-request

authors: Njong392 PriyansuMaurya theselaw

license_type: permissive

license_source: github-api


text:
🛑 rimgo rimgo.nohost.network is down

In 73b93ce, rimgo rimgo.nohost.network (https://rimgo.nohost.network) was down:

HTTP code: 0
Response time: 0 ms

Resolved: rimgo rimgo.nohost.network is back up in 04cd833.

repo: NoPlagiarism/services-personal-upptime

license: MIT


text:
🛑 GotHub gothub.lunar.icu is down

In 1ed347a, GotHub gothub.lunar.icu (https://gothub.lunar.icu) was down:

HTTP code: 0
Response time: 0 ms

Resolved: GotHub gothub.lunar.icu is back up in 4387fd5.


text:
🛑 AnonymousOverflow overflow.r4fo.com is down

In 47129fd, AnonymousOverflow overflow.r4fo.com (https://overflow.r4fo.com) was down:

HTTP code: 0
Response time: 0 ms

Resolved: AnonymousOverflow overflow.r4fo.com is back up in 14281dd after 9 minutes.


text:
🛑 libreddit libreddit.spike.codes is down

In afedeb6, libreddit libreddit.spike.codes (https://libreddit.spike.codes) was down:

HTTP code: 502
Response time: 27614 ms

Resolved: libreddit libreddit.spike.codes is back up in 6662c07 after 15 minutes.


text:
🛑 libreddit libreddit.domain.glass is down

In 178d34c, libreddit libreddit.domain.glass (https://libreddit.domain.glass) was down:

HTTP code: 503
Response time: 243 ms

Resolved: libreddit libreddit.domain.glass is back up in efb5154 after 27 minutes.


text:
🛑 AnonymousOverflow overflow.projectsegfau.lt is down

In a71c54b, AnonymousOverflow overflow.projectsegfau.lt (https://overflow.projectsegfau.lt) was down:

HTTP code: 0
Response time: 0 ms

Resolved: AnonymousOverflow overflow.projectsegfau.lt is back up in f11c4ce after 9 minutes.


text:
🛑 libreddit libreddit.spike.codes is down

In 0752a6d, libreddit libreddit.spike.codes (https://libreddit.spike.codes) was down:

HTTP code: 0
Response time: 0 ms

Resolved: libreddit libreddit.spike.codes is back up in 5be5b8e after 9 minutes.


text:
PyTorch (GPU) not working on Win 11 box

Hi,
I am trying to get Casanovo running on a Windows 11 box with GEForce RTX 3070 and following the instructions I could not get it work. I have Casanovo running but without using the GPU.
I first tried to install it several ways (mostly probably wrong), installing NVIDIA driver directly from NVIDIA website. Not sure if I got all appropriate drivers installed. But I believe I did. Then tried following the instruction in Casanovo FAQ page, uninstalling torch, then following installation as described on Pytorch website (and using the conda command it provided), still Casanovo would not see GPU.
Then I tried the >conda install -c nvidia cuda-toolkit and got error at the very end:
C:\Windows\System32>CALL C:\ProgramData\Anaconda3\etc\conda\activate.d\vs2017_get_vsinstall_dir.bat
Did not find VSINSTALLDIR
File Not Found
Windows SDK version found as: ""
The system cannot find the path specified.
Did not find VSINSTALLDIR
C:\Windows\System32>if defined INCLUDE (set "INCLUDE_CONDA_NVCC_BACKUP=" )
C:\Windows\System32>set "INCLUDE=;\targets\x64"
(base) C:\Windows\System32>
Any suggestion and advice would be greatly appreciated.
Thanks,
Tomas Vaisar

Hi Tomas,
Could you try opening a terminal window and running the command nvidia-smi? This should tell you if CUDA is installed, and if it is installed what version is installed. The output should look something like this:

You should see the CUDA version in the top right corner of the output. Sometimes if there's a mismatch between the CUDA version specified in the PyTorch installation and the actual CUDA version installed on your system. As far as the specific error message your seeing, it looks like the error originates from a package that simply locates the installation directory of vscode. You might find some answers about resolving this specific error message here: https://stackoverflow.com/questions/68780561/long-error-messages-about-vsinstalldir-and-vs2019-whenever-i-start-anaconda-prom

Thanks a lot for the response. The CUDA is installed (v 12.5)  - the command you sent worked.
Regarding the other issue - that post did not help unfortunately.
Is specific version of Visual Studio required? It appears that that it is looking for VS 2017 and I have VS 2022 installed.
Thanks,
Tomas

From: Gwenneth Straub @.>
Sent: Tuesday, July 9, 2024 10:09 AM
To: Noble-Lab/casanovo @.>
Cc: Tomas Vaisar @.>; Author @.>
Subject: Re: [Noble-Lab/casanovo] PyTorch (GPU) not working on Win 11 box (Issue #353)
Hi Tomas,
Could you try opening a terminal window and running the command nvidia-smi? This should tell you if CUDA is installed, and if it is installed what version is installed. The output should look something like this:
image.png (view on web)https://urldefense.com/v3/__https://github.com/Noble-Lab/casanovo/assets/16980750/81d7dace-d1d9-4fe8-ba6b-a2ac28509c53__;!!K-Hz7m0Vt54!nv0sIfGEiMtsPQ70ghpvv7paCVuRoHTY1gFlH6oRSMrsY1y6loeuByWJWsjGHQQz5D1fAmxdf_codEg9pklho9c$
You should see the CUDA version in the top right corner of the output. Sometimes if there's a mismatch between the CUDA version specified in the PyTorch installation and the actual CUDA version installed on your system. As far as the specific error message your seeing, it looks like the error originates from a package that simply locates the installation directory of vscode. You might find some answers about resolving this specific error message here: https://stackoverflow.com/questions/68780561/long-error-messages-about-vsinstalldir-and-vs2019-whenever-i-start-anaconda-promhttps://urldefense.com/v3/__https://stackoverflow.com/questions/68780561/long-error-messages-about-vsinstalldir-and-vs2019-whenever-i-start-anaconda-prom__;!!K-Hz7m0Vt54!nv0sIfGEiMtsPQ70ghpvv7paCVuRoHTY1gFlH6oRSMrsY1y6loeuByWJWsjGHQQz5D1fAmxdf_codEg90_NU2zo$
—
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You are receiving this because you authored the thread.Message ID: @.***>

A specific version of Visual Studio is not required, nor is Visual Studio required at all actually. It looks like something went wrong when installing one of the dependencies for nvidia cuda-toolkit, which AFIK is not required to be installed explicitly in order to use Casanovo with a GPU.
In order to get a better understanding of what's going on, try opening a new terminal window and activating the Casanovo conda environment with conda activate casanovo_env. Then, start an interactive python session by typing the command python. Inside of the interactive python session, first import Pytorch with import torch, and then check to see if PyTorch can see the GPU by typing torch.cuda.is_available(). This should output true. The entire process should look something like this:

If you see False instead of True for the output of torch.cuda.is_available(), try reinstalling PyTorch with:
pip3 install torch torchvision torchaudio --force-reinstall --index-url https://download.pytorch.org/whl/cu121

The --force-reinstall will ensure that the correct PyTorch build that supports CUDA 12.5 is installed.

Thanks a lot. I ended up uninstalling all the NVIDA junk I installed, uninstalled Anaconda (and reinstalled, had to downgrade python for Fragpipe to work) and then I ran the
(base) C:\Windows\System32>conda install -c nvidia cuda-toolkit
from this I ended up getting the errors about visual studio I was seeing before.
I uninstalled the cuda-toolkit - and the error disappeared.
Then I followed your instructions - on the first "force-reinstall" of the pytorch it did not seem to work, but I repeated it making sure I do it within the casanovo environment and this time it works. I can see that the GPU is available by the > torch.cuda.is_available()
And when I run casanovo I see it is now using the GPU.
Although I got some warnings:
(casanovo_env) c:\Users\vaisarlab\Documents\HPPG2023\24Jun_mAb>casanovo sequence -o results.mztab *.mgf
WARNING: Dataloader multiprocessing is currently not supported on Windows or MacOS; using only a single thread.
Seed set to 454
INFO: Model weights file C:\Users\vaisarlab\AppData\Local\casanovo\casanovo_nontryptic_v4_2_0.ckpt retrieved from local cache
INFO: Casanovo version 4.2.1
INFO: Sequencing peptides from:
INFO:   sample_preprocessed_spectra.mgf
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
INFO: Reading 1 files...
sample_preprocessed_spectra.mgf: 128spectra [00:00, 4046.27spectra/s]
You are using a CUDA device ('NVIDIA GeForce RTX 3070') that has Tensor Cores. To properly utilize them, you should set torch.set_float32_matmul_precision('medium' | 'high') which will trade-off precision for performance. For more details, read https://pytorch.org/docs/stable/generated/torch.set_float32_matmul_precision.html#torch.set_float32_matmul_precision
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0]
Predicting DataLoader 0:   0%|                                                                   | 0/1 [00:00<?, ?it/s]WARNING: UserWarning: 1Torch was not compiled with flash attention. (Triggered internally at ..\aten\src\ATen\native\transformers\cuda\sdp_utils.cpp:455.)
WARNING: UserWarning: 1Torch was not compiled with flash attention. (Triggered internally at ..\aten\src\ATen\native\transformers\cuda\sdp_utils.cpp:455.)
Predicting DataLoader 0: 100%|███████████████████████████████████████████████████████████| 1/1 [00:02<00:00,  0.47it/s]
INFO: DONE!
Thank you,
Tomas

From: Gwenneth Straub @.>
Sent: Tuesday, July 9, 2024 4:31 PM
To: Noble-Lab/casanovo @.>
Cc: Tomas Vaisar @.>; Author @.>
Subject: Re: [Noble-Lab/casanovo] PyTorch (GPU) not working on Win 11 box (Issue #353)
A specific version of Visual Studio is not required, nor is Visual Studio required at all actually. It looks like something went wrong when installing one of the dependencies for nvidia cuda-toolkit, which AFIK is not required to be installed explicitly in order to use Casanovo with a GPU.
In order to get a better understanding of what's going on, try opening a new terminal window and activating the Casanovo conda environment with conda activate casanovo_env. Then, start an interactive python session by typing the command python. Inside of the interactive python session, first import Pytorch with import torch, and then check to see if PyTorch can see the GPU by typing torch.cuda.is_available(). This should output true. The entire process should look something like this:
image.png (view on web)https://urldefense.com/v3/__https://github.com/Noble-Lab/casanovo/assets/16980750/4d2ec495-b433-4f02-99ed-78b70d84c03b__;!!K-Hz7m0Vt54!lktk8UGG8XHAL03AHDqshE8TO3QLnyQNHORKd5jcUKMI_5oAhAvATlkmlqc_rw5UGHBMbZCkpgLL2wPbAgcHHxM$
If you see False instead of True for the output of torch.cuda.is_available(), try reinstalling PyTorch with:
pip3 install torch torchvision torchaudio --force-reinstall --index-url https://download.pytorch.org/whl/cu121https://urldefense.com/v3/__https://download.pytorch.org/whl/cu121__;!!K-Hz7m0Vt54!lktk8UGG8XHAL03AHDqshE8TO3QLnyQNHORKd5jcUKMI_5oAhAvATlkmlqc_rw5UGHBMbZCkpgLL2wPbVbW6s7c$
The --force-reinstall will ensure that the correct PyTorch build that supports CUDA 12.5 is installed.
—
Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/Noble-Lab/casanovo/issues/353*issuecomment-2218978080__;Iw!!K-Hz7m0Vt54!lktk8UGG8XHAL03AHDqshE8TO3QLnyQNHORKd5jcUKMI_5oAhAvATlkmlqc_rw5UGHBMbZCkpgLL2wPbqMpXaic$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AYEGTBDSKQE545LJF4KDMYLZLRXEDAVCNFSM6AAAAABKN3JOYWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJYHE3TQMBYGA__;!!K-Hz7m0Vt54!lktk8UGG8XHAL03AHDqshE8TO3QLnyQNHORKd5jcUKMI_5oAhAvATlkmlqc_rw5UGHBMbZCkpgLL2wPbsj51JPE$.
You are receiving this because you authored the thread.Message ID: @.***>

authors: Lilferrit tomvaiuw

repo: Noble-Lab/casanovo


text:
Add artifact function name validation for call and static call (PR 1)

fixes #390

This looks good, but for some reason the CI isn't running.

authors: alcuadrado zoeyTM

repo: NomicFoundation/ignition


text:
Working version for creating and running cases

Working workflow proposal to create and run landsites cases. Obs! It might be necessary for you to update your NREC image - you should be able to use my instance lasse_dev to create a new snapshot.
The documentation of how to execute model simulations is contained in ~/landsites_tools/simulation/README.md (open this directory on GitHub for rendering the Markdown).

Merged as the test run was successful after rebuilding the NREC virtual machine from scratch

authors: emiliano-gelati lasseke


text:
register beacon (EID) return 403, permission_denied error

I configured my G Dev console:

enabled proximity API
added credentials for OAuth2.0 and Client ID. Based on the SHA1 code of my machine.

I used the same SHA1 for debugging my app from android studio.

@vnarendra5a1  sorry for the delayed reply on this issue. I have fixed this issue and let me know how it goes for you. This was basically due to the introduction of Project Delegation where users have to have write access to a Console Project as an Owner or an Editor. If you do not have a project with write access the Proximity API will not let you register beacons. I have included some resources on the read me section. let me know how it goes.

@vnarendra5a1  Since there is no reply on this issue I will close this issue now.


text:
Issue#59 export n conversations

made updates on Floop export data file, as a result, the n conversation json file was created.

Dan left some guidelines on the Tuesday class repo's version of this issue: https://github.com/North-Seattle-College/ad440-winter2022-tuesday-repo/issues/54#issuecomment-1027571054
Looking through the code, I've left some comments on where I think those steps might be interpreted.

I've updated the code to resolve merge mixes with the development branch:

added a quantity command line argument to address the N conversations

launch code by typing in CL:  floop-data-export.py {cred file path} {desired db} {desired quantity}

code will create json and auto-upload to s3 with conversations grouped together.

authors: ZenSorcere fikirmulu


text:
Implemented error catcher & 404 page

Detailed Information

404 page

Error logging UI

Error logger dashboard Sentry
Related Issues
Closes #181

Type of Change

[x] 🐛 Bug fix or ⚙ enhancement
[x] ✨ New feature or Chore (change with no new features or fixes)
[x] 📚 Documentation update

Checklist

[x] The code follows the style guidelines of this project.
[x] All new and existing tests pass.
[x] This pull request is ready to be merged and reviewed.

Looks cool!

Good!. You moved the doc files out of the docs folder. Can you revert them?

Good!. You moved the doc files out of the docs folder. Can you revert them?

Hang on, I am doing it now

LGTM. @Solomonsolomonsolomon

This is my observation:
https://www.loom.com/share/d4cba707ddf34537bfd7a74f76a8fb1c

authors: Kingsuite fishonamos jedstroke

repo: NoshonNetworks/landver


text:
Update verifyUser and add embedMessage

This PR updates the verifyUser method to properly throw errors in the event that "message" or "user" is not fulfilled.
This PR also includes the new embedMessage method, this method aims to simplify the duplication of default code within multiple commands, specifically the footer, color and timestamp.
Original verifyUser method.

Updated, missing Message and User.

Missing User.

Proper usage.

embedMessage method.

Invalid use of, missing Message.

Proper usage.

Semantic versioning classification:

[x] This PR changes the framework's interface (methods or parameters added)
[ ] This PR includes breaking changes (methods removed or renamed, parameters moved or removed)
[ ] This PR only includes non-code changes, like changes to README, etc.

**Going to redo and re-open at a later time while fixing Conflicts.

repo: NotAWeebDev/Misaki


text:
Bad packages kill NuGet.Server - ZIP Archive contains unsupported data structures

I am running NuGet.Server to mirror the top 5000 packages on nuget.org for a customer than doesn't have network connectivity. I used nuget 3.3 to run "nuget init" to extract the packages into hierarchical order to improve performance.
When I try to query the packages NuGet.Server fails with the error "ZIP Archive contains unsupported data structures". Upon debugging, I found that some of the top 5000 packages on nuget.org have corrupted or invalid zip files. Sadly, this kills the entire NuGet.Server app. This should merely prevent those packages from being shown. Three examples of bad packages are: ecocore 7.0.0.8595, jetbrains.annotations 10.1.5, and nice.freya 1.3.20.
Here is a stack trace (retyped simpler since I don't have network connectivity on the machine with the issue):
WindowsBase.Dll!MS.Internal.IO.Zip.ZipArchive.VerifyVersionNeededToExtract(ushort version)
WindowsBase.Dll!MS.Internal.IO.Zip.ZipIOLocalFileHeader.Validate()
WindowsBase.Dll!MS.Internal.IO.Zip.ZipIOLocalFileHeader.ParseRecord(System.IO.BinaryRead reader, System.Text.Encoding encoding)
[...more Zip archive frames...]
NuGet.Core.dll!NuGet.ZipPackage.GetSupportedFrameworks()
NuGet.Server.dll!NuGet.Server.Infrastructure.ServerPackage.ServerPackage(...)
NuGet.Server.dll!NuGet.Server.Infrastructure.ServerPackageRepository.CreateServerPackage(...)
NuGet.Server.dll!NuGet.Server.Infrastructure.ServerPackageRepository.ReadPackagesFromDisk.AnonymousMethod_0(NuGet.IPackage package)
[...threading frames...]

I am a Microsoft employee and would like to help fix this bug. Would someone be willing to point me in the right direction? I believe that if an exception occurs in the CreateServerPackage method it should just not include that package rather than fail the whole server.

It looks like this Parallel.ForEach is what's causing the problem:
private HashSet<ServerPackage> ReadPackagesFromDisk()
        {
            _logger.Log(LogLevel.Info, "Start reading packages from disk...");
            MonitorFileSystem(false);

            try
            {
                var cachedPackages = new ConcurrentBag<ServerPackage>();

                bool enableDelisting = EnableDelisting;

                var packages = _expandedPackageRepository.GetPackages().ToList();

                Parallel.ForEach(packages, package =>
                {
                    // Create server package
                    var serverPackage = CreateServerPackage(package, enableDelisting);

                    // Add the package to the cache, it should not exist already
                    if (cachedPackages.Contains(serverPackage))
                    {
                        _logger.Log(LogLevel.Warning, "Duplicate package found - {0} {1}", package.Id, package.Version);
                    }
                    else
                    {
                        cachedPackages.Add(serverPackage);
                    }
                });

                _logger.Log(LogLevel.Info, "Finished reading packages from disk.");
                return new HashSet<ServerPackage>(cachedPackages, PackageEqualityComparer.IdAndVersion);
            }
            catch (Exception ex)
            {
                _logger.Log(LogLevel.Error, "Error while reading packages from disk: {0} {1}", ex.Message, ex.StackTrace);
                throw;
            }
            finally
            {
                MonitorFileSystem(true);
            }
        }

Wouldn't it be better to do:
private HashSet<ServerPackage> ReadPackagesFromDisk()
        {
            _logger.Log(LogLevel.Info, "Start reading packages from disk...");
            MonitorFileSystem(false);

            try
            {
                var cachedPackages = new ConcurrentBag<ServerPackage>();

                bool enableDelisting = EnableDelisting;

                var packages = _expandedPackageRepository.GetPackages().ToList();

                Parallel.ForEach(packages, package =>
                {
                    // Create server package
                    try {
                        var serverPackage = CreateServerPackage(package, enableDelisting);

                        // Add the package to the cache, it should not exist already
                        if (cachedPackages.Contains(serverPackage))
                        {
                            _logger.Log(LogLevel.Warning, "Duplicate package found - {0} {1}", package.Id, package.Version);
                        }
                        else
                        {
                            cachedPackages.Add(serverPackage);
                        }
                    }
                    catch (Exception e)
                    {
                         _logger.Log(LogLevel.Info, $"Unable to load package : {package}");
                    }
                });

                _logger.Log(LogLevel.Info, "Finished reading packages from disk.");
                return new HashSet<ServerPackage>(cachedPackages, PackageEqualityComparer.IdAndVersion);
            }
            catch (Exception ex)
            {
                _logger.Log(LogLevel.Error, "Error while reading packages from disk: {0} {1}", ex.Message, ex.StackTrace);
                throw;
            }
            finally
            {
                MonitorFileSystem(true);
            }
        }

A PR with this change would be welcome :-) Good catch!

PR was accepted and merged to dev so I'm closing the issue.

authors: adammodlin maartenba

repo: NuGet/NuGetGallery


text:
How to interrogate NuGet for the globalPackagesFolder

Specifically, I am interfacing from a .NET context. I am taking a dependency on a Git package, which I need to invoke from the command line. But to do that I need to know where that dependency potentially landed. I'm assuming in a packages/, but which globalPackagesFolder specifically?
For package references, I'm assuming I can do that through at least NuGet.Common?
Thanks!

Issue moved to NuGet/Home #7974 via ZenHub

authors: joelverhagen mwpowellhtx


text:
Published package with wrong name.

I have published the package TheToolBox.Data.Contracts v1.0.0 with the wrong name.
It should be TheToolbox.Data.Contracts (with lower case "b").
I contacted the support to remove the package but nothing happened.
I've tried to upload a new version (1.0.1) with the new name (after unlisting the old one) but it is still shown the old name.
Please help!!!!!

The packages have been hard deleted, and you should be able to publish the package with the correct name again.

Thanks
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From: zhhyu notifications@github.com
Sent: Monday, June 29, 2020 5:51:50 PM
To: NuGet/NuGetGallery NuGetGallery@noreply.github.com
Cc: Andre Vianna andre.vianna.rj@hotmail.com; Author author@noreply.github.com
Subject: Re: [NuGet/NuGetGallery] Published package with wrong name. (#8069)
The packages have been hard deleted, and you should be able to publish the package with the correct name again.
—
You are receiving this because you authored the thread.
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authors: AndreVianna zhhyu


text:
[Feature]: Move Search Service from .NET Core 3.1 to .NET 6

Related Problem
No response
The Elevator Pitch
.NET Core 3.1 is EOL on December 13, 2022.
https://dotnet.microsoft.com/en-us/platform/support/policy/dotnet-core
We should move the Search Service to .NET 6 before that time.
Additional Context and Details
No response

This is fully deployed to PROD.


text:
Bulk update (C#6.0 and resource strings)

This PR fixes:

Convert gallery to C#6.0 #2815
Move gallery user-visible strings (e.g. in exceptions) to resources #2816

:shipit: from me, this should PR should have another set of eyes looking at it. Particularly at the $"" changes

/cc @xavierdecoster @joyhui @joelverhagen

A couple nits. Otherwise looks like great cleanup. :shipit:

Cleaned up. Will merge after we ship the NuGet.Core refactoring.

Reopened PR here (just the C# 6.0 changes) - https://github.com/NuGet/NuGetGallery/pull/2846

authors: joelverhagen maartenba yishaigalatzer


text:
NuitkaOptimizationError since 0.6.18rc4

Nuitka 0.6.18rc7 (from source)
CPython 3.7.6 on Windows 7 SP1 64bit
Works with Nuitka 0.6.18rc3, fails starting from Nuitka 0.6.18rc4.
Running Nuitka with ..\path\to\python\python -m nuitka --plugin-enable=pylint-warnings --standalone --prefer-source-code --follow-stdlib --lto=yes --include-plugin-files=..\path\to\Pmw.py --python-flag=no_site,no_randomization,no_warnings,no_asserts,no_docstrings --disable-dll-dependency-cache --windows-disable-console ..\path\to\myproject.py
Nuitka prints out the following message and aborts the build process:
Nuitka:INFO: Starting Python compilation with Nuitka '0.6.18rc7' on Python '3.7'
 commercial None.
Nuitka-Plugins:WARNING: Use '--plugin-enable=pmw-freezer' for: Proper freezing o
f Pmw package.
Nuitka-Plugins:INFO: implicit-imports: Implicit dependencies of module 'tkinter'
 added '_tkinter'.
Nuitka-Plugins:INFO: implicit-imports: Implicit dependencies of module 'socket'
added '_socket'.
PASS 1:  93%|██████████████████████████████?  | 346/372, direct.showbase.LoaderP
roblem with statement at D:\p3d\build-hd\panda3d-editor-win64\direct\showbase\Lo
ader.py:139:
->         try:

Problem with statement at D:\p3d\build-hd\panda3d-editor-win64\direct\showbase\L
oader.py:130:
->     @classmethod

Problem with statement at D:\p3d\build-hd\panda3d-editor-win64\direct\showbase\L
oader.py:130:
->     @classmethod

Problem with statement at D:\p3d\build-hd\panda3d-editor-win64\direct\showbase\L
oader.py:19:
-> class Loader(DirectObject):

Problem with statement at D:\p3d\build-hd\panda3d-editor-win64\direct\showbase\L
oader.py:19:
-> class Loader(DirectObject):

Problem with statement at D:\p3d\build-hd\panda3d-editor-win64\direct\showbase\L
oader.py:19:
-> class Loader(DirectObject):

Problem with statement at D:\p3d\build-hd\panda3d-editor-win64\direct\showbase\L
oader.py:19:
-> class Loader(DirectObject):

Nuitka:INFO: Interrupted while working on '<Node 'COMPILED_PYTHON_MODULE' with {
'filename': 'D:\\p3d\\build-hd\\panda3d-editor-win64\\direct\\showbase\\Loader.p
y', 'module_name': <ModuleName direct.showbase.Loader>, 'code_flags': ''}>'.
                                                                               T
raceback (most recent call last):█████████████████████████████████    | 346/372
  File "D:\p3d\build-hd\Nuitka\nuitka\__main__.py", line 187, in <module>
    main()
  File "D:\p3d\build-hd\Nuitka\nuitka\__main__.py", line 173, in main
    MainControl.main()
  File "D:\p3d\build-hd\Nuitka\nuitka\MainControl.py", line 757, in main
    main_module = _createNodeTree(filename=filename)
  File "D:\p3d\build-hd\Nuitka\nuitka\MainControl.py", line 174, in _createNodeT
ree
    Optimization.optimize(main_module.getOutputFilename())
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\Optimization.py", line 349,
in optimize
    finished = makeOptimizationPass()
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\Optimization.py", line 312,
in makeOptimizationPass
    changed = optimizeModule(current_module)
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\Optimization.py", line 207,
in optimizeModule
    changed = optimizeCompiledPythonModule(module)
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\Optimization.py", line 103,
in optimizeCompiledPythonModule
    scopes_were_incomplete = module.computeModule()
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\ModuleNodes.py", line 524, in comput
eModule
    trace_collection=self.trace_collection
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\StatementNodes.py", line 163, in com
puteStatementsSequence
    new_statement = statement.computeStatementsSequence(trace_collection)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\FrameNodes.py", line 182, in compute
StatementsSequence
    new_statement = trace_collection.onStatement(statement=statement)
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\TraceCollections.py", line 6
11, in onStatement
    new_statement, change_tags, change_desc = statement.computeStatement(self)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\TryNodes.py", line 98, in computeSta
tement
    result = tried.computeStatementsSequence(trace_collection=trace_collection)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\StatementNodes.py", line 165, in com
puteStatementsSequence
    new_statement = trace_collection.onStatement(statement=statement)
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\TraceCollections.py", line 6
11, in onStatement
    new_statement, change_tags, change_desc = statement.computeStatement(self)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\AssignNodes.py", line 275, in comput
eStatement
    source = trace_collection.onExpression(self.subnode_source)
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\TraceCollections.py", line 5
92, in onExpression
    r = expression.computeExpressionRaw(trace_collection=self)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\OutlineNodes.py", line 240, in compu
teExpressionRaw
    result = body.computeStatementsSequence(trace_collection=trace_collection)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\StatementNodes.py", line 165, in com
puteStatementsSequence
    new_statement = trace_collection.onStatement(statement=statement)
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\TraceCollections.py", line 6
11, in onStatement
    new_statement, change_tags, change_desc = statement.computeStatement(self)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\TryNodes.py", line 98, in computeSta
tement
    result = tried.computeStatementsSequence(trace_collection=trace_collection)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\StatementNodes.py", line 165, in com
puteStatementsSequence
    new_statement = trace_collection.onStatement(statement=statement)
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\TraceCollections.py", line 6
11, in onStatement
    new_statement, change_tags, change_desc = statement.computeStatement(self)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\TryNodes.py", line 98, in computeSta
tement
    result = tried.computeStatementsSequence(trace_collection=trace_collection)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\StatementNodes.py", line 163, in com
puteStatementsSequence
    new_statement = statement.computeStatementsSequence(trace_collection)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\FrameNodes.py", line 182, in compute
StatementsSequence
    new_statement = trace_collection.onStatement(statement=statement)
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\TraceCollections.py", line 6
11, in onStatement
    new_statement, change_tags, change_desc = statement.computeStatement(self)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\LocalsDictNodes.py", line 404, in co
mputeStatement
    trace_collection=trace_collection
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\NodeBases.py", line 897, in computeS
tatementSubExpressions
    expression = trace_collection.onExpression(expression=expression)
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\TraceCollections.py", line 5
92, in onExpression
    r = expression.computeExpressionRaw(trace_collection=self)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\ExpressionBases.py", line 1165, in c
omputeExpressionRaw
    expression = trace_collection.onExpression(sub_expression)
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\TraceCollections.py", line 5
92, in onExpression
    r = expression.computeExpressionRaw(trace_collection=self)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\ExpressionBases.py", line 1373, in c
omputeExpressionRaw
    expression = trace_collection.onExpression(expression=sub_expression)
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\TraceCollections.py", line 5
92, in onExpression
    r = expression.computeExpressionRaw(trace_collection=self)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\ExpressionBases.py", line 1165, in c
omputeExpressionRaw
    expression = trace_collection.onExpression(sub_expression)
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\TraceCollections.py", line 5
92, in onExpression
    r = expression.computeExpressionRaw(trace_collection=self)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\FunctionNodes.py", line 1089, in com
puteExpressionRaw
    trace_collection.onUsedFunction(self.getFunctionBody())
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\TraceCollections.py", line 4
75, in onUsedFunction
    function_body.computeFunctionRaw(self)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\FunctionNodes.py", line 495, in comp
uteFunctionRaw
    self.computeFunction(trace_collection)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\FunctionNodes.py", line 511, in comp
uteFunction
    trace_collection=trace_collection
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\StatementNodes.py", line 165, in com
puteStatementsSequence
    new_statement = trace_collection.onStatement(statement=statement)
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\TraceCollections.py", line 6
11, in onStatement
    new_statement, change_tags, change_desc = statement.computeStatement(self)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\TryNodes.py", line 98, in computeSta
tement
    result = tried.computeStatementsSequence(trace_collection=trace_collection)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\StatementNodes.py", line 163, in com
puteStatementsSequence
    new_statement = statement.computeStatementsSequence(trace_collection)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\FrameNodes.py", line 182, in compute
StatementsSequence
    new_statement = trace_collection.onStatement(statement=statement)
  File "D:\p3d\build-hd\Nuitka\nuitka\optimizations\TraceCollections.py", line 6
11, in onStatement
    new_statement, change_tags, change_desc = statement.computeStatement(self)
  File "D:\p3d\build-hd\Nuitka\nuitka\nodes\TryNodes.py", line 143, in computeSt
atement
    statement,
nuitka.Errors.NuitkaOptimizationError:
This statement does raise but didn't annotate an exception exit.

    <node is_temp="False" kind="StatementAssignmentVariable" line="140" owner="d
irect$showbase$Loader$$$function__12__loadPythonFileTypes" var_type="object" var
iable_name="pkg_resources">
      <role name="source">
        <node kind="ExpressionImportModuleFixed" line="140" module_name="pkg_res
ources" />
      </role>
    </node>

The above information should be included in a bug report.

The module pkg_resources is present in the environment.
Please let me know if you need a project example.

This report is very incoherent, 0.6.17rc never contained this node. You might mean 0.6.18rc,, but these would be old and I believe it has been fixed since.

Just saw that the title names the 18, OK. I think rc5 or higher should work.

I meant to write 0.6.18rc3/4/7, it's corrected now in the initial report.

I think rc5 or higher should work.

It doesn't, the message above was copied from 0.6.18rc7:
Nuitka:INFO: Starting Python compilation with Nuitka '0.6.18rc7' on Python '3.7'
 commercial None.

Then I indeed need a reproducer, I havent' see that, and it seems impossible to me, very strange.

As an aside, Pmw should work with just the pmw plugin, you are doing it wrong I think there. Not saying it doesn' work, just too complicated.

Likely this Loader.py would be enough.

Example reproducer:
from direct.showbase.ShowBase import ShowBase

class MyApp(ShowBase):

    def __init__(self):
        ShowBase.__init__(self)

app = MyApp()
app.run()

You will need panda3d, e. g. through pip install panda3d.
You can see Loader.py here: https://github.com/panda3d/panda3d/blob/master/direct/src/showbase/Loader.py

As an aside, Pmw should work with just the pmw plugin, you are doing it wrong I think there. Not saying it doesn' work, just too complicated.

Thanks, I'm very well aware of the Pmw plugin, one of the first, if not the first, plugins for Nuitka. I'm "bundling" it manually. I think I set it up this way back when it did not exist yet and didn't touch my scripts, yet.
I don't see a button to re-"open" this issue.

Ok, I managed to reproduce it just now with this import, it's hard to related filenames to PyPI packages.

Due to the severity of the bug, I have rebased develop rc4 with the fixup to the commit, so bisection remains unaffected by this kind of thing.

I forgot to re-open, sorry, probably limited to contributors, because you know, some people like to spam click buttons unfortunately. But I would close now. :)

authors: kamgha kayhayen

repo: Nuitka/Nuitka


text:
Plugin for sqlalchemy or any hints?

Hi,
is there a plugin available for sqlalchemy or any hints what to include?
Thanky you
Traceback (most recent call last):
  File "D:\PROGRA~1\te_tools\spaLab\receiver\receiverWidget.py", line 524, in onStartStop
  File "D:\PROGRA~1\te_tools\spaLab\receiver\receiverWidget.py", line 44, in open
  File "D:\PROGRA~1\te_tools\spaLab\dbIntf\dbIntf.py", line 23, in open
  File "<string>", line 2, in create_engine
  File "D:\PROGRA~1\te_tools\spaLab\sqlalchemy\util\deprecations.py", line 309, in warned
  File "D:\PROGRA~1\te_tools\spaLab\sqlalchemy\engine\create.py", line 534, in create_engine
  File "D:\PROGRA~1\te_tools\spaLab\sqlalchemy\engine\url.py", line 661, in _get_entrypoint
  File "D:\PROGRA~1\te_tools\spaLab\sqlalchemy\util\langhelpers.py", line 343, in load
sqlalchemy.exc.NoSuchModuleError: Can't load plugin: sqlalchemy.dialects:sqlite

No issue template no fun.

authors: kayhayen mcfreis


text:
Breaks Pillow webp support

Installed Nuitka via pip3, Pillow via apt from debian repos.
$ nuitka3 --version
0.8.4
Commercial: None
Python: 3.10.5 (main, Jun  8 2022, 09:26:22) [GCC 11.3.0]
Flavor: Debian Python
Executable: /usr/bin/python3
OS: Linux
Arch: x86_64
Distribution: Debian sid

Pillow v9.1.1.
My wish is to make Pillow code faster and produce single python-independent binary. AppImage is ok for me.
Consider following example:
#!/usr/bin/env python3

from PIL import Image

def main():
    Image.open("in.jpg").save("out.webp")

if __name__ == "__main__":
    main()

Compiling with nuitka and executing:
$ CCFLAGS='-march=native' nuitka3 --quiet --onefile --follow-stdlib --follow-imports --remove-output --enable-plugin=numpy --enable-plugin=pyqt5 -j3 webp.py

produces binary webp.bin
$ ./webp.bin
Traceback (most recent call last):
  File "/tmp/.mount_webp.bzy6UMM/webp.py", line 10, in <module>
    main()
  File "/tmp/.mount_webp.bzy6UMM/webp.py", line 7, in main
    Image.open("in.jpg").save("out.webp")
  File "/tmp/.mount_webp.bzy6UMM/PIL/Image.py", line 2280, in save
ValueError: unknown file extension: .webp

So no WebP support, unfortunate.
Replacing out.webp with e.g. out.png leads to working program, but I need WebP for my specific purpose.
UPD0:
Simplified command:
$ nuitka3 --onefile --full-compat --remove-output --enable-plugin=numpy --enable-plugin=pyqt5 webp.py doesn't work either.

According to
https://github.com/Nuitka/Nuitka/issues/1598#issuecomment-1148413778
I guess that debian packages are bad for building standalone Nuitka executables and I should use only pip packages.

Did you try that and did the problem persinst?

Yes, please look at https://github.com/Nuitka/Nuitka/issues/1607#issuecomment-1156171991
I tried with 100% PyPI (nuitka, pillow, all their dependencies) in Arch Linux, the problem with WebP persists.

Ah, your update annotation was confusing me there, I get it now. Thanks.

My first suspect was a missing PIL plugin, but PIL.WebPImagePlugin is in the implicit imports, not sure what's going on there.

Ah, it's wrongly (?) assigned to imageio which you are not using.

Ah, it's wrongly (?) assigned to imageio which you are not using.

AFAIK, pillow project is independent from imageio, but imageio requires pillow. WebP support is also pillow thing.

Yes, it's changed to that, somebody added a sloppy implicit dependency there, changing it made things just work. These plugins of Pillow are just some of imageio plugins indeed, and it does a proper PIL.Image import that should always have had those.

Part of the of current pre-release, and will be part of 0.9 release.

Can confirm that 0.9rc7 works against full PIL program

Part of the 0.9 release that I just made.


text:
Update NukkitX Network Dependency

Update Network dependency from v1.3.1 to v1.4.2

Do you realize that more than version number has changed?

Do you realize that more than version number was changed?

Yes, yes I do

I have some other changes to add then I'll update here.

authors: Creeperface01 SupremeMortal c-wolfe

repo: NukkitX/Protocol


text:
[FEATURE] Setup script with autoreplace

A setup CLI script that prompts the user what to replace as stated at https://github.com/NullDev/DiscordJS-Template#satellite-things-to-change-in-the-template

https://github.com/NullDev/DiscordJS-Template/commit/79f8958c135afb3b0054a7e54cac47e24ba601be

repo: NullDev/DiscordJS-Template


text:
Search box in the submission table doesn't seem to work

It does filter on something but i can't tell which. I know there's a grant with "Family" in its name, but that grant didn't get returned in the filter.

verified on rev. 1f687411

repo: OA-PASS/pass-ember


text:
Define a policy using draft PRs when waiting on specific approvals

We've had some understandable confusion on when PRs get merged, as we came up with some exceptions to the "2 TSC approvals" rule in TDC calls.  But not everyone is at every TDC call, nor can everyone be expected to remember everything that came up.  So we should put PRs into draft, even if they are otherwise ready for merging, if we want to wait for a specific approval.
Just filing this b/c I don't have time to try to update DEVELOPMENT.md but we should do that at some point.

Another option is that we could define a minimum time for non-trivial PRs to remain open.  (An examle of a trivial PR would be #3804, although we could use labels if we want to avoid vague heuristics).

"in draft" and "waiting for specific approval" seem contradictory to me. Is there a specific label that could be used here? Or assign the review to the tsc team? (Is there a merge policy that could be set up to require N reviews from that team before it can be merged, without getting in the way of other PRs that have a different merge policy?)

I think we have two things here:

we should probably set the system to required two reviews
sometimes we're looking for feedback from someone in particular

Draft is fair enough if the author does not believe that the PR can currently be merged (pending more changes, someone particular to review it, something else).

HI @lornajane , @handrews , @ralfhandl  Did we ever close the loop on this on a prior TDC?

I think we discussed this, in a TDC call and in Slack:

Technically only one approval is required to allow emergency fixes by two TSC members.
We usually merge once there are two approvals and no objections (reviews that requested changes).
If there were requested changes, we usually wait until these reviewers explicitly approved even if there are two other approvals.

[ ] We could use the "review" label in this case to make this more prominent, or add a new specific label such as "re-review required".

We use Draft PRs for changes that depend on other PRs to be merged first, or for decisions to be made by the TSC

Not sure whether these rules belong into DEVELOPMENT.md or CONTRIBUTING.md.

Added notes about reviewers and draft PRs to the contributing file https://github.com/OAI/OpenAPI-Specification/blob/main/CONTRIBUTING.md#pull-requests

authors: handrews karenetheridge lornajane miqui ralfhandl

repo: OAI/OpenAPI-Specification


text:
Update GOVERNANCE.md

Proposing updates to the TSC processes around membership.

A lower threshold for removing a member
Clarification about reasons for removal
Prefer email when stepping down
Change the announcement process to include the weekly calls and agendas.

Regarding "prolonged absenteeism" and the threshold for removal, would it make sense to specify a period of lack-of-contact (including lack of response to direct efforts to contact) that causes a member to no longer be considered a "voting member"?  Basically, lowering the quorum rather than the vote percentage threshold?
Hopefully we'll never again have a situation like the pandemic that disrupts things in so many ways, but we just had 2 out of 6 members become inactive, and with only one more inactive, the available voting members would have been stuck at 50% of the total.

@handrews is making a good point, but I think the other changes proposed here cover the eventualities quite well. By more often adding members, and by defining the process for removing them, I think we're unlikely to return to a place where 66% seems like a difficult number to achieve.
I'm in favour of these changes (but I'll not click the approve button as a bystander in case that confuses the process!)

@lornajane makes sense to me!  I'm fine with this as-is, then.

Discussed on today's call, this is ready to move forward. However, since I'm the author, it makes sense to have one more @OAI/tsc reviewer, so I've added @whitlockjc and @webron . Feel free to merge after approving or else I'll do that as soon as I'm able.

authors: earth2marsh handrews lornajane


text:
Complete normative and informative references

Fixes #3740
Normative

[x] ABNF
[x] CommonMark
[x] HTML 4.01
[x] IANA registries
[x] JSON Schema Core
[x] JSON Schema Validation
[x] OpenAPI registries
[x] OpenID Connect Core
[x] OpenID Connect Discovery
[x] SPDX
[x] WhatWG URL
[x] XML Namespaces
[x] YAML

Informative

[x] OpenAPI learn - informative

Preview of new output

https://ralfhandl.github.io/OpenAPI-Specification/oas/v2.0.html#normative-references
https://ralfhandl.github.io/OpenAPI-Specification/oas/v3.0.0.html#normative-references
https://ralfhandl.github.io/OpenAPI-Specification/oas/v3.0.1.html#normative-references
https://ralfhandl.github.io/OpenAPI-Specification/oas/v3.0.2.html#normative-references
https://ralfhandl.github.io/OpenAPI-Specification/oas/v3.0.3.html#normative-references
https://ralfhandl.github.io/OpenAPI-Specification/oas/v3.0.4.html#normative-references
https://ralfhandl.github.io/OpenAPI-Specification/oas/v3.1.0.html#normative-references
https://ralfhandl.github.io/OpenAPI-Specification/oas/v3.1.1.html#normative-references

We can either merge, or hang on and see if that final https://github.com/tobie/specref/pull/803 gets a review, I'm happy either way

We can either merge, or hang on and see if that final tobie/specref#803 gets a review, I'm happy either way

I'd rather merge and fine-tune in a later PR. We do have more PRs coming, for example

https://github.com/tobie/specref/pull/805 - OpenAPI-Learn and OpenAPI-Registry

Uncertain here whether to use "Registry" as we do predominantly, or "Registries" as we do in a minority of cases

authors: lornajane ralfhandl


text:
FPGA device

Hello ,,,
I am using Intel ® Stratix ® 10 MX FPGA Development Kit for ETH miner. Can i computer use this OPAE software to communicate with my FPGA board to accelerate my ethash algorithm ?
Thanks.

Hello, thank you for your question.  The short answer is, it depends on whether your PCI Device ID is supported.  If you are creating your FIM IP based one a reference design, then it should be supported.  However, if you deviate from the reference design or implement a PCIe DID that the OPAE SDK source does not track, then you may run into issues.  In this case, you would need to modify the OPAE SDK to make it understand your DID.

Closing due to inactivity/age, and because the original question was answered. If you still require assistance, please re-open the issue.

authors: Jiahua-Gong nathanborak tswhison

repo: OFS/opae-sdk


text:
BUG (Low Prio/Edge Case): Create View fails to work when table name capitalized

An edge case occurs when creating a View that does not resolve, but also does not throw any error. Table names are censored for
proprietary reasons.
https://user-images.githubusercontent.com/59004211/184387328-0221b11e-3d19-498d-ada0-a7cd44cc1aea.mov
SELECT DISTINCT pos.*
    FROM table0
	INNER join table1
	    ON table1.pat_id = table0.epic_pat_id
	INNER JOIN TABLE2 AS pos
	    ON table1.cur_prim_loc_id = pos.pos_id

Edge case occurs when TABLE2 is capitalized. Changing it to lowercase allows it to run without issue. Error only occurs when joining using a capitalized table. When simply doing
SELECT DISTINCT *
    FROM TABLE2

the capitalization does not have an effect.
Also, edge case only occurs when joining multiple tables( does not occur when joining exactly 2 tables total)

Hi @Zwky26 ,
Perseus use postgre database and postgre SQL syntax. In postgre syntax there are two types of identifiers: unquoted and quoted. documentation
If original table name in lowercase, Perseuse uses unquoted identifier, in uppercase or various case - quoted.
I tried to reproduce your example, screen below:

Table0 with unquoted identifier can be written with any case in view SQL query and it would be work:

or

But with TABLE2 you should use quoted identifier rules. Your example would be like this:

SELECT DISTINCT * FROM "TABLE2"

Confirmed that it works just as you said. Thank you for letting me know- issue can be closed, and also combined with https://github.com/SoftwareCountry/Perseus/issues/627 for future implementation of sanitization protocol of naming conventions

repo: OHDSI/Perseus


text:
Standalone S3 Viewer is only showing the first .dcm image with an S3 data source?

Hi guys,
Firstly thanks so much for contributing and maintaining this project, it's a great piece of software and I really appreciate the work you do! Secondly, I'm stuck and would appreciate any help you can give me 👍
I'm hosting the viewer itself from an S3 bucket and a data source of dicom files with JSON maps from another S3 bucket which, for the purposes of this is completely public(just as a test case, I'm aware of the security implications). The issue is that when I enter the URL https://example-ohif-viewer-location.com/viewer?url=dicom-map.json it loads all of the data except for, as far as I can tell, anything past the first slice.
What I know:

There's nothing in the network requests indicating any errors but also no GET requests for the other slices.
It loads and displays correct information for every other aspect of the study and series, including the thumbnail of the first slice, the image of the first slice, the fact that it is 1 of 435 slices, see here
Both S3 buckets are completely publicly accessible including appropriate CORS settings on the images/maps bucket
The scrollbar displays but I can't move it with clicking and dragging or my scroll wheel or the up and down arrows hotkeys
Testing with a smaller JSON map does not change or solve the problem
No errors or warnings in the console
The page loads but there is a single GET 404 at the very top of network requests for the viewer?url=map.json link but I assume this is erroneous as the map can be seen in the console

I suspect it might have something to do with my JSON maps so I'll provide a short snippet of one without any sensitive data, although I could be wrong:
{
   "studies":[
      {
         "StudyInstanceUID":"StudyID",
         "StudyDescription":"CT CHEST",
         "StudyDate":"10101010",
         "StudyTime":"100937.000",
         "PatientName":"NA",
         "PatientId":"NA",
         "series":[
            {
               "instances":[
                  {
                     "metadata":{
                        "Columns":512,
                        "Rows":512,
                        "InstanceNumber":8,
                        "AcquisitionNumber":3,
                        "PhotometricInterpretation":"MONOCHROME2",
                        "BitsAllocated":16,
                        "BitsStored":16,
                        "PixelRepresentation":1,
                        "SamplesPerPixel":1,
                        "PixelSpacing":[
                           0.708,
                           0.708
                        ],
                        "HighBit":15,
                        "ImageOrientationPatient":[
                           1,
                           0,
                           0,
                           0,
                           1,
                           0
                        ],
                        "ImagePositionPatient":[
                           -180.896,
                           -180.896,
                           1772.4
                        ],
                        "FrameOfReferenceUID":"FrameOfReferenceUID",
                        "ImageType":[
                           "ORIGINAL",
                           "PRIMARY",
                           "AXIAL"
                        ],
                        "Modality":"CT",
                        "SOPInstanceUID":"SOP",
                        "SeriesInstanceUID":"SeriesID",
                        "StudyInstanceUID":"StudyID"
                     },
                     "url":"dicomweb://aws-bucket.s3.amazonaws.com/folder/filename1.dcm"
                  },
                  {
                     "metadata":{
                        "Columns":512,
                        "Rows":512,
                        "InstanceNumber":301,
                        "AcquisitionNumber":3,
                        "PhotometricInterpretation":"MONOCHROME2",
                        "BitsAllocated":16,
                        "BitsStored":16,
                        "PixelRepresentation":1,
                        "SamplesPerPixel":1,
                        "PixelSpacing":[
                           0.708,
                           0.708
                        ],
                        "HighBit":15,
                        "ImageOrientationPatient":[
                           1,
                           0,
                           0,
                           0,
                           1,
                           0
                        ],
                        "ImagePositionPatient":[
                           -180.896,
                           -180.896,
                           1538
                        ],
                        "FrameOfReferenceUID":"FrameOfReferenceUID",
                        "ImageType":[
                           "ORIGINAL",
                           "PRIMARY",
                           "AXIAL"
                        ],
                        "Modality":"CT",
                        "SOPInstanceUID":"SOPInstanceUID",
                        "SeriesInstanceUID":"SeriesID",
                        "StudyInstanceUID":"StudyID"
                     },
                     "url":"dicomweb://aws-bucket.s3.amazonaws.com/folder/filename2.dcm"
                  },
                  {
                     "metadata":{
                        "Columns":512,
                        "Rows":512,
                        "InstanceNumber":275,
                        "AcquisitionNumber":3,
                        "PhotometricInterpretation":"MONOCHROME2",
                        "BitsAllocated":16,
                        "BitsStored":16,
                        "PixelRepresentation":1,
                        "SamplesPerPixel":1,
                        "PixelSpacing":[
                           0.708,
                           0.708
                        ],
                        "HighBit":15,
                        "ImageOrientationPatient":[
                           1,
                           0,
                           0,
                           0,
                           1,
                           0
                        ],
                        "ImagePositionPatient":[
                           -180.896,
                           -180.896,
                           1558.8
                        ],
                        "FrameOfReferenceUID":"1.2.392.200036.9116.2.6.1.3268.2060387192.1513905058.104502",
                        "ImageType":[
                           "ORIGINAL",
                           "PRIMARY",
                           "AXIAL"
                        ],
                        "Modality":"CT",
                        "SOPInstanceUID":"SOPID",
                        "SeriesInstanceUID":"SeriesID",
                        "StudyInstanceUID":"StudyID"
                     },
                     "url":"dicomweb://aws-bucket.s3.amazonaws.com/folder/filename3.dcm"
                  }
               ],
               "SeriesDate":"10101010",
               "SeriesDescription":"1.0 Lung Std. Volume   Vol.",
               "SeriesInstanceUID":"SeriesID",
               "SeriesNumber":"6",
               "SeriesTime":"101129.105",
               "Modality":"CT"
            }
         ]
      }
   ]
}

Any help is appreciated!

Hi @Signo-Alaris
You may want to consider using an Orthanc Docker container with a plug-in to your choice of cloud provider - details on Orthanc cloud plug-ins here: https://book.orthanc-server.com/plugins/object-storage.html. Interacting with Orthanc via its RESTful API or through dicomWEB is straightforward.

Issue was on my side! The URL I was generating was always pointing at the same dicom file

repo: OHIF/Viewers


text:
detect-icmp-id: add tests

Task: #5622
Redmine ticket: https://redmine.openinfosecfoundation.org/issues/5622
Description;

Convert unittests from detect-icm-id.c that would be better suited for S-V tests.

Merged in #1215, thanks!

authors: AkakiAlice victorjulien

repo: OISF/suricata-verify


text:
Metric value may slightly change depending on required @k

Most likely the reason for instability in torch.topk:
https://github.com/OML-Team/open-metric-learning/blob/c6004e4d2f43de43ca5c480cc69dbbef06599e69/oml/functional/metrics.py#L89
(If some items in the distance matrix are super close, then their order can be undefined.)

@dapladoc in case you are interested ^

Hi, I'm interested in this issue.

Close because of: https://github.com/OML-Team/open-metric-learning/pull/382#issuecomment-2155060075

authors: AlekseySh dapladoc

repo: OML-Team/open-metric-learning


text:
Reset Password without an SMTP Server

Hi,
It would be great it the password could be change in the web app rather than sending a link in an email. This link can be intercepted which isn't a good security practice. Also if the server running onlyoffice doesn't have access to an email server no-one can get a password reset :(

My current solution is:
From the host run the following code as root every minute.
#Variables
file="/tmp/file.txt"
Cleanup
rm ${file} 2> /dev/null
Kill any existing SMTP Process
function kill_process {
process_id=$(sudo netstat -lpn |grep 25 | awk {'print $7'} | cut -f1 -d"/")
sudo kill $process_id 2> /dev/null
echo "[*] Killed running SMTP process"
}
kill_process
#Start SNMP Server
echo "[*] SMTP Server Started"
test=$(sudo python -m smtpd -n -c DebuggingServer 172.17.173.52:25 > ${file}) &
White until file is not empty
while [ ! -s ${file} ]; do
echo "[-] Waiting for Password to be received"
# Sleep for 2 Seconds
sleep 2
done
echo
echo "[+] Password Reset Link"
echo -n " https" && cat ${file} | tr '\n' ' ' | sed -n 's:.https(.)p=3D1.*:\1:p' | sed 's/3D//g;s/= //g' && echo -n "p=1"
echo
echo
Cleanup
rm ${file} 2> /dev/null
kill_process

My current solution is:
From the host run the following code as root every minute.
#Variables
file="/tmp/file.txt"

# Cleanup
rm ${file} 2> /dev/null

# Kill any existing SMTP Process
function kill_process {
    process_id=$(sudo netstat -lpn |grep 25 | awk {'print $7'} | cut -f1 -d"/")
    sudo kill $process_id 2> /dev/null
    echo "[*] Killed running SMTP process"
}

kill_process

#Start SNMP Server
echo "[*] SMTP Server Started"
test=$(sudo python -m smtpd -n -c DebuggingServer YOUR_IP_HERE:25 > ${file}) &

# White until file is not empty
while [ ! -s ${file} ]; do
    echo "[-] Waiting for Password to be received"
    # Sleep for 2 Seconds
    sleep 2
done
echo
echo "[+] Password Reset Link"
echo -n " https" && cat ${file} | tr '\n' ' ' | sed -n 's:.*https\(.*\)p=3D1.*:\1:p' | sed 's/3D//g;s/= //g' && echo -n "p=1"
echo
echo

# Cleanup
rm ${file} 2> /dev/null

kill_process

Unfortunately, there is no way to change a password. We'd recommend to do the following:

Enable logging in file:/var/www/onlyoffice/WebStudio/web.log4net.config

Close the sending port.
Copy the password changing link from the log file.

Could you generate the password reset link then redirect to the user to that, when they do a password reset?

You may change the password only in Web interface (in User Profile).
But the special method should be added to API about in the beginning of next year.

How can the password be changed in the Web Interface? At the moment the only option I see is send a password via email?

Hi, any update on this ? i need to allow user to change their password without accessing their email

Use API.
echo "Getting the token authorization"
curl -i -X POST -v -H "Accept:application/json"
-H "Content-Type: application/json"
http:///api/2.0/authentication.json -d '{"userName":"firstname.lastname@domain.com","password":"xxxxxx"}'
echo "Get a list of all users using the authorization token from a previous request"
curl -i -X GET -v -H "Accept:application/json"
-H "Authorization: NvxkuMxjBQLrpkGbT839q+pwL1JtctgQUwOF5hhtbN38G7nfo8xMfppYYoqoUGA3zqnu43t5kBgo1VKCI7wCF/95jKtojfks27yWcSRadksufrf0bSvvdXQ=="
http:///api/2.0/people/filter.json
echo "Using the access token and user id set the password and activated the email. Access to this method, only the admins."
echo "A known bug that when performing this method flies the current authorization token."
curl -i -X PUT -v -H "Accept:application/json"
-H "Content-Type: application/json"
-H "Authorization: NvxkuMxjBQLrpkGbT03Y0NRP839q+pwL1AMssMfMZAxLegk82k7w9WBZSJtctgQUwOF5hhtbN38G7nfo8xMfppYYoqoUGA3zqnu43t5kBgo1VKCI7wCF/95jKtojfks27yWcSRadksufrf0bSvvdXQ=="
http:///api/2.0/people/c7c0eac5-dae0-40a7-978c-69cb9c6c84a0/password.json -d '{"userName":"fi.rstnamelastname@domain.com","password":"xxxxxx"}'

Hello Alexey.
Thanks for the API, but I have the question:
I tried your first step and the result was displayed:
{"count":1,"status":0,"statusCode":201,"response":{"token":"3lzKX5goHR9IdqrMoDB3Tbl/10VP9qzZTPZA5xEZ3rkDvHX2OILe57MCsksWiY5gQtEcIOhMvRr5x3cUMy7pyg3xHHQOjOwGTQPMjxsyTerVxP2czYEnKf2iBfyYwB81XP6PUfOwqQC6Ml5BxitT6Q==","expires":"2018-10-06T12:37:50.9948890+02:00","sms":false,"phoneNoise":null}}
This is OK. Then I copied the token and put it in step 2 and this step does not work. I tried with a gap without a gap after "Authorization: "
An error is always displayed:
GET /api/2.0/people/filter.json HTTP/1.1

Host: xxx
User-Agent: curl/7.47.0
Accept:application/json
Authorization: 3lzKX5goHR9IdqrMoDB3Tbl/10VP9qzZTPZA5xEZ3rkDvHX2OILe57MCsksWiY5gQtEcIOhMvRr5x3cUMy7pyg3xHHQOjOwGTQPMjxsyTerVxP2czYEnKf2iBfyYwB81XP6PUfOwqQC6Ml5BxitT6Q==

< HTTP/1.1 401 Unauthorized
HTTP/1.1 401 Unauthorized
Can you help me please? Many thans for your time.

Make sure token from 1st command doesn't contain '\/' characters.
You should unescape '/' i.e. '\/' => '/'

Yes, you're right. That was a problem. Well thank you!

Hello. Can anyone help me? I would like to automate this process.
The user enters their email and password in a simple php form. In the background, step 1 is processed to obtain the token, step 2 would add the received token to get the ID, and in step 3 verify the user with the entered email and the selected ID would be sent with the entered password.
It would be best to create this in javascript but I do not know it :-(.

@UjoJano

It would be best to create this in javascript but I do not know it :-(.

If you are interested in any kind of custom development feel free to contact ONLYOFFICE team at support@onlyoffice.com, they will help you with that task.

echo  "A known bug that when performing this method flies the current authorization token."

what do you by this bug ?

authors: AnaMih JohnS42 UjoJano alexeybannov ibnpetr rizkyramadhan robinlennox

repo: ONLYOFFICE/CommunityServer


text:
Explore if we can disaggregate data for transport capacity

@quartm asked:
"was it deemed unattainable to disaggregate data for low capacity (buses) and high capacity (trains, metro, ferries) public transport?"
This is a discussion.
My thoughts on it are that:

This may partially be covered by issue https://github.com/ONSdigital/SDG_11.2.1/issues/123 as this will take into account frequency. i.e. if a bus arrives once a week or once every hour - which is important. Currently this is in our project for version 1.2 https://github.com/ONSdigital/SDG_11.2.1/projects/5 but it can be put into https://github.com/ONSdigital/SDG_11.2.1/projects/1 if this is considered essential. Note: other countries (e.g. Estonia, and Sweden I think) have included transport frequency data into their calculations.
I am quite sure that transport capacity is not part of the calculation under the official methodology but I might have missed something there. Nonetheless, I think it will be an interesting addition, so:

I have created another ticket to develop a feature to consider transport capacity.

@quartm This is a really good catch. I will got back to the data and have a look if we can label stops "high-capacity" or "low-capacity" - then run the distance analysis accordingly. I imagine this will push up the count of those who have access significantly.
With regards to point a. above this would be really difficult to establish. I know there was a method for a very similar analysis suggested quite a while ago by the data science campus, which used Google streetmaps/streetview pictures and machine learning to analyse pictures of the stops. That sounded tricky and very experimental. Also, I just don't think the street view pictures are available like that any more. Obviously it depends on the disability, but things like ramps and lowering step buses are going to be relevant and some of that depends not on the stop but on the facilities on the transport itself.
Again, for point c, I am very unsure how this would be established. We would need to know the criteria (I imagine things like good lighting and just generally being in an area with a lower-incidence of street crime) and get data for those. Again, some of that would be very difficult to get.
With regards to point b. though, this will be solved by #123
It's really useful to look at write-ups about how other countries calculated this indicator.

Estonia
Sweden
Poland
Portugal
Austria
Norway

I have read through Sweden's and Estonia's method and neither seem to have taken disability into account.

Made a branch to implement this: https://github.com/ONSdigital/SDG_11.2.1/tree/transport_capaity_%23176

authors: james-westwood jwestw


text:
Release 1.12.0 - Update filenames that are uploaded to aws s3

What
Filenames are now human friendly:
The filtered csv downloads now use the dataset Id, edition, version and UTC timestamp so the user can easily distinguish the downloaded file to others they have previously downloaded, e.g. filtered-datasets/{filter_output_id}/{dataset_id}-{edition}-v{version}-filtered-2020-09-28T13-40-12Z.csv
The full csv download now looks like the following full-datasets/{dataset_id}-{edition}-v{version}.csv
Also includes:

CI configuration using latest go version - 1.15.2
go modules updated to use latest version of go 1.15
app dependencies updated

How to review

Sanity check changes
Unit tests pass
If possible check you can generate a csv using the cmd filter journey in develop <- if you do this then you will also prove the following pr works - https://github.com/ONSdigital/dp-filter-api/pull/164

Who can review
Anyone

Before releasing this, can we remove the debug logs, please? I will create a PR shortly against this release branch and develop

authors: DavidSubiros nshumoogum

repo: ONSdigital/dp-dataset-exporter


text:
Implement new piping

What is the context of this PR?
Added support for placeholders as defined here: https://github.com/ONSdigital/eq-schema-validator/blob/v3/doc/decisions/0001-define-piping-in-a-structured-way.md.
Includes the following:

PlaceHolder Parser: Extracts placeholder detail from a survey
Placeholder Transforms:  Defines which transforms can be used on placeholder source data
Placeholder Renderer: Replaces keys which contain placeholders with the final interpreted text
A number of test schemas which test the features added

Supports both new an old ways of piping, along with behaviour to support a list as a source so it can easily integrated at a later date.
Depends on https://github.com/ONSdigital/eq-schema-validator/pull/115
How to review
Check the unit tests included cover all scenarios. Walk through the test schemas and determine if any others need to be added.

@iwootten Was this missed from the implemented transforms on purpose?
https://github.com/ONSdigital/eq-schema-validator/blob/v3/schemas/string_interpolation/transforms/format_number.json

@iwootten Was this missed from the implemented transforms on purpose?
https://github.com/ONSdigital/eq-schema-validator/blob/v3/schemas/string_interpolation/transforms/format_number.json

Nope, just missed as I was mainly using the examples from the docs to go by.

authors: MebinAbraham iwootten

repo: ONSdigital/eq-survey-runner


text:
Restrict ECS to access only allow access from Public subnets

The ECS cluster should now only be accessible via the public subnets (e.g. the ALB) and not directly.

 Able to deploy author to ECS (5)

repo: ONSdigital/eq-terraform-ecs


text:
269 remove int casting

Pull Request submission
Got rid of bugs due to mixing integers and strings.
This includes an update of the function to create an imputation class so it includes an underscore.
Closes or fixes

Detail the ticket(s) you are closing with this PR
Closes 269

Code

[ ] Code runs The code runs on my machine and/or CDSW
[ ] Conflicts resolved There are no conflicts (I have performed a rebase if necessary)
[ ] Requirements My/our code functions according to the requirements of the ticket
[ ] Dependencies I have updated the environment yaml so it includes any new libraries I have used
[ ] Configuration file updated any high level parameters that the user may interact with have been put into the config file (and imported to the script)
[ ] Clean Code

[ ] Code is as PEP 8 compliant as I can humanly make it
[ ] Code passess flake8 linting check
[ ] Code adheres to DRY

[ ] Type hints All new functions have type hints

Documentation
Any new code includes all the following forms of documentation:

[ ] Function Documentation Docstrings within the function(s')/methods have been created

[ ] Includes Args and returns for all major functions
[ ] The docstring details data types

[ ] Updated Documentation: User and/or developer working doc has been updated

Data

[ ] All data needed to run this script is available in Dev/Test
[ ] All data is excluded from this pull request
[ ] Secrets checker pre-commit passes

Testing

[ ] Unit tests Unit tests have been created and are passing or a new ticket to create tests has been created

Peer Review Section

[ ] All requirements install from (updated) environment.yaml
[ ] Documentation has been created and is clear - check the working document
[ ] Doctrings (Google format) have been created and accurately describe the function's functionality
[ ] Unit tests pass, or if not present a new ticket to create tests has been created
[ ] Code runs The code runs on reviewer's machine and/or CDSW

Final approval (post-review)
The author has responded to my review and made changes to my satisfaction.

[ ] I recommend merging this request.

Review comments
Insert detailed comments here!
These might include, but not exclusively:

bugs that need fixing (does it work as expected? and does it work with other code
that it is likely to interact with?)
alternative methods (could it be written more efficiently or with more clarity?)
documentation improvements (does the documentation reflect how the code actually works?)
additional tests that should be implemented (do the tests effectively assure that it
works correctly?)
code style improvements (could the code be written more clearly?)
Do the changes represent a change in functionality so the version number should increase? Start a discussion if so.
As a review you can generates the same outputs from running the code

Your suggestions should be tailored to the code that you are reviewing.
Be critical and clear, but not mean. Ask questions and set actions.

@AnneONS  I have looked over the code and it appears sound. I have also run the code on both dev/test and local and it runs fine with no errors. I spotted a warning (not related to your code probably) and I have raised a bug ticket RDRP-283

authors: AnneONS jwestw

repo: ONSdigital/research-and-development


text:
DocsArchive-15.0.0.0Auto archive content

Please don't merge this PR until target archive repo PR https://github.com/OPS-E2E-PPE/docs-archive-test-target/pull/625 is merged into live branch.
Auto archive content to https://github.com/VSC-Service-Account/docs-archive-test-target.git

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text:
DocsArchive-15.0.0.0Auto archive content

Please don't merge this PR until target archive repo PR https://github.com/OPS-E2E-PPE/docs-archive-test-target_2dff5794-06d6-441b-a349-870019c644c7/pull/1 is merged into live branch.
Auto archive content to https://github.com/OPS-E2E-PPE/docs-archive-test-target_2dff5794-06d6-441b-a349-870019c644c7.git

Docs Build status updates of commit e4d1f88:
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For more details, please refer to the build report.
Note: If you changed an existing file name or deleted a file, broken links in other files to the deleted or renamed file are listed only in the full build report.


text:
DocsArchive-15.0.0.0Auto archive content

Please don't merge this PR until target archive repo PR https://github.com/OPS-E2E-PPE/docs-yml-archive-non-versioning-archive/pull/166 is merged into live branch.
Auto archive content to https://github.com/opstest2/docs-yml-archive-non-versioning-archive.git

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text:
Need to assess whether building a bvh from a rank-2 view impacts performance

c.f. https://github.com/ORNL-CEES/DataTransferKit/pull/513#discussion_r243712391

Per https://github.com/ORNL-CEES/DataTransferKit/pull/513#discussion_r243726246 and following posts on the discussion, there is a cost but it vanishes as the size of the problem grows.
#513 was merged as is with Traits::Access<Rank2View>::get(i) returning a point by value hence making a copy.  We intend to revisit this in the future.

repo: ORNL-CEES/DataTransferKit

license_source: bigquery


text:
Added synthetic benchmark script

Test cases are from https://tensornetwork.org/benchmarks/
Signed-off-by: Thien Nguyen nguyentm@ornl.gov

This benchmark script needs to be modified to measure the performance of exatn::contractTensors() instead of evaluating these individual binary tensor contractions as tensor networks which incurs an additional overhead.

@DmitryLyakh It's a good idea. I'll update the script to use contractTensors instead (may need to expose that to Python as well)

authors: DmitryLyakh tnguyen-ornl

repo: ORNL-QCI/exatn


text:
Document LinuxHost adapter

FWIW: I have a meeting Tuesday, 3rd December to discuss possible changes to the adapter. So this may go out of date quickly.

We'll discuss this but can't precreate cgroups when dealing with connections coming from SSH connections that wouldn't also affect regular SSH logins outside LinuxHost adapter.  The solution will be pam_exec like we do on Login nodes at OSC:
In PAM stack
session     required      pam_exec.so type=open_session /etc/security/limits.sh

/etc/security/limits.sh
set -e

PAM_UID=$(id -u "${PAM_USER}")

if [ "${PAM_SERVICE}" = "sshd" -a "${PAM_UID}" -ge 1000 ]; then
        /usr/bin/systemctl set-property "user-${PAM_UID}.slice" \
                MemoryAccounting=true MemoryLimit=64G \
                CPUAccounting=true \
                CPUQuota=700%
fi

We'd have to adjust the limits and also add extra check of PAM_RHOST to only set these limits when connection comes from OnDemand host.
The cgroup cgrules.conf and cgconfig.conf can only match things by user or group, not by remote host. So the cgroups you set can be for like all users or just admins or just members of a specific group. The rules will assign processes to the necessary cgroup hiearchy. This is what we use in RHEL6 on Ruby but the systemd approach is far superior in terms of catching all processes. The downside to systemd approach is the limits are for all login sessions of a given user so if we say "set limit of 1GB for user foo" then user foo will be limited to 1GB even if they SSH in outside OnDemand and that 1GB limit is shared across all logins on that host.
We MAY be able to use cgrules.conf and set the cgroup based on process name if that's possible with how LinuxHost adapter works. I don't think any other approach I'm aware of will work aside from a custom script we execute via pam_exec that sets custom cgroup values and somehow forces the SSH session into that cgroup.
If the LinuxHost adapter is spawning everything inside Singularity then there are ways with Singularity to set cgroup values.

Thanks Trey, it's good to know what's possible. I added the section about cgroups because the adapter does not place any limits on users, so it would be easy for a "use RStudio as an IDE only" session to turn into a resource intensive session. I would expect that sites would want the cgroups settings for regular SSH sessions and adapter launched processes to be the same. Like Dave says, the point of OnDemand isn't to hide the machine, but I do want a section that makes clear that if sites elect not to setup cgroups then nothing in the adapter will prevent a single user from hogging the machine.

I think cgroups are very much a good idea. One more idea I thought of and wanted to write down before I forgot: Wrapping the LinuxHost login node side in a script and setting up cgrules.conf to look for that process. So ideally all interactions would go through like ondemand-linuxhost-adapter script and then we could do something like:
*:ondemand-linuxhost-adapter  cpu linuxhostadapter
*:ondemand-linuxhost-adapter  memory linuxhostadapter

Then in /etc/cgconfig.d/linuxhostadapter.conf we'd set something like:
group linuxhostadapter {
  memory {
    memory_limit_in_bytes = "1G";
  }
  cpu {
   ...
  }
}

The main downside is the cgroup limits would be static and not dynamic, so a site would have to say all linuxhost adapter executions have same limits.

I was wrong about what cgconfig.conf and cgrules.conf do. They are limits applied to everyone so on Ruby all users share 108GB which is just a way to avoid crashing the node. I am working on docs for cgroups.

Thanks.

Added 2 approaches. One is per-user and one is per-node for all users using this new adapter.

authors: MorganRodgers treydock

repo: OSC/ood-documentation

license: mit


text:
making a better presentation of college chapters

Current Behavior

The current ui of the website is of chapters page is not promising and can be made better with fonts and images.
Desired Behavior

I can add good fonts and better images to it's background to make it look attractive.
Screenshots / Mockups

okay thanks

@manoranjanonline  I am already working on it you can find any other issue Thanks.

repo: OSCode-Community/OSCodeCommunitySite


text:
Pull request

Adds features requested in #5.
I added the new features in a way that doesn't break any existing users.
The new features have to be called by additional flags, see --help.
I also added travis tests. These have to be updated when new vulnerabilities are found. npm run update-tests takes care of this.
Maybe one could create packages and add mock vulnerabilities for testing to ossindex?

Visual inspection looks good. I am going to test the new features out tomorrow and will merge as soon as possible.
Once the merge is complete I will look at the travis tests and create mock packages in OSS Index for predictable and stable testing.

authors: OSSIndex qacwnfq

repo: OSSIndex/auditjs


text:
Reimplement using GStreamer and Rust

This PR reimplements the EasySplash using GStreamer as backend. This is the first preview and likely will be changed prior it is released.
To run this, you can use:
ES_RUNTIME_DIR=/tmp/es GST_DEBUG=1 RUST_LOG=trace cargo run -- open data/ossystems-demo

and to send commands to interrupt the animation (current animation is not interruptable) you can use:
ES_RUNTIME_DIR=/tmp/es RUST_LOG=trace cargo run -- client --stop

@Jonathas-Conceicao I'll rework the examples on README but please review the rest of the PR.

repo: OSSystems/EasySplash


text:
Changed MalwareAnalysis prerequisites. Silenced Prerequisites installation. Corrected -y option.

Status
READY
Description

Changed MalwareAnalysis prerequisites
Corrected option -y - -y should be before install
Silenced Prerequisites installation using -qq tag

Todos

[ ] Tests - Multiple tests successfully completed on a clean Ubuntu image
[ ] Documentation - No change in Documentation needed.

Steps to Test or Reproduce

Download the repository using git clone or downloading zip
Install prerequisite using bash install_dependencies_apt.sh

Impacted Areas in Application
No of files changed = 1

install_dependencies_apt.sh

@DigvijayBhosale1729  please fix it https://app.travis-ci.com/github/OWASP/SecureTea-Project/builds/235730825
https://app.travis-ci.com/github/OWASP/SecureTea-Project/builds/235730889

I forgot json module is loaded in python3 by default.
This happened because i was unsure and edited requirements.txt at the last moment.
Requirements.txt without json works fine. Just tested it out.
Sorry for the inconvenience.
@adeyosemanputra

repo: OWASP/SecureTea-Project


text:
Few Fixes

Gemfile is updated to ensure successful installation of phantomJS for running the tests.
While running the test cases, command_injection_spec is going to pending, I have fixed it which ensures successful run all the time.
A justification for this PR

To run tests, phantomJS is needed and there is a need for a gem installation. Hence I have added and sent a PR of the updated Gemfile to make developers life easier.

Coming to the change in command_injection_spec, this particular test is not succeeding all the time. This particular issue is fixed with the proposed changes

Hey @SriHarshaGajavalli 👋 - Thanks for submitting a PR. Can you provide some context as to the changes, their purpose, etc.?

Hello @cktricky - I have updated the description

@SriHarshaGajavalli - How does this PR impact the phantomJS installation instructions in the README file?

Why do you want the poltergeist gem twice in the Gemfile file?

@jasnow poltergeist gem is already existing but it is failing to get installing sometime. Hence I have added. But it is because of some issues on the local machine. However, I have removed it now.
Coming to the change command_injection_spec, everytime a test is running, it is creating a file and the test is going to pending status instead of failing (which is a successful run)

It isn't failing. Instead, it's successful execution leads to the creation of a file which in turn results in the test case status pending

It isn't failing. Instead, it's successful execution leads to the
creation of a file which in turn results in the test case status pending

With or without commenting out line 17?

With commenting, test case executes successfully (which means actually failed). If we uncomment the line, the test case is going to pending status.
I guess there could be bit of confusion with the concept itself

@SriHarshaGajavalli -  As you mention above:
Coming to the change in command_injection_spec, this particular test is not succeeding all the time. This particular issue is fixed with the proposed changes

Do you know why the command_injection_spec  is succeeding sometimes and not others?

@jasnow : Because of the above mentioned reason, it never succeeded for me

Could not reproduce the problem so rejecting the fix.

@SriHarshaGajavalli  - You are welcome to reopen this issue when you have more data to share.

authors: SriHarshaGajavalli cktricky jasnow

repo: OWASP/railsgoat


text:
Upgrade dependency

Upgrade jsonwebtoken@8.5.1 to version 9.0.2

Please ignore this PR and close it. Generated by TestIM


text:
Register WETH gateway during local deployment

accompanies https://github.com/OffchainLabs/nitro-testnode/pull/30

new registerGateway function
the ROLLUP_OWNER env var passed to deployCreatorAndCreateTokenBridge.ts::setupTokenBridgeInLocalEnv is replaced by ROLLUP_OWNER_KEY

this should be squashed because of all the little '...' commits

moved to #71

authors: godzillaba gzeoneth

repo: OffchainLabs/token-bridge-contracts


text:
[patch] Switch from alpha teamsfx-cli to released

Thank you for your pull request!
Please add '[major]', '[minor]', or [patch] to the title to indicate the impact the change has on the code.  Please also provide the following information.

Change Description:
The publish version of the teamsfx-cli package we depend on now includes the functionality we require.  Switching installed package from the alpha version to a released version.

Do these changes impact command syntax of any of the packages? (e.g., add/remove command, add/remove a command parameter, or update required parameters)
No.

Do these changes impact documentation? (e.g., a tutorial on https://docs.microsoft.com/en-us/office/dev/add-ins/overview/office-add-ins)
No.

If you answered yes to any of these please do the following:
> Include 'Rick-Kirkham' in the review
> Make sure the README file is correct
Validation/testing performed:
Ran automated tests.  Also created a test project with the json manifest and tested the script calls that use the teamsfx-cli to make sure they all work.

Can I get a sign off?

repo: OfficeDev/Office-Addin-Scripts