Error in selecting --output-spaces MNIPediatric:cohort-5:res-2

What happened?
Running latest 23.2.0 fmriprep on QTAB OpenNeuro dataset and specifying --output-spaces MNIPediatric:cohort-5:res-2.

Singularity
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
No
Please copy and paste any relevant log output.
## log:
240301-15:16:51,788 nipype.workflow IMPORTANT:
         Running fMRIPrep version 23.2.0

         License NOTICE ##################################################
         fMRIPrep 23.2.0
         Copyright 2023 The NiPreps Developers.

         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).

         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.

         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.

         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
240301-15:17:24,665 nipype.workflow IMPORTANT:
         Building fMRIPrep's workflow:
           * BIDS dataset path: /data.
           * Participant list: ['0005'].
           * Run identifier: 20240301-151603_c1ba3932-78fe-429c-b836-29d64fbe294b.
           * Output spaces: MNIPediatricAsym:cohort-5:res-2 MNI152NLin2009cAsym:res-2.
           * Pre-run FreeSurfer's SUBJECTS_DIR: /derivs/sourcedata/freesurfer.
240301-15:17:48,878 nipype.workflow INFO:
         ANAT Stage 1: Adding template workflow
240301-15:17:50,199 nipype.workflow INFO:
         ANAT Stage 2: Preparing brain extraction workflow
240301-15:17:50,262 nipype.workflow INFO:
         ANAT Stage 3: Preparing segmentation workflow
240301-15:17:50,265 nipype.workflow INFO:
         ANAT Stage 4: Preparing normalization workflow for ['MNIPediatricAsym:cohort-5', 'MNI152NLin2009cAsym', 'MNI152NLin6Asym']
240301-15:17:50,285 nipype.workflow INFO:
         ANAT Stage 5: Preparing surface reconstruction workflow
240301-15:17:50,301 nipype.workflow INFO:
         ANAT Stage 6: Preparing mask refinement workflow
240301-15:17:50,303 nipype.workflow INFO:
         ANAT Stage 7: Creating T2w template
240301-15:17:50,309 nipype.workflow INFO:
         ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
240301-15:17:50,325 nipype.workflow INFO:
         ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
240301-15:17:50,331 nipype.workflow INFO:
         ANAT Stage 8a: Creating cortical ribbon mask
240301-15:17:50,334 nipype.workflow INFO:
         ANAT Stage 9: Creating fsLR registration sphere
240301-15:17:50,337 nipype.workflow INFO:
         ANAT Stage 10: Creating MSM-Sulc registration sphere
240301-15:19:21,170 nipype.workflow INFO:
         No single-band-reference found for sub-0005_ses-01_task-rest_dir-AP_bold.nii.gz.
240301-15:19:21,231 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
240301-15:19:21,236 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
240301-15:19:21,242 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
240301-15:19:21,272 nipype.workflow IMPORTANT:
         BOLD series will be slice-timing corrected to an offset of 0.416s.
…
…
…
240301-21:04:26,746 nipype.workflow INFO:
         [MultiProc] Running 0 tasks, and 32 jobs ready. Free memory (GB): 0.02/0.02, Free processors: 8/8.
240301-21:04:26,869 nipype.workflow INFO:
         [Node] Setting-up "fmriprep_23_2_wf.sub_0005_wf.select_MNI6" in "/work/fmriprep_23_2_wf/sub_0005_wf/select_MNI6".
240301-21:04:26,871 nipype.workflow INFO:
         [Node] Executing "select_MNI6" <niworkflows.interfaces.utility.KeySelect>
240301-21:04:27,135 nipype.workflow INFO:
         [Node] Finished "select_MNI6", elapsed time 0.000601s.
240301-21:04:27,136 nipype.workflow INFO:
         [Job 453] Completed (fmriprep_23_2_wf.sub_0005_wf.select_MNI6).
240301-21:04:27,259 nipype.workflow INFO:
         [Node] Setting-up "fmriprep_23_2_wf.sub_0005_wf.template_iterator_wf.select_xfm" in "/work/fmriprep_23_2_wf/sub_0005_wf/template_iterator_wf/_in_tuple_MNIPediatricAsymcohort-5.cohort5.res2/select_xfm".
240301-21:04:27,261 nipype.workflow INFO:
         [Node] Executing "select_xfm" <niworkflows.interfaces.utility.KeySelect>
240301-21:04:27,526 nipype.workflow INFO:
         [Node] Finished "select_xfm", elapsed time 0.000435s.
240301-21:04:27,526 nipype.workflow WARNING:
         Storing result file without outputs
240301-21:04:27,526 nipype.workflow WARNING:
         [Node] Error on "fmriprep_23_2_wf.sub_0005_wf.template_iterator_wf.select_xfm" (/work/fmriprep_23_2_wf/sub_0005_wf/template_iterator_wf/_in_tuple_MNIPediatricAsymcohort-5.cohort5.res2/select_xfm)
240301-21:04:27,526 nipype.workflow ERROR:
         Node select_xfm.a0 failed to run on host worf.
240301-21:04:27,527 nipype.workflow ERROR:
         Saving crash info to /derivs/sub-0005/log/20240301-151603_c1ba3932-78fe-429c-b836-29d64fbe294b/crash-20240301-210427-uher-select_xfm.a0-68ceb294-2750-489c-acc8-5ab045166844.txt
Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node select_xfm.

Traceback:
        Traceback (most recent call last):
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 400, in run
            outputs = self.aggregate_outputs(runtime)
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 429, in aggregate_outputs
            predicted_outputs = self._list_outputs()  # Predictions from _list_outputs
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/interfaces/utility.py", line 217, in _list_outputs
            index = self.inputs.keys.index(self.inputs.key)
        ValueError: 'MNIPediatricAsym:cohort-5' is not in list

240301-21:04:27,546 nipype.workflow INFO:
         [Job 454] Completed (fmriprep_23_2_wf.sub_0005_wf.template_iterator_wf.select_xfm).
240301-21:04:27,672 nipype.workflow INFO:
         [Node] Setting-up "fmriprep_23_2_wf.sub_0005_wf.template_iterator_wf.select_xfm" in "/work/fmriprep_23_2_wf/sub_0005_wf/template_iterator_wf/_in_tuple_MNI152NLin2009cAsym.res2/select_xfm".
240301-21:04:27,674 nipype.workflow INFO:
         [Node] Executing "select_xfm" <niworkflows.interfaces.utility.KeySelect>
240301-21:04:27,941 nipype.workflow INFO:
         [Node] Finished "select_xfm", elapsed time 0.000498s.
240301-21:04:27,942 nipype.workflow INFO:
         [Job 455] Completed (fmriprep_23_2_wf.sub_0005_wf.template_iterator_wf.select_xfm).

Additional information / screenshots
I think there might be a naming issue including "cohort-5" twice?  (_in_tuple_MNIPediatricAsymcohort-5.cohort5.res2):
Specific line from above log:
240301-21:04:27,259 nipype.workflow INFO:
[Node] Setting-up "fmriprep_23_2_wf.sub_0005_wf.template_iterator_wf.select_xfm" in "/work/fmriprep_23_2_wf/sub_0005_wf/template_iterator_wf/_in_tuple_MNIPediatricAsymcohort-5.cohort5.res2/select_xfm".

This was fixed in https://github.com/nipreps/smriprep/issues/416, hoping to get a new release out with the fix this week.
BTW, I believe the MNIPediatricAsym:res-2:cohort-5 in your command should be MNIPediatricAsym:cohort-5:res-2, as cohort is parsed before resolution.

We should probably not be sensitive to the order of the modifiers.

Hi all @effigies @mgxd
I have the same issue ValueError: ‘MNIPediatricAsym:cohort-1’ is not in list in fmriprep 23.2.1.

And this is the argument --output-spaces MNIPediatricAsym:res-1:cohort-1 used in my script.
Has this issue been solved or can I use other versions released before fmriprep 23.2.1.
Best,
Yunhong

@WangYunHong98 sorry for the delay - this is fixed in 24.0.0

@mgxd It's fine. Thank you for the excellent work you do for fmriprep!


Stacktrace

Using Light Table version 0.7.2 (Binary version 0.8.6) on Windows 7.
Maybe not really useful bug report, but here it comes anyway: I was playing around with tabsets, but can’t say what exactly produced the error. I noticed a red 2 in the lower right corner, and when I clicked it this message on red background popped up:
TypeError: Cannot call method 'call' of null
    at lt.object.has_tag_QMARK_ (file:///C:/Users/athieme/LightTable/core/node_modules/lighttable/bootstrap.js:20799:128)
    at Function.lt.objs.style.__BEH__remove_theme (file:///C:/Users/athieme/LightTable/core/node_modules/lighttable/bootstrap.js:30065:52)
    at c (file:///C:/Users/athieme/LightTable/core/node_modules/lighttable/bootstrap.js:6196:14)
    at a (file:///C:/Users/athieme/LightTable/core/node_modules/lighttable/bootstrap.js:6236:18)
    at c (file:///C:/Users/athieme/LightTable/core/node_modules/lighttable/bootstrap.js:20443:76)
    at a (file:///C:/Users/athieme/LightTable/core/node_modules/lighttable/bootstrap.js:20477:18)
    at a (file:///C:/Users/athieme/LightTable/core/node_modules/lighttable/bootstrap.js:20488:34)
    at b (file:///C:/Users/athieme/LightTable/core/node_modules/lighttable/bootstrap.js:20492:14)
    at lt.object.destroy_BANG_ (file:///C:/Users/athieme/LightTable/core/node_modules/lighttable/bootstrap.js:20731:49)
    at Function.lt.objs.editor.__BEH__destroy_on_close (file:///C:/Users/athieme/LightTable/core/node_modules/lighttable/bootstrap.js:24315:34)

Thanks for the stacktrace but we do need bugs to be reproducible. Judging from the stacktrace it seems a theme was being removed and there was no active tab. If you can get us some reproducible steps that would be great. If not I'll close in a few days

Closing. Feel free to provide reproducible steps and we can reopen


Aliases

It is necessary to be able to define aliases to the data that is ingested, since in different contexts the same base elements (see 1) can have different names and descriptions. It is essential to be able to map synonymous (semantically analogous) fields, without having to change the database schemas to unify those references. In short, the idea is to have a mapping mechanism from one field to one or multiple aliases. For example, we could have in different data sources different fields that mean the same, so it is convenient to be able to define what the base data is and what the aliases are, or derived references.

Hi @Arturo-Penas-Rial, as discussed, defining glossaries and terms can achieve what you are looking for here. Applying those terms as tags can help align data that relates to the same elements


[BIOMAGE-1207] - Fix QC navigation

Background
Link to issue
https://biomage.atlassian.net/browse/BIOMAGE-1207
Link to staging deployment URL
https://ui-agi-ui402.scp-staging.biomage.net/
Links to any Pull Requests related to this
N.A.
Anything else the reviewers should know about the changes here
There are 4 main changes in this PR :

Add tooltips to the disable, prev and next buttons QC navigation buttons
In multisample experiments, choosing "auto" settings and clicking "apply to all samples" will change the other sample's settings to auto
Revamp QC navigation to fit new design, as specified in the mock up (link in Jira ticket)
QC navigation should rearrange gracefully on small screens

These changes can be seen in the deployment URL.
Changes
Code changes
Definition of DONE
Your changes will be ready for merging after each of the steps below have been completed:
Testing

[X] Unit tests written
[X] Tested locally with Inframock (with latest production data downloaded with biomage experiment pull)
[X] Deployed to staging

To set up easy local testing with inframock, follow the instructions here: https://github.com/biomage-ltd/inframock
To deploy to the staging environment, follow the instructions here: https://github.com/biomage-ltd/biomage-utils
Documentation updates
Is all relevant documentation updated to reflect the proposed changes in this PR?

[ ] Relevant Github READMEs updated
[ ] Relevant wiki pages created/updated

Approvers

[ ] Approved by a member of the core engineering team
[ ] (UX changes) Approved by vickymorrison (this is her username, tag her if you need approval)

Just before merging:

[ ] After the PR is approved, the unstage script in here: https://github.com/biomage-ltd/biomage-utils is executed. This script cleans up your deployment to staging

Optional

[ ] Photo of a cute animal attached to this PR

Looks good! 3 comments:

The hovers on the arrow navigation buttons should say 'previous' and 'next' rather than 'previous filter' and 'next filter' because not all the steps are filters.

I thought we agreed that the "7 of 7 steps complete" would appear in the hover? This information needs to be included otherwise the numbers in the step name dropdown menu don't make sense. So for the status hover I suggest:
"Your data processing is finished.
7 of 7 steps complete.
The analysis launched 5 days ago and finished 5 days ago."

I remember also discussing changing the colours on the step indicators. If it's easy to do it could be done as part of this ticket. Steps that are complete should be green (currently blue). The current view could be indicated with black (currently red) or with a solid black border or something. Note that red/green combination should be avoided because it is not colour blind friendly.

Codecov Report

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The diff coverage is n/a.

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==========================================
  Hits               ?     2191
  Misses             ?     1843
  Partials           ?       16

Continue to review full report at Codecov.

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@vickymorrison Can you take a look at the staging again? I've addressed your feedback.
I've changed the status bar colors as requested. I change the active filter color to orange, instead of black, as It contrasts with green and is easier to see. What do you think about the color? If it's not ok, I'll change it to dark gray.


How do i run this on Windows?

pip install -U organize-tool
C:\Users\teonm\Desktop\Coding\organize>**py organize**
Traceback (most recent call last):
  File "C:\Users\teonm\AppData\Local\Programs\Python\Python310\lib\runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "C:\Users\teonm\AppData\Local\Programs\Python\Python310\lib\runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "C:\Users\teonm\Desktop\Coding\organize\organize\__main__.py", line 2, in <module>
    import cli
  File "C:\Users\teonm\Desktop\Coding\organize\organize\cli.py", line 11, in <module>
    import click
ModuleNotFoundError: No module named 'click'

I changed from .cli import cli in main py because i was getting the same error. Ive tried to PIP install click but thats not the solution either it seems?
C:\Users\teonm\Desktop\Coding\organize>pip install click
Requirement already satisfied: click in c:\users\teonm\appdata\local\packages\pythonsoftwarefoundation.python.3.10_qbz5n2kfra8p0\localcache\local-packages\python310\site-packages (8.1.2)
Requirement already satisfied: colorama in c:\users\teonm\appdata\local\packages\pythonsoftwarefoundation.python.3.10_qbz5n2kfra8p0\localcache\local-packages\python310\site-packages (from click) (0.4.4)

Anyone have guidance? thanks again!

I've been running it on windows ok. I think I installed with something like pip install "organize-tool[textract]" into a virtualenv.

Are you trying to run from source? You mention the pip install command, but your stack trace looks like you have downloaded the organize code to your desktop and are running with the windows py launcher, which I'm not familiar with.
If you are just trying to run it and not necessarily from source, I installed with pip, and can now run organize as a command. It is on my path when the virtual env I installed it to is activated.

This is an installation issue. To be safe you can use:
pip uninstall organize-tool
python3 -m pip install organize-tool
python3 -m organize-tool

But normally you should be able to run organize directly after installation.
I'll close this for now, please reopen if this issue persists!


RNA Expression Level Tests

This adds a few tests of the RNA functionality including filtering by feature IDs and threshold values. I believe these tests present the minimum level of request and response functionality.
A few more tests could be added that show that responses are well formed and contain values expected from the test data. @dcolligan @saupchurch

+1


Feature Request Operator | Support to pull MySQL credentials from secrets in the CR

Description
Add support to pull MySQL credentials from Secrets when deploying CRD from yaml file.
helm-charts/charts/operator-wandb/values.yaml at main · wandb/helm-charts
mysql:
  host: ""
  port: 3306
  database: "wandb_local"
  user: "wandb"
  password: ""

This can be the entire configuration like we do here or at least the password pulled from secrets. Ex. what can look like the password
env:
  - name: MYSQL_PASS
    valueFrom:
      secretKeyRef:
        name: mysql-data
        key: mysql-pass
mysql:
  host: ""
  port: 3306
  database: "wandb_local"
  user: "wandb"
  password: $(MYSQL_PASS)

https://github.com/wandb/helm-charts/pull/222

@jsbroks @danielpanzella - Can we please review the PR here, when you get a chance? Thanks.


[Service Bus] Move recordings to assets repo

Description
Moves test recordings to the azure-sdk-assets repository and creates an assets.json file to enable the new setup, using the generate-assets-json.ps1 script.
All SDK Contribution checklist:

[x] The pull request does not introduce [breaking changes]
[ ] CHANGELOG is updated for new features, bug fixes or other significant changes.
[x] I have read the contribution guidelines.

General Guidelines and Best Practices

[x] Title of the pull request is clear and informative.
[x] There are a small number of commits, each of which have an informative message. This means that previously merged commits do not appear in the history of the PR. For more information on cleaning up the commits in your PR, see this page.

Testing Guidelines

[x] Pull request includes test coverage for the included changes.

API change check
API changes are not detected in this pull request.


Pre-encode images using VQGAN to feed to BART decoder.

Closes #16
Uses VQGAN to encode images and saves them to new .json files (headlines_encoded.json and captions_encoded.json)
There was a merge conflict, I think I fixed it correctly, but better to double check just in case.

@ArjunKrishna3367 Can you create a new branch from main and copy your encode_imgs.py and open a new PR. Once you don't we will close this PR. I'm not sure if merge conflicts are handled properly.

Closing as new PR is opened #22


Questions do not show up

Hi everyone,
This conversational form looks great but unfortunately I can't seem to get it to work properly.
For some reasons the questions don't show up on the screen.
Hopefully it's an easy fix and someone can point out my mistake.
Thanks

Can you show us your code?

@mhinc14 you cf-questions contains an problematic characters: https://www.dropbox.com/s/lrsgpje7unh5854/Screenshot 2017-11-03 09.03.46.png?dl=0

@felixnielsen thanks for pointing that out. Even with the problematic character resolved I get the same issue.
@alexgurr here is example code of how i've been trying it
As shown in the picture in my original post, the text input field appears but none of the questions appear.
Im using chrome on mac and am up to date.
`

The HTML5

Hello world

<form id="contact" method="post" action="" cf-form cf-context>
  <fieldset>

    <input type="text" pattern="^hello" cf-questions="Your answer needs to include 'hello'">

    E-mail
    <input type="email" name="email">

    Phone
    <input type="text" name="phone">

    Website
    <input type="url" name="url">

    Question/Comment
    <textarea name="message"></textarea>

    <input type="submit" name="submit" id="submit" value="Send Message" />

  </fieldset>
</form>

`
If someone can provide me a simple example of that I can just copy and paste and overwrite this code that would super helpful.

Try changing
<form id="contact" method="post" action="" cf-form cf-context>

to
<form id="contact" method="post" action="" cf-form-element>

@alexgurr thanks for trying. I've copied your code across and it still isn't working.
I am building a static website and I wanted to use a conversational form instead of a normal one.
** silly question alert ** - should i be bundling / creating a build file of the website for it to work?
Is there any other things you can thing of that could be preventing it from working?

You don't need to do any of that stuff if it's a static site of HTML pages. I literally have just copied that code above into a foo.html file, opened it in chrome, and it loads fine.

@alexgurr I can confirm i am on the latest chrome version.
I get the same issue when i launch it in firefox too.
I just have an 'index.html' with the code you suggested above in it. But I see the following when I open it in the browser or launch a local server.

I've also just tried it on another computer and its the same issue.
here's the code for the entire index file
`<!doctype html>

<input type="text" pattern="^hello" cf-questions="Your answer needs to include 'hello'">

E-mail
<input type="email" name="email">

Phone
<input type="text" name="phone">

Website
<input type="url" name="url">

Question/Comment
<textarea name="message"></textarea>

<input type="submit" name="submit" id="submit" value="Send Message" />

`

Try putting the script inside a  tag.

If it's the one in your repository - you don't need to wrap the

Thanks for the quick replies and pointing out how to include the code.
It is the one i have just added to my repos.
Even without the div tags around the script....same issue.
When i open the file without serving....same issue.
chrome console shows

Have you tried removing the extra HTML tag?

@alexgurr You legend! That has done it. It's working now. Thanks again!

You're welcome :)


Add rubocop.yml to help ensuring the coding style is followed

Since one of the checks when opening a PR is checking the code styling, it would be helpful if there was a rubocop.yml with the same style guide that is being checked when opening the PR.
This could save some time because I believe I'm not the only one that has rubocop linting active on the text editor and we could spot almost immediately some of the comments we would get when opening the PR.

I'm not against this idea. I will very happily accept PR with a template. The hound integration was added a long time ago and I've never really settled on any style in particular apart from having my personal taste 😉

@rpbaltazar Do you have time to submit an initial style guide that matches the current codebase?

Hey @piotrmurach sorry, I've started it, but ended by not finishing it. Got stuck with other things. This weekend though I should have enough time to do it

👀


Delete obsolete branches

Trying to polish up this library I kindly request to delete the following branches if you don’t mind:
Merged branches:

feature/chunk_stream_filter

Obsolete branches:

fix and travis - to me it looks like docker.sh was "fixed" by https://github.com/stage1/docker-php/commit/7926c4f1#diff-1
sneakybobito/structure - contains significant changes that I don’t think we can merge anymore as they don’t take the work of the last 6 months into account

Done!

Thanks :)! It’s a lot of fun working on this library!!

Happy that you feel that way!
And hopefuly, all the activity around docker-php will motivate me to start working on it again :)


[Bug]: Zitadel can't connect to external PostgreSQL database instance

Preflight Checklist

[X] I could not find a solution in the documentation, the existing issues or discussions
[ ] I have joined the ZITADEL chat

Environment
Self-hosted
Describe the bug
I tried to bring up Zitadel with external (related to the Zitadel host) PostgreSQL database instance.
Before the start i've done all steps described here:
https://zitadel.com/docs/self-hosting/manage/database at the "Postgres" sheet.
The following config file zitadel-conf.yml was used:
Log:
  Level: info

Port: 8080
ExternalPort: 8080
ExternalDomain: localhost
ExternalSecure: false

Database:
  postgres:
    Host: pg1.mynet.net
    Port: 6432
    Database: zitadel
    MaxOpenConns: 25
    MaxConnLifetime: 1h
    MaxConnIdleTime: 5m
    Options: ""
    User:
      Username: zitadel
      Password: "supPer-3Pass"
      SSL:
        Mode: disable
        #RootCert:
        #Cert:
        #Key:

The following init steps file zitadel-init.yml was used:
FirstInstance:
  Org:
    Human:
      Username: 'admin'
      Password: 'Adm384-Du'

I tried with the following commands:
export ZITADEL_MASTERKEY="$(tr -dc A-Za-z0-9 </dev/urandom | head -c 32)"
./zitadel start-from-init --masterkeyFromEnv --config zitadel-conf.yml --steps zitadel-init.yml

and has got the following messages:
INFO[0000] initialization started                        caller="/home/runner/work/zitadel/zitadel/cmd/initialise/init.go:72"
WARN[0000] postgres is currently in beta                 caller="/home/runner/work/zitadel/zitadel/internal/database/postgres/config.go:62"
FATA[0000] unable to initialize the database             caller="/home/runner/work/zitadel/zitadel/cmd/initialise/init.go:65" error="ID=DATAB-0pIWD Message=Errors.Database.Connection.Failed Parent=(cannot parse `host=pg1.mynet.net port=6432 user= application_name=zitadel sslmode= dbname=postgres sslrootcert=`: failed to configure TLS (sslmode is invalid))"

I am really don't understand why Zitadel trying connect to the postgress database when config file has direct order to use zitadel database.
To reproduce
The following config file zitadel-conf.yml was used:
Log:
  Level: info

Port: 8080
ExternalPort: 8080
ExternalDomain: localhost
ExternalSecure: false

Database:
  postgres:
    Host: pg1.mynet.net
    Port: 6432
    Database: zitadel
    MaxOpenConns: 25
    MaxConnLifetime: 1h
    MaxConnIdleTime: 5m
    Options: ""
    User:
      Username: zitadel
      Password: "supPer-3Pass"
      SSL:
        Mode: disable
        #RootCert:
        #Cert:
        #Key:

The following init steps file zitadel-init.yml was used:
FirstInstance:
  Org:
    Human:
      Username: 'admin'
      Password: 'Adm384-Du'

I tried with the following commands:
export ZITADEL_MASTERKEY="$(tr -dc A-Za-z0-9 </dev/urandom | head -c 32)"
./zitadel start-from-init --masterkeyFromEnv --config zitadel-conf.yml --steps zitadel-init.yml

Screenshots
No response
Expected behavior
The configured database name - "zitadel" should be used instead of "postgres".
Version
2.25.5
Operating System
Linux tb1 5.15.0-71-generic #78-Ubuntu SMP Tue Apr 18 09:00:29 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Relevant Configuration
No response
Additional Context
I suspect that something wrong with your logic here:
https://github.com/zitadel/zitadel/blob/main/internal/database/postgres/config.go#L146-L150
By my mind - database type = "postgres" and database name it is completly different things.
P.S. I tried to configure database settings via environment variables such as ZITADEL_DATABASE_POSTGRES_... with the same negative results.
P.S.S. I was successfully tested my PG instance via psql CLI command from the host where Zitadel was executed.

@eliobischof Can you help here?

Hei @philipcristiano
Thanks for the feedback.
I looked at the docs right now, I think we already added the admin now.
I will close the issue for now. Feel free to reopen, if it is no solved

Hi,
I don't think this issue should be closed. As described by @nettworker, the logic in https://github.com/zitadel/zitadel/blob/main/internal/database/postgres/config.go#L146-L150 seems to be invalid. When the admin user is used, the database is always set to postgres and it cannot be changed.
Additionally, the docs are misleading:

The admin user is only needed for the installation step but can also be avoided by preparing the necessary requirements

It cannot, because it has to be defined and it has to use the hardcoded database name.

I also fell over this, as I created the DB user and password manually. I now noticed that defining the admin user cannot be avoided when using docker-compose.
This should be clearly highlighted or even avoided as often enough one does not have access to the PG admin user and a user gets created by someone else.

It is a pity this issue still ongoing.
I faced the same as above, admin user should be provided to go through...

I ran into the same problem (I think?) while trying to use the Helm chart and using the init mode zitadel (so it only creates zitadel data). What helped me was defining ZITADEL_DATABASE_POSTGRES_ADMIN_SSL_MODE=require. It seems to me that the code might be reading database.postgres.admin.ssl.mode instead of database.postgres.user.ssl.mode for the init part, even when you are trying to avoid using it (it was using the correct user, host and password from the database.postgres.user section already).
Hope that helps in at least some scenarios where this happens.

Hi guys! One year later ... The same issue.
./zitadel --version
zitadel version v2.53.0

./zitadel start-from-init --masterkeyFromEnv

INFO[0000] initialization started                        caller="/home/runner/work/zitadel/zitadel/cmd/initialise/init.go:75"
FATA[0000] unable to initialize the database             caller="/home/runner/work/zitadel/zitadel/cmd/initialise/init.go:68" error="ID=DATAB-0pIWD Message=Errors.
Database.Connection.Failed Parent=(failed to connect to `host=c9.mdb.mycloud.net user=dbadmin database=postgres`: server error (ERROR: odyssey: cd499cd511e82: route for 'postgres.dbadmin' is not found (SQLSTATE 3D000)))"

I tried to create the "postgres" PG database at my cloud provider with Terraform, but fail again:
Error: error while requesting API to create database in PostgreSQL Cluster "c9qljdegso81slbbb2jh": server-request-id = e3ae1889-3b9f-40a2-a101-ed0d1218ed9f server-trace-id = 2729332f07537bb1:7492ec102cf369c2:2729332f07537bb1:1 client-request-id = 91bba4a4-31e9-46ba-8cc2-be3829e35080 client-trace-id = 4c6487a3-e626-45bd-946e-08649cb7f289 rpc error: code = InvalidArgument desc = The request is invalid.
databaseSpec.name: Database name 'postgres' is not allowed

Trying to init Zitadel by init command. Yohoo - Zitadel found correct database name - zitadb! Really ?
./zitadel init zitadel
INFO[0000] verify zitadel                                caller="/home/runner/work/zitadel/zitadel/cmd/initialise/verify_zitadel.go:78" database=zitadb
INFO[0000] verify system                                 caller="/home/runner/work/zitadel/zitadel/cmd/initialise/verify_zitadel.go:39"
INFO[0000] verify encryption keys                        caller="/home/runner/work/zitadel/zitadel/cmd/initialise/verify_zitadel.go:44"
INFO[0000] verify projections                            caller="/home/runner/work/zitadel/zitadel/cmd/initialise/verify_zitadel.go:49"
INFO[0000] verify eventstore                             caller="/home/runner/work/zitadel/zitadel/cmd/initialise/verify_zitadel.go:54"
INFO[0000] verify events tables                          caller="/home/runner/work/zitadel/zitadel/cmd/initialise/verify_zitadel.go:59"
INFO[0000] verify system sequence                        caller="/home/runner/work/zitadel/zitadel/cmd/initialise/verify_zitadel.go:64"
INFO[0000] verify unique constraints                     caller="/home/runner/work/zitadel/zitadel/cmd/initialise/verify_zitadel.go:69"

I hope, that start-from-init command will start work as expected and documented.
Thank you.
/Alexander

Hm @nettworker can you share what cloud provider you are using?
It kind of looks to me like a provider specific issue.
Does the same config work against a local DB?

Hi team!
I see that fix already merge to Main branch. It's great news! Thank you very much!
Could you please clarify what Zitadel release with this fix I should use?
Unfortunately I didn't see #8045 in release notes history.
P.S. I just tried with 2.54.3 but no success.
Thank you.
/Alexander

Add comments here:
https://github.com/zitadel/zitadel/pull/8045#issuecomment-2180024747
WBR,
/Alexander


[kafka] Test Kafka JMX check against latest Kafka versions

1.0.1 is the latest bugfix version
1.1.0 is the latest released version
NOTE: This feels like a lot of flavors... possibly some should get removed.
However, I'm working on adding a check that requires functionality available from 0.11 onwards, and there are various other features in there that are only enabled from specific versions of Kafka onward, so in some ways it's best to have these... IDK

@masci I appreciate the trust you place in my code that you were willing to merge it even though it failed tests, but sadly I'm afraid your trust is misplaced. 😢
Unfortunately, this failed the tests because the latest docker images on https://hub.docker.com/r/wurstmeister/kafka/tags/ do not include the -1 suffix like they used to. I realized last night and pushed an updated commit, but looks like I forgot to include the patch in my amended commit.
Fixed here: https://github.com/DataDog/integrations-core/pull/1450


main.zeek, line 98: field value missing (genisys::c$genisys_proto)

🐛 Summary
An error I ran into:
worker-08: expression error in <<REDACTED>>/zeek/site/packages/icsnpp-genisys/main.zeek, line 98: field value missing (genisys::c$genisys_proto)

This line needs to check the existence of the field c$genisys_proto before using it: https://github.com/cisagov/icsnpp-genisys/blob/main/analyzer/main.zeek#L98

Resolved with #4


Fix ambiguous column error when joining some relations

Joining the relation returned by #higher_items or #lower_items to a table also having position_column would result in an ambiguous column error.
The new test file might be a bit heavy handed, but test_list.rb is somewhat...opaque. :)
The test cases are pretty close to my actual use case, and I admit that it's a slightly awkward one.
I have a visible scope on Item that joins on Section, but in the case of the query set returned by lower_items, it's already scoped to a particular Section.
So I could just say .where(visible: true) instead of .visible, which would avoid the unnecessary join, and I'll probably just do that in the meantime.
Still, I think this is probably a change for the better.

@natw, could you use quoted_table_name as per: https://github.com/swanandp/acts_as_list/pull/174 and rebase. Looks good otherwise.

done

Thanks for that. I think there are some inconsistencies now regarding the use of quoted_position_column and position_column in queries.
Can you use quoted_position_column instead of position_column?

there you go. Sorry for the slow response.

Thanks for that :) I've merged that now for you. Expect a new gem in the next week or two once a few other issues get closed.


no decimal/float coefficients?

When I declare operands containing non-integer coefficients, solveLinear raises a "several potential instances", e.g. :1234:

let b = sparseList [1,3]
:t b
b :: (Num α, Eq α) => SparseVector α
let b' = sparseList [1,3.1]
:t b'
b' :: (Fractional α, Eq α) => SparseVector α
let a = sparseMx [[1,2],[2,1]]
:t a
a :: (Num α, Eq α) => SparseMatrix α
let a = sparseMx [[1.2,2],[2,1.2]]
:t a
a :: (Fractional α, Eq α) => SparseMatrix α
solveLinear a' b'

:69:1:
No instance for (Show α0) arising from a use of ‘print’
The type variable ‘α0’ is ambiguous
Note: there are several potential instances:
instance Show Double -- Defined in ‘GHC.Float’
instance Show Float -- Defined in ‘GHC.Float’
instance (Integral a, Show a) => Show (GHC.Real.Ratio a)
-- Defined in ‘GHC.Real’
...plus 29 others
In a stmt of an interactive GHCi command: print it
Is this a bug or a feature? Is there a workaround for systems with non-integer coefficients?

Hi @ocramz! This is actually how it's done — only for integer coefficients. I was using it for a project where worked particularly with integer coefficients, so here I implemented just a minimal set of necessary algorithms for that.

thanks for the clarification, very inspiring work!

Thanks ") it's a pity though that I did't have time to maintain it. On the other hand there are already several sparse linear algebra libs for Haskell (~2-3 years ago there were none)...


feat(protocol-designer): memoize compound command creators

Overview
This PR introduces memoization into the complex command creators.
Command creation is a computationally intensive task, and it can get called over and over again with the same values. This PR caches calls to command creators so that needless computation can be avoided.
closes #7021
Changelog

Memoize compound command creators

Review requests
Upload the protocol attached into PD (it'll take a while to import)
Reorder steps/create a new step
You'll should see that the spinner time significantly decreases.
Try to do the same on production and you should see it taking way longer (except for the initial import)
HG Vial Dispense 25ul non complete.json.zip
Risk assessment
Low/med touches command creators but not changing any functionality

No longer needed after #7053


Revising steps for building MXNet on Windows platform

Description
The steps for building MXNet on Windows have been enhanced by adding more details to make it more customer friendly. The GUI version of CMake simplifies generation of Visual Studio project by iteratively
providing feedback on generation errors. Also by using appropriate Visual Studio Command prompt, CMake tool will inherit all the details it needs to know to discover build environment.

There are problems with vs2017 +cuda9.0 now.some cu can't build.

ok,vs 2017 and cuda9.0 compiler problem has been found.the default All use too many arc.cause ptxas is carsh.cut down arc it will work fine.
https://github.com/apache/incubator-mxnet/pull/8624


fix version check

need to not use json if we're just pulling the flat string.
happy to help revise if you're going with something else that I'm overlooking.

closing, looks like other updates were made

yes, your changes caused conflicts but thanks for the PR. I modified the auto update function with your code so that it works as it should!
See https://github.com/unconst/ImageSubnet/commit/b74329de5445a4471df82117c4ea7103f6f3d2b5


merge from template-arlac77-github

.github/workflows/ci.yml

chore(deps): add 20.16.0 (jobs.test-node.strategy.matrix.node-version)

Pull Request Test Coverage Report for Build<PHONE_NUMBER>6
Details

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.009%) to 87.092%

Totals

Change from base Build<PHONE_NUMBER>8:
-0.009%

Covered Lines:
2530

Relevant Lines:
2893

💛  - Coveralls


sed command failing with vagrant and Docker 1.11

While starting the cluster-lab with a vagrant up after vagrant destroy I get the following log output:
==> follower2: Setting up hypriot-cluster-lab-src (0.2.12-1) ...
==> follower2: Created symlink from /etc/systemd/system/multi-user.target.wants/cluster-lab.service to /etc/systemd/system/cluster-lab.service.
==> follower2: cp:
==> follower2: cannot stat ‘/etc/systemd/system/docker.service’
==> follower2: : No such file or directory
==> follower2: sed: can't read /etc/systemd/system/docker.service: No such file or directory

A docker info against Swarm results in the following output:
root@follower1:/home/vagrant# DOCKER_HOST=tcp://<IP_ADDRESS>:2378 docker info
Containers: 0
 Running: 0
 Paused: 0
 Stopped: 0
Images: 0
Role: primary
Strategy: spread
Filters: health, port, dependency, affinity, constraint
Nodes: 3
 (unknown): <IP_ADDRESS>:2375
  └ Status: Pending
  └ Containers: 0
  └ Reserved CPUs: 0 / 0
  └ Reserved Memory: 0 B / 0 B
  └ Labels:
  └ Error: Cannot connect to the docker engine endpoint
  └ UpdatedAt: 2016-06-08T05:03:41Z
 (unknown): <IP_ADDRESS>:2375
  └ Status: Pending
  └ Containers: 0
  └ Reserved CPUs: 0 / 0
  └ Reserved Memory: 0 B / 0 B
  └ Labels:
  └ Error: Cannot connect to the docker engine endpoint
  └ UpdatedAt: 2016-06-08T04:58:31Z
 (unknown): <IP_ADDRESS>:2375
  └ Status: Pending
  └ Containers: 0
  └ Reserved CPUs: 0 / 0
  └ Reserved Memory: 0 B / 0 B
  └ Labels:
  └ Error: Cannot connect to the docker engine endpoint
  └ UpdatedAt: 2016-06-08T05:01:01Z
Plugins:
 Volume:
 Network:
Kernel Version: 4.2.0-30-generic
Operating System: linux
Architecture: amd64
CPUs: 0
Total Memory: 0 B
Name: e62a0f42529d
Docker Root Dir:
Debug mode (client): false
Debug mode (server): false
WARNING: No kernel memory limit support

A docker info against the local Docker installation results in
root@follower1:/home/vagrant# docker info
Containers: 3
 Running: 3
 Paused: 0
 Stopped: 0
Images: 2
Server Version: 1.11.2
Storage Driver: overlay
 Backing Filesystem: extfs
Logging Driver: json-file
Cgroup Driver: cgroupfs
Plugins:
 Volume: local
 Network: bridge null host
Kernel Version: 4.2.0-30-generic
Operating System: Ubuntu 15.10
OSType: linux
Architecture: x86_64
CPUs: 1
Total Memory: 992.9 MiB
Name: follower1
ID: FJYP:QGBI:QQRC:DCXS:OEOW:36JV:JMPV:DTFV:6B6K:C4XO:PEQO:LJYE
Docker Root Dir: /var/lib/docker
Debug mode (client): false
Debug mode (server): false
Registry: https://index.docker.io/v1/
WARNING: No swap limit support

A cluster-lab health shows
root@follower1:/home/vagrant# cluster-lab health

Internet Connection
  [PASS]   eth1 exists
  [PASS]   eth1 has an ip address
  [PASS]   Internet is reachable
  [PASS]   DNS works

Networking
  [PASS]   eth1.200 exists
  [PASS]   eth1.200 has correct IP from vlan network
  [PASS]   Cluster leader is reachable
  [PASS]   eth1.200 has exactly one IP
  [PASS]   eth1.200 has no local link address
  [PASS]   Avahi process exists
  [PASS]   Avahi is using eth1.200

Docker
  [PASS]   Docker is running
  [FAIL]   Docker is configured to use Consul as key-value store
  [FAIL]   Docker is configured to listen via tcp at port 2375
  [FAIL]   Docker listens on <IP_ADDRESS> via tcp at port 2375 (Docker-Engine)

Consul
  [PASS]   Consul Docker image exists
  [PASS]   Consul Docker container is running
  [PASS]   Consul is listening on port 8300
  [PASS]   Consul is listening on port 8301
  [PASS]   Consul is listening on port 8302
  [PASS]   Consul is listening on port 8400
  [PASS]   Consul is listening on port 8500
  [PASS]   Consul is listening on port 8600
  [PASS]   Consul API works
  [PASS]   Cluster-Node is pingable with IP <IP_ADDRESS>
  [PASS]   Cluster-Node is pingable with IP <IP_ADDRESS>
  [PASS]   Cluster-Node is pingable with IP <IP_ADDRESS>
  [PASS]   No Cluster-Node is in status 'failed'
  [FAIL]   Consul is able to talk to Docker-Engine on port 7946 (Serf)

Swarm
  [PASS]   Swarm-Join Docker container is running
  [PASS]   Swarm-Manage Docker container is running
  [PASS]   Number of Swarm and Consul nodes is equal which means our cluster is healthy

It seems the Docker daemon was not configured correctly by the cluster-lab.
I guess the problem is related to the following line:
https://github.com/hypriot/cluster-lab/blob/master/package/usr/local/lib/cluster-lab/docker_lib#L79-L81
@firecyberice What do you think?

@Govinda-Fichtner @firecyberice I Might have a fix for this. Testing now.

@Govinda-Fichtner can you please add the missconfigured /etc/systemd/system/docker.service file

Issue was in the script that copies the service file. Was putting it in /lib instead of /etc.  #49 for the fix.


Fix Vulnerability - alert/4595220

See this security alert description: https://dev.azure.com/FuseLabs/SDK_Public/_componentGovernance/143548/alert/4595220?typeId=2307488
Linked issue: #5354

Resolved: All current botbuilder-dotnet packages referencing System.Text.Encodings.Web specify version 5.0.1. That is a secure version.


Configuration to skip files in certain directories

Context
In our current adoption of packwerk, we've elected to keep our specs directory monolithic.
bundle exec packwerk check skips our specs directory, but when running the check against a list of modified files we potentially include specs which don't currently conform to packages.
Is it possible to include a configuration to packwerk.check that excludes files from certain directories?

Follow up, this can already be accomplished by excluding these in packwerk.yml so closing issue, sorry about the noise.


Panic parsing terminfo

vtebench panic while trying to run a benchmark, apparently parsing terminfo.
The version used is current master at 300768f39d1cb34c958aaff54c4356faeaaeafee
Here follows system info and backtrace. I attached the terminfo file and the output of strace
# lsb_release -a
LSB Version:    :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch
Distributor ID: Fedora
Description:    Fedora release 28 (Twenty Eight)
Release:        28
Codename:       TwentyEight

RUST_BACKTRACE=1 ./target/debug/vtebench -b 50000000 -w $(tput cols) -h $(tput lines) scrolling-in-region --lines-from-bottom 1

thread 'main' panicked at 'called `Result::unwrap()` on an `Err` value: Terminfo(Parse)', libcore/result.rs:945:5
stack backtrace:
   0: std::sys::unix::backtrace::tracing::imp::unwind_backtrace
             at libstd/sys/unix/backtrace/tracing/gcc_s.rs:49
   1: std::sys_common::backtrace::_print
             at libstd/sys_common/backtrace.rs:71
   2: std::panicking::default_hook::{{closure}}
             at libstd/sys_common/backtrace.rs:59
             at libstd/panicking.rs:380
   3: std::panicking::default_hook
             at libstd/panicking.rs:396
   4: std::panicking::rust_panic_with_hook
             at libstd/panicking.rs:576
   5: std::panicking::begin_panic
             at libstd/panicking.rs:537
   6: std::panicking::begin_panic_fmt
             at libstd/panicking.rs:521
   7: rust_begin_unwind
             at libstd/panicking.rs:497
   8: core::panicking::panic_fmt
             at libcore/panicking.rs:71
   9: core::result::unwrap_failed
             at /checkout/src/libcore/macros.rs:23
  10: <core::result::Result<T, E>>::unwrap
             at /checkout/src/libcore/result.rs:782
  11: vtebench::main
             at src/main.rs:43
  12: std::rt::lang_start::{{closure}}
             at /checkout/src/libstd/rt.rs:74
  13: std::panicking::try::do_call
             at libstd/rt.rs:59
             at libstd/panicking.rs:479
  14: __rust_maybe_catch_panic
             at libpanic_unwind/lib.rs:102
  15: std::rt::lang_start_internal
             at libstd/panicking.rs:458
             at libstd/panic.rs:358
             at libstd/rt.rs:58
  16: std::rt::lang_start
             at /checkout/src/libstd/rt.rs:74
  17: main
  18: __libc_start_main
  19: _start

strace_output.txt
terminfo.zip

I'm having a similar issue and this is probably not the fault of vtebench but rather an issue with terminfo (so maybe reporting it there will help more if it's not already reported).
However as a workaround using the flag --term xterm has worked for me.

Have either of you done a cargo update which would result in a newer version of the terminfo crate being used?

Neither cargo update nor bumping it to 0.5 worked for me.


Vehicle Tesla: misleading error on startup

Describe the bug
The error is:
[main  ] ERROR 2024/03/16 07:22:45 creating vehicle ev failed: invalid vehicle type: tesla
but should be:
[main  ] ERROR 2024/03/16 07:50:53 creating vehicle ev failed: cannot create vehicle type 'tesla': token expired
If you comment out the condition:
// vehicle/tesla.go
func init() {
	if id := os.Getenv("TESLA_CLIENT_ID"); id != "" {
		tesla.OAuth2Config.ClientID = id
	}
	if secret := os.Getenv("TESLA_CLIENT_SECRET"); secret != "" {
		tesla.OAuth2Config.ClientSecret = secret
	}
	//if tesla.OAuth2Config.ClientID != "" {
	registry.Add("tesla", NewTeslaFromConfig)
	//}
}

You will see the logs below.
Steps to reproduce

Create a valid Tesla token/refresh-token pair or you already have one
Wait until token exp
Start evcc

Configuration details
vehicles:
  - name: ev
    type: tesla
    title: Model3
    icon: car
    tokens:
      access: eyJhbxxx
      refresh: EU_3115xxx
    capacity: 60
    vin: LRWxxx

    features: ["coarsecurrent"]

Log details
[tesla ] TRACE 2024/03/16 07:50:50 POST https://auth.tesla.com/oauth2/v3/token
[tesla ] TRACE 2024/03/16 07:50:53 grant_type=refresh_token&refresh_token=***
--
{
  "error": "unauthorized_client",
  "error_description": "We don't recognize this client_id and client_secret combination",
  "referenceID": "e7815d65-xxx"
}
[main  ] ERROR 2024/03/16 07:50:53 creating vehicle ev failed: cannot create vehicle type 'tesla': token expired

What type of operating system are you running?
Linux
Version
master d3ae3350

Thats expected when evcc is compiled without Tesla support.

? If you comment it out you will see the real error otherwise it throws unknown template which is still wrong.

It was just a hint for the root cause.

It is the real error. There is no Tesla support.


Pdf reports

Implementation of PDF reports using external service pdfcrowd

Good work. Seems like we are still using the hardcoded pdfcrowd credentials and that we need to sort out where pdfcrowd looks for the css/js files. I suggest both of these things are sorted out before we merge this into master.

Pdfcrowd credentials are now defined in meerkat_infrastructure/dev/docker-compose.yml. For running pdfcrowd in local environment the env variable PDFCROWD_USE_EXTERNAL_STATIC_FILES can be set to 1, in which case the CSS/JS files are fetched from https://console.aws.amazon.com/s3/home?region=us-west-2#&bucket=test-meerkat&prefix=pdfcrowd-files/

We need to change our email on our pdfcrowd account how will I do this


4.0 beta 5 last reboot date error

Tried running the 4.0 beta 5 script to install super and am getting the following error:
Error: Unregonized last reboot date format: Oct 18 10:59
I've attached my log
super 2.log

https://github.com/Macjutsu/super/releases/tag/v4.0.0-beta6

@Macjutsu Using 4.0 Beta6 - Same error. Could open a new issue but it seems to be the same one.
Small typo side note: Unregonized  > Unrecognized
Thu Oct 19 00:34:37 MAC bash[66851]: Installation: Copying super to: /Library/Management/super/super
Thu Oct 19 00:34:37 MAC bash[66851]: Installation: Creating super search path link: /usr/local/bin/super
Thu Oct 19 00:34:37 MAC bash[66851]: Installation: Creating super LaunchDaemon helper: /Library/Management/super/super-starter
Thu Oct 19 00:34:37 MAC bash[66851]: Installation: Removing previous super LaunchDaemon: /Library/LaunchDaemons/com.macjutsu.super.plist
Thu Oct 19 00:34:37 MAC bash[66851]: Installation: Creating super LaunchDaemon: /Library/LaunchDaemons/com.macjutsu.super.plist.
Thu Oct 19 00:34:37 MAC bash[66851]: Installation: Setting permissions for installed super items.

Thu Oct 19 00:34:38 MAC bash[66851]: **** S.U.P.E.R.M.A.N. 4.0.0-beta6 - ERROR EXIT ****```

You are correct that this is still an open bug... but also a duplicate... https://github.com/Macjutsu/super/issues/156


Question: is there a maximum length for a given key?

I have a very long key and I was wondering if I could use it with figaro or just store it in the database.

I don't think there's a maximum. I guess just give it a try!


Injection tarrif

Feature request:
Is it possible to get a sensor with tariff for injection as well?

in latest version, option has been added to add full details of the rates. doing so, injection rates would be listed too I'd expect.
adding it as a separate sensor might be an option too in future


An access token is required to delete a video.

Exception in Youtube.php line 288:
An access token is required to delete a video.
I got an error when upload file.
How to solve it?
I don't know how to add token for it!

Hi,
Have you followed the readme? https://github.com/JoeDawson/youtube/blob/master/README.md

Yes, I created an application on Google and get Client ID, Client secret to updated to .env config file.
In table youtube_access_tokens are empty.

You need to visit your Google console and add your URL as the callback (localhost).
Then in your app, visit http://localhost:8000/youtube/auth - you will be redirected to Google and will be asked to log in. This is when you get a token.

Did you solve this?

Closing due to inactivity.

Sorry, I have just back this issue.
Still not solve
Got new error!
Whoops, looks like something went wrong.
I'm trying to debug, the seems error by getAccessToken of client.
$accessToken = $this->client->getAccessToken(); is null


perl: warning: Setting locale failed

Hi there, I've run this:
singularity exec trust4-singularity.sif /TRUST4/run-trust4 -b M1500497.bam
then met with the following errors:
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
[Mon Apr  6 23:59:06 2020] TRUST4 begins.
Need to use -f to specify the sequence of annotated V/D/J/C genes' sequence.
Please could you help? Thanks!
Dakai

The warning is fine. There are two required option -f and --ref, e.g:
singularity exec trust4-singularity.sif /TRUST4/run-trust4 -b M1500497.bam -f  hg38_bcrtcr.fa --ref human_IMGT+C.fa .
You can add other options like "-t" for multithreading.


The comment can not be parsed when using decorator

Example
class JoinGroupAPIView(APIView):
    def post(self, request):
        """
        加入某个小组的api
        ---
        request_serializer: CreateJoinGroupRequestSerializer
        """
        pass

It works fine

But when I added @login_required decorator, the document it generated has something wrong
class JoinGroupAPIView(APIView):
    @login_required
    def post(self, request):
        """
        加入某个小组的api
        ---
        request_serializer: CreateJoinGroupRequestSerializer
        """
        pass

shouldn't you be using permission_classes or get_permissions in conjunction with permissions.IsAuthenticated instead of login_required?

I added @wraps(func) for my decorator. It worked now.
Because the decorator will change the name of the function.
http://stackoverflow.com/questions/308999/what-does-functools-wraps-do
Thanks!


Make Dataset Folder compatible with WEBP images

It seems like webp is supported in PIL , does the PIL loader not work with it?

@bjuncek we just needed to add it to the list of supported formats.
This has been fixed via #736


Some changes to the code.

Added an array of elements to remove intead of hard-coding it.

Removing the entire element instead of hiding it.


Make room bans hide messages in the room only.

I really don't like this change, but people are going to be complaining about it over and over so I guess I'm doing it


Mongodb does not work with Email auth

Hello,
Thanks for this great library, I'm on version 2.0.0-beta.59 and it seems like Mongodb does not work with Email auth.
After clicking on the link being sent by email I get this error :
EMAIL_CALLBACK_ERROR TypeError: Cannot read property 'id' of undefined     at next-auth/dist/server/lib/callback-handler.js:1:1381
It seems related to this line,
https://github.com/iaincollins/next-auth/blob/50b9743bb6a659c6b3061f07b7f5db1ede00ff04/src/server/lib/callback-handler.js#L68
Shouldn't it be "user._id" when the database is mongodb ?

Thank you for the bug report!
So, the methods in the default database adapter should be handling that abstraction, but I've worked out what is going on.
I'm going to guess you have jwt enabled with mongodb and that this is happening when you are trying to sign in while already having a valid session.
When using a JWT the User ID is extracted from the token, rather than from a query to the session table, this means it's type is not an ObjectID but a string. When getUser was being called, it was failing because it was a regular string and looking up an ObjectID with a string does match.
There were a couple of other related issues which compounded this error, including the order of conditional checks not being very good and another almost identical problem when it ties to link accounts which is in turn a consequence of the sign in page not currently checking to see if you are already signed in (which is intended oddity for now, as account linking isn't complete yet).
To top that off, documentation was also wrong and should have listed npm i mongodb as the driver install instructions for MongoDB.
I've just published a fix as 2.0.0-beta.60 and would appreciate your feedback!


fix: add wrapper ref to wrapper div and use element hook

Description

Adds wrapperRef to all elements to certify the wrapper <div> is in the DOM before trying to mount the element.

Testing required outside of automated testing?

[x] Not Applicable

Screenshots (if appropriate):

[x] Not Applicable

Rollback / Rollforward Procedure

[x] Roll Forward
[ ] Roll Back

Reviewer Checklist

[ ] Description of Change
[ ] Description of outside testing if applicable.
[ ] Description of Roll Forward / Backward Procedure
[ ] Documentation updated for Change

:tada: This PR is included in version 1.4.1 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


Ascend & plain ascend

Dear All,
I have been translating the web platform and I am puzzled what ascend & plain ascend means.

ascend: perhaps the whole elevation difference what should be done to reach the destination
plain ascend: perhaps the elevation difference between start point and destination

However, if I look at the height profile of a route, figures don't exactly match these definitions…
Please, explain me what they are
Thanks

It is as above.
But the ascend seems to me to be "filtered ascend", as named in the final stats of the BRouter itself.
It is the raw ascend as get by applying SRTM altitudes, with applied the 10m hysteresis filter. Hungary may look rather flat for this filter.

As you wrote:

ascend = total ascend = cumulative elevation gain
(" sum of every gain in elevation throughout an entire trip")
plain ascend = height difference (between start and end point)

And as poutnikl already said, "ascend" is really "filtered ascend", not sure if it will get too long, but maybe we should label it as such, while "filtered total ascend" probably is too long.
Personally, I'm not quite happy with the term "plain ascend" and might want to rename it, perhaps to:

height difference
difference in altitude
difference in elevation

Any opinions, other suggestions?

What about Linear elevation ?
Btw, as EN non native, is elevation and altitude the same thing, or is the former rather altitude difference ?

Note: I've added the given context into Transifex to ease future translations :-).


CLOUDP-167804: Migrate serverless instances commands to v2 client

Proposed changes
Migrate Serverless Instances commands to use v2 client.

Jira ticket: CLOUDP-167804

Checklist

[x] I have signed the MongoDB CLA
[ ] I have added tests that prove my fix is effective or that my feature works
[ ] I have added any necessary documentation in document requirements section listed in CONTRIBUTING.md (if appropriate)
[ ] I have addressed the @mongodb/docs-cloud-team comments (if appropriate)
[ ] I have updated test/README.md (if an e2e test has been added)
[x] I have run make fmt and formatted my code

Further comments

For the first commit, the build will be failing as kubernetes/operator is also using the Store, but is accessing the field AutoScaling that is not present in the v2 client.
Checked on the backend model, and this issue is not an OpenAPI annotation issue, but it seems like a bug in operator.
Here is the error from Evergreen:
internal/kubernetes/operator/deployment/deployment.go:442:17: deployment.AutoScaling undefined (type *mongodbatlasv2.ServerlessInstanceDescription has no field or method AutoScaling)

the parts that are passed to operator need to be v1 structures. It looks like we do use the same sdk in both and objects are passed between operator and cli.
We will need to work with Kubernetes team to get models updated later phase.
For now we need to do v2=>v1 mapping for entire kubernetes suite.
CC @igor-karpukhin

As solution, we can duplicate the method used by Kubernetes (leave it untouched) and introduce new one for the CLI itself

Rebase needed.

@andmatei this should be fixed now

Was discussed in the triage call, looks like we don't want to remove atlas commands from mongocli yet, so may have to revert some of these changes 😢
CC @gssbzn @wtrocki @colm-quinn

Should we migrate those commands to use the v2 client, or should duplicate the stores in this case too?

I think just use the v2 client across the board.
No sense duplicating the stores then removing one set a week or two later


Retiring gorpc for vtctl.

@michael-berlin @enisoc

Note the last file is already imported in google3.

LGTM


lxd/firewall/drivers: Fix nft syntax

This fixes the nft syntax, as it causes the following error in LXD:
EROR[05-11|18:09:29] Firewall nftables unable to parse existing ruleset:
invalid character '^' looking for beginning of value

When running the command in a shell, it says:
$ nft list ruleset --json -nn
Error: syntax error, options must be specified before commands
nft list ruleset --json -nn
   ^             ~~

Signed-off-by: Thomas Hipp<EMAIL_ADDRESS>

@monstermunchkin weird, they have have relaxed the ordering in future versions of nft as the json parser option is required to activate nft support, which is happening OK in ubuntu 20.04 as is.
What version of nft and os are you testing this on btw?

@tomponline
$ nft --version
nftables v0.9.4 (Jive at Five)

@monstermunchkin interesting, im running v0.9.3 (Topsy) on ubuntu 20.04.
So they've actually tightened the restrictions in the newer version.

@monstermunchkin the change in this PR works on v0.9.3 too so all good :)

Testsuite passed


Connection Failed

I think the connections to server has been outraged for last couple of days.
Prompts: Fetch errors.

The service has been restored, please try again, or upgrade the plug-in version. Thank you for your feedback


Add Doctor Model, accept Doctor in the file and set up password hashing.

Add Doctor Model
Add test cases for Doctor
Add Password hashing at commons package
Add test case for password hashing util.
Allow retrieval and storing of Doctor into the file.
Add test cases for 6.

Pull Request Test Coverage Report for Build 79

140 of 189 (74.07%)  changed or added relevant lines in 13 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-2.01%) to 90.809%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

src/main/java/seedu/address/commons/util/HashUtil.java
7
8
87.5%

src/main/java/seedu/address/storage/XmlSerializableAddressBook.java
9
10
90.0%

src/main/java/seedu/address/model/doctor/Id.java
6
8
75.0%

src/main/java/seedu/address/model/doctor/UniqueDoctorList.java
37
39
94.87%

src/main/java/seedu/address/model/doctor/Password.java
9
11
81.82%

src/main/java/seedu/address/model/AddressBook.java
13
19
68.42%

src/main/java/seedu/address/model/ModelManager.java
13
20
65.0%

src/main/java/seedu/address/model/doctor/Doctor.java
22
31
70.97%

src/main/java/seedu/address/storage/XmlAdaptedDoctor.java
16
35
45.71%

Totals

Change from base Build 75:
-2.01%

Covered Lines:
1571

Relevant Lines:
1730

💛  - Coveralls

Btw, by custom we need to wait for all assigned reviewers to review before any of us clicks the "Merge pull request" button right? Or should I click it now

No nid. Currently, I set it to at least 1.


sparc64-linux support

This needs to be "cleaned" up to use modules instead of a bunch of cfgs ...
Sadly, sparc64 constants are very different from other architectures so cleaning this will result in a bunch of duplication, I think.
While working on this, I was wondering why the constants are not written like this:
// linux/mod.rs
const COMMON: ::c_int = 3;

cfg_if! {
    if #[cfg(target_arch = "sparc64")] {
        const FOO: ::c_int = 1;
    } else if #[cfg(any(target_arch = "mips64", target_arch = "x86_64"))] {
        const FOO: ::c_int = 2;
    } else {
        // unsupported/unknown architecture
    }
}

I think this might result in less duplicated code. @alexcrichton Has something like that ^ been attempted before?

r? @alexcrichton
(rust_highfive has picked a reviewer for you, use r? to override)

For values that need to be changed for #[cfg]'d, can we just push those down the module hierarchy? It's fine to have a ton of duplication, that's what libc is for!

Looks good to me! Travis has a few failures though?

Looks good to me! Travis has a few failures though?

should be ready to go this time

should be ready to go this time

@bors: r+

@bors: r+

:pushpin: Commit 67615b4 has been approved by alexcrichton

:pushpin: Commit 67615b4 has been approved by alexcrichton

:hourglass: Testing commit 67615b4 with merge 3e89579...

:hourglass: Testing commit 67615b4 with merge 3e89579...

:sunny: Test successful - status-appveyor, status-travis
Approved by: alexcrichton
Pushing 3e895791fb587f56ee533db2f33a215b19495c13 to master...

:sunny: Test successful - status-appveyor, status-travis
Approved by: alexcrichton
Pushing 3e895791fb587f56ee533db2f33a215b19495c13 to master...


When i use api as route method, i can't get the session values.

Laravel Version: 5.5.*
PHP Version: 7.1.12
Database Driver & Version: MySQL 5.7

Description:
When i request url is 'api/test' , i can't get the session values.  my test code:
Route::get('session/test',function(){
    if (session()->has('test'))
    {
        echo 'session storage , data:' . session('test');
    }else{
        session('test','this is test');
        dd(session('test'));
    }
});

### Steps To Reproduce:

the base method session_start() and $_SESSION['test'] are access values.

Hi @Bevis-Liao,
Welcome to Laravel and we are glad to have you as part of the community.
Unfortunately this github area is not a support area for general application issues. This is only for issues/bugs with the framework code itself. The lack of session data in the API is an intended and correct behaviour of the framework.
Can I please suggestion closing your issue ticket here. Instead trying asking your question on one of the many great community support areas that will likely give you a better answer more quickly:

Laravel Slack (https://larachat.co/)
Laravel.io Forum (https://laravel.io/forum)
Laracasts Forum (https://laracasts.com/discuss)
StackOverflow (http://stackoverflow.com/questions/tagged/laravel)

Thanks in advance.

@laurencei  Many thanks for your reply.

This is not a bug. Check the $middlewareGroups in your app/Http/Kernel.php and you'll find that the api does not have sessions enabled.

Solved by adding \Illuminate\Session\Middleware\StartSession::class,
In Kernel.php
Before
'api' => [
'throttle:60,1',
'bindings',
],
After
'api' => [
\Illuminate\Session\Middleware\StartSession::class,
'throttle:60,1',
'bindings',
],

This is not a bug. Check the $middlewareGroups in your app/Http/Kernel.php and you'll find that the api does not have sessions enabled.

I know this is an old post, but would there be some negative outcomes form enabling sessions in the API routes?

@adampatterson I enabled them but it still didn't work

Solved by adding \Illuminate\Session\Middleware\StartSession::class,
In Kernel.php
Before
'api' => [
'throttle:60,1',
'bindings',
],
After
'api' => [
\Illuminate\Session\Middleware\StartSession::class,
'throttle:60,1',
'bindings',
],

It didn't work for me at first but when i cleared my config it now works.
php artisan config:clear

It is still not working for me after the above changed

@marcosdipaolo  I can't even remember what project I was working on at the time but have a look at using Laravel Sanctum


Feature request: Simple way to consider remaining input a failure

I often need to scan a string and check that the entire string was consumed. I can do:
int num;
auto result = scn::scan(filename, "item-{}.txt", num);
if (result && result.range().empty()) {
    // Filename is valid
}

but I would rather type something like:
int num;
if (scn::scan_all(filename, "item-{}.txt", num)) {
    // Filename is valid
}

Could this be considered (or is there some other simple way to do this that I am missing)?

At least for now, I don't consider this worth increasing the API surface.


send an email to the newsletter subscribers

Migrated from GitLab: https://gitlab.com/meltano/meltano/-/issues/917
Originally created by @dmor on 2019-08-22 22:46:04

We have subscribers, let's email them and grow MAUI!
Goals:
Implicit: Get users to update their version so they can be properly tracked by Google Analytics
Explicit: Show traction with list of all we have shipped
Explicit: Request participants for Meltano pilots
Explicit: Promote GitLab Commit London

View 10 previous comments from the original issue on GitLab


Add ability to create Cluster Groups

This is in support of 10,000 cluster and 100,000 nodes.

Issue & design being tracked already so I'm closing this as duplicate.
https://github.com/rancher/dashboard/issues/259


cellsetformatter clean up

done

ok maybe not done.
we should make it more flexible and cleaner, less code redundancy with other formatters...