FieldCode is fragmented

When getting fieldcodes using
document.MainDocumentPart.RootElement.Descendants(Of FieldCode)()
FieldCode  is fragmented  when Word put the instruction text in multiple  <w:instrText>.
the xml looks like these
<w:r>
<w:rPr>
<w:b />
</w:rPr>
<w:fldChar w:fldCharType="begin" />
</w:r>
<w:r>
<w:rPr>
<w:b />
</w:rPr>
<w:instrText xml:space="preserve"> MERGEFIELD CHIL</w:instrText>
</w:r>
<w:r w:rsidRPr="00611B99">
<w:rPr>
<w:b />
<w:szCs w:val="24" />
</w:rPr>
<w:instrText>D2__Person_1_First_Name</w:instrText>
</w:r>
<w:r>
<w:rPr>
<w:b />
</w:rPr>
<w:fldChar w:fldCharType="separate" />
</w:r>
<w:r>
<w:rPr>
<w:b />
</w:rPr>
<w:fldChar w:fldCharType="end" />
</w:r>
I am getting two separate fieldcode

MERGEFIELD CHIL
D2_Person_1_First_Name

Instead of just one MERGEFIELD CHILD2_Person_1_First_Name

Hi @rainierpaul, the FieldCode class is tied to the w:instrText element. And because the instruction text for that field has varied formatting, there are two elements for the one text string.  Descendants is very literal in that it only looks for elements that fit the type T that you pass. It looks like what you're asking for here is an enhancement to the framework specifically to handle these scenarios. Do you agree? I see an opportunity if you'd (or someone would) like to come up with a solution and submit a PR. We'll review it for addition to the Framework.

@rainierpaul Were you able to come up with a fix? If so, we could look at incorporating it into the library

@rainierpaul, @tomjebo, and @twsouthwick In my mind, there is no fix in the Open XML SDK that you can make without changing its nature. The Open XML SDK is simply the lowest-level, strongly-typed API you can think of for producing and working with Open XML markup. Therefore, if Word or other tools produce complex markup (e.g., two w:instrText elements instead of one), you will have to pre-process or simplify that markup before doing whatever you want to do with this.
You should really have a look at the Open XML Power Tools. You would be surprised by how much cleanup or massaging is sometimes necessary before you can do what you'd actually want to do.
By the way, a number of years ago, @EricWhiteDev and I discussed whether it wouldn't make sense to include some higher-level abstractions into the SDK. However, at least at the time there was no desire on Microsoft's side to enhance the SDK in that way. I'm not sure whether that has changed.

@rainierpaul Given what @ThomasBarnekow said, it does seem out of scope of the library. The SDK at this time is designed to help you manage the OpenXML schema in code. Please take a look at the Open XML Power Tools to see if it helps.


Make minCpuPlatform a variable to enable launching Cascade Lake instances on Google Compute Platform

I haven't yet been able to successfully launch a "Cascade Lake" instance. The result coming back from GCP is
[provisioner@mgmt ~]$ sudo tail -f /var/log/slurm/elastic.log
2019-10-20 21:54:28,338 startnode  INFO     Starting c2-standard-4-0001 in citc-test-ce europe-west4-c
2019-10-20 21:54:30,947 startnode  ERROR     problem launching instance: <HttpError 400 when requesting https://compute.googleapis.com/compute/v1/projects/citc-test-ce/zones/europe-west4-c/instances?alt=json returned "The selected machine type 'c2-standard-4' has a required CPU platform of 'cascadelake'. The minimum CPU platform must match this, but was 'skylake'.">

Google documentation
Specifying a Minimum CPU Platform for VM Instances

This is currently set in create_node_config in citc.py
https://github.com/ACRC/slurm-ansible-playbook/blob/b2b687434cbae5a5855399637db130c107d03cac/roles/slurm/files/citc_gcp.py#L105

As a quick YOLO test changing the hard coded value
--- /opt/cloud_sdk/lib/python3.6/site-packages/citc_cloud.py.orig	2019-10-20 22:18:43.864878497 +0000
+++ /opt/cloud_sdk/lib/python3.6/site-packages/citc_cloud.py	2019-10-20 22:19:12.751080593 +0000
@@ -102,7 +102,7 @@
                 ]
             }
         ],
-        'minCpuPlatform': 'Intel Skylake',
+        'minCpuPlatform': 'Intel Cascade Lake',
         'metadata': {
             'items': [{
                 'key': 'startup-script',

works, the node provisions and boots:
2019-10-20 22:20:06,577 startnode  INFO     Starting c2-standard-4-0001 in citc-test-ce europe-west4-c
2019-10-20 22:20:09,602 startnode  INFO     c2-standard-4-0001:  No VNIC attachment yet. Waiting...
2019-10-20 22:20:15,237 startnode  INFO       Private IP <IP_ADDRESS>
2019-10-20 22:20:15,246 startnode  INFO      Started c2-standard-4-0001

Another approach that works is to just remove that attribute:
--- /opt/cloud_sdk/lib64/python3.6/site-packages/citc_cloud.py.orig	2019-10-21 13:45:37.285506506 +0000
+++ /opt/cloud_sdk/lib64/python3.6/site-packages/citc_cloud.py	2019-10-21 15:11:17.601853276 +0000
@@ -102,7 +102,6 @@
                 ]
             }
         ],
-        'minCpuPlatform': 'Intel Skylake',
         'metadata': {
             'items': [{
                 'key': 'startup-script',

What would be the downsides to not specifying minCpuPlatform?

Extend citc_gcp.py: create_node_config() to cater for Slurm Features to allow for specifying minCPUPlatform in the SBatch Slurm job config.  For example:
#! /bin/bash
#SBATCH --job-name=test
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --cpus-per-task=1
#SBATCH --time=10:00
#SBATCH --constraint="minCPUPlatform=Intel Cascade Lake"
srun -l hostname


Change strain to use generics

@andrerfcsantos suggested that "Strain" would be a good exercise for practicing generics. This PR does that.  The old version of the exercise was very clunky, with generics it makes much more sense.
I added a note on generics in the stub file so people know what they are up for. I also increased the difficultly to 4 to avoid people complaining that an easy exercise needs such an "advanced" concept.

Looks good, thanks for this!
CI seems to be failing because of golang.org/x/exp/slices and some kind of conflict with the linter. Maybe upgrading the linter will fix this?
Also, this package is part of the standard library as of Go 1.21, so when upgrading the track to Go 1.21 we can just replace the import to use the standard library and we won't have this problem.
@junedev Do we think we should try to fix the linter issue for now or focus on upgrading to 1.21?

I don't urgently need the slices package for this but it would have been nice.
The real error is this one (which shows when I do "go test" before running the linter):
Error: tmp/lint/practice/strain/strain_test.go:8:2: cannot find package "golang.org/x/exp/slices" in any of:
	/opt/hostedtoolcache/go/1.20.7/x64/src/golang.org/x/exp/slices (from $GOROOT)
	/home/runner/go/src/golang.org/x/exp/slices (from $GOPATH)
ok  	_/home/runner/work/go/go/tmp/lint/concept/airport_robot	0.004s
ok  	_/home/runner/work/go/go/tmp/lint/concept/animal_magic	0.004s

Not sure why the go test command is not downloading things in a way that it can access it.


Add Circular Buffer exercise

This change also applies configlet's formatting on the track's config.json.

@1ethanhansen I've just fixed and pushed the fix for the merge conflict


rabtap: 1.39.1 -> 1.39.3

Automatic update generated by nixpkgs-update tools. This update was made based on information from https://github.com/jandelgado/rabtap/releases.
meta.description for rabtap is: RabbitMQ wire tap and swiss army knife
meta.homepage for rabtap is: https://github.com/jandelgado/rabtap
Updates performed

Golang update

To inspect upstream changes

Release on GitHub

Compare changes on GitHub

Impact
Checks done

built on NixOS
The tests defined in passthru.tests, if any, passed
found 1.39.2 in filename of file in /nix/store/x8aj23vji0cn3di59jq470z1vgxk9gny-rabtap-1.39.2

Rebuild report (if merged into master) (click to expand)

2 total rebuild path(s)

2 package rebuild(s)

First fifty rebuilds by attrpath

rabtap

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/x8aj23vji0cn3di59jq470z1vgxk9gny-rabtap-1.39.2 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A rabtap https://github.com/r-ryantm/nixpkgs/archive/d030fea1319f76b9fc6dced531b2f9bdc892f7bc.tar.gz

Or:
nix build github:r-ryantm/nixpkgs/d030fea1319f76b9fc6dced531b2f9bdc892f7bc#rabtap

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/x8aj23vji0cn3di59jq470z1vgxk9gny-rabtap-1.39.2
ls -la /nix/store/x8aj23vji0cn3di59jq470z1vgxk9gny-rabtap-1.39.2/bin

Pre-merge build results
We have automatically built all packages that will get rebuilt due to
this change.
This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.
Result of nixpkgs-review --extra-nixpkgs-config '{ allowInsecurePredicate = x: true; }' run on x86_64-linux 1

1 package built:

rabtap

Maintainer pings
cc @eigengrau for testing.

Automatic update generated by nixpkgs-update tools. This update was made based on information from https://github.com/jandelgado/rabtap/releases.
meta.description for rabtap is: RabbitMQ wire tap and swiss army knife
meta.homepage for rabtap is: https://github.com/jandelgado/rabtap
Updates performed

Golang update

To inspect upstream changes

Release on GitHub

Compare changes on GitHub

Impact
Checks done

built on NixOS
The tests defined in passthru.tests, if any, passed
found 1.39.3 in filename of file in /nix/store/10475qv8z770gn8jv0f12wgfdlff21vf-rabtap-1.39.3

Rebuild report (if merged into master) (click to expand)

2 total rebuild path(s)

2 package rebuild(s)

First fifty rebuilds by attrpath

rabtap

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/10475qv8z770gn8jv0f12wgfdlff21vf-rabtap-1.39.3 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A rabtap https://github.com/r-ryantm/nixpkgs/archive/715d7d6d140f24ed2316dd43ed7f7e2f6864e31f.tar.gz

Or:
nix build github:r-ryantm/nixpkgs/715d7d6d140f24ed2316dd43ed7f7e2f6864e31f#rabtap

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/10475qv8z770gn8jv0f12wgfdlff21vf-rabtap-1.39.3
ls -la /nix/store/10475qv8z770gn8jv0f12wgfdlff21vf-rabtap-1.39.3/bin

Pre-merge build results
We have automatically built all packages that will get rebuilt due to
this change.
This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.
Result of nixpkgs-review --extra-nixpkgs-config '{ allowInsecurePredicate = x: true; }' run on x86_64-linux 1

1 package built:

rabtap

Maintainer pings
cc @eigengrau for testing.


Issue with updating.

Microsoft PowerToys version
v0.58.0
Running as admin

[X] Yes

Area(s) with issue?
Installer
Steps to reproduce
Unable to update to newer version i,e, 0.59.0. Stuck at downloading stage with message showing an error occurred trying to install this update.
✔ Expected Behavior
Updates to newer version
❌ Actual Behavior
Message showing an error occurred trying to install this update
Other Software
No response

@Aryak-Mohanty Same thing happened to me. I've explained how I've solved it here: https://github.com/microsoft/PowerToys/issues/18652#issuecomment-1152921932
Another similar problem occurred to others when the update completed successfully, but the error persisted. It is explained in details here: https://github.com/microsoft/PowerToys/issues/18663

/bugreport


Reduce bundle size

Reduces main app bundle size by 63% (size goes down from 9.83MB to 3.66MB), by splitting it into chunks that can be loaded asynchronously.
50% of current app.js bundle size is taken up by two big components - cornerstoe-wado-image-loader and react-vtkjs-viewport.
Both are not necessary for rendering initial Study List screen.
In fact react-vtkjs-viewport is not required until we enter into 2D MPR.
By splitting the bundle into chunks and delaying their loading as much as possible, initial load time can improve.

You are definitely my favourite new contributor 🥇

This is awesome, main PWA feels a lot snappier! Awesome job.
Currently /local and the json launch are broken, although these are likely easy to fix, they can be found under these urls:
Local
JSON Launch (this just takes a JSON file and loads a study based on its JSON structure).
Both just seem to need dynamic loading of cornerstone-wado-image-loader added.
Sure @dannyrb  will have some other comments on the PR.
Thanks again for the awesome contribution!

Updated the PR to fix the broken functionalities (Local and JSON Launch) and remove the dead code.

@ckedar, thanks again for your work here 🎉
If you have any other insights to share, we're all ears.
Also more than happy to donate a few hours of my own time if there's anything I can assist you with. You've been incredibly helpful with all of these PRs.

@dannyrb, @swederik Thank you for the appreciation.
Really glad that I could make some meaningful contribution to an open source project.
Kind of first one for me.

This is where we are at now after your changes (just uncomment this line https://github.com/OHIF/Viewers/blob/master/platform/viewer/.webpack/webpack.pwa.js#L50 for anyone that wants to try it themselves):

Some other stuff we could try to dynamically load:

dcmjs (though maybe we are using it to normalize the QIDO response on the study list, I think. Maybe it could still be part of the second chunk to load and not part of the initial bundle)
Cornerstone core, cornerstone tools, dicomParser,  - there's no real reason why these need to be part of the first bundle. They are probably dependencies of react-cornerstone-viewport and maybe one of the platform libraries. Maybe we can find a way to push them to a later bundle as well


Reset EntityEditor auto_ptr properly while clearing the layout #1258

Reset EntityEditor auto_ptr properly while clearing the layout
Update all EntityEditor form widgets with dictionary
Remove unnecessary create_form_layout call

Here is an explanation why it is done with a new interface.
Mostly all project-related entities are derived from EntityItem class, except the frame. Frame is treated in an absolutely different way right now.
The join points for both, FrameItem and EntityItem derivables, are ItemBase and EntityCreatorBase classes.
We can't put a fully virtual method to ItemBase, since it should have a cabability to be constructed on its own, and EntityCreatorBase drives slightly another functions.
So, as you wanted to keep it simple, with dummy logic for AttributeEditor and without signals/slots, I've decided to make a new interface for values retrieval as a compromise between desired solution and desired functionality.

About IEntityValueProvider : couldn't we get rid of it if we modified AttributeEditor::edit() to take a renderer::Entity* rather than just its values?

@dictoon, I've missed that way, sorry, my bad. I'll need just to add an extra argument to AttributeEditor::edit() than and, probably, a getter method to EntityItemBase.

@dictoon, checked out that approach, and here is a problem. This method is used for the entity update after changes has been made through some widget. In fact, it just deletes the old Entity instance and creates a new one, with new values. So, the Entity pointer we are passing to AttributeEditor::edit() became useless straight after the first edit has been applied at all cases, except Frame one, since it is treated in a different manner. Thus, it looks like that we need to go all the way down to EntityVector and handle entity update here somehow, or pass a pointer to renderer::Entity pointer to AttributeEditor::edit()

Merged, thank you!


Fix artifact transforms performance tests

So comparison with old versions is better
Fixes https://github.com/gradle/gradle-private/issues/4175

@bot-gradle test APT

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@bot-gradle test this

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PullRequestFeedback build

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@bot-gradle clean

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@asodja ClearArtifactTransformCacheWithoutInstrumentedJarsMutatorTest coverage is not catching this issue?

@asodja ClearArtifactTransformCacheWithoutInstrumentedJarsMutatorTest coverage is not catching this issue?

@6hundreds Good point, I will add it


Download SSMS Preview link doesn't take you anywhere and doesn't download anything

[Enter feedback here]

Document Details
⚠ Do not edit this section. It is required for learn.microsoft.com ➟ GitHub issue linking.

ID: 45daf2f0-bb22-338f-062b-a9fabcb71a92
Version Independent ID: b6e909fe-15d9-c1cf-c018-d4f6f36ff31f
Content: Download SQL Server Management Studio (SSMS) - SQL Server Management Studio (SSMS)
Content Source: docs/ssms/download-sql-server-management-studio-ssms.md
Service: sql
Sub-service: ssms
GitHub Login: @erinstellato-ms
Microsoft Alias: erinstellato

@MeatRocket Can you please clarify the issue?  When I go to https://learn.microsoft.com/en-us/sql/ssms/download-sql-server-management-studio-ssms?view=sql-server-ver16#feedback and select the text that says "Download SSMS 19":

I then get take to this page:
https://learn.microsoft.com/en-us/sql/ssms/download-sql-server-management-studio-ssms-19?view=sql-server-ver16
From this page, if I select "Download SQL Server Management Studio (SSMS) 19 (Preview) then the download starts for me.

Here is the direct download link:
https://go.microsoft.com/fwlink/?linkid=2203303&clcid=0x409
If this does not work for you, can please provide more details on what does occur?


System.NotImplementedException: The method or operation is not implemented. Facing the same issue even after copying the libraries

I included media plugin in all my projects but still i am getting the same error.
"System.Reflection.TargetInvocationException: Exception has been thrown by the target of an invocation. ---> System.Reflection.TargetInvocationException: Exception has been thrown by the target of an invocation. ---> System.NotImplementedException: The method or operation is not implemented."
when i am trying to access camera with TakePhotoAsync() method.
Please let me know if i am missing any other libraries.

unable to reproduce. try to uninstall and re-install the nugets


GSE120386_Genomic programming of IRF4-expressing human Langerhans cells.

Project short name:
Primary Wrangler:
Secondary Wrangler:

Associated files

Google Drive:

Published study links

Paper: https://doi.org/10.1038/s41467-019-14125-x

Accessioned data: GSE120386.

Key Events

[ ] Convert published metadata to HCA spreadsheet
[ ] Manually curate dataset to meet HCA metadata standard
[ ] Collect any matrix and cell-type annotation files
[ ] Upload sheet to validate metadata
[ ] Check linking using ingest graph validator
[ ] Transfer raw files to ingest to validate data files
[ ] Ask the Secondary Wrangler for an end-to-end review of the project. Ask the Expertise Wrangler to review specific tabs if needed
[ ] Submit dataset to Production
[ ] Complete the Export SOP
[ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

The metadata schema update needed for a treatment/stimulus protocol has been prioritised.

Treatment protocol has now been added to the hca metadata schema. This dataset can now be curated with treatment protocol metadata included.


DE32768-make overlay page able to refetch once there is pinned and un…

…ppined action

Just realized my last commit broke the test, fixing it

I combined all those functions to _appendOrUpdateBustCacheQueryString function which basically add bustCache query string if it does not exist, or replace it with new one if it already existed. And now make everywhere use _appendOrUpdateBustCacheQueryString  instead.


npm global install fails on linux

Dear team,
I am failing to npm install the generator in version 3.0.1 fails with authorization error on linux during the postinstallation.
This is what I do:
sudo npm install generator-easy-ui5 -g
Maybe the sudo run as is not being propagated?
I have attached the result.
installation_output.txt
Installation works fine with version 2.4.6.
Thanks a lot
Michel

jep, the log hints to some dir confusion caused by sudo.
just do a npm i -g yo generator-easy-ui5
(note the yo also being installed globally as a peer dep)
hth, v.

(i closed this by accident, sorry. please reopen if necessary)

Hi Volker,
thanks for looking into this.
It is the default behaviour for npm to install global packages into the folder /usr/lib/node_modules. Without sudo this will not work.
There are workarounds (like this one) for this, but by default, linux users will experience this, i believe. And so do i :-).
Cheers
Michel

I can confirm that the issue is resolved by changing the default folder for global packages for npm.
So it works for me now.
Cheers
Michel


Error in re-creating sciplex analysis

Hello, when running this section of code from 2_perturbations_sciplex3_evaluation.ipynb
model = biolord.Biolord(
adata=adata,
n_latent=256,
model_name="sciplex3",
module_params=module_params,
train_classifiers=False,
split_key="split_ood",
)
I ran into the following error:
TypeError                                 Traceback (most recent call last)
Cell In[10], line 1
----> 1 model = biolord.Biolord(
2     adata=adata,
3     n_latent=256,
4     model_name="sciplex3",
5     module_params=module_params,
6     train_classifiers=False,
7     split_key="split_ood",
8 )
File /lib/python3.9/site-packages/biolord/_model.py:137, in Biolord.init(self, adata, model_name, module_params, n_latent, train_classifiers, split_key, train_split, valid_split, test_split)
126     self.module = BiolordClassifyModule(
127         n_genes=self.n_genes,
128         n_samples=self.n_samples,
(...)
134         **module_params,
135     ).float()
136 else:
--> 137     self.module = BiolordModule(
138         n_genes=self.n_genes,
139         n_samples=self.n_samples,
140         x_loc=self.x_loc,
141         ordered_attributes_map=self.ordered_attributes_map,
142         categorical_attributes_map=self.categorical_attributes_map,
143         n_latent=self.n_latent,
144         **module_params,
145     ).float()
147 self._model_summary_string = self.class.name
148 self._model_name = model_name
TypeError: init() got an unexpected keyword argument 'loss_ae'
Thank you so much for making this tool and your code available!

Hi,
Please excuse the late response!
We have just pushed a fix for this repo that shall resolve this.

I'm now getting a new bug. I think it may be useful if there was a fille that outlined the versions of packages used. For example, chemprop is now version 2 by default, so to get proper featurization I needed to pip install chemprop==1.6.1.
When I run the following line of code:
model.train(
max_epochs=200,
batch_size=512,
plan_kwargs=trainer_params,
early_stopping=True,
early_stopping_patience=20,
check_val_every_n_epoch=10,
num_workers=1,
)
I get this error:
/orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/site-packages/lightning/fabric/plugins/environments/slurm.py:191: The srun command is available on your system but is not used. HINT: If your intention is to run Lightning on SLURM, prepend your python command with srun like so: srun python /orcd/archive/abugoot/001/Projects/dlesman/biolord_e ...
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
IPU available: False, using: 0 IPUs
HPU available: False, using: 0 HPUs
/orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/site-packages/lightning/fabric/plugins/environments/slurm.py:191: The srun command is available on your system but is not used. HINT: If your intention is to run Lightning on SLURM, prepend your python command with srun like so: srun python /orcd/archive/abugoot/001/Projects/dlesman/biolord_e ...
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0]
/orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/multiprocessing/popen_fork.py:66: RuntimeWarning: os.fork() was called. os.fork() is incompatible with multithreaded code, and JAX is multithreaded, so this will likely lead to a deadlock.
self.pid = os.fork()
Epoch 1/200:   0%| | 1/200 [00:33<1:49:27, 33.00s/it, v_num=1, val_generative_mean_accuracy=0.492, val_generative_var_accuracy=-3.87, val_biolord_metric=-1.69, val_LO
/orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/multiprocessing/popen_fork.py:66: RuntimeWarning: os.fork() was called. os.fork() is incompatible with multithreaded code, and JAX is multithreaded, so this will likely lead to a deadlock.
self.pid = os.fork()
MisconfigurationException                 Traceback (most recent call last)
Cell In[15], line 1
----> 1 model.train(
2     max_epochs=200,
3     batch_size=512,
4     plan_kwargs=trainer_params,
5     early_stopping=True,
6     early_stopping_patience=20,
7     check_val_every_n_epoch=10,
8     num_workers=1,
9 )
File /orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/site-packages/biolord/_model.py:729, in Biolord.train(self, max_epochs, accelerator, device, train_size, validation_size, plan_kwargs, batch_size, early_stopping, **trainer_kwargs)
714 trainer_kwargs["default_root_dir"] = trainer_kwargs.pop("default_root_dir", root_dir)
716 runner = TrainRunner(
717     self,
718     training_plan=self.training_plan,
(...)
726     **trainer_kwargs,
727 )
--> 729 return runner()
File /orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/site-packages/scvi/train/_trainrunner.py:98, in TrainRunner.call(self)
95 if hasattr(self.data_splitter, "n_val"):
96     self.training_plan.n_obs_validation = self.data_splitter.n_val
---> 98 self.trainer.fit(self.training_plan, self.data_splitter)
99 self._update_history()
101 # data splitter only gets these attrs after fit
File /orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/site-packages/scvi/train/_trainer.py:219, in Trainer.fit(self, *args, **kwargs)
213 if isinstance(args[0], PyroTrainingPlan):
214     warnings.filterwarnings(
215         action="ignore",
216         category=UserWarning,
217         message="LightningModule.configure_optimizers returned None",
218     )
--> 219 super().fit(*args, **kwargs)
File /orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/site-packages/lightning/pytorch/trainer/trainer.py:544, in Trainer.fit(self, model, train_dataloaders, val_dataloaders, datamodule, ckpt_path)
542 self.state.status = TrainerStatus.RUNNING
543 self.training = True
--> 544 call._call_and_handle_interrupt(
545     self, self._fit_impl, model, train_dataloaders, val_dataloaders, datamodule, ckpt_path
546 )
File /orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/site-packages/lightning/pytorch/trainer/call.py:44, in _call_and_handle_interrupt(trainer, trainer_fn, *args, **kwargs)
42     if trainer.strategy.launcher is not None:
43         return trainer.strategy.launcher.launch(trainer_fn, *args, trainer=trainer, **kwargs)
---> 44     return trainer_fn(*args, **kwargs)
46 except _TunerExitException:
47     _call_teardown_hook(trainer)
File /orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/site-packages/lightning/pytorch/trainer/trainer.py:580, in Trainer._fit_impl(self, model, train_dataloaders, val_dataloaders, datamodule, ckpt_path)
573 assert self.state.fn is not None
574 ckpt_path = self._checkpoint_connector._select_ckpt_path(
575     self.state.fn,
576     ckpt_path,
577     model_provided=True,
578     model_connected=self.lightning_module is not None,
579 )
--> 580 self._run(model, ckpt_path=ckpt_path)
582 assert self.state.stopped
583 self.training = False
File /orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/site-packages/lightning/pytorch/trainer/trainer.py:989, in Trainer._run(self, model, ckpt_path)
984 self._signal_connector.register_signal_handlers()
986 # ----------------------------
987 # RUN THE TRAINER
988 # ----------------------------
--> 989 results = self._run_stage()
991 # ----------------------------
992 # POST-Training CLEAN UP
993 # ----------------------------
994 log.debug(f"{self.class.name}: trainer tearing down")
File /orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/site-packages/lightning/pytorch/trainer/trainer.py:1035, in Trainer._run_stage(self)
1033         self._run_sanity_check()
1034     with torch.autograd.set_detect_anomaly(self._detect_anomaly):
-> 1035         self.fit_loop.run()
1036     return None
1037 raise RuntimeError(f"Unexpected state {self.state}")
File /orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/site-packages/lightning/pytorch/loops/fit_loop.py:203, in _FitLoop.run(self)
201     self.on_advance_start()
202     self.advance()
--> 203     self.on_advance_end()
204     self._restarting = False
205 except StopIteration:
File /orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/site-packages/lightning/pytorch/loops/fit_loop.py:374, in _FitLoop.on_advance_end(self)
372 call._call_callback_hooks(trainer, "on_train_epoch_end", monitoring_callbacks=False)
373 call._call_lightning_module_hook(trainer, "on_train_epoch_end")
--> 374 call._call_callback_hooks(trainer, "on_train_epoch_end", monitoring_callbacks=True)
376 trainer._logger_connector.on_epoch_end()
378 if self.epoch_loop._num_ready_batches_reached():
379     # if we are restarting and the above condition holds, it's because we are reloading an epoch-end checkpoint.
380     # since metric-based schedulers require access to metrics and those are not currently saved in the
381     # checkpoint, the plateau schedulers shouldn't be updated
File /orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/site-packages/lightning/pytorch/trainer/call.py:208, in _call_callback_hooks(trainer, hook_name, monitoring_callbacks, *args, **kwargs)
206     if callable(fn):
207         with trainer.profiler.profile(f"[Callback]{callback.state_key}.{hook_name}"):
--> 208             fn(trainer, trainer.lightning_module, *args, **kwargs)
210 if pl_module:
211     # restore current_fx when nested context
212     pl_module._current_fx_name = prev_fx_name
File /orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/site-packages/lightning/pytorch/callbacks/model_checkpoint.py:313, in ModelCheckpoint.on_train_epoch_end(self, trainer, pl_module)
311 monitor_candidates = self._monitor_candidates(trainer)
312 if self._every_n_epochs >= 1 and (trainer.current_epoch + 1) % self._every_n_epochs == 0:
--> 313     self._save_topk_checkpoint(trainer, monitor_candidates)
314 self._save_last_checkpoint(trainer, monitor_candidates)
File /orcd/archive/abugoot/001/Projects/dlesman/biolord_env/lib/python3.12/site-packages/lightning/pytorch/callbacks/model_checkpoint.py:368, in ModelCheckpoint._save_topk_checkpoint(self, trainer, monitor_candidates)
362     m = (
363         f"ModelCheckpoint(monitor={self.monitor!r}) could not find the monitored key in the returned"
364         f" metrics: {list(monitor_candidates)}."
365         f" HINT: Did you call log({self.monitor!r}, value) in the LightningModule?"
366     )
367     if trainer.fit_loop.epoch_loop.val_loop._has_run:
--> 368         raise MisconfigurationException(m)
369     warning_cache.warn(m)
370 self._save_monitor_checkpoint(trainer, monitor_candidates)
MisconfigurationException: ModelCheckpoint(monitor='validation_loss') could not find the monitored key in the returned metrics: ['val_generative_mean_accuracy', 'val_generative_var_accuracy', 'val_biolord_metric', 'val_LOSS_KEYS.RECONSTRUCTION', 'val_LOSS_KEYS.UNKNOWN_ATTRIBUTE_PENALTY', 'generative_mean_accuracy', 'generative_var_accuracy', 'biolord_metric', <LOSS_KEYS.RECONSTRUCTION: 'reconstruction_loss'>, <LOSS_KEYS.UNKNOWN_ATTRIBUTE_PENALTY: 'unknown_attribute_penalty_loss'>, 'epoch', 'step']. HINT: Did you call log('validation_loss', value) in the LightningModule?

Hi,
Please excuse us, we have the requirements.txt file which lists packages and i realize that chemprop is indeed not there. With that we provide the processed anndata files which contains the required features.
I am afraid your issue is also due to some sort of incompatibility between lightning and scvi, what are the versions you are using?
Also, can you try uninstalling jax from the environment?

Hi,
Thank you for getting back to me! I am now going through the requirements.txt file. It seems that there are some issues with the versions used, like I've gotten these errors so far:
ERROR: Could not find a version that satisfies the requirement alembic==1.4.3.dev0
ERROR: Could not find a version that satisfies the requirement arandr==0.1.10 (from versions: none)
I was wondering if you could let me know which python version I should be using?

Nevermind, I found that it's 3.9.2, will continue trying to get the requirements to install

So the requirements.txt file is not working properly. I run into several issues. To try and get the run to skip over the failing package installations (which happens once every 5-10 packages) I tried cat requirements.txt | xargs -n 1 pip install. But as this runs, eventually pip breaks and I get the following error for all the remaining packages:
Error processing line 1 of /orcd/archive/abugoot/001/Projects/dlesman/biolord_env_new/lib/python3.9/site-packages/distutils-precedence.pth:
Traceback (most recent call last):
File "/orcd/archive/abugoot/001/Projects/dlesman/biolord_env_new/lib/python3.9/site.py", line 177, in addpackage
exec(line)
File "", line 1, in
ModuleNotFoundError: No module named '_distutils_hack'
Pleaset let me know if additional info would be helpful.

Please excuse us for this inconvenience.
Can you please try starting a python 3.9.2 with installation of biolord (+seaborn, umap) in the environment.

I tried and got this error (same as before):
MisconfigurationException: ModelCheckpoint(monitor='validation_loss') could not find the monitored key in the returned metrics: ['val_generative_mean_accuracy', 'val_generative_var_accuracy', 'val_biolord_metric', 'val_reconstruction_loss', 'val_unknown_attribute_penalty_loss', 'generative_mean_accuracy', 'generative_var_accuracy', 'biolord_metric', <LOSS_KEYS.RECONSTRUCTION: 'reconstruction_loss'>, <LOSS_KEYS.UNKNOWN_ATTRIBUTE_PENALTY: 'unknown_attribute_penalty_loss'>, 'epoch', 'step']. HINT: Did you call log('validation_loss', value) in the LightningModule?
Here is the output to pip freeze:
absl-py==2.1.0
accumulation-tree==0.6.2
aiohttp==3.9.5
aiosignal==1.3.1
anndata==0.10.7
anyio==4.3.0
argon2-cffi==23.1.0
argon2-cffi-bindings==21.2.0
array_api_compat==1.6
arrow==1.3.0
asttokens==2.4.1
async-lru==2.0.4
async-timeout==4.0.3
attrs==23.2.0
Babel==2.14.0
backoff==2.2.1
beautifulsoup4==4.12.3
biolord==0.0.3
bleach==6.1.0
blessed==1.20.0
certifi==2024.2.2
cffi==1.16.0
charset-normalizer==3.3.2
chex==0.1.86
comm==0.2.2
contextlib2==21.6.0
contourpy==1.2.1
cycler==0.12.1
debugpy==1.8.1
decorator==5.1.1
defusedxml==0.7.1
dm-tree==0.1.8
docrep==0.3.2
etils==1.5.2
exceptiongroup==1.2.1
executing==2.0.1
fastjsonschema==2.19.1
filelock==3.13.4
flax==0.8.2
fonttools==4.51.0
fqdn==1.5.1
frozenlist==1.4.1
fsspec==2024.3.1
get-annotations==0.1.2
h11==0.14.0
h5py==3.11.0
httpcore==1.0.5
httpx==0.27.0
idna==3.7
importlib_metadata==7.1.0
importlib_resources==6.4.0
ipykernel==6.29.4
ipython==8.18.1
isoduration==20.11.0
jax==0.4.26
jaxlib==0.4.26
jedi==0.19.1
Jinja2==3.1.3
joblib==1.4.0
json5==0.9.25
jsonpointer==2.4
jsonschema==4.21.1
jsonschema-specifications==2023.12.1
jupyter-events==0.10.0
jupyter-lsp==2.2.5
jupyter_client==8.6.1
jupyter_core==5.7.2
jupyter_server==2.14.0
jupyter_server_terminals==0.5.3
jupyterlab==4.1.7
jupyterlab_pygments==0.3.0
jupyterlab_server==2.27.1
kaggle==1.5.16
kiwisolver==1.4.5
legacy-api-wrap==1.4
lightning==2.1.4
lightning-utilities==0.11.2
llvmlite==0.42.0
loompy==3.0.7
markdown-it-py==3.0.0
MarkupSafe==2.1.5
matplotlib==3.8.4
matplotlib-inline==0.1.7
mdurl==0.1.2
mistune==3.0.2
ml-collections==0.1.1
ml-dtypes==0.4.0
mpmath==1.3.0
msgpack==1.0.8
mudata==0.2.3
multidict==6.0.5
multipledispatch==1.0.0
natsort==8.4.0
nbclient==0.10.0
nbconvert==7.16.3
nbformat==5.10.4
nest-asyncio==1.6.0
networkx==3.2.1
notebook==7.1.3
notebook_shim==0.2.4
numba==0.59.1
numpy==1.26.4
numpy-groupies==0.10.2
numpyro==0.14.0
nvidia-cublas-cu12==<IP_ADDRESS>
nvidia-cuda-cupti-cu12==12.1.105
nvidia-cuda-nvrtc-cu12==12.1.105
nvidia-cuda-runtime-cu12==12.1.105
nvidia-cudnn-cu12==<IP_ADDRESS>
nvidia-cufft-cu12==<IP_ADDRESS>
nvidia-curand-cu12==<IP_ADDRESS>
nvidia-cusolver-cu12==<IP_ADDRESS>
nvidia-cusparse-cu12==<IP_ADDRESS>
nvidia-nccl-cu12==2.20.5
nvidia-nvjitlink-cu12==12.4.127
nvidia-nvtx-cu12==12.1.105
opt-einsum==3.3.0
optax==0.2.2
orbax-checkpoint==0.5.10
ordered-set==4.1.0
overrides==7.7.0
packaging==24.0
pandas==2.2.2
pandocfilters==1.5.1
parso==0.8.4
patsy==0.5.6
pexpect==4.9.0
pillow==10.3.0
platformdirs==4.2.1
prometheus_client==0.20.0
prompt-toolkit==3.0.43
protobuf==5.26.1
psutil==5.9.8
ptyprocess==0.7.0
pure-eval==0.2.2
pycparser==2.22
Pygments==2.17.2
pynndescent==0.5.12
pyparsing==3.1.2
pyro-api==0.1.2
pyro-ppl==1.9.0
python-dateutil==2.9.0.post0
python-editor==1.0.4
python-json-logger==2.0.7
python-multipart==0.0.6
pytorch-lightning==2.2.3
pytz==2024.1
pyudorandom==1.0.0
PyYAML==6.0.1
pyzmq==26.0.2
readchar==4.0.5
referencing==0.35.0
requests==2.31.0
rfc3339-validator==0.1.4
rfc3986-validator==0.1.1
rich==13.7.1
rpds-py==0.18.0
scanpy==1.10.1
scikit-learn==1.4.2
scipy==1.13.0
scvi-tools==1.1.2
seaborn==0.13.2
Send2Trash==1.8.3
session-info==1.0.0
six==1.16.0
sniffio==1.3.1
soupsieve==2.5
stack-data==0.6.3
statsmodels==0.14.2
stdlib-list==0.10.0
sympy==1.12
tdigest==<IP_ADDRESS>
tensorstore==0.1.57
terminado==0.18.1
threadpoolctl==3.4.0
tinycss2==1.3.0
tomli==2.0.1
toolz==0.12.1
torch==2.3.0
torchmetrics==1.3.2
tornado==6.4
tqdm==4.66.2
traitlets==5.14.3
triton==2.3.0
types-python-dateutil==<IP_ADDRESS>40316
typing_extensions==4.11.0
tzdata==2024.1
umap==0.1.1
umap-learn==0.5.6
uri-template==1.3.0
urllib3==2.2.1
wcwidth==0.2.13
webcolors==1.13
webencodings==0.5.1
websocket-client==1.8.0
yarl==1.9.4
zipp==3.18.1

Hi Dan,
Please excuse us; this is indeed an error stemming from changes in scvi-tools checkpointing policy which required a modification in the biolord package.
We have just pushed a fix to biolord to resolve it. We will soon release a new version with this fix.
Locally you can simply add enable_checkpointing=False to the model.train() call:
model.train(
    max_epochs=200,
    batch_size=512,
    plan_kwargs=trainer_params,
    early_stopping=True,
    early_stopping_patience=20,
    check_val_every_n_epoch=10,
    num_workers=1,
    enable_checkpointing=False
)

For complete compatibility you shall pull the biolord repo or downgrade  scvi-tools <= 1.0.4.
Please excuse us again for this inconvenience and thank you for spotting it.

Thank you! The new version works now (pip install from the main branch). I was wondering if a method was already implemented for saving and loading model weights.

Yes; we generally follow scVI (lightning API) here with the save() and load functions (see here).
For saving you can also use checkpointing.
# save
model.save(dir_path="your_path", overwrite:bool=.., save_anndata:bool=..)

# load
biolord.Biolord.setup_anndata(adata, ...)  # following the setup of the model
biolord.Biolord.load(dir_path="your_path")

Hi again! Thank you for all the help, another quick question. In the file "1_perturbations_adamson_preprocessing.ipynb"  you have the following line:
subgroup_analysis[seed], subgroup_analysis_deeper, test_metrics = gears_model.train(epochs = epoch)
which gives me an error because gears_model.train(epochs=epoch) does not return anything for me. Did you modify the GEARS code so that it returned something? And if so, could you provide an example or let me know what you have it returning?
Thank you!

Dear Daniel,
I am sorry for this inconvenience, following the discussion here we used the the git version, commit #d6a464e40f9e759706c81edabfda8ac4bccb3a3f
Locally we modified the code to get the same seeds settings, and extended information, attached is the diff file.
Thank you for the interest again.
diff.txt

Hi,
we are sorry for this inconvenience, and thank you for the interest again!
following the discussion here we used the the git version, commit #d6a464e40f9e759706c81edabfda8ac4bccb3a3f
Locally we modified the code to get the same seeds settings, and extended information, attached is the diff.txt file.


build is older than sources

Some fixes exist in the src directory but the build (Chart.js & Chart.min.js) does not reflect those changes.

also the npm build seems older than the version suggests.

I think this is fixed in fdec3462064bf3ca6324b14d65e98edce2b8106b for v2

@zachpanz88 is right. This was fixed for both v1 and v2 already.


The image package might be private

As I mentioned in the title. I am still not able to see the image package. Please feel free to help to check it. Thanks for your time.

My bad - it's public now.

It's normal to forget to set it. And thanks.


Related to #296:Resource download with parameter

issue #296: add a test method test_download_with_parameter(): downloading resource with query parameter.

@ryxx0811 isn't this also in the other PR? We can work on it there, no need to have two PRs for similar work. I think we can close this.

@slobentanzer


faile to compile

:0: error: error opening input file '/Users/xxx/cheyote/Cheyote/Cheyote-Bridging-Header.h' (No such file or directory)

patch that path to read Taurine-bridging-header or rename it to cheyote

:0: error: error opening input file '/Users/xxx/cheyote/Cheyote/Cheyote-Bridging-Header.h' (No such file or directory)

its a fake jailbreak, its just taurine (ios 14)


Focusing

Can you make any general comments on focusing. Should you just set heights so the field of view is 1m wide at the ground and then focus for the clear image of what's on the ground? Does focusing make much difference to the performance of the system?

The way we usually focus the camera is to firstly mount it at the height it will be used in the field and then adjust the focus ring (one is the aperture, and one is the focus) until it becomes clear using the video feed. This adjustment is best done with a ruler or some other writing/tool with clear indications of how sharp the the image is. Usually we do it in a lab/shed/workshop so it's easier to see everything.
A focused image helps a lot with detecting the weeds - an unfocused camera will mean smaller weeds will be blurred into the background and the colours won't be as distinct.

Ta, muchly.
Bill Manning Land Services - Advisory Services (Cropping)
North West Local Land Services
PO Box 546 |35-37 Abbott Street | Gunnedah NSW 2380
T: +61 2 6742 9210 | F:+61 2 6742 4022
M:  0428 607 731
<EMAIL_ADDRESS>W: northwest.lls.nsw.gov.auhttp://northwest.lls.nsw.gov.au/
www.facebook.com/northwestlocallandserviceshttp://www.facebook.com/northwestlocallandservices

From: Guy Coleman @.>
Sent: Saturday, 8 October 2022 10:53 PM
To: geezacoleman/OpenWeedLocator @.>
Cc: Bill Manning @.>; Author @.>
Subject: Re: [geezacoleman/OpenWeedLocator] Focusing (Issue #57)
The way we usually focus the camera is to firstly mount it at the height it will be used in the field and then adjust the focus ring (one is the aperture, and one is the focus) until it becomes clear using the video feed. This adjustment is best done with a ruler or some other writing/tool with clear indications of how sharp the the image is. Usually we do it in a lab/shed/workshop so it's easier to see everything.
A focused image helps a lot with detecting the weeds - an unfocused camera will mean smaller weeds will be blurred into the background and the colours won't be as distinct.
—
Reply to this email directly, view it on GitHubhttps://github.com/geezacoleman/OpenWeedLocator/issues/57#issuecomment-1272301724, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AN3U5AXA6SSUF5PGFKKTTWLWCFOD5ANCNFSM6AAAAAAQ7HYTVQ.
You are receiving this because you authored the thread.Message ID: @.***>


Account summary - your overview - time toggle

Padding doesn't match design.
Design left, build right:

closing -- I fixed this in a previous PR


Prefer Windows release as basis for metric computations

We were getting inaccurate metrics when, by chance, the OSX release of Firefox would be used to calculate some metrics. This ensures that a Windows release is used consistently as the "base release" for metrics computations (except, of course, when there is no Windows release: Safari/WebKit).

Codecov Report

Merging #245 into master will increase coverage by 0.12%.
The diff coverage is 83.33%.

@@            Coverage Diff             @@
##           master     #245      +/-   ##
==========================================
+ Coverage   61.33%   61.45%   +0.12%
==========================================
  Files          38       38
  Lines        2387     2392       +5
  Branches      159      160       +1
==========================================
+ Hits         1464     1470       +6
+ Misses        923      922       -1

Impacted Files
Coverage Δ

lib/confluence/metric_computer_runner.es6.js
76.86% <83.33%> (+1.67%)
:arrow_up:

Continue to review full report at Codecov.

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This is already included in what's deployed to http://web-confluence.appspot.com, right?

@foolip Re: deployed? Yes.


Feature/convert purs to tsx for setting menu

#1337
Checklist

[x] the [contributor license agreement][] is signed
[x] commit message follows [commit guidelines][]

Description of change
Rewrite the Setting Menu and UI Setting Editor in Typescript.

Nice. I see Codebuild is green, hopefully Travis agrees and then you can merge on in. :+1:


Section/Group Dropdown and "Showing [x] Students" Text Not Aligned Horizontally

The section/group dropdown in the "Grades" screen, as well as the "Showing [x] Students" text, appear to be aligned to the top of their grey container, causing them to butt up against the "Add Gradebook Item" button. This makes things at the top of the Grades screen feel a little cramped:

Can we center these horizontally within the grey container, so that they're horizontally aligned with the "Showing [x] of [y] items" text, Show/Hide Items menu, and Group by Category buttons?

Confirmed in master.

Verified on 11.x nightly MySQL server.  Set any label on this to show status?  (we show in Jira if we have verified the fix in the branch, so just asking)


Example: Handling/Parsing Core MIDI Notifications

[x] Demonstrate the notification handler closure in MIDIManager
[x] explain the notifications (MIDIIONotification)
[x] show how to parse the metadata associated with each notification type
[x] add project to examples CI workflow

Done. Pushed to main.


Load shapeFile buffer Array using catiline.js

Baterias.zip
Attached file is getting loaded in http://leaflet.calvinmetcalf.com/#6/-38.212/-66.753
My Requirement

Zip File is saved in Database
loading Zip File in base64 from DB and converting it to buffer Array
var buffer = base64ToBuffer(base64ShapeFile.substr(41));
I want to load this file using worker as shown in your example

worker.data(reader.result,[reader.result]).then(function(data){
//do stuff with data
});
In Place of reader.result I am replacing it with bufferArray
worker.data(buffer, [buffer]).then(function (data) {
//do stuff with data
});
4. Please help me to load this file using Worker object
5. How to initialize the worker object
Help in this regard will be highly appreciated.

Used these files

if you are loading it from just data you have hard coded into the page the worker doesn't really help, that only works if you are loading from a separate url

I have not hard coded, the zip file is saved in database and its been loaded to page in base64 string and convert it to buffer Array. Can I load this buffer Array using catiline.js? If not how can I load via buffer Array or base64 String. Any thoughts?

ok so what you wrote should do the trick, what sort of error are you getting ? if aren't getting an error try chaning
worker.data(buffer, [buffer]).then(function (data) {
//do stuff with data
});

to
worker.data(buffer, [buffer]).then(function (data) {
//do stuff with data
}, function (e) {
console.log(e);
});

also just to double check, you've replaced //do stuff with data with your own code right ?


WIP Identity Platform

@Ikstar Thanks for the invitation! For a clean slate, would it be alright with you if I squashed all your commits so far into one, then rebased the current upstream 5.x branch onto it, and finally do a force-push?
I know, that's probably not the first thing someone should do when they arrive at a repo that doesn't belong to them, but I lack the git skills to fix some issues I'm having during an interactive rebase 🙈 - on the other time, I have some time this weekend to spend it on this 😅


Your account has been suspended

Info
When I login via github, it says:

Your account has been suspended

This happened after I changed email address in account settings.
And when I sign up for a new account, it says:

You seem to be using an IP / HTTP proxy that has been banned

VPNs and ISPs that service consumer homes often use a pool of IPs. If someone else was using that IP from a pool, and they were messing around, the mods may have banned that IP. Public libraries also often use pools of IPs for their computers. Wait and see what the mods say to your post here.


Is the spec generated for server streams reliable?

We want to generate REST API clients from the OpenAPI spec but are unsure how reliable and messy the server streams spec gets.

For streaming RPCs you probably aren't going to get a client out of the box that can do that for you.
If you're lucky you can implement something that can receive a content type of application/connect (or application/grpc or application/grpc-web) and knows how to do the Connect protocol framing which would be required for streaming calls, unfortunately. I'm not aware of anything that does this since it kind of requires a lot of different things to come together that normally don't.
Last time I checked, OpenAPI doesn't really handle streaming data in a special way that generated clients can actually leverage and when they discuss these things it's always about streaming a single response from the server and buffering some amount of it in memory, not streaming of multiple discrete responses... so I wouldn't be surprised if making this work is awkward in most or all OpenAPI client generators.
In summary, I wouldn't expect streaming RPCs to work based on the OpenAPI spec for any OpenAPI client generator. If you need that, you probably want to use a connect, gRPC or gRPC-Web client instead.

Thank you for the answer!
We will probably first try to create the spec just for documentation purposes, so not being able to generate the clients right now should be ok.


RuntimeError: Given groups=1, weight of size 64 3 7 7, expected input[3, 2, 800, 1120] to have 3 channels, but got 2 channels instead

Thanks for your error report and we appreciate it a lot.
Checklist

I have searched related issues but cannot get the expected help.
The bug has not been fixed in the latest version.

when l train faster-rcnn ,this error is happen,but others model is normal.i think it maybe batch-size and channel is error.

Please follow the issue template to fill in the required fields. Without enough information, it would be hard for others to help with this issue.


Add error documentation

Issue #, if available:
n/a.
Description of changes:
Include a building option to avoid "Dynamic require of "stream" is not supported" error.

Thanks! Please run prettier and reformat the code and we're good

Still prettier is complaining. Can you run it like this from the root of the workspace?: npx prettier -w .

Sorry mate it's getting worse! The issue must be that you use another prettier config than the project. I see now that there is no prettier config in the project (which surprises me, didn't notice before), and I am not sure what is going on now ... looks like on your machine prettier finds another config file that you have.
Try this instead: npx prettier --no-config -w . That should skip your config.
We could add prettier config to this project to prevent this. Maybe add an empty prettier key in package.json (empty so we get all defaults): prettier: {}

No problem. Added.
I believe you already merged the code.

All done now. Thanks for your vigilance on our docs!


Fix hashing on windows

Running the most recent commit in this PR locally results in a FileNotFoundException for the GCS lookups to storage.googleapis.com for me.

@respatialized if you can, I'd appreciate if you could try this once more, using the latest sha on this PR as a git dependency and confirm that
(= "3mXdcLQSNAEFTLdDXoAw47rKytXS"
   ((requiring-resolve 'nextjournal.clerk.render.hashing/front-end-hash)))
;;=> true

Yes, I am able to load clerk and that expression evaluates to true on Windows. ✔


How to make the keyboard hidden when drawer show?

If the center vc has some text filed in its view, when the the textfield is focused, and the user pan the center view to show drawer, the keyboard is hidden, and when the drawer is shown, the keyboard shown again.
How to hide the keyboard when the side vc is shown ?

The reason that the keyboard is hide when sidebar is in progress (drag, moving) is that they toggle userInteractionEnabled
Besides, this https://github.com/mutualmobile/MMDrawerController/issues/64 can help

I've tried the solution from @pronebird but once I have the center view a text field, keyboard appears, I open the drawer, go back to the text field, the keyboard will not show up again and the input field is blocked. Any idea why?

override func viewDidLoad() {
super.viewDidLoad()
// detect is a high order function that returns the first found object
if let cRecognisers = self.view.gestureRecognizers{
if let cRecogniser = cRecognisers.first{
cRecogniser.addTarget(self, action: "handlePanGR")
}
}
}

func handlePanGR() {
    UIApplication.sharedApplication().sendAction("resignFirstResponder", to: nil, from: nil, forEvent: nil)
}

@blackyhn  dude, it works perfect thanks!


Premodit for HITEMP available

I made Premodit HITEMP/HITRAN available.
Currently, I assume the same procedure as ExoMol for isotopes: So, the user needs to select a single isotope from HITEMP database. I slightly changed the API for isotopes. See here for the details.

Test cross sections using HITEMP is here
Test spectra using HITEMP is here
See here for XS using hitran

#304


Storybook 7 and React 18 update

Codecov Report
All modified lines are covered by tests :white_check_mark:
:exclamation: Your organization needs to install the Codecov GitHub app to enable full functionality.
see 1 file with indirect coverage changes
:loudspeaker: Thoughts on this report? Let us know!.


[BUG] table video_info has no column named desc_raw

f2 dy -M one -u 'https://www.douyin.com/video/7383551945027423539'

https://github.com/Johnserf-Seed/TikTokDownload/issues/740


Cannot run D435 on fresh Ubuntu 16.04 install

I am trying to get the driver running on a fresh Ubuntu install. The D435 camera I am using and associated USB cable are both functional (I can run the driver fine on a different Ubuntu 16.04 machine). I installed librealsense with pre-built binaries as described here and am using the latest code on development branch for realsense2_camera. As I had no luck with 4.10 kernel, I tried upgrading to 4.15 - the output of both cases is pasted below. Please advise.
4.10.0-28 Kernel
Output of roslaunch realsense2_camera rs_rgbd.launch:
... logging to /home/syler/.ros/log/ba0813d6-e9d9-11e8-a700-c0b6f9704397/roslaunch-bronco-3296.log
Checking log directory for disk usage. This may take awhile.
Press Ctrl-C to interrupt
Done checking log file disk usage. Usage is <1GB.

started roslaunch server http://bronco:37509/

SUMMARY
========

PARAMETERS
 * /camera/realsense2_camera/accel_fps: 1000
 * /camera/realsense2_camera/accel_optical_frame_id: camera_accel_opti...
 * /camera/realsense2_camera/align_depth: True
 * /camera/realsense2_camera/aligned_depth_to_color_frame_id: camera_aligned_de...
 * /camera/realsense2_camera/aligned_depth_to_fisheye_frame_id: camera_aligned_de...
 * /camera/realsense2_camera/aligned_depth_to_infra1_frame_id: camera_aligned_de...
 * /camera/realsense2_camera/aligned_depth_to_infra2_frame_id: camera_aligned_de...
 * /camera/realsense2_camera/base_frame_id: camera_link
 * /camera/realsense2_camera/color_fps: 30
 * /camera/realsense2_camera/color_frame_id: camera_color_frame
 * /camera/realsense2_camera/color_height: 480
 * /camera/realsense2_camera/color_optical_frame_id: camera_color_opti...
 * /camera/realsense2_camera/color_width: 640
 * /camera/realsense2_camera/depth_fps: 30
 * /camera/realsense2_camera/depth_frame_id: camera_depth_frame
 * /camera/realsense2_camera/depth_height: 480
 * /camera/realsense2_camera/depth_optical_frame_id: camera_depth_opti...
 * /camera/realsense2_camera/depth_width: 640
 * /camera/realsense2_camera/enable_color: True
 * /camera/realsense2_camera/enable_depth: True
 * /camera/realsense2_camera/enable_fisheye: True
 * /camera/realsense2_camera/enable_imu: True
 * /camera/realsense2_camera/enable_infra1: True
 * /camera/realsense2_camera/enable_infra2: True
 * /camera/realsense2_camera/enable_pointcloud: False
 * /camera/realsense2_camera/enable_sync: True
 * /camera/realsense2_camera/filters:
 * /camera/realsense2_camera/fisheye_fps: 30
 * /camera/realsense2_camera/fisheye_height: 480
 * /camera/realsense2_camera/fisheye_optical_frame_id: camera_fisheye_op...
 * /camera/realsense2_camera/fisheye_width: 640
 * /camera/realsense2_camera/gyro_fps: 1000
 * /camera/realsense2_camera/gyro_optical_frame_id: camera_gyro_optic...
 * /camera/realsense2_camera/infra1_fps: 30
 * /camera/realsense2_camera/infra1_frame_id: camera_infra1_frame
 * /camera/realsense2_camera/infra1_height: 480
 * /camera/realsense2_camera/infra1_optical_frame_id: camera_infra1_opt...
 * /camera/realsense2_camera/infra1_width: 640
 * /camera/realsense2_camera/infra2_fps: 30
 * /camera/realsense2_camera/infra2_frame_id: camera_infra2_frame
 * /camera/realsense2_camera/infra2_height: 480
 * /camera/realsense2_camera/infra2_optical_frame_id: camera_infra2_opt...
 * /camera/realsense2_camera/infra2_width: 640
 * /camera/realsense2_camera/json_file_path:
 * /camera/realsense2_camera/pointcloud_texture_index: 0
 * /camera/realsense2_camera/pointcloud_texture_stream: RS2_STREAM_COLOR
 * /camera/realsense2_camera/rosbag_filename:
 * /camera/realsense2_camera/serial_no:
 * /rosdistro: kinetic
 * /rosversion: 1.12.14

NODES
  /camera/
    color_rectify_color (nodelet/nodelet)
    points_xyzrgb_hw_registered (nodelet/nodelet)
    realsense2_camera (nodelet/nodelet)
    realsense2_camera_manager (nodelet/nodelet)

auto-starting new master
process[master]: started with pid [3314]
ROS_MASTER_URI=http://localhost:11311

setting /run_id to ba0813d6-e9d9-11e8-a700-c0b6f9704397
process[rosout-1]: started with pid [3327]
started core service [/rosout]
process[camera/realsense2_camera_manager-2]: started with pid [3330]
process[camera/realsense2_camera-3]: started with pid [3339]
process[camera/color_rectify_color-4]: started with pid [3346]
process[camera/points_xyzrgb_hw_registered-5]: started with pid [3347]
[ INFO] [1542398198.069304421]: Initializing nodelet with 32 worker threads.
[ INFO] [1542398198.124774411]: RealSense ROS v2.1.1
[ INFO] [1542398198.124811991]: Running with LibRealSense v2.16.4
[ INFO] [1542398198.286017470]: getParameters...
[ INFO] [1542398198.335060598]: setupDevice...
[ INFO] [1542398198.335088760]: JSON file is not provided
[ INFO] [1542398198.335108507]: ROS Node Namespace: camera
[ INFO] [1542398198.335126601]: Device Name: Intel RealSense D435
[ INFO] [1542398198.335148372]: Device Serial No:<PHONE_NUMBER>84
[ INFO] [1542398198.335159864]: Device FW version: <IP_ADDRESS>
[ INFO] [1542398198.335178268]: Device Product ID: 0x0B07
[ INFO] [1542398198.335190201]: Enable PointCloud: Off
[ INFO] [1542398198.335216530]: Align Depth: On
[ INFO] [1542398198.335232911]: Sync Mode: On
[ INFO] [1542398198.335455869]: Device Sensors:
[ INFO] [1542398198.335575673]: Stereo Module was found.
[ INFO] [1542398198.335601271]: RGB Camera was found.
[ INFO] [1542398198.335739380]: (Fisheye, 0) sensor isn't supported by current device! -- Skipping...
[ INFO] [1542398198.335756082]: (Gyro, 0) sensor isn't supported by current device! -- Skipping...
[ INFO] [1542398198.335774556]: (Accel, 0) sensor isn't supported by current device! -- Skipping...
[ INFO] [1542398198.335807208]: setupPublishers...
[ INFO] [1542398198.341759970]: Expected frequency for depth = 30.00000
[ INFO] [1542398198.374292857]: Expected frequency for infra1 = 30.00000
[ INFO] [1542398198.401504215]: Expected frequency for aligned_depth_to_infra1 = 30.00000
[ INFO] [1542398198.427662969]: Expected frequency for infra2 = 30.00000
[ INFO] [1542398198.453414770]: Expected frequency for aligned_depth_to_infra2 = 30.00000
[ INFO] [1542398198.479899846]: Expected frequency for color = 30.00000
[ INFO] [1542398198.506547316]: Expected frequency for aligned_depth_to_color = 30.00000
[ INFO] [1542398198.534446093]: setupStreams...
 16/11 14:56:38,534 WARNING [140365988620160] (sensor.cpp:338) Unregistered Media formats : [ UYVY ]; Supported: [ ]
[ INFO] [1542398198.540599793]: depth stream is enabled - width: 640, height: 480, fps: 30
[ INFO] [1542398198.540828962]: infra1 stream is enabled - width: 640, height: 480, fps: 30
[ INFO] [1542398198.541008649]: infra2 stream is enabled - width: 640, height: 480, fps: 30
[ INFO] [1542398198.542338413]: color stream is enabled - width: 640, height: 480, fps: 30
[ INFO] [1542398198.582476281]: num_filters: 0
[ INFO] [1542398198.582536244]: publishStaticTransforms...
[ INFO] [1542398198.582913952]: RealSense Node Is Up!
[ INFO] [1542398198.582996577]: Start updating dynamic parameters...
 16/11 14:56:38,642 WARNING [140365988620160] (types.cpp:57) start_streaming(...) failed. UVC device is already streaming!
 16/11 14:56:38,645 WARNING [140365988620160] (types.cpp:57) start_streaming(...) failed. UVC device is already streaming!
 16/11 14:56:38,645 WARNING [140365988620160] (types.cpp:57) start_streaming(...) failed. UVC device is already streaming!
 16/11 14:56:38,645 WARNING [140365988620160] (types.cpp:57) start_streaming(...) failed. UVC device is already streaming!
[ INFO] [1542398198.973507438]: Done updating dynamic parameters...
 16/11 14:56:43,572 WARNING [140364832831232] (backend-v4l2.cpp:1013) Frames didn't arrived within 5 seconds
 16/11 14:56:43,576 WARNING [140364824438528] (backend-v4l2.cpp:1013) Frames didn't arrived within 5 seconds
 16/11 14:56:43,583 WARNING [140364813571840] (backend-v4l2.cpp:1013) Frames didn't arrived within 5 seconds

System Configuration
Output of lsusb for the camera:
Bus 006 Device 003: ID 8086:0b07 Intel Corp.

Output of lsusb -t for the camera:
/:  Bus 06.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/4p, 5000M
    |__ Port 1: Dev 3, If 0, Class=Video, Driver=uvcvideo, 5000M
    |__ Port 1: Dev 3, If 1, Class=Video, Driver=uvcvideo, 5000M
    |__ Port 1: Dev 3, If 2, Class=Video, Driver=uvcvideo, 5000M
    |__ Port 1: Dev 3, If 3, Class=Video, Driver=uvcvideo, 5000M
    |__ Port 1: Dev 3, If 4, Class=Video, Driver=uvcvideo, 5000M

Output of uname -a:
Linux bronco 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

4.15.0-39 Kernel
Output of roslaunch realsense2_camera rs_rgbd.launch:
... logging to /home/syler/.ros/log/4cfbd76e-e9de-11e8-a4f6-c0b6f9704397/roslaunch-bronco-19730.log
Checking log directory for disk usage. This may take awhile.
Press Ctrl-C to interrupt
Done checking log file disk usage. Usage is <1GB.

started roslaunch server http://bronco:36051/

SUMMARY
========

PARAMETERS
 * /camera/realsense2_camera/accel_fps: 1000
 * /camera/realsense2_camera/accel_optical_frame_id: camera_accel_opti...
 * /camera/realsense2_camera/align_depth: True
 * /camera/realsense2_camera/aligned_depth_to_color_frame_id: camera_aligned_de...
 * /camera/realsense2_camera/aligned_depth_to_fisheye_frame_id: camera_aligned_de...
 * /camera/realsense2_camera/aligned_depth_to_infra1_frame_id: camera_aligned_de...
 * /camera/realsense2_camera/aligned_depth_to_infra2_frame_id: camera_aligned_de...
 * /camera/realsense2_camera/base_frame_id: camera_link
 * /camera/realsense2_camera/color_fps: 30
 * /camera/realsense2_camera/color_frame_id: camera_color_frame
 * /camera/realsense2_camera/color_height: 480
 * /camera/realsense2_camera/color_optical_frame_id: camera_color_opti...
 * /camera/realsense2_camera/color_width: 640
 * /camera/realsense2_camera/depth_fps: 30
 * /camera/realsense2_camera/depth_frame_id: camera_depth_frame
 * /camera/realsense2_camera/depth_height: 480
 * /camera/realsense2_camera/depth_optical_frame_id: camera_depth_opti...
 * /camera/realsense2_camera/depth_width: 640
 * /camera/realsense2_camera/enable_color: True
 * /camera/realsense2_camera/enable_depth: True
 * /camera/realsense2_camera/enable_fisheye: True
 * /camera/realsense2_camera/enable_imu: True
 * /camera/realsense2_camera/enable_infra1: True
 * /camera/realsense2_camera/enable_infra2: True
 * /camera/realsense2_camera/enable_pointcloud: False
 * /camera/realsense2_camera/enable_sync: True
 * /camera/realsense2_camera/filters:
 * /camera/realsense2_camera/fisheye_fps: 30
 * /camera/realsense2_camera/fisheye_height: 480
 * /camera/realsense2_camera/fisheye_optical_frame_id: camera_fisheye_op...
 * /camera/realsense2_camera/fisheye_width: 640
 * /camera/realsense2_camera/gyro_fps: 1000
 * /camera/realsense2_camera/gyro_optical_frame_id: camera_gyro_optic...
 * /camera/realsense2_camera/infra1_fps: 30
 * /camera/realsense2_camera/infra1_frame_id: camera_infra1_frame
 * /camera/realsense2_camera/infra1_height: 480
 * /camera/realsense2_camera/infra1_optical_frame_id: camera_infra1_opt...
 * /camera/realsense2_camera/infra1_width: 640
 * /camera/realsense2_camera/infra2_fps: 30
 * /camera/realsense2_camera/infra2_frame_id: camera_infra2_frame
 * /camera/realsense2_camera/infra2_height: 480
 * /camera/realsense2_camera/infra2_optical_frame_id: camera_infra2_opt...
 * /camera/realsense2_camera/infra2_width: 640
 * /camera/realsense2_camera/json_file_path:
 * /camera/realsense2_camera/pointcloud_texture_index: 0
 * /camera/realsense2_camera/pointcloud_texture_stream: RS2_STREAM_COLOR
 * /camera/realsense2_camera/rosbag_filename:
 * /camera/realsense2_camera/serial_no:
 * /rosdistro: kinetic
 * /rosversion: 1.12.14

NODES
  /camera/
    color_rectify_color (nodelet/nodelet)
    points_xyzrgb_hw_registered (nodelet/nodelet)
    realsense2_camera (nodelet/nodelet)
    realsense2_camera_manager (nodelet/nodelet)

auto-starting new master
process[master]: started with pid [19740]
ROS_MASTER_URI=http://localhost:11311

setting /run_id to 4cfbd76e-e9de-11e8-a4f6-c0b6f9704397
process[rosout-1]: started with pid [19753]
started core service [/rosout]
process[camera/realsense2_camera_manager-2]: started with pid [19770]
process[camera/realsense2_camera-3]: started with pid [19771]
process[camera/color_rectify_color-4]: started with pid [19772]
process[camera/points_xyzrgb_hw_registered-5]: started with pid [19774]
[ INFO] [1542400162.612899571]: Initializing nodelet with 32 worker threads.
[ INFO] [1542400162.655125827]: RealSense ROS v2.1.1
[ INFO] [1542400162.655158319]: Running with LibRealSense v2.16.4
[ERROR] [1542400162.670064795]: No RealSense devices were found! Terminating RealSense Node...
[FATAL] [1542400162.846696735]: Failed to load nodelet '/camera/realsense2_camera` of type `realsense2_camera/RealSenseNodeFactory` to manager `realsense2_camera_manager'
[FATAL] [1542400162.846733606]: Failed to load nodelet '/camera/color_rectify_color` of type `image_proc/rectify` to manager `realsense2_camera_manager'
[camera/realsense2_camera_manager-2] process has died [pid 19770, exit code 1, cmd /opt/ros/kinetic/lib/nodelet/nodelet manager __name:=realsense2_camera_manager __log:=/home/syler/.ros/log/4cfbd76e-e9de-11e8-a4f6-c0b6f9704397/camera-realsense2_camera_manager-2.log].
log file: /home/syler/.ros/log/4cfbd76e-e9de-11e8-a4f6-c0b6f9704397/camera-realsense2_camera_manager-2*.log
[camera/realsense2_camera-3] process has died [pid 19771, exit code 255, cmd /opt/ros/kinetic/lib/nodelet/nodelet load realsense2_camera/RealSenseNodeFactory realsense2_camera_manager __name:=realsense2_camera __log:=/home/syler/.ros/log/4cfbd76e-e9de-11e8-a4f6-c0b6f9704397/camera-realsense2_camera-3.log].
log file: /home/syler/.ros/log/4cfbd76e-e9de-11e8-a4f6-c0b6f9704397/camera-realsense2_camera-3*.log
[camera/color_rectify_color-4] process has died [pid 19772, exit code 255, cmd /opt/ros/kinetic/lib/nodelet/nodelet load image_proc/rectify realsense2_camera_manager --no-bond image_mono:=color/image_raw image_rect:=color/image_rect_color __name:=color_rectify_color __log:=/home/syler/.ros/log/4cfbd76e-e9de-11e8-a4f6-c0b6f9704397/camera-color_rectify_color-4.log].
log file: /home/syler/.ros/log/4cfbd76e-e9de-11e8-a4f6-c0b6f9704397/camera-color_rectify_color-4*.log
[camera/points_xyzrgb_hw_registered-5] process has finished cleanly
log file: /home/syler/.ros/log/4cfbd76e-e9de-11e8-a4f6-c0b6f9704397/camera-points_xyzrgb_hw_registered-5*.log

System Configuration
Output of lsusb for the camera:
Bus 006 Device 003: ID 8086:0b07 Intel Corp.

Output of lsusb -t for the camera:
/:  Bus 06.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/4p, 5000M
    |__ Port 1: Dev 3, If 0, Class=Video, Driver=uvcvideo, 5000M
    |__ Port 1: Dev 3, If 1, Class=Video, Driver=uvcvideo, 5000M
    |__ Port 1: Dev 3, If 2, Class=Video, Driver=uvcvideo, 5000M
    |__ Port 1: Dev 3, If 3, Class=Video, Driver=uvcvideo, 5000M
    |__ Port 1: Dev 3, If 4, Class=Video, Driver=uvcvideo, 5000M

Output of uname -a:
Linux bronco 4.15.0-39-generic #42~16.04.1-Ubuntu SMP Wed Oct 24 17:09:54 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

Output of modinfo uvcvideo | grep "version:" :
version:        1.1.2.realsense-1.3.3
srcversion:     C4FB5E9B212E9C39ED6CD7C

'Frames didn't arrived within 5 seconds', i met this problem for quite many times. just plug out and replug in the camera, it can solved for me.

@5yler , this sounds weird. I solved this kind of errors all by replug, or rerun the command. i am using ubantu 16.04 and kernel 4.15

The problem of 'Frames didn't arrived within 5 seconds' could usually be solved by setting the IR and Color sensors to a different frequency. Try running with color_fps:=15. It seems like this is a firmware problem that has something to do with synchronization of the streams.
About the problem 'No RealSense devices were found!', it usually refers to either a kernel or permission problems. Could it be that after upgrading the kernel you didn't install the realsense kernel-patch for that kernel?
modinfo uvcvideo | grep "version: should include realsense string"
If that's ok, try installing Intel Realsense permission scripts located in librealsense source directory:
sudo cp config/99-realsense-libusb.rules /etc/udev/rules.d/  sudo udevadm control --reload-rules && udevadm trigger

Installing the permission scripts didn't work - however I solved the problem by running
sudo usermod -aG dialout $USER

and restarting the computer.


DEID Service Health Check fails

In the test-ingestion-deid namespace in the health-patterns-1 cluster, clinical ingestion with deid is deployed.
NAME: ingestion
LAST DEPLOYED: Thu Jun 17 13:57:47 2021
NAMESPACE: test-ingestion-deid
STATUS: deployed
REVISION: 1
NOTES:
Welcome to the
   d8888 888                                    d8b
  d88888 888                                    Y8P
 d88P888 888
d88P 888 888 888  888  .d88b.   8888b.  888d888 888  .d88b.

d88P  888 888 888  888 d8P  Y8b     "88b 888P"   888 d8P  Y8b
d88P   888 888 Y88  88P 88888888 .d888888<PHONE_NUMBER>8888
d8888888888 888  Y8bd8P  Y8b.     888  888 888     888 Y8b.
d88P     888 888   Y88P    "Y8888  "Y888888 888     888  "Y8888
                           Clinical Data Ingestion Framework

Pattern: De-Identification
The following services have been deployed:

Primary FHIR Server --------- https://test-ingestion-deid-ingestion-fhir.wh-health-patterns.dev.watson-health.ibm.com/fhir-server/api/v4
Secondary FHIR Server ------- https://test-ingestion-deid-ingestion-fhir-deid.wh-health-patterns.dev.watson-health.ibm.com/fhir-server/api/v4
De-Identification Service --- https://test-ingestion-deid-ingestion-deid.wh-health-patterns.dev.watson-health.ibm.com/api/v1/
NiFi Server ----------------- https://test-ingestion-deid-ingestion-nifi.wh-health-patterns.dev.watson-health.ibm.com/nifi
NiFi HTTP Post API ---------- https://test-ingestion-deid-ingestion-nifi-http-post.wh-health-patterns.dev.watson-health.ibm.com
NiFi Registry --------------- https://test-ingestion-deid-ingestion-nifi-registry.wh-health-patterns.dev.watson-health.ibm.com/nifi-registry
Zookeeper
Kafka

Access to the Kafka server is handled via load balancer. It may take a few minutes for the load balancer IP to be available.
Watch the status of the kafka service by running the following command and wait until the external IP address appears:
kubectl get --namespace test-ingestion-deid svc -w | grep kafka-0-external
Once the external IP has been assigned run the following command to identify the kafka server broker:
export KAFKA_IP=$(kubectl get svc --namespace test-ingestion-deid ingestion-kafka-0-external -o jsonpath='{.status.loadBalancer.ingress[0].hostname}')
export KAFKA_PORT=$(kubectl get svc ingestion-kafka-0-external -o jsonpath='{.spec.ports[0].port}')
echo Kafka Broker: $KAFKA_IP:$KAFKA_PORT
Inside the cluster you can access the services at the following locations:

Primary FHIR Server: ingestion-fhir.test-ingestion-deid.svc.
Secondary FHIR Server: ingestion-fhir-deid.test-ingestion-deid.svc.
De-Identification Service: ingestion-deid.test-ingestion-deid.svc.
NiFi Server: ingestion-nifi.test-ingestion-deid.svc.
NiFi Registry: ingestion-nifi-registry.test-ingestion-deid.svc.
Kafka: ingestion-kafka.test-ingestion-deid.svc.
Zookeeper: ingestion-zookeeper.test-ingestion-deid.svc.

The DEID Service healthcheck fails with http 503 Service Temporarily Unavailable.
https://test-ingestion-deid-ingestion-deid.wh-health-patterns.dev.watson-health.ibm.com/api/v1/deid_service}/api/v1/health

Verified fix


Drone CLI fails to install on Windows

Looks like src/env.rs contains some unix-specific code which makes it impossible to install drone on Windows. Would it be possible to replace it with a platform-independent implementation?
Compilation log:
   Compiling drone v0.11.1
error[E0433]: failed to resolve: could not find `unix` in `os`
 --> C:\Users\bugad\.cargo\registry\src\github.com-1ecc6299db9ec823\drone-0.11.1\src\env.rs:5:20
  |
5 | use std::{env, os::unix::process::CommandExt, process::Command};
  |                    ^^^^ could not find `unix` in `os`

error[E0432]: unresolved import `signal_hook::iterator`
  --> C:\Users\bugad\.cargo\registry\src\github.com-1ecc6299db9ec823\drone-0.11.1\src\probe\bmp.rs:13:18
   |
13 | use signal_hook::iterator::Signals;
   |                  ^^^^^^^^ could not find `iterator` in `signal_hook`

error[E0432]: unresolved import `signal_hook::iterator`
  --> C:\Users\bugad\.cargo\registry\src\github.com-1ecc6299db9ec823\drone-0.11.1\src\probe\openocd.rs:14:18
   |
14 | use signal_hook::iterator::Signals;
   |                  ^^^^^^^^ could not find `iterator` in `signal_hook`

error[E0432]: unresolved import `signal_hook::iterator`
  --> C:\Users\bugad\.cargo\registry\src\github.com-1ecc6299db9ec823\drone-0.11.1\src\probe\mod.rs:14:18
   |
14 | use signal_hook::iterator::Signals;
   |                  ^^^^^^^^ could not find `iterator` in `signal_hook`

error[E0433]: failed to resolve: could not find `unix` in `os`
  --> C:\Users\bugad\.cargo\registry\src\github.com-1ecc6299db9ec823\drone-0.11.1\src\utils.rs:12:9
   |
12 |     os::unix::{ffi::OsStrExt, io::AsRawFd, process::CommandExt},
   |         ^^^^ could not find `unix` in `os`

error[E0432]: unresolved imports `signal_hook::iterator`, `signal_hook::SIGQUIT`
 --> C:\Users\bugad\.cargo\registry\src\github.com-1ecc6299db9ec823\drone-0.11.1\src\utils.rs:5:19
  |
5 | use signal_hook::{iterator::Signals, SIGINT, SIGQUIT, SIGTERM};
  |                   ^^^^^^^^                   ^^^^^^^ no `SIGQUIT` in the root
  |                   |
  |                   could not find `iterator` in `signal_hook`

error[E0425]: cannot find function `mkfifo` in crate `libc`
   --> C:\Users\bugad\.cargo\registry\src\github.com-1ecc6299db9ec823\drone-0.11.1\src\utils.rs:115:23
    |
115 |     if unsafe { libc::mkfifo(c_pipe.as_ptr(), 0o644) } == -1 {
    |                       ^^^^^^ not found in `libc`

error[E0425]: cannot find function `fcntl` in crate `libc`
   --> C:\Users\bugad\.cargo\registry\src\github.com-1ecc6299db9ec823\drone-0.11.1\src\utils.rs:124:20
    |
124 |     unsafe { libc::fcntl(fifo.as_raw_fd(), libc::F_SETFL, libc::O_NONBLOCK) };
    |                    ^^^^^ not found in `libc`

error[E0425]: cannot find value `F_SETFL` in crate `libc`
   --> C:\Users\bugad\.cargo\registry\src\github.com-1ecc6299db9ec823\drone-0.11.1\src\utils.rs:124:50
    |
124 |     unsafe { libc::fcntl(fifo.as_raw_fd(), libc::F_SETFL, libc::O_NONBLOCK) };
    |                                                  ^^^^^^^ not found in `libc`

error[E0425]: cannot find value `O_NONBLOCK` in crate `libc`
   --> C:\Users\bugad\.cargo\registry\src\github.com-1ecc6299db9ec823\drone-0.11.1\src\utils.rs:124:65
    |
124 |     unsafe { libc::fcntl(fifo.as_raw_fd(), libc::F_SETFL, libc::O_NONBLOCK) };
    |                                                                 ^^^^^^^^^^ not found in `libc`

error[E0425]: cannot find function `setpgid` in crate `libc`
   --> C:\Users\bugad\.cargo\registry\src\github.com-1ecc6299db9ec823\drone-0.11.1\src\utils.rs:140:19
    |
140 |             libc::setpgid(0, 0);
    |                   ^^^^^^^ help: a function with a similar name exists: `getpid`

error[E0599]: no method named `exec` found for type `std::process::Command` in the current scope
  --> C:\Users\bugad\.cargo\registry\src\github.com-1ecc6299db9ec823\drone-0.11.1\src\env.rs:21:33
   |
21 |             Err(anyhow!(command.exec()))
   |                                 ^^^^ method not found in `std::process::Command`

error[E0599]: no method named `as_bytes` found for type `&std::ffi::OsStr` in the current scope
   --> C:\Users\bugad\.cargo\registry\src\github.com-1ecc6299db9ec823\drone-0.11.1\src\utils.rs:114:48
    |
114 |     let c_pipe = CString::new(pipe.as_os_str().as_bytes())?;
    |                                                ^^^^^^^^ method not found in `&std::ffi::OsStr`
    |
    = help: items from traits can only be used if the trait is in scope
    = note: the following trait is implemented but not in scope; perhaps add a `use` for it:
            `use clap::osstringext::OsStrExt3;`

error[E0599]: no method named `as_raw_fd` found for type `std::fs::File` in the current scope
   --> C:\Users\bugad\.cargo\registry\src\github.com-1ecc6299db9ec823\drone-0.11.1\src\utils.rs:124:31
    |
124 |     unsafe { libc::fcntl(fifo.as_raw_fd(), libc::F_SETFL, libc::O_NONBLOCK) };
    |                               ^^^^^^^^^ method not found in `std::fs::File`

error[E0599]: no method named `pre_exec` found for type `&mut std::process::Command` in the current scope
   --> C:\Users\bugad\.cargo\registry\src\github.com-1ecc6299db9ec823\drone-0.11.1\src\utils.rs:139:17
    |
139 |         openocd.pre_exec(|| {
    |                 ^^^^^^^^ method not found in `&mut std::process::Command`

error: aborting due to 15 previous errors

Would it be possible to replace it with a platform-independent implementation?

I think it's possible, but not trivial. Drone CLI uses pipes, signals, and other unix stuff to glue different external commands together. For example when you run drone probe itm with an OpenOCD probe, it spawns OpenOCD GDB server that connects to your probe, GDB client that connects to the GDB server and sends commands to enable ITM on the chip, itmsink utility that consumes the output of the pipe created by OpenOCD. And all of this should correctly handle Ctrl-C as if it's a single drone command.

I'm trying out drone and hit the same issue. I think it is a really nice project, but being rust only is a really big limitation. Rust has a ton of platform independent libraries to handle this stuff.
If I have time I will give this a shot

Thank you for your comment. We will much appreciate contributions to make drone CLI tools available for non-unix operating systems.

@chemicstry Have you considered using WSL? I am working from Windows this way, and it works just fine!

@chemicstry Have you considered using WSL? I am working from Windows this way, and it works just fine!


[Bug]: Can't install operator using helm chart version 2.0.0

Can't install Camel-K operator using helm chart
Have 2 simple integrations
hello.groovy
from('timer:tick?period=3000')
        .setBody().constant('Hello world from Camel K!')
        .to('log:info')

HttpTest.java
package com.backbase.gc.mambu;
import org.apache.camel.builder.RouteBuilder;
@SuppressWarnings("unused")
public class HttpTest extends RouteBuilder {
    @Override
    public void configure() {
        from("rest://get:/test")
                .setBody().simple("Hello world from test at ${date:now:yyyy-MM-dd HH:mm:ss.SSS}")
                .log("${body}")
        ;
    }
}

If I install Camel-K using cli:
kamel install -n camel-k --force --olm=false \
  --global \
  --organization ecosystemsgctmp \
  --registry ecosystemsgctmp.azurecr.io \
  --registry-secret camel-k-registry-secret \
  --wait

everything work.
If I use helm to install Camel-K operator:
helm -n camel-k upgrade --install -f camel-k.values.yaml \
  --repo https://apache.github.io/camel-k/charts \
  camel-k \
  camel-k \
  --version 2.0.1 --wait

camel-k.values.yaml
---
operator:
  global: "true"
platform:
  build:
    registry:
      organization: ecosystemsgctmp
      address: ecosystemsgctmp.azurecr.io
      secret: camel-k-registry-secret

Steps to reproduce

Kubernetes cluster: AKS v1.26.6
istio, istio-gateway: 1.18.2
knative: v1.11

Install Camel-K operator using following command
helm -n camel-k upgrade --install -f camel-k.values.yaml \
  --repo https://apache.github.io/camel-k/charts \
  camel-k \
  camel-k \
  --version 2.0.1 --wait

camel-k.values.yaml
---
operator:
  global: "true"
platform:
  build:
    registry:
      organization: ecosystemsgctmp
      address: ecosystemsgctmp.azurecr.io
      secret: camel-k-registry-secret

Run integraion
HttpTest.java
package com.backbase.gc.mambu;
import org.apache.camel.builder.RouteBuilder;
@SuppressWarnings("unused")
public class HttpTest extends RouteBuilder {
    @Override
    public void configure() {
        from("rest://get:/test")
                .setBody().simple("Hello world from test at ${date:now:yyyy-MM-dd HH:mm:ss.SSS}")
                .log("${body}")
        ;
    }
}

with command:
kamel run --trait knative-service.min-scale=1 HttpTest.java

Relevant log output
{"level":"info","ts":1693918064.4193337,"logger":"camel-k.traits","msg":"Skipping environment variable POD_NAME (fieldRef)","trait":"container"}
{"level":"error","ts":1693918064.4319084,"msg":"Reconciler error","controller":"integration-controller","controllerGroup":"camel.apache.org","controllerKind":"Integration","Integration":{"name":"http-test","namespace":"default"},"namespace":"default","name":"http-test","reconcileID":"5349f143-288d-4f01-8df0-ee61fb41c5c0","error":"error executing post actions: error during apply resource: default/http-test: services.serving.knative.dev \"http-test\" is forbidden: User \"system:serviceaccount:camel-k:camel-k-operator\" cannot patch resource \"services\" in API group \"serving.knative.dev\" in the namespace \"default\": RBAC: clusterrole.rbac.authorization.k8s.io \"addressable-resolver\" not found","stacktrace":"sigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).reconcileHandler\n\tsigs.k8s.io/controller-runtime@v0.13.1/pkg/internal/controller/controller.go:326\nsigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).processNextWorkItem\n\tsigs.k8s.io/controller-runtime@v0.13.1/pkg/internal/controller/controller.go:273\nsigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).Start.func2.2\n\tsigs.k8s.io/controller-runtime@v0.13.1/pkg/internal/controller/controller.go:234"}

### Camel K version

v2.0.1

Hello. Yes it seems to be a bug when installing a global operator and Knative presence. It requires some RBAC which are not provided by default in the Helm installation procedure. While working on a fix, in order to workaround it please execute: https://raw.githubusercontent.com/apache/camel-k/main/config/rbac/operator-cluster-role-addressable-resolver.yaml

I've applied camel-k-operator-bind-addressable-resolver after helm upgrade --install and still getting error:
{"level":"error","ts":1693989282.0464962,"msg":"Reconciler error","controller":"integration-controller","controllerGroup":"camel.apache.org","controllerKind":"Integration","Integration":{"name":"http-test","namespace":"default"},"namespace":"default","name":"http-test","reconcileID":"95a5ea4f-458e-40b9-9927-673b5182a027","error":"error executing post actions: error during apply resource: default/http-test: services.serving.knative.dev \"http-test\" is forbidden: User \"system:serviceaccount:camel-k:camel-k-operator\" cannot patch resource \"services\" in API group \"serving.knative.dev\" in the namespace \"default\"","stacktrace":"sigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).reconcileHandler\n\tsigs.k8s.io/controller-runtime@v0.13.1/pkg/internal/controller/controller.go:326\nsigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).processNextWorkItem\n\tsigs.k8s.io/controller-runtime@v0.13.1/pkg/internal/controller/controller.go:273\nsigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).Start.func2.2\n\tsigs.k8s.io/controller-runtime@v0.13.1/pkg/internal/controller/controller.go:234"}

Yes, it seems we don't support Knative out of the box in Helm. We will work on it. Please in the while, try to apply the RBACs in: https://github.com/apache/camel-k/blob/main/config/rbac/operator-role-knative.yaml and https://github.com/apache/camel-k/blob/main/config/rbac/operator-role-binding-knative.yaml
Let us know how it goes.

Hi Pasquale,
Applied all manifests after helm upgrade --install. Integration still stuck in "Deploying" state, and error is:
{"level":"error","ts":1694071782.4348025,"msg":"Reconciler error","controller":"integration-controller","controllerGroup":"camel.apache.org","controllerKind":"Integration","Integration":{"name":"http-test","namespace":"default"},"namespace":"default","name":"http-test","reconcileID":"06bde19f-24b0-4489-a73f-db823c355130","error":"error executing post actions: error during apply resource: default/http-test: services.serving.knative.dev \"http-test\" is forbidden: User \"system:serviceaccount:camel-k:camel-k-operator\" cannot patch resource \"services\" in API group \"serving.knative.dev\" in the namespace \"default\"","stacktrace":"sigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).reconcileHandler\n\tsigs.k8s.io/controller-runtime@v0.13.1/pkg/internal/controller/controller.go:326\nsigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).processNextWorkItem\n\tsigs.k8s.io/controller-runtime@v0.13.1/pkg/internal/controller/controller.go:273\nsigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).Start.func2.2\n\tsigs.k8s.io/controller-runtime@v0.13.1/pkg/internal/controller/controller.go:234"}

Hello. In order to troubleshoot the helm installation procedure, please, check the script you find in https://github.com/apache/camel-k/blob/main/script/release_helm.sh which will be called by the make helm procedure.
Basically it wrap the content of https://github.com/apache/camel-k/tree/main/helm/camel-k directory, which contains the CRDs and templates required to provide the proper installation. I suspect in the template directory we miss all the required knative stuff. As a reference, you can follow the trail of the CLI install here: https://github.com/apache/camel-k/blob/6fd445fe2832d5d4de30400e4fbf8296f58a6b44/pkg/install/operator.go#L276
Please, let me know if you require any further help and thanks for taking care.

Thanks for the reply! 🙏🏻

Hey @squakez, it seems that the make release_helm indeed creates the missing RBACs you mentioned above.
~/opensource/camel-k/docs/charts/camel-k > tree
.
|-- Chart.yaml
|-- README.md
|-- crds
|   |-- cluster-role.yaml
|   |-- crd-build.yaml
|   |-- crd-camel-catalog.yaml
|   |-- crd-integration-kit.yaml
|   |-- crd-integration-platform.yaml
|   |-- crd-integration.yaml
|   |-- crd-kamelet-binding.yaml
|   |-- crd-kamelet.yaml
|   `-- crd-pipe.yaml
|-- templates
|   |-- NOTES.txt
|   |-- _helpers.tpl
|   |-- operator-cluster-role-bindings.yaml
|   |-- operator-cluster-roles.yaml
|   |-- operator-role-binding.yaml
|   |-- operator-role.yaml
|   |-- operator-service-account.yaml
|   |-- operator.yaml
|   `-- platform.yaml
`-- values.yaml

3 directories, 21 files

In this case, what might be missing? The direct CRDs and templates of Knative itself?

I don't see any operator-role-knative, etcetera over there. Quickly following the code I've posted above, what it seems we're missing are the following:
		"/rbac/operator-role-knative.yaml",
		"/rbac/operator-role-binding-knative.yaml",
/rbac/operator-cluster-role-binding-addressable-resolver.yaml

however you must consider to install this only when the knative is previously installed. Not sure if there is an easy way to have it done ootb in Helm, reason why this could have been left outside the canonical installation procedure on purpose.

BTW, the above point could be done looking at .Capabilities, see https://stackoverflow.com/questions/59370451/create-kubernetes-resources-with-helm-only-if-custom-resource-definition-exists


does this code support gpu and cpu ?

Is this code support gpu and cpu . If yes, then can you tell me which argument will take cpu cores and gpu (cuda backend).

Priyansh2, the code is based on Google's word2vec project (Apache 2.0 License). So I don't think there is gpu support.

Is this code support gpu and cpu . If yes, then can you tell me which argument will take cpu cores and gpu (cuda backend).

Priyansh2, the code is based on Google's word2vec project (Apache 2.0 License). So I don't think there is gpu support.


Whole actor run randomly crash

Describe the bug
Whole actor randomly crash with error:
2022-01-03T12:52:48.631Z /home/myuser/app/node_modules/puppeteer/lib/cjs/puppeteer/common/FrameManager.js:334
2022-01-03T12:52:48.635Z         const context = new ExecutionContext_js_1.ExecutionContext(frame._client || this._client, contextPayload, world);
2022-01-03T12:52:48.638Z                                                                          ^
2022-01-03T12:52:48.641Z
2022-01-03T12:52:48.644Z TypeError: Cannot read properties of null (reading '_client')
2022-01-03T12:52:48.646Z     at FrameManager._onExecutionContextCreated (/home/myuser/app/node_modules/puppeteer/lib/cjs/puppeteer/common/FrameManager.js:334:74)
2022-01-03T12:52:48.650Z     at /home/myuser/app/node_modules/puppeteer/lib/cjs/puppeteer/common/FrameManager.js:76:18
2022-01-03T12:52:48.653Z     at /home/myuser/app/node_modules/puppeteer/lib/cjs/vendor/mitt/src/index.js:51:62
2022-01-03T12:52:48.656Z     at Array.map (<anonymous>)
2022-01-03T12:52:48.660Z     at Object.emit (/home/myuser/app/node_modules/puppeteer/lib/cjs/vendor/mitt/src/index.js:51:43)
2022-01-03T12:52:48.664Z     at CDPSession.emit (/home/myuser/app/node_modules/puppeteer/lib/cjs/puppeteer/common/EventEmitter.js:72:22)
2022-01-03T12:52:48.667Z     at CDPSession._onMessage (/home/myuser/app/node_modules/puppeteer/lib/cjs/puppeteer/common/Connection.js:245:18)
2022-01-03T12:52:48.669Z     at Connection._onMessage (/home/myuser/app/node_modules/puppeteer/lib/cjs/puppeteer/common/Connection.js:117:25)
2022-01-03T12:52:48.672Z     at WebSocket.<anonymous> (/home/myuser/app/node_modules/puppeteer/lib/cjs/puppeteer/node/NodeWebSocketTransport.js:13:32)
2022-01-03T12:52:48.675Z     at WebSocket.onMessage (/home/myuser/app/node_modules/puppeteer/node_modules/ws/lib/event-target.js:199:18)
2022-01-03T12:52:48.867Z

System information:

docker build: apify/actor-node-puppeteer-chrome:16
Node.js version 16.13.1
Apify SDK version 2.2.0
Puppeteer version 11.0.0

With Puppeteer version 10.4.0 it is not happening. Thanks!

I dont think this is enough to reproduce, we do have puppeteer actors with v11 and sdk 2.2 and they run just fine. I was also testing long running actors (~5 hours) and never seen that.

Looks like puppeteer bug, should be fixed in v12, we will use that version once chrome 97 is out in stable.
https://github.com/puppeteer/puppeteer/issues/7749

Thanks. So maybe docker image apify/actor-node-puppeteer-chrome:16 should not use Puppeteer v11 as default version?

Yeah I guess we should. I will downgrade the version here and ship new SDK to rebuild the images, that should be enough. Locally we would still install latest as there is the * in package.json, but on platform it should pick the version from docker image. I guess we don't want to change that * in the project template, right @mnmkng?

The * is there to say "use whatever is preinstalled in the image" I hope it still works that way.


Having a frustrating problem with one Reveal Modal.

First, let me say the issue does not happen on my local machine - only when it is live.
I have a login form. If you enter incorrect credentials a Reveal appears telling you so. On its way in, the modal background appears briefly but then disappears just as quickly, leaving the Reveal in a broken state. If you then close it, the Reveal is hidden but the background reappears. If you click the link to open the next Reveal, which is a form to submit your e-mail to set a new password, again the Reveal has no background, until you close it, when the background once again reappears.
The first Reveal is called from a jquery script if the login fails. I have tried wrapping the reveal call in a setTimeout function but the problem still occurs. If I change the 'Forgot Password' link next to the Log In button to call the first Reveal directly, it comes in fine. I also have numerous other Reveals that are working as intended. It is only this one, and only when it is live.
Here is the jquery script:
$('.logInForm').on("submit", function(e) {
    e.preventDefault();
    var str = $(this).serialize();
    $.post('lib/login.php', str, function(data) {
             if (data.success) {
                   location.reload();
             } else {
                   $('#badLogin').foundation("reveal", "open");
              }
      });
})

You can see it here at admintest.mascores.com. This is my first attempt at building with Foundation and I am liking it. The site is by no means complete, but I want to figure this issue out before I continue on.
Any thoughts? Thanks in advance.

After lots of tweaks to my code I appear to have fixed the issue and everything seems to be working fine.