Can't pass multiple inputs in custom trainer functions

I need to add two inputs to my model, the first input should take samples from training data set, the second input should take a timestep by which I'll need to calculate time projection later on, I stuck trying to pass second input in custom init function or directly to predict_fn.
The model below doesn't make sense I simplified my example to pass just a random tensor as a timestep input:
Mix.install([
  {:axon, "== 0.6.1"},
  {:kino, ">= 0.9.0"},
  {:scidata, "~> 0.1"}
])

defmodule MyModel do
  import Nx.Defn

  def model do
    sample_shape = {12, 32, 32, 3}
    sample = Axon.input("sample", shape: sample_shape)
    timestep = Axon.input("timestep", shape: {})

    time_emb = Axon.layer(&t_emb/2, [timestep], embedding_size: 128)

    Axon.conv(sample, 32,
      kernel_size: 3,
      padding: [{1, 1}, {1, 1}],
      name: "input_conv",
      activation: :silu
    )
    |> Axon.add(time_emb)
  end

  defn t_emb(timestep, _opts) do
    print_expr(timestep, label: :temestemp?)

    timestep
  end

  deftransform sample_timesteps(_random_key) do
    new_key = Nx.Random.key(123)
    timestep = Nx.iota({1, 32, 32, 3}, names: [:n, :time_x, :time_y, :d])
    {timestep, new_key}
  end
end

out = MyModel.model()
Axon.get_inputs(out) |> IO.inspect()

%{"sample" => {12, 32, 32, 3}, "timestep" => {}}
{init_fn, predict_fn} = Axon.build(out)
{optimizer_init, optimizer} = Polaris.Optimizers.adamw(learning_rate: 1.0e-4)
import Nx.Defn

init = fn template, _state ->
  template = %{
    "sample" => Nx.template({12, 32, 32, 3}, :f32),
    "timestep" => Nx.template({}, :f32)
  }

  params = init_fn.(template, %{})
  key = Nx.Random.key(123)

  %{
    key: key,
    i: Nx.tensor(0),
    model_state: params,
    optimizer_state: optimizer_init.(params),
    loss: Nx.tensor(0.0)
  }
end

step = fn batch, state ->
  iter = state[:i]
  params = state[:model_state]
  key = state[:key]
  {t, key} = MyModel.sample_timesteps(key)
  noise = batch * t

  {loss, grads} =
    value_and_grad(params, fn params ->
      %{prediction: preds} =
        predict_fn.(params, %{
          "sample" => batch,
          "timestep" => t
        })

      Axon.Losses.categorical_cross_entropy(preds, noise, reduction: :mean)
    end)

  optimizer_state = state[:optimizer_state]

  {updates, optimizer_state} = optimizer.(grads, optimizer_state, params)
  params = Polaris.Updates.apply_updates(params, updates)

  new_loss =
    state[:loss]
    |> Nx.multiply(state[:i])
    |> Nx.add(loss)
    |> Nx.divide(Nx.add(state[:i], 1))

  %{
    key: key,
    iteration: iter + 1,
    model_state: params,
    optimizer_state: optimizer_state,
    loss: new_loss
  }
end

batch_size = 12

{{data, type, shape}, _train_labels} = Scidata.CIFAR100.download()
IO.inspect(shape, label: :dataset_shape)

shape = {:auto, 32, 32, 3}

train_data =
  data
  |> Nx.from_binary(type)
  |> Nx.reshape(shape, names: [:images, :height, :width, :channels])
  |> Nx.divide(255)
  |> Nx.to_batched(batch_size)

step
|> Axon.Loop.loop(init)
|> Axon.Loop.run(train_data, %{}, iterations: 10)

The issue with a template in init function:
** (Axon.CompileError) exception found when compiling layer Axon.Layers.conv/4 named input_conv:

    ** (RuntimeError) cannot perform operations on a Nx.TemplateBackend tensor
        (nx 0.7.2) lib/nx/template_backend.ex:31: Nx.TemplateBackend.conv/4
        (nx 0.7.2) lib/nx.ex:13193: Nx.conv/3
        (axon 0.6.1) lib/axon/layers.ex:364: Axon.Layers."__defn:conv_impl__"/4

(pass debug: true to build/compile see where the layer was defined)

Compiling of the model was initiated at:

    #cell:c7byoosengyhscek:11: (file)
    #cell:c7byoosengyhscek:67: (file)

when I comment this lines from init_fn to pass actual input:
# template = %{
#     "sample" => Nx.template({12, 32, 32, 3}, :f32),
#     "timestep" => Nx.template({}, :f32)
#   }

I'm getting an image input in place of timestep:
temestemp?: #Nx.Tensor<
  f32[images: 12][height: 32][width: 32][channels: 3]

  Nx.Defn.Expr
  parameter a:0   f32[12][32][32][3]
>
temestemp?: #Nx.Tensor<
  f32[images: 12][height: 32][width: 32][channels: 3]

  Nx.Defn.Expr
  parameter a:0   f32[12][32][32][3]
>

I'd like to see [:n, :time_x, :time_y, :d] named tensor in the log
Please let me know if I'm doing it wrong or is it a bug? I stuck on this for almost a week before I discovered my timestep input isn't even a timestep

There is definitely something strange going on here. So when you initialize a model, you need to provide all of the inputs and their shape. So if you remove your logic:
template = %{
  "sample" => Nx.template({12, 32, 32, 3}, :f32),
  "timestep" => Nx.template({}, :f32)
}

It actually should just blow up because you're giving it 1 input. I think the issue though is that if you pass a tensor it will just assume that input should be used for every input in the model, and so it doesn't raise. So that is 1 Axon bug.
As for the issues with templates, you should use a tensor there instead. I know it's confusing, but the issue is basically that you are using templates inside of a numerical definition. They are only meant to be used as placeholder parameters outside of numerical definitions. So I can use:
  template = %{
    "sample" => template,
    "timestep" => Nx.tensor(1, type: :f32)
  }

To initialize the model and it works

oh this is it! I can wrap more inputs in init_fn and the original template has only batch from the training dataset :+1: yeah it definitely clarified it, thank you!

it looks like the first forward pass is init_fn where I though I could pas s just a template inputs without passing real data trough, this way I need to add noise to batched images in init_fn where I wanted to specify just a raw parameters :thinking:


Typo in the FAQ page

I have absolutely no idea if this is the right place to post this but it should at least get noticed here.
There’s a small typo in the answer here: https://dolphin-emu.org/docs/faq/#how-much-ram-do-i-need-run-dolphin
It should be “has no effect on […]” instead of “has no affect on […]”.
Sorry if I should have posted this somewhere else. I looked at the CONTRIBUTING.md file but it didn’t help me much and quickly glancing over the code proved unsuccessful too.

@JMC47

Fixed, thank you!


Limit parallelism of nightly tests [skip ci]

Signed-off-by: Peixin Li<EMAIL_ADDRESS>The parallelism could go wild on large GPU-mem instance,
and this could actually slow down the whole process.
Give it a limitation here

build


AutoSave Audit

Forgive if this is an obvoius oversight,
Trying to use SQL Script (for Database First) and pulling the tables in by updating an edmx model from the database.
I am having a challenge with
AuditManager.DefaultConfiguration.AutoSavePreAction = (context, audit) =>
    (context as POCContext).AuditEntries.AddRange(audit.Entries);

Where I am getting an error
Argument 1: cannot convert from 'System.Collections.Generic.List<Z.EntityFramework.Plus.AuditEntry>' to 'System.Collections.Generic.IEnumerable<POC.Test.Data.AuditEntry>'
I appreciate the error just trying to understand the correct implementation strategy for the supplied script with e DB first apporach.
However I tried implementing the Custom solution and am hitting the SaveChangesAsync block
...
if (audit.Configuration.AutoSavePreAction != null)
        {
            audit.Configuration.AutoSavePreAction(this, audit);
            await base.SaveChangesAsync(cancellationToken).ConfigureAwait(false);
        }
...

howerver my save is not working.
Please advise the correct strategy for the audit entity and DB first.
Thanks

The first error happen because you have mapped “POC.Test.Data.AuditEntry” in the context but you try to add a list of “Z.EntityFramework.Plus.AuditEntry” in the context which are not compatible.
We recommend to map "Z.EntityFramework.Plus.AuditEntry" to your context instead but if you really need a custom AuditEntry class, then you can easily do it by importing values:
AuditManager.DefaultConfiguration.AutoSavePreAction = (context, audit) => {
    // Use a constructor to create your own custom audit entry
    var customAuditEntries = audit.Entries.Select(x => new POC.Test.Data.AuditEntry(x));
    (context as POCContext).AuditEntries.AddRange(customAuditEntries) };

That worked. In fact I also got the audit on autosave override working so both ways work. I realized my error before coming back to report my findings. I worked it out by looking through your repo and re-reading the instructions. There was nothing wrong with them. It was just too late in the evening.
This is looking very good btw. Excellent work.
Chris

Thank you Chris ;)
Let me know if you find something else missing from our library.
Jonathan


Remove Arduino RobertaFunctions

There still is RobertaFunctions.h and .cpp in the resources. However, it was already mostly replaced by NEPODefs.h, the only remaining method used by Arduinos is clamp.

[x] Change to inline function with std::min/max (we support STL either with ArduinoSTL or inbuilt by the system)
[x] Remove include & definition from code generation
[x] Change tests
[x] Test robots

[x] Arduino
[x] mBot
[x] senseBox

Yeah!


fix: temporarily disable fully_qualified_strict_types rule

adds to https://github.com/stickeeuk/php-cs-fixer-config/pull/24

:tada: This PR is included in version 2.3.2 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


#26 -  update dockerfile

Update only dockerfile becouse the rest of the dependencies are up-to-date except those that cannot be updated.
psr/container             1.1.2  2.0.2  Common Container Interface (PHP FIG PSR-11)
symfony/service-contracts v2.5.1 v3.0.1 Generic abstractions related to writing services

Why these could not be updated?

Why these could not be updated?

Because  another  dependencies use this concret versions and not have highter versions for this dep


Support arbitrary tag on event to suggest not showing link previews on that event?

Ideally used by bots who spit out enough context around the link to not need a preview. Clients could obviously ignore this, but it could also respect the hint. Example structure:
{
   "msgtype": "m.notice",
   "text": "Hello world! Here's a link to Google: https://google.ca",
   "url_preview_hint": "hide"
}

This might actually be more of a riot-web issue, but having a spec for these kinds of things would also be neat.

Duplicate of #779

Fankx Travis


Update README.md

Translate "contributors" to Spanish.

@all-contributors please add JimmyLoloy98 for tests,doc

@all-contributors please add JimmyLoloy98 for test,doc

@all-contributors please add JimmyLoloy98 for test


Intra-page links

As a web developer
I want links in my navigation section to direct to sections on my main page
So that my website is easy to navigate, and my skills are showcased.

Link functionality added.


Feature Request: Show current GPU at menu icon using a letter

Thanks for this great app!
I think it would be great if we can have the currently active GPU being shown by a letter on the menu icon. Something like gfxCardStatus did. So we can quickly know which GPU is being used.
gfxCardStatus:
 for integrated GPU.
 for dedicated GPU.

There is.  It looks like a gear icon when the gpu is integrated and when it is discrete there is a dot in the middle of it.

Apologies. My bad. I missed that. Thanks!

No worries it's not super obvious.  I'll make a note in the readme so its more clear for everyone.


Unable to use C++ Standard Library

Describe the bug
C++ Standard Library cannot be used with Zephyr 1.14.0. It used to work with 1.14-rc1.
To Reproduce
prj.conf: CONFIG_CPLUSPLUS=y
main.cpp:
#include <zephyr.h>
#include <vector>

int main()
{
  std::vector<int> v;

  v.push_back(10);

  for (int x : v)
    printk("x: %d", x);

  return 0;
}

Command line: D:\zephyr-test>cmake -GNinja -Bbuild -H. -DBOARD=stm32f4_disco && ninja -C build
Output:
Zephyr version: 1.14.0
-- Found PythonInterp: C:/Users/user/AppData/Local/Programs/Python/Python37/
python.exe (found suitable version "3.7.0", minimum required is "3.4")
-- Selected BOARD stm32f4_disco
-- Loading D:/test/zephyr-v1.14.0/boards/arm/stm32f4_disco/stm32f4_disco.dts as
base
-- Overlaying D:/test/zephyr-v1.14.0/dts/common/common.dts
Parsing Kconfig tree in D:/test/zephyr-v1.14.0/Kconfig
Loading D:/test/zephyr-v1.14.0/boards/arm/stm32f4_disco/stm32f4_disco_defconfig
as base
Merging D:/zephyr-test/prj.conf
Configuration written to 'D:/zephyr-test/build/zephyr/.config'
-- Cache files will be written to: C:\Users\user\AppData\Local/.cache/zephyr

-- The C compiler identification is GNU 8.2.1
-- The CXX compiler identification is GNU 8.2.1
-- The ASM compiler identification is GNU
-- Found assembler: C:/Program Files (x86)/GNU Tools Arm Embedded/8 2018-q4-majo
r/bin/arm-none-eabi-gcc.exe
-- Performing Test toolchain_is_ok
-- Performing Test toolchain_is_ok - Success
-- Configuring done
-- Generating done
-- Build files have been written to: D:/zephyr-test/build
ninja: Entering directory `build'
...
../src/main.cpp:2:10: fatal error: vector: No such file or directory
 #include <vector>
          ^~~~~~~~
compilation terminated.
[13/121] Building C object zephyr/arch...__arm__core__cortex_m.dir/prep_c.c.obj
ninja: build stopped: subcommand failed.

Expected behavior
It compiles, as with 1.14-rc1:
D:\zephyr-test>cmake -GNinja -Bbuild -H. -DBOARD=stm32f4_disco && ninja -C build

Zephyr version: 1.14.0
-- Found PythonInterp: C:/Users/user/AppData/Local/Programs/Python/Python37/
python.exe (found suitable version "3.7.0", minimum required is "3.4")
-- Selected BOARD stm32f4_disco
-- Loading D:/test/zephyr-1.14.0-rc1/boards/arm/stm32f4_disco/stm32f4_disco.dts
as base
-- Overlaying D:/test/zephyr-1.14.0-rc1/dts/common/common.dts
Parsing Kconfig tree in D:/test/zephyr-1.14.0-rc1/Kconfig
Loading D:/test/zephyr-1.14.0-rc1/boards/arm/stm32f4_disco/stm32f4_disco_defconf
ig as base
Merging D:/zephyr-test/prj.conf
Configuration written to 'D:/zephyr-test/build/zephyr/.config'
-- Cache files will be written to: C:\Users\user\AppData\Local/.cache/zephyr

-- The C compiler identification is GNU 8.2.1
-- The CXX compiler identification is GNU 8.2.1
-- The ASM compiler identification is GNU
-- Found assembler: C:/Program Files (x86)/GNU Tools Arm Embedded/8 2018-q4-majo
r/bin/arm-none-eabi-gcc.exe
-- Performing Test toolchain_is_ok
-- Performing Test toolchain_is_ok - Success
Including module(s):
-- Configuring done
-- Generating done
-- Build files have been written to: D:/zephyr-test/build
ninja: Entering directory `build'
[116/121] Linking CXX executable zephyr\zephyr_prebuilt.elf
Memory region         Used Size  Region Size  %age Used
           FLASH:       13592 B         1 MB      1.30%
            SRAM:        4348 B       192 KB      2.21%
        IDT_LIST:         120 B         2 KB      5.86%
[121/121] Linking CXX executable zephyr\zephyr.elf

Impact
Cannot update to Zephyr 1.14.0 for current development project.
Environment (please complete the following information):

OS: Windows
Toolchain: GNU ARM Embedded
Version used: Zephyr 1.14.0

Is this a reasonable fix or am I oversimplifying?
diff --git a/cmake/compiler/gcc/target_baremetal.cmake b/cmake/compiler/gcc/target_baremetal.cmake
index d268604435..0c657a61ac 100644
--- a/cmake/compiler/gcc/target_baremetal.cmake
+++ b/cmake/compiler/gcc/target_baremetal.cmake
@@ -5,7 +5,8 @@ macro(toolchain_cc_nostdinc)

   if (NOT CONFIG_NEWLIB_LIBC AND
     NOT COMPILER STREQUAL "xcc" AND
-    NOT CONFIG_NATIVE_APPLICATION)
+    NOT CONFIG_NATIVE_APPLICATION AND
+    NOT CONFIG_CPLUSPLUS)
     zephyr_compile_options( -nostdinc)
     zephyr_system_include_directories(${NOSTDINC})
   endif()

CC @SebastianBoe

@SebastianBoe could you please take a look at this one?

Presumably, this is due to NOSTDINC not pointing to the correct directory, but I am unable to figure out how to set it correctly, so avoiding -nostdinc is OK.

Take a look at the PR here and discussion, we might need to resurrect this:
https://github.com/zephyrproject-rtos/zephyr/pull/13648

The reporter has not enabled CONFIG_NEWLIB_LIBC.
To use the C++ standard library the CONFIG_LIB_CPLUSPLUS must be enabled. And to enable CONFIG_LIB_CPLUSPLUS, the CONFIG_NEWLIB_LIBC option must be enabled. A dependency that enforces this is now added in https://github.com/zephyrproject-rtos/zephyr/pull/18224

It is true that CONFIG_NEWLIB_LIBC is necessary, however, the problem description indicates that the gnumarmemb toolchain is also involved, so #17564 then triggers.  A backport of the patch to newlib from #18242 is required to fully solve the problem.

Backport is now in branch.


[1.5.n] Do not touch the connections in get_available_fcp

We should just set the assigner id and not change the connections
in get_available_fcp. The connections are maintained in attach and detach
steps.
Signed-off-by: dyyang<EMAIL_ADDRESS>


Re-rendering (i.e. responsive = True) broken in 6.0.10, 6.0.11 and 6.0.12

These versions contain the following code not present in the source code repository in wwwroot/Chart.js:
    chart.options.animation.onComplete = function (ctx) {
        window["AnimationComplete1"](ctx);
        DotNet.invokeMethodAsync('PSC.Blazor.Components.Chartjs', 'AnimationCompleted');
    }

    chart.options.scales.x.ticks.callback = function (val, index) {
        window["TickEvent1"](val, index);
        DotNet.invokeMethodAsync('PSC.Blazor.Components.Chartjs', 'ChartScaleXTicks', val, index);
    }

As there are no functions on the window object named AnimationComplete1 and TickEvent1, these cause Javascript errors resulting in no re-rendering taking place. In practice, this means as soon as the window is shrunk to a size that requires a re-render, the chart disappears.
6.0.9 works in this regard, since it does not have these lines of code

Oh, sorry my fault. I tried to create an interaction between the component and a custom function but it is not working.
I'll fix it now.
Enrico

A component update is on its way. In few minutes you will have a new version. Let me know if it is working.
Thank you in advance,
Enrico

I think something may have gone wrong in the build process?

 I think something may have gone wrong in the build process?

i'm facing the same Problem

OK. I don't know why

With the new version 6.0.15, I hope it should be fixed.
Please give it a try and let me know.
Enrico

Sadly it still dont work. On the NuGet Page it is also shown as tool.

The last working version is 6.0.12

I have to check what the NET tool is... I haven't included it but myself

OK, I think I found the issue! A new version is coming...

Version 6.0.16 is deployed. Please check and confirm.

worked perfectly! thank you and have nice Weekend :)

Thank you, you too


dependency on ihe.formatcode.fhir to last published version?

Section Number
https://profiles.ihe.net/ITI/MHD/qa.html
Issue
MHD is dependent on the terminology defined in ihe.formatcode.fhir#current. current is the last built version on the ci-build. the dependency should be probably fixed to the last published version 0.2.4?
https://profiles.ihe.net/fhir/ihe.formatcode.fhir/history.html
Proposed Change
Add dependency  to latest published version, maybe with an X that updated patched versions will be considered: 0.2.x
Priority:

Medium: Significant issue or clarification. Requires discussion, but should not lead to long debate.

I tried to use 0.2.4, but got a build failure.
java.io.IOException: Error reading http://profiles.ihe.net/fhir/ihe.formatcode.fhir/0.2.4/package.tgz: Input is not in the .gz format
I do not know how to resolve this.
I hope that it is related to the ig-registry accepting the pull-request
https://github.com/FHIR/ig-registry/pull/50

I have removed this constraint as it was not really an important constraint. Will continue to promote the IHE FormatCode IG as formally recognized by HL7.


Docker Image failing on failure to install Perl

I just cloned the repository and tried to build the Dockerfile. However the dockerfile is failing while trying to install dependencies, and giving the following error:
> [pfredenv 3/9] RUN yum install -y java perl perl-DBI perl-DBD-mysql wget libgfortran && yum clean all:
#6 0.447 Loaded plugins: ovl, security
#6 0.495 Setting up Install Process
#6 0.620 http://ftp.scientificlinux.org/linux/scientific/6.10/x86_64/os/repodata/repomd.xml: [Errno 14] PYCURL ERROR 22 - "The requested URL returned error: 404 Not Found"
#6 0.621 Trying other mirror.
#6 0.621 To address this issue please refer to the below knowledge base article
#6 0.621
#6 0.621 https://access.redhat.com/articles/1320623
#6 0.621
#6 0.621 If above article doesn't help to resolve this issue please open a ticket with Red Hat Support.
#6 0.621
#6 0.731 http://ftp1.scientificlinux.org/linux/scientific/6.10/x86_64/os/repodata/repomd.xml: [Errno 14] PYCURL ERROR 22 - "The requested URL returned error: 404 Not Found"
#6 0.731 Trying other mirror.
#6 0.824 http://ftp2.scientificlinux.org/linux/scientific/6.10/x86_64/os/repodata/repomd.xml: [Errno 14] PYCURL ERROR 22 - "The requested URL returned error: 404 Not Found"
#6 0.824 Trying other mirror.
#6 1.141 ftp://ftp.scientificlinux.org/linux/scientific/6.10/x86_64/os/repodata/repomd.xml: [Errno 14] PYCURL ERROR 9 - "Server denied you to change to the given directory"
#6 1.141 Trying other mirror.
#6 1.141 Error: Cannot retrieve repository metadata (repomd.xml) for repository: sl. Please verify its path and try again
------

@TianhongZhang @cruzda

It seems that ScientificLinux 6 reached end of life last year (https://scientificlinux.org/downloads/sl-versions/sl6/), and we used the docker image of this version in our Dockerfile. You can try to upgrade to version 7, but through testings are required to assure compatibility with other dependencies. If you can get it to work, can you issue a pull request to merge your changes? Thanks

@JunaidChaudry
Sorry for the typo, We fixed it. Can you run sudo docker build -t pfredimg . to build again?

@alfredyewang  The dockerfile is not building successfully. However, docker-compose logs  show the entrypoint.sh script to be failing. Please take a look at the output of the docker-compose logs:
 docker-compose logs
Attaching to pfredservice
pfredservice     | Setting up environment...
pfredservice     | Downloading Tomcat from port 9090
pfredservice     | --2021-11-05 13:34:02--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/tomcat.tar.gz
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://github-releases.githubusercontent.com/203637909/3f989780-2342-11ea-9544-de650f3e5bda?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133306Z&X-Amz-Expires=300&X-Amz-Signature=15454babf4997feaa8ca9c1eea81049a45b970bee795b2a21b85c7cbd950d234&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dtomcat.tar.gz&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-05 13:34:02--  https://github-releases.githubusercontent.com/203637909/3f989780-2342-11ea-9544-de650f3e5bda?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133306Z&X-Amz-Expires=300&X-Amz-Signature=15454babf4997feaa8ca9c1eea81049a45b970bee795b2a21b85c7cbd950d234&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dtomcat.tar.gz&response-content-type=application%2Foctet-stream
pfredservice     | Resolving github-releases.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to github-releases.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify github-releases.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to github-releases.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | tar: *.tar.gz: Cannot open: No such file or directory
pfredservice     | tar: Error is not recoverable: exiting now
pfredservice     | rm: cannot remove `*.tar.gz': No such file or directory
pfredservice     | Downloading pfred from github
pfredservice     | --2021-11-05 13:34:02--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/pfred.tar.gz
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://github-releases.githubusercontent.com/203637909/3539c480-57ef-11ea-8306-d2db0fa69635?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133307Z&X-Amz-Expires=300&X-Amz-Signature=146c414789f42a4cffc31e7aa43c354004e337db174dc1e23ea82ed611edc972&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dpfred.tar.gz&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-05 13:34:02--  https://github-releases.githubusercontent.com/203637909/3539c480-57ef-11ea-8306-d2db0fa69635?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133307Z&X-Amz-Expires=300&X-Amz-Signature=146c414789f42a4cffc31e7aa43c354004e337db174dc1e23ea82ed611edc972&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dpfred.tar.gz&response-content-type=application%2Foctet-stream
pfredservice     | Resolving github-releases.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to github-releases.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify github-releases.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to github-releases.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | tar: pfred.tar.gz: Cannot open: No such file or directory
pfredservice     | tar: Error is not recoverable: exiting now
pfredservice     | rm: cannot remove `*.tar.gz': No such file or directory
pfredservice     | Downloading BioPerl-1.6.1 from github
pfredservice     | --2021-11-05 13:34:02--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/BioPerl-1.6.1.tar.gz
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/304e2e00-c4b7-11e9-94b2-4d2fe5b19df7?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133307Z&X-Amz-Expires=300&X-Amz-Signature=ed0e3b2b8fce0f96a09a3f6f1a7ff51631470a83f51ae44034a6295433193fcf&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3DBioPerl-1.6.1.tar.gz&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-05 13:34:02--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/304e2e00-c4b7-11e9-94b2-4d2fe5b19df7?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133307Z&X-Amz-Expires=300&X-Amz-Signature=ed0e3b2b8fce0f96a09a3f6f1a7ff51631470a83f51ae44034a6295433193fcf&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3DBioPerl-1.6.1.tar.gz&response-content-type=application%2Foctet-stream
pfredservice     | Resolving objects.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to objects.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify objects.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to objects.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | tar: BioPerl-1.6.1.tar.gz: Cannot open: No such file or directory
pfredservice     | tar: Error is not recoverable: exiting now
pfredservice     | rm: cannot remove `*.tar.gz': No such file or directory
pfredservice     | Downloading oligowalk from github
pfredservice     | --2021-11-05 13:34:03--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/oligowalk.tar.gz
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/20364e80-c4b7-11e9-8414-d5c919055e1f?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133307Z&X-Amz-Expires=300&X-Amz-Signature=155a39eb3be77180908cb2ee7b10f0ca3e9583a0522bd91d244a7286b1a83747&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Doligowalk.tar.gz&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-05 13:34:03--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/20364e80-c4b7-11e9-8414-d5c919055e1f?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133307Z&X-Amz-Expires=300&X-Amz-Signature=155a39eb3be77180908cb2ee7b10f0ca3e9583a0522bd91d244a7286b1a83747&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Doligowalk.tar.gz&response-content-type=application%2Foctet-stream
pfredservice     | Resolving objects.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to objects.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify objects.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to objects.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | tar: oligowalk.tar.gz: Cannot open: No such file or directory
pfredservice     | tar: Error is not recoverable: exiting now
pfredservice     | rm: cannot remove `*.tar.gz': No such file or directory
pfredservice     | Downloading ensemblapi from github
pfredservice     | --2021-11-05 13:34:03--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/ensemblapi.tar.gz
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://github-releases.githubusercontent.com/203637909/2b897a00-c4b7-11e9-965a-0452d1f95c3a?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133308Z&X-Amz-Expires=300&X-Amz-Signature=371503195873865cb2d42c3ad3d1474b76eadd10c456dfdccc0230bbb4133168&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Densemblapi.tar.gz&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-05 13:34:03--  https://github-releases.githubusercontent.com/203637909/2b897a00-c4b7-11e9-965a-0452d1f95c3a?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133308Z&X-Amz-Expires=300&X-Amz-Signature=371503195873865cb2d42c3ad3d1474b76eadd10c456dfdccc0230bbb4133168&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Densemblapi.tar.gz&response-content-type=application%2Foctet-stream
pfredservice     | Resolving github-releases.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to github-releases.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify github-releases.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to github-releases.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | tar: ensemblapi.tar.gz: Cannot open: No such file or directory
pfredservice     | tar: Error is not recoverable: exiting now
pfredservice     | rm: cannot remove `*.tar.gz': No such file or directory
pfredservice     | Downloading bowtie from github
pfredservice     | --2021-11-05 13:34:03--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/bowtie.tar.gz.partaa
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/f3d18600-3df8-11ea-9275-96979b0bd369?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133308Z&X-Amz-Expires=300&X-Amz-Signature=f057d6dce86d9bc615f6b0baa5f28188453374ad0eabe8a8b69d1a8788812f89&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partaa&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-05 13:34:03--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/f3d18600-3df8-11ea-9275-96979b0bd369?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133308Z&X-Amz-Expires=300&X-Amz-Signature=f057d6dce86d9bc615f6b0baa5f28188453374ad0eabe8a8b69d1a8788812f89&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partaa&response-content-type=application%2Foctet-stream
pfredservice     | Resolving objects.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to objects.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify objects.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to objects.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | --2021-11-05 13:34:03--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/bowtie.tar.gz.partab
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://github-releases.githubusercontent.com/203637909/f3d18600-3df8-11ea-80fb-3bf58828eb88?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133308Z&X-Amz-Expires=300&X-Amz-Signature=77c70af4a0914ee13d7d3dabd94c4e6b5a083b095552e12069c9c492ed70d4b6&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partab&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-05 13:34:03--  https://github-releases.githubusercontent.com/203637909/f3d18600-3df8-11ea-80fb-3bf58828eb88?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133308Z&X-Amz-Expires=300&X-Amz-Signature=77c70af4a0914ee13d7d3dabd94c4e6b5a083b095552e12069c9c492ed70d4b6&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partab&response-content-type=application%2Foctet-stream
pfredservice     | Resolving github-releases.githubusercontent.com... ::ffff:<IP_ADDRESS>, ::ffff:<IP_ADDRESS>, ::ffff:<IP_ADDRESS>, ...
pfredservice     | Connecting to github-releases.githubusercontent.com|::ffff:<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify github-releases.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to github-releases.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | --2021-11-05 13:34:04--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/bowtie.tar.gz.partac
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://github-releases.githubusercontent.com/203637909/f3d18600-3df8-11ea-8344-548226049bbd?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133308Z&X-Amz-Expires=300&X-Amz-Signature=e1f33e4d83c97be50f97d0cea4fe3f8d157966a7fc761f16e56468da3c9b8040&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partac&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-05 13:34:04--  https://github-releases.githubusercontent.com/203637909/f3d18600-3df8-11ea-8344-548226049bbd?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133308Z&X-Amz-Expires=300&X-Amz-Signature=e1f33e4d83c97be50f97d0cea4fe3f8d157966a7fc761f16e56468da3c9b8040&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partac&response-content-type=application%2Foctet-stream
pfredservice     | Resolving github-releases.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to github-releases.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify github-releases.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to github-releases.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | --2021-11-05 13:34:04--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/bowtie.tar.gz.partad
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/f3d18600-3df8-11ea-9f6a-25c221e186c6?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133309Z&X-Amz-Expires=300&X-Amz-Signature=b1d7049c5a3f9cc7cc8bf2754384a27b4298ba2bce469ec379004c2d6c2834ce&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partad&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-05 13:34:04--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/f3d18600-3df8-11ea-9f6a-25c221e186c6?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211105%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211105T133309Z&X-Amz-Expires=300&X-Amz-Signature=b1d7049c5a3f9cc7cc8bf2754384a27b4298ba2bce469ec379004c2d6c2834ce&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partad&response-content-type=application%2Foctet-stream
pfredservice     | Resolving objects.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to objects.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify objects.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to objects.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | --2021-11-05 13:34:04--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/bowtie.tar.gz.partae
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 404 Not Found
pfredservice     | 2021-11-05 13:34:04 ERROR 404: Not Found.
pfredservice     |
pfredservice     | cat: bowtie.tar.gz.parta*: No such file or directory
pfredservice     | rm: cannot remove `*.tar.gz.parta*': No such file or directory
pfredservice     | tar: This does not look like a tar archive
pfredservice     |
pfredservice     | gzip: stdin: unexpected end of file
pfredservice     | tar: Child returned status 1
pfredservice     | tar: Error is not recoverable: exiting now
pfredservice     | chmod: cannot access `pfred/*': No such file or directory
pfredservice     | ./entrypoint.sh: line 52: startup.sh: command not found

@JunaidChaudry  I am not able to reproduce your error. Can you share your running environment?

Hi,
I just cleared up everything, rebuilt and re-run , and the error is still the same...  docker build runs fine, however docker-compose logs is still now showing errors as below:
Attaching to pfredservice
pfredservice     | Setting up environment...
pfredservice     | Downloading Tomcat from port 9090
pfredservice     | --2021-11-11 17:23:31--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/tomcat.tar.gz
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://github-releases.githubusercontent.com/203637909/3f989780-2342-11ea-9544-de650f3e5bda?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172331Z&X-Amz-Expires=300&X-Amz-Signature=73b1a62a774dbf42c8c86cd6dc138843871b0a93271c444256b3b58b1fbb82fa&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dtomcat.tar.gz&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-11 17:23:31--  https://github-releases.githubusercontent.com/203637909/3f989780-2342-11ea-9544-de650f3e5bda?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172331Z&X-Amz-Expires=300&X-Amz-Signature=73b1a62a774dbf42c8c86cd6dc138843871b0a93271c444256b3b58b1fbb82fa&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dtomcat.tar.gz&response-content-type=application%2Foctet-stream
pfredservice     | Resolving github-releases.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to github-releases.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify github-releases.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to github-releases.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | tar: *.tar.gz: Cannot open: No such file or directory
pfredservice     | tar: Error is not recoverable: exiting now
pfredservice     | rm: cannot remove `*.tar.gz': No such file or directory
pfredservice     | Downloading pfred from github
pfredservice     | --2021-11-11 17:23:31--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/pfred.tar.gz
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://github-releases.githubusercontent.com/203637909/3539c480-57ef-11ea-8306-d2db0fa69635?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172331Z&X-Amz-Expires=300&X-Amz-Signature=85ef3adf75ede1122dc401d9d8d4e21ad6fec478d37d2b5153f9313bffb6146e&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dpfred.tar.gz&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-11 17:23:31--  https://github-releases.githubusercontent.com/203637909/3539c480-57ef-11ea-8306-d2db0fa69635?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172331Z&X-Amz-Expires=300&X-Amz-Signature=85ef3adf75ede1122dc401d9d8d4e21ad6fec478d37d2b5153f9313bffb6146e&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dpfred.tar.gz&response-content-type=application%2Foctet-stream
pfredservice     | Resolving github-releases.githubusercontent.com... ::ffff:<IP_ADDRESS>, ::ffff:<IP_ADDRESS>, ::ffff:<IP_ADDRESS>, ...
pfredservice     | Connecting to github-releases.githubusercontent.com|::ffff:<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify github-releases.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to github-releases.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | tar: pfred.tar.gz: Cannot open: No such file or directory
pfredservice     | tar: Error is not recoverable: exiting now
pfredservice     | rm: cannot remove `*.tar.gz': No such file or directory
pfredservice     | Downloading BioPerl-1.6.1 from github
pfredservice     | --2021-11-11 17:23:31--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/BioPerl-1.6.1.tar.gz
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/304e2e00-c4b7-11e9-94b2-4d2fe5b19df7?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172332Z&X-Amz-Expires=300&X-Amz-Signature=21841f30be2cda28fec51dd0eaf393bd606b6d8ba97c48f9cb82aa3092c52602&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3DBioPerl-1.6.1.tar.gz&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-11 17:23:32--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/304e2e00-c4b7-11e9-94b2-4d2fe5b19df7?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172332Z&X-Amz-Expires=300&X-Amz-Signature=21841f30be2cda28fec51dd0eaf393bd606b6d8ba97c48f9cb82aa3092c52602&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3DBioPerl-1.6.1.tar.gz&response-content-type=application%2Foctet-stream
pfredservice     | Resolving objects.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to objects.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify objects.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to objects.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | tar: BioPerl-1.6.1.tar.gz: Cannot open: No such file or directory
pfredservice     | tar: Error is not recoverable: exiting now
pfredservice     | rm: cannot remove `*.tar.gz': No such file or directory
pfredservice     | Downloading oligowalk from github
pfredservice     | --2021-11-11 17:23:32--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/oligowalk.tar.gz
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/20364e80-c4b7-11e9-8414-d5c919055e1f?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172332Z&X-Amz-Expires=300&X-Amz-Signature=9b3e1e759be49bdd8f69c75286ea2c3e5fa33f290348eb192743e3aa44988c40&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Doligowalk.tar.gz&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-11 17:23:32--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/20364e80-c4b7-11e9-8414-d5c919055e1f?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172332Z&X-Amz-Expires=300&X-Amz-Signature=9b3e1e759be49bdd8f69c75286ea2c3e5fa33f290348eb192743e3aa44988c40&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Doligowalk.tar.gz&response-content-type=application%2Foctet-stream
pfredservice     | Resolving objects.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to objects.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify objects.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to objects.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | tar: oligowalk.tar.gz: Cannot open: No such file or directory
pfredservice     | tar: Error is not recoverable: exiting now
pfredservice     | rm: cannot remove `*.tar.gz': No such file or directory
pfredservice     | Downloading ensemblapi from github
pfredservice     | --2021-11-11 17:23:32--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/ensemblapi.tar.gz
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://github-releases.githubusercontent.com/203637909/2b897a00-c4b7-11e9-965a-0452d1f95c3a?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172332Z&X-Amz-Expires=300&X-Amz-Signature=09b7baa3677172fd525edd4c64a3092a052aaafa813c15336cef8b7ebd0f1608&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Densemblapi.tar.gz&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-11 17:23:32--  https://github-releases.githubusercontent.com/203637909/2b897a00-c4b7-11e9-965a-0452d1f95c3a?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172332Z&X-Amz-Expires=300&X-Amz-Signature=09b7baa3677172fd525edd4c64a3092a052aaafa813c15336cef8b7ebd0f1608&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Densemblapi.tar.gz&response-content-type=application%2Foctet-stream
pfredservice     | Resolving github-releases.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to github-releases.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify github-releases.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to github-releases.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | tar: ensemblapi.tar.gz: Cannot open: No such file or directory
pfredservice     | tar: Error is not recoverable: exiting now
pfredservice     | rm: cannot remove `*.tar.gz': No such file or directory
pfredservice     | Downloading bowtie from github
pfredservice     | --2021-11-11 17:23:32--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/bowtie.tar.gz.partaa
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/f3d18600-3df8-11ea-9275-96979b0bd369?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172332Z&X-Amz-Expires=300&X-Amz-Signature=07eaf560f840772d8929c2d0adf6541f3e10ecb788ef8cbf1a8c23e2c5ec692e&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partaa&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-11 17:23:33--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/f3d18600-3df8-11ea-9275-96979b0bd369?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172332Z&X-Amz-Expires=300&X-Amz-Signature=07eaf560f840772d8929c2d0adf6541f3e10ecb788ef8cbf1a8c23e2c5ec692e&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partaa&response-content-type=application%2Foctet-stream
pfredservice     | Resolving objects.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to objects.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify objects.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to objects.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | --2021-11-11 17:23:33--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/bowtie.tar.gz.partab
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://github-releases.githubusercontent.com/203637909/f3d18600-3df8-11ea-80fb-3bf58828eb88?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172333Z&X-Amz-Expires=300&X-Amz-Signature=d7ec7aa41f26430d1dccaaea54bb67444416dbc11746ad9610b4e8ffa7630d9f&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partab&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-11 17:23:33--  https://github-releases.githubusercontent.com/203637909/f3d18600-3df8-11ea-80fb-3bf58828eb88?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172333Z&X-Amz-Expires=300&X-Amz-Signature=d7ec7aa41f26430d1dccaaea54bb67444416dbc11746ad9610b4e8ffa7630d9f&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partab&response-content-type=application%2Foctet-stream
pfredservice     | Resolving github-releases.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to github-releases.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify github-releases.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to github-releases.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | --2021-11-11 17:23:33--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/bowtie.tar.gz.partac
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://github-releases.githubusercontent.com/203637909/f3d18600-3df8-11ea-8344-548226049bbd?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172333Z&X-Amz-Expires=300&X-Amz-Signature=b5ba6167dd96aa4e23c016ac1514bfbd5849a2bff91898230e28244878733f06&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partac&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-11 17:23:33--  https://github-releases.githubusercontent.com/203637909/f3d18600-3df8-11ea-8344-548226049bbd?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172333Z&X-Amz-Expires=300&X-Amz-Signature=b5ba6167dd96aa4e23c016ac1514bfbd5849a2bff91898230e28244878733f06&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partac&response-content-type=application%2Foctet-stream
pfredservice     | Resolving github-releases.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to github-releases.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify github-releases.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to github-releases.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | --2021-11-11 17:23:33--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/bowtie.tar.gz.partad
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 302 Found
pfredservice     | Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/f3d18600-3df8-11ea-9f6a-25c221e186c6?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172333Z&X-Amz-Expires=300&X-Amz-Signature=962d2ee688d2c760b8fc95685a5b200513fd8ec42e804da1961fae3dab92033e&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partad&response-content-type=application%2Foctet-stream [following]
pfredservice     | --2021-11-11 17:23:33--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/203637909/f3d18600-3df8-11ea-9f6a-25c221e186c6?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20211111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211111T172333Z&X-Amz-Expires=300&X-Amz-Signature=962d2ee688d2c760b8fc95685a5b200513fd8ec42e804da1961fae3dab92033e&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=203637909&response-content-disposition=attachment%3B%20filename%3Dbowtie.tar.gz.partad&response-content-type=application%2Foctet-stream
pfredservice     | Resolving objects.githubusercontent.com... <IP_ADDRESS>, <IP_ADDRESS>, <IP_ADDRESS>, ...
pfredservice     | Connecting to objects.githubusercontent.com|<IP_ADDRESS>|:443... connected.
pfredservice     | ERROR: cannot verify objects.githubusercontent.com's certificate, issued by `/O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':
pfredservice     |   Unable to locally verify the issuer's authority.
pfredservice     | To connect to objects.githubusercontent.com insecurely, use `--no-check-certificate'.
pfredservice     | --2021-11-11 17:23:33--  https://github.com/pfred/pfred-docker/releases/download/v1.0-alpha/bowtie.tar.gz.partae
pfredservice     | Resolving github.com... <IP_ADDRESS>
pfredservice     | Connecting to github.com|<IP_ADDRESS>|:443... connected.
pfredservice     | HTTP request sent, awaiting response... 404 Not Found
pfredservice     | 2021-11-11 17:23:33 ERROR 404: Not Found.
pfredservice     |
pfredservice     | cat: bowtie.tar.gz.parta*: No such file or directory
pfredservice     | rm: cannot remove `*.tar.gz.parta*': No such file or directory
pfredservice     | tar: This does not look like a tar archive
pfredservice     |
pfredservice     | gzip: stdin: unexpected end of file
pfredservice     | tar: Child returned status 1
pfredservice     | tar: Error is not recoverable: exiting now
pfredservice     | chmod: cannot access `pfred/*': No such file or directory
pfredservice     | ./entrypoint.sh: line 52: startup.sh: command not found

I am running on MacOS Catalina Version 10.15.7
Docker version 20.10.8, build 3967b7d
docker-compose version 1.29.2, build 5becea4c

@alfredyewang Is there any update?

@JunaidChaudry  I tested it on my Mac Catalina, and everything works.
ERROR: cannot verify objects.githubusercontent.com's certificate, issued by /O=Cisco/CN=Cisco Umbrella Secondary SubCA nyc-SG':`
Seems it was a GitHub problem.

Hi @alfredyewang , I was able to get it running, and have the "Tomcat started" message in docker logs. One follow-up question however, on what URL is the service available? The readme says that the service should be available at https://os.biogen.com/PFREDRestService/api. However, I don't see any response on doing a curl to that url.
Do I have to exec into a pod before being able to access the service?
Can you please provide an example if possible?
P.S:  I am able to see the default apache tomcat server page on localhost:8080, since there is a port binding 8080:8080

Hi @alfredyewang , I was able to get it running, and have the "Tomcat started" message in docker logs. One follow-up question however, on what URL is the service available? The readme says that the service should be available at https://os.biogen.com/PFREDRestService/api. However, I don't see any response on doing a curl to that url. Do I have to exec into a pod before being able to access the service? Can you please provide an example if possible?
P.S: I am able to see the default apache tomcat server page on localhost:8080, since there is a port binding 8080:8080

Is there any update to this @alfredyewang currently we want to connect to the server through the pfred java version, but it appears that no ways to connect to the server as the config url doesn't save and keeps reverting to the original server.

@chemist-ian Hi Ian, if you build this docker locally, you can point the pfred java client to https://localhost:8080/PFREDRestService/api. Or you can directly use the remote service that is https://os.biogen.com/PFREDRestService/api

This remote service is still working ?
https://os.biogen.com/PFREDRestService/api

@chemist-ian Hi Ian, if you build this docker locally, you can point the pfred java client to https://localhost:8080/PFREDRestService/api. Or you can directly use the remote service that is https://os.biogen.com/PFREDRestService/api

@alfredyewang @TianhongZhang @cruzda
I am testing PFRED and have successfully installed pfred-docker，Through the Swagger UI webpage in http://<IP_ADDRESS>:8080/PFREDRestService/api , I can test an API such as/ScriptUtilities/Shortcuts  successfully, for example, by using the curl command I can get something:
[root@localhost test]# curl -X GET "http://<IP_ADDRESS>:8080/PFREDRestService/service/ScriptUtilities/Orthologs?enseblID=ENSG00000165175&RunDirectory=run_orthologs_3&RequestedSpecies=rat&Species=human" -H "accept: text/plain"
name,species,length,source
ENST00000614558,homo_sapiens,3758,ENSEMBL
ENST00000457894,homo_sapiens,1812,ENSEMBL
ENST00000378474,homo_sapiens,1889,ENSEMBL
ENST00000336949,homo_sapiens,4814,ENSEMBL
However,  when I was running PFRED.jnlp, I configured Configuration>Configuration Service as http://<IP_ADDRESS>:8080/PFREDRestService/api , and then I ran Analysis>Enumerate Oligo>From ensemble ID and clicked [Retrieve Ortholog Sequence] button, there is always NO data returned and display. I checked the log in the service container and found that the localhost_access_log.2024-03-29.txt log shows the following:
<IP_ADDRESS> - - [29/Mar/2024:03:39:39 +0000] "GET /PFREDRestService/service/ScriptUtilities/Orthologs?enseblID=ENSG00000165175&RunDirectory=run_orthologs_4&RequestedSpecies=rat&Species=human HTTP/1.1" 200 344
<IP_ADDRESS> - - [29/Mar/2024:03:40:33 +0000] "POST /PFREDRestService/api/ HTTP/1.1" 200 4116
<IP_ADDRESS> - - [29/Mar/2024:03:51:32 +0000] "POST /PFREDRestService/api HTTP/1.1" 302 -
when url is http://<IP_ADDRESS>:8080/PFREDRestService/api, client requests  generated "302 -",
when url is http://<IP_ADDRESS>:8080/PFREDRestService/api/, client requests  generated "200 4116",
It seems http://<IP_ADDRESS>:8080/PFREDRestService/api/ is better, but I still don't konw why nothing returned when click [Retrieve Ortholog Sequence] button. Although the api url function seems very OK in swagger page.


Keep history of external imports

[x] Allow for multiple import source
[x] Allow for linking of the imported data to a beneficiary or whatever we want later on
[x] Keep track of the parsed data into a json struct inside postgres
[x] Keep only the latest external_data import (don't allow more history than one import)
[x] Tests
[x] Use sha256 check sum to check if we should update or not

Related to #800

:tada: This PR is included in version 1.113.0 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


Problem with runners (private repo needs private runners, public repo needs public runners)

Try to config that without changing the script when switching privacy (forking).

Should be fixed by requesting 'ubuntu-latest'.
If you'd like privately hosted runners, then you'll just have to label them exactly like that.
Github should prioritize them.


Updating package.json dependencies

For the Web downloaded csv  the "request" package is required but is missing from the dependencies. This pull request has the proposed fix.

the lib does not depend on request. maybe your code is?
thus the request module should be part of your package.json rather than the lib's?
~Keyang

Close due to no response


Docs update

Hello there
In the docs, there is the statement:

As of January 2017 the Neugram scripting language itself is an early prototype and not ready for anything more than experimentation. However the embedded shell has enough features to be used as an interactive shell replacement.

We're heading towards end of the year, might be good to give a status update on the stability of the language.
I am very interested in using it, as it fits perfectly my use case, but can't push it inside my team unless I'm more certain of the stability of it.
If there is anything I can help with, please let me know.

@crawshaw is the gatekeeper of the website, so he may have more comments/insights.
if you are looking for issues to whet your appetite, I've filled a few against the jupyter backend (jupyter: ...).
if you are more interested in the interactive shell replacement aspect of ng, I can't say much (I am less interested by that, I must admit.)

I removed that comment because it's quite out of date.
I have one post to write soon for the advent series, I'll do another at the same time for neugram.io with a status update.


Easy opportunity for a better error message about decreases

I'm getting "subtyping check failed: expected _some_internal_id:τ{ unreadable decreases clause }; got τ.
I think the shape of the error message is simple enough that maybe the error printer could match on it and print something along the lines of "could not find a decreasing argument"?

Seems like a great idea.  Otherwise, that error message is a beast to decipher (I was lucky enough to first encounter it while Nik was in the room, but that doesn't seem like a scalable solution).

Other easy opportunity: using * for multiplication when FStar.Mul is not in scope.
Other easy error message fix: name not found, suggest restarting the emacs mode when in interactive mode.

For the decreases clause, I think we can just wrap a custom message (Meta_labeled) around it when we build it, as we do for other things, instead of matching on the output. Doesn't sound too scary to do, so I might attempt it soon.

Cool, this is a definite improvement!  I agree that the second one could still use some cleaning, but having an actual termination error message should be a lot easier for anyone who bumps into it.  Thanks Guido!

Thanks Guido, this is great. This issue has also been reported by Kevin Kane and numerous other people. I think this will make a huge difference.

Closing this issue, The remaining aspect of not shadowing in the error message in case 2 is an instance of a more precise printing of the expected type in an error message, for which we have issue #2034


Merge upstream intel realsense ros2 branch

Not tested yet. Will post an update in the comments when I test this

@charlielito I tested this on local and on a robot and confirmed that the following is working:
LOCAL:

[ ] RGB Image (checked and local console and rviz)
[ ] Pointcloud (checked in rviz)
[ ] depth image (checked in rviz)
[ ] Get coords service (checke in local console)
[ ] Get pixel service (checked in local console with c2c)
[ ] Get version service (checked in cli)

ROBOT

[ ] RGB Image (checked in console)
[ ] Pointcloud (checked in cli)
[ ] depth image (checked in cli)
[ ] Get coords service (checked in console with waypoint, visual measure and c2c)
[ ] Get pixel service (checked inl console with c2c)
[ ] Get version service (checked in cli)
[ ] Imu data (Pitch calibrated successfully and imu data was generated properly)


Windows Terminal still show vertical scroll bar using WindowsDriver.

This is very annoying even after the EnableConsoleScrolling was disabled as deprecated.
https://github.com/gui-cs/Terminal.Gui/assets/13117724/bb9a2143-fbc6-46e1-a6dd-44012c69ee93

Did you know you can turn off the WT vertical scroll bar in settings?

Emitting [3J deletes all data in the back scroll buffer. Other console apps do not do this. Eg. vim, emacs, midnight commander, etc...
Even with your fix, the scrollbar still re-appears when you resize the terminal:

If you really want to have the back buffer cleared we can add this as a configurable option. In v2 it will be easy to add such an option via configurationmanager.
"WindowsDriver.ClearBackBufferOnResize": true,

Did you know you can turn off the WT vertical scroll bar in settings?

Yes I did, but I don't want change it only to run Terminal.Gui. Windows Terminal must respect the app properties. But there is a misleading about 1047 and 1049 escape sequences. Is the 1049 that handles the alternate buffer and not the 1047.
See here the correct https://learn.microsoft.com/en-us/windows/console/console-virtual-terminal-sequences#alternate-screen-buffer, but https://invisible-island.net/xterm/ctlseqs/ctlseqs.html say that is the 1047. I think that has to do with emulator type, don't know. But 1049 does what I need and the Console.Out.Write ("\x1b[3J") isn't needed.

If you really want to have the back buffer cleared we can add this as a configurable option. In v2 it will be easy to add such an option via configurationmanager.

I only want to clear when we start the Terminal.Gui app but after using the Alternate Screen Buffer to save and restore.
I'll try to find a way to these Alternate Screen Buffer is only used on Windows and only used on Windows Terminal.

But here they refer that's the 1049 code. Since WindowsDriver can only executes escape sequences on Windows Terminal I've ensured with this fix, that they are only executed on WT because on others terminals they are only echoed to the terminal which are visible after exit the app.


Is it possible to call a native method or package function directly without involving the UI?

Description
sample code
import { PassioSDK } from '@passiolife/nutritionai-react-native-sdk-v3'
import { device } from 'detox'

describe('Example', () => {
  beforeAll(async () => {
    jest.setTimeout(300000) // Set timeout to 5 minutes for long-running tests
    await device.launchApp({
      permissions: {
        location: 'inuse',
        camera: 'YES',
        notifications: 'YES',
      },
    })
  })

  beforeEach(async () => {
    await device.reloadReactNative()
  })

  it('should tap on button by id and expect some text to be visible', async () => {
    const result = await PassioSDK.searchForFood('apple')
    expect(result).toBe('Hello from Native!') // Check if the returned value is correct
  }, 300000)
})

Your environment
Detox version:  20.27.3
React Native version: 0.74.3
Node version:  20
Device model: IOS 15 Pro
OS:
Test-runner (select one): jest

Someone has to implement this one for the new React Native architecture: https://github.com/wix/Detox/pull/4208
Unfortunately, a couple of people tried and did not succeed for various reasons, so it's still in the embarrassing limbo state. 😕


Webresource content size is too big

Looks like a great project.
Built from source. When running pac pcf push I get the following message:
Error: Import Solution Failed: CustomControl with name ktcs.BasicGridForCanvas failed to import with error: Webresource content size is too big.
Import Solution Failed: CustomControl with name ktcs.BasicGridForCanvas failed to import with error: Webresource content size is too big.

Thank you that worked :)