Feature support: SLO ResponseLocation (3.1)

I need 1 feature in version 3.1 that I don't see implemented, unless I didn't find them.
a) Our IdP uses ResponseLocation in addition to Location for its SingleLogoutService.
I.E. its metadata contains:
<ns0:SingleLogoutService
  Binding="urn:oasis:names:tc:SAML:2.0:bindings:HTTP-Redirect"
  Location="https://<idp url>/idp/saml2/sls"
  ResponseLocation="https://<idp url>/idp/saml2/slr"  # this extra URL
/>

But it seems that using this second URL (optional in the SAML spec) isn't supported in php-saml.
To implement it, it seems that we would need to:

Support the response location URL in lib/Saml2/Settings.php.
Update logic in ib/Saml2/Auth::process_slo in the case of SAMLResponse to use that URL when available or fall back on the current one.
Add Auth:getSLOResponseUrl() which gets the responseUrl from Settings or use getSLOurl() if responseUrl is not defined
Read ResponseLocation from IdP metadata

I will review and let you know.

We use this feature in productive environment since march and it works perfectly. (3.1.1 patches applied). Will this feature merged into branch 3.xx ?

Merged on 3.2.0 branch

I have difficulties to get this working. When logging out on my sp everything is all right, all other sps logout. But when I logout from another sp a get this response:
Destination url validation failed
My config is:
...
'singleLogoutService' => array(
            'url' => '<idp-url>/nidp/saml2/slo'),
            'responseUrl' => '<idp-url>/nidp/saml2/slo_return',
        ),
...

Comparing working saml meta data with generated meta data by onelogin I found one difference:
Debugging with SAML Tracer:
Working meta-data from other sp:
URL: POST /nidp/saml2/slo_return
<saml2p:LogoutResponse xmlns:saml2p="urn:oasis:names:tc:SAML:2.0:protocol"
                       Destination="<idp-url>/nidp/saml2/slo_return"
                       ID="a41h4j863bd8d9f8210ch337j39f882"
                       InResponseTo="idTH5ZaOnipOXlRCpEkONUy_pkUhA"
                       IssueInstant="2020-09-25T09:05:11.814Z"
                       Version="2.0"
                       >

With my SP I get:
URL: GET https://login.hs-osnabrueck.de/nidp/saml2/slo_return
<samlp:LogoutResponse xmlns:samlp="urn:oasis:names:tc:SAML:2.0:protocol"
                      xmlns:saml="urn:oasis:names:tc:SAML:2.0:assertion"
                      ID="ONELOGIN_533bfe89b6fc2608aa01a371a03781233ab8b381"
                      Version="2.0"
                      IssueInstant="2020-09-25T09:07:32Z"
                      Destination="<idp-url>/nidp/saml2/slo"
                      InResponseTo="idiuK7Sc5VhYnuLHNmMYhXYWHM7zU"
                      >

The difference between POST and GET doesn't matter, but the difference in the SAML-Protocol:
Destination="<idp-url>/nidp/saml2/slo_return"
vs
Destination="<idp-url>/nidp/saml2/slo"

The idp is checking this url and throws the error. In testing I tried this configuration:
...
'singleLogoutService' => array(
            'url' => '<idp-url>/nidp/saml2/slo_return'),
            'responseUrl' => '<idp-url>/nidp/saml2/slo_return',
        ),
...

Now logout from other sp is working, but not log out from my sp.
Obviosly the SAML in using the url of 'singleLogoutService' 'url'. It should use url responseURL when logging out from another sp.

The SLO supported in this toolkit uses the binding HTTP-Redirect.
When you define
'singleLogoutService' => array(
            'url' => '<idp-url>/nidp/saml2/slo_return'),
            'responseUrl' => '<idp-url>/nidp/saml2/slo_return',
        ),

The toolkit will send LogoutRequest to '/nidp/saml2/slo_return' and LogoutResponse to  '/nidp/saml2/slo_return' using a GET parameter.
If you modified it to use a POST parameter instead, you may review how you implemented this, maybe the problem is there.
Have you used SAML Tracer to record the SAML flow and verify the flow are the expected?
Do you know what entity raises the "Destination URL validation failed"? It does not seem related to php-saml.

Thanks for your fast reply.

When you define
'singleLogoutService' => array(
            'url' => '<idp-url>/nidp/saml2/slo_return'),
            'responseUrl' => '<idp-url>/nidp/saml2/slo_return',
        ),

The toolkit will send LogoutRequest to '/nidp/saml2/slo_return' and LogoutResponse to '/nidp/saml2/slo_return' using a GET parameter.

Yeah, you're correct. The URLs are working as expected, but the destination in SAML-protocol doesn't change.
Destination="<idp-url>/nidp/saml2/slo_return"
vs
Destination="<idp-url>/nidp/saml2/slo"

I need the request to "slo", the response to "slo_return", and the Destination should correspond to this.

If you modified it to use a POST parameter instead, you may review how you implemented this, maybe the problem is there.
Have you used SAML Tracer to record the SAML flow and verify the flow are the expected?

This is another SP, that I am not responsible for, but where the flow is working. The SAML flow is the same, only difference is destination

Do you know what entity raises the "Destination URL validation failed"? It does not seem related to php-saml.

It is definitly my sp, when I change the settings of to all 4 possibilities I get different behavior as described above.
'url' => '<idp-url>/nidp/saml2/slo'), // or slo_return
'responseUrl' => '<idp-url>/nidp/saml2/slo_return', // or slo


temp change: use dev NodeNormalizer url with improved UMLS support

I tested using this dev instance of Node Normalizer while testing https://github.com/biothings/bte_trapi_query_graph_handler/pull/121#issuecomment-1254346453.
I think this improves UMLS coverage (however I still noticed some IDs where the names / labels hadn't been retrieved). It seems to run fine (no change in speed).
I think we can run automated tests before merging. I dunno about running demotests - except to try stressing it and see if it still works aka labels are still retrieved for nodes).

you can test it manually with UMLS IDs by going here https://nodenormalization-sri.renci.org/1.3/docs#/default/get_normalized_node_handler_get_normalized_nodes_post

Comparison here. Some changes, a couple increases in results, and a couple decreases in results:

B.2c (minimal)
B.2f
D.1 (minimal)
D.2

The two had minimal changes (labeled), while the other two had substantial enough changes to be worth investigating. I doubt these are due to the PR and are likely due to query success/failure differences, but I haven't yet confirmed this.

(EDITING AS I REVIEW)

One diff I see for B.2c is that Automat Biolink instance was changed (looks like dev in the old one, ITRB prod in the newer one)

also I noticed in the demotests: D4 went from no results to some results. interesting

Actually maybe we want to wait? I've noted the following issues:

CHEBI:CHEBI IDs https://github.com/TranslatorSRI/Babel/issues/69
some MONDO and MESH terms getting null responses o_0 https://github.com/TranslatorSRI/Babel/issues/71

Noting an update:

NodeNorm and NameRes at RENCI have both been updated to the Babel 2022dec2 release! You can try them out at:
https://nodenormalization-sri.renci.org/docs
https://name-resolution-sri.renci.org/docs
Please report any bugs you notice at https://github.com/TranslatorSRI/NodeNormalization/issues/ or https://github.com/TranslatorSRI/NameResolution/issues/ respectively. I would usually try to deploy this to ITRB after about a week of testing, but given the holidays, I’ll do that in the second week of January instead.

Closing because we've decide twice now (back in Sept and now in Dec) that we don't want to migrate to their dev NodeNormalizer to "test it out early".


nixos/hardware: add support for qmk keyboards

Description of changes

nixos/hardware: add support for qmk keyboards
nixos/hardware: clean up "with lib;" for keyboards

Things done

Built on platform(s)

[X] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

[ ] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[X] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
23.05 Release Notes (or backporting 22.11 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[X] Fits CONTRIBUTING.md.

Cc @ngiger


cargo install cargo-c fails on Apple M1, Ventura

Problem
cargo install cargo-c fails with error[E0658]: use of unstable library feature 'scoped_threads'
error[E0658]: use of unstable library feature 'scoped_threads'
  --> /Users/decades/.cargo/registry/src/github.com-1ecc6299db9ec823/cargo-0.66.0/src/cargo/core/compiler/job_queue.rs:58:25
   |
58 | use std::thread::{self, Scope};
   |                         ^^^^^
   |
   = note: see issue #93203 <https://github.com/rust-lang/rust/issues/93203> for more information

error[E0658]: use of unstable library feature 'scoped_threads'
   --> /Users/decades/.cargo/registry/src/github.com-1ecc6299db9ec823/cargo-0.66.0/src/cargo/core/compiler/job_queue.rs:559:9
    |
559 |         thread::scope(
    |         ^^^^^^^^^^^^^
    |
    = note: see issue #93203 <https://github.com/rust-lang/rust/issues/93203> for more information

error[E0658]: use of unstable library feature 'scoped_threads'
   --> /Users/decades/.cargo/registry/src/github.com-1ecc6299db9ec823/cargo-0.66.0/src/cargo/core/compiler/job_queue.rs:573:20
    |
573 |         scope: &'s Scope<'s, '_>,
    |                    ^^^^^^^^^^^^^
    |
    = note: see issue #93203 <https://github.com/rust-lang/rust/issues/93203> for more information

error[E0658]: use of unstable library feature 'scoped_threads'
   --> /Users/decades/.cargo/registry/src/github.com-1ecc6299db9ec823/cargo-0.66.0/src/cargo/core/compiler/job_queue.rs:824:20
    |
824 |         scope: &'s Scope<'s, '_>,
    |                    ^^^^^^^^^^^^^
    |
    = note: see issue #93203 <https://github.com/rust-lang/rust/issues/93203> for more information

error[E0658]: use of unstable library feature 'scoped_threads'
    --> /Users/decades/.cargo/registry/src/github.com-1ecc6299db9ec823/cargo-0.66.0/src/cargo/core/compiler/job_queue.rs:1010:83
     |
1010 |     fn run<'s>(&mut self, unit: &Unit, job: Job, cx: &Context<'_, '_>, scope: &'s Scope<'s, '_>) {
     |                                                                                ^^^^^^^^^^^^^
     |
     = note: see issue #93203 <https://github.com/rust-lang/rust/issues/93203> for more information

error[E0107]: this struct takes 1 lifetime argument but 2 lifetime arguments were supplied
   --> /Users/decades/.cargo/registry/src/github.com-1ecc6299db9ec823/cargo-0.66.0/src/cargo/core/compiler/job_queue.rs:573:20
    |
573 |         scope: &'s Scope<'s, '_>,
    |                    ^^^^^     -- help: remove this lifetime argument
    |                    |
    |                    expected 1 lifetime argument
    |
note: struct defined here, with 1 lifetime parameter: `'env`
   --> /Users/decades/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/src/rust/library/std/src/thread/scoped.rs:12:12
    |
12  | pub struct Scope<'env> {
    |            ^^^^^ ----

error[E0107]: this struct takes 1 lifetime argument but 2 lifetime arguments were supplied
   --> /Users/decades/.cargo/registry/src/github.com-1ecc6299db9ec823/cargo-0.66.0/src/cargo/core/compiler/job_queue.rs:824:20
    |
824 |         scope: &'s Scope<'s, '_>,
    |                    ^^^^^     -- help: remove this lifetime argument
    |                    |
    |                    expected 1 lifetime argument
    |
note: struct defined here, with 1 lifetime parameter: `'env`
   --> /Users/decades/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/src/rust/library/std/src/thread/scoped.rs:12:12
    |
12  | pub struct Scope<'env> {
    |            ^^^^^ ----

error[E0107]: this struct takes 1 lifetime argument but 2 lifetime arguments were supplied
    --> /Users/decades/.cargo/registry/src/github.com-1ecc6299db9ec823/cargo-0.66.0/src/cargo/core/compiler/job_queue.rs:1010:83
     |
1010 |     fn run<'s>(&mut self, unit: &Unit, job: Job, cx: &Context<'_, '_>, scope: &'s Scope<'s, '_>) {
     |                                                                                ^^^^^     -- help: remove this lifetime argument
     |                                                                                |
     |                                                                                expected 1 lifetime argument
     |
note: struct defined here, with 1 lifetime parameter: `'env`
    --> /Users/decades/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/src/rust/library/std/src/thread/scoped.rs:12:12
     |
12   | pub struct Scope<'env> {
     |            ^^^^^ ----

Some errors have detailed explanations: E0107, E0658.
For more information about an error, try `rustc --explain E0107`.
error: could not compile `cargo` due to 8 previous errors
warning: build failed, waiting for other jobs to finish...
error: failed to compile `cargo-c v0.9.14+cargo-0.66`, intermediate artifacts can be found at `/var/folders/7l/rc18f0m564qgtmjlzn6b_n5m0000gn/T/cargo-installR0P574`

Caused by:
  build failed

Steps

cargo install cargo-c

Possible Solution(s)
No response
Notes
No response
Version
cargo 1.60.0 (d1fd9fe2c 2022-03-01)
release: 1.60.0
commit-hash: d1fd9fe2c40a1a56af9132b5c92ab963ac7ae422
commit-date: 2022-03-01
host: aarch64-apple-darwin
libgit2: 1.3.0 (sys:0.13.23 vendored)
libcurl: 7.85.0 (sys:0.4.51+curl-7.80.0 system ssl:(SecureTransport) LibreSSL/3.3.6)
os: Mac OS 13.1.0 [64-bit]

Problem gone with latest cargo
cargo 1.65.0 (4bc8f24d3 2022-10-20)

For the future, this is an error compiling a crate, rather than a bug within cargo, and it would best to reach out to the crate author instead of the cargo team.  The reason the upgrade worked is that the crate requires a minimum version of the Rust standard library to work.  Normally, crates define this with the package.rust-version field which would have produced a nice error but this crate isn't defining that field.  Might be worth asking the crate author to add that field.

Right. Sorry for bother


[Feature request] next- and previous error

Currently I find myself scrolling through the file to find where the error occurred, especially if I have edited in multiple places, and the error is not currently in my view.
I think it would be nice to be able to jump to an error quickly.
It does not seem too hard to do since we have the lsp-diagnostics buffer which can just be parsed for the line and column of the error.
I will probably try implementing it myself soon.
Let me know your opinions

It's easy to put a list of jump positions into an option when publishing diagnostics for the buffer. I think using that list would be easier than scanning *diagnostics* buffer. Do you want me to do Rust part, and you'll then implement Kakoune/shell part? (IIRC you are not interested much in Rust, but I may be wrong).

Sure! I'll take a look at it soon.

How about using the lsp_errors option as the jump list?

Should be totally fine if it's convenient enough to parse. Idea with introducing another option was to ease Kakoune/shell side work, but not to introduce extra entity is generally better, of course.

I think it should be easy to parse, since it is basically a list of coordinates including labels for the kind of diagnostic


Cherrypick #867 to release/1.0 branch.

Cherrypick #867
Signed-off-by: Lantao Liu<EMAIL_ADDRESS>

/test pull-cri-containerd-node-e2e


GopherCon India listed under wrong year.

The GopherCon India is listed under the year 2016, Feb, but it rather should have been under the year 2017, Feb.

@arush-sal Hi, not sure I follow. The list has conferences for both the year 2016 and 2017. GopherCon India is listed both in 2016 and 2017.

Yup you are right, my bad :(

@arush-sal No problem! Thanks for reporting though. Appreciate it! :)


Investigate about dashbaord

Do we a need a dashaboard?

How to get started?
What is this app anyway?
How can I solve my problem?

features could be summaries this way


Charts: Show Bluetooth download popup only first time

Description:

Reopened https://github.com/ruuvi/com.ruuvi.station/issues/873 to improve icon
When we get new icon implemented, show popup only first time and hide if was shown.
Reinstalling app popup will be shown again first time.

Closing this issue, handled with https://github.com/ruuvi/com.ruuvi.station/issues/873


Update to new structure for explanation tests

What is the goal of this PR?
We bring the structure of tests for explanations in line with that of graknlabs/grakn and graknlabs/verification.
What are the changes implemented in this PR?

Moves explanation tests to their own module
Within the module, we have one Feature with reasoning and one without
Updates CI to run these two test Features

@jmsfltchr is this PR still valid?

No we don't need this. We do however need to reintroduce these explanation tests into client-java once we have an implementation for them.


Preference setting to hide the icon on the menubar

It would be great to have the option to hide the icon from the menubar.

I agree, this issue has already been brought up in #25.


Automatic Model Compression Example

I tried to run the automatic model compression example provided in https://github.com/microsoft/nni/blob/master/docs/en_US/Compressor/AutoCompression.md.
Some problems:

format error in search_space.json (line 20, line 37)
what is nni.get_parameters () ? (*.py, line 3)
could you pls provide the full example folder ? (with run_prune.sh, ...etc)

@suiguoxin Currently, this doc is only for guidance, we have not provided the complete example code.
Making model compression completely automatic is an ongoing work item, we will release full fledged version of this feature soon.

@QuanluZhang - the issue is assigned to @suiguoxin for complete this example?


I32 incident and vet buttons and forms

Change Summary
Adds buttons and forms for submitting incident reports and vet concerns on the visits page.  Adds a context for the visit page which we can continue to use.  It autofills some user information based on the currentUser from the auth context.
Change Form

[x] The pull request title has an issue number
[x] The change works by "Smoke testing" or quick testing
[ ] The change has tests
[ ] The change has documentation

Have resolved all merging issues


Command Line Tool not working

When pasting in the link it will print score not found.

I can't reproduce the issue:

Can you share what your node and npm versions are?
node --version
v20.14.0 // my version

npm --version
10.4.0 // my version

ya I wish there were working command line switches for input of file, and selecting output file type and location

Closing in favor of https://github.com/LibreScore/dl-librescore/issues/81


Fix consuming null in DemuxingObjectDecoder

Fixes https://github.com/micronaut-projects/micronaut-oracle-cloud/pull/658

i dont understand why this is necessary, let me check

ohh i understand. i will make a tiny change to the naming because i found this code very confusing :)


Fixes #1976 broken integration test

Fixes #1976
The fix for #1877 changed a tag in _AdminNavigationPartial.cshtml on which the integration tests requires.

Fix is now redundant.  #1978 works.


new example: demonstrate basic ASG integration with Lifecycle Hooks

Autoscaling Groups can be setup with one or more Lifecycle hooks, which can then be used to take specific actions as EC2 instances pass through the various states of their "lifecycle". In essence, lifecycle hooks put EC2 instances in a "paused/pending" state before going into service, and before terminating. However, implementing the full picture requires linking together several components, and there are some options for how it's all setup.
The goal of this ticket is to produce an initial example that we can use to explore specific use cases and implementation ideas when in those scenarios. Future tickets can add to this example or create additional variations on the example to cover other use cases.
We're already using user_data for init (though lifecycle hooks could still bring improvements there), so at least right now, we're primarily interested in taking actions before terminating an EC2 instance.
Specifically, we'd like build out coverage for:

de-registering EC2 instances from an ELB or ALB's target group before terminating each instance
when using a cluster management tool (Kubernetes or Nomad, for example), we should use the manager's APIs to mark the instance to terminate as in-eligible for new tasks and should also be drained of currently running tasks.

We are interested in two main ways to run actions on lifecycle events:

a lambda function
some script or tool that runs from an EC2 instances

Interacting with the AWS API is a pretty easy thing to do with lambda, but using tools like kubectl to interact with cluster management APIs is not. Due to our use of cluster management tools, running the tool/script from an EC2 instance is more useful and desirable than running from lambda. However, we would like to demonstrate how to use lambda for running actions on lifecycle events.
Requirements

Must use an existing example which has an ALB and some webapp servers in an ASG.
Could demo how to run a "cleanup action" on a EC2 webapp instance when it is in the terminated lifecycle hook - that is, each instance would run an action on itself when it is terminating.
Should add an EC2 instance that can be used to run actions on lifecycle events (let's call it the "Monitor")
Must give that EC2 instance the permissions it needs (to access resources on AWS) via IAM instance profile
Should a tool/script/agent (lifecycled or some other demo script), on the Monitor, to handle lifecycle events for all the webapp servers. Do something like de-register it from the ALB
If and where it makes sense, should encapsulate lifecycle components in modules (or at least note that as a task for later).
Should leave running actions from lambda as a task for another example, or to include in this example later, unless everything else is complete and there is time available in this issue.

Resources

Here is more info about Lifecycle Hooks from the AWS docs: https://docs.aws.amazon.com/autoscaling/ec2/userguide/lifecycle-hooks.html
Terraform docs: https://www.terraform.io/docs/providers/aws/r/autoscaling_lifecycle_hooks.html

note the overlap between this resource and using the lifecycle parameter in the ASG resource
ASG docs https://www.terraform.io/docs/providers/aws/r/autoscaling_group.html

lifecycled: https://github.com/buildkite/lifecycled
This is a simple but complete example of the general setup: https://github.com/buildkite/lifecycled/blob/master/terraform/modules/example/main.tf
Another blog post describing some aspects of this: https://aws.amazon.com/blogs/compute/how-to-automate-container-instance-draining-in-amazon-ecs/

Sending to @psibi for review.


Swift Compat for setDrawerVisualStateBlock

If you try to set setDrawerVisualStateBlock with MMDrawerVisualState.swingingDoorVisualStateBlock() there's an error:
accessing members of protocol type value MMDrawerControllerDrawerVisualStateBloack is unimplemented
My bridge contains:
#import <MMDrawerController/MMDrawerController.h>
#import <MMDrawerController/MMDrawerVisualState.h>
How can I set this using swift?

@danielgomezrico  did you ever figure this out?

Running into this issue too. Maybe we'll have to edit the source code because I think the meaning of this error is that Swift couldn't yet understand and utilize that syntax.


Remove extlib from opam.export

We depend on both core and extlib in coda right now. Ideally, we should cut our dependency on extlib as we don't use very much from there, and much of the functionality we use is either easy to replicate or exists in other opam packages already. Removing this will help limit our opam dependencies, decrease our binary size, and avoid confusion over two stdlib extensions existing in the same code base (extlib extends some of the same stuff core does).

Now that #15643 is merged, extlib is unused but still in the opam.export file. I'm repurposing this issue to finalise its removal by deleting it from opam.export.


[GHSA-vp35-85q5-9f25] Container build can leak any path on the host into the container

Updates

Affected products

Comments
github.com/moby/moby is not a valid Go package; github.com/docker/docker is still the canonical name.

Hi there @thaJeztah! A community member has suggested an improvement to your security advisory. If approved, this change will affect the global advisory listed at github.com/advisories. It will not affect the version listed in your project repository.
This change will be reviewed by our Security Curation Team. If you have thoughts or feedback, please share them in a comment here! If this PR has already been closed, you can start a new community contribution for this advisory

👋 This pull request has been marked as stale because it has been open with no activity.  If you do nothing this pull request will be closed eventually by the stale bot. Please see CONTRIBUTING.md for more policy details.

I am unable to add the Keep label, but this PR is still "fresh" and I would like to merge it.


Submit VCell <IP_ADDRESS>

id: vcell
version: <IP_ADDRESS>
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/<IP_ADDRESS>/biosimulators.json
specificationsPatch:
version: <IP_ADDRESS>
image:
url: ghcr.io/virtualcell/biosimulators_vcell:<IP_ADDRESS>
digest: "sha256:7a3c3c5a735f6f432801b384f4cf345f1bbf1f2a739ece11e46864b9783ad9a3"
validateImage: true
commitSimulator: true

Thank you @vcdaemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (1.5 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log: None

cli.CliDisplaysHelpInline (1.9 s)

Test that a command-line interface provides inline help.
Warnings:
Command-line interface should support the `-h` option for displaying help inline.

The command-line interface displayed the following when executed with `-h`:

  usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

Command-line interface should support the `--help` option for displaying help inline.

The command-line interface displayed the following when executed with `--help`:

  usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

Log: None

cli.CliDisplaysVersionInformationInline (1.5 s)

Test that a command-line interface provides version information inline.
Warnings:
Command-line interface should support the `-v` option for displaying version information inline.

The command-line interface displayed the following when executed with `-v`:

  usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

Command-line interface should support the `--version` option for displaying version information inline.

The command-line interface displayed the following when executed with `--version`:

  usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

Log: None

docker_image.DeclaresSupportedEnvironmentVariables (0.5 s)

Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log: None

docker_image.HasBioContainersLabels (0.5 s)

Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

Summary of tests

Executed 73 test cases

Passed 33 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
docker_image.SingularityImageExecutesSimulationsSuccessfully
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 40 test cases:

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsComputeModelChanges
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsRepeatedTasksWithChanges
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
sedml.SimulatorSupportsSubstitutingAlgorithms
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

Skips
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log: None

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:
Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:
Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (8.5 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).
Reason for skip:
Simulator did not produce the following reports:
  - `BIOMD0000000912_sim.sedml/report`

Log:
Jan 25, 2022 8:10:06 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_c0486a65-6fb4-4b92-9dc2-f74a4784c3872288963213465506733

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks...

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=#__source__]

Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

DataGenerator [math=org.jmathml.ASTRootNode@4b14918a, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@6d1ef78d, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@1a6c1270, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, name=I, getId()=data_gen_I]

org.jlibsedml.Report@c84c5553

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

[Fatal Error] :1:1: Content is not allowed in prolog.

[Fatal Error] :1:1: Content is not allowed in prolog.

java.lang.RuntimeException: Error importing from SBML : no SBML source.

	at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449)

	at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:704)

	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:74)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:375)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

Generating report `report`.

java.lang.NullPointerException

	at org.vcell.cli.CLIUtils.generateReportsAsCSV(CLIUtils.java:530)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:404)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

HDF conversion successful

 All sedml documents in this archive failed to execute

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (8.5 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1) and inherit the changes of the model.
Reason for skip:
Simulator did not produce the following reports:
  - `BIOMD0000000912_sim.sedml/report`

Log:
Jan 25, 2022 8:10:15 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_af890d83-3e13-42e8-98b1-ae5bd434cc6d1462260742749602979

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks...

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=#__source__]

Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

DataGenerator [math=org.jmathml.ASTRootNode@1a6c1270, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@77d67cf3, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@6dee4f1b, name=I, getId()=data_gen_I]

org.jlibsedml.Report@c84c5553

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

[Fatal Error] :1:1: Content is not allowed in prolog.

[Fatal Error] :1:1: Content is not allowed in prolog.

java.lang.RuntimeException: Error importing from SBML : no SBML source.

	at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449)

	at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:704)

	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:74)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:375)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

Generating report `report`.

java.lang.NullPointerException

	at org.vcell.cli.CLIUtils.generateReportsAsCSV(CLIUtils.java:530)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:404)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

HDF conversion successful

 All sedml documents in this archive failed to execute

sedml.SimulatorProducesLinear3DPlots (0.3 s)

Test that a simulator produces linear 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)

Test that a simulator produces logarithmic 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (13.0 s)

Test that a simulator supports model changes that involve adding, replacing, and removing model elements.
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

Log:
Jan 25, 2022 8:11:49 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_50104c4a-cc36-4042-8b07-bf68e79cb21d6405940713175473940

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks...

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

DataGenerator [math=org.jmathml.ASTRootNode@1a6c1270, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@77d67cf3, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@6dee4f1b, name=I, getId()=data_gen_I]

org.jlibsedml.Report@c84c5553

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp1285576807986867458.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@65f00478

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 104 ms

-----------------------------------------------------------------------------------------------------

Ran 1 simulations for 1 biomodels.

Generating report `report`.

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsComputeModelChanges (14.0 s)

Test that a simulator supports compute model changes
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

Log:
Jan 25, 2022 8:12:15 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_979071ff-152f-455e-a5f1-4c3c7915ee955967921271139591814

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks...

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

DataGenerator [math=org.jmathml.ASTRootNode@1d0d6318, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@4bc28c33, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@4409e975, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@5c153b9e, name=I, getId()=data_gen_I]

org.jlibsedml.Report@c84c5553

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp7930652319396025519.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@178270b2

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 79 ms

-----------------------------------------------------------------------------------------------------

Ran 1 simulations for 1 biomodels.

Generating report `report`.

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataSetsWithDifferentShapes (13.9 s)

Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmplve0a3ti/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 25, 2022 8:12:43 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_792d7510-e992-4b10-bf93-f14c6a4127d78597365522708876509

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks...

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

UniformTimeCourse [initialTime=0.0, numberOfPoints=20, outputEndTime=4.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim__copy_2]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

Task [modelReference=BIOMD0000000912, name=null, simulationReference=BIOMD0000000912_sim__copy_2, getId()=BIOMD0000000912_task__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@3f270e0a, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@1a760689, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@7241a47d, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@70f59913, name=I, getId()=data_gen_I]

DataGenerator [math=org.jmathml.ASTRootNode@77258e59, name=null, getId()=data_gen_time__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@5dcd8c7a, name=null, getId()=data_gen_T__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@2250b9f2, name=null, getId()=data_gen_E__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@7e3181aa, name=null, getId()=data_gen_I__copy_2]

org.jlibsedml.Report@c84c5553

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp438107534949431801.xml

Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@4564e94b

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 100 ms

-----------------------------------------------------------------------------------------------------

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@7af1cd63

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 37 ms

-----------------------------------------------------------------------------------------------------

Ran 2 simulations for 1 biomodels.

Generating report `report`.

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 421, in <module>

    fire.Fire({

  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire

    component, remaining_args = _CallAndUpdateTrace(

  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 155, in exec_plot_output_sed_doc

    data_set_df = pd.read_csv(report_filename, header=None).T

  File "/usr/local/lib/python3.8/dist-packages/pandas/util/_decorators.py", line 311, in wrapper

    return func(*args, **kwargs)

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 680, in read_csv

    return _read(filepath_or_buffer, kwds)

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 581, in _read

    return parser.read(nrows)

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 1250, in read

    index, columns, col_dict = self._engine.read(nrows)

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read

    chunks = self._reader.read_low_memory(nrows)

  File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory

  File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows

  File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows

  File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error

pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24

HDF conversion failed

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsModelAttributeChanges (14.1 s)

Test that a simulator supports changes to the attributes of model elements
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

Log:
Jan 25, 2022 8:12:56 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_936928c8-fd2b-4ed8-8c34-dbe69ee120555041977811790670153

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks...

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

DataGenerator [math=org.jmathml.ASTRootNode@1a6c1270, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@77d67cf3, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@6dee4f1b, name=I, getId()=data_gen_I]

org.jlibsedml.Report@c84c5553

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp6053933036373457159.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@3c017078

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 85 ms

-----------------------------------------------------------------------------------------------------

Ran 1 simulations for 1 biomodels.

Generating report `report`.

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsRepeatedTasksWithChanges (8.1 s)

Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmplve0a3ti/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 25, 2022 8:13:52 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_f5b355e6-a824-462a-b23e-0b864e25da667477991469103224966

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_f5b355e6-a824-462a-b23e-0b864e25da667477991469103224966/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

Jan 25, 2022 8:13:56 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_59df01c3-4a6b-4cff-8643-88aac3c201fd6561735849691706048

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_59df01c3-4a6b-4cff-8643-88aac3c201fd6561735849691706048/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (8.2 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmplve0a3ti/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 25, 2022 8:14:00 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_bf4bf420-c37f-4c44-adea-1b808249f404938540954082887365

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_bf4bf420-c37f-4c44-adea-1b808249f404938540954082887365/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

Jan 25, 2022 8:14:04 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_e2c74e66-689d-4252-8cbb-326486bbd5f68318844268601542340

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_e2c74e66-689d-4252-8cbb-326486bbd5f68318844268601542340/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (4.0 s)

Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmplve0a3ti/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 25, 2022 8:14:08 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_05bf4f58-fe02-4e90-872d-69bb8e24a9307117499975687183847

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_05bf4f58-fe02-4e90-872d-69bb8e24a9307117499975687183847/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (4.0 s)

Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmplve0a3ti/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 25, 2022 8:14:12 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_27724ffe-5a7b-45b0-a708-6effe0c2813c98341883612773688

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_27724ffe-5a7b-45b0-a708-6effe0c2813c98341883612773688/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (4.0 s)

Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmplve0a3ti/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 25, 2022 8:14:16 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_9f6b5bb8-057f-46a6-9cbf-417b6775d4d4316913023193435515

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_9f6b5bb8-057f-46a6-9cbf-417b6775d4d4316913023193435515/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (4.0 s)

Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmplve0a3ti/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 25, 2022 8:14:20 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_56097405-c8ad-46ca-b8af-1755e4d8cdf84622744140244412782

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_56097405-c8ad-46ca-b8af-1755e4d8cdf84622744140244412782/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (4.0 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmplve0a3ti/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 25, 2022 8:14:24 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_415a5316-67a6-4780-9c26-c62eea259e684025672057728151311

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_415a5316-67a6-4780-9c26-c62eea259e684025672057728151311/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (4.0 s)

Test that a simulator supports nested repeated tasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmplve0a3ti/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 25, 2022 8:14:28 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=<IP_ADDRESS>, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_9f3895fa-9a5f-4247-b60f-de9f76e68cb26268312300790668637

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_9f3895fa-9a5f-4247-b60f-de9f76e68cb26268312300790668637/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithSubTas ...

The image for your simulator is valid!

Your submission was committed to the BioSimulators registry. Thank you!
Future submissions of subsequent versions of VCell to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.


hug became slow to import (1.4s) and call (1.6s)

time hug

Error: must define a file name or module that contains a Hug API.
real	0m1.624s
user	0m1.523s
sys	0m0.113s
time hug -f api.py -c ls # api.py only contains an exit, no importing or anything

real	0m1.404s
user	0m1.318s
sys	0m0.099s
 time python3.7 -c "import hug"

real	0m1.477s
user	0m1.371s
sys	0m0.115s

I'm unable to reproduce this. On every system I've tried it's taking <=130 MS to import hug and <=260 MS to run the hug API including the Python interpreter starting overhead. It's important to note that both of your tests do not separate out Python's overhead itself, making it hard to determine if it's simply Python being slow to start. Are you able to provide additional information such as the OS you're running on, what import time within a running Python instance is, and the exact version of hug being ran?
Thanks!
~Timothy

Another example:
time python3.7 -c "import requests"
real	0m0.251s
user	0m0.239s
sys	0m0.017s
Specs:
OS: Arch Linux
Python: 3.7
Hug: 2.3.0
It's strange, but I also do not know what could be the problem... maybe other people have an idea.

I installed 2.3.2 and it did improve:
time hug -f api.py -c ls
real	0m0.600s
user	0m0.550s
sys	0m0.048s

This also happened to me in a prior release:
https://github.com/timothycrosley/hug/issues/184, unfortunately, I don't know how it was resolved, I'll have to investigate further. 600 MS isn't too bad for REST API usage, but even that is less than ideal for CLI applications, where I'd like to see it take no more than 300 MS maximum.
Note that with the latest release on my machine:
(venv) timothy@timothy-XPS-13-9360:~/projects/hug_website2$ time python3 -c "import hug"

real    0m0.271s
user    0m0.252s
sys     0m0.012s

I'll spend some more time later and see if I can pin down areas that could contribute to import slowness and improve them.
Thanks!
~Timothy

In case this helps: I tried installing the latest commit, and it got a disastrous result (maybe that's a clue to something?)...
pip3.7 install git+git://github.com/timothycrosley/hug.git@af2dd05d18b33fc48596b1ca24323ef10a0f9316
time hug
Error: must define a file name or module that contains a Hug API.
real	0m2.456s
user	0m2.291s
sys	0m0.148s
time hug -f api.py -c ls
real	0m3.684s
user	0m3.514s
sys	0m0.167s

Ok, I noticed that uninstalling and reinstalling the old version it was still slow.
Now, 20 minutes later, it is fast again. This was after I had one shell in which I manually changed PATH to contain only the essentials in that session. It was then ~200ms. Now, it is fast everywhere.
I got the idea from the fact you were using a venv. Maybe this adds to the list of clues.


Modify Comments section

Is your feature request related to a problem? Please describe.
Update comments section
Describe the solution you'd like
I want to add real like use of comment as examples:
// Change heading:
document.getElementById("myH").innerHTML = "My First Page";

// Change paragraph:
document.getElementById("myP").innerHTML = "My first paragraph.";

I would like to restructure the markdown in following format
# Comments
## Types of Comments
### Single Line comments
### Multi Line comments
## Real life examples of comments

Assign me this issue . I want to work on it.


[Bug] uncognized option --yes for archlinux

Steps To Reproduce

run leon create birth

The current behavior
On stdout: ```
✖ Installing packages
Error: Failed to install needed packages
For further information, look at the log file located at<EMAIL_ADDRESS>
when looking at error files:

Error: Command failed with exit code 1: sudo --non-interactive<EMAIL_ADDRESS>pacman: unrecognized option '--yes'

## The expected behavior

correct installation

Hello! @kamaradclimber
Thanks for your report!
Indeed it is a bug, actually --yes doesn't exist for the pacman CLI.
In the CLI part, we already support many famous package managers for different GNU/Linux distributions, but unfortunately, on the Core side, it is not the case.
Being able to run Leon on multiple CPU architectures, and distribution, it's definitely something we would like to support, and we would like to solve it before the v1.0.0 stable release (currently Leon is in beta).
We will try to solve this problem later, when the core of Leon is more mature, just before the v1 stable release.
You can read more here: https://github.com/leon-ai/leon/pull/302#pullrequestreview-914081908.
Meanwhile, you can use Leon without problems on Ubuntu, macOS, and Windows, also you can try Leon with a single click thanks to GitPod: https://github.com/leon-ai/leon#-try-with-a-single-click.


Dynamic tab height

Is this how it's supposed to look?

Except for the footer which is not planned in this PR AFAIK, there seems to be a gap at the top. Do you think we should remove it?

Clearly on chrome there is no gap, so I think this is a browser-dependent behavior. I think we should try to support firefox even though it is not 100% functional at the moment.

Yes, the footer is still not removed in firefox. Not sure how to do this cleanly with polling in mind. I think we really need an event-based method for updating the height.

can you ask gpt4 for a firefox version of this?

#tabs:has( > div#tab_comfyui_webui_root[style*="display: block;"]) ~ #footer {
    display: none;
}

Something like this?
window.onload = function() {
    var tabElement = document.querySelector('#tabs > #tab_comfyui_webui_root');
    var footerElement = document.querySelector('#tabs ~ #footer');
    if (window.getComputedStyle(tabElement).display === 'block') {
        footerElement.style.display = 'none';
    }
};

Probably shouldn't do this on load, but this could work.

If it's possible to call this function on tab change it would work. You just need to keep track of the last activation state of the comfyui tab and toggle the display property when the tab display changes.

nvm, I have a very dumb css/js solution that works

LGTM
Please, make sure to consider fixing the top padding for firefox before merging.

LGTM
Please, make sure to consider fixing the top padding for firefox before merging.

I tried it on my side, it looks fine as is. Is it still broken for you?

It does work after testing again. There's a slight lag but it shouldn't be a problem. Looks good.