fixing/instructions for slivka-bio install via conda on aarch64

[foreveremain]

(slivkafoo) jprocter@M-000764 % mamba install -c slivka -c mmwarowny -c bioconda -c conda-forge slivka-bio
slivka/noarch                                        2.6kB @  13.0kB/s  0.2s
slivka/osx-arm64                                    ??.?MB @  ??.?MB/s  0.3s
bioconda/osx-arm64                                 151.1kB @ 103.0kB/s  0.2s
bioconda/noarch                                      4.7MB @   7.5MB/s  0.6s
conda-forge/osx-arm64                               14.5MB @   8.0MB/s  1.8s
conda-forge/noarch                                  19.2MB @   9.6MB/s  2.0s

error    libmamba Could not solve for environment specs
    The following package could not be installed
    └─ slivka-bio =* * is not installable because it requires
       └─ clustalo =1.2.4 *, which does not exist (perhaps a missing channel).
critical libmamba Could not solve for environment specs
(slivkafoo) jprocter@M-000764 % 

Current status of dependencies:

(slivkafoo) jprocter@M-000764 % mamba repoquery depends -c slivka -c mmwarowny -c bioconda -c conda-forge slivka-bio
Getting repodata from channels...

slivka/noarch                                               Using cache
slivka/osx-arm64                                            Using cache
mmwarowny/noarch                                            Using cache
mmwarowny/osx-arm64                                         Using cache
bioconda/noarch                                             Using cache
bioconda/osx-arm64                                          Using cache
conda-forge/noarch                                          Using cache
conda-forge/osx-arm64                                       Using cache
 Name                                 Version  Build                   Channel     Subdir     
───────────────────────────────────────────────────────────────────────────────────────────────
 biopython                            1.85     py310h078409c_0         conda-forge conda-forge
 clustalo 1.2.4.* >>> NOT FOUND <<<                                                           
 clustalw                             2.1      h4675bf2_12             bioconda    bioconda   
 disembl 1.4.* >>> NOT FOUND <<<                                                              
 globplot 2.3.* >>> NOT FOUND <<<                                                             
 gunicorn                             23.0.0   py310hbe9552e_0         conda-forge conda-forge
 mafft 7.458.* >>> NOT FOUND <<<                                                              
 msaprobs 0.9.7.* >>> NOT FOUND <<<                                                           
 muscle                               3.8.1551 h4675bf2_8              bioconda    bioconda   
 probcons                             1.12     h697fd72_3              bioconda    bioconda   
 python                               3.13.2   h81fe080_100_cp313      conda-forge conda-forge
 requests                             2.32.3   pyhd8ed1ab_0            conda-forge conda-forge
 slivka                               0.8.3b3  py_0                    slivka      slivka     
 slivka-bio                           0.8.3b1  0                       slivka      slivka     
 t_coffee 13.41.0.* >>> NOT FOUND <<<                                                         
 viennarna                            2.6.4    py310pl5321h47cb94a_3   bioconda    bioconda  

[jamesabbott]

Most of bioconda is not build for arm64 as yet, so this will be ‘challenging’…I have an x86_64 mamba setup running under rosetta in order to access bio packages on my M1… J From: Jim Procter ***@***.***> Date: Tuesday, 25 February 2025 at 17:20 To: bartongroup/slivka-bio ***@***.***> Cc: Subscribed ***@***.***> Subject: [bartongroup/slivka-bio] slivka-bio does not install on aarch64 due to missing dependencies (Issue #11) CAUTION: This email originated from outside the University of Dundee. Do not click links or open attachments unless you recognise the sender's email address and know the content is safe. (slivkafoo) ***@***.*** % mamba install -c slivka -c mmwarowny -c bioconda -c conda-forge slivka-bio slivka/noarch 2.6kB @ 13.0kB/s 0.2s slivka/osx-arm64 ??.?MB @ ??.?MB/s 0.3s bioconda/osx-arm64 151.1kB @ 103.0kB/s 0.2s bioconda/noarch 4.7MB @ 7.5MB/s 0.6s conda-forge/osx-arm64 14.5MB @ 8.0MB/s 1.8s conda-forge/noarch 19.2MB @ 9.6MB/s 2.0s error libmamba Could not solve for environment specs The following package could not be installed └─ slivka-bio =* * is not installable because it requires └─ clustalo =1.2.4 *, which does not exist (perhaps a missing channel). critical libmamba Could not solve for environment specs (slivkafoo) ***@***.*** % Current status of dependencies: (slivkafoo) ***@***.*** % mamba repoquery depends -c slivka -c mmwarowny -c bioconda -c conda-forge slivka-bio Getting repodata from channels... slivka/noarch Using cache slivka/osx-arm64 Using cache mmwarowny/noarch Using cache mmwarowny/osx-arm64 Using cache bioconda/noarch Using cache bioconda/osx-arm64 Using cache conda-forge/noarch Using cache conda-forge/osx-arm64 Using cache Name Version Build Channel Subdir ─────────────────────────────────────────────────────────────────────────────────────────────── biopython 1.85 py310h078409c_0 conda-forge conda-forge clustalo 1.2.4.* >>> NOT FOUND <<< clustalw 2.1 h4675bf2_12 bioconda bioconda disembl 1.4.* >>> NOT FOUND <<< globplot 2.3.* >>> NOT FOUND <<< gunicorn 23.0.0 py310hbe9552e_0 conda-forge conda-forge mafft 7.458.* >>> NOT FOUND <<< msaprobs 0.9.7.* >>> NOT FOUND <<< muscle 3.8.1551 h4675bf2_8 bioconda bioconda probcons 1.12 h697fd72_3 bioconda bioconda python 3.13.2 h81fe080_100_cp313 conda-forge conda-forge requests 2.32.3 pyhd8ed1ab_0 conda-forge conda-forge slivka 0.8.3b3 py_0 slivka slivka slivka-bio 0.8.3b1 0 slivka slivka t_coffee 13.41.0.* >>> NOT FOUND <<< viennarna 2.6.4 py310pl5321h47cb94a_3 bioconda bioconda — Reply to this email directly, view it on GitHub<#11>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABIRXSIMLK7UEDXEFDCOL632RSQ4NAVCNFSM6AAAAABX3GMYRWVHI2DSMVQWIX3LMV43ASLTON2WKOZSHA3TSMBYGA3TIMQ>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> [Image removed by sender. foreveremain]foreveremain created an issue (bartongroup/slivka-bio#11)<#11> (slivkafoo) ***@***.*** % mamba install -c slivka -c mmwarowny -c bioconda -c conda-forge slivka-bio slivka/noarch 2.6kB @ 13.0kB/s 0.2s slivka/osx-arm64 ??.?MB @ ??.?MB/s 0.3s bioconda/osx-arm64 151.1kB @ 103.0kB/s 0.2s bioconda/noarch 4.7MB @ 7.5MB/s 0.6s conda-forge/osx-arm64 14.5MB @ 8.0MB/s 1.8s conda-forge/noarch 19.2MB @ 9.6MB/s 2.0s error libmamba Could not solve for environment specs The following package could not be installed └─ slivka-bio =* * is not installable because it requires └─ clustalo =1.2.4 *, which does not exist (perhaps a missing channel). critical libmamba Could not solve for environment specs (slivkafoo) ***@***.*** % Current status of dependencies: (slivkafoo) ***@***.*** % mamba repoquery depends -c slivka -c mmwarowny -c bioconda -c conda-forge slivka-bio Getting repodata from channels... slivka/noarch Using cache slivka/osx-arm64 Using cache mmwarowny/noarch Using cache mmwarowny/osx-arm64 Using cache bioconda/noarch Using cache bioconda/osx-arm64 Using cache conda-forge/noarch Using cache conda-forge/osx-arm64 Using cache Name Version Build Channel Subdir ─────────────────────────────────────────────────────────────────────────────────────────────── biopython 1.85 py310h078409c_0 conda-forge conda-forge clustalo 1.2.4.* >>> NOT FOUND <<< clustalw 2.1 h4675bf2_12 bioconda bioconda disembl 1.4.* >>> NOT FOUND <<< globplot 2.3.* >>> NOT FOUND <<< gunicorn 23.0.0 py310hbe9552e_0 conda-forge conda-forge mafft 7.458.* >>> NOT FOUND <<< msaprobs 0.9.7.* >>> NOT FOUND <<< muscle 3.8.1551 h4675bf2_8 bioconda bioconda probcons 1.12 h697fd72_3 bioconda bioconda python 3.13.2 h81fe080_100_cp313 conda-forge conda-forge requests 2.32.3 pyhd8ed1ab_0 conda-forge conda-forge slivka 0.8.3b3 py_0 slivka slivka slivka-bio 0.8.3b1 0 slivka slivka t_coffee 13.41.0.* >>> NOT FOUND <<< viennarna 2.6.4 py310pl5321h47cb94a_3 bioconda bioconda — Reply to this email directly, view it on GitHub<#11>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABIRXSIMLK7UEDXEFDCOL632RSQ4NAVCNFSM6AAAAABX3GMYRWVHI2DSMVQWIX3LMV43ASLTON2WKOZSHA3TSMBYGA3TIMQ>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> The University of Dundee is a registered Scottish Charity, No: SC015096

[foreveremain]

Indeed. However, it fails even with osx-64 rosetta2 channels:

(/Users/jprocter/miniforge3) jprocter@M-000764 % conda create -n slivkaX64 --platform osx-64 python=3.8 
...

(slivkaX64) jprocter@M-000764 % mamba activate slivkaX64
(slivkaX64) jprocter@M-000764 % mamba install --platform osx-64 -c slivka -c mmwarowny -c bioconda -c conda-forge slivka-bio
bioconda/noarch                                             Using cache
conda-forge/noarch                                          Using cache
mmwarowny/osx-64                                    ??.?MB @  ??.?MB/s  0.3s
bioconda/osx-64                                      4.1MB @  10.0MB/s  0.4s
slivka/osx-64                                       ??.?MB @  ??.?MB/s  0.4s
conda-forge/osx-64                                  36.8MB @  16.1MB/s  2.3s

Pinned packages:

  - python=3.8

error    libmamba Could not solve for environment specs
    The following package could not be installed
    └─ slivka-bio =* * is not installable because it requires
       └─ disembl =1.4 *, which does not exist (perhaps a missing channel).
critical libmamba Could not solve for environment specs
(slivkaX64) jprocter@M-000764 % mamba repoquery depends --platform osx-64 -c slivka -c mmwarowny -c bioconda -c conda-forge slivka-bio
Getting repodata from channels...

slivka/noarch                                               Using cache
slivka/osx-64                                               Using cache
mmwarowny/noarch                                            Using cache
mmwarowny/osx-64                                            Using cache
bioconda/noarch                                             Using cache
bioconda/osx-64                                             Using cache
conda-forge/noarch                                          Using cache
conda-forge/osx-64                                          Using cache
 Name                                 Version  Build                   Channel     Subdir     
───────────────────────────────────────────────────────────────────────────────────────────────
 biopython                            1.85     py310hbb8c376_0         conda-forge conda-forge
 clustalo                             1.2.4    0                       bioconda    bioconda   
 clustalw                             2.1      0                       bioconda    bioconda   
 disembl 1.4.* >>> NOT FOUND <<<                                                              
 globplot 2.3.* >>> NOT FOUND <<<                                                             
 gunicorn                             23.0.0   py310h2ec42d9_0         conda-forge conda-forge
 mafft                                7.458    h01d97ff_0              bioconda    bioconda   
 msaprobs                             0.9.7    h0100bc9_3              bioconda    bioconda   
 muscle                               3.8.1551 1                       bioconda    bioconda   
 probcons                             1.12     h1f6ca2e_3              bioconda    bioconda   
 python                               3.13.2   h2267d90_0_cp313t       conda-forge conda-forge
 requests                             2.32.3   pyhd8ed1ab_0            conda-forge conda-forge
 slivka                               0.8.3b3  py_0                    slivka      slivka     
 slivka-bio                           0.8.3b1  0                       slivka      slivka     
 t_coffee 13.41.0.* >>> NOT FOUND <<<                                                         
 viennarna                            2.6.4    py310pl5321h050e90c_3   bioconda    bioconda   
(slivkaX64) jprocter@M-000764 % 

[warownia1]

Both slivka and slivka-bio are noarch packages. If bioconda doesn't support M1 then there is not much I can do other than removing all the dependencies from slivka-bio recipe which defeats the purpose of packaging it with conda.

I'm working on a slivka-bio-installer that will replace slivka-bio package in the near future.

[foreveremain]

Could we get an issue/roadmap for the installer somewhere please @warownia1 ? I still think one of the ways to go was to have a tool specific subpackage like what is done with debian and other systems, where packages can suggest a bunch of other packages, but don't have hard dependency on them. Each tool has a tool-slivka package which has the hard dependency. For instance, slivka-bio suggests slivka-bio-tcoffee, and there's an incantation that installs all suggested packages, but if one of those fails, slivka bio is still functional.

[foreveremain]

@warownia1 noted that the slivka-bio conda invocation in the docs is stale (latest is in the README.md: https://github.com/bartongroup/slivka-bio/blob/v0.8.3/README.md). I managed to get a conda install of slivka bio on osx-aarch64 with all tools using the following:

mamba config set channel_priority flexible
mamba install --platform osx-64 -c slivka -c bartongroup -c bioconda -c conda-forge slivka-bio

The flexible priority seems to be needed to avoid a pathological conflict due to pinned versions: found the solution via conda/conda#13390

[foreveremain]

OK. Next problem seems to be that "slivka-bio init " throws errors:

(slivkaOsx64) jprocter@M-000764 slivka-bio-from-conda-2025-03-03 % slivka-bio init my-slivka-bio                              
Creating project directory.
Copying files.
Traceback (most recent call last):
  File "/Users/jprocter/uod-development/miniforge3/envs/slivkaOsx64/lib/python3.9/importlib/resources.py", line 97, in open_binary
    return open(full_path, mode='rb')
FileNotFoundError: [Errno 2] No such file or directory: '/Users/jprocter/uod-development/slivka-projects/slivka-bio-from-conda-2025-03-03/settings.yaml'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/jprocter/uod-development/miniforge3/envs/slivkaOsx64/bin/slivka-bio", line 21, in <module>
    slivka.cli.main()
  File "/Users/jprocter/uod-development/miniforge3/envs/slivkaOsx64/lib/python3.9/site-packages/click/core.py", line 1161, in __call__
    return self.main(*args, **kwargs)
  File "/Users/jprocter/uod-development/miniforge3/envs/slivkaOsx64/lib/python3.9/site-packages/click/core.py", line 1082, in main
    rv = self.invoke(ctx)
  File "/Users/jprocter/uod-development/miniforge3/envs/slivkaOsx64/lib/python3.9/site-packages/click/core.py", line 1697, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/jprocter/uod-development/miniforge3/envs/slivkaOsx64/lib/python3.9/site-packages/click/core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/jprocter/uod-development/miniforge3/envs/slivkaOsx64/lib/python3.9/site-packages/click/core.py", line 788, in invoke
    return __callback(*args, **kwargs)
  File "/Users/jprocter/uod-development/miniforge3/envs/slivkaOsx64/lib/python3.9/site-packages/slivka/cli.py", line 37, in init
    init_project(path)
  File "/Users/jprocter/uod-development/miniforge3/envs/slivkaOsx64/lib/python3.9/site-packages/slivka/cli.py", line 59, in init_project
    copy_project_file("settings.yaml", "config.yaml")
  File "/Users/jprocter/uod-development/miniforge3/envs/slivkaOsx64/lib/python3.9/site-packages/slivka/cli.py", line 50, in copy_project_file
    stream = resources.open_binary(
  File "/Users/jprocter/uod-development/miniforge3/envs/slivkaOsx64/lib/python3.9/site-packages/slivka/compat/resources.py", line 21, in open_binary
    return importlib.resources.open_binary(*_shift_path(package, resource))
  File "/Users/jprocter/uod-development/miniforge3/envs/slivkaOsx64/lib/python3.9/importlib/resources.py", line 111, in open_binary
    raise FileNotFoundError(message)
FileNotFoundError: 'settings.yaml' resource not found in 'slivka.project_template'
(slivkaOsx64) jprocter@M-000764 slivka-bio-from-conda-2025-03-03 % 

All that gets written to the directory is a 'manage.py' script.
I get a bit further if I run it again, it adds an empty config.yaml file, but again, looks like we're missing a template file.

This could be covered by a continuous integration test perhaps ?

[foreveremain]

Manually installed mongodb via conda (brew fails due to lack of codsigning signature). Created a minimal mongodb config and slivka-bio config. Everything starts up with python=3.8 (had to downgrade the above), but whilst jobs run, there's an uncaught exception TypeError: Object of type PosixPath is not JSON serializable that causes a 500 response on the api . Looks like we need some judicious 'str(..)' patches (see e.g. https://git.embl.de/grp-itservices/dma-python-client/-/commit/407e0cdfebec9b71cfa285ba32d92a2c329da70b). Stacktrace is below...

127.0.0.1 - - [03/Mar/2025 17:52:25] "POST /api/services/aacon/jobs HTTP/1.1" 500 -
Error on request:
Traceback (most recent call last):
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/werkzeug/serving.py", line 333, in run_wsgi
    execute(self.server.app)
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/werkzeug/serving.py", line 320, in execute
    application_iter = app(environ, start_response)
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 2552, in __call__
    return self.wsgi_app(environ, start_response)
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 2532, in wsgi_app
    response = self.handle_exception(e)
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 2529, in wsgi_app
    response = self.full_dispatch_request()
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 1825, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 1823, in full_dispatch_request
    rv = self.dispatch_request()
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 1799, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/slivka/server/api_views.py", line 109, in service_jobs_view
    response = jsonify(content)
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/json/__init__.py", line 342, in jsonify
    return current_app.json.response(*args, **kwargs)
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/json/provider.py", line 309, in response
    f"{self.dumps(obj, **dump_args)}\n", mimetype=mimetype
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/json/provider.py", line 230, in dumps
    return json.dumps(obj, **kwargs)
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/__init__.py", line 234, in dumps
    return cls(
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/encoder.py", line 201, in encode
    chunks = list(chunks)
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/encoder.py", line 431, in _iterencode
    yield from _iterencode_dict(o, _current_indent_level)
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/encoder.py", line 405, in _iterencode_dict
    yield from chunks
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/encoder.py", line 405, in _iterencode_dict
    yield from chunks
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/encoder.py", line 438, in _iterencode
    o = _default(o)
  File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/json/provider.py", line 122, in _default
    raise TypeError(f"Object of type {type(o).__name__} is not JSON serializable")
TypeError: Object of type PosixPath is not JSON serializable

I'm almost certain this is some yuck arising from the rosetta2-ified python, since I've never seen this in other situations. Offending line is: https://github.com/bartongroup/slivka/blob/48002b0f27486a59322bcb3e503dcc10ce06fa2f/slivka/server/api_views.py#L110
For the record we're also getting a deprecation warning:

/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/slivka/server/forms/form.py:179: DeprecationWarning: Function insert is deprecated
  request.insert(database)

[warownia1]

My guess is that slivka-bio init doesn't work because they introduced some incompatible changes to importlib module. Also, if I remember correctly, you are not supposed to run slivka-bio init. The purpose of slivka-bio conda package is that is comes with already existing slivka project built into the package. It was never meant to be an editable instance, but a quick and easy way to get started. If you want to create projects, then use slivka init.

…

On Mon, Mar 3, 2025, 19:04 Jim Procter ***@***.***> wrote: Manually installed mongodb via conda (brew fails due to lack of codsigning signature). Created a minimal mongodb config and slivka-bio config. Everything starts up with python=3.8 (had to downgrade the above), but whilst jobs run, there's an uncaught exception that causes a 500 response on the api . Looks like we need some judicious 'str(..)' patches (see e.g. https://git.embl.de/grp-itservices/dma-python-client/-/commit/407e0cdfebec9b71cfa285ba32d92a2c329da70b). Stacktrace is below... ''' 127.0.0.1 - - [03/Mar/2025 17:52:25] "POST /api/services/aacon/jobs HTTP/1.1" 500 - Error on request: Traceback (most recent call last): File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/werkzeug/serving.py", line 333, in run_wsgi execute(self.server.app) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/werkzeug/serving.py", line 320, in execute application_iter = app(environ, start_response) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 2552, in *call* return self.wsgi_app(environ, start_response) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 2532, in wsgi_app response = self.handle_exception(e) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 2529, in wsgi_app response = self.full_dispatch_request() File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 1825, in full_dispatch_request rv = self.handle_user_exception(e) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 1823, in full_dispatch_request rv = self.dispatch_request() File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 1799, in dispatch_request return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/slivka/server/api_views.py", line 109, in service_jobs_view response = jsonify(content) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/json/ *init*.py", line 342, in jsonify return current_app.json.response(*args, **kwargs) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/json/provider.py", line 309, in response f"{self.dumps(obj, **dump_args)}\n", mimetype=mimetype File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/json/provider.py", line 230, in dumps return json.dumps(obj, **kwargs) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/*init*.py", line 234, in dumps return cls( File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/encoder.py", line 201, in encode chunks = list(chunks) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/encoder.py", line 431, in _iterencode yield from _iterencode_dict(o, _current_indent_level) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/encoder.py", line 405, in _iterencode_dict yield from chunks File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/encoder.py", line 405, in _iterencode_dict yield from chunks File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/encoder.py", line 438, in _iterencode o = _default(o) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/json/provider.py", line 122, in _default raise TypeError(f"Object of type {type(o).*name*} is not JSON serializable") TypeError: Object of type PosixPath is not JSON serializable /Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/slivka/server/forms/form.py:179: DeprecationWarning: Function insert is deprecated request.insert(database) ''' — Reply to this email directly, view it on GitHub <#11 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADAMLDV4EFI6QTPIJP6MKV32SSKT7AVCNFSM6AAAAABX3GMYRWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMOJVGE3TIMJXGQ> . You are receiving this because you were mentioned.Message ID: ***@***.***> [image: foreveremain]*foreveremain* left a comment (bartongroup/slivka-bio#11) <#11 (comment)> Manually installed mongodb via conda (brew fails due to lack of codsigning signature). Created a minimal mongodb config and slivka-bio config. Everything starts up with python=3.8 (had to downgrade the above), but whilst jobs run, there's an uncaught exception that causes a 500 response on the api . Looks like we need some judicious 'str(..)' patches (see e.g. https://git.embl.de/grp-itservices/dma-python-client/-/commit/407e0cdfebec9b71cfa285ba32d92a2c329da70b). Stacktrace is below... ''' 127.0.0.1 - - [03/Mar/2025 17:52:25] "POST /api/services/aacon/jobs HTTP/1.1" 500 - Error on request: Traceback (most recent call last): File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/werkzeug/serving.py", line 333, in run_wsgi execute(self.server.app) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/werkzeug/serving.py", line 320, in execute application_iter = app(environ, start_response) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 2552, in *call* return self.wsgi_app(environ, start_response) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 2532, in wsgi_app response = self.handle_exception(e) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 2529, in wsgi_app response = self.full_dispatch_request() File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 1825, in full_dispatch_request rv = self.handle_user_exception(e) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 1823, in full_dispatch_request rv = self.dispatch_request() File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/app.py", line 1799, in dispatch_request return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/slivka/server/api_views.py", line 109, in service_jobs_view response = jsonify(content) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/json/ *init*.py", line 342, in jsonify return current_app.json.response(*args, **kwargs) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/json/provider.py", line 309, in response f"{self.dumps(obj, **dump_args)}\n", mimetype=mimetype File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/json/provider.py", line 230, in dumps return json.dumps(obj, **kwargs) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/*init*.py", line 234, in dumps return cls( File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/encoder.py", line 201, in encode chunks = list(chunks) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/encoder.py", line 431, in _iterencode yield from _iterencode_dict(o, _current_indent_level) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/encoder.py", line 405, in _iterencode_dict yield from chunks File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/encoder.py", line 405, in _iterencode_dict yield from chunks File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/json/encoder.py", line 438, in _iterencode o = _default(o) File "/Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/flask/json/provider.py", line 122, in _default raise TypeError(f"Object of type {type(o).*name*} is not JSON serializable") TypeError: Object of type PosixPath is not JSON serializable /Users/jprocter/miniforge3/envs/slivkaX64/lib/python3.8/site-packages/slivka/server/forms/form.py:179: DeprecationWarning: Function insert is deprecated request.insert(database) ''' — Reply to this email directly, view it on GitHub <#11 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADAMLDV4EFI6QTPIJP6MKV32SSKT7AVCNFSM6AAAAABX3GMYRWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMOJVGE3TIMJXGQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>