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C14 schema #1182

Merged
merged 16 commits into from
Jan 24, 2025
Merged

C14 schema #1182

merged 16 commits into from
Jan 24, 2025

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jfy133
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@jfy133 jfy133 commented Jul 23, 2024

This is a PoC for for adding a C14 schema

@jfy133 jfy133 added the WIP label Jul 23, 2024
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jfy133 commented Jul 23, 2024

@maxibor @aidaanva @DianaSpurite

This is the schema draft I made, the issue that applies to all currently (which is a different issue that I had before) is:

## Ancient Metagenome Environmental
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.9.19/x64/bin/AMDirT", line 5, in <module>
    from AMDirT.cli import cli
  File "/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/AMDirT/cli.py", line 319, in <module>
    type=click.Choice(get_amdir_tags()),
    return cached_func(*args, **kwargs)
    return self._get_or_create_cached_value(args, kwargs)
    return self._handle_cache_miss(cache, value_key, func_args, func_kwargs)
    computed_value = self._info.func(*func_args, **func_kwargs)
  File "/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/AMDirT/core/__init__.py", line 63, in get_amdir_tags
    return [
  File "/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/AMDirT/core/__init__.py", line 66, in <listcomp>
    if version.parse(tag["name"]) >= version.parse("v22.09")
  File "/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/packaging/version.py", line 56, in parse
    return Version(version)
  File "/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/packaging/version.py", line 202, in __init__
    raise InvalidVersion(f"Invalid version: '{version}'")
packaging.version.InvalidVersion: Invalid version: 'latest'
# Radiocarbon Dates
## Ancient Single Genome Host Associated
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.9.19/x64/bin/AMDirT", line 5, in <module>
    from AMDirT.cli import cli
  File "/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/AMDirT/cli.py", line 319, in <module>
    type=click.Choice(get_amdir_tags()),
    return cached_func(*args, **kwargs)
    return self._get_or_create_cached_value(args, kwargs)
    return self._handle_cache_miss(cache, value_key, func_args, func_kwargs)
    computed_value = self._info.func(*func_args, **func_kwargs)
  File "/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/AMDirT/core/__init__.py", line 63, in get_amdir_tags
    return [
  File "/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/AMDirT/core/__init__.py", line 66, in <listcomp>
    if version.parse(tag["name"]) >= version.parse("v22.09")
  File "/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/packaging/version.py", line 56, in parse
    return Version(version)
  File "/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/packaging/version.py", line 202, in __init__
    raise InvalidVersion(f"Invalid version: '{version}'")
packaging.version.InvalidVersion: Invalid version: 'latest'

@jfy133 jfy133 force-pushed the master branch 3 times, most recently from 49ac494 to 62f90dc Compare October 5, 2024 04:40
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jfy133 commented Dec 6, 2024

I just had a thought: we should replace the schema here so the columns align with the minas c14 extension (@aidaanva)

@jfy133 jfy133 changed the base branch from master to c14-extension January 24, 2025 07:20
@jfy133 jfy133 marked this pull request as ready for review January 24, 2025 07:21
@jfy133 jfy133 merged commit 91278f0 into SPAAM-community:c14-extension Jan 24, 2025
@jfy133 jfy133 deleted the c14-schema branch January 24, 2025 07:21
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