Artifact inputs must come before parameters in callable signature

Developer Discussion
1

I’m in the process of embedding a qiime2 plugin within my software package. The corresponding PR can be found here

One of the things that I’m currently hung up on at the moment is the function signature.

I’m declaring one of my functions as follows

from gneiss.plugin_setup import plugin
from qiime2.plugin import SemanticType
from ._model import Regression_g
from q2_types.feature_table import FeatureTable
from q2_composition.plugin_setup import Composition
from q2_types.tree import Phylogeny
from qiime2.plugin import Str, Metadata

LinearMixedEffects_g = SemanticType('LinearMixedEffects_g',
                                    variant_of=Regression_g.field['type'])

plugin.methods.register_function(
    function=mixedlm,
    inputs={'table': FeatureTable[Composition],
            'tree': Phylogeny,
            'metadata': Metadata},
    parameters={'formula' : Str},
    outputs=[('linear_mixed_effects_model', Regression_g[LinearMixedEffects_g])],
    name='Simplicial Linear mixed effects models',
    description="Perform linear mixed effects model on balances."
)

And whenever I run qiime dev refresh-cache, I get the following error message

Traceback (most recent call last):
  File "/Users/mortonjt/miniconda3/envs/gneiss/bin/qiime", line 11, in <module>
    load_entry_point('q2cli==2017.3.0.dev0', 'console_scripts', 'qiime')()
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/q2cli/dev.py", line 27, in refresh_cache
    import q2cli.cache
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/q2cli/cache.py", line 299, in <module>
    CACHE = DeploymentCache()
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/q2cli/cache.py", line 107, in _get_cached_state
    self._cache_current_state(current_requirements)
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/q2cli/cache.py", line 196, in _cache_current_state
    state = self._get_current_state()
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/q2cli/cache.py", line 234, in _get_current_state
    plugin_manager = qiime2.sdk.PluginManager()
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 32, in __new__
    self._init()
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 46, in _init
    plugin = entry_point.load()
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2302, in load
    return self.resolve()
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2308, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/Users/mortonjt/Dropbox/UCSD/research/gneiss/gneiss/plugin_setup.py", line 23, in <module>
    importlib.import_module('gneiss.regression')
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/Users/mortonjt/Dropbox/UCSD/research/gneiss/gneiss/regression/__init__.py", line 36, in <module>
    from ._ols import ols, OLSModel
  File "/Users/mortonjt/Dropbox/UCSD/research/gneiss/gneiss/regression/_ols.py", line 14, in <module>
    from ._regression import (_intersect_of_table_metadata_tree,
  File "/Users/mortonjt/Dropbox/UCSD/research/gneiss/gneiss/regression/_regression.py", line 93, in <module>
    from ._mixedlm import LinearMixedEffects_g
  File "/Users/mortonjt/Dropbox/UCSD/research/gneiss/gneiss/regression/_mixedlm.py", line 291, in <module>
    description="Perform linear mixed effects model on balances."
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/qiime2/plugin/plugin.py", line 209, in register_function
    output_descriptions)
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/qiime2/sdk/action.py", line 287, in _init
    output_descriptions)
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/qiime2/core/type/signature.py", line 97, in __init__
    parameter_descriptions, output_descriptions)
  File "/Users/mortonjt/miniconda3/envs/gneiss/lib/python3.5/site-packages/qiime2/core/type/signature.py", line 161, in _parse_signature
    raise TypeError("Artifact inputs must come before"
TypeError: Artifact inputs must come before parameters in callable signature.

If I’m understanding correctly, Phylogenies and Tables are both Artifacts. Is Metadata also considered an artifact? And what does this error message mean?

2

This error is usually associated with the actual function’s signature-line, but I suspect it is actually because you are defining Metadata as in input. We consider metadata to be a parameter in QIIME 2, so that is likely what is happening.

3

Ok. Just to clarify, does Metadata refer to an entire metadata table (i.e. a pd.Dataframe with all of the metadata information such as body_site, ph, …), or is it a single metadata column?

Also, I’ve tried to move Metadata to the parameters section, and I’m getting the exact same error :confused:

4

Metadata is the entire thing, MetadataCategory would be a single column.

Then that means it is the function signature itself which is out of order, not necessarily the registration (although the metadata does need to be in the parameters section).

5

Looks like the reordering the parameters fixed it. Thanks!