Generate a list of the names of all metadata parameters in a rachis deployment.

list-metadata-parameter-names.ipynb

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      "/opt/homebrew/Caskroom/miniforge/base/envs/q2dev-amplicon-2025-11-17/lib/python3.10/site-packages/unifrac/__init__.py:9: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n",
      "  import pkg_resources\n"
     ]
    }
   ],
   "source": [
    "import qiime2.sdk\n",
    "from qiime2.plugin import Metadata\n",
    "pm = qiime2.sdk.PluginManager()"
   ]
  },
  {
   "cell_type": "code",
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   "id": "17981030",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "boots core_metrics: metadata\n",
      "boots kmer_diversity: metadata\n",
      "emperor plot: metadata\n",
      "emperor procrustes_plot: metadata\n",
      "**: emperor biplot: sample_metadata\n",
      "**: emperor biplot: feature_metadata\n",
      "vizard heatmap: metadata\n",
      "vizard scatterplot_2d: metadata\n",
      "vizard lineplot: metadata\n",
      "vizard boxplot: metadata\n",
      "**: rescript get_ncbi_data: accession_ids\n",
      "**: rescript get_ncbi_data_protein: accession_ids\n",
      "**: rescript filter_taxa: ids_to_keep\n",
      "kmerizer core_metrics: metadata\n",
      "phylogeny filter_tree: metadata\n",
      "feature-table filter_samples: metadata\n",
      "feature-table filter_features: metadata\n",
      "feature-table filter_seqs: metadata\n",
      "**: feature-table summarize: sample_metadata\n",
      "feature-table tabulate_seqs: metadata\n",
      "feature-table summarize_plus: metadata\n",
      "sample-classifier metatable: metadata\n",
      "diversity filter_distance_matrix: metadata\n",
      "diversity filter_alpha_diversity: metadata\n",
      "diversity alpha_group_significance: metadata\n",
      "diversity bioenv: metadata\n",
      "diversity alpha_correlation: metadata\n",
      "diversity alpha_rarefaction: metadata\n",
      "diversity beta_rarefaction: metadata\n",
      "diversity adonis: metadata\n",
      "diversity core_metrics_phylogenetic: metadata\n",
      "diversity core_metrics: metadata\n",
      "quality-control decontam_identify: metadata\n",
      "quality-control decontam_identify_batches: metadata\n",
      "longitudinal nmit: metadata\n",
      "longitudinal first_differences: metadata\n",
      "longitudinal first_distances: metadata\n",
      "longitudinal pairwise_differences: metadata\n",
      "longitudinal pairwise_distances: metadata\n",
      "longitudinal linear_mixed_effects: metadata\n",
      "longitudinal anova: metadata\n",
      "longitudinal volatility: metadata\n",
      "longitudinal plot_feature_volatility: metadata\n",
      "longitudinal feature_volatility: metadata\n",
      "longitudinal maturity_index: metadata\n",
      "demux filter_samples: metadata\n",
      "**: metadata merge: metadata1\n",
      "**: metadata merge: metadata2\n",
      "**: metadata tabulate: input\n",
      "taxa barplot: metadata\n",
      "taxa barplot2: metadata\n",
      "stats prep_alpha_distribution: metadata\n",
      "stats alpha_group_significance: metadata\n",
      "composition ancombc: metadata\n",
      "composition ancombc2: metadata\n",
      "**: composition da_barplot: feature_ids\n"
     ]
    }
   ],
   "source": [
    "preferred_metadata_names = set(['metadata'])\n",
    "\n",
    "for plugin_name, plugin in pm.plugins.items():\n",
    "    for action_name, action in plugin.actions.items():\n",
    "        for param_name, param in action.signature.parameters.items():\n",
    "            if param.qiime_type == Metadata:\n",
    "                if param_name not in preferred_metadata_names:\n",
    "                    print('**', end=': ')\n",
    "                print(f'{plugin_name} {action_name}: {param_name}')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "25ffe996",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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