--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kmd_hmdb_interrogator.py	Tue Aug 29 09:45:16 2023 +0000
@@ -0,0 +1,328 @@
+#!/usr/bin/env python3
+
+import csv
+import operator
+
+import click
+
+import kmd_hmdb_api_client.client
+from kmd_hmdb_api_client.api.default import (
+    api_annotation_get,
+    api_compound_find,
+    api_taxonomy_get,
+)
+
+__version__ = "1.0.0"
+
+
+kmd_hmdb_client = kmd_hmdb_api_client.client.Client(
+    "https://kmd-hmdb-rest-api.metabolomics-chopin.e-metabohub.fr",
+    verify_ssl=False,
+    timeout=500,
+)
+
+find_compound = (
+    lambda *args, **kwargs:
+        api_compound_find.sync(*args, **kwargs, client=kmd_hmdb_client)
+)
+get_taxonomy = (
+    lambda *args, **kwargs:
+        api_taxonomy_get.sync(*args, **kwargs, client=kmd_hmdb_client)
+)
+get_annotation = (
+    lambda *args, **kwargs:
+        api_annotation_get.sync(*args, **kwargs, client=kmd_hmdb_client)
+)
+
+positive_adducts = [
+    "M+H",
+    "M+2H",
+    "M+H+NH4",
+    "M+H+Na",
+    "M+H+K",
+    "M+ACN+2H",
+    "M+2Na",
+    "M+H-2H2O",
+    "M+H-H2O",
+    "M+NH4",
+    "M+Na",
+    "M+CH3OH+H",
+    "M+K",
+    "M+ACN+H",
+    "M+2Na-H",
+    "M+IsoProp+H",
+    "M+ACN+Na",
+    "M+2K+H",
+    "M+DMSO+H",
+    "M+2ACN+H",
+    "2M+H",
+    "2M+NH4",
+    "2M+Na",
+    "2M+K",
+]
+
+negative_adducts = [
+    "M-H",
+    "M-2H",
+    "M-H2O-H",
+    "M+Cl",
+    "M+FA-H",
+    "M+Hac-H",
+    "M-H+HCOONa",
+    "M+Br",
+    "M+TFA-H",
+    "2M-H",
+    "2M+FA-H",
+    "2M+Hac-H",
+]
+
+adduct_choices = positive_adducts + negative_adducts
+
+taxonomy_column_choices = [
+    "class",
+    "kingdom",
+    "molecular_framework",
+    "sub_class",
+    "super_class",
+    "id",
+]
+
+annotation_column_choices = [
+    "adduct",
+    "kendricks_mass",
+    "kendricks_mass_defect",
+    "monisotopic_molecular_weight",
+    "nominal_mass",
+    "polarity",
+    "annotation_id",
+]
+
+compound_column_choices = [
+
+    "database",
+    "metabolite_name",
+    "chemical_formula",
+    "hmdb_id",
+    "inchikey",
+    "compound_id",
+] + annotation_column_choices
+
+
+@click.group()
+def cli():
+    pass
+
+
+@cli.command(help="")
+@click.option(
+    "--version",
+    is_flag=True,
+)
+@click.option(
+    "--mz-ratio",
+    default=[303.05],
+    show_default=True,
+    multiple=True,
+    help="Provide the mz-ratio."
+)
+@click.option(
+    "--database",
+    default=["farid"],
+    show_default=True,
+    multiple=True,
+    help="Provide the database."
+)
+@click.option(
+    "--mass-tolerance",
+    default=10.5,
+    show_default=True,
+    help="Provide the mass-tolerance."
+)
+@click.option(
+    "--adducts",
+    default=["M+H"],
+    type=click.Choice(adduct_choices),
+    multiple=True,
+    show_default=True,
+    show_choices=False,
+    help="Provide the adducts."
+)
+@click.option(
+    "--columns",
+    default=compound_column_choices[:],
+    type=click.Choice(compound_column_choices),
+    multiple=True,
+    show_default=True,
+    show_choices=False,
+    help="Provide the outputed columns."
+)
+@click.option(
+    "--output-path",
+    help="Provide the output path."
+)
+def compound(*args, **kwargs):
+
+    if kwargs.pop("version"):
+        print(__version__)
+        exit(0)
+
+    adducts = kwargs.pop("adducts")
+    polarity = get_polarity(adducts)
+
+    other_kwargs, compound_kwargs = build_kwargs(
+        adducts=adducts,
+        polarity=polarity,
+        **kwargs
+    )
+    columns = other_kwargs["columns"]
+    result = find_compound(**compound_kwargs)
+    result = explode_compounds(
+        result,
+        with_annotations=any(map(
+          columns.__contains__,
+          annotation_column_choices
+        ))
+    )
+    check_columns_in_result(result, columns)
+    output_csv_result(
+        result,
+        columns,
+        other_kwargs.get("output_path"),
+        delimiter="\t",
+    )
+
+
+def explode_compounds(result, with_annotations):
+    if with_annotations:
+        return [{
+            "database": cpd.database,
+            "metabolite_name": cpd.metabolite_name,
+            "chemical_formula": cpd.chemical_formula,
+            "hmdb_id": cpd.hmdb_id,
+            "inchikey": cpd.inchikey,
+            "compound_id": cpd.id,
+            "adduct": annotation.name,
+            "kendricks_mass": annotation.kendricks_mass,
+            "kendricks_mass_defect": annotation.kendricks_mass_defect,
+            "monisotopic_molecular_weight":
+                annotation.monisotopic_molecular_weight,
+            "nominal_mass": annotation.nominal_mass,
+            "polarity": annotation.polarity,
+            "annotation_id": annotation.id,
+            }
+            for cpd in result
+            for annotation in cpd.annotations
+        ]
+    else:
+        return [{
+            "database": cpd.database,
+            "metabolite_name": cpd.metabolite_name,
+            "chemical_formula": cpd.chemical_formula,
+            "hmdb_id": cpd.hmdb_id,
+            "inchikey": cpd.inchikey,
+            "compound_id": cpd.id,
+            }
+            for cpd in result
+        ]
+
+
+@cli.command(help="")
+@click.option(
+    "--id",
+    type=int,
+    help="Provide the wanted annotation's id."
+)
+@click.option(
+    "--columns",
+    default=annotation_column_choices[:],
+    type=click.Choice(annotation_column_choices),
+    multiple=True,
+    show_default=True,
+    show_choices=False,
+    help="Provide the outputed columns."
+)
+@click.option(
+    "--output-path",
+    help="Provide the output path."
+)
+def annotation(*args, **kwargs):
+    result = get_annotation(id=kwargs.pop("id"))
+    result = [result]
+    columns = kwargs["columns"]
+    check_columns_in_result(result, columns)
+    output_csv_result(
+        result,
+        columns,
+        kwargs.get("output_path")
+    )
+
+
+def get_polarity(adducts):
+    if any(map(positive_adducts.__contains__, adducts)):
+        return "positive"
+    if any(map(negative_adducts.__contains__, adducts)):
+        return "negative"
+    # polarity = []
+    # if any(map(positive_adducts.__contains__, adducts)):
+    #     polarity.append("positive")
+    # if any(map(negative_adducts.__contains__, adducts)):
+    #     polarity.append("negative")
+
+
+def build_kwargs(**kwargs):
+    for original, replacement in (
+        ("database", "database_list"),
+        ("polarity", "polarity_list"),
+    ):
+        if original in kwargs:
+            kwargs[replacement] = kwargs.pop(original)
+    other_kwargs = {
+        other_arg: kwargs.pop(other_arg)
+        for other_arg in ("columns", "output_path", "with_annotations")
+        if other_arg in kwargs
+    }
+    return other_kwargs, kwargs
+
+
+def check_columns_in_result(result, columns):
+    if not result:
+        return
+    if not isinstance(result[0], dict):
+        result = [item.to_dict() for item in result]
+    keys = result[0].keys()
+    missing = [
+        column for column in columns
+        if column not in keys
+    ]
+    if missing:
+        if len(missing) == 1:
+            raise ValueError(
+                f"Could not find the column {missing[0]} in the results."
+            )
+        else:
+            raise ValueError(
+                "Could not find any of the columns "
+                + ','.join(missing)
+                + " in the results."
+            )
+
+
+def output_csv_result(result, columns, output_path, **csv_parameters):
+    if not output_path:
+        raise ValueError("Missing output path. Cannot output CSV results.")
+    with open(output_path, mode="w", newline='') as output_file:
+        writer = csv.writer(output_file, **csv_parameters)
+        write_result(result, columns, writer)
+
+
+def write_result(result, columns, writer):
+    getters = list(map(operator.itemgetter, columns))
+    writer.writerow(columns)
+    writer.writerows(
+        (getter(compound) for getter in getters)
+        for compound in result
+    )
+
+
+if __name__ == "__main__":
+    cli()