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Added max_phase as an option #13

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Merged
cthoyt merged 8 commits into from
Jan 30, 2024
Merged

Added max_phase as an option #13

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9504457
Added max_phase as an option
jhylin Jan 29, 2024
a0fca2f
Changed max_phase to boolean
jhylin Jan 29, 2024
72cd48a
Minor refactor
cthoyt Jan 29, 2024
51120b5
Removed f-string + rearranged in if/else and moved max_phase sql up
jhylin Jan 30, 2024
848a4bf
Removed files
jhylin Jan 30, 2024
9513d43
Tested mp
jhylin Jan 30, 2024
b35046d
Update tests
cthoyt Jan 30, 2024
98de12c
Reduce files
cthoyt Jan 30, 2024
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5 changes: 4 additions & 1 deletion src/chembl_downloader/queries.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,6 +96,7 @@ def get_target_sql(
standard_relation: Optional[str] = None,
standard_type: Optional[str] = None,
tax_id: Optional[str] = None,
max_phase: bool = False,
) -> str:
"""Get the SQL for all chemicals inhibiting the target."""
ar = (
Expand All @@ -106,6 +107,7 @@ def get_target_sql(
st = "" if standard_relation is None else f"AND ACTIVITIES.standard_type = '{standard_type}'"
tt = "" if target_type is None else f"AND TARGET_DICTIONARY.target_type = '{target_type}'"
tax = "" if tax_id is None else f"AND TARGET_DICTIONARY.tax_id = '{tax_id}'"
mp = "" if max_phase is False else f"MOLECULE_DICTIONARY.max_phase"
return dedent(
f"""\
SELECT
Expand All @@ -115,7 +117,8 @@ def get_target_sql(
COMPOUND_STRUCTURES.canonical_smiles,
MOLECULE_DICTIONARY.chembl_id AS molecule_chembl_id,
ACTIVITIES.standard_type,
ACTIVITIES.pchembl_value
ACTIVITIES.pchembl_value,
{mp}
FROM TARGET_DICTIONARY
JOIN ASSAYS ON TARGET_DICTIONARY.tid == ASSAYS.tid
JOIN ACTIVITIES ON ASSAYS.assay_id == ACTIVITIES.assay_id
Expand Down