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revert config_web
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DylanWelzel authored Jul 12, 2024
1 parent a546c17 commit fef77ae
Showing 1 changed file with 6 additions and 344 deletions.
350 changes: 6 additions & 344 deletions src/config_web.py
Original file line number Diff line number Diff line change
Expand Up @@ -14,348 +14,16 @@
# *****************************************************************************
ES_HOST = 'http://localhost:9200'
ES_INDICES = {
"chem": "index_test_20240612_3kwpduyw",
"drug": "index_test_20240612_3kwpduyw",
"compound": "index_test_20240612_3kwpduyw",
"chem": "mychem_current",
"drug": "mychem_current",
"compound": "mychem_current",
}
ES_SCROLL_TIME = "10m"

# *****************************************************************************
# Endpoint Specifics
# *****************************************************************************
# aoelus

# Essential fields
DEFAULT_FIELDS = [
"aeolus.unii",
"aeolus.drug_id",
"aeolus.rxcui",
"aeolus.drug_name",
"aeolus.no_of_outcomes",
"aeolus.outcomes.name",
"aeolus.outcomes.ror",
"aeolus.outcomes.case_count",

"chebi.id",
"chebi.name",
"chebi.definition",
"chebi.relationship.has_role",
"chebi.relationship.is_enantiomer_of",
"chebi.formulae",
"chebi.monoisotopic_mass",
"chebi.iupac",
"chebi.synonyms",
"chebi.pubchem_database_links.sid",
"chebi.pubchem_database_links.cid",
"chebi.last_modified",
"chebi.xrefs",

"chembl.pref_name",
"chembl.molecule_chembl_id",
"chembl.molecule_properties.full_molformula",
"chembl.molecule_properties.full_mwt",
"chembl.molecule_properties.mw_monoisotopic",
"chembl.molecule_properties.alogp",
"chembl.molecule_properties.cx_logd",
"chembl.molecule_properties.cx_logp",
"chembl.molecule_properties.cx_most_apka",
"chembl.molecule_properties.psa",
"chembl.molecule_properties.qed_weighted",
"chembl.inchi_key",
"chembl.smiles",
"chembl.inchi",

"drugbank.id",
"drugbank.name",
"drugbank.cas",
"drugbank.unii",
"drugbank.synonyms",
"drugbank.inchi_key",
"drugbank.accession_number"

"drugcentral.pharmacology_class.chebi.description",
"drugcentral.pharmacology_class.mesh_pa.description",
"drugcentral.fda_adverse_event.meddra_term",
"drugcentral.bioactivity.target_name",
"drugcentral.bioactivity.act_value",
"drugcentral.bioactivity.act_type",
"drugcentral.bioactivity.organism",
"drugcentral.drug_use.indication.concept_name",
"drugcentral.approval.date",
"drugcentral.approval.agency",
"drugcentral.drug_dosage.dosage",
"drugcentral.drug_dosage.unit",
"drugcentral.drug_dosage.route",
"drugcentral.synonyms",
"drugcentral.structures.inchi",
"drugcentral.structures.inchikey",
"drugcentral.structures.smiles",
"drugcentral.structures.cas_rn",
"drugcentral.xrefs",

"fda_orphan_drug.pubchem_sid",
"fda_orphan_drug.generic_name",
"fda_orphan_drug.designated_date",
"fda_orphan_drug.designation_status",
"fda_orphan_drug.approval_status",
"fda_orphan_drug.sponsor",
"fda_orphan_drug.orphan_designation.parsed_text",

"ginas.preferred_name",
"ginas.unii",
"ginas.names_list",
"ginas.moieties.formula",
"ginas.moieties.mwt",
"ginas.inchikey",
"ginas.approved.$numberLong",
"ginas.definitionLevel",
"ginas.deprecated",
"ginas.structure.formula",
"ginas.structure.mwt",
"ginas.cas_primary",
"ginas.xrefs",

"ndc.product_id",
"ndc.productndc",
"ndc.producttypename",
"ndc.proprietaryname",
"ndc.nonproprietaryname",
"ndc.dosageformname",
"ndc.routename",
"ndc.startmarketingdate",
"ndc.marketingcategoryname",
"ndc.applicationnumber",
"ndc.labelername",
"ndc.substancename",
"ndc.active_numerator_strength",
"ndc.active_ingred_unit",
"ndc.pharm_classes",
"ndc.listing_record_certified_through",

"pharmgkb.id",
"pharmgkb.name",
"pharmgkb.generic_names",
"pharmgkb.type",
"pharmgkb.smiles",
"pharmgkb.inchi",
"pharmgkb.xrefs",

"pubchem.cid",
"pubchem.iupac.preferred",
"pubchem.smiles.canonical",
"pubchem.inchi",
"pubchem.inchikey",
"pubchem.molecular_formula",
"pubchem.molecular_weight",
"pubchem.exact_mass",
"pubchem.monoisotopic_weight",
"pubchem.topological_polar_surface_area",
"pubchem.xlogp",
"pubchem.hydrogen_bond_acceptor_count",
"pubchem.hydrogen_bond_donor_count",
"pubchem.rotatable_bond_count",
"pubchem.formal_charge",
"pubchem.complexity",
"pubchem.heavy_atom_count",

"sider.stitch.flat",
"sider.side_effect.placebo",
"sider.meddra.type",
"sider.meddra.umls_id",
"sider.indication.method_of_detection",
"sider.indication.name",

"umls.cui",
"umls.mesh",
"umls.name",

"unichem.actor",
"unichem.atlas",
"unichem.bindingdb",
"unichem.brenda",
"unichem.carotenoiddb",
"unichem.chebi",
"unichem.chembl",
"unichem.chemicalbook",
"unichem.clinicaltrials",
"unichem.comptox",
"unichem.dailymed",
"unichem.drugbank",
"unichem.drugcentral",
"unichem.emolecules",
"unichem.fdasrs",
"unichem.gtopdb",
"unichem.hmdb",
"unichem.ibm",
"unichem.kegg_ligand",
"unichem.lincs",
"unichem.lipidmaps",
"unichem.mcule",
"unichem.metabolights",
"unichem.molport",
"unichem.nih_ncc",
"unichem.nikkaji",
"unichem.nmrshiftdb2",
"unichem.pdb",
"unichem.pharmgkb",
"unichem.pubchem",
"unichem.pubchem_dotf",
"unichem.pubchem_tpharma",
"unichem.recon",
"unichem.rhea",
"unichem.selleck",
"unichem.surechembl",
"unichem.swisslipids",
"unichem.zinc",

"unii.unii",
"unii.registry_number",
"unii.pubchem",
"unii.molecular_formula",
"unii.inchikey",
"unii.smiles",
"unii.ingredient_type",
"unii.substance_type",
"unii.uuid",
"unii.display_name"
]
[
// Aeolus
"aeolus.outcomes.ror_95_ci",
"aeolus.outcomes.id",
"aeolus.outcomes.prr",
"aeolus.outcomes.meddra_code",
"aeolus.outcomes.prr_95_ci",
"aeolus.pt",

// Chebi
"chebi.secondary_chebi_id",
"chebi.relationship",
"chebi.num_children",
"chebi.num_parents",
"chebi.num_descendants",
"chebi.num_ancestors",
"chebi.parents",
"chebi.ancestors",
"chebi.inchi",
"chebi.smiles",
"chebi.charge",
"chebi.star",
"chebi.mass",
"chebi.monoisotopic_mass",
"chebi.citation",

// Chembl
"chembl.availability_type",
"chembl.black_box_warning",
"chembl.chemical_probe",
"chembl.chirality",
"chembl.dosed_ingredient",
"chembl.first_in_class",
"chembl.inorganic_flag",
"chembl.molecule_hierarchy",
"chembl.molecule_properties.aromatic_rings",
"chembl.molecule_properties.hba",
"chembl.molecule_properties.hba_lipinski",
"chembl.molecule_properties.hbd",
"chembl.molecule_properties.hbd_lipinski",
"chembl.molecule_properties.heavy_atoms",
"chembl.molecule_properties.molecular_species",
"chembl.molecule_properties.mw_freebase",
"chembl.molecule_properties.np_likeness_score",
"chembl.molecule_properties.num_lipinski_ro5_violations",
"chembl.molecule_properties.num_ro5_violations",
"chembl.molecule_properties.ro3_pass",
"chembl.molecule_properties.rtb",
"chembl.molecule_type",
"chembl.natural_product",
"chembl.oral",
"chembl.orphan",
"chembl.parenteral",
"chembl.polymer_flag",
"chembl.prodrug",
"chembl.structure_type",
"chembl.therapeutic_flag",
"chembl.topical",
"chembl.withdrawn_flag",

// DrugBank

// DrugCentral
"drugcentral.fda_adverse_event.level",
"drugcentral.fda_adverse_event.llr",
"drugcentral.fda_adverse_event.llr_threshold",
"drugcentral.fda_adverse_event.drug_ae",
"drugcentral.fda_adverse_event.drug_no_ae",
"drugcentral.fda_adverse_event.no_drug_ae",
"drugcentral.fda_adverse_event.no_drug_no_ar",
"drugcentral.bioactivity.uniprot",
"drugcentral.bioactivity.target_class",
"drugcentral.bioactivity.act_source",
"drugcentral.bioactivity.action_type",
"drugcentral.bioactivity.moa",
"drugcentral.bioactivity.moa_source",
"drugcentral.drug_use.indication.umls_cui",
"drugcentral.drug_use.indication.snomed_full_name",
"drugcentral.drug_use.indication.cui_semantic_type",
"drugcentral.drug_use.indication.snomed_concept_id",
"drugcentral.structures.inchi_key",
"drugcentral.structures.cas_rn",
"drugcentral.xrefs",

// FDA Orphan Drug
"fda_orphan_drug.orphan_designation.original_text",
"fda_orphan_drug.orphan_designation.umls",

// Ginas
"ginas.properties",
"ginas.moieties",
"ginas.relationships",
"ginas.approved",
"ginas.access",
"ginas.xrefs",
"ginas.references",
"ginas.approvedBy",
"ginas.substanceClass",
"ginas.tags",
"ginas.status",
"ginas.codes",
"ginas.names",
"ginas.lastEditedBy",
"ginas.notes",
"ginas.structure",

// NDC
"ndc.ndc_exclude_flag",
"ndc.package",

// PharmGKB
"pharmgkb.dosing_guideline",

// PubChem
"pubchem.iupac.allowed",
"pubchem.iupac.cas_like_style",
"pubchem.iupac.markup",
"pubchem.iupac.systematic",
"pubchem.iupac.traditional",
"pubchem.smiles.isomeric",
"pubchem.formal_charge",
"pubchem.complexity",
"pubchem.hydrogen_bond_acceptor_count",
"pubchem.hydrogen_bond_donor_count",
"pubchem.rotatable_bond_count",
"pubchem.topological_polar_surface_area",
"pubchem.heavy_atom_count",
"pubchem.chiral_atom_count",
"pubchem.defined_chiral_atom_count",
"pubchem.undefined_chiral_atom_count",
"pubchem.chiral_bond_count",
"pubchem.defined_chiral_bond_count",
"pubchem.undefined_chiral_bond_count",
"pubchem.isotope_atom_count",
"pubchem.covalent_unit_count",
"pubchem.tautomers_count"
]
# *** NOTE ***
# The CHEBI prefix must have a regex_term_pattern without a named <term> grouping.
# example query: CHEBI:57966:
Expand Down Expand Up @@ -415,10 +83,8 @@
re.compile(r"((chembl\:(?P<term>chembl[0-9]+))|(chembl[0-9]+))", re.I),
"chembl.molecule_chembl_id",
),
(re.compile(r"chebi\:[0-9]+", re.I),
["chebi.id", "chebi.secondary_chebi_id"]),
(re.compile(
r"((unii\:(?P<term>[A-Z0-9]{10}))|([A-Z0-9]{10}))", re.I), "unii.unii"),
(re.compile(r"chebi\:[0-9]+", re.I), ["chebi.id", "chebi.secondary_chebi_id"]),
(re.compile(r"((unii\:(?P<term>[A-Z0-9]{10}))|([A-Z0-9]{10}))", re.I), "unii.unii"),
(
re.compile(r"((drugbank\:(?P<term>db[0-9]+))|(db[0-9]+))", re.I),
[
Expand Down Expand Up @@ -460,7 +126,7 @@

STATUS_CHECK = {
"id": "USNINKBPBVKHHZ-CYUUQNCZSA-L", # penicillin
"index": "index_test_20240612_3kwpduyw",
"index": "mychem_current",
}

_extra_kwargs = {"list_filter": {"type": str, "default": None}}
Expand All @@ -469,7 +135,3 @@
QUERY_KWARGS = copy.deepcopy(QUERY_KWARGS)
QUERY_KWARGS["*"].update(_extra_kwargs)
ES_RESULT_TRANSFORM = "web.pipeline.MyChemESResultFormatter"

# Set default fields
QUERY_KWARGS["*"]["_source"]["default"] = DEFAULT_FIELDS
QUERY_KWARGS["*"]["_source"]["strict"] = False

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