get rid of deprecated modules in `code/reasoningtool/`

[saramsey]

This will involve deletion and/or edits of scores of modules. Extensive testing will be needed. Specifically, and in addition to the usual testing that we do with our example queries, we will need to make sure to test the pubmed_mesh_ngd_controller.py controller.

[saramsey]

creating a branch issue-2582 for this work

[saramsey]

Verifying that it is safe to remove QueryChEMBL.py, since nothing relies on it:

sramsey-laptop:RTX sramsey$ find . -name \*.py -exec grep 'QueryChEMBL' {} /dev/null \;
./code/reasoningtool/kg-construction/QueryPubChem.py:    #     print(QueryChEMBL.get_target_uniprot_ids_for_drug('clothiapine'))
./code/reasoningtool/kg-construction/QueryChEMBL.py:class QueryChEMBL:
./code/reasoningtool/kg-construction/QueryChEMBL.py:        url = QueryChEMBL.API_BASE_URL + '/' + handler + '?' + url_suffix
./code/reasoningtool/kg-construction/QueryChEMBL.py:                               timeout=QueryChEMBL.TIMEOUT_SEC)
./code/reasoningtool/kg-construction/QueryChEMBL.py:            print('Timeout in QueryChEMBL for URL: ' + url, file=sys.stderr)
./code/reasoningtool/kg-construction/QueryChEMBL.py:            print('%s received in QueryChEMBL for URL: %s' % (e, url), file=sys.stderr)
./code/reasoningtool/kg-construction/QueryChEMBL.py:        res = QueryChEMBL.send_query_get(handler='compound_record.json',
./code/reasoningtool/kg-construction/QueryChEMBL.py:        target_mechanisms_json = QueryChEMBL.get_mechanisms_for_chembl_id(chembl_id)
./code/reasoningtool/kg-construction/QueryChEMBL.py:                target_uniprot_ids = QueryChEMBL.map_chembl_target_to_uniprot_ids(target_chembl_id)
./code/reasoningtool/kg-construction/QueryChEMBL.py:        res = QueryChEMBL.send_query_get(handler='target_prediction.json',
./code/reasoningtool/kg-construction/QueryChEMBL.py:        res_json = QueryChEMBL.send_query_get(handler="target.json",
./code/reasoningtool/kg-construction/QueryChEMBL.py:        chembl_ids_for_drug = QueryChEMBL.get_chembl_ids_for_drug(drug_name)
./code/reasoningtool/kg-construction/QueryChEMBL.py:            uniprot_ids_dict = QueryChEMBL.get_target_uniprot_ids_for_chembl_id(chembl_id)
./code/reasoningtool/kg-construction/QueryChEMBL.py:        res = QueryChEMBL.send_query_get(handler='mechanism.json',
./code/reasoningtool/kg-construction/QueryChEMBL.py:    print(QueryChEMBL.get_target_uniprot_ids_for_chembl_id('CHEMBL521'))
./code/reasoningtool/kg-construction/QueryChEMBL.py:    print(QueryChEMBL.get_target_uniprot_ids_for_chembl_id('CHEMBL2364648'))
./code/reasoningtool/kg-construction/QueryChEMBL.py:#    print(QueryChEMBL.get_mechanisms_for_chembl_id("CHEMBL521"))
./code/reasoningtool/kg-construction/QueryChEMBL.py:#    print(QueryChEMBL.map_chembl_target_to_uniprot_ids("CHEMBL2094253"))
./code/reasoningtool/kg-construction/QueryChEMBL.py:#    print(QueryChEMBL.get_mechanisms_for_chembl_id("CHEMBL521"))

[saramsey]

Verifying that it is safe to remove code/reasoningtool/kg-construction/QueryUniprot.py:

sramsey-laptop:RTX sramsey$ find . -name \*.py -exec grep 'QueryUniprot' {} /dev/null \;
./code/reasoningtool/kg-construction/QueryUniprot.py:""" This module defines the class QueryUniprot which connects to APIs at
./code/reasoningtool/kg-construction/QueryUniprot.py:class QueryUniprot:
./code/reasoningtool/kg-construction/QueryUniprot.py:            url =QueryUniprot.API_BASE_URL
./code/reasoningtool/kg-construction/QueryUniprot.py:            res = requests.post(QueryUniprot.API_BASE_URL, data=payload, headers=header)
./code/reasoningtool/kg-construction/QueryUniprot.py:            print('Timeout in QueryUniprot for URL: ' + QueryUniprot.API_BASE_URL, file=sys.stderr)
./code/reasoningtool/kg-construction/QueryUniprot.py:            print('%s received in QueryUniprot for URL: %s' % (e, url), file=sys.stderr)
./code/reasoningtool/kg-construction/QueryUniprot.py:            print(QueryUniprot.API_BASE_URL, file=sys.stderr)
./code/reasoningtool/kg-construction/QueryUniprot.py:            print('Status code ' + str(status_code) + ' for url: ' + QueryUniprot.API_BASE_URL, file=sys.stderr)
./code/reasoningtool/kg-construction/QueryUniprot.py:            res = requests.get(url, timeout=QueryUniprot.TIMEOUT_SEC, headers=header)
./code/reasoningtool/kg-construction/QueryUniprot.py:            print('Timeout in QueryUniprot for URL: ' + url, file=sys.stderr)
./code/reasoningtool/kg-construction/QueryUniprot.py:            print('%s received in QueryUniprot for URL: %s' % (e, url), file=sys.stderr)
./code/reasoningtool/kg-construction/QueryUniprot.py:        handler = QueryUniprot.HANDLER_MAP['map_enzyme_commission_id_to_uniprot_ids'].format(id=ec_id_encoded)
./code/reasoningtool/kg-construction/QueryUniprot.py:        res = QueryUniprot.__access_api(handler)
./code/reasoningtool/kg-construction/QueryUniprot.py:        handler = QueryUniprot.HANDLER_MAP[entity_type].format(id=entity_id)
./code/reasoningtool/kg-construction/QueryUniprot.py:        results = QueryUniprot.__access_api(handler)
./code/reasoningtool/kg-construction/QueryUniprot.py:        entity_obj = QueryUniprot.__get_entity("get_protein", entity_id)
./code/reasoningtool/kg-construction/QueryUniprot.py:        entity_obj = QueryUniprot.__get_entity(entity_type, entity_id)
./code/reasoningtool/kg-construction/QueryUniprot.py:        return QueryUniprot.__get_name("get_protein", protein_id)
./code/reasoningtool/kg-construction/QueryUniprot.py:        res_tab = QueryUniprot.__access_api("uniprot/" + accession_number + ".tab")
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.get_citeable_accession_for_accession("P35354"))
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.get_citeable_accession_for_accession("A8K802"))
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.get_citeable_accession_for_accession("Q16876"))
./code/reasoningtool/kg-construction/QueryUniprot.py:    # print(QueryUniprot.uniprot_id_to_reactome_pathways("P68871"))
./code/reasoningtool/kg-construction/QueryUniprot.py:    # print(QueryUniprot.uniprot_id_to_reactome_pathways("Q16621"))
./code/reasoningtool/kg-construction/QueryUniprot.py:    # print(QueryUniprot.uniprot_id_to_reactome_pathways("P09601"))
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.map_enzyme_commission_id_to_uniprot_ids("ec:1.4.1.17"))  # small results
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.map_enzyme_commission_id_to_uniprot_ids("ec:1.3.1.110")) # empty result
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.map_enzyme_commission_id_to_uniprot_ids("ec:1.2.1.22"))  # large results
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.map_enzyme_commission_id_to_uniprot_ids("ec:4.4.1.xx"))  # fake id
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.map_enzyme_commission_id_to_uniprot_ids("R-HSA-1912422"))   # wrong id
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.get_protein_gene_symbol('UniProtKB:P20848'))
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.get_protein_gene_symbol("UniProtKB:P01358"))
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.get_protein_gene_symbol("UniProtKB:Q96P88"))
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.get_protein_name('UniProtKB:P01358'))
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.get_protein_name('UniProtKB:P20848'))
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.get_protein_name('UniProtKB:Q9Y471'))
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.get_protein_name('UniProtKB:O60397'))
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.get_protein_name('UniProtKB:Q8IZJ3'))
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.get_protein_name('UniProtKB:Q7Z2Y8'))
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.get_protein_name('UniProtKB:Q8IWN7'))
./code/reasoningtool/kg-construction/QueryUniprot.py:    print(QueryUniprot.get_protein_name('UniProtKB:Q156A1'))

[saramsey]

Verifying it is safe to remove RTX/code/reasoningtool/kg-construction/QueryPubChem.py:

sramsey-laptop:kg-construction sramsey$ find . -name \*.py -exec grep 'QueryPubChem' {} /dev/null \;
./QueryPubChem.py:class QueryPubChem:
./QueryPubChem.py:        url = QueryPubChem.API_BASE_URL + '/' + handler
./QueryPubChem.py:            res = requests.get(url, timeout=QueryPubChem.TIMEOUT_SEC)
./QueryPubChem.py:            print('Timeout in QueryPubChem for URL: ' + url, file=sys.stderr)
./QueryPubChem.py:            print('%s received in QueryPubChem for URL: %s' % (e, url), file=sys.stderr)
./QueryPubChem.py:        url = QueryPubChem.API_BASE_URL + '/' + handler + '/' + url_suffix
./QueryPubChem.py:            res = requests.get(url, timeout=QueryPubChem.TIMEOUT_SEC)
./QueryPubChem.py:            print('Timeout in QueryPubChem for URL: ' + url, file=sys.stderr)
./QueryPubChem.py:            print('%s received in QueryPubChem for URL: %s' % (e, url), file=sys.stderr)
./QueryPubChem.py:        res = QueryPubChem.send_query_get(handler='compound/name',
./QueryPubChem.py:    #     print(QueryPubChem.get_chembl_ids_for_drug('gne-493'))
./QueryPubChem.py:            print('Timeout in QueryPubChem for URL: ' + url, file=sys.stderr)
./QueryPubChem.py:            print('%s received in QueryPubChem for URL: %s' % (e, url), file=sys.stderr)
./QueryPubChem.py:        handler = QueryPubChem.HANDLER_MAP['get_pubchem_cid'].format(sid=pubchem_sid)
./QueryPubChem.py:        res = QueryPubChem.__access_api(handler)
./QueryPubChem.py:        handler = QueryPubChem.HANDLER_MAP['get_description_url'].format(cid=pubchem_cid)
./QueryPubChem.py:        res = QueryPubChem.__access_api(handler)
./QueryPubChem.py:        pubchem_cid = QueryPubChem.get_pubchem_cid(pubchem_sid)
./QueryPubChem.py:            res_url = QueryPubChem.get_description_url_from_cid(pubchem_cid)
./QueryPubChem.py:    print(QueryPubChem.get_chembl_ids_for_drug('gne-493'))
./QueryPubChem.py:    print(QueryPubChem.get_pubchem_id_for_chembl_id('CHEMBL521'))
./QueryPubChem.py:    print(QueryPubChem.get_pubchem_id_for_chembl_id('chembl521'))
./QueryPubChem.py:    print(QueryPubChem.get_pubchem_id_for_chembl_id('3400'))
./QueryPubChem.py:    print(QueryPubChem.get_pubmed_id_for_pubchem_id('3672'))
./QueryPubChem.py:    print(QueryPubChem.get_pubmed_id_for_pubchem_id('3500'))
./QueryPubChem.py:    print(QueryPubChem.get_pubmed_id_for_pubchem_id('3400'))
./QueryPubChem.py:    print(QueryPubChem.get_description_url('6921'))
./QueryPubChem.py:    print(QueryPubChem.get_description_url('3500'))
./QueryPubChem.py:    print(QueryPubChem.get_description_url('3400'))
./QueryPubChem.py:    print(QueryPubChem.get_description_url(3400))
./QueryPubChem.py:    print(QueryPubChem.get_description_url('3324'))

[saramsey]

Following the thread in #130 and based on a review of its commit history, I believe it is safe to remove RTX/code/UI/autocomplete/GenerateQuestionTerms.py.

[saramsey]

Evidence that it is now safe to remove RTX/code/reasoningtool/kg-construction/Neo4jConnection.py:

sramsey-laptop:RTX sramsey$ find . -name \*.py -exec grep 'Neo4jConnection' {} /dev/null \;
./code/reasoningtool/kg-construction/Neo4jConnection.py:''' This module defines the class Neo4jConnection. Neo4jConnection class is designed
./code/reasoningtool/kg-construction/Neo4jConnection.py:class Neo4jConnection:

[saramsey]

Evidence that it is now safe to remove RTX/code/reasoningtool/kg-construction/chemblMap.tsv:

sramsey-laptop:RTX sramsey$ find . -type f -exec grep 'chemblMap.tsv' {} /dev/null \;
Binary file ./.git/index matches

[saramsey]

Verifying that it is safe to remove RTX/code/reasoningtool/kg-construction/SynonymMapper.py, except for breakage of a deprecated module RTX/code/reasoningtool/MLDrugRepurposing/MyChemGT.py which has been addressed via a note in RTX/code/reasoningtool/MLDrugRepurposing/README.md as described below:

sramsey-laptop:RTX sramsey$ find . -name \*.py -exec grep 'SynonymMapper' {} /dev/null \;
./code/reasoningtool/MLDrugRepurposing/MyChemGT.py:from SynonymMapper import SynonymMapper
./code/reasoningtool/MLDrugRepurposing/MyChemGT.py:    sm = SynonymMapper()
./code/reasoningtool/kg-construction/SynonymMapper.py:class SynonymMapper():

Note added to RTX/code/reasoningtool/MLDrugRepurposing/README.md:

On Oct. 9, 2025, a module,
`RTX/code/reasoningtool/kg-construction/SynonymMapper.py`, on which the
`MyChemGT.py` module in this directory depends, was deleted from the
`RTXteam/RTX` project area (see #2582). But if you need this code, you can
obtain it from any earlier RTXteam/RTX [release](https://github.com/RTXteam/RTX/releases).

[saramsey]

Verifying that it is safe to remove RTX/code/reasoningtool/QuestionAnswering/LilGimTestQuestion.py:

sramsey-laptop:RTX sramsey$ find . -name \*.py -exec grep 'LilGimTestQuestion' {} /dev/null \;

[saramsey]

Verifying that it is safe to remove RTX/code/reasoningtool/QuestionAnswering/QueryLilGIM.py:

sramsey-laptop:RTX sramsey$ find . -name \*.py -exec grep 'QueryLilGIM' {} /dev/null \;
./code/reasoningtool/QuestionAnswering/QueryLilGIM.py:""" This module defines the module QueryLilGIM. QueryLilGIM provides
./code/reasoningtool/QuestionAnswering/QueryLilGIM.py:class QueryLilGIM:
./code/reasoningtool/QuestionAnswering/QueryLilGIM.py:            response = QueryLilGIM._get(endpoint, data, base_url)
./code/reasoningtool/QuestionAnswering/QueryLilGIM.py:#            QueryLilGIM._jprint(response)
./code/reasoningtool/QuestionAnswering/QueryLilGIM.py:                QueryLilGIM._jprint(e.response.json(), file=sys.stderr)
./code/reasoningtool/QuestionAnswering/QueryLilGIM.py:                query_status = QueryLilGIM._get('%s/status/%s' % (endpoint.split('/')[0],
./code/reasoningtool/QuestionAnswering/QueryLilGIM.py:#                QueryLilGIM._jprint(query_status)
./code/reasoningtool/QuestionAnswering/QueryLilGIM.py:                QueryLilGIM._jprint(e.response.json(), file=sys.stderr)
./code/reasoningtool/QuestionAnswering/QueryLilGIM.py:    qlg = QueryLilGIM()

[saramsey]

Verifying that it is safe to remove RTX/code/reasoningtool/kg-construction/QueryMyGene.py:

sramsey-laptop:RTX sramsey$ find . -name \*.py -exec grep 'QueryMyGene' {} /dev/null \;
./code/reasoningtool/kg-construction/QueryMyGene.py:""" This module defines the class QueryMyGene.
./code/reasoningtool/kg-construction/QueryMyGene.py:QueryMyGene is written to query gene annotation information via python package
./code/reasoningtool/kg-construction/QueryMyGene.py:class QueryMyGene:
./code/reasoningtool/kg-construction/QueryMyGene.py:            url = QueryMyGene.API_BASE_URL + '/' + handler + '?' + url_suffix
./code/reasoningtool/kg-construction/QueryMyGene.py:            url = QueryMyGene.API_BASE_URL + '/' + handler
./code/reasoningtool/kg-construction/QueryMyGene.py:            res = requests.get(url, params=params, timeout=QueryMyGene.TIMEOUT_SEC, headers=headers)
./code/reasoningtool/kg-construction/QueryMyGene.py:            print('Timeout in QueryMyGene for URL: ' + url, file=sys.stderr)
./code/reasoningtool/kg-construction/QueryMyGene.py:            print('%s received in QueryMyGene for URL: %s' % (e, url), file=sys.stderr)
./code/reasoningtool/kg-construction/QueryMyGene.py:        handler = QueryMyGene.HANDLER_MAP['query']
./code/reasoningtool/kg-construction/QueryMyGene.py:        res = QueryMyGene.__access_api(handler, url_suffix)
./code/reasoningtool/kg-construction/QueryMyGene.py:            uniprot_ids_list = QueryMyGene.unnest(uniprot_ids_list, str)
./code/reasoningtool/kg-construction/QueryMyGene.py:        handler = QueryMyGene.HANDLER_MAP['query']
./code/reasoningtool/kg-construction/QueryMyGene.py:        res = QueryMyGene.__access_api(handler, url_suffix)
./code/reasoningtool/kg-construction/QueryMyGene.py:                print("QueryMyGene.convert_uniprot_id_to_gene_symbol: no \'hits\' result data for uniprot_id: " + uniprot_id, file=sys.stderr)
./code/reasoningtool/kg-construction/QueryMyGene.py:        handler = QueryMyGene.HANDLER_MAP['query']
./code/reasoningtool/kg-construction/QueryMyGene.py:        res = QueryMyGene.__access_api(handler, url_suffix)
./code/reasoningtool/kg-construction/QueryMyGene.py:                print("QueryMyGene.convert_uniprot_id_to_entrez_gene_ID: no \'hits\' result data for uniprot_id: " + uniprot_id, file=sys.stderr)
./code/reasoningtool/kg-construction/QueryMyGene.py:        handler = QueryMyGene.HANDLER_MAP['query']
./code/reasoningtool/kg-construction/QueryMyGene.py:        res = QueryMyGene.__access_api(handler, url_suffix)
./code/reasoningtool/kg-construction/QueryMyGene.py:        handler = QueryMyGene.HANDLER_MAP['query']
./code/reasoningtool/kg-construction/QueryMyGene.py:        res = QueryMyGene.__access_api(handler, url_suffix)
./code/reasoningtool/kg-construction/QueryMyGene.py:        handler = QueryMyGene.HANDLER_MAP['query']
./code/reasoningtool/kg-construction/QueryMyGene.py:        res = QueryMyGene.__access_api(handler, url_suffix)
./code/reasoningtool/kg-construction/QueryMyGene.py:        handler = QueryMyGene.HANDLER_MAP['query']
./code/reasoningtool/kg-construction/QueryMyGene.py:        res = QueryMyGene.__access_api(handler, url_suffix)
./code/reasoningtool/kg-construction/QueryMyGene.py:                        print("QueryMyGene.convert_entrez_gene_ID_to_mirbase_ID result missing miRBase field where it was expected; Entrez Gene ID: " +
./code/reasoningtool/kg-construction/QueryMyGene.py:        handler = QueryMyGene.HANDLER_MAP['query']
./code/reasoningtool/kg-construction/QueryMyGene.py:        q_res = QueryMyGene.__access_api(handler, url_suffix)
./code/reasoningtool/kg-construction/QueryMyGene.py:        handler = QueryMyGene.HANDLER_MAP['query']
./code/reasoningtool/kg-construction/QueryMyGene.py:        q_res = QueryMyGene.__access_api(handler, url_suffix)
./code/reasoningtool/kg-construction/QueryMyGene.py:        handler = QueryMyGene.HANDLER_MAP['query']
./code/reasoningtool/kg-construction/QueryMyGene.py:        q_res = QueryMyGene.__access_api(handler, url_suffix)
./code/reasoningtool/kg-construction/QueryMyGene.py:        handler = QueryMyGene.HANDLER_MAP['query']
./code/reasoningtool/kg-construction/QueryMyGene.py:        res_json = QueryMyGene.__access_api(handler, url_suffix)
./code/reasoningtool/kg-construction/QueryMyGene.py:            handler = QueryMyGene.HANDLER_MAP['gene'] + '/' + str(gene_id)
./code/reasoningtool/kg-construction/QueryMyGene.py:            res = QueryMyGene.__access_api(handler, url_suffix)
./code/reasoningtool/kg-construction/QueryMyGene.py:            handler = QueryMyGene.HANDLER_MAP['query']
./code/reasoningtool/kg-construction/QueryMyGene.py:            res = QueryMyGene.__access_api(handler, url_suffix)
./code/reasoningtool/kg-construction/QueryMyGene.py:        handler = QueryMyGene.HANDLER_MAP['query']
./code/reasoningtool/kg-construction/QueryMyGene.py:        results = str(QueryMyGene.__access_api(handler, None, params=params, return_raw=True))
./code/reasoningtool/kg-construction/QueryMyGene.py:        handler = QueryMyGene.HANDLER_MAP['query']
./code/reasoningtool/kg-construction/QueryMyGene.py:        results = str(QueryMyGene.__access_api(handler, None, params=params, return_raw=True))
./code/reasoningtool/kg-construction/QueryMyGene.py:    mg = QueryMyGene()