moving test to sub-directory and --cov=./

.github/workflows/databases-ci.yaml

@@ -61,14 +61,14 @@ jobs:
         shell: bash -l {0}
         run: |
           pytest -v --cov-report=xml --color=yes  \
-          --cov=missense_kinase_toolkit/databases \
-           tests/test_databases.py
+          --cov=./ \
+           missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/tests/test_databases.py
 
       - name: Upload coverage reports to Codecov
         uses: codecov/[email protected]
         with:
           fail_ci_if_error: false # optional (default = false)
-          file: missense_kinase_toolkit/databases/coverage.xml
+          file: ./coverage.xml
           flags: databases # optional
           name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
           # https://github.com/codecov/codecov-action

missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/tests/test_databases.py

@@ -0,0 +1,257 @@
+"""
+Unit and regression test for the missense_kinase_toolkit package.
+"""
+
+# Import package, test suite, and other packages as needed
+import pytest
+
+
+def test_missense_kinase_toolkit_database_imported():
+    """Test if module is imported."""
+    import sys
+    import missense_kinase_toolkit.databases
+
+    assert "missense_kinase_toolkit.databases" in sys.modules
+
+
+def test_config():
+    from missense_kinase_toolkit.databases import config
+
+    # test that the function to set the output directory works
+    with pytest.raises(SystemExit) as sample:
+        config.get_output_dir()
+    assert sample.type == SystemExit
+    assert sample.value.code == 1
+    config.set_output_dir("test")
+    assert config.get_output_dir() == "test"
+
+    # test that the function to set the request cache works
+    assert config.maybe_get_request_cache() is None
+    config.set_request_cache("test")
+    assert config.maybe_get_request_cache() == "test"
+
+    # test that the function to set the cBioPortal instance works
+    with pytest.raises(SystemExit) as sample:
+        config.get_cbioportal_instance()
+    assert sample.type == SystemExit
+    assert sample.value.code == 1
+    config.set_cbioportal_instance("test")
+    assert config.get_cbioportal_instance() == "test"
+
+    # test that the function to set the cBioPortal token works
+    assert config.maybe_get_cbioportal_token() is None
+    config.set_cbioportal_token("test")
+    assert config.maybe_get_cbioportal_token() == "test"
+
+
+def test_io_utils():
+    import pandas as pd
+    import os
+    from missense_kinase_toolkit.databases import io_utils, config
+
+    # os.environ["OUTPUT_DIR"] = "."
+    config.set_output_dir(".")
+
+    # test that the functions to save and load dataframes work
+    df = pd.DataFrame({"A": [1, 2, 3], "B": [4, 5, 6]})
+    io_utils.save_dataframe_to_csv(df, "test1.csv")
+    df_read = io_utils.load_csv_to_dataframe("test1.csv")
+    assert df.equals(df_read)
+
+    # test that the function to concatenate csv files with glob works
+    io_utils.save_dataframe_to_csv(df, "test2.csv")
+    df_concat = io_utils.concatenate_csv_files_with_glob("*test*.csv")
+    assert df_concat.equals(pd.concat([df, df]))
+
+    # remove the files created
+    os.remove("test1.csv")
+    os.remove("test2.csv")
+
+    # test that the function to convert a string to a list works
+    assert io_utils.convert_str2list("a,b,c") == ["a", "b", "c"]
+    assert io_utils.convert_str2list("a, b, c") == ["a", "b", "c"]
+
+
+def test_requests_wrapper(capsys):
+    import requests
+    from missense_kinase_toolkit.databases import uniprot, utils_requests
+
+    uniprot.UniProt("TEST")
+    out, _ = capsys.readouterr()
+    assert out == "Error code: 400 (Bad request)\n"
+
+    utils_requests.print_status_code_if_res_not_ok(
+        requests.get("https://rest.uniprot.org/uniprotkb/TEST"),
+        dict_status_code = {400: "TEST"}
+    )
+    out, _ = capsys.readouterr()
+    assert out == "Error code: 400 (TEST)\n"
+
+    utils_requests.print_status_code_if_res_not_ok(
+        requests.get("https://rest.uniprot.org/uniprotkb/TEST"),
+        dict_status_code = {200: "TEST"}
+    )
+    out, _ = capsys.readouterr()
+    assert out == "Error code: 400\n"
+
+
+def test_cbioportal():
+    import os
+    from missense_kinase_toolkit.databases import config, cbioportal
+
+    config.set_cbioportal_instance("www.cbioportal.org")
+    config.set_output_dir(".")
+
+    # test that the function to query the cBioPortal API works
+    cbioportal_instance = cbioportal.cBioPortal()
+    assert cbioportal_instance.get_instance() == "www.cbioportal.org"
+    assert cbioportal_instance.get_url() == "https://www.cbioportal.org/api/v2/api-docs"
+    assert cbioportal_instance._cbioportal is not None
+
+    # test that server status is up
+    assert cbioportal_instance._cbioportal.Server_running_status.getServerStatusUsingGET().response().result["status"] == "UP"
+
+    # test that Zehir cohort is available
+    study = "msk_impact_2017"
+    list_studies = cbioportal_instance._cbioportal.Studies.getAllStudiesUsingGET().result()
+    list_study_ids = [study.studyId for study in list_studies]
+    assert study in list_study_ids
+
+    # test that the function to get all mutations by study works
+    df = cbioportal.Mutations(study).get_cbioportal_cohort_mutations()
+    assert df.shape[0] == 78142
+
+    # make sure save works
+    mutations_instance = cbioportal.Mutations(study)
+    mutations_instance.get_cbioportal_cohort_mutations(bool_save=True)
+    assert os.path.isfile(f"{mutations_instance.study_id}_mutations.csv") == True
+    os.remove(f"{mutations_instance.study_id}_mutations.csv")
+
+    assert mutations_instance.get_study_id() == study
+    assert mutations_instance._mutations is not None
+
+
+def test_hgnc():
+    from missense_kinase_toolkit.databases import hgnc
+
+    abl1 = hgnc.HGNC("Abl1", True)
+    abl1.maybe_get_symbol_from_hgnc_search()
+    assert abl1.hgnc == "ABL1"
+    assert abl1.maybe_get_info_from_hgnc_fetch()["locus_type"][0] == "gene with protein product"
+
+    abl1 = hgnc.HGNC("ENSG00000097007", False)
+    abl1.maybe_get_symbol_from_hgnc_search()
+    assert abl1.hgnc == "ABL1"
+    assert abl1.maybe_get_info_from_hgnc_fetch()["locus_type"][0] == "gene with protein product"
+
+    test = hgnc.HGNC("test", True)
+    test.maybe_get_symbol_from_hgnc_search()
+    assert test.ensembl is None
+    assert test.maybe_get_info_from_hgnc_fetch()["locus_type"] is None
+
+    test = hgnc.HGNC("test", False)
+    test.maybe_get_symbol_from_hgnc_search()
+    assert test.hgnc is None
+    assert test.maybe_get_info_from_hgnc_fetch() is None
+
+    test = hgnc.HGNC("temp")
+    test.maybe_get_symbol_from_hgnc_search(
+        custom_field="mane_select",
+        custom_term="ENST00000318560.6"
+    )
+    assert test.hgnc == "ABL1"
+
+
+def test_klifs():
+    from missense_kinase_toolkit.databases import klifs
+
+    dict_egfr = klifs.KinaseInfo("EGFR")._kinase_info
+
+    assert dict_egfr["family"]      ==      "EGFR"
+    assert dict_egfr["full_name"]   ==      "epidermal growth factor receptor"
+    assert dict_egfr["gene_name"]   ==      "EGFR"
+    assert dict_egfr["group"]       ==      "TK"
+    assert dict_egfr["iuphar"]      ==      1797
+    assert dict_egfr["kinase_ID"]   ==      406
+    assert dict_egfr["name"]        ==      "EGFR"
+    assert dict_egfr["pocket"]      ==      "KVLGSGAFGTVYKVAIKELEILDEAYVMASVDPHVCRLLGIQLITQLMPFGCLLDYVREYLEDRRLVHRDLAARNVLVITDFGLA"
+    assert dict_egfr["species"]     ==      "Human"
+    assert dict_egfr["uniprot"]     ==      "P00533"
+
+
+def test_scrapers():
+    from missense_kinase_toolkit.databases import scrapers
+
+    # test that the function to scrape the KinHub database works
+    df_kinhub = scrapers.kinhub()
+    assert df_kinhub.shape[0] == 517
+    assert df_kinhub.shape[1] == 8
+    assert "HGNC Name" in df_kinhub.columns
+    assert "UniprotID" in df_kinhub.columns
+
+
+def test_colors(capsys):
+    from missense_kinase_toolkit.databases import colors
+
+    # correct mappings
+    assert colors.map_aa_to_single_letter_code("Ala")       == "A"
+    assert colors.map_aa_to_single_letter_code("ALA")       == "A"
+    assert colors.map_aa_to_single_letter_code("alanine")   == "A"
+    assert colors.map_aa_to_single_letter_code("ALANINE")   == "A"
+    assert colors.map_aa_to_single_letter_code("A")         == "A"
+    assert colors.map_aa_to_single_letter_code("a")         == "A"
+
+    # incorrect mappings
+    TEST1 = "X"
+    assert colors.map_aa_to_single_letter_code(TEST1) is None
+    out, _ = capsys.readouterr()
+    assert out == f"Invalid single-letter amino acid: {TEST1.upper()}\n"
+    TEST2 = "AL"
+    assert colors.map_aa_to_single_letter_code(TEST2) is None
+    out, _ = capsys.readouterr()
+    assert out == f"Length error and invalid amino acid: {TEST2}\n"
+    TEST3 = "XYZ"
+    assert colors.map_aa_to_single_letter_code(TEST3) is None
+    out, _ = capsys.readouterr()
+    assert out == f"Invalid 3-letter amino acid: {TEST3.upper()}\n"
+    TEST4 = "TEST"
+    assert colors.map_aa_to_single_letter_code(TEST4) is None
+    out, _ = capsys.readouterr()
+    assert out == f"Invalid amino acid name: {TEST4.lower()}\n"
+
+    # color mapping
+    DICT_COLORS = colors.DICT_COLORS
+    assert colors.map_single_letter_aa_to_color("A", DICT_COLORS["ALPHABET_PROJECT"]["DICT_COLORS"]) == "#F0A3FF"
+    assert colors.map_single_letter_aa_to_color("A", DICT_COLORS["ASAP"]["DICT_COLORS"])             == "red"
+    assert colors.map_single_letter_aa_to_color("A", DICT_COLORS["RASMOL"]["DICT_COLORS"])           == "#C8C8C8"
+    assert colors.map_single_letter_aa_to_color("A", DICT_COLORS["SHAPELY"]["DICT_COLORS"])          == "#8CFF8C"
+    assert colors.map_single_letter_aa_to_color("A", DICT_COLORS["CLUSTALX"]["DICT_COLORS"])         == "blue"
+    assert colors.map_single_letter_aa_to_color("A", DICT_COLORS["ZAPPO"]["DICT_COLORS"])            == "#ffafaf"
+
+
+def test_uniprot():
+    from missense_kinase_toolkit.databases import uniprot
+
+    abl1 = uniprot.UniProt("P00519")
+    assert abl1._sequence == "MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSSESRFNTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKELGKQGVRGAVSTLLQAPELPTKTRTSRRAAEHRDTTDVPEMPHSKGQGESDPLDHEPAVSPLLPRKERGPPEGGLNEDERLLPKDKKTNLFSALIKKKKKTAPTPPKRSSSFREMDGQPERRGAGEEEGRDISNGALAFTPLDTADPAKSPKPSNGAGVPNGALRESGGSGFRSPHLWKKSSTLTSSRLATGEEEGGGSSSKRFLRSCSASCVPHGAKDTEWRSVTLPRDLQSTGRQFDSSTFGGHKSEKPALPRKRAGENRSDQVTRGTVTPPPRLVKKNEEAADEVFKDIMESSPGSSPPNLTPKPLRRQVTVAPASGLPHKEEAGKGSALGTPAAAEPVTPTSKAGSGAPGGTSKGPAEESRVRRHKHSSESPGRDKGKLSRLKPAPPPPPAASAGKAGGKPSQSPSQEAAGEAVLGAKTKATSLVDAVNSDAAKPSQPGEGLKKPVLPATPKPQSAKPSGTPISPAPVPSTLPSASSALAGDQPSSTAFIPLISTRVSLRKTRQPPERIASGAITKGVVLDSTEALCLAISRNSEQMASHSAVLEAGKNLYTFCVSYVDSIQQMRNKFAFREAINKLENNLRELQICPATAGSGPAATQDFSKLLSSVKEISDIVQR"
+
+
+def test_pfam():
+    from missense_kinase_toolkit.databases import pfam
+
+    # test that the function to find Pfam domain for a given HGNC symbol and position works
+    df_pfam = pfam.Pfam("P00519")._pfam
+    assert df_pfam.shape[0] == 4
+    assert df_pfam.shape[1] == 18
+    assert "uniprot" in df_pfam.columns
+    assert "start" in df_pfam.columns
+    assert "end" in df_pfam.columns
+    assert "name" in df_pfam.columns
+    assert df_pfam.loc[df_pfam["name"] == "Protein tyrosine and serine/threonine kinase", "start"].values[0] == 242
+    assert df_pfam.loc[df_pfam["name"] == "Protein tyrosine and serine/threonine kinase", "end"].values[0] == 492
+    assert pfam.find_pfam_domain(
+        input_id="p00519",
+        input_position=350,
+        df_ref=df_pfam,
+        col_ref_id="uniprot"
+    ) == "Protein tyrosine and serine/threonine kinase"