BioMCP

from biomcp import render def test_render_full_json(data_dir): input_data = (data_dir / "ct_gov/trials_NCT04280705.json").read_text() expect_markdown = (data_dir / "ct_gov/trials_NCT04280705.txt").read_text() markdown = render.to_markdown(input_data) assert markdown == expect_markdown input_data = ( data_dir / "myvariant/variants_full_braf_v600e.json" ).read_text() expect_markdown = ( data_dir / "myvariant/variants_full_braf_v600e.txt" ).read_text() markdown = render.to_markdown(input_data) print("==" * 100) print(markdown) print("==" * 100) assert markdown == expect_markdown def test_render_with_nones(): markdown = render.to_markdown(data) assert ( markdown == """# Studies ## Protocol Section ### Design Module Study Type: interventional Phases: phase2 ### Identification Module Brief Title: study of autologous tumor infiltrating lymphocytes in patients with solid tumors Nct Id: nct03645928 ### Status Module Overall Status: recruiting #### Completion Date Struct Date: 2029-08-09 #### Start Date Struct Date: 2019-05-07 """ ) data = { "next_page_token": None, "studies": [ { "derived_section": None, "document_section": None, "has_results": None, "protocol_section": { "arms_interventions_module": None, "conditions_module": None, "contacts_locations_module": None, "description_module": None, "design_module": { "design_info": None, "enrollment_info": None, "phases": ["phase2"], "study_type": "interventional", }, "eligibility_module": None, "identification_module": { "acronym": None, "brief_title": "study " "of " "autologous " "tumor " "infiltrating " "lymphocytes " "in " "patients " "with " "solid " "tumors", "nct_id": "nct03645928", "official_title": None, "org_study_id_info": None, "organization": None, "secondary_id_infos": None, }, "outcomes_module": None, "oversight_module": None, "references_module": None, "sponsor_collaborators_module": None, "status_module": { "completion_date_struct": { "date": "2029-08-09", "type": None, }, "expanded_access_info": None, "last_known_status": None, "last_update_post_date_struct": None, "last_update_submit_date": None, "overall_status": "recruiting", "primary_completion_date_struct": None, "results_first_post_date_struct": None, "results_first_submit_date": None, "results_first_submit_qc_date": None, "start_date_struct": {"date": "2019-05-07", "type": None}, "status_verified_date": None, "study_first_post_date_struct": None, "study_first_submit_date": None, "study_first_submit_qc_date": None, "why_stopped": None, }, }, "results_section": None, }, ], } def test_transform_key_protocol_section(): assert render.transform_key("protocol_section") == "Protocol Section" def test_transform_key_nct_number(): assert render.transform_key("nct_number") == "Nct Number" def test_transform_key_study_url(): assert render.transform_key("study_url") == "Study Url" def test_transform_key_allcaps(): assert render.transform_key("allcaps") == "Allcaps" def test_transform_key_primary_purpose(): assert render.transform_key("primary_purpose") == "Primary Purpose" def test_transform_key_underscores(): assert render.transform_key("some_key_name") == "Some Key Name" def test_transform_key_lowercase(): assert render.transform_key("somekey") == "Somekey" def test_transform_key_nctid(): assert render.transform_key("nct_id") == "Nct Id" def test_transform_key_4dct(): assert render.transform_key("4dct") == "4dct" def test_wrap_preserve_newlines_blank(): assert render.wrap_preserve_newlines("", 20) == [] def test_wrap_preserve_newlines_short_line(): text = "hello world" assert render.wrap_preserve_newlines(text, 20) == ["hello world"] def test_wrap_preserve_newlines_long(): text = "this line is definitely longer than twenty characters" lines = render.wrap_preserve_newlines(text, 20) assert len(lines) > 1 assert "this line is" in lines[0] def test_process_scalar_list_fits(): lines = [] render.process_scalar_list( "conditions", lines, ["condition1", "condition2"], ) assert lines == ["Conditions: condition1, condition2"] def test_process_scalar_list_too_long(): lines = [] big_list = ["test_value" * 10, "another" * 5] render.process_scalar_list("giant_field", lines, big_list) assert lines[0].startswith("Giant Field:") assert lines[1].startswith("- test_value") def test_render_key_value_short(): lines = [] render.render_key_value(lines, "nct_number", "nct100") assert lines == ["Nct Number: nct100"] def test_render_key_value_long(): lines = [] render.render_key_value(lines, "brief_summary", "hello " * 15) # first line "brief summary:" assert lines[0] == "Brief Summary:" assert lines[1].startswith(" hello hello")