Fix unit tests and create new ones

tests/test_api_file.py

@@ -0,0 +1,202 @@
+import pytest
+
+from rfam_batch.api import *
+
+
+@pytest.fixture
+def out_text():
+    with open("example_files/out", "r") as file:
+        return file.read()
+
+
+@pytest.fixture
+def sequence():
+    with open("example_files/sequence", "r") as file:
+        return file.read()
+
+
+@pytest.fixture
+def tblout_text():
+    with open("example_files/tblout", "r") as file:
+        return file.read()
+
+
+def test_valid_header():
+    assert SubmittedRequest.validate_header(">valid_header") == ">valid_header"
+
+
+def test_invalid_header():
+    with pytest.raises(ValueError, match="Invalid characters in header"):
+        SubmittedRequest.validate_header(">invalid;header")
+    with pytest.raises(ValueError, match="Invalid characters in header"):
+        SubmittedRequest.validate_header(">invalid\\header")
+    with pytest.raises(ValueError, match="Invalid characters in header"):
+        SubmittedRequest.validate_header(">invalid!header")
+    with pytest.raises(ValueError, match="Invalid characters in header"):
+        SubmittedRequest.validate_header(">invalid*header")
+
+
+def test_valid_sequence():
+    assert SubmittedRequest.validate_sequence("ACGTU") == "ACGTU"
+
+
+def test_sequence_invalid_length():
+    with pytest.raises(
+        ValueError,
+        match="Sequence length must be less than or equal to 7,000 nucleotides",
+    ):
+        SubmittedRequest.validate_sequence("A" * 7001)
+
+
+def test_sequence_invalid_characters():
+    with pytest.raises(ValueError, match="Invalid characters in sequence"):
+        SubmittedRequest.validate_sequence("ACGTX")
+
+
+def test_gap_characters_in_sequence():
+    raw_sequence = "ACGT.U"
+    with pytest.raises(ValueError):
+        SubmittedRequest.parse(raw_sequence)
+
+
+def test_parse_single_sequence():
+    raw_input = ">header1\nACGTACGT"
+    result = SubmittedRequest.parse(raw_input)
+    assert len(result.sequences) == 1
+    assert result.sequences[0] == ">header1\nACGTACGT"
+
+
+def test_parse_multiple_sequences():
+    raw_input = ">header1\nACGT\n>header2\nTGCA"
+    result = SubmittedRequest.parse(raw_input)
+    assert len(result.sequences) == 2
+    assert result.sequences[0] == ">header1\nACGT"
+    assert result.sequences[1] == ">header2\nTGCA"
+
+
+def test_case_insensitivity():
+    raw_sequence = "acgturyswmkbdhn"
+    request = SubmittedRequest.parse(raw_sequence)
+    assert request.sequences[0].strip() == "ACGTURYSWMKBDHN"
+
+
+def test_mixed_case_sequence():
+    raw_sequence = ">Header\nAcGt"
+    request = SubmittedRequest.parse(raw_sequence)
+    assert request.sequences[0] == ">Header\nACGT"
+
+
+def test_parse_cm_scan_result_instance(out_text, sequence, tblout_text):
+    job_id = "test_job_id"
+    result = parse_cm_scan_result(out_text, sequence, tblout_text, job_id)
+    assert isinstance(result, CmScanResult)
+
+
+def test_parse_cm_scan_result_sequence(out_text, sequence, tblout_text):
+    job_id = "test_job_id"
+    result = parse_cm_scan_result(out_text, sequence, tblout_text, job_id)
+    assert (
+        result.searchSequence
+        == "AGTTACGGCCATACCTCAGAGAATATACCGTATCCCGTTCGATCTGCGAAGTTAAGCTCTGAAGGGCGTCGTCAGTACTATAGTGGGTGACCATATGGGAATACGACGTGCTGTAGCTT"
+    )
+
+
+def test_parse_cm_scan_result_num_hits(out_text, sequence, tblout_text):
+    job_id = "test_job_id"
+    result = parse_cm_scan_result(out_text, sequence, tblout_text, job_id)
+    assert result.numHits == 1
+
+
+def test_parse_cm_scan_result_date(out_text, sequence, tblout_text):
+    job_id = "test_job_id"
+    result = parse_cm_scan_result(out_text, sequence, tblout_text, job_id)
+    assert result.opened == "2024-04-03 10:28:27"
+
+
+def test_parse_cm_scan_result_hits(out_text, sequence, tblout_text):
+    job_id = "test_job_id"
+    result = parse_cm_scan_result(out_text, sequence, tblout_text, job_id)
+    hits = {
+        "5S_rRNA": [
+            Hit(
+                id="5S_rRNA",
+                acc="RF00001",
+                start=1,
+                end=119,
+                strand="+",
+                GC=0.49,
+                score=104.9,
+                E=4.5e-24,
+                alignment=Alignment(
+                    nc="#NC                                                                                                                                          ",
+                    ss="#SS                  (((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>>-->>---->>>>>-->><<<-<<----<-<<-----<<____>>----->>->-->>->>>))))))))): ",
+                    hit_seq="#CM 1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCcgAAguUAAGcgcgcUugggCcagggUAGUAcuagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119",
+                    match="#MATCH                  :: U:C:GCCAUACC ::G:GAA ::ACCG AUCCC+U+CGA CU CGAA::UAAGC:C:: +GGGC: :G  AGUACUA  +UGGGUGACC+  UGGGAA+AC:A:GUGC:G:A ::+",
+                    user_seq="#SEQ 1 AGUUACGGCCAUACCUCAGAGAAUAUACCGUAUCCCGUUCGAUCUGCGAAGUUAAGCUCUGAAGGGCGUCGUCAGUACUAUAGUGGGUGACCAUAUGGGAAUACGACGUGCUGUAGCUU 119",
+                    pp="#PP                  *********************************************************************************************************************** ",
+                ),
+            )
+        ]
+    }
+    assert result.hits == hits
+
+
+def test_submission_response_build():
+    job_id = "infernal_cmscan-R20240530-111350-0806-24133014-p1m"
+    result_url = "https://batch.rfam.org/result/infernal_cmscan-R20240530-111350-0806-24133014-p1m/tblout"
+    response = SubmissionResponse.build(job_id, result_url)
+    assert response.job_id == job_id
+    assert response.result_url == result_url
+    assert response.dict(by_alias=True) == {"jobId": job_id, "resultURL": result_url}
+
+
+def test_submission_response_validation():
+    with pytest.raises(ValueError):
+        SubmissionResponse(resultURL="https://batch.rfam.org", jobId=None)
+
+
+def test_submission_response_fields():
+    response = SubmissionResponse(
+        resultURL="https://batch.rfam.org/result", jobId="1234"
+    )
+    assert response.job_id == "1234"
+    assert response.result_url == "https://batch.rfam.org/result"
+
+
+def test_multiple_sequences_initialization():
+    opened = "2023-05-31 12:00:00"
+    hits = [
+        {
+            "id": "hit1",
+            "acc": "acc1",
+            "start": 1,
+            "end": 100,
+            "strand": "+",
+            "GC": 50.0,
+            "score": 100.0,
+            "E": 0.001,
+        },
+        {
+            "id": "hit2",
+            "acc": "acc2",
+            "start": 101,
+            "end": 200,
+            "strand": "-",
+            "GC": 52.0,
+            "score": 200.0,
+            "E": 0.002,
+        },
+    ]
+    multiple_sequences = MultipleSequences(opened=opened, hits=hits)
+    assert multiple_sequences.opened == opened
+    assert len(multiple_sequences.hits) == 2
+    assert multiple_sequences.hits[0]["id"] == "hit1"
+    assert multiple_sequences.hits[1]["id"] == "hit2"
+
+
+def test_multiple_sequences_empty_hits():
+    opened = "2023-05-31 12:00:00"
+    hits = []
+    multiple_sequences = MultipleSequences(opened=opened, hits=hits)
+    assert multiple_sequences.opened == opened
+    assert len(multiple_sequences.hits) == 0