more tests

tests/test_urlsketch.py

@@ -131,4 +131,139 @@ def test_urlsketch_download_only(runtmp, capfd):
     fa_files = os.listdir(out_dir)
     assert set(fa_files) == set(['GCA_000175535.1_genomic.urlsketch.fna.gz', 'GCA_000961135.2_protein.urlsketch.faa.gz', 'GCA_000961135.2_genomic.urlsketch.fna.gz'])
     captured = capfd.readouterr()
-    assert "Failed to send signatures: channel closed" not in captured.err
+    assert "Failed to send signatures: channel closed" not in captured.err
+
+
+def test_urlsketch_bad_acc(runtmp):
+    acc_csv = get_test_data('acc-url.csv')
+    acc_mod = runtmp.output('acc_mod.csv')
+    with open(acc_csv, 'r') as inF, open(acc_mod, 'w') as outF:
+        lines = inF.readlines()
+        for line in lines:
+            # if this acc exist in line, copy it and write an extra line with an invalid accession
+            outF.write(line)
+            print(line)
+            if "GCA_000175535.1" in line:
+                mod_line = line.replace('GCA_000175535.1', 'GCA_0001755559.1')  # add extra digit - should not be valid
+                print(mod_line)
+                outF.write(mod_line)
+
+    output = runtmp.output('simple.zip')
+    failed = runtmp.output('failed.csv')
+
+    sig1 = get_test_data('GCA_000175535.1.sig.gz')
+    sig2 = get_test_data('GCA_000961135.2.sig.gz')
+    sig3 = get_test_data('GCA_000961135.2.protein.sig.gz')
+    ss1 = sourmash.load_one_signature(sig1, ksize=31)
+    ss2 = sourmash.load_one_signature(sig2, ksize=31)
+    # why does this need ksize =30 and not ksize = 10!???
+    ss3 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='protein')
+
+    runtmp.sourmash('scripts', 'urlsketch', acc_mod, '-o', output,
+                    '--failed', failed, '-r', '1',
+                    '--param-str', "dna,k=31,scaled=1000", '-p', "protein,k=10,scaled=200")
+
+    assert os.path.exists(output)
+    assert not runtmp.last_result.out # stdout should be empty
+
+    # Open the failed file
+    assert os.path.exists(failed)
+    with open(failed, 'r') as acc_file:
+        # Read the lines of the file
+        lines = acc_file.readlines()
+        # Check if the modified accession exists in the first column of any line
+        for line in lines:
+            print(line)
+            if "GCA_0001755559.1" in line.split(',')[0]:
+                assert True
+                break
+        else:
+            assert False, "Modified accession not found"
+
+    idx = sourmash.load_file_as_index(output)
+    sigs = list(idx.signatures())
+
+    assert len(sigs) == 3
+    for sig in sigs:
+        if 'GCA_000175535.1' in sig.name:
+            assert sig.name == ss1.name
+            assert sig.md5sum() == ss1.md5sum()
+        elif 'GCA_000961135.2' in sig.name:
+            assert sig.name == ss2.name
+            if sig.minhash.moltype == 'DNA':
+                assert sig.md5sum() == ss2.md5sum()
+            else:
+                assert sig.md5sum() == ss3.md5sum()
+
+def test_urlsketch_missing_accfile(runtmp, capfd):
+    acc_csv = runtmp.output('acc1.csv')
+    output = runtmp.output('simple.zip')
+    failed = runtmp.output('failed.csv')
+
+    with pytest.raises(utils.SourmashCommandFailed):
+        runtmp.sourmash('scripts', 'urlsketch', acc_csv, '-o', output,
+                    '--failed', failed, '-r', '1',
+                    '--param-str', "dna,k=31,scaled=1000", '-p', "protein,k=10,scaled=200")
+
+    captured = capfd.readouterr()
+    print(captured.err)
+    assert "Error: No such file or directory" in captured.err
+
+
+def test_urlsketch_empty_accfile(runtmp, capfd):
+    acc_csv = get_test_data('acc1.csv')
+    with open(acc_csv, 'w') as file:
+        file.write('')
+    output = runtmp.output('simple.zip')
+    failed = runtmp.output('failed.csv')
+
+    with pytest.raises(utils.SourmashCommandFailed):
+        runtmp.sourmash('scripts', 'urlsketch', acc_csv, '-o', output,
+                    '--failed', failed, '-r', '1',
+                    '--param-str', "dna,k=31,scaled=1000", '-p', "protein,k=10,scaled=200")
+
+    captured = capfd.readouterr()
+    print(captured.err)
+    assert 'Error: Invalid column names in CSV file. Columns should be: ["accession", "name", "moltype", "md5sum", "download_filename", "url"]' in captured.err
+
+
+def test_urlsketch_bad_acc_fail(runtmp, capfd):
+    acc_csv = get_test_data('acc-url.csv')
+    acc_mod = runtmp.output('acc_mod.csv')
+    with open(acc_csv, 'r') as inF, open(acc_mod, 'w') as outF:
+        lines = inF.readlines()
+        outF.write(lines[0])  # write the header line
+        for line in lines:
+            # if this acc exist in line, copy it and write
+            if "GCA_000175535.1" in line:
+                mod_line = line.replace('GCA_000175535.1', 'GCA_0001755559.1')  # add extra digit - should not be valid
+                print(mod_line)
+                outF.write(mod_line)
+
+    output = runtmp.output('simple.zip')
+    failed = runtmp.output('failed.csv')
+
+    with pytest.raises(utils.SourmashCommandFailed):
+        runtmp.sourmash('scripts', 'urlsketch', acc_mod, '-o', output,
+                    '--failed', failed, '-r', '1',
+                    '--param-str', "dna,k=31,scaled=1000")
+
+    captured = capfd.readouterr()
+    print(captured.out)
+    print(captured.err)
+    assert "Error: No signatures written, exiting." in captured.err
+
+
+
+def test_urlsketch_missing_output(runtmp):
+    # no output sig zipfile provided but also not --download-only
+    acc_csv = runtmp.output('acc1.csv')
+    output = runtmp.output('simple.zip')
+    failed = runtmp.output('failed.csv')
+
+    with pytest.raises(utils.SourmashCommandFailed):
+        runtmp.sourmash('scripts', 'urlsketch', acc_csv,
+                    '--failed', failed, '-r', '1',
+                    '--param-str', "dna,k=31,scaled=1000")
+
+    assert "Error: output signature zipfile is required if not using '--download-only'." in runtmp.last_result.err