test url input

src/utils.rs

@@ -127,13 +127,13 @@ pub fn load_gbassembly_info(input_csv: String) -> Result<(Vec<GBAssemblyData>, u
             .get(1)
             .ok_or_else(|| anyhow!("Missing 'name' field"))?
             .to_string();
-
         // optionally get url
-        let url = record.get(3).and_then(|s| {
+        let url = record.get(2).and_then(|s| {
             if s.is_empty() {
                 None
             } else {
-                reqwest::Url::parse(s).map_err(|_| ()).ok()
+                let trimmed_s = s.trim_end_matches("/");
+                reqwest::Url::parse(trimmed_s).map_err(|_| ()).ok()
             }
         });
 

tests/test_gbsketch.py

@@ -56,6 +56,43 @@ def test_gbsketch_simple(runtmp):
             else:
                 assert sig.md5sum() == ss3.md5sum()
 
+
+def test_gbsketch_simple_url(runtmp):
+    acc_csv = get_test_data('acc-with-url.csv')
+    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', 'gbsketch', acc_csv, '-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
+
+    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_gbsketch_genomes_only(runtmp):
     acc_csv = get_test_data('acc.csv')
     output = runtmp.output('simple.zip')