Merge pull request #36 from sourmash-bio/fix-fail

- fixes #35. To finish, enable reading failure file as `urlsketch` input in #34.

Changes:
- `url.as_str()` prior to printing
- test output format of failed file

src/directsketch.rs

@@ -527,7 +527,13 @@ pub fn failures_handle(
                     url,
                 }) = recv_failed.recv().await
                 {
-                    let record = format!("{},{},{},{:?}\n", accession, name, moltype, url);
+                    let record = format!(
+                        "{},{},{},{:?}\n",
+                        accession,
+                        name,
+                        moltype,
+                        url.map(|u| u.to_string()).unwrap_or("".to_string())
+                    );
                     // Attempt to write each record
                     if let Err(e) = writer.write_all(record.as_bytes()).await {
                         let error = Error::new(e).context("Failed to write record");

tests/test_gbsketch.py

@@ -55,6 +55,15 @@ def test_gbsketch_simple(runtmp):
                 assert sig.md5sum() == ss2.md5sum()
             else:
                 assert sig.md5sum() == ss3.md5sum()
+    assert os.path.exists(failed)
+    with open(failed, 'r') as failF:
+        next(failF)  # skip header line
+        for line in failF:
+            acc, name, moltype, url = line.strip().split(',')
+            assert acc == "GCA_000175535.1"
+            assert name == "GCA_000175535.1 Chlamydia muridarum MopnTet14 (agent of mouse pneumonitis) strain=MopnTet14"
+            assert moltype == "protein"
+            assert url == '"https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/175/535/GCA_000175535.1_ASM17553v1/GCA_000175535.1_ASM17553v1_protein.faa.gz"'
 
 
 def test_gbsketch_simple_url(runtmp):
@@ -273,7 +282,7 @@ def test_gbsketch_download_only(runtmp, capfd):
     assert set(fa_files) == set(['GCA_000175535.1_genomic.fna.gz', 'GCA_000961135.2_protein.faa.gz', 'GCA_000961135.2_genomic.fna.gz'])
     captured = capfd.readouterr()
     assert "Failed to send signatures: channel closed" not in captured.err
-   
+
 
 def test_gbsketch_bad_acc(runtmp):
     acc_csv = get_test_data('acc.csv')
@@ -335,7 +344,7 @@ def test_gbsketch_bad_acc(runtmp):
                 assert sig.md5sum() == ss2.md5sum()
             else:
                 assert sig.md5sum() == ss3.md5sum()
-    
+
 
 def test_gbsketch_missing_accfile(runtmp, capfd):
     acc_csv = runtmp.output('acc1.csv')
@@ -397,6 +406,7 @@ def test_gbsketch_bad_acc_fail(runtmp, capfd):
 
 
 def test_gbsketch_version_bug(runtmp):
+    # test for bug where we didn't check version correctly
     acc_csv = get_test_data('acc-version.csv')
     output = runtmp.output('simple.zip')
     failed = runtmp.output('failed.csv')