Add option to return sequences from the Genbank file as a stream of sequences #870
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josemduarte
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Apr 15, 2020
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Thanks! One comment about error handling
| } catch (IOException | CompoundNotFoundException e) { | ||
| // TODO Auto-generated catch block | ||
| e.printStackTrace(); | ||
| return null; |
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I'd rather throw the exception forward and let the caller handle it. Returning null means all callers have to handle the null and that they lose the ability to provide a good error message.
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Could you merge master into your branch? The tests should pass then. A problem with them was fixed in #871 |
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I thought I had... I'll double check.
As far as the exception goes, can you actually pass that exception on? If I
try, Eclipse tells me it's an error...
…On Wed, Apr 15, 2020, 3:39 PM Jose Manuel Duarte ***@***.***> wrote:
Could you merge master into your branch? The tests should pass then. A
problem with them was fixed in #871
<#871>
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I successfully merged the new stuff in.
There are ways to get the exception out of the lambda. They are a bit
tedious, but if it is helpful, I can give that a try...
…On Wed, Apr 15, 2020, 4:02 PM Erik McKee ***@***.***> wrote:
I thought I had... I'll double check.
As far as the exception goes, can you actually pass that exception on? If
I try, Eclipse tells me it's an error...
On Wed, Apr 15, 2020, 3:39 PM Jose Manuel Duarte ***@***.***>
wrote:
> Could you merge master into your branch? The tests should pass then. A
> problem with them was fixed in #871
> <#871>
>
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There seems to be an issue with the new test. See logs from travis, there's a timeout after running GenbankReaderTest |
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I'll take a look... if I run it in junit in eclipse it runs fine... that's
odd
…On Sun, Apr 19, 2020, 6:40 PM Jose Manuel Duarte ***@***.***> wrote:
There seems to be an issue with the new test. See logs from travis,
there's a timeout after running GenbankReaderTest
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How do i rerun Travis after adding a new commit? (or what is a better debugging mechanism here?) |
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I've just triggered the travis tests again |
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I commented out the new test to verify that it is the cause. Is there an
easy way to debug?
…On Tue, Apr 21, 2020, 1:41 PM Jose Manuel Duarte ***@***.***> wrote:
I've just triggered the travis tests again
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OK, it still hangs even if not executing my test... |
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Can you try to run |
lafita
requested changes
Apr 22, 2020
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| @Test | ||
| public void testSequenceStream() { | ||
| CheckableInputStream inStream = new CheckableInputStream(this.getClass().getResourceAsStream("/two-dnaseqs.gb")); |
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Did you also include this file in the test resources directory? It seems not to be in this PR
| LinkedHashMap<String,S> sequences = new LinkedHashMap<>(); | ||
| @SuppressWarnings("unchecked") | ||
| int i=0; | ||
| while(true) { |
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This is what is hanging the build. Because the stream returned is null (the file does not exist, see comment below), sequence is always null and this while loop never finishes.
The while loop is not needed anymore, simply take an action if the sequence is null.
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Isn't that the same file used by one of the existing tests?
…On Wed, Apr 22, 2020, 6:41 AM Aleix Lafita ***@***.***> wrote:
***@***.**** requested changes on this pull request.
------------------------------
In
biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
<#870 (comment)>:
> @@ -163,6 +164,27 @@ public void testProcess() throws Exception {
assertEquals(3, dnaSequence.getAccession().getVersion().intValue());
assertTrue(genbankDNA.isClosed());
}
+
+ @test
+ public void testSequenceStream() {
+ CheckableInputStream inStream = new CheckableInputStream(this.getClass().getResourceAsStream("/two-dnaseqs.gb"));
Did you also include this file in the test resources directory? It seems
not to be in this PR
------------------------------
In
biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
<#870 (comment)>:
> @@ -153,35 +154,56 @@ public GenbankReader(
}
LinkedHashMap<String,S> sequences = new LinkedHashMap<>();
- @SuppressWarnings("unchecked")
int i=0;
while(true) {
This is what is hanging the build. Because the stream returned is null
(the file does not exist, see comment below), sequence is always null and
this while loop never finishes.
The while loop is not needed anymore, simply take an action if the
sequence is null.
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True the file exists, but the while loop is not needed anymore and probably the one causing the timeout in travis. @emckee2006 does maven install work locally for you? |
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Why doesn't that method need the while loop? It still needs to support
grabbing multiple sequences...
…On Wed, Apr 22, 2020, 10:55 AM Aleix Lafita ***@***.***> wrote:
True the file exists, but the while loop is not needed anymore and
probably the one causing the timeout in travis. @emckee2006
<https://github.com/emckee2006> does maven install work locally for you?
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This needs help... closing for now... |
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