Re: libbarclay-java needs update, libpicard-java runtime tests by pigx-scrnaseq
Hi again,
On 11.09.20 00:01, Pierre Gruet wrote:
> Hi,
>
> Le 10/09/2020 à 17:11, Andreas Tille a écrit :
>> Hi Steffen,
>>
>> On Thu, Sep 10, 2020 at 03:32:49PM +0200, Steffen Möller wrote:
>>> libpicard-java needs an argparse class from the barclay library. This
>>> was found by the intense build-time testing of the PIGx-scRNAseq.
>>> ...
>>> How shall I/we proceed? My immediate plan was to just update locally to
>>> vesion 4.0.0 (released a few days ago) and see if the two reverse
>>> dependencies still build.
>> From my naive point of view the migration to a recent libbarclay-java
>> should be easy given that only two packages in our hands are rdepends
>> of it. Thus I was running routine-update on barclay[1] but the build
>> is running into:
>>
>> ...
>> radle Test Executor 1 finished executing tests.
>> Results: FAILURE (346 tests, 344 successes, 2 failures, 0 skipped)
>>
>>
>> Pierre, can you help? ;-)
>>
> I have had a really hard time, but I finally found the issue (a
> LinkedHashMap was wrongly iterated over in a Freemarker template), now
> all build tests are passing and the .deb can be built :-)
> I have pushed my changes to Salsa.
>
> Could someone do some final checks (maybe forward the patch I have written)?
https://github.com/broadinstitute/barclay/
You can expect to be listed as a contributor one your patch is accepted.
That
and an unpredictable exchange with upstream is what you earned. The
submission
to upstream is on you :) Should you feel a bit awkward with github then I
happily help ... but since you are doing just fine with gitlab ...
I added
--- a/debian/pom-barclay.xml
+++ b/debian/pom-barclay.xml
@@ -5,7 +5,7 @@
<artifactId>barclay</artifactId>
<packaging>jar</packaging>
<description>barclay</description>
- <version>2.1.0</version>
+ <version>4.0.0</version>
<name>barclay</name>
<organization>
<name>org.broadinstitute</name>
but otherwise left it and it looks good!?:
$ dpkg -c ../libbarclay-java_4.0.0-1_all.deb
drwxr-xr-x root/root 0 2020-09-10 23:55 ./
drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/
drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/share/
drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-09-10 23:55
./usr/share/doc/libbarclay-java/
-rw-r--r-- root/root 709 2020-09-10 23:55
./usr/share/doc/libbarclay-java/changelog.Debian.gz
-rw-r--r-- root/root 3287 2020-09-10 23:55
./usr/share/doc/libbarclay-java/copyright
drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/share/java/
-rw-r--r-- root/root 147669 2020-09-10 23:55
./usr/share/java/barclay-4.0.0.jar
drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/share/maven-repo/
drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/share/maven-repo/org/
drwxr-xr-x root/root 0 2020-09-10 23:55
./usr/share/maven-repo/org/broadinstitute/
drwxr-xr-x root/root 0 2020-09-10 23:55
./usr/share/maven-repo/org/broadinstitute/barclay/
drwxr-xr-x root/root 0 2020-09-10 23:55
./usr/share/maven-repo/org/broadinstitute/barclay/4.0.0/
-rw-r--r-- root/root 2246 2020-09-10 23:55
./usr/share/maven-repo/org/broadinstitute/barclay/4.0.0/barclay-4.0.0.pom
drwxr-xr-x root/root 0 2020-09-10 23:55
./usr/share/maven-repo/org/broadinstitute/barclay/debian/
-rw-r--r-- root/root 2247 2020-09-10 23:55
./usr/share/maven-repo/org/broadinstitute/barclay/debian/barclay-debian.pom
lrwxrwxrwx root/root 0 2020-09-10 23:55
./usr/share/java/barclay.jar -> barclay-4.0.0.jar
lrwxrwxrwx root/root 0 2020-09-10 23:55
./usr/share/maven-repo/org/broadinstitute/barclay/4.0.0/barclay-4.0.0.jar
-> ../../../../../java/barclay.jar
lrwxrwxrwx root/root 0 2020-09-10 23:55
./usr/share/maven-repo/org/broadinstitute/barclay/debian/barclay-debian.jar
-> ../../../../../java/barclay.jar
>
>>> If this update then then happens to also fix
>>> the failed test of PIGx-scRNAseq, then this shall be it. Alternatively,
>>> well, we would need versioned library packages, then, and I'll see how
>>> far version 3 carries me.
>> I do not think we should spent time on a version that just became
>> outdated so version 4 should most probably be our target.
>>
>>> Right? If there is anyone out there who is a
>>> bit closer to the barclay library, please direct me if there is any need
>>> to keep the older version 2 in the archive.
>> Libpicard-java needs an update as well - so I'd suggest to upgrade
>> libbarclay-java first and than see how to continue (may be together
>> with upstream).
>>
>> Disclaimer: All I said is probably absolutely naive and not based on
>> any deeper knowledge about the software involved simply guided by my gut
>> feeling about what usually was a sensible strategy.
>>
> I do not know barclay either but I would say the same.
libpicard-java just finished building and testing (and it tested
intensively), but pigx-scrnaseq will need to wait for another day.
Will upload libbarclay-java - thank to tons!
Steffen
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