Re: libbarclay-java needs update, libpicard-java runtime tests by pigx-scrnaseq
Hi Steffen,
Le 11/09/2020 à 02:23, Steffen Möller a écrit :
> 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 ...
>
Thanks! :-)
I have just forwarded the patch. I was too lazy (or it was too late) to
do it yesterday night. Thanks for your words!
>
> 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!
>
Thanks for the upload and for the information that libpicard-java is
also fine!
>
> Steffen
>
>
Best,
Pierre
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