[MOBY-dev] error installing Biomoby via ant
Edward Kawas
edward.kawas at gmail.com
Wed Mar 11 17:00:29 UTC 2009
I think that I may have figured it out.
Using the datatype SOTest2_validated_cDNA_clone as an example, I think that
the main problem is that the datatype has 2 has relationships. It has
SOTest2_cDNA and SOTest2_validated. The problem, I think, is that they both
have the articlename 'has_quality'.
I am sure that articlenames in Services have to be unique, but I can't find
any documentation online saying that articlenames describing relationships
in Datatypes have to be unique as well.
So, if articlenames have to be unique, then the registry inadvertently
allowed the registration of datatypes without unique articlenames for
container relationships. Alternatively, if this is allowed, then a bug was
discovered in MoSeS.
Anyone have any insight into which one is the correct scenario?
Eddie
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Michael Gerlich
Sent: March-11-09 4:14 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] error installing Biomoby via ant
Hi Eddie,
I'am using Suns JDK 1.5 Version 16. I also encountered this behavivour
with JDK 6 with compliance level 1.5 (as I had trouble with JDK 6
generated services and axis 1.4 and Tomcat5.5).
This problem also occurs when I run install from a fresh CVS checkout
(including a fresh Biomoby cache directory). All SOTEST* datatypes are
only registered at Central registry, so they are fetched when Biomoby
fills its cache (retrieving datatypes).
Regards,
Michael
> Hi Michael,
>
> What version of JAVA are you using? What registry are you generating these
> datatypes from?
>
> Thanks,
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Michael Gerlich
> Sent: March-10-09 4:28 PM
> To: MOBY-dev at lists.open-bio.org
> Subject: [MOBY-dev] error installing Biomoby via ant
>
> Hi all,
>
> I checked out Biomoby from CVS and tried to install it via the
corresponding
> ant tasks, but after fetching all necessary libraries, the compilation
fails
> with a lot of error messages regarding datatypes SOTEST*.
>
> I also encountered this behavior when I tried to run Moses Generator for
one
> of my services with an existing Biomoby instance on another machine. There
> the build also fails.
> I tested this on 3 different machines, including both Ubuntu and XP os.
The
> error log is attached, taken from Dashboad.
>
> Does anyone encounter similar problems? Should I try cleaning Maven
> repository, Biomoby cache and/or new Eclipse workspace?
>
> Thanks in advance and regards,
> Michael
>
>
> Excerpt follows (100 error messages like this):
>
>
home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/datat
> ypes/SOTest2_engineered_foreign_gene.java:152: getMoby_Parent() in
> org.biomoby.shared.datatypes.SOTest2_engineered_foreign_gene cannot
override
> getMoby_Parent() in org.biomoby.shared.datatypes.SOTest2_engineered_gene;
> attempting to use incompatible return type
> [javac] found : org.biomoby.shared.datatypes.SOTest2_foreign_gene
> [javac] required:
org.biomoby.shared.datatypes.SOTest2_engineered_region
> [javac] public SOTest2_foreign_gene getMoby_Parent() {
> [javac] ^
> [javac]
>
/home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/data
> types/SOTest2_engineered_foreign_transposable_element.java:121:
> getMoby_has_quality() in
>
org.biomoby.shared.datatypes.SOTest2_engineered_foreign_transposable_element
> cannot override getMoby_has_quality() in
> org.biomoby.shared.datatypes.SOTest2_mobile_genetic_element; attempting to
> use incompatible return type
> [javac] found : org.biomoby.shared.datatypes.SOTest2_foreign[]
> [javac] required: org.biomoby.shared.datatypes.SOTest2_mobile[]
> [javac] public SOTest2_foreign[] getMoby_has_quality() {
> [javac] ^
> [javac]
>
/home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/data
> types/SOTest2_foreign_transposable_element.java:112: getMoby_has_quality()
> in org.biomoby.shared.datatypes.SOTest2_foreign_transposable_element
cannot
> override getMoby_has_quality() in
> org.biomoby.shared.datatypes.SOTest2_mobile_genetic_element; attempting to
> use incompatible return type
> [javac] found : org.biomoby.shared.datatypes.SOTest2_foreign[]
> [javac] required: org.biomoby.shared.datatypes.SOTest2_mobile[]
> [javac] public SOTest2_foreign[] getMoby_has_quality() {
> [javac] ^
> [javac]
>
/home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/data
> types/SOTest2_engineered_fusion_gene.java:122: getMoby_has_quality() in
> org.biomoby.shared.datatypes.SOTest2_engineered_fusion_gene cannot
override
> getMoby_has_quality() in org.biomoby.shared.datatypes.SOTest2_fusion_gene;
> attempting to use incompatible return type
> [javac] found : org.biomoby.shared.datatypes.SOTest2_engineered[]
> [javac] required: org.biomoby.shared.datatypes.SOTest2_fusion[]
> [javac] public SOTest2_engineered[] getMoby_has_quality() {
> [javac] ^
> [javac]
>
/home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/data
> types/SOTest2_engineered_rescue_region.java:120: getMoby_has_quality() in
> org.biomoby.shared.datatypes.SOTest2_engineered_rescue_region cannot
> override getMoby_has_quality() in
> org.biomoby.shared.datatypes.SOTest2_rescue_region; attempting to use
> incompatible return type
> [javac] found : org.biomoby.shared.datatypes.SOTest2_engineered[]
> [javac] required: org.biomoby.shared.datatypes.SOTest2_rescue[]
> [javac] public SOTest2_engineered[] getMoby_has_quality() {
> [javac] ^
> [javac]
>
/home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/data
> types/SOTest2_engineered_transposable_element.java:121:
> getMoby_has_quality() in
> org.biomoby.shared.datatypes.SOTest2_engineered_transposable_element
cannot
> override getMoby_has_quality() in
> org.biomoby.shared.datatypes.SOTest2_mobile_genetic_element; attempting to
> use incompatible return type
> [javac] found : org.biomoby.shared.datatypes.SOTest2_engineered[]
> [javac] required: org.biomoby.shared.datatypes.SOTest2_mobile[]
> [javac] public SOTest2_engineered[] getMoby_has_quality() {
> [javac] ^
> [javac]
>
/home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/data
> types/SOTest2_five_prime_coding_exon_noncoding_region.java:114:
> getMoby_part_of() in
>
org.biomoby.shared.datatypes.SOTest2_five_prime_coding_exon_noncoding_region
> cannot override getMoby_part_of() in
> org.biomoby.shared.datatypes.SOTest2_transcript_region; attempting to use
> incompatible return type
> [javac] found :
> org.biomoby.shared.datatypes.SOTest2_five_prime_coding_exon[]
> [javac] required: org.biomoby.shared.datatypes.SOTest2_transcript[]
> [javac] public SOTest2_five_prime_coding_exon[] getMoby_part_of()
{
> [javac] ^
> [javac]
>
/home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/data
> types/SOTest2_five_prime_exon_coding_region.java:114: getMoby_part_of() in
> org.biomoby.shared.datatypes.SOTest2_five_prime_exon_coding_region cannot
> override getMoby_part_of() in
> org.biomoby.shared.datatypes.SOTest2_transcript_region; attempting to use
> incompatible return type
> [javac] found :
> org.biomoby.shared.datatypes.SOTest2_five_prime_coding_exon[]
> [javac] required: org.biomoby.shared.datatypes.SOTest2_transcript[]
> [javac] public SOTest2_five_prime_coding_exon[] getMoby_part_of()
{
> [javac]
>
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>
--
Michael Gerlich
Group Bioinformatics & Mass Spectrometry
Leibniz Institute of Plant Biochemistry
06120 Halle, Germany
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