[MOBY-dev] error installing Biomoby via ant
Paul Gordon
gordonp at ucalgary.ca
Wed Mar 11 17:19:59 UTC 2009
I can confirm that member articleNames must be unique. Otherwise there
would be no way to distinguish two HAS and a HAS-A instance.
Edward Kawas wrote:
> 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]
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>>
>>
>
>
>
More information about the MOBY-dev
mailing list