[MOBY-dev] [moby] Re: error installing Biomoby via ant

Wed Mar 11 18:21:08 UTC 2009

Hi,

those datatypes are neither mine nor do I use them. 
They are registered at some French site. I don't use any of these SOTEST*
datatypes. 
I just can't get a fresh Biomoby checkout "installed" correctly or generate
Moses code for one of my services (using pre-defined datatypes like
ArrayString and/or ArrayFloat or one my own datatypes like MSPeakRel, which
is derived from Array and having unique field names ;) ).

Is there a way to circumvent these SOTEST* datatypes when running Moses
and/or install ant script?

Kind regards,
Michael

-----Ursprüngliche Nachricht-----
Von: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] Im Auftrag von Mark Wilkinson
Gesendet: Mittwoch, 11. März 2009 18:44
An: Core developer announcements
Betreff: Re: [MOBY-dev] [moby] Re: error installing Biomoby via ant

I believe that the MOBY Central code is supposed to check that  
articlenames are unique... but it may be bugged!

M

On Wed, 11 Mar 2009 10:00:29 -0700, Edward Kawas <edward.kawas at gmail.com>  
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]
>>
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>>
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>>
>>
>
>

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