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

Edward Kawas edward.kawas at gmail.com
Wed Mar 11 18:32:11 UTC 2009 

I feel bad doing so, but ok. I will back up their definitions and then remove them.

When I am done, I will let everyone know.

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson
Sent: March-11-09 11:32 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] [moby] Re: error installing Biomoby via ant

Eddie, if no service uses them, and if no object uses them, then we should  
probably consider deleting them...  this is allowed by the API.

M



On Wed, 11 Mar 2009 11:21:08 -0700, Michael Gerlich  
<MichaelGerlich at gmx.de> wrote:

> 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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