[MOBY-dev] [moby] Re: error installing Biomoby via ant
Mark Wilkinson
markw at illuminae.com
Wed Mar 11 18:38:39 UTC 2009
No need to feel bad! This is *precisely* how Moby ontology curation is
supposed to work! Objects that are not being used, or that have a
"better" object defined elsewhere in the ontology, should be deleted by
the author of the object, or by anyone who finds it. This is the Web 2.0
aspect of Moby that hasn't really been working well (probably because
everyone feels the same as you about deleting other people's stuff...).
The API prevents you from deleting objects that *are* being used, but
that's the only security we guarantee in Moby.
M
On Wed, 11 Mar 2009 11:32:11 -0700, Edward Kawas <edward.kawas at gmail.com>
wrote:
> 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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