[MOBY-dev] [moby] Re: error installing Biomoby via ant
Paul Gordon
gordonp at ucalgary.ca
Wed Mar 11 19:04:57 UTC 2009
Mark,
Hopefully we can find to the time next week to purge it a bit...
Mark Wilkinson wrote:
> 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]
>>>>>
>>>>> _______________________________________________
>>>>> MOBY-dev mailing list
>>>>> MOBY-dev at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>>
>>>>> _______________________________________________
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>>>>> MOBY-dev at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
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>>
>>
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