[MOBY-dev] error installing Biomoby via ant
Paul Gordon
gordonp at ucalgary.ca
Thu Mar 26 14:31:02 UTC 2009
As there is no unique place to put documentation for the purpose or
usage of a member other than its articleName, I'd suggest that the
articleName be mandatory, if only for the purpose of succinctly
describing the relationship between it and the container class.
Pieter Neerincx wrote:
> Hi,
>
> If I remember correctly for datatypes it's the combination of the
> object's name and articleName attribute value that must be unique. As
> long as the combi is unique you can distinguish two HAS and a HAS-A
> instance. Therefore if an object has multiple relationships involving
> child element of the same type a unique articleName attribute is
> mandatory but otherwise articleName attributes were optional. In
> addition articleNames in service inputs or outputs were mandatory and
> quite some time ago articleNames became also mandatory for primitives
> no matter whether there was only one relationship involving a certain
> type of primitive or whether there were more.
>
> So AFAIK the GCP_* objects mentioned below are correctly registered
> according to the current specs, but to keep things simple it wouldn't
> hurt to make articleName attributes always mandatory. That would
> render quite some currently used objects invalid though...
>
> Cheers,
>
> Pi
>
> On 25 Mar 2009, at 18:29, Edward Kawas wrote:
>
>> Based on what Paul has said, is it true that the datatypes
>> (GCP_BiologicalSample, GCP_Germplasm) are then incorrectly registered?
>>
>> 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 Paul Gordon
>> Sent: March-11-09 10:20 AM
>> To: Core developer announcements
>> Subject: Re: [MOBY-dev] error installing Biomoby via ant
>>
>> 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]
>>>>
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>>>>
>>>>
>>>
>>>
>>>
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>
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