[MOBY-dev] error installing Biomoby via ant

Pieter Neerincx pieter.neerincx at gmail.com
Thu Mar 26 15:47:31 UTC 2009 

Making the articleName attributes mandatory in all cases will also  
help to make MoSeS generated code more readable. If the optional  
articleName attributes are missing, MoSeS will generate some variables  
with "placeholder names". If you have more than one of those, things  
can get rather confusing. So you have my vote for making articleName  
attributes mandatory in all circumstances!

Cheers,

Pi

On 26 Mar 2009, at 16:07, Paul Gordon wrote:

> Sounds good to me.  If the docs don't say articleName is mandatory,  
> that was an error of omission on our part...
>
> Edward Kawas wrote:
>> I thought that the articlename was supposed to be mandatory...  
>> anyways, the
>> 2 services that I mentioned seem to be the only 2 incorrect  
>> datatypes. I
>> created a patch for the registry, but before I committed it, I  
>> wanted to
>> check that I had the general idea down.
>>
>> The patch works like so:
>>
>> User X is registering a datatype. We take all of the direct HAS/HASA
>> articlenames and then traverse the ISA hierarchy towards the root  
>> node
>> ensuring that the articlenames are not used further up the tree.
>>
>> This is how I found those 2 datatypes that I mentioned previously.  
>> I tested
>> my patch against all datatypes in our ontology.
>>
>> If everyone is happy with this, I will commit the patch and update  
>> the
>> documentation.
>>
>> 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-26-09 7:31 AM
>> To: Core developer announcements
>> Subject: Re: [MOBY-dev] error installing Biomoby via ant
>>
>> 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]
>>>>>>
>>>>>> _______________________________________________
>>>>>> MOBY-dev mailing list
>>>>>> MOBY-dev at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>>>
>>>>>> _______________________________________________
>>>>>> MOBY-dev mailing list
>>>>>> MOBY-dev at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> MOBY-dev mailing list
>>>> MOBY-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>
>>>> _______________________________________________
>>>> MOBY-dev mailing list
>>>> MOBY-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>
>>> -------------------------------------------------------------
>>> Wageningen University and Research centre (WUR)
>>> Laboratory of Bioinformatics
>>> Transitorium (building 312) room 1034
>>>
>>> Dreijenlaan 3
>>> 6703 HA Wageningen
>>> The Netherlands
>>>
>>> phone:  +31 (0)317-483 060
>>> mobile: +31 (0)6-143 66 783
>>> e-mail: pieter.neerincx at gmail.com
>>> skype:  pieter.online
>>> -------------------------------------------------------------
>>>
>>>
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>>>
>>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>>
>>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-------------------------------------------------------------
Wageningen University and Research centre (WUR)
Laboratory of Bioinformatics
Transitorium (building 312) room 1034

Dreijenlaan 3
6703 HA Wageningen
The Netherlands

phone:  +31 (0)317-483 060
mobile: +31 (0)6-143 66 783
e-mail: pieter.neerincx at gmail.com
skype:  pieter.online
-------------------------------------------------------------

More information about the MOBY-dev mailing list