[BEXIS2-Dev] Default Data Structure

bexis2-dev at listserv.uni-jena.de bexis2-dev at listserv.uni-jena.de
Fr Feb 3 14:16:12 CET 2017 

Hi all,

first of all -

On 31.01.2017 12:14, bexis2-dev at listserv.uni-jena.de wrote:
> Hello Roman,
>
> I am not a specialist in dealing with XML schema definitions.
> So I have a few questions referring to these definitions.
>
> 1. In the schemas you sent I find the following header in schemaPDwithoutDS.xsd:
>
>> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema"
>> 	targetNamespace="http://www.bgc-jena.mpg.de"
>> 	xmlns:bgc="http://www.bgc-jena.mpg.de"
>>    	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
>> 	xmlns="http://www.bgc-jena.mpg.de" elementFormDefault="qualified"
>> 	xml:lang="en">
> My understanding ist that the namespace bgc is referred to threefold:
> – the target of this XML schema definition is "http://www.bgc-jena.mpg.de"
> – the default namespace in this XML schema is "http://www.bgc-jena.mpg.de"
> – in addition the prefix "bgc" is assigned to the namespace "http://www.bgc-jena.mpg.de"
>
> The last one seems to be superfluous, to me it seems that you need either a specific ("bgc") or a default definition for a given namespace. Or am I mistaken?
The schema was generated a while ago (around 2007). We all were not part 
of the former team. There was never a complete review of the schema. We 
probably review it (during the next 6 month).

>
> The namespace bgc is used in either ref (always "bgc:source")
>
>> <xsd:attribute ref="bgc:source"/>
>
> or several xpath attributes:
>
>> <xsd:selector xpath="bgc:owner"/>
>> <xsd:selector xpath="bgc:keyword"/>
>> …
> While I can understand the latter usage to enforce uniqueness on the respective entries (though not the necessity of the "bgc:"), I don't understand the effect of the former ref attribute. Can you explain?

The ref refers to an attribut called "bgc:source". You will find it in 
the baseTypes.xsd schema. That means on that position an attribute exists.

>
> 2. The other question is that when importing the schema into the BExIS 2.10 system, I am asked for fields giving the title and a description of the data. I didn't find any description in the metadata schema. Is this intentional?
Not intentional but also not intuitional (intuitive) enough. The mapping 
asks you to link to a field in your metadata structure where a 
description (field) is. In the BE(xIS) metadata usually the 
bgc:methodology/bgc:introduction node is used for it. Maybe not the best 
place and having something called description or abstract in metadata 
would fit better. But that is how this metadata structure look at the 
moment...


>
> All the best
> Thomas
>
>> Am 20.01.2017 um 16:25 schrieb bexis2-dev at listserv.uni-jena.de:
>>
>> Hi Thomas,
>>
>> regarding the metadata schema, please find attached a ZIP file with the
>> latest schema of the Exploratories.
>>
>> The main XSD file is: schemaPDwithoutDS.xsd
>>
>> The other 2 files are dependencies.
>>
>> All 3 files need to be uploaded to the system first (Collect > Push Big
>> File). Then in Manage Metadata Structure (in settings/gear symbol) you
>> should be able to import the main XSD file (select from previously
>> uploaded).
>>
>> There is still one small issue with this schema. All fields are
>> indicated as required fields. This is just because we use a different
>> way of defining required fields in the XSD. Not a big deal, just needs
>> someone to go through and change the definition. But haven't got around
>> to do that. So please ignore the red asterisks in the form, once the XSD
>> has been imported.
>>
>>
>> Permissions on system features are managed through the admin menue
>> (settings): Feature Permissions
>> Then click on the Metadata Management (the term, not the checkbox) and
>> you will see all users and their permission on this feature. Note: any
>> change there takes effect immediately, without further confirmation.
>>
>> Regarding your other error message, Sven will reply to you.
>>
>> Best regards,
>> Roman
>>
>>
>>
>> Am 20.01.2017 um 12:07 schrieb bexis2-dev at listserv.uni-jena.de:
>>> Hello Roman,
>>>
>>> thanks for the swift reply.
>>>
>>> We are looking forward to the "Party Package" and would love to take you up on the offer of a "2 day session in Göttingen and do the migration jointly."
>>>
>>> It sounds like a good idea to wait with serious efforts to transfer the data until the next release, but I would like to tinker with the metadata definition, import, export etc., thus any helpful files would be very welcome.
>>>
>>> I still have to work on my local installation, though, right now I get on
>>> 	http://bexis2.10/SAM/Account/MyAccount
>>> an error message
>>> 	42703: Spalte securityqu0_.title existiert nicht
>>> 	Description: An unhandled exception occurred during the execution of the current web request.
>>> 	Please review the stack trace for more information about the error and where it originated in the code.
>>> 	Exception Details: Npgsql.NpgsqlException: 42703: Spalte securityqu0_.title existiert nicht
>>>
>>> Which permissions do I need for the Metadata Schema Management, and where and how are they granted?
>>>
>>> Cheers
>>> Thomas
>>>
>>>> Am 19.01.2017 um 18:48 schrieb bexis2-dev at listserv.uni-jena.de:
>>>>
>>>> Hello Thomas,
>>>>
>>>> I now recall I promised to provide you with the adapted XSD of the
>>>> Exploratories Project a few month ago. Sorry, I didn't follow up on
>>>> that. I just don't have it right now, but will get back to you on this
>>>> by tomorrow.
>>>>
>>>> With this XSD you will have very similar elements of the metadata as you
>>>> are used to in BEXIS 1. And if you like to change something or add
>>>> another schema to the system, thats easily possible. As you know, BEXIS
>>>> 2 can work with multiple schemas at the same time.
>>>>
>>>> However, it will not be exactly the same schema, since a number of
>>>> things have changed in BEXIS 2, e.g. Data Structures are managed
>>>> separately from the metadata in BEXIS 2. Also, we are currently working
>>>> on the linkage between the metadata and the so called "Party Package"
>>>> (managing projects, people, organisations, etc). This will be available
>>>> in the next release in May 2017. BTW, this will be a dedicated release
>>>> to support the migration from B1 to B2.
>>>>
>>>> For the transfer of all entities at database level (data, metadata,
>>>> users, permissions, etc.) most of the scripts are ready by now. I'm not
>>>> sure how self-explanatory they are. Perhaps we have to set up a 2 day
>>>> session in Göttingen and do the migration jointly. I suspect this will
>>>> need some more preparation and testing before-hand. What's your timeline
>>>> on that?
>>>>
>>>> Regarding the Metadata Schema Management, are you sure the required
>>>> feature permissions are set for you? We are not aware of any problem
>>>> there. It works for all our instances.
>>>>
>>>>
>>>> best wishes
>>>> Roman
>>>>
>>>>
>>>>
>>>> Am 18.01.2017 um 16:11 schrieb bexis2-dev at listserv.uni-jena.de:
>>>>> Hello folks,
>>>>>
>>>>> I might have asked this before, but am not aware of any satisfying answer: are there any predefined metadata and data structures available with BExIS 2, in particular to ease the transfer from BExIS 1 to BExIS 2?
>>>>> We have about 200 structured and about 600 unstructured datasets in our current BExIS 1 database and want to move to BExIS 2 in the (near) future.
>>>>>
>>>>> In principle it should be easy to transfer at least the unstructured datasets to BExIS 2, but I don't see the metadata structure required. This should be constructed somehow from the schema definitions used in BExIS 1:
>>>>> 	schema.xsd  which calls
>>>>> 		baseTypes.xsd
>>>>> 		researchObjects.xsd
>>>>> 		dataStructure.xsd
>>>>> but I am not quite sure how to do this.
>>>>> Has somebody done this and can provide a suitable schema definition?
>>>>>
>>>>> And what are the experiences concerning structured datasets?
>>>>>
>>>>> An additional problem is that I am not able to manage Metadata structures, my BExIS 2.10 tells me
>>>>>
>>>>> 	Access denied!
>>>>> 	Reason: You are not authorized.
>>>>>
>>>>> Any help would be highly appreciated…
>>>>>
>>>>> With best regards
>>>>> Thomas Fischer
>>>>>
>>>>> --
>>>>> Thomas Fischer PhD
>>>>> Research and Development
>>>>> SFB 990 EFForTS | INF-Project
>>>>>
>>>>> Georg-August-Universität Göttingen
>>>>> Niedersächsische Staats- und Universitätsbibliothek Göttingen
>>>>> D-37070 Göttingen
>>>>>
>>>>> Papendiek 14  (Historical Building, Room 2.407)
>>>>> +49 551 39-33883 (Tel.)
>>>>> +43 662 621498 (Tel.)
>>>>> +49 551 39-33856 (Fax)
>>>>>
>>>>> fischer at sub.uni-goettingen.de
>>>>> http://www.sub.uni-goettingen.de/
>>>>> http://rdd.sub.uni-goettingen.de/
>>>>> http://vifamath.de/
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> bexis2-dev mailing list
>>>>> bexis2-dev at listserv.uni-jena.de
>>>>> https://lserv.uni-jena.de/mailman/listinfo/bexis2-dev
>>>>>
>>>> --
>>>>
>>>> Roman Gerlach
>>>> Kontaktstelle Forschungsdatenmanagement
>>>> BExIS++ Projektkoordinator
>>>> Friedrich-Schiller-Universität Jena
>>>> Leutragraben 1, Jentower 17N04
>>>> 07743 Jena
>>>>
>>>> Tel.:  +49-(0)3641-948968
>>>> Email: roman.gerlach at uni-jena.de
>>>> Web:   http://www.uni-jena.de/forschungsdatenmanagement.html
>>>>       http://bexis2.uni-jena.de/
>>>>
>>>> _______________________________________________
>>>> bexis2-dev mailing list
>>>> bexis2-dev at listserv.uni-jena.de
>>>> https://lserv.uni-jena.de/mailman/listinfo/bexis2-dev
>>>
>>>
>>> _______________________________________________
>>> bexis2-dev mailing list
>>> bexis2-dev at listserv.uni-jena.de
>>> https://lserv.uni-jena.de/mailman/listinfo/bexis2-dev
>>>
>> --
>>
>> Roman Gerlach
>> Kontaktstelle Forschungsdatenmanagement
>> BExIS++ Projektkoordinator
>> Friedrich-Schiller-Universität Jena
>> Leutragraben 1, Jentower 17N04
>> 07743 Jena
>>
>> Tel.:  +49-(0)3641-948968
>> Email: roman.gerlach at uni-jena.de
>> Web:   http://www.uni-jena.de/forschungsdatenmanagement.html
>>        http://bexis2.uni-jena.de/
>>
>> _______________________________________________
>> bexis2-dev mailing list
>> bexis2-dev at listserv.uni-jena.de
>> https://lserv.uni-jena.de/mailman/listinfo/bexis2-dev
>
>
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-- 
Andreas Ostrowski
Datenmanagement Biodiversitaets-Exploratorien
Friedrich-Schiller-Universität Jena
Institut für Informatik
Leutragraben 1, Jentower
07743 Jena

Tel.:   ++ 49 3641 9 46431

E-Mail: andreas.ostrowski at uni-jena.de
WWW:    http://www.biodiversity-exploratories.de
--

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