pywrapper-devel

Re: [PyWrapper-devel] Managing the concept server

[<wi...@go...>]

Milko,

comment #1: try not to use :: in the full concepts but make them look like a
simple URL. for example
http://www.ipgri.org/schemas/mcpd_eurisco/1.00/NICODE

comment #2: the error says: "biocase.CNS.NonUniqueConceptError". so it looks
as if the aliases or qualified names are not unique. check. another problem
could be that the alias.txt should have "=" between an alias and the
qualified concept. But I think its not required.

commen #3: the idea is that the server CANNOT start up with conflicting or
broken alias files. this shoulkd be fixed before. dont you agree with that?
otherwise you could get unforseen weird results.

markus


On 11/13/06, Skofic A. Milko (IPGRI) <M.S...@cg...> wrote:
>
> Hi guys, I am trying to create an alias file to use other schemas and test
> mapping and output models. I have created a schema, run it through TAPIR's
> schema parser and tried to set up another concept server.
> I get an error whenever I startup TAPIR, and I am sure it has to do with
> the alias file and its other related files.
> The error is:
>
> Traceback (most recent call last):
>   File "../webapp/start_server.py", line 56, in ?
>     import root, page
>   File "/Library/WebServer/Services/pywrapper/webapp/root.py", line 17, in
> ?
>     import page, biocase.configuration
>   File "/Library/WebServer/Services/pywrapper/webapp/page.py", line 24, in
> ?
>     class Page(object):
>   File "/Library/WebServer/Services/pywrapper/webapp/page.py", line 26, in
> Page
>     _dsaObjDict = biocase.pywrapper.datasource_factory.getDsaDict()
>   File
> "/Library/WebServer/Services/pywrapper/lib/biocase/pywrapper/datasource_factory.py",
> line 49, in getDsaDict
>     dsaObj.readPrefsFile()
>   File
> "/Library/WebServer/Services/pywrapper/lib/biocase/pywrapper/datasource.py",
> line 218, in readPrefsFile
>     parse(filename, handler)
>   File
> "/Library/WebServer/Services/pywrapper/tools/python/lib/python2.4/site-packages/_xmlplus/sax/__init__.py",
> line 31, in parse
>     parser.parse(filename_or_stream)
>   File
> "/Library/WebServer/Services/pywrapper/tools/python/lib/python2.4/site-packages/_xmlplus/sax/expatreader.py",
> line 109, in parse
>     xmlreader.IncrementalParser.parse(self, source)
>   File
> "/Library/WebServer/Services/pywrapper/tools/python/lib/python2.4/site-packages/_xmlplus/sax/xmlreader.py",
> line 123, in parse
>     self.feed(buffer)
>   File
> "/Library/WebServer/Services/pywrapper/tools/python/lib/python2.4/site-packages/_xmlplus/sax/expatreader.py",
> line 216, in feed
>     self._parser.Parse(data, isFinal)
>   File
> "/Library/WebServer/Services/pywrapper/tools/python/lib/python2.4/site-packages/_xmlplus/sax/expatreader.py",
> line 312, in start_element
>     self._cont_handler.startElement(name, AttributesImpl(attrs))
>   File
> "/Library/WebServer/Services/pywrapper/lib/biocase/pywrapper/datasource_handler.py",
> line 73, in startElement
>     self._lastConceptObj = buildConceptFromAttrs(attrs,
> ns=self._lastSchemaNS)
>   File
> "/Library/WebServer/Services/pywrapper/lib/biocase/pywrapper/filter/concept.py",
> line 215, in buildConceptFromAttrs
>     conceptObj = buildConcept(qname, ns)
>   File
> "/Library/WebServer/Services/pywrapper/lib/biocase/pywrapper/filter/concept.py",
> line 239, in buildConcept
>     CNServer = createCNServer(aliasList=cfgObj.ConceptNameServer.AliasList,
> cachedir=cfgObj.cacheLocator)
>   File "/Library/WebServer/Services/pywrapper/lib/biocase/CNS.py", line
> 433, in createCNServer
>     CNS.addAliasLocation(alias)
>   File "/Library/WebServer/Services/pywrapper/lib/biocase/CNS.py", line
> 168, in addAliasLocation
>     self._read(fh)
>   File "/Library/WebServer/Services/pywrapper/lib/biocase/CNS.py", line
> 241, in _read
>     self.addConcept( c, additionalAliases=[] )
>   File "/Library/WebServer/Services/pywrapper/lib/biocase/CNS.py", line
> 346, in addConcept
>     raise NonUniqueConcept(conceptObj)
> biocase.CNS.NonUniqueConceptError in atexit._run_exitfuncs:
> Traceback (most recent call last):
>   File
> "/Library/WebServer/Services/pywrapper/tools/python/lib/python2.4/atexit.py",
> line 24, in _run_exitfuncs
>     func(*targs, **kargs)
>   File
> "/Library/WebServer/Services/pywrapper/tools/python/lib/python2.4/logging/__init__.py",
> line 1333, in shutdown
>     h.close()
>   File
> "/Library/WebServer/Services/pywrapper/tools/python/lib/python2.4/logging/__init__.py",
> line 674, in close
>     del _handlers[self]
> KeyError: <logging.StreamHandler instance at 0x1385418>
> Error in sys.exitfunc:
> Traceback (most recent call last):
>   File
> "/Library/WebServer/Services/pywrapper/tools/python/lib/python2.4/atexit.py",
> line 24, in _run_exitfuncs
>     func(*targs, **kargs)
>   File
> "/Library/WebServer/Services/pywrapper/tools/python/lib/python2.4/logging/__init__.py",
> line 1333, in shutdown
>     h.close()
>   File
> "/Library/WebServer/Services/pywrapper/tools/python/lib/python2.4/logging/__init__.py",
> line 674, in close
>     del _handlers[self]
> KeyError: <logging.StreamHandler instance at 0x1385418>
>
> This listing comes from the terminal. I am sure I did something wrong with
> the files, however it should not crash like this. Anyways here are the
> files:
>
> The alias file is at http://eurisco.ecpgr.org/schemas/alias.txt
> The schema file is at:
> http://eurisco.ecpgr.org/schemas/MCPD_EURISCO_1.00.xsd
> And the model file is at:
> http://eurisco.ecpgr.org/schemas/MCPD_EURISCO_1.00.xml
>
> I have now removed the reference to that alias file so the system can
> work.
> Looking at the alias file I see a strange syntax: is that correct? I only
> changed the label, alias and added the models section.
>
> Thanks!
>
> Milko
>

Re: [PyWrapper-devel] Managing the concept server

[<wi...@go...>]

just quick:

- just ot avoid confusion. the root"table" is a root Alias!

- not available I am working on. it means the following: for a given model
pywrapper analyses the mappings and comes up with a list of aliases used fo=
r
the IndexingRecord. If this list includes the preferred alias, it uses this
to build the tablealias tree from, otherwise just picks one randomly. So no=
t
available means your alias is not usable for a record definition. otherwise
a single datasource would only be allowed to represent one kind of object. =
a
specimen with identifications could also serve taxon data in theory for
example - with a different root alias. we maybe should have avoided this in
TAPIR, but its like this now.

- pywrapper tries to reduce the list of available aliases. This gives bette=
r
performance. For example if a metadata table and a specimen table both are
found to be used as root aliases, but the specimen table contains a FK to
metadata, pywrapper knows it can ignore the metadata table, cause its ID
will depend on the specimen ID. I gotta check this routine again to be sure
it makes sense.


And: in the configtools mapping pane (overview) there is now a section that
lists all shared models if there are any configured. Together with the
number of dontrepeats, the preferred and required root alias.

Markus



On 11/14/06, Skofic A. Milko (IPGRI) <M.S...@cg...> wrote:
>
> OK I added the preferredRootTable to the preferences and it sees it
> alright, except that it says it cannot use it:
> <diagnostic time=3D"2006-11-14T09:44:05.92" level=3D"warn">
> Preferred root alias 'ACC' not available. Use alias 'ACC_STORAGE' out
> of [u'ACC_STORAGE']
> </diagnostic>
>
> What does "not available" mean? If you want to try for yourself the
> address is:
> http://tapir.grinfo.net:8080/pywrapper
> the passwords are the usual ACDC, the data source is EURISCO and the
> query I use is:
> <?xml version=3D'1.0' encoding=3D'UTF-8'?>
> <request>
>         <header>
>                 <source accesspoint=3D"
> http://tapir.grinfo.net:8080/pywrapper/
> pywrapper?dsa=3DEURISCO" sendtime=3D"2006-11-13T12:54:29.43"/>
>         </header>
>         <search count=3D'true' start=3D'0' limit=3D'50'>
>                 <externalOutputModel location=3D"
> http://eurisco.ecpgr.org/schemas/
> MCPD_EURISCO_1.00.xml"/>
>                 <filter>
>                         <like>
>                                 <concept id=3D'GENUS@mcpd_eurisco_100' />
>                                 <literal value=3D'B*' />
>                         </like>
>                 </filter>
>                 <orderBy>
>                         <concept id=3D'INSTCODE@mcpd_eurisco_100' />
>                         <concept id=3D'GENUS@mcpd_eurisco_100' />
>                         <concept id=3D'ACCENUMB@mcpd_eurisco_100' />
>                 </orderBy>
>         </search>
> </request>
>
> Hope it helps!
>
> Milko
>
> P.S. Shouldn't the preferredRootTable be set in the structure pane,
> like it was with BioCASE?
>
>
> On Nov 13, 2006, at 23:57 , Markus D=F6ring wrote:
>
> > alright.
> > looks as if it works. can you try milko?
> > m
> >
> >
> > On 13.11.2006, at 23:43, Markus D=F6ring wrote:
> >
> > ahh man.
> > its close to work but not yet. but I removed the serious error with
> > models. you can update now, but the preferred root alias selection
> > doesnt yet work fully.
> > the idea is that you can assign a preferred root alias in the
> > dsa_prefs for a shared model. but it will only be used if the alias
> > is one of the potential ones. Otherwise you can also assign a
> > "requiredRootAlias" which is always added to the root alias list no
> > matter what. but that still doesnt work...
> >
> > heres what it look likes in the prefs:
> >
> > <model location=3D"http://rs.tdwg.org/tapir/cs/abcd2.06/model/
> > abcd206.xml" preferredRootAlias=3D"herbariumsheets">
> >
> > good night gringos,
> > markus
> >
> >
> >
> > On 13.11.2006, at 21:41, Javier de la Torre wrote:
> >
> > Thats the biocase way by the way.
> >
> > We will not be able to solve this problem at the TAPIR level
> > without a more complete mapping... the idea of being able to map
> > tables, or kind of objects, to the XML tree will solve that... but
> > thats TAPIR 1.5
> >
> > Cheers.
> >
> > On 13/11/2006, at 18:54, Markus D=F6ring wrote:
> >
> >> for fixed models we could surely cheat that way. assign a root
> >> table that HAS to be used first.
> >> should be the easiest (still requires some hours Id suspect).
> >> markus
> >>
> >>
> >> On 13.11.2006, at 18:17, Skofic A. Milko (IPGRI) wrote:
> >>
> >> I finally fixed the alias file: the strange thing is that the
> >> TAPIR schema parser gave something like:
> >>
> >> NICODE                                                      http://
> >> www.ipgri.org/schemas/mcpd_eurisco/1.00::NICODE
> >> INSTCODE                                                    http://
> >> www.ipgri.org/schemas/mcpd_eurisco/1.00::INSTCODE
> >> ACCENUMB                                                    http://
> >> www.ipgri.org/schemas/mcpd_eurisco/1.00::ACCENUMB
> >>
> >> but it's OK, once one gets the feel for the alias file you can do
> >> it by hand... except if you have a schema like ABCD... -:)
> >>
> >>> comment #1: try not to use :: in the full concepts but make them
> >>> look like a simple URL. for example http://www.ipgri.org/schemas/
> >>> mcpd_eurisco/1.00/NICODE
> >> I now have this form:
> >>  http://www.ipgri.org/schemas/mcpd_eurisco/1.00/Accessions/
> >> Accession/NICODE
> >>
> >>> commen #3: the idea is that the server CANNOT start up with
> >>> conflicting or broken alias files. this shoulkd be fixed before.
> >>> dont you agree with that? otherwise you could get unforseen weird
> >>> results.
> >> I agree, alias files are usually not going to be managed by users,
> >> so this error is not too problematic.
> >>
> >> Now, regarding the structure, I did a bunch of tests, I managed to
> >> create an output model from ABCD to EURISCO and it works. The only
> >> problem is trying to use directly the EURISCO model. EURISCO has
> >> ACC as the main table, but ACC is linked to other tables with
> >> repeating values, although no required field is in these tables.
> >>
> >> When I try to query and look at the SQL it produces, it uses the
> >> repeating tables as the origin of the joins, which is correct if
> >> you translate the database graph into a tree, but there must be
> >> some way to indicate that the root of the joins is ACC, not the
> >> other tables.
> >>
> >> After some testing I realised that when you clear the cache files
> >> from the ConfigTool, it doesn't cleat the http cache files, so I
> >> could make any change in the schema and it would not be reflected
> >> in TAPIR.
> >>
> >> So, let me know if you have some ideas about the structure problem
> >> we have, there should be some way to indicate or force the main
> >> table (Table A, in this case) to be the root of the tree.
> >>
> >> Thanks!
> >>
> >> Milko
> >>
> >>
> >> On Nov 13, 2006, at 16:25 , Markus D=F6ring wrote:
> >>
> >>> Milko,
> >>>
> >>> comment #1: try not to use :: in the full concepts but make them
> >>> look like a simple URL. for example http://www.ipgri.org/schemas/
> >>> mcpd_eurisco/1.00/NICODE
> >>>
> >>> comment #2: the error says: "biocase.CNS.NonUniqueConceptError".
> >>> so it looks as if the aliases or qualified names are not unique.
> >>> check. another problem could be that the alias.txt should have
> >>> "=3D" between an alias and the qualified concept. But I think its
> >>> not required.
> >>>
> >>> commen #3: the idea is that the server CANNOT start up with
> >>> conflicting or broken alias files. this shoulkd be fixed before.
> >>> dont you agree with that? otherwise you could get unforseen weird
> >>> results.
> >>>
> >>> markus
> >>>
> >>>
> >>> On 11/13/06, Skofic A. Milko (IPGRI) <M.S...@cg...> wrote:
> >>> Hi guys, I am trying to create an alias file to use other schemas
> >>> and test mapping and output models. I have created a schema, run
> >>> it through TAPIR's schema parser and tried to set up another
> >>> concept server.
> >>>
> >>> I get an error whenever I startup TAPIR, and I am sure it has to
> >>> do with the alias file and its other related files.
> >>> The error is:
> >>>
> >>> Traceback (most recent call last):
> >>>   File "../webapp/start_server.py", line 56, in ?
> >>>     import root, page
> >>>   File "/Library/WebServer/Services/pywrapper/webapp/root.py",
> >>> line 17, in ?
> >>>     import page, biocase.configuration
> >>>   File "/Library/WebServer/Services/pywrapper/webapp/page.py",
> >>> line 24, in ?
> >>>     class Page(object):
> >>>   File "/Library/WebServer/Services/pywrapper/webapp/page.py",
> >>> line 26, in Page
> >>>     _dsaObjDict =3D biocase.pywrapper.datasource_factory.getDsaDict()
> >>>   File "/Library/WebServer/Services/pywrapper/lib/biocase/
> >>> pywrapper/datasource_factory.py", line 49, in getDsaDict
> >>>     dsaObj.readPrefsFile ()
> >>>   File "/Library/WebServer/Services/pywrapper/lib/biocase/
> >>> pywrapper/datasource.py", line 218, in readPrefsFile
> >>>     parse(filename, handler)
> >>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/
> >>> python2.4/site-packages/_xmlplus/sax/__init__.py", line 31, in parse
> >>>     parser.parse(filename_or_stream)
> >>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/
> >>> python2.4/site-packages/_xmlplus/sax/expatreader.py", line 109,
> >>> in parse
> >>>     xmlreader.IncrementalParser.parse(self, source)
> >>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/
> >>> python2.4/site-packages/_xmlplus/sax/xmlreader.py", line 123, in
> >>> parse
> >>>     self.feed(buffer)
> >>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/
> >>> python2.4/site-packages/_xmlplus/sax/expatreader.py", line 216,
> >>> in feed
> >>>     self._parser.Parse(data, isFinal)
> >>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/
> >>> python2.4/site-packages/_xmlplus/sax/expatreader.py", line 312,
> >>> in start_element
> >>>     self._cont_handler.startElement(name, AttributesImpl(attrs))
> >>>   File "/Library/WebServer/Services/pywrapper/lib/biocase/
> >>> pywrapper/datasource_handler.py", line 73, in startElement
> >>>     self._lastConceptObj =3D buildConceptFromAttrs(attrs,
> >>> ns=3Dself._lastSchemaNS)
> >>>   File "/Library/WebServer/Services/pywrapper/lib/biocase/
> >>> pywrapper/filter/concept.py", line 215, in buildConceptFromAttrs
> >>>     conceptObj =3D buildConcept(qname, ns)
> >>>   File "/Library/WebServer/Services/pywrapper/lib/biocase/
> >>> pywrapper/filter/concept.py", line 239, in buildConcept
> >>>     CNServer =3D createCNServer
> >>> (aliasList=3DcfgObj.ConceptNameServer.AliasList,
> >>> cachedir=3DcfgObj.cacheLocator)
> >>>   File "/Library/WebServer/Services/pywrapper/lib/biocase/
> >>> CNS.py", line 433, in createCNServer
> >>>     CNS.addAliasLocation(alias)
> >>>   File "/Library/WebServer/Services/pywrapper/lib/biocase/
> >>> CNS.py", line 168, in addAliasLocation
> >>>     self._read(fh)
> >>>   File "/Library/WebServer/Services/pywrapper/lib/biocase/
> >>> CNS.py", line 241, in _read
> >>>     self.addConcept( c, additionalAliases=3D[] )
> >>>   File "/Library/WebServer/Services/pywrapper/lib/biocase/
> >>> CNS.py", line 346, in addConcept
> >>>     raise NonUniqueConcept(conceptObj)
> >>> biocase.CNS.NonUniqueConceptError in atexit._run_exitfuncs:
> >>> Traceback (most recent call last):
> >>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/
> >>> python2.4/atexit.py", line 24, in _run_exitfuncs
> >>>     func(*targs, **kargs)
> >>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/
> >>> python2.4/logging/__init__.py", line 1333, in shutdown
> >>>     h.close()
> >>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/
> >>> python2.4/logging/__init__.py", line 674, in close
> >>>     del _handlers[self]
> >>> KeyError: <logging.StreamHandler instance at 0x1385418>
> >>> Error in sys.exitfunc:
> >>> Traceback (most recent call last):
> >>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/
> >>> python2.4/atexit.py", line 24, in _run_exitfuncs
> >>>     func(*targs, **kargs)
> >>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/
> >>> python2.4/logging/__init__.py", line 1333, in shutdown
> >>>     h.close()
> >>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/
> >>> python2.4/logging/__init__.py", line 674, in close
> >>>     del _handlers[self]
> >>> KeyError: <logging.StreamHandler instance at 0x1385418>
> >>>
> >>> This listing comes from the terminal. I am sure I did something
> >>> wrong with the files, however it should not crash like this.
> >>> Anyways here are the files:
> >>>
> >>> The alias file is at http://eurisco.ecpgr.org/schemas/alias.txt
> >>> The schema file is at: http://eurisco.ecpgr.org/schemas/
> >>> MCPD_EURISCO_1.00.xsd
> >>> And the model file is at: http://eurisco.ecpgr.org/schemas/
> >>> MCPD_EURISCO_1.00.xml
> >>>
> >>> I have now removed the reference to that alias file so the system
> >>> can work.
> >>> Looking at the alias file I see a strange syntax: is that
> >>> correct? I only changed the label, alias and added the models
> >>> section.
> >>>
> >>> Thanks!
> >>>
> >>> Milko
> >>>
> >>
> >>
> >
> >
> >
>
>

[PyWrapper-devel] SVN Server

[Peter B. <p.w...@re...>]

I'm having problems connecting to the SVN server.  Can anyone confirm if 
the server is up/down?

Regards

Peter

Re: [PyWrapper-devel] SVN Server

[Javier de la T. <ja...@gm...>]

Here is working fine.
But I am not behind a firewall.

Javier.

On 15/11/2006, at 16:13, Peter Brewer wrote:

> I'm having problems connecting to the SVN server.  Can anyone  
> confirm if
> the server is up/down?
>
> Regards
>
> Peter
>
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