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From: Langtry C. <se...@ce...> - 2008-07-20 20:12:41
|
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From: Carylon B. <cu...@ss...> - 2008-07-13 17:37:16
|
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From: Joana G. M. <jgo...@gm...> - 2008-07-10 14:28:43
|
So,my connection is in Broken status. But I have configured with the correct parameters. I´m using postgreSQL 8.3 my Database´s name is BDColetas. I´m using too ENCODING = 'WIN1252'. But in the connection settings pywrapper there isn´t this code and I choose iso8859_1 for test. My user is postgres and my password is Xis003! and my Host is localhost. I don´t know why is happen this error because my connection settings are right. Some idea that what might be happening? thanks again! Database Connection The connection to the database is Broken . Please adjust your connection settings so that the status above shows a green OK. Database Structure -- Joana G. Malaverri Mestranda em Ciências da Computação IC-UNICAMP Fono: 3305-4514 |
From: Joana G. M. <jgo...@gm...> - 2008-07-10 14:06:17
|
Hi everybody, I 'm trying to config pywrapper. But when I was click in one of these links: http://rs.tdwg.org/dwc/dwcore/<http://localhost:8000/pywrapper/configtool/biocore/mappings/schema?ns=http%3A%2F%2Frs.tdwg.org%2Fdwc%2Fdwcore%2F>or http://rs.tdwg.org/dwc/geospatial/<http://localhost:8000/pywrapper/configtool/biocore/mappings/schema?ns=http%3A%2F%2Frs.tdwg.org%2Fdwc%2Fgeospatial%2F> Concept lists These are the conceptual XML schemas mapped to your database and the number of existing mappings. Follow the link to edit the mappings as lists of concepts: - 007 concepts in http://rs.tdwg.org/dwc/dwcore/<http://localhost:8000/pywrapper/configtool/biocore/mappings/schema?ns=http%3A%2F%2Frs.tdwg.org%2Fdwc%2Fdwcore%2F> - 002 concepts in http://rs.tdwg.org/dwc/geospatial/<http://localhost:8000/pywrapper/configtool/biocore/mappings/schema?ns=http%3A%2F%2Frs.tdwg.org%2Fdwc%2Fgeospatial%2F> Show this error!!!. I'm new using pywrapper. Do you know how I can do to resolve this problem? thanks for your help!! Joana 500 Internal Server Error The server encountered an unexpected condition which prevented it from fulfilling the request. Traceback (most recent call last): File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\cherrypy\_cprequest.py", line 551, in respond cherrypy.response.body = self.handler() File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\cherrypy\_cpdispatch.py", line 24, in __call__ return self.callable(*self.args, **self.kwargs) File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\webapp\configtool\cfgtool.py", line 90, in default return getattr(self.dsaAdminObj, action)(dsa, *morePosArgs, **kwargs) File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\webapp\configtool\dsaAdmin.py", line 366, in mappings return getattr(self.mapperObj, action)(dsa, *args, **kwargs) File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\webapp\configtool\mappings\mapper.py", line 102, in schema CNS=self.CNServer File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\webapp\configtool\mappings\mapper.py", line 44, in render return page.Page.render(self, logout=True, menu_items=submenu, curr_menu_idx=4, title=title, dsa=dsa, dsaObj=dsaObj, dbmodObj=dbmodObj, **kwargs) File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\webapp\page.py", line 99, in render return tmpl.serialize(output='html') File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\kid\__init__.py", line 299, in serialize raise_template_error(module=self.__module__) File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\kid\__init__.py", line 297, in serialize return serializer.serialize(self, encoding, fragment, format) File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\kid\serialization.py", line 105, in serialize text = ''.join(self.generate(stream, encoding, fragment, format)) File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\kid\serialization.py", line 630, in generate for ev, item in self.apply_filters(stream, format): File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\kid\serialization.py", line 163, in format_stream for ev, item in stream: File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\kid\parser.py", line 219, in _coalesce for ev, item in stream: File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\kid\serialization.py", line 478, in inject_meta_tags for ev, item in stream: File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\kid\parser.py", line 177, in _track for p in stream: File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\kid\filter.py", line 30, in apply_matches item = stream.expand() File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\kid\parser.py", line 106, in expand for ev, item in self._iter: File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\kid\parser.py", line 177, in _track for p in stream: File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\kid\parser.py", line 219, in _coalesce for ev, item in stream: File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\webapp\configtool/mappings/schema.py", line 390, in _pull File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\kid\parser.py", line 177, in _track for p in stream: File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\webapp\lib.py", line 266, in __attrtype_select File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\biocase\pywrapper\datasource.py", line 204, in getDbModObj self.dbModObj = DBModuleClass(dsaObj=self, opStatusObj=opStatusObj) File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\biocase\pywrapper\dbmod\dbmod_postgres.py", line 66, in __init__ DBBasemodule.__init__(self, dsaObj, opStatusObj, integrateSqlParameters=False) File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\biocase\pywrapper\dbmod\base_dbmod.py", line 53, in __init__ self.conn = self.createDBconnection() File "C:\Documents and Settings\joana\Desktop\pywrapper_3.1.0a\pywrapper_3.1.0alpha\lib\biocase\pywrapper\dbmod\dbmod_postgres.py", line 80, in createDBconnection raise DbModuleMissingError(log, 'pyPgSQL') NameError: global name 'DbModuleMissingError' is not defined Error location in template file 'C:\\Documents and Settings\\joana\\Desktop\\pywrapper_3.1.0a\\pywrapper_3.1.0alpha\\webapp\\configtool/mappings/schema.kid' between line 113, column 9 and line 114: ... </h3> -- Joana G. Malaverri Mestranda em Ciências da Computação IC-UNICAMP Fono: 3305-4514 |
From: Strauf O. <dye...@dm...> - 2008-07-08 00:39:16
|
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From: Mumme R. <yo...@di...> - 2008-06-29 16:19:38
|
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|
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|
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|
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From: Shiela S. <so...@ac...> - 2007-12-18 16:42:11
|
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From: Javier de la T. <ja...@gm...> - 2007-12-18 09:14:52
|
Hi all, I just returned today from a week of holidays. I will take a look at =20 the emails this afternoon when i have a little bit more of time. Cheers. On 14/12/2007, at 14:30, D=C3=B6ring, Markus wrote: > Ricardo, > Ill have to look at it more closely, but I was the one to add this =20 > "save > http body" stuff to pywrapper. I guess the moby part from javier =20 > was working > correctly before. > > The situation with http body is a difficlut one unfortunately. > When the streamed request comes in, we dont know what it is apart =20 > from the > http content header and the content length header. It is streamed =20 > so you > need to decide what to do just then inspecting the http headers. > > The idea is to only save the body if it is an xml content header, =20 > otherwise > (for example html content from the webapps) leave it alone so that =20= > other > libraries will not get confused (if you "save" the body, the stream =20= > is gone > and this will cause troubles for analysing request parameters later =20= > via > cherrypy.request). > > XML based messages that we use for TAPIR (but also for SOAP or others) > should be send immediately in the http (POST) body and not encoded =20 > as a POST > parameters in a http request. This is also part of the TAPIR spec =20 > but you > can find that in OGC too. The idea is that all parameters are =20 > encoded in the > XML message already. So you need to access the entire http body, =20 > something I > didnt manage to do with CherryPy cause the framework already parses =20= > a lot of > http stuff by default for you. So I intercepted the http requests =20 > pretty > early with custom cherrypy filters. > > I believe we should check why moby fails and simple fix the moby =20 > module to > read the saved http body. Wouldnt that work? > > > Markus > > > > > > > > "Ricardo Scachetti Pereira" wrote on 13.12.2007 19:42 Uhr: > >> Hi Markus and Javi, >> >> I'm trying to get PyWrapper to process BioMoby requests, but I =20= >> got >> stuck with the following problem. >> >> The function saveHttpBody() (which I copy below - from file >> ./webapp/pywrapper.py) looks at the request URL and decide whether or >> not to save the http request body. >> >> The problem is that the moby handler needs that the http body is >> saved, but I don't know how to save it when a moby request comes. =20 >> To be >> honest, I found the check n =3D=3D 'pywrapper' a little obscure. When = =20 >> does >> the http body gets saved anyway? >> >> In any case, if I change the code so that the http body is always >> saved, moby requests are handled without problems, but then the >> PyWrapper config tool webapp breaks. >> >> Is there a way for me to detect that the request is a moby one at >> that point? But the request hasn't been parsed yet at that point, =20 >> right? >> >> Anyway, I would really appreciate if you could shed some light on >> the matter. >> >> Thanks, >> >> Ricardo >> >> >> PS: Here is the function: >> >> def saveHttpBody(): >> """ Called after the request header has been read/parsed""" >> request =3D cherrypy.request >> # only process hook if pywrapper is being called >> n=3Drequest.path_info.lower().replace('/','') >> #print request.path_info / script_name >> log.debug("SaveHttpBody is looking at the request: %s"%n) >> if n =3D=3D 'pywrapper': >> para=3DcfgObj.PyWrapper.httpBodyParameter >> # get http body data >> dataLength =3D int(request.headers.get('Content-Length') or = 0) >> data =3D request.rfile.read(dataLength) >> # save http body & content-length as a new parameter. usually >> __HTTP_BODY__ >> request.params[para]=3D(cStringIO.StringIO(data), dataLength) >> # fake the input stream so CP can parse the body regularly >> if hasattr(request.rfile, 'maxlen'): >> request.rfile =3D >> http.SizeCheckWrapper(rfile=3DcStringIO.StringIO(data), >> maxlen=3Drequest.rfile.maxlen) >> else: >> request.rfile =3D >> http.SizeCheckWrapper(rfile=3DcStringIO.StringIO(data), maxlen=3D0) >> >> cherrypy.request.hooks.attach('before_request_body', saveHttpBody, >> failsafe=3DNone, priority=3DNone) >> > |
From: Dring, M. <m.d...@BG...> - 2007-12-14 13:41:52
|
Ricardo, Ill have to look at it more closely, but I was the one to add this "save http body" stuff to pywrapper. I guess the moby part from javier was working correctly before. The situation with http body is a difficlut one unfortunately. When the streamed request comes in, we dont know what it is apart from the http content header and the content length header. It is streamed so you need to decide what to do just then inspecting the http headers. The idea is to only save the body if it is an xml content header, otherwise (for example html content from the webapps) leave it alone so that other libraries will not get confused (if you "save" the body, the stream is gone and this will cause troubles for analysing request parameters later via cherrypy.request). XML based messages that we use for TAPIR (but also for SOAP or others) should be send immediately in the http (POST) body and not encoded as a POST parameters in a http request. This is also part of the TAPIR spec but you can find that in OGC too. The idea is that all parameters are encoded in the XML message already. So you need to access the entire http body, something I didnt manage to do with CherryPy cause the framework already parses a lot of http stuff by default for you. So I intercepted the http requests pretty early with custom cherrypy filters. I believe we should check why moby fails and simple fix the moby module to read the saved http body. Wouldnt that work? Markus "Ricardo Scachetti Pereira" wrote on 13.12.2007 19:42 Uhr: > Hi Markus and Javi, > > I'm trying to get PyWrapper to process BioMoby requests, but I got > stuck with the following problem. > > The function saveHttpBody() (which I copy below - from file > ./webapp/pywrapper.py) looks at the request URL and decide whether or > not to save the http request body. > > The problem is that the moby handler needs that the http body is > saved, but I don't know how to save it when a moby request comes. To be > honest, I found the check n == 'pywrapper' a little obscure. When does > the http body gets saved anyway? > > In any case, if I change the code so that the http body is always > saved, moby requests are handled without problems, but then the > PyWrapper config tool webapp breaks. > > Is there a way for me to detect that the request is a moby one at > that point? But the request hasn't been parsed yet at that point, right? > > Anyway, I would really appreciate if you could shed some light on > the matter. > > Thanks, > > Ricardo > > > PS: Here is the function: > > def saveHttpBody(): > """ Called after the request header has been read/parsed""" > request = cherrypy.request > # only process hook if pywrapper is being called > n=request.path_info.lower().replace('/','') > #print request.path_info / script_name > log.debug("SaveHttpBody is looking at the request: %s"%n) > if n == 'pywrapper': > para=cfgObj.PyWrapper.httpBodyParameter > # get http body data > dataLength = int(request.headers.get('Content-Length') or 0) > data = request.rfile.read(dataLength) > # save http body & content-length as a new parameter. usually > __HTTP_BODY__ > request.params[para]=(cStringIO.StringIO(data), dataLength) > # fake the input stream so CP can parse the body regularly > if hasattr(request.rfile, 'maxlen'): > request.rfile = > http.SizeCheckWrapper(rfile=cStringIO.StringIO(data), > maxlen=request.rfile.maxlen) > else: > request.rfile = > http.SizeCheckWrapper(rfile=cStringIO.StringIO(data), maxlen=0) > > cherrypy.request.hooks.attach('before_request_body', saveHttpBody, > failsafe=None, priority=None) > |
From: Gideon G. <gg...@et...> - 2007-11-14 12:59:15
|
Hi Ricardo, I would like to test it when you get there. It would be good to include this in the maual then. It was very =20 dissatisfying that I could not get it to work. Contact me if you need more detailed information. Gideon On Nov 14, 2007, at 2:54 PM, Ricardo Scachetti Pereira wrote: > Thanks Gideon and Markus for your input. > > I think that to make PyWrapper more robust and easier to install =20= > on Windows (part of my goals for 2008) I'll definitely have to work =20= > on this specific task. I'll keep all that you said in mind when I =20 > start working on PyWrapper early next year. > > Cheers, > > Ricardo > > > D=F6ring, Markus wrote: >> Ricardo, >> It might be best to evaluate if we cant move to mod_python/apache =20 >> as the >> recommended installation (apart from standalone which is really =20 >> useful for >> testing and quick setups). I havent followed the CherryPy =20 >> developments, but >> there must have been some changes happening there. As PyWrapper is =20= >> based on >> CherryPy thats the first source we should investigate: >> >> http://www.cherrypy.org/ >> >> I agree it's the most disturbing part in setting up pywrapper, =20 >> especially on >> windows. Now that fastcgi doesnt seem to be supported anymore, I'd =20= >> prefer to >> ignore IIS and require apache on windows. If that works painlessly =20= >> I think >> we are fine. >> >> Markus >> >> >> >> "Gideon Gijswijt" wrote on 13.11.2007 12:26 Uhr: >> >> >>> Hi Ricardo, >>> >>> According to Markus, the fastGCI option is the only option with >>> sufficient performance, so we went on with this option. >>> >>> I tried to get it working under Apache 1.3, 2.0 and 2.2 on =20 >>> Windows XP >>> and on Server 2003. >>> I also tried FastCGI but also FCGI, since FastCGI does not work with >>> Apache 2.2 anymore. >>> After trying for 5 days, I had to give up because of the deadline. >>> >>> It may be possible that with some rewriting of the wrapper =20 >>> itself, it >>> is possible to use the FCGI, but we lacked the time to work this =20 >>> out. >>> This is why we could only suggest the stand-alone option for =20 >>> Windows. >>> >>> Cheers, >>> >>> Gideon >>> >>> On Nov 12, 2007, at 12:09 PM, Ricardo Scachetti Pereira wrote: >>> >>> >>>> Hi guys, >>>> >>>> I've been running PyWrapper on Windows for sometime now using >>>> standalone CherryPy web app server. >>>> >>>> Now I tried to run PyWrapper using Apache 2.0 on Windows without >>>> success and I was wondering whether you could help me with that. >>>> >>>> First, I tried to run PyWrapper with mod_python and >>>> modpython_gateway without success. I realized that there was a >>>> script modpython_gateway.py on the webapp directory (that is needed >>>> to run PyWrapper with mod_python) but that file was later deleted. >>>> My reading is that you guys gave up on that combination of >>>> mod_python and modpython_gateway. Is that right? >>>> >>>> Then I tried FastCGI, without success either. I've used the >>>> sample Apache configuration for FastCGI but couldn't get PyWrapper >>>> to work. >>>> >>>> I've noticed that the documentation on PyWrapper 3.1 from ETI >>>> says PyWrapper doesn't run on Windows/Apache nor explains how to >>>> set it up. If that's the case, is there any specific reasons why >>>> you give up on it? >>>> >>>> In any case, do you guys have any hints for me on how to run >>>> PyWrapper on Windows with Apache, or hints on how to make PyWrapper >>>> run on that platform again? >>>> >>>> Cheers, >>>> >>>> Ricardo >>>> >>>> >>>> >>>> >>>> >>>> >>>> >> >> >> > > |
From: Ricardo S. P. <ri...@td...> - 2007-11-14 12:55:44
|
Thanks Gideon and Markus for your input. I think that to make PyWrapper more robust and easier to install on Windows (part of my goals for 2008) I'll definitely have to work on this specific task. I'll keep all that you said in mind when I start working on PyWrapper early next year. Cheers, Ricardo Döring, Markus wrote: > Ricardo, > It might be best to evaluate if we cant move to mod_python/apache as the > recommended installation (apart from standalone which is really useful for > testing and quick setups). I havent followed the CherryPy developments, but > there must have been some changes happening there. As PyWrapper is based on > CherryPy thats the first source we should investigate: > > http://www.cherrypy.org/ > > I agree it's the most disturbing part in setting up pywrapper, especially on > windows. Now that fastcgi doesnt seem to be supported anymore, I'd prefer to > ignore IIS and require apache on windows. If that works painlessly I think > we are fine. > > Markus > > > > "Gideon Gijswijt" wrote on 13.11.2007 12:26 Uhr: > > >> Hi Ricardo, >> >> According to Markus, the fastGCI option is the only option with >> sufficient performance, so we went on with this option. >> >> I tried to get it working under Apache 1.3, 2.0 and 2.2 on Windows XP >> and on Server 2003. >> I also tried FastCGI but also FCGI, since FastCGI does not work with >> Apache 2.2 anymore. >> After trying for 5 days, I had to give up because of the deadline. >> >> It may be possible that with some rewriting of the wrapper itself, it >> is possible to use the FCGI, but we lacked the time to work this out. >> This is why we could only suggest the stand-alone option for Windows. >> >> Cheers, >> >> Gideon >> >> On Nov 12, 2007, at 12:09 PM, Ricardo Scachetti Pereira wrote: >> >> >>> Hi guys, >>> >>> I've been running PyWrapper on Windows for sometime now using >>> standalone CherryPy web app server. >>> >>> Now I tried to run PyWrapper using Apache 2.0 on Windows without >>> success and I was wondering whether you could help me with that. >>> >>> First, I tried to run PyWrapper with mod_python and >>> modpython_gateway without success. I realized that there was a >>> script modpython_gateway.py on the webapp directory (that is needed >>> to run PyWrapper with mod_python) but that file was later deleted. >>> My reading is that you guys gave up on that combination of >>> mod_python and modpython_gateway. Is that right? >>> >>> Then I tried FastCGI, without success either. I've used the >>> sample Apache configuration for FastCGI but couldn't get PyWrapper >>> to work. >>> >>> I've noticed that the documentation on PyWrapper 3.1 from ETI >>> says PyWrapper doesn't run on Windows/Apache nor explains how to >>> set it up. If that's the case, is there any specific reasons why >>> you give up on it? >>> >>> In any case, do you guys have any hints for me on how to run >>> PyWrapper on Windows with Apache, or hints on how to make PyWrapper >>> run on that platform again? >>> >>> Cheers, >>> >>> Ricardo >>> >>> >>> >>> >>> >>> >>> > > > |
From: Dring, M. <m.d...@BG...> - 2007-11-14 10:51:53
|
Ricardo, It might be best to evaluate if we cant move to mod_python/apache as the recommended installation (apart from standalone which is really useful for testing and quick setups). I havent followed the CherryPy developments, but there must have been some changes happening there. As PyWrapper is based on CherryPy thats the first source we should investigate: http://www.cherrypy.org/ I agree it's the most disturbing part in setting up pywrapper, especially on windows. Now that fastcgi doesnt seem to be supported anymore, I'd prefer to ignore IIS and require apache on windows. If that works painlessly I think we are fine. Markus "Gideon Gijswijt" wrote on 13.11.2007 12:26 Uhr: > Hi Ricardo, > > According to Markus, the fastGCI option is the only option with > sufficient performance, so we went on with this option. > > I tried to get it working under Apache 1.3, 2.0 and 2.2 on Windows XP > and on Server 2003. > I also tried FastCGI but also FCGI, since FastCGI does not work with > Apache 2.2 anymore. > After trying for 5 days, I had to give up because of the deadline. > > It may be possible that with some rewriting of the wrapper itself, it > is possible to use the FCGI, but we lacked the time to work this out. > This is why we could only suggest the stand-alone option for Windows. > > Cheers, > > Gideon > > On Nov 12, 2007, at 12:09 PM, Ricardo Scachetti Pereira wrote: > >> Hi guys, >> >> I've been running PyWrapper on Windows for sometime now using >> standalone CherryPy web app server. >> >> Now I tried to run PyWrapper using Apache 2.0 on Windows without >> success and I was wondering whether you could help me with that. >> >> First, I tried to run PyWrapper with mod_python and >> modpython_gateway without success. I realized that there was a >> script modpython_gateway.py on the webapp directory (that is needed >> to run PyWrapper with mod_python) but that file was later deleted. >> My reading is that you guys gave up on that combination of >> mod_python and modpython_gateway. Is that right? >> >> Then I tried FastCGI, without success either. I've used the >> sample Apache configuration for FastCGI but couldn't get PyWrapper >> to work. >> >> I've noticed that the documentation on PyWrapper 3.1 from ETI >> says PyWrapper doesn't run on Windows/Apache nor explains how to >> set it up. If that's the case, is there any specific reasons why >> you give up on it? >> >> In any case, do you guys have any hints for me on how to run >> PyWrapper on Windows with Apache, or hints on how to make PyWrapper >> run on that platform again? >> >> Cheers, >> >> Ricardo >> >> >> >> >> >> > |
From: <m.d...@bg...> - 2007-07-23 10:06:54
|
Milko, pywrapper cant handle mixed content yet so you should assign it a simple datatype. in your example this would be sth like this (note the extension base xs:string): <xs:element name="Dataset" maxOccurs="unbounded"> <xs:complexType> <xs:simpleContent> <xs:extension base="xs:string"> <xs:attribute name="identifier" type="xs:string"/> <xs:attribute name="domain" type="xs:string"/> <xs:attribute name="URN" type="xs:string"/> </xs:extension> </xs:simpleContent> </xs:complexType> </xs:element> markus On Jul 20, 2007, at 5:47 PM, Skofic A. Milko (Bioversity - HQ) wrote: > Hi Markus, > > I have installed TAPIR in Peru and Colombia, as I told you we had > some problems in Peru with the libraryes, but we managed to solve > them, in Colombia everything went well and the service is running. > > I am creating new structures and I was trying to implement a > construct in which an element has both attributes and a simple > type, here is an example of the XML: > > <?xml version="1.0" encoding="UTF-8"?> > <Datasets > xmlns="http://grinfo.net/test" > xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" > xsi:schemaLocation="http://grinfo.net/test http://localhost/cns/ > test/Schema/test.xsd"> > <Dataset identifier="ID1">Dataset 1</Dataset> > <Dataset identifier="ID2">Dataset 2</Dataset> > <Dataset identifier="ID3" URN="http://someurl" > domain="Taxonomy">Dataset 3</Dataset> > </Datasets> > > The schema that I use is as follows: > > <?xml version="1.0" encoding="UTF-8"?> > <xs:schema > xmlns:xs="http://www.w3.org/2001/XMLSchema" > xmlns="http://grinfo.net/test" > targetNamespace="http://grinfo.net/test" > elementFormDefault="qualified" > attributeFormDefault="unqualified"> > <xs:element name="Datasets"> > <xs:complexType> > <xs:sequence> > <xs:element name="Dataset" maxOccurs="unbounded"> > <xs:complexType mixed="true"> > <xs:attribute name="identifier" type="xs:string"/> > <xs:attribute name="domain" type="xs:string"/> > <xs:attribute name="URN" type="xs:string"/> > </xs:complexType> > </xs:element> > </xs:sequence> > </xs:complexType> > </xs:element> > </xs:schema> > > When I feed the schema to TAPIR's alias file generator, TAPIR will > generate an ID for the <Dataset> attributes, but not for the > element itself. I tried to add manually the ID of the element in > the alias file, but when I tried to query with this structure TAPIR > returned in the end the following warning: > > <diagnostic time="2007-07-20T17:18:39.10" level="WARNING"> > The element /Datasets/Dataset was emptied 1 times because of > missing xml datatype in the view structure > </diagnostic> > > From that message I understand that TAPIR skipped the element > because it cannot make up its data type. I am not an expert in XML, > so is there is a way to indicate a simple data type of an element > that has attributes, or must I add an element with a simple type? > > Thanks for the help > > Ciao! > > Milko |
From: Wouter A. <wo...@et...> - 2007-07-17 11:35:16
|
On second thought, I do not think it is really a bug in the Schema parser, but an unclarity in the schema. Since it is not clear from the schema that there will be text content it is logical not to treat the element like that. But it will mean that we will have to treat the results from the schema parser with care. Wouter ----- Original Message ----- From: "Markus Döring" <m.d...@bg...> To: "Wouter Addink" <wo...@et...> Sent: Monday, July 16, 2007 2:02 PM Subject: Re: [PyWrapper-devel] bug in TAPIR Schema Parser ok, they use mixed content which is not really supported by pywrapper I believe. Genus is of type ReferenceType which is: <xs:complexType name="ReferenceType" mixed="true"> <xs:annotation><xs:documentation> Elements of this type are used to refer to other resources. They can be used in the following ways. 1) With text content and no attributes - a simple text representation of the resource. 2) With no text content but a ref attribute pointing to the location or the resource. 3) A combination of the two above. The text content is a summary or the resource referenced to in the ref attribute. </xs:documentation></xs:annotation> <xs:attribute name="ref" type="xs:token" use="optional"> Would it be correct to automatically assign a string datatype to an element that allows mixed content? markus On Jul 16, 2007, at 1:27 PM, Wouter Addink wrote: > No simple type attached to the missing ones I think. > Example in TCS: > DataSet/TaxonNames/TaxonName/CanonicalName/Genus > > Wouter > > ----- Original Message ----- From: "Markus Döring" <m.d...@bg...> > To: "PyWrapper Developers mailing list" <pywrapper- > de...@li...>; "Wouter Addink" <wo...@et...> > Sent: Monday, July 16, 2007 1:22 PM > Subject: Re: [PyWrapper-devel] bug in TAPIR Schema Parser > > >> thanks wouter, >> do you have an example of this at hand? are you sure that the element >> has a simple type attached to it? otherwise it is not recognised as a >> concept on purpose. >> markus >> >> >> >> On Jul 13, 2007, at 4:22 PM, Wouter Addink wrote: >> >>> Hi, >>> Pywrapper contains a handy tool to genereate concept paths from a >>> schema (CNS aliases.txt). However this tool contains a bug. >>> >From concepts with attributes only the paths to the attributes >>> are generated, not the path to the concept itself. >>> >>> Regards, >>> Wouter Addink >>> -------------------------------------------------------------------- >>> -- --- >>> This SF.net email is sponsored by DB2 Express >>> Download DB2 Express C - the FREE version of DB2 express and take >>> control of your XML. No limits. Just data. Click to get it now. >>> http://sourceforge.net/powerbar/db2/ >>> _______________________________________________ >>> PyWrapper-devel mailing list >>> PyW...@li... >>> https://lists.sourceforge.net/lists/listinfo/pywrapper-devel >> >> > > |
From: <m.d...@bg...> - 2007-07-16 11:19:46
|
thanks wouter, do you have an example of this at hand? are you sure that the element has a simple type attached to it? otherwise it is not recognised as a concept on purpose. markus On Jul 13, 2007, at 4:22 PM, Wouter Addink wrote: > Hi, > Pywrapper contains a handy tool to genereate concept paths from a > schema (CNS aliases.txt). However this tool contains a bug. >From > concepts with attributes only the paths to the attributes are > generated, not the path to the concept itself. > > Regards, > Wouter Addink > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > PyWrapper-devel mailing list > PyW...@li... > https://lists.sourceforge.net/lists/listinfo/pywrapper-devel |
From: Wouter A. <wo...@et...> - 2007-07-13 14:22:42
|
Hi, Pywrapper contains a handy tool to genereate concept paths from a schema = (CNS aliases.txt). However this tool contains a bug. From concepts with = attributes only the paths to the attributes are generated, not the path = to the concept itself. Regards, Wouter Addink |
From: Dring, M. <m.d...@BG...> - 2007-07-02 09:56:33
|
Milko, The problem is that the setuptools module needed to install lxml has released a new version. In the pywrapper packages there is a script called = " ez_setup.py" which installs setuptools. This script needs to be the latest version which can be found here: http://peak.telecommunity.com/dist/ez_setup.py Or as part of the setuptools distribution here: http://cheeseshop.python.org/packages/source/s/setuptools/ I have updated the pywrapper SVN with the 0.6c6 version of the script so th= e installer script should hopefully work now (both for trunk and stable) Sorry, but I dont have time now to test it. It would probably best to update the installer script to download the ez_script file from the above URL (if the URL doesnt change...) Hope everything works now. Markus Am 02.07.2007 8:14 Uhr schrieb "Milko A. =A9kofi=E8" unter <mi...@ma...>: > Hi Markus, I am in Peru and tomorrow morning I have to install and > demonstrate TAPIR, i was trying to install TAPIR on my laptop and the > installation process always failed. I managed to track the problem, > it is when it tries to install lxml, here is the log: >=20 > E07-Laptop-1:/Library/WebServer/Services/pywrapper/tools/build milko > $ ../python/bin/easy_install lxml > Searching for lxml > Reading http://www.python.org/pypi/lxml/ > Reading http://www.python.org/pypi/lxml/1.3 > Reading http://codespeak.net/lxml > Reading http://www.python.org/pypi/lxml/1.2 > Reading http://www.python.org/pypi/lxml/1.1 > Reading http://www.python.org/pypi/lxml/1.0 > Reading http://www.python.org/pypi/lxml/0.9.2 > Reading http://www.python.org/pypi/lxml/1.2.1 > Reading http://www.python.org/pypi/lxml/0.9.1 > Reading http://www.python.org/pypi/lxml/1.1.2 > Reading http://www.python.org/pypi/lxml/1.1.1 > Reading http://www.python.org/pypi/lxml/0.9 > Reading http://www.python.org/pypi/lxml/1.0.4 > Reading http://www.python.org/pypi/lxml/1.0.3 > Reading http://www.python.org/pypi/lxml/1.0.2 > Reading http://www.python.org/pypi/lxml/1.0.1 > Best match: lxml 1.3 > Downloading http://codespeak.net/lxml/lxml-1.3.tgz > Processing lxml-1.3.tgz > Running lxml-1.3/setup.py -q bdist_egg --dist-dir /private/tmp/ > easy_install-sGupKh/lxml-1.3/egg-dist-tmp-W2POGM > The required version of setuptools (>=3D0.6c5) is not available, and > can't be installed while this script is running. Please install > a more recent version first. >=20 > (Currently using setuptools 0.6c3 (/Library/WebServer/Services/ > pywrapper/tools/python/lib/python2.4/site-packages/setuptools-0.6c3- > py2.4.egg)) > error: Setup script exited with 2 >=20 > I really don't know how to modify or change the installation script > to cope with this problem, in fact I don't know how to fix this. >=20 > It is about 1:00 here, if you manage to read this e-mail before I go > to do the installation tomorrow morning (in 6 hours) can you please > send me some info on how to fix this? >=20 > Thank you very much in advance! >=20 > Milko |
From: Dring, M. <m.d...@BG...> - 2007-06-22 14:38:56
|
Milko, The latest svn trunk fixes the alias generator bug. I had to do a mayor change in how I treat full qualified concepts internally to accomodate the latest TAPIR changes, thats why the generator was broken. I use the clark notation for fully qualified paths {NS}ELEMENT-NAME now internally. Unfortunately Ive broken the bgbm installation now :) Well, something you shouldnt do on a Friday afternoon. Markus Am 21.06.2007 18:33 Uhr schrieb "Skofic A. Milko (Bioversity - HQ)" unter <M.S...@CG...>: > Indeed, the alias file generator in the utilities section generates > paths with {} parenthesis that probably get either interpreted or > stripped somewhere in the process, so the alias is unusable. > > I removed all the parenthesis parts and set all the paths to standard > paths (http://namespace/Element) and I finally managed to query. > > It would be a good thing to fix this, since we will be working with > big schemas and making the file by hand will take too much time; > also, before it used to make the correct paths, why did you change this? > > Bye! > > Milko |
From: Dring, M. <m.d...@BG...> - 2007-06-20 13:45:32
|
Well,m to be honest Ive never tried that. If you experience a problem then there might be one. What does the sql logging say? And what happens if you execute the exact sql directly? Am 20.06.2007 11:55 Uhr schrieb "Skofic A. Milko (Bioversity - HQ)" unter <m.s...@cg...>: > I was trying to understand why the models I was testing don't work > and I fell into a possible problem (which still does not answer my > previous problem): > > In my databases I like to use binary strings formed by hashing a > series of significant fields of the table. Normally you get a 32 > hexadecimal string (if you use the MD5 MySQL function or the old md5 > () function in PHP), but when you have more than 1 million records it > is nice to reduce the size of the key, so I use the PHP function that > creates the same hash as a 16 character binary string, which I use in > the database. When trying queries I noticed that if I use an ASCII > string as the primary key TAPIR at least performs the query, if I use > the binary string it does not even do the query: is there a problem > using binary fields as primary keys? > > Thanks > > Milko |
From: Roger H. <ro...@td...> - 2007-06-15 09:42:10
|
I think MySQL unicode support if pretty perfect now (version 5) you =20 seem to be able to specify encodings right down to column level and =20 do just about anything you might want to - if you can work out what =20 it is you need to do that is ;). I believe the big changes came in 4.1 http://dev.mysql.com/tech-resources/articles/4.1/unicode.html It comes down to doing some detective work. Tracing right through the =20= data path from the original thing you imported into the db. Good luck, Roger On 15 Jun 2007, at 10:20, D=F6ring, Markus wrote: > well, > im not sure about the very latest mysql version, but mysql is very =20 > lazy when it comes to character encodings and to my knowledge it =20 > *doesnt* support unicode at all. What most people do is encode =20 > their data as utf8 and dump it in mysql as latin1. that causes some =20= > confusion sometimes. for pywrapper I think the utf8 setting would =20 > be correct in this case. have you tried different settings? what =20 > happens? and are you sure the =C3 is not inside your db? > > pywrapper has only one setting for character encodings, yes, the =20 > one you pointed to. > for serious debugging you could try to connect to the db via the =20 > terminal using python interactively. take a look at the dbmod =20 > dmod_mysql.py inside lib/biocase/pywrapper/dbmod (or sth like this) =20= > how to do a connection. just retype the commands in the python =20 > shell and see what you get. > > markus > > > -----Original Message----- > From: pyw...@li... on behalf of =20 > Shunde Zhang > Sent: Thu 6/14/2007 2:42 AM > To: PyWrapper Developers mailing list > Cc:=09 > Subject: Re: [PyWrapper-devel] Unicode > > Hi Markus, > > The raw XML from your server has the correct value, eg. Punb=E4cken. =20= > However, in > my raw XML, this character is shown as "=C3=A4", which is not correct. > Could you tell me how you configured it in detail? Did you just set =20= > it in: > > Home =BB Configtool =BB <datasource> =BB Connection >> Encoding > > Is there any other place I need to look at? > > I am using mysql and when I created the database, I didn't set any =20 > character > set. so it is using the default one, utf-8. since if I dump the =20 > database, I can > see: > > /*!40101 SET NAMES utf8 */; > > I think this means my database is using utf8. also I set utf8 in =20 > pywrapper. but > it doesn't work. is it possible to debug it? thanks a lot. > > Cheers, > Shunde. > > > Quoting Markus D=F6ring <m.d...@bg...>: > >> shunde, >> pywrapper definitely supports unicode. >> you can configure the character encoding for each datasource (the >> character encoding used in the database, output should always be >> utf8) and it works fine for the training dataset where there are at >> least latin1 characters. see here: >> >> http://search.biocase.org/tapir/pywrapper?dsa=3Dtraining&op=3Di&c=3Dhtt= p:// >> rs.tdwg.org/dwc/dwcore/Locality&limit=3D100 >> >> -- >> Markus >> >> >> >> On 13.06.2007, at 07:08, Shunde Zhang wrote: >> >>> Hi all, >>> >>> Does pywrapper support unicode? I've done a test. In database, my >>> value is >>> "Universit=E4t". and in the XML returned from pywrapper it becomes >>> "Universit=C3=A4t". It seems not correct. Could anybody tell >>> me how to >>> configure pywrapper to support Unicode? thanks in advance. >>> >>> Cheers, >>> Shunde. >>> >>> >>> >>> --------------------------------------------------------------------=20= >>> -- >>> --- >>> This SF.net email is sponsored by DB2 Express >>> Download DB2 Express C - the FREE version of DB2 express and take >>> control of your XML. No limits. Just data. Click to get it now. >>> http://sourceforge.net/powerbar/db2/ >>> _______________________________________________ >>> PyWrapper-devel mailing list >>> PyW...@li... >>> https://lists.sourceforge.net/lists/listinfo/pywrapper-devel >> >> >> ---------------------------------------------------------------------=20= >> ---- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> PyWrapper-devel mailing list >> PyW...@li... >> https://lists.sourceforge.net/lists/listinfo/pywrapper-devel >> > > ----------------------------------------------------------------------=20= > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > PyWrapper-devel mailing list > PyW...@li... > https://lists.sourceforge.net/lists/listinfo/pywrapper-devel > > > > > ----------------------------------------------------------------------=20= > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > PyWrapper-devel mailing list > PyW...@li... > https://lists.sourceforge.net/lists/listinfo/pywrapper-devel |
From: <m.d...@BG...> - 2007-06-15 09:23:36
|
It might or should. but im not 100% sure and it can be quite some work = if you have to compile the fastcgi module for apache yourself. on linux = its probably part of the distribution. see here: http://trac.pywrapper.org/pywrapper/wiki/InstallationGuide#Behindawebserv= erviaFastCGI There is also a cherrypy configuration in config/pywrapper.cfg that has = this line: server.thread_pool =3D 3 try increasing the thread pool. that should allow the cherrypy server to = answer more requests simultaneously. markus -----Original Message----- From: pyw...@li... on behalf of Shunde = Zhang Sent: Thu 6/14/2007 2:45 AM To: PyWrapper Developers mailing list Cc:=09 Subject: Re: [PyWrapper-devel] GENERATING_CONTENT_FAILED withparallel = queries Hi Markus, I am using cherrypy for testing. could you please tell me how to use = production mode? would it be solved if I use apache? thanks again. Cheers, Shunde. Quoting Markus D=F6ring <m.d...@bg...>: > shunde, > are you running pywrapper behind apache via fastcgi or standalone via > cherrypy? if cherrypy, are you using the produciton mode? > -- > Markus > > > > On 13.06.2007, at 02:10, Shunde Zhang wrote: > > > Hi all, > > > > I've written a program using multi-threads to send queries at the > > same time. I > > was working before. Yesterday I put in more records to my database > > (~300000). > > Today I ran my program, I found that it works if I send one only > > query at one > > time. If I sent 2 queries at the same time, it gives me an error. > > > > <!-- CONTENT START --> > > <error xmlns=3D"http://rs.tdwg.org/tapir/1.0" time=3D"2007-06-07 > > 11:13:10.23" > > level=3D"ERROR">Response preparation and data retrieval = error</error> > > <!-- CONTENT END --> > > <diagnostics> > > <diagnostic time=3D"2007-06-07T11:13:02.44" level=3D"INFO">Reading > > request</diagnostic> > > <diagnostic time=3D"2007-06-07T11:13:02.49" level=3D"INFO">Read = model > > http://rs.tdwg.org/tapir/cs/abcd/2.06/model/abcd206.xml</diagnostic> > > <diagnostic time=3D"2007-06-07T11:13:02.51" level=3D"INFO">Request = fully > > parsed</diagnostic> > > <diagnostic time=3D"2007-06-07T11:13:02.51" level=3D"INFO">Get = distinct > > records...</diagnostic> > > <diagnostic time=3D"2007-06-07T11:13:02.52" level=3D"INFO">Executing > > SQL: "SELECT > > DISTINCT TaxonName.Genus, TaxonName.Species FROM TaxonName AS > > TaxonName > > ORDER BY TaxonName.Genus, TaxonName.Species LIMIT 21 OFFSET 0"</ > > diagnostic> > > <diagnostic time=3D"2007-06-07T11:13:03.47" level=3D"INFO">Parsed > > response structure > > contains 991 leaf concepts with type out of 1663 nodes in = total</diag > > nostic> > > <diagnostic time=3D"2007-06-07T11:13:04.14" level=3D"INFO">Request = fully > > parsed</diagnostic> > > <diagnostic time=3D"2007-06-07T11:13:04.15" level=3D"INFO">Init = model > > ACBD 2.06 with > > datasource preferences</diagnostic> > > <diagnostic time=3D"2007-06-07T11:13:04.55" level=3D"INFO">Model = init > > finished. The > > model contains 1324 mapped concepts for datasource 'avh' out of 1324 = m > > odel nodes mapped.</diagnostic> > > <diagnostic time=3D"2007-06-07T11:13:04.55" level=3D"INFO">Update = model > > structure > > with datasource preferences</diagnostic> > > <diagnostic time=3D"2007-06-07T11:13:10.17" level=3D"INFO">DB query > > finished</diagnostic> > > <diagnostic time=3D"2007-06-07T11:13:10.17" > > level=3D"ERROR">GENERATING_CONTENT_FAILED</diagnostic> > > <diagnostic time=3D"2007-06-07T11:13:10.23" level=3D"ERROR">Response > > preparation and > > data retrieval error</diagnostic> > > <diagnostic time=3D"2007-06-07T11:13:10.24" > > level=3D"ERROR">GENERATING_CONTENT_FAILED</diagnostic> > > > > Strangely, i sent one inventory and one search, but the errors I > > got are the > > same, which is like doing an inventory query as above. Could you > > please give me > > some idea of how to solve it? thanks a lot. > > > > Cheers, > > Shunde. > > > > > > > > > > = ---------------------------------------------------------------------- > > --- > > This SF.net email is sponsored by DB2 Express > > Download DB2 Express C - the FREE version of DB2 express and take > > control of your XML. No limits. Just data. Click to get it now. > > http://sourceforge.net/powerbar/db2/ > > _______________________________________________ > > PyWrapper-devel mailing list > > PyW...@li... > > https://lists.sourceforge.net/lists/listinfo/pywrapper-devel > > > = -------------------------------------------------------------------------= > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > PyWrapper-devel mailing list > PyW...@li... > https://lists.sourceforge.net/lists/listinfo/pywrapper-devel > -------------------------------------------------------------------------= This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ PyWrapper-devel mailing list PyW...@li... https://lists.sourceforge.net/lists/listinfo/pywrapper-devel |