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[Biogeosdi] Who is working on the code?
by Javier de la Torre 28 Jun '07

28 Jun '07

Hey guys, While editing the code to improve a little bit the documentation I am more and more realizing that there has been some work on it after the workshop. I see ocurrencesModel now have methids to serialize to RSS and things like that... Who is working on this? For what purpose? Just for curiosity! Thanks Javier.

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Fwd: [Biogeosdi] Re: Search on the GBIF REST services
by Javier de la Torre 27 Jun '07

27 Jun '07

Here is a comment from Donald, I have to say I have no idea why this statement is on the report... was like this in the previous too no? Cheers. Begin forwarded message: > From: Donald Hobern <dhobern(a)gbif.org> > Date: 27 de junio de 2007 12:17:27 GMT+02:00 > To: Javier de la Torre <jatorre(a)gmail.com> > Subject: Re: [Biogeosdi] Re: Search on the GBIF REST services > > Thanks, Javier. > > I'll take a look. By the way, the report says: > > */ GBIF data does not reference the original data providers > > Are you having a problem with this? Every occurrence record (and > every taxon concept) is nested within a DataResource metadata > block, which is itself nested within a DataProvider block. For > each you can use the appropriate web service (with the supplied key > values) to retrieve full information (including access points for > DataResources). > > If you need help, please let me know. > > Many thanks, > > Donald > > Javier de la Torre wrote: >> jaja. >> >> Well, >> >> Let me send you the report as it is today. The doxygen still looks >> very bad, maybe is easier for you to just try the service >> interface we have for the code: >> >> http://omtest.cria.org.br/biogeosdi/backend/libs/amfphp/browser/ >> >> The doxygen is here (we are working to clean it): >> >> http://omtest.cria.org.br/biogeosdi/doc/html/ >> >> The two prototypes themselves can be found at: >> >> http://omtest.cria.org.br/biogeosdi/doc/html/ >> >> >> Have fun. >> >> Javier. >> >> >> >> >> On 27/06/2007, at 10:36, Donald Hobern wrote: >> >> >> >>> Do you have any current presentation/document outlining what you >>> are doing in BioGeoSDI? A web search tells me that you have >>> exceptionally well commented code... >>> >>> >>> >>> Donald >>> >>> >>> >>> Javier de la Torre wrote: >>> >>>> Buff... that is more than enough!! >>>> >>>> I suppose you also drop latitude=longitude=0 right? >>>> >>>> >>>> >>>> I think we have to change our report on this topic jeje. >>>> >>>> >>>> >>>> Cheers. >>>> >>>> >>>> >>>> On 26/06/2007, at 22:13, Donald Hobern wrote: >>>> >>>> >>>> >>>>> Right now the dodginess is only detected for records where we >>>>> interpret the Country name as a particular country and also >>>>> have coordinates and the coordinates do not intersect the >>>>> country. In many cases we actually also determine that the >>>>> latitude is negated, the longitude is negated and/or the >>>>> latitude and longitude are transposed. >>>>> >>>>> >>>>> >>>>> Donald >>>>> >>>>> >>>>> >>>>> Tim Sutton wrote: >>>>> >>>>>> Hi >>>>>> >>>>>> >>>>>> >>>>>> Great stuff that we can now exclude dodgy / non existant >>>>>> occurrences - >>>>>> >>>>>> we could probably make th e second (coordinate issues) option >>>>>> user >>>>>> >>>>>> settable (or at the least a setting in our global config file). >>>>>> >>>>>> >>>>>> >>>>>> Regards >>>>>> >>>>>> >>>>>> >>>>>> Tim >>>>>> >>>>>> >>>>>> >>>>>> 2007/6/26, Javier de la Torre <jatorre(a)gmail.com>: >>>>>> >>>>>>> Great, >>>>>>> >>>>>>> >>>>>>> >>>>>>> I will then uncomment the code :) >>>>>>> >>>>>>> >>>>>>> >>>>>>> Javier. >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 26/06/2007, at 17:24, Donald Hobern wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> > Thanks, Javier - found the problem - will get the fix deployed >>>>>>> >>>>>>> > tomorrow. >>>>>>> >>>>>>> > >>>>>>> >>>>>>> > Best wishes, >>>>>>> >>>>>>> > >>>>>>> >>>>>>> > Donald >>>>>>> >>>>>>> > >>>>>>> >>>>>>> > Javier de la Torre wrote: >>>>>>> >>>>>>> >> Great Donald, >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> We have now some comments to remove on the report about >>>>>>> the GBIF >>>>>>> >>>>>>> >> REST service ;) >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> Still I have an issue when using the &coordinateissues=false >>>>>>> >>>>>>> >> parameter >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> This URL returns 195 records: >>>>>>> >>>>>>> >> http://data.gbif.org/ws/rest/occurrence/list? >>>>>>> >>>>>>> >> format=brief&scientificname=Puma+concolor >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> This one none: >>>>>>> >>>>>>> >> http://data.gbif.org/ws/rest/occurrence/list? >>>>>>> >>>>>>> >> format=brief&coordinateissues=false&scientificname=Puma >>>>>>> +concolor >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> And I suppose not all coordinates are wrong no? >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> Cheers. >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> On 26/06/2007, at 14:29, Donald Hobern wrote: >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >>> Dear Javier, >>>>>>> >>>>>>> >>> >>>>>>> >>>>>>> >>> The structures are now stable. Sorry not to have copied >>>>>>> you on >>>>>>> >>>>>>> >>> my emails on what was changing. Adding >>>>>>> "&coordinatestatus=true" >>>>>>> >>>>>>> >>> should limit responses to those with coordinates. You >>>>>>> can also >>>>>>> >>>>>>> >>> use "&coordinateissues=false" to exclude records where we >>>>>>> have >>>>>>> >>>>>>> >>> detected that the coordinates do not match the supplied >>>>>>> country >>>>>>> >>>>>>> >>> name. >>>>>>> >>>>>>> >>> >>>>>>> >>>>>>> >>> Donald >>>>>>> >>>>>>> >>> >>>>>>> >>>>>>> >>> Javier de la Torre wrote: >>>>>>> >>>>>>> >>>> Hey Donald, >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> I am fixing some stuff on the prototype we did in Brasil >>>>>>> and I >>>>>>> >>>>>>> >>>> had to change my code to reflect the new format that the >>>>>>> rest >>>>>>> >>>>>>> >>>> services are sending now. Is this more or less stable now? >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> And another question, would be possible to ask the >>>>>>> service to >>>>>>> >>>>>>> >>>> return only occurrences with coordinates. For us is not >>>>>>> of much >>>>>>> >>>>>>> >>>> use occurrences without coordinates. >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> Thats the query I am trying >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> http://newportal.gbif.org/ws/rest/occurrence/list? >>>>>>> >>>>>>> >>>> >>>>>>> format=brief&minLatitude=-90&maxLatitude=90&scientificname=Puma >>>>>>> >>>>>>> >>>> +concolor >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> Thanks in advance. >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> Javier. >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>> >>>>>>> >>>>>>> >>> -- >>>>>>> >>>>>>> >>> ------------------------------------------------------------ >>>>>>> >>>>>>> >>> Donald Hobern (dhobern(a)gbif.org) >>>>>>> >>>>>>> >>> Deputy Director for Informatics Global Biodiversity >>>>>>> Information >>>>>>> >>>>>>> >>> Facility Secretariat Universitetsparken 15, DK-2100 >>>>>>> Copenhagen, >>>>>>> >>>>>>> >>> Denmark >>>>>>> >>>>>>> >>> Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 >>>>>>> >>>>>>> >>> ------------------------------------------------------------ >>>>>>> >>>>>>> >>> >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> > >>>>>>> >>>>>>> > -- >>>>>>> >>>>>>> > ------------------------------------------------------------ >>>>>>> >>>>>>> > Donald Hobern (dhobern(a)gbif.org) >>>>>>> >>>>>>> > Deputy Director for Informatics Global Biodiversity >>>>>>> Information >>>>>>> >>>>>>> > Facility Secretariat Universitetsparken 15, DK-2100 >>>>>>> Copenhagen, >>>>>>> >>>>>>> > Denmark >>>>>>> >>>>>>> > Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 >>>>>>> >>>>>>> > ------------------------------------------------------------ >>>>>>> >>>>>>> > >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> >>>>>>> biogeosdi mailing list >>>>>>> >>>>>>> biogeosdi(a)lists.tdwg.org >>>>>>> >>>>>>> http://lists.tdwg.org/mailman/listinfo/biogeosdi >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> >>> -- >>> ------------------------------------------------------------ >>> >>> Donald Hobern (dhobern(a)gbif.org) >>> >>> Deputy Director for Informatics Global Biodiversity Information >>> Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, >>> Denmark >>> >>> Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 >>> >>> ------------------------------------------------------------ >>> >>> >>> >> >> >> > > -- > ------------------------------------------------------------ > Donald Hobern (dhobern(a)gbif.org) > Deputy Director for Informatics > Global Biodiversity Information Facility Secretariat > Universitetsparken 15, DK-2100 Copenhagen, Denmark > Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 > ------------------------------------------------------------

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[Biogeosdi] Re: itineraries in openmodeller
by Meganck Bart 27 Jun '07

27 Jun '07

Hi Tim, A new week and the rain has started again... time for : Some paragraphs on itinerary modelling With itineraries, we want to retrace the actual expedition route as accurately as possible. For this, we want to make use of all possible data sources, the first of which are of course the georeferenced specimen records (such as come from GBIF et al.). Besides that, we are also looking for other information sources, for example field notes, old maps and the like. When properly encoded in some system of "boundaries", these extra information sources create a set of restrictions that can be used for quality control on the data. For example : if a point by its lat/lon values looks like an outlier of the general set, we could find clues in the other information sources about what is going on. Either some indication that, yes, the point is correct (e.g. its field number fits perfectly in the field number series) or some proof that, indeed, the point is incorrect (e.g. some notes about the camping sites, proving that the expedition was not near that place at the time). Both the data set (points) and the "info set" are fed into the modeller tool, and two outputs are generated : 1/ a judgement about the points in the data set (+ visualisation, indication of faulty points) and 2/ a new "info set", if the points yielded some new information to be used in the future. So, it would be a system that grows in knowledge as more data sets are processed, and more extra information is encoded. In a first stage though, we'll be mostly looking at the internal coherence in the data set points - and that would make the process more "mainstream" and "OM-ready". Later on, the process will add more "semantics" to the geospatial aspect, and I don't see very clear yet how that would fit into OM. The temporal aspect will, however, play a very important part from the beginning - an it's great news that OM will incorporate this. Have you seen the Mapbuilder timeseries demo : http://geoservices.cgdi.ca/mapbuilder/demo/timeSeries/index.html Basically, they perform as many WMS-requests as there are "time slices" on the WMS-server, then store the result and display one after the other in an animation. Best regards, Bart. On Sat, 2007-05-05 at 22:43 -0300, Tim Sutton wrote: > Hi > > Yes a couple of paragraphs of your ideas for itinerary modelling would > probably make your requirements a bit clearer. Currently the > openModeller library has no in built support for temporal analysis. In > a future release of openModeller Desktop, I will add support for > projection of niche models into multiple 'time slices' and producing > an animation of the result. Typically we would use this when > predicting changes in distribution in future climate scenarios. > > PS I dont know if I mentioned the new linux binary thats available > with the 1.0.5 release of openModeller. > > Regardsbiogeosdi(a)lists.tdwg.org > > Tim > > 2007/5/4, Meganck Bart <bart.meganck(a)africamuseum.be>: > > Hi Tim, > > > > > * could OM take in data layers other than environmental data ? > > > > > > > > > > It can use pretty much any raster layer - what did you have in mind? > > > > Well, it would be a bit more difficult than just a raster layer : > > in fact, we try to gather extra information from the data as we process > > it, so there > > would have to be some kind of (temporary) storage. > > > > Also, the data would be more time-oriented, not only spatially (as rasters > > are). > > I don't know if that would be feasible for OM - and if I'm expressing > > myself clearly > > here... ;-) > > > > Perhaps I'll make a short text with some explanation of what exactly > > we would try to do ? > > > > best regards, > > > > Bart. > > > > > > > > On Thu, 2007-05-03 at 13:21 -0300, Tim Sutton wrote: > > > Hi Bart! > > > > > > 2007/5/3, Meganck Bart <bart.meganck(a)africamuseum.be>: > > > > Hi Tim, > > > > > > > > I have been thinking about how to make the "itinerary" project a > > > > use-case for our GeoAppInter workflow. > > > > > > > > It's clear that until now I've been working a bit too enclosed - so > > the > > > > Campinas workshop was an eye-opener. > > > > > > > > In fact the itinerary implementation would not be that different from > > > > the demo we did. It's just another way of looking at the modeling > > part. > > > > For that I have some questions about OpenModeler : > > > > > > > > > > Cool it would be great to include itineray support. > > > > > > > * how easy or how difficult is it to make your own algorithms for OM ? > > > > In what language do they have to be implemented ? > > > > > > > > > > Its pretty easy - requires a basic knowledge of C++ though. > > > > > > > * could OM take in data layers other than environmental data ? > > > > > > > > > > It can use pretty much any raster layer - what did you have in mind? > > > > > > > > > Regards > > > > > > Tim > > > > > > > best regards, > > > > > > > > Bart. > > > > > > > > -- > > > > Bart Meganck, > > > > > > > > ICT & GIS engineer, > > > > African Zoology Department. > > > > > > > > Royal Museum for Central Africa, > > > > Leuvensesteenweg 13, > > > > B-3080 Tervuren, > > > > Belgium. > > > > > > > > Tel : +32(0)2 769 56 92 > > > > Fax : +32(0)2 767 02 42 > > > > Email : bart.meganck(a)africamuseum.be > > > > Website : www.africamuseum.be > > > > > > > > ########################################### > > > > > > > > This message has been scanned by ICT - Africa Museum > > > > > > > > ________________________________________ > > > > 3/5/2007 - Filtered through antispam by ICT > > > > > > > > > > > > > > > > > -- > > -- > > Bart Meganck, > > > > ICT & GIS engineer, > > African Zoology Department. > > > > Royal Museum for Central Africa, > > Leuvensesteenweg 13, > > B-3080 Tervuren, > > Belgium. > > > > Tel : +32(0)2 769 56 92 > > Fax : +32(0)2 767 02 42 > > Email : bart.meganck(a)africamuseum.be > > Website : www.africamuseum.be > > > > ########################################### > > > > This message has been scanned by ICT - Africa Museum > > > > ________________________________________ > > 4/5/2007 - Filtered through antispam by ICT > > > > > > > -- -- Bart Meganck, ICT & GIS engineer, African Zoology Department. Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium. Tel : +32(0)2 769 56 92 Fax : +32(0)2 767 02 42 Email : bart.meganck(a)africamuseum.be Website : www.africamuseum.be ########################################### This message has been scanned by ICT - Africa Museum ________________________________________ 7/5/2007 - Filtered through antispam by ICT

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Fwd: [Biogeosdi] Re: Search on the GBIF REST services
by Javier de la Torre 26 Jun '07

26 Jun '07

Begin forwarded message: > From: Donald Hobern <dhobern(a)gbif.org> > Date: 26 de junio de 2007 22:47:00 GMT+02:00 > To: Javier de la Torre <jatorre(a)gmail.com> > Cc: Tim Sutton <tim(a)linfiniti.com>, biogeosdi(a)lists.tdwg.org > Subject: Re: [Biogeosdi] Re: Search on the GBIF REST services > > The tests we perform correspond to the following bits: > > /** > * Set if latitude appears to have the wrong sign > */ > public static final int > GEOSPATIAL_PRESUMED_NEGATED_LATITUDE = 0x01; > /** > * Set if longitude appears to have the wrong sign > */ > public static final int > GEOSPATIAL_PRESUMED_NEGATED_LONGITUDE = 0x02; > /** > * Set if latitude and longitude appears to have been switched > */ > public static final int > GEOSPATIAL_PRESUMED_INVERTED_COORDINATES = 0x04; > /** > * Set if coordinates are (0,0) > */ > public static final int > GEOSPATIAL_ZERO_COORDINATES = 0x08; > /** > * Set if coordinates not in range -90 to 90 and -180 to 180 > */ > public static final int > GEOSPATIAL_COORDINATES_OUT_OF_RANGE = 0x10; > /** > * Set if coordinates do not match country name (covers > cases not handled above) > */ > public static final int > GEOSPATIAL_COUNTRY_COORDINATE_MISMATCH = 0x20; > > Donald > > Javier de la Torre wrote: >> Buff... that is more than enough!! >> I suppose you also drop latitude=longitude=0 right? >> >> I think we have to change our report on this topic jeje. >> >> Cheers. >> >> On 26/06/2007, at 22:13, Donald Hobern wrote: >> >>> Right now the dodginess is only detected for records where we >>> interpret the Country name as a particular country and also have >>> coordinates and the coordinates do not intersect the country. In >>> many cases we actually also determine that the latitude is >>> negated, the longitude is negated and/or the latitude and >>> longitude are transposed. >>> >>> Donald >>> >>> Tim Sutton wrote: >>>> Hi >>>> >>>> Great stuff that we can now exclude dodgy / non existant >>>> occurrences - >>>> we could probably make th e second (coordinate issues) option user >>>> settable (or at the least a setting in our global config file). >>>> >>>> Regards >>>> >>>> Tim >>>> >>>> 2007/6/26, Javier de la Torre <jatorre(a)gmail.com>: >>>>> Great, >>>>> >>>>> I will then uncomment the code :) >>>>> >>>>> Javier. >>>>> >>>>> On 26/06/2007, at 17:24, Donald Hobern wrote: >>>>> >>>>> > Thanks, Javier - found the problem - will get the fix deployed >>>>> > tomorrow. >>>>> > >>>>> > Best wishes, >>>>> > >>>>> > Donald >>>>> > >>>>> > Javier de la Torre wrote: >>>>> >> Great Donald, >>>>> >> >>>>> >> We have now some comments to remove on the report about the >>>>> GBIF >>>>> >> REST service ;) >>>>> >> >>>>> >> Still I have an issue when using the &coordinateissues=false >>>>> >> parameter >>>>> >> >>>>> >> This URL returns 195 records: >>>>> >> http://data.gbif.org/ws/rest/occurrence/list? >>>>> >> format=brief&scientificname=Puma+concolor >>>>> >> >>>>> >> This one none: >>>>> >> http://data.gbif.org/ws/rest/occurrence/list? >>>>> >> format=brief&coordinateissues=false&scientificname=Puma >>>>> +concolor >>>>> >> >>>>> >> >>>>> >> And I suppose not all coordinates are wrong no? >>>>> >> >>>>> >> Cheers. >>>>> >> >>>>> >> >>>>> >> On 26/06/2007, at 14:29, Donald Hobern wrote: >>>>> >> >>>>> >>> Dear Javier, >>>>> >>> >>>>> >>> The structures are now stable. Sorry not to have copied >>>>> you on >>>>> >>> my emails on what was changing. Adding >>>>> "&coordinatestatus=true" >>>>> >>> should limit responses to those with coordinates. You can >>>>> also >>>>> >>> use "&coordinateissues=false" to exclude records where we have >>>>> >>> detected that the coordinates do not match the supplied >>>>> country >>>>> >>> name. >>>>> >>> >>>>> >>> Donald >>>>> >>> >>>>> >>> Javier de la Torre wrote: >>>>> >>>> Hey Donald, >>>>> >>>> >>>>> >>>> I am fixing some stuff on the prototype we did in Brasil >>>>> and I >>>>> >>>> had to change my code to reflect the new format that the rest >>>>> >>>> services are sending now. Is this more or less stable now? >>>>> >>>> >>>>> >>>> And another question, would be possible to ask the service to >>>>> >>>> return only occurrences with coordinates. For us is not of >>>>> much >>>>> >>>> use occurrences without coordinates. >>>>> >>>> >>>>> >>>> Thats the query I am trying >>>>> >>>> >>>>> >>>> http://newportal.gbif.org/ws/rest/occurrence/list? >>>>> >>>> >>>>> format=brief&minLatitude=-90&maxLatitude=90&scientificname=Puma >>>>> >>>> +concolor >>>>> >>>> >>>>> >>>> Thanks in advance. >>>>> >>>> >>>>> >>>> Javier. >>>>> >>>> >>>>> >>>> >>>>> >>>> >>>>> >>> >>>>> >>> -- >>>>> >>> ------------------------------------------------------------ >>>>> >>> Donald Hobern (dhobern(a)gbif.org) >>>>> >>> Deputy Director for Informatics Global Biodiversity >>>>> Information >>>>> >>> Facility Secretariat Universitetsparken 15, DK-2100 >>>>> Copenhagen, >>>>> >>> Denmark >>>>> >>> Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 >>>>> >>> ------------------------------------------------------------ >>>>> >>> >>>>> >> >>>>> >> >>>>> >> >>>>> > >>>>> > -- >>>>> > ------------------------------------------------------------ >>>>> > Donald Hobern (dhobern(a)gbif.org) >>>>> > Deputy Director for Informatics Global Biodiversity Information >>>>> > Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, >>>>> > Denmark >>>>> > Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 >>>>> > ------------------------------------------------------------ >>>>> > >>>>> >>>>> _______________________________________________ >>>>> biogeosdi mailing list >>>>> biogeosdi(a)lists.tdwg.org >>>>> http://lists.tdwg.org/mailman/listinfo/biogeosdi >>>>> >>>> >>>> >> >> >>

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[Biogeosdi] Fwd: Auto-discard notification
by Javier de la Torre 26 Jun '07

26 Jun '07

I think Donald is not on the mailing list... Begin forwarded message: > From: biogeosdi-bounces(a)lists.tdwg.org > Date: 26 de junio de 2007 22:12:59 GMT+02:00 > To: biogeosdi-owner(a)lists.tdwg.org > Subject: Auto-discard notification > > The attached message has been automatically discarded. > From: Donald Hobern <dhobern(a)gbif.org> > Date: 26 de junio de 2007 22:13:02 GMT+02:00 > To: Tim Sutton <tim(a)linfiniti.com> > Cc: Javier de la Torre <jatorre(a)gmail.com>, biogeosdi(a)lists.tdwg.org > Subject: Re: [Biogeosdi] Re: Search on the GBIF REST services > > > Right now the dodginess is only detected for records where we > interpret the Country name as a particular country and also have > coordinates and the coordinates do not intersect the country. In > many cases we actually also determine that the latitude is negated, > the longitude is negated and/or the latitude and longitude are > transposed. > > Donald > > Tim Sutton wrote: >> Hi >> >> Great stuff that we can now exclude dodgy / non existant >> occurrences - >> we could probably make th e second (coordinate issues) option user >> settable (or at the least a setting in our global config file). >> >> Regards >> >> Tim >> >> 2007/6/26, Javier de la Torre <jatorre(a)gmail.com>: >>> Great, >>> >>> I will then uncomment the code :) >>> >>> Javier. >>> >>> On 26/06/2007, at 17:24, Donald Hobern wrote: >>> >>> > Thanks, Javier - found the problem - will get the fix deployed >>> > tomorrow. >>> > >>> > Best wishes, >>> > >>> > Donald >>> > >>> > Javier de la Torre wrote: >>> >> Great Donald, >>> >> >>> >> We have now some comments to remove on the report about the GBIF >>> >> REST service ;) >>> >> >>> >> Still I have an issue when using the &coordinateissues=false >>> >> parameter >>> >> >>> >> This URL returns 195 records: >>> >> http://data.gbif.org/ws/rest/occurrence/list? >>> >> format=brief&scientificname=Puma+concolor >>> >> >>> >> This one none: >>> >> http://data.gbif.org/ws/rest/occurrence/list? >>> >> format=brief&coordinateissues=false&scientificname=Puma+concolor >>> >> >>> >> >>> >> And I suppose not all coordinates are wrong no? >>> >> >>> >> Cheers. >>> >> >>> >> >>> >> On 26/06/2007, at 14:29, Donald Hobern wrote: >>> >> >>> >>> Dear Javier, >>> >>> >>> >>> The structures are now stable. Sorry not to have copied you on >>> >>> my emails on what was changing. Adding "&coordinatestatus=true" >>> >>> should limit responses to those with coordinates. You can also >>> >>> use "&coordinateissues=false" to exclude records where we have >>> >>> detected that the coordinates do not match the supplied country >>> >>> name. >>> >>> >>> >>> Donald >>> >>> >>> >>> Javier de la Torre wrote: >>> >>>> Hey Donald, >>> >>>> >>> >>>> I am fixing some stuff on the prototype we did in Brasil and I >>> >>>> had to change my code to reflect the new format that the rest >>> >>>> services are sending now. Is this more or less stable now? >>> >>>> >>> >>>> And another question, would be possible to ask the service to >>> >>>> return only occurrences with coordinates. For us is not of much >>> >>>> use occurrences without coordinates. >>> >>>> >>> >>>> Thats the query I am trying >>> >>>> >>> >>>> http://newportal.gbif.org/ws/rest/occurrence/list? >>> >>>> format=brief&minLatitude=-90&maxLatitude=90&scientificname=Puma >>> >>>> +concolor >>> >>>> >>> >>>> Thanks in advance. >>> >>>> >>> >>>> Javier. >>> >>>> >>> >>>> >>> >>>> >>> >>> >>> >>> -- >>> >>> ------------------------------------------------------------ >>> >>> Donald Hobern (dhobern(a)gbif.org) >>> >>> Deputy Director for Informatics Global Biodiversity Information >>> >>> Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, >>> >>> Denmark >>> >>> Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 >>> >>> ------------------------------------------------------------ >>> >>> >>> >> >>> >> >>> >> >>> > >>> > -- >>> > ------------------------------------------------------------ >>> > Donald Hobern (dhobern(a)gbif.org) >>> > Deputy Director for Informatics Global Biodiversity Information >>> > Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, >>> > Denmark >>> > Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 >>> > ------------------------------------------------------------ >>> > >>> >>> _______________________________________________ >>> biogeosdi mailing list >>> biogeosdi(a)lists.tdwg.org >>> http://lists.tdwg.org/mailman/listinfo/biogeosdi >>> >> >> >> >>

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Re: [Biogeosdi] Re: Search on the GBIF REST services
by Javier de la Torre 26 Jun '07

26 Jun '07

Buff... that is more than enough!! I suppose you also drop latitude=longitude=0 right? I think we have to change our report on this topic jeje. Cheers. On 26/06/2007, at 22:13, Donald Hobern wrote: > Right now the dodginess is only detected for records where we > interpret the Country name as a particular country and also have > coordinates and the coordinates do not intersect the country. In > many cases we actually also determine that the latitude is negated, > the longitude is negated and/or the latitude and longitude are > transposed. > > Donald > > Tim Sutton wrote: >> Hi >> >> Great stuff that we can now exclude dodgy / non existant >> occurrences - >> we could probably make th e second (coordinate issues) option user >> settable (or at the least a setting in our global config file). >> >> Regards >> >> Tim >> >> 2007/6/26, Javier de la Torre <jatorre(a)gmail.com>: >>> Great, >>> >>> I will then uncomment the code :) >>> >>> Javier. >>> >>> On 26/06/2007, at 17:24, Donald Hobern wrote: >>> >>> > Thanks, Javier - found the problem - will get the fix deployed >>> > tomorrow. >>> > >>> > Best wishes, >>> > >>> > Donald >>> > >>> > Javier de la Torre wrote: >>> >> Great Donald, >>> >> >>> >> We have now some comments to remove on the report about the GBIF >>> >> REST service ;) >>> >> >>> >> Still I have an issue when using the &coordinateissues=false >>> >> parameter >>> >> >>> >> This URL returns 195 records: >>> >> http://data.gbif.org/ws/rest/occurrence/list? >>> >> format=brief&scientificname=Puma+concolor >>> >> >>> >> This one none: >>> >> http://data.gbif.org/ws/rest/occurrence/list? >>> >> format=brief&coordinateissues=false&scientificname=Puma+concolor >>> >> >>> >> >>> >> And I suppose not all coordinates are wrong no? >>> >> >>> >> Cheers. >>> >> >>> >> >>> >> On 26/06/2007, at 14:29, Donald Hobern wrote: >>> >> >>> >>> Dear Javier, >>> >>> >>> >>> The structures are now stable. Sorry not to have copied you on >>> >>> my emails on what was changing. Adding "&coordinatestatus=true" >>> >>> should limit responses to those with coordinates. You can also >>> >>> use "&coordinateissues=false" to exclude records where we have >>> >>> detected that the coordinates do not match the supplied country >>> >>> name. >>> >>> >>> >>> Donald >>> >>> >>> >>> Javier de la Torre wrote: >>> >>>> Hey Donald, >>> >>>> >>> >>>> I am fixing some stuff on the prototype we did in Brasil and I >>> >>>> had to change my code to reflect the new format that the rest >>> >>>> services are sending now. Is this more or less stable now? >>> >>>> >>> >>>> And another question, would be possible to ask the service to >>> >>>> return only occurrences with coordinates. For us is not of much >>> >>>> use occurrences without coordinates. >>> >>>> >>> >>>> Thats the query I am trying >>> >>>> >>> >>>> http://newportal.gbif.org/ws/rest/occurrence/list? >>> >>>> format=brief&minLatitude=-90&maxLatitude=90&scientificname=Puma >>> >>>> +concolor >>> >>>> >>> >>>> Thanks in advance. >>> >>>> >>> >>>> Javier. >>> >>>> >>> >>>> >>> >>>> >>> >>> >>> >>> -- >>> >>> ------------------------------------------------------------ >>> >>> Donald Hobern (dhobern(a)gbif.org) >>> >>> Deputy Director for Informatics Global Biodiversity Information >>> >>> Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, >>> >>> Denmark >>> >>> Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 >>> >>> ------------------------------------------------------------ >>> >>> >>> >> >>> >> >>> >> >>> > >>> > -- >>> > ------------------------------------------------------------ >>> > Donald Hobern (dhobern(a)gbif.org) >>> > Deputy Director for Informatics Global Biodiversity Information >>> > Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, >>> > Denmark >>> > Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 >>> > ------------------------------------------------------------ >>> > >>> >>> _______________________________________________ >>> biogeosdi mailing list >>> biogeosdi(a)lists.tdwg.org >>> http://lists.tdwg.org/mailman/listinfo/biogeosdi >>> >> >>

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[Biogeosdi] Re: Search on the GBIF REST services
by Javier de la Torre 26 Jun '07

26 Jun '07

Great, I will then uncomment the code :) Javier. On 26/06/2007, at 17:24, Donald Hobern wrote: > Thanks, Javier - found the problem - will get the fix deployed > tomorrow. > > Best wishes, > > Donald > > Javier de la Torre wrote: >> Great Donald, >> >> We have now some comments to remove on the report about the GBIF >> REST service ;) >> >> Still I have an issue when using the &coordinateissues=false >> parameter >> >> This URL returns 195 records: >> http://data.gbif.org/ws/rest/occurrence/list? >> format=brief&scientificname=Puma+concolor >> >> This one none: >> http://data.gbif.org/ws/rest/occurrence/list? >> format=brief&coordinateissues=false&scientificname=Puma+concolor >> >> >> And I suppose not all coordinates are wrong no? >> >> Cheers. >> >> >> On 26/06/2007, at 14:29, Donald Hobern wrote: >> >>> Dear Javier, >>> >>> The structures are now stable. Sorry not to have copied you on >>> my emails on what was changing. Adding "&coordinatestatus=true" >>> should limit responses to those with coordinates. You can also >>> use "&coordinateissues=false" to exclude records where we have >>> detected that the coordinates do not match the supplied country >>> name. >>> >>> Donald >>> >>> Javier de la Torre wrote: >>>> Hey Donald, >>>> >>>> I am fixing some stuff on the prototype we did in Brasil and I >>>> had to change my code to reflect the new format that the rest >>>> services are sending now. Is this more or less stable now? >>>> >>>> And another question, would be possible to ask the service to >>>> return only occurrences with coordinates. For us is not of much >>>> use occurrences without coordinates. >>>> >>>> Thats the query I am trying >>>> >>>> http://newportal.gbif.org/ws/rest/occurrence/list? >>>> format=brief&minLatitude=-90&maxLatitude=90&scientificname=Puma >>>> +concolor >>>> >>>> Thanks in advance. >>>> >>>> Javier. >>>> >>>> >>>> >>> >>> -- >>> ------------------------------------------------------------ >>> Donald Hobern (dhobern(a)gbif.org) >>> Deputy Director for Informatics Global Biodiversity Information >>> Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, >>> Denmark >>> Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 >>> ------------------------------------------------------------ >>> >> >> >> > > -- > ------------------------------------------------------------ > Donald Hobern (dhobern(a)gbif.org) > Deputy Director for Informatics Global Biodiversity Information > Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, > Denmark > Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 > ------------------------------------------------------------ >

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[Biogeosdi] Fwd: Search on the GBIF REST services
by Javier de la Torre 26 Jun '07

26 Jun '07

Cool!! Begin forwarded message: > From: Donald Hobern <dhobern(a)gbif.org> > Date: 26 de junio de 2007 14:29:18 GMT+02:00 > To: Javier de la Torre <jatorre(a)gmail.com> > Subject: Re: Search on the GBIF REST services > > Dear Javier, > > The structures are now stable. Sorry not to have copied you on my > emails on what was changing. Adding "&coordinatestatus=true" > should limit responses to those with coordinates. You can also use > "&coordinateissues=false" to exclude records where we have detected > that the coordinates do not match the supplied country name. > > Donald > > Javier de la Torre wrote: >> Hey Donald, >> >> I am fixing some stuff on the prototype we did in Brasil and I had >> to change my code to reflect the new format that the rest services >> are sending now. Is this more or less stable now? >> >> And another question, would be possible to ask the service to >> return only occurrences with coordinates. For us is not of much >> use occurrences without coordinates. >> >> Thats the query I am trying >> >> http://newportal.gbif.org/ws/rest/occurrence/list? >> format=brief&minLatitude=-90&maxLatitude=90&scientificname=Puma >> +concolor >> >> Thanks in advance. >> >> Javier. >> >> >> > > -- > ------------------------------------------------------------ > Donald Hobern (dhobern(a)gbif.org) > Deputy Director for Informatics Global Biodiversity Information > Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, > Denmark > Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 > ------------------------------------------------------------ >

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[Biogeosdi] Long time ago...
by Javier de la Torre 26 Jun '07

26 Jun '07

Hey people!! Long time ago there was a meeting in Campinas... 6 incredible person met there to create an amazing prototype that would save the world... but they forgot to finish the documentation!! What a pity, the world would have been a much better place.... We can be different! We still have the opportunity to save the world if we finish the report from our last meeting! I have edited several parts of the document and sent it to Lee to ask him for comments. He is very happy with the status of the report, but I have to say I would still edit a little bit more... in any case I think we can start a fast process... let say we put the document under ask for comments until wednesday, if no one complain before I will send it then. If someone, for any reason, does not have access to the document on the SVN server Lee also asked me to present the report and the prototype on the next OGC meeting in Paris, the 12th of June. Flip will give us 20min and 5 more for questions... I hope everybody is fine with me going there. This is part of the TDWG-OGC MoU, we have to demonstrate that we take them seriously. I will be on holidays from the 28th til the 8th of July. I will travel to the states for a friends wedding in Kentucky. If things get crazy I might finish getting marriage in Las Vegas as Elvis Presley, but if not I will probably fly then directly tom Paris. My trip is NY- Chicago-Kentucky if someone is on the road those days. So... I did it again... I will use my holidays to work on the presentation and on the prototype. Ideally I will present a finish prototype on HTML and Flex, with the design that the designer did here and with Yahoo maps integration. Of course also with a nice presentation, not a boring one, and with lot of preparation. But somewhere between this ideal situation and a total disaster I will finish, if someone want to help please go ahead!! First thing I need to have is a title for the presentation. I have some ideas but more are welcome: -90 coconuts and an old Dell laptop to save biodiversity using geospatial standards. -Demonstration on how tropical weather influence programming productivity and happiness... using OGC standards! -OGC is not enough -Biodioversity 2.0 And some more classical, and more probable like: -OGC standards and biodiversity: the biogeosdi experiment. Javier de la Torre IMASTE-IPS Dtor. Tecnología Tel: 91 536 05 03 Mov: 629 69 38 70 skype:jatorre555 jatorre(a)imaste-ips.com

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Re: [Biogeosdi] the EDIT connection
by Javier de la Torre 25 Jun '07

25 Jun '07

Hey Tim, Well, this is definetly wired but I am on it... In any case I get a lot of layers like .svn/text-base/meanRad.asc.svn- base that I suspect are not real layers but is just that the omws fetch the layers from the file system and does not exclude hidden files like the ones from subversion. We are gonna get a lot of wrong layers like this. But in any case this is not the problem... it is the nusoap library... Did we mention enough in the report that SOAP document style web services are almost impossible to use from PHP? There is only nusoap available and is pretty buggy... I am really considering rewriting the piece of code that connect to the service and get the data... at the end we are not really making use of any serialization deserialization mechanism... definelty AMF rules!! JAvi. On 25/06/2007, at 20:22, Tim Sutton wrote: > Hi > > Yup I should have said I checked using openModeller desktop and the ws > is working fine so the issue seems to be a nusoapy one. If its still > using the omtest ws url (it was last I checked) then no the available > layers list should not have changed and it should return a result > pretty quickly since it has only a handful of layers in it... > > I think a swift conk on the nusoap lib with a coconut may fix it... > > Regards > > Tim > > 2007/6/25, Javier de la Torre <jatorre(a)gmail.com>: >> Hey, >> >> This is very weird. I checked with another tool and the OMWS is >> working fine returning layers as it should... then I check on the >> NUSOAP library and it seems that the problem is that the call to the >> method >> >> $omSoapService->document >> >> which should return the document that the omws returned is truncated >> almost at the end and therefore the XML does not validate... >> accessing the response inna an object way seems to work so I am >> checking if I can solve that. >> >> So... the difference from the workshop might be that there more >> layers now available under omws? >> >> Cheers. >> >> On 25/06/2007, at 18:00, Tim Sutton wrote: >> >> > Hi Javi >> > >> > If you watch the logs (/tmp/phperrors.log) while clicking onto the >> > getlayers link you will see only this: >> > >> > [25-Jun-2001 09:50:42] nlayers: 1 >> > [25-Jun-2001 09:50:46] >> > http://omtest.cria.org.br:80/cgi-bin/om_soap_server.cgi<-- ctor >> om end >> > point >> > [25-Jun-2001 09:50:46] >> > http://omtest.cria.org.br:80/cgi-bin/om_soap_server.cgi <-- >> > getAvailable Layers endpoint >> > >> > When I installed the omtest code on my mac here the mac console >> gives >> > me a bit more detail: >> > >> > [Mon Jun 25 12:59:57 2007] [error] nlayers: 1 >> > [Mon Jun 25 13:00:02 2007] [error] [client 200.144.120.115] File >> does >> > not exist: /Users/timlinux/Sites/biogeosdi/frontend/openlayers/ >> > theme/default/style.css >> > [Mon Jun 25 13:02:06 2007] [error] >> > http://omtest.cria.org.br:80/cgi-bin/om_soap_server.cgi<-- ctor >> om end >> > point >> > [Mon Jun 25 13:02:06 2007] [error] >> > http://omtest.cria.org.br:80/cgi-bin/om_soap_server.cgi <-- >> > getAvailable Layers endpoint >> > [Mon Jun 25 13:02:06 2007] [error] PHP Notice: Undefined property: >> > nusoapclient::$operation in >> > /Users/timlinux/dev/php/biogeosdi/backend/libs/nusoap/nusoap.php on >> > line 6837 >> > >> > Does that mean anything to you? >> > >> > Regards >> > >> > Tim >> > >> > 2007/6/7, Javier de la Torre <jatorre(a)gmail.com>: >> >> Give it to me!! I am the master of strange nusoap errors and >> you know >> >> it :D >> >> >> >> >> >> On 06/06/2007, at 20:49, Tim Sutton wrote: >> >> >> >> > Hi Guys >> >> > >> >> > Yes absolutely its all available as opensource already - they >> >> can get >> >> > it using anonymouse svn account. I've been working on getting >> the >> >> > prototype completed yesterday and on and off this week. >> Something >> >> > seems to have been broken with the layer selection screen and Im >> >> > gettin g a strange error from nusoap at this point. Ill post >> the >> >> > exact message in a follow up email. >> >> > >> >> > Regards >> >> > >> >> > Tim >> >> > >> >> > 2007/5/30, Javier de la Torre <jatorre(a)gmail.com>: >> >> >> Hi all, >> >> >> >> >> >> I am trying to finish what we did in the biodgeosdi meeting >> and >> >> >> going through the emails. >> >> >> >> >> >> > Some people from partner institutes are visiting us now >> for the >> >> >> EDIT >> >> >> > project. I have shown them what we have done in Campinas, and >> >> they >> >> >> > were >> >> >> > really interested. >> >> >> > >> >> >> > We got some nice interaction from them concerning >> Mapbuilder and >> >> >> other >> >> >> > softwares, and they were asking specifically for how we went >> >> >> about to >> >> >> > get the XMl from the OGC services, and pass it on to PHP. >> >> >> > >> >> >> > So, a quick check with all of the team : am I right that our >> >> code, >> >> >> > once >> >> >> > finished, will be available on the web as open source ? >> For the >> >> >> moment >> >> >> > you have to log into the CVS server. >> >> >> >> >> >> >> >> >> From my side this is clearly the idea. And expect it really >> soon. >> >> >> >> >> >> Cheers. >> >> >> _______________________________________________ >> >> >> biogeosdi mailing list >> >> >> biogeosdi(a)lists.tdwg.org >> >> >> http://lists.tdwg.org/mailman/listinfo/biogeosdi >> >> >> >> >> > >> >> > >> >> > -- >> >> > -- >> >> > Tim Sutton >> >> > >> >> > Visit http://qgis.org for a great Open Source GIS >> >> > Home Page: http://linfiniti.com >> >> > Skype: timlinux >> >> > MSN: tim_bdworld(a)msn.com >> >> > Yahoo: tim_bdworld(a)yahoo.com >> >> > Jabber: timlinux >> >> > Irc: timlinux on #qgis at freenode.net >> >> >> >> >> > >> > >> > -- >> > Tim Sutton >> > QGIS Project Steering Committee Member - Release Manager >> > Visit http://qgis.org for a great open source GIS >> > openModeller Desktop Developer >> > Visit http://openModeller.sf.net for a great open source ecological >> > niche modelling tool >> > Home Page: http://tim.linfiniti.com >> > Skype: timlinux >> > Irc: timlinux on #qgis at freenode.net >> >> > > > -- > Tim Sutton > QGIS Project Steering Committee Member - Release Manager > Visit http://qgis.org for a great open source GIS > openModeller Desktop Developer > Visit http://openModeller.sf.net for a great open source ecological > niche modelling tool > Home Page: http://tim.linfiniti.com > Skype: timlinux > Irc: timlinux on #qgis at freenode.net

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