Dear list members, (Sorry for cross-posting.) I would like to let you know that we've just updated these two pages on the wiki: 1. Essential tools and environment configurations: http://dev.gbif.org/wiki/display/ALA/01+Essential+tools+and+environment+conf... 2. Installation: http://dev.gbif.org/wiki/display/ALA/02+Installation We are able to install the ALA portal demo by following these steps. Any suggestions on improving the documentation are highly appreciated! Cheers, Burke
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Burke, Have you tried indexing a resource through their DwCA using biocache-store tool on Mac OS? Kind Regard. Sama - ------------------------------------------------------------ Santiago Martínez de la Riva Vivanco GBIF.ES, Unidad de Coordinación Real Jardín Botánico CSIC Plaza de Murillo, 2 28014 Madrid, Spain Tel: +34 91 4293917 x 273 - sama@gbif.es - www.gbif.es - https://twitter.com/smr_sama El 28/05/2014 17:34, Burke Chih-Jen Ko [GBIF] escribió:
Dear list members, (Sorry for cross-posting.)
I would like to let you know that we've just updated these two pages on the wiki:
1. Essential tools and environment configurations: http://dev.gbif.org/wiki/display/ALA/01+Essential+tools+and+environment+conf... 2. Installation: http://dev.gbif.org/wiki/display/ALA/02+Installation
We are able to install the ALA portal demo by following these steps. Any suggestions on improving the documentation are highly appreciated!
Cheers,
Burke
-----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQEcBAEBAgAGBQJThgQvAAoJEMV2/tf+QnQD3/IH+gPfKtkZy6YMAhOY0xZSVW32 cA6mHSqP6kwtxkTPhnNHbLQg83UOMb4WyB7VXgIDuKBYqkzN43TEU6ZmzX66war+ PLyn3H1dnks/clAEUYFNqXOPtt4xcUZs2jUG5z9GIqNo6Nw4WOto03Wye5Nbe7qH AXxchdr3JWu4jiJi7OlMtcxgNl2kkkiXB/3mB+e84N82NXmVQdk5wOW5/0hmgBkN xQSWMusX5TxT+k4MRyF7AFzl9GJSp6fIP8nCLQe1VZ7rYdP0d1uIZugDCSkI3kN8 pLi+jjd3zQm1cdXT8JjWF78XpUCuqrc+FQl2mYAXEPpVlk3egyMPoWzLWOT23ao= =1lOb -----END PGP SIGNATURE-----
Hi Sama, Yes I did but I use country DwC-A downloaded from GBIF Portal. I basically follow the instruction on https://code.google.com/p/ala-portal/wiki/LoadBiocacheData. Precisely it's done inside the ubuntu box. After that I can see indexed records but for now it seems the mapping needs some configuration. I am still looking for configurations. Did you get the map shown before? Cheers, Burke On May 28, 2014, at 5:43 PM, sama <sama@gbif.es> wrote:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
Dear Burke,
Have you tried indexing a resource through their DwCA using biocache-store tool on Mac OS?
Kind Regard. Sama - ------------------------------------------------------------ Santiago Martínez de la Riva Vivanco GBIF.ES, Unidad de Coordinación Real Jardín Botánico CSIC Plaza de Murillo, 2 28014 Madrid, Spain Tel: +34 91 4293917 x 273 - sama@gbif.es - www.gbif.es - https://twitter.com/smr_sama
El 28/05/2014 17:34, Burke Chih-Jen Ko [GBIF] escribió:
Dear list members, (Sorry for cross-posting.)
I would like to let you know that we've just updated these two pages on the wiki:
1. Essential tools and environment configurations: http://dev.gbif.org/wiki/display/ALA/01+Essential+tools+and+environment+conf... 2. Installation: http://dev.gbif.org/wiki/display/ALA/02+Installation
We are able to install the ALA portal demo by following these steps. Any suggestions on improving the documentation are highly appreciated!
Cheers,
Burke
-----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/
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Hi Burke, I think that you can use the instructions that you refer in your mail when you are running from inside CSIRO/ALA, please someone correct me if Im wrong. I´m going to tell you my experience: When I want to index a resource I use biocache.jar. I use two options: Load a resource via CSV or via Dwc-A. I attach a mail in which Natasha explains how we can load a resource via Dwc-A. If I want to load a resource through CSV, I execute the next command: java -cp .:biocache.jar au.org.ala.util.DwcCSVLoader drtest -l path-to-file.csv -b true When you have loaded the resource you have to enter in the biocache command line, then you must execute >biocache and then you can process and index the loaded resource. > process drtest and >index drtest. My problem is that when I want to load a resource via Dwc-A and I execute: java -cp .:biocache.jar au.org.ala.util.DwCALoader drtest The system doesnt find the class: au.org.ala.util.DwCALoader. It´s very weird. Could you check if you can do this? I mean, could you check if you can load a resource in the way Natasha explained in her mail? The mappings. I dont understand one thing. How is it possible that in the demo-portal <http://ala-ono.it.csiro.au/generic-hub/occurrences/de34b076-e436-4314-a769- 969f8ef36273> http://ala-ono.it.csiro.au/generic-hub/occurrences/de34b076-e436-4314-a769-9 69f8ef36273, I can see the information in the right way? This is an example of a Spanish resource from GBIF.org. The occurrences are been loaded, processed and indexed. How is that in our installation we must to do something else if in that installation we can see the indexed occurrences correctly, It is the same installation, right?? Kind regards. SaMa De: Burke Chih-Jen Ko [GBIF] [mailto:bko@gbif.org] Enviado el: jueves, 29 de mayo de 2014 9:48 Para: Santiago Martinez de la Riva CC: Ala-portal@lists.gbif.org Asunto: Re: [Ala-portal] Installation page updated Hi Sama, Yes I did but I use country DwC-A downloaded from GBIF Portal. I basically follow the instruction on https://code.google.com/p/ala-portal/wiki/LoadBiocacheData. Precisely it's done inside the ubuntu box. After that I can see indexed records but for now it seems the mapping needs some configuration. I am still looking for configurations. Did you get the map shown before? Cheers, Burke On May 28, 2014, at 5:43 PM, sama <sama@gbif.es> wrote: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Burke, Have you tried indexing a resource through their DwCA using biocache-store tool on Mac OS? Kind Regard. Sama - ------------------------------------------------------------ Santiago Martínez de la Riva Vivanco GBIF.ES, Unidad de Coordinación Real Jardín Botánico CSIC Plaza de Murillo, 2 28014 Madrid, Spain Tel: +34 91 4293917 x 273 - sama@gbif.es - www.gbif.es - https://twitter.com/smr_sama El 28/05/2014 17:34, Burke Chih-Jen Ko [GBIF] escribió: Dear list members, (Sorry for cross-posting.) I would like to let you know that we've just updated these two pages on the wiki: 1. Essential tools and environment configurations: http://dev.gbif.org/wiki/display/ALA/01+Essential+tools+and+environment+conf igurations 2. Installation: http://dev.gbif.org/wiki/display/ALA/02+Installation We are able to install the ALA portal demo by following these steps. Any suggestions on improving the documentation are highly appreciated! Cheers, Burke -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQEcBAEBAgAGBQJThgQvAAoJEMV2/tf+QnQD3/IH+gPfKtkZy6YMAhOY0xZSVW32 cA6mHSqP6kwtxkTPhnNHbLQg83UOMb4WyB7VXgIDuKBYqkzN43TEU6ZmzX66war+ PLyn3H1dnks/clAEUYFNqXOPtt4xcUZs2jUG5z9GIqNo6Nw4WOto03Wye5Nbe7qH AXxchdr3JWu4jiJi7OlMtcxgNl2kkkiXB/3mB+e84N82NXmVQdk5wOW5/0hmgBkN xQSWMusX5TxT+k4MRyF7AFzl9GJSp6fIP8nCLQe1VZ7rYdP0d1uIZugDCSkI3kN8 pLi+jjd3zQm1cdXT8JjWF78XpUCuqrc+FQl2mYAXEPpVlk3egyMPoWzLWOT23ao= =1lOb -----END PGP SIGNATURE-----
Thanks Santiago, Burke. The recommended approach for all projects is to load data following the instructions that Burke included in his last email [1]. One of the requirements for this to work is that an instance of the collectory is installed. What Natasha described (and which is now out of date) is a mechanism for loading data without a collectory instance. This is useful for local development purposes only. This can be done on the command line with version 1.1 with the command: biocache>> load-local-csv dr0 /tmp/my-csv.txt The way we load data in our production environment is as follows: 1) Create a data resource in the collectory 2) Upload a CSV or DwC-A zip file into the collectory using the "Upload file" option 3) Use the command line tool describe in [1] to load, sample (optional), process and index the data Hope this helps. Dave Martin ALA [1] https://code.google.com/p/ala-portal/wiki/LoadBiocacheData ________________________________ From: ala-portal-bounces@lists.gbif.org [ala-portal-bounces@lists.gbif.org] on behalf of Santiago [sama@gbif.es] Sent: 29 May 2014 19:08 To: 'Burke Chih-Jen Ko [GBIF]' Cc: Ala-portal@lists.gbif.org Subject: Re: [Ala-portal] Installation page updated Hi Burke, I think that you can use the instructions that you refer in your mail when you are running from inside CSIRO/ALA, please someone correct me if I’m wrong. I´m going to tell you my experience: When I want to index a resource I use biocache.jar. I use two options: Load a resource via CSV or via Dwc-A. I attach a mail in which Natasha explains how we can load a resource via Dwc-A. If I want to load a resource through CSV, I execute the next command: java -cp .:biocache.jar au.org.ala.util.DwcCSVLoader drtest -l path-to-file.csv -b true When you have loaded the resource you have to enter in the biocache command line, then you must execute “ >biocache” and then you can process and index the loaded resource. “> process drtest” and “>index drtest”. My problem is that when I want to load a resource via Dwc-A and I execute: java -cp .:biocache.jar au.org.ala.util.DwCALoader drtest The system doesn’t find the class: au.org.ala.util.DwCALoader. It´s very weird. Could you check if you can do this? I mean, could you check if you can load a resource in the way Natasha explained in her mail? The mappings. I don’t understand one thing. How is it possible that in the demo-portal http://ala-ono.it.csiro.au/generic-hub/occurrences/de34b076-e436-4314-a769-9..., I can see the information in the right way? This is an example of a Spanish resource from GBIF.org. The occurrences are been loaded, processed and indexed. How is that in our installation we must to do something else if in that installation we can see the indexed occurrences correctly, It is the same installation, right?? Kind regards. SaMa De: Burke Chih-Jen Ko [GBIF] [mailto:bko@gbif.org] Enviado el: jueves, 29 de mayo de 2014 9:48 Para: Santiago Martinez de la Riva CC: Ala-portal@lists.gbif.org Asunto: Re: [Ala-portal] Installation page updated Hi Sama, Yes I did but I use country DwC-A downloaded from GBIF Portal. I basically follow the instruction on https://code.google.com/p/ala-portal/wiki/LoadBiocacheData. Precisely it's done inside the ubuntu box. After that I can see indexed records but for now it seems the mapping needs some configuration. I am still looking for configurations. Did you get the map shown before? Cheers, Burke On May 28, 2014, at 5:43 PM, sama <sama@gbif.es<mailto:sama@gbif.es>> wrote: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Burke, Have you tried indexing a resource through their DwCA using biocache-store tool on Mac OS? Kind Regard. Sama - ------------------------------------------------------------ Santiago Martínez de la Riva Vivanco GBIF.ES, Unidad de Coordinación Real Jardín Botánico CSIC Plaza de Murillo, 2 28014 Madrid, Spain Tel: +34 91 4293917 x 273 - sama@gbif.es<mailto:sama@gbif.es> - www.gbif.es<http://www.gbif.es> - https://twitter.com/smr_sama El 28/05/2014 17:34, Burke Chih-Jen Ko [GBIF] escribió: Dear list members, (Sorry for cross-posting.) I would like to let you know that we've just updated these two pages on the wiki: 1. Essential tools and environment configurations: http://dev.gbif.org/wiki/display/ALA/01+Essential+tools+and+environment+conf... 2. Installation: http://dev.gbif.org/wiki/display/ALA/02+Installation We are able to install the ALA portal demo by following these steps. Any suggestions on improving the documentation are highly appreciated! Cheers, Burke -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQEcBAEBAgAGBQJThgQvAAoJEMV2/tf+QnQD3/IH+gPfKtkZy6YMAhOY0xZSVW32 cA6mHSqP6kwtxkTPhnNHbLQg83UOMb4WyB7VXgIDuKBYqkzN43TEU6ZmzX66war+ PLyn3H1dnks/clAEUYFNqXOPtt4xcUZs2jUG5z9GIqNo6Nw4WOto03Wye5Nbe7qH AXxchdr3JWu4jiJi7OlMtcxgNl2kkkiXB/3mB+e84N82NXmVQdk5wOW5/0hmgBkN xQSWMusX5TxT+k4MRyF7AFzl9GJSp6fIP8nCLQe1VZ7rYdP0d1uIZugDCSkI3kN8 pLi+jjd3zQm1cdXT8JjWF78XpUCuqrc+FQl2mYAXEPpVlk3egyMPoWzLWOT23ao= =1lOb -----END PGP SIGNATURE-----
Dear David, Thanks so much for the info. I´ll check it on my VM. Kind regards. SaMa. De: David.Martin@csiro.au [mailto:David.Martin@csiro.au] Enviado el: jueves, 29 de mayo de 2014 11:43 Para: Santiago Martinez de la Riva; bko@gbif.org CC: Ala-portal@lists.gbif.org Asunto: RE: [Ala-portal] Installation page updated Thanks Santiago, Burke. The recommended approach for all projects is to load data following the instructions that Burke included in his last email [1]. One of the requirements for this to work is that an instance of the collectory is installed. What Natasha described (and which is now out of date) is a mechanism for loading data without a collectory instance. This is useful for local development purposes only. This can be done on the command line with version 1.1 with the command: biocache>> load-local-csv dr0 /tmp/my-csv.txt The way we load data in our production environment is as follows: 1) Create a data resource in the collectory 2) Upload a CSV or DwC-A zip file into the collectory using the "Upload file" option 3) Use the command line tool describe in [1] to load, sample (optional), process and index the data Hope this helps. Dave Martin ALA [1] <https://code.google.com/p/ala-portal/wiki/LoadBiocacheData> https://code.google.com/p/ala-portal/wiki/LoadBiocacheData _____ From: ala-portal-bounces@lists.gbif.org [ala-portal-bounces@lists.gbif.org] on behalf of Santiago [sama@gbif.es] Sent: 29 May 2014 19:08 To: 'Burke Chih-Jen Ko [GBIF]' Cc: Ala-portal@lists.gbif.org Subject: Re: [Ala-portal] Installation page updated Hi Burke, I think that you can use the instructions that you refer in your mail when you are running from inside CSIRO/ALA, please someone correct me if Im wrong. I´m going to tell you my experience: When I want to index a resource I use biocache.jar. I use two options: Load a resource via CSV or via Dwc-A. I attach a mail in which Natasha explains how we can load a resource via Dwc-A. If I want to load a resource through CSV, I execute the next command: java -cp .:biocache.jar au.org.ala.util.DwcCSVLoader drtest -l path-to-file.csv -b true When you have loaded the resource you have to enter in the biocache command line, then you must execute >biocache and then you can process and index the loaded resource. > process drtest and >index drtest. My problem is that when I want to load a resource via Dwc-A and I execute: java -cp .:biocache.jar au.org.ala.util.DwCALoader drtest The system doesnt find the class: au.org.ala.util.DwCALoader. It´s very weird. Could you check if you can do this? I mean, could you check if you can load a resource in the way Natasha explained in her mail? The mappings. I dont understand one thing. How is it possible that in the demo-portal <http://ala-ono.it.csiro.au/generic-hub/occurrences/de34b076-e436-4314-a769- 969f8ef36273> http://ala-ono.it.csiro.au/generic-hub/occurrences/de34b076-e436-4314-a769-9 69f8ef36273, I can see the information in the right way? This is an example of a Spanish resource from GBIF.org. The occurrences are been loaded, processed and indexed. How is that in our installation we must to do something else if in that installation we can see the indexed occurrences correctly, It is the same installation, right?? Kind regards. SaMa De: Burke Chih-Jen Ko [GBIF] [mailto:bko@gbif.org] Enviado el: jueves, 29 de mayo de 2014 9:48 Para: Santiago Martinez de la Riva CC: Ala-portal@lists.gbif.org Asunto: Re: [Ala-portal] Installation page updated Hi Sama, Yes I did but I use country DwC-A downloaded from GBIF Portal. I basically follow the instruction on https://code.google.com/p/ala-portal/wiki/LoadBiocacheData. Precisely it's done inside the ubuntu box. After that I can see indexed records but for now it seems the mapping needs some configuration. I am still looking for configurations. Did you get the map shown before? Cheers, Burke On May 28, 2014, at 5:43 PM, sama <sama@gbif.es> wrote: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Burke, Have you tried indexing a resource through their DwCA using biocache-store tool on Mac OS? Kind Regard. Sama - ------------------------------------------------------------ Santiago Martínez de la Riva Vivanco GBIF.ES, Unidad de Coordinación Real Jardín Botánico CSIC Plaza de Murillo, 2 28014 Madrid, Spain Tel: +34 91 4293917 x 273 - sama@gbif.es - www.gbif.es - https://twitter.com/smr_sama El 28/05/2014 17:34, Burke Chih-Jen Ko [GBIF] escribió: Dear list members, (Sorry for cross-posting.) I would like to let you know that we've just updated these two pages on the wiki: 1. Essential tools and environment configurations: http://dev.gbif.org/wiki/display/ALA/01+Essential+tools+and+environment+conf igurations 2. Installation: http://dev.gbif.org/wiki/display/ALA/02+Installation We are able to install the ALA portal demo by following these steps. Any suggestions on improving the documentation are highly appreciated! Cheers, Burke -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQEcBAEBAgAGBQJThgQvAAoJEMV2/tf+QnQD3/IH+gPfKtkZy6YMAhOY0xZSVW32 cA6mHSqP6kwtxkTPhnNHbLQg83UOMb4WyB7VXgIDuKBYqkzN43TEU6ZmzX66war+ PLyn3H1dnks/clAEUYFNqXOPtt4xcUZs2jUG5z9GIqNo6Nw4WOto03Wye5Nbe7qH AXxchdr3JWu4jiJi7OlMtcxgNl2kkkiXB/3mB+e84N82NXmVQdk5wOW5/0hmgBkN xQSWMusX5TxT+k4MRyF7AFzl9GJSp6fIP8nCLQe1VZ7rYdP0d1uIZugDCSkI3kN8 pLi+jjd3zQm1cdXT8JjWF78XpUCuqrc+FQl2mYAXEPpVlk3egyMPoWzLWOT23ao= =1lOb -----END PGP SIGNATURE-----
participants (4)
-
Burke Chih-Jen Ko [GBIF] -
David.Martin＠csiro.au -
sama -
Santiago