February 2014 - Echobase-devel - mailman.cloud.codelutin.com

Mise à jour des requètes (mathieu)
by Tony Chemit 28 Feb '14

28 Feb '14

Hello, Je pense avoir fini avec la préparation des vues, voici le fichier en pièce-jointe. J'ai juste un doute sur la somme des meanLenght pour une espèce donnée et une cellule donnée, ça me paraît bizarre de sommer des moyennes, à toi de me dire si c'est ok. On le validera demain matin si tu veux. Bonne soirée. tony. -- Tony Chemit -------------------- tél: +33 (0) 2 40 50 29 28 http://www.codelutin.com email: chemit(a)codelutin.com twitter: https://twitter.com/tchemit

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Import FishMap
by Tony Chemit 28 Feb '14

28 Feb '14

Mathieu, Je n'ai pas pu importé le fichier car il me manque une espèces BIGG-FISH. On voit ça demain matin. tony. -- Tony Chemit -------------------- tél: +33 (0) 2 40 50 29 28 http://www.codelutin.com email: chemit(a)codelutin.com twitter: https://twitter.com/tchemit

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Concernant les vues pour les résultats esdu - espèces
by Tony Chemit 27 Feb '14

27 Feb '14

Salut, je suis encore sur le travail de ces vues, le fait de faire des regroupements c'est pas si simple si on veut garder de bonnes performances. Je vais donc dans un premier temps tout limiter aux espèces principales et aux métas concernés qu'on veut traiter. On verra plus tard si d'autres besoins surgissent. Mathieu, je t'envoie ça quand c'est prêt. tony. -- Tony Chemit -------------------- tél: +33 (0) 2 40 50 29 28 http://www.codelutin.com email: chemit(a)codelutin.com twitter: https://twitter.com/tchemit

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Fwd: RE: Implementation of metadata standard
by Mathieu Doray 27 Feb '14

27 Feb '14

Hola! Echobase envahit le monde! J'ai des collègues english qui voudraient tester Echobase, et notamment le lien avec QGIS (cf. ci-dessous). Vois tu une possibilité de faire ça? sur demo? Et je voulais traduire d'avantage le site Echobase en anglais mais le restructured text il ne veut pas enregistrer mes modifs... (j'ai créé un ticket) A+ M -------- Message original -------- Sujet: RE: Implementation of metadata standard Date : Wed, 26 Feb 2014 22:01:40 +0000 De : Adam Dunford <Adam.Dunford(a)niwa.co.nz> Pour : Mathieu Doray <mathieu.doray(a)ifremer.fr> RE: Implementation of metadata standard Hi Matthieu, Thank you for the information. I am very interested as that is what we are trying to do also. We have made some progress towards having a web interface to our fisheries acoustic data and I would be interested in seeing what you've done. Can you give me the web link or tell me how to access via QGis? Thanks, Adam *From:*Mathieu Doray [mailto:mathieu.doray@ifremer.fr] *Sent:* Thursday, 27 February 2014 6:59 a.m. *To:* Gauthier, Stephane; Adam Dunford; Carrie Wall Bell - NOAA Affiliate; Michael Jech - NOAA Federal *Cc:* Tim.Ryan(a)csiro.au; alex.derobertis(a)noaa.gov; Chris Taylor - NOAA Federal; ddoolittle(a)ku.edu; davidm(a)echoview.com; Ryan.Downie(a)csiro.au; erwan.josse(a)ird.fr; gavinj(a)imr.no; nilsolav(a)imr.no; Hassan.Moustahfid(a)noaa.gov; jeff.condiotty(a)simrad.com; jhorne(a)u.washington.edu; julien.barde(a)ird.fr; Gordon.Keith(a)csiro.au; lars.nonboe.andersen(a)simrad.com; Laura Kracker - NOAA Federal; Laurent.Berger(a)ifremer.fr; Melvin, Gary D; niklas.larson(a)slu.se; nolwenn.behagle(a)ird.fr; hector.pena(a)imr.no; Reka Domokos - NOAA Federal; Richard O'Driscoll; Rick Towler - NOAA Federal; s_elayoubi(a)hotmail.com; sascha.fassler(a)wur.nl; sigurdur(a)hafro.is; sof(a)bas.ac.uk; sromain(a)gmail.com; Taina.Honkalehto(a)noaa.gov; tomasz.laczkowski(a)mir.gdynia.pl; Verena.Trenkel(a)ifremer.fr; Brent Wood *Subject:* Re: Implementation of metadata standard Dear all, good question, indeed... We, at Ifremer, have designed Echobase, an open source, server-based, relational database, which is fully aligned on the ICES metadata standard. It is powered by a postgreSQL database, and can be queried within a web browser, through a java interface, LibreOffice base, R, or Quantum GIS. I have attached a slideshow describing the Echobase main features. The software includes English menus and can be freely downloaded here: http://maven-site.forge.codelutin.com/echobase/en/index.html The database model is available there: http://maven-site.forge.codelutin.com/echobase/en/model.html The ICES metadata standard works quite well for us. We collect all mandatory metadata. Data inputs in Echobase are based on text files automatically generated in R, so inputing lots of metadata is not a problem, as long as they can be automatically produced by R, based on raw informations from the cruise. I unfortunately will not attend the WAST meeting this year (I will at sea, echo-counting anchovies in the Bay of Biscay...). However, Laurent, who actively participated in the Echobase design, should be there. Also, feel free to ask me questions on Echobase. Cheers, Mathieu Le 25/02/2014 04:37, Gauthier, Stephane a écrit : Hi Adam (& co), I also have someone here in Canada who is working on a relational database fully aligned with the ICES metadata standard. I'll get in touch with him and get back to you. -sg -----Original Message----- From: Adam Dunford [mailto:Adam.Dunford@niwa.co.nz] Sent: Mon 2/24/2014 7:23 PM To: Carrie Wall Bell - NOAA Affiliate; Michael Jech - NOAA Federal Cc: Tim.Ryan(a)csiro.au <mailto:Tim.Ryan@csiro.au>; alex.derobertis(a)noaa.gov <mailto:alex.derobertis@noaa.gov>; Chris Taylor - NOAA Federal; ddoolittle(a)ku.edu <mailto:ddoolittle@ku.edu>; davidm(a)echoview.com <mailto:davidm@echoview.com>; Ryan.Downie(a)csiro.au <mailto:Ryan.Downie@csiro.au>; erwan.josse(a)ird.fr <mailto:erwan.josse@ird.fr>; gavinj(a)imr.no <mailto:gavinj@imr.no>; nilsolav(a)imr.no <mailto:nilsolav@imr.no>; Hassan.Moustahfid(a)noaa.gov <mailto:Hassan.Moustahfid@noaa.gov>; jeff.condiotty(a)simrad.com <mailto:jeff.condiotty@simrad.com>; jhorne(a)u.washington.edu <mailto:jhorne@u.washington.edu>; julien.barde(a)ird.fr <mailto:julien.barde@ird.fr>; Gordon.Keith(a)csiro.au <mailto:Gordon.Keith@csiro.au>; lars.nonboe.andersen(a)simrad.com <mailto:lars.nonboe.andersen@simrad.com>; Laura Kracker - NOAA Federal; Laurent.Berger(a)ifremer.fr <mailto:Laurent.Berger@ifremer.fr>; Mathieu.Doray(a)ifremer.fr <mailto:Mathieu.Doray@ifremer.fr>; Melvin, Gary D; niklas.larson(a)slu.se <mailto:niklas.larson@slu.se>; nolwenn.behagle(a)ird.fr <mailto:nolwenn.behagle@ird.fr>; hector.pena(a)imr.no <mailto:hector.pena@imr.no>; Reka Domokos - NOAA Federal; Richard O'Driscoll; Rick Towler - NOAA Federal; s_elayoubi(a)hotmail.com <mailto:s_elayoubi@hotmail.com>; sascha.fassler(a)wur.nl <mailto:sascha.fassler@wur.nl>; sigurdur(a)hafro.is <mailto:sigurdur@hafro.is>; sof(a)bas.ac.uk <mailto:sof@bas.ac.uk>; Gauthier, Stephane; sromain(a)gmail.com <mailto:sromain@gmail.com>; Taina.Honkalehto(a)noaa.gov <mailto:Taina.Honkalehto@noaa.gov>; tomasz.laczkowski(a)mir.gdynia.pl <mailto:tomasz.laczkowski@mir.gdynia.pl>; Verena.Trenkel(a)ifremer.fr <mailto:Verena.Trenkel@ifremer.fr>; Brent Wood Subject: RE: Implementation of metadata standard Hi all, We also have implemented a relational database for our acoustic metadata. The ERD is attached, and like the NOAA WCD one from Carrie, we've also implemented an organisation/hierarchy that is closely aligned with the ICES metadata convention. We've provided WFS access to our acoustic metadata via QGIS and, using QGIS's action feature (developed by Gavin Macaulay, one of the lead DB creators), we can provide access to echogram images for all transects in the database. The echogram images for all transects are stored in an Atlas database which NIWA hosts and public access is available via atlas.niwa.co.nz/public.jsp (click on toggle images/documents on the RH sidebar once logged in to display all 70K pictures - note not all are echograms) As the database is slightly customised to our own system, and as we're now moving to a different system paradigm with its own particularities I'm designing a multi-schema database which will have a public-facing schema which is fully ICES metadata compliant. Probably as a materialised view, drawn from a number of private schema which are more data/format/system specific. So I'm particularly interested in whether anyone has tried to implement a relational model which is totally based on the ICES metadata convention. Cheers, Adam From: Carrie Wall Bell - NOAA Affiliate [mailto:carrie.wall@noaa.gov] Sent: Tuesday, 25 February 2014 9:50 a.m. To: Michael Jech - NOAA Federal Cc: Tim.Ryan(a)csiro.au <mailto:Tim.Ryan@csiro.au>; alex.derobertis(a)noaa.gov <mailto:alex.derobertis@noaa.gov>; Chris Taylor - NOAA Federal; ddoolittle(a)ku.edu <mailto:ddoolittle@ku.edu>; davidm(a)echoview.com <mailto:davidm@echoview.com>; Ryan.Downie(a)csiro.au <mailto:Ryan.Downie@csiro.au>; erwan.josse(a)ird.fr <mailto:erwan.josse@ird.fr>; gavinj(a)imr.no <mailto:gavinj@imr.no>; nilsolav(a)imr.no <mailto:nilsolav@imr.no>; Hassan.Moustahfid(a)noaa.gov <mailto:Hassan.Moustahfid@noaa.gov>; jeff.condiotty(a)simrad.com <mailto:jeff.condiotty@simrad.com>; jhorne(a)u.washington.edu <mailto:jhorne@u.washington.edu>; julien.barde(a)ird.fr <mailto:julien.barde@ird.fr>; Gordon.Keith(a)csiro.au <mailto:Gordon.Keith@csiro.au>; lars.nonboe.andersen(a)simrad.com <mailto:lars.nonboe.andersen@simrad.com>; Laura Kracker - NOAA Federal; Laurent.Berger(a)ifremer.fr <mailto:Laurent.Berger@ifremer.fr>; Mathieu.Doray(a)ifremer.fr <mailto:Mathieu.Doray@ifremer.fr>; Gary.Melvin(a)dfo-mpo.gc.ca <mailto:Gary.Melvin@dfo-mpo.gc.ca>; niklas.larson(a)slu.se <mailto:niklas.larson@slu.se>; nolwenn.behagle(a)ird.fr <mailto:nolwenn.behagle@ird.fr>; hector.pena(a)imr.no <mailto:hector.pena@imr.no>; Reka Domokos - NOAA Federal; Richard O'Driscoll; Rick Towler - NOAA Federal; s_elayoubi(a)hotmail.com <mailto:s_elayoubi@hotmail.com>; sascha.fassler(a)wur.nl <mailto:sascha.fassler@wur.nl>; sigurdur(a)hafro.is <mailto:sigurdur@hafro.is>; sof(a)bas.ac.uk <mailto:sof@bas.ac.uk>; Stephane.Gauthier(a)dfo-mpo.gc.ca <mailto:Stephane.Gauthier@dfo-mpo.gc.ca>; sromain(a)gmail.com <mailto:sromain@gmail.com>; Taina.Honkalehto(a)noaa.gov <mailto:Taina.Honkalehto@noaa.gov>; tomasz.laczkowski(a)mir.gdynia.pl <mailto:tomasz.laczkowski@mir.gdynia.pl>; Verena.Trenkel(a)ifremer.fr <mailto:Verena.Trenkel@ifremer.fr>; Adam Dunford Subject: Re: Implementation of metadata standard Hi all, I provided the attached metadata schematic to Tim earlier today but perhaps it's more prudent to disseminate it to the group and thus directly to Adam. We have implemented a relational database and it seems to be working quite well for us currently. Some of our terminology is slightly different from that of ICES but the general hierarchy and fields are very closely aligned. Please note the floating dark green cubes are views for our web-based map service and can be ignored. I will be at WGFAST in May and am looking forward to presenting an update on the archive and our metadata efforts. I would be delighted to have a follow-up discussion at the meeting and am open to either an informal or formal setting. Until then, if you have any questions about the attached or other aspects of our metadata/archive project, please don't hesitate to let me know. Carrie. -- Carrie C. Wall, PhD Fisheries Acoustician Cooperative Institute for Research in Environmental Sciences (CIRES) University of Colorado at Boulder NOAA/NGDC Marine Geology and Geophysics Division 325 Broadway E/GC3, Boulder, CO 80305 T: 303-497-4459, F: 303-497-6513 Office: 1B121, NOAA David Skaggs Research Center On Mon, Feb 24, 2014 at 1:38 PM, Michael Jech - NOAA Federal <michael.jech(a)noaa.gov <mailto:michael.jech@noaa.gov><mailto:michael.jech@noaa.gov>> wrote: Hi Tim and Adam, I'm glad Carrie Wall is on this list because she and Chuck Anderson are leading the US effort to archive and set up metadata for the water column acoustic data coming off the NOAA vessels. Adam should contact her directly, and hopefully can avoid re-inventing the wheel in different hemispheres. I'm hoping Carrie will give a presentation at the WGFAST meeting this year, to give everyone an update on our progress. If there is enough interest, we could get together after a day of the meeting, or we could meet informally for beers and discussion. If you want to meet a bit more formally, let me know - I know the co-hosts of the meeting to set up a room :) Thanks, mike On 2/23/14, Tim.Ryan(a)csiro.au <mailto:Tim.Ryan@csiro.au><mailto:Tim.Ryan@csiro.au> <Tim.Ryan(a)csiro.au <mailto:Tim.Ryan@csiro.au><mailto:Tim.Ryan@csiro.au>> wrote: > Hi all, > > I trust everybody is well. > > Email below from Adam Dunford (NIWA) asking about implementation of the > metadata convention in a relational database. If you have some experience of > this and can help please contact Adam. > > > I'm trying to get my head around the ICES metadata convention with the > intention of implementing it in a relational database. Scary, I know - and > making my head hurt at times as I try and talk to our DB people and metadata > experts :) > But I was wondering if you knew of anyone else trying to do the same sort of > thing and if so what relational model they ended up with. No point > re-inventing the wheel. > > I know that the final report carefully avoids both recommending any > particular implementation or even being so closely aligned to one particular > methodology that it's obvious for (e.g. netCDF). I just wondered if at > various times through the iteration of the metadata convention you had any > discussions as to how it might be done as an RDB if one was going to do so. > Adam Dunford [Adam.Dunford(a)niwa.co.nz <mailto:Adam.Dunford@niwa.co.nz><mailto:Adam.Dunford@niwa.co.nz>] > > > More generically, as people implement the metadata they are bound to find > aspects that could be improved or elements that are missing. Are people on > this mailing list happy to continue as a group that can serve to update the > metadata convention in response to user feedback? Hopefully this would not > be too much work and could be done mostly by email, but with the possibility > of meeting up either formally or informally at FAST if warranted. > > If you want out, let me know and I can take you off the email list, > otherwise I'll renew your free lifetime membership :). > > > Best regards > > > > > Tim > -- ######################################################## # J. Michael Jech # NEFSC # 166 Water St. (voice) 508-495-2353<tel:508-495-2353> # Woods Hole, MA 02543 (fax) 508-495-2115<tel:508-495-2115> # michael.jech(a)noaa.gov <mailto:michael.jech@noaa.gov><mailto:michael.jech@noaa.gov> ######################################################## -- Please consider the environment before printing this email. NIWA is the trading name of the National Institute of Water & Atmospheric Research Ltd. -- Mathieu Doray, PhD Ifremer Département Ecologie et Modèles pour l'Halieutique rue de l'Ile d'Yeu B.P. 21105 44311 Nantes Cedex 03 mathieu.doray(a)ifremer.fr <mailto:mathieu.doray@ifremer.fr> Tel./Phone: 02 40 37 41 65 / International: 332 40 37 41 65 Fax : 02.40.37.40.01 / International: 332 40 37 40 01 CV / resume:http://annuaire.ifremer.fr/cv/17093/ -- Please consider the environment before printing this email. NIWA is the trading name of the National Institute of Water & Atmospheric Research Ltd.

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Ouf! pas besoin de dédoubler la colonne resultvalue
by Tony Chemit 26 Feb '14

26 Feb '14

cool, j'ai trouvé au final un moyen pour ne pas à avoir à dédoubler la colonne en utilisant une function... Je t'envoie le fichier sql dans la soirée pour que tu puisses valider ça demain. merci, tony. -- Tony Chemit -------------------- tél: +33 (0) 2 40 50 29 28 http://www.codelutin.com email: chemit(a)codelutin.com twitter: https://twitter.com/tchemit

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[ANN] - EchoBase 2.5.2 released
by Tony Chemit 18 Feb '14

18 Feb '14

The EchoBase team is pleased to announce the echobase-2.5.2 release! The French Institute for the Exploitation of the Sea (Ifremer) has designed an open software suite for storing fisheries acoustic data and computing acoustic indicators for survey-based ecosystem monitoring. It comprises a postgreSQL database designed to store acoustic, navigation and fishing data from ecosystemic surveys (EchoBase) and a suite of R codes (EchoR) for computing fish population indicators based on Echobase data. Documentation of the project can be found here: https://maven-site.forge.codelutin.com/echobase Changes ------- Changes in this version include: Fixed Bugs: o Pb de connexion et d'ajout de données dans base de travail Issue: 4443. Thanks to Mathieu Doray. Resolved by tchemit. o Erreur à la création d'une nouvelle mission Issue: 4445. Thanks to Tony Chemit. Resolved by tchemit. Changes: o Updates I18n to 3.0 and all the nuiton-xxx libs Issue: 4425. Thanks to Tony Chemit. Resolved by tchemit. o Updates mavenpom to 4.7 Issue: 4061. Thanks to Tony Chemit. Resolved by tchemit. o Updates to topia 3.0 Issue: 4062. Thanks to Tony Chemit. Resolved by tchemit. Downloads --------- For a manual installation, you can download files here: https://forge.codelutin.com/projects/echobase/files * echobase-embedded-2.5.2.zip - https://forge.codelutin.com/attachments/download/1450 * echobase-full-2.5.2.war - https://forge.codelutin.com/attachments/download/1451 Have fun! -EchoBase team -- Tony Chemit -------------------- tél: +33 (0) 2 40 50 29 28 http://www.codelutin.com email: chemit(a)codelutin.com twitter: https://twitter.com/tchemit

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Import des données 2011
by Tony Chemit 16 Feb '14

16 Feb '14

Hello, Juste pour confirmer que l'import des données fonctionne bien sur le jeu 2011. Je viens de tout réimporter sur l'une des instances de démo [1] tony. [1] http://demo.codelutin.com/echobase-latest -- Tony Chemit -------------------- tél: +33 (0) 2 40 50 29 28 http://www.codelutin.com email: chemit(a)codelutin.com twitter: https://twitter.com/tchemit

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