ࡱ>  @ ibjbjVV r<r<i4$̾̾̾̾$$QyhxxxxxxxzR }xxx y xxdl 5Y8̾xgLp4!y0Qyg}N}l$$l}dm\d,xx$$Dhd5 $$hOBIS Technical Workshop Intergovernmental Oceanographic Commission (IOC) Member States have been asked to assist in the maintenance and further development of the Ocean Biogeographic Information System (OBIS) and in order to start the development process; a technical workshop was organized and was held at the Bedford Institute of Oceanography, Dartmouth, Canada from June 8 to 10, 2011. Representatives from the group of five institutes comprising the OBIS Development Consortium (Rutgers University, New Jersey, USA; Indian National Centre for Ocean Information Services, Hyderabad, India; the Flanders Marine Institute, Oostende, Belgium; the Marine Geospatial Ecology Laboratory of Duke University, North Carolina, USA; the Centre for Marine Biodiversity of the University Simon Bolivar, Caracas, Venezuela) and representatives from OBIS Canada participated. Due to unforeseen circumstances the representatives traveling from Belgium and Venezuela were unable to be physically present but were able to participate remotely thru the use of Skype. Mikogo ( HYPERLINK "http://www.mikogo.com/" http://www.mikogo.com/) was used to share computer screens at multiple locations. Draft Agenda Day 1 09:00-09:20 - Welcome (Dr. Alain Vezina, Regional Director of Science, Maritimes Region, Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS) 09:20-09:30 - practicalities (M. Kennedy, OBIS Canada, Bedford Institute of Oceanography, Dartmouth, NS) 09:30-10:00 - Opening presentation (Edward Vanden Berghe, OBIS secretariat, Rutgers University, USA) 10:15-12:00 - presentations - representatives of Rutgers, MGEL and USB will present the existing infrastructure. Presentations will focus on the search interface, systems, content management (Drupal) and the database. Identified issues and further development will be discussed. Examples of these issues are whether and how to make available OGC services, REST services, direct database access from GIS systems including Arc, Postgres 8.4 vs 9.0. A work plan will be created including coordinators name, timeline, deadlines, and deliverables. 12:00 - 13:00 - lunch (not provided) 13:00 - 17:00 - continuation Day two 09:00-12:00 - 'hands on' demonstrations 12:00-13:00 - lunch break (not provided) (Note during this period a short tour of BIO will be offered) 13:00-17:00 - continuation Day three 09-00-12:00 - discussions to focus on long term plans where do we want to be by when? What should our system look like to make sure the marine community sees added value to OBIS, over and above GBIF? What applications, search interfaces, etc do we need to serve our specific community? 12:00-13:00 lunch (not provided) 13:00-17:00 - continuation of discussions and preparation of a draft report documenting the outcomes of the workshop. Health breaks each day between 10:00-10:15 and 15:00-15:15 List of participants Edward Vanden Berghe, OBIS, Rutgers University Institute of Marine and Coastal Sciences, New Brunswick New Jersey 08901, USA Aditya Naik Kakodkar, IT Expert, UNESCO/IOC project office for IODE, Wandelaarkaai 7/61, 8400 Oostende, Belgium Mr. T.V.S. Udaya Bhaskar, Data and information Management Group,Indian National Centre for Ocean Information Services, Ocean Valley, Hyderabad, India Julio Castillo, Simon Bolivar University in Venezuela Bart Vanhoorne, Flanders Marine Institute Vlaams Instituut voor de Zee (VLIZ), Wandelaarkaai7, Oostende 8400, Belgium Francisco Hernandez, Flanders Marine Institute Vlaams Instituut voor de Zee (VLIZ), Wandelaarkaai7, Oostende 8400, Belgium Jesse Cleary, Marine Geospatial Ecology Lab, Nicholas School of the Environment, Duke University, NC, USA Ben Donnelly, Nicholas School of the Environment, Duke University, NC, USA Ei Fujioka, Nicholas School of the Environment, Duke University, NC, USA Lenore Bajona, OBIS Canada and Portal Manager, Ocean Tracking Network, Dalhousie University, Halifax, NS, Canada Mary Kennedy, OBIS Canada, Fisheries and Oceans Canada, BIO, Dartmouth, NS, Canada Transition from cloud to VLIZ - TimeLine & Action Items Friday am EVDB - start transfer of dump to postgres machine Friday am Bart - add a second VM disk mounted on /obis/db Friday pm - EVDB start of the restore of the dump Saturday EVDB test speed of the machine/ cross checking memory settings Monday Bendy check and update directory structure Tuesday VLIZ creates the new machine with input from Bendy to create new production database Monday/Tuesday Jesse & Bendy performance testing later in the week skype call to discuss future change the URL from www.VLIZ/be/obis to www.iobis.org future - postgres 9 replication procedures might help keep databases in sync. (Jesse) future - performance test using 2 servers IOC assembly end of June 22-July 5 Friday July 8th?? change DNS to VLIZ (production system) week later shut down Amazon instance September INCOIS - email re specifications required at INCOIS has been sent. notes EDVD dump into VLIZ; restore the dump ( Jesse to run performance tests this afternoon at that time the machines will not be available to others VLIZ & Bendy set up production server; need to reconfigure the machine so that the directory structure is similar on the cloud this can be done before the next data load. Jesse to create upgrade directions for 1.5; the default for the new machine will be to 1.4 so need directions to upgrade.. or VLIZ can take a copy of the virtual machine and start on the new hard drive. set the machine up as a 10gigabyete root disk and a 400 gigabyte var disk VLIZ ( 8Giga and 500 gig) - ACTION someone type df ?can the sizes be made smaller. better for machines. current postgres is 125gig cloud 215 and we are using less so a 300 or 250 will be ok (need larger size for dev machine) july 8 staging and dev machine will be the same next cycle there will be 3 machines (sometime in July) VLIZ to investigate another method for staging SEPT ( INCOIS will only have production; email re specifications required at INCOIS has been sent. INCOIS to start experimentating with VMware, investigate XEN INCOIS to get VMware images from Duke organize a download of the dbase to INCOIS. how much time does it take. will download be an option or will syncronization be required? if yes then this will impact the timescale. Now is the time to ask for a better bandwidth. (VLIZ bandwith is 1GB) Vliz to setup VMware and develop expertise with this machine; document comments re setup and various issues encountered. when to switch dev and what is needed? develop locally Ei has a local machine but will need to test on DEV machine that is as close as possible to the PROD machine. VLIZ will have a data staging (public test machine for ad hoc queries by 50-100 queries) machine running apache and geoserver and ? is it possible for VLIZ to create another machine only for postgres. this one will be used for data loading ? data flow data from dev to staging (dump) and then from staging to production (disc swap) data dev machine on different hardware staging and production on one machine talking 10gigabyes size for the dump. transferring this into the other machine should not be an issue. Friday & action points for immediate needs (no order) PriorityStatusMetadata - get metadata in order and then open up DiGIR metadata does not flow from ver v2 to new system (stored in html files and not in oracle tables) sync postgres with gcmd; sync eurobis with postgres; update obis seamap in GCMD; preference is to get content from GCMD - give credit from multiple data centres keep local copy of metadata in GCMD format perhaps OBIS can build means to send stuff to GCMD. high priority deliver metadata thru DiGIR.. must have a minimum content before the trip to Paris. (IOC assembly end of June 22-July 5) EVDB create a new separate schema called GCMD and this will get populated write scripts to read DIF files generate metadata in DiGIR for GBIF - find a way to shoehorn GCMD data into DiGIR so that we can pass it along on our DiGIR provider (to GBIF). example in GCMD there is a summary and a purpose ( will combine. Bart short term - send DIF files??create DiGIR like data which Evdb will push into resources table. long term - create GCMD pages (?) Ei send dif files to Evdb (as opposed to creating GCMD pages) Lenore we have had a problem with the length of abstract in DiGIR will check to see if there is a maximum number of characters or if this is an internal problem at OBIS CanadahighOAI functionality and responsibility to maintain and expand and working process ( wish to pass this on to someone else. (strategic planning)lowIPT Bart to test/provide comments MK to provide feedback from GBIF Canada testingxData transfer: postgres to postgres - method other than DiGIR EVDB & Lenore explore transfer options for OTNDatasets: Tracking data EVDB/Lenore what subset of tracking datasets should be sent. what has been done for POST and TOPP send only release or 1degree square? summarized data provide URL to get complete track Lenore write up an explanation of how to treat tracking data MK include this document as part of the managers guidexDatasets: Seabird & Aerial survey data sets what fields are required by Seamap EI- to send list of fields to MK MK - include as part of the managers guidexSteering Group (RON managers) to send comments re expanded schema example add animal ID in OBIS schema MK to organize consulting the SGxUsage of older v2 version of OBIS MK ask SG/RON managers to check to see they reference the old version of OBIS Duke? check apache logs to see who is using v2. Jesse was google analytics running on this site? Does analytics know that there was a change in machines? Evdb add a warning window web site to disappear include link to the new website and tutorial EVDB to ensure that v2 can be accessed now that the machine has moved. Lenore google search who is using www?xACON - doesnt work on v2. perhaps result of moving machine. EDVDB to check and change IP address if too complicated then it will be dropped Mary/Lenore to document what functionality currently exists and what functionality users would like to see retained Jesse - how do we convert this to the new search interfacexmap of a particular species URL. Ei to provide script for taxon and taxonID (works for resource: http://iobis.org/mapper/?resource_id=33) EVDB to provide a species list with taxonIDs (with other codes.AphiaID, TSN)revise any documentation etc to refer to taxon code as AphiaID and not WoRMS id. or refer to it as WoRMS code (AphiaID)include the AphiaIDs in the download. (perhaps include other codes such as TSNs) internally generated fields do not need to be seen Lenore to provide list of codes to excludeEVDB record_ID # should not change when data reloaded (Lenore can provide more info if needed here)select multiple areas example Bay of Fundy and Gulf of MainelowEVDB add FAO areas to the area selection criteria (and NAFO areas)Investigate adding Marine Protected AreasxMK contact WoRMS re adding a more obvious/prominent link to OBIS (at the moment the link to OBIS is at the bottom of the species page under distribution map)xxxxEVDB - EoL has depth range 330 to 0 and MK would prefer to see 0 to 330 (see gadus morhua). perhaps send depths as negative values?xEVDB - EOL doesnt show OBIS nameOBIS top page EVDB has a task for Ei ( which page shows up first map/taxon tree and details/resources parameters and details perhaps a museum wishes to link to their dataset. something about the information buttonAd hoc queries VLIZ? create new sever for ad hoc queries by privileged users; machine to be outside the firewall with username/password usage to be tracked and monitored tracked usage to be discussed - if a lot of use then a small fee should be requested perhaps this could be used for Amazon cloud. (Bendy has an idea about the cloud and census data add more lines)xsearch for specific species and create maps Ei & Jesse /VLIZget metadata for specific datasets. Ei/Bart create an inventory of taxa generate the pages and then cache them refresh once a month if continue monthly cycle of loading dataBulletin board Discussion Forum on Drupal (to solicit input) EVDB - set up the bulletin Brook to sign up RON managers, technical group, steering group INNER circle group someone to manager users someone to monitor the discussions and summarize someone to assign priorities to issues evdb Ei ( add threads from correspondenceEVDB - should evdb ask for amazon grant as well as Duke?Bendy - show EVDB to do a bug tracker in subversion instead of mantis.GBIF: GBIF marine content not in OBIS EVDB - GBIF is on the cloud. check to see what marine datasets are in GBIF RONs to check GBIF for marine data that is not available on OBIS following example of iOBIS(?)xGBIF: OBIS data in GBIF VLIZ contact GBIF to see when they last harvested. monitor the currency (up to date) as seen on GBIF and correctness.GBIF new role does anyone wish to take over the cloud version of GBIF? Someone to document details on what is required and then someone might volunteerGBIF reply VLIZ - GBIF needs a reply (to what????)integration of Drupal into php Julio and Eduardo - someone has to look into difficulty to make a formal drupal module out of PHP scriptsOBIS Page and SEARCH option EVDB clean up drupal search to indicate that searching text on the web pages and not searching the database for data. add line to bottom of page to say GO TO SEARCH DATA TAB remove the advanced search optionEVDB contact Julio re Big Pink Box re Drupal librariesEVDB to place disclaimer on iOBIS home page currently it is hidden  HYPERLINK "http://www.iobis.org/data/policy/disclaimer" http://www.iobis.org/data/policy/disclaimer Transfer between dev and prod All - correct way is to create content on the production server but keep it unpublished as opposed to having it on the dev server and then transferringnew versions and when to update Jesse write up a document as to when to update versions. need to make an inventory of everything used plus version. compile list of arguments why to upgrade and list why not upgrade.Google site map. what do we wish to find in google search? where does this link to? ACTION item develop a page that return stuff for Google search (Urgent loosing traffic)Synonyms Ei and EVDB to resolvelogging and reporting Ei and EVDB someone to analyse the apache logs. google analytics is still running. need to track access to resources. MK to contact Mark and EVDB to send out message to RON managers to determine what managers wish to have trackedxLatitude/longitude EVDB- check the number of significant digits in real numbers in postgres (number of digits for latitude/longitude)funding Steering Group needs to find money. Ei/Jesse/Ben - provide document what they anticipate/what they need so that the SG can go get funding.Portal performance how to make a responsive portal at VLIZ. Who?? what should be broken out stuff is the mapper too slow as it is now is this the database connections testing web serves. making calls to species timing results slowRoles and responsibilities ALL to review and comment on the diagram in Ei presentation see google docs 201106_OBIS_Poratal_ai Someone - make rules as to how to make tags or branches, and then who takes responsibility for which parts of the codes.translation need to know when new content added; need to know who the translation contacts are; who adds the content MK draft note to send to RON managers/SG requesting a volunteer willing to take on the role and responsibility of the translation coordinator. (Draft note and list tasks and send to Mark and EVDB for comments)xTranslated content not all pages are translated EVDB to organize the following: add stub to each translated page to say see english version for more content EVDB - v2 version need to push QCd records done at the postgres level back to the oracle dbaseFrench translation is on the DEV only add to PROD EI add French version to the search interface EVDB- update the Drupal pageCREDITS how and where to assign credit Example translation pagesOGC services over and above GBIF/REST (users access OBIS data thru GBIF because of REST services such as ) inventory to make a list of species within a taxa - VLIZ has offered to do REST not urgent if we create the URL - put this on the strategic issues listSloany Jesse - how configurable is sloany? can you update only one tabl?QC procedures - node to node duplicates (OBIS USA to OBIS SeaMap and to iOBIS) EVDB - send Brook to Duke for the meeting between SeaMap and OBIS USA (July) Appendix - Meeting Notes welcome from Alain Vezina Regional Director of Science, Maritimes Region, with the Department of Fisheries and Oceans (DFO) and Director of the Bedford Institute of Oceanography (BIO).  HYPERLINK "http://www.marinebiodiversity.ca/CHONe/Members/alain-v/bio/bio" http://www.marinebiodiversity.ca/CHONe/Members/alain-v/bio/bio present at BIO Ei, Jesse, Bendy, Edward, Lenore, Mary, Udaya skype Bart, Tjess, Adi Julio general work plan from Edward for the 3 days presentations - representatives of Rutgers, MGEL and USB will present the existing infrastructure. Presentations will focus on the search interface, systems, content management (Drupal) and the database. Identified issues and further development will be discussed. Examples of these issues are whether and how to make available OGC services, REST services, direct database access from GIS systems including Arc, Postgres 8.4 vs 9.0. A work plan will be created including coordinators name, timeline, deadlines, and deliverables. discussions to focus on long term plans where do we want to be by when? What should our system look like to make sure the marine community sees added value to OBIS, over and above GBIF? What applications, search interfaces, etc do we need to serve our specific community? General Introductions adi iode programmer extensions of IOBIS, php and sql, drupal, jumla(cms), database mysql and postgres types of analysis Bendy systems, LINUX, plone, wordpress, drupal, web proraming, security jesse gis and remote sensing web gis, mapping server, geoserver, postgres map engines Ei development of obis portal and seampap php arcgis Julio drupal systems administration Udaya, incois Presentations are on Google docs  HYPERLINK "https://docs.google.com/" https://docs.google.com/ Ei presentation amazon cloud consumes $$ 2 databases: prod and dev what is the digir provider used for used to feed data into gbif and they use the old version and not the new version. needs a few days more work to ..? database data comes in thru digir into oracle then do a dump and up to postgres (hope to swap those 2 things around) DiGIR ( Oracle ( Postgres(dev) ( Postgres(prod) ( web page data comes into oracle index in oracle and index in postgres indexing in oracle automated but no QC in postgres lots of manual QC control need to back port the qc checks QC - part on postgres and part on oracle oracle check if all mandatory fields filled in postgres taxonomic names checked edits are not pushed back down to the Oracle version and it is this version that feeds the older V2 site 2 databases are out of sync after the QC process next load should have edits in postgres pushed back to oracle postgres taxonomic checks based upon WoRMS oracle version taxonomic checks is based upon cataloque of life Why use oracle? (answer legacy) used to populate the v2 old version which is still being used digir is still attached to oracle uploading and digir harvesting still talking to digir Examples of links to v2 in OBIS Canada dataset abstracts were lin ked to the v2 site but have be updated and now link to the new web site ( metadata pages include a line stating for more info on the schema go to the following OBIS page NEW -  HYPERLINK "http://www.iobis.org/node/304" http://www.iobis.org/node/304 for data access to see the general rules and disclaimer go here OLD -  HYPERLINK "http://v2.iobis.org/data/policy/disclaimer/" http://v2.iobis.org/data/policy/disclaimer/ NEW -  HYPERLINK "http://www.iobis.org/data/policy/disclaimer" http://www.iobis.org/data/policy/disclaimer the GCMD get data links are broken why are people using the old version? contact Jerry Black re ACON Action - check usage of the v2 version google analytics?? Perhaps add a window suggesting users go look at the new version; RON to update metadata links; EVDB to ensure that v2 can be accessed now that the machine has moved; EVDB to place disclaimer on iOBIS home page; look at the old functionality and determine what would be useful and what could be implemented in the new version need to discuss how to mirror each site (drupal and database) how do we keep everything in sync logistics resources immediate need to address the above crawled seamap and it took 2 days. need an alternative to ?? for large datasets GBIFusing Darwin core iOBIS can accept EXEL OTN would like to see a postgres to postgres PO has done it with OBIS USA and POST in an ad hoc way VLIZ how many machines can you serve? how many do you want??? they can have the prod on a dedicated machine web services can be on the same or separate another one for data portal and search interface ? do you and how much would you like to do the data management on a machine at VLIZ. they can provide the machine and we have the connection but it might be harder to import a file in excel, etc evdb worry machine on the cloud and used to flexible access so access to a machine at VLIZ might be more difficult. jesse will introduce later thinking about postversion9. might be easier to have database to dbase replication. see later Bendy needs a mental picture of hardware at VLIZ as opposed to virtual machine. do know what requirements really are to run on a machine as opposed to the cloud. jesse can VLIZ send a list of what they are using evdb lets have a presentation from Bart. ei next slide collaboration and responsibilities come back to this later portal infrastructure jesse geoserver that is running geoserver now is a custom version but the geoserver sent to Vliz is the newest version so there is a slight difference. need to update the iobis version bart openlayers has new version 2.10; dont know new features need to develop a strategy as to when and why we should upgrade to new version what new features do they need. data access slide what is obis store? definition inside geoserver that defines the connection (namespace in geoserver) database schema everytime the database is updated must run scripts to update the denormalized stuff ? Tjess are all these different layers defined in geo server? YES do you use filters to show datasets and species? original geoserver was not able to handle dynamic queries so asked open geo to create means now queries go into a layer open layers can hand CQL and then these get sent to geoserver main question how to access map to search for specific species?? how can VLIZ learn how to do this. Ei provided a link to a document that explains how . see Google docs layers defined in geoserver. back to presentation Structure details server side is it described what the php does? Example species_info.php or dataset_info.php See below  HYPERLINK "http://iobis.org/mapper/species_info.php" http://iobis.org/mapper/species_info.php  HYPERLINK "http://iobis.org/mapper/species_info.php?id=458789" http://iobis.org/mapper/species_info.php?id=458789 or  HYPERLINK "http://iobis.org/mapper/dataset_info.php?id=601" http://iobis.org/mapper/dataset_info.php?id=601 structure details client side all in java script ?? EXTJS do we need to pay for this? no just for support ? Jess - re we using GEOEXTJS? Ei-yes ( for legend display, not flexible to customize) upper right corner rs_front_page_xx.js (international standardize --- language code) example French no questions slide parameterized layers in geoserver go to google docs for more details includes definition query in the docs Tjess arent you afraid that someone will generate a weird query right corner of screen will restrict characters in the parameter should restrict possibility of inserting stuff another topic to explore jesse this is why developers of geoserver were reluctant to introduce this functionality. next development environment Bart has done one commit and it seems to work. Tjess do you expect us to contribute in this way? Ei this is a topic for discussion but need to make rules as to how to make tags or branches, and then who takes responsibility for which parts of the codes. Jesse consistent symbology and layer definitions. Ei there should be a master geoserver and whoever edits and commits to repository then other nodes check out the updates. Tjess is there a way to use this version to regulate the updates? at regular intervals? Jesse is the question about the database or the data? geoserver layer definitions and portals is the SVN a way of doing updates? Bendy this is a topic for discussion. tend to clone things now Bart suggestion - ?????? use the SVN and . Edward scripts under subversion EI scripts to build portal and Edward made modifications. can these be sent out? next development environment 9.2 not free ($300) latest version based upon eclipse Bendy there is a firebug extension but hard to use. next subversion control master copy is called TRUNK once comfortable to make public then gets version number tag always edit under trunk next multi-language support need to discuss how to notify when new content in English investigate to make the search interface a DRUPAL interface at the moment it is 2 parts ids used for PHP scripts. not standardized but are they persistant. species_id will remain the same for all versions. if a dataset is updated then all records are updated then the re-imported the dataset id will remain if it is a problem that the recordID changes they are incremental IDs. we should try to standardize these .later NEXT slide DiGIR OBIS is using the old platform? where is it running v2 . but subdomain name has changed.. Bart it is not there. BIO we could do an alias or an error page. Tjess digir provider is running on an oracle machine at Rutgers. this is our intention and if it is not functional then we need to repair it. bart - it doesnt work. lets use the new one and not fix the old one. Edward will do stuff and contact others using the old digir and advise them to use the new one VLIZ need to contact GBIF to see when they last harvested. OBIS Canada - we need an updated DIGIR at OBIS Canada. Bart and Ei are the 2 experts with DiGIR 95% of GBIF runs on DiGIR. bart use the IPT toolkit. everytime the database is updated Edward runs an R script to update metadata shoud the r script be in the subversion. reads the postgres.and where do the postgres get their metadata from. need discussion on metadata discussion on Friday - need to do a better job on metadata expand capabilities to acknowledge different data centres Tjess important to have a way to update these XML files EVDB have a way to providers to vet the files; use the GCMD. brazil, scarmarbin use gcmd. VLIZ uses IMIS. Tjess discuss this tomorrow. DiGIR Configuration Ei there is no way to get metadata for specific datasets. Bart can get an inventory of taxa need to generate the page and then cache it. this would change once a month if continue monthly cycle. explore more .but if takes half a day then it is ok. next OGC consideration OGC consideration2 Tjess content of xml file on geoserver is this not something that could be controlled? you mean which attributes? you can specify attributeswhen you do WFS query you can specify Technical Issues (1) lets check this afternoon the number of digits for latitude/longitude resources. duplicates add animal ID in OBIS schema maps - questions about the squares 1degree or 5degree. client or geoserver? General discussion telemetry datasets related catalogue ID summary of OTN data just released need to write up an explanation of how to treat tracking data V2 and ACON advanced search KGS and ACON Day 2 - Thursday sign up for . mikogo to share screens at multiple locations start session and get link so not everyone needs to install the complete version join.mikogo.com then skype for voice over introduction from Udaya from INCOIS and will give a presentation later this morning Julio presentation on Drupal OBIS system based on 2 components (EI mapper ( geoserver, postgres etc) other is the drupal cms initial home page is drupal the mapper also uses a bit of content managed by drupal to display unified interface eg the tabs come from cms the administration of the drupal installation has 2 parts: system admin (install new modules, backup, etc) and content (text and content) type in text and graphics must know how to insert a link from one page to another see iobis.org/node/67/edit ?(Bendy) describe how page translations stay together One of the reasons why they chose drupal tell the system that you wish to translate the page iobis.org/node/78/translate ? is there a way to inform the translators that the page has been translated. PO to create a means to check if pages have been updated see iobis.org/admin/content/node can be done manually evdb-more important the big pink box that state security risk perhaps use Eis php module of drupal the database that serves the drupal part is on a separate machine than the database that has the data and the mapper. education and outreach on translated pages add a stub to say go to English for more info. evdb how to sync the dev and the prod sites example French on the dev only is there an easy way to bring blocks of stuff from dev to prod? Jc correct way is to create content on the production server but keep it unpublished as opposed to having it on the dev server. moving from one instance to another is difficult. Drupal keeps stats about access and if we dump then loose all the stats. find out how to transfer the content now so that we dont clobber the production instance. use dev for new modules use prod for adding new content but keep private for now just cut and past and do not dump and load. pump stuff back from production to development on a regular basis for replication or keeping in sync different mirrors (sloaning???) Tjess? problem with the drupal site to be sync between mirror sites. and do we need to do this? should we have only one site and then offer the users the choice of which mirror site they wish to access for the data. JC depends upon the usage. plus potential problem drupal and mapper run on same machine might be latency if on different machine. mapper gets tabs from drupal. Jesse/Ei will think about integrating but dont see any advantage. JC what if mapper and drupal on different machines. perhaps the fetch can be once a day TJ what is fetched? Ei header and footer fetched from drupal front page, the search interface is standalone but to make it look similar the header/footer is fetched. Bendy/Ei search interface doent care about what is in drupal but wishes to look alike JC will splitting Drupal and mapper cause any problems? ei extjs styles, etc. jesse one drupal and many mirrored search interface ei dont see any problemsget header/foot from iOBIS Bendy figure out how to take drupal search and return a simple species page. discussion about the phrase search OBIS web pages  HYPERLINK "http://iobis.org/search/node/krill" http://iobis.org/search/node/krill need to let user know that they are searching the website and not the database ( add line go to search data tab remove the advanced search this is just confusing! backup JC backup configuration files, modules, etc Bendy everything contained; could import into subversion but not necessary Jesse imbedded mappers JC iobis.org/maps/distribution imbed simple maps drupal module fetches code to imbed into drupal presentation home / maps/ (example add maps to RON pages) Bendy create a web form the legend is not part of the module. can see in the EDIT tab AphiaID vs OBIS_ID and ITIS TSN search by IDs include IDs in download discussion about which part on which machine (Tjess, Ei and Bendy) database and web services need to be mirrored. mirror other stuff if problems with servers virtual in having full mirrors just in case problems arise this implies that drupal content around. can we do this as the last step now have implementation running at VLIZ and could run on amazon we could do this with the dev server to see how it works Jesse - perhaps tomorrow have a prioritization list Ei _ want to take all machine off Amazon too expensive Jesse applied for a grant but spent all the money so wish to rely on other resources. Tjess VLIZ has the machines ready Jess want to do a bit of performance tweaking Bendy with obis launch and using cloud kept scaling up but another way will be to use different machines and split up the load. Tjess Bart had a look at performance and perhaps database may not have all indexes. some work at the dbase level and not just a machine Ei yesterday tried performance tests on VLIZ machine and tried graph data but always timed out. need to investigate. JC database is running on machine with 6GB. Jesse Edward yesterday looked at way postgres was configured. and memory setting in Linux itself. Edward feels that dev is better in performance at the moment amazon machine is 16GB. dev and vliz machine are about the same did vm start yesterday look into this this afternoon Udaya presentation INCOIS infrastrucature (add presentation to google docs) TVS Udaya Bhaskar ChloroGin, Ocean Tutor, netcdf format no biological bit at INCOIS where is the Indian OBIS node? division of labour , INCOIS help the global network. How will this work in practice? from presentation saw hardware and manpower do they need new hardware NO. if they cant do it there then they cant do it anywhere evdb want INCOIS to start experimenting the VMware will be provided by Duke they have created the images. as VLIZ tunes their machines we should use what they learn and then try to reproduce this on the INCOIS machine. the VLIZ machines should become the master. but to get INCOIS started they should get images from Duke Is INCOIS ready to start on Monday? . . need a timeline Tjess for timeline INCOIS has 20mg internet connection will that be upgraded soon? will it fall short? not for hosting the portsl. but wondering how long to download databits with this size. Bart took took 3-4hrs to download to portal only. Edward it took several hours to download postgres image. Tjess perhaps the bottlenect was Amazon Evdb had to transfer the dbase 2x but now have improved the method and it took 4hrs. this is a monthly cost. Tjess as a test organize a download of the dbase to INCOIS. how much time does it take. will download be an option or will syncronization be require. if yes then this will impact the timescale. if need a better bandwith then now is the time to ask. (VLIZ bandwith is 1GB) Tjess do you have a VM machine running NO; need time to set this up and time to develop expertise with this machine; this combined with comments to wait and see what issues VLIZ encounters then we are talking about setting up system in VLIZ in June and the INCOIS in September. will VM machine be installed and download of dbase be done by then. Udaya good idea to have VLIZ go first Evdb need to get VM and bandwith the database is on disk is 120gigabytes Ei what is the plan? production machines developed on VLIZ and then transfer INCOIS to test when complete there will be 2 mirror sites. will the dev stay on cloud no --- they should go to vliz or incois. no money. when performance problems at vliz sorted out and way of accessing the server (extra step to connect to the domain), makes terminal windows slow must look into this Tjess using direct network connection e connect vliz.be screen to choose between 2 virtual machines (juniper network). e start a terminal session Tjess use direct connection Bendy to explain to Edward set up a secure connection. file transfer etc. Bendy to walk Edward thru. Tjess can do it on the screen.. will try this afternoon and sort out tomorrow. a direct connection should be the same as working on the cloud. can use existing machines as the dev machines and use new machine (32gig) for OBIS. must share with other applications. if there is a problem can be made bigger but having different geoservers will boost performance better than having larger machines. set up machine to make size 16gig to make it similar to what exists now on the cloud. so set up the new machine to be the same size as the cloud. then copy over the existing cloud config file. should work.. jesse Udaya will it be ok for outsiders to access machine directly (will there be firewall problems/security). is INCOIS comfortable? evdb not sure if we need to use INCOIS as development so shouldnt need direct access. might wish to make use of their computing power for other stuff other than development. end of Udaya presentation set up map interface on webdev to use server at VLIZ (server array on open layers Vliz geoserver) how will this affect performance. do this after other performance issues sorted out. the content might be different. so update database at vliz to the same as webdev and then run test. Edward IMBIS metadata how to populate postgres database for EurOBIS datasets the existing resources table does not have the proper metadata for EurOBIS look at resources table and many are calculated fields the problem is the structure for resources is not flat Oracle v2 looks at GCMD and disregards what is in DiGIR what we have now --- ignore (it is a mess) what is the relation between RESOURCES and DiGIR of VLIZ and DiGIR of OBIS (needed for GBIF) or VLIZ can generate GCMD make sure that they are in OBIS collection. evdb just provide DIF VLIZ to generate dif and made this service on top of IMIS. this will go into a separate schema in postgres ( then to go to RESOURCES ( then use R to go to DiGIR (for GBIF) currently using R scripts to harvest GCMD info. Tjess to have a chat about architecture and different mirrors. VLIZ presentation (see google docs) slide1- providers ( EurOBIS RON ( iOBIS iOBIS gets data from other nodes, etc iOBIS sends it to the cloud website/geoserver/digir/webservices access the cloud next slide iOBIS send to OBIS IODE PO then INCOIS takes copy of IODE version evdb and Bendy make the 2 mirrors identical main change for 2011 get out of cloud and get mirror at INCOIS evdv agrees with the final slide. the red and blue is good need to update a few slides and indicate iOBIS PO more prominently current slides look as if EurOBIS going directly to the IODE version and not passing thru iOBIS. Tier I, II and III types of nodes write the qc and managers documents for different levels need handbook and procedures. need to share with different nodes re organization plus need to work on automation this is now done thru DiGIR but clear it is not sufficient. one solution does not fit all. large datasets and small datasets need separate tools EOL is not harvesting web servers, evdb makes a dump and sends it to them what is the preferred method for large dataset postgres to postgres, IPT cpr to use IPT to transfer data. Jesse presentation foreword looking postpone till after lunch Arcgis 10 & OBIS see google docs takes sloany and its it into postgres how configurable is sloany? can you update only one table Jesse to look into this OBIS VM framework need to script build up make amazon image 6 months later make another image amazon cloud to continue as the master? NO should evdb ask for amazon grant as well as Duke? be using $1200 per month Bendy - should we be using XEN instead of VM ware since we should be using opensource. dont need to look into this now.. need to discuss this with VLIZ and also when INCOIS is online. con not as good in windows as in unix. jesse is VLIZ using a paid version of the VMware. Duke is using the free version. (no tools to create an image) Bendy can do images. harder to transfer between machines must be done manually. paying for management tools not for functionality. need to make an inventory of everything used plus version. compile list of arguments why to upgrade and list why not upgrade. stay bound to buntu services evdb would like to move to postgis 1.5?? (from 1.4) (for calc and analysis the geographies will be useful) does 1.5 work with geoserver webdev.iobis.org:8080/geoserver/web/ geoserver 2.1 Friday web services look into DiGIR but before that we need make sure that metadata is in order metadata does not flow from ver v2 to new system (stored in html files and not in oracle tables) sync postgres with gcmd; sync eurobis with postgers; update obis seamap in GCMD; *** get metada in order and then open up DiGIR part in GCMD, part in IMIS and part with Ei/Seamap. need to pull all together. evdb hopes to write scripts to read DIF files; Bart will try to produce DIFs for Eurobis datasets. evdb can read DiGIR and can store this info into the oracle tables. preference is to get content from GCMD. must be able to give credit from multiple data centres cant do this using DiGIR. keep local copy of metadata in GCMD format Ei dont need to submit all data into GCMD but can generate DIFs and send this. in the past all metadata has been sent thru DiGIR. Tjess will also have to generate metadata in DiGIR for GBIF evdb- need to find a way to shoehorn GCMD data into DiGIR so that we can pass it along on our DiGIR provider (to GBIF). example in GCMD there is a summary and a purpose ( will combine. Lenore we have had a problem with the length of abstract in DiGIR will check to see if there is a maximum number of characters or if this is an internal problem at OBIS Canada GBIF is looking into other method (OAI- open access information). have this functionality on OBIS (java application) give responsibility to maintain and expand and working process ( wish to pass this on to someone else. Tjess we have OAI at VLIZ. can perhaps use this to read the OBIS content. not a great problem to implement.drop java script and use php. ACTION new sever mirror for ad hoc query VLIZ and INCOIS internal access to this machine dont want to tie down the general public queries.. example if a map imbedded on another web site it wouldnt pull down the public site for privilidged users. usage could be tracked and monitored and if a lot of use then a small fee should be requested perhaps this could be used for Amazon cloud. (Bendy has an idea about the cloud and census data add more lines) machine to be outside the firewall with username/password probably 50-100 Bob Branton POKM USGS etc Bulletin board Discussion Forum on Drupal EVDB - set up the bulletin permission open to OBIS community Brook to sign up RON managers, technical group, steering group INNER CIRCLE need someone to monitor this and summarize this evdb Ei ( add correspondence who to manager users bulletin board to solicit input others summarize and assign prioritize. Duke to show EVDB to do a bug tracker in subversion instead of mantis. funding discussion steering group needs to find money. seamap writing grants for tech stuff never successful. need new developments and products. computer science funding OBIS NSF for Phoebe ACTION ITEM - tech guys needs to provide document what they anticipate what they need so that the SG can go get funding. QC procedures - check for duplicates node to node (OBIS USA to OBIS SeaMap and to iOBIS) if dataset has a new digir resource name there is no way for iOBIS to know museum vs surveys Sharing - ACTION ITEM: send Brook to Duke for the meeting between SeaMap and OBIS USA OTN some other method than DiGIR postgres to postgres need to know what should be sent. what has been done for POST and TOPP send only release or 1degree square? summarized data provide URL to get complet track need to discuss metadata. create DIF and not GCMD. perhaps OBIS can build means to send stuff to GCMD. Transfer between dev and prod is there an easy way to bring blocks of stuff from dev to prod? Jc correct way is to create content on the production server but keep it unpublished as opposed to having it on the dev server. moving from one instance to another is difficult. Drupal keeps stats about access and if we dump then loose all the stats. 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