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Remote sensing of global biodiversity
Task #970: Write perspectives paper
Working Groups
BIEN 3
Task #887: fix disk space leak that fills the disk and crashes the import
Task #902: fix bug that causes joining on the wrong columns in the import
Task #905: narrow down the cause of the import bug (incorrect join columns and disk space leak)
Bug #955: fix geovalidation duplicated rows
Task #285: CSV to XML mappings for NYBG, SALVIAS
Task #286: CSV-XML-database mapping script
Task #287: XML to database conversion script (merged into CSV-XML-database mapping script)
Task #288: VegX-VegBank mapping
Task #289: look for formal mapping mechanism
Task #290: benchmark tests for database loading
Task #291: list of milestones
Task #292: VegBank metadata query mechanism
Task #293: mapping inversion script
Task #294: find plot data source provider to work with Aaron
Task #295: provide benchmark queries for NYBG data
Task #296: Direct mapping from native salvias_plots MySQL database to VegBIEN
Task #297: Request new data dump of specimen data from GBIF, this time in DwC format
Task #298: Try to find source of DwCA (DwC Archives) data
Task #299: Mapping from NVS to VegX and VegBIEN
Task #300: TurboVeg data
Task #301: RAINFOR data
Task #302: Make changes to VegBIEN schema
Task #303: Mapping from VegBIEN to original VegBank
Task #304: Complete full dataset imports to VegBIEN via VegX of NYBG and SALVIAS
Task #305: Complete full-dataset validations for NYBG & SALVIAS
Task #306: Acquire additional plot data sets from providers willing to work with Aaron on mappings and validations
Task #307: Acquire additional specimen data sets in both DwC and DwCA format, esp. GBIF
Task #308: do a direct transfer of some public data from VegBank
Task #309: mapping and export utility from VegBank to VegX
Task #310: automated build process
Task #311: Decouple VegBIEN from VegBank and map directly from VegX to VegBIEN
Task #312: Finish importing SALVIAS data
Task #313: Import full NYBG data
Task #314: Import CTFS data
Task #315: Import TurboVeg data
Task #317: Direct mapping from VegX to VegBIEN
Task #318: decide whether to switch to VegX 1.5.2
Task #319: Update statistics/lists of user-defined fields in use in VegX and VegBIEN
Task #320: Convert user-defined VegX fields to first-class fields
Task #321: Convert user-defined VegBIEN fields to first-class fields
Task #322: get access to raw CTFS data
Task #323: map NYBG data
Task #324: NYBG validations
Task #325: map CTFS data
Task #326: generic MOU template to request data
Task #327: look into Clio
Task #328: get raw data rather than flat file exports from RAINFOR
Task #329: make website user-protected
Task #330: DwC extension to VegX
Task #331: use VegX's individualOrganismObservation/relatedItem to model stems
Task #332: switch to VegX 1.5.3
Task #333: add traits table to VegBIEN
Task #334: which DarwinCore attributes do we want to include in the specimen table?
Task #335: Look into using Sybase Powerbuilder or IBM Enterprise Vision to map data
Task #336: create VegBIEN ERD
Task #337: VegBIEN table renames
Task #338: put together samples of SALVIAS data that aggregates individuals and stems in different ways
Task #339: have "schema showdown"
Task #340: put together definitions of abstract BIEN terms
Task #341: create verbal descriptions of edge cases
Task #342: make DwC_BIEN schema
Task #343: integrate TNRS into VegBIEN
Task #344: contact John about GNRS/georeferencing
Task #345: integrate GNRS into VegBIEN
Task #346: add georeferencing support to schema
Task #347: revise milestones
Task #348: 1st draft of schema
Task #349: make ERD of full schema
Task #350: implement methods in VegBIEN
Task #351: list of fields and method attributes needed to know whether can combine data from different plots
Task #352: create way to represent methods hierarchically in schema
Task #353: add terms from previous versions of DwC to DwC-BIEN
Task #354: list of deliverables for next week (2/6-2/10)
Task #355: implement morphospecies using a scoped plantconcept
Task #356: support subplot events that link to parent plot events
Task #357: make shortlist of 1st-level fields a method should have
Task #358: make shortlist of 1st-level fields a method should have
Task #365: retrieve taxonomic hierarchy in analytical layer by using dynamic queries to external sources
Task #366: refactor VegX
Task #367: get Univ of Arizona DwC data
Task #368: get TEAM VegX data
Task #369: get CTFS data dictionary
Task #370: create ERD of final schema
Task #371: formalize proposed changes to VegX
Task #372: talk to Nick about proposed changes to VegX
Task #373: map all specimens data in raw_data
Task #374: mechanism to export VegBIEN data to flat file
Task #377: ask NYBG for direct access to server
Task #378: create automated feedback mechanism
Task #383: convert VegBank data dictionary to database comments
Task #384: prototype tree traversal algorithm
Task #385: implement mechanism to determine which specimenreplicates refer to the same specimen
Task #386: load Canadensys data
Task #387: count how many duplicates between Canadensys and GBIF
Task #424: Finish translating XML functions to SQL functions for column-based import
Task #425: Reimplement row-based logging mechanism for column-based import
Task #426: Reload DB using column-based import
Task #427: Load all plots data
Task #440: aggregating validations of imports
Task #441: import CTFS data using JOINs from DB export, not VegX
Task #442: test restoring of import backups
Task #443: back up staging tables
Task #444: test backing up entire DB
Task #446: fix deadlock in INSERT IGNORE replacement
Task #448: timeout ANALYZE queries
Task #449: optimize JOINs on existing rows
Task #450: cast all untyped literals as text using cast_literal()
Task #451: verify database contents as part of automated testing
Task #452: add column-based import to automated testing
Task #453: cluster vegbien tables periodically
Task #454: update summarizing queries for current schema
Task #455: change summarizing queries to use vegbien staging tables
Task #456: test that querying the DB uses the unique indexes instead of a seq scan
Task #457: use driver-native autocommit mode instead of our custom autocommit implementation
Task #458: map all VegX sources to stems table
Task #459: data provider feedback: propagate srcs (input columns for an intermediate column) for all tables, not just SQL functions?
Task #461: don't display warning when nullable boolean columns are handled without using COALESCE()
Task #462: name backups according to svn revision instead of or in addition to the date
Task #463: allow an input to appear multiple times in the same map spreadsheet
Task #464: reverse XPaths so that they start with location instead of plantobservation or specimenreplicate
Task #465: move issue tracker comments to wiki pages to ensure version history
Task #466: column-based import: avoid most exceptions by introspecting the DB structure instead of waiting for a parseable exception to be raised
Task #467: underline all to do items in meetings notes
Task #468: rename/delete and recreate public schema in one transaction
Task #469: give everyone their own account on vegbien
Task #470: source terms from old versions of DwC to the DwC history page
Task #471: add make actions so new dependent maps are rebuilt automatically when their source map changes
Task #472: replace accessioncodes with datasource_id+sourceaccessioncode
Task #473: use _merge instead of _alt to avoid losing source data on import
Task #474: use svn to figure out when a map file has changed and needs to be cleaned up
Task #476: develop map spreadsheet -> header override file translation utility
Task #477: allow putting specimens data directly in the top level of the datasource directory
Task #480: automate adding a new table to an existing datasource
Task #482: translate README.TXT to wiki page
Task #483: rename staging table columns according to map.csv
Task #484: support installing staging tables directly from a MySQL export
Task #485: track data provider's citation requirements in VegBIEN
Task #486: add unit-conversion mechanism
Task #490: change import.stats.xls to use field rather than row count
Task #494: add indexes for the analytical_db_view joins
Task #495: add separate datasource table rather than using party for this
Task #497: create examples of taxonomic names to test the limits of the new taxonomic schema
Task #498: add definitions to columns in "green tables"
Task #499: map example terms into the taxonomic schema
Task #500: when lower rank has name concatenated together, use lowest rank as the scientific name
Task #501: find out which datasources won't allow their data to be publicly accessible
Task #521: make place* tables use a structure similar to taxonconcept
Task #522: fix deadlock when multiple testers are running simultaneously
Task #539: get analytical_stem_view to use merge joins instead of hash joins
Task #544: integrate creation of analytical DB into automated testing
Task #548: remove benign errors from the data provider feedback tables
Task #549: add covering indexes on fkeys
Task #560: move VegCore data dictionary to a phpPgAdmin-accessible database
Task #561: make VegBIEN ID fields plain-text instead of numeric
Task #562: flatten the mappings
Task #563: refactor VegBIEN to use VegCore terms
Task #564: make all VegBIEN column names globally unique
Task #565: partition the TaxonDetermination table by row into the different types of determinations
Task #566: automatically adjust staging tables for easier mapping
Task #573: automap the analytical DB columns
Task #574: mechanism to manually override the CSV dialect, encoding, etc.
Task #575: put all wiki attachments in svn
Task #576: merge the datasources' mappings into the VegCore data dictionary
Task #577: use views instead of map spreadsheets to store the datasource mappings
Task #578: replace all fields of type text with a domain type that ensures the value is non-empty (not '')
Task #579: in sql_gen.EnsureNotNull, use ARRAY[] instead of COALESCE() to wrap values where NULL should be compared literally
Task #580: automap each word *in* a VegCore term instead of just the whole term
Task #581: mechanism to dynamically autopopulate NOT NULL values
Task #584: enable running all the import steps from one runscript
Task #636: support TNRS-matching names in "", insted of encoding them and letting TNRS return no match
Task #767: autodetect column mismatches
Task #814: rename columns by name, not position
Task #815: auto-prepend table name to columns
Task #816: re-run TNRS on mis-scrubbed names
Task #831: make tests use their own public schema
Task #856: data provider feedback tables: include the individual records that have errors
Task #857: standardize taxon ranks to a common vocabulary
Task #859: fix slowness in _taxonlabel_set_parent_id()
Task #898: remove dependencies on the development machine
Task #869: enable schema changes to be made on vegbiendev rather than the development machine
Task #886: move test DB to vegbiendev VM
Task #870: grant bien_read access to publishable staging tables
Task #871: grant bien_read access to validation result tables
Task #878: fix crow's foot notation in ERD
Task #882: add limit on the # of parallel import processes
Task #883: have import scripts regularly check disk space and pause processes if getting close to limit
Task #884: fix Postgres bug that causes query planner to use seq scans and slow sorts instead of index scans in the import
Task #899: remove dependencies on Mac
Task #901: schedule regular pg_dump backups of the DB
Task #903: fix Ubuntu 14.04 upgrade bug that prevents Apache from displaying vegbiendev.nceas.ucsb.edu properly
Task #904: add MySQL public user to allow accessing the normalized VegCore data dictionary
Task #907: troubleshoot rsync verification errors
Task #908: generate the source-general derived columns directly on the denormalized staging table
Task #909: in aggregating validations pipeline, support using input result sets from CSVs instead of only by querying the staging tables
Task #928: switch to new TNRS setup
Task #916: Taxon name validation: VegBank
Task #917: TNRS: Instructions for new version with TPL
Task #927: move morphospecies name formation to normalized DB
Task #915: Taxon Name Validation
Task #938: Enquist's taxon validation
Task #929: change TNRS client to store metadata
Task #931: BIEN db at iPlant
Task #932: Discovering BIEN data through iPlant
Task #934: Data Dictionary
Task #935: TNRS crashes when scrubbing names with two infraspecific epithets
Task #936: in TNRS client, detect Internal Server Errors when they occur instead of after the pauses have timed out
Task #937: fix missing date fields
Task #940: resequence datasources in dependency order
Bug #943: in TNRS, the Constrain by Source option is applied incorrectly to the results download
Bug #944: fix phpPgAdmin bug that crashes the DB when browsing large tables
Bug #945: incorrect synonym being selected in TNRS
Task #946: update the column names in the VegBIEN example queries to reflect Brian M's renamings
Task #947: have all scripts that replace DB items rename the existing item out of the way rather than dropping it
Bug #948: fix duplicated rows in view_full_occurrence_individual
Bug #949: fix shortened view_full_occurrence_individual column names that are now ambiguous
Bug #950: fix view_full_occurrence_individual_view rows with is_geovalid NULL
Task #951: test that `make install` is able to fully re-create vegbiendev
Task #952: refresh GBIF so it can be published
Bug #953: CVS and VegBank data
Task #957: add mechanism to customize NULL-equivalent strings used by staging table import
Task #961: test that staging tables can be reloaded from scratch
Task #962: walk through loading of datasources from scratch
Bug #963: fix slow loading of pages hosted on vegbiendev
Bug #965: some VegBank plots are missing the plot name
Bug #966: figure out why some rows are not getting geoscrubbed
Environment and organisms
Task #359: Test GAM method to produce Tmax for one day (OREGON): r script
Task #92: Create subversion repository
Task #118: Provide shared server access to 50-100GB of data
Task #207: Produce global fused DEM layer
Task #209: Produce global slope layer
Task #210: Produce global aspect layer
Task #211: Produce global flow accumulation layer
Task #213: Confirm with Project Scientists: CGIAR Level 4 SRTM project supports planned Terrain Analysis
Task #208: Evaluate existing E&O AML scripts
Task #215: Establish file organization and possible 'tiling' scheme for Fused Global Terrain data set
Task #212: Validate fused DEM at SRTM/ASTER boundary
Task #219: Good News: JPL provides comprehensive Global List of ALL ASTER DEM files
Task #225: Organize and document SRTM input DEM files
Task #262: Organize and document ASTER input DEM files
Task #360: Producing, formatting and extracting variables for the GAM regression (OREGON)
Task #361: Test and compare the GAM method on several days (10 days for now) for Oregon
Task #362: Decide on a map projection for the Oregon case study
Task #364: Integrate spatial variables and structure in the GAM methodology
Task #375: Assemble monthly mean MODIS LST values for the complete record (2000-2012) for Oregon
Task #376: Assemble monthly mean TRMM precipitation values for the complete record for Oregon
Task #411: Insert DEM adaptive smoothing procedure into terrain workflow
Task #393: Identify Focal Regions
Task #406: OR-GAM predictions-model assessment over 365 dates, year 2010
Task #408: Capturing LST spatial structure using spatial eigenvectors
Task #409: Effect of sampling on GAM: hold out proportions and sampling observations
Task #363: Assemble all GHCN data into a single database
Task #416: Scope out workflow for calculating monthly LST climatologies
Task #415: Process MOD06_L2 Cloud data
Task #418: Explore Landcover - LST interactions
Task #419: Assessment of results in the context of the literature: Literature review and accuracy
Task #423: Develop stratified station sampling procedure
Task #430: Estimate total storage size of daily 1970-2010 1km dataset
Task #438: Add buffer to station subsetting algorithm
Task #479: Climatic Stationarity
Task #491: Methods comparison
Task #552: Facilitate raster buffering across antimeridian
Task #568: Interpolation of temperatures in the Venezuela region
Task #583: MODIS Cloud Mask - landcover interaction
Task #612: DEM Evaluation
Task #744: Create Global Grid for Interpolation
Task #745: Run interpolation over tiles for North America
Task #746: Generate Global Monthly Median (Climatologies) MODIS LST
Task #747: Run interpolation over all five case study regions

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Assignee

Rick Reeves
Rick Reeves
Rick Reeves
Rick Reeves
Rick Reeves

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10/31/2014 03:24 PM
11/08/2013 10:10 PM
01/09/2014 09:44 AM
07/28/2014 04:50 PM
01/16/2014 10:42 AM
01/16/2014 10:40 AM
01/20/2014 09:14 PM
11/17/2014 08:47 AM
11/17/2014 08:47 AM
11/17/2014 08:27 AM
02/23/2014 08:02 PM
02/23/2014 08:03 PM
04/16/2014 10:16 PM
04/02/2014 10:10 AM
10/03/2014 03:21 PM
04/23/2014 04:00 PM
04/16/2014 10:14 PM
04/23/2014 03:16 PM
04/28/2017 04:41 AM
04/28/2017 04:40 AM
09/10/2014 05:45 PM
04/28/2017 04:39 AM
05/03/2014 05:30 PM
08/25/2014 05:19 PM
06/19/2014 11:00 AM
04/28/2017 04:38 AM
05/27/2014 09:24 PM
04/28/2017 04:21 AM
06/25/2014 01:19 PM
06/26/2014 05:24 PM
05/22/2014 04:32 PM
05/22/2014 04:43 PM
10/03/2014 03:19 PM
06/17/2014 05:25 PM
06/05/2014 04:42 AM
10/03/2014 03:18 PM
07/14/2014 01:25 PM
10/24/2014 03:18 PM
04/28/2017 04:35 AM
10/17/2014 03:40 PM
04/28/2017 04:34 AM
10/03/2014 03:17 PM
09/04/2014 10:04 AM
10/03/2014 03:22 PM
10/17/2014 11:27 AM
10/16/2014 09:28 AM
09/16/2014 05:12 PM
04/28/2017 04:30 AM
10/14/2014 10:16 AM
10/26/2014 05:16 PM
10/16/2014 09:38 AM
10/16/2014 12:47 PM
10/19/2014 06:35 PM
10/25/2014 03:29 PM
02/29/2012 06:27 PM
03/17/2011 09:19 AM
03/17/2011 09:19 AM
10/10/2012 05:15 PM
04/29/2011 11:04 AM
04/29/2011 11:05 AM
04/14/2011 02:29 PM
04/18/2011 01:12 PM
05/15/2012 09:57 AM
01/12/2012 10:45 AM
01/12/2012 11:59 AM
10/17/2011 11:12 AM
01/25/2012 04:42 PM
09/21/2011 12:50 PM
07/03/2012 09:40 AM
05/01/2012 02:24 PM
07/17/2012 10:37 AM
06/05/2012 12:27 AM
05/17/2012 03:44 PM
03/07/2012 08:38 AM
05/15/2012 11:22 AM
05/02/2012 02:16 PM
05/08/2012 04:31 PM
05/09/2012 03:40 PM
05/01/2012 02:16 PM
07/03/2012 09:45 AM
05/17/2012 11:38 PM
06/01/2012 12:43 PM
06/22/2012 09:47 AM
08/24/2012 01:40 PM
06/01/2012 12:54 PM
06/14/2012 12:34 PM
07/06/2012 06:36 AM
08/24/2012 01:32 PM
12/12/2012 04:36 PM
01/18/2013 05:41 PM
03/08/2013 10:24 AM
03/08/2013 10:21 AM
05/09/2013 08:10 AM
08/22/2013 11:58 AM
08/22/2013 12:01 PM
08/22/2013 12:19 PM
08/22/2013 12:23 PM

Due date

01/15/2015
02/29/2012
05/16/2014
05/16/2014
06/06/2014
10/11/2010
05/31/2011
05/31/2011
05/31/2011
05/31/2011
04/18/2011
05/04/2011
05/15/2011
06/15/2011
05/06/2011
06/04/2011

% Done
 
2024-5
2024-6
2024-7
2024-8
2024-9
2024-10
 
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
Remote sensing of global biodiversity
New 0%
BIEN 3
Resolved 100%
New 60%
New 60%
New 70%
Environment and organisms
Closed 100%
In Progress 100%
New 0%
New 0%
New 0%
Resolved 100%
In Progress 30%
Rejected 100%
Closed 70%
Rejected 100%
In Progress 80%
 

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