05/22/2014

04:43 PM Task #932 (New): Discovering BIEN data through iPlant

iPlant will assign DOIs to datasets made public through its infrastructure. For the BIEN db data, the plan is:
* t... Martha Narro

04:32 PM Task #931 (New): BIEN db at iPlant

Parent issue for tasks related to moving BIEN3 relational database and associated analytical views to iPlant. Martha Narro

05/20/2014

04:26 PM Task #929 (New): change TNRS client to store metadata

* see details in [[2013-06-13 conference call#include-TNRS-version-and-settings-in-TNRS-cache]]
* after implementi... Aaron Marcuse-Kubitza

04:17 PM Task #928 (New): switch to new TNRS setup

# #927 (part of #915)
# #917
# #916 (using rescrubbed names)
# #915
# -#929 (metadata)- _postponed_ Aaron Marcuse-Kubitza

03:26 PM Task #927 (Resolved): move morphospecies name formation to normalized DB

* currently, it's only in the analytical_stem view Aaron Marcuse-Kubitza

05/15/2014

09:43 AM Task #917: TNRS: Instructions for new version with TPL

Aaron, for now (next couple of months, this must be done on the development TNRS web app since TPL is only on the dev... Martha Narro

05/13/2014

02:32 PM Task #917 (New): TNRS: Instructions for new version with TPL

From Brad:
I’ve given some thought to the TPL matter. The algorithm isn’t hard, but Aaron will have to do the sort... Martha Narro

05/12/2014

05:03 PM Task #916: Taxon name validation: VegBank

regarding:
Line 617: TNRS gives a synonym for Aronia prunifolia in a different genus, but this is missed here
L... Martha Narro

04:35 PM Task #916 (New): Taxon name validation: VegBank

Hi Aaron,
Bob only had time to get part way through the VegBank taxon validation file you sent, but there are some... Martha Narro

03:13 PM Task #915 (New): Taxon Name Validation

1. Please correct the following in taxonMorphospecies:
1.1. -Family should be included in taxonMorphospecies only ... Martha Narro

05/03/2014

05:30 PM Task #909 (New): in aggregating validations pipeline, support using input result sets from CSVs instead of only by querying the staging tables

* allows using input query results run on the raw data rather than the preprocessed staging tables
* enables providi... Aaron Marcuse-Kubitza

04/30/2014

02:33 PM Task #908 (New): generate the source-general derived columns directly on the denormalized staging table

* avoids needing to run the full Python import, which is the part that is currently buggy
* see [[New-style_import#s... Aaron Marcuse-Kubitza

04/29/2014

05:46 PM Task #907 (Resolved): troubleshoot rsync verification errors

* normally only happens when a file is concurrently modified, but this file was not in use
* this may indicate disk ... Aaron Marcuse-Kubitza

04/25/2014

05:58 AM Task #905 (Resolved): narrow down the cause of the import bug (incorrect join columns and disk space leak)

_see #887, #902_
h3. -alternate OS approach-
p(. _tried, and problem also occurs on Mac, so using other approac... Aaron Marcuse-Kubitza

04/23/2014

07:22 PM Task #887: fix disk space leak that fills the disk and crashes the import

VM upgraded to Ubuntu 14.04 and using the official Ubuntu version of Postgres, but problem still occurs Aaron Marcuse-Kubitza

06:06 PM Task #903 (Resolved): fix Ubuntu 14.04 upgrade bug that prevents Apache from displaying vegbiendev.nceas.ucsb.edu properly

Aaron Marcuse-Kubitza

06:00 PM Task #903: fix Ubuntu 14.04 upgrade bug that prevents Apache from displaying vegbiendev.nceas.ucsb.edu properly

added workaround for broken MultiViews Aaron Marcuse-Kubitza

04:14 PM Task #903 (Resolved): fix Ubuntu 14.04 upgrade bug that prevents Apache from displaying vegbiendev.nceas.ucsb.edu properly

this consists of 2 problems:
# -http://vegbiendev.nceas.ucsb.edu/index.php now includes the VegCore wiki page inst... Aaron Marcuse-Kubitza

04:42 PM Task #904 (Resolved): add MySQL public user to allow accessing the normalized VegCore data dictionary

__* see "normalized VegCore data dictionary":http://vegbiendev.nceas.ucsb.edu/vegbiendev/db/my/VegCore Aaron Marcuse-Kubitza

04:00 PM Task #884 (Rejected): fix Postgres bug that causes query planner to use seq scans and slow sorts instead of index scans in the import

duplicate of #902: slow sorts are caused by joining on the wrong columns, not query planner settings Aaron Marcuse-Kubitza

03:52 PM Task #902 (Resolved): fix bug that causes joining on the wrong columns in the import

_bug fixed in r14074_
h3. issue
* in some queries, the columns being joined on are completely the wrong set (co... Aaron Marcuse-Kubitza

03:16 PM Task #901: schedule regular pg_dump backups of the DB

see @backups/pg_snapshot@, @backups/mysql_snapshot@ Aaron Marcuse-Kubitza