upload new sampling data: chilcas.ar 2017 (Year 4)

[nutnetadmin]

Received from Enrique Chaneton 2-April-2018 All data saved in individual .csv files in working directory, ready to upload.

Originally was sent w/o biomass data (I think?). These new data are complete.

2018 data are forthcoming.

[nutnetadmin]

stuck on line 182 of import-chilcas-2017.sql, importing NOTHOSCORDUM INODORUM into site_taxon table is messing up, not sure why.

29-aug-2018 Oh this is because they've two synonyms of this taxon, and the taxon currently in site_taxon table is the accepted name, not this current synonym.

Updating to accepted species name in cover_temp file fixes this: update cover_temp set taxa = 'ALLIUM NEAPOLITANUM' where taxa = 'NOTHOSCORDUM INODORUM';

[nutnetadmin]

Two misspelling update cover_temp set taxa = 'DICHONDRA MICROCALYX' where taxa = 'Dichondra mycrocalix'; update cover_temp set taxa = 'TRIFURCIA LAHUE' where taxa = 'Trifurcia lauhe';

[nutnetadmin]

beware for future years taxa separator in cover file is a space taxa separator in taxa file is an underscore

[nutnetadmin]

misspellings in taxa info file: Trifurcia_lauhe Bromus_brachyanthera

update taxa_info temp set taxa = 'BROMUS_BRACHYANTHERUS' where taxa = 'Bromus_brachyanthera'; update taxa_info_temp set species = 'BRACHYANTHERUS' where species = 'brachyanthera'; update taxa_info_temp set taxa = 'Trifurcia_lahue' where taxa = 'Trifurcia_lauhe'; update taxa_info_temp set species = 'lahue' where species = 'lauhe';

[nutnetadmin]

Missing taxa (provenance, lifeform) information: VICIA GRAMINEA We do have Vicia Sp.; is this the same?

[nutnetadmin]

noticed that cover information from non-core subplots has not been uploaded 2014/15/16/17 should update site plan information (upload subplot IDs) and cover for these years in a separate script line 542 query that revealed missing subplotIDs for non-core subplots in database: select distinct a.block, a.plot, a.subplot, plot.plot_ID, subplot.subplot_ID from cover_temp a left join plot on (plot.site_ID = @siteid and plot.block = a.block and plot.plot = a.plot) left join subplot on (subplot.plot_id = plot.plot_ID and a.subplot = subplot.subplot);

[nutnetadmin]

this growing season straddles the new year, so year numbering is a bit strange plus they measured 2x per year in some years, not in others

select distinct year, date from cover left join subplot using (subplot_id) left join plot using (plot_id) left join site using (site_id) left join site_taxon using (site_taxon_id) where site_code =@site limit 3000;

two samplings per year? 2013,'2012-12-01' # December 2012 -> 2013 (Spring??) 2013,'2013-02-28' # March 2013 = 2013 ("fall"?)

2014,'2013-12-06' # December 2013 -> 2014 (Spring)

2015,'2014-12-03' # December 2014 -> 2015 (Spring) 2015,'2015-03-13' # March 2015 = 2015 ("fall"?)

2016,'2015-12-11' # December 2015 -> 2016 (Spring) 2016,'2016-03-04' # March 2016 = 2016 ("fall"?)

2017,'2017-03-03' # March 2017 = 2017 ("fall"?)

two observations per year in 2013, 2015, 2016 only fall in 2017 only spring in 2014

[nutnetadmin]

OK this is a bigger bug - these duplicate observations looks like in 2015 and 2016 we uploaded non-core subplots but did not designate them as such

[nutnetadmin]

see issue #121

[nutnetadmin]

did not upload biomass from non-core subplots

[nutnetadmin]

did not upload par from non-core subplots and from December 2016; only March 2017 PAR was uploaded

[nutnetadmin]

well at least this is all uploaded. will tackle #121 next while chilcas is still fresh.

[nutnetadmin]

ugh. should have uploaded data from November 2016 into the 2017 data. will do in fix-chilcas-non-core-subplot-data-2014-2015-2016.sql

[nutnetadmin]

fixed with fix-chilcas-non-core-subplot-data-2015-2016-2017.sql