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Revision 4016

Added by Aaron Marcuse-Kubitza over 12 years ago

input via maps: Removed _date/date filter from date fields because the main mappings now have _date around all dates, so this filter is redundant

View differences:

inputs/CVS/test/import.organisms.xml.ref
57 57 
        </locationdetermination>
58 58 
        <locationevent>
59 59 
            <authoreventcode>$authorObsCode</authoreventcode>
60 
            <obsstartdate><_date><date><_dateRangeStart><value><_date><date>$obsStartDate</date></_date></value></_dateRangeStart></date></_date></obsstartdate>
60 
            <obsstartdate><_date><date><_dateRangeStart><value>$obsStartDate</value></_dateRangeStart></date></_date></obsstartdate>
61 61 
            <taxonoccurrence>
62 62 
                <aggregateoccurrence><cover>$%cover</cover></aggregateoccurrence>
63 63 
                <sourceaccessioncode><_alt><3>$currentTaxonName sec Weakley 2006</3></_alt></sourceaccessioncode>
inputs/CVS/maps/VegCSV.organisms.csv
1 1 
CVS,VegCSV[DwC],Comments
2 2 
authorObsCode,fieldNumber,
3 
obsStartDate,plotEventStartDate/_*/date,
3 
obsStartDate,plotEventStartDate,
4 4 
realLatitude,decimalLatitude/_alt/1,
5 5 
realLongitude,decimalLongitude/_alt/1,
6 6 
locationAccuracy-m,coordinateUncertaintyInMeters,
inputs/CVS/maps/VegCSV.organisms.full.csv
7 7 
realLongitude,decimalLongitude/_alt/1,
8 8 
publicLongitude,decimalLongitude/_alt/2,
9 9 
authorObsCode,fieldNumber,
10 
obsStartDate,plotEventStartDate/_*/date,
10 
obsStartDate,plotEventStartDate,
11 11 
currentTaxonName sec Weakley 2006,scientificName,
12 12 
state,stateProvince,
13 13 
confidentialityStatus,,
inputs/CVS/maps/VegBIEN.organisms.csv
8 8 
county,"/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",
9 9 
state,"/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=stateProvince]/placename",
10 10 
authorObsCode,/location/locationevent/authoreventcode,
11 
obsStartDate,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value/_*/date,
11 
obsStartDate,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value,
12 12 
%cover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover,
13 13 
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/3,
14 14 
currentTaxonName sec Weakley 2006,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname",
inputs/SALVIAS-CSV/test/import.plots.xml.ref
162 162 
                    </commconcept_id>
163 163 
                </commdetermination>
164 164 
            </commclass>
165 
            <obsenddate><_date><date><_dateRangeEnd><value><_date><date>$date_finish</date></_date></value></_dateRangeEnd></date></_date></obsenddate>
166 
            <obsstartdate><_date><date><_dateRangeStart><value><_date><date>$date_start</date></_date></value></_dateRangeStart></date></_date></obsstartdate>
165 
            <obsenddate><_date><date><_dateRangeEnd><value>$date_finish</value></_dateRangeEnd></date></_date></obsenddate>
166 
            <obsstartdate><_date><date><_dateRangeStart><value>$date_start</value></_dateRangeStart></date></_date></obsstartdate>
167 167 
            <precipitation>$precip_mm</precipitation>
168 168 
            <soilobs>
169 169 
                <acidity>
inputs/SALVIAS-CSV/maps/VegCSV.plots.csv
39 39 
plot_methodology,samplingProtocol,
40 40 
plot_area_ha,plotArea,"Brad: Area in hectares. Is there any way to store units?; Aaron: VegX plot area annotation says ""Total area of the plot in square meters."" so units are fixed"
41 41 
recensused,,"Brad: This is a 0/1 value, internal to SALVIAS. 1 indicates that a  plot has >1 set of values, from different census events.; Aaron: Different censuses are distinguished in organisms data by different census_no values"
42 
date_start,plotEventStartDate/_*/date,
43 
date_finish,plotEventEndDate/_*/date,
42 
date_start,plotEventStartDate,
43 
date_finish,plotEventEndDate,
inputs/SALVIAS-CSV/maps/VegCSV.plots.full.csv
23 23 
pH,ph,"Brad: For all these soil variables, how do we store information on method, units. Seems like an ontological structure would be more appropriate (measurementName, measurementValue, measurementUnits, measurementMethod). Same as BIEN traits table. Something to discuss."
24 24 
soil_P,"phosphorus/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value",
25 25 
plot_area_ha,plotArea,"Brad: Area in hectares. Is there any way to store units?; Aaron: VegX plot area annotation says ""Total area of the plot in square meters."" so units are fixed"
26 
date_finish,plotEventEndDate/_*/date,
27 
date_start,plotEventStartDate/_*/date,
26 
date_finish,plotEventEndDate,
27 
date_start,plotEventStartDate,
28 28 
plot_code,plotName,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
29 29 
soil_K,"potassium/_units:[default=""%"",to=]/value",
30 30 
precip_mm,precipitation,
inputs/SALVIAS-CSV/maps/VegBIEN.plots.csv
17 17 
project,/location/locationevent/*_id/project/projectname,
18 18 
holdridge_life_zone,/location/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname,
19 19 
life_zone_code,/location/locationevent/commclass/commdetermination/*_id/commconcept/commdescription,
20 
date_finish,/location/locationevent/obsenddate/_*/date/_dateRangeEnd/value/_*/date,
21 
date_start,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value/_*/date,
20 
date_finish,/location/locationevent/obsenddate/_*/date/_dateRangeEnd/value,
21 
date_start,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value,
22 22 
precip_mm,/location/locationevent/precipitation,
23 23 
soil_acidity,"/location/locationevent/soilobs/acidity/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value",
24 24 
soil_base,"/location/locationevent/soilobs/basesaturation/_units:[default=""%"",to=]/value",
inputs/SALVIAS/test/import.plots.xml.ref
162 162 
                    </commconcept_id>
163 163 
                </commdetermination>
164 164 
            </commclass>
165 
            <obsenddate><_date><date><_dateRangeEnd><value><_date><date>$date_finish</date></_date></value></_dateRangeEnd></date></_date></obsenddate>
166 
            <obsstartdate><_date><date><_dateRangeStart><value><_date><date>$date_start</date></_date></value></_dateRangeStart></date></_date></obsstartdate>
165 
            <obsenddate><_date><date><_dateRangeEnd><value>$date_finish</value></_dateRangeEnd></date></_date></obsenddate>
166 
            <obsstartdate><_date><date><_dateRangeStart><value>$date_start</value></_dateRangeStart></date></_date></obsstartdate>
167 167 
            <precipitation>$Precip</precipitation>
168 168 
            <soilobs>
169 169 
                <acidity>
inputs/SALVIAS/test/import.organisms.xml.ref
5 5 
        <locationevent>
6 6 
            <taxonoccurrence>
7 7 
                <aggregateoccurrence>
8 
                    <collectiondate><_date><date><_dateRangeStart><value><_date><date>$census_date</date></_date></value></_dateRangeStart></date></_date></collectiondate>
8 
                    <collectiondate><_date><date><_dateRangeStart><value>$census_date</value></_dateRangeStart></date></_date></collectiondate>
9 9 
                    <count>$NoInd</count>
10 10 
                    <cover>$cover_percent</cover>
11 11 
                    <definedvalue fkey="tablerecord_id">
inputs/SALVIAS/maps/VegCSV.plots.csv
58 58 
MethodCode,,
59 59 
plot_area_ha,plotArea,"Brad: Area in hectares. Is there any way to store units?; Aaron: VegX plot area annotation says ""Total area of the plot in square meters."" so units are fixed"
60 60 
recensused,,"Brad: This is a 0/1 value, internal to SALVIAS. 1 indicates that a  plot has >1 set of values, from different census events.; Aaron: Different censuses are distinguished in organisms data by different census_no values"
61 
date_start,plotEventStartDate/_*/date,
62 
date_finish,plotEventEndDate/_*/date,
61 
date_start,plotEventStartDate,
62 
date_finish,plotEventEndDate,
63 63 
plot_administrator,,
64 64 
plot_notes,,
65 65 
tmp_del,,
inputs/SALVIAS/maps/VegCSV.organisms.csv
3 3 
PlotID,parentLocationID,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
4 4 
PlotCode,parentPlotName,"Brad: Same as plotCode, above"
5 5 
census_no,censusNumber,"Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."
6 
census_date,eventDate/_*/date,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
7 
-----
8 
SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count
9 
FROM ""SALVIAS"".organisms
10 
WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL
11 
GROUP BY ""PlotID"", ""Line""
12 
HAVING count(DISTINCT census_date) > 1
6 
census_date,eventDate,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
7 
-----
8 
SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count
9 
FROM ""SALVIAS"".organisms
10 
WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL
11 
GROUP BY ""PlotID"", ""Line""
12 
HAVING count(DISTINCT census_date) > 1
13 13 
-----"
14 14 
OrigRecordID,,
15 15 
Line,plotName,
inputs/SALVIAS/maps/VegCSV.plots.full.csv
23 23 
pH,ph,"Brad: For all these soil variables, how do we store information on method, units. Seems like an ontological structure would be more appropriate (measurementName, measurementValue, measurementUnits, measurementMethod). Same as BIEN traits table. Something to discuss."
24 24 
soil_P,"phosphorus/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value",
25 25 
plot_area_ha,plotArea,"Brad: Area in hectares. Is there any way to store units?; Aaron: VegX plot area annotation says ""Total area of the plot in square meters."" so units are fixed"
26 
date_finish,plotEventEndDate/_*/date,
27 
date_start,plotEventStartDate/_*/date,
26 
date_finish,plotEventEndDate,
27 
date_start,plotEventStartDate,
28 28 
SiteCode,plotName,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
29 29 
soil_K,"potassium/_units:[default=""%"",to=]/value",
30 30 
Precip,precipitation,
inputs/SALVIAS/maps/VegCSV.organisms.full.csv
12 12 
infra_rank_1,computer.taxonRank,
13 13 
cover_percent,coverPercent,
14 14 
temp_dbh,diameterBreastHeight,
15 
census_date,eventDate/_*/date,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
16 
-----
17 
SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count
18 
FROM ""SALVIAS"".organisms
19 
WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL
20 
GROUP BY ""PlotID"", ""Line""
21 
HAVING count(DISTINCT census_date) > 1
15 
census_date,eventDate,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
16 
-----
17 
SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count
18 
FROM ""SALVIAS"".organisms
19 
WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL
20 
GROUP BY ""PlotID"", ""Line""
21 
HAVING count(DISTINCT census_date) > 1
22 22 
-----"
23 23 
OrigFamily,family,Brad: OMIT
24 24 
Notes,fieldNotes,
inputs/SALVIAS/maps/VegBIEN.plots.csv
17 17 
project_id,/location/locationevent/*_id/project/projectname,
18 18 
life_zone_code,/location/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname,
19 19 
life_zone,/location/locationevent/commclass/commdetermination/*_id/commconcept/commdescription,
20 
date_finish,/location/locationevent/obsenddate/_*/date/_dateRangeEnd/value/_*/date,
21 
date_start,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value/_*/date,
20 
date_finish,/location/locationevent/obsenddate/_*/date/_dateRangeEnd/value,
21 
date_start,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value,
22 22 
Precip,/location/locationevent/precipitation,
23 23 
soil_acidity,"/location/locationevent/soilobs/acidity/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value",
24 24 
soil_base,"/location/locationevent/soilobs/basesaturation/_units:[default=""%"",to=]/value",
inputs/SALVIAS/maps/VegBIEN.organisms.csv
1 1 
SALVIAS,VegBIEN:,Comments
2 2 
Line,/location/authorlocationcode/_alt/1,
3 
census_date,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_*/date/_dateRangeStart/value/_*/date,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
4 
-----
5 
SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count
6 
FROM ""SALVIAS"".organisms
7 
WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL
8 
GROUP BY ""PlotID"", ""Line""
9 
HAVING count(DISTINCT census_date) > 1
3 
census_date,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_*/date/_dateRangeStart/value,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
4 
-----
5 
SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count
6 
FROM ""SALVIAS"".organisms
7 
WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL
8 
GROUP BY ""PlotID"", ""Line""
9 
HAVING count(DISTINCT census_date) > 1
10 10 
-----"
11 11 
NoInd,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
12 12 
cover_percent,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover,

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