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Revision 1817

Added by Aaron Marcuse-Kubitza over 12 years ago

input.Makefile: Maps building: full via maps (maps/$(via).%.full.csv): $(makeFullCsv): Sort all maps so that rows are re-ordered whether or not a core self map exists. This way, if a core self map is created, it will not cause the sort order of the generated via-format XMLs to change. This makes it easier to accept any changes to test outputs that result from adding a core self map.

View differences:

inputs/SALVIAS-CSV/test/VegX.plots.xml.ref
3 3 
    <plotObservations>
4 4 
        <plotObservation id="0">
5 5 
            <projectID>0</projectID>
6 
            <plotUniqueIdentifierID>0</plotUniqueIdentifierID>
7 
            <obsStartDate>1990-11-16</obsStartDate>
8 
            <simpleUserdefined>
9 
                <name>method</name>
10 
                <methodID><method><name>1 ha, stems &gt;= 10 cm dbh</name></method></methodID>
11 
            </simpleUserdefined>
6 12 
            <partyWithRole><partyID>0</partyID></partyWithRole>
7 13 
            <simpleUserdefined>
8 14 
                <name>sourceAccessionCode</name>
9 15 
                <value>26102</value>
10 16 
            </simpleUserdefined>
11 
            <plotUniqueIdentifierID>0</plotUniqueIdentifierID>
17 
        </plotObservation>
18 
        <plotObservation id="1">
19 
            <projectID>1</projectID>
20 
            <plotUniqueIdentifierID>1</plotUniqueIdentifierID>
21 
            <obsStartDate>1990-11-16</obsStartDate>
12 22 
            <simpleUserdefined>
13 23 
                <name>method</name>
14 24 
                <methodID><method><name>1 ha, stems &gt;= 10 cm dbh</name></method></methodID>
15 25 
            </simpleUserdefined>
16 
            <obsStartDate>1990-11-16</obsStartDate>
17 
        </plotObservation>
18 
        <plotObservation id="1">
19 
            <projectID>1</projectID>
20 26 
            <partyWithRole><partyID>1</partyID></partyWithRole>
21 27 
            <simpleUserdefined>
22 28 
                <name>sourceAccessionCode</name>
23 29 
                <value>26103</value>
24 30 
            </simpleUserdefined>
25 
            <plotUniqueIdentifierID>1</plotUniqueIdentifierID>
26 
            <simpleUserdefined>
27 
                <name>method</name>
28 
                <methodID><method><name>1 ha, stems &gt;= 10 cm dbh</name></method></methodID>
29 
            </simpleUserdefined>
30 
            <obsStartDate>1990-11-16</obsStartDate>
31 31 
        </plotObservation>
32 32 
    </plotObservations>
33 33 
    <projects>
......
46 46 
            <title>RAINFOR - 1 ha Peru</title>
47 47 
        </project>
48 48 
    </projects>
49 
    <parties>
50 
        <party id="0"><organizationName>SALVIAS-CSV</organizationName></party>
51 
        <party id="1"><organizationName>SALVIAS-CSV</organizationName></party>
52 
    </parties>
53 49 
    <plots>
54 50 
        <plot id="0">
55 
            <plotUniqueIdentifier>ALP-11</plotUniqueIdentifier>
51 
            <area>0.44</area>
52 
            <geospatial>
53 
                <DecimalLatitude>-3.95</DecimalLatitude>
54 
                <DecimalLongitude>-73.4333</DecimalLongitude>
55 
                <verbatimElevation>200</verbatimElevation>
56 
            </geospatial>
57 
            <locationNarrative>pre-Holocene; clay</locationNarrative>
56 58 
            <location>
57 59 
                <placeType>continent</placeType>
58 60 
                <placeName>South America</placeName>
......
65 67 
                <placeType>state</placeType>
66 68 
                <placeName>Loreto</placeName>
67 69 
            </location>
68 
            <locationNarrative>pre-Holocene; clay</locationNarrative>
70 
            <plotUniqueIdentifier>ALP-11</plotUniqueIdentifier>
71 
        </plot>
72 
        <plot id="1">
73 
            <area>0.4</area>
69 74 
            <geospatial>
70 75 
                <DecimalLatitude>-3.95</DecimalLatitude>
71 76 
                <DecimalLongitude>-73.4333</DecimalLongitude>
72 77 
                <verbatimElevation>200</verbatimElevation>
73 78 
            </geospatial>
74 
            <area>0.44</area>
75 
        </plot>
76 
        <plot id="1">
77 
            <plotUniqueIdentifier>ALP-12</plotUniqueIdentifier>
79 
            <locationNarrative>pre-Holocene; white and brown sand</locationNarrative>
78 80 
            <location>
79 81 
                <placeType>continent</placeType>
80 82 
                <placeName>South America</placeName>
......
87 89 
                <placeType>state</placeType>
88 90 
                <placeName>Loreto</placeName>
89 91 
            </location>
90 
            <locationNarrative>pre-Holocene; white and brown sand</locationNarrative>
91 
            <geospatial>
92 
                <DecimalLatitude>-3.95</DecimalLatitude>
93 
                <DecimalLongitude>-73.4333</DecimalLongitude>
94 
                <verbatimElevation>200</verbatimElevation>
95 
            </geospatial>
96 
            <area>0.4</area>
92 
            <plotUniqueIdentifier>ALP-12</plotUniqueIdentifier>
97 93 
        </plot>
98 94 
    </plots>
95 
    <parties>
96 
        <party id="0"><organizationName>SALVIAS-CSV</organizationName></party>
97 
        <party id="1"><organizationName>SALVIAS-CSV</organizationName></party>
98 
    </parties>
99 99 
</VegX>
inputs/SALVIAS-CSV/maps/VegX.plots.full.csv
1 1 
SALVIAS-CSV,VegX:/*s/plotObservation,Comments
2 
project,/*ID->/*s/project:[personnel[role=metadataProvider]/organizationName=$/_ignore/inLabel]/title,
3 
PLOT_ID,:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceAccessionCode]/value,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
4 
plot_code,:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
5 
major_geo,/*UniqueIdentifierID->/*s/plot/location[placeType=continent]/placeName,
6 
country,/*UniqueIdentifierID->/*s/plot/location[placeType=country]/placeName,
7 
pol1,/*UniqueIdentifierID->/*s/plot/location[placeType=state]/placeName,Brad: No; pol1=stateProvince
8 
pol2,/*UniqueIdentifierID->/*s/plot/location[placeType=county]/placeName,Brad: No pol2=countyParish
9 
locality_description,/*UniqueIdentifierID->/*s/plot/locationNarrative,"Brad: No; this is free text description of locality where plot was situated, same as for DwC. Not a description of vegetation. Most likely='namedPlace.placeDescription' in VB; not sure about VX, again need to ask Nick where locality descriptions live in VX"
10 
lat_decimal,/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLatitude,
11 
long_decimal,/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLongitude,
12 
elev_m,/*UniqueIdentifierID->/*s/plot/geospatial/verbatimElevation,Brad: Mean elevation in meters. This is a constrained decimal value; is there no place for this in VegX other than verbatimElevation? Check with Nick.
13 
elev_max_m,/*UniqueIdentifierID->/*s/plot/geospatial/maximumElevationInMeters,
14 
elev_min_m,/*UniqueIdentifierID->/*s/plot/geospatial/minimumElevationInMeters,
15 
temp_c,/temperature,
16 
precip_mm,/simpleUserdefined[name=precipitation]/value,
17 
slope_aspect,/*UniqueIdentifierID->/*s/plot/slopeAspect,
18 
slope_gradient,/*UniqueIdentifierID->/*s/plot/slopeGradient,
19 
clay_percent,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=clay]/value/_units:[default=""%"",to=]/value",
20 
silt_percent,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=silt]/value/_units:[default=""%"",to=]/value",
21 
sand_percent,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=sand]/value/_units:[default=""%"",to=]/value",
22 
organic_percent,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=organic]/value/_units:[default=""%"",to=]/value",
2 
soil_Mg,"->/*s/abioticObservation[*ID]/magnesium/_units:[default=""%"",to=]/value",
3 
soil_N,"->/*s/abioticObservation[*ID]/nitrogen/_units:[default=""%"",to=]/value",
23 4 
pH,->/*s/abioticObservation[*ID]/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 
soil_N,"->/*s/abioticObservation[*ID]/nitrogen/_units:[default=""%"",to=]/value",
25 5 
soil_P,"->/*s/abioticObservation[*ID]/phosphorus/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value",
26 
soil_C,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=carbon]/value/_units:[default=""%"",to=]/value",
27 6 
soil_K,"->/*s/abioticObservation[*ID]/potassium/_units:[default=""%"",to=]/value",
28 
soil_Mg,"->/*s/abioticObservation[*ID]/magnesium/_units:[default=""%"",to=]/value",
29 
soil_Ca,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=calcium]/value/_units:[default=""%"",to=]/value",
30 
soil_Na,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=sodium]/value/_units:[default=""%"",to=]/value",
31 7 
soil_acidity,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=acidity]/value/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value",
32 8 
soil_base,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=base]/value/_units:[default=""%"",to=]/value",
9 
soil_Ca,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=calcium]/value/_units:[default=""%"",to=]/value",
10 
soil_C,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=carbon]/value/_units:[default=""%"",to=]/value",
33 11 
soil_cation_cap,->/*s/abioticObservation[*ID]/simpleUserdefined[name=cationExchangeCapacity]/value,
12 
clay_percent,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=clay]/value/_units:[default=""%"",to=]/value",
34 13 
soil_conductivity,->/*s/abioticObservation[*ID]/simpleUserdefined[name=conductivity]/value,
14 
organic_percent,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=organic]/value/_units:[default=""%"",to=]/value",
15 
sand_percent,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=sand]/value/_units:[default=""%"",to=]/value",
16 
silt_percent,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=silt]/value/_units:[default=""%"",to=]/value",
17 
soil_Na,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=sodium]/value/_units:[default=""%"",to=]/value",
35 18 
soil_texture,->/*s/abioticObservation[*ID]/simpleUserdefined[name=texture]/value,
36 19 
holdridge_life_zone,->/*s/communityDetermination[*ID]/*s/communityConcept/commonName,
37 20 
life_zone_code,->/*s/communityDetermination[*ID]/*s/communityConcept/name,
21 
project,/*ID->/*s/project:[personnel[role=metadataProvider]/organizationName=$/_ignore/inLabel]/title,
22 
plot_area_ha,/*UniqueIdentifierID->/*s/plot/area,"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"
23 
lat_decimal,/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLatitude,
24 
long_decimal,/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLongitude,
25 
elev_max_m,/*UniqueIdentifierID->/*s/plot/geospatial/maximumElevationInMeters,
26 
elev_min_m,/*UniqueIdentifierID->/*s/plot/geospatial/minimumElevationInMeters,
27 
elev_m,/*UniqueIdentifierID->/*s/plot/geospatial/verbatimElevation,Brad: Mean elevation in meters. This is a constrained decimal value; is there no place for this in VegX other than verbatimElevation? Check with Nick.
28 
locality_description,/*UniqueIdentifierID->/*s/plot/locationNarrative,"Brad: No; this is free text description of locality where plot was situated, same as for DwC. Not a description of vegetation. Most likely='namedPlace.placeDescription' in VB; not sure about VX, again need to ask Nick where locality descriptions live in VX"
29 
major_geo,/*UniqueIdentifierID->/*s/plot/location[placeType=continent]/placeName,
30 
country,/*UniqueIdentifierID->/*s/plot/location[placeType=country]/placeName,
31 
pol2,/*UniqueIdentifierID->/*s/plot/location[placeType=county]/placeName,Brad: No pol2=countyParish
32 
pol1,/*UniqueIdentifierID->/*s/plot/location[placeType=state]/placeName,Brad: No; pol1=stateProvince
33 
slope_aspect,/*UniqueIdentifierID->/*s/plot/slopeAspect,
34 
slope_gradient,/*UniqueIdentifierID->/*s/plot/slopeGradient,
35 
date_finish,/obsEndDate/_*/date,
36 
date_start,/obsStartDate/_*/date,
37 
plot_methodology,/simpleUserdefined[name=method]/*ID/method/name,
38 
precip_mm,/simpleUserdefined[name=precipitation]/value,
39 
temp_c,/temperature,
40 
plot_code,:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
41 
PLOT_ID,:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceAccessionCode]/value,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
38 42 
observation_type,,"Brad: SALVIAS internal metadata indicating whether the record represents an individual or aggregate observation. Rather than storing, use to decide where to store in VegX.; Aaron: VegX aggregateOrganismObservation table is missing many fields available in individualOrganismObservation, so we're mapping to individualOrganismObservation regardless of observation type"
39 
plot_methodology,/simpleUserdefined[name=method]/*ID/method/name,
40 
plot_area_ha,/*UniqueIdentifierID->/*s/plot/area,"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 43 
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,/obsStartDate/_*/date,
43 
date_finish,/obsEndDate/_*/date,
inputs/SALVIAS/test/VegX.plots.xml.ref
2 2 
<VegX>
3 3 
    <plotObservations>
4 4 
        <plotObservation id="0">
5 
            <partyWithRole><partyID>0</partyID></partyWithRole>
6 
            <simpleUserdefined>
7 
                <name>sourceAccessionCode</name>
8 
                <value>1</value>
9 
            </simpleUserdefined>
10 5 
            <projectID>0</projectID>
11 6 
            <plotUniqueIdentifierID>0</plotUniqueIdentifierID>
12 7 
            <simpleUserdefined>
8 
                <name>method</name>
9 
                <methodID><method><name>0.1 ha  transect, stems &gt;= 2.5 cm dbh</name></method></methodID>
10 
            </simpleUserdefined>
11 
            <simpleUserdefined>
13 12 
                <name>precipitation</name>
14 13 
                <value>2500.0</value>
15 14 
            </simpleUserdefined>
15 
            <partyWithRole><partyID>0</partyID></partyWithRole>
16 16 
            <simpleUserdefined>
17 
                <name>method</name>
18 
                <methodID><method><name>0.1 ha  transect, stems &gt;= 2.5 cm dbh</name></method></methodID>
17 
                <name>sourceAccessionCode</name>
18 
                <value>1</value>
19 19 
            </simpleUserdefined>
20 20 
        </plotObservation>
21 21 
        <plotObservation id="1">
22 
            <partyWithRole><partyID>1</partyID></partyWithRole>
23 
            <simpleUserdefined>
24 
                <name>sourceAccessionCode</name>
25 
                <value>2</value>
26 
            </simpleUserdefined>
27 22 
            <projectID>1</projectID>
28 23 
            <plotUniqueIdentifierID>1</plotUniqueIdentifierID>
29 24 
            <simpleUserdefined>
25 
                <name>method</name>
26 
                <methodID><method><name>0.1 ha  transect, stems &gt;= 2.5 cm dbh</name></method></methodID>
27 
            </simpleUserdefined>
28 
            <simpleUserdefined>
30 29 
                <name>precipitation</name>
31 30 
                <value>866.0</value>
32 31 
            </simpleUserdefined>
33 32 
            <temperature>7.4</temperature>
33 
            <partyWithRole><partyID>1</partyID></partyWithRole>
34 34 
            <simpleUserdefined>
35 
                <name>method</name>
36 
                <methodID><method><name>0.1 ha  transect, stems &gt;= 2.5 cm dbh</name></method></methodID>
35 
                <name>sourceAccessionCode</name>
36 
                <value>2</value>
37 37 
            </simpleUserdefined>
38 38 
        </plotObservation>
39 39 
    </plotObservations>
40 
    <parties>
41 
        <party id="0"><organizationName>SALVIAS</organizationName></party>
42 
        <party id="1"><organizationName>SALVIAS</organizationName></party>
43 
    </parties>
40 
    <communityDeterminations>
41 
        <communityDetermination>
42 
            <plotObservationID>0</plotObservationID>
43 
            <communityConcepts>
44 
                <communityConcept>
45 
                    <commonName>T-LMw</commonName>
46 
                    <name>Tropical lower montane wet forest</name>
47 
                </communityConcept>
48 
            </communityConcepts>
49 
        </communityDetermination>
50 
        <communityDetermination>
51 
            <plotObservationID>1</plotObservationID>
52 
            <communityConcepts>
53 
                <communityConcept>
54 
                    <commonName>cT-m</commonName>
55 
                    <name>Cool temperate moist forest</name>
56 
                </communityConcept>
57 
            </communityConcepts>
58 
        </communityDetermination>
59 
    </communityDeterminations>
44 60 
    <projects>
45 61 
        <project id="0">
46 62 
            <personnel>
......
59 75 
    </projects>
60 76 
    <plots>
61 77 
        <plot id="0">
62 
            <plotUniqueIdentifier>ACHUPALL</plotUniqueIdentifier>
78 
            <area>0.06</area>
79 
            <geospatial>
80 
                <DecimalLatitude>-3.45</DecimalLatitude>
81 
                <DecimalLongitude>-78.3667</DecimalLongitude>
82 
                <verbatimElevation>2100.0</verbatimElevation>
83 
            </geospatial>
63 84 
            <location>
64 85 
                <placeType>continent</placeType>
65 86 
                <placeName>South America</placeName>
......
68 89 
                <placeType>country</placeType>
69 90 
                <placeName>Ecuador</placeName>
70 91 
            </location>
92 
            <plotUniqueIdentifier>ACHUPALL</plotUniqueIdentifier>
93 
        </plot>
94 
        <plot id="1">
95 
            <area>0.1</area>
71 96 
            <geospatial>
72 
                <DecimalLatitude>-3.45</DecimalLatitude>
73 
                <DecimalLongitude>-78.3667</DecimalLongitude>
74 
                <verbatimElevation>2100.0</verbatimElevation>
97 
                <DecimalLatitude>48.0667</DecimalLatitude>
98 
                <DecimalLongitude>11.5</DecimalLongitude>
99 
                <verbatimElevation>530.0</verbatimElevation>
75 100 
            </geospatial>
76 
            <area>0.06</area>
77 
        </plot>
78 
        <plot id="1">
79 
            <plotUniqueIdentifier>ALLACHER</plotUniqueIdentifier>
80 101 
            <location>
81 102 
                <placeType>continent</placeType>
82 103 
                <placeName>Europe</placeName>
......
85 106 
                <placeType>country</placeType>
86 107 
                <placeName>Germany</placeName>
87 108 
            </location>
88 
            <geospatial>
89 
                <DecimalLatitude>48.0667</DecimalLatitude>
90 
                <DecimalLongitude>11.5</DecimalLongitude>
91 
                <verbatimElevation>530.0</verbatimElevation>
92 
            </geospatial>
93 
            <area>0.1</area>
109 
            <plotUniqueIdentifier>ALLACHER</plotUniqueIdentifier>
94 110 
        </plot>
95 111 
    </plots>
96 
    <communityDeterminations>
97 
        <communityDetermination>
98 
            <plotObservationID>0</plotObservationID>
99 
            <communityConcepts>
100 
                <communityConcept>
101 
                    <commonName>T-LMw</commonName>
102 
                    <name>Tropical lower montane wet forest</name>
103 
                </communityConcept>
104 
            </communityConcepts>
105 
        </communityDetermination>
106 
        <communityDetermination>
107 
            <plotObservationID>1</plotObservationID>
108 
            <communityConcepts>
109 
                <communityConcept>
110 
                    <commonName>cT-m</commonName>
111 
                    <name>Cool temperate moist forest</name>
112 
                </communityConcept>
113 
            </communityConcepts>
114 
        </communityDetermination>
115 
    </communityDeterminations>
112 
    <parties>
113 
        <party id="0"><organizationName>SALVIAS</organizationName></party>
114 
        <party id="1"><organizationName>SALVIAS</organizationName></party>
115 
    </parties>
116 116 
</VegX>
inputs/SALVIAS/test/VegX.stems.xml.ref
6 6 
                <relationshipType>stemParent</relationshipType>
7 7 
                <relatedItemID>1</relatedItemID>
8 8 
            </relatedItem>
9 
            <individualOrganismID>1</individualOrganismID>
9 
            <individualOrganismID>0</individualOrganismID>
10 10 
            <diameterBaseDistance>
11 11 
                <baseDistance><value>1.37</value></baseDistance>
12 12 
                <diameter>6.59</diameter>
13 13 
            </diameterBaseDistance>
14 14 
        </individualOrganismObservation>
15 
        <individualOrganismObservation id="1"><individualOrganismID>0</individualOrganismID></individualOrganismObservation>
15 
        <individualOrganismObservation id="1"><individualOrganismID>1</individualOrganismID></individualOrganismObservation>
16 16 
        <individualOrganismObservation id="1">
17 17 
            <relatedItem>
18 18 
                <relationshipType>stemParent</relationshipType>
19 19 
                <relatedItemID>2</relatedItemID>
20 20 
            </relatedItem>
21 
            <individualOrganismID>3</individualOrganismID>
21 
            <individualOrganismID>2</individualOrganismID>
22 22 
            <diameterBaseDistance>
23 23 
                <baseDistance><value>1.37</value></baseDistance>
24 24 
                <diameter>3.09</diameter>
25 25 
            </diameterBaseDistance>
26 26 
        </individualOrganismObservation>
27 
        <individualOrganismObservation id="2"><individualOrganismID>2</individualOrganismID></individualOrganismObservation>
27 
        <individualOrganismObservation id="2"><individualOrganismID>3</individualOrganismID></individualOrganismObservation>
28 28 
    </individualOrganismObservations>
29 29 
    <individualOrganisms>
30 30 
        <individualOrganism id="0"><taxonNameUsageConceptsID>0</taxonNameUsageConceptsID></individualOrganism>
......
33 33 
        <individualOrganism id="3"><taxonNameUsageConceptsID>3</taxonNameUsageConceptsID></individualOrganism>
34 34 
    </individualOrganisms>
35 35 
    <taxonNameUsageConcepts>
36 
        <taxonNameUsageConcept id="0"><voucher>1</voucher></taxonNameUsageConcept>
37 
        <taxonNameUsageConcept id="1"/>
38 
        <taxonNameUsageConcept id="2"><voucher>2</voucher></taxonNameUsageConcept>
39 
        <taxonNameUsageConcept id="3"/>
36 
        <taxonNameUsageConcept id="0"/>
37 
        <taxonNameUsageConcept id="1"><voucher>1</voucher></taxonNameUsageConcept>
38 
        <taxonNameUsageConcept id="2"/>
39 
        <taxonNameUsageConcept id="3"><voucher>2</voucher></taxonNameUsageConcept>
40 40 
    </taxonNameUsageConcepts>
41 41 
    <aggregateOrganismObservations>
42 42 
        <aggregateOrganismObservation>
43 
            <taxonNameUsageConceptID>1</taxonNameUsageConceptID>
43 
            <taxonNameUsageConceptID>0</taxonNameUsageConceptID>
44 44 
            <aggregateValue><aggregateValue><value>1</value></aggregateValue></aggregateValue>
45 45 
        </aggregateOrganismObservation>
46 46 
        <aggregateOrganismObservation>
47 
            <taxonNameUsageConceptID>3</taxonNameUsageConceptID>
47 
            <taxonNameUsageConceptID>2</taxonNameUsageConceptID>
48 48 
            <aggregateValue><aggregateValue><value>0</value></aggregateValue></aggregateValue>
49 49 
        </aggregateOrganismObservation>
50 50 
    </aggregateOrganismObservations>
inputs/SALVIAS/maps/VegX.plots.full.csv
1 1 
SALVIAS:plotMetadata,VegX:/*s/plotObservation,Comments
2 
PlotID,:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceAccessionCode]/value,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
3 
orig_filename,,
4 
AccessCode,,
5 
project_id,/*ID->/*s/project:[personnel[role=metadataProvider]/organizationName=$/_ignore/inLabel]/title,
6 
PrimOwnerID,,
7 
SiteCode,:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
8 
SiteName,,
9 
new_world,,
10 
MajorGeo,/*UniqueIdentifierID->/*s/plot/location[placeType=continent]/placeName,
11 
Country,/*UniqueIdentifierID->/*s/plot/location[placeType=country]/placeName,
12 
PolDiv1,/*UniqueIdentifierID->/*s/plot/location[placeType=state]/placeName,Brad: No; pol1=stateProvince
13 
pol1_type,,
14 
pol2,/*UniqueIdentifierID->/*s/plot/location[placeType=county]/placeName,Brad: No pol2=countyParish
15 
pol2_type,,
16 
lat_string,,
17 
long_string,,
18 
LatDec,/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLatitude,
19 
LongDec,/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLongitude,
20 
lat_long_accuracy,,
21 
Elev,/*UniqueIdentifierID->/*s/plot/geospatial/verbatimElevation,Brad: Mean elevation in meters. This is a constrained decimal value; is there no place for this in VegX other than verbatimElevation? Check with Nick.
22 
elev_max_m,/*UniqueIdentifierID->/*s/plot/geospatial/maximumElevationInMeters,
23 
elev_min_m,/*UniqueIdentifierID->/*s/plot/geospatial/minimumElevationInMeters,
24 
Precip,/simpleUserdefined[name=precipitation]/value,
25 
ElevSource,,
26 
Temp,/temperature,
27 
PrecipSource,,
28 
TempSource,,
29 
bearing,,
30 
slope_aspect,/*UniqueIdentifierID->/*s/plot/slopeAspect,
31 
slope_gradient,/*UniqueIdentifierID->/*s/plot/slopeGradient,
32 
clay_percent,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=clay]/value/_units:[default=""%"",to=]/value",
33 
silt_percent,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=silt]/value/_units:[default=""%"",to=]/value",
34 
sand_percent,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=sand]/value/_units:[default=""%"",to=]/value",
2 
soil_Mg,"->/*s/abioticObservation[*ID]/magnesium/_units:[default=""%"",to=]/value",
3 
soil_N,"->/*s/abioticObservation[*ID]/nitrogen/_units:[default=""%"",to=]/value",
35 4 
pH,->/*s/abioticObservation[*ID]/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."
36 
soil_N,"->/*s/abioticObservation[*ID]/nitrogen/_units:[default=""%"",to=]/value",
37 5 
soil_P,"->/*s/abioticObservation[*ID]/phosphorus/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value",
38 
soil_C,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=carbon]/value/_units:[default=""%"",to=]/value",
39 6 
soil_K,"->/*s/abioticObservation[*ID]/potassium/_units:[default=""%"",to=]/value",
40 
soil_Mg,"->/*s/abioticObservation[*ID]/magnesium/_units:[default=""%"",to=]/value",
41 
soil_Ca,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=calcium]/value/_units:[default=""%"",to=]/value",
42 
soil_Na,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=sodium]/value/_units:[default=""%"",to=]/value",
43 7 
soil_acidity,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=acidity]/value/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value",
44 8 
soil_base,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=base]/value/_units:[default=""%"",to=]/value",
9 
soil_Ca,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=calcium]/value/_units:[default=""%"",to=]/value",
10 
soil_C,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=carbon]/value/_units:[default=""%"",to=]/value",
45 11 
soil_cation_cap,->/*s/abioticObservation[*ID]/simpleUserdefined[name=cationExchangeCapacity]/value,
12 
clay_percent,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=clay]/value/_units:[default=""%"",to=]/value",
46 13 
soil_conductivity,->/*s/abioticObservation[*ID]/simpleUserdefined[name=conductivity]/value,
47 14 
organic_percent,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=organic]/value/_units:[default=""%"",to=]/value",
15 
sand_percent,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=sand]/value/_units:[default=""%"",to=]/value",
16 
silt_percent,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=silt]/value/_units:[default=""%"",to=]/value",
17 
soil_Na,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=sodium]/value/_units:[default=""%"",to=]/value",
48 18 
soil_texture,"->/*s/abioticObservation[*ID]/simpleUserdefined[name=texture]/value/_units:[default=""%"",to=]/value",
49 
RevisionComments,,
50 
Locality_Description,/*UniqueIdentifierID->/*s/plot/locationNarrative,"Brad: No; this is free text description of locality where plot was situated, same as for DwC. Not a description of vegetation. Most likely='namedPlace.placeDescription' in VB; not sure about VX, again need to ask Nick where locality descriptions live in VX"
51 
topography_desc,,
52 
vegetation_1,,
53 
vegetation_2,,
54 
Habitat,,
55 19 
life_zone_code,->/*s/communityDetermination[*ID]/*s/communityConcept/commonName,
56 20 
life_zone,->/*s/communityDetermination[*ID]/*s/communityConcept/name,
21 
project_id,/*ID->/*s/project:[personnel[role=metadataProvider]/organizationName=$/_ignore/inLabel]/title,
22 
plot_area_ha,/*UniqueIdentifierID->/*s/plot/area,"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"
23 
LatDec,/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLatitude,
24 
LongDec,/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLongitude,
25 
elev_max_m,/*UniqueIdentifierID->/*s/plot/geospatial/maximumElevationInMeters,
26 
elev_min_m,/*UniqueIdentifierID->/*s/plot/geospatial/minimumElevationInMeters,
27 
Elev,/*UniqueIdentifierID->/*s/plot/geospatial/verbatimElevation,Brad: Mean elevation in meters. This is a constrained decimal value; is there no place for this in VegX other than verbatimElevation? Check with Nick.
28 
Locality_Description,/*UniqueIdentifierID->/*s/plot/locationNarrative,"Brad: No; this is free text description of locality where plot was situated, same as for DwC. Not a description of vegetation. Most likely='namedPlace.placeDescription' in VB; not sure about VX, again need to ask Nick where locality descriptions live in VX"
29 
MajorGeo,/*UniqueIdentifierID->/*s/plot/location[placeType=continent]/placeName,
30 
Country,/*UniqueIdentifierID->/*s/plot/location[placeType=country]/placeName,
31 
pol2,/*UniqueIdentifierID->/*s/plot/location[placeType=county]/placeName,Brad: No pol2=countyParish
32 
PolDiv1,/*UniqueIdentifierID->/*s/plot/location[placeType=state]/placeName,Brad: No; pol1=stateProvince
33 
slope_aspect,/*UniqueIdentifierID->/*s/plot/slopeAspect,
34 
slope_gradient,/*UniqueIdentifierID->/*s/plot/slopeGradient,
35 
date_finish,/obsEndDate/_*/date,
36 
date_start,/obsStartDate/_*/date,
57 37 
PlotMethod,/simpleUserdefined[name=method]/*ID/method/name,
38 
Precip,/simpleUserdefined[name=precipitation]/value,
39 
Temp,/temperature,
40 
SiteCode,:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
41 
PlotID,:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceAccessionCode]/value,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
42 
AccessCode,,
43 
ElevSource,,
44 
Habitat,,
58 45 
MethodCode,,
59 
plot_area_ha,/*UniqueIdentifierID->/*s/plot/area,"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 
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,/obsStartDate/_*/date,
62 
date_finish,/obsEndDate/_*/date,
46 
PrecipSource,,
47 
PrimOwnerID,,
48 
RevisionComments,,
49 
SiteName,,
50 
TempSource,,
51 
bearing,,
52 
lat_long_accuracy,,
53 
lat_string,,
54 
long_string,,
55 
new_world,,
56 
orig_filename,,
63 57 
plot_administrator,,
64 58 
plot_notes,,
59 
pol1_type,,
60 
pol2_type,,
61 
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"
65 62 
tmp_del,,
63 
topography_desc,,
64 
vegetation_1,,
65 
vegetation_2,,
inputs/SALVIAS/maps/VegX.stems.full.csv
1 1 
SALVIAS:stems,VegX:/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID],Comments
2 
stem_id,,
3 
origrecord_id_stems,,
4 
PlotObsID,/relatedItem[relationshipType=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,
5 2 
NoInd,/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/aggregateOrganismObservation[*ID]/*/aggregateValue/value,
3 
stem_notes,/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/note/text,
4 
stem_tag1,/*ID->/*s/individualOrganism/identificationLabel[@id=1],
5 
stem_tag2,/*ID->/*s/individualOrganism/identificationLabel[@id=2],
6 6 
basal_diam,/diameterBaseDistance[baseDistance/value=0]/diameter,
7 7 
stem_dbh,/diameterBaseDistance[baseDistance[!attributeID]/value=1.37]/diameter,
8 8 
gentry_dbh,/diameterBaseDistance[baseDistance[*ID/*s/attribute/quantitative/*ID/*s/method(/name=Gentry)]/value=1.37]/diameter,
9 
stem_notes,/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/note/text,
10 
stem_tag1,/*ID->/*s/individualOrganism/identificationLabel[@id=1],
11 
stem_tag2,/*ID->/*s/individualOrganism/identificationLabel[@id=2],
12 
stem_height_m,/simpleUserdefined[name=height]/value,
13 
stem_height_first_branch_m,/simpleUserdefined[name=heightFirstBranch]/value,
9 
PlotObsID,/relatedItem[relationshipType=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,
14 10 
stem_canopy_form,/simpleUserdefined[name=canopyForm]/value,
15 11 
stem_canopy_position,/simpleUserdefined[name=canopyPosition]/value,
12 
stem_height_first_branch_m,/simpleUserdefined[name=heightFirstBranch]/value,
13 
stem_height_m,/simpleUserdefined[name=height]/value,
16 14 
stem_liana_infestation,/simpleUserdefined[name=lianaInfestation]/value,
15 
origrecord_id_stems,,
16 
stem_id,,
17 17 
tmp_del,,
inputs/input.Makefile
174 174 
$(bin)/intersect maps/src.$*.csv 0)
175 175 

  		




  176
  176
  
    
makeFullCsv = $(if $(shell test -e $(word 2,$+) && echo t),\


  		




  177
  
  
    
env ignore=1 $(bin)/union <$+|$(bin)/sort_map >$@,$(CP) $< $@)


  		




  
  177
  
    
env ignore=1 $(bin)/union <$+|,<$< )$(bin)/sort_map >$@


  		




  178
  178
  
    
# can't use $(wildcard) because it won't recheck file after $(coreSelfMap) runs


  		




  179
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  180
  180
  
    
maps/$(via).%.full.csv: maps/$(via).%.csv $(coreSelfMap)


  		












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