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Revision 1056

Added by Aaron Marcuse-Kubitza almost 13 years ago

VegX-VegBIEN mapping: Map datasource name (/_ignore/inLabel) to new locationevent.datasource instead of location.reference

View differences:

inputs/SALVIAS/test/VegBIEN.plots.xml.ref
26 26 
                    <latitude>-3.45</latitude>
27 27 
                    <longitude>-78.3667</longitude>
28 28 
                </locationdetermination>
29 
                <reference_id><reference><shortname>SALVIAS</shortname></reference></reference_id>
30 29 
            </location>
31 30 
        </location_id>
32 31 
        <project_id><project><projectname>1</projectname></project></project_id>
......
50 49 
            <definedvalue>2500.0</definedvalue>
51 50 
        </definedvalue>
52 51 
        <methodnarrative>0.1 ha  transect, stems &gt;= 2.5 cm dbh</methodnarrative>
52 
        <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
53 53 
        <authoreventcode>1</authoreventcode>
54 54 
    </locationevent>
55 55 
    <locationevent id="1">
......
78 78 
                    <latitude>48.0667</latitude>
79 79 
                    <longitude>11.5</longitude>
80 80 
                </locationdetermination>
81 
                <reference_id><reference><shortname>SALVIAS</shortname></reference></reference_id>
82 81 
            </location>
83 82 
        </location_id>
84 83 
        <project_id><project><projectname>1</projectname></project></project_id>
......
111 110 
            <definedvalue>7.4</definedvalue>
112 111 
        </definedvalue>
113 112 
        <methodnarrative>0.1 ha  transect, stems &gt;= 2.5 cm dbh</methodnarrative>
113 
        <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
114 114 
        <authoreventcode>2</authoreventcode>
115 115 
    </locationevent>
116 116 
</VegBIEN>
inputs/SALVIAS/test/VegBIEN.organisms.xml.ref
3 3 
    <taxonoccurrence id="0">
4 4 
        <locationevent_id>
5 5 
            <locationevent>
6 
                <location_id><location><reference_id><reference><shortname>SALVIAS</shortname></reference></reference_id></location></location_id>
6 
                <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
7 7 
                <authoreventcode>295</authoreventcode>
8 8 
            </locationevent>
9 9 
        </locationevent_id>
......
119 119 
    <taxonoccurrence id="1">
120 120 
        <locationevent_id>
121 121 
            <locationevent>
122 
                <location_id><location><reference_id><reference><shortname>SALVIAS</shortname></reference></reference_id></location></location_id>
122 
                <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
123 123 
                <authoreventcode>295</authoreventcode>
124 124 
            </locationevent>
125 125 
        </locationevent_id>
inputs/SALVIAS/test/import.plots.out.ref
1 
Inserted 32 new rows into database
1 
Inserted 31 new rows into database
inputs/SALVIAS/test/import.organisms.out.ref
1 
Inserted 88 new rows into database
1 
Inserted 85 new rows into database
inputs/SALVIAS/maps/VegBIEN.plots.csv
38 38 
sand_percent,/soilobs:[soilhorizon=unknown]/soilsand,
39 39 
silt_percent,/soilobs:[soilhorizon=unknown]/soilsilt,
40 40 
soil_texture,/soilobs:[soilhorizon=unknown]/soiltexture,
41 
PlotID,:[*_id/location/*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/authoreventcode,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
41 
PlotID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authoreventcode,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
42 42 
AccessCode,,
43 43 
ElevSource,,
44 44 
Habitat,,
inputs/SALVIAS/maps/VegBIEN.organisms.csv
1 1 
SALVIAS:plotObservations,VegBIEN:/taxonoccurrence,Comments
2 
PlotID,/*_id/locationevent:[*_id/location/*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/authoreventcode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
2 
PlotID,/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authoreventcode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
3 3 
PlotObsID,/aggregateoccurrence/*_id/plantobservation/authorplantcode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
4 4 
height_m,/aggregateoccurrence/*_id/plantobservation/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
5 5 
tag2,/aggregateoccurrence/*_id/plantobservation/stemobservation/authorstemcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
inputs/SALVIAS-CSV/test/VegBIEN.plots.xml.ref
35 35 
                    <longitude>-73.4333</longitude>
36 36 
                </locationdetermination>
37 37 
                <locationnarrative>pre-Holocene; clay</locationnarrative>
38 
                <reference_id><reference><shortname>SALVIAS</shortname></reference></reference_id>
39 38 
            </location>
40 39 
        </location_id>
41 40 
        <project_id><project><projectname>RAINFOR - 1 ha Peru</projectname></project></project_id>
42 41 
        <methodnarrative>1 ha, stems &gt;= 10 cm dbh</methodnarrative>
43 42 
        <obsstartdate>1990-11-16</obsstartdate>
43 
        <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
44 44 
        <authoreventcode>26102</authoreventcode>
45 45 
    </locationevent>
46 46 
    <locationevent id="1">
......
78 78 
                    <longitude>-73.4333</longitude>
79 79 
                </locationdetermination>
80 80 
                <locationnarrative>pre-Holocene; white and brown sand</locationnarrative>
81 
                <reference_id><reference><shortname>SALVIAS</shortname></reference></reference_id>
82 81 
            </location>
83 82 
        </location_id>
84 83 
        <project_id><project><projectname>RAINFOR - 1 ha Peru</projectname></project></project_id>
85 84 
        <methodnarrative>1 ha, stems &gt;= 10 cm dbh</methodnarrative>
86 85 
        <obsstartdate>1990-11-16</obsstartdate>
86 
        <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
87 87 
        <authoreventcode>26103</authoreventcode>
88 88 
    </locationevent>
89 89 
</VegBIEN>
inputs/SALVIAS-CSV/test/VegBIEN.organisms.xml.ref
7 7 
                    <location>
8 8 
                        <authorlocationcode>1</authorlocationcode>
9 9 
                        <parent_id><location><authorlocationcode>ALP-11</authorlocationcode></location></parent_id>
10 
                        <reference_id><reference><shortname>SALVIAS</shortname></reference></reference_id>
11 10 
                    </location>
12 11 
                </location_id>
13 12 
                <obsstartdate>2001-01-01</obsstartdate>
13 
                <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
14 14 
                <authoreventcode>26102</authoreventcode>
15 15 
            </locationevent>
16 16 
        </locationevent_id>
......
123 123 
                    <location>
124 124 
                        <authorlocationcode>4</authorlocationcode>
125 125 
                        <parent_id><location><authorlocationcode>ALP-11</authorlocationcode></location></parent_id>
126 
                        <reference_id><reference><shortname>SALVIAS</shortname></reference></reference_id>
127 126 
                    </location>
128 127 
                </location_id>
129 128 
                <obsstartdate>2001-01-01</obsstartdate>
129 
                <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
130 130 
                <authoreventcode>26102</authoreventcode>
131 131 
            </locationevent>
132 132 
        </locationevent_id>
inputs/SALVIAS-CSV/test/import.plots.out.ref
1 
Inserted 19 new rows into database
1 
Inserted 18 new rows into database
inputs/SALVIAS-CSV/test/import.organisms.out.ref
1 
Inserted 81 new rows into database
1 
Inserted 79 new rows into database
inputs/SALVIAS-CSV/maps/VegBIEN.plots.csv
38 38 
sand_percent,/soilobs:[soilhorizon=unknown]/soilsand,
39 39 
silt_percent,/soilobs:[soilhorizon=unknown]/soilsilt,
40 40 
soil_texture,/soilobs:[soilhorizon=unknown]/soiltexture,
41 
PLOT_ID,:[*_id/location/*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/authoreventcode,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
41 
PLOT_ID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authoreventcode,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
42 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"
43 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"
inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv
2 2 
subplot,/*_id/locationevent/*_id/location/authorlocationcode,
3 3 
plot_code,/*_id/locationevent/*_id/location/parent_id/location/authorlocationcode,"Brad: Same as plotCode, above"
4 4 
census_date,/*_id/locationevent/obsstartdate/_date/year,
5 
PLOT_ID,/*_id/locationevent:[*_id/location/*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/authoreventcode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
5 
PLOT_ID,/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authoreventcode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
6 6 
OBSERVATION_ID,/aggregateoccurrence/*_id/plantobservation/authorplantcode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
7 7 
height_m,/aggregateoccurrence/*_id/plantobservation/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
8 8 
stem_height_m,/aggregateoccurrence/*_id/plantobservation/overallheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
mappings/VegX-VegBIEN.plots.csv
48 48 
->/*s/abioticObservation[*ID]/simpleUserdefined[name=texture]/value,/soilobs:[soilhorizon=unknown]/soiltexture,
49 49 
/*UniqueIdentifierID->/*s/plot/geospatial/maximumDepthInMeters,/waterdepth/max,
50 50 
/*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters,/waterdepth/min,
51 
/partyWithRole/*ID->/parties/party/organizationName,:[*_id/location/*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/*_id/location/*_id/reference/shortname/_alt/1,
52 
:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=authorCode]/value,:[*_id/location/*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/authoreventcode,
51 
:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=authorCode]/value,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authoreventcode,
52 
/partyWithRole/*ID->/parties/party/organizationName,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1,
mappings/VegX-VegBIEN.organisms.csv
48 48 
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=texture]/value,/*_id/locationevent/soilobs:[soilhorizon=unknown]/soiltexture,
49 49 
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/maximumDepthInMeters,/*_id/locationevent/waterdepth/max,
50 50 
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters,/*_id/locationevent/waterdepth/min,
51 
/*ID->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,/*_id/locationevent:[*_id/location/*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/*_id/location/*_id/reference/shortname/_alt/1,
52 
/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=authorCode]/value,/*_id/locationevent:[*_id/location/*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/authoreventcode,
51 
/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=authorCode]/value,/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authoreventcode,
52 
/*ID->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1,
53 53 
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher,/aggregateoccurrence/*_id/plantobservation/authorplantcode,
54 54 
/height,/aggregateoccurrence/*_id/plantobservation/overallheight,
55 55 
/simpleUserdefined[name=stemHeightM]/value,/aggregateoccurrence/*_id/plantobservation/overallheight,
mappings/for_review/VegX-VegBIEN.plots.csv
48 48 
//*s/abioticObservation/simpleUserdefined[name=texture]/value,//soilobs/soiltexture,
49 49 
//geospatial/maximumDepthInMeters,//waterdepth/max,
50 50 
//geospatial/minimumDepthInMeters,//waterdepth/min,
51 
//party/organizationName,//reference/shortname/_alt/1,
52 51 
/simpleUserdefined[name=authorCode]/value,/authoreventcode,
52 
//party/organizationName,//party/organizationname/_alt/1,
mappings/for_review/VegX-VegBIEN.organisms.csv
48 48 
//*s/abioticObservation/simpleUserdefined[name=texture]/value,//soilobs/soiltexture,
49 49 
//geospatial/maximumDepthInMeters,//waterdepth/max,
50 50 
//geospatial/minimumDepthInMeters,//waterdepth/min,
51 
//party/organizationName,//reference/shortname/_alt/1,
52 51 
//plotObservation/simpleUserdefined[name=authorCode]/value,//locationevent/authoreventcode,
52 
//party/organizationName,//party/organizationname/_alt/1,
53 53 
//taxonNameUsageConcept/voucher,//plantobservation/authorplantcode,
54 54 
/height,//plantobservation/overallheight,
55 55 
/simpleUserdefined[name=stemHeightM]/value,//plantobservation/overallheight,

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