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Revision 1077

Added by Aaron Marcuse-Kubitza about 13 years ago

SALVIAS mappings: Fixed PlotID mapping to go to locationevent.sourceaccessioncode

View differences:

inputs/SALVIAS/test/VegBIEN.plots.xml.ref
57 57 
            <definedvalue>2500.0</definedvalue>
58 58 
        </definedvalue>
59 59 
        <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
60 
        <authorlocationcode>1</authorlocationcode>
60 
        <sourceaccessioncode>1</sourceaccessioncode>
61 61 
    </locationevent>
62 62 
    <locationevent id="1">
63 63 
        <location_id>
......
125 125 
            <definedvalue>7.4</definedvalue>
126 126 
        </definedvalue>
127 127 
        <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
128 
        <authorlocationcode>2</authorlocationcode>
128 
        <sourceaccessioncode>2</sourceaccessioncode>
129 129 
    </locationevent>
130 130 
</VegBIEN>
inputs/SALVIAS/test/VegBIEN.organisms.xml.ref
4 4 
        <locationevent_id>
5 5 
            <locationevent>
6 6 
                <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
7 
                <authorlocationcode>295</authorlocationcode>
7 
                <sourceaccessioncode>295</sourceaccessioncode>
8 8 
            </locationevent>
9 9 
        </locationevent_id>
10 10 
        <aggregateoccurrence>
......
124 124 
        <locationevent_id>
125 125 
            <locationevent>
126 126 
                <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
127 
                <authorlocationcode>295</authorlocationcode>
127 
                <sourceaccessioncode>295</sourceaccessioncode>
128 128 
            </locationevent>
129 129 
        </locationevent_id>
130 130 
        <aggregateoccurrence>
inputs/SALVIAS/test/import.organisms.out.ref
1 
Inserted 87 new rows into database
1 
Inserted 86 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,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
41 
PlotID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"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:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
2 
PlotID,/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
3 3 
height_m,/aggregateoccurrence/*_id/plantobservation/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
4 4 
PlotObsID,/aggregateoccurrence/*_id/plantobservation/sourceaccessioncode,"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."
5 5 
ht_first_branch_m,"/aggregateoccurrence/*_id/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
inputs/SALVIAS-CSV/test/VegBIEN.plots.xml.ref
48 48 
        </project_id>
49 49 
        <obsstartdate>1990-11-16</obsstartdate>
50 50 
        <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
51 
        <authorlocationcode>26102</authorlocationcode>
51 
        <sourceaccessioncode>26102</sourceaccessioncode>
52 52 
    </locationevent>
53 53 
    <locationevent id="1">
54 54 
        <location_id>
......
98 98 
        </project_id>
99 99 
        <obsstartdate>1990-11-16</obsstartdate>
100 100 
        <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
101 
        <authorlocationcode>26103</authorlocationcode>
101 
        <sourceaccessioncode>26103</sourceaccessioncode>
102 102 
    </locationevent>
103 103 
</VegBIEN>
inputs/SALVIAS-CSV/test/VegBIEN.organisms.xml.ref
11 11 
                </location_id>
12 12 
                <obsstartdate>2001-01-01</obsstartdate>
13 13 
                <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
14 
                <authorlocationcode>26102</authorlocationcode>
14 
                <sourceaccessioncode>26102</sourceaccessioncode>
15 15 
            </locationevent>
16 16 
        </locationevent_id>
17 17 
        <aggregateoccurrence>
......
134 134 
                </location_id>
135 135 
                <obsstartdate>2001-01-01</obsstartdate>
136 136 
                <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
137 
                <authorlocationcode>26102</authorlocationcode>
137 
                <sourceaccessioncode>26102</sourceaccessioncode>
138 138 
            </locationevent>
139 139 
        </locationevent_id>
140 140 
        <aggregateoccurrence>
inputs/SALVIAS-CSV/test/import.organisms.out.ref
1 
Inserted 83 new rows into database
1 
Inserted 82 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,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
41 
PLOT_ID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"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:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
5 
PLOT_ID,/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
6 6 
height_m,/aggregateoccurrence/*_id/plantobservation/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
7 7 
stem_height_m,/aggregateoccurrence/*_id/plantobservation/overallheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
8 8 
OBSERVATION_ID,/aggregateoccurrence/*_id/plantobservation/sourceaccessioncode,"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."
mappings/VegX-VegBIEN.plots.csv
49 49 
->/*s/abioticObservation[*ID]/simpleUserdefined[name=texture]/value,/soilobs:[soilhorizon=unknown]/soiltexture,
50 50 
/*UniqueIdentifierID->/*s/plot/geospatial/maximumDepthInMeters,/waterdepth/max,
51 51 
/*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters,/waterdepth/min,
52 
:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=authorCode]/value,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode,
53 52 
/partyWithRole/*ID->/parties/party/organizationName,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1,
53 
:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=authorCode]/value,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,
mappings/VegX-VegBIEN.organisms.csv
49 49 
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=texture]/value,/*_id/locationevent/soilobs:[soilhorizon=unknown]/soiltexture,
50 50 
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/maximumDepthInMeters,/*_id/locationevent/waterdepth/max,
51 51 
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters,/*_id/locationevent/waterdepth/min,
52 
/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=authorCode]/value,/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode,
53 52 
/*ID->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1,
53 
/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=authorCode]/value,/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,
54 54 
/height,/aggregateoccurrence/*_id/plantobservation/overallheight,
55 55 
/simpleUserdefined[name=stemHeightM]/value,/aggregateoccurrence/*_id/plantobservation/overallheight,
56 56 
:[*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceaccessioncode]/value,/aggregateoccurrence/*_id/plantobservation/sourceaccessioncode,
mappings/for_review/VegX-VegBIEN.plots.csv
49 49 
//*s/abioticObservation/simpleUserdefined[name=texture]/value,//soilobs/soiltexture,
50 50 
//geospatial/maximumDepthInMeters,//waterdepth/max,
51 51 
//geospatial/minimumDepthInMeters,//waterdepth/min,
52 
/simpleUserdefined[name=authorCode]/value,/authorlocationcode,
53 52 
//party/organizationName,//party/organizationname/_alt/1,
53 
/simpleUserdefined[name=authorCode]/value,/sourceaccessioncode,
mappings/for_review/VegX-VegBIEN.organisms.csv
49 49 
//*s/abioticObservation/simpleUserdefined[name=texture]/value,//soilobs/soiltexture,
50 50 
//geospatial/maximumDepthInMeters,//waterdepth/max,
51 51 
//geospatial/minimumDepthInMeters,//waterdepth/min,
52 
//plotObservation/simpleUserdefined[name=authorCode]/value,//locationevent/authorlocationcode,
53 52 
//party/organizationName,//party/organizationname/_alt/1,
53 
//plotObservation/simpleUserdefined[name=authorCode]/value,//locationevent/sourceaccessioncode,
54 54 
/height,//plantobservation/overallheight,
55 55 
/simpleUserdefined[name=stemHeightM]/value,//plantobservation/overallheight,
56 56 
/simpleUserdefined[name=sourceaccessioncode]/value,//plantobservation/sourceaccessioncode,

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