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Revision 506

Added by Aaron Marcuse-Kubitza about 13 years ago

VegX mappings: Use baseDistance/value instead of baseDistance so we can later use complexUserDefined to distinguish between different types of dbh

View differences:

test/accepted_output/SALVIAS.organisms.VegX.xml
21 21 
                <value>1</value>
22 22 
            </simpleUserdefined>
23 23 
            <diameterBaseDistance>
24 
                <baseDistance>1.37</baseDistance>
24 
                <baseDistance>
25 
                    <value>1.37</value>
26 
                </baseDistance>
25 27 
                <diameter>662</diameter>
26 28 
            </diameterBaseDistance>
27 29 
        </individualOrganismObservation>
......
45 47 
                <value>1</value>
46 48 
            </simpleUserdefined>
47 49 
            <diameterBaseDistance>
48 
                <baseDistance>1.37</baseDistance>
50 
                <baseDistance>
51 
                    <value>1.37</value>
52 
                </baseDistance>
49 53 
                <diameter>215</diameter>
50 54 
            </diameterBaseDistance>
51 55 
        </individualOrganismObservation>
mappings/VegX-VegBIEN.organisms.csv
53 53 
/simpleUserdefined[name=count]/value,/aggregateoccurrence/count/_alt/1
54 54 
/simpleUserdefined[name=coverPercent]/value,/aggregateoccurrence/cover
55 55 
/simpleUserdefined[name=interceptCm]/value,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
56 
/diameterBaseDistance[baseDistance=1.37]/diameter,/aggregateoccurrence/individualplant/diameter
56 
/diameterBaseDistance[baseDistance/value=1.37]/diameter,/aggregateoccurrence/individualplant/diameter
57 57 
/height,/aggregateoccurrence/individualplant/height
58 58 
/simpleUserdefined[name=stemHeightM]/value,/aggregateoccurrence/individualplant/height
59 59 
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/authorCode,/aggregateoccurrence/individualplant/specimen:[*_id/reference]/catalognumber_dwc
......
65 65 
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/note/text,/aggregateoccurrence/individualplant/stem
66 66 
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/identificationLabel,/aggregateoccurrence/individualplant/stem
67 67 
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/*ID->/*s/individualOrganism/identificationLabel,/aggregateoccurrence/individualplant/stem
68 
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance=0]/diameter,/aggregateoccurrence/individualplant/stem
69 
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance=1.37]/diameter,/aggregateoccurrence/individualplant/stem
70 
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance=1.37]/diameter,/aggregateoccurrence/individualplant/stem
68 
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance/value=0]/diameter,/aggregateoccurrence/individualplant/stem
69 
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance/value=1.37]/diameter,/aggregateoccurrence/individualplant/stem
70 
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance/value=1.37]/diameter,/aggregateoccurrence/individualplant/stem
71 71 
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/relatedItem[relationshipType=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,/aggregateoccurrence/individualplant/stem
72 72 
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=count]/value,/aggregateoccurrence/individualplant/stem
73 73 
->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=stemCanopyForm]/value,/aggregateoccurrence/individualplant/stem
......
78 78 
/*ID->/*s/individualOrganism/identificationLabel,/aggregateoccurrence/individualplant/stem/authorcode
79 79 
/*ID->/*s/individualOrganism/identificationLabel/_alt/1,/aggregateoccurrence/individualplant/stem/authorcode/_alt/1
80 80 
/*ID->/*s/individualOrganism/identificationLabel/_alt/2,/aggregateoccurrence/individualplant/stem/authorcode/_alt/2
81 
/diameterBaseDistance[baseDistance=0]/diameter,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=basalDiameter]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
81 
/diameterBaseDistance[baseDistance/value=0]/diameter,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=basalDiameter]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
82 82 
/simpleUserdefined[name=stemCanopyForm]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=canopyForm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
83 83 
/simpleUserdefined[name=stemCanopyPosition]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=canopyPosition]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
84 84 
/simpleUserdefined[name=habitat]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=habitat]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
mappings/SALVIAS-VegX.organisms.csv
36 36 
"ht_first_branch_m","/simpleUserdefined[name=htFirstBranchM]/value","Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob"
37 37 
"stem_tag1","/*ID->/*s/individualOrganism/identificationLabel","Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."
38 38 
"stem_tag2","/*ID->/*s/individualOrganism/identificationLabel","Brad: see above"
39 
"stem_dbh","/diameterBaseDistance[baseDistance=1.37]/diameter",
40 
"basal_diam","/diameterBaseDistance[baseDistance=0]/diameter",
39 
"stem_dbh","/diameterBaseDistance[baseDistance/value=1.37]/diameter",
40 
"basal_diam","/diameterBaseDistance[baseDistance/value=0]/diameter",
41 41 
"stem_height_m","/simpleUserdefined[name=stemHeightM]/value","Brad: Same as for height, but applies to individuals stems, not trees. Rare."
42 42 
"stem_height_first_branch_m","/simpleUserdefined[name=stemHeightFirstBranchM]/value","Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
43 43 
"stem_canopy_form","/simpleUserdefined[name=stemCanopyForm]/value","Brad: Should also be userDefined for VegBank. "
mappings/for_review/VegX-VegBIEN.organisms.csv
53 53 
/simpleUserdefined[name=count]/value,//aggregateoccurrence/count/_alt/1
54 54 
/simpleUserdefined[name=coverPercent]/value,//aggregateoccurrence/cover
55 55 
/simpleUserdefined[name=interceptCm]/value,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]/definedvalue"
56 
/diameterBaseDistance[baseDistance=1.37]/diameter,//individualplant/diameter
56 
/diameterBaseDistance[value=1.37]/diameter,//individualplant/diameter
57 57 
/height,//individualplant/height
58 58 
/simpleUserdefined[name=stemHeightM]/value,//individualplant/height
59 59 
//taxonNameUsageConcept/authorCode,//specimen/catalognumber_dwc
......
65 65 
//note/text,//individualplant/stem
66 66 
//individualOrganism/identificationLabel,//individualplant/stem
67 67 
//individualOrganism/identificationLabel,//individualplant/stem
68 
//*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance=0]/diameter,//individualplant/stem
69 
//*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance=1.37]/diameter,//individualplant/stem
70 
//*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[baseDistance=1.37]/diameter,//individualplant/stem
68 
//*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[value=0]/diameter,//individualplant/stem
69 
//*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[value=1.37]/diameter,//individualplant/stem
70 
//*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/diameterBaseDistance[value=1.37]/diameter,//individualplant/stem
71 71 
//taxonNameUsageConcept/voucher,//individualplant/stem
72 72 
//*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=count]/value,//individualplant/stem
73 73 
//*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]/simpleUserdefined[name=stemCanopyForm]/value,//individualplant/stem
......
78 78 
//individualOrganism/identificationLabel,//stem/authorcode
79 79 
//individualOrganism/identificationLabel/_alt/1,//stem/authorcode/_alt/1
80 80 
//individualOrganism/identificationLabel/_alt/2,//stem/authorcode/_alt/2
81 
/diameterBaseDistance[baseDistance=0]/diameter,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=basalDiameter]]/definedvalue"
81 
/diameterBaseDistance[value=0]/diameter,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=basalDiameter]]/definedvalue"
82 82 
/simpleUserdefined[name=stemCanopyForm]/value,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=canopyForm]]/definedvalue"
83 83 
/simpleUserdefined[name=stemCanopyPosition]/value,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=canopyPosition]]/definedvalue"
84 84 
/simpleUserdefined[name=habitat]/value,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=habitat]]/definedvalue"
mappings/for_review/SALVIAS-VegX.organisms.csv
36 36 
ht_first_branch_m,/simpleUserdefined[name=htFirstBranchM]/value,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
37 37 
stem_tag1,//individualOrganism/identificationLabel,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."
38 38 
stem_tag2,//individualOrganism/identificationLabel,Brad: see above
39 
stem_dbh,/diameterBaseDistance[baseDistance=1.37]/diameter,
40 
basal_diam,/diameterBaseDistance[baseDistance=0]/diameter,
39 
stem_dbh,/diameterBaseDistance[value=1.37]/diameter,
40 
basal_diam,/diameterBaseDistance[value=0]/diameter,
41 41 
stem_height_m,/simpleUserdefined[name=stemHeightM]/value,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
42 42 
stem_height_first_branch_m,/simpleUserdefined[name=stemHeightFirstBranchM]/value,"Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
43 43 
stem_canopy_form,/simpleUserdefined[name=stemCanopyForm]/value,Brad: Should also be userDefined for VegBank.
mappings/for_review/SALVIAS_db-VegX.organisms.csv
58 58 
canopy_form,/simpleUserdefined[name=canopyForm]/value,Brad: Should also be userDefined for VegBank.
59 59 
liana_infestation,/simpleUserdefined[name=lianaInfestation]/value,Brad: Should also be userDefined for VegBank.
60 60 
Notes,//note/text,
61 
temp_dbh,/diameterBaseDistance[baseDistance=1.37]/diameter,
61 
temp_dbh,/diameterBaseDistance[value=1.37]/diameter,
62 62 
temp_liandbh,,
63 63 
tmp_del,,
mappings/SALVIAS_db-VegX.organisms.csv
58 58 
"canopy_form","/simpleUserdefined[name=canopyForm]/value","Brad: Should also be userDefined for VegBank. "
59 59 
"liana_infestation","/simpleUserdefined[name=lianaInfestation]/value","Brad: Should also be userDefined for VegBank. "
60 60 
"Notes","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/note/text",
61 
"temp_dbh","/diameterBaseDistance[baseDistance=1.37]/diameter",
61 
"temp_dbh","/diameterBaseDistance[baseDistance/value=1.37]/diameter",
62 62 
"temp_liandbh",,
63 63 
"tmp_del",,
mappings/VegX-VegBIEN.stems.csv
2 2 
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/note/text,
3 3 
/*ID->/*s/individualOrganism/identificationLabel,
4 4 
/*ID->/*s/individualOrganism/identificationLabel,
5 
/diameterBaseDistance[baseDistance=0]/diameter,
6 
/diameterBaseDistance[baseDistance=1.37]/diameter,
7 
/diameterBaseDistance[baseDistance=1.37]/diameter,
5 
/diameterBaseDistance[baseDistance/value=0]/diameter,
6 
/diameterBaseDistance[baseDistance/value=1.37]/diameter,
7 
/diameterBaseDistance[baseDistance/value=1.37]/diameter,
8 8 
/relatedItem[relationshipType=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,
9 9 
/simpleUserdefined[name=count]/value,
10 10 
/simpleUserdefined[name=stemCanopyForm]/value,

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