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Revision 6761

Added by Aaron Marcuse-Kubitza over 11 years ago

inputs/CVS/: Joined together stemCount and stemLocation tables to create stemLocation_, in order to include the stem size class's measurements in each tagged stem's stemobservation (in addition to in the stemobservation for the aggregateoccurrence as a whole)

View differences:

inputs/CVS/stemLocation/new_terms.csv
1 
STEMLOCATION_ID,stemID,,
2 
STEMLOCATION_ID,individualID,,
3 
STEMCOUNT_ID,aggregateOccurrenceID,,
4 
stemCode,authorStemCode,,
5 
stemXPosition,organismX_m,,
6 
stemYPosition,organismY_m,,
inputs/CVS/stemLocation/unmapped_terms.csv
1 
*stemHealth
2 
*dba_src_ID
3 
*cust_cvs_stemSource
4 
*cust_cvs_stemComment
5 
*cust_cvs_resprout
6 
*entry_sortOrder
inputs/CVS/stemLocation/header.csv
1 
STEMLOCATION_ID,STEMCOUNT_ID,stemCode,stemXPosition,stemYPosition,stemHealth,dba_src_ID,cust_cvs_stemSource,cust_cvs_stemComment,cust_cvs_resprout,entry_sortOrder
inputs/CVS/stemLocation/map.csv
1 
CVS,VegCore,Filter,Comments
2 
STEMLOCATION_ID,stemID,,
3 
STEMLOCATION_ID,individualID,,
4 
STEMCOUNT_ID,aggregateOccurrenceID,,
5 
stemCode,authorStemCode,,
6 
stemXPosition,organismX_m,,
7 
stemYPosition,organismY_m,,
8 
stemHealth,*stemHealth,,
9 
dba_src_ID,*dba_src_ID,,
10 
cust_cvs_stemSource,*cust_cvs_stemSource,,
11 
cust_cvs_stemComment,*cust_cvs_stemComment,,
12 
cust_cvs_resprout,*cust_cvs_resprout,,
13 
entry_sortOrder,*entry_sortOrder,,
inputs/CVS/stemLocation/test.xml.ref
1 
Put template:
2 
<VegBIEN>
3 
    <_setDefault id="-1">
4 
        <source_id><source><shortname>CVS</shortname></source></source_id>
5 
        <path>
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            <_simplifyPath>
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                <next>parent_id</next>
8 
                <path>
9 
                    <location>
10 
                        <locationevent>
11 
                            <taxonoccurrence>
12 
                                <aggregateoccurrence>
13 
                                    <plantobservation>
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                                        <sourceaccessioncode>$STEMLOCATION_ID</sourceaccessioncode>
15 
                                        <stemobservation>
16 
                                            <authorstemcode>$stemCode</authorstemcode>
17 
                                            <sourceaccessioncode>$STEMLOCATION_ID</sourceaccessioncode>
18 
                                            <xposition_m>$stemXPosition</xposition_m>
19 
                                            <yposition_m>$stemYPosition</yposition_m>
20 
                                        </stemobservation>
21 
                                    </plantobservation>
22 
                                    <sourceaccessioncode>$STEMCOUNT_ID</sourceaccessioncode>
23 
                                </aggregateoccurrence>
24 
                            </taxonoccurrence>
25 
                        </locationevent>
26 
                    </location>
27 
                </path>
28 
            </_simplifyPath>
29 
        </path>
30 
    </_setDefault>
31 
</VegBIEN>
32 
Inserted 0 new rows into database
inputs/CVS/stemLocation/VegBIEN.csv
1 
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
2 
STEMLOCATION_ID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
3 
STEMLOCATION_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,
4 
stemCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode,
5 
STEMLOCATION_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/sourceaccessioncode,
6 
stemXPosition,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,
7 
stemYPosition,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,
8 
STEMCOUNT_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/sourceaccessioncode,
9 
STEMLOCATION_ID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
10 
STEMCOUNT_ID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists",
11 
STEMLOCATION_ID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else",
12 
cust_cvs_resprout,,** No join mapping for *cust_cvs_resprout **
13 
cust_cvs_stemComment,,** No join mapping for *cust_cvs_stemComment **
14 
cust_cvs_stemSource,,** No join mapping for *cust_cvs_stemSource **
15 
dba_src_ID,,** No join mapping for *dba_src_ID **
16 
entry_sortOrder,,** No join mapping for *entry_sortOrder **
17 
stemHealth,,** No join mapping for *stemHealth **
inputs/CVS/import_order.txt
3 3 
observation_
4 4 
taxonObservation_
5 5 
stemCount_
6 
stemLocation
6 
stemLocation_
inputs/CVS/cvs.~.clean_up.sql
13 13 
ALTER TABLE "stemCount" RENAME "dba_src_ID" TO "stemCount_dba_src_ID";
14 14 
ALTER TABLE "stemCount" RENAME "entry_herbLineID" TO "stemCount_entry_herbLineID";
15 15 
ALTER TABLE "stemCount" RENAME "entry_treeLineID" TO "stemCount_entry_treeLineID";
16 
ALTER TABLE "stemCount" RENAME "entry_sortOrder" TO "stemCount_entry_sortOrder";
17 
ALTER TABLE "stemLocation" RENAME "entry_sortOrder" TO "stemLocation_entry_sortOrder";
16 18 
ALTER TABLE "taxonInterpretation" RENAME "PARTY_ID" TO "taxonInterpretation_PARTY_ID";
17 19 
ALTER TABLE "taxonInterpretation" RENAME "PLANTNAME_ID" TO "taxonInterpretation_PLANTNAME_ID";
18 20 
ALTER TABLE "taxonInterpretation" RENAME "dba_src_ID" TO "taxonInterpretation_dba_src_ID";
inputs/CVS/stemLocation_/create.sql
1 
SELECT *
2 
FROM "stemCount"
3 
LEFT JOIN "stemLocation" USING ("STEMCOUNT_ID")
4 
;
inputs/CVS/stemLocation_/header.csv
1 
STEMCOUNT_ID,taxonImportance_ID,stemDiameter,stemDiameterAccuracy,stemHeight,stemHeightAccuracy,stemCount,stemTaxonArea,stemCount_dba_src_ID,cust_cvs_ddh,cust_cvs_ddhAccuracy,cust_cvs_isPlanted,cust_cvs_subsamplingFactor,stemCount_entry_herbLineID,stemCount_entry_treeLineID,entry_recordCount,stemCount_entry_sortOrder,STEMLOCATION_ID,stemCode,stemXPosition,stemYPosition,stemHealth,dba_src_ID,cust_cvs_stemSource,cust_cvs_stemComment,cust_cvs_resprout,stemLocation_entry_sortOrder
inputs/CVS/stemLocation_/map.csv
1 
CVS,VegCore,Filter,Comments
2 
STEMCOUNT_ID,aggregateOccurrenceID,,
3 
taxonImportance_ID,OMIT,,Omitted because STEMCOUNT_ID is more specific
4 
stemDiameter,diameterBreastHeight_cm,,
5 
stemDiameterAccuracy,*stemdiameteraccuracy,,
6 
stemHeight,height_m,,
7 
stemHeightAccuracy,*stemheightaccuracy,,
8 
stemCount,individualCount,,
9 
stemTaxonArea,*stemtaxonarea,,
10 
stemCount_dba_src_ID,*stemCount_dba_src_ID,,
11 
cust_cvs_ddh,*cust_cvs_ddh,,
12 
cust_cvs_ddhAccuracy,*cust_cvs_ddhAccuracy,,
13 
cust_cvs_isPlanted,*cust_cvs_isPlanted,,
14 
cust_cvs_subsamplingFactor,*cust_cvs_subsamplingFactor,,
15 
stemCount_entry_herbLineID,*stemCount_entry_herbLineID,,
16 
stemCount_entry_treeLineID,*stemCount_entry_treeLineID,,
17 
entry_recordCount,*entry_recordCount,,
18 
stemCount_entry_sortOrder,*stemCount_entry_sortOrder,,
19 
STEMLOCATION_ID,stemID,,
20 
STEMLOCATION_ID,individualID,,
21 
stemCode,authorStemCode,,
22 
stemXPosition,organismX_m,,
23 
stemYPosition,organismY_m,,
24 
stemHealth,*stemhealth,,
25 
dba_src_ID,*dba_src_ID,,
26 
cust_cvs_stemSource,*cust_cvs_stemSource,,
27 
cust_cvs_stemComment,*cust_cvs_stemComment,,
28 
cust_cvs_resprout,*cust_cvs_resprout,,
29 
stemLocation_entry_sortOrder,*stemLocation_entry_sortOrder,,
inputs/CVS/stemLocation_/VegBIEN.csv
1 
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
2 
STEMLOCATION_ID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
3 
stemCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,
4 
STEMLOCATION_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,
5 
stemCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode,
6 
stemDiameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,
7 
stemHeight,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m,
8 
STEMLOCATION_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/sourceaccessioncode,
9 
stemXPosition,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,
10 
stemYPosition,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,
11 
STEMCOUNT_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/sourceaccessioncode,
12 
STEMLOCATION_ID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
13 
STEMCOUNT_ID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists",
14 
STEMLOCATION_ID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else",
15 
cust_cvs_ddh,,** No join mapping for *cust_cvs_ddh **
16 
cust_cvs_ddhAccuracy,,** No join mapping for *cust_cvs_ddhAccuracy **
17 
cust_cvs_isPlanted,,** No join mapping for *cust_cvs_isPlanted **
18 
cust_cvs_resprout,,** No join mapping for *cust_cvs_resprout **
19 
cust_cvs_stemComment,,** No join mapping for *cust_cvs_stemComment **
20 
cust_cvs_stemSource,,** No join mapping for *cust_cvs_stemSource **
21 
cust_cvs_subsamplingFactor,,** No join mapping for *cust_cvs_subsamplingFactor **
22 
dba_src_ID,,** No join mapping for *dba_src_ID **
23 
entry_recordCount,,** No join mapping for *entry_recordCount **
24 
stemCount_dba_src_ID,,** No join mapping for *stemCount_dba_src_ID **
25 
stemCount_entry_herbLineID,,** No join mapping for *stemCount_entry_herbLineID **
26 
stemCount_entry_sortOrder,,** No join mapping for *stemCount_entry_sortOrder **
27 
stemCount_entry_treeLineID,,** No join mapping for *stemCount_entry_treeLineID **
28 
stemDiameterAccuracy,,** No join mapping for *stemdiameteraccuracy **
29 
stemHealth,,** No join mapping for *stemhealth **
30 
stemHeightAccuracy,,** No join mapping for *stemheightaccuracy **
31 
stemLocation_entry_sortOrder,,** No join mapping for *stemLocation_entry_sortOrder **
32 
stemTaxonArea,,** No join mapping for *stemtaxonarea **
33 
taxonImportance_ID,,** No non-empty join mapping for OMIT ** Omitted because STEMCOUNT_ID is more specific
inputs/CVS/stemLocation_/test.xml.ref
1 
Put template:
2 
<VegBIEN>
3 
    <_setDefault id="-1">
4 
        <source_id><source><shortname>CVS</shortname></source></source_id>
5 
        <path>
6 
            <_simplifyPath>
7 
                <next>parent_id</next>
8 
                <path>
9 
                    <location>
10 
                        <locationevent>
11 
                            <taxonoccurrence>
12 
                                <aggregateoccurrence>
13 
                                    <count>$stemCount</count>
14 
                                    <plantobservation>
15 
                                        <sourceaccessioncode>$STEMLOCATION_ID</sourceaccessioncode>
16 
                                        <stemobservation>
17 
                                            <authorstemcode>$stemCode</authorstemcode>
18 
                                            <diameterbreastheight_m><_cm_to_m><value>$stemDiameter</value></_cm_to_m></diameterbreastheight_m>
19 
                                            <height_m>$stemHeight</height_m>
20 
                                            <sourceaccessioncode>$STEMLOCATION_ID</sourceaccessioncode>
21 
                                            <xposition_m>$stemXPosition</xposition_m>
22 
                                            <yposition_m>$stemYPosition</yposition_m>
23 
                                        </stemobservation>
24 
                                    </plantobservation>
25 
                                    <sourceaccessioncode>$STEMCOUNT_ID</sourceaccessioncode>
26 
                                </aggregateoccurrence>
27 
                            </taxonoccurrence>
28 
                        </locationevent>
29 
                    </location>
30 
                </path>
31 
            </_simplifyPath>
32 
        </path>
33 
    </_setDefault>
34 
</VegBIEN>
35 
Inserted 7 new rows into database
inputs/CVS/stemLocation_/unmapped_terms.csv
1 
*stemdiameteraccuracy
2 
*stemheightaccuracy
3 
*stemtaxonarea
4 
*stemCount_dba_src_ID
5 
*cust_cvs_ddh
6 
*cust_cvs_ddhAccuracy
7 
*cust_cvs_isPlanted
8 
*cust_cvs_subsamplingFactor
9 
*stemCount_entry_herbLineID
10 
*stemCount_entry_treeLineID
11 
*entry_recordCount
12 
*stemCount_entry_sortOrder
13 
*stemhealth
14 
*dba_src_ID
15 
*cust_cvs_stemSource
16 
*cust_cvs_stemComment
17 
*cust_cvs_resprout
18 
*stemLocation_entry_sortOrder
inputs/CVS/stemLocation_/new_terms.csv
1 
STEMCOUNT_ID,aggregateOccurrenceID,,
2 
taxonImportance_ID,OMIT,,Omitted because STEMCOUNT_ID is more specific
3 
stemDiameter,diameterBreastHeight_cm,,
4 
stemHeight,height_m,,
5 
STEMLOCATION_ID,stemID,,
6 
STEMLOCATION_ID,individualID,,
7 
stemCode,authorStemCode,,
8 
stemXPosition,organismX_m,,
9 
stemYPosition,organismY_m,,

Also available in: Unified diff