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Revision 4110

Added by Aaron Marcuse-Kubitza over 12 years ago

inputs: Renamed stems table to 2.stems so import order would be inherent in the dir name, using steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV_subfolders#Rename-subfolders-with-import-order>

View differences:

inputs/SALVIAS/test/import.stems.xml.ref
1 
Put template:
2 
<VegBIEN>
3 
    <location id="-1">
4 
        <locationevent>
5 
            <taxonoccurrence>
6 
                <aggregateoccurrence>
7 
                    <plantobservation>
8 
                        <sourceaccessioncode>$PlotObsID</sourceaccessioncode>
9 
                        <stemcount>$NoInd</stemcount>
10 
                        <stemobservation>
11 
                            <basaldiameter>$basal_diam</basaldiameter>
12 
                            <definedvalue fkey="tablerecord_id">
13 
                                <userdefined_id>
14 
                                    <userdefined>
15 
                                        <tablename>stemobservation</tablename>
16 
                                        <userdefinedname>canopyForm</userdefinedname>
17 
                                    </userdefined>
18 
                                </userdefined_id>
19 
                                <definedvalue>$stem_canopy_form</definedvalue>
20 
                            </definedvalue>
21 
                            <definedvalue fkey="tablerecord_id">
22 
                                <userdefined_id>
23 
                                    <userdefined>
24 
                                        <tablename>stemobservation</tablename>
25 
                                        <userdefinedname>canopyPosition</userdefinedname>
26 
                                    </userdefined>
27 
                                </userdefined_id>
28 
                                <definedvalue>$stem_canopy_position</definedvalue>
29 
                            </definedvalue>
30 
                            <definedvalue fkey="tablerecord_id">
31 
                                <userdefined_id>
32 
                                    <userdefined>
33 
                                        <tablename>stemobservation</tablename>
34 
                                        <userdefinedname>gentryDiameter</userdefinedname>
35 
                                    </userdefined>
36 
                                </userdefined_id>
37 
                                <definedvalue>$gentry_dbh</definedvalue>
38 
                            </definedvalue>
39 
                            <definedvalue fkey="tablerecord_id">
40 
                                <userdefined_id>
41 
                                    <userdefined>
42 
                                        <tablename>stemobservation</tablename>
43 
                                        <userdefinedname>lianaInfestation</userdefinedname>
44 
                                    </userdefined>
45 
                                </userdefined_id>
46 
                                <definedvalue>$stem_liana_infestation</definedvalue>
47 
                            </definedvalue>
48 
                            <definedvalue fkey="tablerecord_id">
49 
                                <userdefined_id>
50 
                                    <userdefined>
51 
                                        <tablename>stemobservation</tablename>
52 
                                        <userdefinedname>notes</userdefinedname>
53 
                                    </userdefined>
54 
                                </userdefined_id>
55 
                                <definedvalue>$stem_notes</definedvalue>
56 
                            </definedvalue>
57 
                            <diameterbreastheight>$stem_dbh</diameterbreastheight>
58 
                            <height>$stem_height_m</height>
59 
                            <heightfirstbranch>$stem_height_first_branch_m</heightfirstbranch>
60 
                            <stemtag>
61 
                                <iscurrent>
62 
                                    <_alt>
63 
                                        <2>true</2>
64 
                                        <1>false</1>
65 
                                    </_alt>
66 
                                </iscurrent>
67 
                                <tag>$stem_tag1</tag>
68 
                            </stemtag>
69 
                            <stemtag>
70 
                                <iscurrent>true</iscurrent>
71 
                                <tag>$stem_tag2</tag>
72 
                            </stemtag>
73 
                        </stemobservation>
74 
                    </plantobservation>
75 
                </aggregateoccurrence>
76 
                <sourceaccessioncode>$PlotObsID</sourceaccessioncode>
77 
            </taxonoccurrence>
78 
        </locationevent>
79 
    </location>
80 
</VegBIEN>
81 
Inserted 24 new rows into database
inputs/SALVIAS/maps/src.stems.csv
1 
SALVIAS,Veg+,Comments
2 
stem_id,,
3 
origrecord_id_stems,,
4 
PlotObsID,,
5 
NoInd,,
6 
basal_diam,,
7 
stem_dbh,,
8 
gentry_dbh,,
9 
stem_notes,,
10 
stem_tag1,,
11 
stem_tag2,,
12 
stem_height_m,,
13 
stem_height_first_branch_m,,
14 
stem_canopy_form,,
15 
stem_canopy_position,,
16 
stem_liana_infestation,,
17 
tmp_del,,
inputs/SALVIAS/maps/Veg+.stems.full.csv
1 
SALVIAS,Veg+,Comments
2 
basal_diam,basalDiameter,
3 
stem_canopy_form,canopyForm,
4 
stem_canopy_position,canopyPosition,
5 
stem_dbh,diameterBreastHeight,
6 
gentry_dbh,diameterBreastHeightGentry,
7 
stem_height_m,height,
8 
stem_height_first_branch_m,heightFirstBranch,
9 
PlotObsID,individualID,
10 
stem_liana_infestation,lianaInfestation,
11 
stem_tag2,previousTag,
12 
NoInd,stemCount,
13 
stem_notes,stemNotes,
14 
stem_tag1,tag,
15 
origrecord_id_stems,,
16 
stem_id,,
17 
tmp_del,,
inputs/SALVIAS/maps/VegBIEN.stems.csv
1 
SALVIAS,VegBIEN:,Comments
2 
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,
3 
NoInd,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount,
4 
basal_diam,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter,
5 
stem_canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue",
6 
stem_canopy_position,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue",
7 
gentry_dbh,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=gentryDiameter]]:[@fkey=tablerecord_id]/definedvalue",
8 
stem_liana_infestation,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue",
9 
stem_notes,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=notes]]:[@fkey=tablerecord_id]/definedvalue",
10 
stem_dbh,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight,
11 
stem_height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height,
12 
stem_height_first_branch_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch,
13 
stem_tag1,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2
14 
stem_tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag,
15 
PlotObsID,/location/locationevent/taxonoccurrence/sourceaccessioncode,
16 
origrecord_id_stems,,** No input mapping for origrecord_id_stems **
17 
stem_id,,** No input mapping for stem_id **
18 
tmp_del,,** No input mapping for tmp_del **
inputs/SALVIAS/maps/Veg+.stems.csv
1 
SALVIAS,Veg+,Comments
2 
stem_id,,
3 
origrecord_id_stems,,
4 
PlotObsID,individualID,
5 
NoInd,stemCount,
6 
basal_diam,basalDiameter,
7 
stem_dbh,diameterBreastHeight,
8 
gentry_dbh,diameterBreastHeightGentry,
9 
stem_notes,stemNotes,
10 
stem_tag1,tag,
11 
stem_tag2,previousTag,
12 
stem_height_m,height,
13 
stem_height_first_branch_m,heightFirstBranch,
14 
stem_canopy_form,canopyForm,
15 
stem_canopy_position,canopyPosition,
16 
stem_liana_infestation,lianaInfestation,
17 
tmp_del,,
inputs/SALVIAS/test/import.2.stems.xml.ref
1 
Put template:
2 
<VegBIEN>
3 
    <location id="-1">
4 
        <locationevent>
5 
            <taxonoccurrence>
6 
                <aggregateoccurrence>
7 
                    <plantobservation>
8 
                        <sourceaccessioncode>$PlotObsID</sourceaccessioncode>
9 
                        <stemcount>$NoInd</stemcount>
10 
                        <stemobservation>
11 
                            <basaldiameter>$basal_diam</basaldiameter>
12 
                            <definedvalue fkey="tablerecord_id">
13 
                                <userdefined_id>
14 
                                    <userdefined>
15 
                                        <tablename>stemobservation</tablename>
16 
                                        <userdefinedname>canopyForm</userdefinedname>
17 
                                    </userdefined>
18 
                                </userdefined_id>
19 
                                <definedvalue>$stem_canopy_form</definedvalue>
20 
                            </definedvalue>
21 
                            <definedvalue fkey="tablerecord_id">
22 
                                <userdefined_id>
23 
                                    <userdefined>
24 
                                        <tablename>stemobservation</tablename>
25 
                                        <userdefinedname>canopyPosition</userdefinedname>
26 
                                    </userdefined>
27 
                                </userdefined_id>
28 
                                <definedvalue>$stem_canopy_position</definedvalue>
29 
                            </definedvalue>
30 
                            <definedvalue fkey="tablerecord_id">
31 
                                <userdefined_id>
32 
                                    <userdefined>
33 
                                        <tablename>stemobservation</tablename>
34 
                                        <userdefinedname>gentryDiameter</userdefinedname>
35 
                                    </userdefined>
36 
                                </userdefined_id>
37 
                                <definedvalue>$gentry_dbh</definedvalue>
38 
                            </definedvalue>
39 
                            <definedvalue fkey="tablerecord_id">
40 
                                <userdefined_id>
41 
                                    <userdefined>
42 
                                        <tablename>stemobservation</tablename>
43 
                                        <userdefinedname>lianaInfestation</userdefinedname>
44 
                                    </userdefined>
45 
                                </userdefined_id>
46 
                                <definedvalue>$stem_liana_infestation</definedvalue>
47 
                            </definedvalue>
48 
                            <definedvalue fkey="tablerecord_id">
49 
                                <userdefined_id>
50 
                                    <userdefined>
51 
                                        <tablename>stemobservation</tablename>
52 
                                        <userdefinedname>notes</userdefinedname>
53 
                                    </userdefined>
54 
                                </userdefined_id>
55 
                                <definedvalue>$stem_notes</definedvalue>
56 
                            </definedvalue>
57 
                            <diameterbreastheight>$stem_dbh</diameterbreastheight>
58 
                            <height>$stem_height_m</height>
59 
                            <heightfirstbranch>$stem_height_first_branch_m</heightfirstbranch>
60 
                            <stemtag>
61 
                                <iscurrent>
62 
                                    <_alt>
63 
                                        <2>true</2>
64 
                                        <1>false</1>
65 
                                    </_alt>
66 
                                </iscurrent>
67 
                                <tag>$stem_tag1</tag>
68 
                            </stemtag>
69 
                            <stemtag>
70 
                                <iscurrent>true</iscurrent>
71 
                                <tag>$stem_tag2</tag>
72 
                            </stemtag>
73 
                        </stemobservation>
74 
                    </plantobservation>
75 
                </aggregateoccurrence>
76 
                <sourceaccessioncode>$PlotObsID</sourceaccessioncode>
77 
            </taxonoccurrence>
78 
        </locationevent>
79 
    </location>
80 
</VegBIEN>
81 
Inserted 24 new rows into database
inputs/SALVIAS/maps/Veg+.2.stems.csv
1 
SALVIAS,Veg+,Comments
2 
stem_id,,
3 
origrecord_id_stems,,
4 
PlotObsID,individualID,
5 
NoInd,stemCount,
6 
basal_diam,basalDiameter,
7 
stem_dbh,diameterBreastHeight,
8 
gentry_dbh,diameterBreastHeightGentry,
9 
stem_notes,stemNotes,
10 
stem_tag1,tag,
11 
stem_tag2,previousTag,
12 
stem_height_m,height,
13 
stem_height_first_branch_m,heightFirstBranch,
14 
stem_canopy_form,canopyForm,
15 
stem_canopy_position,canopyPosition,
16 
stem_liana_infestation,lianaInfestation,
17 
tmp_del,,
inputs/SALVIAS/maps/Veg+.2.stems.full.csv
1 
SALVIAS,Veg+,Comments
2 
basal_diam,basalDiameter,
3 
stem_canopy_form,canopyForm,
4 
stem_canopy_position,canopyPosition,
5 
stem_dbh,diameterBreastHeight,
6 
gentry_dbh,diameterBreastHeightGentry,
7 
stem_height_m,height,
8 
stem_height_first_branch_m,heightFirstBranch,
9 
PlotObsID,individualID,
10 
stem_liana_infestation,lianaInfestation,
11 
stem_tag2,previousTag,
12 
NoInd,stemCount,
13 
stem_notes,stemNotes,
14 
stem_tag1,tag,
15 
origrecord_id_stems,,
16 
stem_id,,
17 
tmp_del,,
inputs/SALVIAS/maps/VegBIEN.2.stems.csv
1 
SALVIAS,VegBIEN:,Comments
2 
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,
3 
NoInd,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount,
4 
basal_diam,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter,
5 
stem_canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue",
6 
stem_canopy_position,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue",
7 
gentry_dbh,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=gentryDiameter]]:[@fkey=tablerecord_id]/definedvalue",
8 
stem_liana_infestation,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue",
9 
stem_notes,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=notes]]:[@fkey=tablerecord_id]/definedvalue",
10 
stem_dbh,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight,
11 
stem_height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height,
12 
stem_height_first_branch_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch,
13 
stem_tag1,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2
14 
stem_tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag,
15 
PlotObsID,/location/locationevent/taxonoccurrence/sourceaccessioncode,
16 
origrecord_id_stems,,** No input mapping for origrecord_id_stems **
17 
stem_id,,** No input mapping for stem_id **
18 
tmp_del,,** No input mapping for tmp_del **
inputs/SALVIAS/maps/src.2.stems.csv
1 
SALVIAS,Veg+,Comments
2 
stem_id,,
3 
origrecord_id_stems,,
4 
PlotObsID,,
5 
NoInd,,
6 
basal_diam,,
7 
stem_dbh,,
8 
gentry_dbh,,
9 
stem_notes,,
10 
stem_tag1,,
11 
stem_tag2,,
12 
stem_height_m,,
13 
stem_height_first_branch_m,,
14 
stem_canopy_form,,
15 
stem_canopy_position,,
16 
stem_liana_infestation,,
17 
tmp_del,,
inputs/input.Makefile
13 13 
use_staged ?= $(by_col)
14 14 

  		




  15
  15
  
    
# Makefile


  		




  16
  
  
    
tablesSort ?= 0.plots 1.organisms stems specimens


  		




  
  16
  
    
tablesSort ?= 0.plots 1.organisms 2.stems specimens


  		




  17
  17
  
    
exts ?= csv tsv txt xml


  		




  18
  18
  
    
test_n ?= 2


  		




  19
  19
  
    

  		












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