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Revision 475

VegBIEN: Renamed stemobservation.stemcode to authorcode

View differences:

test/accepted_output/SALVIAS.organisms.VegBIEN.xml
24 24
            <individualplant>
25 25
                <stemdiameter>662</stemdiameter>
26 26
                <stemobservation>
27
                    <stemcode>8</stemcode>
27
                    <authorcode>8</authorcode>
28 28
                </stemobservation>
29 29
            </individualplant>
30 30
        </collectiveobservation>
......
304 304
            <individualplant>
305 305
                <stemdiameter>215</stemdiameter>
306 306
                <stemobservation>
307
                    <stemcode>91</stemcode>
307
                    <authorcode>91</authorcode>
308 308
                </stemobservation>
309 309
            </individualplant>
310 310
        </collectiveobservation>
inputs/SALVIAS/map.VegBIEN.organisms.csv
6 6
intercept_cm,"/collectiveobservation/definedvalue[*_id/userdefined[tablename=collectiveobservation,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
7 7
temp_dbh,/collectiveobservation/individualplant/stemdiameter,
8 8
height_m,/collectiveobservation/individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
9
tag2,/collectiveobservation/individualplant/stemobservation/authorcode/_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."
10
tag1,/collectiveobservation/individualplant/stemobservation/authorcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
9 11
ht_first_branch_m,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
10
tag2,/collectiveobservation/individualplant/stemobservation/stemcode/_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."
11
tag1,/collectiveobservation/individualplant/stemobservation/stemcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
12 12
x_position,/collectiveobservation/individualplant/stemobservation/stemxposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
13 13
y_position,/collectiveobservation/individualplant/stemobservation/stemyposition,Brad: See comment above for x_position
14 14
census_date,/taxondetermination[role_id/aux_role/rolecode=collector]/collectiondate/_date/date,
schemas/vegbien.sql
2225 2225
CREATE TABLE stemobservation (
2226 2226
    stemobservation_id integer NOT NULL,
2227 2227
    individualplant_id integer NOT NULL,
2228
    stemcode character varying(20),
2228
    authorcode character varying(20),
2229 2229
    stemxposition double precision,
2230 2230
    stemyposition double precision,
2231 2231
    stemhealth character varying(50),
......
4179 4179
--
4180 4180

  
4181 4181
ALTER TABLE ONLY stemobservation
4182
    ADD CONSTRAINT stemobservation_keys UNIQUE (individualplant_id, stemcode);
4182
    ADD CONSTRAINT stemobservation_keys UNIQUE (individualplant_id, authorcode);
4183 4183

  
4184 4184

  
4185 4185
--
mappings/SALVIAS_db-VegBIEN.organisms.csv
6 6
intercept_cm,"/collectiveobservation/definedvalue[*_id/userdefined[tablename=collectiveobservation,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
7 7
temp_dbh,/collectiveobservation/individualplant/stemdiameter,
8 8
height_m,/collectiveobservation/individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
9
tag2,/collectiveobservation/individualplant/stemobservation/authorcode/_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."
10
tag1,/collectiveobservation/individualplant/stemobservation/authorcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
9 11
ht_first_branch_m,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
10
tag2,/collectiveobservation/individualplant/stemobservation/stemcode/_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."
11
tag1,/collectiveobservation/individualplant/stemobservation/stemcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
12 12
x_position,/collectiveobservation/individualplant/stemobservation/stemxposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
13 13
y_position,/collectiveobservation/individualplant/stemobservation/stemyposition,Brad: See comment above for x_position
14 14
census_date,/taxondetermination[role_id/aux_role/rolecode=collector]/collectiondate/_date/date,
mappings/VegX-VegBIEN.organisms.csv
56 56
/diameterBaseDistance[baseDistance=1.37]/diameter,/collectiveobservation/individualplant/stemdiameter
57 57
/height,/collectiveobservation/individualplant/stemheight
58 58
/simpleUserdefined[name=stemHeightM]/value,/collectiveobservation/individualplant/stemheight
59
/*ID->/*s/individualOrganism/identificationLabel,/collectiveobservation/individualplant/stemobservation/authorcode
60
/*ID->/*s/individualOrganism/identificationLabel/_alt/1,/collectiveobservation/individualplant/stemobservation/authorcode/_alt/1
61
/*ID->/*s/individualOrganism/identificationLabel/_alt/2,/collectiveobservation/individualplant/stemobservation/authorcode/_alt/2
59 62
/simpleUserdefined[name=habitat]/value,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=habitat]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
60 63
/simpleUserdefined[name=htFirstBranchM]/value,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
61 64
/simpleUserdefined[name=plantFungusDescription]/value,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=plantFungusDescription]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
......
66 69
/simpleUserdefined[name=stemLianaInfestation]/value,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemLianaInfestation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
67 70
/simpleUserdefined[name=substrate]/value,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=substrate]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
68 71
/simpleUserdefined[name=vegetation]/value,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=vegetation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
69
/*ID->/*s/individualOrganism/identificationLabel,/collectiveobservation/individualplant/stemobservation/stemcode
70
/*ID->/*s/individualOrganism/identificationLabel/_alt/1,/collectiveobservation/individualplant/stemobservation/stemcode/_alt/1
71
/*ID->/*s/individualOrganism/identificationLabel/_alt/2,/collectiveobservation/individualplant/stemobservation/stemcode/_alt/2
72 72
/simpleUserdefined[name=xPosition]/value,/collectiveobservation/individualplant/stemobservation/stemxposition
73 73
/simpleUserdefined[name=yPosition]/value,/collectiveobservation/individualplant/stemobservation/stemyposition
74 74
/simpleUserdefined[name=collectionDate]/value,/taxondetermination[role_id/aux_role/rolecode=collector]/collectiondate
mappings/for_review/SALVIAS_db-VegBIEN.organisms.csv
6 6
intercept_cm,"//collectiveobservation/definedvalue[*_id/userdefined[tablename=collectiveobservation,userdefinedname=interceptCm]]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
7 7
temp_dbh,//individualplant/stemdiameter,
8 8
height_m,//individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
9
tag2,//stemobservation/authorcode/_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."
10
tag1,//stemobservation/authorcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
9 11
ht_first_branch_m,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
10
tag2,//stemobservation/stemcode/_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."
11
tag1,//stemobservation/stemcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
12 12
x_position,//stemobservation/stemxposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
13 13
y_position,//stemobservation/stemyposition,Brad: See comment above for x_position
14 14
census_date,/taxondetermination[rolecode=collector]/collectiondate/_date/date,
mappings/for_review/VegX-VegBIEN.organisms.csv
56 56
/diameterBaseDistance[baseDistance=1.37]/diameter,//individualplant/stemdiameter
57 57
/height,//individualplant/stemheight
58 58
/simpleUserdefined[name=stemHeightM]/value,//individualplant/stemheight
59
//individualOrganism/identificationLabel,//stemobservation/authorcode
60
//individualOrganism/identificationLabel/_alt/1,//stemobservation/authorcode/_alt/1
61
//individualOrganism/identificationLabel/_alt/2,//stemobservation/authorcode/_alt/2
59 62
/simpleUserdefined[name=habitat]/value,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=habitat]]/definedvalue"
60 63
/simpleUserdefined[name=htFirstBranchM]/value,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]]/definedvalue"
61 64
/simpleUserdefined[name=plantFungusDescription]/value,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=plantFungusDescription]]/definedvalue"
......
66 69
/simpleUserdefined[name=stemLianaInfestation]/value,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemLianaInfestation]]/definedvalue"
67 70
/simpleUserdefined[name=substrate]/value,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=substrate]]/definedvalue"
68 71
/simpleUserdefined[name=vegetation]/value,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=vegetation]]/definedvalue"
69
//individualOrganism/identificationLabel,//stemobservation/stemcode
70
//individualOrganism/identificationLabel/_alt/1,//stemobservation/stemcode/_alt/1
71
//individualOrganism/identificationLabel/_alt/2,//stemobservation/stemcode/_alt/2
72 72
/simpleUserdefined[name=xPosition]/value,//stemobservation/stemxposition
73 73
/simpleUserdefined[name=yPosition]/value,//stemobservation/stemyposition
74 74
/simpleUserdefined[name=collectionDate]/value,/taxondetermination[rolecode=collector]/collectiondate
mappings/for_review/SALVIAS-VegBIEN.organisms.csv
8 8
stem_dbh,//individualplant/stemdiameter,
9 9
height_m,//individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
10 10
stem_height_m,//individualplant/stemheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
11
stem_tag1,//stemobservation/authorcode,"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."
12
stem_tag2,//stemobservation/authorcode,Brad: see above
13
tag2,//stemobservation/authorcode/_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."
14
tag1,//stemobservation/authorcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
11 15
ht_first_branch_m,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
12 16
basal_diam,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemBasalDiameter]]/definedvalue",
13 17
stem_canopy_form,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyForm]]/definedvalue",Brad: Should also be userDefined for VegBank. 
14 18
stem_canopy_position,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyPosition]]/definedvalue",Brad: Should also be userDefined for VegBank. 
15 19
stem_height_first_branch_m,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemHeightFirstBranchM]]/definedvalue","Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
16 20
stem_liana_infestation,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemLianaInfestation]]/definedvalue",Brad: Should also be userDefined for VegBank. 
17
stem_tag1,//stemobservation/stemcode,"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."
18
stem_tag2,//stemobservation/stemcode,Brad: see above
19
tag2,//stemobservation/stemcode/_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."
20
tag1,//stemobservation/stemcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
21 21
x_position,//stemobservation/stemxposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
22 22
y_position,//stemobservation/stemyposition,Brad: See comment above for x_position
23 23
coll_number,/taxondetermination[rolecode=collector]/collectionnumber,Brad: Incorrect. Map instead as for voucher_string
mappings/SALVIAS-VegBIEN.organisms.csv
8 8
stem_dbh,/collectiveobservation/individualplant/stemdiameter,
9 9
height_m,/collectiveobservation/individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
10 10
stem_height_m,/collectiveobservation/individualplant/stemheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
11
stem_tag1,/collectiveobservation/individualplant/stemobservation/authorcode,"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."
12
stem_tag2,/collectiveobservation/individualplant/stemobservation/authorcode,Brad: see above
13
tag2,/collectiveobservation/individualplant/stemobservation/authorcode/_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."
14
tag1,/collectiveobservation/individualplant/stemobservation/authorcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
11 15
ht_first_branch_m,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
12 16
basal_diam,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemBasalDiameter]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",
13 17
stem_canopy_form,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyForm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. 
14 18
stem_canopy_position,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyPosition]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. 
15 19
stem_height_first_branch_m,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemHeightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
16 20
stem_liana_infestation,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemLianaInfestation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. 
17
stem_tag1,/collectiveobservation/individualplant/stemobservation/stemcode,"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."
18
stem_tag2,/collectiveobservation/individualplant/stemobservation/stemcode,Brad: see above
19
tag2,/collectiveobservation/individualplant/stemobservation/stemcode/_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."
20
tag1,/collectiveobservation/individualplant/stemobservation/stemcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
21 21
x_position,/collectiveobservation/individualplant/stemobservation/stemxposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
22 22
y_position,/collectiveobservation/individualplant/stemobservation/stemyposition,Brad: See comment above for x_position
23 23
coll_number,/taxondetermination[role_id/aux_role/rolecode=collector]/collectionnumber,Brad: Incorrect. Map instead as for voucher_string

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