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Revision 10425

Added by Aaron Marcuse-Kubitza over 11 years ago

bugfix: inputs/*/*/map.csv for specimen tables: remapped eventDate,day,month,year to *Collected, because a general date always applies to the observation itself rather than to any parent event (specimens don't have a parent event)

View differences:

inputs/MO/Specimen/new_terms.csv
11 11 
lower,county,,
12 12 
minlatdecdeg,decimalLatitude,,
13 13 
minlongdecdeg,decimalLongitude,,
14 
minimumday,day,,
15 
minimummonth,month,,
16 
minimumyear,year,,
14 
minimumday,dayCollected,,
15 
minimummonth,monthCollected,,
16 
minimumyear,yearCollected,,
17 17 
description,specimenDescription,,
18 18 
acronyms,specimenHolderInstitutions,,
19 19 
determinationyear,yearIdentified,,
inputs/TRTE/Specimen/map.csv
5 5 
genus,genus,,
6 6 
bibliographicCitation,bibliographicCitation,,
7 7 
verbatimLongitude,verbatimLongitude,,
8 
eventDate,eventDate,,
8 
eventDate,dateCollected,,
9 9 
decimalLongitude,decimalLongitude,,
10 10 
catalogNumber,accessionNumber,,
11 11 
language,language,,
inputs/HVAA/Specimen/map.csv
22 22 
typeStatus,typeStatus,,
23 23 
recordedBy,recordedBy,,
24 24 
recordNumber,collectorNumber,,
25 
eventDate,eventDate,,
26 
year,year,,
27 
month,month,,
28 
day,day,,
25 
eventDate,dateCollected,,
26 
year,yearCollected,,
27 
month,monthCollected,,
28 
day,dayCollected,,
29 29 
startDayOfYear,startDayOfYear,,
30 30 
endDayOfYear,endDayOfYear,,
31 31 
verbatimEventDate,verbatimEventDate,,
inputs/HVAA/Specimen/VegBIEN.csv
20 20 
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1,
21 21 
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3,
22 22 
samplingProtocol,/location/locationevent/*_id/method/name,
23 
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists",
24 
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value",
25 
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value",
26 
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value,
27 
eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value,
28 23 
dateIdentified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/1/_dateRangeStart/value",
29 24 
taxonRemarks,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/notes",
30 25 
identificationQualifier,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/taxonfit",
26 
eventDate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1,
27 
day,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
28 
month,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
29 
year,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
31 30 
individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,
32 31 
occurrenceRemarks,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1/_merge/1,
33 32 
dynamicProperties,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1/_merge/2,Contains occurrenceRemarks data
......
102 101 
associatedTaxa,,** No join mapping for associatedTaxa **
103 102 
basisOfRecord,,** No join mapping for basisOfRecord **
104 103 
coordinatePrecision,,** No non-empty join mapping for UNUSED#coordinatePrecision **
105 
day,,** No join mapping for day **
106 104 
disposition,,** No join mapping for disposition **
107 105 
endDayOfYear,,** No join mapping for endDayOfYear **
108 106 
fieldNotes,,** No non-empty join mapping for UNUSED#fieldNotes **
......
117 115 
language,,** No join mapping for language **
118 116 
lifeStage,,** No join mapping for lifeStage **
119 117 
modified,,** No join mapping for modified **
120 
month,,** No join mapping for month **
121 118 
municipality,,** No join mapping for municipality **
122 119 
otherCatalogNumbers,,** No join mapping for otherCatalogNumbers **
123 120 
ownerInstitutionCode,,** No join mapping for specimenOwner **
......
128 125 
typeStatus,,** No join mapping for typeStatus **
129 126 
verbatimCoordinateSystem,,** No join mapping for coordinateUnits **
130 127 
verbatimEventDate,,** No join mapping for verbatimEventDate **
131 
year,,** No join mapping for year **
inputs/HVAA/Specimen/test.xml.ref
50 50 
                        </iscultivated>
51 51 
                        <locationevent>
52 52 
                            <method_id><method><name>$samplingProtocol</name></method></method_id>
53 
                            <obsenddate><_dateRangeEnd><value>$eventDate</value></_dateRangeEnd></obsenddate>
54 
                            <obsstartdate><_dateRangeStart><value>$eventDate</value></_dateRangeStart></obsstartdate>
55 53 
                            <taxonoccurrence>
56 54 
                                <aggregateoccurrence>
55 
                                    <collectiondate>
56 
                                        <_alt>
57 
                                            <1>$eventDate</1>
58 
                                            <2>
59 
                                                <_date>
60 
                                                    <day>
61 
                                                        <_nullIf>
62 
                                                            <null>0</null>
63 
                                                            <type>float</type>
64 
                                                            <value>$day</value>
65 
                                                        </_nullIf>
66 
                                                    </day>
67 
                                                    <month>
68 
                                                        <_nullIf>
69 
                                                            <null>0</null>
70 
                                                            <type>float</type>
71 
                                                            <value>$month</value>
72 
                                                        </_nullIf>
73 
                                                    </month>
74 
                                                    <year>
75 
                                                        <_nullIf>
76 
                                                            <null>0</null>
77 
                                                            <type>float</type>
78 
                                                            <value>$year</value>
79 
                                                        </_nullIf>
80 
                                                    </year>
81 
                                                </_date>
82 
                                            </2>
83 
                                        </_alt>
84 
                                    </collectiondate>
57 85 
                                    <count>$individualCount</count>
58 86 
                                    <notes>
59 87 
                                        <_merge>
inputs/HVAA/Specimen/unmapped_terms.csv
5 5 
identificationReferences
6 6 
identificationRemarks
7 7 
typeStatus
8 
year
9 
month
10 
day
11 8 
startDayOfYear
12 9 
endDayOfYear
13 10 
verbatimEventDate
inputs/ACAD/Specimen/map.csv
28 28 
identificationRemarks,identificationRemarks,,
29 29 
rightsHolder,dataOwners,,
30 30 
recordNumber,collectorNumber,,
31 
eventDate,eventDate,,
31 
eventDate,dateCollected,,
32 32 
rights,rights,,
33 33 
occurrenceRemarks,occurrenceRemarks,,
34 34 
habitat,habitat,,
inputs/WIN/Specimen/map.csv
14 14 
rights,rights,,
15 15 
occurrenceRemarks,occurrenceRemarks,,
16 16 
verbatimElevation,verbatimElevation,,
17 
eventDate,eventDate,,
17 
eventDate,dateCollected,,
18 18 
recordNumber,collectorNumber,,
19 19 
county,county,,
20 20 
type,type,,
inputs/GBIF/raw_occurrence_record_plants/map.csv
33 33 
county,county,,
34 34 
collector_name,recordedBy,,
35 35 
locality,locality,,
36 
year,year,,
37 
month,month,,
38 
day,day,,
36 
year,yearCollected,,
37 
month,monthCollected,,
38 
day,dayCollected,,
39 39 
basis_of_record,basisOfRecord,,
40 40 
identifier_name,identifiedBy,,
41 41 
identification_date,dateIdentified,,
inputs/GBIF/raw_occurrence_record_plants/new_terms.csv
1 1 
row_num,raw_occurrence_record-row_num,,
2 2 
catalogue_number,accessionNumber,,
3 
author,scientificNameAuthorship,,
3 4 
rank,taxonRank,,
4 5 
order_rank,order,,
5 6 
lat_long_precision,coordinatePrecision_deg,,Tentative
inputs/GBIF/raw_occurrence_record_plants/unmapped_terms.csv
5 5 
coordinatePrecision_deg
6 6 
*altitude_precision
7 7 
*depth_precision
8 
year
9 
month
10 
day
11 8 
basisOfRecord
12 9 
*unit_qualifier
13 10 
*created
inputs/GBIF/map.csv
33 33 
county,county,,
34 34 
collector_name,recordedBy,,
35 35 
locality,locality,,
36 
year,year,,
37 
month,month,,
38 
day,day,,
36 
year,yearCollected,,
37 
month,monthCollected,,
38 
day,dayCollected,,
39 39 
basis_of_record,basisOfRecord,,
40 40 
identifier_name,identifiedBy,,
41 41 
identification_date,dateIdentified,,
inputs/QFA/Specimen/map.csv
40 40 
infraspecificEpithet,infraspecificEpithet,,
41 41 
country,country,,
42 42 
language,language,,
43 
eventDate,eventDate,,
43 
eventDate,dateCollected,,
44 44 
collectionCode,collection,,
45 45 
scientificName,scientificName,,
46 46 
stateProvince,stateProvince,,
inputs/JBM/Specimen/map.csv
26 26 
family,family,,
27 27 
datasetName,dataset,,
28 28 
scientificName,scientificName,,
29 
eventDate,eventDate,,
29 
eventDate,dateCollected,,
30 30 
habitat,habitat,,
31 31 
country,country,,
32 32 
rights,rights,,
inputs/UBC/Specimen/map.csv
26 26 
family,family,,
27 27 
datasetName,dataset,,
28 28 
modified,modified,,
29 
eventDate,eventDate,,
29 
eventDate,dateCollected,,
30 30 
georeferencedDate,georeferencedDate,,
31 31 
georeferenceSources,georeferenceSources,,
32 32 
bibliographicCitation,bibliographicCitation,,
inputs/UBC/Specimen/VegBIEN.csv
15 15 
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
16 16 
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1,
17 17 
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3,
18 
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists",
19 
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value",
20 
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value",
21 
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value,
22 
eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value,
23 18 
dateIdentified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/1/_dateRangeStart/value",
24 19 
taxonRemarks,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/notes",
25 20 
identificationQualifier,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/taxonfit",
21 
eventDate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1,
26 22 
occurrenceRemarks,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1,
27 23 
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2,
28 24 
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
inputs/UBC/Specimen/test.xml.ref
43 43 
                            </_locationnarrative_is_cultivated>
44 44 
                        </iscultivated>
45 45 
                        <locationevent>
46 
                            <obsenddate><_dateRangeEnd><value>$eventDate</value></_dateRangeEnd></obsenddate>
47 
                            <obsstartdate><_dateRangeStart><value>$eventDate</value></_dateRangeStart></obsstartdate>
48 46 
                            <taxonoccurrence>
49 47 
                                <aggregateoccurrence>
48 
                                    <collectiondate>$eventDate</collectiondate>
50 49 
                                    <notes>$occurrenceRemarks</notes>
51 50 
                                    <plantobservation>
52 51 
                                        <authorplantcode>$recordNumber</authorplantcode>
inputs/SpeciesLink/Specimen/map.csv
61 61 
dwc_terms_eventTime,eventTime,,
62 62 
dwc_terms_startDayOfYear,UNUSED#dwc_terms_startDayOfYear,,
63 63 
dwc_terms_endDayOfYear,UNUSED#dwc_terms_endDayOfYear,,
64 
dwc_terms_year,year,,
65 
dwc_terms_month,month,,
66 
dwc_terms_day,day,,
64 
dwc_terms_year,yearCollected,,
65 
dwc_terms_month,monthCollected,,
66 
dwc_terms_day,dayCollected,,
67 67 
dwc_terms_fieldNumber,collectorNumber,/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
68 68 
-----
69 69 
SELECT count(*) FROM ""SpeciesLink"".specimens
inputs/SpeciesLink/Specimen/VegBIEN.csv
57 57 
conceptual_darwin_2003_1_0_MonthIdentified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
58 58 
conceptual_darwin_2003_1_0_YearIdentified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
59 59 
conceptual_darwin_2003_1_0_DayCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
60 
dwc_terms_day,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
60 61 
conceptual_darwin_2003_1_0_MonthCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
62 
dwc_terms_month,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
61 63 
conceptual_darwin_2003_1_0_YearCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
64 
dwc_terms_year,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
62 65 
conceptual_darwin_2003_1_0_IndividualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,
63 66 
dwc_curatorial_IndividualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,
64 67 
dwc_terms_individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,
......
316 319 
dwc_dwcore_DateLastModified,,** No join mapping for modified **
317 320 
dwc_dwcore_DayOfYear,,** No non-empty join mapping for UNUSED#dwc_dwcore_DayOfYear **
318 321 
dwc_terms_basisOfRecord,,** No join mapping for basisOfRecord **
319 
dwc_terms_day,,** No join mapping for day **
320 322 
dwc_terms_endDayOfYear,,** No non-empty join mapping for UNUSED#dwc_terms_endDayOfYear **
321 323 
dwc_terms_eventTime,,** No join mapping for eventTime **
322 
dwc_terms_month,,** No join mapping for month **
323 324 
dwc_terms_otherCatalogNumbers,,** No join mapping for otherCatalogNumbers **
324 325 
dwc_terms_preparations,,** No join mapping for preparations **
325 326 
dwc_terms_startDayOfYear,,** No non-empty join mapping for UNUSED#dwc_terms_startDayOfYear **
326 327 
dwc_terms_typeStatus,,** No join mapping for typeStatus **
327 
dwc_terms_year,,** No join mapping for year **
328 328 
http__purl_org_dc_terms_modified,,** No join mapping for modified **
329 329 
row_num,,** No join mapping for *row_num **
inputs/SpeciesLink/Specimen/test.xml.ref
80 80 
                                                <_nullIf>
81 81 
                                                    <null>0</null>
82 82 
                                                    <type>float</type>
83 
                                                    <value>$conceptual_darwin_2003_1_0_DayCollected</value>
83 
                                                    <value>
84 
                                                        <_alt>
85 
                                                            <0>$conceptual_darwin_2003_1_0_DayCollected</0>
86 
                                                            <1>$dwc_terms_day</1>
87 
                                                        </_alt>
88 
                                                    </value>
84 89 
                                                </_nullIf>
85 90 
                                            </day>
86 91 
                                            <month>
87 92 
                                                <_nullIf>
88 93 
                                                    <null>0</null>
89 94 
                                                    <type>float</type>
90 
                                                    <value>$conceptual_darwin_2003_1_0_MonthCollected</value>
95 
                                                    <value>
96 
                                                        <_alt>
97 
                                                            <0>$conceptual_darwin_2003_1_0_MonthCollected</0>
98 
                                                            <1>$dwc_terms_month</1>
99 
                                                        </_alt>
100 
                                                    </value>
91 101 
                                                </_nullIf>
92 102 
                                            </month>
93 103 
                                            <year>
94 104 
                                                <_nullIf>
95 105 
                                                    <null>0</null>
96 106 
                                                    <type>float</type>
97 
                                                    <value>$conceptual_darwin_2003_1_0_YearCollected</value>
107 
                                                    <value>
108 
                                                        <_alt>
109 
                                                            <0>$conceptual_darwin_2003_1_0_YearCollected</0>
110 
                                                            <1>$dwc_terms_year</1>
111 
                                                        </_alt>
112 
                                                    </value>
98 113 
                                                </_nullIf>
99 114 
                                            </year>
100 115 
                                        </_date>
inputs/SpeciesLink/Specimen/new_terms.csv
56 56 
dwc_terms_preparations,preparations,,
57 57 
dwc_terms_otherCatalogNumbers,otherCatalogNumbers,,
58 58 
dwc_terms_eventTime,eventTime,,
59 
dwc_terms_year,year,,
60 
dwc_terms_month,month,,
61 
dwc_terms_day,day,,
59 
dwc_terms_year,yearCollected,,
60 
dwc_terms_month,monthCollected,,
61 
dwc_terms_day,dayCollected,,
62 62 
dwc_terms_fieldNumber,collectorNumber,/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
63 63 
-----
64 64 
SELECT count(*) FROM ""SpeciesLink"".specimens
inputs/SpeciesLink/Specimen/unmapped_terms.csv
8 8 
preparations
9 9 
otherCatalogNumbers
10 10 
eventTime
11 
year
12 
month
13 
day
14 11 
modified
15 12 
basisOfRecord
16 13 
typeStatus
inputs/HIBG/Specimen/map.csv
51 51 
genus,genus,,
52 52 
taxonRank,taxonRank,,
53 53 
type,type,,
54 
eventDate,eventDate,,
54 
eventDate,dateCollected,,
55 55 
scientificName,scientificName,,
56 56 
verbatimElevation,verbatimElevation,,
57 57 
scientificNameAuthorship,scientificNameAuthorship,,
inputs/ARIZ/omoccurrences/map.csv
32 32 
recordNumber,collectorNumber,,
33 33 
recordedById,*recordedById,,
34 34 
associatedCollectors,*associatedCollectors,,
35 
eventDate,eventDate,,
36 
year,year,,
37 
month,month,,
38 
day,day,,
35 
eventDate,dateCollected,,
36 
year,yearCollected,,
37 
month,monthCollected,,
38 
day,dayCollected,,
39 39 
startDayOfYear,startDayOfYear,,
40 40 
endDayOfYear,endDayOfYear,,
41 41 
verbatimEventDate,verbatimEventDate,,
inputs/ARIZ/omoccurrences/unmapped_terms.csv
10 10 
typeStatus
11 11 
*recordedById
12 12 
*associatedCollectors
13 
year
14 
month
15 
day
16 13 
startDayOfYear
17 14 
endDayOfYear
18 15 
verbatimEventDate
inputs/TRT/Specimen/map.csv
41 41 
associatedMedia,associatedMedia,,
42 42 
datasetID,datasetURL,,
43 43 
georeferencedDate,georeferencedDate,,
44 
eventDate,eventDate,,
44 
eventDate,dateCollected,,
45 45 
kingdom,kingdom,,
46 46 
bibliographicCitation,bibliographicCitation,,
47 47 
taxonRank,taxonRank,,
inputs/MO/Specimen/map.csv
21 21 
elevationunits,*elevationunits,,
22 22 
minlatdecdeg,decimalLatitude,,
23 23 
minlongdecdeg,decimalLongitude,,
24 
minimumday,day,,
25 
minimummonth,month,,
26 
minimumyear,year,,
24 
minimumday,dayCollected,,
25 
minimummonth,monthCollected,,
26 
minimumyear,yearCollected,,
27 27 
description,specimenDescription,,
28 28 
acronyms,specimenHolderInstitutions,,
29 29 
notes,locationRemarks,,
inputs/MO/Specimen/unmapped_terms.csv
1 1 
*row_num
2 2 
*elevationunits
3 
day
4 
month
5 
year
6 3 
specimenDescription
7 4 
*elev_method
8 5 
georeferenceProtocol

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