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Revision 1801

Added by Aaron Marcuse-Kubitza over 12 years ago

join: Also print "No join mapping" warning if a join mapping was found but it was empty. The warning in that case is actually "No non-empty join mapping" to distinguish it from a mapping that's missing entirely. input.Makefile: missing_mappings: Support new "No join mapping" error message.

View differences:

inputs/XAL/maps/VegBIEN.specimens.csv
35 35 
CatalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
36 36 
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
37 37 
FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
38 
BasisOfRecord,,** No join mapping for BasisOfRecord **
39 
DateLastModified,,** No join mapping for DateLastModified **
40 
IndividualCount,,** No join mapping for IndividualCount **
41 
InstitutionCode,,** No join mapping for InstitutionCode **
42 
JulianDay,,** No join mapping for JulianDay **
43 
PreparationType,,** No join mapping for PreparationType **
44 
PreviousCatalogNumber,,** No join mapping for PreviousCatalogNumber **
45 
RelatedCatalogItem,,** No join mapping for RelatedCatalogItem **
46 
RelationshipType,,** No join mapping for RelationshipType **
47 
TimeOfDay,,** No join mapping for TimeOfDay **
48 
TypeStatus,,** No join mapping for TypeStatus **
38 
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord **
39 
DateLastModified,,** No non-empty join mapping for DateLastModified **
40 
IndividualCount,,** No non-empty join mapping for IndividualCount **
41 
InstitutionCode,,** No non-empty join mapping for InstitutionCode **
42 
JulianDay,,** No non-empty join mapping for JulianDay **
43 
PreparationType,,** No non-empty join mapping for PreparationType **
44 
PreviousCatalogNumber,,** No non-empty join mapping for PreviousCatalogNumber **
45 
RelatedCatalogItem,,** No non-empty join mapping for RelatedCatalogItem **
46 
RelationshipType,,** No non-empty join mapping for RelationshipType **
47 
TimeOfDay,,** No non-empty join mapping for TimeOfDay **
48 
TypeStatus,,** No non-empty join mapping for TypeStatus **
inputs/NY/maps/VegBIEN.specimens.csv
41 41 
UniqueNYInternalRecordNumber,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/sourceaccessioncode","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
42 42 
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
43 43 
FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
44 
BasisOfRecord,,** No join mapping for BasisOfRecord **
45 
DateLastModified,,** No join mapping for DateLastModified **
46 
IndividualCount,,** No join mapping for IndividualCount **
47 
InstitutionCode,,** No join mapping for InstitutionCode **
48 
JulianDay,,** No join mapping for JulianDay **
49 
PreparationType,,** No join mapping for PreparationType **
50 
PreviousCatalogNumber,,** No join mapping for PreviousCatalogNumber **
51 
RelatedCatalogItem,,** No join mapping for RelatedCatalogItem **
52 
RelationshipType,,** No join mapping for RelationshipType **
53 
TimeOfDay,,** No join mapping for TimeOfDay **
54 
TypeStatus,,** No join mapping for TypeStatus **
44 
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord **
45 
DateLastModified,,** No non-empty join mapping for DateLastModified **
46 
IndividualCount,,** No non-empty join mapping for IndividualCount **
47 
InstitutionCode,,** No non-empty join mapping for InstitutionCode **
48 
JulianDay,,** No non-empty join mapping for JulianDay **
49 
PreparationType,,** No non-empty join mapping for PreparationType **
50 
PreviousCatalogNumber,,** No non-empty join mapping for PreviousCatalogNumber **
51 
RelatedCatalogItem,,** No non-empty join mapping for RelatedCatalogItem **
52 
RelationshipType,,** No non-empty join mapping for RelationshipType **
53 
TimeOfDay,,** No non-empty join mapping for TimeOfDay **
54 
TypeStatus,,** No non-empty join mapping for TypeStatus **
55 55 
key,,Not used because UniqueNYInternalRecordNumber is a better pkey
inputs/ACAD/maps/VegBIEN.specimens.csv
26 26 
id,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/sourceaccessioncode","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
27 27 
recordNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
28 28 
collectionID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/2,,9
29 
basisOfRecord,,** No join mapping for basisOfRecord **
30 
bibliographicCitation,,** No join mapping for bibliographicCitation **
31 
dynamicProperties,,** No join mapping for dynamicProperties **
32 
geodeticDatum,,** No join mapping for geodeticDatum **
33 
georeferenceSources,,** No join mapping for georeferenceSources **
34 
georeferenceVerificationStatus,,** No join mapping for georeferenceVerificationStatus **
35 
identificationRemarks,,** No join mapping for identificationRemarks **
36 
institutionCode,,** No join mapping for institutionCode **
37 
language,,** No join mapping for language **
38 
locationRemarks,,** No join mapping for locationRemarks **
39 
modified,,** No join mapping for modified **
40 
municipality,,** No join mapping for municipality **
41 
occurrenceRemarks,,** No join mapping for occurrenceRemarks **
42 
ownerInstitutionCode,,** No join mapping for ownerInstitutionCode **
43 
reproductiveCondition,,** No join mapping for reproductiveCondition **
44 
rights,,** No join mapping for rights **
45 
rightsHolder,,** No join mapping for rightsHolder **
46 
taxonRank,,** No join mapping for taxonRank **
47 
type,,** No join mapping for type **
48 
verbatimDepth,,** No join mapping for verbatimDepth **
49 
verbatimElevation,,** No join mapping for verbatimElevation **
29 
basisOfRecord,,** No non-empty join mapping for basisOfRecord **
30 
bibliographicCitation,,** No non-empty join mapping for bibliographicCitation **
31 
dynamicProperties,,** No non-empty join mapping for dynamicProperties **
32 
geodeticDatum,,** No non-empty join mapping for geodeticDatum **
33 
georeferenceSources,,** No non-empty join mapping for georeferenceSources **
34 
georeferenceVerificationStatus,,** No non-empty join mapping for georeferenceVerificationStatus **
35 
identificationRemarks,,** No non-empty join mapping for identificationRemarks **
36 
institutionCode,,** No non-empty join mapping for institutionCode **
37 
language,,** No non-empty join mapping for language **
38 
locationRemarks,,** No non-empty join mapping for locationRemarks **
39 
modified,,** No non-empty join mapping for modified **
40 
municipality,,** No non-empty join mapping for municipality **
41 
occurrenceRemarks,,** No non-empty join mapping for occurrenceRemarks **
42 
ownerInstitutionCode,,** No non-empty join mapping for ownerInstitutionCode **
43 
reproductiveCondition,,** No non-empty join mapping for reproductiveCondition **
44 
rights,,** No non-empty join mapping for rights **
45 
rightsHolder,,** No non-empty join mapping for rightsHolder **
46 
taxonRank,,** No non-empty join mapping for taxonRank **
47 
type,,** No non-empty join mapping for type **
48 
verbatimDepth,,** No non-empty join mapping for verbatimDepth **
49 
verbatimElevation,,** No non-empty join mapping for verbatimElevation **
inputs/UNCC/maps/VegBIEN.specimens.csv
29 29 
accession,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/sourceaccessioncode","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
30 30 
collectno,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
31 31 
filler,,"Where used, same as family"
32 
flower,,"** No join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?"
33 
fruit,,"** No join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?"
34 
infrarank,,** No join mapping for taxonRank/_alt/2 **
35 
leaves,,"** No join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?"
36 
root,,"** No join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?"
37 
sheetno,,** No join mapping for associatedMedia ** ?
38 
usdaRank,,** No join mapping for taxonRank/_alt/1 **
32 
flower,,"** No non-empty join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?"
33 
fruit,,"** No non-empty join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?"
34 
infrarank,,** No non-empty join mapping for taxonRank/_alt/2 **
35 
leaves,,"** No non-empty join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?"
36 
root,,"** No non-empty join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?"
37 
sheetno,,** No non-empty join mapping for associatedMedia ** ?
38 
usdaRank,,** No non-empty join mapping for taxonRank/_alt/1 **
inputs/REMIB/maps/VegBIEN.specimens.csv
19 19 
lat_sec,,** No input mapping for lat_sec **
20 20 
long_min,,** No input mapping for long_min **
21 21 
long_sec,,** No input mapping for long_sec **
22 
preparation,,** No join mapping for preparation **
22 
preparation,,** No non-empty join mapping for preparation **
inputs/U/maps/VegBIEN.specimens.csv
26 26 
Majorarea,,** No input mapping for Majorarea **
27 27 
NS,,** No input mapping for NS **
28 28 
Newgazett,,** No input mapping for Newgazett **
29 
Phenology,,** No join mapping for ReproductiveCondition **
29 
Phenology,,** No non-empty join mapping for ReproductiveCondition **
30 30 
Prefix,,Not used
31 31 
Suffix,,Not used
32 
cf,,** No join mapping for IdentificationQualifier **
32 
cf,,** No non-empty join mapping for IdentificationQualifier **
inputs/ARIZ/maps/VegBIEN.specimens.csv
41 41 
GlobalUniqueIdentifier,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/sourceaccessioncode","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
42 42 
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
43 43 
FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
44 
AgeClass,,** No join mapping for lifeStage **
45 
BasisOfRecord,,** No join mapping for BasisOfRecord **
44 
AgeClass,,** No non-empty join mapping for lifeStage **
45 
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord **
46 46 
CatalogNumber,,Map to nothing so it doesn't overwrite CatalogNumberNumeric
47 
DateLastModified,,** No join mapping for DateLastModified **
48 
GenBankNum,,"** No join mapping for associatedSequences/_label[label=""GenBank""]/value ** "
49 
GeorefMethod,,** No join mapping for georeferenceProtocol **
50 
HigherGeography,,** No join mapping for HigherGeography **
47 
DateLastModified,,** No non-empty join mapping for DateLastModified **
48 
GenBankNum,,"** No non-empty join mapping for associatedSequences/_label[label=""GenBank""]/value ** "
49 
GeorefMethod,,** No non-empty join mapping for georeferenceProtocol **
50 
HigherGeography,,** No non-empty join mapping for HigherGeography **
51 51 
HorizontalDatum,,Not used
52 
IdentificationModifier,,** No join mapping for identificationQualifier **
53 
IndividualCount,,** No join mapping for IndividualCount **
54 
InstitutionCode,,** No join mapping for InstitutionCode **
55 
Island,,** No join mapping for Island **
56 
IslandGroup,,** No join mapping for IslandGroup **
57 
JulianDay,,** No join mapping for JulianDay **
58 
LatLongComments,,** No join mapping for georeferenceRemarks **
59 
OriginalCoordinateSystem,,** No join mapping for verbatimSRS **
60 
OtherCatalogNumbers,,** No join mapping for RelatedCatalogItem **
61 
Preparations,,** No join mapping for Preparations **
62 
RelatedCatalogedItems,,"** No join mapping for RelatedCatalogItem ** Used only when OtherCatalogNumbers is NULL, so _alt not needed"
63 
TimeCollected,,** No join mapping for TimeOfDay **
52 
IdentificationModifier,,** No non-empty join mapping for identificationQualifier **
53 
IndividualCount,,** No non-empty join mapping for IndividualCount **
54 
InstitutionCode,,** No non-empty join mapping for InstitutionCode **
55 
Island,,** No non-empty join mapping for Island **
56 
IslandGroup,,** No non-empty join mapping for IslandGroup **
57 
JulianDay,,** No non-empty join mapping for JulianDay **
58 
LatLongComments,,** No non-empty join mapping for georeferenceRemarks **
59 
OriginalCoordinateSystem,,** No non-empty join mapping for verbatimSRS **
60 
OtherCatalogNumbers,,** No non-empty join mapping for RelatedCatalogItem **
61 
Preparations,,** No non-empty join mapping for Preparations **
62 
RelatedCatalogedItems,,"** No non-empty join mapping for RelatedCatalogItem ** Used only when OtherCatalogNumbers is NULL, so _alt not needed"
63 
TimeCollected,,** No non-empty join mapping for TimeOfDay **
64 64 
Tissues,,Not used
65 
TypeStatus,,** No join mapping for TypeStatus **
66 
VerbatimDepth,,** No join mapping for VerbatimDepth **
67 
VerbatimElevation,,** No join mapping for VerbatimElevation **
65 
TypeStatus,,** No non-empty join mapping for TypeStatus **
66 
VerbatimDepth,,** No non-empty join mapping for VerbatimDepth **
67 
VerbatimElevation,,** No non-empty join mapping for VerbatimElevation **
inputs/GBIF/maps/VegBIEN.specimens.csv
20 20 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
21 21 
CollectionCD,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
22 22 
CatalogNO,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
23 
GBIFFamilyOriginal,,** No join mapping for originalNameUsage/_alt/2/_name/first ** DwC doesn't fully support taxonomic redeterminations
24 
GBIFGenusOriginal,,** No join mapping for originalNameUsage/_alt/2/_name/middle ** DwC doesn't fully support taxonomic redeterminations
25 
InstitutionCD,,** No join mapping for InstitutionCode **
26 
LastDateModified,,** No join mapping for DateLastModified **
27 
ScientificNameOriginal,,** No join mapping for originalNameUsage/_alt/1 ** DwC doesn't fully support taxonomic redeterminations
23 
GBIFFamilyOriginal,,** No non-empty join mapping for originalNameUsage/_alt/2/_name/first ** DwC doesn't fully support taxonomic redeterminations
24 
GBIFGenusOriginal,,** No non-empty join mapping for originalNameUsage/_alt/2/_name/middle ** DwC doesn't fully support taxonomic redeterminations
25 
InstitutionCD,,** No non-empty join mapping for InstitutionCode **
26 
LastDateModified,,** No non-empty join mapping for DateLastModified **
27 
ScientificNameOriginal,,** No non-empty join mapping for originalNameUsage/_alt/1 ** DwC doesn't fully support taxonomic redeterminations
inputs/NCU-NCSC/maps/VegBIEN.specimens.csv
13 13 
Accession Number,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/sourceaccessioncode","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
14 14 
Alt E/W,,** No input mapping for Alt E/W **
15 15 
Alt N/S,,** No input mapping for Alt N/S **
16 
Elevation,,** No join mapping for VerbatimElevation **
16 
Elevation,,** No non-empty join mapping for VerbatimElevation **
17 17 
FIPS,,FIPS county code
18 
Format,,** No join mapping for PreparationType **
18 
Format,,** No non-empty join mapping for PreparationType **
19 19 
Typology,,** No input mapping for Typology **
inputs/SpeciesLink/maps/VegBIEN.specimens.csv
83 83 
collectionID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/2,,9
84 84 
FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
85 85 
fieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
86 
BasisOfRecord,,** No join mapping for BasisOfRecord **
87 
DateLastModified,,** No join mapping for DateLastModified **
88 
DayOfYear,,** No join mapping for JulianDay **
89 
IndividualCount,,** No join mapping for IndividualCount **
90 
InstitutionCode,,** No join mapping for InstitutionCode **
91 
JulianDay,,** No join mapping for JulianDay **
92 
PreparationType,,** No join mapping for PreparationType **
93 
PreviousCatalogNumber,,** No join mapping for PreviousCatalogNumber **
94 
RelatedCatalogItem,,** No join mapping for RelatedCatalogItem **
95 
RelationshipType,,** No join mapping for RelationshipType **
96 
TimeOfDay,,** No join mapping for TimeOfDay **
97 
TypeStatus,,** No join mapping for TypeStatus **
98 
basisOfRecord,,** No join mapping for basisOfRecord **
99 
day,,** No join mapping for day **
100 
dc_terms_modified,,** No join mapping for dcterms:modified **
101 
endDayOfYear,,** No join mapping for endDayOfYear **
102 
eventTime,,** No join mapping for eventTime **
103 
individualCount,,** No join mapping for individualCount **
104 
institutionCode,,** No join mapping for institutionCode **
105 
month,,** No join mapping for month **
106 
occurrenceRemarks,,** No join mapping for occurrenceRemarks **
107 
otherCatalogNumbers,,** No join mapping for otherCatalogNumbers **
108 
preparations,,** No join mapping for preparations **
109 
startDayOfYear,,** No join mapping for startDayOfYear **
110 
typeStatus,,** No join mapping for typeStatus **
111 
year,,** No join mapping for year **
86 
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord **
87 
DateLastModified,,** No non-empty join mapping for DateLastModified **
88 
DayOfYear,,** No non-empty join mapping for JulianDay **
89 
IndividualCount,,** No non-empty join mapping for IndividualCount **
90 
InstitutionCode,,** No non-empty join mapping for InstitutionCode **
91 
JulianDay,,** No non-empty join mapping for JulianDay **
92 
PreparationType,,** No non-empty join mapping for PreparationType **
93 
PreviousCatalogNumber,,** No non-empty join mapping for PreviousCatalogNumber **
94 
RelatedCatalogItem,,** No non-empty join mapping for RelatedCatalogItem **
95 
RelationshipType,,** No non-empty join mapping for RelationshipType **
96 
TimeOfDay,,** No non-empty join mapping for TimeOfDay **
97 
TypeStatus,,** No non-empty join mapping for TypeStatus **
98 
basisOfRecord,,** No non-empty join mapping for basisOfRecord **
99 
day,,** No non-empty join mapping for day **
100 
dc_terms_modified,,** No non-empty join mapping for dcterms:modified **
101 
endDayOfYear,,** No non-empty join mapping for endDayOfYear **
102 
eventTime,,** No non-empty join mapping for eventTime **
103 
individualCount,,** No non-empty join mapping for individualCount **
104 
institutionCode,,** No non-empty join mapping for institutionCode **
105 
month,,** No non-empty join mapping for month **
106 
occurrenceRemarks,,** No non-empty join mapping for occurrenceRemarks **
107 
otherCatalogNumbers,,** No non-empty join mapping for otherCatalogNumbers **
108 
preparations,,** No non-empty join mapping for preparations **
109 
startDayOfYear,,** No non-empty join mapping for startDayOfYear **
110 
typeStatus,,** No non-empty join mapping for typeStatus **
111 
year,,** No non-empty join mapping for year **
inputs/MO/maps/VegBIEN.specimens.csv
24 24 
notes,/description/_merge/1,,
25 25 
CatalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
26 26 
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
27 
BasisOfRecord,,** No join mapping for BasisOfRecord **
28 
DateLastModified,,** No join mapping for DateLastModified **
29 
IndividualCount,,** No join mapping for IndividualCount **
30 
InstitutionCode,,** No join mapping for InstitutionCode **
31 
TypeStatus,,** No join mapping for TypeStatus **
27 
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord **
28 
DateLastModified,,** No non-empty join mapping for DateLastModified **
29 
IndividualCount,,** No non-empty join mapping for IndividualCount **
30 
InstitutionCode,,** No non-empty join mapping for InstitutionCode **
31 
TypeStatus,,** No non-empty join mapping for TypeStatus **
32 32 
convertednotes,,** No input mapping for convertednotes **

Also available in: Unified diff