Revision 10385
Added by Aaron Marcuse-Kubitza over 11 years ago
| inputs/BRIT/specimen_flat/postprocess.sql | ||
|---|---|---|
| 26 | 26 |
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| 27 | 27 |
SELECT mk_derived_col((:table_str, 'diameterBreastHeight_cm'), $$_avg("DBH_Min" , "DBH_Max" )$$); -- runtime: 0.3 s ("Time: 326.615 ms") @starscream
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| 28 | 28 |
SELECT mk_derived_col((:table_str, 'height_m'), $$_avg("Height_Min", "Height_Max")$$); -- runtime: 0.3 s ("Time: 346.548 ms") @starscream
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SELECT mk_derived_col((:table_str, 'recordedBy'), |
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$$_join("Collector_Abbrev_Name", "Collection_Team")$$)
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; -- runtime: 0.3 s ("Time: 281.817 ms") @starscream
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SELECT mk_derived_col((:table_str, 'locality'), |
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$$_join("Locality_Summary", "Locality_Description", "Locality_Site_Specific")$$)
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; -- runtime: 0.3 s ("Time: 254.771 ms") @starscream
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| inputs/BRIT/specimen_flat/map.csv | ||
|---|---|---|
| 2 | 2 |
specimen_id,dataProviderRecordID,, |
| 3 | 3 |
Institution_Code,specimenHolderInstitutions,, |
| 4 | 4 |
Global_Unique_Identifier,UNUSED#Global_Unique_Identifier,, |
| 5 |
Collector_Abbrev_Name,recordedBy,/_join/1,
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| 6 |
Collection_Team,recordedBy,/_join/2,
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| 5 |
Collector_Abbrev_Name,recordedBy_primary,,the primary collector
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| 6 |
Collection_Team,recordedBy_additional,,additional collectors
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| 7 | 7 |
Collection_Number,collectorNumber,, |
| 8 | 8 |
Date_of_Collection,dateCollected,, |
| 9 | 9 |
Year_Collected,yearCollected,, |
| ... | ... | |
| 30 | 30 |
Closest_Town,UNUSED#Closest_Town,, |
| 31 | 31 |
Research_Site_Name,*Research_Site_Name,, |
| 32 | 32 |
Project_Name,projectName,, |
| 33 |
Locality_Summary,locality,/_join/1,
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Locality_Description,locality,/_join/2,
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Locality_Site_Specific,locality,/_join/3,
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Locality_Summary,locality__area__prefix,,rarely populated
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Locality_Description,locality__area__main,,
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Locality_Site_Specific,locality__spot,,"location within area, including landmarks"
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| 36 | 36 |
Habitat_Description,habitat,, |
| 37 | 37 |
Habitat_Summary,UNUSED#Habitat_Summary,, |
| 38 | 38 |
Soil_Description,*Soil_Description,, |
| ... | ... | |
| 66 | 66 |
occurrenceRemarks,occurrenceRemarks,, |
| 67 | 67 |
diameterBreastHeight_cm,diameterBreastHeight_cm,, |
| 68 | 68 |
height_m,height_m,, |
| 69 |
recordedBy,recordedBy,, |
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| 70 |
locality,locality,, |
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| inputs/BRIT/specimen_flat/VegBIEN.csv | ||
|---|---|---|
| 11 | 11 |
Elevation_Min,/location/elevation_m/_alt/2/_avg/1,Assuming units based on the range and precision of values |
| 12 | 12 |
Elevation_Max,/location/elevation_m/_alt/2/_avg/2,Assuming units based on the range and precision of values |
| 13 | 13 |
Collection_Number,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 14 |
Locality_Summary,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1/_join/1, |
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| 15 |
Locality_Description,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1/_join/2, |
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| 16 |
Locality_Site_Specific,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1/_join/3, |
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locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
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| 17 | 15 |
Habitat_Description,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
| 18 | 16 |
Collection_Method,/location/locationevent/*_id/method/name, |
| 19 | 17 |
Project_Name,/location/locationevent/*_id/project/projectname, |
| ... | ... | |
| 39 | 37 |
height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m, |
| 40 | 38 |
Collection_Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
| 41 | 39 |
Scientific_Name,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2", |
| 42 |
Collector_Abbrev_Name,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join/1, |
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Collection_Team,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join/2, |
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recordedBy,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
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| 44 | 41 |
Collection_Number,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 45 | 42 |
specimen_id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 46 | 43 |
specimen_id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| ... | ... | |
| 71 | 68 |
Year_Identified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| 72 | 69 |
Catalog_Number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
| 73 | 70 |
Collection_Number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then", |
| 74 |
Locality_Summary,/location/locationnarrative/_merge/1/_join/1, |
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Locality_Description,/location/locationnarrative/_merge/1/_join/2, |
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Locality_Site_Specific,/location/locationnarrative/_merge/1/_join/3, |
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locality,/location/locationnarrative/_merge/1, |
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| 77 | 72 |
Habitat_Description,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
| 78 | 73 |
Coordinate_Uncertainity,/location/locationplace/*_id/place/*_id/coordinates/coordsaccuracy_m/_noCV/value,Assuming units based on the range and precision of values |
| 79 | 74 |
Latitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
| ... | ... | |
| 90 | 85 |
Auxilirary_Collections,,** No non-empty join mapping for UNUSED#Auxilirary_Collections ** |
| 91 | 86 |
Basis_Of_Specimen,,** No join mapping for basisOfRecord ** |
| 92 | 87 |
Closest_Town,,** No non-empty join mapping for UNUSED#Closest_Town ** |
| 88 |
Collection_Team,,** No join mapping for recordedBy_additional ** additional collectors |
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Collector_Abbrev_Name,,** No join mapping for recordedBy_primary ** the primary collector |
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| 93 | 90 |
DBH_Max,,** No join mapping for diameterBreastHeight_max_cm_verbatim ** Assuming units based on the range and precision of values |
| 94 | 91 |
DBH_Min,,** No join mapping for diameterBreastHeight_min_cm_verbatim ** Assuming units based on the range and precision of values |
| 95 | 92 |
Dubpliate_Herbarium,,** No non-empty join mapping for UNUSED#Dubpliate_Herbarium ** |
| ... | ... | |
| 100 | 97 |
Height_Min,,** No join mapping for height_min_m_verbatim ** Assuming units based on the range and precision of values |
| 101 | 98 |
Infra_Rank,,** No join mapping for infraspecificRank ** |
| 102 | 99 |
Local_Name,,** No join mapping for vernacularName ** |
| 100 |
Locality_Description,,** No join mapping for locality__area__main ** |
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Locality_Site_Specific,,"** No join mapping for locality__spot ** location within area, including landmarks" |
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Locality_Summary,,** No join mapping for locality__area__prefix ** rarely populated |
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| 103 | 103 |
Notes_Plant,,** No join mapping for occurrenceRemarks_verbatim ** |
| 104 | 104 |
Research_Site_Name,,** No join mapping for *Research_Site_Name ** |
| 105 | 105 |
Soil_Description,,** No join mapping for *Soil_Description ** |
| inputs/BRIT/specimen_flat/test.xml.ref | ||
|---|---|---|
| 28 | 28 |
<_locationnarrative_is_cultivated> |
| 29 | 29 |
<locationnarrative> |
| 30 | 30 |
<_join> |
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<1> |
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<_join> |
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<1>$Locality_Summary</1> |
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<2>$Locality_Description</2> |
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<3>$Locality_Site_Specific</3> |
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</_join> |
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</1> |
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<1>$locality</1> |
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| 38 | 32 |
<3>$Habitat_Description</3> |
| 39 | 33 |
</_join> |
| 40 | 34 |
</locationnarrative> |
| ... | ... | |
| 103 | 97 |
</stemobservation> |
| 104 | 98 |
</plantobservation> |
| 105 | 99 |
</aggregateoccurrence> |
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<collector_id> |
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<party> |
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<fullname> |
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<_join> |
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<1>$Collector_Abbrev_Name</1> |
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<2>$Collection_Team</2> |
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</_join> |
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</fullname> |
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</party> |
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</collector_id> |
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<collector_id><party><fullname>$recordedBy</fullname></party></collector_id> |
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| 116 | 101 |
<sourceaccessioncode>$specimen_id</sourceaccessioncode> |
| 117 | 102 |
<taxondetermination> |
| 118 | 103 |
<party_id><party><fullname>$Determined_By_Name</fullname></party></party_id> |
| ... | ... | |
| 253 | 238 |
</locationevent> |
| 254 | 239 |
<locationnarrative> |
| 255 | 240 |
<_merge> |
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<1> |
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<_join> |
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<1>$Locality_Summary</1> |
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<2>$Locality_Description</2> |
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<3>$Locality_Site_Specific</3> |
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</_join> |
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</1> |
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<1>$locality</1> |
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| 263 | 242 |
<3> |
| 264 | 243 |
<_label> |
| 265 | 244 |
<label>habitat</label> |
| inputs/BRIT/specimen_flat/new_terms.csv | ||
|---|---|---|
| 1 | 1 |
specimen_id,dataProviderRecordID,, |
| 2 |
Collector_Abbrev_Name,recordedBy,/_join/1,
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| 3 |
Collection_Team,recordedBy,/_join/2,
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| 2 |
Collector_Abbrev_Name,recordedBy_primary,,the primary collector
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| 3 |
Collection_Team,recordedBy_additional,,additional collectors
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| 4 | 4 |
Date_of_Collection,dateCollected,, |
| 5 | 5 |
Kingdom_Name,kingdom,, |
| 6 | 6 |
Division_Name,phylum,, |
| ... | ... | |
| 16 | 16 |
Continent_Name,continent,, |
| 17 | 17 |
Region_Name,stateProvince,, |
| 18 | 18 |
Subregion_Name,county,, |
| 19 |
Locality_Summary,locality,/_join/1,
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Locality_Description,locality,/_join/2,
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Locality_Site_Specific,locality,/_join/3,
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| 19 |
Locality_Summary,locality__area__prefix,,rarely populated
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| 20 |
Locality_Description,locality__area__main,,
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| 21 |
Locality_Site_Specific,locality__spot,,"location within area, including landmarks"
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| 22 | 22 |
Habitat_Description,habitat,, |
| 23 | 23 |
Notes_Plant,occurrenceRemarks_verbatim,, |
| 24 | 24 |
Phenology_Stage,reproductiveCondition,, |
| inputs/BRIT/specimen_flat/unmapped_terms.csv | ||
|---|---|---|
| 1 |
recordedBy_primary |
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| 2 |
recordedBy_additional |
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| 1 | 3 |
*subclass |
| 2 | 4 |
infraspecificRank |
| 3 | 5 |
vernacularName |
| 4 | 6 |
*Research_Site_Name |
| 7 |
locality__area__prefix |
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| 8 |
locality__area__main |
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| 9 |
locality__spot |
|
| 5 | 10 |
*Soil_Description |
| 6 | 11 |
occurrenceRemarks_verbatim |
| 7 | 12 |
height_min_m_verbatim |
Also available in: Unified diff
inputs/BRIT/specimen_flat/: translated multi-column filters with _join() to postprocessing derived columns, using the steps at wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns