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AtlasOfLivingAustralia / biocache-store

Occurrence processing, indexing and batch processing
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Inconsistent field counts in files produced by ExportFromIndexStream #238

Open ansell opened 6 years ago

ansell commented 6 years ago

Some files created by ExportFromIndexStream contain inconsistent field counts compared to the header row:

Line and header sizes were different: expected 661, found 652 

headers=["Record ID", "dcterms:bibliographicCitation", "dcterms:bibliographicCitation", "collectionID", "collectionCode", "dataGeneralizations", "Data Resource ID", "datasetID", "datasetName", "dynamicProperties", "informationWithheld", "institutionID", "institutionCode", "dcterms:language", "dcterms:license", "dcterms:modified", "ownerInstitutionCode", "basisOfRecord", "dcterms:references", "dcterms:accessRights", "dcterms:rightsHolder", "dcterms:type", "associatedMedia", "associatedReferences", "associatedSequences", "associatedTaxa", "behavior", "catalogNumber", "recordedBy", "disposition", "establishmentMeans", "individualCount", "lifeStage", "occurrenceRemarks", "occurrenceStatus", "occurrenceID", "organismQuantity", "organismQuantityType", "otherCatalogNumbers", "preparations", "sex", "recordNumber", "reproductiveCondition", "associatedOrganisms", "associatedOccurrences", "organismID", "organismName", "organismRemarks", "organismScope", "previousIdentifications", "day", "endDayOfYear", "eventRemarks", "eventTime", "eventID", "fieldNotes", "fieldNumber", "habitat", "month", "eventDate", "parentEventID", "sampleSizeUnit", "samplingEffort", "samplingProtocol", "startDayOfYear", "verbatimEventDate", "year", "continent", "coordinatePrecision", "coordinateUncertaintyInMeters", "country", "countryCode", "county", "verbatimDepth", "verbatimElevation", "footprintSRS", "footprintSpatialFit", "footprintWKT", "geodeticDatum", "georeferenceProtocol", "georeferenceRemarks", "georeferenceSources", "georeferenceVerificationStatus", "georeferencedBy", "georeferencedDate", "higherGeography", "higherGeographyID", "island", "islandGroup", "decimalLatitude", "locality", "locationAccordingTo", "locationRemarks", "locationID", "decimalLongitude", "maximumDepthInMeters", "maximumElevationInMeters", "maximumDistanceAboveSurfaceInMeters", "minimumDepthInMeters", "minimumElevationInMeters", "minimumDistanceAboveSurfaceInMeters", "municipality", "pointRadiusSpatialFit", "stateProvince", "verbatimCoordinateSystem", "verbatimCoordinates", "verbatimLatitude", "verbatimLocality", "verbatimLongitude", "verbatimSRS", "waterBody", "identificationID", "identificationReferences", "identificationRemarks", "identificationVerificationStatus", "identifiedBy", "dateIdentified", "identificationQualifier", "typeStatus", "acceptedNameUsage", "acceptedNameUsageID", "class", "class", "vernacularName", "family", "genus", "higherClassification", "infraspecificEpithet", "kingdom", "nameAccordingTo", "nameAccordingToID", "namePublishedIn", "namePublishedInID", "namePublishedInYear", "nomenclaturalCode", "nomenclaturalStatus", "order", "originalNameUsageID", "originalNameUsage", "parentNameUsage", "parentNameUsageID", "phylum", "taxonRank", "scientificNameAuthorship", "scientificNameID", "specificEpithet", "specificEpithet", "subgenus", "taxonID", "taxonRemarks", "taxonConceptID", "scientificName", "taxonomicStatus", "verbatimTaxonRank", "measurementAccuracy", "measurementDeterminedBy", "measurementDeterminedDate", "measurementID", "measurementMethod", "measurementRemarks", "measurementType", "measurementUnit", "measurementValue", "austConservation.p", "stateConservation.p", "speciesGroups.p", "Species subgroups", "Subspecies - matched", "Outlier for layer", "Taxon identification issue", "Location Quality", "Australia's Indigenous forest estate (2013) v2.0", "Forests of Australia (2013) v2.0", "Tenure of Australia's forests (2013) v2.0", "ph", "NVIS 4.1 MVG", "NVIS 4.1 MVS", "Nitrogen", "IGBP Land Cover vegetation classification scheme (2011)", "Fruit Fly Exclusion Zone - Tri State", "Precipitation - annual mean", "National Dynamic Land Cover", "2030A1BMk35M: Evaporation - month max", "2030A1BMk35M: Evaporation - annual mean", "Phylloxera Infection Zone - Maroondah, Victoria", "WoFS", "Phenology max 1 2002", "Phenology max 1 2012", "Shannon Diversity (H)", "Occurrence Density", "Species Richness", "Endemism", "Endemism (Non-marine)", "Phylogenetic Tree 2857", "Phylogenetic Tree 4152", "Phylogenetic Tree 5", "Marspec Annual Variance in SST", "2030A1BMk35M: Evaporation - month min", "Marspec Annual Range in SST", "Marspec SST of the warmest ice-free month", "Marspec SST of the coldest ice-free month", "Marspec Mean Annual SST", "Marspec Annual Variance in SSS", "Marspec Annual Range in SSS", "Marspec Maximum Monthly SSS", "Marspec Minimum Monthly SSS", "Marspec Mean Annual SSS", "Marspec Concavity", "Marspec Bathymetric Slope", "Marspec Distance to Shore", "Marspec Profile Curvature", "Marspec Plan Curvature ", "Marspec North/South Aspect", "Fractional Cover - Bare Soil (2012-03-05)", "Marspec East/West Aspect", "Weathering Intensity V2", "Euclidean Distance to Coast (metres)", "Euclidean Distance to Coast (metres)", "Leaf Area Index (LAI) - 2012-03-05", "Fraction of Photosynthetically Active Radiation (fPAR)", "2030A1BMk35M: Temperature - annual max mean", "Enhanced Vegetation Index (2012-03-05)", "Normalized Difference Vegetation Index (2012-03-05)", "Gross Primary Productivity (2012-03-13)", "Fractional Cover - Non-persistent Vegetation (2012-03-05)", "Fractional Cover - Persistent Vegetation (2012-03-05)", "2030A1BMk35M: Water potential - month max", "2030A1BMk35M: Water potential - month min", "2030A1BMk35M: Water potential - annual mean", "2030A1BMk35M: Water deficit - month min", "2030A1BMk35M: Water deficit - month mean", "2030A1BMk35M: Water deficit - month max", "2030A1BMk35M: Temperature - max month diurnal range", "2030A1BMk35M: Temperature - mean annual diurnal range", "2030A1BMk35M: Temperature - min month diurnal range", "2030A1BMk35M: Temperature - annual range", "2030A1BMk35M: Precipitation - equinox seasonality ratio", "2030A1BMk35M: Precipitation - spring or autumn season", "2030A1BMk35M: Precipitation - solstice seasonality ratio", "2030A1BMk35M: Precipitation - summer or winter season", "2030A1BMk35M: Water surplus - month min", "2030A1BMk35M: Water surplus - annual mean", "2030A1BMk35M: Water surplus - month max", "2030A1BMk35M: Temperature - min difference in max", "2030A1BMk35M: Temperature - max difference in max", "2030A1BMk35M: Temperature - min difference in min", "2030A1BMk35M: Temperature - max difference in min", "2030A1BMk35M: Precipitation - min difference between successive months", "2030A1BMk35M: Precipitation - max difference between successive months", "2030A1BMk35M: Humidity - month max relative 3pm", "2030A1BMk35M: Humidity - annual mean relative 3pm", "2030A1BMk35M: Humidity - month min relative 3pm", "2030A1BMk35M: Precipitation - wettest month", "2030A1BMk35M: Precipitation - annual mean", "2030A1BMk35M: Precipitation - driest month", "2030A1BMk35M: Radiation - max month precipitation modified", "2030A1BMk35M: Radiation - mean annual precipitation modified", "2030A1BMk35M: Radiation - min month precipitation modified", "2030A1BMk35M: Water stress index - month min", "2030A1BMk35M: Water stress index - annual mean", "2030A1BMk35M: Temperature - coolest month max", "2030A1BMk35M: Water stress index - month max", "2030A1BMk35M: Temperature - warmest month min", "2030A1BMk35M: Temperature - annual min mean", "2030A1BMk35M: Temperature - coldest month min", "2030A1BMk35M: Growth index C3 mesotherm plants - annual mean", "2030A1BMk35M: Growth index C3 macrotherm plants - annual mean", "2030A1BMk35M: Temperature - month hottest maximum", "2030A1BMk35M: Crop factor - month min", "2030A1BMk35M: Crop factor - annual mean", "2030A1BMk35M: Crop factor - month max", "2030A1BMk35M: Growth index C4 megatherm plants - annual mean", "2030A1BMk35M: Aridity index - month min", "2030A1BMk35M: Aridity index - annual mean", "2030A1BMk35M: Aridity index - month max", "2030A1BMk35M: Precipitation deficit - month min", "2030A1BMk35M: Precipitation deficit - annual mean", "2030A1BMk35M: Precipitation deficit - month max", "Great Barrier Reef 100m DEM", "Euclidean Distance to the Australian Coastline", "Phylloxera Infection Zone - Mooroopna, Victoria", "Phosphorus", "Potassium", "Carbon - organic", "Population - change", "Unemployment rate", "Age - prime group", "Population - density SLA 2006 p/sqkm)", "Work force - older", "Age", "Internet", "Income - low", "Employment", "Income - high", "Education - vocational training", "Home ownership", "Education - degrees", "Disadvantaged ", "Weathering Intensity", "Averaged Topographic Relief", "Sea Surface Temperature - MODIS Terra", "Topographic slope (%)", "SeaWiFS Chlorophyll Mean", "Unreliable water retention parameters", "Valley bottom %", "Topographic wetness index", "Water holding capacity - plant-available ", "Soil depth", "Topographic roughness", "Ridge top flatness - proportion", "Topographic relief", "Phosphorus - plant-available total pre-European", "Phosphorus - plant-available pre-European", "Phosphorus pre-European", "Soil pedality", "Magnetic anomalies", "Nutrient status", "Nitrogen - plant-available pre-European", "Nitrogen store pre-European", "Nitrogen concentration pre-European", "Valley bottom flatness index", "Ridge top flatness", "Hydrological conductivity - uncertainty", "Hydrologic conductivity - average saturated", "Pedality hydrological score", "Bouguer gravity anomalies", "Lithology - age range", "Lithology - mean age", "Lithology - mean age range (log)", "Lithology - mean age (log)", "Lithology - fertility", "Erosional surfaces - proportion", "Distance - to permanent water (weighted)", "Distance - to non-permanent water (weighted)", "Distance - to coast", "Precipitation deficit - month max", "Substrate data reliability", "Distance - to any water (weighted)", "Carbon store pre-European", "Soils - coarse", "Calcrete", "Clay %", "Temperature - min absolute mean min", "Bulk density", "GEOMACS - geometric mean", "ASRIS 0-1m Plant Available Water Capacity (250m raster)", "ASRIS 0-30cm Clay Content (250m raster)", "ASRIS 0-30cm Bulk Density (250m raster)", "Topographic Slope (degrees)", "Sheep numbers", "SeaWIFS K490 Mean", "Gypsum", "Natural resource management expenditure - additional", "Dolomite (physical)", "Dolomite (acidity)", "Lime", "Dairy numbers", "Beef numbers", "Fire frequency", "Time since last burn", "Threatened communities (2008)", "Precipitation deficit - annual mean", "Moisture - average", "Threatened species (2008)", "Moisture - variability", "Slope length", "Runoff - average", "Precipitation - summer reliability", "Precipitation - winter reliability", "Precipitation - autumn reliability", "Precipitation - spring reliability", "Precipitation - summer", "Precipitation - winter", "Precipitation - autumn", "Precipitation - spring", "Precipitation - annual", "Water holding capacity", "NPP Mean", "Natural resource management expenditure", "Erodibility", "Migratory species (2008)", "NDVI Mean", "Evaporation - average", "Erosivity", "Evaporation - variability", "Elevation ", "Drainage - variability", "Drainage - average", "Remoteness index", "Aspect", "Nitrate - mean (cars2006)", "Water potential - month min", "Phosphate - mean (cars2006)", "Silicate - mean (cars2006)", "oxygen - mean (cars2006)", "Salinity - mean (cars2009a)", "Temperature - mean (cars2009a)", "Phylloxera Infection Zone - Nagambie, Victoria", "Water potential - annual mean", "Water potential - month max", "WorldClim: Temperature - driest quarter mean", "WorldClim: Temperature - wettest quarter mean", "WorldClim: Temperature - annual range", "WorldClim: Temperature - coldest month min", "WorldClim: Temperature - warmest month max", "WorldClim: Temperature - seasonality", "WorldClim: Temperature - isothermality", "WorldClim: Temperature - diurnal range mean", "WorldClim: Precipitation - coldest quarter", "WorldClim: Precipitation - warmest quarter", "WorldClim: Precipitation - driest quarter", "WorldClim: Precipitation - wettest quarter", "WorldClim: Precipitation - seasonality", "WorldClim: Precipitation - driest month", "WorldClim: Precipitation - wettest month", "WorldClim: Precipitation - annual", "WorldClim: Temperature - coldest quarter mean", "WorldClim: Temperature - warmest quarter mean", "WorldClim: Temperature - annual mean", "Wind speed - month min 9am or 3pm ", "Wind speed - annual mean 9am or 3pm", "Wind speed - month max 9am or 3pm", "Wind speed - month max 9am ", "Vapour pressure deficit - month max 9am", "Wind speed - annual mean 9am", "Wind speed - month min 9am", "Wind speed - month max 3pm", "Wind speed - annual mean 3pm", "Wind speed - month min 3pm", "Wind run - month max", "Wind run - annual mean", "Wind run - month min", "Water deficit - month min", "Water deficit - month mean", "Water deficit - month max", "Vapour pressure deficit - month min", "Vapour pressure deficit - annual mean", "Vapour pressure deficit - month max", "Vapour pressure deficit - annual mean 9am", "Vapour pressure deficit - month min 9am", "Temperature - max month diurnal range", "Temperature - mean annual diurnal range", "Temperature - min month diurnal range", "Temperature - annual range", "Temperature - mean annual absolute mean min", "Temperature - max absolute mean max", "Temperature - month mean absolute max", "Precipitation - equinox seasonality ratio", "Precipitation - spring or autumn season", "Precipitation - solstice seasonality ratio", "Precipitation - summer or winter season", "Precipitation - annual seasonality ratio", "Precipitation - annual seasonality", "Water surplus - month min", "Water surplus - annual mean", "Water surplus - month max", "Precipitation - spring or autumn (log) season", "Precipitation - summer or winter (log) season", "Precipitation - annual (log) seasonality index", "Temperature - min difference in max", "Temperature - max difference in max", "Temperature - min difference in min", "Temperature - max difference in min", "Precipitation - min difference between successive months", "Precipitation - max difference between successive months", "Humidity - month max relative 3pm ", "Humidity - annual mean relative 3pm ", "Humidity - month min relative 3pm ", "Humidity - month min relative", "Humidity - annual mean relative", "Humidity - month max relative", "Precipitation - wettest month", "Precipitation - driest month", "Radiation - max month precipitation modified", "Radiation - mean annual precipitation modified", "Radiation - min month precipitation modified", "Water stress index - month min", "Water stress index - annual mean", "Water stress index - month max", "Temperature - warmest month min", "Temperature - annual min mean", "Temperature - coldest month min", "Growth index C3 mesotherm plants - annual mean", "Growth index C3 macrotherm plants - annual mean", "Temperature - month hottest maximum", "Temperature - annual max mean", "Temperature - coolest month max", "Crop factor - month min", "Evaporation - month max", "Evaporation - annual mean", "Evaporation - month min", "Temperature - driest quarter mean (Bio09)", "Crop factor - annual mean", "Crop factor - month max", "Growth index C4 megatherm plants - annual mean", "Temperature - wettest quarter mean", "Temperature - annual range (Bio07)", "Temperature - coldest period min (Bio06)", "Temperature - warmest period max (Bio05)", "Temperature - seasonality (Bio04)", "Moisture Index - coldest quarter mean (Bio35)", "Moisture Index - warmest quarter mean (Bio34)", "Moisture Index - lowest quarter mean (Bio33)", "Moisture Index - highest quarter mean (Bio32)", "Moisture Index - seasonality (Bio31)", "Moisture Index - lowest period (Bio30)", "Temperature - isothermality (Bio03)", "Moisture Index - highest period (Bio29)", "Moisture Index - annual mean (Bio28)", "Radiation - coldest quarter (Bio27)", "Radiation - warmest quarter  (Bio26)", "Radiation - driest quarter (Bio25)", "Radiation - wettest quarter (Bio24)", "Radiation - seasonality (Bio23)", "Radiation - lowest period (Bio22)", "Radiation - highest period (Bio21)", "Radiation - annual mean (Bio20)", "Temperature - diurnal range mean (Bio02)", "Precipitation - coldest quarter (Bio19)", "PSMA State Electoral Boundaries (2016)", "Precipitation - warmest quarter (Bio18)", "Precipitation - driest quarter  (Bio17)", "Precipitation - wettest quarter (Bio16)", "Precipitation - seasonality (Bio15)", "Precipitation - driest period (Bio14)", "Precipitation - wettest period (Bio13)", "Precipitation - annual (Bio12)", "Temperature - coldest quarter mean (Bio11)", "Bush Heritage Reserves", "Temperature - warmest quarter (Bio10)", "Temperature - annual mean (Bio01)", "Bathymetry and Topography 9 sec", "Aridity index - month min", "Aridity index - annual mean", "Aridity index - month max", "Precipitation deficit - month min", "MDBA Water Resource Planning Areas Traditional Owners - Surface Water - Nation names", "MDBA Water Resource Planning Areas Traditional Owners - Ground Water - Nation names", "PSMA Commonwealth Electoral Boundaries (2016)", "mdb_ground_water_sdl_resource_units", "mdb_ground_water_water_resource_plan_areas", "mdb_surface_water_water_resource_plan_areas", "Physiographic Provinces 2011", "wetlands_mdb_name_only", "wetlands_mdb_group_only", "mdb_surface_water_sdl_resource_units", "Local Government Areas", "Murray-Darling Basin Water Resource Plan Areas Groundwater", "Murray-Darling Basin Sustainable Rivers Audit (SRA) Zones", "Murray-Darling Basin Sustainable Rivers Audit (SRA) Valleys", "Wetlands GIS of the Murray-Darling Basin Series 2.0", "NRM Regions 2015", "NRM Regions 2014", "New Zealand Ecological Districts", "New Zealand Land Districts", "New Zealand Provinces", "Murray Darling Basin Authority Water Quality Zones", "FAO Fishing areas (Marine)", "Murray-Darling Basin Boundary", "World Anthropogenic Biomes (2000)", "Important Bird Areas (IBA) Australia", "seagrass", "Global 200 Fresh Water", "Global 200 Terrestrial", "Global 200 Marine", "Physiographic Regions 2011", "capad 2014 marine", "capad 2014 terrestrial", "Fire regime niches", "capad 2012 marine", "capad 2012", "aus_agroclimate_grp", "Geological Regions of Australia", "ASGS Australian States and Territories", "GER Kanangra-Boyd to Wyangala Link", "GER Great Eastern Ranges Initiative", "GER Central Victorial Biolinks", "GER Standard Boundary 31-12-2013", "GER Border Ranges", "Phylloxera Infection Zone - North East, Victoria", "Indigenous Protected Areas (Aug 2013)", "Indigenous Land Use Agreements", "Native Title Determinations", "NSW Local Land Services", "Koppen Climate Classification (All Classes)", "Koppen Climate Classification", "Collaborative Australian Protected Areas Database (CAPAD) 2010", "Collaborative Australian Protected Areas Database (CAPAD) 2010", "ACT TAMS Reserves", "Australian Tropical Savanna", "Drainage Divisions Level 2", "Drainage Divisions Level 1", "Statistical Local Areas", "River Regions", "GER Southern Highlands", "GER Slopes To Summit", "GER National Corridor", "GER Kosciuszko to Coast", "GER Kanangra-Boyd to Wyangala Link", "GER Jaliigirr", "GER Illawarra to Shoalhaven", "GER Hunter Valley", "Terrestrial Ecoregional Boundaries", "Freshwater Ecoregions of the World", "IBRA 7 Subregions", "IBRA 7 Regions", "Collaborative Australian Protected Areas Database (CAPAD) marine 2010", "Collaborative Australian Protected Areas Database (CAPAD) marine 2010", "Tillage practice - dominant (area)", "Tillage practice - dominant (number)", "Fallow practice - dominant (area)", "Fallow practice - dominant (number)", "Irrigation practice - dominant", "Stubble practice - dominant (area)", "stubble practice - dominant (number)", "Australian Coral Ecoregions", "Land cover", "Land use", "Marine Ecoregions of the World", "Antarctic Protected Areas", "Special Quarantine Zone - Torres Strait", "cl937", "Phylloxera Infection Zone - Sydney, New South Wales", "Phylloxera Infection Zone - Albury, New South Wales", "Commonwealth Electoral Boundaries", "Geomorphology of the Australian Margin and adjacent seafloor", "Atlas of Life in the Coastal Wilderness", "Phylloxera Infection Zone - Upton, Victoria", "Phylloxera Infection Zone - Whitebridge, Victoria", "IMCRA Meso-scale Bioregions", "Potato Cyst Nematode Zones - Victoria", "NRM Regions", "IBRA 6 Sub Regions", "Directory of Important Wetlands", "RAMSAR wetland regions", "Surface Geology of Australia", "Estuary habitat mapping", "Areas for Further Assessment within the East Marine Region", "World Country Boundaries", "Territorial Sea", "Vegetation - condition", "Vegetation types - present", "Sodicity", "Vegetation types - native", "IBRA 6 Regions", "IMCRA Regions", "Australian States and Territories", "LGA Boundaries (deprecated)", "Continental Shelf", "States including coastal waters", "Contiguous Zone", "Exclusive Economic Zone", "userQualityAssertion"] 

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Mesibov commented 6 years ago

Hi, Peter.

You realise you're still exporting pseudo-duplicate fields (https://github.com/AtlasOfLivingAustralia/ala-downloads/issues/17)?

class class Collaborative Australian Protected Areas Database (CAPAD) 2010 Collaborative Australian Protected Areas Database (CAPAD) 2010 Collaborative Australian Protected Areas Database (CAPAD) marine 2010 Collaborative Australian Protected Areas Database (CAPAD) marine 2010 dcterms:bibliographicCitation dcterms:bibliographicCitation Euclidean Distance to Coast (metres) Euclidean Distance to Coast (metres) GER Kanangra-Boyd to Wyangala Link GER Kanangra-Boyd to Wyangala Link specificEpithet specificEpithet

Regards, Bob -- Dr Robert Mesibov West Ulverstone, Tasmania, Australia Home phone: 64252630 [61 3 64252630] https://www.polydesmida.info (science and coding) https://www.datafix.com.au (data auditing)