Thredds harvest #86

jyucsiro · 2018-11-21T00:25:02Z

This PR features a tool called threddsnc2rdf.py.

threddsnc2rdf.py provides the ability to pass in a THREDDS or THREDDS catalog endpoint to then crawl any netCDF file and output BALD RDF or Schema.org json-ld descriptions .

Examples:

#output BALD RDF
$python threddsnc2rdf.py https://data.nodc.noaa.gov/thredds/catalog/ncei/gocd/a0000068/catalog.xml

#output Schema.org JSON-LD
$ python threddsnc2rdf.py --schema-org https://data.nodc.noaa.gov/thredds/catalog/ncei/gocd/a0000068/catalog.xml

Example BALD RDF output

@prefix bald: <http://binary-array-ld.net/latest/> .
@prefix ns1: <https://data.nodc.noaa.gov/thredds/dodsC/ncei/gocd/a0000068/gocd_a0000068_46023_199909.nc/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

<https://data.nodc.noaa.gov/thredds/dodsC/ncei/gocd/a0000068/gocd_a0000068_46023_199909.nc> a bald:Container ;
    bald:contains ns1:crs,
        ns1:depth,
        ns1:depth_quality_flag,
        ns1:latitude,
        ns1:latitude_quality_flag,
        ns1:longitude,
        ns1:longitude_quality_flag,
        ns1:time,
        ns1:time_quality_flag,
        ns1:u,
        ns1:u_quality_flag,
        ns1:u_quality_flag_time_ref,
        ns1:u_time_ref,
        ns1:v,
        ns1:v_quality_flag,
        ns1:v_quality_flag_time_ref,
        ns1:v_time_ref ;
    ns1:Conventions "CF-1.6, ACDD-1.3" ;
    ns1:QC_Manual "Reference Manual for Quality Control Subsurface Currents Data, Version 1.0" ;
    ns1:QC_Software "qcscd.R, 1.4, 2017-06-08" ;
    ns1:QC_Version "1.0" ;
    ns1:QC_indicator "1" ;
    ns1:QC_test_codes "1, 1, 1, 1, 1, 1, 1, 1, 1" ;
    ns1:QC_test_names "Platform_Identification, Impossible_Date/Time, Impossible_Location, Position_on_Land, Global_Impossible_Parameter_Values, Spike, Constant_Speed, Constant_Direction, Rate_of_Change_in_Time" ;
    ns1:QC_test_results "1, 1, 1, -9, 1, 1, 1, 1, 1" ;
    ns1:acknowledgment "The most important contributors are the collectors of the original data. Without their efforts, this compilation of data would not have been possible. These data were acquired from the US NOAA National Centers for Environmental Information (NCEI). This work was supported by the NCEI management." ;
    ns1:cdm_data_type "Profile" ;
    ns1:comment " " ;
    ns1:contributor_name "NDBC" ;
    ns1:contributor_role "data originator" ;
    ns1:creator_email "[email protected]" ;
    ns1:creator_institution "NOAA National Centers for Environmental Information " ;
    ns1:creator_name "Charles Sun" ;
    ns1:creator_type "person" ;
    ns1:creator_url <https://www.nodc.noaa.gov/gocd/> ;
    ns1:date_created "2017-06-08T16:47:04Z" ;
    ns1:date_issued "2017-06-08T16:47:09Z" ;
    ns1:date_metadata_modified "2017-06-08T16:47:04Z" ;
    ns1:date_modified "2017-06-08T16:47:09Z" ;
    ns1:featureType "timeSeriesProfile" ;
    ns1:geospatial_bounds "POLYGON((34.71389 -120.96667, 34.71389 -120.96667, 34.71389 -120.96667, 34.71389 -120.96667, 34.71389 -120.96667))" ;
    ns1:geospatial_bounds_crs "EPSG:4326" ;
    ns1:geospatial_bounds_vertical_crs "EPSG:4326" ;
    ns1:geospatial_lat_max 34.71389 ;
    ns1:geospatial_lat_min 34.71389 ;
    ns1:geospatial_lat_resolution "point" ;
    ns1:geospatial_lat_units "degrees_north" ;
    ns1:geospatial_lon_max -120.96667 ;
    ns1:geospatial_lon_min -120.96667 ;
    ns1:geospatial_lon_resolution "point" ;
    ns1:geospatial_lon_units "degrees_east" ;
    ns1:geospatial_vertical_max 328.0 ;
    ns1:geospatial_vertical_min 24.0 ;
    ns1:geospatial_vertical_positive "down" ;
    ns1:geospatial_vertical_resolution "point" ;
    ns1:geospatial_vertical_units "meters" ;
    ns1:gocd_format_version "GOCD-3.0" ;
    ns1:gocd_id "gocd_a0000068_46023_199909.nc" ;
    ns1:history "2017-06-08T16:47:04Z csun writeF291ADCPnc.R 1.0" ;
    ns1:id "0093183" ;
    ns1:institution "NDBC" ;
    ns1:instrument "ADCP" ;
    ns1:instrument_vocabulary "NCEI Ocean Archive System database" ;
    ns1:keywords "EARTH SCIENCE,OCEANS,OCEAN CIRCULATION,OCEAN CURRENTS" ;
    ns1:keywords_vocabulary "GCMD Science Keywords" ;
    ns1:license "These data are openly available to the public Please acknowledge the use of these data with the text given in the acknowledgment attribute." ;
    ns1:metadata_link <https://www.nodc.noaa.gov/cgi-bin/OAS/prd/text/query> ;
    ns1:naming_authority "gov.noaa.nodc" ;
    ns1:ncei_template_version "NCEI_NetCDF_TimeSeriesProfile_Orthogonal_Template_v1.1" ;
    ns1:platform "FIXED PLATFORM" ;
    ns1:platform_vocabulary "NCEI Ocean Archive System database" ;
    ns1:processing_level "not applicable" ;
    ns1:product_version "GOCD 3.0" ;
    ns1:program "NDBC C-MAN stations and moored buoys program" ;
    ns1:project "NDBC C-MAN stations and moored buoys program" ;
    ns1:publisher_email "[email protected]" ;
    ns1:publisher_institution "US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION - IN295" ;
    ns1:publisher_name "US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION - IN295" ;
    ns1:publisher_type "institution" ;
    ns1:publisher_url <https://www.nodc.noaa.gov> ;
    ns1:references <https://www.nodc.noaa.gov/> ;
    ns1:source "global ocean currents in the NCEI archive holdings" ;
    ns1:standard_name_vocabulary "NetCDF Climate and Forecast (CF) Metadata Convention" ;
    ns1:summary "global ocean currents in the NCEI archive holdings" ;
    ns1:time_coverage_duration "P0Y029DT23H00M00S" ;
    ns1:time_coverage_end "1999-09-30T23:49:59Z" ;
    ns1:time_coverage_resolution "R000001/1999-09-01T00:49:59Z/P0Y029DT23H00M00S" ;
    ns1:time_coverage_start "1999-09-01T00:49:59Z" ;
    ns1:title "Global Ocean Currents Database - gocd_a0000068_46023_199909.nc" ;
    ns1:uuid "9fb84bea-612d-4838-bc1c-4393269585bc" .

ns1:latitude_quality_flag a bald:Subject ;
    ns1:_FillValue "-9" ;
    ns1:flag_meanings "good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value" ;
    ns1:flag_values ( 1 2 3 4 5 6 7 8 9 ) ;
    ns1:long_name "Latitude Quality Flags" .

ns1:longitude_quality_flag a bald:Subject ;
    ns1:_FillValue "-9" ;
    ns1:flag_meanings "good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value" ;
    ns1:flag_values ( 1 2 3 4 5 6 7 8 9 ) ;
    ns1:long_name "Longitude Quality Flags" .

ns1:u a bald:Array ;
    bald:references ns1:u_time_ref ;
    bald:shape "(719, 20)" ;
    ns1:C_format "%7.4f" ;
    ns1:FORTRAN_format "F7.4" ;
    ns1:_FillValue "9999.9" ;
    ns1:ancillary_variables ns1:u_quality_flag ;
    ns1:cell_methods "time: point depth:point" ;
    ns1:coordinates ns1:depth,
        ns1:latitude,
        ns1:longitude,
        ns1:time ;
    ns1:coverage_content_type "physicalMeasurement" ;
    ns1:data_max 0.0305 ;
    ns1:data_min -0.031 ;
    ns1:grid_mapping ns1:crs ;
    ns1:long_name "Eastward Velocity Component" ;
    ns1:standard_name "eastward_sea_water_velocity" ;
    ns1:units "m s-1" ;
    ns1:valid_max 5.0 ;
    ns1:valid_min -5.0 .

ns1:v a bald:Array ;
    bald:references ns1:v_time_ref ;
    bald:shape "(719, 20)" ;
    ns1:C_format "%7.4f" ;
    ns1:FORTRAN_format "F7.4" ;
    ns1:_FillValue "9999.9" ;
    ns1:ancillary_variables ns1:v_quality_flag ;
    ns1:cell_methods "time: point depth:point" ;
    ns1:coordinates ns1:depth,
        ns1:latitude,
        ns1:longitude,
        ns1:time ;
    ns1:coverage_content_type "physicalMeasurement" ;
    ns1:data_max 0.045 ;
    ns1:data_min -0.0205 ;
    ns1:grid_mapping ns1:crs ;
    ns1:long_name "Northward Velocity Component" ;
    ns1:standard_name "northward_sea_water_velocity" ;
    ns1:units "m s-1" ;
    ns1:valid_max 5.0 ;
    ns1:valid_min -5.0 .

ns1:depth_quality_flag a bald:Array ;
    bald:shape "(20,)" ;
    ns1:_FillValue "-9" ;
    ns1:flag_meanings "good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value" ;
    ns1:flag_values ( 1 2 3 4 5 6 7 8 9 ) ;
    ns1:long_name "Depth Quality Flags" .

ns1:time_quality_flag a bald:Array ;
    bald:references ns1:time ;
    bald:shape "(719,)" ;
    ns1:_FillValue "-9" ;
    ns1:flag_meanings "good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value" ;
    ns1:flag_values ( 1 2 3 4 5 6 7 8 9 ) ;
    ns1:long_name "Time Quality Flags" .

ns1:u_quality_flag a bald:Array ;
    bald:references ns1:u_quality_flag_time_ref ;
    bald:shape "(719, 20)" ;
    ns1:_FillValue "-9" ;
    ns1:flag_meanings "good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value" ;
    ns1:flag_values ( 1 2 3 4 5 6 7 8 9 ) ;
    ns1:long_name "Eastward Velocity component QC Flags" .

ns1:u_quality_flag_time_ref a bald:Reference,
        bald:Subject ;
    bald:array ns1:time ;
    bald:childBroadcast "(719, 1)" .

ns1:u_time_ref a bald:Reference,
        bald:Subject ;
    bald:array ns1:time ;
    bald:childBroadcast "(719, 1)" .

ns1:v_quality_flag a bald:Array ;
    bald:references ns1:v_quality_flag_time_ref ;
    bald:shape "(719, 20)" ;
    ns1:_FillValue "-9" ;
    ns1:flag_meanings "good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value" ;
    ns1:flag_values ( 1 2 3 4 5 6 7 8 9 ) ;
    ns1:long_name "Northward Velocity component QC Flags" .

ns1:v_quality_flag_time_ref a bald:Reference,
        bald:Subject ;
    bald:array ns1:time ;
    bald:childBroadcast "(719, 1)" .

ns1:v_time_ref a bald:Reference,
        bald:Subject ;
    bald:array ns1:time ;
    bald:childBroadcast "(719, 1)" .

ns1:depth a bald:Array ;
    bald:shape "(20,)" ;
    ns1:C_format "%7.2f" ;
    ns1:FORTRAN_format "F7.2" ;
    ns1:_FillValue "9999.9" ;
    ns1:ancillary_variables ns1:depth_quality_flag ;
    ns1:coverage_content_type "coordinate" ;
    ns1:data_max 328.0 ;
    ns1:data_min 24.0 ;
    ns1:long_name "Depth" ;
    ns1:positive "down" ;
    ns1:standard_name ns1:depth ;
    ns1:units "meters" .

ns1:latitude a bald:Subject ;
    ns1:_FillValue "9999.9" ;
    ns1:axis "Y" ;
    ns1:coverage_content_type "coordinate" ;
    ns1:data_max 34.71389 ;
    ns1:data_min 34.71389 ;
    ns1:grid_mapping ns1:crs ;
    ns1:long_name "Latitude" ;
    ns1:standard_name ns1:latitude ;
    ns1:units "degrees_north" ;
    ns1:valid_max 90.0 ;
    ns1:valid_min -90.0 .

ns1:longitude a bald:Subject ;
    ns1:_FillValue "9999.9" ;
    ns1:axis "X" ;
    ns1:coverage_content_type "coordinate" ;
    ns1:data_max -120.96667 ;
    ns1:data_min -120.96667 ;
    ns1:grid_mapping ns1:crs ;
    ns1:long_name "Longitude" ;
    ns1:standard_name ns1:longitude ;
    ns1:units "degrees_east" ;
    ns1:valid_max 180.0 ;
    ns1:valid_min -180.0 .

ns1:crs a bald:Subject ;
    ns1:coverage_content_type "auxiliaryInformation" ;
    ns1:epsg_code "EPSG:4326" ;
    ns1:grid_mapping_name "latitude_longitude" ;
    ns1:inverse_flattening "298.257223563" ;
    ns1:long_name "Coordinate Reference System" ;
    ns1:longitude_of_prime_meridian "0.0" ;
    ns1:semi_major_axis "6378137.0" .

ns1:time a bald:Array,
        bald:Reference ;
    bald:array ns1:time ;
    bald:first_value 36402.034722222015 ;
    bald:last_value 36431.993055555504 ;
    bald:shape "(719,)" ;
    ns1:C_format "%9.4f" ;
    ns1:FORTRAN_format "F9.4" ;
    ns1:ancillary_variables ns1:time_quality_flag ;
    ns1:axis "T" ;
    ns1:calendar "julian" ;
    ns1:cf_role "timeseries_id" ;
    ns1:coverage_content_type "coordinate" ;
    ns1:data_max 36431.99306 ;
    ns1:data_min 36402.03472 ;
    ns1:long_name ns1:time ;
    ns1:standard_name ns1:time ;
    ns1:units "days since 1900-01-01 00:00:00" .

Example schema.org output

{
    "@context": "http://schema.org/",
    "description": "global ocean currents in the NCEI archive holdings",
    "http://schema.org/identifier": "0093183",
    "http://schema.org/license": "These data are openly available to the public Please acknowledge the use of these data with the text given in the acknowledgment attribute.",
    "id": "https://data.nodc.noaa.gov/thredds/dodsC/ncei/gocd/a0000068/gocd_a0000068_46054_199909.nc",
    "keywords": [
        "OCEANS",
        "OCEAN CIRCULATION",
        "OCEAN CURRENTS",
        "EARTH SCIENCE"
    ],
    "name": "Global Ocean Currents Database - gocd_a0000068_46054_199909.nc",
    "type": "Dataset",
    "url": "https://data.nodc.noaa.gov/thredds/dodsC/ncei/gocd/a0000068/gocd_a0000068_46054_199909.nc"
}

…rn them into rdf

… test-schema-org

…to thredds_harvest

marqh

there are some dependencies listed here that don't appear to be used.

i'd like to avoid urllib3 and focus url interactions on requests, for example

please confirm whether these dependencies are needed

marqh · 2018-12-11T16:26:14Z

nc2rdf/requirements.txt

+pydap
+requests-futures
+owslib
+urllib3


this dependency doesn't appear to be used anywhere

threddsnc2rdf.py uses the urljoin/split/parse functions of urllib3/urllib.

marqh · 2018-12-11T16:26:21Z

nc2rdf/requirements.txt

+requests-futures
+owslib
+urllib3
+python-dateutil


this dependency doesn't appear to be used anywhere

the code used to use the parser function. seems like it doesn't now. it can go.

marqh · 2018-12-11T16:26:36Z

nc2rdf/requirements.txt

@@ -0,0 +1,6 @@
+lxml
+pydap
+requests-futures


this dependency doesn't appear to be used anywhere

requests-futures could probably go

jyucsiro and others added 16 commits September 20, 2017 17:11

adding handling for outputting to file and default uris

dd3a607

adding default prefixes handling

61eb279

adding requirements.txt and script to harvest thredds nc files and tu…

dc1f020

…rn them into rdf

Adding threddsnc2rdf cmd line tool and readme doc

1b0168e

adding nc2schemaorg function

9301915

ad reame

2678a9b

adding comments that this is a hack

974d779

Commenting print

80347e4

Merge branch 'test-schema-org' into thredds_harvest

b77940c

enable nc2rdf for urls

616e471

adding feature to add url if input is a http/https url

cd7b1db

Merge branch 'test-schema-org' into thredds_harvest

04cacc4

Merge branch 'master' of https://github.com/binary-array-ld/bald into…

c07f764

… test-schema-org

Merge branch 'test-schema-org' of https://github.com/jyucsiro/bald in…

0550a31

…to thredds_harvest

using bnode as id

b85819a

using bnode instead

40960b4

marqh reviewed Dec 11, 2018

View reviewed changes

removing unused dependencies

17eb6ea

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Thredds harvest #86

Thredds harvest #86

jyucsiro commented Nov 21, 2018

marqh left a comment

marqh Dec 11, 2018

jyucsiro Dec 17, 2018

marqh Dec 11, 2018

jyucsiro Dec 17, 2018

marqh Dec 11, 2018

jyucsiro Dec 17, 2018

Thredds harvest #86

Are you sure you want to change the base?

Thredds harvest #86

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jyucsiro commented Nov 21, 2018

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jyucsiro Dec 17, 2018

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