,
Kara Woo [aut],
Andrew MacDonald [aut],
Naupaka Zimmerman [aut],
Gavin Simpson [aut]| Title: | Client for the 'Pangaea' Database |
|---|---|
| Description: | Tools to interact with the 'Pangaea' Database (<https://www.pangaea.de>), including functions for searching for data, fetching 'datasets' by 'dataset' 'ID', and working with the 'Pangaea' 'OAI-PMH' service. |
| Authors: | Scott Chamberlain [aut, cre] ,
Kara Woo [aut],
Andrew MacDonald [aut],
Naupaka Zimmerman [aut],
Gavin Simpson [aut] |
| Maintainer: | Scott Chamberlain <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.1.0 |
| Built: | 2024-09-17 05:28:09 UTC |
| Source: | https://github.com/ropensci/pangaear |
Package includes tools to interact with the Pangaea Database, including functions for searching for data, fetching datasets by dataset ID, working with the Pangaea OAI-PMH service, and Elasticsearch service.
The main workhorse function for getting data is pg_data().
One thing you may want to do is set a different path for caching
the data you download: see pg_cache for details
Manage cached pangaear files with hoardr
The dafault cache directory is
paste0(rappdirs::user_cache_dir(), "/R/pangaear"), but you can set
your own path using cache_path_set()
cache_delete only accepts 1 file name, while
cache_delete_all doesn't accept any names, but deletes all files.
For deleting many specific files, use cache_delete in a lapply()
type call
pg_cache$cache_path_get() get cache path
pg_cache$cache_path_set() set cache path
pg_cache$list() returns a character vector of full path file names
pg_cache$files() returns file objects with metadata
pg_cache$details() returns files with details
pg_cache$delete() delete specific files
pg_cache$delete_all() delete all files, returns nothing
## Not run: pg_cache # list files in cache pg_cache$list() # delete certain database files # pg_cache$delete("file path") # pg_cache$list() # delete all files in cache # pg_cache$delete_all() # pg_cache$list() # set a different cache path from the default # pg_cache$cache_path_set(full_path = "/Foo/Bar") ## End(Not run)## Not run: pg_cache # list files in cache pg_cache$list() # delete certain database files # pg_cache$delete("file path") # pg_cache$list() # delete all files in cache # pg_cache$delete_all() # pg_cache$list() # set a different cache path from the default # pg_cache$cache_path_set(full_path = "/Foo/Bar") ## End(Not run)
cache path clear
pg_cache_clear(...)pg_cache_clear(...)
... |
ignored |
Grabs data as a dataframe or list of dataframes from a Pangaea data repository URI; see: https://www.pangaea.de/
pg_data(doi, overwrite = TRUE, mssgs = TRUE, ...)pg_data(doi, overwrite = TRUE, mssgs = TRUE, ...)
doi |
DOI of Pangaeae single dataset, or of a collection of datasets.
Expects either just a DOI of the form |
overwrite |
(logical) Ovewrite a file if one is found with the same name |
mssgs |
(logical) print information messages. Default: |
... |
Curl options passed on to crul::verb-GET |
Data files are stored in an operating system appropriate location.
Run pg_cache$cache_path_get() to get the storage location
on your machine. See pg_cache for more information, including how to
set a different base path for downloaded files.
Some files/datasets require the user to be logged in. For now we just pass on these - that is, give back nothing other than metadata.
One or more items of class pangaea, each with the doi, parent doi
(if many dois within a parent doi), url, citation, path, and data object.
Data object depends on what kind of file it is. For tabular data, we print
the first 10 columns or so; for a zip file we list the files in the zip
(but leave it up to the user to dig unzip and get files from the zip file);
for png files, we point the user to read the file in with png::readPNG()
Naupaka Zimmerman, Scott Chamberlain
## Not run: # a single file (res <- pg_data(doi='10.1594/PANGAEA.807580')) res[[1]]$doi res[[1]]$citation res[[1]]$data res[[1]]$metadata # another single file pg_data(doi='10.1594/PANGAEA.807584') # Many files (res <- pg_data(doi='10.1594/PANGAEA.761032')) res[[1]] res[[2]] # Manipulating the cache ## list files in the cache pg_cache$list() ## clear all data # pg_cache$delete_all() pg_cache$list() ## clear a single dataset by DOI pg_data(doi='10.1594/PANGAEA.812093') pg_cache$list() path <- grep("PANGAEA.812093", pg_cache$list(), value = TRUE) pg_cache$delete(path) pg_cache$list() # search for datasets, then pass in DOIs (searchres <- pg_search(query = 'birds', count = 20)) pg_data(searchres$doi[1]) # png file pg_data(doi = "10.1594/PANGAEA.825428") # zip file pg_data(doi = "10.1594/PANGAEA.860500") # login required ## we skip file download pg_data("10.1594/PANGAEA.788547") ## End(Not run)## Not run: # a single file (res <- pg_data(doi='10.1594/PANGAEA.807580')) res[[1]]$doi res[[1]]$citation res[[1]]$data res[[1]]$metadata # another single file pg_data(doi='10.1594/PANGAEA.807584') # Many files (res <- pg_data(doi='10.1594/PANGAEA.761032')) res[[1]] res[[2]] # Manipulating the cache ## list files in the cache pg_cache$list() ## clear all data # pg_cache$delete_all() pg_cache$list() ## clear a single dataset by DOI pg_data(doi='10.1594/PANGAEA.812093') pg_cache$list() path <- grep("PANGAEA.812093", pg_cache$list(), value = TRUE) pg_cache$delete(path) pg_cache$list() # search for datasets, then pass in DOIs (searchres <- pg_search(query = 'birds', count = 20)) pg_data(searchres$doi[1]) # png file pg_data(doi = "10.1594/PANGAEA.825428") # zip file pg_data(doi = "10.1594/PANGAEA.860500") # login required ## we skip file download pg_data("10.1594/PANGAEA.788547") ## End(Not run)
Get record from the Pangaea repository
pg_get_record(identifier, prefix = "oai_dc", as = "df", ...)pg_get_record(identifier, prefix = "oai_dc", as = "df", ...)
identifier |
Dataset identifier. See Examples. |
prefix |
A character string to specify the metadata format in OAI-PMH
requests issued to the repository. The default ( |
as |
(character) What to return. One of "df" (for data.frame; default), "list", or "raw" (raw text) |
... |
Curl debugging options passed on to |
XML character string, data.frame, or list, depending on what
requested with the as parameter
wraps oai::get_records()
Other oai methods:
pg_identify(),
pg_list_identifiers(),
pg_list_metadata_formats(),
pg_list_records(),
pg_list_sets()
## Not run: pg_get_record(identifier = "oai:pangaea.de:doi:10.1594/PANGAEA.788382") pg_get_record(identifier = "oai:pangaea.de:doi:10.1594/PANGAEA.269656", prefix="iso19139") pg_get_record(identifier = "oai:pangaea.de:doi:10.1594/PANGAEA.269656", prefix="dif") # invalid record id # pg_get_record(identifier = "oai:pangaea.de:doi:10.1594/PANGAEA.11111") # pg_get_record(identifier = "oai:pangaea.de:doi:10.1594/PANGAEA.11111", # prefix="adfadf") ## End(Not run)## Not run: pg_get_record(identifier = "oai:pangaea.de:doi:10.1594/PANGAEA.788382") pg_get_record(identifier = "oai:pangaea.de:doi:10.1594/PANGAEA.269656", prefix="iso19139") pg_get_record(identifier = "oai:pangaea.de:doi:10.1594/PANGAEA.269656", prefix="dif") # invalid record id # pg_get_record(identifier = "oai:pangaea.de:doi:10.1594/PANGAEA.11111") # pg_get_record(identifier = "oai:pangaea.de:doi:10.1594/PANGAEA.11111", # prefix="adfadf") ## End(Not run)
Identify information about the Pangaea repository
pg_identify(...)pg_identify(...)
... |
Curl debugging options passed on to |
list
wraps oai::id()
Other oai methods:
pg_get_record(),
pg_list_identifiers(),
pg_list_metadata_formats(),
pg_list_records(),
pg_list_sets()
## Not run: pg_identify() ## End(Not run)## Not run: pg_identify() ## End(Not run)
List identifiers of the Pangaea repository
pg_list_identifiers( prefix = "oai_dc", from = NULL, until = NULL, set = NULL, token = NULL, as = "df", ... )pg_list_identifiers( prefix = "oai_dc", from = NULL, until = NULL, set = NULL, token = NULL, as = "df", ... )
prefix |
A character string to specify the metadata format in OAI-PMH
requests issued to the repository. The default ( |
from |
Character string giving datestamp to be used as lower bound for datestamp-based selective harvesting (i.e., only harvest records with datestamps in the given range). Dates and times must be encoded using ISO 8601. The trailing Z must be used when including time. OAI-PMH implies UTC for data/time specifications. |
until |
Character string giving a datestamp to be used as an upper bound, for datestamp-based selective harvesting (i.e., only harvest records with datestamps in the given range). |
set |
A character string giving a set to be used for selective harvesting (i.e., only harvest records in the given set). |
token |
(character) a token previously provided by the server to resume a request where it last left off. 50 is max number of records returned. We will loop for you internally to get all the records you asked for. |
as |
(character) What to return. One of "df" (for data.frame; default), "list", or "raw" (raw text) |
... |
Curl debugging options passed on to |
XML character string, data.frame, or list, depending on what
requested with the as parameter
wraps oai::list_identifiers()
Other oai methods:
pg_get_record(),
pg_identify(),
pg_list_metadata_formats(),
pg_list_records(),
pg_list_sets()
## Not run: pg_list_identifiers( from = paste0(Sys.Date() - 4, "T00:00:00Z"), until = paste0(Sys.Date() - 3, "T18:00:00Z") ) pg_list_identifiers(set="geocode1", from=Sys.Date()-1, until=Sys.Date()) pg_list_identifiers(prefix="iso19139", from=Sys.Date()-1, until=Sys.Date()) pg_list_identifiers(prefix="dif", from = paste0(Sys.Date() - 2, "T00:00:00Z"), until = paste0(Sys.Date() - 1, "T18:00:00Z") ) ## End(Not run)## Not run: pg_list_identifiers( from = paste0(Sys.Date() - 4, "T00:00:00Z"), until = paste0(Sys.Date() - 3, "T18:00:00Z") ) pg_list_identifiers(set="geocode1", from=Sys.Date()-1, until=Sys.Date()) pg_list_identifiers(prefix="iso19139", from=Sys.Date()-1, until=Sys.Date()) pg_list_identifiers(prefix="dif", from = paste0(Sys.Date() - 2, "T00:00:00Z"), until = paste0(Sys.Date() - 1, "T18:00:00Z") ) ## End(Not run)
Get metadata formats from the Pangaea repository
pg_list_metadata_formats(...)pg_list_metadata_formats(...)
... |
Curl debugging options passed on to |
data.frame
wraps oai::list_metadataformats()
Other oai methods:
pg_get_record(),
pg_identify(),
pg_list_identifiers(),
pg_list_records(),
pg_list_sets()
## Not run: pg_list_metadata_formats() ## End(Not run)## Not run: pg_list_metadata_formats() ## End(Not run)
List records from Pangaea
pg_list_records( prefix = "oai_dc", from = NULL, until = NULL, set = NULL, token = NULL, as = "df", ... )pg_list_records( prefix = "oai_dc", from = NULL, until = NULL, set = NULL, token = NULL, as = "df", ... )
prefix |
A character string to specify the metadata format in OAI-PMH
requests issued to the repository. The default ( |
from |
Character string giving datestamp to be used as lower bound for datestamp-based selective harvesting (i.e., only harvest records with datestamps in the given range). Dates and times must be encoded using ISO 8601. The trailing Z must be used when including time. OAI-PMH implies UTC for data/time specifications. |
until |
Character string giving a datestamp to be used as an upper bound, for datestamp-based selective harvesting (i.e., only harvest records with datestamps in the given range). |
set |
A character string giving a set to be used for selective harvesting (i.e., only harvest records in the given set). |
token |
(character) a token previously provided by the server to resume a request where it last left off. 50 is max number of records returned. We will loop for you internally to get all the records you asked for. |
as |
(character) What to return. One of "df" (for data.frame; default), "list", or "raw" (raw text) |
... |
Curl debugging options passed on to |
XML character string, data.frame, or list, depending on what
requested witht the as parameter
wraps oai::list_records()
Other oai methods:
pg_get_record(),
pg_identify(),
pg_list_identifiers(),
pg_list_metadata_formats(),
pg_list_sets()
## Not run: pg_list_records(set='citable', from=Sys.Date()-1, until=Sys.Date()) # When no results found > "'noRecordsMatch'" # pg_list_records(set='geomound', from='2015-01-01', until='2015-01-01') pg_list_records(prefix="iso19139", set='citable', from=Sys.Date()-1, until=Sys.Date()) ## FIXME - below are broken # pg_list_records(prefix="dif", set='citable', from=Sys.Date()-4, # until=Sys.Date()) # pg_list_records(prefix="dif", set='project4094', from=Sys.Date()-4, # until=Sys.Date()) ## End(Not run)## Not run: pg_list_records(set='citable', from=Sys.Date()-1, until=Sys.Date()) # When no results found > "'noRecordsMatch'" # pg_list_records(set='geomound', from='2015-01-01', until='2015-01-01') pg_list_records(prefix="iso19139", set='citable', from=Sys.Date()-1, until=Sys.Date()) ## FIXME - below are broken # pg_list_records(prefix="dif", set='citable', from=Sys.Date()-4, # until=Sys.Date()) # pg_list_records(prefix="dif", set='project4094', from=Sys.Date()-4, # until=Sys.Date()) ## End(Not run)
List the set structure of the Pangaea repository
pg_list_sets(token = NULL, as = "df", ...)pg_list_sets(token = NULL, as = "df", ...)
token |
(character) a token previously provided by the server to resume a request where it last left off. 50 is max number of records returned. We will loop for you internally to get all the records you asked for. |
as |
(character) What to return. One of "df" (for data.frame; default), "list", or "raw" (raw text) |
... |
Curl debugging options passed on to |
XML character string, data.frame, or list, depending on what
requested with the as parameter
wraps oai::list_sets()
Other oai methods:
pg_get_record(),
pg_identify(),
pg_list_identifiers(),
pg_list_metadata_formats(),
pg_list_records()
## Not run: pg_list_sets() pg_list_sets(as = "list") pg_list_sets(as = "raw") ## End(Not run)## Not run: pg_list_sets() pg_list_sets(as = "list") pg_list_sets(as = "raw") ## End(Not run)
Search the Pangaea database
pg_search( query, count = 10, offset = 0, topic = NULL, bbox = NULL, mindate = NULL, maxdate = NULL, ... )pg_search( query, count = 10, offset = 0, topic = NULL, bbox = NULL, mindate = NULL, maxdate = NULL, ... )
query |
(character) Query terms. You can refine a search by prefixing the term(s) with a category, one of citation, reference, parameter, event, project, campaign, or basis. See examples. |
count |
(integer) Number of items to return. Default: 10. Maximum: 500.
Use |
offset |
(integer) Record number to start at. Default: 0 |
topic |
(character) topic area: one of NULL (all areas), "Agriculture", "Atomosphere", "Biological Classification", "Biospshere", "Chemistry", "Cryosphere", "Ecology", "Fisheries", "Geophysics", "Human Dimensions", "Lakes & Rivers", "Land Surface", "Lithosphere", "Oceans", "Paleontology" |
bbox |
(numeric) A bounding box, of the form: minlon, minlat, maxlon, maxlat |
mindate, maxdate
|
(character) Dates to search for, of the form "2014-10-28" |
... |
Curl options passed on to crul::verb-GET |
This is a thin wrapper around the GUI search interface on the page https://www.pangaea.de. Everything you can do there, you can do here.
tibble/data.frame with the structure:
score: match score, higher is a better match
doi: the DOI for the data package
size: size number
size_measure: size measure, one of "data points" or "datasets"
citation: citation for the data package
supplement_to: citation for what the data package is a supplement to
## Not run: pg_search(query='water') pg_search(query='water', count=2) pg_search(query='water', count=20) pg_search(query='water', mindate="2013-06-01", maxdate="2013-07-01") pg_search(query='water', bbox=c(-124.2, 41.8, -116.8, 46.1)) pg_search(query='reference:Archer') pg_search(query='parameter:"carbon dioxide"') pg_search(query='event:M2-track') pg_search(query='event:TT011_2-CTD31') pg_search(query='project:Joint Global Ocean Flux Study') pg_search(query='campaign:M2') pg_search(query='basis:Meteor') # paging with count and offset # max is 500 records per request - if you need > 500, use offset and count res1 <- pg_search(query = "florisphaera", count = 500, offset = 0) res2 <- pg_search(query = "florisphaera", count = 500, offset = 500) res3 <- pg_search(query = "florisphaera", count = 500, offset = 1000) do.call("rbind.data.frame", list(res1, res2, res3)) # get attributes: maxScore, totalCount, and offset res <- pg_search(query='water', bbox=c(-124.2, 41.8, -116.8, 46.1)) attributes(res) attr(res, "maxScore") attr(res, "totalCount") attr(res, "offset") # curl options pg_search(query='citation:Archer', verbose = TRUE) ## End(Not run)## Not run: pg_search(query='water') pg_search(query='water', count=2) pg_search(query='water', count=20) pg_search(query='water', mindate="2013-06-01", maxdate="2013-07-01") pg_search(query='water', bbox=c(-124.2, 41.8, -116.8, 46.1)) pg_search(query='reference:Archer') pg_search(query='parameter:"carbon dioxide"') pg_search(query='event:M2-track') pg_search(query='event:TT011_2-CTD31') pg_search(query='project:Joint Global Ocean Flux Study') pg_search(query='campaign:M2') pg_search(query='basis:Meteor') # paging with count and offset # max is 500 records per request - if you need > 500, use offset and count res1 <- pg_search(query = "florisphaera", count = 500, offset = 0) res2 <- pg_search(query = "florisphaera", count = 500, offset = 500) res3 <- pg_search(query = "florisphaera", count = 500, offset = 1000) do.call("rbind.data.frame", list(res1, res2, res3)) # get attributes: maxScore, totalCount, and offset res <- pg_search(query='water', bbox=c(-124.2, 41.8, -116.8, 46.1)) attributes(res) attr(res, "maxScore") attr(res, "totalCount") attr(res, "offset") # curl options pg_search(query='citation:Archer', verbose = TRUE) ## End(Not run)
Search the Pangaea database with Elasticsearch
pg_search_es( query = NULL, size = 10, from = NULL, source = NULL, df = NULL, analyzer = NULL, default_operator = NULL, explain = NULL, sort = NULL, track_scores = NULL, timeout = NULL, terminate_after = NULL, search_type = NULL, lowercase_expanded_terms = NULL, analyze_wildcard = NULL, version = FALSE, ... )pg_search_es( query = NULL, size = 10, from = NULL, source = NULL, df = NULL, analyzer = NULL, default_operator = NULL, explain = NULL, sort = NULL, track_scores = NULL, timeout = NULL, terminate_after = NULL, search_type = NULL, lowercase_expanded_terms = NULL, analyze_wildcard = NULL, version = FALSE, ... )
query |
(character) Query terms.. |
size |
(character) The number of hits to return. Pass in as a
character string to avoid problems with large number conversion to
scientific notation. Default: 10. The default maximum is 10,000 - however,
you can change this default maximum by changing the
|
from |
(character) The starting from index of the hits to return. Pass in as a character string to avoid problems with large number conversion to scientific notation. Default: 0 |
source |
(character) character vector of fields to return |
df |
(character) The default field to use when no field prefix is defined within the query. |
analyzer |
(character) The analyzer name to be used when analyzing the query string. |
default_operator |
(character) The default operator to be used, can be
|
explain |
(logical) For each hit, contain an explanation of how
scoring of the hits was computed. Default: |
sort |
(character) Sorting to perform. Can either be in the form of
fieldName, or |
track_scores |
(logical) When sorting, set to |
timeout |
(numeric) A search timeout, bounding the search request to be executed within the specified time value and bail with the hits accumulated up to that point when expired. Default: no timeout. |
terminate_after |
(numeric) The maximum number of documents to collect for each shard, upon reaching which the query execution will terminate early. If set, the response will have a boolean field terminated_early to indicate whether the query execution has actually terminated_early. Default: no terminate_after |
search_type |
(character) The type of the search operation to perform.
Can be |
lowercase_expanded_terms |
(logical) Should terms be automatically
lowercased or not. Default: |
analyze_wildcard |
(logical) Should wildcard and prefix queries be
analyzed or not. Default: |
version |
(logical) Print the document version with each document. |
... |
Curl options passed on to crul::verb-GET |
An interface to Pangaea's Elasticsearch query interface. You can also just use elastic package to interact with it. The base URL is https://ws.pangaea.de/es/pangaea/panmd/_search
tibble/data.frame, empty if no results
## Not run: (res <- pg_search_es()) attributes(res) attr(res, "total") attr(res, "max_score") pg_search_es(query = 'water', source = c('parentURI', 'minElevation')) pg_search_es(query = 'water', size = 3) pg_search_es(query = 'water', size = 3, from = 10) pg_search_es(query = 'water sky', default_operator = "OR") pg_search_es(query = 'water sky', default_operator = "AND") pg_search_es(query = 'water', sort = "minElevation") pg_search_es(query = 'water', sort = "minElevation:desc") ## End(Not run)## Not run: (res <- pg_search_es()) attributes(res) attr(res, "total") attr(res, "max_score") pg_search_es(query = 'water', source = c('parentURI', 'minElevation')) pg_search_es(query = 'water', size = 3) pg_search_es(query = 'water', size = 3, from = 10) pg_search_es(query = 'water sky', default_operator = "OR") pg_search_es(query = 'water sky', default_operator = "AND") pg_search_es(query = 'water', sort = "minElevation") pg_search_es(query = 'water', sort = "minElevation:desc") ## End(Not run)