-
Notifications
You must be signed in to change notification settings - Fork 4
/
oai.Rmd
235 lines (190 loc) · 8.54 KB
/
oai.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
<!--
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{oai introduction}
%\VignetteEncoding{UTF-8}
-->
oai introduction
================
A general purpose client to work with any 'OAI-PMH' service.
The 'OAI-PMH' protocol is described at <http://www.openarchives.org/OAI/openarchivesprotocol.html>.
The main functions follow the OAI-PMH verbs:
* `GetRecord`
* `Identify`
* `ListIdentifiers`
* `ListMetadataFormats`
* `ListRecords`
* `ListSets`
## Get oai
Install from CRAN
```r
install.packages("oai")
```
Or install the development version from GitHub
```r
devtools::install_github("ropensci/oai")
```
Load `oai`
```r
library("oai")
```
## Identify
```r
id("http://oai.datacite.org/oai")
#> repositoryName baseURL protocolVersion
#> 1 DataCite MDS https://oai.datacite.org/oai 2.0
#> adminEmail earliestDatestamp deletedRecord
#> 1 support@datacite.org 2011-01-01T00:00:00Z persistent
#> granularity compression compression.1
#> 1 YYYY-MM-DDThh:mm:ssZ gzip deflate
#> description
#> 1 oaioai.datacite.org:oai:oai.datacite.org:12425
```
## ListIdentifiers
```r
list_identifiers(from = '2018-05-01T', until = '2018-09-01T')
#> # A tibble: 2,904 x 5
#> identifier datestamp setSpec setSpec.1 setSpec.2
#> <chr> <chr> <chr> <chr> <chr>
#> 1 cbe4cdda-2045-41… 2018-08-30T… installation:842… dataset_type… country:…
#> 2 3fb7ddd8-07c0-49… 2018-08-28T… installation:842… dataset_type… country:…
#> 3 34585f24-1ffe-47… 2018-08-28T… installation:842… dataset_type… country:…
#> 4 8ac24ec8-1e7b-40… 2018-08-28T… installation:842… dataset_type… country:…
#> 5 e381b970-9b62-46… 2018-08-28T… installation:842… dataset_type… country:…
#> 6 4496b1b1-1ea9-4e… 2018-08-28T… installation:842… dataset_type… country:…
#> 7 fc5d68a6-b511-4c… 2018-08-27T… installation:73e… dataset_type… country:…
#> 8 5e0073bc-de2a-4b… 2018-08-27T… installation:688… dataset_type… country:…
#> 9 ab2684cf-62e5-4f… 2018-08-27T… installation:804… dataset_type… country:…
#> 10 34fbcf59-d9bb-47… 2018-08-27T… installation:7c5… dataset_type… country:…
#> # … with 2,894 more rows
```
## Count Identifiers
```r
count_identifiers()
```
## ListRecords
```r
list_records(from = '2018-05-01T', until = '2018-05-15T')
#> # A tibble: 44 x 26
#> identifier datestamp setSpec setSpec.1 setSpec.2 title publisher
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 18799ce9-… 2018-05-… instal… dataset_… country:… Bird… Sokoine …
#> 2 79f51633-… 2018-05-… instal… dataset_… country:… Impl… Aïgos SAS
#> 3 f83746ee-… 2018-05-… instal… dataset_… country:… NDFF… Dutch Na…
#> 4 a3533a61-… 2018-05-… instal… dataset_… country:… EDP … EDP - En…
#> 5 ba9b66a3-… 2018-05-… instal… dataset_… country:… Ende… Sokoine …
#> 6 78b696d9-… 2018-05-… instal… dataset_… country:… Ende… Sokoine …
#> 7 c791b255-… 2018-05-… instal… dataset_… country:… Ende… Sokoine …
#> 8 b929ccda-… 2018-05-… instal… dataset_… country:… List… Sokoine …
#> 9 da285c2a-… 2018-05-… instal… dataset_… country:… Moni… Corporac…
#> 10 87372877-… 2018-05-… instal… dataset_… country:… Moni… Corporac…
#> # … with 34 more rows, and 19 more variables: identifier.1 <chr>,
#> # subject <chr>, source <chr>, description <chr>, description.1 <chr>,
#> # type <chr>, creator <chr>, date <chr>, language <chr>, coverage <chr>,
#> # coverage.1 <chr>, format <chr>, source.1 <chr>, subject.1 <chr>,
#> # coverage.2 <chr>, creator.1 <chr>, description.2 <chr>,
#> # creator.2 <chr>, subject.2 <chr>
```
## GetRecords
```r
ids <- c("87832186-00ea-44dd-a6bf-c2896c4d09b4", "d981c07d-bc43-40a2-be1f-e786e25106ac")
get_records(ids)
#> $`87832186-00ea-44dd-a6bf-c2896c4d09b4`
#> $`87832186-00ea-44dd-a6bf-c2896c4d09b4`$header
#> # A tibble: 1 x 3
#> identifier datestamp setSpec
#> <chr> <chr> <chr>
#> 1 87832186-00ea-44dd-a6… 2018-06-29T12… installation:729a7375-b120-4e4f-bb…
#>
#> $`87832186-00ea-44dd-a6bf-c2896c4d09b4`$metadata
#> # A tibble: 0 x 0
#>
#>
#> $`d981c07d-bc43-40a2-be1f-e786e25106ac`
#> $`d981c07d-bc43-40a2-be1f-e786e25106ac`$header
#> # A tibble: 1 x 3
#> identifier datestamp setSpec
#> <chr> <chr> <chr>
#> 1 d981c07d-bc43-40a2-be… 2018-01-21T21… installation:804b8dd0-07ac-4a30-bf…
#>
#> $`d981c07d-bc43-40a2-be1f-e786e25106ac`$metadata
#> # A tibble: 1 x 12
#> title publisher identifier subject source description type creator date
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Pece… Institut… https://w… peces,… http:… Caracteriz… Data… Fernan… 2018…
#> # … with 3 more variables: language <chr>, coverage <chr>, format <chr>
```
## List MetadataFormats
```r
list_metadataformats(id = "87832186-00ea-44dd-a6bf-c2896c4d09b4")
#> $`87832186-00ea-44dd-a6bf-c2896c4d09b4`
#> metadataPrefix schema
#> 1 oai_dc http://www.openarchives.org/OAI/2.0/oai_dc.xsd
#> 2 eml http://rs.gbif.org/schema/eml-gbif-profile/1.0.2/eml.xsd
#> metadataNamespace
#> 1 http://www.openarchives.org/OAI/2.0/oai_dc/
#> 2 eml://ecoinformatics.org/eml-2.1.1
```
## List Sets
```r
list_sets("http://api.gbif.org/v1/oai-pmh/registry")
#> # A tibble: 572 x 2
#> setSpec setName
#> <chr> <chr>
#> 1 dataset_type per dataset type
#> 2 dataset_type:OCCURRENCE occurrence
#> 3 dataset_type:CHECKLIST checklist
#> 4 dataset_type:METADATA metadata
#> 5 dataset_type:SAMPLING_EVENT sampling_event
#> 6 country per country
#> 7 country:AD Andorra
#> 8 country:AO Angola
#> 9 country:AR Argentina
#> 10 country:AT Austria
#> # … with 562 more rows
```
### Biodiversity Heritage Library
Identify
```r
id("http://www.biodiversitylibrary.org/oai")
#> repositoryName
#> 1 Biodiversity Heritage Library OAI Repository
#> baseURL protocolVersion
#> 1 https://www.biodiversitylibrary.org/oai 2.0
#> adminEmail earliestDatestamp deletedRecord granularity
#> 1 oai@biodiversitylibrary.org 2006-01-01 no YYYY-MM-DD
#> description
#> 1 oaibiodiversitylibrary.org:oai:biodiversitylibrary.org:item/1000
```
Get records
```r
get_records(c("oai:biodiversitylibrary.org:item/7", "oai:biodiversitylibrary.org:item/9"),
url = "http://www.biodiversitylibrary.org/oai")
#> $`oai:biodiversitylibrary.org:item/7`
#> $`oai:biodiversitylibrary.org:item/7`$header
#> # A tibble: 1 x 3
#> identifier datestamp setSpec
#> <chr> <chr> <chr>
#> 1 oai:biodiversitylibrary.org:item/7 2016-07-13T09:13:41Z item
#>
#> $`oai:biodiversitylibrary.org:item/7`$metadata
#> # A tibble: 1 x 11
#> title creator subject description publisher contributor date type
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Die … Fleisc… Bogor;… pt.5:v.1 (… Leiden :… Missouri B… 1900… text…
#> # … with 3 more variables: identifier <chr>, language <chr>, rights <chr>
#>
#>
#> $`oai:biodiversitylibrary.org:item/9`
#> $`oai:biodiversitylibrary.org:item/9`$header
#> # A tibble: 1 x 3
#> identifier datestamp setSpec
#> <chr> <chr> <chr>
#> 1 oai:biodiversitylibrary.org:item/9 2016-07-13T09:13:41Z item
#>
#> $`oai:biodiversitylibrary.org:item/9`$metadata
#> # A tibble: 1 x 11
#> title creator subject description publisher contributor date type
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Die … Fleisc… Bogor;… pt.5:v.3 (… Leiden :… Missouri B… 1906… text…
#> # … with 3 more variables: identifier <chr>, language <chr>, rights <chr>
```