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Correct spelling errors

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gothub committed Jan 28, 2019
1 parent eb03e72 commit 947f4b90d81522125a8e4b79ede9170eee5c64f7
@@ -67,7 +67,7 @@ if (!exists("tableDescriber.registry")) tableDescriber.registry <- list()
## @param x the TableDescriber
## @param ...
## @returnType character
## @return vector of dataONE formatIds
## @return vector of DataONE formatIds
##
## @author rnahf
## @export
@@ -56,7 +56,7 @@
#' \item{\code{\link{getAuthSubject}}}{: Get the authentication subject.}
#' \item{\code{\link{getAuthExpires}}}{: Get the expiration date of the current authentication method.}
#' \item{\code{\link{isAuthExpired}}}{: Check if the currently valid authentication method has reached the expiration time.}
#' \item{\code{\link{obscureAuth}}}{: Temporarity disable DataONE authentication.}
#' \item{\code{\link{obscureAuth}}}{: Temporarily disable DataONE authentication.}
#' \item{\code{\link{restoreAuth}}}{: Restore authentication (after being disabled with \code{obscureAuth}).}
#' \item{\code{\link{showAuth}}}{: Display all authentication information.}
#' \item{\code{\link{getTokenInfo}}}{: Display all authentication token information.}
@@ -216,7 +216,7 @@ setMethod("getAuthSubject", signature("AuthenticationManager"), function(.Object

#' Get the expiration date of the current authentication method.
#' @description The expiration date of the current authentication method, either
#' authentication token or X.509 certificate, is returned as a Greenich Mean Time (GMT) value.
#' authentication token or X.509 certificate, is returned as a Greenwich Mean Time (GMT) value.
#' @rdname getAuthExpires
#' @aliases getAuthExpires
#' @param .Object An AuthenticationManager instance
@@ -248,7 +248,7 @@ setMethod("isAuthExpired", signature("AuthenticationManager"), function(.Object,
return(authInfo$expired)
})

#' Temporarity disable DataONE authentication.
#' Temporarily disable DataONE authentication.
#' @description Calling \code{obscureAuth} temporarily disables authentication so that
#' @details This method is intended to be used for authentication testing.
#' \code{isAuthValid} will return FALSE. Authentication can be re-enabled by calling
@@ -284,7 +284,7 @@ setGeneric("listNodes", function(x, ...) {
})

#' @rdname listNodes
#' @param url Optianal - the url of the CN.
#' @param url Optional - the url of the CN.
#' @export
setMethod("listNodes", signature("CNode"), function(x, url=as.character(NA), ...) {
# If an optional url argument is specified, use that. This might be used if
@@ -361,7 +361,7 @@ setMethod("reserveIdentifier", signature("CNode"), function(x, id) {
})

#' Checks to determine if the supplied subject is the owner of the reservation of id.
#' @description The hasReservation method checks the reservation of an identfier that has
#' @description The hasReservation method checks the reservation of an identifier that has
#' previously been reserved with the \code{reserveIdentifier} method. The identifier must have
#' been reserved by the specified DataONE user identity (\code{subject}).
#' @details To determine the DataONE identity that is currently being used for DataONE
@@ -573,7 +573,7 @@ setMethod("resolve", signature("CNode"), function(x, pid){
#' Get a reference to a node based on its identifier
#' @rdname getMNode
#' @aliases getMNode
#' @details For an explanation of DataONE Coordinatine Nodes and Member Node
#' @details For an explanation of DataONE Coordinating Nodes and Member Node
#' identifiers, see the section \emph{"DataONE Environments"} in the overview vignette
#' by entering the R command: \code{vignette("dataone-overview")}.
#' @param x The coordinating node to query for its registered Member Nodes
@@ -179,7 +179,7 @@ setMethod("createD1Object", signature("D1Client", "D1Object"), function(x, d1Obj
#' Download a data object from the DataONE Federation.
#' @description An object is download from the DataONE network for the identifier that is provided.
#' @param x A D1Client instance
#' @param identifier The identifier of the object to download from DatONE
#' @param identifier The identifier of the object to download from DataONE
#' @param ... (not yet used)
#' @rdname getD1Object
#' @aliases getD1Object
@@ -835,7 +835,7 @@ setMethod("getCN", signature("D1Client"), function(x) {
#' @details The DataPackage describes the collection of data object and their associated
#' metadata object, with the relationships and members serialized into a document
#' stored under, and retrievable with, the packageId as it's own distinct object.
#' Any objects in the data map that have a dataUploaded value are assumed to be
#' Any objects in the data map that have a dateUploaded value are assumed to be
#' pre-existing in the system, and skipped.
#' @note Member objects are created serially, and most errors in creating one object will
#' interrupt the create process for the whole, with the result that some members will
@@ -1528,7 +1528,7 @@ setMethod("getMetadataMember", signature("D1Client", "DataPackage"), function(x,
#' The SystemMetadata is used to assign a name to the file that is output to disk. If a fileName is specified in
#' the SystemMetadata, then the file output to disk will be named according to the SystemMetadata fileName.
#' If there is not a specified SystemMetadata fileName, the identifier will be used as the file name output to disk.
#' If the indentifier is used as the file name, a file name extesion will be determined using the SystemMetadata
#' If the identifier is used as the file name, a file name extension will be determined using the SystemMetadata
#' formatID along with information from CNCore.listFormats(). If the SystemMetadata formatID is
#' "application/octet-stream" no extension will be written.
#' @param x A D1Client object.
@@ -92,7 +92,7 @@ result[1,c("id", "title")]
id <- result[1,'id']
```

The metadata file that describes the located research can be downloaed and viewed in an XML viewer, text
The metadata file that describes the located research can be downloaded and viewed in an XML viewer, text
editor after being written to disk, or in R via the commands below:
```
library(XML)
@@ -141,7 +141,7 @@ pkg <- getDataPackage(d1c, id="urn:uuid:04cd34fd-25d4-447f-ab6e-73a572c5d383", q
See the R vignette [dataone R Package ](https://github.com/DataONEorg/rdataone/blob/master/vignettes/dataone-overview.Rmd) for
more information.

## Acknowledgements
## Acknowledgments
Work on this package was supported by:

- NSF-ABI grant #1262458 to C. Gries, M. B. Jones, and S. Collins.

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@@ -36,7 +36,7 @@ For additional overview information about the DataONE Federation, please https:/
The following features are available via the `dataone` package, for member nodes that have implemented the DataONE version 2.0 API.

### 1. Series Identifiers
Each data, metadata, and resource map object in DataONE has a unique identifier, refered to in DataONE documentation as a Persistent
Each data, metadata, and resource map object in DataONE has a unique identifier, referred to in DataONE documentation as a Persistent
Identifier (PID). A PID is associated with one object in DataONE and always refers to the same object, the same set of bytes that are
stored on the DataONE network.

@@ -58,7 +58,7 @@ can be sent to DataONE services to prove a user's identity.

Authentication tokens can be used with Member Nodes that have been upgraded to the DataONE Version 2.0 Member Node API

The process of providing user identity information either via an X.509 certificate or via an authentication token is refered to as *authentication*.
The process of providing user identity information either via an X.509 certificate or via an authentication token is referred to as *authentication*.

Authentication tokens can be obtained from a user's DataONE account settings web page. To create an authentication token:

@@ -71,7 +71,7 @@ Authentication tokens can be obtained from a user's DataONE account settings web
- Click "Renew authentication token" if the token you have been using has expired.
- Click on the "Copy" button below the text window to copy the authentication string to the paste buffer.
- Note the identity string and expiration date of the token.
- In the R console, paste the string which is similiar to this example:
- In the R console, paste the string which is similar to this example:
```
options(dataone_token = "eyJhbGciOiJSUzI1NiJ9...")
```
@@ -165,7 +165,7 @@ dev | DEV |
dev2 | DEV2 |

Each DataONE environment has a CN that maintains a registry of all MNs in that network. The CN can be queried for a list of
all MNs in a network, for example, to see the MNs that are currently in the production environmemt:
all MNs in a network, for example, to see the MNs that are currently in the production environment:
```{r, eval=F}
cn <- CNode("PROD")
unlist(lapply(listNodes(cn), function(x) x@name))
@@ -177,7 +177,7 @@ To see the URL service endpoint for a CN, you can view the `endpoint` slot:
cn@endpoint
```

To see the member nodes that are currenly in the STAGE2 environment:
To see the member nodes that are currently in the STAGE2 environment:
```{r, eval=F}
cn <- CNode("STAGING2")
unlist(lapply(listNodes(cn), function(x) x@name))
@@ -76,7 +76,7 @@ uploadDataObject(d1c, d1Object, public=TRUE)

## Additional Resources

The `dataone` R package vignettes can be viewed using the R `vignette` comand,
The `dataone` R package vignettes can be viewed using the R `vignette` command,
for example `vignette("dataone-overview")`.

The `dataone` vignettes describe these topics:
@@ -66,8 +66,8 @@ mnId <- locations$data[2, "nodeIdentifier"]
mn <- getMNode(cn, mnId)
```

Multiple MNs may hold the data, depending on the DataONE replication policy that is in effect for the dataset and which member nodes are currenctly available. (DataONE copies or 'replicates' datasets from one MN to other MNs, depending on what was requested by the user
when a dataset was first uploaded to DatqONE). In this example the second location from the resolve list will be downloaded. Now the call can be made that downloads the object itself:
Multiple MNs may hold the data, depending on the DataONE replication policy that is in effect for the dataset and which member nodes are currently available. (DataONE copies or 'replicates' datasets from one MN to other MNs, depending on what was requested by the user
when a dataset was first uploaded to DataONE). In this example the second location from the resolve list will be downloaded. Now the call can be made that downloads the object itself:
```{r, warning=FALSE,eval=FALSE}
obj <- getObject(mn, pid)
```
@@ -11,7 +11,7 @@ vignette: >
## Known Issues With dataone R Package Version 2.0
### Error Using X.509 Certificates

Using an X.509 certificate for DataONE authenticatin on certain versions of Mac OS X can cause the following error:
Using an X.509 certificate for DataONE authentication on certain versions of Mac OS X can cause the following error:

```
Error in curl::curl_fetch_memory(url, handle = handle) :
@@ -10,7 +10,7 @@ vignette: >

The primary method to locate data in the DataONE network is to use the web based search tool located at https://search.dataone.org.

Data can also be discovered programatically from R using the *dataone* R package method `query`. Both the web page and the R method
Data can also be discovered programmatically from R using the *dataone* R package method `query`. Both the web page and the R method
access the same
underlying search mechanism, the Apache Foundation Solr search engine that runs on the
[DataONE Coordinating Node](https://www.dataone.org/coordinating-nodes). The DataONE Solr index, similar to a catalog or database, contains
@@ -28,7 +28,7 @@ Additional information about searching DataONE can be viewed at [Content Discove

Some familiarity with Solr is helpful when using the `query` method
effectively, however basic queries can be very powerful and the examples in this document can provide a starting point. As an alternative to
composing queries using Solr syntax, a simplier search mechanism is available with the `query` method that uses name, value pairs (See the section: *A Simplied Search").
composing queries using Solr syntax, a simpler search mechanism is available with the `query` method that uses name, value pairs (See the section: *A Simplified Search").
Additional information about the `query` method can be obtained from the R help facility, e.g. `?query` from the R command line.
@@ -105,7 +105,7 @@ result[,'id']

### Using a Simplified Search.
A search may be performed by just specifying query fields and values using the *searchTerms* parameter.
For example, to search for datasets that mention 'kelp' in the abstract and have an attribute discription that contains the word 'biomass', the following query could be used:
For example, to search for datasets that mention 'kelp' in the abstract and have an attribute description that contains the word 'biomass', the following query could be used:
```{r, eval=F}
cn <- CNode("PROD")
mn <- getMNode(cn, "urn:node:KNB")
@@ -123,7 +123,7 @@ using a web browser to view https://cn.dataone.org/cn/v2/query/solr.
### Search just a member node
If it is known which Member Node holds the data of interest, then a search can be limited to just that
MN by sending the search directly to that MN instead of the CN. For example, if the dataset of interest
is on The Knowledge Network for Biocomplexity (KNB) Member Node, then the search is performed with the statments:
is on The Knowledge Network for Biocomplexity (KNB) Member Node, then the search is performed with the statements:

```{r, eval=F}
# Query the data holdings on a member node
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