Misc updates/fixes: labkey.domain.createAndLoad fix for strictFieldValidation, labkey.webdav.put description support, add labkey.query.import

Rlabkey/NAMESPACE

@@ -44,6 +44,7 @@ export(labkey.pipeline.getPipelineContainer)
 export(labkey.pipeline.getProtocols)
 export(labkey.pipeline.getFileStatus)
 export(labkey.pipeline.startAnalysis)
+export(labkey.query.import)
 
 S3method(print, LabkeySession)
 S3method(print, LabkeySchemaList)

Rlabkey/R/labkey.domain.R

@@ -214,8 +214,11 @@ labkey.domain.createAndLoad <- function(baseUrl=NULL, folderPath, name, descript
         stop (paste("A value must be specified for each of baseUrl, folderPath, name, df or domainKind."))
 
     if (is.null(options))
-        options <- list(strictFieldValidation = FALSE)
-    else
+        options <- list()
+
+    # Add option for study dataset and data class creation to skip validation check for required properties,
+    # see DataSetDomainKind.createDomain and ExperimentServiceImpl.createDataClass
+    if (domainKind == "StudyDatasetVisit" || domainKind == "StudyDatatsetDate" || domainKind == "DataClass")
         options <- c(options, list(strictFieldValidation = FALSE))
 
     if (is.null(schemaName))
@@ -241,7 +244,7 @@ labkey.domain.createAndLoad <- function(baseUrl=NULL, folderPath, name, descript
     labkey.domain.create(baseUrl = baseUrl, folderPath = folderPath, domainKind = domainKind,
         domainDesign = design, options = options)
 
-    labkey.insertRows(baseUrl = baseUrl, folderPath = folderPath, schemaName = schemaName, queryName= name, df)
+    labkey.query.import(baseUrl, folderPath, schemaName, queryName= name, toImport = df)
 }
 
 labkey.domain.createConditionalFormat <- function(queryFilter, bold=FALSE, italic=FALSE, strikeThrough=FALSE, textColor="", backgroundColor="")

Rlabkey/R/labkey.query.import.R

@@ -0,0 +1,49 @@
+##
+#  Copyright (c) 2013-2018 LabKey Corporation
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+##
+
+labkey.query.import <- function(baseUrl=NULL, folderPath, schemaName, queryName, toImport, options = NULL)
+{
+    baseUrl=labkey.getBaseUrl(baseUrl)
+
+    ## check required parameters
+    if (missing(baseUrl) || is.null(baseUrl) || missing(folderPath) || missing(schemaName) || missing(queryName) || missing(toImport))
+        stop (paste("A value must be specified for each of baseUrl, folderPath, schemaName, queryName, and toImport."))
+    if (!missing(options) & !is.list(options))
+        stop (paste("options must be a list data structure."))
+
+    ## normalize the folder path
+    folderPath <- encodeFolderPath(folderPath)
+
+    ## write the dataframe to a tempfile to post to the server
+    tf <- tempfile(fileext=".tsv")
+    write.table(toImport, file=tf, sep="\t", quote=FALSE, row.names=FALSE)
+
+    ## build the options param list
+    if (is.null(options))
+        options <- list()
+    options <- c(options, list(schemaName=schemaName, queryName=queryName, file=upload_file(tf)))
+
+    ## Execute via our standard POST function
+    url <- paste(baseUrl, "query", folderPath, "import.api", sep="")
+    rawdata <- labkey.post(url, options, encoding="multipart")
+    response <- fromJSON(rawdata, simplifyVector=FALSE, simplifyDataFrame=FALSE)
+
+    ## delete the temp file
+    file.remove(tf)
+
+    return(response)
+}
+

Rlabkey/R/labkey.webdav.R

@@ -69,7 +69,7 @@ labkey.webdav.getByUrl <- function(url, localFilePath, overwrite=TRUE)
     processResponse(response)
 }
 
-labkey.webdav.put <- function(localFile, baseUrl=NULL, folderPath, remoteFilePath, fileSet="@files")
+labkey.webdav.put <- function(localFile, baseUrl=NULL, folderPath, remoteFilePath, fileSet="@files", description=NULL)
 {
     if (missing(localFile)) {
         stop (paste("A value must be specified for localFile"))
@@ -84,6 +84,10 @@ labkey.webdav.put <- function(localFile, baseUrl=NULL, folderPath, remoteFilePat
 
     pbody <- upload_file(localFile)
 
+    if (!is.null(description)) {
+        url <- paste0(url, "?description=", URLencode(description))
+    }
+
     if (!is.null(.lkdefaults[["debug"]]) && .lkdefaults[["debug"]] == TRUE) {
         print(paste0("URL: ", url))
         response <- PUT(url=url, config=options, body=pbody, verbose(data_in=TRUE, info=TRUE, ssl=TRUE))

Rlabkey/man/labkey.importRows.Rd

@@ -11,18 +11,18 @@ labkey.importRows(baseUrl, folderPath,
 \arguments{
   \item{baseUrl}{a string specifying the \code{baseUrl}for the labkey server}
   \item{folderPath}{a string specifying the \code{folderPath} }
-  \item{schemaName}{a string specifying the  \code{schemaName} for the query}
-  \item{queryName}{a string specifying the  \code{queryName} }
+  \item{schemaName}{a string specifying the \code{schemaName} for the query}
+  \item{queryName}{a string specifying the \code{queryName} }
   \item{toImport}{a data frame containing rows of data to be imported}
   \item{na}{(optional) the value to convert NA's to, defaults to NULL}
 }
 \details{
 Multiple rows of data can be imported in bulk.  The \code{toImport} data frame must contain
 values for each column in the dataset and must be created with the \code{stringsAsFactors} option
 set to FALSE. The names of the data in the data frame must be the column names from the
-LabKey Server.To import a value of NULL, use an empty string ("") in the data frame (regardless of the database column type).
-Also, when importing data into a study dataset, the sequence number must be specified. \cr \cr
-Note: requires LabKey server version 13.3 or greater.
+LabKey Server. To import a value of NULL, use an empty string ("") in the data frame
+(regardless of the database column type). Also, when importing data into a study dataset, the
+sequence number must be specified.
 }
 
 \value{
@@ -35,8 +35,8 @@ number as passed in the request.
 \author{Cory Nathe}
 \seealso{
 \code{\link{labkey.selectRows}}, \code{\link{labkey.executeSql}}, \code{\link{makeFilter}},
-\code{\link{labkey.insertRows}}, \code{\link{labkey.updateRows}}, \cr
-\code{\link{labkey.deleteRows}}
+\code{\link{labkey.insertRows}}, \code{\link{labkey.updateRows}}, \code{\link{labkey.deleteRows}},
+\code{\link{labkey.query.import}}
 }
 \examples{
 \donttest{

Rlabkey/man/labkey.insertRows.Rd

@@ -40,6 +40,7 @@ inserted.
 \code{\link{labkey.selectRows}}, \code{\link{labkey.executeSql}}, \code{\link{makeFilter}}, 
 \code{\link{labkey.importRows}}, \code{\link{labkey.updateRows}}, \cr
 \code{\link{labkey.deleteRows}},
+\code{\link{labkey.query.import}},
 \code{\link{labkey.provenance.createProvenanceParams}},
 \code{\link{labkey.provenance.startRecording}},
 \code{\link{labkey.provenance.addRecordingStep}},

Rlabkey/man/labkey.query.import.Rd

@@ -0,0 +1,80 @@
+\name{labkey.query.import}
+\alias{labkey.query.import}
+\title{Bulk import an R data frame into a LabKey Server table using file import.}
+\description{
+Bulk import an R data frame into a LabKey Server table using file import.
+}
+\usage{
+labkey.query.import(baseUrl, folderPath,
+    schemaName, queryName, toImport, options = NULL)
+}
+\arguments{
+  \item{baseUrl}{a string specifying the \code{baseUrl}for the labkey server}
+  \item{folderPath}{a string specifying the \code{folderPath} }
+  \item{schemaName}{a string specifying the \code{schemaName} for the query}
+  \item{queryName}{a string specifying the \code{queryName}}
+  \item{toImport}{a data frame containing rows of data to be imported}
+  \item{options}{(optional) a list containing options specific to the import
+  action of the query}
+}
+\details{
+This command mimics the "Import bulk data" option that you see in the LabKey server UI
+for a table/query. It takes the passed in \code{toImport} data frame and writes it to a
+temp file to be posted to the import action for the given LabKey query. It is very similar
+to the \code{labkey.importRows} command but will be much more performant.
+\cr \cr
+Multiple rows of data can be imported in bulk using the \code{toImport} data frame.
+The names of the data in the data frame must be the column names from the
+LabKey Server.
+\cr \cr
+LabKey data types support different import options. The list of valid options for each
+query will vary, but some common examples include:
+    \itemize{
+        \item{ \code{insertOption (string)} : Whether the import action should be done as an insert, creating new
+            rows for each provided row of the data frame, or a merge. When merging during import, any data you provide
+            for the rows representing records that already exist will replace the previous values.
+            Note that when updating an existing record, you only need to provide the columns you wish to update,
+            existing data for other columns will be left as is. Available options are "INSERT" and "MERGE".
+            Defaults to "INSERT".}
+        \item{ \code{auditBehavior (string)} : Set the level of auditing details for this import action.
+            Available options are "SUMMARY" and "DETAILED". SUMMARY - Audit log reflects that a change was made,
+            but does not mention the nature of the change. DETAILED - Provides full details on what change was made,
+            including values before and after the change. Defaults to the setting as specified by the LabKey query.}
+        \item{ \code{importLookupByAlternateKey (boolean)} : Allows lookup target rows to be resolved by values
+            rather than the target's primary key. This option will only be available for lookups that are
+            configured with unique column information. Defaults to FALSE.}
+    }
+}
+
+\value{
+A list is returned with the row count for the number of affected rows. If options are provided,
+additional details may be included in the response object related to those options.
+}
+\author{Cory Nathe}
+\seealso{
+\code{\link{labkey.insertRows}}, \code{\link{labkey.updateRows}}, \code{\link{labkey.importRows}}
+}
+\examples{
+\donttest{
+
+## Note that users must have the necessary permissions in the database
+## to be able to modify data through the use of these functions
+# library(Rlabkey)
+
+df <- data.frame(
+    name=c("test1","test2","test3"),
+    customInt=c(1:3),
+    customString=c("aaa", "bbb", "ccc")
+)
+
+importedInfo <- labkey.query.import(
+    "http://localhost:8080/labkey",
+    folderPath="/apisamples", schemaName="samples", queryName="SampleType1",
+    toImport=df, options=list(insertOption = "MERGE", auditBehavior = "DETAILED")
+)
+
+importedInfo$rowCount
+
+}
+}
+\keyword{IO}

Rlabkey/man/labkey.setCurlOptions.Rd

@@ -58,4 +58,10 @@ For Variable Name: enter RLABKEY_CAINFO_FILE\cr
 For Variable Value: enter the path of the ca-bundle.crt you created above.\cr
 Hit the Ok buttons to close all the windows.\cr
 Now you can start R and begin working.
+
+\cr \cr
+
+This command can also be used to provide an alternate location / path to your
+\code{.netrc} file. Example:\cr
+\code{labkey.setCurlOptions(NETRC_FILE = '/path/to/alternate/_netrc')}
 }

Rlabkey/man/labkey.updateRows.Rd

@@ -38,6 +38,7 @@ updated.
 \code{\link{labkey.selectRows}}, \code{\link{labkey.executeSql}}, \code{\link{makeFilter}}, 
 \code{\link{labkey.insertRows}}, \code{\link{labkey.importRows}}, \cr
 \code{\link{labkey.deleteRows}},
+\code{\link{labkey.query.import}},
 \code{\link{labkey.provenance.createProvenanceParams}},
 \code{\link{labkey.provenance.startRecording}},
 \code{\link{labkey.provenance.addRecordingStep}},

Rlabkey/man/labkey.webdav.put.Rd

@@ -10,15 +10,17 @@ labkey.webdav.put(
     baseUrl=NULL,
     folderPath,
     remoteFilePath,
-    fileSet='@files'
-    )
+    fileSet='@files',
+    description=NULL
+)
 }
 \arguments{
   \item{localFile}{the local filepath to upload }
   \item{baseUrl}{a string specifying the \code{baseUrl} for the labkey server}
   \item{folderPath}{a string specifying the \code{folderPath} }
   \item{remoteFilePath}{the destination path of this file on the remote server, relative to the folder root. }
   \item{fileSet}{(optional) the name of file server fileSet, which is typically "@files" (the default value for this argument). In some cases this might be "@pipeline" or "@fileset". }
+  \item{description}{(optional) the description to attach to this file on the remote server. }
 }
 \details{
 Upload a single file from the local machine to a LabKey Server using WebDAV.